Multidisciplinary Tool for Systems Analysis of Planetary Entry, Descent, and Landing

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

2011-01-01

Systems analysis of a planetary entry (SAPE), descent, and landing (EDL) is a multidisciplinary activity in nature. SAPE improves the performance of the systems analysis team by automating and streamlining the process, and this improvement can reduce the errors that stem from manual data transfer among discipline experts. SAPE is a multidisciplinary tool for systems analysis of planetary EDL for Venus, Earth, Mars, Jupiter, Saturn, Uranus, Neptune, and Titan. It performs EDL systems analysis for any planet, operates cross-platform (i.e., Windows, Mac, and Linux operating systems), uses existing software components and open-source software to avoid software licensing issues, performs low-fidelity systems analysis in one hour on a computer that is comparable to an average laptop, and keeps discipline experts in the analysis loop. SAPE uses Python, a platform-independent, open-source language, for integration and for the user interface. Development has relied heavily on the object-oriented programming capabilities that are available in Python. Modules are provided to interface with commercial and government off-the-shelf software components (e.g., thermal protection systems and finite-element analysis). SAPE currently includes the following analysis modules: geometry, trajectory, aerodynamics, aerothermal, thermal protection system, and interface for structural sizing.

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.

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

Volumetric neuroimage analysis extensions for the MIPAV software package.

PubMed

Bazin, Pierre-Louis; Cuzzocreo, Jennifer L; Yassa, Michael A; Gandler, William; McAuliffe, Matthew J; Bassett, Susan S; Pham, Dzung L

2007-09-15

We describe a new collection of publicly available software tools for performing quantitative neuroimage analysis. The tools perform semi-automatic brain extraction, tissue classification, Talairach alignment, and atlas-based measurements within a user-friendly graphical environment. They are implemented as plug-ins for MIPAV, a freely available medical image processing software package from the National Institutes of Health. Because the plug-ins and MIPAV are implemented in Java, both can be utilized on nearly any operating system platform. In addition to the software plug-ins, we have also released a digital version of the Talairach atlas that can be used to perform regional volumetric analyses. Several studies are conducted applying the new tools to simulated and real neuroimaging data sets.

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.

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

Performance analysis and optimization of an advanced pharmaceutical wastewater treatment plant through a visual basic software tool (PWWT.VB).

PubMed

Pal, Parimal; Thakura, Ritwik; Chakrabortty, Sankha

2016-05-01

A user-friendly, menu-driven simulation software tool has been developed for the first time to optimize and analyze the system performance of an advanced continuous membrane-integrated pharmaceutical wastewater treatment plant. The software allows pre-analysis and manipulation of input data which helps in optimization and shows the software performance visually on a graphical platform. Moreover, the software helps the user to "visualize" the effects of the operating parameters through its model-predicted output profiles. The software is based on a dynamic mathematical model, developed for a systematically integrated forward osmosis-nanofiltration process for removal of toxic organic compounds from pharmaceutical wastewater. The model-predicted values have been observed to corroborate well with the extensive experimental investigations which were found to be consistent under varying operating conditions like operating pressure, operating flow rate, and draw solute concentration. Low values of the relative error (RE = 0.09) and high values of Willmott-d-index (d will = 0.981) reflected a high degree of accuracy and reliability of the software. This software is likely to be a very efficient tool for system design or simulation of an advanced membrane-integrated treatment plant for hazardous wastewater.

An analysis of functional shoulder movements during task performance using Dartfish movement analysis software.

PubMed

Khadilkar, Leenesh; MacDermid, Joy C; Sinden, Kathryn E; Jenkyn, Thomas R; Birmingham, Trevor B; Athwal, George S

2014-01-01

Video-based movement analysis software (Dartfish) has potential for clinical applications for understanding shoulder motion if functional measures can be reliably obtained. The primary purpose of this study was to describe the functional range of motion (ROM) of the shoulder used to perform a subset of functional tasks. A second purpose was to assess the reliability of functional ROM measurements obtained by different raters using Dartfish software. Ten healthy participants, mean age 29 ± 5 years, were videotaped while performing five tasks selected from the Disabilities of the Arm, Shoulder and Hand (DASH). Video cameras and markers were used to obtain video images suitable for analysis in Dartfish software. Three repetitions of each task were performed. Shoulder movements from all three repetitions were analyzed using Dartfish software. The tracking tool of the Dartfish software was used to obtain shoulder joint angles and arcs of motion. Test-retest and inter-rater reliability of the measurements were evaluated using intraclass correlation coefficients (ICC). Maximum (coronal plane) abduction (118° ± 16°) and (sagittal plane) flexion (111° ± 15°) was observed during 'washing one's hair;' maximum extension (-68° ± 9°) was identified during 'washing one's own back.' Minimum shoulder ROM was observed during 'opening a tight jar' (33° ± 13° abduction and 13° ± 19° flexion). Test-retest reliability (ICC = 0.45 to 0.94) suggests high inter-individual task variability, and inter-rater reliability (ICC = 0.68 to 1.00) showed moderate to excellent agreement. KEY FINDINGS INCLUDE: 1) functional shoulder ROM identified in this study compared to similar studies; 2) healthy individuals require less than full ROM when performing five common ADL tasks 3) high participant variability was observed during performance of the five ADL tasks; and 4) Dartfish software provides a clinically relevant tool to analyze shoulder function.

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.

Automated daily quality control analysis for mammography in a multi-unit imaging center.

PubMed

Sundell, Veli-Matti; Mäkelä, Teemu; Meaney, Alexander; Kaasalainen, Touko; Savolainen, Sauli

2018-01-01

Background The high requirements for mammography image quality necessitate a systematic quality assurance process. Digital imaging allows automation of the image quality analysis, which can potentially improve repeatability and objectivity compared to a visual evaluation made by the users. Purpose To develop an automatic image quality analysis software for daily mammography quality control in a multi-unit imaging center. Material and Methods An automated image quality analysis software using the discrete wavelet transform and multiresolution analysis was developed for the American College of Radiology accreditation phantom. The software was validated by analyzing 60 randomly selected phantom images from six mammography systems and 20 phantom images with different dose levels from one mammography system. The results were compared to a visual analysis made by four reviewers. Additionally, long-term image quality trends of a full-field digital mammography system and a computed radiography mammography system were investigated. Results The automated software produced feature detection levels comparable to visual analysis. The agreement was good in the case of fibers, while the software detected somewhat more microcalcifications and characteristic masses. Long-term follow-up via a quality assurance web portal demonstrated the feasibility of using the software for monitoring the performance of mammography systems in a multi-unit imaging center. Conclusion Automated image quality analysis enables monitoring the performance of digital mammography systems in an efficient, centralized manner.

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.

Cardiovascular imaging environment: will the future be cloud-based?

PubMed

Kawel-Boehm, Nadine; Bluemke, David A

2017-07-01

In cardiovascular CT and MR imaging large datasets have to be stored, post-processed, analyzed and distributed. Beside basic assessment of volume and function in cardiac magnetic resonance imaging e.g., more sophisticated quantitative analysis is requested requiring specific software. Several institutions cannot afford various types of software and provide expertise to perform sophisticated analysis. Areas covered: Various cloud services exist related to data storage and analysis specifically for cardiovascular CT and MR imaging. Instead of on-site data storage, cloud providers offer flexible storage services on a pay-per-use basis. To avoid purchase and maintenance of specialized software for cardiovascular image analysis, e.g. to assess myocardial iron overload, MR 4D flow and fractional flow reserve, evaluation can be performed with cloud based software by the consumer or complete analysis is performed by the cloud provider. However, challenges to widespread implementation of cloud services include regulatory issues regarding patient privacy and data security. Expert commentary: If patient privacy and data security is guaranteed cloud imaging is a valuable option to cope with storage of large image datasets and offer sophisticated cardiovascular image analysis for institutions of all sizes.

Classification software technique assessment

NASA Technical Reports Server (NTRS)

Jayroe, R. R., Jr.; Atkinson, R.; Dasarathy, B. V.; Lybanon, M.; Ramapryian, H. K.

1976-01-01

A catalog of software options is presented for the use of local user communities to obtain software for analyzing remotely sensed multispectral imagery. The resources required to utilize a particular software program are described. Descriptions of how a particular program analyzes data and the performance of that program for an application and data set provided by the user are shown. An effort is made to establish a statistical performance base for various software programs with regard to different data sets and analysis applications, to determine the status of the state-of-the-art.

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

PubMed

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

2014-10-01

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

Technology Infusion of CodeSonar into the Space Network Ground Segment (RII07)

NASA Technical Reports Server (NTRS)

Benson, Markland

2008-01-01

The NASA Software Assurance Research Program (in part) performs studies as to the feasibility of technologies for improving the safety, quality, reliability, cost, and performance of NASA software. This study considers the application of commercial automated source code analysis tools to mission critical ground software that is in the operations and sustainment portion of the product lifecycle.

Representation of the Physiological Factors Contributing to Postflight Changes in Functional Performance Using Motion Analysis Software

NASA Technical Reports Server (NTRS)

Parks, Kelsey

2010-01-01

Astronauts experience changes in multiple physiological systems due to exposure to the microgravity conditions of space flight. To understand how changes in physiological function influence functional performance, a testing procedure has been developed that evaluates both astronaut postflight functional performance and related physiological changes. Astronauts complete seven functional and physiological tests. The objective of this project is to use motion tracking and digitizing software to visually display the postflight decrement in the functional performance of the astronauts. The motion analysis software will be used to digitize astronaut data videos into stick figure videos to represent the astronauts as they perform the Functional Tasks Tests. This project will benefit NASA by allowing NASA scientists to present data of their neurological studies without revealing the identities of the astronauts.

Automatic sample changer control software for automation of neutron activation analysis process in Malaysian Nuclear Agency

NASA Astrophysics Data System (ADS)

Yussup, N.; Ibrahim, M. M.; Rahman, N. A. A.; Mokhtar, M.; Salim, N. A. A.; Soh@Shaari, S. C.; Azman, A.; Lombigit, L.; Azman, A.; Omar, S. A.

2018-01-01

Most of the procedures in neutron activation analysis (NAA) process that has been established in Malaysian Nuclear Agency (Nuclear Malaysia) since 1980s were performed manually. These manual procedures carried out by the NAA laboratory personnel are time consuming and inefficient especially for sample counting and measurement process. The sample needs to be changed and the measurement software needs to be setup for every one hour counting time. Both of these procedures are performed manually for every sample. Hence, an automatic sample changer system (ASC) that consists of hardware and software is developed to automate sample counting process for up to 30 samples consecutively. This paper describes the ASC control software for NAA process which is designed and developed to control the ASC hardware and call GammaVision software for sample measurement. The software is developed by using National Instrument LabVIEW development package.

Data analysis and software support for the Earth radiation budget experiment

NASA Technical Reports Server (NTRS)

Edmonds, W.; Natarajan, S.

1987-01-01

Computer programming and data analysis efforts were performed in support of the Earth Radiation Budget Experiment (ERBE) at NASA/Langley. A brief description of the ERBE followed by sections describing software development and data analysis for both prelaunch and postlaunch instrument data are presented.

For operation of the Computer Software Management and Information Center (COSMIC)

NASA Technical Reports Server (NTRS)

Carmon, J. L.

1983-01-01

Computer programs for large systems of normal equations, an interactive digital signal process, structural analysis of cylindrical thrust chambers, swirling turbulent axisymmetric recirculating flows in practical isothermal combustor geometrics, computation of three dimensional combustor performance, a thermal radiation analysis system, transient response analysis, and a software design analysis are summarized.

Orbit Software Suite

NASA Technical Reports Server (NTRS)

Osgood, Cathy; Williams, Kevin; Gentry, Philip; Brownfield, Dana; Hallstrom, John; Stuit, Tim

2012-01-01

Orbit Software Suite is used to support a variety of NASA/DM (Dependable Multiprocessor) mission planning and analysis activities on the IPS (Intrusion Prevention System) platform. The suite of Orbit software tools (Orbit Design and Orbit Dynamics) resides on IPS/Linux workstations, and is used to perform mission design and analysis tasks corresponding to trajectory/ launch window, rendezvous, and proximity operations flight segments. A list of tools in Orbit Software Suite represents tool versions established during/after the Equipment Rehost-3 Project.

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.

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.

Space shuttle orbiter avionics software: Post review report for the entry FACI (First Article Configuration Inspection). [including orbital flight tests integrated system

NASA Technical Reports Server (NTRS)

Markos, H.

1978-01-01

Status of the computer programs dealing with space shuttle orbiter avionics is reported. Specific topics covered include: delivery status; SSW software; SM software; DL software; GNC software; level 3/4 testing; level 5 testing; performance analysis, SDL readiness for entry first article configuration inspection; and verification assessment.

High Performance Computing Software Applications for Space Situational Awareness

NASA Astrophysics Data System (ADS)

Giuliano, C.; Schumacher, P.; Matson, C.; Chun, F.; Duncan, B.; Borelli, K.; Desonia, R.; Gusciora, G.; Roe, K.

The High Performance Computing Software Applications Institute for Space Situational Awareness (HSAI-SSA) has completed its first full year of applications development. The emphasis of our work in this first year was in improving space surveillance sensor models and image enhancement software. These applications are the Space Surveillance Network Analysis Model (SSNAM), the Air Force Space Fence simulation (SimFence), and physically constrained iterative de-convolution (PCID) image enhancement software tool. Specifically, we have demonstrated order of magnitude speed-up in those codes running on the latest Cray XD-1 Linux supercomputer (Hoku) at the Maui High Performance Computing Center. The software applications improvements that HSAI-SSA has made, has had significant impact to the warfighter and has fundamentally changed the role of high performance computing in SSA.

A Critical Appraisal of Techniques, Software Packages, and Standards for Quantitative Proteomic Analysis

PubMed Central

Lawless, Craig; Hubbard, Simon J.; Fan, Jun; Bessant, Conrad; Hermjakob, Henning; Jones, Andrew R.

2012-01-01

Abstract New methods for performing quantitative proteome analyses based on differential labeling protocols or label-free techniques are reported in the literature on an almost monthly basis. In parallel, a correspondingly vast number of software tools for the analysis of quantitative proteomics data has also been described in the literature and produced by private companies. In this article we focus on the review of some of the most popular techniques in the field and present a critical appraisal of several software packages available to process and analyze the data produced. We also describe the importance of community standards to support the wide range of software, which may assist researchers in the analysis of data using different platforms and protocols. It is intended that this review will serve bench scientists both as a useful reference and a guide to the selection and use of different pipelines to perform quantitative proteomics data analysis. We have produced a web-based tool (http://www.proteosuite.org/?q=other_resources) to help researchers find appropriate software for their local instrumentation, available file formats, and quantitative methodology. PMID:22804616

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.

ConcreteWorks v3 training/user manual (P1) : ConcreteWorks software (P2).

DOT National Transportation Integrated Search

2017-04-01

ConcreteWorks is designed to be a user-friendly software package that can help concrete : professionals optimize concrete mixture proportioning, perform a concrete thermal analysis, and : increase the chloride diffusion service life. The software pac...

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.

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.

PuMA: the Porous Microstructure Analysis software

NASA Astrophysics Data System (ADS)

Ferguson, Joseph C.; Panerai, Francesco; Borner, Arnaud; Mansour, Nagi N.

2018-01-01

The Porous Microstructure Analysis (PuMA) software has been developed in order to compute effective material properties and perform material response simulations on digitized microstructures of porous media. PuMA is able to import digital three-dimensional images obtained from X-ray microtomography or to generate artificial microstructures. PuMA also provides a module for interactive 3D visualizations. Version 2.1 includes modules to compute porosity, volume fractions, and surface area. Two finite difference Laplace solvers have been implemented to compute the continuum tortuosity factor, effective thermal conductivity, and effective electrical conductivity. A random method has been developed to compute tortuosity factors from the continuum to rarefied regimes. Representative elementary volume analysis can be performed on each property. The software also includes a time-dependent, particle-based model for the oxidation of fibrous materials. PuMA was developed for Linux operating systems and is available as a NASA software under a US & Foreign release.

Analysis of key technologies for virtual instruments metrology

NASA Astrophysics Data System (ADS)

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

2008-12-01

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

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

A program downloader and other utility software for the DATAC bus monitor unit

NASA Technical Reports Server (NTRS)

Novacki, Stanley M., III

1987-01-01

A set or programs designed to facilitate software testing on the DATAC Bus Monitor is described. By providing a means to simplify program loading, firmware generation, and subsequent testing of programs, the overhead involved in software evaluation is reduced and that time is used more productively in performance, analysis and improvement of current software.

Precision Attitude Determination System (PADS) design and analysis. Two-axis gimbal star tracker

NASA Technical Reports Server (NTRS)

1973-01-01

Development of the Precision Attitude Determination System (PADS) focused chiefly on the two-axis gimballed star tracker and electronics design improved from that of Precision Pointing Control System (PPCS), and application of the improved tracker for PADS at geosynchronous altitude. System design, system analysis, software design, and hardware design activities are reported. The system design encompasses the PADS configuration, system performance characteristics, component design summaries, and interface considerations. The PADS design and performance analysis includes error analysis, performance analysis via attitude determination simulation, and star tracker servo design analysis. The design of the star tracker and electronics are discussed. Sensor electronics schematics are included. A detailed characterization of the application software algorithms and computer requirements is provided.

Team Software Development for Aerothermodynamic and Aerodynamic Analysis and Design

NASA Technical Reports Server (NTRS)

Alexandrov, N.; Atkins, H. L.; Bibb, K. L.; Biedron, R. T.; Carpenter, M. H.; Gnoffo, P. A.; Hammond, D. P.; Jones, W. T.; Kleb, W. L.; Lee-Rausch, E. M.

2003-01-01

A collaborative approach to software development is described. The approach employs the agile development techniques: project retrospectives, Scrum status meetings, and elements of Extreme Programming to efficiently develop a cohesive and extensible software suite. The software product under development is a fluid dynamics simulator for performing aerodynamic and aerothermodynamic analysis and design. The functionality of the software product is achieved both through the merging, with substantial rewrite, of separate legacy codes and the authorship of new routines. Examples of rapid implementation of new functionality demonstrate the benefits obtained with this agile software development process. The appendix contains a discussion of coding issues encountered while porting legacy Fortran 77 code to Fortran 95, software design principles, and a Fortran 95 coding standard.

Numerical Analysis of Coolant Flow and Heat Transfer in ITER Diagnostic First Wall

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

Khodak, A.; Loesser, G.; Zhai, Y.

2015-07-24

We performed numerical simulations of the ITER Diagnostic First Wall (DFW) using ANSYS workbench. During operation DFW will include solid main body as well as liquid coolant. Thus thermal and hydraulic analysis of the DFW was performed using conjugated heat transfer approach, in which heat transfer was resolved in both solid and liquid parts, and simultaneously fluid dynamics analysis was performed only in the liquid part. This approach includes interface between solid and liquid part of the systemAnalysis was performed using ANSYS CFX software. CFX software allows solution of heat transfer equations in solid and liquid part, and solution ofmore » the flow equations in the liquid part. Coolant flow in the DFW was assumed turbulent and was resolved using Reynolds averaged Navier-Stokes equations with Shear Stress Transport turbulence model. Meshing was performed using CFX method available within ANSYS. The data cloud for thermal loading consisting of volumetric heating and surface heating was imported into CFX Volumetric heating source was generated using Attila software. Surface heating was obtained using radiation heat transfer analysis. Our results allowed us to identify areas of excessive heating. Proposals for cooling channel relocation were made. Additional suggestions were made to improve hydraulic performance of the cooling system.« less

Arsenic removal from contaminated groundwater by membrane-integrated hybrid plant: optimization and control using Visual Basic platform.

PubMed

Chakrabortty, S; Sen, M; Pal, P

2014-03-01

A simulation software (ARRPA) has been developed in Microsoft Visual Basic platform for optimization and control of a novel membrane-integrated arsenic separation plant in the backdrop of absence of such software. The user-friendly, menu-driven software is based on a dynamic linearized mathematical model, developed for the hybrid treatment scheme. The model captures the chemical kinetics in the pre-treating chemical reactor and the separation and transport phenomena involved in nanofiltration. The software has been validated through extensive experimental investigations. The agreement between the outputs from computer simulation program and the experimental findings are excellent and consistent under varying operating conditions reflecting high degree of accuracy and reliability of the software. High values of the overall correlation coefficient (R (2) = 0.989) and Willmott d-index (0.989) are indicators of the capability of the software in analyzing performance of the plant. The software permits pre-analysis, manipulation of input data, helps in optimization and exhibits performance of an integrated plant visually on a graphical platform. Performance analysis of the whole system as well as the individual units is possible using the tool. The software first of its kind in its domain and in the well-known Microsoft Excel environment is likely to be very useful in successful design, optimization and operation of an advanced hybrid treatment plant for removal of arsenic from contaminated groundwater.

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.

Dataflow Design Tool: User's Manual

NASA Technical Reports Server (NTRS)

Jones, Robert L., III

1996-01-01

The Dataflow Design Tool is a software tool for selecting a multiprocessor scheduling solution for a class of computational problems. The problems of interest are those that can be described with a dataflow graph and are intended to be executed repetitively on a set of identical processors. Typical applications include signal processing and control law problems. The software tool implements graph-search algorithms and analysis techniques based on the dataflow paradigm. Dataflow analyses provided by the software are introduced and shown to effectively determine performance bounds, scheduling constraints, and resource requirements. The software tool provides performance optimization through the inclusion of artificial precedence constraints among the schedulable tasks. The user interface and tool capabilities are described. Examples are provided to demonstrate the analysis, scheduling, and optimization functions facilitated by the tool.

Department-Generated Microcomputer Software.

ERIC Educational Resources Information Center

Mantei, Erwin J.

1986-01-01

Explains how self-produced software can be used to perform rapid number analysis or number-crunching duties in geology classes. Reviews programs in mineralogy and petrology and identifies areas in geology where computers can be used effectively. Discusses the advantages and benefits of integrating department-generated software into a geology…

Scalable Performance Environments for Parallel Systems

NASA Technical Reports Server (NTRS)

Reed, Daniel A.; Olson, Robert D.; Aydt, Ruth A.; Madhyastha, Tara M.; Birkett, Thomas; Jensen, David W.; Nazief, Bobby A. A.; Totty, Brian K.

1991-01-01

As parallel systems expand in size and complexity, the absence of performance tools for these parallel systems exacerbates the already difficult problems of application program and system software performance tuning. Moreover, given the pace of technological change, we can no longer afford to develop ad hoc, one-of-a-kind performance instrumentation software; we need scalable, portable performance analysis tools. We describe an environment prototype based on the lessons learned from two previous generations of performance data analysis software. Our environment prototype contains a set of performance data transformation modules that can be interconnected in user-specified ways. It is the responsibility of the environment infrastructure to hide details of module interconnection and data sharing. The environment is written in C++ with the graphical displays based on X windows and the Motif toolkit. It allows users to interconnect and configure modules graphically to form an acyclic, directed data analysis graph. Performance trace data are represented in a self-documenting stream format that includes internal definitions of data types, sizes, and names. The environment prototype supports the use of head-mounted displays and sonic data presentation in addition to the traditional use of visual techniques.

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.

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

PubMed

Mägi, Reedik; Morris, Andrew P

2010-05-28

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

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)

Evaluating Games-Based Learning

ERIC Educational Resources Information Center

Hainey, Thomas; Connolly, Thomas

2010-01-01

A highly important part of software engineering education is requirements collection and analysis, one of the initial stages of the Software Development Lifecycle. No other conceptual work is as difficult to rectify at a later stage or as damaging to the overall system if performed incorrectly. As software engineering is a field with a reputation…

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.

New software for 3D fracture network analysis and visualization

NASA Astrophysics Data System (ADS)

Song, J.; Noh, Y.; Choi, Y.; Um, J.; Hwang, S.

2013-12-01

This study presents new software to perform analysis and visualization of the fracture network system in 3D. The developed software modules for the analysis and visualization, such as BOUNDARY, DISK3D, FNTWK3D, CSECT and BDM, have been developed using Microsoft Visual Basic.NET and Visualization TookKit (VTK) open-source library. Two case studies revealed that each module plays a role in construction of analysis domain, visualization of fracture geometry in 3D, calculation of equivalent pipes, production of cross-section map and management of borehole data, respectively. The developed software for analysis and visualization of the 3D fractured rock mass can be used to tackle the geomechanical problems related to strength, deformability and hydraulic behaviors of the fractured rock masses.

Database Performance Monitoring for the Photovoltaic Systems

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

Klise, Katherine A.

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

A near-infrared fluorescence-based surgical navigation system imaging software for sentinel lymph node detection

NASA Astrophysics Data System (ADS)

Ye, Jinzuo; Chi, Chongwei; Zhang, Shuang; Ma, Xibo; Tian, Jie

2014-02-01

Sentinel lymph node (SLN) in vivo detection is vital in breast cancer surgery. A new near-infrared fluorescence-based surgical navigation system (SNS) imaging software, which has been developed by our research group, is presented for SLN detection surgery in this paper. The software is based on the fluorescence-based surgical navigation hardware system (SNHS) which has been developed in our lab, and is designed specifically for intraoperative imaging and postoperative data analysis. The surgical navigation imaging software consists of the following software modules, which mainly include the control module, the image grabbing module, the real-time display module, the data saving module and the image processing module. And some algorithms have been designed to achieve the performance of the software, for example, the image registration algorithm based on correlation matching. Some of the key features of the software include: setting the control parameters of the SNS; acquiring, display and storing the intraoperative imaging data in real-time automatically; analysis and processing of the saved image data. The developed software has been used to successfully detect the SLNs in 21 cases of breast cancer patients. In the near future, we plan to improve the software performance and it will be extensively used for clinical purpose.

Simulation of Attacks for Security in Wireless Sensor Network.

PubMed

Diaz, Alvaro; Sanchez, Pablo

2016-11-18

The increasing complexity and low-power constraints of current Wireless Sensor Networks (WSN) require efficient methodologies for network simulation and embedded software performance analysis of nodes. In addition, security is also a very important feature that has to be addressed in most WSNs, since they may work with sensitive data and operate in hostile unattended environments. In this paper, a methodology for security analysis of Wireless Sensor Networks is presented. The methodology allows designing attack-aware embedded software/firmware or attack countermeasures to provide security in WSNs. The proposed methodology includes attacker modeling and attack simulation with performance analysis (node's software execution time and power consumption estimation). After an analysis of different WSN attack types, an attacker model is proposed. This model defines three different types of attackers that can emulate most WSN attacks. In addition, this paper presents a virtual platform that is able to model the node hardware, embedded software and basic wireless channel features. This virtual simulation analyzes the embedded software behavior and node power consumption while it takes into account the network deployment and topology. Additionally, this simulator integrates the previously mentioned attacker model. Thus, the impact of attacks on power consumption and software behavior/execution-time can be analyzed. This provides developers with essential information about the effects that one or multiple attacks could have on the network, helping them to develop more secure WSN systems. This WSN attack simulator is an essential element of the attack-aware embedded software development methodology that is also introduced in this work.

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

PubMed

Pecoraro, F; Luzi, D

2014-01-01

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

Dynamic CT myocardial perfusion imaging: performance of 3D semi-automated evaluation software.

PubMed

Ebersberger, Ullrich; Marcus, Roy P; Schoepf, U Joseph; Lo, Gladys G; Wang, Yining; Blanke, Philipp; Geyer, Lucas L; Gray, J Cranston; McQuiston, Andrew D; Cho, Young Jun; Scheuering, Michael; Canstein, Christian; Nikolaou, Konstantin; Hoffmann, Ellen; Bamberg, Fabian

2014-01-01

To evaluate the performance of three-dimensional semi-automated evaluation software for the assessment of myocardial blood flow (MBF) and blood volume (MBV) at dynamic myocardial perfusion computed tomography (CT). Volume-based software relying on marginal space learning and probabilistic boosting tree-based contour fitting was applied to CT myocardial perfusion imaging data of 37 subjects. In addition, all image data were analysed manually and both approaches were compared with SPECT findings. Study endpoints included time of analysis and conventional measures of diagnostic accuracy. Of 592 analysable segments, 42 showed perfusion defects on SPECT. Average analysis times for the manual and software-based approaches were 49.1 ± 11.2 and 16.5 ± 3.7 min respectively (P < 0.01). There was strong agreement between the two measures of interest (MBF, ICC = 0.91, and MBV, ICC = 0.88, both P < 0.01) and no significant difference in MBF/MBV with respect to diagnostic accuracy between the two approaches for both MBF and MBV for manual versus software-based approach; respectively; all comparisons P > 0.05. Three-dimensional semi-automated evaluation of dynamic myocardial perfusion CT data provides similar measures and diagnostic accuracy to manual evaluation, albeit with substantially reduced analysis times. This capability may aid the integration of this test into clinical workflows. • Myocardial perfusion CT is attractive for comprehensive coronary heart disease assessment. • Traditional image analysis methods are cumbersome and time-consuming. • Automated 3D perfusion software shortens analysis times. • Automated 3D perfusion software increases standardisation of myocardial perfusion CT. • Automated, standardised analysis fosters myocardial perfusion CT integration into clinical practice.

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.

A quantitative analysis of the relationship between an online homework system and student achievement in pre-calculus

NASA Astrophysics Data System (ADS)

Babaali, Parisa; Gonzalez, Lidia

2015-07-01

Supporting student success in entry-level mathematics courses at the undergraduate level has and continues to be a challenge. Recently we have seen an increased reliance on technological supports including software to supplement more traditional in-class instruction. In this paper, we explore the effects on student performance of the use of a computer software program to supplement instruction in an entry-level mathematics course at the undergraduate level, specifically, a pre-calculus course. Relying on data from multiple sections of the course over various semesters, we compare student performance in those classes utilizing the software against those in which it was not used. Quantitative analysis of the data then leads us to conclusions about the effectiveness of the software as well as recommendations for future iterations of the course and others like it.

Efficient, Multi-Scale Designs Take Flight

NASA Technical Reports Server (NTRS)

2003-01-01

Engineers can solve aerospace design problems faster and more efficiently with a versatile software product that performs automated structural analysis and sizing optimization. Collier Research Corporation's HyperSizer Structural Sizing Software is a design, analysis, and documentation tool that increases productivity and standardization for a design team. Based on established aerospace structural methods for strength, stability, and stiffness, HyperSizer can be used all the way from the conceptual design to in service support. The software originated from NASA s efforts to automate its capability to perform aircraft strength analyses, structural sizing, and weight prediction and reduction. With a strategy to combine finite element analysis with an automated design procedure, NASA s Langley Research Center led the development of a software code known as ST-SIZE from 1988 to 1995. Collier Research employees were principal developers of the code along with Langley researchers. The code evolved into one that could analyze the strength and stability of stiffened panels constructed of any material, including light-weight, fiber-reinforced composites.

An Assessmant of a Beofulf System for a Wide Class of Analysis and Design Software

NASA Technical Reports Server (NTRS)

Katz, D. S.; Cwik, T.; Kwan, B. H.; Lou, J. Z.; Springer, P. L.; Sterling, T. L.; Wang, P.

1997-01-01

This paper discusses Beowulf systems, focusing on Hyglac, the Beowulf system installed at the Jet Propulsion Laboratory. The purpose of the paper is to assess how a system of this type will perform while running a variety of scientific and engineering analysis and design software.

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.

IMCS reflight certification requirements and design specifications

NASA Technical Reports Server (NTRS)

1984-01-01

The requirements for reflight certification are established. Software requirements encompass the software programs that are resident in the PCC, DEP, PDSS, EC, or any related GSE. A design approach for the reflight software packages is recommended. These designs will be of sufficient detail to permit the implementation of reflight software. The PDSS/IMC Reflight Certification system provides the tools and mechanisms for the user to perform the reflight certification test procedures, test data capture, test data display, and test data analysis. The system as defined will be structured to permit maximum automation of reflight certification procedures and test data analysis.

Automating Risk Analysis of Software Design Models

PubMed Central

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

2014-01-01

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

Automating risk analysis of software design models.

PubMed

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

2014-01-01

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

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.

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.

Development of automation software for neutron activation analysis process in Malaysian nuclear agency

NASA Astrophysics Data System (ADS)

Yussup, N.; Rahman, N. A. A.; Ibrahim, M. M.; Mokhtar, M.; Salim, N. A. A.; Soh@Shaari, S. C.; Azman, A.

2017-01-01

Neutron Activation Analysis (NAA) process has been established in Malaysian Nuclear Agency (Nuclear Malaysia) since 1980s. Most of the procedures established especially from sample registration to sample analysis are performed manually. These manual procedures carried out by the NAA laboratory personnel are time consuming and inefficient. Hence, a software to support the system automation is developed to provide an effective method to replace redundant manual data entries and produce faster sample analysis and calculation process. This paper describes the design and development of automation software for NAA process which consists of three sub-programs. The sub-programs are sample registration, hardware control and data acquisition; and sample analysis. The data flow and connection between the sub-programs will be explained. The software is developed by using National Instrument LabView development package.

FieldTrip: Open source software for advanced analysis of MEG, EEG, and invasive electrophysiological data.

PubMed

Oostenveld, Robert; Fries, Pascal; Maris, Eric; Schoffelen, Jan-Mathijs

2011-01-01

This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete set of consistent and user-friendly high-level functions that allow experimental neuroscientists to analyze experimental data. It includes algorithms for simple and advanced analysis, such as time-frequency analysis using multitapers, source reconstruction using dipoles, distributed sources and beamformers, connectivity analysis, and nonparametric statistical permutation tests at the channel and source level. The implementation as toolbox allows the user to perform elaborate and structured analyses of large data sets using the MATLAB command line and batch scripting. Furthermore, users and developers can easily extend the functionality and implement new algorithms. The modular design facilitates the reuse in other software packages.

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.

IAC level "O" program development

NASA Technical Reports Server (NTRS)

Vos, R. G.

1982-01-01

The current status of the IAC development activity is summarized. The listed prototype software and documentation was delivered, and details were planned for development of the level 1 operational system. The planned end product IAC is required to support LSST design analysis and performance evaluation, with emphasis on the coupling of required technical disciplines. The long term IAC effectively provides two distinct features: a specific set of analysis modules (thermal, structural, controls, antenna radiation performance and instrument optical performance) that will function together with the IAC supporting software in an integrated and user friendly manner; and a general framework whereby new analysis modules can readily be incorporated into IAC or be allowed to communicate with it.

Software Tools on the Peregrine System | High-Performance Computing | NREL

Science.gov Websites

Debugger or performance analysis Tool for understanding the behavior of MPI applications. Intel VTune environment for statistical computing and graphics. VirtualGL/TurboVNC Visualization and analytics Remote Tools on the Peregrine System Software Tools on the Peregrine System NREL has a variety of

CPE--A New Perspective: The Impact of the Technology Revolution. Proceedings of the Computer Performance Evaluation Users Group Meeting (19th, San Francisco, California, October 25-28, 1983). Final Report. Reports on Computer Science and Technology.

ERIC Educational Resources Information Center

Mobray, Deborah, Ed.

Papers on local area networks (LANs), modelling techniques, software improvement, capacity planning, software engineering, microcomputers and end user computing, cost accounting and chargeback, configuration and performance management, and benchmarking presented at this conference include: (1) "Theoretical Performance Analysis of Virtual…

Comparing direct and iterative equation solvers in a large structural analysis software system

NASA Technical Reports Server (NTRS)

Poole, E. L.

1991-01-01

Two direct Choleski equation solvers and two iterative preconditioned conjugate gradient (PCG) equation solvers used in a large structural analysis software system are described. The two direct solvers are implementations of the Choleski method for variable-band matrix storage and sparse matrix storage. The two iterative PCG solvers include the Jacobi conjugate gradient method and an incomplete Choleski conjugate gradient method. The performance of the direct and iterative solvers is compared by solving several representative structural analysis problems. Some key factors affecting the performance of the iterative solvers relative to the direct solvers are identified.

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.

Image Classification Workflow Using Machine Learning Methods

NASA Astrophysics Data System (ADS)

Christoffersen, M. S.; Roser, M.; Valadez-Vergara, R.; Fernández-Vega, J. A.; Pierce, S. A.; Arora, R.

2016-12-01

Recent increases in the availability and quality of remote sensing datasets have fueled an increasing number of scientifically significant discoveries based on land use classification and land use change analysis. However, much of the software made to work with remote sensing data products, specifically multispectral images, is commercial and often prohibitively expensive. The free to use solutions that are currently available come bundled up as small parts of much larger programs that are very susceptible to bugs and difficult to install and configure. What is needed is a compact, easy to use set of tools to perform land use analysis on multispectral images. To address this need, we have developed software using the Python programming language with the sole function of land use classification and land use change analysis. We chose Python to develop our software because it is relatively readable, has a large body of relevant third party libraries such as GDAL and Spectral Python, and is free to install and use on Windows, Linux, and Macintosh operating systems. In order to test our classification software, we performed a K-means unsupervised classification, Gaussian Maximum Likelihood supervised classification, and a Mahalanobis Distance based supervised classification. The images used for testing were three Landsat rasters of Austin, Texas with a spatial resolution of 60 meters for the years of 1984 and 1999, and 30 meters for the year 2015. The testing dataset was easily downloaded using the Earth Explorer application produced by the USGS. The software should be able to perform classification based on any set of multispectral rasters with little to no modification. Our software makes the ease of land use classification using commercial software available without an expensive license.

Simulation of Attacks for Security in Wireless Sensor Network

PubMed Central

Diaz, Alvaro; Sanchez, Pablo

2016-01-01

The increasing complexity and low-power constraints of current Wireless Sensor Networks (WSN) require efficient methodologies for network simulation and embedded software performance analysis of nodes. In addition, security is also a very important feature that has to be addressed in most WSNs, since they may work with sensitive data and operate in hostile unattended environments. In this paper, a methodology for security analysis of Wireless Sensor Networks is presented. The methodology allows designing attack-aware embedded software/firmware or attack countermeasures to provide security in WSNs. The proposed methodology includes attacker modeling and attack simulation with performance analysis (node’s software execution time and power consumption estimation). After an analysis of different WSN attack types, an attacker model is proposed. This model defines three different types of attackers that can emulate most WSN attacks. In addition, this paper presents a virtual platform that is able to model the node hardware, embedded software and basic wireless channel features. This virtual simulation analyzes the embedded software behavior and node power consumption while it takes into account the network deployment and topology. Additionally, this simulator integrates the previously mentioned attacker model. Thus, the impact of attacks on power consumption and software behavior/execution-time can be analyzed. This provides developers with essential information about the effects that one or multiple attacks could have on the network, helping them to develop more secure WSN systems. This WSN attack simulator is an essential element of the attack-aware embedded software development methodology that is also introduced in this work. PMID:27869710

SIMREL: Software for Coefficient Alpha and Its Confidence Intervals with Monte Carlo Studies

ERIC Educational Resources Information Center

Yurdugul, Halil

2009-01-01

This article describes SIMREL, a software program designed for the simulation of alpha coefficients and the estimation of its confidence intervals. SIMREL runs on two alternatives. In the first one, if SIMREL is run for a single data file, it performs descriptive statistics, principal components analysis, and variance analysis of the item scores…

A multi-center study benchmarks software tools for label-free proteome quantification

PubMed Central

Gillet, Ludovic C; Bernhardt, Oliver M.; MacLean, Brendan; Röst, Hannes L.; Tate, Stephen A.; Tsou, Chih-Chiang; Reiter, Lukas; Distler, Ute; Rosenberger, George; Perez-Riverol, Yasset; Nesvizhskii, Alexey I.; Aebersold, Ruedi; Tenzer, Stefan

2016-01-01

The consistent and accurate quantification of proteins by mass spectrometry (MS)-based proteomics depends on the performance of instruments, acquisition methods and data analysis software. In collaboration with the software developers, we evaluated OpenSWATH, SWATH2.0, Skyline, Spectronaut and DIA-Umpire, five of the most widely used software methods for processing data from SWATH-MS (sequential window acquisition of all theoretical fragment ion spectra), a method that uses data-independent acquisition (DIA) for label-free protein quantification. We analyzed high-complexity test datasets from hybrid proteome samples of defined quantitative composition acquired on two different MS instruments using different SWATH isolation windows setups. For consistent evaluation we developed LFQbench, an R-package to calculate metrics of precision and accuracy in label-free quantitative MS, and report the identification performance, robustness and specificity of each software tool. Our reference datasets enabled developers to improve their software tools. After optimization, all tools provided highly convergent identification and reliable quantification performance, underscoring their robustness for label-free quantitative proteomics. PMID:27701404

A multicenter study benchmarks software tools for label-free proteome quantification.

PubMed

Navarro, Pedro; Kuharev, Jörg; Gillet, Ludovic C; Bernhardt, Oliver M; MacLean, Brendan; Röst, Hannes L; Tate, Stephen A; Tsou, Chih-Chiang; Reiter, Lukas; Distler, Ute; Rosenberger, George; Perez-Riverol, Yasset; Nesvizhskii, Alexey I; Aebersold, Ruedi; Tenzer, Stefan

2016-11-01

Consistent and accurate quantification of proteins by mass spectrometry (MS)-based proteomics depends on the performance of instruments, acquisition methods and data analysis software. In collaboration with the software developers, we evaluated OpenSWATH, SWATH 2.0, Skyline, Spectronaut and DIA-Umpire, five of the most widely used software methods for processing data from sequential window acquisition of all theoretical fragment-ion spectra (SWATH)-MS, which uses data-independent acquisition (DIA) for label-free protein quantification. We analyzed high-complexity test data sets from hybrid proteome samples of defined quantitative composition acquired on two different MS instruments using different SWATH isolation-window setups. For consistent evaluation, we developed LFQbench, an R package, to calculate metrics of precision and accuracy in label-free quantitative MS and report the identification performance, robustness and specificity of each software tool. Our reference data sets enabled developers to improve their software tools. After optimization, all tools provided highly convergent identification and reliable quantification performance, underscoring their robustness for label-free quantitative proteomics.

Some Methods of Applied Numerical Analysis to 3d Facial Reconstruction Software

NASA Astrophysics Data System (ADS)

Roşu, Şerban; Ianeş, Emilia; Roşu, Doina

2010-09-01

This paper deals with the collective work performed by medical doctors from the University Of Medicine and Pharmacy Timisoara and engineers from the Politechnical Institute Timisoara in the effort to create the first Romanian 3d reconstruction software based on CT or MRI scans and to test the created software in clinical practice.

MOFA Software for the COBRA Toolbox

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

Griesemer, Marc; Navid, Ali

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

Computer program for design and performance analysis of navigation-aid power systems. Program documentation. Volume 1: Software requirements document

NASA Technical Reports Server (NTRS)

Goltz, G.; Kaiser, L. M.; Weiner, H.

1977-01-01

A computer program has been developed for designing and analyzing the performance of solar array/battery power systems for the U.S. Coast Guard Navigational Aids. This program is called the Design Synthesis/Performance Analysis (DSPA) Computer Program. The basic function of the Design Synthesis portion of the DSPA program is to evaluate functional and economic criteria to provide specifications for viable solar array/battery power systems. The basic function of the Performance Analysis portion of the DSPA program is to simulate the operation of solar array/battery power systems under specific loads and environmental conditions. This document establishes the software requirements for the DSPA computer program, discusses the processing that occurs within the program, and defines the necessary interfaces for operation.

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

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.

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.

Toward an Efficient Icing CFD Process Using an Interactive Software Toolkit: Smagglce 2D

NASA Technical Reports Server (NTRS)

Vickerman, Mary B.; Choo, Yung K.; Schilling, Herbert W.; Baez, Marivell; Braun, Donald C.; Cotton, Barbara J.

2001-01-01

Two-dimensional CID analysis for iced airfoils can be a labor-intensive task. The software toolkit SmaggIce 2D is being developed to help streamline the CID process and provide the unique features needed for icing. When complete, it will include a combination of partially automated and fully interactive tools for all aspects of the tasks leading up to the flow analysis: geometry preparation, domain decomposition. block boundary demoralization. gridding, and linking with a flow solver. It also includes tools to perform ice shape characterization, an important aid in determining the relationship between ice characteristics and their effects on aerodynamic performance. Completed tools, work-in-progress, and planned features of the software toolkit are presented here.

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

Probabilistic structural analysis methods for select space propulsion system components

NASA Technical Reports Server (NTRS)

Millwater, H. R.; Cruse, T. A.

1989-01-01

The Probabilistic Structural Analysis Methods (PSAM) project developed at the Southwest Research Institute integrates state-of-the-art structural analysis techniques with probability theory for the design and analysis of complex large-scale engineering structures. An advanced efficient software system (NESSUS) capable of performing complex probabilistic analysis has been developed. NESSUS contains a number of software components to perform probabilistic analysis of structures. These components include: an expert system, a probabilistic finite element code, a probabilistic boundary element code and a fast probability integrator. The NESSUS software system is shown. An expert system is included to capture and utilize PSAM knowledge and experience. NESSUS/EXPERT is an interactive menu-driven expert system that provides information to assist in the use of the probabilistic finite element code NESSUS/FEM and the fast probability integrator (FPI). The expert system menu structure is summarized. The NESSUS system contains a state-of-the-art nonlinear probabilistic finite element code, NESSUS/FEM, to determine the structural response and sensitivities. A broad range of analysis capabilities and an extensive element library is present.

FieldTrip: Open Source Software for Advanced Analysis of MEG, EEG, and Invasive Electrophysiological Data

PubMed Central

Oostenveld, Robert; Fries, Pascal; Maris, Eric; Schoffelen, Jan-Mathijs

2011-01-01

This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete set of consistent and user-friendly high-level functions that allow experimental neuroscientists to analyze experimental data. It includes algorithms for simple and advanced analysis, such as time-frequency analysis using multitapers, source reconstruction using dipoles, distributed sources and beamformers, connectivity analysis, and nonparametric statistical permutation tests at the channel and source level. The implementation as toolbox allows the user to perform elaborate and structured analyses of large data sets using the MATLAB command line and batch scripting. Furthermore, users and developers can easily extend the functionality and implement new algorithms. The modular design facilitates the reuse in other software packages. PMID:21253357

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.

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.

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.

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

PubMed

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

2011-06-01

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

Implementation of interconnect simulation tools in spice

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

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

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;

Using SFOC to fly the Magellan Venus mapping mission

NASA Technical Reports Server (NTRS)

Bucher, Allen W.; Leonard, Robert E., Jr.; Short, Owen G.

1993-01-01

Traditionally, spacecraft flight operations at the Jet Propulsion Laboratory (JPL) have been performed by teams of spacecraft experts utilizing ground software designed specifically for the current mission. The Jet Propulsion Laboratory set out to reduce the cost of spacecraft mission operations by designing ground data processing software that could be used by multiple spacecraft missions, either sequentially or concurrently. The Space Flight Operations Center (SFOC) System was developed to provide the ground data system capabilities needed to monitor several spacecraft simultaneously and provide enough flexibility to meet the specific needs of individual projects. The Magellan Spacecraft Team utilizes the SFOC hardware and software designed for engineering telemetry analysis, both real-time and non-real-time. The flexibility of the SFOC System has allowed the spacecraft team to integrate their own tools with SFOC tools to perform the tasks required to operate a spacecraft mission. This paper describes how the Magellan Spacecraft Team is utilizing the SFOC System in conjunction with their own software tools to perform the required tasks of spacecraft event monitoring as well as engineering data analysis and trending.

Requirements for Next Generation Comprehensive Analysis of Rotorcraft

NASA Technical Reports Server (NTRS)

Johnson, Wayne; Data, Anubhav

2008-01-01

The unique demands of rotorcraft aeromechanics analysis have led to the development of software tools that are described as comprehensive analyses. The next generation of rotorcraft comprehensive analyses will be driven and enabled by the tremendous capabilities of high performance computing, particularly modular and scaleable software executed on multiple cores. Development of a comprehensive analysis based on high performance computing both demands and permits a new analysis architecture. This paper describes a vision of the requirements for this next generation of comprehensive analyses of rotorcraft. The requirements are described and substantiated for what must be included and justification provided for what should be excluded. With this guide, a path to the next generation code can be found.

Performing Verification and Validation in Reuse-Based Software Engineering

NASA Technical Reports Server (NTRS)

Addy, Edward A.

1999-01-01

The implementation of reuse-based software engineering not only introduces new activities to the software development process, such as domain analysis and domain modeling, it also impacts other aspects of software engineering. Other areas of software engineering that are affected include Configuration Management, Testing, Quality Control, and Verification and Validation (V&V). Activities in each of these areas must be adapted to address the entire domain or product line rather than a specific application system. This paper discusses changes and enhancements to the V&V process, in order to adapt V&V to reuse-based software engineering.

Application of Elements of Numerical Methods in the Analysis of Journal Bearings in AC Induction Motors: An Industry Case Study

ERIC Educational Resources Information Center

Ahrens, Fred; Mistry, Rajendra

2005-01-01

In product engineering there often arise design analysis problems for which a commercial software package is either unavailable or cost prohibitive. Further, these calculations often require successive iterations that can be time intensive when performed by hand, thus development of a software application is indicated. This case relates to the…

Phobos lander coding system: Software and analysis

NASA Technical Reports Server (NTRS)

Cheung, K.-M.; Pollara, F.

1988-01-01

The software developed for the decoding system used in the telemetry link of the Phobos Lander mission is described. Encoders and decoders are provided to cover the three possible telemetry configurations. The software can be used to decode actual data or to simulate the performance of the telemetry system. The theoretical properties of the codes chosen for this mission are analyzed and discussed.

Effects of photographic distance on tree crown atributes calculated using urbancrowns image analysis software

Treesearch

Mason F. Patterson; P. Eric Wiseman; Matthew F. Winn; Sang-mook Lee; Philip A. Araman

2011-01-01

UrbanCrowns is a software program developed by the USDA Forest Service that computes crown attributes using a side-view digital photograph and a few basic field measurements. From an operational standpoint, it is not known how well the software performs under varying photographic conditions for trees of diverse size, which could impact measurement reproducibility and...

An Analysis of Botnet Vulnerabilities

DTIC Science & Technology

2007-06-01

Definition Currently, the primary defense against botnets is prompt patching of vulnerable systems and antivirus software . Network monitoring can identify...IRCd software , none were identified during this effort. AFIT iv For my wife, for her caring and support throughout the course of this...are software agents designed to automatically perform tasks. Examples include web-spiders that catalog the Internet and bots found in popular online

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.

State analysis requirements database for engineering complex embedded systems

NASA Technical Reports Server (NTRS)

Bennett, Matthew B.; Rasmussen, Robert D.; Ingham, Michel D.

2004-01-01

It has become clear that spacecraft system complexity is reaching a threshold where customary methods of control are no longer affordable or sufficiently reliable. At the heart of this problem are the conventional approaches to systems and software engineering based on subsystem-level functional decomposition, which fail to scale in the tangled web of interactions typically encountered in complex spacecraft designs. Furthermore, there is a fundamental gap between the requirements on software specified by systems engineers and the implementation of these requirements by software engineers. Software engineers must perform the translation of requirements into software code, hoping to accurately capture the systems engineer's understanding of the system behavior, which is not always explicitly specified. This gap opens up the possibility for misinterpretation of the systems engineer's intent, potentially leading to software errors. This problem is addressed by a systems engineering tool called the State Analysis Database, which provides a tool for capturing system and software requirements in the form of explicit models. This paper describes how requirements for complex aerospace systems can be developed using the State Analysis Database.

A digital acquisition and elaboration system for nuclear fast pulse detection

NASA Astrophysics Data System (ADS)

Esposito, B.; Riva, M.; Marocco, D.; Kaschuck, Y.

2007-03-01

A new digital acquisition and elaboration system has been developed and assembled in ENEA-Frascati for the direct sampling of fast pulses from nuclear detectors such as scintillators and diamond detectors. The system is capable of performing the digital sampling of the pulses (200 MSamples/s, 14-bit) and the simultaneous (compressed) data transfer for further storage and software elaboration. The design (FPGA-based) is oriented to real-time applications and has been developed in order to allow acquisition with no loss of pulses and data storage for long-time intervals (tens of s at MHz pulse count rates) without the need of large on-board memory. A dedicated pulse analysis software, written in LabVIEWTM, performs the treatment of the acquired pulses, including pulse recognition, pile-up rejection, baseline removal, pulse shape particle separation and pulse height spectra analysis. The acquisition and pre-elaboration programs have been fully integrated with the analysis software.

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.

Rotorcraft performance data for AEDT : Methods of using the NASA Design and Analysis of Rotorcraft tool for developing data for AEDT's Rotorcraft Performance Model

DOT National Transportation Integrated Search

2016-09-01

This report documents use of the NASA Design and Analysis of Rotorcraft (NDARC) helicopter performance software tool in developing data for the FAAs Aviation Environmental Design Tool (AEDT). These data support the Rotorcraft Performance Model (RP...

BeadArray Expression Analysis Using Bioconductor

PubMed Central

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

2011-01-01

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

Stackfile Database

NASA Technical Reports Server (NTRS)

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

2013-01-01

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

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.

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.

Online Learning Flight Control for Intelligent Flight Control Systems (IFCS)

NASA Technical Reports Server (NTRS)

Niewoehner, Kevin R.; Carter, John (Technical Monitor)

2001-01-01

The research accomplishments for the cooperative agreement 'Online Learning Flight Control for Intelligent Flight Control Systems (IFCS)' include the following: (1) previous IFC program data collection and analysis; (2) IFC program support site (configured IFC systems support network, configured Tornado/VxWorks OS development system, made Configuration and Documentation Management Systems Internet accessible); (3) Airborne Research Test Systems (ARTS) II Hardware (developed hardware requirements specification, developing environmental testing requirements, hardware design, and hardware design development); (4) ARTS II software development laboratory unit (procurement of lab style hardware, configured lab style hardware, and designed interface module equivalent to ARTS II faceplate); (5) program support documentation (developed software development plan, configuration management plan, and software verification and validation plan); (6) LWR algorithm analysis (performed timing and profiling on algorithm); (7) pre-trained neural network analysis; (8) Dynamic Cell Structures (DCS) Neural Network Analysis (performing timing and profiling on algorithm); and (9) conducted technical interchange and quarterly meetings to define IFC research goals.

Engineering Complex Embedded Systems with State Analysis and the Mission Data System

NASA Technical Reports Server (NTRS)

Ingham, Michel D.; Rasmussen, Robert D.; Bennett, Matthew B.; Moncada, Alex C.

2004-01-01

It has become clear that spacecraft system complexity is reaching a threshold where customary methods of control are no longer affordable or sufficiently reliable. At the heart of this problem are the conventional approaches to systems and software engineering based on subsystem-level functional decomposition, which fail to scale in the tangled web of interactions typically encountered in complex spacecraft designs. Furthermore, there is a fundamental gap between the requirements on software specified by systems engineers and the implementation of these requirements by software engineers. Software engineers must perform the translation of requirements into software code, hoping to accurately capture the systems engineer's understanding of the system behavior, which is not always explicitly specified. This gap opens up the possibility for misinterpretation of the systems engineer s intent, potentially leading to software errors. This problem is addressed by a systems engineering methodology called State Analysis, which provides a process for capturing system and software requirements in the form of explicit models. This paper describes how requirements for complex aerospace systems can be developed using State Analysis and how these requirements inform the design of the system software, using representative spacecraft examples.

Prediction of ball and roller bearing thermal and kinematic performance by computer analysis

NASA Technical Reports Server (NTRS)

Pirvics, J.; Kleckner, R. J.

1983-01-01

Characteristics of good computerized analysis software are suggested. These general remarks and an overview of representative software precede a more detailed discussion of load support system analysis program structure. Particular attention is directed at a recent cylindrical roller bearing analysis as an example of the available design tools. Selected software modules are then examined to reveal the detail inherent in contemporary analysis. This leads to a brief section on current design computation which seeks to suggest when and why computerized analysis is warranted. An example concludes the argument offered for such design methodology. Finally, remarks are made concerning needs for model development to address effects which are now considered to be secondary but are anticipated to emerge to primary status in the near future.

Lean and Efficient Software: Whole-Program Optimization of Executables

DTIC Science & Technology

2015-09-30

libraries. Many levels of library interfaces—where some libraries are dynamically linked and some are provided in binary form only—significantly limit...software at build time. The opportunity: Our objective in this project is to substantially improve the performance, size, and robustness of binary ...executables by using static and dynamic binary program analysis techniques to perform whole-program optimization directly on compiled programs

Scout: high-performance heterogeneous computing made simple

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

Jablin, James; Mc Cormick, Patrick; Herlihy, Maurice

2011-01-26

Researchers must often write their own simulation and analysis software. During this process they simultaneously confront both computational and scientific problems. Current strategies for aiding the generation of performance-oriented programs do not abstract the software development from the science. Furthermore, the problem is becoming increasingly complex and pressing with the continued development of many-core and heterogeneous (CPU-GPU) architectures. To acbieve high performance, scientists must expertly navigate both software and hardware. Co-design between computer scientists and research scientists can alleviate but not solve this problem. The science community requires better tools for developing, optimizing, and future-proofing codes, allowing scientists to focusmore » on their research while still achieving high computational performance. Scout is a parallel programming language and extensible compiler framework targeting heterogeneous architectures. It provides the abstraction required to buffer scientists from the constantly-shifting details of hardware while still realizing higb-performance by encapsulating software and hardware optimization within a compiler framework.« less

Autonomous Aerobraking: Thermal Analysis and Response Surface Development

NASA Technical Reports Server (NTRS)

Dec, John A.; Thornblom, Mark N.

2011-01-01

A high-fidelity thermal model of the Mars Reconnaissance Orbiter was developed for use in an autonomous aerobraking simulation study. Response surface equations were derived from the high-fidelity thermal model and integrated into the autonomous aerobraking simulation software. The high-fidelity thermal model was developed using the Thermal Desktop software and used in all phases of the analysis. The use of Thermal Desktop exclusively, represented a change from previously developed aerobraking thermal analysis methodologies. Comparisons were made between the Thermal Desktop solutions and those developed for the previous aerobraking thermal analyses performed on the Mars Reconnaissance Orbiter during aerobraking operations. A variable sensitivity screening study was performed to reduce the number of variables carried in the response surface equations. Thermal analysis and response surface equation development were performed for autonomous aerobraking missions at Mars and Venus.

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

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.

PyPWA: A partial-wave/amplitude analysis software framework

NASA Astrophysics Data System (ADS)

Salgado, Carlos

2016-05-01

The PyPWA project aims to develop a software framework for Partial Wave and Amplitude Analysis of data; providing the user with software tools to identify resonances from multi-particle final states in photoproduction. Most of the code is written in Python. The software is divided into two main branches: one general-shell where amplitude's parameters (or any parametric model) are to be estimated from the data. This branch also includes software to produce simulated data-sets using the fitted amplitudes. A second branch contains a specific realization of the isobar model (with room to include Deck-type and other isobar model extensions) to perform PWA with an interface into the computer resources at Jefferson Lab. We are currently implementing parallelism and vectorization using the Intel's Xeon Phi family of coprocessors.

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.

Modern Computational Techniques for the HMMER Sequence Analysis

PubMed Central

2013-01-01

This paper focuses on the latest research and critical reviews on modern computing architectures, software and hardware accelerated algorithms for bioinformatics data analysis with an emphasis on one of the most important sequence analysis applications—hidden Markov models (HMM). We show the detailed performance comparison of sequence analysis tools on various computing platforms recently developed in the bioinformatics society. The characteristics of the sequence analysis, such as data and compute-intensive natures, make it very attractive to optimize and parallelize by using both traditional software approach and innovated hardware acceleration technologies. PMID:25937944

A semi-automated volumetric software for segmentation and perfusion parameter quantification of brain tumors using 320-row multidetector computed tomography: a validation study.

PubMed

Chae, Soo Young; Suh, Sangil; Ryoo, Inseon; Park, Arim; Noh, Kyoung Jin; Shim, Hackjoon; Seol, Hae Young

2017-05-01

We developed a semi-automated volumetric software, NPerfusion, to segment brain tumors and quantify perfusion parameters on whole-brain CT perfusion (WBCTP) images. The purpose of this study was to assess the feasibility of the software and to validate its performance compared with manual segmentation. Twenty-nine patients with pathologically proven brain tumors who underwent preoperative WBCTP between August 2012 and February 2015 were included. Three perfusion parameters, arterial flow (AF), equivalent blood volume (EBV), and Patlak flow (PF, which is a measure of permeability of capillaries), of brain tumors were generated by a commercial software and then quantified volumetrically by NPerfusion, which also semi-automatically segmented tumor boundaries. The quantification was validated by comparison with that of manual segmentation in terms of the concordance correlation coefficient and Bland-Altman analysis. With NPerfusion, we successfully performed segmentation and quantified whole volumetric perfusion parameters of all 29 brain tumors that showed consistent perfusion trends with previous studies. The validation of the perfusion parameter quantification exhibited almost perfect agreement with manual segmentation, with Lin concordance correlation coefficients (ρ c ) for AF, EBV, and PF of 0.9988, 0.9994, and 0.9976, respectively. On Bland-Altman analysis, most differences between this software and manual segmentation on the commercial software were within the limit of agreement. NPerfusion successfully performs segmentation of brain tumors and calculates perfusion parameters of brain tumors. We validated this semi-automated segmentation software by comparing it with manual segmentation. NPerfusion can be used to calculate volumetric perfusion parameters of brain tumors from WBCTP.

A neural net-based approach to software metrics

NASA Technical Reports Server (NTRS)

Boetticher, G.; Srinivas, Kankanahalli; Eichmann, David A.

1992-01-01

Software metrics provide an effective method for characterizing software. Metrics have traditionally been composed through the definition of an equation. This approach is limited by the fact that all the interrelationships among all the parameters be fully understood. This paper explores an alternative, neural network approach to modeling metrics. Experiments performed on two widely accepted metrics, McCabe and Halstead, indicate that the approach is sound, thus serving as the groundwork for further exploration into the analysis and design of software metrics.

The Expanded Capabilities Of The Cementitious Barriers Partnership Software Toolbox Version 2.0 - 14331

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

Burns, Heather; Flach, Greg; Smith, Frank

2014-01-10

The Cementitious Barriers Partnership (CBP) Project is a multi-disciplinary, multi-institutional collaboration supported by the U.S. Department of Energy (US DOE) Office of Tank Waste Management. The CBP program has developed a set of integrated tools (based on state-of-the-art models and leaching test methods) that help improve understanding and predictions of the long-term structural, hydraulic and chemical performance of cementitious barriers used in nuclear applications. The CBP Software Toolbox – “Version 1.0” was released early in FY2013 and was used to support DOE-EM performance assessments in evaluating various degradation mechanisms that included sulfate attack, carbonation and constituent leaching. The sulfate attackmore » analysis predicted the extent and damage that sulfate ingress will have on concrete vaults over extended time (i.e., > 1000 years) and the carbonation analysis provided concrete degradation predictions from rebar corrosion. The new release “Version 2.0” includes upgraded carbonation software and a new software module to evaluate degradation due to chloride attack. Also included in the newer version are a dual regime module allowing evaluation of contaminant release in two regimes – both fractured and un-fractured. The integrated software package has also been upgraded with new plotting capabilities and many other features that increase the “user-friendliness” of the package. Experimental work has been generated to provide data to calibrate the models to improve the credibility of the analysis and reduce the uncertainty. Tools selected for and developed under this program have been used to evaluate and predict the behavior of cementitious barriers used in near-surface engineered waste disposal systems for periods of performance up to or longer than 100 years for operating facilities and longer than 1000 years for waste disposal. The CBP Software Toolbox is and will continue to produce tangible benefits to the working DOE Performance Assessment (PA) community.« less

A Flexible Method for Producing F.E.M. Analysis of Bone Using Open-Source Software

NASA Technical Reports Server (NTRS)

Boppana, Abhishektha; Sefcik, Ryan; Meyers, Jerry G.; Lewandowski, Beth E.

2016-01-01

This project, performed in support of the NASA GRC Space Academy summer program, sought to develop an open-source workflow methodology that segmented medical image data, created a 3D model from the segmented data, and prepared the model for finite-element analysis. In an initial step, a technological survey evaluated the performance of various existing open-source software that claim to perform these tasks. However, the survey concluded that no single software exhibited the wide array of functionality required for the potential NASA application in the area of bone, muscle and bio fluidic studies. As a result, development of a series of Python scripts provided the bridging mechanism to address the shortcomings of the available open source tools. The implementation of the VTK library provided the most quick and effective means of segmenting regions of interest from the medical images; it allowed for the export of a 3D model by using the marching cubes algorithm to build a surface mesh. To facilitate the development of the model domain from this extracted information required a surface mesh to be processed in the open-source software packages Blender and Gmsh. The Preview program of the FEBio suite proved to be sufficient for volume filling the model with an unstructured mesh and preparing boundaries specifications for finite element analysis. To fully allow FEM modeling, an in house developed Python script allowed assignment of material properties on an element by element basis by performing a weighted interpolation of voxel intensity of the parent medical image correlated to published information of image intensity to material properties, such as ash density. A graphical user interface combined the Python scripts and other software into a user friendly interface. The work using Python scripts provides a potential alternative to expensive commercial software and inadequate, limited open-source freeware programs for the creation of 3D computational models. More work will be needed to validate this approach in creating finite-element models.

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.

IMMAN: free software for information theory-based chemometric analysis.

PubMed

Urias, Ricardo W Pino; Barigye, Stephen J; Marrero-Ponce, Yovani; García-Jacas, César R; Valdes-Martiní, José R; Perez-Gimenez, Facundo

2015-05-01

The features and theoretical background of a new and free computational program for chemometric analysis denominated IMMAN (acronym for Information theory-based CheMoMetrics ANalysis) are presented. This is multi-platform software developed in the Java programming language, designed with a remarkably user-friendly graphical interface for the computation of a collection of information-theoretic functions adapted for rank-based unsupervised and supervised feature selection tasks. A total of 20 feature selection parameters are presented, with the unsupervised and supervised frameworks represented by 10 approaches in each case. Several information-theoretic parameters traditionally used as molecular descriptors (MDs) are adapted for use as unsupervised rank-based feature selection methods. On the other hand, a generalization scheme for the previously defined differential Shannon's entropy is discussed, as well as the introduction of Jeffreys information measure for supervised feature selection. Moreover, well-known information-theoretic feature selection parameters, such as information gain, gain ratio, and symmetrical uncertainty are incorporated to the IMMAN software ( http://mobiosd-hub.com/imman-soft/ ), following an equal-interval discretization approach. IMMAN offers data pre-processing functionalities, such as missing values processing, dataset partitioning, and browsing. Moreover, single parameter or ensemble (multi-criteria) ranking options are provided. Consequently, this software is suitable for tasks like dimensionality reduction, feature ranking, as well as comparative diversity analysis of data matrices. Simple examples of applications performed with this program are presented. A comparative study between IMMAN and WEKA feature selection tools using the Arcene dataset was performed, demonstrating similar behavior. In addition, it is revealed that the use of IMMAN unsupervised feature selection methods improves the performance of both IMMAN and WEKA supervised algorithms. Graphic representation for Shannon's distribution of MD calculating software.

Inclusion of LCCA in Alaska flexible pavement design software manual.

DOT National Transportation Integrated Search

2012-10-01

Life cycle cost analysis is a key part for selecting materials and techniques that optimize the service life of a pavement in terms of cost and performance. While the Alaska : Flexible Pavement Design software has been in use since 2004, there is no ...

A new software for dimensional measurements in 3D endodontic root canal instrumentation.

PubMed

Sinibaldi, Raffaele; Pecci, Raffaella; Somma, Francesco; Della Penna, Stefania; Bedini, Rossella

2012-01-01

The main issue to be faced to get size estimates of 3D modification of the dental canal after endodontic treatment is the co-registration of the image stacks obtained through micro computed tomography (micro-CT) scans before and after treatment. Here quantitative analysis of micro-CT images have been performed by means of new dedicated software targeted to the analysis of root canal after endodontic instrumentation. This software analytically calculates the best superposition between the pre and post structures using the inertia tensor of the tooth. This strategy avoid minimization procedures, which can be user dependent, and time consuming. Once the co-registration have been achieved dimensional measurements have then been performed by contemporary evaluation of quantitative parameters over the two superimposed stacks of micro-CT images. The software automatically calculated the changes of volume, surface and symmetry axes in 3D occurring after the instrumentation. The calculation is based on direct comparison of the canal and canal branches selected by the user on the pre treatment image stack.

DAISY: a new software tool to test global identifiability of biological and physiological systems.

PubMed

Bellu, Giuseppina; Saccomani, Maria Pia; Audoly, Stefania; D'Angiò, Leontina

2007-10-01

A priori global identifiability is a structural property of biological and physiological models. It is considered a prerequisite for well-posed estimation, since it concerns the possibility of recovering uniquely the unknown model parameters from measured input-output data, under ideal conditions (noise-free observations and error-free model structure). Of course, determining if the parameters can be uniquely recovered from observed data is essential before investing resources, time and effort in performing actual biomedical experiments. Many interesting biological models are nonlinear but identifiability analysis for nonlinear system turns out to be a difficult mathematical problem. Different methods have been proposed in the literature to test identifiability of nonlinear models but, to the best of our knowledge, so far no software tools have been proposed for automatically checking identifiability of nonlinear models. In this paper, we describe a software tool implementing a differential algebra algorithm to perform parameter identifiability analysis for (linear and) nonlinear dynamic models described by polynomial or rational equations. Our goal is to provide the biological investigator a completely automatized software, requiring minimum prior knowledge of mathematical modelling and no in-depth understanding of the mathematical tools. The DAISY (Differential Algebra for Identifiability of SYstems) software will potentially be useful in biological modelling studies, especially in physiology and clinical medicine, where research experiments are particularly expensive and/or difficult to perform. Practical examples of use of the software tool DAISY are presented. DAISY is available at the web site http://www.dei.unipd.it/~pia/.

PSGMiner: A modular software for polysomnographic analysis.

PubMed

Umut, İlhan

2016-06-01

Sleep disorders affect a great percentage of the population. The diagnosis of these disorders is usually made by polysomnography. This paper details the development of new software to carry out feature extraction in order to perform robust analysis and classification of sleep events using polysomnographic data. The software, called PSGMiner, is a tool, which visualizes, processes and classifies bioelectrical data. The purpose of this program is to provide researchers with a platform with which to test new hypotheses by creating tests to check for correlations that are not available in commercially available software. The software is freely available under the GPL3 License. PSGMiner is composed of a number of diverse modules such as feature extraction, annotation, and machine learning modules, all of which are accessible from the main module. Using the software, it is possible to extract features of polysomnography using digital signal processing and statistical methods and to perform different analyses. The features can be classified through the use of five classification algorithms. PSGMiner offers an architecture designed for integrating new methods. Automatic scoring, which is available in almost all commercial PSG software, is not inherently available in this program, though it can be implemented by two different methodologies (machine learning and algorithms). While similar software focuses on a certain signal or event composed of a small number of modules with no expansion possibility, the software introduced here can handle all polysomnographic signals and events. The software simplifies the processing of polysomnographic signals for researchers and physicians that are not experts in computer programming. It can find correlations between different events which could help predict an oncoming event such as sleep apnea. The software could also be used for educational purposes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Software Design Improvements. Part 1; Software Benefits and Limitations

NASA Technical Reports Server (NTRS)

Lalli, Vincent R.; Packard, Michael H.; Ziemianski, Tom

1997-01-01

Computer hardware and associated software have been used for many years to process accounting information, to analyze test data and to perform engineering analysis. Now computers and software also control everything from automobiles to washing machines and the number and type of applications are growing at an exponential rate. The size of individual program has shown similar growth. Furthermore, software and hardware are used to monitor and/or control potentially dangerous products and safety-critical systems. These uses include everything from airplanes and braking systems to medical devices and nuclear plants. The question is: how can this hardware and software be made more reliable? Also, how can software quality be improved? What methodology needs to be provided on large and small software products to improve the design and how can software be verified?

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.

SEURAT: visual analytics for the integrated analysis of microarray data.

PubMed

Gribov, Alexander; Sill, Martin; Lück, Sonja; Rücker, Frank; Döhner, Konstanze; Bullinger, Lars; Benner, Axel; Unwin, Antony

2010-06-03

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. 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. The SEURAT software meets the growing needs of researchers to perform joint analysis of gene expression, genomical and clinical data.

HSCT4.0 Application: Software Requirements Specification

NASA Technical Reports Server (NTRS)

Salas, A. O.; Walsh, J. L.; Mason, B. H.; Weston, R. P.; Townsend, J. C.; Samareh, J. A.; Green, L. L.

2001-01-01

The software requirements for the High Performance Computing and Communication Program High Speed Civil Transport application project, referred to as HSCT4.0, are described. The objective of the HSCT4.0 application project is to demonstrate the application of high-performance computing techniques to the problem of multidisciplinary design optimization of a supersonic transport configuration, using high-fidelity analysis simulations. Descriptions of the various functions (and the relationships among them) that make up the multidisciplinary application as well as the constraints on the software design arc provided. This document serves to establish an agreement between the suppliers and the customer as to what the HSCT4.0 application should do and provides to the software developers the information necessary to design and implement the system.

Advanced Automation for Ion Trap Mass Spectrometry-New Opportunities for Real-Time Autonomous Analysis

NASA Technical Reports Server (NTRS)

Palmer, Peter T.; Wong, C. M.; Salmonson, J. D.; Yost, R. A.; Griffin, T. P.; Yates, N. A.; Lawless, James G. (Technical Monitor)

1994-01-01

The utility of MS/MS for both target compound analysis and the structure elucidation of unknowns has been described in a number of references. A broader acceptance of this technique has not yet been realized as it requires large, complex, and costly instrumentation which has not been competitive with more conventional techniques. Recent advancements in ion trap mass spectrometry promise to change this situation. Although the ion trap's small size, sensitivity, and ability to perform multiple stages of mass spectrometry have made it eminently suitable for on-line, real-time monitoring applications, advance automation techniques are required to make these capabilities more accessible to non-experts. Towards this end we have developed custom software for the design and implementation of MS/MS experiments. This software allows the user to take full advantage of the ion trap's versatility with respect to ionization techniques, scan proxies, and ion accumulation/ejection methods. Additionally, expert system software has been developed for autonomous target compound analysis. This software has been linked to ion trap control software and a commercial data system to bring all of the steps in the analysis cycle under control of the expert system. These software development efforts and their utilization for a number of trace analysis applications will be described.

Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data.

PubMed

Robertson, Charles E; Harris, J Kirk; Wagner, Brandie D; Granger, David; Browne, Kathy; Tatem, Beth; Feazel, Leah M; Park, Kristin; Pace, Norman R; Frank, Daniel N

2013-12-01

Studies of the human microbiome, and microbial community ecology in general, have blossomed of late and are now a burgeoning source of exciting research findings. Along with the advent of next-generation sequencing platforms, which have dramatically increased the scope of microbiome-related projects, several high-performance sequence analysis pipelines (e.g. QIIME, MOTHUR, VAMPS) are now available to investigators for microbiome analysis. The subject of our manuscript, the graphical user interface-based Explicet software package, fills a previously unmet need for a robust, yet intuitive means of integrating the outputs of the software pipelines with user-specified metadata and then visualizing the combined data.

MIDAS - A microcomputer-based image display and analysis system with full Landsat frame processing capabilities

NASA Technical Reports Server (NTRS)

Hofman, L. B.; Erickson, W. K.; Donovan, W. E.

1984-01-01

Image Display and Analysis Systems (MIDAS) developed at NASA/Ames for the analysis of Landsat MSS images is described. The MIDAS computer power and memory, graphics, resource-sharing, expansion and upgrade, environment and maintenance, and software/user-interface requirements are outlined; the implementation hardware (including 32-bit microprocessor, 512K error-correcting RAM, 70 or 140-Mbyte formatted disk drive, 512 x 512 x 24 color frame buffer, and local-area-network transceiver) and applications software (ELAS, CIE, and P-EDITOR) are characterized; and implementation problems, performance data, and costs are examined. Planned improvements in MIDAS hardware and design goals and areas of exploration for MIDAS software are discussed.

Reliability and availability analysis of a 10 kW@20 K helium refrigerator

NASA Astrophysics Data System (ADS)

Li, J.; Xiong, L. Y.; Liu, L. Q.; Wang, H. R.; Wang, B. M.

2017-02-01

A 10 kW@20 K helium refrigerator has been established in the Technical Institute of Physics and Chemistry, Chinese Academy of Sciences. To evaluate and improve this refrigerator’s reliability and availability, a reliability and availability analysis is performed. According to the mission profile of this refrigerator, a functional analysis is performed. The failure data of the refrigerator components are collected and failure rate distributions are fitted by software Weibull++ V10.0. A Failure Modes, Effects & Criticality Analysis (FMECA) is performed and the critical components with higher risks are pointed out. Software BlockSim V9.0 is used to calculate the reliability and the availability of this refrigerator. The result indicates that compressors, turbine and vacuum pump are the critical components and the key units of this refrigerator. The mitigation actions with respect to design, testing, maintenance and operation are proposed to decrease those major and medium risks.

Shadow analysis via the C+K Visioline: A technical note.

PubMed

Houser, T; Zerweck, C; Grove, G; Wickett, R

2017-11-01

This research investigated the ability of shadow analysis (via the Courage + Khazaka Visioline and Image Pro Premiere 9.0 software) to accurately assess the differences in skin topography associated with photo aging. Analyses were performed on impressions collected from a microfinish comparator scale (GAR Electroforming) as well a series of impressions collected from the crow's feet region of 9 women who represent each point on the Zerweck Crow's Feet classification scale. Analyses were performed using a Courage + Khazaka Visioline VL 650 as well as Image Pro Premiere 9.0 software. Shadow analysis showed an ability to accurately measure the groove depth when measuring impressions collected from grooves of known depth. Several shadow analysis parameters showed a correlation with the expert grader ratings of crow's feet when averaging measurements taken from the North and South directions. The Max Depth parameter in particular showed a strong correlation with the expert grader's ratings which improved when a more sophisticated analysis was performed using Image Pro Premiere. When used properly, shadow analysis is effective at accurately measuring skin surface impressions for differences in skin topography. Shadow analysis is shown to accurately assess the differences across a range of crow's feet severity correlating to a 0-8 grader scale. The Visioline VL 650 is a good tool for this measurement, with room for improvement in analysis which can be achieved through third party image analysis software. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

WISE: Automated support for software project management and measurement. M.S. Thesis

NASA Technical Reports Server (NTRS)

Ramakrishnan, Sudhakar

1995-01-01

One important aspect of software development and IV&V is measurement. Unless a software development effort is measured in some way, it is difficult to judge the effectiveness of current efforts and predict future performances. Collection of metrics and adherence to a process are difficult tasks in a software project. Change activity is a powerful indicator of project status. Automated systems that can handle change requests, issues, and other process documents provide an excellent platform for tracking the status of the project. A World Wide Web based architecture is developed for (a) making metrics collection an implicit part of the software process, (b) providing metric analysis dynamically, (c) supporting automated tools that can complement current practices of in-process improvement, and (d) overcoming geographical barrier. An operational system (WISE) instantiates this architecture allowing for the improvement of software process in a realistic environment. The tool tracks issues in software development process, provides informal communication between the users with different roles, supports to-do lists (TDL), and helps in software process improvement. WISE minimizes the time devoted to metrics collection, analysis, and captures software change data. Automated tools like WISE focus on understanding and managing the software process. The goal is improvement through measurement.

Program Aids Design Of Fluid-Circulating Systems

NASA Technical Reports Server (NTRS)

Bacskay, Allen; Dalee, Robert

1992-01-01

Computer Aided Systems Engineering and Analysis (CASE/A) program is interactive software tool for trade study and analysis, designed to increase productivity during all phases of systems engineering. Graphics-based command-driven software package provides user-friendly computing environment in which engineer analyzes performance and interface characteristics of ECLS/ATC system. Useful during all phases of spacecraft-design program, from initial conceptual design trade studies to actual flight, including pre-flight prediction and in-flight analysis of anomalies. Written in FORTRAN 77.

Realtime Decision Making on EO-1 Using Onboard Science Analysis

NASA Technical Reports Server (NTRS)

Sherwood, Robert; Chien, Steve; Davies, Ashley; Mandl, Dan; Frye, Stu

2004-01-01

Recent autonomy experiments conducted on Earth Observing 1 (EO-1) using the Autonomous Sciencecraft Experiment (ASE) flight software has been used to classify key features in hyperspectral images captured by EO-1. Furthermore, analysis is performed by this software onboard EO-1 and then used to modify the operational plan without interaction from the ground. This paper will outline the overall operations concept and provide some details and examples of the onboard science processing, science analysis, and replanning.

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.

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

NASA Technical Reports Server (NTRS)

Rainey, J. A.

1976-01-01

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

Static analysis techniques for semiautomatic synthesis of message passing software skeletons

DOE PAGES

Sottile, Matthew; Dagit, Jason; Zhang, Deli; ...

2015-06-29

The design of high-performance computing architectures demands performance analysis of large-scale parallel applications to derive various parameters concerning hardware design and software development. The process of performance analysis and benchmarking an application can be done in several ways with varying degrees of fidelity. One of the most cost-effective ways is to do a coarse-grained study of large-scale parallel applications through the use of program skeletons. The concept of a “program skeleton” that we discuss in this article is an abstracted program that is derived from a larger program where source code that is determined to be irrelevant is removed formore » the purposes of the skeleton. In this work, we develop a semiautomatic approach for extracting program skeletons based on compiler program analysis. Finally, we demonstrate correctness of our skeleton extraction process by comparing details from communication traces, as well as show the performance speedup of using skeletons by running simulations in the SST/macro simulator.« less

A new ImageJ plug-in "ActogramJ" for chronobiological analyses.

PubMed

Schmid, Benjamin; Helfrich-Förster, Charlotte; Yoshii, Taishi

2011-10-01

While the rapid development of personal computers and high-throughput recording systems for circadian rhythms allow chronobiologists to produce huge amounts of data, the software to analyze them often lags behind. Here, we announce newly developed chronobiology software that is easy to use, compatible with many different systems, and freely available. Our system can perform the most frequently used analyses: actogram drawing, periodogram analysis, and waveform analysis. The software is distributed as a pure Java plug-in for ImageJ and so works on the 3 main operating systems: Linux, Macintosh, and Windows. We believe that this free software raises the speed of data analyses and makes studying chronobiology accessible to newcomers. © 2011 The Author(s)

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.

A Biosequence-based Approach to Software Characterization

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

Oehmen, Christopher S.; Peterson, Elena S.; Phillips, Aaron R.

For many applications, it is desirable to have some process for recognizing when software binaries are closely related without relying on them to be identical or have identical segments. Some examples include monitoring utilization of high performance computing centers or service clouds, detecting freeware in licensed code, and enforcing application whitelists. But doing so in a dynamic environment is a nontrivial task because most approaches to software similarity require extensive and time-consuming analysis of a binary, or they fail to recognize executables that are similar but nonidentical. Presented herein is a novel biosequence-based method for quantifying similarity of executable binaries.more » Using this method, it is shown in an example application on large-scale multi-author codes that 1) the biosequence-based method has a statistical performance in recognizing and distinguishing between a collection of real-world high performance computing applications better than 90% of ideal; and 2) an example of using family tree analysis to tune identification for a code subfamily can achieve better than 99% of ideal performance.« less

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.

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.

ETICS: the international software engineering service for the grid

NASA Astrophysics Data System (ADS)

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

2008-07-01

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

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.

SIMPATIQCO: a server-based software suite which facilitates monitoring the time course of LC-MS performance metrics on Orbitrap instruments.

PubMed

Pichler, Peter; Mazanek, Michael; Dusberger, Frederico; Weilnböck, Lisa; Huber, Christian G; Stingl, Christoph; Luider, Theo M; Straube, Werner L; Köcher, Thomas; Mechtler, Karl

2012-11-02

While the performance of liquid chromatography (LC) and mass spectrometry (MS) instrumentation continues to increase, applications such as analyses of complete or near-complete proteomes and quantitative studies require constant and optimal system performance. For this reason, research laboratories and core facilities alike are recommended to implement quality control (QC) measures as part of their routine workflows. Many laboratories perform sporadic quality control checks. However, successive and systematic longitudinal monitoring of system performance would be facilitated by dedicated automatic or semiautomatic software solutions that aid an effortless analysis and display of QC metrics over time. We present the software package SIMPATIQCO (SIMPle AuTomatIc Quality COntrol) designed for evaluation of data from LTQ Orbitrap, Q-Exactive, LTQ FT, and LTQ instruments. A centralized SIMPATIQCO server can process QC data from multiple instruments. The software calculates QC metrics supervising every step of data acquisition from LC and electrospray to MS. For each QC metric the software learns the range indicating adequate system performance from the uploaded data using robust statistics. Results are stored in a database and can be displayed in a comfortable manner from any computer in the laboratory via a web browser. QC data can be monitored for individual LC runs as well as plotted over time. SIMPATIQCO thus assists the longitudinal monitoring of important QC metrics such as peptide elution times, peak widths, intensities, total ion current (TIC) as well as sensitivity, and overall LC-MS system performance; in this way the software also helps identify potential problems. The SIMPATIQCO software package is available free of charge.

SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC–MS Performance Metrics on Orbitrap Instruments

PubMed Central

2012-01-01

While the performance of liquid chromatography (LC) and mass spectrometry (MS) instrumentation continues to increase, applications such as analyses of complete or near-complete proteomes and quantitative studies require constant and optimal system performance. For this reason, research laboratories and core facilities alike are recommended to implement quality control (QC) measures as part of their routine workflows. Many laboratories perform sporadic quality control checks. However, successive and systematic longitudinal monitoring of system performance would be facilitated by dedicated automatic or semiautomatic software solutions that aid an effortless analysis and display of QC metrics over time. We present the software package SIMPATIQCO (SIMPle AuTomatIc Quality COntrol) designed for evaluation of data from LTQ Orbitrap, Q-Exactive, LTQ FT, and LTQ instruments. A centralized SIMPATIQCO server can process QC data from multiple instruments. The software calculates QC metrics supervising every step of data acquisition from LC and electrospray to MS. For each QC metric the software learns the range indicating adequate system performance from the uploaded data using robust statistics. Results are stored in a database and can be displayed in a comfortable manner from any computer in the laboratory via a web browser. QC data can be monitored for individual LC runs as well as plotted over time. SIMPATIQCO thus assists the longitudinal monitoring of important QC metrics such as peptide elution times, peak widths, intensities, total ion current (TIC) as well as sensitivity, and overall LC–MS system performance; in this way the software also helps identify potential problems. The SIMPATIQCO software package is available free of charge. PMID:23088386

Pilot-in-the-Loop CFD Method Development

DTIC Science & Technology

2014-06-16

CFD analysis. Coupled simulations will be run at PSU on the COCOA -4 cluster, a high performance computing cluster. The CRUNCH CFD software has...been installed on the COCOA -4 servers and initial software tests are being conducted. Initial efforts will use the Generic Frigate Shape SFS-2 to

GSFC VLBI Analysis center

NASA Technical Reports Server (NTRS)

Gordon, David; Ma, Chopo; MacMillan, Dan; Petrov, Leonid; Baver, Karen

2005-01-01

This report presents the activities of the GSFC VLBI Analysis Center during 2004. The GSFC Analysis Center analyzes all IVS sessions, makes regular IVS submissions of data and analysis products, and performs research and software development activities aimed at improving the VLBI technique.

GSFC VLBI Analysis Center

NASA Technical Reports Server (NTRS)

Gordon, David; Ma, Chopo; MacMillan, Dan; Gipson, John; Bolotin, Sergei; Le Bail, Karine; Baver, Karen

2013-01-01

This report presents the activities of the GSFC VLBI Analysis Center during 2012. The GSFC VLBI Analysis Center analyzes all IVS sessions, makes regular IVS submissions of data and analysis products, and performs research and software development aimed at improving the VLBI technique.

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.

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

NASA Astrophysics Data System (ADS)

Lelièvre, Peter G.; Grey, Melissa

2017-08-01

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

A LabVIEW®-based software for the control of the AUTORAD platform: a fully automated multisequential flow injection analysis Lab-on-Valve (MSFIA-LOV) system for radiochemical analysis.

PubMed

Barbesi, Donato; Vicente Vilas, Víctor; Millet, Sylvain; Sandow, Miguel; Colle, Jean-Yves; Aldave de Las Heras, Laura

2017-01-01

A LabVIEW ® -based software for the control of the fully automated multi-sequential flow injection analysis Lab-on-Valve (MSFIA-LOV) platform AutoRAD performing radiochemical analysis is described. The analytical platform interfaces an Arduino ® -based device triggering multiple detectors providing a flexible and fit for purpose choice of detection systems. The different analytical devices are interfaced to the PC running LabVIEW ® VI software using USB and RS232 interfaces, both for sending commands and receiving confirmation or error responses. The AUTORAD platform has been successfully applied for the chemical separation and determination of Sr, an important fission product pertinent to nuclear waste.

Knowledge-Based Parallel Performance Technology for Scientific Application Competitiveness Final Report

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

Malony, Allen D; Shende, Sameer

The primary goal of the University of Oregon's DOE "œcompetitiveness" project was to create performance technology that embodies and supports knowledge of performance data, analysis, and diagnosis in parallel performance problem solving. The target of our development activities was the TAU Performance System and the technology accomplishments reported in this and prior reports have all been incorporated in the TAU open software distribution. In addition, the project has been committed to maintaining strong interactions with the DOE SciDAC Performance Engineering Research Institute (PERI) and Center for Technology for Advanced Scientific Component Software (TASCS). This collaboration has proved valuable for translationmore » of our knowledge-based performance techniques to parallel application development and performance engineering practice. Our outreach has also extended to the DOE Advanced CompuTational Software (ACTS) collection and project. Throughout the project we have participated in the PERI and TASCS meetings, as well as the ACTS annual workshops.« less

Libre Software in Spanish Public Administrations

NASA Astrophysics Data System (ADS)

Ortega, Felipe; Lafuente, Isabel; Gato, Jose; González-Barahona, Jesús M.

Libre software started to be used in Public Administrations in Spain during the 1990s, in some isolated but interesting experiences.During the early 2000s, and specially in some regional governments, libre software started to be considered as an integral part of ITrelated policies. In 2007, it was evident that many experiences related to libre software were running in Public Administrations with different levels of success. However, no study had looked into the details of these experiences, and no comprehensive analysis had been performed to better understand the different factors that affect them.

Atmosphere Explorer control system software (version 1.0)

NASA Technical Reports Server (NTRS)

Villasenor, A.

1972-01-01

The basic design is described of the Atmosphere Explorer Control System (AECS) software used in the testing, integration, and flight contol of the AE spacecraft and experiments. The software performs several vital functions, such as issuing commands to the spacecraft and experiments, receiving and processing telemetry data, and allowing for extensive data processing by experiment analysis programs. The major processing sections are: executive control section, telemetry decommutation section, command generation section, and utility section.

Harnessing the power of emerging petascale platforms

NASA Astrophysics Data System (ADS)

Mellor-Crummey, John

2007-07-01

As part of the US Department of Energy's Scientific Discovery through Advanced Computing (SciDAC-2) program, science teams are tackling problems that require computational simulation and modeling at the petascale. A grand challenge for computer science is to develop software technology that makes it easier to harness the power of these systems to aid scientific discovery. As part of its activities, the SciDAC-2 Center for Scalable Application Development Software (CScADS) is building open source software tools to support efficient scientific computing on the emerging leadership-class platforms. In this paper, we describe two tools for performance analysis and tuning that are being developed as part of CScADS: a tool for analyzing scalability and performance, and a tool for optimizing loop nests for better node performance. We motivate these tools by showing how they apply to S3D, a turbulent combustion code under development at Sandia National Laboratory. For S3D, our node performance analysis tool helped uncover several performance bottlenecks. Using our loop nest optimization tool, we transformed S3D's most costly loop nest to reduce execution time by a factor of 2.94 for a processor working on a 503 domain.

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.

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.

Easily extensible unix software for spectral analysis, display, modification, and synthesis of musical sounds

NASA Astrophysics Data System (ADS)

Beauchamp, James W.

2002-11-01

Software has been developed which enables users to perform time-varying spectral analysis of individual musical tones or successions of them and to perform further processing of the data. The package, called sndan, is freely available in source code, uses EPS graphics for display, and is written in ansi c for ease of code modification and extension. Two analyzers, a fixed-filter-bank phase vocoder (''pvan'') and a frequency-tracking analyzer (''mqan'') constitute the analysis front end of the package. While pvan's output consists of continuous amplitudes and frequencies of harmonics, mqan produces disjoint ''tracks.'' However, another program extracts a fundamental frequency and separates harmonics from the tracks, resulting in a continuous harmonic output. ''monan'' is a program used to display harmonic data in a variety of formats, perform various spectral modifications, and perform additive resynthesis of the harmonic partials, including possible pitch-shifting and time-scaling. Sounds can also be synthesized according to a musical score using a companion synthesis language, Music 4C. Several other programs in the sndan suite can be used for specialized tasks, such as signal display and editing. Applications of the software include producing specialized sounds for music compositions or psychoacoustic experiments or as a basis for developing new synthesis algorithms.

INFOS: spectrum fitting software for NMR analysis.

PubMed

Smith, Albert A

2017-02-01

Software for fitting of NMR spectra in MATLAB is presented. Spectra are fitted in the frequency domain, using Fourier transformed lineshapes, which are derived using the experimental acquisition and processing parameters. This yields more accurate fits compared to common fitting methods that use Lorentzian or Gaussian functions. Furthermore, a very time-efficient algorithm for calculating and fitting spectra has been developed. The software also performs initial peak picking, followed by subsequent fitting and refinement of the peak list, by iteratively adding and removing peaks to improve the overall fit. Estimation of error on fitting parameters is performed using a Monte-Carlo approach. Many fitting options allow the software to be flexible enough for a wide array of applications, while still being straightforward to set up with minimal user input.

Evaluation methodologies for an advanced information processing system

NASA Technical Reports Server (NTRS)

Schabowsky, R. S., Jr.; Gai, E.; Walker, B. K.; Lala, J. H.; Motyka, P.

1984-01-01

The system concept and requirements for an Advanced Information Processing System (AIPS) are briefly described, but the emphasis of this paper is on the evaluation methodologies being developed and utilized in the AIPS program. The evaluation tasks include hardware reliability, maintainability and availability, software reliability, performance, and performability. Hardware RMA and software reliability are addressed with Markov modeling techniques. The performance analysis for AIPS is based on queueing theory. Performability is a measure of merit which combines system reliability and performance measures. The probability laws of the performance measures are obtained from the Markov reliability models. Scalar functions of this law such as the mean and variance provide measures of merit in the AIPS performability evaluations.

Integrated optomechanical analysis and testing software development at MIT Lincoln Laboratory

NASA Astrophysics Data System (ADS)

Stoeckel, Gerhard P.; Doyle, Keith B.

2013-09-01

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

Confirmatory Factor Analysis Alternative: Free, Accessible CBID Software.

PubMed

Bott, Marjorie; Karanevich, Alex G; Garrard, Lili; Price, Larry R; Mudaranthakam, Dinesh Pal; Gajewski, Byron

2018-02-01

New software that performs Classical and Bayesian Instrument Development (CBID) is reported that seamlessly integrates expert (content validity) and participant data (construct validity) to produce entire reliability estimates with smaller sample requirements. The free CBID software can be accessed through a website and used by clinical investigators in new instrument development. Demonstrations are presented of the three approaches using the CBID software: (a) traditional confirmatory factor analysis (CFA), (b) Bayesian CFA using flat uninformative prior, and (c) Bayesian CFA using content expert data (informative prior). Outcomes of usability testing demonstrate the need to make the user-friendly, free CBID software available to interdisciplinary researchers. CBID has the potential to be a new and expeditious method for instrument development, adding to our current measurement toolbox. This allows for the development of new instruments for measuring determinants of health in smaller diverse populations or populations of rare diseases.

DAISY: a new software tool to test global identifiability of biological and physiological systems

PubMed Central

Bellu, Giuseppina; Saccomani, Maria Pia; Audoly, Stefania; D’Angiò, Leontina

2009-01-01

A priori global identifiability is a structural property of biological and physiological models. It is considered a prerequisite for well-posed estimation, since it concerns the possibility of recovering uniquely the unknown model parameters from measured input-output data, under ideal conditions (noise-free observations and error-free model structure). Of course, determining if the parameters can be uniquely recovered from observed data is essential before investing resources, time and effort in performing actual biomedical experiments. Many interesting biological models are nonlinear but identifiability analysis for nonlinear system turns out to be a difficult mathematical problem. Different methods have been proposed in the literature to test identifiability of nonlinear models but, to the best of our knowledge, so far no software tools have been proposed for automatically checking identifiability of nonlinear models. In this paper, we describe a software tool implementing a differential algebra algorithm to perform parameter identifiability analysis for (linear and) nonlinear dynamic models described by polynomial or rational equations. Our goal is to provide the biological investigator a completely automatized software, requiring minimum prior knowledge of mathematical modelling and no in-depth understanding of the mathematical tools. The DAISY (Differential Algebra for Identifiability of SYstems) software will potentially be useful in biological modelling studies, especially in physiology and clinical medicine, where research experiments are particularly expensive and/or difficult to perform. Practical examples of use of the software tool DAISY are presented. DAISY is available at the web site http://www.dei.unipd.it/~pia/. PMID:17707944

A four-alternative forced choice (4AFC) software for observer performance evaluation in radiology

NASA Astrophysics Data System (ADS)

Zhang, Guozhi; Cockmartin, Lesley; Bosmans, Hilde

2016-03-01

Four-alternative forced choice (4AFC) test is a psychophysical method that can be adopted for observer performance evaluation in radiological studies. While the concept of this method is well established, difficulties to handle large image data, perform unbiased sampling, and keep track of the choice made by the observer have restricted its application in practice. In this work, we propose an easy-to-use software that can help perform 4AFC tests with DICOM images. The software suits for any experimental design that follows the 4AFC approach. It has a powerful image viewing system that favorably simulates the clinical reading environment. The graphical interface allows the observer to adjust various viewing parameters and perform the selection with very simple operations. The sampling process involved in 4AFC as well as the speed and accuracy of the choice made by the observer is precisely monitored in the background and can be easily exported for test analysis. The software has also a defensive mechanism for data management and operation control that minimizes the possibility of mistakes from user during the test. This software can largely facilitate the use of 4AFC approach in radiological observer studies and is expected to have widespread applicability.

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.

Interactive system for geomagnetic data analysis

NASA Astrophysics Data System (ADS)

Solovev, Igor

2017-10-01

The paper suggests the methods for analyzing geomagnetic field variations, which are implemented in "Aurora" software system for complex analysis of geophysical parameters. The software system allows one to perform a detailed magnetic data analysis. The methods allow one to estimate the intensity of geomagnetic perturbations and to allocate increased geomagnetic activity periods. The software system is publicly available (http://aurorasa.ikir.ru:8580, http://www.ikir.ru:8280/lsaserver/MagneticPage.jsp). This research was supported by the Russian Science Foundation (Project No. 14-11-00194).

BAM/DASS: Data Analysis Software for Sub-Microarcsecond Astrometry Device

NASA Astrophysics Data System (ADS)

Gardiol, D.; Bonino, D.; Lattanzi, M. G.; Riva, A.; Russo, F.

2010-12-01

The INAF - Osservatorio Astronomico di Torino is part of the Data Processing and Analysis Consortium (DPAC) for Gaia, a cornerstone mission of the European Space Agency. Gaia will perform global astrometry by means of two telescopes looking at the sky along two different lines of sight oriented at a fixed angle, also called basic angle. Knowledge of the basic angle fluctuations at the sub-microarcsecond level over periods of the order of the minute is crucial to reach the mission goals. A specific device, the Basic Angle Monitoring, will be dedicated to this purpose. We present here the software system we are developing to analyze the BAM data and recover the basic angle variations. This tool is integrated into the whole DPAC data analysis software.

Comparative investigation of body composition in male dogs using CT and body fat analysis software.

PubMed

Kobayashi, Toyokazu; Koie, Hiroshi; Kusumi, Akiko; Kitagawa, Masato; Kanayama, Kiichi; Otsuji, Kazuya

2014-03-01

In small animal veterinary practices, body condition score (BCS) is generally used to diagnose obesity. However, BCS does not constitute objective data. In this study, we investigated the value of using human body fat analysis software for male dogs. We also compared changes in body fat after neutering. Changes in body fat at the time of neutering (age 1 year) and 1 year later were compared by performing CT scanning and using human body fat analysis software. We found that body fat increased in all the individuals tested. In terms of the site of fat accumulation, subcutaneous fat was more pronounced than visceral fat with a marked increase on the dorsal side of the abdomen rather than the thorax.

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.

Development of program package for investigation and modeling of carbon nanostructures in diamond like carbon films with the help of Raman scattering and infrared absorption spectra line resolving

NASA Astrophysics Data System (ADS)

Hayrapetyan, David B.; Hovhannisyan, Levon; Mantashyan, Paytsar A.

2013-04-01

The analysis of complex spectra is an actual problem for modern science. The work is devoted to the creation of a software package, which analyzes spectrum in the different formats, possesses by dynamic knowledge database and self-study mechanism, performs automated analysis of the spectra compound based on knowledge database by application of certain algorithms. In the software package as searching systems, hyper-spherical random search algorithms, gradient algorithms and genetic searching algorithms were used. The analysis of Raman and IR spectrum of diamond-like carbon (DLC) samples were performed by elaborated program. After processing the data, the program immediately displays all the calculated parameters of DLC.

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

PubMed Central

2011-01-01

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

Space tug economic analysis study. Volume 2: Tug concepts analysis. Part 1: Overall approach and data generation

NASA Technical Reports Server (NTRS)

1972-01-01

An economic analysis of space tug operations is presented. The subjects discussed are: (1) data base for orbit injection stages, (2) data base for reusable space tug, (3) performance equations, (4) data integration and interpretation, (5) tug performance and mission model accomodation, (6) total program cost, (7) payload analysis, (8) computer software, and (9) comparison of tug concepts.

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 Rose and Compass for Authentication

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

White, G

2009-07-09

Many recent non-proliferation software projects include a software authentication component. In this context, 'authentication' is defined as determining that a software package performs only its intended purpose and performs that purpose correctly and reliably over many years. In addition to visual inspection by knowledgeable computer scientists, automated tools are needed to highlight suspicious code constructs both to aid the visual inspection and to guide program development. While many commercial tools are available for portions of the authentication task, they are proprietary, and have limited extensibility. An open-source, extensible tool can be customized to the unique needs of each project. ROSEmore » is an LLNL-developed robust source-to-source analysis and optimization infrastructure currently addressing large, million-line DOE applications in C, C++, and FORTRAN. It continues to be extended to support the automated analysis of binaries (x86, ARM, and PowerPC). We continue to extend ROSE to address a number of security specific requirements and apply it to software authentication for non-proliferation projects. We will give an update on the status of our work.« less

A 20-year period of orthotopic liver transplantation activity in a single center: a time series analysis performed using the R Statistical Software.

PubMed

Santori, G; Andorno, E; Morelli, N; Casaccia, M; Bottino, G; Di Domenico, S; Valente, U

2009-05-01

In many Western countries a "minimum volume rule" policy has been adopted as a quality measure for complex surgical procedures. In Italy, the National Transplant Centre set the minimum number of orthotopic liver transplantation (OLT) procedures/y at 25/center. OLT procedures performed in a single center for a reasonably large period may be treated as a time series to evaluate trend, seasonal cycles, and nonsystematic fluctuations. Between January 1, 1987 and December 31, 2006, we performed 563 cadaveric donor OLTs to adult recipients. During 2007, there were another 28 procedures. The greatest numbers of OLTs/y were performed in 2001 (n = 51), 2005 (n = 50), and 2004 (n = 49). A time series analysis performed using R Statistical Software (Foundation for Statistical Computing, Vienna, Austria), a free software environment for statistical computing and graphics, showed an incremental trend after exponential smoothing as well as after seasonal decomposition. The predicted OLT/mo for 2007 calculated with the Holt-Winters exponential smoothing applied to the previous period 1987-2006 helped to identify the months where there was a major difference between predicted and performed procedures. The time series approach may be helpful to establish a minimum volume/y at a single-center level.

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

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.

[Evaluation of performance of five bioinformatics software for the prediction of missense mutations].

PubMed

Chen, Qianting; Dai, Congling; Zhang, Qianjun; Du, Juan; Li, Wen

2016-10-01

To study the prediction performance evaluation with five kinds of bioinformatics software (SIFT, PolyPhen2, MutationTaster, Provean, MutationAssessor). From own database for genetic mutations collected over the past five years, Chinese literature database, Human Gene Mutation Database, and dbSNP, 121 missense mutations confirmed by functional studies, and 121 missense mutations suspected to be pathogenic by pedigree analysis were used as positive gold standard, while 242 missense mutations with minor allele frequency (MAF)>5% in dominant hereditary diseases were used as negative gold standard. The selected mutations were predicted with the five software. Based on the results, the performance of the five software was evaluated for their sensitivity, specificity, positive predict value, false positive rate, negative predict value, false negative rate, false discovery rate, accuracy, and receiver operating characteristic curve (ROC). In terms of sensitivity, negative predictive value and false negative rate, the rank was MutationTaster, PolyPhen2, Provean, SIFT, and MutationAssessor. For specificity and false positive rate, the rank was MutationTaster, Provean, MutationAssessor, SIFT, and PolyPhen2. For positive predict value and false discovery rate, the rank was MutationTaster, Provean, MutationAssessor, PolyPhen2, and SIFT. For area under the ROC curve (AUC) and accuracy, the rank was MutationTaster, Provean, PolyPhen2, MutationAssessor, and SIFT. The prediction performance of software may be different when using different parameters. Among the five software, MutationTaster has the best prediction performance.

Perfusion CT in acute stroke: effectiveness of automatically-generated colour maps.

PubMed

Ukmar, Maja; Degrassi, Ferruccio; Pozzi Mucelli, Roberta Antea; Neri, Francesca; Mucelli, Fabio Pozzi; Cova, Maria Assunta

2017-04-01

To evaluate the accuracy of perfusion CT (pCT) in the definition of the infarcted core and the penumbra, comparing the data obtained from the evaluation of parametric maps [cerebral blood volume (CBV), cerebral blood flow (CBF) and mean transit time (MTT)] with software-generated colour maps. A retrospective analysis was performed to identify patients with suspected acute ischaemic strokes and who had undergone unenhanced CT and pCT carried out within 4.5 h from the onset of the symptoms. A qualitative evaluation of the CBV, CBF and MTT maps was performed, followed by an analysis of the colour maps automatically generated by the software. 26 patients were identified, but a direct CT follow-up was performed only on 19 patients after 24-48 h. In the qualitative analysis, 14 patients showed perfusion abnormalities. Specifically, 29 perfusion deficit areas were detected, of which 15 areas suggested the penumbra and the remaining 14 areas suggested the infarct. As for automatically software-generated maps, 12 patients showed perfusion abnormalities. 25 perfusion deficit areas were identified, 15 areas of which suggested the penumbra and the other 10 areas the infarct. The McNemar's test showed no statistically significant difference between the two methods of evaluation in highlighting infarcted areas proved later at CT follow-up. We demonstrated how pCT provides good diagnostic accuracy in the identification of acute ischaemic lesions. The limits of identification of the lesions mainly lie at the pons level and in the basal ganglia area. Qualitative analysis has proven to be more efficient in identification of perfusion lesions in comparison with software-generated maps. However, software-generated maps have proven to be very useful in the emergency setting. Advances in knowledge: The use of CT perfusion is requested in increasingly more patients in order to optimize the treatment, thanks also to the technological evolution of CT, which now allows a whole-brain study. The need for performing CT perfusion study also in the emergency setting could represent a problem for physicians who are not used to interpreting the parametric maps (CBV, MTT etc.). The software-generated maps could be of value in these settings, helping the less expert physician in the differentiation between different areas.

Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules.

PubMed

Solernou, Albert; Hanson, Benjamin S; Richardson, Robin A; Welch, Robert; Read, Daniel J; Harlen, Oliver G; Harris, Sarah A

2018-03-01

Fluctuating Finite Element Analysis (FFEA) is a software package designed to perform continuum mechanics simulations of proteins and other globular macromolecules. It combines conventional finite element methods with stochastic thermal noise, and is appropriate for simulations of large proteins and protein complexes at the mesoscale (length-scales in the range of 5 nm to 1 μm), where there is currently a paucity of modelling tools. It requires 3D volumetric information as input, which can be low resolution structural information such as cryo-electron tomography (cryo-ET) maps or much higher resolution atomistic co-ordinates from which volumetric information can be extracted. In this article we introduce our open source software package for performing FFEA simulations which we have released under a GPLv3 license. The software package includes a C ++ implementation of FFEA, together with tools to assist the user to set up the system from Electron Microscopy Data Bank (EMDB) or Protein Data Bank (PDB) data files. We also provide a PyMOL plugin to perform basic visualisation and additional Python tools for the analysis of FFEA simulation trajectories. This manuscript provides a basic background to the FFEA method, describing the implementation of the core mechanical model and how intermolecular interactions and the solvent environment are included within this framework. We provide prospective FFEA users with a practical overview of how to set up an FFEA simulation with reference to our publicly available online tutorials and manuals that accompany this first release of the package.

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

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.

Multidisciplinary High-Fidelity Analysis and Optimization of Aerospace Vehicles. Part 1; Formulation

NASA Technical Reports Server (NTRS)

Walsh, J. L.; Townsend, J. C.; Salas, A. O.; Samareh, J. A.; Mukhopadhyay, V.; Barthelemy, J.-F.

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 highspeed civil transport configuration. The paper describes the engineering aspects of formulating the optimization by integrating these analysis codes and associated interface codes into the system. The discipline codes are integrated by using the Java programming language and a Common Object Request Broker Architecture (CORBA) compliant software product. A companion paper presents currently available results.

SEP thrust subsystem performance sensitivity analysis

NASA Technical Reports Server (NTRS)

Atkins, K. L.; Sauer, C. G., Jr.; Kerrisk, D. J.

1973-01-01

This is a two-part report on solar electric propulsion (SEP) performance sensitivity analysis. The first part describes the preliminary analysis of the SEP thrust system performance for an Encke rendezvous mission. A detailed description of thrust subsystem hardware tolerances on mission performance is included together with nominal spacecraft parameters based on these tolerances. The second part describes the method of analysis and graphical techniques used in generating the data for Part 1. Included is a description of both the trajectory program used and the additional software developed for this analysis. Part 2 also includes a comprehensive description of the use of the graphical techniques employed in this performance analysis.

Lessons Learned from Autonomous Sciencecraft Experiment

NASA Technical Reports Server (NTRS)

Chien, Steve A.; Sherwood, Rob; Tran, Daniel; Cichy, Benjamin; Rabideau, Gregg; Castano, Rebecca; Davies, Ashley; Mandl, Dan; Frye, Stuart; Trout, Bruce;

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

PubMed

Baig, Hasan; Madsen, Jan

2017-01-15

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

Quantitative assessment of human motion using video motion analysis

NASA Technical Reports Server (NTRS)

Probe, John D.

1993-01-01

In the study of the dynamics and kinematics of the human body a wide variety of technologies has been developed. Photogrammetric techniques are well documented and are known to provide reliable positional data from recorded images. Often these techniques are used in conjunction with cinematography and videography for analysis of planar motion, and to a lesser degree three-dimensional motion. Cinematography has been the most widely used medium for movement analysis. Excessive operating costs and the lag time required for film development, coupled with recent advances in video technology, have allowed video based motion analysis systems to emerge as a cost effective method of collecting and analyzing human movement. The Anthropometric and Biomechanics Lab at Johnson Space Center utilizes the video based Ariel Performance Analysis System (APAS) to develop data on shirtsleeved and space-suited human performance in order to plan efficient on-orbit intravehicular and extravehicular activities. APAS is a fully integrated system of hardware and software for biomechanics and the analysis of human performance and generalized motion measurement. Major components of the complete system include the video system, the AT compatible computer, and the proprietary software.

Tools for 3D scientific visualization in computational aerodynamics at NASA Ames Research Center

NASA Technical Reports Server (NTRS)

Bancroft, Gordon; Plessel, Todd; Merritt, Fergus; Watson, Val

1989-01-01

Hardware, software, and techniques used by the Fluid Dynamics Division (NASA) for performing visualization of computational aerodynamics, which can be applied to the visualization of flow fields from computer simulations of fluid dynamics about the Space Shuttle, are discussed. Three visualization techniques applied, post-processing, tracking, and steering, are described, as well as the post-processing software packages used, PLOT3D, SURF (Surface Modeller), GAS (Graphical Animation System), and FAST (Flow Analysis software Toolkit). Using post-processing methods a flow simulation was executed on a supercomputer and, after the simulation was complete, the results were processed for viewing. It is shown that the high-resolution, high-performance three-dimensional workstation combined with specially developed display and animation software provides a good tool for analyzing flow field solutions obtained from supercomputers.

A data dictionary approach to multilingual documentation and decision support for the diagnosis of acute abdominal pain. (COPERNICUS 555, an European concerted action).

PubMed

Ohmann, C; Eich, H P; Sippel, H

1998-01-01

This paper describes the design and development of a multilingual documentation and decision support system for the diagnosis of acute abdominal pain. The work was performed within a multi-national COPERNICUS European concerted action dealing with information technology for quality assurance in acute abdominal pain in Europe (EURO-AAP, 555). The software engineering was based on object-oriented analysis design and programming. The program cover three modules: a data dictionary, a documentation program and a knowledge based system. National versions of the software were provided and introduced into 16 centers from Central and Eastern Europe. A prospective data collection was performed in which 4020 patients were recruited. The software design has been proven to be very efficient and useful for the development of multilingual software.

Robot-operated quality control station based on the UTT method

NASA Astrophysics Data System (ADS)

Burghardt, Andrzej; Kurc, Krzysztof; Szybicki, Dariusz; Muszyńska, Magdalena; Nawrocki, Jacek

2017-03-01

This paper presents a robotic test stand for the ultrasonic transmission tomography (UTT) inspection of stator vane thickness. The article presents the method of the test stand design in Autodesk Robot Structural Analysis Professional 2013 software suite. The performance of the designed test stand solution was simulated in the RobotStudio software suite. The operating principle of the test stand measurement system is presented with a specific focus on the measurement strategy. The results of actual wall thickness measurements performed on stator vanes are presented.

GPS-based system for satellite tracking and geodesy

NASA Technical Reports Server (NTRS)

Bertiger, Willy I.; Thornton, Catherine L.

1989-01-01

High-performance receivers and data processing systems developed for GPS are reviewed. The GPS Inferred Positioning System (GIPSY) and the Orbiter Analysis and Simulation Software (OASIS) are described. The OASIS software is used to assess GPS system performance using GIPSY for data processing. Consideration is given to parameter estimation for multiday arcs, orbit repeatability, orbit prediction, daily baseline repeatability, agreement with VLBI, and ambiguity resolution. Also, the dual-frequency Rogue receiver, which can track up to eight GPS satellites simultaneously, is discussed.

Meta-analysis in Stata using gllamm.

PubMed

Bagos, Pantelis G

2015-12-01

There are several user-written programs for performing meta-analysis in Stata (Stata Statistical Software: College Station, TX: Stata Corp LP). These include metan, metareg, mvmeta, and glst. However, there are several cases for which these programs do not suffice. For instance, there is no software for performing univariate meta-analysis with correlated estimates, for multilevel or hierarchical meta-analysis, or for meta-analysis of longitudinal data. In this work, we show with practical applications that many disparate models, including but not limited to the ones mentioned earlier, can be fitted using gllamm. The software is very versatile and can handle a wide variety of models with applications in a wide range of disciplines. The method presented here takes advantage of these modeling capabilities and makes use of appropriate transformations, based on the Cholesky decomposition of the inverse of the covariance matrix, known as generalized least squares, in order to handle correlated data. The models described earlier can be thought of as special instances of a general linear mixed-model formulation, but to the author's knowledge, a general exposition in order to incorporate all the available models for meta-analysis as special cases and the instructions to fit them in Stata has not been presented so far. Source code is available at http:www.compgen.org/tools/gllamm. Copyright © 2015 John Wiley & Sons, Ltd.

Program Analyzes Radar Altimeter Data

NASA Technical Reports Server (NTRS)

Vandemark, Doug; Hancock, David; Tran, Ngan

2004-01-01

A computer program has been written to perform several analyses of radar altimeter data. The program was designed to improve on previous methods of analysis of altimeter engineering data by (1) facilitating and accelerating the analysis of large amounts of data in a more direct manner and (2) improving the ability to estimate performance of radar-altimeter instrumentation and provide data corrections. The data in question are openly available to the international scientific community and can be downloaded from anonymous file-transfer- protocol (FTP) locations that are accessible via links from altimetry Web sites. The software estimates noise in range measurements, estimates corrections for electromagnetic bias, and performs statistical analyses on various parameters for comparison of different altimeters. Whereas prior techniques used to perform similar analyses of altimeter range noise require comparison of data from repetitions of satellite ground tracks, the present software uses a high-pass filtering technique to obtain similar results from single satellite passes. Elimination of the requirement for repeat-track analysis facilitates the analysis of large amounts of satellite data to assess subtle variations in range noise.

ConfocalCheck - A Software Tool for the Automated Monitoring of Confocal Microscope Performance

PubMed Central

Hng, Keng Imm; Dormann, Dirk

2013-01-01

Laser scanning confocal microscopy has become an invaluable tool in biomedical research but regular quality testing is vital to maintain the system’s performance for diagnostic and research purposes. Although many methods have been devised over the years to characterise specific aspects of a confocal microscope like measuring the optical point spread function or the field illumination, only very few analysis tools are available. Our aim was to develop a comprehensive quality assurance framework ranging from image acquisition to automated analysis and documentation. We created standardised test data to assess the performance of the lasers, the objective lenses and other key components required for optimum confocal operation. The ConfocalCheck software presented here analyses the data fully automatically. It creates numerous visual outputs indicating potential issues requiring further investigation. By storing results in a web browser compatible file format the software greatly simplifies record keeping allowing the operator to quickly compare old and new data and to spot developing trends. We demonstrate that the systematic monitoring of confocal performance is essential in a core facility environment and how the quantitative measurements obtained can be used for the detailed characterisation of system components as well as for comparisons across multiple instruments. PMID:24224017

MSiReader v1.0: Evolving Open-Source Mass Spectrometry Imaging Software for Targeted and Untargeted Analyses.

PubMed

Bokhart, Mark T; Nazari, Milad; Garrard, Kenneth P; Muddiman, David C

2018-01-01

A major update to the mass spectrometry imaging (MSI) software MSiReader is presented, offering a multitude of newly added features critical to MSI analyses. MSiReader is a free, open-source, and vendor-neutral software written in the MATLAB platform and is capable of analyzing most common MSI data formats. A standalone version of the software, which does not require a MATLAB license, is also distributed. The newly incorporated data analysis features expand the utility of MSiReader beyond simple visualization of molecular distributions. The MSiQuantification tool allows researchers to calculate absolute concentrations from quantification MSI experiments exclusively through MSiReader software, significantly reducing data analysis time. An image overlay feature allows the incorporation of complementary imaging modalities to be displayed with the MSI data. A polarity filter has also been incorporated into the data loading step, allowing the facile analysis of polarity switching experiments without the need for data parsing prior to loading the data file into MSiReader. A quality assurance feature to generate a mass measurement accuracy (MMA) heatmap for an analyte of interest has also been added to allow for the investigation of MMA across the imaging experiment. Most importantly, as new features have been added performance has not degraded, in fact it has been dramatically improved. These new tools and the improvements to the performance in MSiReader v1.0 enable the MSI community to evaluate their data in greater depth and in less time. Graphical Abstract ᅟ.

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

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

PubMed

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

2008-08-15

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. 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. SBML-SAT provides the community of systems biologists a new tool for the analysis of their SBML models of biochemical and cellular processes.

Cooperation on Improved Isotopic Identification and Analysis Software for Portable, Electrically Cooled High-Resolution Gamma Spectrometry Systems Final Report

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

Dreyer, Jonathan G.; Wang, Tzu-Fang; Vo, Duc T.

Under a 2006 agreement between the Department of Energy (DOE) of the United States of America and the Institut de Radioprotection et de Sûreté Nucléaire (IRSN) of France, the National Nuclear Security Administration (NNSA) within DOE and IRSN initiated a collaboration to improve isotopic identification and analysis of nuclear material [i.e., plutonium (Pu) and uranium (U)]. The specific aim of the collaborative project was to develop new versions of two types of isotopic identification and analysis software: (1) the fixed-energy response-function analysis for multiple energies (FRAM) codes and (2) multi-group analysis (MGA) codes. The project is entitled Action Sheet 4more » – Cooperation on Improved Isotopic Identification and Analysis Software for Portable, Electrically Cooled, High-Resolution Gamma Spectrometry Systems (Action Sheet 4). FRAM and MGA/U235HI are software codes used to analyze isotopic ratios of U and Pu. FRAM is an application that uses parameter sets for the analysis of U or Pu. MGA and U235HI are two separate applications that analyze Pu or U, respectively. They have traditionally been used by safeguards practitioners to analyze gamma spectra acquired with high-resolution gamma spectrometry (HRGS) systems that are cooled by liquid nitrogen. However, it was discovered that these analysis programs were not as accurate when used on spectra acquired with a newer generation of more portable, electrically cooled HRGS (ECHRGS) systems. In response to this need, DOE/NNSA and IRSN collaborated to update the FRAM and U235HI codes to improve their performance with newer ECHRGS systems. Lawrence Livermore National Laboratory (LLNL) and Los Alamos National Laboratory (LANL) performed this work for DOE/NNSA.« less

Comparative Investigation of Body Composition in Male Dogs Using CT and Body Fat Analysis Software

PubMed Central

KOBAYASHI, Toyokazu; KOIE, Hiroshi; KUSUMI, Akiko; KITAGAWA, Masato; KANAYAMA, Kiichi; OTSUJI, Kazuya

2013-01-01

ABSTRACT In small animal veterinary practices, body condition score (BCS) is generally used to diagnose obesity. However, BCS does not constitute objective data. In this study, we investigated the value of using human body fat analysis software for male dogs. We also compared changes in body fat after neutering. Changes in body fat at the time of neutering (age 1 year) and 1 year later were compared by performing CT scanning and using human body fat analysis software. We found that body fat increased in all the individuals tested. In terms of the site of fat accumulation, subcutaneous fat was more pronounced than visceral fat with a marked increase on the dorsal side of the abdomen rather than the thorax. PMID:24212506

A medical software system for volumetric analysis of cerebral pathologies in magnetic resonance imaging (MRI) data.

PubMed

Egger, Jan; Kappus, Christoph; Freisleben, Bernd; Nimsky, Christopher

2012-08-01

In this contribution, a medical software system for volumetric analysis of different cerebral pathologies in magnetic resonance imaging (MRI) data is presented. The software system is based on a semi-automatic segmentation algorithm and helps to overcome the time-consuming process of volume determination during monitoring of a patient. After imaging, the parameter settings-including a seed point-are set up in the system and an automatic segmentation is performed by a novel graph-based approach. Manually reviewing the result leads to reseeding, adding seed points or an automatic surface mesh generation. The mesh is saved for monitoring the patient and for comparisons with follow-up scans. Based on the mesh, the system performs a voxelization and volume calculation, which leads to diagnosis and therefore further treatment decisions. The overall system has been tested with different cerebral pathologies-glioblastoma multiforme, pituitary adenomas and cerebral aneurysms- and evaluated against manual expert segmentations using the Dice Similarity Coefficient (DSC). Additionally, intra-physician segmentations have been performed to provide a quality measure for the presented system.

MNE Scan: Software for real-time processing of electrophysiological data.

PubMed

Esch, Lorenz; Sun, Limin; Klüber, Viktor; Lew, Seok; Baumgarten, Daniel; Grant, P Ellen; Okada, Yoshio; Haueisen, Jens; Hämäläinen, Matti S; Dinh, Christoph

2018-06-01

Magnetoencephalography (MEG) and Electroencephalography (EEG) are noninvasive techniques to study the electrophysiological activity of the human brain. Thus, they are well suited for real-time monitoring and analysis of neuronal activity. Real-time MEG/EEG data processing allows adjustment of the stimuli to the subject's responses for optimizing the acquired information especially by providing dynamically changing displays to enable neurofeedback. We introduce MNE Scan, an acquisition and real-time analysis software based on the multipurpose software library MNE-CPP. MNE Scan allows the development and application of acquisition and novel real-time processing methods in both research and clinical studies. The MNE Scan development follows a strict software engineering process to enable approvals required for clinical software. We tested the performance of MNE Scan in several device-independent use cases, including, a clinical epilepsy study, real-time source estimation, and Brain Computer Interface (BCI) application. Compared to existing tools we propose a modular software considering clinical software requirements expected by certification authorities. At the same time the software is extendable and freely accessible. We conclude that MNE Scan is the first step in creating a device-independent open-source software to facilitate the transition from basic neuroscience research to both applied sciences and clinical applications. Copyright © 2018 Elsevier B.V. All rights reserved.

DigitalVHI--a freeware open-source software application to capture the Voice Handicap Index and other questionnaire data in various languages.

PubMed

Herbst, Christian T; Oh, Jinook; Vydrová, Jitka; Švec, Jan G

2015-07-01

In this short report we introduce DigitalVHI, a free open-source software application for obtaining Voice Handicap Index (VHI) and other questionnaire data, which can be put on a computer in clinics and used in clinical practice. The software can simplify performing clinical studies since it makes the VHI scores directly available for analysis in a digital form. It can be downloaded from http://www.christian-herbst.org/DigitalVHI/.

Optimization of Skill Retention in the U.S. Army through Initial Training Analysis and Design. Volume 1.

DTIC Science & Technology

1983-05-01

observed end-of-course scores for tasks .- trained to criterion. e MGA software was calibrated to provide retention estimates at two levels of...exceed the MGA estimates. Thirty-five out of forty, or 87.5,o0 of the tasks met this expectation. . * For these first trial data, MGA software predicts...Objective: The objective of this effort was to perform an operational test of the capability of MGA Skill Training and Retention (STAR©) software to

A CAMAC-VME-Macintosh data acquisition system for nuclear experiments

NASA Astrophysics Data System (ADS)

Anzalone, A.; Giustolisi, F.

1989-10-01

A multiprocessor system for data acquisition and analysis in low-energy nuclear physics has been realized. The system is built around CAMAC, the VMEbus, and the Macintosh PC. Multiprocessor software has been developed, using RTF, MACsys, and CERN cross-software. The execution of several programs that run on several VME CPUs and on an external PC is coordinated by a mailbox protocol. No operating system is used on the VME CPUs. The hardware, software, and system performance are described.

JCMT COADD: UKT14 continuum and photometry data reduction

NASA Astrophysics Data System (ADS)

Hughes, David; Oliveira, Firmin J.; Tilanus, Remo P. J.; Jenness, Tim

2014-11-01

COADD was used to reduce photometry and continuum data from the UKT14 instrument on the James Clerk Maxwell Telescope in the 1990s. The software can co-add multiple observations and perform sigma clipping and Kolmogorov-Smirnov statistical analysis. Additional information on the software is available in the JCMT Spring 1993 newsletter (large PDF).

NASA Applications for Computational Electromagnetic Analysis

NASA Technical Reports Server (NTRS)

Lewis, Catherine C.; Trout, Dawn H.; Krome, Mark E.; Perry, Thomas A.

2011-01-01

Computational Electromagnetic Software is used by NASA to analyze the compatibility of systems too large or too complex for testing. Recent advances in software packages and computer capabilities have made it possible to determine the effects of a transmitter inside a launch vehicle fairing, better analyze the environment threats, and perform on-orbit replacements with assured electromagnetic compatibility.

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.

Performance Analysis of Saturated Induction Motors by Virtual Tests

ERIC Educational Resources Information Center

Ojaghi, M.; Faiz, J.; Kazemi, M.; Rezaei, M.

2012-01-01

Many undergraduate-level electrical machines textbooks give detailed treatments of the performance of induction motors. Students can deepen this understanding of motor performance by performing the appropriate practical work in laboratories or in simulation using proper software packages. This paper considers various common and less-common tests…

RMP Guidance for Offsite Consequence Analysis

EPA Pesticide Factsheets

Offsite consequence analysis (OCA) consists of a worst-case release scenario and alternative release scenarios. OCA is required from facilities with chemicals above threshold quantities. RMP*Comp software can be used to perform calculations described here.

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.

Neutron imaging data processing using the Mantid framework

NASA Astrophysics Data System (ADS)

Pouzols, Federico M.; Draper, Nicholas; Nagella, Sri; Yang, Erica; Sajid, Ahmed; Ross, Derek; Ritchie, Brian; Hill, John; Burca, Genoveva; Minniti, Triestino; Moreton-Smith, Christopher; Kockelmann, Winfried

2016-09-01

Several imaging instruments are currently being constructed at neutron sources around the world. The Mantid software project provides an extensible framework that supports high-performance computing for data manipulation, analysis and visualisation of scientific data. At ISIS, IMAT (Imaging and Materials Science & Engineering) will offer unique time-of-flight neutron imaging techniques which impose several software requirements to control the data reduction and analysis. Here we outline the extensions currently being added to Mantid to provide specific support for neutron imaging requirements.

CWA 15793 2011 Planning and Implementation Tool

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

Gross, Alan; Nail, George

This software, built on an open source platform called Electron (runs on Chromium and Node.js), is designed to assist organizations in the implementation of a biorisk management system consistent with the requirements of the international, publicly available guidance document CEN Workshop Agreement 15793:2011 (CWA 15793). The software includes tools for conducting organizational gap analysis against CWA 15793 requirements, planning tools to support the implementation of CWA 15793 requirements, and performance monitoring support. The gap analysis questions are based on the text of CWA 15793, and its associated guidance document, CEN Workshop Agreement 16393:2012. The authors have secured permission from themore » publisher of CWA 15793, the European Committee for Standardization (CEN), to use language from the document in the software, with the understanding that the software will be made available freely, without charge.« less

Automatic Generation of Overlays and Offset Values Based on Visiting Vehicle Telemetry and RWS Visuals

NASA Technical Reports Server (NTRS)

Dunne, Matthew J.

2011-01-01

The development of computer software as a tool to generate visual displays has led to an overall expansion of automated computer generated images in the aerospace industry. These visual overlays are generated by combining raw data with pre-existing data on the object or objects being analyzed on the screen. The National Aeronautics and Space Administration (NASA) uses this computer software to generate on-screen overlays when a Visiting Vehicle (VV) is berthing with the International Space Station (ISS). In order for Mission Control Center personnel to be a contributing factor in the VV berthing process, computer software similar to that on the ISS must be readily available on the ground to be used for analysis. In addition, this software must perform engineering calculations and save data for further analysis.

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.

Choosing a software design method for real-time Ada applications: JSD process inversion as a means to tailor a design specification to the performance requirements and target machine

NASA Technical Reports Server (NTRS)

Withey, James V.

1986-01-01

The validity of real-time software is determined by its ability to execute on a computer within the time constraints of the physical system it is modeling. In many applications the time constraints are so critical that the details of process scheduling are elevated to the requirements analysis phase of the software development cycle. It is not uncommon to find specifications for a real-time cyclic executive program included to assumed in such requirements. It was found that prelininary designs structured around this implementation abscure the data flow of the real world system that is modeled and that it is consequently difficult and costly to maintain, update and reuse the resulting software. A cyclic executive is a software component that schedules and implicitly synchronizes the real-time software through periodic and repetitive subroutine calls. Therefore a design method is sought that allows the deferral of process scheduling to the later stages of design. The appropriate scheduling paradigm must be chosen given the performance constraints, the largest environment and the software's lifecycle. The concept of process inversion is explored with respect to the cyclic executive.

OpenMSI: A High-Performance Web-Based Platform for Mass Spectrometry Imaging

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

Rubel, Oliver; Greiner, Annette; Cholia, Shreyas

Mass spectrometry imaging (MSI) enables researchers to directly probe endogenous molecules directly within the architecture of the biological matrix. Unfortunately, efficient access, management, and analysis of the data generated by MSI approaches remain major challenges to this rapidly developing field. Despite the availability of numerous dedicated file formats and software packages, it is a widely held viewpoint that the biggest challenge is simply opening, sharing, and analyzing a file without loss of information. Here we present OpenMSI, a software framework and platform that addresses these challenges via an advanced, high-performance, extensible file format and Web API for remote data accessmore » (http://openmsi.nersc.gov). The OpenMSI file format supports storage of raw MSI data, metadata, and derived analyses in a single, self-describing format based on HDF5 and is supported by a large range of analysis software (e.g., Matlab and R) and programming languages (e.g., C++, Fortran, and Python). Careful optimization of the storage layout of MSI data sets using chunking, compression, and data replication accelerates common, selective data access operations while minimizing data storage requirements and are critical enablers of rapid data I/O. The OpenMSI file format has shown to provide >2000-fold improvement for image access operations, enabling spectrum and image retrieval in less than 0.3 s across the Internet even for 50 GB MSI data sets. To make remote high-performance compute resources accessible for analysis and to facilitate data sharing and collaboration, we describe an easy-to-use yet powerful Web API, enabling fast and convenient access to MSI data, metadata, and derived analysis results stored remotely to facilitate high-performance data analysis and enable implementation of Web based data sharing, visualization, and analysis.« less

Paramedir: A Tool for Programmable Performance Analysis

NASA Technical Reports Server (NTRS)

Jost, Gabriele; Labarta, Jesus; Gimenez, Judit

2004-01-01

Performance analysis of parallel scientific applications is time consuming and requires great expertise in areas such as programming paradigms, system software, and computer hardware architectures. In this paper we describe a tool that facilitates the programmability of performance metric calculations thereby allowing the automation of the analysis and reducing the application development time. We demonstrate how the system can be used to capture knowledge and intuition acquired by advanced parallel programmers in order to be transferred to novice users.

User manual of the CATSS system (version 1.0) communication analysis tool for space station

NASA Technical Reports Server (NTRS)

Tsang, C. S.; Su, Y. T.; Lindsey, W. C.

1983-01-01

The Communication Analysis Tool for the Space Station (CATSS) is a FORTRAN language software package capable of predicting the communications links performance for the Space Station (SS) communication and tracking (C & T) system. An interactive software package was currently developed to run on the DEC/VAX computers. The CATSS models and evaluates the various C & T links of the SS, which includes the modulation schemes such as Binary-Phase-Shift-Keying (BPSK), BPSK with Direct Sequence Spread Spectrum (PN/BPSK), and M-ary Frequency-Shift-Keying with Frequency Hopping (FH/MFSK). Optical Space Communication link is also included. CATSS is a C & T system engineering tool used to predict and analyze the system performance for different link environment. Identification of system weaknesses is achieved through evaluation of performance with varying system parameters. System tradeoff for different values of system parameters are made based on the performance prediction.

Plateletpheresis efficiency and mathematical correction of software-derived platelet yield prediction: A linear regression and ROC modeling approach.

PubMed

Jaime-Pérez, José Carlos; Jiménez-Castillo, Raúl Alberto; Vázquez-Hernández, Karina Elizabeth; Salazar-Riojas, Rosario; Méndez-Ramírez, Nereida; Gómez-Almaguer, David

2017-10-01

Advances in automated cell separators have improved the efficiency of plateletpheresis and the possibility of obtaining double products (DP). We assessed cell processor accuracy of predicted platelet (PLT) yields with the goal of a better prediction of DP collections. This retrospective proof-of-concept study included 302 plateletpheresis procedures performed on a Trima Accel v6.0 at the apheresis unit of a hematology department. Donor variables, software predicted yield and actual PLT yield were statistically evaluated. Software prediction was optimized by linear regression analysis and its optimal cut-off to obtain a DP assessed by receiver operating characteristic curve (ROC) modeling. Three hundred and two plateletpheresis procedures were performed; in 271 (89.7%) occasions, donors were men and in 31 (10.3%) women. Pre-donation PLT count had the best direct correlation with actual PLT yield (r = 0.486. P < .001). Means of software machine-derived values differed significantly from actual PLT yield, 4.72 × 10 11 vs.6.12 × 10 11 , respectively, (P < .001). The following equation was developed to adjust these values: actual PLT yield= 0.221 + (1.254 × theoretical platelet yield). ROC curve model showed an optimal apheresis device software prediction cut-off of 4.65 × 10 11 to obtain a DP, with a sensitivity of 82.2%, specificity of 93.3%, and an area under the curve (AUC) of 0.909. Trima Accel v6.0 software consistently underestimated PLT yields. Simple correction derived from linear regression analysis accurately corrected this underestimation and ROC analysis identified a precise cut-off to reliably predict a DP. © 2016 Wiley Periodicals, Inc.

Object-Oriented Multi-Disciplinary Design, Analysis, and Optimization Tool

NASA Technical Reports Server (NTRS)

Pak, Chan-gi

2011-01-01

An Object-Oriented Optimization (O3) tool was developed that leverages existing tools and practices, and allows the easy integration and adoption of new state-of-the-art software. At the heart of the O3 tool is the Central Executive Module (CEM), which can integrate disparate software packages in a cross platform network environment so as to quickly perform optimization and design tasks in a cohesive, streamlined manner. This object-oriented framework can integrate the analysis codes for multiple disciplines instead of relying on one code to perform the analysis for all disciplines. The CEM was written in FORTRAN and the script commands for each performance index were submitted through the use of the FORTRAN Call System command. In this CEM, the user chooses an optimization methodology, defines objective and constraint functions from performance indices, and provides starting and side constraints for continuous as well as discrete design variables. The structural analysis modules such as computations of the structural weight, stress, deflection, buckling, and flutter and divergence speeds have been developed and incorporated into the O3 tool to build an object-oriented Multidisciplinary Design, Analysis, and Optimization (MDAO) tool.

ExaSAT: An exascale co-design tool for performance modeling

DOE PAGES

Unat, Didem; Chan, Cy; Zhang, Weiqun; ...

2015-02-09

One of the emerging challenges to designing HPC systems is understanding and projecting the requirements of exascale applications. In order to determine the performance consequences of different hardware designs, analytic models are essential because they can provide fast feedback to the co-design centers and chip designers without costly simulations. However, current attempts to analytically model program performance typically rely on the user manually specifying a performance model. Here we introduce the ExaSAT framework that automates the extraction of parameterized performance models directly from source code using compiler analysis. The parameterized analytic model enables quantitative evaluation of a broad range ofmore » hardware design trade-offs and software optimizations on a variety of different performance metrics, with a primary focus on data movement as a metric. Finally, we demonstrate the ExaSAT framework’s ability to perform deep code analysis of a proxy application from the Department of Energy Combustion Co-design Center to illustrate its value to the exascale co-design process. ExaSAT analysis provides insights into the hardware and software trade-offs and lays the groundwork for exploring a more targeted set of design points using cycle-accurate architectural simulators.« less

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.

A system for automatic evaluation of simulation software

NASA Technical Reports Server (NTRS)

Ryan, J. P.; Hodges, B. C.

1976-01-01

Within the field of computer software, simulation and verification are complementary processes. Simulation methods can be used to verify software by performing variable range analysis. More general verification procedures, such as those described in this paper, can be implicitly, viewed as attempts at modeling the end-product software. From software requirement methodology, each component of the verification system has some element of simulation to it. Conversely, general verification procedures can be used to analyze simulation software. A dynamic analyzer is described which can be used to obtain properly scaled variables for an analog simulation, which is first digitally simulated. In a similar way, it is thought that the other system components and indeed the whole system itself have the potential of being effectively used in a simulation environment.

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.

The use of lower resolution viewing devices for mammographic interpretation: implications for education and training.

PubMed

Chen, Yan; James, Jonathan J; Turnbull, Anne E; Gale, Alastair G

2015-10-01

To establish whether lower resolution, lower cost viewing devices have the potential to deliver mammographic interpretation training. On three occasions over eight months, fourteen consultant radiologists and reporting radiographers read forty challenging digital mammography screening cases on three different displays: a digital mammography workstation, a standard LCD monitor, and a smartphone. Standard image manipulation software was available for use on all three devices. Receiver operating characteristic (ROC) analysis and ANOVA (Analysis of Variance) were used to determine the significance of differences in performance between the viewing devices with/without the application of image manipulation software. The effect of reader's experience was also assessed. Performance was significantly higher (p < .05) on the mammography workstation compared to the other two viewing devices. When image manipulation software was applied to images viewed on the standard LCD monitor, performance improved to mirror levels seen on the mammography workstation with no significant difference between the two. Image interpretation on the smartphone was uniformly poor. Film reader experience had no significant effect on performance across all three viewing devices. Lower resolution standard LCD monitors combined with appropriate image manipulation software are capable of displaying mammographic pathology, and are potentially suitable for delivering mammographic interpretation training. • This study investigates potential devices for training in mammography interpretation. • Lower resolution standard LCD monitors are potentially suitable for mammographic interpretation training. • The effect of image manipulation tools on mammography workstation viewing is insignificant. • Reader experience had no significant effect on performance in all viewing devices. • Smart phones are not suitable for displaying mammograms.

An easy and inexpensive method for quantitative analysis of endothelial damage by using vital dye staining and Adobe Photoshop software.

PubMed

Saad, Hisham A; Terry, Mark A; Shamie, Neda; Chen, Edwin S; Friend, Daniel F; Holiman, Jeffrey D; Stoeger, Christopher

2008-08-01

We developed a simple, practical, and inexpensive technique to analyze areas of endothelial cell loss and/or damage over the entire corneal area after vital dye staining by using a readily available, off-the-shelf, consumer software program, Adobe Photoshop. The purpose of this article is to convey a method of quantifying areas of cell loss and/or damage. Descemet-stripping automated endothelial keratoplasty corneal transplant surgery was performed by using 5 precut corneas on a human cadaver eye. Corneas were removed and stained with trypan blue and alizarin red S and subsequently photographed. Quantitative assessment of endothelial damage was performed by using Adobe Photoshop 7.0 software. The average difference for cell area damage for analyses performed by 1 observer twice was 1.41%. For analyses performed by 2 observers, the average difference was 1.71%. Three masked observers were 100% successful in matching the randomized stained corneas to their randomized processed Adobe images. Vital dye staining of corneal endothelial cells can be combined with Adobe Photoshop software to yield a quantitative assessment of areas of acute endothelial cell loss and/or damage. This described technique holds promise for a more consistent and accurate method to evaluate the surgical trauma to the endothelial cell layer in laboratory models. This method of quantitative analysis can probably be generalized to any area of research that involves areas that are differentiated by color or contrast.

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.

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

NASA Technical Reports Server (NTRS)

Cheng, U.

1989-01-01

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

The Imagery of Sound

NASA Technical Reports Server (NTRS)

2000-01-01

Automated Analysis Corporation's COMET is a suite of acoustic analysis software for advanced noise prediction. It analyzes the origin, radiation, and scattering of noise, and supplies information on how to achieve noise reduction and improve sound characteristics. COMET's Structural Acoustic Foam Engineering (SAFE) module extends the sound field analysis capability of foam and other materials. SAFE shows how noise travels while airborne, how it travels within a structure, and how these media interact to affect other aspects of the transmission of noise. The COMET software reduces design time and expense while optimizing a final product's acoustical performance. COMET was developed through SBIR funding and Langley Research Center for Automated Analysis Corporation.

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

Salama, A.; Mikhail, M.

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

Monitoring the CMS strip tracker readout system

NASA Astrophysics Data System (ADS)

Mersi, S.; Bainbridge, R.; Baulieu, G.; Bel, S.; Cole, J.; Cripps, N.; Delaere, C.; Drouhin, F.; Fulcher, J.; Giassi, A.; Gross, L.; Hahn, K.; Mirabito, L.; Nikolic, M.; Tkaczyk, S.; Wingham, M.

2008-07-01

The CMS Silicon Strip Tracker at the LHC comprises a sensitive area of approximately 200 m2 and 10 million readout channels. Its data acquisition system is based around a custom analogue front-end chip. Both the control and the readout of the front-end electronics are performed by off-detector VME boards in the counting room, which digitise the raw event data and perform zero-suppression and formatting. The data acquisition system uses the CMS online software framework to configure, control and monitor the hardware components and steer the data acquisition. The first data analysis is performed online within the official CMS reconstruction framework, which provides many services, such as distributed analysis, access to geometry and conditions data, and a Data Quality Monitoring tool based on the online physics reconstruction. The data acquisition monitoring of the Strip Tracker uses both the data acquisition and the reconstruction software frameworks in order to provide real-time feedback to shifters on the operational state of the detector, archiving for later analysis and possibly trigger automatic recovery actions in case of errors. Here we review the proposed architecture of the monitoring system and we describe its software components, which are already in place, the various monitoring streams available, and our experiences of operating and monitoring a large-scale system.

Theoretical and software considerations for general dynamic analysis using multilevel substructured models

NASA Technical Reports Server (NTRS)

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

1985-01-01

The dynamic analysis of complex structural systems using the finite element method and multilevel substructured models is presented. The fixed-interface method is selected for substructure reduction because of its efficiency, accuracy, and adaptability to restart and reanalysis. This method is extended to reduction of substructures which are themselves composed of reduced substructures. The implementation and performance of the method in a general purpose software system is emphasized. Solution algorithms consistent with the chosen data structures are presented. It is demonstrated that successful finite element software requires the use of software executives to supplement the algorithmic language. The complexity of the implementation of restart and reanalysis porcedures illustrates the need for executive systems to support the noncomputational aspects of the software. It is shown that significant computational efficiencies can be achieved through proper use of substructuring and reduction technbiques without sacrificing solution accuracy. The restart and reanalysis capabilities and the flexible procedures for multilevel substructured modeling gives economical yet accurate analyses of complex structural systems.

Development of Software to Model AXAF-I Image Quality

NASA Technical Reports Server (NTRS)

Ahmad, Anees; Hawkins, Lamar

1996-01-01

This draft final report describes the work performed under the delivery order number 145 from May 1995 through August 1996. The scope of work included a number of software development tasks for the performance modeling of AXAF-I. A number of new capabilities and functions have been added to the GT software, which is the command mode version of the GRAZTRACE software, originally developed by MSFC. A structural data interface has been developed for the EAL (old SPAR) finite element analysis FEA program, which is being used by MSFC Structural Analysis group for the analysis of AXAF-I. This interface utility can read the structural deformation file from the EAL and other finite element analysis programs such as NASTRAN and COSMOS/M, and convert the data to a suitable format that can be used for the deformation ray-tracing to predict the image quality for a distorted mirror. There is a provision in this utility to expand the data from finite element models assuming 180 degrees symmetry. This utility has been used to predict image characteristics for the AXAF-I HRMA, when subjected to gravity effects in the horizontal x-ray ground test configuration. The development of the metrology data processing interface software has also been completed. It can read the HDOS FITS format surface map files, manipulate and filter the metrology data, and produce a deformation file, which can be used by GT for ray tracing for the mirror surface figure errors. This utility has been used to determine the optimum alignment (axial spacing and clocking) for the four pairs of AXAF-I mirrors. Based on this optimized alignment, the geometric images and effective focal lengths for the as built mirrors were predicted to cross check the results obtained by Kodak.

A Review of CEFA Software: Comprehensive Exploratory Factor Analysis Program

ERIC Educational Resources Information Center

Lee, Soon-Mook

2010-01-01

CEFA 3.02(Browne, Cudeck, Tateneni, & Mels, 2008) is a factor analysis computer program designed to perform exploratory factor analysis. It provides the main properties that are needed for exploratory factor analysis, namely a variety of factoring methods employing eight different discrepancy functions to be minimized to yield initial…

Analysis of wheel rim - Material and manufacturing aspects

NASA Astrophysics Data System (ADS)

Misra, Sheelam; Singh, Abhiraaj; James, Eldhose

2018-05-01

The tire in an automobile is supported by the rim of the wheel and its shape and dimensions should be adjusted to accommodate a specified tire. In this study, a tire of car wheel rim belonging to the disc wheel category is considered. Design is an important industrial operation used to define and specify the quality of the product. The design and modelling reduces the risk of damage involved in the manufacturing process. The design performed on this wheel rim is done on modelling software. After designing the model, it is imported for analysis purposes. The analysis software is used to calculate the different types of force, stresses, torque, and pressures acting upon the rim of the wheel and it reduces the time spent by a human for mathematical calculations. The analysis carried out considers two different materials namely structural steel and aluminium. Both materials are analyzed and their performance is noted.

High-performance equation solvers and their impact on finite element analysis

NASA Technical Reports Server (NTRS)

Poole, Eugene L.; Knight, Norman F., Jr.; Davis, D. Dale, Jr.

1990-01-01

The role of equation solvers in modern structural analysis software is described. Direct and iterative equation solvers which exploit vectorization on modern high-performance computer systems are described and compared. The direct solvers are two Cholesky factorization methods. The first method utilizes a novel variable-band data storage format to achieve very high computation rates and the second method uses a sparse data storage format designed to reduce the number of operations. The iterative solvers are preconditioned conjugate gradient methods. Two different preconditioners are included; the first uses a diagonal matrix storage scheme to achieve high computation rates and the second requires a sparse data storage scheme and converges to the solution in fewer iterations that the first. The impact of using all of the equation solvers in a common structural analysis software system is demonstrated by solving several representative structural analysis problems.

High-performance equation solvers and their impact on finite element analysis

NASA Technical Reports Server (NTRS)

Poole, Eugene L.; Knight, Norman F., Jr.; Davis, D. D., Jr.

1992-01-01

The role of equation solvers in modern structural analysis software is described. Direct and iterative equation solvers which exploit vectorization on modern high-performance computer systems are described and compared. The direct solvers are two Cholesky factorization methods. The first method utilizes a novel variable-band data storage format to achieve very high computation rates and the second method uses a sparse data storage format designed to reduce the number od operations. The iterative solvers are preconditioned conjugate gradient methods. Two different preconditioners are included; the first uses a diagonal matrix storage scheme to achieve high computation rates and the second requires a sparse data storage scheme and converges to the solution in fewer iterations that the first. The impact of using all of the equation solvers in a common structural analysis software system is demonstrated by solving several representative structural analysis problems.

Technical note on the validation of a semi-automated image analysis software application for estrogen and progesterone receptor detection in breast cancer.

PubMed

Krecsák, László; Micsik, Tamás; Kiszler, Gábor; Krenács, Tibor; Szabó, Dániel; Jónás, Viktor; Császár, Gergely; Czuni, László; Gurzó, Péter; Ficsor, Levente; Molnár, Béla

2011-01-18

The immunohistochemical detection of estrogen (ER) and progesterone (PR) receptors in breast cancer is routinely used for prognostic and predictive testing. Whole slide digitalization supported by dedicated software tools allows quantization of the image objects (e.g. cell membrane, nuclei) and an unbiased analysis of immunostaining results. Validation studies of image analysis applications for the detection of ER and PR in breast cancer specimens provided strong concordance between the pathologist's manual assessment of slides and scoring performed using different software applications. The effectiveness of two connected semi-automated image analysis software (NuclearQuant v. 1.13 application for Pannoramic™ Viewer v. 1.14) for determination of ER and PR status in formalin-fixed paraffin embedded breast cancer specimens immunostained with the automated Leica Bond Max system was studied. First the detection algorithm was calibrated to the scores provided an independent assessors (pathologist), using selected areas from 38 small digital slides (created from 16 cases) containing a mean number of 195 cells. Each cell was manually marked and scored according to the Allred-system combining frequency and intensity scores. The performance of the calibrated algorithm was tested on 16 cases (14 invasive ductal carcinoma, 2 invasive lobular carcinoma) against the pathologist's manual scoring of digital slides. The detection was calibrated to 87 percent object detection agreement and almost perfect Total Score agreement (Cohen's kappa 0.859, quadratic weighted kappa 0.986) from slight or moderate agreement at the start of the study, using the un-calibrated algorithm. The performance of the application was tested against the pathologist's manual scoring of digital slides on 53 regions of interest of 16 ER and PR slides covering all positivity ranges, and the quadratic weighted kappa provided almost perfect agreement (κ = 0.981) among the two scoring schemes. NuclearQuant v. 1.13 application for Pannoramic™ Viewer v. 1.14 software application proved to be a reliable image analysis tool for pathologists testing ER and PR status in breast cancer.

Study of fault tolerant software technology for dynamic systems

NASA Technical Reports Server (NTRS)

Caglayan, A. K.; Zacharias, G. L.

1985-01-01

The major aim of this study is to investigate the feasibility of using systems-based failure detection isolation and compensation (FDIC) techniques in building fault-tolerant software and extending them, whenever possible, to the domain of software fault tolerance. First, it is shown that systems-based FDIC methods can be extended to develop software error detection techniques by using system models for software modules. In particular, it is demonstrated that systems-based FDIC techniques can yield consistency checks that are easier to implement than acceptance tests based on software specifications. Next, it is shown that systems-based failure compensation techniques can be generalized to the domain of software fault tolerance in developing software error recovery procedures. Finally, the feasibility of using fault-tolerant software in flight software is investigated. In particular, possible system and version instabilities, and functional performance degradation that may occur in N-Version programming applications to flight software are illustrated. Finally, a comparative analysis of N-Version and recovery block techniques in the context of generic blocks in flight software is presented.

Automotive Design

NASA Technical Reports Server (NTRS)

1991-01-01

Analytical Design Service Corporation, Ann Arbor, MI, used NASTRAN (a NASA Structural Analysis program that analyzes a design and predicts how parts will perform) in tests of transmissions, engine cooling systems, internal engine parts, and body components. They also use it to design future automobiles. Analytical software can save millions by allowing computer simulated analysis of performance even before prototypes are built.

Automated Sensitivity Analysis of Interplanetary Trajectories

NASA Technical Reports Server (NTRS)

Knittel, Jeremy; Hughes, Kyle; Englander, Jacob; Sarli, Bruno

2017-01-01

This work describes a suite of Python tools known as the Python EMTG Automated Trade Study Application (PEATSA). PEATSA was written to automate the operation of trajectory optimization software, simplify the process of performing sensitivity analysis, and was ultimately found to out-perform a human trajectory designer in unexpected ways. These benefits will be discussed and demonstrated on sample mission designs.

Performance analysis of mini-propellers based on FlightGear

NASA Astrophysics Data System (ADS)

Vogeltanz, Tomáš

2016-06-01

This paper presents a performance analysis of three mini-propellers based on the FlightGear flight simulator. Although a basic propeller analysis has to be performed before the use of FlightGear, for a complex and more practical performance analysis, it is advantageous to use a propeller model in cooperation with a particular aircraft model. This approach may determine whether the propeller has sufficient quality in respect of aircraft requirements. In the first section, the software used for the analysis is illustrated. Then, the parameters of the analyzed mini-propellers and the tested UAV are described. Finally, the main section shows and discusses the results of the performance analysis of the mini-propellers.

j5 DNA assembly design automation.

PubMed

Hillson, Nathan J

2014-01-01

Modern standardized methodologies, described in detail in the previous chapters of this book, have enabled the software-automated design of optimized DNA construction protocols. This chapter describes how to design (combinatorial) scar-less DNA assembly protocols using the web-based software j5. j5 assists biomedical and biotechnological researchers construct DNA by automating the design of optimized protocols for flanking homology sequence as well as type IIS endonuclease-mediated DNA assembly methodologies. Unlike any other software tool available today, j5 designs scar-less combinatorial DNA assembly protocols, performs a cost-benefit analysis to identify which portions of an assembly process would be less expensive to outsource to a DNA synthesis service provider, and designs hierarchical DNA assembly strategies to mitigate anticipated poor assembly junction sequence performance. Software integrated with j5 add significant value to the j5 design process through graphical user-interface enhancement and downstream liquid-handling robotic laboratory automation.

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.

The contaminant analysis automation robot implementation for the automated laboratory

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

Younkin, J.R.; Igou, R.E.; Urenda, T.D.

1995-12-31

The Contaminant Analysis Automation (CAA) project defines the automated laboratory as a series of standard laboratory modules (SLM) serviced by a robotic standard support module (SSM). These SLMs are designed to allow plug-and-play integration into automated systems that perform standard analysis methods (SAM). While the SLMs are autonomous in the execution of their particular chemical processing task, the SAM concept relies on a high-level task sequence controller (TSC) to coordinate the robotic delivery of materials requisite for SLM operations, initiate an SLM operation with the chemical method dependent operating parameters, and coordinate the robotic removal of materials from the SLMmore » when its commands and events has been established to allow ready them for transport operations as well as performing the Supervisor and Subsystems (GENISAS) software governs events from the SLMs and robot. The Intelligent System Operating Environment (ISOE) enables the inter-process communications used by GENISAS. CAA selected the Hewlett-Packard Optimized Robot for Chemical Analysis (ORCA) and its associated Windows based Methods Development Software (MDS) as the robot SSM. The MDS software is used to teach the robot each SLM position and required material port motions. To allow the TSC to command these SLM motions, a hardware and software implementation was required that allowed message passing between different operating systems. This implementation involved the use of a Virtual Memory Extended (VME) rack with a Force CPU-30 computer running VxWorks; a real-time multitasking operating system, and a Radiuses PC compatible VME computer running MDS. A GENISAS server on The Force computer accepts a transport command from the TSC, a GENISAS supervisor, over Ethernet and notifies software on the RadiSys PC of the pending command through VMEbus shared memory. The command is then delivered to the MDS robot control software using a Windows Dynamic Data Exchange conversation.« less

cluster trials v. 1.0

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

Mitchell, John; Castillo, Andrew

2016-09-21

This software contains a set of python modules – input, search, cluster, analysis; these modules read input files containing spatial coordinates and associated attributes which can be used to perform nearest neighbor search (spatial indexing via kdtree), cluster analysis/identification, and calculation of spatial statistics for analysis.

Manual on performance of traffic signal systems: assessment of operations and maintenance : [summary].

DOT National Transportation Integrated Search

2017-05-01

In this project, Florida Atlantic University researchers developed a methodology and software tools that allow objective, quantitative analysis of the performance of signal systems. : The researchers surveyed the state of practice for traffic signal ...

Waste management facility accident analysis (WASTE ACC) system: software for analysis of waste management alternatives

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

Kohout, E.F.; Folga, S.; Mueller, C.

1996-03-01

This paper describes the Waste Management Facility Accident Analysis (WASTE{underscore}ACC) software, which was developed at Argonne National Laboratory (ANL) to support the US Department of Energy`s (DOE`s) Waste Management (WM) Programmatic Environmental Impact Statement (PEIS). WASTE{underscore}ACC is a decision support and database system that is compatible with Microsoft{reg_sign} Windows{trademark}. It assesses potential atmospheric releases from accidents at waste management facilities. The software provides the user with an easy-to-use tool to determine the risk-dominant accident sequences for the many possible combinations of process technologies, waste and facility types, and alternative cases described in the WM PEIS. In addition, its structure willmore » allow additional alternative cases and assumptions to be tested as part of the future DOE programmatic decision-making process. The WASTE{underscore}ACC system demonstrates one approach to performing a generic, systemwide evaluation of accident risks at waste management facilities. The advantages of WASTE{underscore}ACC are threefold. First, the software gets waste volume and radiological profile data that were used to perform other WM PEIS-related analyses directly from the WASTE{underscore}MGMT system. Second, the system allows for a consistent analysis across all sites and waste streams, which enables decision makers to understand more fully the trade-offs among various policy options and scenarios. Third, the system is easy to operate; even complex scenario runs are completed within minutes.« less

Software Cost Estimation Using a Decision Graph Process: A Knowledge Engineering Approach

NASA Technical Reports Server (NTRS)

Stukes, Sherry; Spagnuolo, John, Jr.

2011-01-01

This paper is not a description per se of the efforts by two software cost analysts. Rather, it is an outline of the methodology used for FSW cost analysis presented in a form that would serve as a foundation upon which others may gain insight into how to perform FSW cost analyses for their own problems at hand.

DoD Key Technologies Plan

DTIC Science & Technology

1992-07-01

methodologies ; software performance analysis; software testing; and concurrent languages. Finally, efforts in algorithms, which are primarily designed to upgrade...These codes provide a powerful research tool for testing new concepts and designs prior to experimental implementation. DoE’s laser program has also...development, and specially designed production facilities. World leadership in bth non -fluorinated and fluorinated materials resides in the U.S. but Japan

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

NASA Technical Reports Server (NTRS)

1981-01-01

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

Analysis of Performance of Stereoscopic-Vision Software

NASA Technical Reports Server (NTRS)

Kim, Won; Ansar, Adnan; Steele, Robert; Steinke, Robert

2007-01-01

A team of JPL researchers has analyzed stereoscopic vision software and produced a document describing its performance. This software is of the type used in maneuvering exploratory robotic vehicles on Martian terrain. The software in question utilizes correlations between portions of the images recorded by two electronic cameras to compute stereoscopic disparities, which, in conjunction with camera models, are used in computing distances to terrain points to be included in constructing a three-dimensional model of the terrain. The analysis included effects of correlation- window size, a pyramidal image down-sampling scheme, vertical misalignment, focus, maximum disparity, stereo baseline, and range ripples. Contributions of sub-pixel interpolation, vertical misalignment, and foreshortening to stereo correlation error were examined theoretically and experimentally. It was found that camera-calibration inaccuracy contributes to both down-range and cross-range error but stereo correlation error affects only the down-range error. Experimental data for quantifying the stereo disparity error were obtained by use of reflective metrological targets taped to corners of bricks placed at known positions relative to the cameras. For the particular 1,024-by-768-pixel cameras of the system analyzed, the standard deviation of the down-range disparity error was found to be 0.32 pixel.

Sampling and sensitivity analyses tools (SaSAT) for computational modelling

PubMed Central

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

2008-01-01

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

Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules

PubMed Central

Solernou, Albert

2018-01-01

Fluctuating Finite Element Analysis (FFEA) is a software package designed to perform continuum mechanics simulations of proteins and other globular macromolecules. It combines conventional finite element methods with stochastic thermal noise, and is appropriate for simulations of large proteins and protein complexes at the mesoscale (length-scales in the range of 5 nm to 1 μm), where there is currently a paucity of modelling tools. It requires 3D volumetric information as input, which can be low resolution structural information such as cryo-electron tomography (cryo-ET) maps or much higher resolution atomistic co-ordinates from which volumetric information can be extracted. In this article we introduce our open source software package for performing FFEA simulations which we have released under a GPLv3 license. The software package includes a C ++ implementation of FFEA, together with tools to assist the user to set up the system from Electron Microscopy Data Bank (EMDB) or Protein Data Bank (PDB) data files. We also provide a PyMOL plugin to perform basic visualisation and additional Python tools for the analysis of FFEA simulation trajectories. This manuscript provides a basic background to the FFEA method, describing the implementation of the core mechanical model and how intermolecular interactions and the solvent environment are included within this framework. We provide prospective FFEA users with a practical overview of how to set up an FFEA simulation with reference to our publicly available online tutorials and manuals that accompany this first release of the package. PMID:29570700

Improving the performance of minimizers and winnowing schemes.

PubMed

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

2017-07-15

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. 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. The software used for this analysis is available on GitHub: https://github.com/gmarcais/minimizers.git . gmarcais@cs.cmu.edu or carlk@cs.cmu.edu. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Software Development Standard Processes (SDSP)

NASA Technical Reports Server (NTRS)

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

Off-the-shelf mobile handset environments for deploying accelerometer based gait and activity analysis algorithms.

PubMed

Hynes, Martin; Wang, Han; Kilmartin, Liam

2009-01-01

Over the last decade, there has been substantial research interest in the application of accelerometry data for many forms of automated gait and activity analysis algorithms. This paper introduces a summary of new "of-the-shelf" mobile phone handset platforms containing embedded accelerometers which support the development of custom software to implement real time analysis of the accelerometer data. An overview of the main software programming environments which support the development of such software, including Java ME based JSR 256 API, C++ based Motion Sensor API and the Python based "aXYZ" module, is provided. Finally, a sample application is introduced and its performance evaluated in order to illustrate how a standard mobile phone can be used to detect gait activity using such a non-intrusive and easily accepted sensing platform.

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.

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.

Quantitative Analysis of Color Differences within High Contrast, Low Power Reversible Electrophoretic Displays

DOE PAGES

Giera, Brian; Bukosky, Scott; Lee, Elaine; ...

2018-01-23

Here, quantitative color analysis is performed on videos of high contrast, low power reversible electrophoretic deposition (EPD)-based displays operated under different applied voltages. This analysis is coded in an open-source software, relies on a color differentiation metric, ΔE * 00, derived from digital video, and provides an intuitive relationship between the operating conditions of the devices and their performance. Time-dependent ΔE * 00 color analysis reveals color relaxation behavior, recoverability for different voltage sequences, and operating conditions that can lead to optimal performance.

Quantitative Analysis of Color Differences within High Contrast, Low Power Reversible Electrophoretic Displays

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

Giera, Brian; Bukosky, Scott; Lee, Elaine

Here, quantitative color analysis is performed on videos of high contrast, low power reversible electrophoretic deposition (EPD)-based displays operated under different applied voltages. This analysis is coded in an open-source software, relies on a color differentiation metric, ΔE * 00, derived from digital video, and provides an intuitive relationship between the operating conditions of the devices and their performance. Time-dependent ΔE * 00 color analysis reveals color relaxation behavior, recoverability for different voltage sequences, and operating conditions that can lead to optimal performance.

Software Tools to Support the Assessment of System Health

NASA Technical Reports Server (NTRS)

Melcher, Kevin J.

2013-01-01

This presentation provides an overview of three software tools that were developed by the NASA Glenn Research Center to support the assessment of system health: the Propulsion Diagnostic Method Evaluation Strategy (ProDIMES), the Systematic Sensor Selection Strategy (S4), and the Extended Testability Analysis (ETA) tool. Originally developed to support specific NASA projects in aeronautics and space, these software tools are currently available to U.S. citizens through the NASA Glenn Software Catalog. The ProDiMES software tool was developed to support a uniform comparison of propulsion gas path diagnostic methods. Methods published in the open literature are typically applied to dissimilar platforms with different levels of complexity. They often address different diagnostic problems and use inconsistent metrics for evaluating performance. As a result, it is difficult to perform a one ]to ]one comparison of the various diagnostic methods. ProDIMES solves this problem by serving as a theme problem to aid in propulsion gas path diagnostic technology development and evaluation. The overall goal is to provide a tool that will serve as an industry standard, and will truly facilitate the development and evaluation of significant Engine Health Management (EHM) capabilities. ProDiMES has been developed under a collaborative project of The Technical Cooperation Program (TTCP) based on feedback provided by individuals within the aircraft engine health management community. The S4 software tool provides a framework that supports the optimal selection of sensors for health management assessments. S4 is structured to accommodate user ]defined applications, diagnostic systems, search techniques, and system requirements/constraints. One or more sensor suites that maximize this performance while meeting other user ]defined system requirements that are presumed to exist. S4 provides a systematic approach for evaluating combinations of sensors to determine the set or sets of sensors that optimally meet the performance goals and the constraints. It identifies optimal sensor suite solutions by utilizing a merit (i.e., cost) function with one of several available optimization approaches. As part of its analysis, S4 can expose fault conditions that are difficult to diagnose due to an incomplete diagnostic philosophy and/or a lack of sensors. S4 was originally developed and applied to liquid rocket engines. It was subsequently used to study the optimized selection of sensors for a simulation ]based aircraft engine diagnostic system. The ETA Tool is a software ]based analysis tool that augments the testability analysis and reporting capabilities of a commercial ]off ]the ]shelf (COTS) package. An initial diagnostic assessment is performed by the COTS software using a user ]developed, qualitative, directed ]graph model of the system being analyzed. The ETA Tool accesses system design information captured within the model and the associated testability analysis output to create a series of six reports for various system engineering needs. These reports are highlighted in the presentation. The ETA Tool was developed by NASA to support the verification of fault management requirements early in the Launch Vehicle process. Due to their early development during the design process, the TEAMS ]based diagnostic model and the ETA Tool were able to positively influence the system design by highlighting gaps in failure detection, fault isolation, and failure recovery.

Runtime Speculative Software-Only Fault Tolerance

DTIC Science & Technology

2012-06-01

reliability of RSFT, a in-depth analysis on its window of vulnerability is also discussed and measured via simulated fault injection. The performance...propagation of faults through the entire program. For optimal performance, these techniques have to use herotic alias analysis to find the minimum set of...affect program output. No program source code or alias analysis is needed to analyze the fault propagation ahead of time. 2.3 Limitations of Existing

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.

On the release of cppxfel for processing X-ray free-electron laser images.

PubMed

Ginn, Helen Mary; Evans, Gwyndaf; Sauter, Nicholas K; Stuart, David Ian

2016-06-01

As serial femtosecond crystallography expands towards a variety of delivery methods, including chip-based methods, and smaller collected data sets, the requirement to optimize the data analysis to produce maximum structure quality is becoming increasingly pressing. Here cppxfel , a software package primarily written in C++, which showcases several data analysis techniques, is released. This software package presently indexes images using DIALS (diffraction integration for advanced light sources) and performs an initial orientation matrix refinement, followed by post-refinement of individual images against a reference data set. Cppxfel is released with the hope that the unique and useful elements of this package can be repurposed for existing software packages. However, as released, it produces high-quality crystal structures and is therefore likely to be also useful to experienced users of X-ray free-electron laser (XFEL) software who wish to maximize the information extracted from a limited number of XFEL images.

SSME Bearing and Seal Tester Data Compilation, Analysis and Reporting; and Refinement of the Cryogenic Bearing Analysis Mathematical Model

NASA Technical Reports Server (NTRS)

Moore, James; Marty, Dave; Cody, Joe

2000-01-01

SRS and NASA/MSFC have developed software with unique capabilities to couple bearing kinematic modeling with high fidelity thermal modeling. The core thermomechanical modeling software was developed by SRS and others in the late 1980's and early 1990's under various different contractual efforts. SRS originally developed software that enabled SHABERTH (Shaft Bearing Thermal Model) and SINDA (Systems Improved Numerical Differencing Analyzer) to exchange data and autonomously allowing bearing component temperature effects to propagate into the steady state bearing mechanical model. A separate contract was issued in 1990 to create a personal computer version of the software. At that time SRS performed major improvements to the code. Both SHABERTH and SINDA were independently ported to the PC and compiled. SRS them integrated the two programs into a single program that was named SINSHA. This was a major code improvement.

SSME Bearing and Seal Tester Data Compilation, Analysis, and Reporting; and Refinement of the Cryogenic Bearing Analysis Mathematical Model

NASA Technical Reports Server (NTRS)

Moore, James; Marty, Dave; Cody, Joe

2000-01-01

SRS and NASA/MSFC have developed software with unique capabilities to couple bearing kinematic modeling with high fidelity thermal modeling. The core thermomechanical modeling software was developed by SRS and others in the late 1980's and early 1990's under various different contractual efforts. SRS originally developed software that enabled SHABERTH (Shaft Bearing Thermal Model) and SINDA (Systems Improved Numerical Differencing Analyzer) to exchange data and autonomously allowing bearing component temperature effects to propagate into the steady state bearing mechanical model. A separate contract was issued in 1990 to create a personal computer version of the software. At that time SRS performed major improvements to the code. Both SHABERTH and SINDA were independently ported to the PC and compiled. SRS them integrated the two programs into a single program that was named SINSHA. This was a major code improvement.

On the release of cppxfel for processing X-ray free-electron laser images

DOE PAGES

Ginn, Helen Mary; Evans, Gwyndaf; Sauter, Nicholas K.; ...

2016-05-11

As serial femtosecond crystallography expands towards a variety of delivery methods, including chip-based methods, and smaller collected data sets, the requirement to optimize the data analysis to produce maximum structure quality is becoming increasingly pressing. Herecppxfel, a software package primarily written in C++, which showcases several data analysis techniques, is released. This software package presently indexes images using DIALS (diffraction integration for advanced light sources) and performs an initial orientation matrix refinement, followed by post-refinement of individual images against a reference data set.Cppxfelis released with the hope that the unique and useful elements of this package can be repurposed formore » existing software packages. However, as released, it produces high-quality crystal structures and is therefore likely to be also useful to experienced users of X-ray free-electron laser (XFEL) software who wish to maximize the information extracted from a limited number of XFEL images.« less

A proven approach for more effective software development and maintenance

NASA Technical Reports Server (NTRS)

Pajerski, Rose; Hall, Dana; Sinclair, Craig

1994-01-01

Modern space flight mission operations and associated ground data systems are increasingly dependent upon reliable, quality software. Critical functions such as command load preparation, health and status monitoring, communications link scheduling and conflict resolution, and transparent gateway protocol conversion are routinely performed by software. Given budget constraints and the ever increasing capabilities of processor technology, the next generation of control centers and data systems will be even more dependent upon software across all aspects of performance. A key challenge now is to implement improved engineering, management, and assurance processes for the development and maintenance of that software; processes that cost less, yield higher quality products, and that self-correct for continual improvement evolution. The NASA Goddard Space Flight Center has a unique experience base that can be readily tapped to help solve the software challenge. Over the past eighteen years, the Software Engineering Laboratory within the code 500 Flight Dynamics Division has evolved a software development and maintenance methodology that accommodates the unique characteristics of an organization while optimizing and continually improving the organization's software capabilities. This methodology relies upon measurement, analysis, and feedback much analogous to that of control loop systems. It is an approach with a time-tested track record proven through repeated applications across a broad range of operational software development and maintenance projects. This paper describes the software improvement methodology employed by the Software Engineering Laboratory, and how it has been exploited within the Flight Dynamics Division with GSFC Code 500. Examples of specific improvement in the software itself and its processes are presented to illustrate the effectiveness of the methodology. Finally, the initial findings are given when this methodology was applied across the mission operations and ground data systems software domains throughout Code 500.

Highway User Benefit Analysis System Research Project #128

DOT National Transportation Integrated Search

2000-10-01

In this research, a methodology for estimating road user costs of various competing alternatives was developed. Also, software was developed to calculate the road user cost, perform economic analysis and update cost tables. The methodology is based o...

2012 Eco-Logical grant program annual report

DOT National Transportation Integrated Search

2000-01-01

What is IDAS? IDAS, which stands for the ITS Deployment Analysis System, is software developed by the Federal Highway Administration that can be used to perform sketch planning analysis for ITS deployments. Planners and others can use IDAS to calcula...

MSiReader v1.0: Evolving Open-Source Mass Spectrometry Imaging Software for Targeted and Untargeted Analyses

NASA Astrophysics Data System (ADS)

Bokhart, Mark T.; Nazari, Milad; Garrard, Kenneth P.; Muddiman, David C.

2018-01-01

A major update to the mass spectrometry imaging (MSI) software MSiReader is presented, offering a multitude of newly added features critical to MSI analyses. MSiReader is a free, open-source, and vendor-neutral software written in the MATLAB platform and is capable of analyzing most common MSI data formats. A standalone version of the software, which does not require a MATLAB license, is also distributed. The newly incorporated data analysis features expand the utility of MSiReader beyond simple visualization of molecular distributions. The MSiQuantification tool allows researchers to calculate absolute concentrations from quantification MSI experiments exclusively through MSiReader software, significantly reducing data analysis time. An image overlay feature allows the incorporation of complementary imaging modalities to be displayed with the MSI data. A polarity filter has also been incorporated into the data loading step, allowing the facile analysis of polarity switching experiments without the need for data parsing prior to loading the data file into MSiReader. A quality assurance feature to generate a mass measurement accuracy (MMA) heatmap for an analyte of interest has also been added to allow for the investigation of MMA across the imaging experiment. Most importantly, as new features have been added performance has not degraded, in fact it has been dramatically improved. These new tools and the improvements to the performance in MSiReader v1.0 enable the MSI community to evaluate their data in greater depth and in less time. [Figure not available: see fulltext.

Real-Time Processing Library for Open-Source Hardware Biomedical Sensors

PubMed Central

Castro-García, Juan A.; Lebrato-Vázquez, Clara

2018-01-01

Applications involving data acquisition from sensors need samples at a preset frequency rate, the filtering out of noise and/or analysis of certain frequency components. We propose a novel software architecture based on open-software hardware platforms which allows programmers to create data streams from input channels and easily implement filters and frequency analysis objects. The performances of the different classes given in the size of memory allocated and execution time (number of clock cycles) were analyzed in the low-cost platform Arduino Genuino. In addition, 11 people took part in an experiment in which they had to implement several exercises and complete a usability test. Sampling rates under 250 Hz (typical for many biomedical applications) makes it feasible to implement filters, sliding windows and Fourier analysis, operating in real time. Participants rated software usability at 70.2 out of 100 and the ease of use when implementing several signal processing applications was rated at just over 4.4 out of 5. Participants showed their intention of using this software because it was percieved as useful and very easy to use. The performances of the library showed that it may be appropriate for implementing small biomedical real-time applications or for human movement monitoring, even in a simple open-source hardware device like Arduino Genuino. The general perception about this library is that it is easy to use and intuitive. PMID:29596394

Real-Time Processing Library for Open-Source Hardware Biomedical Sensors.

PubMed

Molina-Cantero, Alberto J; Castro-García, Juan A; Lebrato-Vázquez, Clara; Gómez-González, Isabel M; Merino-Monge, Manuel

2018-03-29

Applications involving data acquisition from sensors need samples at a preset frequency rate, the filtering out of noise and/or analysis of certain frequency components. We propose a novel software architecture based on open-software hardware platforms which allows programmers to create data streams from input channels and easily implement filters and frequency analysis objects. The performances of the different classes given in the size of memory allocated and execution time (number of clock cycles) were analyzed in the low-cost platform Arduino Genuino. In addition, 11 people took part in an experiment in which they had to implement several exercises and complete a usability test. Sampling rates under 250 Hz (typical for many biomedical applications) makes it feasible to implement filters, sliding windows and Fourier analysis, operating in real time. Participants rated software usability at 70.2 out of 100 and the ease of use when implementing several signal processing applications was rated at just over 4.4 out of 5. Participants showed their intention of using this software because it was percieved as useful and very easy to use. The performances of the library showed that it may be appropriate for implementing small biomedical real-time applications or for human movement monitoring, even in a simple open-source hardware device like Arduino Genuino. The general perception about this library is that it is easy to use and intuitive.

Integrated software health management for aerospace guidance, navigation, and control systems: A probabilistic reasoning approach

NASA Astrophysics Data System (ADS)

Mbaya, Timmy

Embedded Aerospace Systems have to perform safety and mission critical operations in a real-time environment where timing and functional correctness are extremely important. Guidance, Navigation, and Control (GN&C) systems substantially rely on complex software interfacing with hardware in real-time; any faults in software or hardware, or their interaction could result in fatal consequences. Integrated Software Health Management (ISWHM) provides an approach for detection and diagnosis of software failures while the software is in operation. The ISWHM approach is based on probabilistic modeling of software and hardware sensors using a Bayesian network. To meet memory and timing constraints of real-time embedded execution, the Bayesian network is compiled into an Arithmetic Circuit, which is used for on-line monitoring. This type of system monitoring, using an ISWHM, provides automated reasoning capabilities that compute diagnoses in a timely manner when failures occur. This reasoning capability enables time-critical mitigating decisions and relieves the human agent from the time-consuming and arduous task of foraging through a multitude of isolated---and often contradictory---diagnosis data. For the purpose of demonstrating the relevance of ISWHM, modeling and reasoning is performed on a simple simulated aerospace system running on a real-time operating system emulator, the OSEK/Trampoline platform. Models for a small satellite and an F-16 fighter jet GN&C (Guidance, Navigation, and Control) system have been implemented. Analysis of the ISWHM is then performed by injecting faults and analyzing the ISWHM's diagnoses.

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.

NeuroMatic: An Integrated Open-Source Software Toolkit for Acquisition, Analysis and Simulation of Electrophysiological Data

PubMed Central

Rothman, Jason S.; Silver, R. Angus

2018-01-01

Acquisition, analysis and simulation of electrophysiological properties of the nervous system require multiple software packages. This makes it difficult to conserve experimental metadata and track the analysis performed. It also complicates certain experimental approaches such as online analysis. To address this, we developed NeuroMatic, an open-source software toolkit that performs data acquisition (episodic, continuous and triggered recordings), data analysis (spike rasters, spontaneous event detection, curve fitting, stationarity) and simulations (stochastic synaptic transmission, synaptic short-term plasticity, integrate-and-fire and Hodgkin-Huxley-like single-compartment models). The merging of a wide range of tools into a single package facilitates a more integrated style of research, from the development of online analysis functions during data acquisition, to the simulation of synaptic conductance trains during dynamic-clamp experiments. Moreover, NeuroMatic has the advantage of working within Igor Pro, a platform-independent environment that includes an extensive library of built-in functions, a history window for reviewing the user's workflow and the ability to produce publication-quality graphics. Since its original release, NeuroMatic has been used in a wide range of scientific studies and its user base has grown considerably. NeuroMatic version 3.0 can be found at http://www.neuromatic.thinkrandom.com and https://github.com/SilverLabUCL/NeuroMatic. PMID:29670519

Network Meta-Analysis Using R: A Review of Currently Available Automated Packages

PubMed Central

Neupane, Binod; Richer, Danielle; Bonner, Ashley Joel; Kibret, Taddele; Beyene, Joseph

2014-01-01

Network meta-analysis (NMA) – a statistical technique that allows comparison of multiple treatments in the same meta-analysis simultaneously – has become increasingly popular in the medical literature in recent years. The statistical methodology underpinning this technique and software tools for implementing the methods are evolving. Both commercial and freely available statistical software packages have been developed to facilitate the statistical computations using NMA with varying degrees of functionality and ease of use. This paper aims to introduce the reader to three R packages, namely, gemtc, pcnetmeta, and netmeta, which are freely available software tools implemented in R. Each automates the process of performing NMA so that users can perform the analysis with minimal computational effort. We present, compare and contrast the availability and functionality of different important features of NMA in these three packages so that clinical investigators and researchers can determine which R packages to implement depending on their analysis needs. Four summary tables detailing (i) data input and network plotting, (ii) modeling options, (iii) assumption checking and diagnostic testing, and (iv) inference and reporting tools, are provided, along with an analysis of a previously published dataset to illustrate the outputs available from each package. We demonstrate that each of the three packages provides a useful set of tools, and combined provide users with nearly all functionality that might be desired when conducting a NMA. PMID:25541687

Network meta-analysis using R: a review of currently available automated packages.

PubMed

Neupane, Binod; Richer, Danielle; Bonner, Ashley Joel; Kibret, Taddele; Beyene, Joseph

2014-01-01

Network meta-analysis (NMA)--a statistical technique that allows comparison of multiple treatments in the same meta-analysis simultaneously--has become increasingly popular in the medical literature in recent years. The statistical methodology underpinning this technique and software tools for implementing the methods are evolving. Both commercial and freely available statistical software packages have been developed to facilitate the statistical computations using NMA with varying degrees of functionality and ease of use. This paper aims to introduce the reader to three R packages, namely, gemtc, pcnetmeta, and netmeta, which are freely available software tools implemented in R. Each automates the process of performing NMA so that users can perform the analysis with minimal computational effort. We present, compare and contrast the availability and functionality of different important features of NMA in these three packages so that clinical investigators and researchers can determine which R packages to implement depending on their analysis needs. Four summary tables detailing (i) data input and network plotting, (ii) modeling options, (iii) assumption checking and diagnostic testing, and (iv) inference and reporting tools, are provided, along with an analysis of a previously published dataset to illustrate the outputs available from each package. We demonstrate that each of the three packages provides a useful set of tools, and combined provide users with nearly all functionality that might be desired when conducting a NMA.

Probability and Statistics in Sensor Performance Modeling

DTIC Science & Technology

2010-12-01

language software program is called Environmental Awareness for Sensor and Emitter Employment. Some important numerical issues in the implementation...3 Statistical analysis for measuring sensor performance...complementary cumulative distribution function cdf cumulative distribution function DST decision-support tool EASEE Environmental Awareness of

Optimizing the Performance of Radionuclide Identification Software in the Hunt for Nuclear Security Threats

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

Fotion, Katherine A.

2016-08-18

The Radionuclide Analysis Kit (RNAK), my team’s most recent nuclide identification software, is entering the testing phase. A question arises: will removing rare nuclides from the software’s library improve its overall performance? An affirmative response indicates fundamental errors in the software’s framework, while a negative response confirms the effectiveness of the software’s key machine learning algorithms. After thorough testing, I found that the performance of RNAK cannot be improved with the library choice effect, thus verifying the effectiveness of RNAK’s algorithms—multiple linear regression, Bayesian network using the Viterbi algorithm, and branch and bound search.

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

IRACproc: IRAC Post-BCD Processing

NASA Astrophysics Data System (ADS)

Schuster, Mike; Marengo, Massimo; Patten, Brian

2012-09-01

IRACproc is a software suite that facilitates the co-addition of dithered or mapped Spitzer/IRAC data to make them ready for further analysis with application to a wide variety of IRAC observing programs. The software runs within PDL, a numeric extension for Perl available from pdl.perl.org, and as stand alone perl scripts. In acting as a wrapper for the Spitzer Science Center's MOPEX software, IRACproc improves the rejection of cosmic rays and other transients in the co-added data. In addition, IRACproc performs (optional) Point Spread Function (PSF) fitting, subtraction, and masking of saturated stars.

Hybrid PV/diesel solar power system design using multi-level factor analysis optimization

NASA Astrophysics Data System (ADS)

Drake, Joshua P.

Solar power systems represent a large area of interest across a spectrum of organizations at a global level. It was determined that a clear understanding of current state of the art software and design methods, as well as optimization methods, could be used to improve the design methodology. Solar power design literature was researched for an in depth understanding of solar power system design methods and algorithms. Multiple software packages for the design and optimization of solar power systems were analyzed for a critical understanding of their design workflow. In addition, several methods of optimization were studied, including brute force, Pareto analysis, Monte Carlo, linear and nonlinear programming, and multi-way factor analysis. Factor analysis was selected as the most efficient optimization method for engineering design as it applied to solar power system design. The solar power design algorithms, software work flow analysis, and factor analysis optimization were combined to develop a solar power system design optimization software package called FireDrake. This software was used for the design of multiple solar power systems in conjunction with an energy audit case study performed in seven Tibetan refugee camps located in Mainpat, India. A report of solar system designs for the camps, as well as a proposed schedule for future installations was generated. It was determined that there were several improvements that could be made to the state of the art in modern solar power system design, though the complexity of current applications is significant.

Automated Sensitivity Analysis of Interplanetary Trajectories for Optimal Mission Design

NASA Technical Reports Server (NTRS)

Knittel, Jeremy; Hughes, Kyle; Englander, Jacob; Sarli, Bruno

2017-01-01

This work describes a suite of Python tools known as the Python EMTG Automated Trade Study Application (PEATSA). PEATSA was written to automate the operation of trajectory optimization software, simplify the process of performing sensitivity analysis, and was ultimately found to out-perform a human trajectory designer in unexpected ways. These benefits will be discussed and demonstrated on sample mission designs.

IDL Object Oriented Software for Hinode/XRT Image Analysis

NASA Astrophysics Data System (ADS)

Higgins, P. A.; Gallagher, P. T.

2008-09-01

We have developed a set of object oriented IDL routines that enable users to search, download and analyse images from the X-Ray Telescope (XRT) on-board Hinode. In this paper, we give specific examples of how the object can be used and how multi-instrument data analysis can be performed. The XRT object is a highly versatile and powerful IDL object, which will prove to be a useful tool for solar researchers. This software utilizes the generic Framework object available within the GEN branch of SolarSoft.

Dakota, a multilevel parallel object-oriented framework for design optimization, parameter estimation, uncertainty quantification, and sensitivity analysis :

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

Adams, Brian M.; Ebeida, Mohamed Salah; Eldred, Michael S.

The Dakota (Design Analysis Kit for Optimization and Terascale Applications) toolkit provides a exible and extensible interface between simulation codes and iterative analysis methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quanti cation with sampling, reliability, and stochastic expansion methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components requiredmore » for iterative systems analyses, the Dakota toolkit provides a exible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a user's manual for the Dakota software and provides capability overviews and procedures for software execution, as well as a variety of example studies.« less

Diagnostic performance of an automated analysis software for the diagnosis of Alzheimer’s dementia with 18F FDG PET

PubMed Central

Partovi, Sasan; Yuh, Roger; Pirozzi, Sara; Lu, Ziang; Couturier, Spencer; Grosse, Ulrich; Schluchter, Mark D; Nelson, Aaron; Jones, Robert; O’Donnell, James K; Faulhaber, Peter

2017-01-01

The objective of this study was to assess the ability of a quantitative software-aided approach to improve the diagnostic accuracy of 18F FDG PET for Alzheimer’s dementia over visual analysis alone. Twenty normal subjects (M:F-12:8; mean age 80.6 years) and twenty mild AD subjects (M:F-12:8; mean age 70.6 years) with 18F FDG PET scans were obtained from the ADNI database. Three blinded readers interpreted these PET images first using a visual qualitative approach and then using a quantitative software-aided approach. Images were classified on two five-point scales based on normal/abnormal (1-definitely normal; 5-definitely abnormal) and presence of AD (1-definitely not AD; 5-definitely AD). Diagnostic sensitivity, specificity, and accuracy for both approaches were compared based on the aforementioned scales. The sensitivity, specificity, and accuracy for the normal vs. abnormal readings of all readers combined were higher when comparing the software-aided vs. visual approach (sensitivity 0.93 vs. 0.83 P = 0.0466; specificity 0.85 vs. 0.60 P = 0.0005; accuracy 0.89 vs. 0.72 P<0.0001). The specificity and accuracy for absence vs. presence of AD of all readers combined were higher when comparing the software-aided vs. visual approach (specificity 0.90 vs. 0.70 P = 0.0008; accuracy 0.81 vs. 0.72 P = 0.0356). Sensitivities of the software-aided and visual approaches did not differ significantly (0.72 vs. 0.73 P = 0.74). The quantitative software-aided approach appears to improve the performance of 18F FDG PET for the diagnosis of mild AD. It may be helpful for experienced 18F FDG PET readers analyzing challenging cases. PMID:28123864

Next generation of decision making software for nanopatterns characterization: application to semiconductor industry

NASA Astrophysics Data System (ADS)

Dervilllé, A.; Labrosse, A.; Zimmermann, Y.; Foucher, J.; Gronheid, R.; Boeckx, C.; Singh, A.; Leray, P.; Halder, S.

2016-03-01

The dimensional scaling in IC manufacturing strongly drives the demands on CD and defect metrology techniques and their measurement uncertainties. Defect review has become as important as CD metrology and both of them create a new metrology paradigm because it creates a completely new need for flexible, robust and scalable metrology software. Current, software architectures and metrology algorithms are performant but it must be pushed to another higher level in order to follow roadmap speed and requirements. For example: manage defect and CD in one step algorithm, customize algorithms and outputs features for each R&D team environment, provide software update every day or every week for R&D teams in order to explore easily various development strategies. The final goal is to avoid spending hours and days to manually tune algorithm to analyze metrology data and to allow R&D teams to stay focus on their expertise. The benefits are drastic costs reduction, more efficient R&D team and better process quality. In this paper, we propose a new generation of software platform and development infrastructure which can integrate specific metrology business modules. For example, we will show the integration of a chemistry module dedicated to electronics materials like Direct Self Assembly features. We will show a new generation of image analysis algorithms which are able to manage at the same time defect rates, images classifications, CD and roughness measurements with high throughput performances in order to be compatible with HVM. In a second part, we will assess the reliability, the customization of algorithm and the software platform capabilities to follow new specific semiconductor metrology software requirements: flexibility, robustness, high throughput and scalability. Finally, we will demonstrate how such environment has allowed a drastic reduction of data analysis cycle time.

Information Technology.

ERIC Educational Resources Information Center

Marcum, Deanna; Boss, Richard

1983-01-01

Relates office automation to its application in libraries, discussing computer software packages for microcomputers performing tasks involved in word processing, accounting, statistical analysis, electronic filing cabinets, and electronic mail systems. (EJS)

77 FR 24541 - Virginia Electric and Power Company, North Anna Power Station Units 1 and 2, Independent Spent...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-24

... submitted TN Calculation No. 10494-174, which performed a bounding thermal analysis using ANSYS finite element software to evaluate the misloading events. The ANSYS analysis consists of a half-symmetric, three...

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.

Preparing systems engineering and computing science students in disciplined methods, quantitative, and advanced statistical techniques to improve process performance

NASA Astrophysics Data System (ADS)

McCray, Wilmon Wil L., Jr.

The research was prompted by a need to conduct a study that assesses process improvement, quality management and analytical techniques taught to students in U.S. colleges and universities undergraduate and graduate systems engineering and the computing science discipline (e.g., software engineering, computer science, and information technology) degree programs during their academic training that can be applied to quantitatively manage processes for performance. Everyone involved in executing repeatable processes in the software and systems development lifecycle processes needs to become familiar with the concepts of quantitative management, statistical thinking, process improvement methods and how they relate to process-performance. Organizations are starting to embrace the de facto Software Engineering Institute (SEI) Capability Maturity Model Integration (CMMI RTM) Models as process improvement frameworks to improve business processes performance. High maturity process areas in the CMMI model imply the use of analytical, statistical, quantitative management techniques, and process performance modeling to identify and eliminate sources of variation, continually improve process-performance; reduce cost and predict future outcomes. The research study identifies and provides a detail discussion of the gap analysis findings of process improvement and quantitative analysis techniques taught in U.S. universities systems engineering and computing science degree programs, gaps that exist in the literature, and a comparison analysis which identifies the gaps that exist between the SEI's "healthy ingredients " of a process performance model and courses taught in U.S. universities degree program. The research also heightens awareness that academicians have conducted little research on applicable statistics and quantitative techniques that can be used to demonstrate high maturity as implied in the CMMI models. The research also includes a Monte Carlo simulation optimization model and dashboard that demonstrates the use of statistical methods, statistical process control, sensitivity analysis, quantitative and optimization techniques to establish a baseline and predict future customer satisfaction index scores (outcomes). The American Customer Satisfaction Index (ACSI) model and industry benchmarks were used as a framework for the simulation model.

X-Graphs: Language and Algorithms for Heterogeneous Graph Streams

DTIC Science & Technology

2017-09-01

INTRODUCTION 1 3 METHODS , ASUMPTIONS, AND PROCEDURES 2 Software Abstractions for Graph Analytic Applications 2 High performance Platforms for Graph Processing...data is stored in a distributed file system. 3 METHODS , ASUMPTIONS, AND PROCEDURES Software Abstractions for Graph Analytic Applications To...implementations of novel methods for networks analysis: several methods for detection of overlapping communities, personalized PageRank, node embeddings into a d

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.

MemAxes Visualization Software

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

Hardware advancements such as Intel's PEBS and AMD's IBS, as well as software developments such as the perf_event API in Linux have made available the acquisition of memory access samples with performance information. MemAxes is a visualization and analysis tool for memory access sample data. By mapping the samples to their associated code, variables, node topology, and application dataset, MemAxes provides intuitive views of the data.

Selecting information technology for physicians' practices: a cross-sectional study.

PubMed

Eden, Karen Beekman

2002-04-05

Many physicians are transitioning from paper to electronic formats for billing, scheduling, medical charts, communications, etc. The primary objective of this research was to identify the relationship (if any) between the software selection process and the office staff's perceptions of the software's impact on practice activities. A telephone survey was conducted with office representatives of 407 physician practices in Oregon who had purchased information technology. The respondents, usually office managers, answered scripted questions about their selection process and their perceptions of the software after implementation. Multiple logistic regression revealed that software type, selection steps, and certain factors influencing the purchase were related to whether the respondents felt the software improved the scheduling and financial analysis practice activities. Specifically, practices that selected electronic medical record or practice management software, that made software comparisons, or that considered prior user testimony as important were more likely to have perceived improvements in the scheduling process than were other practices. Practices that considered value important, that did not consider compatibility important, that selected managed care software, that spent less than 10,000 dollars, or that provided learning time (most dramatic increase in odds ratio, 8.2) during implementation were more likely to perceive that the software had improved the financial analysis process than were other practices. Perhaps one of the most important predictors of improvement was providing learning time during implementation, particularly when the software involves several practice activities. Despite this importance, less than half of the practices reported performing this step.

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

NASA Astrophysics Data System (ADS)

Ramkilowan, A.; Griffith, D. J.

2017-10-01

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

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;

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

PubMed

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

2016-10-01

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

Final Report Scalable Analysis Methods and In Situ Infrastructure for Extreme Scale Knowledge Discovery

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

O'Leary, Patrick

The primary challenge motivating this project is the widening gap between the ability to compute information and to store it for subsequent analysis. This gap adversely impacts science code teams, who can perform analysis only on a small fraction of the data they calculate, resulting in the substantial likelihood of lost or missed science, when results are computed but not analyzed. Our approach is to perform as much analysis or visualization processing on data while it is still resident in memory, which is known as in situ processing. The idea in situ processing was not new at the time ofmore » the start of this effort in 2014, but efforts in that space were largely ad hoc, and there was no concerted effort within the research community that aimed to foster production-quality software tools suitable for use by Department of Energy (DOE) science projects. Our objective was to produce and enable the use of production-quality in situ methods and infrastructure, at scale, on DOE high-performance computing (HPC) facilities, though we expected to have an impact beyond DOE due to the widespread nature of the challenges, which affect virtually all large-scale computational science efforts. To achieve this objective, we engaged in software technology research and development (R&D), in close partnerships with DOE science code teams, to produce software technologies that were shown to run efficiently at scale on DOE HPC platforms.« less

Radiological performance assessment for the E-Area Vaults Disposal Facility. Appendices A through M

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

Cook, J.R.

1994-04-15

These document contains appendices A-M for the performance assessment. They are A: details of models and assumptions, B: computer codes, C: data tabulation, D: geochemical interactions, E: hydrogeology of the Savannah River Site, F: software QA plans, G: completeness review guide, H: performance assessment peer review panel recommendations, I: suspect soil performance analysis, J: sensitivity/uncertainty analysis, K: vault degradation study, L: description of naval reactor waste disposal, M: porflow input file. (GHH)

The Identification of Software Failure Regions

DTIC Science & Technology

1990-06-01

be used to detect non-obviously redundant test cases. A preliminary examination of the manual analysis method is performed with a set of programs ...failure regions are defined and a method of failure region analysis is described in detail. The thesis describes how this analysis may be used to detect...is the termination of the ability of a functional unit to perform its required function. (Glossary, 1983) The presence of faults in program code

A Comparison and Evaluation of Real-Time Software Systems Modeling Languages

NASA Technical Reports Server (NTRS)

Evensen, Kenneth D.; Weiss, Kathryn Anne

2010-01-01

A model-driven approach to real-time software systems development enables the conceptualization of software, fostering a more thorough understanding of its often complex architecture and behavior while promoting the documentation and analysis of concerns common to real-time embedded systems such as scheduling, resource allocation, and performance. Several modeling languages have been developed to assist in the model-driven software engineering effort for real-time systems, and these languages are beginning to gain traction with practitioners throughout the aerospace industry. This paper presents a survey of several real-time software system modeling languages, namely the Architectural Analysis and Design Language (AADL), the Unified Modeling Language (UML), Systems Modeling Language (SysML), the Modeling and Analysis of Real-Time Embedded Systems (MARTE) UML profile, and the AADL for UML profile. Each language has its advantages and disadvantages, and in order to adequately describe a real-time software system's architecture, a complementary use of multiple languages is almost certainly necessary. This paper aims to explore these languages in the context of understanding the value each brings to the model-driven software engineering effort and to determine if it is feasible and practical to combine aspects of the various modeling languages to achieve more complete coverage in architectural descriptions. To this end, each language is evaluated with respect to a set of criteria such as scope, formalisms, and architectural coverage. An example is used to help illustrate the capabilities of the various languages.

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.

Computational System For Rapid CFD Analysis In Engineering

NASA Technical Reports Server (NTRS)

Barson, Steven L.; Ascoli, Edward P.; Decroix, Michelle E.; Sindir, Munir M.

1995-01-01

Computational system comprising modular hardware and software sub-systems developed to accelerate and facilitate use of techniques of computational fluid dynamics (CFD) in engineering environment. Addresses integration of all aspects of CFD analysis process, including definition of hardware surfaces, generation of computational grids, CFD flow solution, and postprocessing. Incorporates interfaces for integration of all hardware and software tools needed to perform complete CFD analysis. Includes tools for efficient definition of flow geometry, generation of computational grids, computation of flows on grids, and postprocessing of flow data. System accepts geometric input from any of three basic sources: computer-aided design (CAD), computer-aided engineering (CAE), or definition by user.

Software for Data Analysis with Graphical Models

NASA Technical Reports Server (NTRS)

Buntine, Wray L.; Roy, H. Scott

1994-01-01

Probabilistic graphical models are being used widely in artificial intelligence and statistics, for instance, in diagnosis and expert systems, as a framework for representing and reasoning with probabilities and independencies. They come with corresponding algorithms for performing statistical inference. This offers a unifying framework for prototyping and/or generating data analysis algorithms from graphical specifications. This paper illustrates the framework with an example and then presents some basic techniques for the task: problem decomposition and the calculation of exact Bayes factors. Other tools already developed, such as automatic differentiation, Gibbs sampling, and use of the EM algorithm, make this a broad basis for the generation of data analysis software.

Computer-aided modelling and analysis of PV systems: a comparative study.

PubMed

Koukouvaos, Charalambos; Kandris, Dionisis; Samarakou, Maria

2014-01-01

Modern scientific advances have enabled remarkable efficacy for photovoltaic systems with regard to the exploitation of solar energy, boosting them into having a rapidly growing position among the systems developed for the production of renewable energy. However, in many cases the design, analysis, and control of photovoltaic systems are tasks which are quite complex and thus difficult to be carried out. In order to cope with this kind of problems, appropriate software tools have been developed either as standalone products or parts of general purpose software platforms used to model and simulate the generation, transmission, and distribution of solar energy. The utilization of this kind of software tools may be extremely helpful to the successful performance evaluation of energy systems with maximum accuracy and minimum cost in time and effort. The work presented in this paper aims on a first level at the performance analysis of various configurations of photovoltaic systems through computer-aided modelling. On a second level, it provides a comparative evaluation of the credibility of two of the most advanced graphical programming environments, namely, Simulink and LabVIEW, with regard to their application in photovoltaic systems.

Computer-Aided Modelling and Analysis of PV Systems: A Comparative Study

PubMed Central

Koukouvaos, Charalambos

2014-01-01

Modern scientific advances have enabled remarkable efficacy for photovoltaic systems with regard to the exploitation of solar energy, boosting them into having a rapidly growing position among the systems developed for the production of renewable energy. However, in many cases the design, analysis, and control of photovoltaic systems are tasks which are quite complex and thus difficult to be carried out. In order to cope with this kind of problems, appropriate software tools have been developed either as standalone products or parts of general purpose software platforms used to model and simulate the generation, transmission, and distribution of solar energy. The utilization of this kind of software tools may be extremely helpful to the successful performance evaluation of energy systems with maximum accuracy and minimum cost in time and effort. The work presented in this paper aims on a first level at the performance analysis of various configurations of photovoltaic systems through computer-aided modelling. On a second level, it provides a comparative evaluation of the credibility of two of the most advanced graphical programming environments, namely, Simulink and LabVIEW, with regard to their application in photovoltaic systems. PMID:24772007

KSC management training system project

NASA Technical Reports Server (NTRS)

Sepulveda, Jose A.

1993-01-01

The stated objectives for the summer of 1993 were: to review the Individual Development Plan Surveys for 1994 in order to automate the analysis of the Needs Assessment effort; and to develop and implement evaluation methodologies to perform ongoing program-wide course-to-course assessment. This includes the following: to propose a methodology to develop and implement objective, performance-based assessment instruments for each training effort; to mechanize course evaluation forms and develop software to facilitate the data gathering, analysis, and reporting processes; and to implement the methodology, forms, and software in at lease one training course or seminar selected among those normally offered in the summer at KSC. Section two of this report addresses the work done in regard to the Individual Development Plan Surveys for 1994. Section three presents the methodology proposed to develop and implement objective, performance-based assessment instruments for each training course offered at KSC.

Recoding low-level simulator data into a record of meaningful task performance: the integrated task modeling environment (ITME).

PubMed

King, Robert; Parker, Simon; Mouzakis, Kon; Fletcher, Winston; Fitzgerald, Patrick

2007-11-01

The Integrated Task Modeling Environment (ITME) is a user-friendly software tool that has been developed to automatically recode low-level data into an empirical record of meaningful task performance. The present research investigated and validated the performance of the ITME software package by conducting complex simulation missions and comparing the task analyses produced by ITME with taskanalyses produced by experienced video analysts. A very high interrater reliability (> or = .94) existed between experienced video analysts and the ITME for the task analyses produced for each mission. The mean session time:analysis time ratio was 1:24 using video analysis techniques and 1:5 using the ITME. It was concluded that the ITME produced task analyses that were as reliable as those produced by experienced video analysts, and significantly reduced the time cost associated with these analyses.

OpenMS: a flexible open-source software platform for mass spectrometry data analysis.

PubMed

Röst, Hannes L; Sachsenberg, Timo; Aiche, Stephan; Bielow, Chris; Weisser, Hendrik; Aicheler, Fabian; Andreotti, Sandro; Ehrlich, Hans-Christian; Gutenbrunner, Petra; Kenar, Erhan; Liang, Xiao; Nahnsen, Sven; Nilse, Lars; Pfeuffer, Julianus; Rosenberger, George; Rurik, Marc; Schmitt, Uwe; Veit, Johannes; Walzer, Mathias; Wojnar, David; Wolski, Witold E; Schilling, Oliver; Choudhary, Jyoti S; Malmström, Lars; Aebersold, Ruedi; Reinert, Knut; Kohlbacher, Oliver

2016-08-30

High-resolution mass spectrometry (MS) has become an important tool in the life sciences, contributing to the diagnosis and understanding of human diseases, elucidating biomolecular structural information and characterizing cellular signaling networks. However, the rapid growth in the volume and complexity of MS data makes transparent, accurate and reproducible analysis difficult. We present OpenMS 2.0 (http://www.openms.de), a robust, open-source, cross-platform software specifically designed for the flexible and reproducible analysis of high-throughput MS data. The extensible OpenMS software implements common mass spectrometric data processing tasks through a well-defined application programming interface in C++ and Python and through standardized open data formats. OpenMS additionally provides a set of 185 tools and ready-made workflows for common mass spectrometric data processing tasks, which enable users to perform complex quantitative mass spectrometric analyses with ease.

Expert system verification and validation study: ES V/V Workshop

NASA Technical Reports Server (NTRS)

French, Scott; Hamilton, David

1992-01-01

The primary purpose of this document is to build a foundation for applying principles of verification and validation (V&V) of expert systems. To achieve this, some V&V as applied to conventionally implemented software is required. Part one will discuss the background of V&V from the perspective of (1) what is V&V of software and (2) V&V's role in developing software. Part one will also overview some common analysis techniques that are applied when performing V&V of software. All of these materials will be presented based on the assumption that the reader has little or no background in V&V or in developing procedural software. The primary purpose of part two is to explain the major techniques that have been developed for V&V of expert systems.

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

APMS 3.0 Flight Analyst Guide: Aviation Performance Measuring System

NASA Technical Reports Server (NTRS)

Jay, Griff; Prothero, Gary; Romanowski, Timothy; Lynch, Robert; Lawrence, Robert; Rosenthal, Loren

2004-01-01

The Aviation Performance Measuring System (APMS) is a method-embodied in software-that uses mathematical algorithms and related procedures to analyze digital flight data extracted from aircraft flight data recorders. APMS consists of an integrated set of tools used to perform two primary functions: a) Flight Data Importation b) Flight Data Analysis.

ACQ4: an open-source software platform for data acquisition and analysis in neurophysiology research.

PubMed

Campagnola, Luke; Kratz, Megan B; Manis, Paul B

2014-01-01

The complexity of modern neurophysiology experiments requires specialized software to coordinate multiple acquisition devices and analyze the collected data. We have developed ACQ4, an open-source software platform for performing data acquisition and analysis in experimental neurophysiology. This software integrates the tasks of acquiring, managing, and analyzing experimental data. ACQ4 has been used primarily for standard patch-clamp electrophysiology, laser scanning photostimulation, multiphoton microscopy, intrinsic imaging, and calcium imaging. The system is highly modular, which facilitates the addition of new devices and functionality. The modules included with ACQ4 provide for rapid construction of acquisition protocols, live video display, and customizable analysis tools. Position-aware data collection allows automated construction of image mosaics and registration of images with 3-dimensional anatomical atlases. ACQ4 uses free and open-source tools including Python, NumPy/SciPy for numerical computation, PyQt for the user interface, and PyQtGraph for scientific graphics. Supported hardware includes cameras, patch clamp amplifiers, scanning mirrors, lasers, shutters, Pockels cells, motorized stages, and more. ACQ4 is available for download at http://www.acq4.org.

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.

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

Automating Structural Analysis of Spacecraft Vehicles

NASA Technical Reports Server (NTRS)

Hrinda, Glenn A.

2004-01-01

A major effort within NASA's vehicle analysis discipline has been to automate structural analysis and sizing optimization during conceptual design studies of advanced spacecraft. Traditional spacecraft structural sizing has involved detailed finite element analysis (FEA) requiring large degree-of-freedom (DOF) finite element models (FEM). Creation and analysis of these models can be time consuming and limit model size during conceptual designs. The goal is to find an optimal design that meets the mission requirements but produces the lightest structure. A structural sizing tool called HyperSizer has been successfully used in the conceptual design phase of a reusable launch vehicle and planetary exploration spacecraft. The program couples with FEA to enable system level performance assessments and weight predictions including design optimization of material selections and sizing of spacecraft members. The software's analysis capabilities are based on established aerospace structural methods for strength, stability and stiffness that produce adequately sized members and reliable structural weight estimates. The software also helps to identify potential structural deficiencies early in the conceptual design so changes can be made without wasted time. HyperSizer's automated analysis and sizing optimization increases productivity and brings standardization to a systems study. These benefits will be illustrated in examining two different types of conceptual spacecraft designed using the software. A hypersonic air breathing, single stage to orbit (SSTO), reusable launch vehicle (RLV) will be highlighted as well as an aeroshell for a planetary exploration vehicle used for aerocapture at Mars. By showing the two different types of vehicles, the software's flexibility will be demonstrated with an emphasis on reducing aeroshell structural weight. Member sizes, concepts and material selections will be discussed as well as analysis methods used in optimizing the structure. Analysis based on the HyperSizer structural sizing software will be discussed. Design trades required to optimize structural weight will be presented.

TransFit: Finite element analysis data fitting software

NASA Technical Reports Server (NTRS)

Freeman, Mark

1993-01-01

The Advanced X-Ray Astrophysics Facility (AXAF) mission support team has made extensive use of geometric ray tracing to analyze the performance of AXAF developmental and flight optics. One important aspect of this performance modeling is the incorporation of finite element analysis (FEA) data into the surface deformations of the optical elements. TransFit is software designed for the fitting of FEA data of Wolter I optical surface distortions with a continuous surface description which can then be used by SAO's analytic ray tracing software, currently OSAC (Optical Surface Analysis Code). The improved capabilities of Transfit over previous methods include bicubic spline fitting of FEA data to accommodate higher spatial frequency distortions, fitted data visualization for assessing the quality of fit, the ability to accommodate input data from three FEA codes plus other standard formats, and options for alignment of the model coordinate system with the ray trace coordinate system. TransFit uses the AnswerGarden graphical user interface (GUI) to edit input parameters and then access routines written in PV-WAVE, C, and FORTRAN to allow the user to interactively create, evaluate, and modify the fit. The topics covered include an introduction to TransFit: requirements, designs philosophy, and implementation; design specifics: modules, parameters, fitting algorithms, and data displays; a procedural example; verification of performance; future work; and appendices on online help and ray trace results of the verification section.

Software Package Completed for Alloy Design at the Atomic Level

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo H.; Noebe, Ronald D.; Abel, Phillip B.; Good, Brian S.

2001-01-01

As a result of a multidisciplinary effort involving solid-state physics, quantum mechanics, and materials and surface science, the first version of a software package dedicated to the atomistic analysis of multicomponent systems was recently completed. Based on the BFS (Bozzolo, Ferrante, and Smith) method for the calculation of alloy and surface energetics, this package includes modules devoted to the analysis of many essential features that characterize any given alloy or surface system, including (1) surface structure analysis, (2) surface segregation, (3) surface alloying, (4) bulk crystalline material properties and atomic defect structures, and (5) thermal processes that allow us to perform phase diagram calculations. All the modules of this Alloy Design Workbench 1.0 (ADW 1.0) are designed to run in PC and workstation environments, and their operation and performance are substantially linked to the needs of the user and the specific application.

OpenStereo: Open Source, Cross-Platform Software for Structural Geology Analysis

NASA Astrophysics Data System (ADS)

Grohmann, C. H.; Campanha, G. A.

2010-12-01

Free and open source software (FOSS) are increasingly seen as synonyms of innovation and progress. Freedom to run, copy, distribute, study, change and improve the software (through access to the source code) assure a high level of positive feedback between users and developers, which results in stable, secure and constantly updated systems. Several software packages for structural geology analysis are available to the user, with commercial licenses or that can be downloaded at no cost from the Internet. Some provide basic tools of stereographic projections such as plotting poles, great circles, density contouring, eigenvector analysis, data rotation etc, while others perform more specific tasks, such as paleostress or geotechnical/rock stability analysis. This variety also means a wide range of data formating for input, Graphical User Interface (GUI) design and graphic export format. The majority of packages is built for MS-Windows and even though there are packages for the UNIX-based MacOS, there aren't native packages for *nix (UNIX, Linux, BSD etc) Operating Systems (OS), forcing the users to run these programs with emulators or virtual machines. Those limitations lead us to develop OpenStereo, an open source, cross-platform software for stereographic projections and structural geology. The software is written in Python, a high-level, cross-platform programming language and the GUI is designed with wxPython, which provide a consistent look regardless the OS. Numeric operations (like matrix and linear algebra) are performed with the Numpy module and all graphic capabilities are provided by the Matplolib library, including on-screen plotting and graphic exporting to common desktop formats (emf, eps, ps, pdf, png, svg). Data input is done with simple ASCII text files, with values of dip direction and dip/plunge separated by spaces, tabs or commas. The user can open multiple file at the same time (or the same file more than once), and overlay different elements of each dataset (poles, great circles etc). The GUI shows the opened files in a tree structure, similar to “layers” of many illustration software, where the vertical order of the files in the tree reflects the drawing order of the selected elements. At this stage, the software performs plotting operations of poles to planes, lineations, great circles, density contours and rose diagrams. A set of statistics is calculated for each file and its eigenvalues and eigenvectors are used to suggest if the data is clustered about a mean value or distributed along a girdle. Modified Flinn, Triangular and histograms plots are also available. Next step of development will focus on tools as merging and rotation of datasets, possibility to save 'projects' and paleostress analysis. In its current state, OpenStereo requires Python, wxPython, Numpy and Matplotlib installed in the system. We recommend installing PythonXY or the Enthought Python Distribution on MS-Windows and MacOS machines, since all dependencies are provided. Most Linux distributions provide an easy way to install all dependencies through software repositories. OpenStereo is released under the GNU General Public License. Programmers willing to contribute are encouraged to contact the authors directly. FAPESP Grant #09/17675-5

Performance of the engineering analysis and data system 2 common file system

NASA Technical Reports Server (NTRS)

Debrunner, Linda S.

1993-01-01

The Engineering Analysis and Data System (EADS) was used from April 1986 to July 1993 to support large scale scientific and engineering computation (e.g. computational fluid dynamics) at Marshall Space Flight Center. The need for an updated system resulted in a RFP in June 1991, after which a contract was awarded to Cray Grumman. EADS II was installed in February 1993, and by July 1993 most users were migrated. EADS II is a network of heterogeneous computer systems supporting scientific and engineering applications. The Common File System (CFS) is a key component of this system. The CFS provides a seamless, integrated environment to the users of EADS II including both disk and tape storage. UniTree software is used to implement this hierarchical storage management system. The performance of the CFS suffered during the early months of the production system. Several of the performance problems were traced to software bugs which have been corrected. Other problems were associated with hardware. However, the use of NFS in UniTree UCFM software limits the performance of the system. The performance issues related to the CFS have led to a need to develop a greater understanding of the CFS organization. This paper will first describe the EADS II with emphasis on the CFS. Then, a discussion of mass storage systems will be presented, and methods of measuring the performance of the Common File System will be outlined. Finally, areas for further study will be identified and conclusions will be drawn.

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

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.

BROCCOLI: Software for fast fMRI analysis on many-core CPUs and GPUs

PubMed Central

Eklund, Anders; Dufort, Paul; Villani, Mattias; LaConte, Stephen

2014-01-01

Analysis of functional magnetic resonance imaging (fMRI) data is becoming ever more computationally demanding as temporal and spatial resolutions improve, and large, publicly available data sets proliferate. Moreover, methodological improvements in the neuroimaging pipeline, such as non-linear spatial normalization, non-parametric permutation tests and Bayesian Markov Chain Monte Carlo approaches, can dramatically increase the computational burden. Despite these challenges, there do not yet exist any fMRI software packages which leverage inexpensive and powerful graphics processing units (GPUs) to perform these analyses. Here, we therefore present BROCCOLI, a free software package written in OpenCL (Open Computing Language) that can be used for parallel analysis of fMRI data on a large variety of hardware configurations. BROCCOLI has, for example, been tested with an Intel CPU, an Nvidia GPU, and an AMD GPU. These tests show that parallel processing of fMRI data can lead to significantly faster analysis pipelines. This speedup can be achieved on relatively standard hardware, but further, dramatic speed improvements require only a modest investment in GPU hardware. BROCCOLI (running on a GPU) can perform non-linear spatial normalization to a 1 mm3 brain template in 4–6 s, and run a second level permutation test with 10,000 permutations in about a minute. These non-parametric tests are generally more robust than their parametric counterparts, and can also enable more sophisticated analyses by estimating complicated null distributions. Additionally, BROCCOLI includes support for Bayesian first-level fMRI analysis using a Gibbs sampler. The new software is freely available under GNU GPL3 and can be downloaded from github (https://github.com/wanderine/BROCCOLI/). PMID:24672471

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.

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

PubMed Central

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

2012-01-01

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

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.

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

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

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

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

Uses of software in digital image analysis: a forensic report

NASA Astrophysics Data System (ADS)

Sharma, Mukesh; Jha, Shailendra

2010-02-01

Forensic image analysis is required an expertise to interpret the content of an image or the image itself in legal matters. Major sub-disciplines of forensic image analysis with law enforcement applications include photo-grammetry, photographic comparison, content analysis and image authentication. It has wide applications in forensic science range from documenting crime scenes to enhancing faint or indistinct patterns such as partial fingerprints. The process of forensic image analysis can involve several different tasks, regardless of the type of image analysis performed. Through this paper authors have tried to explain these tasks, which are described in to three categories: Image Compression, Image Enhancement & Restoration and Measurement Extraction. With the help of examples like signature comparison, counterfeit currency comparison and foot-wear sole impression using the software Canvas and Corel Draw.

Strengthening Software Authentication with the ROSE Software Suite

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

White, G

2006-06-15

Many recent nonproliferation and arms control software projects include a software authentication regime. These include U.S. Government-sponsored projects both in the United States and in the Russian Federation (RF). This trend toward requiring software authentication is only accelerating. Demonstrating assurance that software performs as expected without hidden ''backdoors'' is crucial to a project's success. In this context, ''authentication'' is defined as determining that a software package performs only its intended purpose and performs said purpose correctly and reliably over the planned duration of an agreement. In addition to visual inspections by knowledgeable computer scientists, automated tools are needed to highlightmore » suspicious code constructs, both to aid visual inspection and to guide program development. While many commercial tools are available for portions of the authentication task, they are proprietary and not extensible. An open-source, extensible tool can be customized to the unique needs of each project (projects can have both common and custom rules to detect flaws and security holes). Any such extensible tool has to be based on a complete language compiler. ROSE is precisely such a compiler infrastructure developed within the Department of Energy (DOE) and targeted at the optimization of scientific applications and user-defined libraries within large-scale applications (typically applications of a million lines of code). ROSE is a robust, source-to-source analysis and optimization infrastructure currently addressing large, million-line DOE applications in C and C++ (handling the full C, C99, C++ languages and with current collaborations to support Fortran90). We propose to extend ROSE to address a number of security-specific requirements, and apply it to software authentication for nonproliferation and arms control projects.« less

Advanced Cell Classifier: User-Friendly Machine-Learning-Based Software for Discovering Phenotypes in High-Content Imaging Data.

PubMed

Piccinini, Filippo; Balassa, Tamas; Szkalisity, Abel; Molnar, Csaba; Paavolainen, Lassi; Kujala, Kaisa; Buzas, Krisztina; Sarazova, Marie; Pietiainen, Vilja; Kutay, Ulrike; Smith, Kevin; Horvath, Peter

2017-06-28

High-content, imaging-based screens now routinely generate data on a scale that precludes manual verification and interrogation. Software applying machine learning has become an essential tool to automate analysis, but these methods require annotated examples to learn from. Efficiently exploring large datasets to find relevant examples remains a challenging bottleneck. Here, we present Advanced Cell Classifier (ACC), a graphical software package for phenotypic analysis that addresses these difficulties. ACC applies machine-learning and image-analysis methods to high-content data generated by large-scale, cell-based experiments. It features methods to mine microscopic image data, discover new phenotypes, and improve recognition performance. We demonstrate that these features substantially expedite the training process, successfully uncover rare phenotypes, and improve the accuracy of the analysis. ACC is extensively documented, designed to be user-friendly for researchers without machine-learning expertise, and distributed as a free open-source tool at www.cellclassifier.org. Copyright © 2017 Elsevier Inc. All rights reserved.

Design sensitivity analysis and optimization tool (DSO) for sizing design applications

NASA Technical Reports Server (NTRS)

Chang, Kuang-Hua; Choi, Kyung K.; Perng, Jyh-Hwa

1992-01-01

The DSO tool, a structural design software system that provides the designer with a graphics-based menu-driven design environment to perform easy design optimization for general applications, is presented. Three design stages, preprocessing, design sensitivity analysis, and postprocessing, are implemented in the DSO to allow the designer to carry out the design process systematically. A framework, including data base, user interface, foundation class, and remote module, has been designed and implemented to facilitate software development for the DSO. A number of dedicated commercial software/packages have been integrated in the DSO to support the design procedures. Instead of parameterizing an FEM, design parameters are defined on a geometric model associated with physical quantities, and the continuum design sensitivity analysis theory is implemented to compute design sensitivity coefficients using postprocessing data from the analysis codes. A tracked vehicle road wheel is given as a sizing design application to demonstrate the DSO's easy and convenient design optimization process.

Development of an automated analysis system for data from flow cytometric intracellular cytokine staining assays from clinical vaccine trials

PubMed Central

Shulman, Nick; Bellew, Matthew; Snelling, George; Carter, Donald; Huang, Yunda; Li, Hongli; Self, Steven G.; McElrath, M. Juliana; De Rosa, Stephen C.

2008-01-01

Background Intracellular cytokine staining (ICS) by multiparameter flow cytometry is one of the primary methods for determining T cell immunogenicity in HIV-1 clinical vaccine trials. Data analysis requires considerable expertise and time. The amount of data is quickly increasing as more and larger trials are performed, and thus there is a critical need for high throughput methods of data analysis. Methods A web based flow cytometric analysis system, LabKey Flow, was developed for analyses of data from standardized ICS assays. A gating template was created manually in commercially-available flow cytometric analysis software. Using this template, the system automatically compensated and analyzed all data sets. Quality control queries were designed to identify potentially incorrect sample collections. Results Comparison of the semi-automated analysis performed by LabKey Flow and the manual analysis performed using FlowJo software demonstrated excellent concordance (concordance correlation coefficient >0.990). Manual inspection of the analyses performed by LabKey Flow for 8-color ICS data files from several clinical vaccine trials indicates that template gates can appropriately be used for most data sets. Conclusions The semi-automated LabKey Flow analysis system can analyze accurately large ICS data files. Routine use of the system does not require specialized expertise. This high-throughput analysis will provide great utility for rapid evaluation of complex multiparameter flow cytometric measurements collected from large clinical trials. PMID:18615598

The Implications of Using Integrated Software Support Environment for Design of Guidance and Control Systems Software

DTIC Science & Technology

1990-02-01

inspections are performed before each formal review of each software life cycle phase. * Required software audits are performed . " The software is acceptable... Audits : Software audits are performed bySQA consistent with thegeneral audit rules and an auditreportis prepared. Software Quality Inspection (SQI...DSD Software Development Method 3-34 DEFINITION OF ACRONYMS Acronym Full Name or Description MACH Methode d’Analyse et de Conception Flierarchisee

The integration of automated knowledge acquisition with computer-aided software engineering for space shuttle expert systems

NASA Technical Reports Server (NTRS)

Modesitt, Kenneth L.

1990-01-01

A prediction was made that the terms expert systems and knowledge acquisition would begin to disappear over the next several years. This is not because they are falling into disuse; it is rather that practitioners are realizing that they are valuable adjuncts to software engineering, in terms of problem domains addressed, user acceptance, and in development methodologies. A specific problem was discussed, that of constructing an automated test analysis system for the Space Shuttle Main Engine. In this domain, knowledge acquisition was part of requirements systems analysis, and was performed with the aid of a powerful inductive ESBT in conjunction with a computer aided software engineering (CASE) tool. The original prediction is not a very risky one -- it has already been accomplished.

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

PubMed

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

2009-08-01

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

CytoSpectre: a tool for spectral analysis of oriented structures on cellular and subcellular levels.

PubMed

Kartasalo, Kimmo; Pölönen, Risto-Pekka; Ojala, Marisa; Rasku, Jyrki; Lekkala, Jukka; Aalto-Setälä, Katriina; Kallio, Pasi

2015-10-26

Orientation and the degree of isotropy are important in many biological systems such as the sarcomeres of cardiomyocytes and other fibrillar structures of the cytoskeleton. Image based analysis of such structures is often limited to qualitative evaluation by human experts, hampering the throughput, repeatability and reliability of the analyses. Software tools are not readily available for this purpose and the existing methods typically rely at least partly on manual operation. We developed CytoSpectre, an automated tool based on spectral analysis, allowing the quantification of orientation and also size distributions of structures in microscopy images. CytoSpectre utilizes the Fourier transform to estimate the power spectrum of an image and based on the spectrum, computes parameter values describing, among others, the mean orientation, isotropy and size of target structures. The analysis can be further tuned to focus on targets of particular size at cellular or subcellular scales. The software can be operated via a graphical user interface without any programming expertise. We analyzed the performance of CytoSpectre by extensive simulations using artificial images, by benchmarking against FibrilTool and by comparisons with manual measurements performed for real images by a panel of human experts. The software was found to be tolerant against noise and blurring and superior to FibrilTool when analyzing realistic targets with degraded image quality. The analysis of real images indicated general good agreement between computational and manual results while also revealing notable expert-to-expert variation. Moreover, the experiment showed that CytoSpectre can handle images obtained of different cell types using different microscopy techniques. Finally, we studied the effect of mechanical stretching on cardiomyocytes to demonstrate the software in an actual experiment and observed changes in cellular orientation in response to stretching. CytoSpectre, a versatile, easy-to-use software tool for spectral analysis of microscopy images was developed. The tool is compatible with most 2D images and can be used to analyze targets at different scales. We expect the tool to be useful in diverse applications dealing with structures whose orientation and size distributions are of interest. While designed for the biological field, the software could also be useful in non-biological applications.

Assistant for Specifying Quality Software (ASQS) Mission Area Analysis

DTIC Science & Technology

1990-12-01

somewhat arbitrary, it was a reasonable and fast approach for partitioning the mission and software domains. The MAD builds on work done by Boeing Aerospace...Reliability ++ Reliability +++ Response 2: NO Discussion: A NO response implies intermittent burns -- most likely to perform attitude control functions...Propulsion Reliability +++ Reliability ++ 4-15 4.8.3 Query BT.3 Query: For intermittent thruster firing requirements, will the average burn time be less than

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

Jarocki, John Charles; Zage, David John; Fisher, Andrew N.

LinkShop is a software tool for applying the method of Linkography to the analysis time-sequence data. LinkShop provides command line, web, and application programming interfaces (API) for input and processing of time-sequence data, abstraction models, and ontologies. The software creates graph representations of the abstraction model, ontology, and derived linkograph. Finally, the tool allows the user to perform statistical measurements of the linkograph and refine the ontology through direct manipulation of the linkograph.

Applying the Goal-Question-Indicator-Metric (GQIM) Method to Perform Military Situational Analysis

DTIC Science & Technology

2016-05-11

www.sei.cmu.edu CMU/SEI-2016-TN-003 | SOFTWARE ENGINEERING INSTITUTE | CARNEGIE MELLON UNIVERSITY Distribution Statement A: Approved for Public Release...Distribution is Unlimited Copyright 2016 Carnegie Mellon University This material is based upon work funded and supported by the Department of...Defense under Contract No. FA8721-05-C-0003 with Carnegie Mellon University for the operation of the Software Engineering Institute, a federally

A Survey of Techniques for Security Architecture Analysis

DTIC Science & Technology

2003-05-01

to be corrected immediately. 49 DSTO-TR-1438 A software phenomenon is the "user innovation network", examples of such networks being "free" and "open...source" software projects. These networks have innovation development, production, distribution and consumption all being performed by users/self...manufacturers. "User innovation networks can function entirely independently of manufacturers because (1) at least some users have sufficient incentive to

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.

Unified Engineering Software System

NASA Technical Reports Server (NTRS)

Purves, L. R.; Gordon, S.; Peltzman, A.; Dube, M.

1989-01-01

Collection of computer programs performs diverse functions in prototype engineering. NEXUS, NASA Engineering Extendible Unified Software system, is research set of computer programs designed to support full sequence of activities encountered in NASA engineering projects. Sequence spans preliminary design, design analysis, detailed design, manufacturing, assembly, and testing. Primarily addresses process of prototype engineering, task of getting single or small number of copies of product to work. Written in FORTRAN 77 and PROLOG.

Models for Threat Assessment in Networks

DTIC Science & Technology

2006-09-01

Software International and Command AntiVirus . [Online]. Available: http://www.commandsoftware.com/virus/newlove.html [38] C. Ng and P. Ferrie. (2000...28 2.3 False positive trends across all population sizes for r=0.7 and m=0.1 . . . . 33 2.4 False negative trends across all population...benefits analysis is often performed to determine the list of mitigation procedures. Traditionally, risk assessment has been done in part with software

2016 Research Outreach Program report

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

Lee, Hye Young; Kim, Yangkyu

2016-10-13

This paper is the research activity report for 4 weeks in LANL. Under the guidance of Dr. Lee, who performs nuclear physics research at LANSCE, LANL, I studied the Low Energy NZ (LENZ) setup and how to use the LENZ. First, I studied the LENZ chamber and Si detectors, and worked on detector calibrations, using the computer software, ROOT (CERN developed data analysis tool) and EXCEL (Microsoft office software). I also performed the calibration experiments that measure alpha particles emitted from a Th-229 source by using a S1-type detector (Si detector). And with Dr. Lee, we checked the result.

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.

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.

Introduction on Using the FastPCR Software and the Related Java Web Tools for PCR and Oligonucleotide Assembly and Analysis.

PubMed

Kalendar, Ruslan; Tselykh, Timofey V; Khassenov, Bekbolat; Ramanculov, Erlan M

2017-01-01

This chapter introduces the FastPCR software as an integrated tool environment for PCR primer and probe design, which predicts properties of oligonucleotides based on experimental studies of the PCR efficiency. The software provides comprehensive facilities for designing primers for most PCR applications and their combinations. These include the standard PCR as well as the multiplex, long-distance, inverse, real-time, group-specific, unique, overlap extension PCR for multi-fragments assembling cloning and loop-mediated isothermal amplification (LAMP). It also contains a built-in program to design oligonucleotide sets both for long sequence assembly by ligase chain reaction and for design of amplicons that tile across a region(s) of interest. The software calculates the melting temperature for the standard and degenerate oligonucleotides including locked nucleic acid (LNA) and other modifications. It also provides analyses for a set of primers with the prediction of oligonucleotide properties, dimer and G/C-quadruplex detection, linguistic complexity as well as a primer dilution and resuspension calculator. The program consists of various bioinformatical tools for analysis of sequences with the GC or AT skew, CG% and GA% content, and the purine-pyrimidine skew. It also analyzes the linguistic sequence complexity and performs generation of random DNA sequence as well as restriction endonucleases analysis. The program allows to find or create restriction enzyme recognition sites for coding sequences and supports the clustering of sequences. It performs efficient and complete detection of various repeat types with visual display. The FastPCR software allows the sequence file batch processing that is essential for automation. The program is available for download at http://primerdigital.com/fastpcr.html , and its online version is located at http://primerdigital.com/tools/pcr.html .

Efficient Process Migration for Parallel Processing on Non-Dedicated Networks of Workstations

NASA Technical Reports Server (NTRS)

Chanchio, Kasidit; Sun, Xian-He

1996-01-01

This paper presents the design and preliminary implementation of MpPVM, a software system that supports process migration for PVM application programs in a non-dedicated heterogeneous computing environment. New concepts of migration point as well as migration point analysis and necessary data analysis are introduced. In MpPVM, process migrations occur only at previously inserted migration points. Migration point analysis determines appropriate locations to insert migration points; whereas, necessary data analysis provides a minimum set of variables to be transferred at each migration pint. A new methodology to perform reliable point-to-point data communications in a migration environment is also discussed. Finally, a preliminary implementation of MpPVM and its experimental results are presented, showing the correctness and promising performance of our process migration mechanism in a scalable non-dedicated heterogeneous computing environment. While MpPVM is developed on top of PVM, the process migration methodology introduced in this study is general and can be applied to any distributed software environment.

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.

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).

Data Packages for the Hanford Immobilized Low Activity Tank Waste Performance Assessment 2001 Version [SEC 1 THRU 5

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

MANN, F.M.

Data package supporting the 2001 Immobilized Low-Activity Waste Performance Analysis. Geology, hydrology, geochemistry, facility, waste form, and dosimetry data based on recent investigation are provided. Verification and benchmarking packages for selected software codes are provided.

Integrated Sensitivity Analysis Workflow

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

Friedman-Hill, Ernest J.; Hoffman, Edward L.; Gibson, Marcus J.

2014-08-01

Sensitivity analysis is a crucial element of rigorous engineering analysis, but performing such an analysis on a complex model is difficult and time consuming. The mission of the DART Workbench team at Sandia National Laboratories is to lower the barriers to adoption of advanced analysis tools through software integration. The integrated environment guides the engineer in the use of these integrated tools and greatly reduces the cycle time for engineering analysis.

Methodology issues concerning the accuracy of kinematic data collection and analysis using the ariel performance analysis system

NASA Technical Reports Server (NTRS)

Wilmington, R. P.; Klute, Glenn K. (Editor); Carroll, Amy E. (Editor); Stuart, Mark A. (Editor); Poliner, Jeff (Editor); Rajulu, Sudhakar (Editor); Stanush, Julie (Editor)

1992-01-01

Kinematics, the study of motion exclusive of the influences of mass and force, is one of the primary methods used for the analysis of human biomechanical systems as well as other types of mechanical systems. The Anthropometry and Biomechanics Laboratory (ABL) in the Crew Interface Analysis section of the Man-Systems Division performs both human body kinematics as well as mechanical system kinematics using the Ariel Performance Analysis System (APAS). The APAS supports both analysis of analog signals (e.g. force plate data collection) as well as digitization and analysis of video data. The current evaluations address several methodology issues concerning the accuracy of the kinematic data collection and analysis used in the ABL. This document describes a series of evaluations performed to gain quantitative data pertaining to position and constant angular velocity movements under several operating conditions. Two-dimensional as well as three-dimensional data collection and analyses were completed in a controlled laboratory environment using typical hardware setups. In addition, an evaluation was performed to evaluate the accuracy impact due to a single axis camera offset. Segment length and positional data exhibited errors within 3 percent when using three-dimensional analysis and yielded errors within 8 percent through two-dimensional analysis (Direct Linear Software). Peak angular velocities displayed errors within 6 percent through three-dimensional analyses and exhibited errors of 12 percent when using two-dimensional analysis (Direct Linear Software). The specific results from this series of evaluations and their impacts on the methodology issues of kinematic data collection and analyses are presented in detail. The accuracy levels observed in these evaluations are also presented.

solveTruss v1.0: Static, global buckling and frequency analysis of 2D and 3D trusses with Mathematica

NASA Astrophysics Data System (ADS)

Ozbasaran, Hakan

Trusses have an important place amongst engineering structures due to many advantages such as high structural efficiency, fast assembly and easy maintenance. Iterative truss design procedures, which require analysis of a large number of candidate structural systems such as size, shape and topology optimization with stochastic methods, mostly lead the engineer to establish a link between the development platform and external structural analysis software. By increasing number of structural analyses, this (probably slow-response) link may climb to the top of the list of performance issues. This paper introduces a software for static, global member buckling and frequency analysis of 2D and 3D trusses to overcome this problem for Mathematica users.

Software Design Challenges in Time Series Prediction Systems Using Parallel Implementation of Artificial Neural Networks.

PubMed

Manikandan, Narayanan; Subha, Srinivasan

2016-01-01

Software development life cycle has been characterized by destructive disconnects between activities like planning, analysis, design, and programming. Particularly software developed with prediction based results is always a big challenge for designers. Time series data forecasting like currency exchange, stock prices, and weather report are some of the areas where an extensive research is going on for the last three decades. In the initial days, the problems with financial analysis and prediction were solved by statistical models and methods. For the last two decades, a large number of Artificial Neural Networks based learning models have been proposed to solve the problems of financial data and get accurate results in prediction of the future trends and prices. This paper addressed some architectural design related issues for performance improvement through vectorising the strengths of multivariate econometric time series models and Artificial Neural Networks. It provides an adaptive approach for predicting exchange rates and it can be called hybrid methodology for predicting exchange rates. This framework is tested for finding the accuracy and performance of parallel algorithms used.

Software Design Challenges in Time Series Prediction Systems Using Parallel Implementation of Artificial Neural Networks

PubMed Central

Manikandan, Narayanan; Subha, Srinivasan

2016-01-01

Software development life cycle has been characterized by destructive disconnects between activities like planning, analysis, design, and programming. Particularly software developed with prediction based results is always a big challenge for designers. Time series data forecasting like currency exchange, stock prices, and weather report are some of the areas where an extensive research is going on for the last three decades. In the initial days, the problems with financial analysis and prediction were solved by statistical models and methods. For the last two decades, a large number of Artificial Neural Networks based learning models have been proposed to solve the problems of financial data and get accurate results in prediction of the future trends and prices. This paper addressed some architectural design related issues for performance improvement through vectorising the strengths of multivariate econometric time series models and Artificial Neural Networks. It provides an adaptive approach for predicting exchange rates and it can be called hybrid methodology for predicting exchange rates. This framework is tested for finding the accuracy and performance of parallel algorithms used. PMID:26881271

High-Performance Mixed Models Based Genome-Wide Association Analysis with omicABEL software

PubMed Central

Fabregat-Traver, Diego; Sharapov, Sodbo Zh.; Hayward, Caroline; Rudan, Igor; Campbell, Harry; Aulchenko, Yurii; Bientinesi, Paolo

2014-01-01

To raise the power of genome-wide association studies (GWAS) and avoid false-positive results in structured populations, one can rely on mixed model based tests. When large samples are used, and when multiple traits are to be studied in the ’omics’ context, this approach becomes computationally challenging. Here we consider the problem of mixed-model based GWAS for arbitrary number of traits, and demonstrate that for the analysis of single-trait and multiple-trait scenarios different computational algorithms are optimal. We implement these optimal algorithms in a high-performance computing framework that uses state-of-the-art linear algebra kernels, incorporates optimizations, and avoids redundant computations, increasing throughput while reducing memory usage and energy consumption. We show that, compared to existing libraries, our algorithms and software achieve considerable speed-ups. The OmicABEL software described in this manuscript is available under the GNU GPL v. 3 license as part of the GenABEL project for statistical genomics at http: //www.genabel.org/packages/OmicABEL. PMID:25717363

High-Performance Mixed Models Based Genome-Wide Association Analysis with omicABEL software.

PubMed

Fabregat-Traver, Diego; Sharapov, Sodbo Zh; Hayward, Caroline; Rudan, Igor; Campbell, Harry; Aulchenko, Yurii; Bientinesi, Paolo

2014-01-01

To raise the power of genome-wide association studies (GWAS) and avoid false-positive results in structured populations, one can rely on mixed model based tests. When large samples are used, and when multiple traits are to be studied in the 'omics' context, this approach becomes computationally challenging. Here we consider the problem of mixed-model based GWAS for arbitrary number of traits, and demonstrate that for the analysis of single-trait and multiple-trait scenarios different computational algorithms are optimal. We implement these optimal algorithms in a high-performance computing framework that uses state-of-the-art linear algebra kernels, incorporates optimizations, and avoids redundant computations, increasing throughput while reducing memory usage and energy consumption. We show that, compared to existing libraries, our algorithms and software achieve considerable speed-ups. The OmicABEL software described in this manuscript is available under the GNU GPL v. 3 license as part of the GenABEL project for statistical genomics at http: //www.genabel.org/packages/OmicABEL.

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

PubMed

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

2017-12-01

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

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.

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

PubMed

Giancarlo, R; Scaturro, D; Utro, F

2015-02-01

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

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.

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

PubMed

Gross, Arnd; Ziepert, Marita; Scholz, Markus

2012-01-01

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

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

PubMed Central

Gross, Arnd; Ziepert, Marita; Scholz, Markus

2012-01-01

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

Application of mixsep software package: Performance verification of male-mixed DNA analysis

PubMed Central

HU, NA; CONG, BIN; GAO, TAO; CHEN, YU; SHEN, JUNYI; LI, SHUJIN; MA, CHUNLING

2015-01-01

An experimental model of male-mixed DNA (n=297) was constructed according to the mixed DNA construction principle. This comprised the use of the Applied Biosystems (ABI) 7500 quantitative polymerase chain reaction system, with scientific validation of mixture proportion (Mx; root-mean-square error ≤0.02). Statistical analysis was performed on locus separation accuracy using mixsep, a DNA mixture separation R-package, and the analytical performance of mixsep was assessed by examining the data distribution pattern of different mixed gradients, short tandem repeat (STR) loci and mixed DNA types. The results showed that locus separation accuracy had a negative linear correlation with the mixed gradient (R2=−0.7121). With increasing mixed gradient imbalance, locus separation accuracy first increased and then decreased, with the highest value detected at a gradient of 1:3 (≥90%). The mixed gradient, which is the theoretical Mx, was one of the primary factors that influenced the success of mixed DNA analysis. Among the 16 STR loci detected by Identifiler®, the separation accuracy was relatively high (>88%) for loci D5S818, D8S1179 and FGA, whereas the median separation accuracy value was lowest for the D7S820 locus. STR loci with relatively large numbers of allelic drop-out (ADO; >15) were all located in the yellow and red channels, including loci D18S51, D19S433, FGA, TPOX and vWA. These five loci featured low allele peak heights, which was consistent with the low sensitivity of the ABI 3130xl Genetic Analyzer to yellow and red fluorescence. The locus separation accuracy of the mixsep package was substantially different with and without the inclusion of ADO loci; inclusion of ADO significantly reduced the analytical performance of the mixsep package, which was consistent with the lack of an ADO functional module in this software. The present study demonstrated that the mixsep software had a number of advantages and was recommended for analysis of mixed DNA. This software was easy to operate and produced understandable results with a degree of controllability. PMID:25936428

Shuttle avionics software development trials: Tribulations and successes, the backup flight system

NASA Technical Reports Server (NTRS)

Chevers, E. S.

1985-01-01

The development and verification of the Backup Flight System software (BFS) is discussed. The approach taken for the BFS was to develop a very simple and straightforward software program and then test it in every conceivable manner. The result was a program that contained approximately 12,000 full words including ground checkout and the built in test program for the computer. To perform verification, a series of tests was defined using the actual flight type hardware and simulated flight conditions. Then simulated flights were flown and detailed performance analysis was conducted. The intent of most BFS tests was to demonstrate that a stable flightpath could be obtained after engagement from an anomalous initial condition. The extention of the BFS to meet the requirements of the orbital flight test phase is also described.

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

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

PubMed

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

2015-01-01

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

Welding process modelling and control

NASA Technical Reports Server (NTRS)

Romine, Peter L.; Adenwala, Jinen A.

1993-01-01

The research and analysis performed, and software developed, and hardware/software recommendations made during 1992 in development of the PC-based data acquisition system for support of Welding Process Modeling and Control is reported. A need was identified by the Metals Processing Branch of NASA Marshall Space Flight Center, for a mobile data aquisition and analysis system, customized for welding measurement and calibration. Several hardware configurations were evaluated and a PC-based system was chosen. The Welding Measurement System (WMS) is a dedicated instrument, strictly for the use of data aquisition and analysis. Although the WMS supports many of the functions associated with the process control, it is not the intention for this system to be used for welding process control.

Application of CT-PSF-based computer-simulated lung nodules for evaluating the accuracy of computer-aided volumetry.

PubMed

Funaki, Ayumu; Ohkubo, Masaki; Wada, Shinichi; Murao, Kohei; Matsumoto, Toru; Niizuma, Shinji

2012-07-01

With the wide dissemination of computed tomography (CT) screening for lung cancer, measuring the nodule volume accurately with computer-aided volumetry software is increasingly important. Many studies for determining the accuracy of volumetry software have been performed using a phantom with artificial nodules. These phantom studies are limited, however, in their ability to reproduce the nodules both accurately and in the variety of sizes and densities required. Therefore, we propose a new approach of using computer-simulated nodules based on the point spread function measured in a CT system. The validity of the proposed method was confirmed by the excellent agreement obtained between computer-simulated nodules and phantom nodules regarding the volume measurements. A practical clinical evaluation of the accuracy of volumetry software was achieved by adding simulated nodules onto clinical lung images, including noise and artifacts. The tested volumetry software was revealed to be accurate within an error of 20 % for nodules >5 mm and with the difference between nodule density and background (lung) (CT value) being 400-600 HU. Such a detailed analysis can provide clinically useful information on the use of volumetry software in CT screening for lung cancer. We concluded that the proposed method is effective for evaluating the performance of computer-aided volumetry software.

Processing of on-board recorded data for quick analysis of aircraft performance. [rotor systems research aircraft

NASA Technical Reports Server (NTRS)

Michaud, N. H.

1979-01-01

A system of independent computer programs for the processing of digitized pulse code modulated (PCM) and frequency modulated (FM) data is described. Information is stored in a set of random files and accessed to produce both statistical and graphical output. The software system is designed primarily to present these reports within a twenty-four hour period for quick analysis of the helicopter's performance.

Development and Integration of Control System Models

NASA Technical Reports Server (NTRS)

Kim, Young K.

1998-01-01

The computer simulation tool, TREETOPS, has been upgraded and used at NASA/MSFC to model various complicated mechanical systems and to perform their dynamics and control analysis with pointing control systems. A TREETOPS model of Advanced X-ray Astrophysics Facility - Imaging (AXAF-1) dynamics and control system was developed to evaluate the AXAF-I pointing performance for Normal Pointing Mode. An optical model of Shooting Star Experiment (SSE) was also developed and its optical performance analysis was done using the MACOS software.

SHAPA: An interactive software tool for protocol analysis applied to aircrew communications and workload

NASA Technical Reports Server (NTRS)

James, Jeffrey M.; Sanderson, Penelope M.; Seidler, Karen S.

1990-01-01

As modern transport environments become increasingly complex, issues such as crew communication, interaction with automation, and workload management have become crucial. Much research is being focused on holistic aspects of social and cognitive behavior, such as the strategies used to handle workload, the flow of information, the scheduling of tasks, the verbal and non-verbal interactions between crew members. Traditional laboratory performance measures no longer sufficiently meet the needs of researchers addressing these issues. However observational techniques are better equipped to capture the type of data needed and to build models of the requisite level of sophistication. Presented here is SHAPA, an interactive software tool for performing both verbal and non-verbal protocol analysis. It has been developed with the idea of affording the researchers the closest possible degree of engagement with protocol data. The researcher can configure SHAPA to encode protocols using any theoretical framework or encoding vocabulary that is desired. SHAPA allows protocol analysis to be performed at any level of analysis, and it supplies a wide variety of tools for data aggregation, manipulation. The output generated by SHAPA can be used alone or in combination with other performance variables to get a rich picture of the influences on sequences of verbal or nonverbal behavior.

Model-based engineering for laser weapons systems

NASA Astrophysics Data System (ADS)

Panthaki, Malcolm; Coy, Steve

2011-10-01

The Comet Performance Engineering Workspace is an environment that enables integrated, multidisciplinary modeling and design/simulation process automation. One of the many multi-disciplinary applications of the Comet Workspace is for the integrated Structural, Thermal, Optical Performance (STOP) analysis of complex, multi-disciplinary space systems containing Electro-Optical (EO) sensors such as those which are designed and developed by and for NASA and the Department of Defense. The CometTM software is currently able to integrate performance simulation data and processes from a wide range of 3-D CAD and analysis software programs including CODE VTM from Optical Research Associates and SigFitTM from Sigmadyne Inc. which are used to simulate the optics performance of EO sensor systems in space-borne applications. Over the past year, Comet Solutions has been working with MZA Associates of Albuquerque, NM, under a contract with the Air Force Research Laboratories. This funded effort is a "risk reduction effort", to help determine whether the combination of Comet and WaveTrainTM, a wave optics systems engineering analysis environment developed and maintained by MZA Associates and used by the Air Force Research Laboratory, will result in an effective Model-Based Engineering (MBE) environment for the analysis and design of laser weapons systems. This paper will review the results of this effort and future steps.

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.

New technologies for supporting real-time on-board software development

NASA Astrophysics Data System (ADS)

Kerridge, D.

1995-03-01

The next generation of on-board data management systems will be significantly more complex than current designs, and will be required to perform more complex and demanding tasks in software. Improved hardware technology, in the form of the MA31750 radiation hard processor, is one key component in addressing the needs of future embedded systems. However, to complement these hardware advances, improved support for the design and implementation of real-time data management software is now needed. This will help to control the cost and risk assoicated with developing data management software development as it becomes an increasingly significant element within embedded systems. One particular problem with developing embedded software is managing the non-functional requirements in a systematic way. This paper identifies how Logica has exploited recent developments in hard real-time theory to address this problem through the use of new hard real-time analysis and design methods which can be supported by specialized tools. The first stage in transferring this technology from the research domain to industrial application has already been completed. The MA37150 Hard Real-Time Embedded Software Support Environment (HESSE) is a loosely integrated set of hardware and software tools which directly support the process of hard real-time analysis for software targeting the MA31750 processor. With further development, this HESSE promises to provide embedded system developers with software tools which can reduce the risks associated with developing complex hard real-time software. Supported in this way by more sophisticated software methods and tools, it is foreseen that MA31750 based embedded systems can meet the processing needs for the next generation of on-board data management systems.

How Game Location Affects Soccer Performance: T-Pattern Analysis of Attack Actions in Home and Away Matches.

PubMed

Diana, Barbara; Zurloni, Valentino; Elia, Massimiliano; Cavalera, Cesare M; Jonsson, Gudberg K; Anguera, M Teresa

2017-01-01

The influence of game location on performance has been widely examined in sport contexts. Concerning soccer, game-location affects positively the secondary and tertiary level of performance; however, there are fewer evidences about its effect on game structure (primary level of performance). This study aimed to detect the effect of game location on a primary level of performance in soccer. In particular, the objective was to reveal the hidden structures underlying the attack actions, in both home and away matches played by a top club (Serie A 2012/2013-First Leg). The methodological approach was based on systematic observation, supported by digital recordings and T-pattern analysis. Data were analyzed with THEME 6.0 software. A quantitative analysis, with nonparametric Mann-Whitney test and descriptive statistics, was carried out to test the hypotheses. A qualitative analysis on complex patterns was performed to get in-depth information on the game structure. This study showed that game tactics were significantly different, with home matches characterized by a more structured and varied game than away matches. In particular, a higher number of different patterns, with a higher level of complexity and including more unique behaviors was detected in home matches than in the away ones. No significant differences were found in the number of events coded per game between the two conditions. THEME software, and the corresponding T-pattern detection algorithm, enhance research opportunities by going further than frequency-based analyses, making this method an effective tool in supporting sport performance analysis and training.

How Game Location Affects Soccer Performance: T-Pattern Analysis of Attack Actions in Home and Away Matches

PubMed Central

Diana, Barbara; Zurloni, Valentino; Elia, Massimiliano; Cavalera, Cesare M.; Jonsson, Gudberg K.; Anguera, M. Teresa

2017-01-01

The influence of game location on performance has been widely examined in sport contexts. Concerning soccer, game-location affects positively the secondary and tertiary level of performance; however, there are fewer evidences about its effect on game structure (primary level of performance). This study aimed to detect the effect of game location on a primary level of performance in soccer. In particular, the objective was to reveal the hidden structures underlying the attack actions, in both home and away matches played by a top club (Serie A 2012/2013—First Leg). The methodological approach was based on systematic observation, supported by digital recordings and T-pattern analysis. Data were analyzed with THEME 6.0 software. A quantitative analysis, with nonparametric Mann–Whitney test and descriptive statistics, was carried out to test the hypotheses. A qualitative analysis on complex patterns was performed to get in-depth information on the game structure. This study showed that game tactics were significantly different, with home matches characterized by a more structured and varied game than away matches. In particular, a higher number of different patterns, with a higher level of complexity and including more unique behaviors was detected in home matches than in the away ones. No significant differences were found in the number of events coded per game between the two conditions. THEME software, and the corresponding T-pattern detection algorithm, enhance research opportunities by going further than frequency-based analyses, making this method an effective tool in supporting sport performance analysis and training. PMID:28878712

Open access for ALICE analysis based on virtualization technology

NASA Astrophysics Data System (ADS)

Buncic, P.; Gheata, M.; Schutz, Y.

2015-12-01

Open access is one of the important leverages for long-term data preservation for a HEP experiment. To guarantee the usability of data analysis tools beyond the experiment lifetime it is crucial that third party users from the scientific community have access to the data and associated software. The ALICE Collaboration has developed a layer of lightweight components built on top of virtualization technology to hide the complexity and details of the experiment-specific software. Users can perform basic analysis tasks within CernVM, a lightweight generic virtual machine, paired with an ALICE specific contextualization. Once the virtual machine is launched, a graphical user interface is automatically started without any additional configuration. This interface allows downloading the base ALICE analysis software and running a set of ALICE analysis modules. Currently the available tools include fully documented tutorials for ALICE analysis, such as the measurement of strange particle production or the nuclear modification factor in Pb-Pb collisions. The interface can be easily extended to include an arbitrary number of additional analysis modules. We present the current status of the tools used by ALICE through the CERN open access portal, and the plans for future extensions of this system.

Effectiveness of Simulation in a Hybrid and Online Networking Course.

ERIC Educational Resources Information Center

Cameron, Brian H.

2003-01-01

Reports on a study that compares the performance of students enrolled in two sections of a Web-based computer networking course: one utilizing a simulation package and the second utilizing a static, graphical software package. Analysis shows statistically significant improvements in performance in the simulation group compared to the…

Geomagnetic field modeling by optimal recursive filtering

NASA Technical Reports Server (NTRS)

1980-01-01

Data sets selected for mini-batches and the software modifications required for processing these sets are described. Initial analysis was performed on minibatch field model recovery. Studies are being performed to examine the convergence of the solutions and the maximum expansion order the data will support in the constant and secular terms.

A research program in empirical computer science

NASA Technical Reports Server (NTRS)

Knight, J. C.

1991-01-01

During the grant reporting period our primary activities have been to begin preparation for the establishment of a research program in experimental computer science. The focus of research in this program will be safety-critical systems. Many questions that arise in the effort to improve software dependability can only be addressed empirically. For example, there is no way to predict the performance of the various proposed approaches to building fault-tolerant software. Performance models, though valuable, are parameterized and cannot be used to make quantitative predictions without experimental determination of underlying distributions. In the past, experimentation has been able to shed some light on the practical benefits and limitations of software fault tolerance. It is common, also, for experimentation to reveal new questions or new aspects of problems that were previously unknown. A good example is the Consistent Comparison Problem that was revealed by experimentation and subsequently studied in depth. The result was a clear understanding of a previously unknown problem with software fault tolerance. The purpose of a research program in empirical computer science is to perform controlled experiments in the area of real-time, embedded control systems. The goal of the various experiments will be to determine better approaches to the construction of the software for computing systems that have to be relied upon. As such it will validate research concepts from other sources, provide new research results, and facilitate the transition of research results from concepts to practical procedures that can be applied with low risk to NASA flight projects. The target of experimentation will be the production software development activities undertaken by any organization prepared to contribute to the research program. Experimental goals, procedures, data analysis and result reporting will be performed for the most part by the University of Virginia.

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

NASA Astrophysics Data System (ADS)

Jaggi, S.

1993-02-01

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

A dedicated software application for treatment verification with off-line PET/CT imaging at the Heidelberg Ion Beam Therapy Center

NASA Astrophysics Data System (ADS)

Chen, W.; Bauer, J.; Kurz, C.; Tessonnier, T.; Handrack, J.; Haberer, T.; Debus, J.; Parodi, K.

2017-01-01

We present the workflow of the offline-PET based range verification method used at the Heidelberg Ion Beam Therapy Center, detailing the functionalities of an in-house developed software application, SimInterface14, with which range analysis is performed. Moreover, we introduce the design of a decision support system assessing uncertainties and facilitating physicians in decisions making for plan adaptation.

Performance Improvements to the Naval Postgraduate School Turbopropulsion Labs Transonic Axially Splittered Rotor

DTIC Science & Technology

2013-12-01

Implementation of current NPS TPL design procedure that uses COTS software (MATLAB, SolidWorks, and ANSYS - CFX ) for the geometric rendering and...procedure that uses commercial-off-the-shelf software (MATLAB, SolidWorks, and ANSYS - CFX ) for the geometric rendering and analysis was modified and... CFX The CFD simulation program in ANSYS Workbench. CFX -Pre CFX boundary conditions and solver settings module. CFX -Solver CFX solver program. CFX

Cybersecurity and medical devices: A practical guide for cardiac electrophysiologists

PubMed Central

Kramer, Daniel B.; Foo Kune, Denis; Auto de Medeiros, Julio; Yan, Chen; Xu, Wenyuan; Crawford, Thomas; Fu, Kevin

2017-01-01

Abstract Medical devices increasingly depend on software. While this expands the ability of devices to perform key therapeutic and diagnostic functions, reliance on software inevitably causes exposure to hazards of security vulnerabilities. This article uses a recent high‐profile case example to outline a proactive approach to security awareness that incorporates a scientific, risk‐based analysis of security concerns that supports ongoing discussions with patients about their medical devices. PMID:28512774

Virtual airway simulation to improve dexterity among novices performing fibreoptic intubation.

PubMed

De Oliveira, G S; Glassenberg, R; Chang, R; Fitzgerald, P; McCarthy, R J

2013-10-01

We developed a virtual reality software application (iLarynx) using built-in accelerometer properties of the iPhone(®) or iPad(®) (Apple Inc., Cupertino, CA, USA) that mimics hand movements for the performance of fibreoptic skills. Twenty novice medical students were randomly assigned to virtual airway training with the iLarynx software or no additional training. Eight out of the 10 subjects in the standard training group had at least one failed (> 120 s) attempt compared with two out of the 10 participants in the iLarynx group (p = 0.01). There were a total of 24 failed attempts in the standard training group and four in the iLarynx group (p < 0.005). Cusum analysis demonstrated continued group improvement in the iLarynx, but not in the standard training group. Virtual airway simulation using freely available software on a smartphone/tablet device improves dexterity among novices performing upper airway endoscopy. © 2013 The Association of Anaesthetists of Great Britain and Ireland.

OPAD-EDIFIS Real-Time Processing

NASA Technical Reports Server (NTRS)

Katsinis, Constantine

1997-01-01

The Optical Plume Anomaly Detection (OPAD) detects engine hardware degradation of flight vehicles through identification and quantification of elemental species found in the plume by analyzing the plume emission spectra in a real-time mode. Real-time performance of OPAD relies on extensive software which must report metal amounts in the plume faster than once every 0.5 sec. OPAD software previously written by NASA scientists performed most necessary functions at speeds which were far below what is needed for real-time operation. The research presented in this report improved the execution speed of the software by optimizing the code without changing the algorithms and converting it into a parallelized form which is executed in a shared-memory multiprocessor system. The resulting code was subjected to extensive timing analysis. The report also provides suggestions for further performance improvement by (1) identifying areas of algorithm optimization, (2) recommending commercially available multiprocessor architectures and operating systems to support real-time execution and (3) presenting an initial study of fault-tolerance requirements.

Prediction of rodent carcinogenic potential of naturally occurring chemicals in the human diet using high-throughput QSAR predictive modeling

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

Valerio, Luis G.; Arvidson, Kirk B.; Chanderbhan, Ronald F.

2007-07-01

Consistent with the U.S. Food and Drug Administration (FDA) Critical Path Initiative, predictive toxicology software programs employing quantitative structure-activity relationship (QSAR) models are currently under evaluation for regulatory risk assessment and scientific decision support for highly sensitive endpoints such as carcinogenicity, mutagenicity and reproductive toxicity. At the FDA's Center for Food Safety and Applied Nutrition's Office of Food Additive Safety and the Center for Drug Evaluation and Research's Informatics and Computational Safety Analysis Staff (ICSAS), the use of computational SAR tools for both qualitative and quantitative risk assessment applications are being developed and evaluated. One tool of current interest ismore » MDL-QSAR predictive discriminant analysis modeling of rodent carcinogenicity, which has been previously evaluated for pharmaceutical applications by the FDA ICSAS. The study described in this paper aims to evaluate the utility of this software to estimate the carcinogenic potential of small, organic, naturally occurring chemicals found in the human diet. In addition, a group of 19 known synthetic dietary constituents that were positive in rodent carcinogenicity studies served as a control group. In the test group of naturally occurring chemicals, 101 were found to be suitable for predictive modeling using this software's discriminant analysis modeling approach. Predictions performed on these compounds were compared to published experimental evidence of each compound's carcinogenic potential. Experimental evidence included relevant toxicological studies such as rodent cancer bioassays, rodent anti-carcinogenicity studies, genotoxic studies, and the presence of chemical structural alerts. Statistical indices of predictive performance were calculated to assess the utility of the predictive modeling method. Results revealed good predictive performance using this software's rodent carcinogenicity module of over 1200 chemicals, comprised primarily of pharmaceutical, industrial and some natural products developed under an FDA-MDL cooperative research and development agreement (CRADA). The predictive performance for this group of dietary natural products and the control group was 97% sensitivity and 80% concordance. Specificity was marginal at 53%. This study finds that the in silico QSAR analysis employing this software's rodent carcinogenicity database is capable of identifying the rodent carcinogenic potential of naturally occurring organic molecules found in the human diet with a high degree of sensitivity. It is the first study to demonstrate successful QSAR predictive modeling of naturally occurring carcinogens found in the human diet using an external validation test. Further test validation of this software and expansion of the training data set for dietary chemicals will help to support the future use of such QSAR methods for screening and prioritizing the risk of dietary chemicals when actual animal data are inadequate, equivocal, or absent.« less

Large-scale structural analysis: The structural analyst, the CSM Testbed and the NAS System

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr.; Mccleary, Susan L.; Macy, Steven C.; Aminpour, Mohammad A.

1989-01-01

The Computational Structural Mechanics (CSM) activity is developing advanced structural analysis and computational methods that exploit high-performance computers. Methods are developed in the framework of the CSM testbed software system and applied to representative complex structural analysis problems from the aerospace industry. An overview of the CSM testbed methods development environment is presented and some numerical methods developed on a CRAY-2 are described. Selected application studies performed on the NAS CRAY-2 are also summarized.

High-performance liquid chromatography coupled with tandem mass spectrometry technology in the analysis of Chinese Medicine Formulas: A bibliometric analysis (1997-2015).

PubMed

He, Xi-Ran; Li, Chun-Guang; Zhu, Xiao-Shu; Li, Yuan-Qing; Jarouche, Mariam; Bensoussan, Alan; Li, Ping-Ping

2017-01-01

There is a recognized challenge in analyzing traditional Chinese medicine formulas because of their complex chemical compositions. The application of modern analytical techniques such as high-performance liquid chromatography coupled with a tandem mass spectrometry has improved the characterization of various compounds from traditional Chinese medicine formulas significantly. This study aims to conduct a bibliometric analysis to recognize the overall trend of high-performance liquid chromatography coupled with tandem mass spectrometry approaches in the analysis of traditional Chinese medicine formulas, its significance and possible underlying interactions between individual herbs in these formulas. Electronic databases were searched systematically, and the identified studies were collected and analyzed using Microsoft Access 2010, Graph Pad 5.0 software and Ucinet software package. 338 publications between 1997 and 2015 were identified, and analyzed in terms of annual growth and accumulated publications, top journals, forms of traditional Chinese medicine preparations and highly studied formulas and single herbs, as well as social network analysis of single herbs. There is a significant increase trend in using high-performance liquid chromatography coupled with tandem mass spectrometry related techniques in analysis of commonly used forms of traditional Chinese medicine formulas in the last 3 years. Stringent quality control is of great significance for the modernization and globalization of traditional Chinese medicine, and this bibliometric analysis provided the first and comprehensive summary within this field. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Apollo experience report: Engineering and analysis mission support

NASA Technical Reports Server (NTRS)

Fricke, R. W., Jr.

1975-01-01

The tasks performed by the team of specialists that evaluated hardware performance during prelaunch checkout and in-flight operation are discussed. The organizational structure, operational procedures, and interfaces as well as the facilities and software required to perform these tasks are discussed. The scope of the service performed by the team and the evaluation philosophy are described. Summaries of problems and their resolution are included as appendixes.

Integrated analysis of large space systems

NASA Technical Reports Server (NTRS)

Young, J. P.

1980-01-01

Based on the belief that actual flight hardware development of large space systems will necessitate a formalized method of integrating the various engineering discipline analyses, an efficient highly user oriented software system capable of performing interdisciplinary design analyses with tolerable solution turnaround time is planned Specific analysis capability goals were set forth with initial emphasis given to sequential and quasi-static thermal/structural analysis and fully coupled structural/control system analysis. Subsequently, the IAC would be expanded to include a fully coupled thermal/structural/control system, electromagnetic radiation, and optical performance analyses.

A Ballistic Limit Analysis Program for Shielding Against Micrometeoroids and Orbital Debris

NASA Technical Reports Server (NTRS)

Ryan, Shannon; Christiansen, Erie

2010-01-01

A software program has been developed that enables the user to quickly and simply perform ballistic limit calculations for common spacecraft structures that are subject to hypervelocity impact of micrometeoroid and orbital debris (MMOD) projectiles. This analysis program consists of two core modules: design, and; performance. The design module enables a user to calculate preliminary dimensions of a shield configuration (e.g., thicknesses/areal densities, spacing, etc.) for a ?design? particle (diameter, density, impact velocity, incidence). The performance module enables a more detailed shielding analysis, providing the performance of a user-defined shielding configuration over the range of relevant in-orbit impact conditions.

Large-scale structural optimization

NASA Technical Reports Server (NTRS)

Sobieszczanski-Sobieski, J.

1983-01-01

Problems encountered by aerospace designers in attempting to optimize whole aircraft are discussed, along with possible solutions. Large scale optimization, as opposed to component-by-component optimization, is hindered by computational costs, software inflexibility, concentration on a single, rather than trade-off, design methodology and the incompatibility of large-scale optimization with single program, single computer methods. The software problem can be approached by placing the full analysis outside of the optimization loop. Full analysis is then performed only periodically. Problem-dependent software can be removed from the generic code using a systems programming technique, and then embody the definitions of design variables, objective function and design constraints. Trade-off algorithms can be used at the design points to obtain quantitative answers. Finally, decomposing the large-scale problem into independent subproblems allows systematic optimization of the problems by an organization of people and machines.

Open source pipeline for ESPaDOnS reduction and analysis

NASA Astrophysics Data System (ADS)

Martioli, Eder; Teeple, Doug; Manset, Nadine; Devost, Daniel; Withington, Kanoa; Venne, Andre; Tannock, Megan

2012-09-01

OPERA is a Canada-France-Hawaii Telescope (CFHT) open source collaborative software project currently under development for an ESPaDOnS echelle spectro-polarimetric image reduction pipeline. OPERA is designed to be fully automated, performing calibrations and reduction, producing one-dimensional intensity and polarimetric spectra. The calibrations are performed on two-dimensional images. Spectra are extracted using an optimal extraction algorithm. While primarily designed for CFHT ESPaDOnS data, the pipeline is being written to be extensible to other echelle spectrographs. A primary design goal is to make use of fast, modern object-oriented technologies. Processing is controlled by a harness, which manages a set of processing modules, that make use of a collection of native OPERA software libraries and standard external software libraries. The harness and modules are completely parametrized by site configuration and instrument parameters. The software is open- ended, permitting users of OPERA to extend the pipeline capabilities. All these features have been designed to provide a portable infrastructure that facilitates collaborative development, code re-usability and extensibility. OPERA is free software with support for both GNU/Linux and MacOSX platforms. The pipeline is hosted on SourceForge under the name "opera-pipeline".

Image analysis software versus direct anthropometry for breast measurements.

PubMed

Quieregatto, Paulo Rogério; Hochman, Bernardo; Furtado, Fabianne; Machado, Aline Fernanda Perez; Sabino Neto, Miguel; Ferreira, Lydia Masako

2014-10-01

To compare breast measurements performed using the software packages ImageTool(r), AutoCAD(r) and Adobe Photoshop(r) with direct anthropometric measurements. Points were marked on the breasts and arms of 40 volunteer women aged between 18 and 60 years. When connecting the points, seven linear segments and one angular measurement on each half of the body, and one medial segment common to both body halves were defined. The volunteers were photographed in a standardized manner. Photogrammetric measurements were performed by three independent observers using the three software packages and compared to direct anthropometric measurements made with calipers and a protractor. Measurements obtained with AutoCAD(r) were the most reproducible and those made with ImageTool(r) were the most similar to direct anthropometry, while measurements with Adobe Photoshop(r) showed the largest differences. Except for angular measurements, significant differences were found between measurements of line segments made using the three software packages and those obtained by direct anthropometry. AutoCAD(r) provided the highest precision and intermediate accuracy; ImageTool(r) had the highest accuracy and lowest precision; and Adobe Photoshop(r) showed intermediate precision and the worst accuracy among the three software packages.

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

PubMed

Bennett, Christopher L; McNeer, Richard R

2012-03-01

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

Java Web Start based software for automated quantitative nuclear analysis of prostate cancer and benign prostate hyperplasia.

PubMed

Singh, Swaroop S; Kim, Desok; Mohler, James L

2005-05-11

Androgen acts via androgen receptor (AR) and accurate measurement of the levels of AR protein expression is critical for prostate research. The expression of AR in paired specimens of benign prostate and prostate cancer from 20 African and 20 Caucasian Americans was compared to demonstrate an application of this system. A set of 200 immunopositive and 200 immunonegative nuclei were collected from the images using a macro developed in Image Pro Plus. Linear Discriminant and Logistic Regression analyses were performed on the data to generate classification coefficients. Classification coefficients render the automated image analysis software independent of the type of immunostaining or image acquisition system used. The image analysis software performs local segmentation and uses nuclear shape and size to detect prostatic epithelial nuclei. AR expression is described by (a) percentage of immunopositive nuclei; (b) percentage of immunopositive nuclear area; and (c) intensity of AR expression among immunopositive nuclei or areas. The percent positive nuclei and percent nuclear area were similar by race in both benign prostate hyperplasia and prostate cancer. In prostate cancer epithelial nuclei, African Americans exhibited 38% higher levels of AR immunostaining than Caucasian Americans (two sided Student's t-tests; P < 0.05). Intensity of AR immunostaining was similar between races in benign prostate. The differences measured in the intensity of AR expression in prostate cancer were consistent with previous studies. Classification coefficients are required due to non-standardized immunostaining and image collection methods across medical institutions and research laboratories and helps customize the software for the specimen under study. The availability of a free, automated system creates new opportunities for testing, evaluation and use of this image analysis system by many research groups who study nuclear protein expression.

Analysis of Head Response to Torso Acceleration. Vol. II - Description of Data Retrieval, Analysis and Display Software.

DOT National Transportation Integrated Search

1987-11-01

Performance requirements are developed which define the kinematic and kinetic response of the head for a seated subject exposed to frontal, lateral or oblique impact. Response is expressed in terms of variables which are readily measured in an anthro...

The Equivalence of Three Statistical Packages for Performing Hierarchical Cluster Analysis

ERIC Educational Resources Information Center

Blashfield, Roger

1977-01-01

Three different software programs which contain hierarchical agglomerative cluster analysis procedures were shown to generate different solutions on the same data set using apparently the same options. The basis for the differences in the solutions was the formulae used to calculate Euclidean distance. (Author/JKS)

RootScan: Software for high-throughput analysis of root anatomical traits

USDA-ARS?s Scientific Manuscript database

RootScan is a program for semi-automated image analysis of anatomical phenes in root cross-sections. RootScan uses pixel value thresholds to separate the cross-section from its background and to visually dissect it into tissue regions. Area measurements and object counts are performed within various...

PIRATE: pediatric imaging response assessment and targeting environment

NASA Astrophysics Data System (ADS)

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

2010-02-01

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

Quantitative contrast-enhanced ultrasound for monitoring vedolizumab therapy in inflammatory bowel disease patients: a pilot study.

PubMed

Goertz, Ruediger S; Klett, Daniel; Wildner, Dane; Atreya, Raja; Neurath, Markus F; Strobel, Deike

2018-01-01

Background Microvascularization of the bowel wall can be visualized and quantified non-invasively by software-assisted analysis of derived time-intensity curves. Purpose To perform software-based quantification of bowel wall perfusion using quantitative contrast-enhanced ultrasound (CEUS) according to clinical response in patients with inflammatory bowel disease treated with vedolizumab. Material and Methods In a prospective study, in 18 out of 34 patients, high-frequency ultrasound of bowel wall thickness using color Doppler flow combined with CEUS was performed at baseline and after 14 weeks of treatment with vedolizumab. Clinical activity scores at week 14 were used to differentiate between responders and non-responders. CEUS parameters were calculated by software analysis of the video loops. Results Nine of 18 patients (11 with Crohn's disease and seven with ulcerative colitis) showed response to treatment with vedolizumab. Overall, the responder group showed a significant decrease in the semi-quantitative color Doppler vascularization score. Amplitude-derived CEUS parameters of mural microvascularization such as peak enhancement or wash-in rate decreased in responders, in contrast with non-responders. Time-derived parameters remained stable or increased during treatment in all patients. Conclusion Analysis of bowel microvascularization by CEUS shows statistically significant changes in the wash-in-rate related to response of vedolizumab therapy.

Comparison of performance of object-based image analysis techniques available in open source software (Spring and Orfeo Toolbox/Monteverdi) considering very high spatial resolution data

NASA Astrophysics Data System (ADS)

Teodoro, Ana C.; Araujo, Ricardo

2016-01-01

The use of unmanned aerial vehicles (UAVs) for remote sensing applications is becoming more frequent. However, this type of information can result in several software problems related to the huge amount of data available. Object-based image analysis (OBIA) has proven to be superior to pixel-based analysis for very high-resolution images. The main objective of this work was to explore the potentialities of the OBIA methods available in two different open source software applications, Spring and OTB/Monteverdi, in order to generate an urban land cover map. An orthomosaic derived from UAVs was considered, 10 different regions of interest were selected, and two different approaches were followed. The first one (Spring) uses the region growing segmentation algorithm followed by the Bhattacharya classifier. The second approach (OTB/Monteverdi) uses the mean shift segmentation algorithm followed by the support vector machine (SVM) classifier. Two strategies were followed: four classes were considered using Spring and thereafter seven classes were considered for OTB/Monteverdi. The SVM classifier produces slightly better results and presents a shorter processing time. However, the poor spectral resolution of the data (only RGB bands) is an important factor that limits the performance of the classifiers applied.

SACA: Software Assisted Call Analysis--an interactive tool supporting content exploration, online guidance and quality improvement of counseling dialogues.

PubMed

Trinkaus, Hans L; Gaisser, Andrea E

2010-09-01

Nearly 30,000 individual inquiries are answered annually by the telephone cancer information service (CIS, KID) of the German Cancer Research Center (DKFZ). The aim was to develop a tool for evaluating these calls, and to support the complete counseling process interactively. A novel software tool is introduced, based on a structure similar to a music score. Treating the interaction as a "duet", guided by the CIS counselor, the essential contents of the dialogue are extracted automatically. For this, "trained speech recognition" is applied to the (known) counselor's part, and "keyword spotting" is used on the (unknown) client's part to pick out specific items from the "word streams". The outcomes fill an abstract score representing the dialogue. Pilot tests performed on a prototype of SACA (Software Assisted Call Analysis) resulted in a basic proof of concept: Demographic data as well as information regarding the situation of the caller could be identified. The study encourages following up on the vision of an integrated SACA tool for supporting calls online and performing statistics on its knowledge database offline. Further research perspectives are to check SACA's potential in comparison with established interaction analysis systems like RIAS. Copyright (c) 2010 Elsevier Ireland Ltd. All rights reserved.

Simple Sensitivity Analysis for Orion GNC

NASA Technical Reports Server (NTRS)

Pressburger, Tom; Hoelscher, Brian; Martin, Rodney; Sricharan, Kumar

2013-01-01

The performance of Orion flight software, especially its GNC software, is being analyzed by running Monte Carlo simulations of Orion spacecraft flights. The simulated performance is analyzed for conformance with flight requirements, expressed as performance constraints. Flight requirements include guidance (e.g. touchdown distance from target) and control (e.g., control saturation) as well as performance (e.g., heat load constraints). The Monte Carlo simulations disperse hundreds of simulation input variables, for everything from mass properties to date of launch.We describe in this paper a sensitivity analysis tool (Critical Factors Tool or CFT) developed to find the input variables or pairs of variables which by themselves significantly influence satisfaction of requirements or significantly affect key performance metrics (e.g., touchdown distance from target). Knowing these factors can inform robustness analysis, can inform where engineering resources are most needed, and could even affect operations. The contributions of this paper include the introduction of novel sensitivity measures, such as estimating success probability, and a technique for determining whether pairs of factors are interacting dependently or independently. The tool found that input variables such as moments, mass, thrust dispersions, and date of launch were found to be significant factors for success of various requirements. Examples are shown in this paper as well as a summary and physics discussion of EFT-1 driving factors that the tool found.

Scalable and Power Efficient Data Analytics for Hybrid Exascale Systems

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

Choudhary, Alok; Samatova, Nagiza; Wu, Kesheng

This project developed a generic and optimized set of core data analytics functions. These functions organically consolidate a broad constellation of high performance analytical pipelines. As the architectures of emerging HPC systems become inherently heterogeneous, there is a need to design algorithms for data analysis kernels accelerated on hybrid multi-node, multi-core HPC architectures comprised of a mix of CPUs, GPUs, and SSDs. Furthermore, the power-aware trend drives the advances in our performance-energy tradeoff analysis framework which enables our data analysis kernels algorithms and software to be parameterized so that users can choose the right power-performance optimizations.

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

NASA Technical Reports Server (NTRS)

Gupta, Pramod; Schumann, Johann

2004-01-01

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

SU-C-201-04: Quantification of Perfusion Heterogeneity Based On Texture Analysis for Fully Automatic Detection of Ischemic Deficits From Myocardial Perfusion Imaging

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

Fang, Y; Huang, H; Su, T

Purpose: Texture-based quantification of image heterogeneity has been a popular topic for imaging studies in recent years. As previous studies mainly focus on oncological applications, we report our recent efforts of applying such techniques on cardiac perfusion imaging. A fully automated procedure has been developed to perform texture analysis for measuring the image heterogeneity. Clinical data were used to evaluate the preliminary performance of such methods. Methods: Myocardial perfusion images of Thallium-201 scans were collected from 293 patients with suspected coronary artery disease. Each subject underwent a Tl-201 scan and a percutaneous coronary intervention (PCI) within three months. The PCImore » Result was used as the gold standard of coronary ischemia of more than 70% stenosis. Each Tl-201 scan was spatially normalized to an image template for fully automatic segmentation of the LV. The segmented voxel intensities were then carried into the texture analysis with our open-source software Chang Gung Image Texture Analysis toolbox (CGITA). To evaluate the clinical performance of the image heterogeneity for detecting the coronary stenosis, receiver operating characteristic (ROC) analysis was used to compute the overall accuracy, sensitivity and specificity as well as the area under curve (AUC). Those indices were compared to those obtained from the commercially available semi-automatic software QPS. Results: With the fully automatic procedure to quantify heterogeneity from Tl-201 scans, we were able to achieve a good discrimination with good accuracy (74%), sensitivity (73%), specificity (77%) and AUC of 0.82. Such performance is similar to those obtained from the semi-automatic QPS software that gives a sensitivity of 71% and specificity of 77%. Conclusion: Based on fully automatic procedures of data processing, our preliminary data indicate that the image heterogeneity of myocardial perfusion imaging can provide useful information for automatic determination of the myocardial ischemia.« less

A Simplified Mesh Deformation Method Using Commercial Structural Analysis Software

NASA Technical Reports Server (NTRS)

Hsu, Su-Yuen; Chang, Chau-Lyan; Samareh, Jamshid

2004-01-01

Mesh deformation in response to redefined or moving aerodynamic surface geometries is a frequently encountered task in many applications. Most existing methods are either mathematically too complex or computationally too expensive for usage in practical design and optimization. We propose a simplified mesh deformation method based on linear elastic finite element analyses that can be easily implemented by using commercially available structural analysis software. Using a prescribed displacement at the mesh boundaries, a simple structural analysis is constructed based on a spatially varying Young s modulus to move the entire mesh in accordance with the surface geometry redefinitions. A variety of surface movements, such as translation, rotation, or incremental surface reshaping that often takes place in an optimization procedure, may be handled by the present method. We describe the numerical formulation and implementation using the NASTRAN software in this paper. The use of commercial software bypasses tedious reimplementation and takes advantage of the computational efficiency offered by the vendor. A two-dimensional airfoil mesh and a three-dimensional aircraft mesh were used as test cases to demonstrate the effectiveness of the proposed method. Euler and Navier-Stokes calculations were performed for the deformed two-dimensional meshes.

Identification of genes in anonymous DNA sequences. Annual performance report, February 1, 1991--January 31, 1992

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

Fields, C.A.

1996-06-01

The objective of this project is the development of practical software to automate the identification of genes in anonymous DNA sequences from the human, and other higher eukaryotic genomes. A software system for automated sequence analysis, gm (gene modeler) has been designed, implemented, tested, and distributed to several dozen laboratories worldwide. A significantly faster, more robust, and more flexible version of this software, gm 2.0 has now been completed, and is being tested by operational use to analyze human cosmid sequence data. A range of efforts to further understand the features of eukaryoyic gene sequences are also underway. This progressmore » report also contains papers coming out of the project including the following: gm: a Tool for Exploratory Analysis of DNA Sequence Data; The Human THE-LTR(O) and MstII Interspersed Repeats are subfamilies of a single widely distruted highly variable repeat family; Information contents and dinucleotide compostions of plant intron sequences vary with evolutionary origin; Splicing signals in Drosophila: intron size, information content, and consensus sequences; Integration of automated sequence analysis into mapping and sequencing projects; Software for the C. elegans genome project.« less

ACQ4: an open-source software platform for data acquisition and analysis in neurophysiology research

PubMed Central

Campagnola, Luke; Kratz, Megan B.; Manis, Paul B.

2014-01-01

The complexity of modern neurophysiology experiments requires specialized software to coordinate multiple acquisition devices and analyze the collected data. We have developed ACQ4, an open-source software platform for performing data acquisition and analysis in experimental neurophysiology. This software integrates the tasks of acquiring, managing, and analyzing experimental data. ACQ4 has been used primarily for standard patch-clamp electrophysiology, laser scanning photostimulation, multiphoton microscopy, intrinsic imaging, and calcium imaging. The system is highly modular, which facilitates the addition of new devices and functionality. The modules included with ACQ4 provide for rapid construction of acquisition protocols, live video display, and customizable analysis tools. Position-aware data collection allows automated construction of image mosaics and registration of images with 3-dimensional anatomical atlases. ACQ4 uses free and open-source tools including Python, NumPy/SciPy for numerical computation, PyQt for the user interface, and PyQtGraph for scientific graphics. Supported hardware includes cameras, patch clamp amplifiers, scanning mirrors, lasers, shutters, Pockels cells, motorized stages, and more. ACQ4 is available for download at http://www.acq4.org. PMID:24523692

The EOSDIS software challenge

NASA Astrophysics Data System (ADS)

Jaworski, Allan

1993-08-01

The Earth Observing System (EOS) Data and Information System (EOSDIS) will serve as a major resource for the earth science community, supporting both command and control of complex instruments onboard the EOS spacecraft and the archiving, distribution, and analysis of data. The scale of EOSDIS and the volume of multidisciplinary research to be conducted using EOSDIS resources will produce unparalleled needs for technology transparency, data integration, and system interoperability. The scale of this effort far outscopes any previous scientific data system in its breadth or operational and performance needs. Modern hardware technology can meet the EOSDIS technical challenge. Multiprocessing speeds of many giga-flops are being realized by modern computers. Online storage disk, optical disk, and videocassette libraries with storage capacities of many terabytes are now commercially available. Radio frequency and fiber optics communications networks with gigabit rates are demonstrable today. It remains, of course, to perform the system engineering to establish the requirements, architectures, and designs that will implement the EOSDIS systems. Software technology, however, has not enjoyed the price/performance advances of hardware. Although we have learned to engineer hardware systems which have several orders of magnitude greater complexity and performance than those built in the 1960's, we have not made comparable progress in dramatically reducing the cost of software development. This lack of progress may significantly reduce our capabilities to achieve economically the types of highly interoperable, responsive, integraded, and productive environments which are needed by the earth science community. This paper describes some of the EOSDIS software requirements and current activities in the software community which are applicable to meeting the EOSDIS challenge. Some of these areas include intelligent user interfaces, software reuse libraries, and domain engineering. Also included are discussions of applicable standards in the areas of operating systems interfaces, user interfaces, communications interfaces, data transport, and science algorithm support, and their role in supporting the software development process.

NCI's High Performance Computing (HPC) and High Performance Data (HPD) Computing Platform for Environmental and Earth System Data Science

NASA Astrophysics Data System (ADS)

Evans, Ben; Allen, Chris; Antony, Joseph; Bastrakova, Irina; Gohar, Kashif; Porter, David; Pugh, Tim; Santana, Fabiana; Smillie, Jon; Trenham, Claire; Wang, Jingbo; Wyborn, Lesley

2015-04-01

The National Computational Infrastructure (NCI) has established a powerful and flexible in-situ petascale computational environment to enable both high performance computing and Data-intensive Science across a wide spectrum of national environmental and earth science data collections - in particular climate, observational data and geoscientific assets. This paper examines 1) the computational environments that supports the modelling and data processing pipelines, 2) the analysis environments and methods to support data analysis, and 3) the progress so far to harmonise the underlying data collections for future interdisciplinary research across these large volume data collections. NCI has established 10+ PBytes of major national and international data collections from both the government and research sectors based on six themes: 1) weather, climate, and earth system science model simulations, 2) marine and earth observations, 3) geosciences, 4) terrestrial ecosystems, 5) water and hydrology, and 6) astronomy, social and biosciences. Collectively they span the lithosphere, crust, biosphere, hydrosphere, troposphere, and stratosphere. The data is largely sourced from NCI's partners (which include the custodians of many of the major Australian national-scale scientific collections), leading research communities, and collaborating overseas organisations. New infrastructures created at NCI mean the data collections are now accessible within an integrated High Performance Computing and Data (HPC-HPD) environment - a 1.2 PFlop supercomputer (Raijin), a HPC class 3000 core OpenStack cloud system and several highly connected large-scale high-bandwidth Lustre filesystems. The hardware was designed at inception to ensure that it would allow the layered software environment to flexibly accommodate the advancement of future data science. New approaches to software technology and data models have also had to be developed to enable access to these large and exponentially increasing data volumes at NCI. Traditional HPC and data environments are still made available in a way that flexibly provides the tools, services and supporting software systems on these new petascale infrastructures. But to enable the research to take place at this scale, the data, metadata and software now need to evolve together - creating a new integrated high performance infrastructure. The new infrastructure at NCI currently supports a catalogue of integrated, reusable software and workflows from earth system and ecosystem modelling, weather research, satellite and other observed data processing and analysis. One of the challenges for NCI has been to support existing techniques and methods, while carefully preparing the underlying infrastructure for the transition needed for the next class of Data-intensive Science. In doing so, a flexible range of techniques and software can be made available for application across the corpus of data collections available, and to provide a new infrastructure for future interdisciplinary research.

Design tool for multiprocessor scheduling and evaluation of iterative dataflow algorithms

NASA Technical Reports Server (NTRS)

Jones, Robert L., III

1995-01-01

A graph-theoretic design process and software tool is defined for selecting a multiprocessing scheduling solution for a class of computational problems. The problems of interest are those that can be described with a dataflow graph and are intended to be executed repetitively on a set of identical processors. Typical applications include signal processing and control law problems. Graph-search algorithms and analysis techniques are introduced and shown to effectively determine performance bounds, scheduling constraints, and resource requirements. The software tool applies the design process to a given problem and includes performance optimization through the inclusion of additional precedence constraints among the schedulable tasks.

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.

Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis

PubMed Central

2011-01-01

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

Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis.

PubMed

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

2011-01-25

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

Software Performs Complex Design Analysis

NASA Technical Reports Server (NTRS)

2008-01-01

Designers use computational fluid dynamics (CFD) to gain greater understanding of the fluid flow phenomena involved in components being designed. They also use finite element analysis (FEA) as a tool to help gain greater understanding of the structural response of components to loads, stresses and strains, and the prediction of failure modes. Automated CFD and FEA engineering design has centered on shape optimization, which has been hindered by two major problems: 1) inadequate shape parameterization algorithms, and 2) inadequate algorithms for CFD and FEA grid modification. Working with software engineers at Stennis Space Center, a NASA commercial partner, Optimal Solutions Software LLC, was able to utilize its revolutionary, one-of-a-kind arbitrary shape deformation (ASD) capability-a major advancement in solving these two aforementioned problems-to optimize the shapes of complex pipe components that transport highly sensitive fluids. The ASD technology solves the problem of inadequate shape parameterization algorithms by allowing the CFD designers to freely create their own shape parameters, therefore eliminating the restriction of only being able to use the computer-aided design (CAD) parameters. The problem of inadequate algorithms for CFD grid modification is solved by the fact that the new software performs a smooth volumetric deformation. This eliminates the extremely costly process of having to remesh the grid for every shape change desired. The program can perform a design change in a markedly reduced amount of time, a process that would traditionally involve the designer returning to the CAD model to reshape and then remesh the shapes, something that has been known to take hours, days-even weeks or months-depending upon the size of the model.

A UML Profile for State Analysis

NASA Technical Reports Server (NTRS)

Murray, Alex; Rasmussen, Robert

2010-01-01

State Analysis is a systems engineering methodology for the specification and design of control systems, developed at the Jet Propulsion Laboratory. The methodology emphasizes an analysis of the system under control in terms of States and their properties and behaviors and their effects on each other, a clear separation of the control system from the controlled system, cognizance in the control system of the controlled system's State, goal-based control built on constraining the controlled system's States, and disciplined techniques for State discovery and characterization. State Analysis (SA) introduces two key diagram types: State Effects and Goal Network diagrams. The team at JPL developed a tool for performing State Analysis. The tool includes a drawing capability, backed by a database that supports the diagram types and the organization of the elements of the SA models. But the tool does not support the usual activities of software engineering and design - a disadvantage, since systems to which State Analysis can be applied tend to be very software-intensive. This motivated the work described in this paper: the development of a preliminary Unified Modeling Language (UML) profile for State Analysis. Having this profile would enable systems engineers to specify a system using the methods and graphical language of State Analysis, which is easily linked with a larger system model in SysML (Systems Modeling Language), while also giving software engineers engaged in implementing the specified control system immediate access to and use of the SA model, in the same language, UML, used for other software design. That is, a State Analysis profile would serve as a shared modeling bridge between system and software models for the behavior aspects of the system. This paper begins with an overview of State Analysis and its underpinnings, followed by an overview of the mapping of SA constructs to the UML metamodel. It then delves into the details of these mappings and the constraints associated with them. Finally, we give an example of the use of the profile for expressing an example SA model.

NASA Technical Management Report (533Q)

NASA Technical Reports Server (NTRS)

Klosko, S. M.; Sanchez, B. (Technical Monitor)

2001-01-01

The objective of this task is analytical support of the NASA Satellite Laser Ranging (SLR) program in the areas of SLR data analysis, software development, assessment of SLR station performance, development of improved models for atmospheric propagation and interpretation of station calibration techniques, and science coordination and analysis functions for the NASA led Central Bureau of the International Laser Ranging Service (ILRS). The contractor shall in each year of the five year contract: (1) Provide software development and analysis support to the NASA SLR program and the ILRS. Attend and make analysis reports at the monthly meetings of the Central Bureau of the ILRS covering data received during the previous period. Provide support to the Analysis Working Group of the ILRS including special tiger teams that are established to handle unique analysis problems. Support the updating of the SLR Bibliography contained on the ILRS web site; (2) Perform special assessments of SLR station performance from available data to determine unique biases and technical problems at the station; (3) Develop improvements to models of atmospheric propagation and for handling pre- and post-pass calibration data provided by global network stations; (4) Provide review presentation of overall ILRS network data results at one major scientific meeting per year; (5) Contribute to and support the publication of NASA SLR and ILRS reports highlighting the results of SLR analysis activity.

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.

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 .

Evaluation of interaction dynamics of concurrent processes

NASA Astrophysics Data System (ADS)

Sobecki, Piotr; Białasiewicz, Jan T.; Gross, Nicholas

2017-03-01

The purpose of this paper is to present the wavelet tools that enable the detection of temporal interactions of concurrent processes. In particular, the determination of interaction coherence of time-varying signals is achieved using a complex continuous wavelet transform. This paper has used electrocardiogram (ECG) and seismocardiogram (SCG) data set to show multiple continuous wavelet analysis techniques based on Morlet wavelet transform. MATLAB Graphical User Interface (GUI), developed in the reported research to assist in quick and simple data analysis, is presented. These software tools can discover the interaction dynamics of time-varying signals, hence they can reveal their correlation in phase and amplitude, as well as their non-linear interconnections. The user-friendly MATLAB GUI enables effective use of the developed software what enables to load two processes under investigation, make choice of the required processing parameters, and then perform the analysis. The software developed is a useful tool for researchers who have a need for investigation of interaction dynamics of concurrent processes.

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.

Gaia DR1 documentation Chapter 6: Variability

NASA Astrophysics Data System (ADS)

Eyer, L.; Rimoldini, L.; Guy, L.; Holl, B.; Clementini, G.; Cuypers, J.; Mowlavi, N.; Lecoeur-Taïbi, I.; De Ridder, J.; Charnas, J.; Nienartowicz, K.

2017-12-01

This chapter describes the photometric variability processing of the Gaia DR1 data. Coordination Unit 7 is responsible for the variability analysis of over a billion celestial sources. In particular the definition, design, development, validation and provision of a software package for the data processing of photometrically variable objects. Data Processing Centre Geneva (DPCG) responsibilities cover all issues related to the computational part of the CU7 analysis. These span: hardware provisioning, including selection, deployment and optimisation of suitable hardware, choosing and developing software architecture, defining data and scientific workflows as well as operational activities such as configuration management, data import, time series reconstruction, storage and processing handling, visualisation and data export. CU7/DPCG is also responsible for interaction with other DPCs and CUs, software and programming training for the CU7 members, scientific software quality control and management of software and data lifecycle. Details about the specific data treatment steps of the Gaia DR1 data products are found in Eyer et al. (2017) and are not repeated here. The variability content of the Gaia DR1 focusses on a subsample of Cepheids and RR Lyrae stars around the South ecliptic pole, showcasing the performance of the Gaia photometry with respect to variable objects.

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.

Development and prospective evaluation of an automated software system for quality control of quantitative 99mTc-MAG3 renal studies.

PubMed

Folks, Russell D; Garcia, Ernest V; Taylor, Andrew T

2007-03-01

Quantitative nuclear renography has numerous potential sources of error. We previously reported the initial development of a computer software module for comprehensively addressing the issue of quality control (QC) in the analysis of radionuclide renal images. The objective of this study was to prospectively test the QC software. The QC software works in conjunction with standard quantitative renal image analysis using a renal quantification program. The software saves a text file that summarizes QC findings as possible errors in user-entered values, calculated values that may be unreliable because of the patient's clinical condition, and problems relating to acquisition or processing. To test the QC software, a technologist not involved in software development processed 83 consecutive nontransplant clinical studies. The QC findings of the software were then tabulated. QC events were defined as technical (study descriptors that were out of range or were entered and then changed, unusually sized or positioned regions of interest, or missing frames in the dynamic image set) or clinical (calculated functional values judged to be erroneous or unreliable). Technical QC events were identified in 36 (43%) of 83 studies. Clinical QC events were identified in 37 (45%) of 83 studies. Specific QC events included starting the camera after the bolus had reached the kidney, dose infiltration, oversubtraction of background activity, and missing frames in the dynamic image set. QC software has been developed to automatically verify user input, monitor calculation of renal functional parameters, summarize QC findings, and flag potentially unreliable values for the nuclear medicine physician. Incorporation of automated QC features into commercial or local renal software can reduce errors and improve technologist performance and should improve the efficiency and accuracy of image interpretation.

Automated Hazard Analysis

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

Riddle, F. J.

2003-06-26

The Automated Hazard Analysis (AHA) application is a software tool used to conduct job hazard screening and analysis of tasks to be performed in Savannah River Site facilities. The AHA application provides a systematic approach to the assessment of safety and environmental hazards associated with specific tasks, and the identification of controls regulations, and other requirements needed to perform those tasks safely. AHA is to be integrated into existing Savannah River site work control and job hazard analysis processes. Utilization of AHA will improve the consistency and completeness of hazard screening and analysis, and increase the effectiveness of the workmore » planning process.« less

Structural reliability methods: Code development status

NASA Astrophysics Data System (ADS)

Millwater, Harry R.; Thacker, Ben H.; Wu, Y.-T.; Cruse, T. A.

1991-05-01

The Probabilistic Structures Analysis Method (PSAM) program integrates state of the art probabilistic algorithms with structural analysis methods in order to quantify the behavior of Space Shuttle Main Engine structures subject to uncertain loadings, boundary conditions, material parameters, and geometric conditions. An advanced, efficient probabilistic structural analysis software program, NESSUS (Numerical Evaluation of Stochastic Structures Under Stress) was developed as a deliverable. NESSUS contains a number of integrated software components to perform probabilistic analysis of complex structures. A nonlinear finite element module NESSUS/FEM is used to model the structure and obtain structural sensitivities. Some of the capabilities of NESSUS/FEM are shown. A Fast Probability Integration module NESSUS/FPI estimates the probability given the structural sensitivities. A driver module, PFEM, couples the FEM and FPI. NESSUS, version 5.0, addresses component reliability, resistance, and risk.

Structural reliability methods: Code development status

NASA Technical Reports Server (NTRS)

Millwater, Harry R.; Thacker, Ben H.; Wu, Y.-T.; Cruse, T. A.

1991-01-01

The Probabilistic Structures Analysis Method (PSAM) program integrates state of the art probabilistic algorithms with structural analysis methods in order to quantify the behavior of Space Shuttle Main Engine structures subject to uncertain loadings, boundary conditions, material parameters, and geometric conditions. An advanced, efficient probabilistic structural analysis software program, NESSUS (Numerical Evaluation of Stochastic Structures Under Stress) was developed as a deliverable. NESSUS contains a number of integrated software components to perform probabilistic analysis of complex structures. A nonlinear finite element module NESSUS/FEM is used to model the structure and obtain structural sensitivities. Some of the capabilities of NESSUS/FEM are shown. A Fast Probability Integration module NESSUS/FPI estimates the probability given the structural sensitivities. A driver module, PFEM, couples the FEM and FPI. NESSUS, version 5.0, addresses component reliability, resistance, and risk.

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.

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

Arbitrary Shape Deformation in CFD Design

NASA Technical Reports Server (NTRS)

Landon, Mark; Perry, Ernest

2014-01-01

Sculptor(R) is a commercially available software tool, based on an Arbitrary Shape Design (ASD), which allows the user to perform shape optimization for computational fluid dynamics (CFD) design. The developed software tool provides important advances in the state-of-the-art of automatic CFD shape deformations and optimization software. CFD is an analysis tool that is used by engineering designers to help gain a greater understanding of the fluid flow phenomena involved in the components being designed. The next step in the engineering design process is to then modify, the design to improve the components' performance. This step has traditionally been performed manually via trial and error. Two major problems that have, in the past, hindered the development of an automated CFD shape optimization are (1) inadequate shape parameterization algorithms, and (2) inadequate algorithms for CFD grid modification. The ASD that has been developed as part of the Sculptor(R) software tool is a major advancement in solving these two issues. First, the ASD allows the CFD designer to freely create his own shape parameters, thereby eliminating the restriction of only being able to use the CAD model parameters. Then, the software performs a smooth volumetric deformation, which eliminates the extremely costly process of having to remesh the grid for every shape change (which is how this process had previously been achieved). Sculptor(R) can be used to optimize shapes for aerodynamic and structural design of spacecraft, aircraft, watercraft, ducts, and other objects that affect and are affected by flows of fluids and heat. Sculptor(R) makes it possible to perform, in real time, a design change that would manually take hours or days if remeshing were needed.

Summary of Technical Operations, 1991

DTIC Science & Technology

1992-01-01

exploit commonality. The project is using the Feature-Oriented Domain Analysis ( FODA ) method, developed by the project in 1990, to perform this...the development of new movement control software. The analysis will also serve as a means of improving the FODA method. The results of this analysis ...STARS environment. The NASA Program Office has officially decided to expand the use of Rate Monotonic Analysis (RMA), which was originally isolated to

Constructing a working taxonomy of functional Ada software components for real-time embedded system applications

NASA Technical Reports Server (NTRS)

Wallace, Robert

1986-01-01

A major impediment to a systematic attack on Ada software reusability is the lack of an effective taxonomy for software component functions. The scope of all possible applications of Ada software is considered too great to allow the practical development of a working taxonomy. Instead, for the purposes herein, the scope of Ada software application is limited to device and subsystem control in real-time embedded systems. A functional approach is taken in constructing the taxonomy tree for identified Ada domain. The use of modular software functions as a starting point fits well with the object oriented programming philosophy of Ada. Examples of the types of functions represented within the working taxonomy are real time kernels, interrupt service routines, synchronization and message passing, data conversion, digital filtering and signal conditioning, and device control. The constructed taxonomy is proposed as a framework from which a need analysis can be performed to reveal voids in current Ada real-time embedded programming efforts for Space Station.

Hypersonic Navier Stokes Comparisons to Orbiter Flight Data

NASA Technical Reports Server (NTRS)

Campbell, Charles H.; Nompelis, Ioannis; Candler, Graham; Barnhart, Michael; Yoon, Seokkwan

2009-01-01

Hypersonic chemical nonequilibrium simulations of low earth orbit entry flow fields are becoming increasingly commonplace as software and computational capabilities become more capable. However, development of robust and accurate software to model these environments will always encounter a significant barrier in developing a suite of high quality calibration cases. The US3D hypersonic nonequilibrium Navier Stokes analysis capability has been favorably compared to a number of wind tunnel test cases. Extension of the calibration basis for this software to Orbiter flight conditions will provide an incremental increase in confidence. As part of the Orbiter Boundary Layer Transition Flight Experiment and the Hypersonic Thermodynamic Infrared Measurements project, NASA is performing entry flight testing on the Orbiter to provide valuable aerothermodynamic heating data. An increase in interest related to orbiter entry environments is resulting from this activity. With the advent of this new data, comparisons of the US3D software to the new flight testing data is warranted. This paper will provide information regarding the framework of analyses that will be applied with the US3D analysis tool. In addition, comparisons will be made to entry flight testing data provided by the Orbiter BLT Flight Experiment and HYTHIRM projects. If data from digital scans of the Orbiter windward surface become available, simulations will also be performed to characterize the difference in surface heating between the CAD reference OML and the digitized surface provided by the surface scans.

Analysing the Zenith Tropospheric Delay Estimates in On-line Precise Point Positioning (PPP) Services and PPP Software Packages.

PubMed

Mendez Astudillo, Jorge; Lau, Lawrence; Tang, Yu-Ting; Moore, Terry

2018-02-14

As Global Navigation Satellite System (GNSS) signals travel through the troposphere, a tropospheric delay occurs due to a change in the refractive index of the medium. The Precise Point Positioning (PPP) technique can achieve centimeter/millimeter positioning accuracy with only one GNSS receiver. The Zenith Tropospheric Delay (ZTD) is estimated alongside with the position unknowns in PPP. Estimated ZTD can be very useful for meteorological applications, an example is the estimation of water vapor content in the atmosphere from the estimated ZTD. PPP is implemented with different algorithms and models in online services and software packages. In this study, a performance assessment with analysis of ZTD estimates from three PPP online services and three software packages is presented. The main contribution of this paper is to show the accuracy of ZTD estimation achievable in PPP. The analysis also provides the GNSS users and researchers the insight of the processing algorithm dependence and impact on PPP ZTD estimation. Observation data of eight whole days from a total of nine International GNSS Service (IGS) tracking stations spread in the northern hemisphere, the equatorial region and the southern hemisphere is used in this analysis. The PPP ZTD estimates are compared with the ZTD obtained from the IGS tropospheric product of the same days. The estimates of two of the three online PPP services show good agreement (<1 cm) with the IGS ZTD values at the northern and southern hemisphere stations. The results also show that the online PPP services perform better than the selected PPP software packages at all stations.

Electrophoresis gel image processing and analysis using the KODAK 1D software.

PubMed

Pizzonia, J

2001-06-01

The present article reports on the performance of the KODAK 1D Image Analysis Software for the acquisition of information from electrophoresis experiments and highlights the utility of several mathematical functions for subsequent image processing, analysis, and presentation. Digital images of Coomassie-stained polyacrylamide protein gels containing molecular weight standards and ethidium bromide stained agarose gels containing DNA mass standards are acquired using the KODAK Electrophoresis Documentation and Analysis System 290 (EDAS 290). The KODAK 1D software is used to optimize lane and band identification using features such as isomolecular weight lines. Mathematical functions for mass standard representation are presented, and two methods for estimation of unknown band mass are compared. Given the progressive transition of electrophoresis data acquisition and daily reporting in peer-reviewed journals to digital formats ranging from 8-bit systems such as EDAS 290 to more expensive 16-bit systems, the utility of algorithms such as Gaussian modeling, which can correct geometric aberrations such as clipping due to signal saturation common at lower bit depth levels, is discussed. Finally, image-processing tools that can facilitate image preparation for presentation are demonstrated.

Earthscape, a Multi-Purpose Interactive 3d Globe Viewer for Hybrid Data Visualization and Analysis

NASA Astrophysics Data System (ADS)

Sarthou, A.; Mas, S.; Jacquin, M.; Moreno, N.; Salamon, A.

2015-08-01

The hybrid visualization and interaction tool EarthScape is presented here. The software is able to display simultaneously LiDAR point clouds, draped videos with moving footprint, volume scientific data (using volume rendering, isosurface and slice plane), raster data such as still satellite images, vector data and 3D models such as buildings or vehicles. The application runs on touch screen devices such as tablets. The software is based on open source libraries, such as OpenSceneGraph, osgEarth and OpenCV, and shader programming is used to implement volume rendering of scientific data. The next goal of EarthScape is to perform data analysis using ENVI Services Engine, a cloud data analysis solution. EarthScape is also designed to be a client of Jagwire which provides multisource geo-referenced video fluxes. When all these components will be included, EarthScape will be a multi-purpose platform that will provide at the same time data analysis, hybrid visualization and complex interactions. The software is available on demand for free at france@exelisvis.com.

Advances in the production of freeform optical surfaces

NASA Astrophysics Data System (ADS)

Tohme, Yazid E.; Luniya, Suneet S.

2007-05-01

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

Intelligent software for laboratory automation.

PubMed

Whelan, Ken E; King, Ross D

2004-09-01

The automation of laboratory techniques has greatly increased the number of experiments that can be carried out in the chemical and biological sciences. Until recently, this automation has focused primarily on improving hardware. Here we argue that future advances will concentrate on intelligent software to integrate physical experimentation and results analysis with hypothesis formulation and experiment planning. To illustrate our thesis, we describe the 'Robot Scientist' - the first physically implemented example of such a closed loop system. In the Robot Scientist, experimentation is performed by a laboratory robot, hypotheses concerning the results are generated by machine learning and experiments are allocated and selected by a combination of techniques derived from artificial intelligence research. The performance of the Robot Scientist has been evaluated by a rediscovery task based on yeast functional genomics. The Robot Scientist is proof that the integration of programmable laboratory hardware and intelligent software can be used to develop increasingly automated laboratories.

A Business Analytics Software Tool for Monitoring and Predicting Radiology Throughput Performance.

PubMed

Jones, Stephen; Cournane, Seán; Sheehy, Niall; Hederman, Lucy

2016-12-01

Business analytics (BA) is increasingly being utilised by radiology departments to analyse and present data. It encompasses statistical analysis, forecasting and predictive modelling and is used as an umbrella term for decision support and business intelligence systems. The primary aim of this study was to determine whether utilising BA technologies could contribute towards improved decision support and resource management within radiology departments. A set of information technology requirements were identified with key stakeholders, and a prototype BA software tool was designed, developed and implemented. A qualitative evaluation of the tool was carried out through a series of semi-structured interviews with key stakeholders. Feedback was collated, and emergent themes were identified. The results indicated that BA software applications can provide visibility of radiology performance data across all time horizons. The study demonstrated that the tool could potentially assist with improving operational efficiencies and management of radiology resources.

Generic trending and analysis system

NASA Technical Reports Server (NTRS)

Keehan, Lori; Reese, Jay

1994-01-01

The Generic Trending and Analysis System (GTAS) is a generic spacecraft performance monitoring tool developed by NASA Code 511 and Loral Aerosys. It is designed to facilitate quick anomaly resolution and trend analysis. Traditionally, the job of off-line analysis has been performed using hardware and software systems developed for real-time spacecraft contacts; then, the systems were supplemented with a collection of tools developed by Flight Operations Team (FOT) members. Since the number of upcoming missions is increasing, NASA can no longer afford to operate in this manner. GTAS improves control center productivity and effectiveness because it provides a generic solution across multiple missions. Thus, GTAS eliminates the need for each individual mission to develop duplicate capabilities. It also allows for more sophisticated tools to be developed because it draws resources from several projects. In addition, the GTAS software system incorporates commercial off-the-shelf tools software (COTS) packages and reuses components of other NASA-developed systems wherever possible. GTAS has incorporated lessons learned from previous missions by involving the users early in the development process. GTAS users took a proactive role in requirements analysis, design, development, and testing. Because of user involvement, several special tools were designed and are now being developed. GTAS users expressed considerable interest in facilitating data collection for long term trending and analysis. As a result, GTAS provides easy access to large volumes of processed telemetry data directly in the control center. The GTAS archival and retrieval capabilities are supported by the integration of optical disk technology and a COTS relational database management system.

Models and techniques for evaluating the effectiveness of aircraft computing systems

NASA Technical Reports Server (NTRS)

Meyer, J. F.

1978-01-01

Progress in the development of system models and techniques for the formulation and evaluation of aircraft computer system effectiveness is reported. Topics covered include: analysis of functional dependence: a prototype software package, METAPHOR, developed to aid the evaluation of performability; and a comprehensive performability modeling and evaluation exercise involving the SIFT computer.

Impact of Requirements Quality on Project Success or Failure

NASA Astrophysics Data System (ADS)

Tamai, Tetsuo; Kamata, Mayumi Itakura

We are interested in the relationship between the quality of the requirements specifications for software projects and the subsequent outcome of the projects. To examine this relationship, we investigated 32 projects started and completed between 2003 and 2005 by the software development division of a large company in Tokyo. The company has collected reliable data on requirements specification quality, as evaluated by software quality assurance teams, and overall project performance data relating to cost and time overruns. The data for requirements specification quality were first converted into a multiple-dimensional space, with each dimension corresponding to an item of the recommended structure for software requirements specifications (SRS) defined in IEEE Std. 830-1998. We applied various statistical analysis methods to the SRS quality data and project outcomes.

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

A. Alfonsi; C. Rabiti; D. Mandelli

The Reactor Analysis and Virtual control ENviroment (RAVEN) code is a software tool that acts as the control logic driver and post-processing engine for the newly developed Thermal-Hydraulic code RELAP-7. RAVEN is now a multi-purpose Probabilistic Risk Assessment (PRA) software framework that allows dispatching different functionalities: Derive and actuate the control logic required to simulate the plant control system and operator actions (guided procedures), allowing on-line monitoring/controlling in the Phase Space Perform both Monte-Carlo sampling of random distributed events and Dynamic Event Tree based analysis Facilitate the input/output handling through a Graphical User Interface (GUI) and a post-processing data miningmore » module« less

Digital 3D Microstructure Analysis of Concrete using X-Ray Micro Computed Tomography SkyScan 1173: A Preliminary Study

NASA Astrophysics Data System (ADS)

Latief, F. D. E.; Mohammad, I. H.; Rarasati, A. D.

2017-11-01

Digital imaging of a concrete sample using high resolution tomographic imaging by means of X-Ray Micro Computed Tomography (μ-CT) has been conducted to assess the characteristic of the sample’s structure. A standard procedure of image acquisition, reconstruction, image processing of the method using a particular scanning device i.e., the Bruker SkyScan 1173 High Energy Micro-CT are elaborated. A qualitative and a quantitative analysis were briefly performed on the sample to deliver some basic ideas of the capability of the system and the bundled software package. Calculation of total VOI volume, object volume, percent of object volume, total VOI surface, object surface, object surface/volume ratio, object surface density, structure thickness, structure separation, total porosity were conducted and analysed. This paper should serve as a brief description of how the device can produce the preferred image quality as well as the ability of the bundled software packages to help in performing qualitative and quantitative analysis.

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

Chen, Yixing; Zhang, Jianshun; Pelken, Michael

Executive Summary The objective of this study was to develop a “Virtual Design Studio (VDS)”: a software platform for integrated, coordinated and optimized design of green building systems with low energy consumption, high indoor environmental quality (IEQ), and high level of sustainability. This VDS is intended to assist collaborating architects, engineers and project management team members throughout from the early phases to the detailed building design stages. It can be used to plan design tasks and workflow, and evaluate the potential impacts of various green building strategies on the building performance by using the state of the art simulation toolsmore » as well as industrial/professional standards and guidelines for green building system design. Engaged in the development of VDS was a multi-disciplinary research team that included architects, engineers, and software developers. Based on the review and analysis of how existing professional practices in building systems design operate, particularly those used in the U.S., Germany and UK, a generic process for performance-based building design, construction and operation was proposed. It distinguishes the whole process into five distinct stages: Assess, Define, Design, Apply, and Monitoring (ADDAM). The current VDS is focused on the first three stages. The VDS considers building design as a multi-dimensional process, involving multiple design teams, design factors, and design stages. The intersection among these three dimensions defines a specific design task in terms of “who”, “what” and “when”. It also considers building design as a multi-objective process that aims to enhance the five aspects of performance for green building systems: site sustainability, materials and resource efficiency, water utilization efficiency, energy efficiency and impacts to the atmospheric environment, and IEQ. The current VDS development has been limited to energy efficiency and IEQ performance, with particular focus on evaluating thermal performance, air quality and lighting environmental quality because of their strong interaction with the energy performance of buildings. The VDS software framework contains four major functions: 1) Design coordination: It enables users to define tasks using the Input-Process-Output flow approach, which specifies the anticipated activities (i.e., the process), required input and output information, and anticipated interactions with other tasks. It also allows task scheduling to define the work flow, and sharing of the design data and information via the internet. 2) Modeling and simulation: It enables users to perform building simulations to predict the energy consumption and IEQ conditions at any of the design stages by using EnergyPlus and a combined heat, air, moisture and pollutant simulation (CHAMPS) model. A method for co-simulation was developed to allow the use of both models at the same time step for the combined energy and indoor air quality analysis. 3) Results visualization: It enables users to display a 3-D geometric design of the building by reading BIM (building information model) file generated by design software such as SketchUp, and the predicted results of heat, air, moisture, pollutant and light distributions in the building. 4) Performance evaluation: It enables the users to compare the performance of a proposed building design against a reference building that is defined for the same type of buildings under the same climate condition, and predicts the percent of improvements over the minimum requirements specified in ASHRAE Standard 55-2010, 62.1-2010 and 90.1-2010. An approach was developed to estimate the potential impact of a design factor on the whole building performance, and hence can assist the user to identify areas that have most pay back for investment. The VDS software was developed by using C++ with the conventional Model, View and Control (MVC) software architecture. The software has been verified by using a simple 3-zone case building. The application of the VDS concepts and framework for building design and performance analysis has been illustrated by using a medium-sized, five story office building that received LEED Platinum Certification from USGBC.« less

Comparison of requirements and capabilities of major multipurpose software packages.

PubMed

Igo, Robert P; Schnell, Audrey H

2012-01-01

The aim of this chapter is to introduce the reader to commonly used software packages and illustrate their input requirements, analysis options, strengths, and limitations. We focus on packages that perform more than one function and include a program for quality control, linkage, and association analyses. Additional inclusion criteria were (1) programs that are free to academic users and (2) currently supported, maintained, and developed. Using those criteria, we chose to review three programs: Statistical Analysis for Genetic Epidemiology (S.A.G.E.), PLINK, and Merlin. We will describe the required input format and analysis options. We will not go into detail about every possible program in the packages, but we will give an overview of the packages requirements and capabilities.

RETScreen Plus Software Tutorial

NASA Technical Reports Server (NTRS)

Ganoe, Rene D.; Stackhouse, Paul W., Jr.; DeYoung, Russell J.

2014-01-01

Greater emphasis is being placed on reducing both the carbon footprint and energy cost of buildings. A building's energy usage depends upon many factors one of the most important is the local weather and climate conditions to which it's electrical, heating and air conditioning systems must respond. Incorporating renewable energy systems, including solar systems, to supplement energy supplies and increase energy efficiency is important to saving costs and reducing emissions. Also retrofitting technologies to buildings requires knowledge of building performance in its current state, potential future climate state, projection of potential savings with capital investment, and then monitoring the performance once the improvements are made. RETScreen Plus is a performance analysis software module that supplies the needed functions of monitoring current building performance, targeting projected energy efficiency improvements and verifying improvements once completed. This tutorial defines the functions of RETScreen Plus as well as outlines the general procedure for monitoring and reporting building energy performance.

Language workbench user interfaces for data analysis

PubMed Central

Benson, Victoria M.

2015-01-01

Biological data analysis is frequently performed with command line software. While this practice provides considerable flexibility for computationally savy individuals, such as investigators trained in bioinformatics, this also creates a barrier to the widespread use of data analysis software by investigators trained as biologists and/or clinicians. Workflow systems such as Galaxy and Taverna have been developed to try and provide generic user interfaces that can wrap command line analysis software. These solutions are useful for problems that can be solved with workflows, and that do not require specialized user interfaces. However, some types of analyses can benefit from custom user interfaces. For instance, developing biomarker models from high-throughput data is a type of analysis that can be expressed more succinctly with specialized user interfaces. Here, we show how Language Workbench (LW) technology can be used to model the biomarker development and validation process. We developed a language that models the concepts of Dataset, Endpoint, Feature Selection Method and Classifier. These high-level language concepts map directly to abstractions that analysts who develop biomarker models are familiar with. We found that user interfaces developed in the Meta-Programming System (MPS) LW provide convenient means to configure a biomarker development project, to train models and view the validation statistics. We discuss several advantages of developing user interfaces for data analysis with a LW, including increased interface consistency, portability and extension by language composition. The language developed during this experiment is distributed as an MPS plugin (available at http://campagnelab.org/software/bdval-for-mps/). PMID:25755929

STAMPS: development and verification of swallowing kinematic analysis software.

PubMed

Lee, Woo Hyung; Chun, Changmook; Seo, Han Gil; Lee, Seung Hak; Oh, Byung-Mo

2017-10-17

Swallowing impairment is a common complication in various geriatric and neurodegenerative diseases. Swallowing kinematic analysis is essential to quantitatively evaluate the swallowing motion of the oropharyngeal structures. This study aims to develop a novel swallowing kinematic analysis software, called spatio-temporal analyzer for motion and physiologic study (STAMPS), and verify its validity and reliability. STAMPS was developed in MATLAB, which is one of the most popular platforms for biomedical analysis. This software was constructed to acquire, process, and analyze the data of swallowing motion. The target of swallowing structures includes bony structures (hyoid bone, mandible, maxilla, and cervical vertebral bodies), cartilages (epiglottis and arytenoid), soft tissues (larynx and upper esophageal sphincter), and food bolus. Numerous functions are available for the spatiotemporal parameters of the swallowing structures. Testing for validity and reliability was performed in 10 dysphagia patients with diverse etiologies and using the instrumental swallowing model which was designed to mimic the motion of the hyoid bone and the epiglottis. The intra- and inter-rater reliability tests showed excellent agreement for displacement and moderate to excellent agreement for velocity. The Pearson correlation coefficients between the measured and instrumental reference values were nearly 1.00 (P < 0.001) for displacement and velocity. The Bland-Altman plots showed good agreement between the measurements and the reference values. STAMPS provides precise and reliable kinematic measurements and multiple practical functionalities for spatiotemporal analysis. The software is expected to be useful for researchers who are interested in the swallowing motion analysis.

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.

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.

An Example of the Informative Potential of Polar Coordinate Analysis: Sprint Tactics in Elite 1,500-m Track Events

ERIC Educational Resources Information Center

Aragón, Sonia; Lapresa, Daniel; Arana, Javier; Anguera, M. Teresa; Garzón, Belén

2017-01-01

Polar coordinate analysis is a powerful data reduction technique based on the Zsum statistic, which is calculated from adjusted residuals obtained by lag sequential analysis. Its use has been greatly simplified since the addition of a module in the free software program HOISAN for performing the necessary computations and producing…

Assessment of three different software systems in the evaluation of dynamic MRI of the breast.

PubMed

Kurz, K D; Steinhaus, D; Klar, V; Cohnen, M; Wittsack, H J; Saleh, A; Mödder, U; Blondin, D

2009-02-01

The aim was to compare the diagnostic performance and handling of dynamic contrast-enhanced MRI of the breast with two commercial software solutions ("CADstream" and "3TP") and one self-developed software system ("Mammatool"). Identical data sets of dynamic breast MRI from 21 patients were evaluated retrospectively with all three software systems. The exams were classified according to the BI-RADS classification. The number of lesions in the parametric mapping was compared to histology or follow-up of more than 2 years. In addition, 25 quality criteria were judged by 3 independent investigators with a score from 0 to 5. Statistical analysis was performed to document the quality ranking of the different software systems. There were 9 invasive carcinomas, one pure DCIS, one papilloma, one radial scar, three histologically proven changes due to mastopathy, one adenosis and two fibroadenomas. Additionally two patients with enhancing parenchyma followed with MRI for more than 3 years and one scar after breast conserving therapy were included. All malignant lesions were classified as BI-RADS 4 or 5 using all software systems and showed significant enhancement in the parametric mapping. "CADstream" showed the best score on subjective quality criteria. "3TP" showed the lowest number of false-positive results. "Mammatool" produced the lowest number of benign tissues indicated with parametric overlay. All three software programs tested were adequate for sensitive and efficient assessment of dynamic MRI of the breast. Improvements in specificity may be achievable.

Advanced Online Survival Analysis Tool for Predictive Modelling in Clinical Data Science.

PubMed

Montes-Torres, Julio; Subirats, José Luis; Ribelles, Nuria; Urda, Daniel; Franco, Leonardo; Alba, Emilio; Jerez, José Manuel

2016-01-01

One of the prevailing applications of machine learning is the use of predictive modelling in clinical survival analysis. In this work, we present our view of the current situation of computer tools for survival analysis, stressing the need of transferring the latest results in the field of machine learning to biomedical researchers. We propose a web based software for survival analysis called OSA (Online Survival Analysis), which has been developed as an open access and user friendly option to obtain discrete time, predictive survival models at individual level using machine learning techniques, and to perform standard survival analysis. OSA employs an Artificial Neural Network (ANN) based method to produce the predictive survival models. Additionally, the software can easily generate survival and hazard curves with multiple options to personalise the plots, obtain contingency tables from the uploaded data to perform different tests, and fit a Cox regression model from a number of predictor variables. In the Materials and Methods section, we depict the general architecture of the application and introduce the mathematical background of each of the implemented methods. The study concludes with examples of use showing the results obtained with public datasets.

Advanced Online Survival Analysis Tool for Predictive Modelling in Clinical Data Science

PubMed Central

Montes-Torres, Julio; Subirats, José Luis; Ribelles, Nuria; Urda, Daniel; Franco, Leonardo; Alba, Emilio; Jerez, José Manuel

2016-01-01

One of the prevailing applications of machine learning is the use of predictive modelling in clinical survival analysis. In this work, we present our view of the current situation of computer tools for survival analysis, stressing the need of transferring the latest results in the field of machine learning to biomedical researchers. We propose a web based software for survival analysis called OSA (Online Survival Analysis), which has been developed as an open access and user friendly option to obtain discrete time, predictive survival models at individual level using machine learning techniques, and to perform standard survival analysis. OSA employs an Artificial Neural Network (ANN) based method to produce the predictive survival models. Additionally, the software can easily generate survival and hazard curves with multiple options to personalise the plots, obtain contingency tables from the uploaded data to perform different tests, and fit a Cox regression model from a number of predictor variables. In the Materials and Methods section, we depict the general architecture of the application and introduce the mathematical background of each of the implemented methods. The study concludes with examples of use showing the results obtained with public datasets. PMID:27532883

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.

Orbiter subsystem hardware/software interaction analysis. Volume 8: AFT reaction control system, part 2

NASA Technical Reports Server (NTRS)

Becker, D. D.

1980-01-01

The orbiter subsystems and interfacing program elements which interact with the orbiter computer flight software are analyzed. The failure modes identified in the subsystem/element failure mode and effects analysis are examined. Potential interaction with the software is examined through an evaluation of the software requirements. The analysis is restricted to flight software requirements and excludes utility/checkout software. The results of the hardware/software interaction analysis for the forward reaction control system are presented.

Fragment-Based Docking: Development of the CHARMMing Web User Interface as a Platform for Computer-Aided Drug Design

PubMed Central

2015-01-01

Web-based user interfaces to scientific applications are important tools that allow researchers to utilize a broad range of software packages with just an Internet connection and a browser.1 One such interface, CHARMMing (CHARMM interface and graphics), facilitates access to the powerful and widely used molecular software package CHARMM. CHARMMing incorporates tasks such as molecular structure analysis, dynamics, multiscale modeling, and other techniques commonly used by computational life scientists. We have extended CHARMMing’s capabilities to include a fragment-based docking protocol that allows users to perform molecular docking and virtual screening calculations either directly via the CHARMMing Web server or on computing resources using the self-contained job scripts generated via the Web interface. The docking protocol was evaluated by performing a series of “re-dockings” with direct comparison to top commercial docking software. Results of this evaluation showed that CHARMMing’s docking implementation is comparable to many widely used software packages and validates the use of the new CHARMM generalized force field for docking and virtual screening. PMID:25151852