Software Certification for Temporal Properties With Affordable Tool Qualification

NASA Technical Reports Server (NTRS)

Xia, Songtao; DiVito, Benedetto L.

2005-01-01

It has been recognized that a framework based on proof-carrying code (also called semantic-based software certification in its community) could be used as a candidate software certification process for the avionics industry. To meet this goal, tools in the "trust base" of a proof-carrying code system must be qualified by regulatory authorities. A family of semantic-based software certification approaches is described, each different in expressive power, level of automation and trust base. Of particular interest is the so-called abstraction-carrying code, which can certify temporal properties. When a pure abstraction-carrying code method is used in the context of industrial software certification, the fact that the trust base includes a model checker would incur a high qualification cost. This position paper proposes a hybrid of abstraction-based and proof-based certification methods so that the model checker used by a client can be significantly simplified, thereby leading to lower cost in tool qualification.

Predicting tool life in turning operations using neural networks and image processing

NASA Astrophysics Data System (ADS)

Mikołajczyk, T.; Nowicki, K.; Bustillo, A.; Yu Pimenov, D.

2018-05-01

A two-step method is presented for the automatic prediction of tool life in turning operations. First, experimental data are collected for three cutting edges under the same constant processing conditions. In these experiments, the parameter of tool wear, VB, is measured with conventional methods and the same parameter is estimated using Neural Wear, a customized software package that combines flank wear image recognition and Artificial Neural Networks (ANNs). Second, an ANN model of tool life is trained with the data collected from the first two cutting edges and the subsequent model is evaluated on two different subsets for the third cutting edge: the first subset is obtained from the direct measurement of tool wear and the second is obtained from the Neural Wear software that estimates tool wear using edge images. Although the complete-automated solution, Neural Wear software for tool wear recognition plus the ANN model of tool life prediction, presented a slightly higher error than the direct measurements, it was within the same range and can meet all industrial requirements. These results confirm that the combination of image recognition software and ANN modelling could potentially be developed into a useful industrial tool for low-cost estimation of tool life in turning operations.

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

PubMed

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

2014-01-01

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

Bringing your tools to CyVerse Discovery Environment using Docker

PubMed Central

Devisetty, Upendra Kumar; Kennedy, Kathleen; Sarando, Paul; Merchant, Nirav; Lyons, Eric

2016-01-01

Docker has become a very popular container-based virtualization platform for software distribution that has revolutionized the way in which scientific software and software dependencies (software stacks) can be packaged, distributed, and deployed. Docker makes the complex and time-consuming installation procedures needed for scientific software a one-time process. Because it enables platform-independent installation, versioning of software environments, and easy redeployment and reproducibility, Docker is an ideal candidate for the deployment of identical software stacks on different compute environments such as XSEDE and Amazon AWS. CyVerse’s Discovery Environment also uses Docker for integrating its powerful, community-recommended software tools into CyVerse’s production environment for public use. This paper will help users bring their tools into CyVerse Discovery Environment (DE) which will not only allows users to integrate their tools with relative ease compared to the earlier method of tool deployment in DE but will also help users to share their apps with collaborators and release them for public use. PMID:27803802

Bringing your tools to CyVerse Discovery Environment using Docker.

PubMed

Devisetty, Upendra Kumar; Kennedy, Kathleen; Sarando, Paul; Merchant, Nirav; Lyons, Eric

2016-01-01

Docker has become a very popular container-based virtualization platform for software distribution that has revolutionized the way in which scientific software and software dependencies (software stacks) can be packaged, distributed, and deployed. Docker makes the complex and time-consuming installation procedures needed for scientific software a one-time process. Because it enables platform-independent installation, versioning of software environments, and easy redeployment and reproducibility, Docker is an ideal candidate for the deployment of identical software stacks on different compute environments such as XSEDE and Amazon AWS. CyVerse's Discovery Environment also uses Docker for integrating its powerful, community-recommended software tools into CyVerse's production environment for public use. This paper will help users bring their tools into CyVerse Discovery Environment (DE) which will not only allows users to integrate their tools with relative ease compared to the earlier method of tool deployment in DE but will also help users to share their apps with collaborators and release them for public use.

Applications of AN OO Methodology and Case to a Daq System

NASA Astrophysics Data System (ADS)

Bee, C. P.; Eshghi, S.; Jones, R.; Kolos, S.; Magherini, C.; Maidantchik, C.; Mapelli, L.; Mornacchi, G.; Niculescu, M.; Patel, A.; Prigent, D.; Spiwoks, R.; Soloviev, I.; Caprini, M.; Duval, P. Y.; Etienne, F.; Ferrato, D.; Le van Suu, A.; Qian, Z.; Gaponenko, I.; Merzliakov, Y.; Ambrosini, G.; Ferrari, R.; Fumagalli, G.; Polesello, G.

The RD13 project has evaluated the use of the Object Oriented Information Engineering (OOIE) method during the development of several software components connected to the DAQ system. The method is supported by a sophisticated commercial CASE tool (Object Management Workbench) and programming environment (Kappa) which covers the full life-cycle of the software including model simulation, code generation and application deployment. This paper gives an overview of the method, CASE tool, DAQ components which have been developed and we relate our experiences with the method and tool, its integration into our development environment and the spiral lifecycle it supports.

A Quantitative Study of a Software Tool that Supports a Part-Complete Solution Method on Learning Outcomes

ERIC Educational Resources Information Center

Garner, Stuart

2009-01-01

This paper reports on the findings from a quantitative research study into the use of a software tool that was built to support a part-complete solution method (PCSM) for the learning of computer programming. The use of part-complete solutions to programming problems is one of the methods that can be used to reduce the cognitive load that students…

A software tool for determination of breast cancer treatment methods using data mining approach.

PubMed

Cakır, Abdülkadir; Demirel, Burçin

2011-12-01

In this work, breast cancer treatment methods are determined using data mining. For this purpose, software is developed to help to oncology doctor for the suggestion of application of the treatment methods about breast cancer patients. 462 breast cancer patient data, obtained from Ankara Oncology Hospital, are used to determine treatment methods for new patients. This dataset is processed with Weka data mining tool. Classification algorithms are applied one by one for this dataset and results are compared to find proper treatment method. Developed software program called as "Treatment Assistant" uses different algorithms (IB1, Multilayer Perception and Decision Table) to find out which one is giving better result for each attribute to predict and by using Java Net beans interface. Treatment methods are determined for the post surgical operation of breast cancer patients using this developed software tool. At modeling step of data mining process, different Weka algorithms are used for output attributes. For hormonotherapy output IB1, for tamoxifen and radiotherapy outputs Multilayer Perceptron and for the chemotherapy output decision table algorithm shows best accuracy performance compare to each other. In conclusion, this work shows that data mining approach can be a useful tool for medical applications particularly at the treatment decision step. Data mining helps to the doctor to decide in a short time.

Methodology for automating software systems. Task 1 of the foundations for automating software systems

NASA Technical Reports Server (NTRS)

Moseley, Warren

1989-01-01

The early stages of a research program designed to establish an experimental research platform for software engineering are described. Major emphasis is placed on Computer Assisted Software Engineering (CASE). The Poor Man's CASE Tool is based on the Apple Macintosh system, employing available software including Focal Point II, Hypercard, XRefText, and Macproject. These programs are functional in themselves, but through advanced linking are available for operation from within the tool being developed. The research platform is intended to merge software engineering technology with artificial intelligence (AI). In the first prototype of the PMCT, however, the sections of AI are not included. CASE tools assist the software engineer in planning goals, routes to those goals, and ways to measure progress. The method described allows software to be synthesized instead of being written or built.

Success Factors for Using Case Method in Teaching and Learning Software Engineering

ERIC Educational Resources Information Center

Razali, Rozilawati; Zainal, Dzulaiha Aryanee Putri

2013-01-01

The Case Method (CM) has long been used effectively in Social Science education. Its potential use in Applied Science such as Software Engineering (SE) however has yet to be further explored. SE is an engineering discipline that concerns the principles, methods and tools used throughout the software development lifecycle. In CM, subjects are…

An object-oriented description method of EPMM process

NASA Astrophysics Data System (ADS)

Jiang, Zuo; Yang, Fan

2017-06-01

In order to use the object-oriented mature tools and language in software process model, make the software process model more accord with the industrial standard, it’s necessary to study the object-oriented modelling of software process. Based on the formal process definition in EPMM, considering the characteristics that Petri net is mainly formal modelling tool and combining the Petri net modelling with the object-oriented modelling idea, this paper provides this implementation method to convert EPMM based on Petri net into object models based on object-oriented description.

GenePRIMP: A software quality control tool

ScienceCinema

Amrita Pati

2017-12-09

Amrita Pati of the DOE Joint Genome Institute's Genome Biology group describes the software tool GenePRIMP and how it fits into the quality control pipeline for microbial genomics. Further details regarding GenePRIMP appear in a paper published online May 2, 2010 in Nature Methods.

Space Shuttle Software Development and Certification

NASA Technical Reports Server (NTRS)

Orr, James K.; Henderson, Johnnie A

2000-01-01

Man-rated software, "software which is in control of systems and environments upon which human life is critically dependent," must be highly reliable. The Space Shuttle Primary Avionics Software System is an excellent example of such a software system. Lessons learn from more than 20 years of effort have identified basic elements that must be present to achieve this high degree of reliability. The elements include rigorous application of appropriate software development processes, use of trusted tools to support those processes, quantitative process management, and defect elimination and prevention. This presentation highlights methods used within the Space Shuttle project and raises questions that must be addressed to provide similar success in a cost effective manner on future long-term projects where key application development tools are COTS rather than internally developed custom application development tools

NASA software specification and evaluation system design, part 2

NASA Technical Reports Server (NTRS)

1976-01-01

A survey and analysis of the existing methods, tools and techniques employed in the development of software are presented along with recommendations for the construction of reliable software. Functional designs for software specification language, and the data base verifier are presented.

The design of real time infrared image generation software based on Creator and Vega

NASA Astrophysics Data System (ADS)

Wang, Rui-feng; Wu, Wei-dong; Huo, Jun-xiu

2013-09-01

Considering the requirement of high reality and real-time quality dynamic infrared image of an infrared image simulation, a method to design real-time infrared image simulation application on the platform of VC++ is proposed. This is based on visual simulation software Creator and Vega. The functions of Creator are introduced simply, and the main features of Vega developing environment are analyzed. The methods of infrared modeling and background are offered, the designing flow chart of the developing process of IR image real-time generation software and the functions of TMM Tool and MAT Tool and sensor module are explained, at the same time, the real-time of software is designed.

The Business Case for Automated Software Engineering

NASA Technical Reports Server (NTRS)

Menzies, Tim; Elrawas, Oussama; Hihn, Jairus M.; Feather, Martin S.; Madachy, Ray; Boehm, Barry

2007-01-01

Adoption of advanced automated SE (ASE) tools would be more favored if a business case could be made that these tools are more valuable than alternate methods. In theory, software prediction models can be used to make that case. In practice, this is complicated by the 'local tuning' problem. Normally. predictors for software effort and defects and threat use local data to tune their predictions. Such local tuning data is often unavailable. This paper shows that assessing the relative merits of different SE methods need not require precise local tunings. STAR 1 is a simulated annealer plus a Bayesian post-processor that explores the space of possible local tunings within software prediction models. STAR 1 ranks project decisions by their effects on effort and defects and threats. In experiments with NASA systems. STARI found one project where ASE were essential for minimizing effort/ defect/ threats; and another project were ASE tools were merely optional.

Expert system verification and validation study. Delivery 3A and 3B: Trip summaries

NASA Technical Reports Server (NTRS)

French, Scott

1991-01-01

Key results are documented from attending the 4th workshop on verification, validation, and testing. The most interesting part of the workshop was when representatives from the U.S., Japan, and Europe presented surveys of VV&T within their respective regions. Another interesting part focused on current efforts to define industry standards for artificial intelligence and how that might affect approaches to VV&T of expert systems. The next part of the workshop focused on VV&T methods of applying mathematical techniques to verification of rule bases and techniques for capturing information relating to the process of developing software. The final part focused on software tools. A summary is also presented of the EPRI conference on 'Methodologies, Tools, and Standards for Cost Effective Reliable Software Verification and Validation. The conference was divided into discussion sessions on the following issues: development process, automated tools, software reliability, methods, standards, and cost/benefit considerations.

Formal Analysis of the Remote Agent Before and After Flight

NASA Technical Reports Server (NTRS)

Havelund, Klaus; Lowry, Mike; Park, SeungJoon; Pecheur, Charles; Penix, John; Visser, Willem; White, Jon L.

2000-01-01

This paper describes two separate efforts that used the SPIN model checker to verify deep space autonomy flight software. The first effort occurred at the beginning of a spiral development process and found five concurrency errors early in the design cycle that the developers acknowledge would not have been found through testing. This effort required a substantial manual modeling effort involving both abstraction and translation from the prototype LISP code to the PROMELA language used by SPIN. This experience and others led to research to address the gap between formal method tools and the development cycle used by software developers. The Java PathFinder tool which directly translates from Java to PROMELA was developed as part of this research, as well as automatic abstraction tools. In 1999 the flight software flew on a space mission, and a deadlock occurred in a sibling subsystem to the one which was the focus of the first verification effort. A second quick-response "cleanroom" verification effort found the concurrency error in a short amount of time. The error was isomorphic to one of the concurrency errors found during the first verification effort. The paper demonstrates that formal methods tools can find concurrency errors that indeed lead to loss of spacecraft functions, even for the complex software required for autonomy. Second, it describes progress in automatic translation and abstraction that eventually will enable formal methods tools to be inserted directly into the aerospace software development cycle.

Pointo - a Low Cost Solution to Point Cloud Processing

NASA Astrophysics Data System (ADS)

Houshiar, H.; Winkler, S.

2017-11-01

With advance in technology access to data especially 3D point cloud data becomes more and more an everyday task. 3D point clouds are usually captured with very expensive tools such as 3D laser scanners or very time consuming methods such as photogrammetry. Most of the available softwares for 3D point cloud processing are designed for experts and specialists in this field and are usually very large software packages containing variety of methods and tools. This results in softwares that are usually very expensive to acquire and also very difficult to use. Difficulty of use is caused by complicated user interfaces that is required to accommodate a large list of features. The aim of these complex softwares is to provide a powerful tool for a specific group of specialist. However they are not necessary required by the majority of the up coming average users of point clouds. In addition to complexity and high costs of these softwares they generally rely on expensive and modern hardware and only compatible with one specific operating system. Many point cloud customers are not point cloud processing experts or willing to spend the high acquisition costs of these expensive softwares and hardwares. In this paper we introduce a solution for low cost point cloud processing. Our approach is designed to accommodate the needs of the average point cloud user. To reduce the cost and complexity of software our approach focuses on one functionality at a time in contrast with most available softwares and tools that aim to solve as many problems as possible at the same time. Our simple and user oriented design improve the user experience and empower us to optimize our methods for creation of an efficient software. In this paper we introduce Pointo family as a series of connected softwares to provide easy to use tools with simple design for different point cloud processing requirements. PointoVIEWER and PointoCAD are introduced as the first components of the Pointo family to provide a fast and efficient visualization with the ability to add annotation and documentation to the point clouds.

Software Tools for Formal Specification and Verification of Distributed Real-Time Systems.

DTIC Science & Technology

1997-09-30

set of software tools for specification and verification of distributed real time systems using formal methods. The task of this SBIR Phase II effort...to be used by designers of real - time systems for early detection of errors. The mathematical complexity of formal specification and verification has

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.

Modular Analytical Multicomponent Analysis in Gas Sensor Aarrays

PubMed Central

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

2006-01-01

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

Scalable collaborative risk management technology for complex critical systems

NASA Technical Reports Server (NTRS)

Campbell, Scott; Torgerson, Leigh; Burleigh, Scott; Feather, Martin S.; Kiper, James D.

2004-01-01

We describe here our project and plans to develop methods, software tools, and infrastructure tools to address challenges relating to geographically distributed software development. Specifically, this work is creating an infrastructure that supports applications working over distributed geographical and organizational domains and is using this infrastructure to develop a tool that supports project development using risk management and analysis techniques where the participants are not collocated.

Three Software Tools for Viewing Sectional Planes, Volume Models, and Surface Models of a Cadaver Hand

PubMed Central

2018-01-01

Background The hand anatomy, including the complicated hand muscles, can be grasped by using computer-assisted learning tools with high quality two-dimensional images and three-dimensional models. The purpose of this study was to present up-to-date software tools that promote learning of stereoscopic morphology of the hand. Methods On the basis of horizontal sectioned images and outlined images of a male cadaver, vertical planes, volume models, and surface models were elaborated. Software to browse pairs of the sectioned and outlined images in orthogonal planes and software to peel and rotate the volume models, as well as a portable document format (PDF) file to select and rotate the surface models, were produced. Results All of the software tools were downloadable free of charge and usable off-line. The three types of tools for viewing multiple aspects of the hand could be adequately employed according to individual needs. Conclusion These new tools involving the realistic images of a cadaver and the diverse functions are expected to improve comprehensive knowledge of the hand shape. PMID:29441756

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

NASA Astrophysics Data System (ADS)

Mueller, David S.

2013-04-01

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

FunRich proteomics software analysis, let the fun begin!

PubMed

Benito-Martin, Alberto; Peinado, Héctor

2015-08-01

Protein MS analysis is the preferred method for unbiased protein identification. It is normally applied to a large number of both small-scale and high-throughput studies. However, user-friendly computational tools for protein analysis are still needed. In this issue, Mathivanan and colleagues (Proteomics 2015, 15, 2597-2601) report the development of FunRich software, an open-access software that facilitates the analysis of proteomics data, providing tools for functional enrichment and interaction network analysis of genes and proteins. FunRich is a reinterpretation of proteomic software, a standalone tool combining ease of use with customizable databases, free access, and graphical representations. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Role of Computers in Research and Development at Langley Research Center

NASA Technical Reports Server (NTRS)

Wieseman, Carol D. (Compiler)

1994-01-01

This document is a compilation of presentations given at a workshop on the role cf computers in research and development at the Langley Research Center. The objectives of the workshop were to inform the Langley Research Center community of the current software systems and software practices in use at Langley. The workshop was organized in 10 sessions: Software Engineering; Software Engineering Standards, methods, and CASE tools; Solutions of Equations; Automatic Differentiation; Mosaic and the World Wide Web; Graphics and Image Processing; System Design Integration; CAE Tools; Languages; and Advanced Topics.

Using component technology to facilitate external software reuse in ground-based planning systems

NASA Technical Reports Server (NTRS)

Chase, A.

2003-01-01

APGEN (Activity Plan GENerator - 314), a multi-mission planning tool, must interface with external software to vest serve its users. AP-GEN's original method for incorporating external software, the User-Defined library mechanism, has been very successful in allowing APGEN users access to external software functionality.

Reverse engineering of integrated circuits

DOEpatents

Chisholm, Gregory H.; Eckmann, Steven T.; Lain, Christopher M.; Veroff, Robert L.

2003-01-01

Software and a method therein to analyze circuits. The software comprises several tools, each of which perform particular functions in the Reverse Engineering process. The analyst, through a standard interface, directs each tool to the portion of the task to which it is most well suited, rendering previously intractable problems solvable. The tools are generally used iteratively to produce a successively more abstract picture of a circuit, about which incomplete a priori knowledge exists.

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

NASA Technical Reports Server (NTRS)

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

1982-01-01

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

Verification and Validation in a Rapid Software Development Process

NASA Technical Reports Server (NTRS)

Callahan, John R.; Easterbrook, Steve M.

1997-01-01

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

An online database for plant image analysis software tools.

PubMed

Lobet, Guillaume; Draye, Xavier; Périlleux, Claire

2013-10-09

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

Generation of Controlled Analog Emissions from Embedded Devices using Software Stress Methods

DTIC Science & Technology

2017-03-01

Generation of Controlled Analog Emissions from Embedded Devices using Software Stress Methods Oren Sternberg, Jonathan H. Nelson, Israel Perez...Abstract: In this paper, we present a new method that uses software diagnostic tools to study the generation of induced spurious physical emissions from...types of attacks warrants an understanding of unwanted signal generation. We examine this connection by observing the emission profile of an embedded

Basic to Advanced InSAR Processing: GMTSAR

NASA Astrophysics Data System (ADS)

Sandwell, D. T.; Xu, X.; Baker, S.; Hogrelius, A.; Mellors, R. J.; Tong, X.; Wei, M.; Wessel, P.

2017-12-01

Monitoring crustal deformation using InSAR is becoming a standard technique for the science and application communities. Optimal use of the new data streams from Sentinel-1 and NISAR will require open software tools as well as education on the strengths and limitations of the InSAR methods. Over the past decade we have developed freely available, open-source software for processing InSAR data. The software relies on the Generic Mapping Tools (GMT) for the back-end data analysis and display and is thus called GMTSAR. With startup funding from NSF, we accelerated the development of GMTSAR to include more satellite data sources and provide better integration and distribution with GMT. In addition, with support from UNAVCO we have offered 6 GMTSAR short courses to educate mostly novice InSAR users. Currently, the software is used by hundreds of scientists and engineers around the world to study deformation at more than 4300 different sites. The most challenging aspect of the recent software development was the transition from image alignment using the cross-correlation method to a completely new alignment algorithm that uses only the precise orbital information to geometrically align images to an accuracy of better than 7 cm. This development was needed to process a new data type that is being acquired by the Sentinel-1A/B satellites. This combination of software and open data is transforming radar interferometry from a research tool into a fully operational time series analysis tool. Over the next 5 years we are planning to continue to broaden the user base through: improved software delivery methods; code hardening; better integration with data archives; support for high level products being developed for NISAR; and continued education and outreach.

Computerized assessment of placental calcification post-ultrasound: a novel software tool.

PubMed

Moran, M; Higgins, M; Zombori, G; Ryan, J; McAuliffe, F M

2013-05-01

Placental calcification is associated with an increased risk of perinatal morbidity and mortality. The subjectivity of current ultrasound methods of assessment of placental calcification indicates that a more objective method is required. The aim of this study was to correlate the percentage of calcification defined by the clinician using a new software tool for calculating the extent of placental calcification with traditional ultrasound methods and with pregnancy outcome. Ninety placental images were individually assessed. An upper threshold was defined, based on high intensity, to quantify calcification within the placenta. Output metrics were then produced including the overall percentage of calcification with respect to the total number of pixels within the region of interest. The results were correlated with traditional ultrasound methods of assessment of placental calcification and with pregnancy outcome. The results demonstrate a significant correlation between placental calcification, as defined using the software, and traditional methods of Grannum grading of placental calcification. Whilst correlation with perinatal outcome and cord pH was not significant as a result of small numbers, patients with placental calcification assessed using the computerized software at the upper quartile had higher rates of poor perinatal outcome when compared with those at the lower quartile (8/22 (36%) vs 3/23 (13%); P = 0.069). These results suggest that this computerized software tool has the potential to become an alternative method of assessing placental calcification. Copyright © 2012 ISUOG. Published by John Wiley & Sons Ltd.

NASA software specification and evaluation system design, part 1

NASA Technical Reports Server (NTRS)

1976-01-01

The research to develop methods for reducing the effort expended in software and verification is reported. The development of a formal software requirements methodology, a formal specifications language, a programming language, a language preprocessor, and code analysis tools are discussed.

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

DTIC Science & Technology

2008-02-01

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

Cognitive Foundry v. 3.0 (OSS)

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

Basilico, Justin; Dixon, Kevin; McClain, Jonathan

2009-11-18

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

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

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

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

1980-05-01

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

ConvAn: a convergence analyzing tool for optimization of biochemical networks.

PubMed

Kostromins, Andrejs; Mozga, Ivars; Stalidzans, Egils

2012-01-01

Dynamic models of biochemical networks usually are described as a system of nonlinear differential equations. In case of optimization of models for purpose of parameter estimation or design of new properties mainly numerical methods are used. That causes problems of optimization predictability as most of numerical optimization methods have stochastic properties and the convergence of the objective function to the global optimum is hardly predictable. Determination of suitable optimization method and necessary duration of optimization becomes critical in case of evaluation of high number of combinations of adjustable parameters or in case of large dynamic models. This task is complex due to variety of optimization methods, software tools and nonlinearity features of models in different parameter spaces. A software tool ConvAn is developed to analyze statistical properties of convergence dynamics for optimization runs with particular optimization method, model, software tool, set of optimization method parameters and number of adjustable parameters of the model. The convergence curves can be normalized automatically to enable comparison of different methods and models in the same scale. By the help of the biochemistry adapted graphical user interface of ConvAn it is possible to compare different optimization methods in terms of ability to find the global optima or values close to that as well as the necessary computational time to reach them. It is possible to estimate the optimization performance for different number of adjustable parameters. The functionality of ConvAn enables statistical assessment of necessary optimization time depending on the necessary optimization accuracy. Optimization methods, which are not suitable for a particular optimization task, can be rejected if they have poor repeatability or convergence properties. The software ConvAn is freely available on www.biosystems.lv/convan. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Formal Methods for Life-Critical Software

NASA Technical Reports Server (NTRS)

Butler, Ricky W.; Johnson, Sally C.

1993-01-01

The use of computer software in life-critical applications, such as for civil air transports, demands the use of rigorous formal mathematical verification procedures. This paper demonstrates how to apply formal methods to the development and verification of software by leading the reader step-by-step through requirements analysis, design, implementation, and verification of an electronic phone book application. The current maturity and limitations of formal methods tools and techniques are then discussed, and a number of examples of the successful use of formal methods by industry are cited.

Leveraging Existing Mission Tools in a Re-Usable, Component-Based Software Environment

NASA Technical Reports Server (NTRS)

Greene, Kevin; Grenander, Sven; Kurien, James; z,s (fshir. z[orttr); z,scer; O'Reilly, Taifun

2006-01-01

Emerging methods in component-based software development offer significant advantages but may seem incompatible with existing mission operations applications. In this paper we relate our positive experiences integrating existing mission applications into component-based tools we are delivering to three missions. In most operations environments, a number of software applications have been integrated together to form the mission operations software. In contrast, with component-based software development chunks of related functionality and data structures, referred to as components, can be individually delivered, integrated and re-used. With the advent of powerful tools for managing component-based development, complex software systems can potentially see significant benefits in ease of integration, testability and reusability from these techniques. These benefits motivate us to ask how component-based development techniques can be relevant in a mission operations environment, where there is significant investment in software tools that are not component-based and may not be written in languages for which component-based tools even exist. Trusted and complex software tools for sequencing, validation, navigation, and other vital functions cannot simply be re-written or abandoned in order to gain the advantages offered by emerging component-based software techniques. Thus some middle ground must be found. We have faced exactly this issue, and have found several solutions. Ensemble is an open platform for development, integration, and deployment of mission operations software that we are developing. Ensemble itself is an extension of an open source, component-based software development platform called Eclipse. Due to the advantages of component-based development, we have been able to vary rapidly develop mission operations tools for three surface missions by mixing and matching from a common set of mission operation components. We have also had to determine how to integrate existing mission applications for sequence development, sequence validation, and high level activity planning, and other functions into a component-based environment. For each of these, we used a somewhat different technique based upon the structure and usage of the existing application.

Automated real-time software development

NASA Technical Reports Server (NTRS)

Jones, Denise R.; Walker, Carrie K.; Turkovich, John J.

1993-01-01

A Computer-Aided Software Engineering (CASE) system has been developed at the Charles Stark Draper Laboratory (CSDL) under the direction of the NASA Langley Research Center. The CSDL CASE tool provides an automated method of generating source code and hard copy documentation from functional application engineering specifications. The goal is to significantly reduce the cost of developing and maintaining real-time scientific and engineering software while increasing system reliability. This paper describes CSDL CASE and discusses demonstrations that used the tool to automatically generate real-time application code.

Debris Examination Using Ballistic and Radar Integrated Software

NASA Technical Reports Server (NTRS)

Griffith, Anthony; Schottel, Matthew; Lee, David; Scully, Robert; Hamilton, Joseph; Kent, Brian; Thomas, Christopher; Benson, Jonathan; Branch, Eric; Hardman, Paul;

OPTHYLIC: An Optimised Tool for Hybrid Limits Computation

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Cosimulation of embedded system using RTOS software simulator

NASA Astrophysics Data System (ADS)

Wang, Shihao; Duan, Zhigang; Liu, Mingye

2003-09-01

Embedded system design often employs co-simulation to verify system's function; one efficient verification tool of software is Instruction Set Simulator (ISS). As a full functional model of target CPU, ISS interprets instruction of embedded software step by step, which usually is time-consuming since it simulates at low-level. Hence ISS often becomes the bottleneck of co-simulation in a complicated system. In this paper, a new software verification tools, the RTOS software simulator (RSS) was presented. The mechanism of its operation was described in a full details. In RSS method, RTOS API is extended and hardware simulator driver is adopted to deal with data-exchange and synchronism between the two simulators.

Learning Theories Applied to Teaching Technology: Constructivism versus Behavioral Theory for Instructing Multimedia Software Programs

ERIC Educational Resources Information Center

Reed, Cajah S.

2012-01-01

This study sought to find evidence for a beneficial learning theory to teach computer software programs. Additionally, software was analyzed for each learning theory's applicability to resolve whether certain software requires a specific method of education. The results are meant to give educators more effective teaching tools, so students…

Stability analysis using SDSA tool

NASA Astrophysics Data System (ADS)

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

2011-11-01

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

Virtual Immunology: Software for Teaching Basic Immunology

ERIC Educational Resources Information Center

Berçot, Filipe Faria; Fidalgo-Neto, Antônio Augusto; Lopes, Renato Matos; Faggioni, Thais; Alves, Luiz Anastácio

2013-01-01

As immunology continues to evolve, many educational methods have found difficulty in conveying the degree of complexity inherent in its basic principles. Today, the teaching-learning process in such areas has been improved with tools such as educational software. This article introduces "Virtual Immunology," a software program available…

A software technology evaluation program

NASA Technical Reports Server (NTRS)

Novaes-Card, David N.

1985-01-01

A set of quantitative approaches is presented for evaluating software development methods and tools. The basic idea is to generate a set of goals which are refined into quantifiable questions which specify metrics to be collected on the software development and maintenance process and product. These metrics can be used to characterize, evaluate, predict, and motivate. They can be used in an active as well as passive way by learning form analyzing the data and improving the methods and tools based upon what is learned from that analysis. Several examples were given representing each of the different approaches to evaluation. The cost of the approaches varied inversely with the level of confidence in the interpretation of the results.

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.

Teaching meta-analysis using MetaLight.

PubMed

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

2012-10-18

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

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

NASA Technical Reports Server (NTRS)

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

2005-01-01

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

HITCal: a software tool for analysis of video head impulse test responses.

PubMed

Rey-Martinez, Jorge; Batuecas-Caletrio, Angel; Matiño, Eusebi; Perez Fernandez, Nicolás

2015-09-01

The developed software (HITCal) may be a useful tool in the analysis and measurement of the saccadic video head impulse test (vHIT) responses and with the experience obtained during its use the authors suggest that HITCal is an excellent method for enhanced exploration of vHIT outputs. To develop a (software) method to analyze and explore the vHIT responses, mainly saccades. HITCal was written using a computational development program; the function to access a vHIT file was programmed; extended head impulse exploration and measurement tools were created and an automated saccade analysis was developed using an experimental algorithm. For pre-release HITCal laboratory tests, a database of head impulse tests (HITs) was created with the data collected retrospectively in three reference centers. This HITs database was evaluated by humans and was also computed with HITCal. The authors have successfully built HITCal and it has been released as open source software; the developed software was fully operative and all the proposed characteristics were incorporated in the released version. The automated saccades algorithm implemented in HITCal has good concordance with the assessment by human observers (Cohen's kappa coefficient = 0.7).

Multidisciplinary and Active/Collaborative Approaches in Teaching Requirements Engineering

ERIC Educational Resources Information Center

Rosca, Daniela

2005-01-01

The requirements engineering course is a core component of the curriculum for the Master's in Software Engineering programme, at Monmouth University (MU). It covers the process, methods and tools specific to this area, together with the corresponding software quality issues. The need to produce software engineers with strong teamwork and…

Quantitative fluorescence angiography for neurosurgical interventions.

PubMed

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

2013-06-01

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

Center for Efficient Exascale Discretizations Software Suite

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

Kolev, Tzanio; Dobrev, Veselin; Tomov, Vladimir

The CEED Software suite is a collection of generally applicable software tools focusing on the following computational motives: PDE discretizations on unstructured meshes, high-order finite element and spectral element methods and unstructured adaptive mesh refinement. All of this software is being developed as part of CEED, a co-design Center for Efficient Exascale Discretizations, within DOE's Exascale Computing Project (ECP) program.

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

PubMed Central

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

2013-01-01

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

AnClim and ProClimDB software for data quality control and homogenization of time series

NASA Astrophysics Data System (ADS)

Stepanek, Petr

2015-04-01

During the last decade, a software package consisting of AnClim, ProClimDB and LoadData for processing (mainly climatological) data has been created. This software offers a complex solution for processing of climatological time series, starting from loading the data from a central database (e.g. Oracle, software LoadData), through data duality control and homogenization to time series analysis, extreme value evaluations and RCM outputs verification and correction (ProClimDB and AnClim software). The detection of inhomogeneities is carried out on a monthly scale through the application of AnClim, or newly by R functions called from ProClimDB, while quality control, the preparation of reference series and the correction of found breaks is carried out by the ProClimDB software. The software combines many statistical tests, types of reference series and time scales (monthly, seasonal and annual, daily and sub-daily ones). These can be used to create an "ensemble" of solutions, which may be more reliable than any single method. AnClim software is suitable for educational purposes: e.g. for students getting acquainted with methods used in climatology. Built-in graphical tools and comparison of various statistical tests help in better understanding of a given method. ProClimDB is, on the contrary, tool aimed for processing of large climatological datasets. Recently, functions from R may be used within the software making it more efficient in data processing and capable of easy inclusion of new methods (when available under R). An example of usage is easy comparison of methods for correction of inhomogeneities in daily data (HOM of Paul Della-Marta, SPLIDHOM method of Olivier Mestre, DAP - own method, QM of Xiaolan Wang and others). The software is available together with further information on www.climahom.eu . Acknowledgement: this work was partially funded by the project "Building up a multidisciplinary scientific team focused on drought" No. CZ.1.07/2.3.00/20.0248.

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

PubMed

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

2017-11-01

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

Two New Tools for Glycopeptide Analysis Researchers: A Glycopeptide Decoy Generator and a Large Data Set of Assigned CID Spectra of Glycopeptides.

PubMed

Lakbub, Jude C; Su, Xiaomeng; Zhu, Zhikai; Patabandige, Milani W; Hua, David; Go, Eden P; Desaire, Heather

2017-08-04

The glycopeptide analysis field is tightly constrained by a lack of effective tools that translate mass spectrometry data into meaningful chemical information, and perhaps the most challenging aspect of building effective glycopeptide analysis software is designing an accurate scoring algorithm for MS/MS data. We provide the glycoproteomics community with two tools to address this challenge. The first tool, a curated set of 100 expert-assigned CID spectra of glycopeptides, contains a diverse set of spectra from a variety of glycan types; the second tool, Glycopeptide Decoy Generator, is a new software application that generates glycopeptide decoys de novo. We developed these tools so that emerging methods of assigning glycopeptides' CID spectra could be rigorously tested. Software developers or those interested in developing skills in expert (manual) analysis can use these tools to facilitate their work. We demonstrate the tools' utility in assessing the quality of one particular glycopeptide software package, GlycoPep Grader, which assigns glycopeptides to CID spectra. We first acquired the set of 100 expert assigned CID spectra; then, we used the Decoy Generator (described herein) to generate 20 decoys per target glycopeptide. The assigned spectra and decoys were used to test the accuracy of GlycoPep Grader's scoring algorithm; new strengths and weaknesses were identified in the algorithm using this approach. Both newly developed tools are freely available. The software can be downloaded at http://glycopro.chem.ku.edu/GPJ.jar.

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

"I Have a Love-Hate Relationship with ATLAS.ti"™: Integrating Qualitative Data Analysis Software into a Graduate Research Methods Course

ERIC Educational Resources Information Center

Paulus, Trena M.; Bennett, Ann M.

2017-01-01

While research on teaching qualitative methods in education has increased, few studies explore teaching qualitative data analysis software within graduate-level methods courses. During 2013, we required students in several such courses to use ATLAS.ti™ as a project management tool for their assignments. By supporting students' early experiences…

CASE tools and UML: state of the ART.

PubMed

Agarwal, S

2001-05-01

With increasing need for automated tools to assist complex systems development, software design methods are becoming popular. This article analyzes the state of art in computer-aided software engineering (CASE) tools and unified modeling language (UML), focusing on their evolution, merits, and industry usage. It identifies managerial issues for the tools' adoption and recommends an action plan to select and implement them. While CASE and UML offer inherent advantages like cheaper, shorter, and efficient development cycles, they suffer from poor user satisfaction. The critical success factors for their implementation include, among others, management and staff commitment, proper corporate infrastructure, and user training.

Navigating freely-available software tools for metabolomics analysis.

PubMed

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

2017-01-01

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

System and Software Reliability (C103)

NASA Technical Reports Server (NTRS)

Wallace, Dolores

2003-01-01

Within the last decade better reliability models (hardware. software, system) than those currently used have been theorized and developed but not implemented in practice. Previous research on software reliability has shown that while some existing software reliability models are practical, they are no accurate enough. New paradigms of development (e.g. OO) have appeared and associated reliability models have been proposed posed but not investigated. Hardware models have been extensively investigated but not integrated into a system framework. System reliability modeling is the weakest of the three. NASA engineers need better methods and tools to demonstrate that the products meet NASA requirements for reliability measurement. For the new models for the software component of the last decade, there is a great need to bring them into a form that they can be used on software intensive systems. The Statistical Modeling and Estimation of Reliability Functions for Systems (SMERFS'3) tool is an existing vehicle that may be used to incorporate these new modeling advances. Adapting some existing software reliability modeling changes to accommodate major changes in software development technology may also show substantial improvement in prediction accuracy. With some additional research, the next step is to identify and investigate system reliability. System reliability models could then be incorporated in a tool such as SMERFS'3. This tool with better models would greatly add value in assess in GSFC projects.

Evaluation of whole genome sequencing and software tools for drug susceptibility testing of Mycobacterium tuberculosis.

PubMed

van Beek, J; Haanperä, M; Smit, P W; Mentula, S; Soini, H

2018-04-11

Culture-based assays are currently the reference standard for drug susceptibility testing for Mycobacterium tuberculosis. They provide good sensitivity and specificity but are time consuming. The objective of this study was to evaluate whether whole genome sequencing (WGS), combined with software tools for data analysis, can replace routine culture-based assays for drug susceptibility testing of M. tuberculosis. M. tuberculosis cultures sent to the Finnish mycobacterial reference laboratory in 2014 (n = 211) were phenotypically tested by Mycobacteria Growth Indicator Tube (MGIT) for first-line drug susceptibilities. WGS was performed for all isolates using the Illumina MiSeq system, and data were analysed using five software tools (PhyResSE, Mykrobe Predictor, TB Profiler, TGS-TB and KvarQ). Diagnostic time and reagent costs were estimated for both methods. The sensitivity of the five software tools to predict any resistance among strains was almost identical, ranging from 74% to 80%, and specificity was more than 95% for all software tools except for TGS-TB. The sensitivity and specificity to predict resistance to individual drugs varied considerably among the software tools. Reagent costs for MGIT and WGS were €26 and €143 per isolate respectively. Turnaround time for MGIT was 19 days (range 10-50 days) for first-line drugs, and turnaround time for WGS was estimated to be 5 days (range 3-7 days). WGS could be used as a prescreening assay for drug susceptibility testing with confirmation of resistant strains by MGIT. The functionality and ease of use of the software tools need to be improved. Copyright © 2018 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Managers Handbook for Software Development

NASA Technical Reports Server (NTRS)

Agresti, W.; Mcgarry, F.; Card, D.; Page, J.; Church, V.; Werking, R.

1984-01-01

Methods and aids for the management of software development projects are presented. The recommendations are based on analyses and experiences with flight dynamics software development. The management aspects of organizing the project, producing a development plan, estimation costs, scheduling, staffing, preparing deliverable documents, using management tools, monitoring the project, conducting reviews, auditing, testing, and certifying are described.

Product assurance policies and procedures for flight dynamics software development

NASA Technical Reports Server (NTRS)

Perry, Sandra; Jordan, Leon; Decker, William; Page, Gerald; Mcgarry, Frank E.; Valett, Jon

1987-01-01

The product assurance policies and procedures necessary to support flight dynamics software development projects for Goddard Space Flight Center are presented. The quality assurance and configuration management methods and tools for each phase of the software development life cycles are described, from requirements analysis through acceptance testing; maintenance and operation are not addressed.

Propulsion Diagnostic Method Evaluation Strategy (ProDiMES) User's Guide

NASA Technical Reports Server (NTRS)

Simon, Donald L.

2010-01-01

This report is a User's Guide for the Propulsion Diagnostic Method Evaluation Strategy (ProDiMES). ProDiMES is a standard benchmarking problem and a set of evaluation metrics to enable the comparison of candidate aircraft engine gas path diagnostic methods. This Matlab (The Mathworks, Inc.) based software tool enables users to independently develop and evaluate diagnostic methods. Additionally, a set of blind test case data is also distributed as part of the software. This will enable the side-by-side comparison of diagnostic approaches developed by multiple users. The Users Guide describes the various components of ProDiMES, and provides instructions for the installation and operation of the tool.

Manager's handbook for software development, revision 1

NASA Technical Reports Server (NTRS)

1990-01-01

Methods and aids for the management of software development projects are presented. The recommendations are based on analyses and experiences of the Software Engineering Laboratory (SEL) with flight dynamics software development. The management aspects of the following subjects are described: organizing the project, producing a development plan, estimating costs, scheduling, staffing, preparing deliverable documents, using management tools, monitoring the project, conducting reviews, auditing, testing, and certifying.

Dependency visualization for complex system understanding

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

Smart, J. Allison Cory

1994-09-01

With the volume of software in production use dramatically increasing, the importance of software maintenance has become strikingly apparent. Techniques now sought and developed for reverse engineering and design extraction and recovery. At present, numerous commercial products and research tools exist which are capable of visualizing a variety of programming languages and software constructs. The list of new tools and services continues to grow rapidly. Although the scope of the existing commercial and academic product set is quite broad, these tools still share a common underlying problem. The ability of each tool to visually organize object representations is increasingly impairedmore » as the number of components and component dependencies within systems increases. Regardless of how objects are defined, complex ``spaghetti`` networks result in nearly all large system cases. While this problem is immediately apparent in modem systems analysis involving large software implementations, it is not new. As will be discussed in Chapter 2, related problems involving the theory of graphs were identified long ago. This important theoretical foundation provides a useful vehicle for representing and analyzing complex system structures. While the utility of directed graph based concepts in software tool design has been demonstrated in literature, these tools still lack the capabilities necessary for large system comprehension. This foundation must therefore be expanded with new organizational and visualization constructs necessary to meet this challenge. This dissertation addresses this need by constructing a conceptual model and a set of methods for interactively exploring, organizing, and understanding the structure of complex software systems.« less

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.

Specification Improvement Through Analysis of Proof Structure (SITAPS): High Assurance Software Development

DTIC Science & Technology

2016-02-01

proof in mathematics. For example, consider the proof of the Pythagorean Theorem illustrated at: http://www.cut-the-knot.org/ pythagoras / where 112...methods and tools have made significant progress in their ability to model software designs and prove correctness theorems about the systems modeled...assumption criticality” or “ theorem root set size” SITAPS detects potentially brittle verification cases. SITAPS provides tools and techniques that

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

PubMed

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

2014-09-01

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

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

PubMed

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

2017-10-01

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

Test-driven programming

NASA Astrophysics Data System (ADS)

Georgiev, Bozhidar; Georgieva, Adriana

2013-12-01

In this paper, are presented some possibilities concerning the implementation of a test-driven development as a programming method. Here is offered a different point of view for creation of advanced programming techniques (build tests before programming source with all necessary software tools and modules respectively). Therefore, this nontraditional approach for easier programmer's work through building tests at first is preferable way of software development. This approach allows comparatively simple programming (applied with different object-oriented programming languages as for example JAVA, XML, PYTHON etc.). It is predictable way to develop software tools and to provide help about creating better software that is also easier to maintain. Test-driven programming is able to replace more complicated casual paradigms, used by many programmers.

3D graphics hardware accelerator programming methods for real-time visualization systems

NASA Astrophysics Data System (ADS)

Souetov, Andrew E.

2001-02-01

The paper deals with new approaches in software design for creating real-time applications that use modern graphics acceleration hardware. The growing complexity of such type of software compels programmers to use different types of CASE systems in design and development process. The subject under discussion is integration of such systems in a development process, their effective use, and the combination of these new methods with the necessity to produce optimal codes. A method of simulation integration and modeling tools in real-time software development cycle is described.

3D graphics hardware accelerator programming methods for real-time visualization systems

NASA Astrophysics Data System (ADS)

Souetov, Andrew E.

2000-02-01

The paper deals with new approaches in software design for creating real-time applications that use modern graphics acceleration hardware. The growing complexity of such type of software compels programmers to use different types of CASE systems in design and development process. The subject under discussion is integration of such systems in a development process, their effective use, and the combination of these new methods with the necessity to produce optimal codes. A method of simulation integration and modeling tools in real-time software development cycle is described.

EPA's Benchmark Dose Modeling Software

EPA Science Inventory

The EPA developed the Benchmark Dose Software (BMDS) as a tool to help Agency risk assessors facilitate applying benchmark dose (BMD) method’s to EPA’s human health risk assessment (HHRA) documents. The application of BMD methods overcomes many well know limitations ...

Formal Assurance Certifiable Tooling Formal Assurance Certifiable Tooling Strategy Final Report

NASA Technical Reports Server (NTRS)

Bush, Eric; Oglesby, David; Bhatt, Devesh; Murugesan, Anitha; Engstrom, Eric; Mueller, Joe; Pelican, Michael

2017-01-01

This is the Final Report of a research project to investigate issues and provide guidance for the qualification of formal methods tools under the DO-330 qualification process. It consisted of three major subtasks spread over two years: 1) an assessment of theoretical soundness issues that may affect qualification for three categories of formal methods tools, 2) a case study simulating the DO-330 qualification of two actual tool sets, and 3) an investigation of risk mitigation strategies that might be applied to chains of such formal methods tools in order to increase confidence in their certification of airborne software.

Constructing Benchmark Databases and Protocols for Medical Image Analysis: Diabetic Retinopathy

PubMed Central

Kauppi, Tomi; Kämäräinen, Joni-Kristian; Kalesnykiene, Valentina; Sorri, Iiris; Uusitalo, Hannu; Kälviäinen, Heikki

2013-01-01

We address the performance evaluation practices for developing medical image analysis methods, in particular, how to establish and share databases of medical images with verified ground truth and solid evaluation protocols. Such databases support the development of better algorithms, execution of profound method comparisons, and, consequently, technology transfer from research laboratories to clinical practice. For this purpose, we propose a framework consisting of reusable methods and tools for the laborious task of constructing a benchmark database. We provide a software tool for medical image annotation helping to collect class label, spatial span, and expert's confidence on lesions and a method to appropriately combine the manual segmentations from multiple experts. The tool and all necessary functionality for method evaluation are provided as public software packages. As a case study, we utilized the framework and tools to establish the DiaRetDB1 V2.1 database for benchmarking diabetic retinopathy detection algorithms. The database contains a set of retinal images, ground truth based on information from multiple experts, and a baseline algorithm for the detection of retinopathy lesions. PMID:23956787

An overview of very high level software design methods

NASA Technical Reports Server (NTRS)

Asdjodi, Maryam; Hooper, James W.

1988-01-01

Very High Level design methods emphasize automatic transfer of requirements to formal design specifications, and/or may concentrate on automatic transformation of formal design specifications that include some semantic information of the system into machine executable form. Very high level design methods range from general domain independent methods to approaches implementable for specific applications or domains. Applying AI techniques, abstract programming methods, domain heuristics, software engineering tools, library-based programming and other methods different approaches for higher level software design are being developed. Though one finds that a given approach does not always fall exactly in any specific class, this paper provides a classification for very high level design methods including examples for each class. These methods are analyzed and compared based on their basic approaches, strengths and feasibility for future expansion toward automatic development of software systems.

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

PubMed

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

2013-06-15

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

A Virtual World of Visualization

NASA Technical Reports Server (NTRS)

1998-01-01

In 1990, Sterling Software, Inc., developed the Flow Analysis Software Toolkit (FAST) for NASA Ames on contract. FAST is a workstation based modular analysis and visualization tool. It is used to visualize and animate grids and grid oriented data, typically generated by finite difference, finite element and other analytical methods. FAST is now available through COSMIC, NASA's software storehouse.

An application generator for rapid prototyping of Ada real-time control software

NASA Technical Reports Server (NTRS)

Johnson, Jim; Biglari, Haik; Lehman, Larry

1990-01-01

The need to increase engineering productivity and decrease software life cycle costs in real-time system development establishes a motivation for a method of rapid prototyping. The design by iterative rapid prototyping technique is described. A tool which facilitates such a design methodology for the generation of embedded control software is described.

Myths and realities: Defining re-engineering for a large organization

NASA Technical Reports Server (NTRS)

Yin, Sandra; Mccreary, Julia

1992-01-01

This paper describes the background and results of three studies concerning software reverse engineering, re-engineering, and reuse (R3) hosted by the Internal Revenue Service in 1991 and 1992. The situation at the Internal Revenue--aging, piecemeal computer systems and outdated technology maintained by a large staff--is familiar to many institutions, especially among management information systems. The IRS is distinctive for the sheer magnitude and diversity of its problems; the country's tax records are processed using assembly language and COBOL and spread across tape and network DBMS files. How do we proceed with replacing legacy systems? The three software re-engineering studies looked at methods, CASE tool support, and performed a prototype project using re-engineering methods and tools. During the course of these projects, we discovered critical issues broader than the mechanical definitions of methods and tool technology.

Tools and Methods for Teaching Informatics at School: An Advanced Logo Course.

ERIC Educational Resources Information Center

Nikolov, Rumen

1992-01-01

Describes a course in educational informatics for preservice teachers and students in educational software development that emphasizes the use of LOGO, and summarizes course modules that cover tools and methods for teaching informatics, informatics curriculum design, introducing the basic notions of informatics, integrating informatics into the…

Experiences with a generator tool for building clinical application modules.

PubMed

Kuhn, K A; Lenz, R; Elstner, T; Siegele, H; Moll, R

2003-01-01

To elaborate main system characteristics and relevant deployment experiences for the health information system (HIS) Orbis/OpenMed, which is in widespread use in Germany, Austria, and Switzerland. In a deployment phase of 3 years in a 1.200 bed university hospital, where the system underwent significant improvements, the system's functionality and its software design have been analyzed in detail. We focus on an integrated CASE tool for generating embedded clinical applications and for incremental system evolution. We present a participatory and iterative software engineering process developed for efficient utilization of such a tool. The system's functionality is comparable to other commercial products' functionality; its components are embedded in a vendor-specific application framework, and standard interfaces are being used for connecting subsystems. The integrated generator tool is a remarkable feature; it became a key factor of our project. Tool generated applications are workflow enabled and embedded into the overall data base schema. Rapid prototyping and iterative refinement are supported, so application modules can be adapted to the users' work practice. We consider tools supporting an iterative and participatory software engineering process highly relevant for health information system architects. The potential of a system to continuously evolve and to be effectively adapted to changing needs may be more important than sophisticated but hard-coded HIS functionality. More work will focus on HIS software design and on software engineering. Methods and tools are needed for quick and robust adaptation of systems to health care processes and changing requirements.

Assessing ergonomic risks of software: Development of the SEAT.

PubMed

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

2017-03-01

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

The COLA Collision Avoidance Method

NASA Astrophysics Data System (ADS)

Assmann, K.; Berger, J.; Grothkopp, S.

2009-03-01

In the following we present a collision avoidance method named COLA. The method has been designed to predict collisions for Earth orbiting spacecraft on any orbits, including orbit changes, with other space-born objects. The point in time of a collision and the collision probability are determined. To guarantee effective processing the COLA method uses a modular design and is composed of several components which are either developed within this work or deduced from existing algorithms: A filtering module, the close approach determination, the collision detection and the collision probability calculation. A software tool which implements the COLA method has been verified using various test cases built from sample missions. This software has been implemented in the C++ programming language and serves as a universal collision detection tool at LSE Space Engineering & Operations AG.

A Comprehensive Software and Database Management System for Glomerular Filtration Rate Estimation by Radionuclide Plasma Sampling and Serum Creatinine Methods.

PubMed

Jha, Ashish Kumar

2015-01-01

Glomerular filtration rate (GFR) estimation by plasma sampling method is considered as the gold standard. However, this method is not widely used because the complex technique and cumbersome calculations coupled with the lack of availability of user-friendly software. The routinely used Serum Creatinine method (SrCrM) of GFR estimation also requires the use of online calculators which cannot be used without internet access. We have developed user-friendly software "GFR estimation software" which gives the options to estimate GFR by plasma sampling method as well as SrCrM. We have used Microsoft Windows(®) as operating system and Visual Basic 6.0 as the front end and Microsoft Access(®) as database tool to develop this software. We have used Russell's formula for GFR calculation by plasma sampling method. GFR calculations using serum creatinine have been done using MIRD, Cockcroft-Gault method, Schwartz method, and Counahan-Barratt methods. The developed software is performing mathematical calculations correctly and is user-friendly. This software also enables storage and easy retrieval of the raw data, patient's information and calculated GFR for further processing and comparison. This is user-friendly software to calculate the GFR by various plasma sampling method and blood parameter. This software is also a good system for storing the raw and processed data for future analysis.

CrossTalk. The Journal of Defense Software Engineering. Volume 13, Number 6, June 2000

DTIC Science & Technology

2000-06-01

Techniques for Efficiently Generating and Testing Software This paper presents a proven process that uses advanced tools to design, develop and test... optimal software. by Keith R. Wegner Large Software Systems—Back to Basics Development methods that work on small problems seem to not scale well to...Ability Requirements for Teamwork: Implications for Human Resource Management, Journal of Management, Vol. 20, No. 2, 1994. 11. Ferguson, Pat, Watts S

Designing Test Suites for Software Interactions Testing

DTIC Science & Technology

2004-01-01

the annual cost of insufficient software testing methods and tools in the United States is between 22.2 to 59.5 billion US dollars [13, 14]. This study...10 (2004), 1–29. [21] Cheng, C., Dumitrescu, A., and Schroeder , P. Generating small com- binatorial test suites to cover input-output relationships... Proceedings of the Conference on the Future of Software Engineering (May 2000), pp. 61 – 72. [51] Hartman, A. Software and hardware testing using

AOFlagger: RFI Software

NASA Astrophysics Data System (ADS)

Offringa, A. R.

2010-10-01

The RFI software presented here can automatically flag data and can be used to analyze the data in a measurement. The purpose of flagging is to mark samples that are affected by interfering sources such as radio stations, airplanes, electrical fences or other transmitting interferers. The tools in the package are meant for offline use. The software package contains a graphical interface ("rfigui") that can be used to visualize a measurement set and analyze mitigation techniques. It also contains a console flagger ("rficonsole") that can execute a script of mitigation functions without the overhead of a graphical environment. All tools were written in C++. The software has been tested extensively on low radio frequencies (150 MHz or lower) produced by the WSRT and LOFAR telescopes. LOFAR is the Low Frequency Array that is built in and around the Netherlands. Higher frequencies should work as well. Some of the methods implemented are the SumThreshold, the VarThreshold and the singular value decomposition (SVD) method. Included also are several surface fitting algorithms. The software is published under the GNU General Public License version 3.

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/.

Evaluation of an educational technology regarding clinical evaluation of preterm newborns.

PubMed

Fonseca, Luciana Mara Monti; Aredes, Natália Del'Angelo; Leite, Adriana Moraes; dos Santos, Claudia Benedita; de Lima, Regina Aparecida Garcia; Scochi, Carmen Gracinda Silvan

2013-02-01

To evaluate, from the students' point of view, educational software developed as a tool to help teachers and students in neonatal nursing. The study evaluates the contents and simulations addressed in the software. A total of 57 undergraduate nursing students affiliated with five Brazilian public colleges participated. The general assessment of the software was highly satisfactory: 82.4% of the sample characterized the software as quite effective as a teaching tool. Most components were assessed as good or very good. The participants' suggestions and comments are being considered in the improvement and adaptation of the new software version. The results show that the product is adequate for use in neonatal nursing courses and nursing training on the physical examination techniques and semiology of preterm newborns, falling within the pedagogical framework of active methods.

Oxygen octahedra picker: A software tool to extract quantitative information from STEM images.

PubMed

Wang, Yi; Salzberger, Ute; Sigle, Wilfried; Eren Suyolcu, Y; van Aken, Peter A

2016-09-01

In perovskite oxide based materials and hetero-structures there are often strong correlations between oxygen octahedral distortions and functionality. Thus, atomistic understanding of the octahedral distortion, which requires accurate measurements of atomic column positions, will greatly help to engineer their properties. Here, we report the development of a software tool to extract quantitative information of the lattice and of BO6 octahedral distortions from STEM images. Center-of-mass and 2D Gaussian fitting methods are implemented to locate positions of individual atom columns. The precision of atomic column distance measurements is evaluated on both simulated and experimental images. The application of the software tool is demonstrated using practical examples. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Recent development in software and automation tools for high-throughput discovery bioanalysis.

PubMed

Shou, Wilson Z; Zhang, Jun

2012-05-01

Bioanalysis with LC-MS/MS has been established as the method of choice for quantitative determination of drug candidates in biological matrices in drug discovery and development. The LC-MS/MS bioanalytical support for drug discovery, especially for early discovery, often requires high-throughput (HT) analysis of large numbers of samples (hundreds to thousands per day) generated from many structurally diverse compounds (tens to hundreds per day) with a very quick turnaround time, in order to provide important activity and liability data to move discovery projects forward. Another important consideration for discovery bioanalysis is its fit-for-purpose quality requirement depending on the particular experiments being conducted at this stage, and it is usually not as stringent as those required in bioanalysis supporting drug development. These aforementioned attributes of HT discovery bioanalysis made it an ideal candidate for using software and automation tools to eliminate manual steps, remove bottlenecks, improve efficiency and reduce turnaround time while maintaining adequate quality. In this article we will review various recent developments that facilitate automation of individual bioanalytical procedures, such as sample preparation, MS/MS method development, sample analysis and data review, as well as fully integrated software tools that manage the entire bioanalytical workflow in HT discovery bioanalysis. In addition, software tools supporting the emerging high-resolution accurate MS bioanalytical approach are also discussed.

CytoBayesJ: software tools for Bayesian analysis of cytogenetic radiation dosimetry data.

PubMed

Ainsbury, Elizabeth A; Vinnikov, Volodymyr; Puig, Pedro; Maznyk, Nataliya; Rothkamm, Kai; Lloyd, David C

2013-08-30

A number of authors have suggested that a Bayesian approach may be most appropriate for analysis of cytogenetic radiation dosimetry data. In the Bayesian framework, probability of an event is described in terms of previous expectations and uncertainty. Previously existing, or prior, information is used in combination with experimental results to infer probabilities or the likelihood that a hypothesis is true. It has been shown that the Bayesian approach increases both the accuracy and quality assurance of radiation dose estimates. New software entitled CytoBayesJ has been developed with the aim of bringing Bayesian analysis to cytogenetic biodosimetry laboratory practice. CytoBayesJ takes a number of Bayesian or 'Bayesian like' methods that have been proposed in the literature and presents them to the user in the form of simple user-friendly tools, including testing for the most appropriate model for distribution of chromosome aberrations and calculations of posterior probability distributions. The individual tools are described in detail and relevant examples of the use of the methods and the corresponding CytoBayesJ software tools are given. In this way, the suitability of the Bayesian approach to biological radiation dosimetry is highlighted and its wider application encouraged by providing a user-friendly software interface and manual in English and Russian. Copyright © 2013 Elsevier B.V. All rights reserved.

FAST Simulation Tool Containing Methods for Predicting the Dynamic Response of Wind Turbines

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

Jonkman, Jason

2015-08-12

FAST is a simulation tool (computer software) for modeling tlie dynamic response of horizontal-axis wind turbines. FAST employs a combined modal and multibody structural-dynamics formulation in the time domain.

PC graphics generation and management tool for real-time applications

NASA Technical Reports Server (NTRS)

Truong, Long V.

1992-01-01

A graphics tool was designed and developed for easy generation and management of personal computer graphics. It also provides methods and 'run-time' software for many common artificial intelligence (AI) or expert system (ES) applications.

Software-engineering challenges of building and deploying reusable problem solvers.

PubMed

O'Connor, Martin J; Nyulas, Csongor; Tu, Samson; Buckeridge, David L; Okhmatovskaia, Anna; Musen, Mark A

2009-11-01

Problem solving methods (PSMs) are software components that represent and encode reusable algorithms. They can be combined with representations of domain knowledge to produce intelligent application systems. A goal of research on PSMs is to provide principled methods and tools for composing and reusing algorithms in knowledge-based systems. The ultimate objective is to produce libraries of methods that can be easily adapted for use in these systems. Despite the intuitive appeal of PSMs as conceptual building blocks, in practice, these goals are largely unmet. There are no widely available tools for building applications using PSMs and no public libraries of PSMs available for reuse. This paper analyzes some of the reasons for the lack of widespread adoptions of PSM techniques and illustrate our analysis by describing our experiences developing a complex, high-throughput software system based on PSM principles. We conclude that many fundamental principles in PSM research are useful for building knowledge-based systems. In particular, the task-method decomposition process, which provides a means for structuring knowledge-based tasks, is a powerful abstraction for building systems of analytic methods. However, despite the power of PSMs in the conceptual modeling of knowledge-based systems, software engineering challenges have been seriously underestimated. The complexity of integrating control knowledge modeled by developers using PSMs with the domain knowledge that they model using ontologies creates a barrier to widespread use of PSM-based systems. Nevertheless, the surge of recent interest in ontologies has led to the production of comprehensive domain ontologies and of robust ontology-authoring tools. These developments present new opportunities to leverage the PSM approach.

Software-engineering challenges of building and deploying reusable problem solvers

PubMed Central

O’CONNOR, MARTIN J.; NYULAS, CSONGOR; TU, SAMSON; BUCKERIDGE, DAVID L.; OKHMATOVSKAIA, ANNA; MUSEN, MARK A.

2012-01-01

Problem solving methods (PSMs) are software components that represent and encode reusable algorithms. They can be combined with representations of domain knowledge to produce intelligent application systems. A goal of research on PSMs is to provide principled methods and tools for composing and reusing algorithms in knowledge-based systems. The ultimate objective is to produce libraries of methods that can be easily adapted for use in these systems. Despite the intuitive appeal of PSMs as conceptual building blocks, in practice, these goals are largely unmet. There are no widely available tools for building applications using PSMs and no public libraries of PSMs available for reuse. This paper analyzes some of the reasons for the lack of widespread adoptions of PSM techniques and illustrate our analysis by describing our experiences developing a complex, high-throughput software system based on PSM principles. We conclude that many fundamental principles in PSM research are useful for building knowledge-based systems. In particular, the task–method decomposition process, which provides a means for structuring knowledge-based tasks, is a powerful abstraction for building systems of analytic methods. However, despite the power of PSMs in the conceptual modeling of knowledge-based systems, software engineering challenges have been seriously underestimated. The complexity of integrating control knowledge modeled by developers using PSMs with the domain knowledge that they model using ontologies creates a barrier to widespread use of PSM-based systems. Nevertheless, the surge of recent interest in ontologies has led to the production of comprehensive domain ontologies and of robust ontology-authoring tools. These developments present new opportunities to leverage the PSM approach. PMID:23565031

Requirements UML Tool (RUT) Expanded for Extreme Programming (CI02)

NASA Technical Reports Server (NTRS)

McCoy, James R.

2003-01-01

A procedure for capturing and managing system requirements that incorporates XP user stories. Because costs associated with identifying problems in requirements increase dramatically over the lifecycle of a project, a method for identifying sources of software risks in user stories is urgently needed. This initiative aims to determine a set of guide-lines for user stories that will result in high-quality requirement. To further this initiative, a tool is needed to analyze user stories that can assess the quality of individual user stories, detect sources cf software risk's, produce software metrics, and identify areas in user stories that can be improved.

Developing tools for digital radar image data evaluation

NASA Technical Reports Server (NTRS)

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

1986-01-01

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

X-ray system simulation software tools for radiology and radiography education.

PubMed

Kengyelics, Stephen M; Treadgold, Laura A; Davies, Andrew G

2018-02-01

To develop x-ray simulation software tools to support delivery of radiological science education for a range of learning environments and audiences including individual study, lectures, and tutorials. Two software tools were developed; one simulated x-ray production for a simple two dimensional radiographic system geometry comprising an x-ray source, beam filter, test object and detector. The other simulated the acquisition and display of two dimensional radiographic images of complex three dimensional objects using a ray casting algorithm through three dimensional mesh objects. Both tools were intended to be simple to use, produce results accurate enough to be useful for educational purposes, and have an acceptable simulation time on modest computer hardware. The radiographic factors and acquisition geometry could be altered in both tools via their graphical user interfaces. A comparison of radiographic contrast measurements of the simulators to a real system was performed. The contrast output of the simulators had excellent agreement with measured results. The software simulators were deployed to 120 computers on campus. The software tools developed are easy-to-use, clearly demonstrate important x-ray physics and imaging principles, are accessible within a standard University setting and could be used to enhance the teaching of x-ray physics to undergraduate students. Current approaches to teaching x-ray physics in radiological science lack immediacy when linking theory with practice. This method of delivery allows students to engage with the subject in an experiential learning environment. Copyright © 2017. Published by Elsevier Ltd.

Assessment of ICount software, a precise and fast egg counting tool for the mosquito vector Aedes aegypti.

PubMed

Gaburro, Julie; Duchemin, Jean-Bernard; Paradkar, Prasad N; Nahavandi, Saeid; Bhatti, Asim

2016-11-18

Widespread in the tropics, the mosquito Aedes aegypti is an important vector of many viruses, posing a significant threat to human health. Vector monitoring often requires fecundity estimation by counting eggs laid by female mosquitoes. Traditionally, manual data analyses have been used but this requires a lot of effort and is the methods are prone to errors. An easy tool to assess the number of eggs laid would facilitate experimentation and vector control operations. This study introduces a built-in software called ICount allowing automatic egg counting of the mosquito vector, Aedes aegypti. ICount egg estimation compared to manual counting is statistically equivalent, making the software effective for automatic and semi-automatic data analysis. This technique also allows rapid analysis compared to manual methods. Finally, the software has been used to assess p-cresol oviposition choices under laboratory conditions in order to test the system with different egg densities. ICount is a powerful tool for fast and precise egg count analysis, freeing experimenters from manual data processing. Software access is free and its user-friendly interface allows easy use by non-experts. Its efficiency has been tested in our laboratory with oviposition dual choices of Aedes aegypti females. The next step will be the development of a mobile application, based on the ICount platform, for vector monitoring surveys in the field.

Reuse Metrics for Object Oriented Software

NASA Technical Reports Server (NTRS)

Bieman, James M.

1998-01-01

One way to increase the quality of software products and the productivity of software development is to reuse existing software components when building new software systems. In order to monitor improvements in reuse, the level of reuse must be measured. In this NASA supported project we (1) derived a suite of metrics which quantify reuse attributes for object oriented, object based, and procedural software, (2) designed prototype tools to take these measurements in Ada, C++, Java, and C software, (3) evaluated the reuse in available software, (4) analyzed the relationship between coupling, cohesion, inheritance, and reuse, (5) collected object oriented software systems for our empirical analyses, and (6) developed quantitative criteria and methods for restructuring software to improve reusability.

A SOFTWARE TOOL TO COMPARE MEASURED AND SIMULATED BUILDING ENERGY PERFORMANCE DATA

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

Maile, Tobias; Bazjanac, Vladimir; O'Donnell, James

2011-11-01

Building energy performance is often inadequate when compared to design goals. To link design goals to actual operation one can compare measured with simulated energy performance data. Our previously developed comparison approach is the Energy Performance Comparison Methodology (EPCM), which enables the identification of performance problems based on a comparison of measured and simulated performance data. In context of this method, we developed a software tool that provides graphing and data processing capabilities of the two performance data sets. The software tool called SEE IT (Stanford Energy Efficiency Information Tool) eliminates the need for manual generation of data plots andmore » data reformatting. SEE IT makes the generation of time series, scatter and carpet plots independent of the source of data (measured or simulated) and provides a valuable tool for comparing measurements with simulation results. SEE IT also allows assigning data points on a predefined building object hierarchy and supports different versions of simulated performance data. This paper briefly introduces the EPCM, describes the SEE IT tool and illustrates its use in the context of a building case study.« less

DataRocket: Interactive Visualisation of Data Structures

NASA Astrophysics Data System (ADS)

Parkes, Steve; Ramsay, Craig

2010-08-01

CodeRocket is a software engineering tool that provides cognitive support to the software engineer for reasoning about a method or procedure and for documenting the resulting code [1]. DataRocket is a software engineering tool designed to support visualisation and reasoning about program data structures. DataRocket is part of the CodeRocket family of software tools developed by Rapid Quality Systems [2] a spin-out company from the Space Technology Centre at the University of Dundee. CodeRocket and DataRocket integrate seamlessly with existing architectural design and coding tools and provide extensive documentation with little or no effort on behalf of the software engineer. Comprehensive, abstract, detailed design documentation is available early on in a project so that it can be used for design reviews with project managers and non expert stakeholders. Code and documentation remain fully synchronised even when changes are implemented in the code without reference to the existing documentation. At the end of a project the press of a button suffices to produce the detailed design document. Existing legacy code can be easily imported into CodeRocket and DataRocket to reverse engineer detailed design documentation making legacy code more manageable and adding substantially to its value. This paper introduces CodeRocket. It then explains the rationale for DataRocket and describes the key features of this new tool. Finally the major benefits of DataRocket for different stakeholders are considered.

Open source software integrated into data services of Japanese planetary explorations

NASA Astrophysics Data System (ADS)

Yamamoto, Y.; Ishihara, Y.; Otake, H.; Imai, K.; Masuda, K.

2015-12-01

Scientific data obtained by Japanese scientific satellites and lunar and planetary explorations are archived in DARTS (Data ARchives and Transmission System). DARTS provides the data with a simple method such as HTTP directory listing for long-term preservation while DARTS tries to provide rich web applications for ease of access with modern web technologies based on open source software. This presentation showcases availability of open source software through our services. KADIAS is a web-based application to search, analyze, and obtain scientific data measured by SELENE(Kaguya), a Japanese lunar orbiter. KADIAS uses OpenLayers to display maps distributed from Web Map Service (WMS). As a WMS server, open source software MapServer is adopted. KAGUYA 3D GIS (KAGUYA 3D Moon NAVI) provides a virtual globe for the SELENE's data. The main purpose of this application is public outreach. NASA World Wind Java SDK is used to develop. C3 (Cross-Cutting Comparisons) is a tool to compare data from various observations and simulations. It uses Highcharts to draw graphs on web browsers. Flow is a tool to simulate a Field-Of-View of an instrument onboard a spacecraft. This tool itself is open source software developed by JAXA/ISAS, and the license is BSD 3-Caluse License. SPICE Toolkit is essential to compile FLOW. SPICE Toolkit is also open source software developed by NASA/JPL, and the website distributes many spacecrafts' data. Nowadays, open source software is an indispensable tool to integrate DARTS services.

Translating expert system rules into Ada code with validation and verification

NASA Technical Reports Server (NTRS)

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

1991-01-01

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

P-TRAP: a Panicle TRAit Phenotyping tool.

PubMed

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

2013-08-29

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

P-TRAP: a Panicle Trait Phenotyping tool

PubMed Central

2013-01-01

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

Method for automation of tool preproduction

NASA Astrophysics Data System (ADS)

Rychkov, D. A.; Yanyushkin, A. S.; Lobanov, D. V.; Arkhipov, P. V.

2018-03-01

The primary objective of tool production is a creation or selection of such tool design which could make it possible to secure high process efficiency, tool availability as well as a quality of received surfaces with minimum means and resources spent on it. It takes much time of application people, being engaged in tool preparation, to make a correct selection of the appropriate tool among the set of variants. Program software has been developed to solve the problem, which helps to create, systematize and carry out a comparative analysis of tool design to identify the rational variant under given production conditions. The literature indicates that systematization and selection of the tool rational design has been carried out in accordance with the developed modeling technology and comparative design analysis. Software application makes it possible to reduce the period of design by 80....85% and obtain a significant annual saving.

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.

Impacts of software and its engineering on the carbon footprint of ICT

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

Kern, Eva, E-mail: e.kern@umwelt-campus.de; Dick, Markus, E-mail: sustainablesoftwareblog@gmail.com; Naumann, Stefan, E-mail: s.naumann@umwelt-campus.de

2015-04-15

The energy consumption of information and communication technology (ICT) is still increasing. Even though several solutions regarding the hardware side of Green IT exist, the software contribution to Green IT is not well investigated. The carbon footprint is one way to rate the environmental impacts of ICT. In order to get an impression of the induced CO{sub 2} emissions of software, we will present a calculation method for the carbon footprint of a software product over its life cycle. We also offer an approach on how to integrate some aspects of carbon footprint calculation into software development processes and discussmore » impacts and tools regarding this calculation method. We thus show the relevance of energy measurements and the attention to impacts on the carbon footprint by software within Green Software Engineering.« less

Evaluation of MTANNs for eliminating false-positive with different computer aided pulmonary nodules detection software.

PubMed

Shi, Zhenghao; Ma, Jiejue; Feng, Yaning; He, Lifeng; Suzuki, Kenji

2015-11-01

MTANN (Massive Training Artificial Neural Network) is a promising tool, which applied to eliminate false-positive for thoracic CT in recent years. In order to evaluate whether this method is feasible to eliminate false-positive of different CAD schemes, especially, when it is applied to commercial CAD software, this paper evaluate the performance of the method for eliminating false-positives produced by three different versions of commercial CAD software for lung nodules detection in chest radiographs. Experimental results demonstrate that the approach is useful in reducing FPs for different computer aided lung nodules detection software in chest radiographs.

Free and Open Source Software for Geospatial in the field of planetary science

NASA Astrophysics Data System (ADS)

Frigeri, A.

2012-12-01

Information technology applied to geospatial analyses has spread quickly in the last ten years. The availability of OpenData and data from collaborative mapping projects increased the interest on tools, procedures and methods to handle spatially-related information. Free Open Source Software projects devoted to geospatial data handling are gaining a good success as the use of interoperable formats and protocols allow the user to choose what pipeline of tools and libraries is needed to solve a particular task, adapting the software scene to his specific problem. In particular, the Free Open Source model of development mimics the scientific method very well, and researchers should be naturally encouraged to take part to the development process of these software projects, as this represent a very agile way to interact among several institutions. When it comes to planetary sciences, geospatial Free Open Source Software is gaining a key role in projects that commonly involve different subjects in an international scenario. Very popular software suites for processing scientific mission data (for example, ISIS) and for navigation/planning (SPICE) are being distributed along with the source code and the interaction between user and developer is often very strict, creating a continuum between these two figures. A very widely spread library for handling geospatial data (GDAL) has started to support planetary data from the Planetary Data System, and recent contributions enabled the support to other popular data formats used in planetary science, as the Vicar one. The use of Geographic Information System in planetary science is now diffused, and Free Open Source GIS, open GIS formats and network protocols allow to extend existing tools and methods developed to solve Earth based problems, also to the case of the study of solar system bodies. A day in the working life of a researcher using Free Open Source Software for geospatial will be presented, as well as benefits and solutions to possible detriments coming from the effort required by using, supporting and contributing.

Online survey software as a data collection tool for medical education: A case study on lesson plan assessment.

PubMed

Kimiafar, Khalil; Sarbaz, Masoumeh; Sheikhtaheri, Abbas

2016-01-01

Background: There are no general strategies or tools to evaluate daily lesson plans; however, assessments conducted using traditional methods usually include course plans. This study aimed to evaluate the strengths and weaknesses of online survey software in collecting data on education in medical fields and the application of such softwares to evaluate students' views and modification of lesson plans. Methods: After investigating the available online survey software, esurveypro was selected for assessing daily lesson plans. After using the software for one semester, a questionnaire was prepared to assess the advantages and disadvantages of this method and students' views in a cross-sectional study. Results: The majority of the students (51.7%) rated the evaluation of classes per session (lesson plans) using the online survey as useful or very useful. About 51% (n=36) of the students considered this method effective in improving the management of each session, 67.1% (n=47) considered it effective in improving the management of sessions for the next semester, and 51.4% (n=36) said it had a high impact on improving the educational content of subsequent sessions. Finally, 61.4% (n=43) students expressed high and very high levels of satisfaction with using an online survey at each session. Conclusion: The use of online surveys may be appropriate to improve lesson plans and educational planning at different levels. This method can be used for other evaluations and for assessing people's opinions at different levels of an educational system.

Community-driven computational biology with Debian Linux.

PubMed

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

2010-12-21

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

Teaching structure: student use of software tools for understanding macromolecular structure in an undergraduate biochemistry course.

PubMed

Jaswal, Sheila S; O'Hara, Patricia B; Williamson, Patrick L; Springer, Amy L

2013-01-01

Because understanding the structure of biological macromolecules is critical to understanding their function, students of biochemistry should become familiar not only with viewing, but also with generating and manipulating structural representations. We report a strategy from a one-semester undergraduate biochemistry course to integrate use of structural representation tools into both laboratory and homework activities. First, early in the course we introduce the use of readily available open-source software for visualizing protein structure, coincident with modules on amino acid and peptide bond properties. Second, we use these same software tools in lectures and incorporate images and other structure representations in homework tasks. Third, we require a capstone project in which teams of students examine a protein-nucleic acid complex and then use the software tools to illustrate for their classmates the salient features of the structure, relating how the structure helps explain biological function. To ensure engagement with a range of software and database features, we generated a detailed template file that can be used to explore any structure, and that guides students through specific applications of many of the software tools. In presentations, students demonstrate that they are successfully interpreting structural information, and using representations to illustrate particular points relevant to function. Thus, over the semester students integrate information about structural features of biological macromolecules into the larger discussion of the chemical basis of function. Together these assignments provide an accessible introduction to structural representation tools, allowing students to add these methods to their biochemical toolboxes early in their scientific development. © 2013 by The International Union of Biochemistry and Molecular Biology.

GSC configuration management plan

NASA Technical Reports Server (NTRS)

Withers, B. Edward

1990-01-01

The tools and methods used for the configuration management of the artifacts (including software and documentation) associated with the Guidance and Control Software (GCS) project are described. The GCS project is part of a software error studies research program. Three implementations of GCS are being produced in order to study the fundamental characteristics of the software failure process. The Code Management System (CMS) is used to track and retrieve versions of the documentation and software. Application of the CMS for this project is described and the numbering scheme is delineated for the versions of the project artifacts.

Simulink/PARS Integration Support

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

Vacaliuc, B.; Nakhaee, N.

2013-12-18

The state of the art for signal processor hardware has far out-paced the development tools for placing applications on that hardware. In addition, signal processors are available in a variety of architectures, each uniquely capable of handling specific types of signal processing efficiently. With these processors becoming smaller and demanding less power, it has become possible to group multiple processors, a heterogeneous set of processors, into single systems. Different portions of the desired problem set can be assigned to different processor types as appropriate. As software development tools do not keep pace with these processors, especially when multiple processors ofmore » different types are used, a method is needed to enable software code portability among multiple processors and multiple types of processors along with their respective software environments. Sundance DSP, Inc. has developed a software toolkit called “PARS”, whose objective is to provide a framework that uses suites of tools provided by different vendors, along with modeling tools and a real time operating system, to build an application that spans different processor types. The software language used to express the behavior of the system is a very high level modeling language, “Simulink”, a MathWorks product. ORNL has used this toolkit to effectively implement several deliverables. This CRADA describes this collaboration between ORNL and Sundance DSP, Inc.« less

Technology, Pedagogy, and Epistemology: Opportunities and Challenges of Using Computer Modeling and Simulation Tools in Elementary Science Methods

ERIC Educational Resources Information Center

Schwarz, Christina V.; Meyer, Jason; Sharma, Ajay

2007-01-01

This study infused computer modeling and simulation tools in a 1-semester undergraduate elementary science methods course to advance preservice teachers' understandings of computer software use in science teaching and to help them learn important aspects of pedagogy and epistemology. Preservice teachers used computer modeling and simulation tools…

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.

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...

Virtual Observatory and Colitec Software: Modules, Features, Methods

NASA Astrophysics Data System (ADS)

Pohorelov, A. V.; Khlamov, S. V.; Savanevych, V. E.; Briukhovetskyi, A. B.; Vlasenko, V. P.

In this article we described complex processing system created by the CoLiTec project. This system includes features, user-friendly tools for processing control, results reviewing, integration with online catalogs and a lot of different computational modules that are based on the developed methods. Some of them are described in the article.The main directions of the CoLiTec software development are the Virtual Observatory, software for automated asteroids and comets detection and software for brightness equalization.The CoLiTec software is widely used in a number of observatories in the CIS. It has been used in about 700 000 observations, during which 1560 asteroids, including 5 NEO, 21 Trojan asteroids of Jupiter, 1 Centaur and four comets were discovered.

Tools for Embedded Computing Systems Software

NASA Technical Reports Server (NTRS)

1978-01-01

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

An experience of qualified preventive screening: shiraz smart screening software.

PubMed

Islami Parkoohi, Parisa; Zare, Hashem; Abdollahifard, Gholamreza

2015-01-01

Computerized preventive screening software is a cost effective intervention tool to address non-communicable chronic diseases. Shiraz Smart Screening Software (SSSS) was developed as an innovative tool for qualified screening. It allows simultaneous smart screening of several high-burden chronic diseases and supports reminder notification functionality. The extent in which SSSS affects screening quality is also described. Following software development, preventive screening and annual health examinations of 261 school staff (Medical School of Shiraz, Iran) was carried out in a software-assisted manner. To evaluate the quality of the software-assisted screening, we used quasi-experimental study design and determined coverage, irregular attendance and inappropriateness proportions in relation with the manual and software-assisted screening as well as the corresponding number of requested tests. In manual screening method, 27% of employees were covered (with 94% irregular attendance) while by software-assisted screening, the coverage proportion was 79% (attendance status will clear after the specified time). The frequency of inappropriate screening test requests, before the software implementation, was 41.37% for fasting plasma glucose, 41.37% for lipid profile, 0.84% for occult blood, 0.19% for flexible sigmoidoscopy/colonoscopy, 35.29% for Pap smear, 19.20% for mammography and 11.2% for prostate specific antigen. All of the above were corrected by the software application. In total, 366 manual screening and 334 software-assisted screening tests were requested. SSSS is an innovative tool to improve the quality of preventive screening plans in terms of increased screening coverage, reduction in inappropriateness and the total number of requested tests.

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

USGS Publications Warehouse

Mueller, David S.

2013-01-01

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

Index of Workplace & Adult Basic Skills Software.

ERIC Educational Resources Information Center

Askov, Eunice N.; Clark, Cindy Jo

This index of workplace and adult basic skills computer software includes 108 listings. Each listing is described according to the following classifications: (1) teacher/tutor tools (customizable or mini-authoring systems); (2) assessment and skills; (3) content; (4) instruction method; (5) system requirements; and (6) name, address, and phone…

Software Safety Risk in Legacy Safety-Critical Computer Systems

NASA Technical Reports Server (NTRS)

Hill, Janice; Baggs, Rhoda

2007-01-01

Safety-critical computer systems must be engineered to meet system and software safety requirements. For legacy safety-critical computer systems, software safety requirements may not have been formally specified during development. When process-oriented software safety requirements are levied on a legacy system after the fact, where software development artifacts don't exist or are incomplete, the question becomes 'how can this be done?' The risks associated with only meeting certain software safety requirements in a legacy safety-critical computer system must be addressed should such systems be selected as candidates for reuse. This paper proposes a method for ascertaining formally, a software safety risk assessment, that provides measurements for software safety for legacy systems which may or may not have a suite of software engineering documentation that is now normally required. It relies upon the NASA Software Safety Standard, risk assessment methods based upon the Taxonomy-Based Questionnaire, and the application of reverse engineering CASE tools to produce original design documents for legacy systems.

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

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

Ditzler, Gregory; Morrison, J. Calvin; Lan, Yemin

Background: Some of the current software tools for comparative metagenomics provide ecologists with the ability to investigate and explore bacterial communities using α– & β–diversity. Feature subset selection – a sub-field of machine learning – can also provide a unique insight into the differences between metagenomic or 16S phenotypes. In particular, feature subset selection methods can obtain the operational taxonomic units (OTUs), or functional features, that have a high-level of influence on the condition being studied. For example, in a previous study we have used information-theoretic feature selection to understand the differences between protein family abundances that best discriminate betweenmore » age groups in the human gut microbiome. Results: We have developed a new Python command line tool, which is compatible with the widely adopted BIOM format, for microbial ecologists that implements information-theoretic subset selection methods for biological data formats. We demonstrate the software tools capabilities on publicly available datasets. Conclusions: We have made the software implementation of Fizzy available to the public under the GNU GPL license. The standalone implementation can be found at http://github.com/EESI/Fizzy.« less

Fizzy: feature subset selection for metagenomics.

PubMed

Ditzler, Gregory; Morrison, J Calvin; Lan, Yemin; Rosen, Gail L

2015-11-04

Some of the current software tools for comparative metagenomics provide ecologists with the ability to investigate and explore bacterial communities using α- & β-diversity. Feature subset selection--a sub-field of machine learning--can also provide a unique insight into the differences between metagenomic or 16S phenotypes. In particular, feature subset selection methods can obtain the operational taxonomic units (OTUs), or functional features, that have a high-level of influence on the condition being studied. For example, in a previous study we have used information-theoretic feature selection to understand the differences between protein family abundances that best discriminate between age groups in the human gut microbiome. We have developed a new Python command line tool, which is compatible with the widely adopted BIOM format, for microbial ecologists that implements information-theoretic subset selection methods for biological data formats. We demonstrate the software tools capabilities on publicly available datasets. We have made the software implementation of Fizzy available to the public under the GNU GPL license. The standalone implementation can be found at http://github.com/EESI/Fizzy.

Fizzy. Feature subset selection for metagenomics

DOE PAGES

Ditzler, Gregory; Morrison, J. Calvin; Lan, Yemin; ...

2015-11-04

Background: Some of the current software tools for comparative metagenomics provide ecologists with the ability to investigate and explore bacterial communities using α– & β–diversity. Feature subset selection – a sub-field of machine learning – can also provide a unique insight into the differences between metagenomic or 16S phenotypes. In particular, feature subset selection methods can obtain the operational taxonomic units (OTUs), or functional features, that have a high-level of influence on the condition being studied. For example, in a previous study we have used information-theoretic feature selection to understand the differences between protein family abundances that best discriminate betweenmore » age groups in the human gut microbiome. Results: We have developed a new Python command line tool, which is compatible with the widely adopted BIOM format, for microbial ecologists that implements information-theoretic subset selection methods for biological data formats. We demonstrate the software tools capabilities on publicly available datasets. Conclusions: We have made the software implementation of Fizzy available to the public under the GNU GPL license. The standalone implementation can be found at http://github.com/EESI/Fizzy.« less

Reengineering legacy software to object-oriented systems

NASA Technical Reports Server (NTRS)

Pitman, C.; Braley, D.; Fridge, E.; Plumb, A.; Izygon, M.; Mears, B.

1994-01-01

NASA has a legacy of complex software systems that are becoming increasingly expensive to maintain. Reengineering is one approach to modemizing these systems. Object-oriented technology, other modem software engineering principles, and automated tools can be used to reengineer the systems and will help to keep maintenance costs of the modemized systems down. The Software Technology Branch at the NASA/Johnson Space Center has been developing and testing reengineering methods and tools for several years. The Software Technology Branch is currently providing training and consulting support to several large reengineering projects at JSC, including the Reusable Objects Software Environment (ROSE) project, which is reengineering the flight analysis and design system (over 2 million lines of FORTRAN code) into object-oriented C++. Many important lessons have been learned during the past years; one of these is that the design must never be allowed to diverge from the code during maintenance and enhancement. Future work on open, integrated environments to support reengineering is being actively planned.

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

Science.gov Websites

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

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

PubMed

Cavaliere, Roberto

2015-12-01

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

OsiriX software as a preoperative planning tool in cranial neurosurgery: A step-by-step guide for neurosurgical residents

PubMed Central

Spiriev, Toma; Nakov, Vladimir; Laleva, Lili; Tzekov, Christo

2017-01-01

Background: OsiriX (Pixmeo, Switzerland) is an open-source Digital Imaging and Communications in Medicine (DICOM) viewer that is gaining more and more attention in the neurosurgical community because of its user-friendly interface, powerful three-dimensional (3D) volumetric rendering capabilities, and various options for data integration. This paper presents in detail the use of OsiriX software as a preoperative planning tool in cranial neurosurgery. Methods: In January 2013, OsiriX software was introduced into our clinical practice as a preoperative planning tool. Its capabilities are being evaluated on an ongoing basis in routine elective cranial cases. Results: The program has proven to be highly effective at volumetrically representing data from radiological examinations in 3D. Among its benefits in preoperative planning are simulating the position and exact location of the lesion in 3D, tailoring the skin incision and craniotomy bone flap, enhancing the representation of normal and pathological anatomy, and aiding in planning the reconstruction of the affected area. Conclusion: OsiriX is a useful tool for preoperative planning and visualization in neurosurgery. The software greatly facilitates the surgeon's understanding of the relationship between normal and pathological anatomy and can be used as a teaching tool. PMID:29119039

Software Estimation: Developing an Accurate, Reliable Method

DTIC Science & Technology

2011-08-01

Lake, CA ,93555- 6110 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10. SPONSOR/MONITOR’S ACRONYM(S...Activity, the systems engineering team is responsible for system and software requirements. 2 . Process Dashboard is a software planning and tracking tool... CA 93555- 6110 760-939-6989 Brad Hodgins is an interim TSP Mentor Coach, SEI-Authorized TSP Coach, SEI-Certified PSP/TSP Instructor, and SEI

The software-cycle model for re-engineering and reuse

NASA Technical Reports Server (NTRS)

Bailey, John W.; Basili, Victor R.

1992-01-01

This paper reports on the progress of a study which will contribute to our ability to perform high-level, component-based programming by describing means to obtain useful components, methods for the configuration and integration of those components, and an underlying economic model of the costs and benefits associated with this approach to reuse. One goal of the study is to develop and demonstrate methods to recover reusable components from domain-specific software through a combination of tools, to perform the identification, extraction, and re-engineering of components, and domain experts, to direct the applications of those tools. A second goal of the study is to enable the reuse of those components by identifying techniques for configuring and recombining the re-engineered software. This component-recovery or software-cycle model addresses not only the selection and re-engineering of components, but also their recombination into new programs. Once a model of reuse activities has been developed, the quantification of the costs and benefits of various reuse options will enable the development of an adaptable economic model of reuse, which is the principal goal of the overall study. This paper reports on the conception of the software-cycle model and on several supporting techniques of software recovery, measurement, and reuse which will lead to the development of the desired economic model.

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.

Towards early software reliability prediction for computer forensic tools (case study).

PubMed

Abu Talib, Manar

2016-01-01

Versatility, flexibility and robustness are essential requirements for software forensic tools. Researchers and practitioners need to put more effort into assessing this type of tool. A Markov model is a robust means for analyzing and anticipating the functioning of an advanced component based system. It is used, for instance, to analyze the reliability of the state machines of real time reactive systems. This research extends the architecture-based software reliability prediction model for computer forensic tools, which is based on Markov chains and COSMIC-FFP. Basically, every part of the computer forensic tool is linked to a discrete time Markov chain. If this can be done, then a probabilistic analysis by Markov chains can be performed to analyze the reliability of the components and of the whole tool. The purposes of the proposed reliability assessment method are to evaluate the tool's reliability in the early phases of its development, to improve the reliability assessment process for large computer forensic tools over time, and to compare alternative tool designs. The reliability analysis can assist designers in choosing the most reliable topology for the components, which can maximize the reliability of the tool and meet the expected reliability level specified by the end-user. The approach of assessing component-based tool reliability in the COSMIC-FFP context is illustrated with the Forensic Toolkit Imager case study.

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.

Decision Analysis Tools for Volcano Observatories

NASA Astrophysics Data System (ADS)

Hincks, T. H.; Aspinall, W.; Woo, G.

2005-12-01

Staff at volcano observatories are predominantly engaged in scientific activities related to volcano monitoring and instrumentation, data acquisition and analysis. Accordingly, the academic education and professional training of observatory staff tend to focus on these scientific functions. From time to time, however, staff may be called upon to provide decision support to government officials responsible for civil protection. Recognizing that Earth scientists may have limited technical familiarity with formal decision analysis methods, specialist software tools that assist decision support in a crisis should be welcome. A review is given of two software tools that have been under development recently. The first is for probabilistic risk assessment of human and economic loss from volcanic eruptions, and is of practical use in short and medium-term risk-informed planning of exclusion zones, post-disaster response, etc. A multiple branch event-tree architecture for the software, together with a formalism for ascribing probabilities to branches, have been developed within the context of the European Community EXPLORIS project. The second software tool utilizes the principles of the Bayesian Belief Network (BBN) for evidence-based assessment of volcanic state and probabilistic threat evaluation. This is of practical application in short-term volcano hazard forecasting and real-time crisis management, including the difficult challenge of deciding when an eruption is over. An open-source BBN library is the software foundation for this tool, which is capable of combining synoptically different strands of observational data from diverse monitoring sources. A conceptual vision is presented of the practical deployment of these decision analysis tools in a future volcano observatory environment. Summary retrospective analyses are given of previous volcanic crises to illustrate the hazard and risk insights gained from use of these tools.

A new optimization tool path planning for 3-axis end milling of free-form surfaces based on efficient machining intervals

NASA Astrophysics Data System (ADS)

Vu, Duy-Duc; Monies, Frédéric; Rubio, Walter

2018-05-01

A large number of studies, based on 3-axis end milling of free-form surfaces, seek to optimize tool path planning. Approaches try to optimize the machining time by reducing the total tool path length while respecting the criterion of the maximum scallop height. Theoretically, the tool path trajectories that remove the most material follow the directions in which the machined width is the largest. The free-form surface is often considered as a single machining area. Therefore, the optimization on the entire surface is limited. Indeed, it is difficult to define tool trajectories with optimal feed directions which generate largest machined widths. Another limiting point of previous approaches for effectively reduce machining time is the inadequate choice of the tool. Researchers use generally a spherical tool on the entire surface. However, the gains proposed by these different methods developed with these tools lead to relatively small time savings. Therefore, this study proposes a new method, using toroidal milling tools, for generating toolpaths in different regions on the machining surface. The surface is divided into several regions based on machining intervals. These intervals ensure that the effective radius of the tool, at each cutter-contact points on the surface, is always greater than the radius of the tool in an optimized feed direction. A parallel plane strategy is then used on the sub-surfaces with an optimal specific feed direction for each sub-surface. This method allows one to mill the entire surface with efficiency greater than with the use of a spherical tool. The proposed method is calculated and modeled using Maple software to find optimal regions and feed directions in each region. This new method is tested on a free-form surface. A comparison is made with a spherical cutter to show the significant gains obtained with a toroidal milling cutter. Comparisons with CAM software and experimental validations are also done. The results show the efficiency of the method.

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

NASA Technical Reports Server (NTRS)

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

1985-01-01

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

Debugging and Performance Analysis Software Tools for Peregrine System |

Science.gov Websites

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

Morphogenic designer--an efficient tool to digitally design tooth forms.

PubMed

Hajtó, J; Marinescu, C; Silva, N R F A

2014-01-01

Different digital software tools are available today for the purpose of designing anatomically correct anterior and posterior restorations. The current concepts present weaknesses, which can be potentially addressed by more advanced modeling tools, such as the ones already available in professional CAD (Computer Aided Design) graphical software. This study describes the morphogenic designer (MGD) as an efficient and easy method for digitally designing tooth forms for the anterior and posterior dentition. Anterior and posterior tooth forms were selected from a collection of digitalized natural teeth and subjectively assessed as "average". The models in the form of STL files were filtered, cleaned, idealized, and re-meshed to match the specifications of the software used. The shapes were then imported as wavefront ".obj" model into Modo 701, software built for modeling, texturing, visualization, and animation. In order to create a parametric design system, intentional interactive deformations were performed on the average tooth shapes and then further defined as morph targets. By combining various such parameters, several tooth shapes were formed virtually and their images presented. MGD proved to be a versatile and powerful tool for the purpose of esthetic and functional digital crown designs.

Simplified formulae for the estimation of offshore wind turbines clutter on marine radars.

PubMed

Grande, Olatz; Cañizo, Josune; Angulo, Itziar; Jenn, David; Danoon, Laith R; Guerra, David; de la Vega, David

2014-01-01

The potential impact that offshore wind farms may cause on nearby marine radars should be considered before the wind farm is installed. Strong radar echoes from the turbines may degrade radars' detection capability in the area around the wind farm. Although conventional computational methods provide accurate results of scattering by wind turbines, they are not directly implementable in software tools that can be used to conduct the impact studies. This paper proposes a simple model to assess the clutter that wind turbines may generate on marine radars. This method can be easily implemented in the system modeling software tools for the impact analysis of a wind farm in a real scenario.

Simplified Formulae for the Estimation of Offshore Wind Turbines Clutter on Marine Radars

PubMed Central

Grande, Olatz; Cañizo, Josune; Jenn, David; Danoon, Laith R.; Guerra, David

2014-01-01

The potential impact that offshore wind farms may cause on nearby marine radars should be considered before the wind farm is installed. Strong radar echoes from the turbines may degrade radars' detection capability in the area around the wind farm. Although conventional computational methods provide accurate results of scattering by wind turbines, they are not directly implementable in software tools that can be used to conduct the impact studies. This paper proposes a simple model to assess the clutter that wind turbines may generate on marine radars. This method can be easily implemented in the system modeling software tools for the impact analysis of a wind farm in a real scenario. PMID:24782682

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.

Multi-version software reliability through fault-avoidance and fault-tolerance

NASA Technical Reports Server (NTRS)

Vouk, Mladen A.; Mcallister, David F.

1989-01-01

A number of experimental and theoretical issues associated with the practical use of multi-version software to provide run-time tolerance to software faults were investigated. A specialized tool was developed and evaluated for measuring testing coverage for a variety of metrics. The tool was used to collect information on the relationships between software faults and coverage provided by the testing process as measured by different metrics (including data flow metrics). Considerable correlation was found between coverage provided by some higher metrics and the elimination of faults in the code. Back-to-back testing was continued as an efficient mechanism for removal of un-correlated faults, and common-cause faults of variable span. Software reliability estimation methods was also continued based on non-random sampling, and the relationship between software reliability and code coverage provided through testing. New fault tolerance models were formulated. Simulation studies of the Acceptance Voting and Multi-stage Voting algorithms were finished and it was found that these two schemes for software fault tolerance are superior in many respects to some commonly used schemes. Particularly encouraging are the safety properties of the Acceptance testing scheme.

Knickpoint finder: A software tool that improves neotectonic analysis

NASA Astrophysics Data System (ADS)

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

2015-03-01

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

User’s Guide for T.E.S.T. (version 4.2) (Toxicity Estimation Software Tool) A Program to Estimate Toxicity from Molecular Structure

EPA Science Inventory

The user's guide describes the methods used by TEST to predict toxicity and physical properties (including the new mode of action based method used to predict acute aquatic toxicity). It describes all of the experimental data sets included in the tool. It gives the prediction res...

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.

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.

Logic flowgraph methodology - A tool for modeling embedded systems

NASA Technical Reports Server (NTRS)

Muthukumar, C. T.; Guarro, S. B.; Apostolakis, G. E.

1991-01-01

The logic flowgraph methodology (LFM), a method for modeling hardware in terms of its process parameters, has been extended to form an analytical tool for the analysis of integrated (hardware/software) embedded systems. In the software part of a given embedded system model, timing and the control flow among different software components are modeled by augmenting LFM with modified Petrinet structures. The objective of the use of such an augmented LFM model is to uncover possible errors and the potential for unanticipated software/hardware interactions. This is done by backtracking through the augmented LFM mode according to established procedures which allow the semiautomated construction of fault trees for any chosen state of the embedded system (top event). These fault trees, in turn, produce the possible combinations of lower-level states (events) that may lead to the top event.

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

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

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

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

Development of a comprehensive software engineering environment

NASA Technical Reports Server (NTRS)

Hartrum, Thomas C.; Lamont, Gary B.

1987-01-01

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

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

PubMed

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

2009-12-01

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

Developing Teaching Material Software Assisted for Numerical Methods

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

Validation of highly reliable, real-time knowledge-based systems

NASA Technical Reports Server (NTRS)

Johnson, Sally C.

1988-01-01

Knowledge-based systems have the potential to greatly increase the capabilities of future aircraft and spacecraft and to significantly reduce support manpower needed for the space station and other space missions. However, a credible validation methodology must be developed before knowledge-based systems can be used for life- or mission-critical applications. Experience with conventional software has shown that the use of good software engineering techniques and static analysis tools can greatly reduce the time needed for testing and simulation of a system. Since exhaustive testing is infeasible, reliability must be built into the software during the design and implementation phases. Unfortunately, many of the software engineering techniques and tools used for conventional software are of little use in the development of knowledge-based systems. Therefore, research at Langley is focused on developing a set of guidelines, methods, and prototype validation tools for building highly reliable, knowledge-based systems. The use of a comprehensive methodology for building highly reliable, knowledge-based systems should significantly decrease the time needed for testing and simulation. A proven record of delivering reliable systems at the beginning of the highly visible testing and simulation phases is crucial to the acceptance of knowledge-based systems in critical applications.

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.

Examining the Effect of the Die Angle on Tool Load and Wear in the Extrusion Process

NASA Astrophysics Data System (ADS)

Nowotyńska, Irena; Kut, Stanisław

2014-04-01

The tool durability is a crucial factor in each manufacturing process, and this also includes the extrusion process. Striving to achieve the higher product quality should be accompanied by a long-term tool life and production cost reduction. This article presents the comparative research of load and wear of die at various angles of working cone during the concurrent extrusion. The numerical calculations of a tool load during the concurrent extrusion were performed using the MSC MARC software using the finite element method (FEM). Archard model was used to determine and compare die wear. This model was implemented in the software using the FEM. The examined tool deformations and stress distribution were determined based on the performed analyses. The die wear depth at various working cone angles was determined. Properly shaped die has an effect on the extruded material properties, but also controls loads, elastic deformation, and the tool life.

WaveAR: A software tool for calculating parameters for water waves with incident and reflected components

NASA Astrophysics Data System (ADS)

Landry, Blake J.; Hancock, Matthew J.; Mei, Chiang C.; García, Marcelo H.

2012-09-01

The ability to determine wave heights and phases along a spatial domain is vital to understanding a wide range of littoral processes. The software tool presented here employs established Stokes wave theory and sampling methods to calculate parameters for the incident and reflected components of a field of weakly nonlinear waves, monochromatic at first order in wave slope and propagating in one horizontal dimension. The software calculates wave parameters over an entire wave tank and accounts for reflection, weak nonlinearity, and a free second harmonic. Currently, no publicly available program has such functionality. The included MATLAB®-based open source code has also been compiled for Windows®, Mac® and Linux® operating systems. An additional companion program, VirtualWave, is included to generate virtual wave fields for WaveAR. Together, the programs serve as ideal analysis and teaching tools for laboratory water wave systems.

Programming Languages or Generic Software Tools, for Beginners' Courses in Computer Literacy?

ERIC Educational Resources Information Center

Neuwirth, Erich

1987-01-01

Discussion of methods that can be used to teach beginner courses in computer literacy focuses on students aged 10-12. The value of using a programing language versus using a generic software package is highlighted; Logo and Prolog are reviewed; and the use of databases is discussed. (LRW)

TOWARD DEVELOPMENT OF A COMMON SOFTWARE APPLICATION PROGRAMMING INTERFACE (API) FOR UNCERTAINTY, SENSITIVITY, AND PARAMETER ESTIMATION METHODS AND TOOLS

EPA Science Inventory

The final session of the workshop considered the subject of software technology and how it might be better constructed to support those who develop, evaluate, and apply multimedia environmental models. Two invited presentations were featured along with an extended open discussio...

Evolving software reengineering technology for the emerging innovative-competitive era

NASA Technical Reports Server (NTRS)

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

1994-01-01

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

ARX - A Comprehensive Tool for Anonymizing Biomedical Data

PubMed Central

Prasser, Fabian; Kohlmayer, Florian; Lautenschläger, Ronald; Kuhn, Klaus A.

2014-01-01

Collaboration and data sharing have become core elements of biomedical research. Especially when sensitive data from distributed sources are linked, privacy threats have to be considered. Statistical disclosure control allows the protection of sensitive data by introducing fuzziness. Reduction of data quality, however, needs to be balanced against gains in protection. Therefore, tools are needed which provide a good overview of the anonymization process to those responsible for data sharing. These tools require graphical interfaces and the use of intuitive and replicable methods. In addition, extensive testing, documentation and openness to reviews by the community are important. Existing publicly available software is limited in functionality, and often active support is lacking. We present ARX, an anonymization tool that i) implements a wide variety of privacy methods in a highly efficient manner, ii) provides an intuitive cross-platform graphical interface, iii) offers a programming interface for integration into other software systems, and iv) is well documented and actively supported. PMID:25954407

Proceedings of the Eighteenth Annual Software Engineering Workshop

NASA Technical Reports Server (NTRS)

1993-01-01

The workshop provided a forum for software practitioners from around the world to exchange information on the measurement, use, and evaluation of software methods, models, and tools. This year, approximately 450 people attended the workshop, which consisted of six sessions on the following topics: the Software Engineering Laboratory, measurement, technology assessment, advanced concepts, process, and software engineering issues in NASA. Three presentations were given in each of the topic areas. The content of those presentations and the research papers detailing the work reported are included in these proceedings. The workshop concluded with a tutorial session on how to start an Experience Factory.

Online survey software as a data collection tool for medical education: A case study on lesson plan assessment

PubMed Central

Kimiafar, Khalil; Sarbaz, Masoumeh; Sheikhtaheri, Abbas

2016-01-01

Background: There are no general strategies or tools to evaluate daily lesson plans; however, assessments conducted using traditional methods usually include course plans. This study aimed to evaluate the strengths and weaknesses of online survey software in collecting data on education in medical fields and the application of such softwares to evaluate students' views and modification of lesson plans. Methods: After investigating the available online survey software, esurveypro was selected for assessing daily lesson plans. After using the software for one semester, a questionnaire was prepared to assess the advantages and disadvantages of this method and students’ views in a cross-sectional study. Results: The majority of the students (51.7%) rated the evaluation of classes per session (lesson plans) using the online survey as useful or very useful. About 51% (n=36) of the students considered this method effective in improving the management of each session, 67.1% (n=47) considered it effective in improving the management of sessions for the next semester, and 51.4% (n=36) said it had a high impact on improving the educational content of subsequent sessions. Finally, 61.4% (n=43) students expressed high and very high levels of satisfaction with using an online survey at each session. Conclusion: The use of online surveys may be appropriate to improve lesson plans and educational planning at different levels. This method can be used for other evaluations and for assessing people’s opinions at different levels of an educational system. PMID:28491839

The Chandra X-ray Center data system: supporting the mission of the Chandra X-ray Observatory

NASA Astrophysics Data System (ADS)

Evans, Janet D.; Cresitello-Dittmar, Mark; Doe, Stephen; Evans, Ian; Fabbiano, Giuseppina; Germain, Gregg; Glotfelty, Kenny; Hall, Diane; Plummer, David; Zografou, Panagoula

2006-06-01

The Chandra X-ray Center Data System provides end-to-end scientific software support for Chandra X-ray Observatory mission operations. The data system includes the following components: (1) observers' science proposal planning tools; (2) science mission planning tools; (3) science data processing, monitoring, and trending pipelines and tools; and (4) data archive and database management. A subset of the science data processing component is ported to multiple platforms and distributed to end-users as a portable data analysis package. Web-based user tools are also available for data archive search and retrieval. We describe the overall architecture of the data system and its component pieces, and consider the design choices and their impacts on maintainability. We discuss the many challenges involved in maintaining a large, mission-critical software system with limited resources. These challenges include managing continually changing software requirements and ensuring the integrity of the data system and resulting data products while being highly responsive to the needs of the project. We describe our use of COTS and OTS software at the subsystem and component levels, our methods for managing multiple release builds, and adapting a large code base to new hardware and software platforms. We review our experiences during the life of the mission so-far, and our approaches for keeping a small, but highly talented, development team engaged during the maintenance phase of a mission.

Community-driven computational biology with Debian Linux

PubMed Central

2010-01-01

Background The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for research. In order to feed the steady demand for updates on software and associated data, a service infrastructure is required for sharing and providing these tools to heterogeneous computing environments. Results The Debian Med initiative provides ready and coherent software packages for medical informatics and bioinformatics. These packages can be used together in Taverna workflows via the UseCase plugin to manage execution on local or remote machines. If such packages are available in cloud computing environments, the underlying hardware and the analysis pipelines can be shared along with the software. Conclusions Debian Med closes the gap between developers and users. It provides a simple method for offering new releases of software and data resources, thus provisioning a local infrastructure for computational biology. For geographically distributed teams it can ensure they are working on the same versions of tools, in the same conditions. This contributes to the world-wide networking of researchers. PMID:21210984

A Simulated Learning Environment for Teaching Medicine Dispensing Skills

PubMed Central

Styles, Kim; Sewell, Keith; Trinder, Peta; Marriott, Jennifer; Maher, Sheryl; Naidu, Som

2016-01-01

Objective. To develop an authentic simulation of the professional practice dispensary context for students to develop their dispensing skills in a risk-free environment. Design. A development team used an Agile software development method to create MyDispense, a web-based simulation. Modeled on virtual learning environments elements, the software employed widely available standards-based technologies to create a virtual community pharmacy environment. Assessment. First-year pharmacy students who used the software in their tutorials, were, at the end of the second semester, surveyed on their prior dispensing experience and their perceptions of MyDispense as a tool to learn dispensing skills. Conclusion. The dispensary simulation is an effective tool for helping students develop dispensing competency and knowledge in a safe environment. PMID:26941437

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

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

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

2008-09-01

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

Next Generation Nuclear Plant Methods Technical Program Plan

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

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

2010-12-01

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

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

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

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

2010-09-01

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

Controls/CFD Interdisciplinary Research Software Generates Low-Order Linear Models for Control Design From Steady-State CFD Results

NASA Technical Reports Server (NTRS)

Melcher, Kevin J.

1997-01-01

The NASA Lewis Research Center is developing analytical methods and software tools to create a bridge between the controls and computational fluid dynamics (CFD) disciplines. Traditionally, control design engineers have used coarse nonlinear simulations to generate information for the design of new propulsion system controls. However, such traditional methods are not adequate for modeling the propulsion systems of complex, high-speed vehicles like the High Speed Civil Transport. To properly model the relevant flow physics of high-speed propulsion systems, one must use simulations based on CFD methods. Such CFD simulations have become useful tools for engineers that are designing propulsion system components. The analysis techniques and software being developed as part of this effort are an attempt to evolve CFD into a useful tool for control design as well. One major aspect of this research is the generation of linear models from steady-state CFD results. CFD simulations, often used during the design of high-speed inlets, yield high resolution operating point data. Under a NASA grant, the University of Akron has developed analytical techniques and software tools that use these data to generate linear models for control design. The resulting linear models have the same number of states as the original CFD simulation, so they are still very large and computationally cumbersome. Model reduction techniques have been successfully applied to reduce these large linear models by several orders of magnitude without significantly changing the dynamic response. The result is an accurate, easy to use, low-order linear model that takes less time to generate than those generated by traditional means. The development of methods for generating low-order linear models from steady-state CFD is most complete at the one-dimensional level, where software is available to generate models with different kinds of input and output variables. One-dimensional methods have been extended somewhat so that linear models can also be generated from two- and three-dimensional steady-state results. Standard techniques are adequate for reducing the order of one-dimensional CFD-based linear models. However, reduction of linear models based on two- and three-dimensional CFD results is complicated by very sparse, ill-conditioned matrices. Some novel approaches are being investigated to solve this problem.

The advanced software development workstation project

NASA Technical Reports Server (NTRS)

Fridge, Ernest M., III; Pitman, Charles L.

1991-01-01

The Advanced Software Development Workstation (ASDW) task is researching and developing the technologies required to support Computer Aided Software Engineering (CASE) with the emphasis on those advanced methods, tools, and processes that will be of benefit to support all NASA programs. Immediate goals are to provide research and prototype tools that will increase productivity, in the near term, in projects such as the Software Support Environment (SSE), the Space Station Control Center (SSCC), and the Flight Analysis and Design System (FADS) which will be used to support the Space Shuttle and Space Station Freedom. Goals also include providing technology for development, evolution, maintenance, and operations. The technologies under research and development in the ASDW project are targeted to provide productivity enhancements during the software life cycle phase of enterprise and information system modeling, requirements generation and analysis, system design and coding, and system use and maintenance. On-line user's guides will assist users in operating the developed information system with knowledge base expert assistance.

Recent trends related to the use of formal methods in software engineering

NASA Technical Reports Server (NTRS)

Prehn, Soren

1986-01-01

An account is given of some recent developments and trends related to the development and use of formal methods in software engineering. Ongoing activities in Europe are focussed on, since there seems to be a notable difference in attitude towards industrial usage of formal methods in Europe and in the U.S. A more detailed account is given of the currently most widespread formal method in Europe: the Vienna Development Method. Finally, the use of Ada is discussed in relation to the application of formal methods, and the potential for constructing Ada-specific tools based on that method is considered.

Link Analysis in the Mission Planning Lab

NASA Technical Reports Server (NTRS)

McCarthy, Jessica A.; Cervantes, Benjamin W.; Daugherty, Sarah C.; Arroyo, Felipe; Mago, Divyang

2011-01-01

The legacy communications link analysis software currently used at Wallops Flight Facility involves processes that are different for command destruct, radar, and telemetry. There is a clear advantage to developing an easy-to-use tool that combines all the processes in one application. Link Analysis in the Mission Planning Lab (MPL) uses custom software and algorithms integrated with Analytical Graphics Inc. Satellite Toolkit (AGI STK). The MPL link analysis tool uses pre/post-mission data to conduct a dynamic link analysis between ground assets and the launch vehicle. Just as the legacy methods do, the MPL link analysis tool calculates signal strength and signal- to-noise according to the accepted processes for command destruct, radar, and telemetry assets. Graphs and other custom data are generated rapidly in formats for reports and presentations. STK is used for analysis as well as to depict plume angles and antenna gain patterns in 3D. The MPL has developed two interfaces with the STK software (see figure). The first interface is an HTML utility, which was developed in Visual Basic to enhance analysis for plume modeling and to offer a more user friendly, flexible tool. A graphical user interface (GUI) written in MATLAB (see figure upper right-hand corner) is also used to quickly depict link budget information for multiple ground assets. This new method yields a dramatic decrease in the time it takes to provide launch managers with the required link budgets to make critical pre-mission decisions. The software code used for these two custom utilities is a product of NASA's MPL.

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

Building a virtual ligand screening pipeline using free software: a survey.

PubMed

Glaab, Enrico

2016-03-01

Virtual screening, the search for bioactive compounds via computational methods, provides a wide range of opportunities to speed up drug development and reduce the associated risks and costs. While virtual screening is already a standard practice in pharmaceutical companies, its applications in preclinical academic research still remain under-exploited, in spite of an increasing availability of dedicated free databases and software tools. In this survey, an overview of recent developments in this field is presented, focusing on free software and data repositories for screening as alternatives to their commercial counterparts, and outlining how available resources can be interlinked into a comprehensive virtual screening pipeline using typical academic computing facilities. Finally, to facilitate the set-up of corresponding pipelines, a downloadable software system is provided, using platform virtualization to integrate pre-installed screening tools and scripts for reproducible application across different operating systems. © The Author 2015. Published by Oxford University Press.

Building a virtual ligand screening pipeline using free software: a survey

PubMed Central

2016-01-01

Virtual screening, the search for bioactive compounds via computational methods, provides a wide range of opportunities to speed up drug development and reduce the associated risks and costs. While virtual screening is already a standard practice in pharmaceutical companies, its applications in preclinical academic research still remain under-exploited, in spite of an increasing availability of dedicated free databases and software tools. In this survey, an overview of recent developments in this field is presented, focusing on free software and data repositories for screening as alternatives to their commercial counterparts, and outlining how available resources can be interlinked into a comprehensive virtual screening pipeline using typical academic computing facilities. Finally, to facilitate the set-up of corresponding pipelines, a downloadable software system is provided, using platform virtualization to integrate pre-installed screening tools and scripts for reproducible application across different operating systems. PMID:26094053

Interactive Web Graphs with Fewer Restrictions

NASA Technical Reports Server (NTRS)

Fiedler, James

2012-01-01

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

Improvement of Computer Software Quality through Software Automated Tools.

DTIC Science & Technology

1986-08-30

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

DVS-SOFTWARE: An Effective Tool for Applying Highly Parallelized Hardware To Computational Geophysics

NASA Astrophysics Data System (ADS)

Herrera, I.; Herrera, G. S.

2015-12-01

Most geophysical systems are macroscopic physical systems. The behavior prediction of such systems is carried out by means of computational models whose basic models are partial differential equations (PDEs) [1]. Due to the enormous size of the discretized version of such PDEs it is necessary to apply highly parallelized super-computers. For them, at present, the most efficient software is based on non-overlapping domain decomposition methods (DDM). However, a limiting feature of the present state-of-the-art techniques is due to the kind of discretizations used in them. Recently, I. Herrera and co-workers using 'non-overlapping discretizations' have produced the DVS-Software which overcomes this limitation [2]. The DVS-software can be applied to a great variety of geophysical problems and achieves very high parallel efficiencies (90%, or so [3]). It is therefore very suitable for effectively applying the most advanced parallel supercomputers available at present. In a parallel talk, in this AGU Fall Meeting, Graciela Herrera Z. will present how this software is being applied to advance MOD-FLOW. Key Words: Parallel Software for Geophysics, High Performance Computing, HPC, Parallel Computing, Domain Decomposition Methods (DDM)REFERENCES [1]. Herrera Ismael and George F. Pinder, Mathematical Modelling in Science and Engineering: An axiomatic approach", John Wiley, 243p., 2012. [2]. Herrera, I., de la Cruz L.M. and Rosas-Medina A. "Non Overlapping Discretization Methods for Partial, Differential Equations". NUMER METH PART D E, 30: 1427-1454, 2014, DOI 10.1002/num 21852. (Open source) [3]. Herrera, I., & Contreras Iván "An Innovative Tool for Effectively Applying Highly Parallelized Software To Problems of Elasticity". Geofísica Internacional, 2015 (In press)

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

Belley, M; Schmidt, M; Knutson, N

Purpose: Physics second-checks for external beam radiation therapy are performed, in-part, to verify that the machine parameters in the Record-and-Verify (R&V) system that will ultimately be sent to the LINAC exactly match the values initially calculated by the Treatment Planning System (TPS). While performing the second-check, a large portion of the physicists’ time is spent navigating and arranging display windows to locate and compare the relevant numerical values (MLC position, collimator rotation, field size, MU, etc.). Here, we describe the development of a software tool that guides the physicist by aggregating and succinctly displaying machine parameter data relevant to themore » physics second-check process. Methods: A data retrieval software tool was developed using Python to aggregate data and generate a list of machine parameters that are commonly verified during the physics second-check process. This software tool imported values from (i) the TPS RT Plan DICOM file and (ii) the MOSAIQ (R&V) Structured Query Language (SQL) database. The machine parameters aggregated for this study included: MLC positions, X&Y jaw positions, collimator rotation, gantry rotation, MU, dose rate, wedges and accessories, cumulative dose, energy, machine name, couch angle, and more. Results: A GUI interface was developed to generate a side-by-side display of the aggregated machine parameter values for each field, and presented to the physicist for direct visual comparison. This software tool was tested for 3D conformal, static IMRT, sliding window IMRT, and VMAT treatment plans. Conclusion: This software tool facilitated the data collection process needed in order for the physicist to conduct a second-check, thus yielding an optimized second-check workflow that was both more user friendly and time-efficient. Utilizing this software tool, the physicist was able to spend less time searching through the TPS PDF plan document and the R&V system and focus the second-check efforts on assessing the patient-specific plan-quality.« less

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

PubMed

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

2012-11-09

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

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

NASA Technical Reports Server (NTRS)

1982-01-01

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

A Modular GIS-Based Software Architecture for Model Parameter Estimation using the Method of Anchored Distributions (MAD)

NASA Astrophysics Data System (ADS)

Ames, D. P.; Osorio-Murillo, C.; Over, M. W.; Rubin, Y.

2012-12-01

The Method of Anchored Distributions (MAD) is an inverse modeling technique that is well-suited for estimation of spatially varying parameter fields using limited observations and Bayesian methods. This presentation will discuss the design, development, and testing of a free software implementation of the MAD technique using the open source DotSpatial geographic information system (GIS) framework, R statistical software, and the MODFLOW groundwater model. This new tool, dubbed MAD-GIS, is built using a modular architecture that supports the integration of external analytical tools and models for key computational processes including a forward model (e.g. MODFLOW, HYDRUS) and geostatistical analysis (e.g. R, GSLIB). The GIS-based graphical user interface provides a relatively simple way for new users of the technique to prepare the spatial domain, to identify observation and anchor points, to perform the MAD analysis using a selected forward model, and to view results. MAD-GIS uses the Managed Extensibility Framework (MEF) provided by the Microsoft .NET programming platform to support integration of different modeling and analytical tools at run-time through a custom "driver." Each driver establishes a connection with external programs through a programming interface, which provides the elements for communicating with core MAD software. This presentation gives an example of adapting the MODFLOW to serve as the external forward model in MAD-GIS for inferring the distribution functions of key MODFLOW parameters. Additional drivers for other models are being developed and it is expected that the open source nature of the project will engender the development of additional model drivers by 3rd party scientists.

TU-C-17A-03: An Integrated Contour Evaluation Software Tool Using Supervised Pattern Recognition for Radiotherapy

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

Chen, H; Tan, J; Kavanaugh, J

Purpose: Radiotherapy (RT) contours delineated either manually or semiautomatically require verification before clinical usage. Manual evaluation is very time consuming. A new integrated software tool using supervised pattern contour recognition was thus developed to facilitate this process. Methods: The contouring tool was developed using an object-oriented programming language C# and application programming interfaces, e.g. visualization toolkit (VTK). The C# language served as the tool design basis. The Accord.Net scientific computing libraries were utilized for the required statistical data processing and pattern recognition, while the VTK was used to build and render 3-D mesh models from critical RT structures in real-timemore » and 360° visualization. Principal component analysis (PCA) was used for system self-updating geometry variations of normal structures based on physician-approved RT contours as a training dataset. The inhouse design of supervised PCA-based contour recognition method was used for automatically evaluating contour normality/abnormality. The function for reporting the contour evaluation results was implemented by using C# and Windows Form Designer. Results: The software input was RT simulation images and RT structures from commercial clinical treatment planning systems. Several abilities were demonstrated: automatic assessment of RT contours, file loading/saving of various modality medical images and RT contours, and generation/visualization of 3-D images and anatomical models. Moreover, it supported the 360° rendering of the RT structures in a multi-slice view, which allows physicians to visually check and edit abnormally contoured structures. Conclusion: This new software integrates the supervised learning framework with image processing and graphical visualization modules for RT contour verification. This tool has great potential for facilitating treatment planning with the assistance of an automatic contour evaluation module in avoiding unnecessary manual verification for physicians/dosimetrists. In addition, its nature as a compact and stand-alone tool allows for future extensibility to include additional functions for physicians’ clinical needs.« less

Developing Learning Tool of Control System Engineering Using Matrix Laboratory Software Oriented on Industrial Needs

NASA Astrophysics Data System (ADS)

Isnur Haryudo, Subuh; Imam Agung, Achmad; Firmansyah, Rifqi

2018-04-01

The purpose of this research is to develop learning media of control technique using Matrix Laboratory software with industry requirement approach. Learning media serves as a tool for creating a better and effective teaching and learning situation because it can accelerate the learning process in order to enhance the quality of learning. Control Techniques using Matrix Laboratory software can enlarge the interest and attention of students, with real experience and can grow independent attitude. This research design refers to the use of research and development (R & D) methods that have been modified by multi-disciplinary team-based researchers. This research used Computer based learning method consisting of computer and Matrix Laboratory software which was integrated with props. Matrix Laboratory has the ability to visualize the theory and analysis of the Control System which is an integration of computing, visualization and programming which is easy to use. The result of this instructional media development is to use mathematical equations using Matrix Laboratory software on control system application with DC motor plant and PID (Proportional-Integral-Derivative). Considering that manufacturing in the field of Distributed Control systems (DCSs), Programmable Controllers (PLCs), and Microcontrollers (MCUs) use PID systems in production processes are widely used in industry.

Evaluation of three methods for retrospective correction of vignetting on medical microscopy images utilizing two open source software tools.

PubMed

Babaloukas, Georgios; Tentolouris, Nicholas; Liatis, Stavros; Sklavounou, Alexandra; Perrea, Despoina

2011-12-01

Correction of vignetting on images obtained by a digital camera mounted on a microscope is essential before applying image analysis. The aim of this study is to evaluate three methods for retrospective correction of vignetting on medical microscopy images and compare them with a prospective correction method. One digital image from four different tissues was used and a vignetting effect was applied on each of these images. The resulted vignetted image was replicated four times and in each replica a different method for vignetting correction was applied with fiji and gimp software tools. The highest peak signal-to-noise ratio from the comparison of each method to the original image was obtained from the prospective method in all tissues. The morphological filtering method provided the highest peak signal-to-noise ratio value amongst the retrospective methods. The prospective method is suggested as the method of choice for correction of vignetting and if it is not applicable, then the morphological filtering may be suggested as the retrospective alternative method. © 2011 The Authors Journal of Microscopy © 2011 Royal Microscopical Society.

Architectural Analysis of Complex Evolving Systems of Systems

NASA Technical Reports Server (NTRS)

Lindvall, Mikael; Stratton, William C.; Sibol, Deane E.; Ray, Arnab; Ackemann, Chris; Yonkwa, Lyly; Ganesan, Dharma

2009-01-01

The goal of this collaborative project between FC-MD, APL, and GSFC and supported by NASA IV&V Software Assurance Research Program (SARP), was to develop a tool, Dynamic SAVE, or Dyn-SAVE for short, for analyzing architectures of systems of systems. The project team was comprised of the principal investigator (PI) from FC-MD and four other FC-MD scientists (part time) and several FC-MD students (full time), as well as, two APL software architects (part time), and one NASA POC (part time). The PI and FC-MD scientists together with APL architects were responsible for requirements analysis, and for applying and evaluating the Dyn-SAVE tool and method. The PI and a group of FC-MD scientists were responsible for improving the method and conducting outreach activities, while another group of FC-MD scientists were responsible for development and improvement of the tool. Oversight and reporting was conducted by the PI and NASA POC. The project team produced many results including several prototypes of the Dyn-SAVE tool and method, several case studies documenting how the tool and method was applied to APL s software systems, and several published papers in highly respected conferences and journals. Dyn-SAVE as developed and enhanced throughout this research period, is a software tool intended for software developers and architects, software integration testers, and persons who need to analyze software systems from the point of view of how it communicates with other systems. Using the tool, the user specifies the planned communication behavior of the system modeled as a sequence diagram. The user then captures and imports the actual communication behavior of the system, which is then converted and visualized as a sequence diagram by Dyn-SAVE. After mapping the planned to the actual and specifying parameter and timing constraints, Dyn-SAVE detects and highlights deviations between the planned and the actual behavior. Requirements based on the need to analyze two inter-system communication protocols that are representative of protocols used in the Aerospace industry have been specified. The protocols are related: APL s Common Ground System (CGS) as used in the MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) and the Radiation Belt Space Probes (RBSP) missions. The analyzed communications were implementations of the Telemetry protocol and the CCSDS File Delivery Protocol (CFDP) protocol. Based on these requirements, three prototypes of Dyn-SAVE were developed and applied to these protocols. The application of Dyn-SAVE to these protocols resulted in the detection of several issues. Dyn-SAVE was also applied to several Testbeds that have previously been used for experimentation earlier on this project, as well as, to other protocols and logs for testing its broader applicability. For example, Dyn-SAVE was used to analyze 1) the communication pattern between a web browser and a web server, 2) the system log of a computer in order to detect offnominal computer shut-down behavior, and 3) the actual test cases of NASA Goddard s Core Flight System (CFS) and automatically generated test cases in order to determine the overlap between the two sets of test cases. In all cases, Dyn-SAVE assisted in providing insightful conclusions about each of the cases identified above.

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

PubMed Central

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

2013-01-01

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

Automated support for experience-based software management

NASA Technical Reports Server (NTRS)

Valett, Jon D.

1992-01-01

To effectively manage a software development project, the software manager must have access to key information concerning a project's status. This information includes not only data relating to the project of interest, but also, the experience of past development efforts within the environment. This paper describes the concepts and functionality of a software management tool designed to provide this information. This tool, called the Software Management Environment (SME), enables the software manager to compare an ongoing development effort with previous efforts and with models of the 'typical' project within the environment, to predict future project status, to analyze a project's strengths and weaknesses, and to assess the project's quality. In order to provide these functions the tool utilizes a vast corporate memory that includes a data base of software metrics, a set of models and relationships that describe the software development environment, and a set of rules that capture other knowledge and experience of software managers within the environment. Integrating these major concepts into one software management tool, the SME is a model of the type of management tool needed for all software development organizations.

Dynamic optimization case studies in DYNOPT tool

NASA Astrophysics Data System (ADS)

Ozana, Stepan; Pies, Martin; Docekal, Tomas

2016-06-01

Dynamic programming is typically applied to optimization problems. As the analytical solutions are generally very difficult, chosen software tools are used widely. These software packages are often third-party products bound for standard simulation software tools on the market. As typical examples of such tools, TOMLAB and DYNOPT could be effectively applied for solution of problems of dynamic programming. DYNOPT will be presented in this paper due to its licensing policy (free product under GPL) and simplicity of use. DYNOPT is a set of MATLAB functions for determination of optimal control trajectory by given description of the process, the cost to be minimized, subject to equality and inequality constraints, using orthogonal collocation on finite elements method. The actual optimal control problem is solved by complete parameterization both the control and the state profile vector. It is assumed, that the optimized dynamic model may be described by a set of ordinary differential equations (ODEs) or differential-algebraic equations (DAEs). This collection of functions extends the capability of the MATLAB Optimization Tool-box. The paper will introduce use of DYNOPT in the field of dynamic optimization problems by means of case studies regarding chosen laboratory physical educational models.

An Intracranial Electroencephalography (iEEG) Brain Function Mapping Tool with an Application to Epilepsy Surgery Evaluation

PubMed Central

Wang, Yinghua; Yan, Jiaqing; Wen, Jianbin; Yu, Tao; Li, Xiaoli

2016-01-01

Objects: Before epilepsy surgeries, intracranial electroencephalography (iEEG) is often employed in function mapping and epileptogenic foci localization. Although the implanted electrodes provide crucial information for epileptogenic zone resection, a convenient clinical tool for electrode position registration and Brain Function Mapping (BFM) visualization is still lacking. In this study, we developed a BFM Tool, which facilitates electrode position registration and BFM visualization, with an application to epilepsy surgeries. Methods: The BFM Tool mainly utilizes electrode location registration and function mapping based on pre-defined brain models from other software. In addition, the electrode node and mapping properties, such as the node size/color, edge color/thickness, mapping method, can be adjusted easily using the setting panel. Moreover, users may manually import/export location and connectivity data to generate figures for further application. The role of this software is demonstrated by a clinical study of language area localization. Results: The BFM Tool helps clinical doctors and researchers visualize implanted electrodes and brain functions in an easy, quick and flexible manner. Conclusions: Our tool provides convenient electrode registration, easy brain function visualization, and has good performance. It is clinical-oriented and is easy to deploy and use. The BFM tool is suitable for epilepsy and other clinical iEEG applications. PMID:27199729

Software project management tools in global software development: a systematic mapping study.

PubMed

Chadli, Saad Yasser; Idri, Ali; Ros, Joaquín Nicolás; Fernández-Alemán, José Luis; de Gea, Juan M Carrillo; Toval, Ambrosio

2016-01-01

Global software development (GSD) which is a growing trend in the software industry is characterized by a highly distributed environment. Performing software project management (SPM) in such conditions implies the need to overcome new limitations resulting from cultural, temporal and geographic separation. The aim of this research is to discover and classify the various tools mentioned in literature that provide GSD project managers with support and to identify in what way they support group interaction. A systematic mapping study has been performed by means of automatic searches in five sources. We have then synthesized the data extracted and presented the results of this study. A total of 102 tools were identified as being used in SPM activities in GSD. We have classified these tools, according to the software life cycle process on which they focus and how they support the 3C collaboration model (communication, coordination and cooperation). The majority of the tools found are standalone tools (77%). A small number of platforms (8%) also offer a set of interacting tools that cover the software development lifecycle. Results also indicate that SPM areas in GSD are not adequately supported by corresponding tools and deserve more attention from tool builders.

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

PubMed Central

2015-01-01

Nowadays, we live in the “data era” where the use of statistical or data analysis software is inevitable, in any research field. This means that the choice of the right software tool or platform is a strategic issue for a research department. Nevertheless, in many cases decision makers do not pay the right attention to a comprehensive and appropriate evaluation of what the market offers. Indeed, the choice still depends on few factors like, for instance, researcher’s personal inclination, e.g., which software have been used at the university or is already known. This is not wrong in principle, but in some cases it’s not enough at all and might lead to a “dead end” situation, typically after months or years of investments already done on the wrong software. This article, far from being a full and complete guide to statistical software evaluation, aims to illustrate some key points of the decision process and introduce an extended range of factors which can help to undertake the right choice, at least in potential. There is not enough literature about that topic, most of the time underestimated, both in the traditional literature and even in the so called “gray literature”, even if some documents or short pages can be found online. Anyhow, it seems there is not a common and known standpoint about the process of software evaluation from the final user perspective. We suggests a multi-factor analysis leading to an evaluation matrix tool, to be intended as a flexible and customizable tool, aimed to provide a clearer picture of the software alternatives available, not in abstract but related to the researcher’s own context and needs. This method is a result of about twenty years of experience of the author in the field of evaluating and using technical-computing software and partially arises from a research made about such topics as part of a project funded by European Commission under the Lifelong Learning Programme 2011. PMID:26793368

Open source tools for fluorescent imaging.

PubMed

Hamilton, Nicholas A

2012-01-01

As microscopy becomes increasingly automated and imaging expands in the spatial and time dimensions, quantitative analysis tools for fluorescent imaging are becoming critical to remove both bottlenecks in throughput as well as fully extract and exploit the information contained in the imaging. In recent years there has been a flurry of activity in the development of bio-image analysis tools and methods with the result that there are now many high-quality, well-documented, and well-supported open source bio-image analysis projects with large user bases that cover essentially every aspect from image capture to publication. These open source solutions are now providing a viable alternative to commercial solutions. More importantly, they are forming an interoperable and interconnected network of tools that allow data and analysis methods to be shared between many of the major projects. Just as researchers build on, transmit, and verify knowledge through publication, open source analysis methods and software are creating a foundation that can be built upon, transmitted, and verified. Here we describe many of the major projects, their capabilities, and features. We also give an overview of the current state of open source software for fluorescent microscopy analysis and the many reasons to use and develop open source methods. Copyright © 2012 Elsevier Inc. All rights reserved.

VIP Barcoding: composition vector-based software for rapid species identification based on DNA barcoding.

PubMed

Fan, Long; Hui, Jerome H L; Yu, Zu Guo; Chu, Ka Hou

2014-07-01

Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/. © 2014 John Wiley & Sons Ltd.

Software Quality Assurance Metrics

NASA Technical Reports Server (NTRS)

McRae, Kalindra A.

2004-01-01

Software Quality Assurance (SQA) is a planned and systematic set of activities that ensures conformance of software life cycle processes and products conform to requirements, standards and procedures. In software development, software quality means meeting requirements and a degree of excellence and refinement of a project or product. Software Quality is a set of attributes of a software product by which its quality is described and evaluated. The set of attributes includes functionality, reliability, usability, efficiency, maintainability, and portability. Software Metrics help us understand the technical process that is used to develop a product. The process is measured to improve it and the product is measured to increase quality throughout the life cycle of software. Software Metrics are measurements of the quality of software. Software is measured to indicate the quality of the product, to assess the productivity of the people who produce the product, to assess the benefits derived from new software engineering methods and tools, to form a baseline for estimation, and to help justify requests for new tools or additional training. Any part of the software development can be measured. If Software Metrics are implemented in software development, it can save time, money, and allow the organization to identify the caused of defects which have the greatest effect on software development. The summer of 2004, I worked with Cynthia Calhoun and Frank Robinson in the Software Assurance/Risk Management department. My task was to research and collect, compile, and analyze SQA Metrics that have been used in other projects that are not currently being used by the SA team and report them to the Software Assurance team to see if any metrics can be implemented in their software assurance life cycle process.

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

PubMed

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

2016-10-01

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

Integrating and Managing Bim in GIS, Software Review

NASA Astrophysics Data System (ADS)

El Meouche, R.; Rezoug, M.; Hijazi, I.

2013-08-01

Since the advent of Computer-Aided Design (CAD) and Geographical Information System (GIS) tools, project participants have been increasingly leveraging these tools throughout the different phases of a civil infrastructure project. In recent years the number of GIS software that provides tools to enable the integration of Building information in geo context has risen sharply. More and more GIS software are added tools for this purposes and other software projects are regularly extending these tools. However, each software has its different strength and weakness and its purpose of use. This paper provides a thorough review to investigate the software capabilities and clarify its purpose. For this study, Autodesk Revit 2012 i.e. BIM editor software was used to create BIMs. In the first step, three building models were created, the resulted models were converted to BIM format and then the software was used to integrate it. For the evaluation of the software, general characteristics was studied such as the user interface, what formats are supported (import/export), and the way building information are imported.

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

NASA Astrophysics Data System (ADS)

Nieciąg, Halina

2015-10-01

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

A free software for the calculation of T2* values for iron overload assessment.

PubMed

Fernandes, Juliano Lara; Fioravante, Luciana Andrea Barozi; Verissimo, Monica P; Loggetto, Sandra R

2017-06-01

Background Iron overload assessment with magnetic resonance imaging (MRI) using T2* has become a key diagnostic method in the management of many diseases. Quantitative analysis of the MRI images with a cost-effective tool has been a limitation to increased use of the method. Purpose To provide a free software solution for this purpose comparing the results with a commercial solution. Material and Methods The free tool was developed as a standalone program to be directly downloaded and ran in a common personal computer platform without the need of a dedicated workstation. Liver and cardiac T2* values were calculated using both tools and the values obtained compared between them in a group of 56 patients with suspected iron overload using Bland-Altman plots and concordance correlation coefficients (CCC). Results In the heart, the mean T2* differences between the two methods was 0.46 ms (95% confidence interval [CI], -0.037 -0.965) and in the liver 0.49 ms (95% CI, 0.257-0.722). The CCC for both the heart and the liver were significantly high (0.98 [95% CI, 0.966-0.988] with a Pearson ρ of 0.9811 and 0.991 [95% CI, 0.986-0.994] with a Pearson ρ of 0.996, respectively. No significant differences were observed when analyzing only patients with abnormal concentrations of iron in both organs compared to the whole cohort. Conclusion The proposed free software tool is accurate for calculation of T2* values of the liver and heart and might be a solution for centers that cannot use paid commercial solutions.

The Effects of Development Team Skill on Software Product Quality

NASA Technical Reports Server (NTRS)

Beaver, Justin M.; Schiavone, Guy A.

2006-01-01

This paper provides an analysis of the effect of the skill/experience of the software development team on the quality of the final software product. A method for the assessment of software development team skill and experience is proposed, and was derived from a workforce management tool currently in use by the National Aeronautics and Space Administration. Using data from 26 smallscale software development projects, the team skill measures are correlated to 5 software product quality metrics from the ISO/IEC 9126 Software Engineering Product Quality standard. in the analysis of the results, development team skill is found to be a significant factor in the adequacy of the design and implementation. In addition, the results imply that inexperienced software developers are tasked with responsibilities ill-suited to their skill level, and thus have a significant adverse effect on the quality of the software product. Keywords: software quality, development skill, software metrics

Virtual acoustic environments for comprehensive evaluation of model-based hearing devices.

PubMed

Grimm, Giso; Luberadzka, Joanna; Hohmann, Volker

2018-06-01

Create virtual acoustic environments (VAEs) with interactive dynamic rendering for applications in audiology. A toolbox for creation and rendering of dynamic virtual acoustic environments (TASCAR) that allows direct user interaction was developed for application in hearing aid research and audiology. The software architecture and the simulation methods used to produce VAEs are outlined. Example environments are described and analysed. With the proposed software, a tool for simulation of VAEs is available. A set of VAEs rendered with the proposed software was described.

[Analysis of software for identifying spectral line of laser-induced breakdown spectroscopy based on LabVIEW].

PubMed

Hu, Zhi-yu; Zhang, Lei; Ma, Wei-guang; Yan, Xiao-juan; Li, Zhi-xin; Zhang, Yong-zhi; Wang, Le; Dong, Lei; Yin, Wang-bao; Jia, Suo-tang

2012-03-01

Self-designed identifying software for LIBS spectral line was introduced. Being integrated with LabVIEW, the soft ware can smooth spectral lines and pick peaks. The second difference and threshold methods were employed. Characteristic spectrum of several elements matches the NIST database, and realizes automatic spectral line identification and qualitative analysis of the basic composition of sample. This software can analyze spectrum handily and rapidly. It will be a useful tool for LIBS.

Software development for airborne radar

NASA Astrophysics Data System (ADS)

Sundstrom, Ingvar G.

Some aspects for development of software in a modern multimode airborne nose radar are described. First, an overview of where software is used in the radar units is presented. The development phases-system design, functional design, detailed design, function verification, and system verification-are then used as the starting point for the discussion. Methods, tools, and the most important documents are described. The importance of video flight recording in the early stages and use of a digital signal generators for performance verification is emphasized. Some future trends are discussed.

Freely available compound data sets and software tools for chemoinformatics and computational medicinal chemistry applications

PubMed Central

Bajorath, Jurgen

2012-01-01

We have generated a number of  compound data sets and programs for different types of applications in pharmaceutical research. These data sets and programs were originally designed for our research projects and are made publicly available. Without consulting original literature sources, it is difficult to understand specific features of data sets and software tools, basic ideas underlying their design, and applicability domains. Currently, 30 different entries are available for download from our website. In this data article, we provide an overview of the data and tools we make available and designate the areas of research for which they should be useful. For selected data sets and methods/programs, detailed descriptions are given. This article should help interested readers to select data and tools for specific computational investigations. PMID:24358818

MRIVIEW: An interactive computational tool for investigation of brain structure and function

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

Ranken, D.; George, J.

MRIVIEW is a software system which uses image processing and visualization to provide neuroscience researchers with an integrated environment for combining functional and anatomical information. Key features of the software include semi-automated segmentation of volumetric head data and an interactive coordinate reconciliation method which utilizes surface visualization. The current system is a precursor to a computational brain atlas. We describe features this atlas will incorporate, including methods under development for visualizing brain functional data obtained from several different research modalities.

Improving Cognitive Abilities and e-Inclusion in Children with Cerebral Palsy

NASA Astrophysics Data System (ADS)

Martinengo, Chiara; Curatelli, Francesco

Besides overcoming the motor barriers for accessing to computers and Internet, ICT tools can provide a very useful, and often necessary, support for the cognitive development of motor-impaired children with cerebral palsy. In fact, software tools for computation and communication allow teachers to put into effect, in a more complete and efficient way, the learning methods and the educational plans studied for the child. In the present article, after a brief analysis of the general objectives to be pursued for favouring the learning for children with cerebral palsy, we take account of some specific difficulties in the logical-linguistic and logical-mathematical fields, and we show how they can be overcome using general ICT tools and specifically implemented software programs.

Software attribute visualization for high integrity software

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

Pollock, G.M.

1998-03-01

This report documents a prototype tool developed to investigate the use of visualization and virtual reality technologies for improving software surety confidence. The tool is utilized within the execution phase of the software life cycle. It provides a capability to monitor an executing program against prespecified requirements constraints provided in a program written in the requirements specification language SAGE. The resulting Software Attribute Visual Analysis Tool (SAVAnT) also provides a technique to assess the completeness of a software specification.

Transana Qualitative Video and Audio Analysis Software as a Tool for Teaching Intellectual Assessment Skills to Graduate Psychology Students

ERIC Educational Resources Information Center

Rush, S. Craig

2014-01-01

This article draws on the author's experience using qualitative video and audio analysis, most notably through use of the Transana qualitative video and audio analysis software program, as an alternative method for teaching IQ administration skills to students in a graduate psychology program. Qualitative video and audio analysis may be useful for…

Towards an Interoperability Ontology for Software Development Tools

DTIC Science & Technology

2003-03-01

The description of feature models was tied to the introduction of the Feature-Oriented Domain Analysis ( FODA *) [KANG90] approach in the late eighties...Feature-oriented domain analysis ( FODA ) is a domain analysis method developed at the Software...ese obstacles was to construct a “pilot” ontology that is extensible. We applied the Feature-Oriented Domain Analysis approach to capture the

Reducing maintenance costs in agreement with CNC machine tools reliability

NASA Astrophysics Data System (ADS)

Ungureanu, A. L.; Stan, G.; Butunoi, P. A.

2016-08-01

Aligning maintenance strategy with reliability is a challenge due to the need to find an optimal balance between them. Because the various methods described in the relevant literature involve laborious calculations or use of software that can be costly, this paper proposes a method that is easier to implement on CNC machine tools. The new method, called the Consequence of Failure Analysis (CFA) is based on technical and economic optimization, aimed at obtaining a level of required performance with minimum investment and maintenance costs.

An Inverse Modeling Plugin for HydroDesktop using the Method of Anchored Distributions (MAD)

NASA Astrophysics Data System (ADS)

Ames, D. P.; Osorio, C.; Over, M. W.; Rubin, Y.

2011-12-01

The CUAHSI Hydrologic Information System (HIS) software stack is based on an open and extensible architecture that facilitates the addition of new functions and capabilities at both the server side (using HydroServer) and the client side (using HydroDesktop). The HydroDesktop client plugin architecture is used here to expose a new scripting based plugin that makes use of the R statistics software as a means for conducting inverse modeling using the Method of Anchored Distributions (MAD). MAD is a Bayesian inversion technique for conditioning computational model parameters on relevant field observations yielding probabilistic distributions of the model parameters, related to the spatial random variable of interest, by assimilating multi-type and multi-scale data. The implementation of a desktop software tool for using the MAD technique is expected to significantly lower the barrier to use of inverse modeling in education, research, and resource management. The HydroDesktop MAD plugin is being developed following a community-based, open-source approach that will help both its adoption and long term sustainability as a user tool. This presentation will briefly introduce MAD, HydroDesktop, and the MAD plugin and software development effort.

Software Users Manual (SUM): Extended Testability Analysis (ETA) Tool

NASA Technical Reports Server (NTRS)

Maul, William A.; Fulton, Christopher E.

2011-01-01

This software user manual describes the implementation and use the Extended Testability Analysis (ETA) Tool. The ETA Tool is a software program that augments the analysis and reporting capabilities of a commercial-off-the-shelf (COTS) testability analysis software package called the Testability Engineering And Maintenance System (TEAMS) Designer. An initial diagnostic assessment is performed by the TEAMS Designer software using a qualitative, directed-graph model of the system being analyzed. The ETA Tool utilizes system design information captured within the diagnostic model and testability analysis output from the TEAMS Designer software to create a series of six reports for various system engineering needs. The ETA Tool allows the user to perform additional studies on the testability analysis results by determining the detection sensitivity to the loss of certain sensors or tests. The ETA Tool was developed to support design and development of the NASA Ares I Crew Launch Vehicle. The diagnostic analysis provided by the ETA Tool was proven to be valuable system engineering output that provided consistency in the verification of system engineering requirements. This software user manual provides a description of each output report generated by the ETA Tool. The manual also describes the example diagnostic model and supporting documentation - also provided with the ETA Tool software release package - that were used to generate the reports presented in the manual

The MATH--Open Source Application for Easier Learning of Numerical Mathematics

ERIC Educational Resources Information Center

Glaser-Opitz, Henrich; Budajová, Kristina

2016-01-01

The article introduces a software application (MATH) supporting an education of Applied Mathematics, with focus on Numerical Mathematics. The MATH is an easy to use tool supporting various numerical methods calculations with graphical user interface and integrated plotting tool for graphical representation written in Qt with extensive use of Qwt…

Analyzing the Scientific Evolution of Social Work Using Science Mapping

ERIC Educational Resources Information Center

Martínez, Ma Angeles; Cobo, Manuel Jesús; Herrera, Manuel; Herrera-Viedma, Enrique

2015-01-01

Objectives: This article reports the first science mapping analysis of the social work field, which shows its conceptual structure and scientific evolution. Methods: Science Mapping Analysis Software Tool, a bibliometric science mapping tool based on co-word analysis and h-index, is applied using a sample of 18,794 research articles published from…

An Examination of Selected Software Testing Tools: 1992

DTIC Science & Technology

1992-12-01

Report ....................................................... 27-19 Figure 27-17. Metrics Manager Database Full Report...historical test database , the test management and problem reporting tools were examined using the sample test database provided by each supplier. 4-4...track the impact of new methods, organi- zational structures, and technologies. Metrics Manager is supported by an industry database that allows

Lessons learned in deploying software estimation technology and tools

NASA Technical Reports Server (NTRS)

Panlilio-Yap, Nikki; Ho, Danny

1994-01-01

Developing a software product involves estimating various project parameters. This is typically done in the planning stages of the project when there is much uncertainty and very little information. Coming up with accurate estimates of effort, cost, schedule, and reliability is a critical problem faced by all software project managers. The use of estimation models and commercially available tools in conjunction with the best bottom-up estimates of software-development experts enhances the ability of a product development group to derive reasonable estimates of important project parameters. This paper describes the experience of the IBM Software Solutions (SWS) Toronto Laboratory in selecting software estimation models and tools and deploying their use to the laboratory's product development groups. It introduces the SLIM and COSTAR products, the software estimation tools selected for deployment to the product areas, and discusses the rationale for their selection. The paper also describes the mechanisms used for technology injection and tool deployment, and concludes with a discussion of important lessons learned in the technology and tool insertion process.

Evaluation of the efficiency and reliability of software generated by code generators

NASA Technical Reports Server (NTRS)

Schreur, Barbara

1994-01-01

There are numerous studies which show that CASE Tools greatly facilitate software development. As a result of these advantages, an increasing amount of software development is done with CASE Tools. As more software engineers become proficient with these tools, their experience and feedback lead to further development with the tools themselves. What has not been widely studied, however, is the reliability and efficiency of the actual code produced by the CASE Tools. This investigation considered these matters. Three segments of code generated by MATRIXx, one of many commercially available CASE Tools, were chosen for analysis: ETOFLIGHT, a portion of the Earth to Orbit Flight software, and ECLSS and PFMC, modules for Environmental Control and Life Support System and Pump Fan Motor Control, respectively.

Application of Nexus copy number software for CNV detection and analysis.

PubMed

Darvishi, Katayoon

2010-04-01

Among human structural genomic variation, copy number variants (CNVs) are the most frequently known component, comprised of gains/losses of DNA segments that are generally 1 kb in length or longer. Array-based comparative genomic hybridization (aCGH) has emerged as a powerful tool for detecting genomic copy number variants (CNVs). With the rapid increase in the density of array technology and with the adaptation of new high-throughput technology, a reliable and computationally scalable method for accurate mapping of recurring DNA copy number aberrations has become a main focus in research. Here we introduce Nexus Copy Number software, a platform-independent tool, to analyze the output files of all types of commercial and custom-made comparative genomic hybridization (CGH) and single-nucleotide polymorphism (SNP) arrays, such as those manufactured by Affymetrix, Agilent Technologies, Illumina, and Roche NimbleGen. It also supports data generated by various array image-analysis software tools such as GenePix, ImaGene, and BlueFuse. (c) 2010 by John Wiley & Sons, Inc.

WinHPC System Software | High-Performance Computing | NREL

Science.gov Websites

Software WinHPC System Software Learn about the software applications, tools, toolchains, and for industrial applications. Intel Compilers Development Tool, Toolchain Suite featuring an industry

Applications of Formal Methods to Specification and Safety of Avionics Software

NASA Technical Reports Server (NTRS)

Hoover, D. N.; Guaspari, David; Humenn, Polar

1996-01-01

This report treats several topics in applications of formal methods to avionics software development. Most of these topics concern decision tables, an orderly, easy-to-understand format for formally specifying complex choices among alternative courses of action. The topics relating to decision tables include: generalizations fo decision tables that are more concise and support the use of decision tables in a refinement-based formal software development process; a formalism for systems of decision tables with behaviors; an exposition of Parnas tables for users of decision tables; and test coverage criteria and decision tables. We outline features of a revised version of ORA's decision table tool, Tablewise, which will support many of the new ideas described in this report. We also survey formal safety analysis of specifications and software.

Installing and Setting Up the Git Software Tool on OS X | High-Performance

Science.gov Websites

Computing | NREL the Git Software Tool on OS X Installing and Setting Up the Git Software Tool on OS X Learn how to install the Git software tool on OS X for use with the Peregrine system. You can . Binary Installer for OS X - Easiest! You can download the latest version of git from http://git-scm.com

SU-E-T-211: Comparison of Seven New TrueBeam Linacs with Enhanced Beam Data Conformance Using a Beam Comparison Software Tool

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

Grzetic, S; Hessler, J; Gupta, N

2015-06-15

Purpose: To develop an independent software tool to assist in commissioning linacs with enhanced beam conformance, as well as perform ongoing QA for dosimetrically equivalent linacs. Methods: Linac manufacturers offer enhanced beam conformance as an option to allow for clinics to complete commissioning efficiently, as well as implement dosimetrically equivalent linacs. The specification for enhanced conformance includes PDD as well as profiles within 80% FWHM. Recently, we commissioned seven Varian TrueBeam linacs with enhanced beam conformance. We developed a software tool in Visual Basic to allow us to load the reference beam data and compare our beam data during commissioningmore » to evaluate enhanced beam conformance. This tool also allowed us to upload our beam data used for commissioning our dosimetrically equivalent beam models to compare and tweak each of our linac beams to match our modelled data in Varian’s Eclipse TPS. This tool will also be used during annual QA of the linacs to compare our beam data to our baseline data, as required by TG-142. Results: Our software tool was used to check beam conformance for seven TrueBeam linacs that we commissioned in the past six months. Using our tool we found that the factory conformed linacs showed up to 3.82% difference in their beam profile data upon installation. Using our beam comparison tool, we were able to adjust the energy and profiles of our beams to accomplish a better than 1.00% point by point data conformance. Conclusion: The availability of quantitative comparison tools is essential to accept and commission linacs with enhanced beam conformance, as well as to beam match multiple linacs. We further intend to use the same tool to ensure our beam data conforms to the commissioning beam data during our annual QA in keeping with the requirements of TG-142.« less

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

NASA Technical Reports Server (NTRS)

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

2006-01-01

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

Cementitious Barriers Partnership (CBP): Training and Release of CBP Toolbox Software, Version 1.0 - 13480

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

Brown, K.G.; Kosson, D.S.; Garrabrants, A.C.

2013-07-01

The Cementitious Barriers Partnership (CBP) Project is a multi-disciplinary, multi-institutional collaboration supported by the Office of Tank Waste Management within the Office of Environmental Management of U.S. Department of Energy (US DOE). The CBP program has developed a set of integrated tools (based on state-of-the-art models and leaching test methods) that improve understanding and predictions of the long-term hydraulic and chemical performance of cementitious barriers used in nuclear applications. Tools selected for and developed under this program are intended to evaluate and predict the behavior of cementitious barriers used in near-surface engineered waste disposal systems for periods of performance upmore » to or longer than 100 years for operating facilities and longer than 1,000 years for waste management purposes. CBP software tools were made available to selected DOE Office of Environmental Management and field site users for training and evaluation based on a set of important degradation scenarios, including sulfate ingress/attack and carbonation of cementitious materials. The tools were presented at two-day training workshops held at U.S. National Institute of Standards and Technology (NIST), Savannah River, and Hanford included LeachXS{sup TM}/ORCHESTRA, STADIUM{sup R}, and a CBP-developed GoldSim Dashboard interface. Collectively, these components form the CBP Software Toolbox. The new U.S. Environmental Protection Agency leaching test methods based on the Leaching Environmental Assessment Framework (LEAF) were also presented. The CBP Dashboard uses a custom Dynamic-link library developed by CBP to couple to the LeachXS{sup TM}/ORCHESTRA and STADIUM{sup R} codes to simulate reactive transport and degradation in cementitious materials for selected performance assessment scenarios. The first day of the workshop introduced participants to the software components via presentation materials, and the second day included hands-on tutorial exercises followed by discussions of enhancements desired by participants. Tools were revised based on feedback obtained during the workshops held from April through June 2012. The resulting improved CBP Software Toolbox, including evaluation versions of and LeachXS{sup TM}/ORCHESTRA and STADIUM{sup R} has been made available to workshop and selected other participants for further assessment. Inquiries about future workshops and requests for access to the Toolbox software can be made via the CBP web site [1]. (authors)« less

Digital image rectification tool for metrification of gusset plate connections in steel truss bridges.

DOT National Transportation Integrated Search

2009-03-01

A method was developed to obtain dimensional data from photographs for analyzing steel truss gusset plate : connections. The method relies on a software application to correct photographic distortion and to scale the : photographs for analysis. The a...

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

Applying CASE Tools for On-Board Software Development

NASA Astrophysics Data System (ADS)

Brammer, U.; Hönle, A.

For many space projects the software development is facing great pressure with respect to quality, costs and schedule. One way to cope with these challenges is the application of CASE tools for automatic generation of code and documentation. This paper describes two CASE tools: Rhapsody (I-Logix) featuring UML and ISG (BSSE) that provides modeling of finite state machines. Both tools have been used at Kayser-Threde in different space projects for the development of on-board software. The tools are discussed with regard to the full software development cycle.

CONRAD—A software framework for cone-beam imaging in radiology

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

Maier, Andreas; Choi, Jang-Hwan; Riess, Christian

2013-11-15

Purpose: In the community of x-ray imaging, there is a multitude of tools and applications that are used in scientific practice. Many of these tools are proprietary and can only be used within a certain lab. Often the same algorithm is implemented multiple times by different groups in order to enable comparison. In an effort to tackle this problem, the authors created CONRAD, a software framework that provides many of the tools that are required to simulate basic processes in x-ray imaging and perform image reconstruction with consideration of nonlinear physical effects.Methods: CONRAD is a Java-based state-of-the-art software platform withmore » extensive documentation. It is based on platform-independent technologies. Special libraries offer access to hardware acceleration such as OpenCL. There is an easy-to-use interface for parallel processing. The software package includes different simulation tools that are able to generate up to 4D projection and volume data and respective vector motion fields. Well known reconstruction algorithms such as FBP, DBP, and ART are included. All algorithms in the package are referenced to a scientific source.Results: A total of 13 different phantoms and 30 processing steps have already been integrated into the platform at the time of writing. The platform comprises 74.000 nonblank lines of code out of which 19% are used for documentation. The software package is available for download at http://conrad.stanford.edu. To demonstrate the use of the package, the authors reconstructed images from two different scanners, a table top system and a clinical C-arm system. Runtimes were evaluated using the RabbitCT platform and demonstrate state-of-the-art runtimes with 2.5 s for the 256 problem size and 12.4 s for the 512 problem size.Conclusions: As a common software framework, CONRAD enables the medical physics community to share algorithms and develop new ideas. In particular this offers new opportunities for scientific collaboration and quantitative performance comparison between the methods of different groups.« less

Application of AI methods to aircraft guidance and control

NASA Technical Reports Server (NTRS)

Hueschen, Richard M.; Mcmanus, John W.

1988-01-01

A research program for integrating artificial intelligence (AI) techniques with tools and methods used for aircraft flight control system design, development, and implementation is discussed. The application of the AI methods for the development and implementation of the logic software which operates with the control mode panel (CMP) of an aircraft is presented. The CMP is the pilot control panel for the automatic flight control system of a commercial-type research aircraft of Langley Research Center's Advanced Transport Operating Systems (ATOPS) program. A mouse-driven color-display emulation of the CMP, which was developed with AI methods and used to test the AI software logic implementation, is discussed. The operation of the CMP was enhanced with the addition of a display which was quickly developed with AI methods. The display advises the pilot of conditions not satisfied when a mode does not arm or engage. The implementation of the CMP software logic has shown that the time required to develop, implement, and modify software systems can be significantly reduced with the use of the AI methods.

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

PubMed

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

2017-08-01

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

Software for predictive microbiology and risk assessment: a description and comparison of tools presented at the ICPMF8 Software Fair.

PubMed

Tenenhaus-Aziza, Fanny; Ellouze, Mariem

2015-02-01

The 8th International Conference on Predictive Modelling in Food was held in Paris, France in September 2013. One of the major topics of this conference was the transfer of knowledge and tools between academics and stakeholders of the food sector. During the conference, a "Software Fair" was held to provide information and demonstrations of predictive microbiology and risk assessment software. This article presents an overall description of the 16 software tools demonstrated at the session and provides a comparison based on several criteria such as the modeling approach, the different modules available (e.g. databases, predictors, fitting tools, risk assessment tools), the studied environmental factors (temperature, pH, aw, etc.), the type of media (broth or food) and the number and type of the provided micro-organisms (pathogens and spoilers). The present study is a guide to help users select the software tools which are most suitable to their specific needs, before they test and explore the tool(s) in more depth. Copyright © 2014 Elsevier Ltd. All rights reserved.

Extrusion Process by Finite Volume Method Using OpenFoam Software

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

Matos Martins, Marcelo; Tonini Button, Sergio; Divo Bressan, Jose

The computational codes are very important tools to solve engineering problems. In the analysis of metal forming process, such as extrusion, this is not different because the computational codes allow analyzing the process with reduced cost. Traditionally, the Finite Element Method is used to solve solid mechanic problems, however, the Finite Volume Method (FVM) have been gaining force in this field of applications. This paper presents the velocity field and friction coefficient variation results, obtained by numerical simulation using the OpenFoam Software and the FVM to solve an aluminum direct cold extrusion process.

EpHLA software: a timesaving and accurate tool for improving identification of acceptable mismatches for clinical purposes.

PubMed

Filho, Herton Luiz Alves Sales; da Mata Sousa, Luiz Claudio Demes; von Glehn, Cristina de Queiroz Carrascosa; da Silva, Adalberto Socorro; dos Santos Neto, Pedro de Alcântara; do Nascimento, Ferraz; de Castro, Adail Fonseca; do Nascimento, Liliane Machado; Kneib, Carolina; Bianchi Cazarote, Helena; Mayumi Kitamura, Daniele; Torres, Juliane Roberta Dias; da Cruz Lopes, Laiane; Barros, Aryela Loureiro; da Silva Edlin, Evelin Nildiane; de Moura, Fernanda Sá Leal; Watanabe, Janine Midori Figueiredo; do Monte, Semiramis Jamil Hadad

2012-06-01

The HLAMatchmaker algorithm, which allows the identification of “safe” acceptable mismatches (AMMs) for recipients of solid organ and cell allografts, is rarely used in part due to the difficulty in using it in the current Excel format. The automation of this algorithm may universalize its use to benefit the allocation of allografts. Recently, we have developed a new software called EpHLA, which is the first computer program automating the use of the HLAMatchmaker algorithm. Herein, we present the experimental validation of the EpHLA program by showing the time efficiency and the quality of operation. The same results, obtained by a single antigen bead assay with sera from 10 sensitized patients waiting for kidney transplants, were analyzed either by conventional HLAMatchmaker or by automated EpHLA method. Users testing these two methods were asked to record: (i) time required for completion of the analysis (in minutes); (ii) number of eplets obtained for class I and class II HLA molecules; (iii) categorization of eplets as reactive or non-reactive based on the MFI cutoff value; and (iv) determination of AMMs based on eplets' reactivities. We showed that although both methods had similar accuracy, the automated EpHLA method was over 8 times faster in comparison to the conventional HLAMatchmaker method. In particular the EpHLA software was faster and more reliable but equally accurate as the conventional method to define AMMs for allografts. The EpHLA software is an accurate and quick method for the identification of AMMs and thus it may be a very useful tool in the decision-making process of organ allocation for highly sensitized patients as well as in many other applications.

Toolpack mathematical software development environment

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

Osterweil, L.

1982-07-21

The purpose of this research project was to produce a well integrated set of tools for the support of numerical computation. The project entailed the specification, design and implementation of both a diversity of tools and an innovative tool integration mechanism. This large configuration of tightly integrated tools comprises an environment for numerical software development, and has been named Toolpack/IST (Integrated System of Tools). Following the creation of this environment in prototype form, the environment software was readied for widespread distribution by transitioning it to a development organization for systematization, documentation and distribution. It is expected that public release ofmore » Toolpack/IST will begin imminently and will provide a basis for evaluation of the innovative software approaches taken as well as a uniform set of development tools for the numerical software community.« less

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

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

NASA Technical Reports Server (NTRS)

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

2005-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2012-09-01

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

Computer-aided diagnosis software for vulvovaginal candidiasis detection from Pap smear images.

PubMed

Momenzadeh, Mohammadreza; Vard, Alireza; Talebi, Ardeshir; Mehri Dehnavi, Alireza; Rabbani, Hossein

2018-01-01

Vulvovaginal candidiasis (VVC) is a common gynecologic infection and it occurs when there is overgrowth of the yeast called Candida. VVC diagnosis is usually done by observing a Pap smear sample under a microscope and searching for the conidium and mycelium components of Candida. This manual method is time consuming, subjective and tedious. Any diagnosis tools that detect VVC, semi- or full-automatically, can be very helpful to pathologists. This article presents a computer aided diagnosis (CAD) software to improve human diagnosis of VVC from Pap smear samples. The proposed software is designed based on phenotypic and morphology features of the Candida in Pap smear sample images. This software provide a user-friendly interface which consists of a set of image processing tools and analytical results that helps to detect Candida and determine severity of illness. The software was evaluated on 200 Pap smear sample images and obtained specificity of 91.04% and sensitivity of 92.48% to detect VVC. As a result, the use of the proposed software reduces diagnostic time and can be employed as a second objective opinion for pathologists. © 2017 Wiley Periodicals, Inc.

Crux: Rapid Open Source Protein Tandem Mass Spectrometry Analysis

PubMed Central

2015-01-01

Efficiently and accurately analyzing big protein tandem mass spectrometry data sets requires robust software that incorporates state-of-the-art computational, machine learning, and statistical methods. The Crux mass spectrometry analysis software toolkit (http://cruxtoolkit.sourceforge.net) is an open source project that aims to provide users with a cross-platform suite of analysis tools for interpreting protein mass spectrometry data. PMID:25182276

Final Report: Quantification of Uncertainty in Extreme Scale Computations (QUEST)

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

Marzouk, Youssef; Conrad, Patrick; Bigoni, Daniele

QUEST (\\url{www.quest-scidac.org}) is a SciDAC Institute that is focused on uncertainty quantification (UQ) in large-scale scientific computations. Our goals are to (1) advance the state of the art in UQ mathematics, algorithms, and software; and (2) provide modeling, algorithmic, and general UQ expertise, together with software tools, to other SciDAC projects, thereby enabling and guiding a broad range of UQ activities in their respective contexts. QUEST is a collaboration among six institutions (Sandia National Laboratories, Los Alamos National Laboratory, the University of Southern California, Massachusetts Institute of Technology, the University of Texas at Austin, and Duke University) with a historymore » of joint UQ research. Our vision encompasses all aspects of UQ in leadership-class computing. This includes the well-founded setup of UQ problems; characterization of the input space given available data/information; local and global sensitivity analysis; adaptive dimensionality and order reduction; forward and inverse propagation of uncertainty; handling of application code failures, missing data, and hardware/software fault tolerance; and model inadequacy, comparison, validation, selection, and averaging. The nature of the UQ problem requires the seamless combination of data, models, and information across this landscape in a manner that provides a self-consistent quantification of requisite uncertainties in predictions from computational models. Accordingly, our UQ methods and tools span an interdisciplinary space across applied math, information theory, and statistics. The MIT QUEST effort centers on statistical inference and methods for surrogate or reduced-order modeling. MIT personnel have been responsible for the development of adaptive sampling methods, methods for approximating computationally intensive models, and software for both forward uncertainty propagation and statistical inverse problems. A key software product of the MIT QUEST effort is the MIT Uncertainty Quantification library, called MUQ (\\url{muq.mit.edu}).« less

Closing the Certification Gaps in Adaptive Flight Control Software

NASA Technical Reports Server (NTRS)

Jacklin, Stephen A.

2008-01-01

Over the last five decades, extensive research has been performed to design and develop adaptive control systems for aerospace systems and other applications where the capability to change controller behavior at different operating conditions is highly desirable. Although adaptive flight control has been partially implemented through the use of gain-scheduled control, truly adaptive control systems using learning algorithms and on-line system identification methods have not seen commercial deployment. The reason is that the certification process for adaptive flight control software for use in national air space has not yet been decided. The purpose of this paper is to examine the gaps between the state-of-the-art methodologies used to certify conventional (i.e., non-adaptive) flight control system software and what will likely to be needed to satisfy FAA airworthiness requirements. These gaps include the lack of a certification plan or process guide, the need to develop verification and validation tools and methodologies to analyze adaptive controller stability and convergence, as well as the development of metrics to evaluate adaptive controller performance at off-nominal flight conditions. This paper presents the major certification gap areas, a description of the current state of the verification methodologies, and what further research efforts will likely be needed to close the gaps remaining in current certification practices. It is envisioned that closing the gap will require certain advances in simulation methods, comprehensive methods to determine learning algorithm stability and convergence rates, the development of performance metrics for adaptive controllers, the application of formal software assurance methods, the application of on-line software monitoring tools for adaptive controller health assessment, and the development of a certification case for adaptive system safety of flight.

A high-level 3D visualization API for Java and ImageJ.

PubMed

Schmid, Benjamin; Schindelin, Johannes; Cardona, Albert; Longair, Mark; Heisenberg, Martin

2010-05-21

Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set. Here we present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Our framework is seamlessly integrated into ImageJ, a free image processing package with a vast collection of community-developed biological image analysis tools. Our framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment. In particular, we provide high-level access to volume rendering, volume editing, surface extraction, and image annotation. The ability to rely on a library that removes the low-level details enables concentrating software development efforts on the algorithm implementation parts. Our framework enables biomedical image software development to be built with 3D visualization capabilities with very little effort. We offer the source code and convenient binary packages along with extensive documentation at http://3dviewer.neurofly.de.

Fault tolerant testbed evaluation, phase 1

NASA Technical Reports Server (NTRS)

Caluori, V., Jr.; Newberry, T.

1993-01-01

In recent years, avionics systems development costs have become the driving factor in the development of space systems, military aircraft, and commercial aircraft. A method of reducing avionics development costs is to utilize state-of-the-art software application generator (autocode) tools and methods. The recent maturity of application generator technology has the potential to dramatically reduce development costs by eliminating software development steps that have historically introduced errors and the need for re-work. Application generator tools have been demonstrated to be an effective method for autocoding non-redundant, relatively low-rate input/output (I/O) applications on the Space Station Freedom (SSF) program; however, they have not been demonstrated for fault tolerant, high-rate I/O, flight critical environments. This contract will evaluate the use of application generators in these harsh environments. Using Boeing's quad-redundant avionics system controller as the target system, Space Shuttle Guidance, Navigation, and Control (GN&C) software will be autocoded, tested, and evaluated in the Johnson (Space Center) Avionics Engineering Laboratory (JAEL). The response of the autocoded system will be shown to match the response of the existing Shuttle General Purpose Computers (GPC's), thereby demonstrating the viability of using autocode techniques in the development of future avionics systems.

Using Penelope to assess the correctness of NASA Ada software: A demonstration of formal methods as a counterpart to testing

NASA Technical Reports Server (NTRS)

Eichenlaub, Carl T.; Harper, C. Douglas; Hird, Geoffrey

1993-01-01

Life-critical applications warrant a higher level of software reliability than has yet been achieved. Since it is not certain that traditional methods alone can provide the required ultra reliability, new methods should be examined as supplements or replacements. This paper describes a mathematical counterpart to the traditional process of empirical testing. ORA's Penelope verification system is demonstrated as a tool for evaluating the correctness of Ada software. Grady Booch's Ada calendar utility package, obtained through NASA, was specified in the Larch/Ada language. Formal verification in the Penelope environment established that many of the package's subprograms met their specifications. In other subprograms, failed attempts at verification revealed several errors that had escaped detection by testing.

Decision Support Methods and Tools

NASA Technical Reports Server (NTRS)

Green, Lawrence L.; Alexandrov, Natalia M.; Brown, Sherilyn A.; Cerro, Jeffrey A.; Gumbert, Clyde r.; Sorokach, Michael R.; Burg, Cecile M.

2006-01-01

This paper is one of a set of papers, developed simultaneously and presented within a single conference session, that are intended to highlight systems analysis and design capabilities within the Systems Analysis and Concepts Directorate (SACD) of the National Aeronautics and Space Administration (NASA) Langley Research Center (LaRC). This paper focuses on the specific capabilities of uncertainty/risk analysis, quantification, propagation, decomposition, and management, robust/reliability design methods, and extensions of these capabilities into decision analysis methods within SACD. These disciplines are discussed together herein under the name of Decision Support Methods and Tools. Several examples are discussed which highlight the application of these methods within current or recent aerospace research at the NASA LaRC. Where applicable, commercially available, or government developed software tools are also discussed

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.

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

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

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

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

Construction of integrated case environments.

PubMed

Losavio, Francisca; Matteo, Alfredo; Pérez, María

2003-01-01

The main goal of Computer-Aided Software Engineering (CASE) technology is to improve the entire software system development process. The CASE approach is not merely a technology; it involves a fundamental change in the process of software development. The tendency of the CASE approach, technically speaking, is the integration of tools that assist in the application of specific methods. In this sense, the environment architecture, which includes the platform and the system's hardware and software, constitutes the base of the CASE environment. The problem of tools integration has been proposed for two decades. Current integration efforts emphasize the interoperability of tools, especially in distributed environments. In this work we use the Brown approach. The environment resulting from the application of this model is called a federative environment, focusing on the fact that this architecture pays special attention to the connections among the components of the environment. This approach is now being used in component-based design. This paper describes a concrete experience in civil engineering and architecture fields, for the construction of an integrated CASE environment. A generic architectural framework based on an intermediary architectural pattern is applied to achieve the integration of the different tools. This intermediary represents the control perspective of the PAC (Presentation-Abstraction-Control) style, which has been implemented as a Mediator pattern and it has been used in the interactive systems domain. In addition, a process is given to construct the integrated CASE.

Virtual tool mark generation for efficient striation analysis in forensic science

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

Ekstrand, Laura

In 2009, a National Academy of Sciences report called for investigation into the scienti c basis behind tool mark comparisons (National Academy of Sciences, 2009). Answering this call, Chumbley et al. (2010) attempted to prove or disprove the hypothesis that tool marks are unique to a single tool. They developed a statistical algorithm that could, in most cases, discern matching and non-matching tool marks made at di erent angles by sequentially numbered screwdriver tips. Moreover, in the cases where the algorithm misinterpreted a pair of marks, an experienced forensics examiner could discern the correct outcome. While this research served tomore » con rm the basic assumptions behind tool mark analysis, it also suggested that statistical analysis software could help to reduce the examiner's workload. This led to a new tool mark analysis approach, introduced in this thesis, that relies on 3D scans of screwdriver tip and marked plate surfaces at the micrometer scale from an optical microscope. These scans are carefully cleaned to remove noise from the data acquisition process and assigned a coordinate system that mathematically de nes angles and twists in a natural way. The marking process is then simulated by using a 3D graphics software package to impart rotations to the tip and take the projection of the tip's geometry in the direction of tool travel. The edge of this projection, retrieved from the 3D graphics software, becomes a virtual tool mark. Using this method, virtual marks are made at increments of 5 and compared to a scan of the evidence mark. The previously developed statistical package from Chumbley et al. (2010) performs the comparison, comparing the similarity of the geometry of both marks to the similarity that would occur due to random chance. The resulting statistical measure of the likelihood of the match informs the examiner of the angle of the best matching virtual mark, allowing the examiner to focus his/her mark analysis on a smaller range of angles. Preliminary results are quite promising. In a study with both sides of 6 screwdriver tips and 34 corresponding marks, the method distinguished known matches from known non-matches with zero false positive matches and only two matches mistaken for non-matches. For matches, it could predict the correct marking angle within 5-10 . Moreover, on a standard desktop computer, the virtual marking software is capable of cleaning 3D tip and plate scans in minutes and producing a virtual mark and comparing it to a real mark in seconds. These results support several of the professional conclusions of the tool mark analysis com- munity, including the idea that marks produced by the same tool only match if they are made at similar angles. The method also displays the potential to automate part of the comparison process, freeing the examiner to focus on other tasks, which is important in busy, backlogged crime labs. Finally, the method o ers the unique chance to directly link an evidence mark to the tool that produced it while reducing potential damage to the evidence.« less

An Aerodynamic Simulation Process for Iced Lifting Surfaces and Associated Issues

NASA Technical Reports Server (NTRS)

Choo, Yung K.; Vickerman, Mary B.; Hackenberg, Anthony W.; Rigby, David L.

2003-01-01

This paper discusses technologies and software tools that are being implemented in a software toolkit currently under development at NASA Glenn Research Center. Its purpose is to help study the effects of icing on airfoil performance and assist with the aerodynamic simulation process which consists of characterization and modeling of ice geometry, application of block topology and grid generation, and flow simulation. Tools and technologies for each task have been carefully chosen based on their contribution to the overall process. For the geometry characterization and modeling, we have chosen an interactive rather than automatic process in order to handle numerous ice shapes. An Appendix presents features of a software toolkit developed to support the interactive process. Approaches taken for the generation of block topology and grids, and flow simulation, though not yet implemented in the software, are discussed with reasons for why particular methods are chosen. Some of the issues that need to be addressed and discussed by the icing community are also included.

Current trends for customized biomedical software tools.

PubMed

Khan, Haseeb Ahmad

2017-01-01

In the past, biomedical scientists were solely dependent on expensive commercial software packages for various applications. However, the advent of user-friendly programming languages and open source platforms has revolutionized the development of simple and efficient customized software tools for solving specific biomedical problems. Many of these tools are designed and developed by biomedical scientists independently or with the support of computer experts and often made freely available for the benefit of scientific community. The current trends for customized biomedical software tools are highlighted in this short review.

AZTEC. Parallel Iterative method Software for Solving Linear Systems

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

Hutchinson, S.; Shadid, J.; Tuminaro, R.

1995-07-01

AZTEC is an interactive library that greatly simplifies the parrallelization process when solving the linear systems of equations Ax=b where A is a user supplied n X n sparse matrix, b is a user supplied vector of length n and x is a vector of length n to be computed. AZTEC is intended as a software tool for users who want to avoid cumbersome parallel programming details but who have large sparse linear systems which require an efficiently utilized parallel processing system. A collection of data transformation tools are provided that allow for easy creation of distributed sparse unstructured matricesmore » for parallel solutions.« less

Analysing Culture and Interculture in Saudi EFL Textbooks: A Corpus Linguistic Approach

ERIC Educational Resources Information Center

Almujaiwel, Sultan

2018-01-01

This paper combines corpus processing tools to investigate the cultural elements of Saudi education of English as a foreign language (EFL). The latest Saudi EFL textbooks (2016 onwards) are available in researchable PDF formats. This helps process them through corpus search software tools. The method adopted is based on analysing 20 cultural…

MFV-class: a multi-faceted visualization tool of object classes.

PubMed

Zhang, Zhi-meng; Pan, Yun-he; Zhuang, Yue-ting

2004-11-01

Classes are key software components in an object-oriented software system. In many industrial OO software systems, there are some classes that have complicated structure and relationships. So in the processes of software maintenance, testing, software reengineering, software reuse and software restructure, it is a challenge for software engineers to understand these classes thoroughly. This paper proposes a class comprehension model based on constructivist learning theory, and implements a software visualization tool (MFV-Class) to help in the comprehension of a class. The tool provides multiple views of class to uncover manifold facets of class contents. It enables visualizing three object-oriented metrics of classes to help users focus on the understanding process. A case study was conducted to evaluate our approach and the toolkit.

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.

Open environments to support systems engineering tool integration: A study using the Portable Common Tool Environment (PCTE)

NASA Technical Reports Server (NTRS)

Eckhardt, Dave E., Jr.; Jipping, Michael J.; Wild, Chris J.; Zeil, Steven J.; Roberts, Cathy C.

1993-01-01

A study of computer engineering tool integration using the Portable Common Tool Environment (PCTE) Public Interface Standard is presented. Over a 10-week time frame, three existing software products were encapsulated to work in the Emeraude environment, an implementation of the PCTE version 1.5 standard. The software products used were a computer-aided software engineering (CASE) design tool, a software reuse tool, and a computer architecture design and analysis tool. The tool set was then demonstrated to work in a coordinated design process in the Emeraude environment. The project and the features of PCTE used are described, experience with the use of Emeraude environment over the project time frame is summarized, and several related areas for future research are summarized.

Open-source Software for Demand Forecasting of Clinical Laboratory Test Volumes Using Time-series Analysis

PubMed Central

Mohammed, Emad A.; Naugler, Christopher

2017-01-01

Background: Demand forecasting is the area of predictive analytics devoted to predicting future volumes of services or consumables. Fair understanding and estimation of how demand will vary facilitates the optimal utilization of resources. In a medical laboratory, accurate forecasting of future demand, that is, test volumes, can increase efficiency and facilitate long-term laboratory planning. Importantly, in an era of utilization management initiatives, accurately predicted volumes compared to the realized test volumes can form a precise way to evaluate utilization management initiatives. Laboratory test volumes are often highly amenable to forecasting by time-series models; however, the statistical software needed to do this is generally either expensive or highly technical. Method: In this paper, we describe an open-source web-based software tool for time-series forecasting and explain how to use it as a demand forecasting tool in clinical laboratories to estimate test volumes. Results: This tool has three different models, that is, Holt-Winters multiplicative, Holt-Winters additive, and simple linear regression. Moreover, these models are ranked and the best one is highlighted. Conclusion: This tool will allow anyone with historic test volume data to model future demand. PMID:28400996

HTAPP: High-Throughput Autonomous Proteomic Pipeline

PubMed Central

Yu, Kebing; Salomon, Arthur R.

2011-01-01

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

ELISA, a demonstrator environment for information systems architecture design

NASA Technical Reports Server (NTRS)

Panem, Chantal

1994-01-01

This paper describes an approach of reusability of software engineering technology in the area of ground space system design. System engineers have lots of needs similar to software developers: sharing of a common data base, capitalization of knowledge, definition of a common design process, communication between different technical domains. Moreover system designers need to simulate dynamically their system as early as possible. Software development environments, methods and tools now become operational and widely used. Their architecture is based on a unique object base, a set of common management services and they host a family of tools for each life cycle activity. In late '92, CNES decided to develop a demonstrative software environment supporting some system activities. The design of ground space data processing systems was chosen as the application domain. ELISA (Integrated Software Environment for Architectures Specification) was specified as a 'demonstrator', i.e. a sufficient basis for demonstrations, evaluation and future operational enhancements. A process with three phases was implemented: system requirements definition, design of system architectures models, and selection of physical architectures. Each phase is composed of several activities that can be performed in parallel, with the provision of Commercial Off the Shelves Tools. ELISA has been delivered to CNES in January 94, currently used for demonstrations and evaluations on real projects (e.g. SPOT4 Satellite Control Center). It is on the way of new evolutions.

ProphTools: general prioritization tools for heterogeneous biological networks.

PubMed

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

2017-12-01

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

A multiparametric automatic method to monitor long-term reproducibility in digital mammography: results from a regional screening programme.

PubMed

Gennaro, G; Ballaminut, A; Contento, G

2017-09-01

This study aims to illustrate a multiparametric automatic method for monitoring long-term reproducibility of digital mammography systems, and its application on a large scale. Twenty-five digital mammography systems employed within a regional screening programme were controlled weekly using the same type of phantom, whose images were analysed by an automatic software tool. To assess system reproducibility levels, 15 image quality indices (IQIs) were extracted and compared with the corresponding indices previously determined by a baseline procedure. The coefficients of variation (COVs) of the IQIs were used to assess the overall variability. A total of 2553 phantom images were collected from the 25 digital mammography systems from March 2013 to December 2014. Most of the systems showed excellent image quality reproducibility over the surveillance interval, with mean variability below 5%. Variability of each IQI was 5%, with the exception of one index associated with the smallest phantom objects (0.25 mm), which was below 10%. The method applied for reproducibility tests-multi-detail phantoms, cloud automatic software tool to measure multiple image quality indices and statistical process control-was proven to be effective and applicable on a large scale and to any type of digital mammography system. • Reproducibility of mammography image quality should be monitored by appropriate quality controls. • Use of automatic software tools allows image quality evaluation by multiple indices. • System reproducibility can be assessed comparing current index value with baseline data. • Overall system reproducibility of modern digital mammography systems is excellent. • The method proposed and applied is cost-effective and easily scalable.

ToxPredictor: a Toxicity Estimation Software Tool

EPA Science Inventory

The Computational Toxicology Team within the National Risk Management Research Laboratory has developed a software tool that will allow the user to estimate the toxicity for a variety of endpoints (such as acute aquatic toxicity). The software tool is coded in Java and can be ac...

Transforming Clinical Imaging Data for Virtual Reality Learning Objects

ERIC Educational Resources Information Center

Trelease, Robert B.; Rosset, Antoine

2008-01-01

Advances in anatomical informatics, three-dimensional (3D) modeling, and virtual reality (VR) methods have made computer-based structural visualization a practical tool for education. In this article, the authors describe streamlined methods for producing VR "learning objects," standardized interactive software modules for anatomical sciences…

Analyzing the economic impacts of transportation projects.

DOT National Transportation Integrated Search

2013-09-01

The main goal of the study is to explore methods, approaches and : analytical software tools for analyzing economic activity that results from largescale : transportation investments in Connecticut. The primary conclusion is that the : transportation...

Monte Carlo Methodology Serves Up a Software Success

NASA Technical Reports Server (NTRS)

2003-01-01

Widely used for the modeling of gas flows through the computation of the motion and collisions of representative molecules, the Direct Simulation Monte Carlo method has become the gold standard for producing research and engineering predictions in the field of rarefied gas dynamics. Direct Simulation Monte Carlo was first introduced in the early 1960s by Dr. Graeme Bird, a professor at the University of Sydney, Australia. It has since proved to be a valuable tool to the aerospace and defense industries in providing design and operational support data, as well as flight data analysis. In 2002, NASA brought to the forefront a software product that maintains the same basic physics formulation of Dr. Bird's method, but provides effective modeling of complex, three-dimensional, real vehicle simulations and parallel processing capabilities to handle additional computational requirements, especially in areas where computational fluid dynamics (CFD) is not applicable. NASA's Direct Simulation Monte Carlo Analysis Code (DAC) software package is now considered the Agency s premier high-fidelity simulation tool for predicting vehicle aerodynamics and aerothermodynamic environments in rarified, or low-density, gas flows.

Statistical analysis of water-quality data containing multiple detection limits: S-language software for regression on order statistics

USGS Publications Warehouse

Lee, L.; Helsel, D.

2005-01-01

Trace contaminants in water, including metals and organics, often are measured at sufficiently low concentrations to be reported only as values below the instrument detection limit. Interpretation of these "less thans" is complicated when multiple detection limits occur. Statistical methods for multiply censored, or multiple-detection limit, datasets have been developed for medical and industrial statistics, and can be employed to estimate summary statistics or model the distributions of trace-level environmental data. We describe S-language-based software tools that perform robust linear regression on order statistics (ROS). The ROS method has been evaluated as one of the most reliable procedures for developing summary statistics of multiply censored data. It is applicable to any dataset that has 0 to 80% of its values censored. These tools are a part of a software library, or add-on package, for the R environment for statistical computing. This library can be used to generate ROS models and associated summary statistics, plot modeled distributions, and predict exceedance probabilities of water-quality standards. ?? 2005 Elsevier Ltd. All rights reserved.

Playbook Data Analysis Tool: Collecting Interaction Data from Extremely Remote Users

NASA Technical Reports Server (NTRS)

Kanefsky, Bob; Zheng, Jimin; Deliz, Ivonne; Marquez, Jessica J.; Hillenius, Steven

2017-01-01

Typically, user tests for software tools are conducted in person. At NASA, the users may be located at the bottom of the ocean in a pressurized habitat, above the atmosphere in the International Space Station, or in an isolated capsule on a simulated asteroid mission. The Playbook Data Analysis Tool (P-DAT) is a human-computer interaction (HCI) evaluation tool that the NASA Ames HCI Group has developed to record user interactions with Playbook, the group's existing planning-and-execution software application. Once the remotely collected user interaction data makes its way back to Earth, researchers can use P-DAT for in-depth analysis. Since a critical component of the Playbook project is to understand how to develop more intuitive software tools for astronauts to plan in space, P-DAT helps guide us in the development of additional easy-to-use features for Playbook, informing the design of future crew autonomy tools.P-DAT has demonstrated the capability of discreetly capturing usability data in amanner that is transparent to Playbook’s end-users. In our experience, P-DAT data hasalready shown its utility, revealing potential usability patterns, helping diagnose softwarebugs, and identifying metrics and events that are pertinent to Playbook usage aswell as spaceflight operations. As we continue to develop this analysis tool, P-DATmay yet provide a method for long-duration, unobtrusive human performance collectionand evaluation for mission controllers back on Earth and researchers investigatingthe effects and mitigations related to future human spaceflight performance.

Proceedings of the Ninth Annual Software Engineering Workshop

NASA Technical Reports Server (NTRS)

1984-01-01

Experiences in measurement, utilization, and evaluation of software methodologies, models, and tools are discussed. NASA's involvement in ever larger and more complex systems, like the space station project, provides a motive for the support of software engineering research and the exchange of ideas in such forums. The topics of current SEL research are software error studies, experiments with software development, and software tools.

Software Management Environment (SME): Components and algorithms

NASA Technical Reports Server (NTRS)

Hendrick, Robert; Kistler, David; Valett, Jon

1994-01-01

This document presents the components and algorithms of the Software Management Environment (SME), a management tool developed for the Software Engineering Branch (Code 552) of the Flight Dynamics Division (FDD) of the Goddard Space Flight Center (GSFC). The SME provides an integrated set of visually oriented experienced-based tools that can assist software development managers in managing and planning software development projects. This document describes and illustrates the analysis functions that underlie the SME's project monitoring, estimation, and planning tools. 'SME Components and Algorithms' is a companion reference to 'SME Concepts and Architecture' and 'Software Engineering Laboratory (SEL) Relationships, Models, and Management Rules.'

The GeoViz Toolkit: Using component-oriented coordination methods for geographic visualization and analysis

PubMed Central

Hardisty, Frank; Robinson, Anthony C.

2010-01-01

In this paper we present the GeoViz Toolkit, an open-source, internet-delivered program for geographic visualization and analysis that features a diverse set of software components which can be flexibly combined by users who do not have programming expertise. The design and architecture of the GeoViz Toolkit allows us to address three key research challenges in geovisualization: allowing end users to create their own geovisualization and analysis component set on-the-fly, integrating geovisualization methods with spatial analysis methods, and making geovisualization applications sharable between users. Each of these tasks necessitates a robust yet flexible approach to inter-tool coordination. The coordination strategy we developed for the GeoViz Toolkit, called Introspective Observer Coordination, leverages and combines key advances in software engineering from the last decade: automatic introspection of objects, software design patterns, and reflective invocation of methods. PMID:21731423

Spectrum analysis on quality requirements consideration in software design documents.

PubMed

Kaiya, Haruhiko; Umemura, Masahiro; Ogata, Shinpei; Kaijiri, Kenji

2013-12-01

Software quality requirements defined in the requirements analysis stage should be implemented in the final products, such as source codes and system deployment. To guarantee this meta-requirement, quality requirements should be considered in the intermediate stages, such as the design stage or the architectural definition stage. We propose a novel method for checking whether quality requirements are considered in the design stage. In this method, a technique called "spectrum analysis for quality requirements" is applied not only to requirements specifications but also to design documents. The technique enables us to derive the spectrum of a document, and quality requirements considerations in the document are numerically represented in the spectrum. We can thus objectively identify whether the considerations of quality requirements in a requirements document are adapted to its design document. To validate the method, we applied it to commercial software systems with the help of a supporting tool, and we confirmed that the method worked well.

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

PubMed

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

2015-03-01

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

Fault Tolerant Considerations and Methods for Guidance and Control Systems

DTIC Science & Technology

1987-07-01

multifunction devices such as microprocessors with software. In striving toward the economic goal, however, a cost is incurred in a different coin, i.e...therefore been developed which reduces the software risk to acceptable proportions. Several of the techniques thus developed incur no significant cost ...complex that their design and implementation need computerized tools in order to be cost -effective (in a broad sense, including the capability of

Radio frequency tags systems to initiate system processing

NASA Astrophysics Data System (ADS)

Madsen, Harold O.; Madsen, David W.

1994-09-01

This paper describes the automatic identification technology which has been installed at Applied Magnetic Corp. MR fab. World class manufacturing requires technology exploitation. This system combines (1) FluoroTrac cassette and operator tracking, (2) CELLworks cell controller software tools, and (3) Auto-Soft Inc. software integration services. The combined system eliminates operator keystrokes and errors during normal processing within a semiconductor fab. The methods and benefits of this system are described.

NSWC-NADC interactive communication links for AN/UYS-1 loadtape creation and retrieval

NASA Astrophysics Data System (ADS)

Greathouse, D. M.

1984-09-01

This report contains an alternative method of communication (interactive vs. remote batch) with the Naval Air Development Center for the creation and retrieval of AN/UYS-1 Advanced Signal Processor (ASP) operational software loadtapes. Operational software for the Digital Acoustic Sensor Simulator (DASS) program is developed and maintained at the Naval Air Development Center (NADC). The Facility for Automated Software Production (FASP), an NADC-resident software generation facility, provides the support tools necessary for data base creation, software development and maintenance, and loadtape generation. Once a loadtape file is generated at NADC, it must be retrieved via telephone transmission and placed in a format suitable for loading into the AN/UYS-1 Advanced Signal Processor (ASP).

Graphical Technique to Support the Teaching/Learning Process of Software Process Reference Models

NASA Astrophysics Data System (ADS)

Espinosa-Curiel, Ismael Edrein; Rodríguez-Jacobo, Josefina; Fernández-Zepeda, José Alberto

In this paper, we propose a set of diagrams to visualize software process reference models (PRM). The diagrams, called dimods, are the combination of some visual and process modeling techniques such as rich pictures, mind maps, IDEF and RAD diagrams. We show the use of this technique by designing a set of dimods for the Mexican Software Industry Process Model (MoProSoft). Additionally, we perform an evaluation of the usefulness of dimods. The result of the evaluation shows that dimods may be a support tool that facilitates the understanding, memorization, and learning of software PRMs in both, software development organizations and universities. The results also show that dimods may have advantages over the traditional description methods for these types of models.

Survey of Non-Rigid Registration Tools in Medicine.

PubMed

Keszei, András P; Berkels, Benjamin; Deserno, Thomas M

2017-02-01

We catalogue available software solutions for non-rigid image registration to support scientists in selecting suitable tools for specific medical registration purposes. Registration tools were identified using non-systematic search in Pubmed, Web of Science, IEEE Xplore® Digital Library, Google Scholar, and through references in identified sources (n = 22). Exclusions are due to unavailability or inappropriateness. The remaining (n = 18) tools were classified by (i) access and technology, (ii) interfaces and application, (iii) living community, (iv) supported file formats, and (v) types of registration methodologies emphasizing the similarity measures implemented. Out of the 18 tools, (i) 12 are open source, 8 are released under a permissive free license, which imposes the least restrictions on the use and further development of the tool, 8 provide graphical processing unit (GPU) support; (ii) 7 are built on software platforms, 5 were developed for brain image registration; (iii) 6 are under active development but only 3 have had their last update in 2015 or 2016; (iv) 16 support the Analyze format, while 7 file formats can be read with only one of the tools; and (v) 6 provide multiple registration methods and 6 provide landmark-based registration methods. Based on open source, licensing, GPU support, active community, several file formats, algorithms, and similarity measures, the tools Elastics and Plastimatch are chosen for the platform ITK and without platform requirements, respectively. Researchers in medical image analysis already have a large choice of registration tools freely available. However, the most recently published algorithms may not be included in the tools, yet.

Reviews of Instructional Software in Scholarly Journals: A Selected Bibliography.

ERIC Educational Resources Information Center

Bantz, David A.; And Others

This bibliography lists reviews of more than 100 instructional software packages, which are arranged alphabetically by discipline. Information provided for each entry includes the topical emphasis, type of software (i.e., simulation, tutorial, analysis tool, test generator, database, writing tool, drill, plotting tool, videodisc), the journal…

Modeling and MBL: Software Tools for Science.

ERIC Educational Resources Information Center

Tinker, Robert F.

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

Assistive Software Tools for Secondary-Level Students with Literacy Difficulties

ERIC Educational Resources Information Center

Lange, Alissa A.; McPhillips, Martin; Mulhern, Gerry; Wylie, Judith

2006-01-01

The present study assessed the compensatory effectiveness of four assistive software tools (speech synthesis, spellchecker, homophone tool, and dictionary) on literacy. Secondary-level students (N = 93) with reading difficulties completed computer-based tests of literacy skills. Training on their respective software followed for those assigned to…

Estimation of toxicity using a Java based software tool

EPA Science Inventory

A software tool has been developed that will allow a user to estimate the toxicity for a variety of endpoints (such as acute aquatic toxicity). The software tool is coded in Java and can be accessed using a web browser (or alternatively downloaded and ran as a stand alone applic...

Software Construction and Analysis Tools for Future Space Missions

NASA Technical Reports Server (NTRS)

Lowry, Michael R.; Clancy, Daniel (Technical Monitor)

2002-01-01

NASA and its international partners will increasingly depend on software-based systems to implement advanced functions for future space missions, such as Martian rovers that autonomously navigate long distances exploring geographic features formed by surface water early in the planet's history. The software-based functions for these missions will need to be robust and highly reliable, raising significant challenges in the context of recent Mars mission failures attributed to software faults. After reviewing these challenges, this paper describes tools that have been developed at NASA Ames that could contribute to meeting these challenges; 1) Program synthesis tools based on automated inference that generate documentation for manual review and annotations for automated certification. 2) Model-checking tools for concurrent object-oriented software that achieve memorability through synergy with program abstraction and static analysis tools.

Software tool for portal dosimetry research.

PubMed

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

2008-09-01

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

OptFlux: an open-source software platform for in silico metabolic engineering.

PubMed

Rocha, Isabel; Maia, Paulo; Evangelista, Pedro; Vilaça, Paulo; Soares, Simão; Pinto, José P; Nielsen, Jens; Patil, Kiran R; Ferreira, Eugénio C; Rocha, Miguel

2010-04-19

Over the last few years a number of methods have been proposed for the phenotype simulation of microorganisms under different environmental and genetic conditions. These have been used as the basis to support the discovery of successful genetic modifications of the microbial metabolism to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other expert researchers. The main aim of this work is, therefore, to provide a user-friendly computational tool for Metabolic Engineering applications. OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the previously proposed OptKnock algorithm. It also allows the use of stoichiometric metabolic models for (i) phenotype simulation of both wild-type and mutant organisms, using the methods of Flux Balance Analysis, Minimization of Metabolic Adjustment or Regulatory on/off Minimization of Metabolic flux changes, (ii) Metabolic Flux Analysis, computing the admissible flux space given a set of measured fluxes, and (iii) pathway analysis through the calculation of Elementary Flux Modes. OptFlux also contemplates several methods for model simplification and other pre-processing operations aimed at reducing the search space for optimization algorithms. The software supports importing/exporting to several flat file formats and it is compatible with the SBML standard. OptFlux has a visualization module that allows the analysis of the model structure that is compatible with the layout information of Cell Designer, allowing the superimposition of simulation results with the model graph. The OptFlux software is freely available, together with documentation and other resources, thus bridging the gap from research in strain optimization algorithms and the final users. It is a valuable platform for researchers in the field that have available a number of useful tools. Its open-source nature invites contributions by all those interested in making their methods available for the community. Given its plug-in based architecture it can be extended with new functionalities. Currently, several plug-ins are being developed, including network topology analysis tools and the integration with Boolean network based regulatory models.

OptFlux: an open-source software platform for in silico metabolic engineering

PubMed Central

2010-01-01

Background Over the last few years a number of methods have been proposed for the phenotype simulation of microorganisms under different environmental and genetic conditions. These have been used as the basis to support the discovery of successful genetic modifications of the microbial metabolism to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other expert researchers. The main aim of this work is, therefore, to provide a user-friendly computational tool for Metabolic Engineering applications. Results OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the previously proposed OptKnock algorithm. It also allows the use of stoichiometric metabolic models for (i) phenotype simulation of both wild-type and mutant organisms, using the methods of Flux Balance Analysis, Minimization of Metabolic Adjustment or Regulatory on/off Minimization of Metabolic flux changes, (ii) Metabolic Flux Analysis, computing the admissible flux space given a set of measured fluxes, and (iii) pathway analysis through the calculation of Elementary Flux Modes. OptFlux also contemplates several methods for model simplification and other pre-processing operations aimed at reducing the search space for optimization algorithms. The software supports importing/exporting to several flat file formats and it is compatible with the SBML standard. OptFlux has a visualization module that allows the analysis of the model structure that is compatible with the layout information of Cell Designer, allowing the superimposition of simulation results with the model graph. Conclusions The OptFlux software is freely available, together with documentation and other resources, thus bridging the gap from research in strain optimization algorithms and the final users. It is a valuable platform for researchers in the field that have available a number of useful tools. Its open-source nature invites contributions by all those interested in making their methods available for the community. Given its plug-in based architecture it can be extended with new functionalities. Currently, several plug-ins are being developed, including network topology analysis tools and the integration with Boolean network based regulatory models. PMID:20403172

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.

Imaging and quantitative methods for studying cytoskeletal rearrangements during root development and gravitropism.

PubMed

Jacques, Eveline; Wells, Darren M; Bennett, Malcolm J; Vissenberg, Kris

2015-01-01

High-resolution imaging of cytoskeletal structures paves the way for standardized methods to quantify cytoskeletal organization. Here we provide a detailed description of the analysis performed to determine the microtubule patterns in gravistimulated roots, using the recently developed software tool MicroFilament Analyzer.

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.

Tapping into Graduate Students' Collaborative Technology Experience in a Research Methods Class: Insights on Teaching Research Methods in a Malaysian and American Setting

ERIC Educational Resources Information Center

Vasquez-Colina, Maria D.; Maslin-Ostrowski, Pat; Baba, Suria

2017-01-01

This case study used qualitative and quantitative methods to investigate challenges of learning and teaching research methods by examining graduate students' use of collaborative technology (i.e., digital tools that enable collaboration and information seeking such as software and social media) and students' computer self-efficacy. We conducted…

The Synthesis Map Is a Multidimensional Educational Tool That Provides Insight into Students' Mental Models and Promotes Students' Synthetic Knowledge Generation

ERIC Educational Resources Information Center

Ortega, Ryan A.; Brame, Cynthia J.

2015-01-01

Concept mapping was developed as a method of displaying and organizing hierarchical knowledge structures. Using the new, multidimensional presentation software Prezi, we have developed a new teaching technique designed to engage higher-level skills in the cognitive domain. This tool, synthesis mapping, is a natural evolution of concept mapping,…

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

PubMed

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

2016-08-01

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

Web-based interactive 2D/3D medical image processing and visualization software.

PubMed

Mahmoudi, Seyyed Ehsan; Akhondi-Asl, Alireza; Rahmani, Roohollah; Faghih-Roohi, Shahrooz; Taimouri, Vahid; Sabouri, Ahmad; Soltanian-Zadeh, Hamid

2010-05-01

There are many medical image processing software tools available for research and diagnosis purposes. However, most of these tools are available only as local applications. This limits the accessibility of the software to a specific machine, and thus the data and processing power of that application are not available to other workstations. Further, there are operating system and processing power limitations which prevent such applications from running on every type of workstation. By developing web-based tools, it is possible for users to access the medical image processing functionalities wherever the internet is available. In this paper, we introduce a pure web-based, interactive, extendable, 2D and 3D medical image processing and visualization application that requires no client installation. Our software uses a four-layered design consisting of an algorithm layer, web-user-interface layer, server communication layer, and wrapper layer. To compete with extendibility of the current local medical image processing software, each layer is highly independent of other layers. A wide range of medical image preprocessing, registration, and segmentation methods are implemented using open source libraries. Desktop-like user interaction is provided by using AJAX technology in the web-user-interface. For the visualization functionality of the software, the VRML standard is used to provide 3D features over the web. Integration of these technologies has allowed implementation of our purely web-based software with high functionality without requiring powerful computational resources in the client side. The user-interface is designed such that the users can select appropriate parameters for practical research and clinical studies. Copyright (c) 2009 Elsevier Ireland Ltd. All rights reserved.

Methylation Integration (Mint) | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

A comprehensive software pipeline and set of Galaxy tools/workflows for integrative analysis of genome-wide DNA methylation and hydroxymethylation data. Data types can be either bisulfite sequencing and/or pull-down methods.

ProUCL version 4.1.00 Documentation Downloads

EPA Pesticide Factsheets

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

Parallel software tools at Langley Research Center

NASA Technical Reports Server (NTRS)

Moitra, Stuti; Tennille, Geoffrey M.; Lakeotes, Christopher D.; Randall, Donald P.; Arthur, Jarvis J.; Hammond, Dana P.; Mall, Gerald H.

1993-01-01

This document gives a brief overview of parallel software tools available on the Intel iPSC/860 parallel computer at Langley Research Center. It is intended to provide a source of information that is somewhat more concise than vendor-supplied material on the purpose and use of various tools. Each of the chapters on tools is organized in a similar manner covering an overview of the functionality, access information, how to effectively use the tool, observations about the tool and how it compares to similar software, known problems or shortfalls with the software, and reference documentation. It is primarily intended for users of the iPSC/860 at Langley Research Center and is appropriate for both the experienced and novice user.

AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis

PubMed Central

Boyle, Thomas J; Bao, Zhirong; Murray, John I; Araya, Carlos L; Waterston, Robert H

2006-01-01

Background The invariant lineage of the nematode Caenorhabditis elegans has potential as a powerful tool for the description of mutant phenotypes and gene expression patterns. We previously described procedures for the imaging and automatic extraction of the cell lineage from C. elegans embryos. That method uses time-lapse confocal imaging of a strain expressing histone-GFP fusions and a software package, StarryNite, processes the thousands of images and produces output files that describe the location and lineage relationship of each nucleus at each time point. Results We have developed a companion software package, AceTree, which links the images and the annotations using tree representations of the lineage. This facilitates curation and editing of the lineage. AceTree also contains powerful visualization and interpretive tools, such as space filling models and tree-based expression patterning, that can be used to extract biological significance from the data. Conclusion By pairing a fast lineaging program written in C with a user interface program written in Java we have produced a powerful software suite for exploring embryonic development. PMID:16740163

AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis.

PubMed

Boyle, Thomas J; Bao, Zhirong; Murray, John I; Araya, Carlos L; Waterston, Robert H

2006-06-01

The invariant lineage of the nematode Caenorhabditis elegans has potential as a powerful tool for the description of mutant phenotypes and gene expression patterns. We previously described procedures for the imaging and automatic extraction of the cell lineage from C. elegans embryos. That method uses time-lapse confocal imaging of a strain expressing histone-GFP fusions and a software package, StarryNite, processes the thousands of images and produces output files that describe the location and lineage relationship of each nucleus at each time point. We have developed a companion software package, AceTree, which links the images and the annotations using tree representations of the lineage. This facilitates curation and editing of the lineage. AceTree also contains powerful visualization and interpretive tools, such as space filling models and tree-based expression patterning, that can be used to extract biological significance from the data. By pairing a fast lineaging program written in C with a user interface program written in Java we have produced a powerful software suite for exploring embryonic development.

IDEAL: Images Across Domains, Experiments, Algorithms and Learning

NASA Astrophysics Data System (ADS)

Ushizima, Daniela M.; Bale, Hrishikesh A.; Bethel, E. Wes; Ercius, Peter; Helms, Brett A.; Krishnan, Harinarayan; Grinberg, Lea T.; Haranczyk, Maciej; Macdowell, Alastair A.; Odziomek, Katarzyna; Parkinson, Dilworth Y.; Perciano, Talita; Ritchie, Robert O.; Yang, Chao

2016-11-01

Research across science domains is increasingly reliant on image-centric data. Software tools are in high demand to uncover relevant, but hidden, information in digital images, such as those coming from faster next generation high-throughput imaging platforms. The challenge is to analyze the data torrent generated by the advanced instruments efficiently, and provide insights such as measurements for decision-making. In this paper, we overview work performed by an interdisciplinary team of computational and materials scientists, aimed at designing software applications and coordinating research efforts connecting (1) emerging algorithms for dealing with large and complex datasets; (2) data analysis methods with emphasis in pattern recognition and machine learning; and (3) advances in evolving computer architectures. Engineering tools around these efforts accelerate the analyses of image-based recordings, improve reusability and reproducibility, scale scientific procedures by reducing time between experiments, increase efficiency, and open opportunities for more users of the imaging facilities. This paper describes our algorithms and software tools, showing results across image scales, demonstrating how our framework plays a role in improving image understanding for quality control of existent materials and discovery of new compounds.

A Quantitative Analysis of Open Source Software's Acceptability as Production-Quality Code

ERIC Educational Resources Information Center

Fischer, Michael

2011-01-01

The difficulty in writing defect-free software has been long acknowledged both by academia and industry. A constant battle occurs as developers seek to craft software that works within aggressive business schedules and deadlines. Many tools and techniques are used in attempt to manage these software projects. Software metrics are a tool that has…

Voxel Datacubes for 3D Visualization in Blender

NASA Astrophysics Data System (ADS)

Gárate, Matías

2017-05-01

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

The enhanced Software Life Cyle Support Environment (ProSLCSE): Automation for enterprise and process modeling

NASA Technical Reports Server (NTRS)

Milligan, James R.; Dutton, James E.

1993-01-01

In this paper, we have introduced a comprehensive method for enterprise modeling that addresses the three important aspects of how an organization goes about its business. FirstEP includes infrastructure modeling, information modeling, and process modeling notations that are intended to be easy to learn and use. The notations stress the use of straightforward visual languages that are intuitive, syntactically simple, and semantically rich. ProSLCSE will be developed with automated tools and services to facilitate enterprise modeling and process enactment. In the spirit of FirstEP, ProSLCSE tools will also be seductively easy to use. Achieving fully managed, optimized software development and support processes will be long and arduous for most software organizations, and many serious problems will have to be solved along the way. ProSLCSE will provide the ability to document, communicate, and modify existing processes, which is the necessary first step.

The mission events graphic generator software: A small tool with big results

NASA Technical Reports Server (NTRS)

Lupisella, Mark; Leibee, Jack; Scaffidi, Charles

1993-01-01

Utilization of graphics has long been a useful methodology for many aspects of spacecraft operations. A personal computer based software tool that implements straight-forward graphics and greatly enhances spacecraft operations is presented. This unique software tool is the Mission Events Graphic Generator (MEGG) software which is used in support of the Hubble Space Telescope (HST) Project. MEGG reads the HST mission schedule and generates a graphical timeline.

Usefulness of the automatic quantitative estimation tool for cerebral blood flow: clinical assessment of the application software tool AQCEL.

PubMed

Momose, Mitsuhiro; Takaki, Akihiro; Matsushita, Tsuyoshi; Yanagisawa, Shin; Yano, Kesato; Miyasaka, Tadashi; Ogura, Yuka; Kadoya, Masumi

2011-01-01

AQCEL enables automatic reconstruction of single-photon emission computed tomogram (SPECT) without image degradation and quantitative analysis of cerebral blood flow (CBF) after the input of simple parameters. We ascertained the usefulness and quality of images obtained by the application software AQCEL in clinical practice. Twelve patients underwent brain perfusion SPECT using technetium-99m ethyl cysteinate dimer at rest and after acetazolamide (ACZ) loading. Images reconstructed using AQCEL were compared with those reconstructed using conventional filtered back projection (FBP) method for qualitative estimation. Two experienced nuclear medicine physicians interpreted the image quality using the following visual scores: 0, same; 1, slightly superior; 2, superior. For quantitative estimation, the mean CBF values of the normal hemisphere of the 12 patients using ACZ calculated by the AQCEL method were compared with those calculated by the conventional method. The CBF values of the 24 regions of the 3-dimensional stereotaxic region of interest template (3DSRT) calculated by the AQCEL method at rest and after ACZ loading were compared to those calculated by the conventional method. No significant qualitative difference was observed between the AQCEL and conventional FBP methods in the rest study. The average score by the AQCEL method was 0.25 ± 0.45 and that by the conventional method was 0.17 ± 0.39 (P = 0.34). There was a significant qualitative difference between the AQCEL and conventional methods in the ACZ loading study. The average score for AQCEL was 0.83 ± 0.58 and that for the conventional method was 0.08 ± 0.29 (P = 0.003). During quantitative estimation using ACZ, the mean CBF values of 12 patients calculated by the AQCEL method were 3-8% higher than those calculated by the conventional method. The square of the correlation coefficient between these methods was 0.995. While comparing the 24 3DSRT regions of 12 patients, the squares of the correlation coefficient between AQCEL and conventional methods were 0.973 and 0.986 for the normal and affected sides at rest, respectively, and 0.977 and 0.984 for the normal and affected sides after ACZ loading, respectively. The quality of images reconstructed using the application software AQCEL were superior to that obtained using conventional method after ACZ loading, and high correlations were shown in quantity at rest and after ACZ loading. This software can be applied to clinical practice and is a useful tool for improvement of reproducibility and throughput.

User Studies: Developing Learning Strategy Tool Software for Children.

ERIC Educational Resources Information Center

Fitzgerald, Gail E.; Koury, Kevin A.; Peng, Hsinyi

This paper is a report of user studies for developing learning strategy tool software for children. The prototype software demonstrated is designed for children with learning and behavioral disabilities. The tools consist of easy-to-use templates for creating organizational, memory, and learning approach guides for use in classrooms and at home.…

MUST - An integrated system of support tools for research flight software engineering. [Multipurpose User-oriented Software Technology

NASA Technical Reports Server (NTRS)

Straeter, T. A.; Foudriat, E. C.; Will, R. W.

1977-01-01

The objectives of NASA's MUST (Multipurpose User-oriented Software Technology) program at Langley Research Center are to cut the cost of producing software which effectively utilizes digital systems for flight research. These objectives will be accomplished by providing an integrated system of support software tools for use throughout the research flight software development process. A description of the overall MUST program and its progress toward the release of a first MUST system will be presented. This release includes: a special interactive user interface, a library of subroutines, assemblers, a compiler, automatic documentation tools, and a test and simulation system.

Managing Digital Archives Using Open Source Software Tools

NASA Astrophysics Data System (ADS)

Barve, S.; Dongare, S.

2007-10-01

This paper describes the use of open source software tools such as MySQL and PHP for creating database-backed websites. Such websites offer many advantages over ones built from static HTML pages. This paper will discuss how OSS tools are used and their benefits, and after the successful implementation of these tools how the library took the initiative in implementing an institutional repository using DSpace open source software.

Tools for Administration of a UNIX-Based Network

NASA Technical Reports Server (NTRS)

LeClaire, Stephen; Farrar, Edward

2004-01-01

Several computer programs have been developed to enable efficient administration of a large, heterogeneous, UNIX-based computing and communication network that includes a variety of computers connected to a variety of subnetworks. One program provides secure software tools for administrators to create, modify, lock, and delete accounts of specific users. This program also provides tools for users to change their UNIX passwords and log-in shells. These tools check for errors. Another program comprises a client and a server component that, together, provide a secure mechanism to create, modify, and query quota levels on a network file system (NFS) mounted by use of the VERITAS File SystemJ software. The client software resides on an internal secure computer with a secure Web interface; one can gain access to the client software from any authorized computer capable of running web-browser software. The server software resides on a UNIX computer configured with the VERITAS software system. Directories where VERITAS quotas are applied are NFS-mounted. Another program is a Web-based, client/server Internet Protocol (IP) address tool that facilitates maintenance lookup of information about IP addresses for a network of computers.

Ffuzz: Towards full system high coverage fuzz testing on binary executables.

PubMed

Zhang, Bin; Ye, Jiaxi; Bi, Xing; Feng, Chao; Tang, Chaojing

2018-01-01

Bugs and vulnerabilities in binary executables threaten cyber security. Current discovery methods, like fuzz testing, symbolic execution and manual analysis, both have advantages and disadvantages when exercising the deeper code area in binary executables to find more bugs. In this paper, we designed and implemented a hybrid automatic bug finding tool-Ffuzz-on top of fuzz testing and selective symbolic execution. It targets full system software stack testing including both the user space and kernel space. Combining these two mainstream techniques enables us to achieve higher coverage and avoid getting stuck both in fuzz testing and symbolic execution. We also proposed two key optimizations to improve the efficiency of full system testing. We evaluated the efficiency and effectiveness of our method on real-world binary software and 844 memory corruption vulnerable programs in the Juliet test suite. The results show that Ffuzz can discover software bugs in the full system software stack effectively and efficiently.

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.

Tracking and Quantifying Developmental Processes in C. elegans Using Open-source Tools.

PubMed

Dutta, Priyanka; Lehmann, Christina; Odedra, Devang; Singh, Deepika; Pohl, Christian

2015-12-16

Quantitatively capturing developmental processes is crucial to derive mechanistic models and key to identify and describe mutant phenotypes. Here protocols are presented for preparing embryos and adult C. elegans animals for short- and long-term time-lapse microscopy and methods for tracking and quantification of developmental processes. The methods presented are all based on C. elegans strains available from the Caenorhabditis Genetics Center and on open-source software that can be easily implemented in any laboratory independently of the microscopy system used. A reconstruction of a 3D cell-shape model using the modelling software IMOD, manual tracking of fluorescently-labeled subcellular structures using the multi-purpose image analysis program Endrov, and an analysis of cortical contractile flow using PIVlab (Time-Resolved Digital Particle Image Velocimetry Tool for MATLAB) are shown. It is discussed how these methods can also be deployed to quantitatively capture other developmental processes in different models, e.g., cell tracking and lineage tracing, tracking of vesicle flow.

Exploiting Software Tool Towards Easier Use And Higher Efficiency

NASA Astrophysics Data System (ADS)

Lin, G. H.; Su, J. T.; Deng, Y. Y.

2006-08-01

In developing countries, using data based on instrument made by themselves in maximum extent is very important. It is not only related to maximizing science returns upon prophase investment -- deep accumulations in every aspects but also science output. Based on the idea, we are exploiting a software (called THDP: Tool of Huairou Data Processing). It is used for processing a series of issues, which is met necessary in processing data. This paper discusses its designed purpose, functions, method and specialities. The primary vehicle for general data interpretation is through various techniques of data visualization, techniques of interactive. In the software, we employed Object Oriented approach. It is appropriate to the vehicle. it is imperative that the approach provide not only function, but do so in as convenient a fashion as possible. As result of the software exploiting, it is not only easier to learn data processing for beginner and more convenienter to need further improvement for senior but also increase greatly efficiency in every phrases include analyse, parameter adjusting, result display. Under frame of virtual observatory, for developing countries, we should study more and newer related technologies, which can advance ability and efficiency in science research, like the software we are developing

Ada developers' supplement to the recommended approach

NASA Technical Reports Server (NTRS)

Kester, Rush; Landis, Linda

1993-01-01

This document is a collection of guidelines for programmers and managers who are responsible for the development of flight dynamics applications in Ada. It is intended to be used in conjunction with the Recommended Approach to Software Development (SEL-81-305), which describes the software development life cycle, its products, reviews, methods, tools, and measures. The Ada Developers' Supplement provides additional detail on such topics as reuse, object-oriented analysis, and object-oriented design.

The State of Software for Evolutionary Biology.

PubMed

Darriba, Diego; Flouri, Tomáš; Stamatakis, Alexandros

2018-05-01

With Next Generation Sequencing data being routinely used, evolutionary biology is transforming into a computational science. Thus, researchers have to rely on a growing number of increasingly complex software. All widely used core tools in the field have grown considerably, in terms of the number of features as well as lines of code and consequently, also with respect to software complexity. A topic that has received little attention is the software engineering quality of widely used core analysis tools. Software developers appear to rarely assess the quality of their code, and this can have potential negative consequences for end-users. To this end, we assessed the code quality of 16 highly cited and compute-intensive tools mainly written in C/C++ (e.g., MrBayes, MAFFT, SweepFinder, etc.) and JAVA (BEAST) from the broader area of evolutionary biology that are being routinely used in current data analysis pipelines. Because, the software engineering quality of the tools we analyzed is rather unsatisfying, we provide a list of best practices for improving the quality of existing tools and list techniques that can be deployed for developing reliable, high quality scientific software from scratch. Finally, we also discuss journal as well as science policy and, more importantly, funding issues that need to be addressed for improving software engineering quality as well as ensuring support for developing new and maintaining existing software. Our intention is to raise the awareness of the community regarding software engineering quality issues and to emphasize the substantial lack of funding for scientific software development.

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.

Hemodynamics model of fluid–solid interaction in internal carotid artery aneurysms

PubMed Central

Fu-Yu, Wang; Lei, Liu; Xiao-Jun, Zhang; Hai-Yue, Ju

2010-01-01

The objective of this study is to present a relatively simple method to reconstruct cerebral aneurysms as 3D numerical grids. The method accurately duplicates the geometry to provide computer simulations of the blood flow. Initial images were obtained by using CT angiography and 3D digital subtraction angiography in DICOM format. The image was processed by using MIMICS software, and the 3D fluid model (blood flow) and 3D solid model (wall) were generated. The subsequent output was exported to the ANSYS workbench software to generate the volumetric mesh for further hemodynamic study. The fluid model was defined and simulated in CFX software while the solid model was calculated in ANSYS software. The force data calculated firstly in the CFX software were transferred to the ANSYS software, and after receiving the force data, total mesh displacement data were calculated in the ANSYS software. Then, the mesh displacement data were transferred back to the CFX software. The data exchange was processed in workbench software. The results of simulation could be visualized in CFX-post. Two examples of grid reconstruction and blood flow simulation for patients with internal carotid artery aneurysms were presented. The wall shear stress, wall total pressure, and von Mises stress could be visualized. This method seems to be relatively simple and suitable for direct use by neurosurgeons or neuroradiologists, and maybe a practical tool for planning treatment and follow-up of patients after neurosurgical or endovascular interventions with 3D angiography. PMID:20812022

Hemodynamics model of fluid-solid interaction in internal carotid artery aneurysms.

PubMed

Bai-Nan, Xu; Fu-Yu, Wang; Lei, Liu; Xiao-Jun, Zhang; Hai-Yue, Ju

2011-01-01

The objective of this study is to present a relatively simple method to reconstruct cerebral aneurysms as 3D numerical grids. The method accurately duplicates the geometry to provide computer simulations of the blood flow. Initial images were obtained by using CT angiography and 3D digital subtraction angiography in DICOM format. The image was processed by using MIMICS software, and the 3D fluid model (blood flow) and 3D solid model (wall) were generated. The subsequent output was exported to the ANSYS workbench software to generate the volumetric mesh for further hemodynamic study. The fluid model was defined and simulated in CFX software while the solid model was calculated in ANSYS software. The force data calculated firstly in the CFX software were transferred to the ANSYS software, and after receiving the force data, total mesh displacement data were calculated in the ANSYS software. Then, the mesh displacement data were transferred back to the CFX software. The data exchange was processed in workbench software. The results of simulation could be visualized in CFX-post. Two examples of grid reconstruction and blood flow simulation for patients with internal carotid artery aneurysms were presented. The wall shear stress, wall total pressure, and von Mises stress could be visualized. This method seems to be relatively simple and suitable for direct use by neurosurgeons or neuroradiologists, and maybe a practical tool for planning treatment and follow-up of patients after neurosurgical or endovascular interventions with 3D angiography.

Assessing the Robustness of Complete Bacterial Genome Segmentations

NASA Astrophysics Data System (ADS)

Devillers, Hugo; Chiapello, Hélène; Schbath, Sophie; El Karoui, Meriem

Comparison of closely related bacterial genomes has revealed the presence of highly conserved sequences forming a "backbone" that is interrupted by numerous, less conserved, DNA fragments. Segmentation of bacterial genomes into backbone and variable regions is particularly useful to investigate bacterial genome evolution. Several software tools have been designed to compare complete bacterial chromosomes and a few online databases store pre-computed genome comparisons. However, very few statistical methods are available to evaluate the reliability of these software tools and to compare the results obtained with them. To fill this gap, we have developed two local scores to measure the robustness of bacterial genome segmentations. Our method uses a simulation procedure based on random perturbations of the compared genomes. The scores presented in this paper are simple to implement and our results show that they allow to discriminate easily between robust and non-robust bacterial genome segmentations when using aligners such as MAUVE and MGA.

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

DOE PAGES

Kang, Dongwan D.; Froula, Jeff; Egan, Rob; ...

2015-01-01

Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. Because of the complex nature of these communities, existing metagenome binning methods often miss a large number of microbial species. In addition, most of the tools are not scalable to large datasets. Here we introduce automated software called MetaBAT that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency for accurate metagenome binning. MetaBAT outperforms alternative methods in accuracy and computational efficiency on both synthetic and real metagenome datasets. Lastly, it automatically formsmore » hundreds of high quality genome bins on a very large assembly consisting millions of contigs in a matter of hours on a single node. MetaBAT is open source software and available at https://bitbucket.org/berkeleylab/metabat.« less

ClusCo: clustering and comparison of protein models.

PubMed

Jamroz, Michal; Kolinski, Andrzej

2013-02-22

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

47 CFR 73.9007 - Robustness requirements for covered demodulator products.

Code of Federal Regulations, 2010 CFR

2010-10-01

... RADIO SERVICES RADIO BROADCAST SERVICES Digital Broadcast Television Redistribution Control § 73.9007...-available tools or equipment also means specialized electronic tools or software tools that are widely... requirements set forth in this subpart. Such specialized electronic tools or software tools includes, but is...

Configuring the Orion Guidance, Navigation, and Control Flight Software for Automated Sequencing

NASA Technical Reports Server (NTRS)

Odegard, Ryan G.; Siliwinski, Tomasz K.; King, Ellis T.; Hart, Jeremy J.

2010-01-01

The Orion Crew Exploration Vehicle is being designed with greater automation capabilities than any other crewed spacecraft in NASA s history. The Guidance, Navigation, and Control (GN&C) flight software architecture is designed to provide a flexible and evolvable framework that accommodates increasing levels of automation over time. Within the GN&C flight software, a data-driven approach is used to configure software. This approach allows data reconfiguration and updates to automated sequences without requiring recompilation of the software. Because of the great dependency of the automation and the flight software on the configuration data, the data management is a vital component of the processes for software certification, mission design, and flight operations. To enable the automated sequencing and data configuration of the GN&C subsystem on Orion, a desktop database configuration tool has been developed. The database tool allows the specification of the GN&C activity sequences, the automated transitions in the software, and the corresponding parameter reconfigurations. These aspects of the GN&C automation on Orion are all coordinated via data management, and the database tool provides the ability to test the automation capabilities during the development of the GN&C software. In addition to providing the infrastructure to manage the GN&C automation, the database tool has been designed with capabilities to import and export artifacts for simulation analysis and documentation purposes. Furthermore, the database configuration tool, currently used to manage simulation data, is envisioned to evolve into a mission planning tool for generating and testing GN&C software sequences and configurations. A key enabler of the GN&C automation design, the database tool allows both the creation and maintenance of the data artifacts, as well as serving the critical role of helping to manage, visualize, and understand the data-driven parameters both during software development and throughout the life of the Orion project.

Processing methods for differential analysis of LC/MS profile data

PubMed Central

Katajamaa, Mikko; Orešič, Matej

2005-01-01

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

Processing methods for differential analysis of LC/MS profile data.

PubMed

Katajamaa, Mikko; Oresic, Matej

2005-07-18

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

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

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

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

2012-01-15

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

A New Look at NASA: Strategic Research In Information Technology

NASA Technical Reports Server (NTRS)

Alfano, David; Tu, Eugene (Technical Monitor)

2002-01-01

This viewgraph presentation provides information on research undertaken by NASA to facilitate the development of information technologies. Specific ideas covered here include: 1) Bio/nano technologies: biomolecular and nanoscale systems and tools for assembly and computing; 2) Evolvable hardware: autonomous self-improving, self-repairing hardware and software for survivable space systems in extreme environments; 3) High Confidence Software Technologies: formal methods, high-assurance software design, and program synthesis; 4) Intelligent Controls and Diagnostics: Next generation machine learning, adaptive control, and health management technologies; 5) Revolutionary computing: New computational models to increase capability and robustness to enable future NASA space missions.

BYMUR software: a free and open source tool for quantifying and visualizing multi-risk analyses

NASA Astrophysics Data System (ADS)

Tonini, Roberto; Selva, Jacopo

2013-04-01

The BYMUR software aims to provide an easy-to-use open source tool for both computing multi-risk and managing/visualizing/comparing all the inputs (e.g. hazard, fragilities and exposure) as well as the corresponding results (e.g. risk curves, risk indexes). For all inputs, a complete management of inter-model epistemic uncertainty is considered. The BYMUR software will be one of the final products provided by the homonymous ByMuR project (http://bymur.bo.ingv.it/) funded by Italian Ministry of Education, Universities and Research (MIUR), focused to (i) provide a quantitative and objective general method for a comprehensive long-term multi-risk analysis in a given area, accounting for inter-model epistemic uncertainty through Bayesian methodologies, and (ii) apply the methodology to seismic, volcanic and tsunami risks in Naples (Italy). More specifically, the BYMUR software will be able to separately account for the probabilistic hazard assessment of different kind of hazardous phenomena, the relative (time-dependent/independent) vulnerabilities and exposure data, and their possible (predefined) interactions: the software will analyze these inputs and will use them to estimate both single- and multi- risk associated to a specific target area. In addition, it will be possible to connect the software to further tools (e.g., a full hazard analysis), allowing a dynamic I/O of results. The use of Python programming language guarantees that the final software will be open source and platform independent. Moreover, thanks to the integration of some most popular and rich-featured Python scientific modules (Numpy, Matplotlib, Scipy) with the wxPython graphical user toolkit, the final tool will be equipped with a comprehensive Graphical User Interface (GUI) able to control and visualize (in the form of tables, maps and/or plots) any stage of the multi-risk analysis. The additional features of importing/exporting data in MySQL databases and/or standard XML formats (for instance, the global standards defined in the frame of GEM project for seismic hazard and risk) will grant the interoperability with other FOSS software and tools and, at the same time, to be on hand of the geo-scientific community. An already available example of connection is represented by the BET_VH(**) tool, which probabilistic volcanic hazard outputs will be used as input for BYMUR. Finally, the prototype version of BYMUR will be used for the case study of the municipality of Naples, by considering three different natural hazards (volcanic eruptions, earthquakes and tsunamis) and by assessing the consequent long-term risk evaluation. (**)BET_VH (Bayesian Event Tree for Volcanic Hazard) is probabilistic tool for long-term volcanic hazard assessment, recently re-designed and adjusted to be run on the Vhub cyber-infrastructure, a free web-based collaborative tool in volcanology research (see http://vhub.org/resources/betvh).

Error correction and diversity analysis of population mixtures determined by NGS

PubMed Central

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

2014-01-01

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

TCGA Expedition: A Data Acquisition and Management System for TCGA Data

PubMed Central

Chandran, Uma R.; Medvedeva, Olga P.; Barmada, M. Michael; Blood, Philip D.; Chakka, Anish; Luthra, Soumya; Ferreira, Antonio; Wong, Kim F.; Lee, Adrian V.; Zhang, Zhihui; Budden, Robert; Scott, J. Ray; Berndt, Annerose; Berg, Jeremy M.; Jacobson, Rebecca S.

2016-01-01

Background The Cancer Genome Atlas Project (TCGA) is a National Cancer Institute effort to profile at least 500 cases of 20 different tumor types using genomic platforms and to make these data, both raw and processed, available to all researchers. TCGA data are currently over 1.2 Petabyte in size and include whole genome sequence (WGS), whole exome sequence, methylation, RNA expression, proteomic, and clinical datasets. Publicly accessible TCGA data are released through public portals, but many challenges exist in navigating and using data obtained from these sites. We developed TCGA Expedition to support the research community focused on computational methods for cancer research. Data obtained, versioned, and archived using TCGA Expedition supports command line access at high-performance computing facilities as well as some functionality with third party tools. For a subset of TCGA data collected at University of Pittsburgh, we also re-associate TCGA data with de-identified data from the electronic health records. Here we describe the software as well as the architecture of our repository, methods for loading of TCGA data to multiple platforms, and security and regulatory controls that conform to federal best practices. Results TCGA Expedition software consists of a set of scripts written in Bash, Python and Java that download, extract, harmonize, version and store all TCGA data and metadata. The software generates a versioned, participant- and sample-centered, local TCGA data directory with metadata structures that directly reference the local data files as well as the original data files. The software supports flexible searches of the data via a web portal, user-centric data tracking tools, and data provenance tools. Using this software, we created a collaborative repository, the Pittsburgh Genome Resource Repository (PGRR) that enabled investigators at our institution to work with all TCGA data formats, and to interrogate these data with analysis pipelines, and associated tools. WGS data are especially challenging for individual investigators to use, due to issues with downloading, storage, and processing; having locally accessible WGS BAM files has proven invaluable. Conclusion Our open-source, freely available TCGA Expedition software can be used to create a local collaborative infrastructure for acquiring, managing, and analyzing TCGA data and other large public datasets. PMID:27788220

Technology Transfer Challenges for High-Assurance Software Engineering Tools

NASA Technical Reports Server (NTRS)

Koga, Dennis (Technical Monitor); Penix, John; Markosian, Lawrence Z.

2003-01-01

In this paper, we describe our experience with the challenges thar we are currently facing in our effort to develop advanced software verification and validation tools. We categorize these challenges into several areas: cost benefits modeling, tool usability, customer application domain, and organizational issues. We provide examples of challenges in each area and identrfj, open research issues in areas which limit our ability to transfer high-assurance software engineering tools into practice.

Caesy: A software tool for computer-aided engineering

NASA Technical Reports Server (NTRS)

Wette, Matt

1993-01-01

A new software tool, Caesy, is described. This tool provides a strongly typed programming environment for research in the development of algorithms and software for computer-aided control system design. A description of the user language and its implementation as they currently stand are presented along with a description of work in progress and areas of future work.

Software Tools for Battery Design | Transportation Research | NREL

Science.gov Websites

battery designers, developers, and manufacturers create affordable, high-performance lithium-ion (Li-ion Software Tools for Battery Design Software Tools for Battery Design Under the Computer-Aided ) batteries for next-generation electric-drive vehicles (EDVs). An image of a simulation of a battery pack

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

PubMed

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

2016-04-01

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

Software and the Scientist: Coding and Citation Practices in Geodynamics

NASA Astrophysics Data System (ADS)

Hwang, Lorraine; Fish, Allison; Soito, Laura; Smith, MacKenzie; Kellogg, Louise H.

2017-11-01

In geodynamics as in other scientific areas, computation has become a core component of research, complementing field observation, laboratory analysis, experiment, and theory. Computational tools for data analysis, mapping, visualization, modeling, and simulation are essential for all aspects of the scientific workflow. Specialized scientific software is often developed by geodynamicists for their own use, and this effort represents a distinctive intellectual contribution. Drawing on a geodynamics community that focuses on developing and disseminating scientific software, we assess the current practices of software development and attribution, as well as attitudes about the need and best practices for software citation. We analyzed publications by participants in the Computational Infrastructure for Geodynamics and conducted mixed method surveys of the solid earth geophysics community. From this we learned that coding skills are typically learned informally. Participants considered good code as trusted, reusable, readable, and not overly complex and considered a good coder as one that participates in the community in an open and reasonable manor contributing to both long- and short-term community projects. Participants strongly supported citing software reflected by the high rate a software package was named in the literature and the high rate of citations in the references. However, lacking are clear instructions from developers on how to cite and education of users on what to cite. In addition, citations did not always lead to discoverability of the resource. A unique identifier to the software package itself, community education, and citation tools would contribute to better attribution practices.

Implementing a modeling software for animated protein-complex interactions using a physics simulation library.

PubMed

Ueno, Yutaka; Ito, Shuntaro; Konagaya, Akihiko

2014-12-01

To better understand the behaviors and structural dynamics of proteins within a cell, novel software tools are being developed that can create molecular animations based on the findings of structural biology. This study proposes our method developed based on our prototypes to detect collisions and examine the soft-body dynamics of molecular models. The code was implemented with a software development toolkit for rigid-body dynamics simulation and a three-dimensional graphics library. The essential functions of the target software system included the basic molecular modeling environment, collision detection in the molecular models, and physical simulations of the movement of the model. Taking advantage of recent software technologies such as physics simulation modules and interpreted scripting language, the functions required for accurate and meaningful molecular animation were implemented efficiently.

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

PubMed

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

2016-12-15

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

Sentiment Analysis of Health Care Tweets: Review of the Methods Used.

PubMed

Gohil, Sunir; Vuik, Sabine; Darzi, Ara

2018-04-23

Twitter is a microblogging service where users can send and read short 140-character messages called "tweets." There are several unstructured, free-text tweets relating to health care being shared on Twitter, which is becoming a popular area for health care research. Sentiment is a metric commonly used to investigate the positive or negative opinion within these messages. Exploring the methods used for sentiment analysis in Twitter health care research may allow us to better understand the options available for future research in this growing field. The first objective of this study was to understand which tools would be available for sentiment analysis of Twitter health care research, by reviewing existing studies in this area and the methods they used. The second objective was to determine which method would work best in the health care settings, by analyzing how the methods were used to answer specific health care questions, their production, and how their accuracy was analyzed. A review of the literature was conducted pertaining to Twitter and health care research, which used a quantitative method of sentiment analysis for the free-text messages (tweets). The study compared the types of tools used in each case and examined methods for tool production, tool training, and analysis of accuracy. A total of 12 papers studying the quantitative measurement of sentiment in the health care setting were found. More than half of these studies produced tools specifically for their research, 4 used open source tools available freely, and 2 used commercially available software. Moreover, 4 out of the 12 tools were trained using a smaller sample of the study's final data. The sentiment method was trained against, on an average, 0.45% (2816/627,024) of the total sample data. One of the 12 papers commented on the analysis of accuracy of the tool used. Multiple methods are used for sentiment analysis of tweets in the health care setting. These range from self-produced basic categorizations to more complex and expensive commercial software. The open source and commercial methods are developed on product reviews and generic social media messages. None of these methods have been extensively tested against a corpus of health care messages to check their accuracy. This study suggests that there is a need for an accurate and tested tool for sentiment analysis of tweets trained using a health care setting-specific corpus of manually annotated tweets first. ©Sunir Gohil, Sabine Vuik, Ara Darzi. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 23.04.2018.

Building Flexible User Interfaces for Solving PDEs

NASA Astrophysics Data System (ADS)

Logg, Anders; Wells, Garth N.

2010-09-01

FEniCS is a collection of software tools for the automated solution of differential equations by finite element methods. In this note, we describe how FEniCS can be used to solve a simple nonlinear model problem with varying levels of automation. At one extreme, FEniCS provides tools for the fully automated and adaptive solution of nonlinear partial differential equations. At the other extreme, FEniCS provides a range of tools that allow the computational scientist to experiment with novel solution algorithms.

Using Modern Design Tools for Digital Avionics Development

NASA Technical Reports Server (NTRS)

Hyde, David W.; Lakin, David R., II; Asquith, Thomas E.

2000-01-01

Using Modem Design Tools for Digital Avionics Development Shrinking development time and increased complexity of new avionics forces the designer to use modem tools and methods during hardware development. Engineers at the Marshall Space Flight Center have successfully upgraded their design flow and used it to develop a Mongoose V based radiation tolerant processor board for the International Space Station's Water Recovery System. The design flow, based on hardware description languages, simulation, synthesis, hardware models, and full functional software model libraries, allowed designers to fully simulate the processor board from reset, through initialization before any boards were built. The fidelity of a digital simulation is limited to the accuracy of the models used and how realistically the designer drives the circuit's inputs during simulation. By using the actual silicon during simulation, device modeling errors are reduced. Numerous design flaws were discovered early in the design phase when they could be easily fixed. The use of hardware models and actual MIPS software loaded into full functional memory models also provided checkout of the software development environment. This paper will describe the design flow used to develop the processor board and give examples of errors that were found using the tools. An overview of the processor board firmware will also be covered.

Ultrasound Doppler method of remote elastometry

NASA Astrophysics Data System (ADS)

Timanin, E. M.; Eremin, E. V.; Belyaev, R. V.; Mansfel'd, A. D.

2015-03-01

The paper presents the theoretical relations constituting the basis of remote measurements of the shear elasticity of biological tissues using the ultrasound Doppler method. It also describes the hardware-software setup implementing this approach, as well as the results of experiments with these tools on a biological tissue phantom and on human liver in vivo.

A software tool for ecosystem services assessments

NASA Astrophysics Data System (ADS)

Riegels, Niels; Klinting, Anders; Butts, Michael; Middelboe, Anne Lise; Mark, Ole

2017-04-01

The EU FP7 DESSIN project is developing methods and tools for assessment of ecosystem services (ESS) and associated economic values, with a focus on freshwater ESS in urban settings. Although the ESS approach has gained considerable visibility over the past ten years, operationalizing the approach remains a challenge. Therefore, DESSSIN is also supporting development of a free software tool to support users implementing the DESSIN ESS evaluation framework. The DESSIN ESS evaluation framework is a structured approach to measuring changes in ecosystem services. The main purpose of the framework is to facilitate the application of the ESS approach in the appraisal of projects that have impacts on freshwater ecosystems and their services. The DESSIN framework helps users evaluate changes in ESS by linking biophysical, economic, and sustainability assessments sequentially. It was developed using the Common International Classification of Ecosystem Services (CICES) and the DPSIR (Drivers, Pressures, States, Impacts, Responses) adaptive management cycle. The former is a standardized system for the classification of ESS developed by the European Union to enhance the consistency and comparability of ESS assessments. The latter is a well-known concept to disentangle the biophysical and social aspects of a system under study. As part of its analytical component, the DESSIN framework also integrates elements of the Final Ecosystem Goods and Services-Classification System (FEGS-CS) of the US Environmental Protection Agency (USEPA). As implemented in the software tool, the DESSIN framework consists of five parts: • In part I of the evaluation, the ecosystem is defined and described and the local stakeholders are identified. In addition, administrative details and objectives of the assessment are defined. • In part II, drivers and pressures are identified. Once these first two elements of the DPSIR scheme have been characterized, the claimed/expected capabilities of a proposed project can be estimated to determine whether the project affects drivers, pressures, states or a combination of these. • In part III, information about impacts on drivers, pressures, and states is used to identify ESS impacted by a proposed project. Potential beneficiaries of impacted ESS are also identified. • In part IV, changes in ESS are estimated. These estimates include changes in the provision of ESS, the use of ESS, and the value of ESS. • A sustainability assessment in Part V estimates the broader impact of a proposed project according to social, environmental, governance and other criteria. The ESS evaluation software tool is designed to assist an evaluation or study leader carrying out an ESS assessment. The tool helps users move through the logic of the ESS evaluation and make sense of relationships between elements of the DPSIR framework, the CICES classification scheme, and the FEGS approach. The tool also provides links to useful indicators and assessment methods in order to help users quantify changes in ESS and ESS values. The software tool is developed in collaboration with the DESSIN user group, who will use the software to estimate changes in ESS resulting from the implementation of green technologies addressing water quality and water scarcity issues. Although the software is targeted to this user group, it will be made available for free to the public after the conclusion of the project.

Digital modeling of end-mill cutting tools for FEM applications from the active cutting contour

NASA Astrophysics Data System (ADS)

Salguero, Jorge; Marcos, M.; Batista, M.; Gómez, A.; Mayuet, P.; Bienvenido, R.

2012-04-01

A very current technique in the research field of machining by material removal is the use of simulations using the Finite Element Method (FEM). Nevertheless, and although is widely used in processes that allows approximations to orthogonal cutting, such as shaping, is scarcely used in more complexes processes, such as milling. This fact is due principally to the complex geometry of the cutting tools in these processes, and the need to realize the studi es in an oblique cutting configuration. This paper shows a methodology for the geometrical characterization of commercial endmill cutting tools, by the extraction of the cutting tool contour, making use of optical metrology, and using this geometry to model the active cutting zone with a 3D CAD software. This model is easily exportable to different CAD formats, such as IGES or STEP, and importable from FEM software, where is possible to study the behavior in service of the same ones.

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

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

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

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

A simple rapid process for semi-automated brain extraction from magnetic resonance images of the whole mouse head.

PubMed

Delora, Adam; Gonzales, Aaron; Medina, Christopher S; Mitchell, Adam; Mohed, Abdul Faheem; Jacobs, Russell E; Bearer, Elaine L

2016-01-15

Magnetic resonance imaging (MRI) is a well-developed technique in neuroscience. Limitations in applying MRI to rodent models of neuropsychiatric disorders include the large number of animals required to achieve statistical significance, and the paucity of automation tools for the critical early step in processing, brain extraction, which prepares brain images for alignment and voxel-wise statistics. This novel timesaving automation of template-based brain extraction ("skull-stripping") is capable of quickly and reliably extracting the brain from large numbers of whole head images in a single step. The method is simple to install and requires minimal user interaction. This method is equally applicable to different types of MR images. Results were evaluated with Dice and Jacquard similarity indices and compared in 3D surface projections with other stripping approaches. Statistical comparisons demonstrate that individual variation of brain volumes are preserved. A downloadable software package not otherwise available for extraction of brains from whole head images is included here. This software tool increases speed, can be used with an atlas or a template from within the dataset, and produces masks that need little further refinement. Our new automation can be applied to any MR dataset, since the starting point is a template mask generated specifically for that dataset. The method reliably and rapidly extracts brain images from whole head images, rendering them useable for subsequent analytical processing. This software tool will accelerate the exploitation of mouse models for the investigation of human brain disorders by MRI. Copyright © 2015 Elsevier B.V. All rights reserved.

FAMIAS - A userfriendly new software tool for the mode identification of photometric and spectroscopic times series

NASA Astrophysics Data System (ADS)

Zima, W.

2008-12-01

FAMIAS (Frequency Analysis and Mode Identification for AsteroSeismology) is a collection of state-of-the-art software tools for the analysis of photometric and spectroscopic time series data. It is one of the deliverables of the Work Package NA5: Asteroseismology of the European Coordination Action in Helio- and Asteroseismology (HELAS1 ). Two main sets of tools are incorporated in FAMIAS. The first set allows to search for pe- riodicities in the data using Fourier and non-linear least-squares fitting algorithms. The other set allows to carry out a mode identification for the detected pulsation frequencies to deter- mine their pulsational quantum numbers, the harmonic degree, ℓ, and the azimuthal order, m. For the spectroscopic mode identification, the Fourier parameter fit method and the moment method are available. The photometric mode identification is based on pre-computed grids of atmospheric parameters and non-adiabatic observables, and uses the method of amplitude ratios and phase differences in different filters. The types of stars to which FAMIAS is appli- cable are main-sequence pulsators hotter than the Sun. This includes the Gamma Dor stars, Delta Sct stars, the slowly pulsating B stars and the Beta Cep stars - basically all pulsating main-sequence stars, for which empirical mode identification is required to successfully carry out asteroseismology. The complete manual for FAMIAS is published in a special issue of Communications in Asteroseismology, Vol 155. The homepage of FAMIAS2 provides the possibility to download the software and to read the on-line documentation.

Observation-Driven Configuration of Complex Software Systems

NASA Astrophysics Data System (ADS)

Sage, Aled

2010-06-01

The ever-increasing complexity of software systems makes them hard to comprehend, predict and tune due to emergent properties and non-deterministic behaviour. Complexity arises from the size of software systems and the wide variety of possible operating environments: the increasing choice of platforms and communication policies leads to ever more complex performance characteristics. In addition, software systems exhibit different behaviour under different workloads. Many software systems are designed to be configurable so that policies can be chosen to meet the needs of various stakeholders. For complex software systems it can be difficult to accurately predict the effects of a change and to know which configuration is most appropriate. This thesis demonstrates that it is useful to run automated experiments that measure a selection of system configurations. Experiments can find configurations that meet the stakeholders' needs, find interesting behavioural characteristics, and help produce predictive models of the system's behaviour. The design and use of ACT (Automated Configuration Tool) for running such experiments is described, in combination a number of search strategies for deciding on the configurations to measure. Design Of Experiments (DOE) is discussed, with emphasis on Taguchi Methods. These statistical methods have been used extensively in manufacturing, but have not previously been used for configuring software systems. The novel contribution here is an industrial case study, applying the combination of ACT and Taguchi Methods to DC-Directory, a product from Data Connection Ltd (DCL). The case study investigated the applicability of Taguchi Methods for configuring complex software systems. Taguchi Methods were found to be useful for modelling and configuring DC- Directory, making them a valuable addition to the techniques available to system administrators and developers.

Managing Written Directives: A Software Solution to Streamline Workflow.

PubMed

Wagner, Robert H; Savir-Baruch, Bital; Gabriel, Medhat S; Halama, James R; Bova, Davide

2017-06-01

A written directive is required by the U.S. Nuclear Regulatory Commission for any use of 131 I above 1.11 MBq (30 μCi) and for patients receiving radiopharmaceutical therapy. This requirement has also been adopted and must be enforced by the agreement states. As the introduction of new radiopharmaceuticals increases therapeutic options in nuclear medicine, time spent on regulatory paperwork also increases. The pressure of managing these time-consuming regulatory requirements may heighten the potential for inaccurate or incomplete directive data and subsequent regulatory violations. To improve on the paper-trail method of directive management, we created a software tool using a Health Insurance Portability and Accountability Act (HIPAA)-compliant database. This software allows for secure data-sharing among physicians, technologists, and managers while saving time, reducing errors, and eliminating the possibility of loss and duplication. Methods: The software tool was developed using Visual Basic, which is part of the Visual Studio development environment for the Windows platform. Patient data are deposited in an Access database on a local HIPAA-compliant secure server or hard disk. Once a working version had been developed, it was installed at our institution and used to manage directives. Updates and modifications of the software were released regularly until no more significant problems were found with its operation. Results: The software has been used at our institution for over 2 y and has reliably kept track of all directives. All physicians and technologists use the software daily and find it superior to paper directives. They can retrieve active directives at any stage of completion, as well as completed directives. Conclusion: We have developed a software solution for the management of written directives that streamlines and structures the departmental workflow. This solution saves time, centralizes the information for all staff to share, and decreases confusion about the creation, completion, filing, and retrieval of directives. © 2017 by the Society of Nuclear Medicine and Molecular Imaging.

Software engineering methodologies and tools

NASA Technical Reports Server (NTRS)

Wilcox, Lawrence M.

1993-01-01

Over the years many engineering disciplines have developed, including chemical, electronic, etc. Common to all engineering disciplines is the use of rigor, models, metrics, and predefined methodologies. Recently, a new engineering discipline has appeared on the scene, called software engineering. For over thirty years computer software has been developed and the track record has not been good. Software development projects often miss schedules, are over budget, do not give the user what is wanted, and produce defects. One estimate is there are one to three defects per 1000 lines of deployed code. More and more systems are requiring larger and more complex software for support. As this requirement grows, the software development problems grow exponentially. It is believed that software quality can be improved by applying engineering principles. Another compelling reason to bring the engineering disciplines to software development is productivity. It has been estimated that productivity of producing software has only increased one to two percent a year in the last thirty years. Ironically, the computer and its software have contributed significantly to the industry-wide productivity, but computer professionals have done a poor job of using the computer to do their job. Engineering disciplines and methodologies are now emerging supported by software tools that address the problems of software development. This paper addresses some of the current software engineering methodologies as a backdrop for the general evaluation of computer assisted software engineering (CASE) tools from actual installation of and experimentation with some specific tools.

The Software Architecture of the Upgraded ESA DRAMA Software Suite

NASA Astrophysics Data System (ADS)

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

2013-08-01

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

Tool for analysis of early age transverse cracking of composite bridge decks.

DOT National Transportation Integrated Search

2011-08-29

"Executive Summary: Computational methods and associated software were developed : to compute stresses in HP concrete composite bridge decks due to temperature, shrinkage, and : vehicle loading. The structural analysis program uses a layered finite e...

CEMENTITIOUS BARRIERS PARTNERSHIP FY13 MID-YEAR REPORT

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

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

2013-05-01

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

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.

Using Automation to Improve the Flight Software Testing Process

NASA Technical Reports Server (NTRS)

ODonnell, James R., Jr.; Andrews, Stephen F.; Morgenstern, Wendy M.; Bartholomew, Maureen O.; McComas, David C.; Bauer, Frank H. (Technical Monitor)

2001-01-01

One of the critical phases in the development of a spacecraft attitude control system (ACS) is the testing of its flight software. The testing (and test verification) of ACS flight software requires a mix of skills involving software, attitude control, data manipulation, and analysis. The process of analyzing and verifying flight software test results often creates a bottleneck which dictates the speed at which flight software verification can be conducted. In the development of the Microwave Anisotropy Probe (MAP) spacecraft ACS subsystem, an integrated design environment was used that included a MAP high fidelity (HiFi) simulation, a central database of spacecraft parameters, a script language for numeric and string processing, and plotting capability. In this integrated environment, it was possible to automate many of the steps involved in flight software testing, making the entire process more efficient and thorough than on previous missions. In this paper, we will compare the testing process used on MAP to that used on previous missions. The software tools that were developed to automate testing and test verification will be discussed, including the ability to import and process test data, synchronize test data and automatically generate HiFi script files used for test verification, and an automated capability for generating comparison plots. A summary of the perceived benefits of applying these test methods on MAP will be given. Finally, the paper will conclude with a discussion of re-use of the tools and techniques presented, and the ongoing effort to apply them to flight software testing of the Triana spacecraft ACS subsystem.

Using Automation to Improve the Flight Software Testing Process

NASA Technical Reports Server (NTRS)

ODonnell, James R., Jr.; Morgenstern, Wendy M.; Bartholomew, Maureen O.

2001-01-01

One of the critical phases in the development of a spacecraft attitude control system (ACS) is the testing of its flight software. The testing (and test verification) of ACS flight software requires a mix of skills involving software, knowledge of attitude control, and attitude control hardware, data manipulation, and analysis. The process of analyzing and verifying flight software test results often creates a bottleneck which dictates the speed at which flight software verification can be conducted. In the development of the Microwave Anisotropy Probe (MAP) spacecraft ACS subsystem, an integrated design environment was used that included a MAP high fidelity (HiFi) simulation, a central database of spacecraft parameters, a script language for numeric and string processing, and plotting capability. In this integrated environment, it was possible to automate many of the steps involved in flight software testing, making the entire process more efficient and thorough than on previous missions. In this paper, we will compare the testing process used on MAP to that used on other missions. The software tools that were developed to automate testing and test verification will be discussed, including the ability to import and process test data, synchronize test data and automatically generate HiFi script files used for test verification, and an automated capability for generating comparison plots. A summary of the benefits of applying these test methods on MAP will be given. Finally, the paper will conclude with a discussion of re-use of the tools and techniques presented, and the ongoing effort to apply them to flight software testing of the Triana spacecraft ACS subsystem.

Development of a Software Tool to Automate ADCO Flight Controller Console Planning Tasks

NASA Technical Reports Server (NTRS)

Anderson, Mark G.

2011-01-01

This independent study project covers the development of the International Space Station (ISS) Attitude Determination and Control Officer (ADCO) Planning Exchange APEX Tool. The primary goal of the tool is to streamline existing manual and time-intensive planning tools into a more automated, user-friendly application that interfaces with existing products and allows the ADCO to produce accurate products and timelines more effectively. This paper will survey the current ISS attitude planning process and its associated requirements, goals, documentation and software tools and how a software tool could simplify and automate many of the planning actions which occur at the ADCO console. The project will be covered from inception through the initial prototype delivery in November 2011 and will include development of design requirements and software as well as design verification and testing.

The Development of a Novel High Throughput Computational Tool for Studying Individual and Collective Cellular Migration

PubMed Central

Chapnick, Douglas A.; Jacobsen, Jeremy; Liu, Xuedong

2013-01-01

Understanding how cells migrate individually and collectively during development and cancer metastasis can be significantly aided by a computation tool to accurately measure not only cellular migration speed, but also migration direction and changes in migration direction in a temporal and spatial manner. We have developed such a tool for cell migration researchers, named Pathfinder, which is capable of simultaneously measuring the migration speed, migration direction, and changes in migration directions of thousands of cells both instantaneously and over long periods of time from fluorescence microscopy data. Additionally, we demonstrate how the Pathfinder software can be used to quantify collective cell migration. The novel capability of the Pathfinder software to measure the changes in migration direction of large populations of cells in a spatiotemporal manner will aid cellular migration research by providing a robust method for determining the mechanisms of cellular guidance during individual and collective cell migration. PMID:24386097

The State of Software for Evolutionary Biology

PubMed Central

Darriba, Diego; Flouri, Tomáš; Stamatakis, Alexandros

2018-01-01

Abstract With Next Generation Sequencing data being routinely used, evolutionary biology is transforming into a computational science. Thus, researchers have to rely on a growing number of increasingly complex software. All widely used core tools in the field have grown considerably, in terms of the number of features as well as lines of code and consequently, also with respect to software complexity. A topic that has received little attention is the software engineering quality of widely used core analysis tools. Software developers appear to rarely assess the quality of their code, and this can have potential negative consequences for end-users. To this end, we assessed the code quality of 16 highly cited and compute-intensive tools mainly written in C/C++ (e.g., MrBayes, MAFFT, SweepFinder, etc.) and JAVA (BEAST) from the broader area of evolutionary biology that are being routinely used in current data analysis pipelines. Because, the software engineering quality of the tools we analyzed is rather unsatisfying, we provide a list of best practices for improving the quality of existing tools and list techniques that can be deployed for developing reliable, high quality scientific software from scratch. Finally, we also discuss journal as well as science policy and, more importantly, funding issues that need to be addressed for improving software engineering quality as well as ensuring support for developing new and maintaining existing software. Our intention is to raise the awareness of the community regarding software engineering quality issues and to emphasize the substantial lack of funding for scientific software development. PMID:29385525

Software-defined Quantum Networking Ecosystem

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

Humble, Travis S.; Sadlier, Ronald

The software enables a user to perform modeling and simulation of software-defined quantum networks. The software addresses the problem of how to synchronize transmission of quantum and classical signals through multi-node networks and to demonstrate quantum information protocols such as quantum teleportation. The software approaches this problem by generating a graphical model of the underlying network and attributing properties to each node and link in the graph. The graphical model is then simulated using a combination of discrete-event simulators to calculate the expected state of each node and link in the graph at a future time. A user interacts withmore » the software by providing an initial network model and instantiating methods for the nodes to transmit information with each other. This includes writing application scripts in python that make use of the software library interfaces. A user then initiates the application scripts, which invokes the software simulation. The user then uses the built-in diagnostic tools to query the state of the simulation and to collect statistics on synchronization.« less

Automatic extraction and visualization of object-oriented software design metrics

NASA Astrophysics Data System (ADS)

Lakshminarayana, Anuradha; Newman, Timothy S.; Li, Wei; Talburt, John

2000-02-01

Software visualization is a graphical representation of software characteristics and behavior. Certain modes of software visualization can be useful in isolating problems and identifying unanticipated behavior. In this paper we present a new approach to aid understanding of object- oriented software through 3D visualization of software metrics that can be extracted from the design phase of software development. The focus of the paper is a metric extraction method and a new collection of glyphs for multi- dimensional metric visualization. Our approach utilize the extensibility interface of a popular CASE tool to access and automatically extract the metrics from Unified Modeling Language class diagrams. Following the extraction of the design metrics, 3D visualization of these metrics are generated for each class in the design, utilizing intuitively meaningful 3D glyphs that are representative of the ensemble of metrics. Extraction and visualization of design metrics can aid software developers in the early study and understanding of design complexity.

The NASA Software Research Infusion Initiative: Successful Technology Transfer for Software Assurance

NASA Technical Reports Server (NTRS)

Hinchey, Michael G.; Pressburger, Thomas; Markosian, Lawrence; Feather, Martin S.

2006-01-01

New processes, methods and tools are constantly appearing in the field of software engineering. Many of these augur great potential in improving software development processes, resulting in higher quality software with greater levels of assurance. However, there are a number of obstacles that impede their infusion into software development practices. These are the recurring obstacles common to many forms of research. Practitioners cannot readily identify the emerging techniques that may most benefit them, and cannot afford to risk time and effort in evaluating and experimenting with them while there is still uncertainty about whether they will have payoff in this particular context. Similarly, researchers cannot readily identify those practitioners whose problems would be amenable to their techniques and lack the feedback from practical applications necessary to help them to evolve their techniques to make them more likely to be successful. This paper describes an ongoing effort conducted by a software engineering research infusion team, and the NASA Research Infusion Initiative, established by NASA s Software Engineering Initiative, to overcome these obstacles.

A software platform for statistical evaluation of patient respiratory patterns in radiation therapy.

PubMed

Dunn, Leon; Kenny, John

2017-10-01

The aim of this work was to design and evaluate a software tool for analysis of a patient's respiration, with the goal of optimizing the effectiveness of motion management techniques during radiotherapy imaging and treatment. A software tool which analyses patient respiratory data files (.vxp files) created by the Varian Real-Time Position Management System (RPM) was developed to analyse patient respiratory data. The software, called RespAnalysis, was created in MATLAB and provides four modules, one each for determining respiration characteristics, providing breathing coaching (biofeedback training), comparing pre and post-training characteristics and performing a fraction-by-fraction assessment. The modules analyse respiratory traces to determine signal characteristics and specifically use a Sample Entropy algorithm as the key means to quantify breathing irregularity. Simulated respiratory signals, as well as 91 patient RPM traces were analysed with RespAnalysis to test the viability of using the Sample Entropy for predicting breathing regularity. Retrospective assessment of patient data demonstrated that the Sample Entropy metric was a predictor of periodic irregularity in respiration data, however, it was found to be insensitive to amplitude variation. Additional waveform statistics assessing the distribution of signal amplitudes over time coupled with Sample Entropy method were found to be useful in assessing breathing regularity. The RespAnalysis software tool presented in this work uses the Sample Entropy method to analyse patient respiratory data recorded for motion management purposes in radiation therapy. This is applicable during treatment simulation and during subsequent treatment fractions, providing a way to quantify breathing irregularity, as well as assess the need for breathing coaching. It was demonstrated that the Sample Entropy metric was correlated to the irregularity of the patient's respiratory motion in terms of periodicity, whilst other metrics, such as percentage deviation of inhale/exhale peak positions provided insight into respiratory amplitude regularity. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Desktop software to identify patients eligible for recruitment into a clinical trial: using SARMA to recruit to the ROAD feasibility trial.

PubMed

Treweek, Shaun; Pearson, Ewan; Smith, Natalie; Neville, Ron; Sargeant, Paul; Boswell, Brian; Sullivan, Frank

2010-01-01

Recruitment to trials in primary care is often difficult, particularly when practice staff need to identify study participants with acute conditions during consultations. The Scottish Acute Recruitment Management Application (SARMA) system is linked to general practice electronic medical record (EMR) systems and is designed to provide recruitment support to multi-centre trials by screening patients against trial inclusion criteria and alerting practice staff if the patient appears eligible. For patients willing to learn more about the trial, the software allows practice staff to send the patient's contact details to the research team by text message. To evaluate the ability of the software to support trial recruitment. Software evaluation embedded in a randomised controlled trial. Five general practices in Tayside and Fife, Scotland. SARMA was used to support recruitment to a feasibility trial (the Response to Oral Agents in Diabetes, or ROAD trial) looking at users of oral therapy in diabetes. The technical performance of the software and its utility as a recruitment tool were evaluated. The software was successfully installed at four of the five general practices and recruited 11 of the 29 participants for ROAD (other methods were letter and direct invitation by a practice nurse) and had a recruitment return of 35% (11 of 31 texts sent led to a recruitment). Screen failures were relatively low (7 of 31 referred). Practice staff members were positive about the system. An automated recruitment tool can support primary care trials in Scotland and has the potential to support recruitment in other jurisdictions. It offers a low-cost supplement to other trial recruitment methods and is likely to have a much lower screen failure rate than blanket approaches such as mailshots and newspaper campaigns.

Agile: From Software to Mission Systems

NASA Technical Reports Server (NTRS)

Trimble, Jay; Shirley, Mark; Hobart, Sarah

2017-01-01

To maximize efficiency and flexibility in Mission Operations System (MOS) design, we are evolving principles from agile and lean methods for software, to the complete mission system. This allows for reduced operational risk at reduced cost, and achieves a more effective design through early integration of operations into mission system engineering and flight system design. The core principles are assessment of capability through demonstration, risk reduction through targeted experiments, early test and deployment, and maturation of processes and tools through use.

Methods, Software and Tools for Three Numerical Applications. Final report

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

E. R. Jessup

2000-03-01

This is a report of the results of the authors work supported by DOE contract DE-FG03-97ER25325. They proposed to study three numerical problems. They are: (1) the extension of the PMESC parallel programming library; (2) the development of algorithms and software for certain generalized eigenvalue and singular value (SVD) problems, and (3) the application of techniques of linear algebra to an information retrieval technique known as latent semantic indexing (LSI).

Planetary Data Workshop, Part 2

NASA Technical Reports Server (NTRS)

1984-01-01

Technical aspects of the Planetary Data System (PDS) are addressed. Methods and tools for maintaining and accessing large, complex sets of data are discussed. The specific software and applications needed for processing imaging and non-imaging science data are reviewed. The need for specific software that provides users with information on the location and geometry of scientific observations is discussed. Computer networks and user interface to the PDS are covered along with Computer hardware available to this data system.

SU-F-I-43: A Software-Based Statistical Method to Compute Low Contrast Detectability in Computed Tomography Images

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

Chacko, M; Aldoohan, S

Purpose: The low contrast detectability (LCD) of a CT scanner is its ability to detect and display faint lesions. The current approach to quantify LCD is achieved using vendor-specific methods and phantoms, typically by subjectively observing the smallest size object at a contrast level above phantom background. However, this approach does not yield clinically applicable values for LCD. The current study proposes a statistical LCD metric using software tools to not only to assess scanner performance, but also to quantify the key factors affecting LCD. This approach was developed using uniform QC phantoms, and its applicability was then extended undermore » simulated clinical conditions. Methods: MATLAB software was developed to compute LCD using a uniform image of a QC phantom. For a given virtual object size, the software randomly samples the image within a selected area, and uses statistical analysis based on Student’s t-distribution to compute the LCD as the minimal Hounsfield Unit’s that can be distinguished from the background at the 95% confidence level. Its validity was assessed by comparison with the behavior of a known QC phantom under various scan protocols and a tissue-mimicking phantom. The contributions of beam quality and scattered radiation upon the computed LCD were quantified by using various external beam-hardening filters and phantom lengths. Results: As expected, the LCD was inversely related to object size under all scan conditions. The type of image reconstruction kernel filter and tissue/organ type strongly influenced the background noise characteristics and therefore, the computed LCD for the associated image. Conclusion: The proposed metric and its associated software tools are vendor-independent and can be used to analyze any LCD scanner performance. Furthermore, the method employed can be used in conjunction with the relationships established in this study between LCD and tissue type to extend these concepts to patients’ clinical CT images.« less

A component-based software environment for visualizing large macromolecular assemblies.

PubMed

Sanner, Michel F

2005-03-01

The interactive visualization of large biological assemblies poses a number of challenging problems, including the development of multiresolution representations and new interaction methods for navigating and analyzing these complex systems. An additional challenge is the development of flexible software environments that will facilitate the integration and interoperation of computational models and techniques from a wide variety of scientific disciplines. In this paper, we present a component-based software development strategy centered on the high-level, object-oriented, interpretive programming language: Python. We present several software components, discuss their integration, and describe some of their features that are relevant to the visualization of large molecular assemblies. Several examples are given to illustrate the interoperation of these software components and the integration of structural data from a variety of experimental sources. These examples illustrate how combining visual programming with component-based software development facilitates the rapid prototyping of novel visualization tools.

Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data

PubMed Central

Kumar, Shailesh; Vo, Angie Duy; Qin, Fujun; Li, Hui

2016-01-01

RNA-Seq made possible the global identification of fusion transcripts, i.e. “chimeric RNAs”. Even though various software packages have been developed to serve this purpose, they behave differently in different datasets provided by different developers. It is important for both users, and developers to have an unbiased assessment of the performance of existing fusion detection tools. Toward this goal, we compared the performance of 12 well-known fusion detection software packages. We evaluated the sensitivity, false discovery rate, computing time, and memory usage of these tools in four different datasets (positive, negative, mixed, and test). We conclude that some tools are better than others in terms of sensitivity, positive prediction value, time consumption and memory usage. We also observed small overlaps of the fusions detected by different tools in the real dataset (test dataset). This could be due to false discoveries by various tools, but could also be due to the reason that none of the tools are inclusive. We have found that the performance of the tools depends on the quality, read length, and number of reads of the RNA-Seq data. We recommend that users choose the proper tools for their purpose based on the properties of their RNA-Seq data. PMID:26862001

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

PubMed

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

2013-08-01

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

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

PubMed Central

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

2013-01-01

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

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

PubMed Central

2011-01-01

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

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

PubMed

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

2011-05-17

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

Multiobjective optimization of hybrid regenerative life support technologies. Topic D: Technology Assessment

NASA Technical Reports Server (NTRS)

Manousiouthakis, Vasilios

1995-01-01

We developed simple mathematical models for many of the technologies constituting the water reclamation system in a space station. These models were employed for subsystem optimization and for the evaluation of the performance of individual water reclamation technologies, by quantifying their operational 'cost' as a linear function of weight, volume, and power consumption. Then we performed preliminary investigations on the performance improvements attainable by simple hybrid systems involving parallel combinations of technologies. We are developing a software tool for synthesizing a hybrid water recovery system (WRS) for long term space missions. As conceptual framework, we are employing the state space approach. Given a number of available technologies and the mission specifications, the state space approach would help design flowsheets featuring optimal process configurations, including those that feature stream connections in parallel, series, or recycles. We visualize this software tool to function as follows: given the mission duration, the crew size, water quality specifications, and the cost coefficients, the software will synthesize a water recovery system for the space station. It should require minimal user intervention. The following tasks need to be solved for achieving this goal: (1) formulate a problem statement that will be used to evaluate the advantages of a hybrid WRS over a single technology WBS; (2) model several WRS technologies that can be employed in the space station; (3) propose a recycling network design methodology (since the WRS synthesis task is a recycling network design problem, it is essential to employ a systematic method in synthesizing this network); (4) develop a software implementation for this design methodology, design a hybrid system using this software, and compare the resulting WRS with a base-case WRS; and (5) create a user-friendly interface for this software tool.

Computer modeling in the practice of acoustical consulting: An evolving variety of uses from marketing and diagnosis through design to eventually research

NASA Astrophysics Data System (ADS)

Madaras, Gary S.

2002-05-01

The use of computer modeling as a marketing, diagnosis, design, and research tool in the practice of acoustical consulting is discussed. From the time it is obtained, the software can be used as an effective marketing tool. It is not until the software basics are learned and some amount of testing and verification occurs that the software can be used as a tool for diagnosing the acoustics of existing rooms. A greater understanding of the output types and formats as well as experience in interpreting the results is required before the software can be used as an efficient design tool. Lastly, it is only after repetitive use as a design tool that the software can be used as a cost-effective means of conducting research in practice. The discussion is supplemented with specific examples of actual projects provided by various consultants within multiple firms. Focus is placed on the use of CATT-Acoustic software and predicting the room acoustics of large performing arts halls as well as other public assembly spaces.

Knowledge-based approach for generating target system specifications from a domain model

NASA Technical Reports Server (NTRS)

Gomaa, Hassan; Kerschberg, Larry; Sugumaran, Vijayan

1992-01-01

Several institutions in industry and academia are pursuing research efforts in domain modeling to address unresolved issues in software reuse. To demonstrate the concepts of domain modeling and software reuse, a prototype software engineering environment is being developed at George Mason University to support the creation of domain models and the generation of target system specifications. This prototype environment, which is application domain independent, consists of an integrated set of commercial off-the-shelf software tools and custom-developed software tools. This paper describes the knowledge-based tool that was developed as part of the environment to generate target system specifications from a domain model.

C-C1-04: Building a Health Services Information Technology Research Environment

PubMed Central

Gehrum, David W; Jones, JB; Romania, Gregory J; Young, David L; Lerch, Virginia R; Bruce, Christa A; Donkochik, Diane; Stewart, Walter F

2010-01-01

Background: The electronic health record (EHR) has opened a new era for health services research (HSR) where information technology (IT) is used to re-engineer care processes. While the EHR provides one means of advancing novel solutions, a promising strategy is to develop tools (e.g., online questionnaires, visual display tools, decision support) distinct from, but which interact with, the EHR. Development of such software tools outside the EHR offers an advantage in flexibility, sophistication, and ultimately in portability to other settings. However, institutional IT departments have an imperative to protect patient data and to standardize IT processes to ensure system-level security and support traditional business needs. Such imperatives usually present formidable process barriers to testing novel software solutions. We describe how, in collaboration with our IT department, we are creating an environment and a process that allows for routine and rapid testing of novel software solutions. Methods: We convened a working group consisting of IT and research personnel with expertise in information security, database design/management, web design, EHR programming, and health services research. The working group was tasked with developing a research IT environment to accomplish two objectives: maintain network/ data security and regulatory compliance; allow researchers working with external vendors to rapidly prototype and, in a clinical setting, test web-based tools. Results: Two parallel solutions, one focused on hardware, the second on oversight and management, were developed. First, we concluded that three separate, staged development environments were required to allow external vendor access for testing software and for transitioning software to be used in a clinic. In parallel, the extant oversight process for approving/managing access to internal/external personnel had to be altered to reflect the scope and scale of discrete research projects, as opposed to an enterpriselevel approach to IT management. Conclusions: Innovation in health services software development requires a flexible, scalable IT environment adapted to the unique objectives of a HSR software development model. In our experience, implementing the hardware solution is less challenging than the cultural change required to implement such a model and the modifications to administrative and oversight processes to sustain an environment for rapid product development and testing.

Rapid Development of Custom Software Architecture Design Environments

DTIC Science & Technology

1999-08-01

the tools themselves. This dissertation describes a new approach to capturing and using architectural design expertise in software architecture design environments...A language and tools are presented for capturing and encapsulating software architecture design expertise within a conceptual framework...of architectural styles and design rules. The design expertise thus captured is supported with an incrementally configurable software architecture

Evaluating Business Intelligence/Business Analytics Software for Use in the Information Systems Curriculum

ERIC Educational Resources Information Center

Davis, Gary Alan; Woratschek, Charles R.

2015-01-01

Business Intelligence (BI) and Business Analytics (BA) Software has been included in many Information Systems (IS) curricula. This study surveyed current and past undergraduate and graduate students to evaluate various BI/BA tools. Specifically, this study compared several software tools from two of the major software providers in the BI/BA field.…

cisprimertool: software to implement a comparative genomics strategy for the development of conserved intron scanning (CIS) markers.

PubMed

Jayashree, B; Jagadeesh, V T; Hoisington, D

2008-05-01

The availability of complete, annotated genomic sequence information in model organisms is a rich resource that can be extended to understudied orphan crops through comparative genomic approaches. We report here a software tool (cisprimertool) for the identification of conserved intron scanning regions using expressed sequence tag alignments to a completely sequenced model crop genome. The method used is based on earlier studies reporting the assessment of conserved intron scanning primers (called CISP) within relatively conserved exons located near exon-intron boundaries from onion, banana, sorghum and pearl millet alignments with rice. The tool is freely available to academic users at http://www.icrisat.org/gt-bt/CISPTool.htm. © 2007 ICRISAT.

BH-ShaDe: A Software Tool That Assists Architecture Students in the III-Structured Task of Housing Design

ERIC Educational Resources Information Center

Millan, Eva; Belmonte, Maria-Victoria; Ruiz-Montiel, Manuela; Gavilanes, Juan; Perez-de-la-Cruz, Jose-Luis

2016-01-01

In this paper, we present BH-ShaDe, a new software tool to assist architecture students learning the ill-structured domain/task of housing design. The software tool provides students with automatic or interactively generated floor plan schemas for basic houses. The students can then use the generated schemas as initial seeds to develop complete…

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

PubMed

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

2005-04-06

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

Estimation of toxicity using the Toxicity Estimation Software Tool (TEST)

EPA Science Inventory

Tens of thousands of chemicals are currently in commerce, and hundreds more are introduced every year. Since experimental measurements of toxicity are extremely time consuming and expensive, it is imperative that alternative methods to estimate toxicity are developed.

The Hyperspectral Imager for the Coastal Ocean (HICO): Sensor and Data Processing Overview

DTIC Science & Technology

2010-01-20

backscattering coefficients, and others. Several of these software modules will be developed within the Automated Processing System (APS), a data... Automated Processing System (APS) NRL developed APS, which processes satellite data into ocean color data products. APS is a collection of methods...used for ocean color processing which provide the tools for the automated processing of satellite imagery [1]. These tools are in the process of

iMindMap as an Innovative Tool in Teaching and Learning Accounting: An Exploratory Study

ERIC Educational Resources Information Center

Wan Jusoh, Wan Noor Hazlina; Ahmad, Suraya

2016-01-01

Purpose: The purpose of this study is to explore the use of iMindMap software as an interactive tool in the teaching and learning method and also to be able to consider iMindMap as an alternative instrument in achieving the ultimate learning outcome. Design/Methodology/Approach: Out of 268 students of the management accounting at the University of…

GPM Timeline Inhibits For IT Processing

NASA Technical Reports Server (NTRS)

Dion, Shirley K.

2014-01-01

The Safety Inhibit Timeline Tool was created as one approach to capturing and understanding inhibits and controls from IT through launch. Global Precipitation Measurement (GPM) Mission, which launched from Japan in March 2014, was a joint mission under a partnership between the National Aeronautics and Space Administration (NASA) and the Japan Aerospace Exploration Agency (JAXA). GPM was one of the first NASA Goddard in-house programs that extensively used software controls. Using this tool during the GPM buildup allowed a thorough review of inhibit and safety critical software design for hazardous subsystems such as the high gain antenna boom, solar array, and instrument deployments, transmitter turn-on, propulsion system release, and instrument radar turn-on. The GPM safety team developed a methodology to document software safety as part of the standard hazard report. As a result of this process, a new tool safety inhibit timeline was created for management of inhibits and their controls during spacecraft buildup and testing during IT at GSFC and at the launch range in Japan. The Safety Inhibit Timeline Tool was a pathfinder approach for reviewing software that controls the electrical inhibits. The Safety Inhibit Timeline Tool strengthens the Safety Analysts understanding of the removal of inhibits during the IT process with safety critical software. With this tool, the Safety Analyst can confirm proper safe configuration of a spacecraft during each IT test, track inhibit and software configuration changes, and assess software criticality. In addition to understanding inhibits and controls during IT, the tool allows the Safety Analyst to better communicate to engineers and management the changes in inhibit states with each phase of hardware and software testing and the impact of safety risks. Lessons learned from participating in the GPM campaign at NASA and JAXA will be discussed during this session.

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.

The Delphi Method Online: Medical Expert Consensus Via the Internet

PubMed Central

Cam, Kenneth M.; McKnight, Patrick E.; Doctor, Jason N.

2002-01-01

Delphi is an expert consensus method. The theory behind the Delphi method is that the interaction of experts may lead to a reduction in individual bias. We have developed software that carries out all aspects of the Delphi method via the Internet. The Delphi method online consists of three components: 1) authorship, 2) interactive polling, and 3) reporting/results. We hope that researchers use this tool in future medical expert systems.

adwTools Developed: New Bulk Alloy and Surface Analysis Software for the Alloy Design Workbench

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Morse, Jeffrey A.; Noebe, Ronald D.; Abel, Phillip B.

2004-01-01

A suite of atomistic modeling software, called the Alloy Design Workbench, has been developed by the Computational Materials Group at the NASA Glenn Research Center and the Ohio Aerospace Institute (OAI). The main goal of this software is to guide and augment experimental materials research and development efforts by creating powerful, yet intuitive, software that combines a graphical user interface with an operating code suitable for real-time atomistic simulations of multicomponent alloy systems. Targeted for experimentalists, the interface is straightforward and requires minimum knowledge of the underlying theory, allowing researchers to focus on the scientific aspects of the work. The centerpiece of the Alloy Design Workbench suite is the adwTools module, which concentrates on the atomistic analysis of surfaces and bulk alloys containing an arbitrary number of elements. An additional module, adwParams, handles ab initio input for the parameterization used in adwTools. Future modules planned for the suite include adwSeg, which will provide numerical predictions for segregation profiles to alloy surfaces and interfaces, and adwReport, which will serve as a window into the database, providing public access to the parameterization data and a repository where users can submit their own findings from the rest of the suite. The entire suite is designed to run on desktop-scale computers. The adwTools module incorporates a custom OAI/Glenn-developed Fortran code based on the BFS (Bozzolo- Ferrante-Smith) method for alloys, ref. 1). The heart of the suite, this code is used to calculate the energetics of different compositions and configurations of atoms.

State-of-the-art Hydrology Education: Development of Windows-based and Web-based Interactive Teaching-Learning Software

NASA Astrophysics Data System (ADS)

Chu, X.

2011-12-01

This study, funded by the NSF CAREER program, focuses on developing new methods to quantify microtopography-controlled overland flow processes and integrating the cutting-edge hydrologic research with all-level education and outreach activities. To achieve the educational goal, an interactive teaching-learning software package has been developed. This software, with enhanced visualization capabilities, integrates the new modeling techniques, computer-guided learning processes, and education-oriented tools in a user-friendly interface. Both Windows-based and web-based versions have been developed. The software is specially designed for three major user levels: elementary level (Level 1: K-12 and outreach education), medium level (Level 2: undergraduate education), and advanced level (Level 3: graduate education). Depending on the levels, users are guided to different educational systems. Each system consists of a series of mini "libraries" featured with movies, pictures, and documentation that cover fundamental theories, varying scale experiments, and computer modeling of overland flow generation, surface runoff, and infiltration processes. Testing and practical use of this educational software in undergraduate and graduate teaching demonstrate its effectiveness to promote students' learning and interest in hydrologic sciences. This educational software also has been used as a hydrologic demonstration tool for K-12 students and Native American students through the Nurturing American Tribal Undergraduate Research Education (NATURE) program and Science, Technology, Engineering and Mathematics (STEM) outreach activities.

Certification of Safety-Critical Software Under DO-178C and DO-278A

NASA Technical Reports Server (NTRS)

Jacklin, Stephen A.

2012-01-01

The RTCA has recently released DO-178C and DO-278A as new certification guidance for the production of airborne and ground-based air traffic management software, respectively. Additionally, RTCA special committee SC-205 has also produced, at the same time, five other companion documents. These documents are RTCA DO-248C, DO-330, DO-331, DO- 332, and DO-333. These supplements address frequently asked questions about software certification, provide guidance on tool qualification requirements, and illustrate the modifications recommended to DO-178C when using model-based software design, object oriented programming, and formal methods. The objective of this paper is to first explain the relationship of DO-178C to the former DO-178B in order to give those familiar with DO- 178B an indication of what has been changed and what has not been changed. With this background, the relationship of DO-178C and DO-278 to the new DO-278A document for ground-based software development is shown. Last, an overview of the new guidance contained in the tool qualification document and the three new supplements to DO-178C and DO-278A is presented. For those unfamiliar with DO-178B, this paper serves to provide an entry point to this new certification guidance for airborne and ground-based CNS/ATM software certification.

A Guide to Analyzing Message-Response Sequences and Group Interaction Patterns in Computer-Mediated Communication

ERIC Educational Resources Information Center

Jeong, Allan

2005-01-01

This paper proposes a set of methods and a framework for evaluating, modeling, and predicting group interactions in computer-mediated communication. The method of sequential analysis is described along with specific software tools and techniques to facilitate the analysis of message-response sequences. In addition, the Dialogic Theory and its…

Towards "Inverse" Character Tables? A One-Step Method for Decomposing Reducible Representations

ERIC Educational Resources Information Center

Piquemal, J.-Y.; Losno, R.; Ancian, B.

2009-01-01

In the framework of group theory, a new procedure is described for a one-step automated reduction of reducible representations. The matrix inversion tool, provided by standard spreadsheet software, is applied to the central part of the character table that contains the characters of the irreducible representation. This method is not restricted to…

Three Software Tools for Viewing Sectional Planes, Volume Models, and Surface Models of a Cadaver Hand.

PubMed

Chung, Beom Sun; Chung, Min Suk; Shin, Byeong Seok; Kwon, Koojoo

2018-02-19

The hand anatomy, including the complicated hand muscles, can be grasped by using computer-assisted learning tools with high quality two-dimensional images and three-dimensional models. The purpose of this study was to present up-to-date software tools that promote learning of stereoscopic morphology of the hand. On the basis of horizontal sectioned images and outlined images of a male cadaver, vertical planes, volume models, and surface models were elaborated. Software to browse pairs of the sectioned and outlined images in orthogonal planes and software to peel and rotate the volume models, as well as a portable document format (PDF) file to select and rotate the surface models, were produced. All of the software tools were downloadable free of charge and usable off-line. The three types of tools for viewing multiple aspects of the hand could be adequately employed according to individual needs. These new tools involving the realistic images of a cadaver and the diverse functions are expected to improve comprehensive knowledge of the hand shape. © 2018 The Korean Academy of Medical Sciences.

Formal functional test designs with a test representation language

NASA Technical Reports Server (NTRS)

Hops, J. M.

1993-01-01

The application of the category-partition method to the test design phase of hardware, software, or system test development is discussed. The method provides a formal framework for reducing the total number of possible test cases to a minimum logical subset for effective testing. An automatic tool and a formal language were developed to implement the method and produce the specification of test cases.

Software Management Environment (SME) concepts and architecture, revision 1

NASA Technical Reports Server (NTRS)

Hendrick, Robert; Kistler, David; Valett, Jon

1992-01-01

This document presents the concepts and architecture of the Software Management Environment (SME), developed for the Software Engineering Branch of the Flight Dynamic Division (FDD) of GSFC. The SME provides an integrated set of experience-based management tools that can assist software development managers in managing and planning flight dynamics software development projects. This document provides a high-level description of the types of information required to implement such an automated management tool.

Use of a quality improvement tool, the prioritization matrix, to identify and prioritize triage software algorithm enhancement.

PubMed

North, Frederick; Varkey, Prathiba; Caraballo, Pedro; Vsetecka, Darlene; Bartel, Greg

2007-10-11

Complex decision support software can require significant effort in maintenance and enhancement. A quality improvement tool, the prioritization matrix, was successfully used to guide software enhancement of algorithms in a symptom assessment call center.

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

Evaluation of 3D Gamma index calculation implemented in two commercial dosimetry systems

NASA Astrophysics Data System (ADS)

Xing, Aitang; Arumugam, Sankar; Deshpande, Shrikant; George, Armia; Vial, Philip; Holloway, Lois; Goozee, Gary

2015-01-01

3D Gamma index is one of the metrics which have been widely used for clinical routine patient specific quality assurance for IMRT, Tomotherapy and VMAT. The algorithms for calculating the 3D Gamma index using global and local methods implemented in two software tools: PTW- VeriSoft® as a part of OCTIVIUS 4D dosimeter systems and 3DVHTM from Sun Nuclear were assessed. The Gamma index calculated by the two systems was compared with manual calculated for one data set. The Gamma pass rate calculated by the two systems was compared using 3%/3mm, 2%/2mm, 3%/2mm and 2%/3mm for two additional data sets. The Gamma indexes calculated by the two systems were accurate, but Gamma pass rates calculated by the two software tools for same data set with the same dose threshold were different due to the different interpolation of raw dose data by the two systems and different implementation of Gamma index calculation and other modules in the two software tools. The mean difference was -1.3%±3.38 (1SD) with a maximum difference of 11.7%.

An evaluation of software tools for the design and development of cockpit displays

NASA Technical Reports Server (NTRS)

Ellis, Thomas D., Jr.

1993-01-01

The use of all-glass cockpits at the NASA Langley Research Center (LaRC) simulation facility has changed the means of design, development, and maintenance of instrument displays. The human-machine interface has evolved from a physical hardware device to a software-generated electronic display system. This has subsequently caused an increased workload at the facility. As computer processing power increases and the glass cockpit becomes predominant in facilities, software tools used in the design and development of cockpit displays are becoming both feasible and necessary for a more productive simulation environment. This paper defines LaRC requirements of a display software development tool and compares two available applications against these requirements. As a part of the software engineering process, these tools reduce development time, provide a common platform for display development, and produce exceptional real-time results.

Chimera Grid Tools

NASA Technical Reports Server (NTRS)

Chan, William M.; Rogers, Stuart E.; Nash, Steven M.; Buning, Pieter G.; Meakin, Robert

2005-01-01

Chimera Grid Tools (CGT) is a software package for performing computational fluid dynamics (CFD) analysis utilizing the Chimera-overset-grid method. For modeling flows with viscosity about geometrically complex bodies in relative motion, the Chimera-overset-grid method is among the most computationally cost-effective methods for obtaining accurate aerodynamic results. CGT contains a large collection of tools for generating overset grids, preparing inputs for computer programs that solve equations of flow on the grids, and post-processing of flow-solution data. The tools in CGT include grid editing tools, surface-grid-generation tools, volume-grid-generation tools, utility scripts, configuration scripts, and tools for post-processing (including generation of animated images of flows and calculating forces and moments exerted on affected bodies). One of the tools, denoted OVERGRID, is a graphical user interface (GUI) that serves to visualize the grids and flow solutions and provides central access to many other tools. The GUI facilitates the generation of grids for a new flow-field configuration. Scripts that follow the grid generation process can then be constructed to mostly automate grid generation for similar configurations. CGT is designed for use in conjunction with a computer-aided-design program that provides the geometry description of the bodies, and a flow-solver program.

Analysis of High-Throughput ELISA Microarray Data

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

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

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

ESSAA: Embedded system safety analysis assistant

NASA Technical Reports Server (NTRS)

Wallace, Peter; Holzer, Joseph; Guarro, Sergio; Hyatt, Larry

1987-01-01

The Embedded System Safety Analysis Assistant (ESSAA) is a knowledge-based tool that can assist in identifying disaster scenarios. Imbedded software issues hazardous control commands to the surrounding hardware. ESSAA is intended to work from outputs to inputs, as a complement to simulation and verification methods. Rather than treating the software in isolation, it examines the context in which the software is to be deployed. Given a specified disasterous outcome, ESSAA works from a qualitative, abstract model of the complete system to infer sets of environmental conditions and/or failures that could cause a disasterous outcome. The scenarios can then be examined in depth for plausibility using existing techniques.

Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field.

PubMed

Wójcikowski, Maciej; Zielenkiewicz, Piotr; Siedlecki, Pawel

2015-01-01

There has been huge progress in the open cheminformatics field in both methods and software development. Unfortunately, there has been little effort to unite those methods and software into one package. We here describe the Open Drug Discovery Toolkit (ODDT), which aims to fulfill the need for comprehensive and open source drug discovery software. The Open Drug Discovery Toolkit was developed as a free and open source tool for both computer aided drug discovery (CADD) developers and researchers. ODDT reimplements many state-of-the-art methods, such as machine learning scoring functions (RF-Score and NNScore) and wraps other external software to ease the process of developing CADD pipelines. ODDT is an out-of-the-box solution designed to be easily customizable and extensible. Therefore, users are strongly encouraged to extend it and develop new methods. We here present three use cases for ODDT in common tasks in computer-aided drug discovery. Open Drug Discovery Toolkit is released on a permissive 3-clause BSD license for both academic and industrial use. ODDT's source code, additional examples and documentation are available on GitHub (https://github.com/oddt/oddt).

STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB.

PubMed

Klingbeil, Guido; Erban, Radek; Giles, Mike; Maini, Philip K

2011-04-15

The importance of stochasticity in biological systems is becoming increasingly recognized and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU that exploits graphics processing units (GPUs) for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB. The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM) and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user's models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2. The software is open source under the GPL v3 and available at http://www.maths.ox.ac.uk/cmb/STOCHSIMGPU. The web site also contains supplementary information. klingbeil@maths.ox.ac.uk Supplementary data are available at Bioinformatics online.

Ensemble: an Architecture for Mission-Operations Software

NASA Technical Reports Server (NTRS)

Norris, Jeffrey; Powell, Mark; Fox, Jason; Rabe, Kenneth; Shu, IHsiang; McCurdy, Michael; Vera, Alonso

2008-01-01

Ensemble is the name of an open architecture for, and a methodology for the development of, spacecraft mission operations software. Ensemble is also potentially applicable to the development of non-spacecraft mission-operations- type software. Ensemble capitalizes on the strengths of the open-source Eclipse software and its architecture to address several issues that have arisen repeatedly in the development of mission-operations software: Heretofore, mission-operations application programs have been developed in disparate programming environments and integrated during the final stages of development of missions. The programs have been poorly integrated, and it has been costly to develop, test, and deploy them. Users of each program have been forced to interact with several different graphical user interfaces (GUIs). Also, the strategy typically used in integrating the programs has yielded serial chains of operational software tools of such a nature that during use of a given tool, it has not been possible to gain access to the capabilities afforded by other tools. In contrast, the Ensemble approach offers a low-risk path towards tighter integration of mission-operations software tools.

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

NASA Astrophysics Data System (ADS)

Novakov, Ognian; Sicard, Claude-Henri

1994-12-01

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

Family-Based Benchmarking of Copy Number Variation Detection Software.

PubMed

Nutsua, Marcel Elie; Fischer, Annegret; Nebel, Almut; Hofmann, Sylvia; Schreiber, Stefan; Krawczak, Michael; Nothnagel, Michael

2015-01-01

The analysis of structural variants, in particular of copy-number variations (CNVs), has proven valuable in unraveling the genetic basis of human diseases. Hence, a large number of algorithms have been developed for the detection of CNVs in SNP array signal intensity data. Using the European and African HapMap trio data, we undertook a comparative evaluation of six commonly used CNV detection software tools, namely Affymetrix Power Tools (APT), QuantiSNP, PennCNV, GLAD, R-gada and VEGA, and assessed their level of pair-wise prediction concordance. The tool-specific CNV prediction accuracy was assessed in silico by way of intra-familial validation. Software tools differed greatly in terms of the number and length of the CNVs predicted as well as the number of markers included in a CNV. All software tools predicted substantially more deletions than duplications. Intra-familial validation revealed consistently low levels of prediction accuracy as measured by the proportion of validated CNVs (34-60%). Moreover, up to 20% of apparent family-based validations were found to be due to chance alone. Software using Hidden Markov models (HMM) showed a trend to predict fewer CNVs than segmentation-based algorithms albeit with greater validity. PennCNV yielded the highest prediction accuracy (60.9%). Finally, the pairwise concordance of CNV prediction was found to vary widely with the software tools involved. We recommend HMM-based software, in particular PennCNV, rather than segmentation-based algorithms when validity is the primary concern of CNV detection. QuantiSNP may be used as an additional tool to detect sets of CNVs not detectable by the other tools. Our study also reemphasizes the need for laboratory-based validation, such as qPCR, of CNVs predicted in silico.

Remote Sensing Image Analysis Without Expert Knowledge - A Web-Based Classification Tool On Top of Taverna Workflow Management System

NASA Astrophysics Data System (ADS)

Selsam, Peter; Schwartze, Christian

2016-10-01

Providing software solutions via internet has been known for quite some time and is now an increasing trend marketed as "software as a service". A lot of business units accept the new methods and streamlined IT strategies by offering web-based infrastructures for external software usage - but geospatial applications featuring very specialized services or functionalities on demand are still rare. Originally applied in desktop environments, the ILMSimage tool for remote sensing image analysis and classification was modified in its communicating structures and enabled for running on a high-power server and benefiting from Tavema software. On top, a GIS-like and web-based user interface guides the user through the different steps in ILMSimage. ILMSimage combines object oriented image segmentation with pattern recognition features. Basic image elements form a construction set to model for large image objects with diverse and complex appearance. There is no need for the user to set up detailed object definitions. Training is done by delineating one or more typical examples (templates) of the desired object using a simple vector polygon. The template can be large and does not need to be homogeneous. The template is completely independent from the segmentation. The object definition is done completely by the software.

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

NASA Astrophysics Data System (ADS)

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

2014-02-01

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

Ground-Based Correction of Remote-Sensing Spectral Imagery

NASA Technical Reports Server (NTRS)

Alder-Golden, Steven M.; Rochford, Peter; Matthew, Michael; Berk, Alexander

2007-01-01

Software has been developed for an improved method of correcting for the atmospheric optical effects (primarily, effects of aerosols and water vapor) in spectral images of the surface of the Earth acquired by airborne and spaceborne remote-sensing instruments. In this method, the variables needed for the corrections are extracted from the readings of a radiometer located on the ground in the vicinity of the scene of interest. The software includes algorithms that analyze measurement data acquired from a shadow-band radiometer. These algorithms are based on a prior radiation transport software model, called MODTRAN, that has been developed through several versions up to what are now known as MODTRAN4 and MODTRAN5 . These components have been integrated with a user-friendly Interactive Data Language (IDL) front end and an advanced version of MODTRAN4. Software tools for handling general data formats, performing a Langley-type calibration, and generating an output file of retrieved atmospheric parameters for use in another atmospheric-correction computer program known as FLAASH have also been incorporated into the present soft-ware. Concomitantly with the soft-ware described thus far, there has been developed a version of FLAASH that utilizes the retrieved atmospheric parameters to process spectral image data.

AceTree: a major update and case study in the long term maintenance of open-source scientific software.

PubMed

Katzman, Braden; Tang, Doris; Santella, Anthony; Bao, Zhirong

2018-04-04

AceTree, a software application first released in 2006, facilitates exploration, curation and editing of tracked C. elegans nuclei in 4-dimensional (4D) fluorescence microscopy datasets. Since its initial release, AceTree has been continuously used to interact with, edit and interpret C. elegans lineage data. In its 11 year lifetime, AceTree has been periodically updated to meet the technical and research demands of its community of users. This paper presents the newest iteration of AceTree which contains extensive updates, demonstrates the new applicability of AceTree in other developmental contexts, and presents its evolutionary software development paradigm as a viable model for maintaining scientific software. Large scale updates have been made to the user interface for an improved user experience. Tools have been grouped according to functionality and obsolete methods have been removed. Internal requirements have been changed that enable greater flexibility of use both in C. elegans contexts and in other model organisms. Additionally, the original 3-dimensional (3D) viewing window has been completely reimplemented. The new window provides a new suite of tools for data exploration. By responding to technical advancements and research demands, AceTree has remained a useful tool for scientific research for over a decade. The updates made to the codebase have extended AceTree's applicability beyond its initial use in C. elegans and enabled its usage with other model organisms. The evolution of AceTree demonstrates a viable model for maintaining scientific software over long periods of time.

A software tool for advanced MRgFUS prostate therapy planning and follow up

NASA Astrophysics Data System (ADS)

van Straaten, Dörte; Hoogenboom, Martijn; van Amerongen, Martinus J.; Weiler, Florian; Issawi, Jumana Al; Günther, Matthias; Fütterer, Jurgen; Jenne, Jürgen W.

2017-03-01

US guided HIFU/FUS ablation for the therapy of prostate cancer is a clinical established method, while MR guided HIFU/FUS applications for prostate recently started clinical evaluation. Even if MRI examination is an excellent diagnostic tool for prostate cancer, it is a time consuming procedure and not practicable within an MRgFUS therapy session. The aim of our ongoing work is to develop software to support therapy planning and post-therapy follow-up for MRgFUS on localized prostate cancer, based on multi-parametric MR protocols. The clinical workflow of diagnosis, therapy and follow-up of MR guided FUS on prostate cancer was deeply analyzed. Based on this, the image processing workflow was designed and all necessary components, e.g. GUI, viewer, registration tools etc. were defined and implemented. The software bases on MeVisLab with several implemented C++ modules for the image processing tasks. The developed software, called LTC (Local Therapy Control) will register and visualize automatically all images (T1w, T2w, DWI etc.) and ADC or perfusion maps gained from the diagnostic MRI session. This maximum of diagnostic information helps to segment all necessary ROIs, e.g. the tumor, for therapy planning. Final therapy planning will be performed based on these segmentation data in the following MRgFUS therapy session. In addition, the developed software should help to evaluate the therapy success, by synchronization and display of pre-therapeutic, therapy and follow-up image data including the therapy plan and thermal dose information. In this ongoing project, the first stand-alone prototype was completed and will be clinically evaluated.

Visual programming for next-generation sequencing data analytics.

PubMed

Milicchio, Franco; Rose, Rebecca; Bian, Jiang; Min, Jae; Prosperi, Mattia

2016-01-01

High-throughput or next-generation sequencing (NGS) technologies have become an established and affordable experimental framework in biological and medical sciences for all basic and translational research. Processing and analyzing NGS data is challenging. NGS data are big, heterogeneous, sparse, and error prone. Although a plethora of tools for NGS data analysis has emerged in the past decade, (i) software development is still lagging behind data generation capabilities, and (ii) there is a 'cultural' gap between the end user and the developer. Generic software template libraries specifically developed for NGS can help in dealing with the former problem, whilst coupling template libraries with visual programming may help with the latter. Here we scrutinize the state-of-the-art low-level software libraries implemented specifically for NGS and graphical tools for NGS analytics. An ideal developing environment for NGS should be modular (with a native library interface), scalable in computational methods (i.e. serial, multithread, distributed), transparent (platform-independent), interoperable (with external software interface), and usable (via an intuitive graphical user interface). These characteristics should facilitate both the run of standardized NGS pipelines and the development of new workflows based on technological advancements or users' needs. We discuss in detail the potential of a computational framework blending generic template programming and visual programming that addresses all of the current limitations. In the long term, a proper, well-developed (although not necessarily unique) software framework will bridge the current gap between data generation and hypothesis testing. This will eventually facilitate the development of novel diagnostic tools embedded in routine healthcare.

Estimating Computer-Based Training Development Times

DTIC Science & Technology

1987-10-14

beginners , must be sure they interpret terms correctly. As a result of this informal validation, the authors suggest refinements in the tool which...Productivity tools available: automated design tools, text processor interfaces, flowcharting software, software interfaces a Multimedia interfaces e

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

Svetlana Shasharina

The goal of the Center for Technology for Advanced Scientific Component Software is to fundamentally changing the way scientific software is developed and used by bringing component-based software development technologies to high-performance scientific and engineering computing. The role of Tech-X work in TASCS project is to provide an outreach to accelerator physics and fusion applications by introducing TASCS tools into applications, testing tools in the applications and modifying the tools to be more usable.

Easy Handling of Sensors and Actuators over TCP/IP Networks by Open Source Hardware/Software

PubMed Central

Mejías, Andrés; Herrera, Reyes S.; Márquez, Marco A.; Calderón, Antonio José; González, Isaías; Andújar, José Manuel

2017-01-01

There are several specific solutions for accessing sensors and actuators present in any process or system through a TCP/IP network, either local or a wide area type like the Internet. The usage of sensors and actuators of different nature and diverse interfaces (SPI, I2C, analogue, etc.) makes access to them from a network in a homogeneous and secure way more complex. A framework, including both software and hardware resources, is necessary to simplify and unify networked access to these devices. In this paper, a set of open-source software tools, specifically designed to cover the different issues concerning the access to sensors and actuators, and two proposed low-cost hardware architectures to operate with the abovementioned software tools are presented. They allow integrated and easy access to local or remote sensors and actuators. The software tools, integrated in the free authoring tool Easy Java and Javascript Simulations (EJS) solve the interaction issues between the subsystem that integrates sensors and actuators into the network, called convergence subsystem in this paper, and the Human Machine Interface (HMI)—this one designed using the intuitive graphical system of EJS—located on the user’s computer. The proposed hardware architectures and software tools are described and experimental implementations with the proposed tools are presented. PMID:28067801

Easy Handling of Sensors and Actuators over TCP/IP Networks by Open Source Hardware/Software.

PubMed

Mejías, Andrés; Herrera, Reyes S; Márquez, Marco A; Calderón, Antonio José; González, Isaías; Andújar, José Manuel

2017-01-05

There are several specific solutions for accessing sensors and actuators present in any process or system through a TCP/IP network, either local or a wide area type like the Internet. The usage of sensors and actuators of different nature and diverse interfaces (SPI, I2C, analogue, etc.) makes access to them from a network in a homogeneous and secure way more complex. A framework, including both software and hardware resources, is necessary to simplify and unify networked access to these devices. In this paper, a set of open-source software tools, specifically designed to cover the different issues concerning the access to sensors and actuators, and two proposed low-cost hardware architectures to operate with the abovementioned software tools are presented. They allow integrated and easy access to local or remote sensors and actuators. The software tools, integrated in the free authoring tool Easy Java and Javascript Simulations (EJS) solve the interaction issues between the subsystem that integrates sensors and actuators into the network, called convergence subsystem in this paper, and the Human Machine Interface (HMI)-this one designed using the intuitive graphical system of EJS-located on the user's computer. The proposed hardware architectures and software tools are described and experimental implementations with the proposed tools are presented.

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

PubMed

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

2018-04-01

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

Scrutinizing UML Activity Diagrams

NASA Astrophysics Data System (ADS)

Al-Fedaghi, Sabah

Building an information system involves two processes: conceptual modeling of the “real world domain” and designing the software system. Object-oriented methods and languages (e.g., UML) are typically used for describing the software system. For the system analysis process that produces the conceptual description, object-oriented techniques or semantics extensions are utilized. Specifically, UML activity diagrams are the “flow charts” of object-oriented conceptualization tools. This chapter proposes an alternative to UML activity diagrams through the development of a conceptual modeling methodology based on the notion of flow.

Characterization of Cloud Water-Content Distribution

NASA Technical Reports Server (NTRS)

Lee, Seungwon

2010-01-01

The development of realistic cloud parameterizations for climate models requires accurate characterizations of subgrid distributions of thermodynamic variables. To this end, a software tool was developed to characterize cloud water-content distributions in climate-model sub-grid scales. This software characterizes distributions of cloud water content with respect to cloud phase, cloud type, precipitation occurrence, and geo-location using CloudSat radar measurements. It uses a statistical method called maximum likelihood estimation to estimate the probability density function of the cloud water content.

Software Analysis of New Space Gravity Data for Geophysics and Climate Research

NASA Technical Reports Server (NTRS)

Deese, Rupert; Ivins, Erik R.; Fielding, Eric J.

2012-01-01

Both the Gravity Recovery and Climate Experiment (GRACE) and Gravity field and steady-state Ocean Circulation Explorer (GOCE) satellites are returning rich data for the study of the solid earth, the oceans, and the climate. Current software analysis tools do not provide researchers with the ease and flexibility required to make full use of this data. We evaluate the capabilities and shortcomings of existing software tools including Mathematica, the GOCE User Toolbox, the ICGEM's (International Center for Global Earth Models) web server, and Tesseroids. Using existing tools as necessary, we design and implement software with the capability to produce gridded data and publication quality renderings from raw gravity data. The straight forward software interface marks an improvement over previously existing tools and makes new space gravity data more useful to researchers. Using the software we calculate Bouguer anomalies of the gravity tensor's vertical component in the Gulf of Mexico, Antarctica, and the 2010 Maule earthquake region. These maps identify promising areas of future research.

Scientific Computation Application Partnerships in Materials and Chemical Sciences, Charge Transfer and Charge Transport in Photoactivated Systems, Developing Electron-Correlated Methods for Excited State Structure and Dynamics in the NWChem Software Suite

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

Cramer, Christopher J.

Charge transfer and charge transport in photoactivated systems are fundamental processes that underlie solar energy capture, solar energy conversion, and photoactivated catalysis, both organometallic and enzymatic. We developed methods, algorithms, and software tools needed for reliable treatment of the underlying physics for charge transfer and charge transport, an undertaking with broad applicability to the goals of the fundamental-interaction component of the Department of Energy Office of Basic Energy Sciences and the exascale initiative of the Office of Advanced Scientific Computing Research.

Atrioventricular junction (AVJ) motion tracking: a software tool with ITK/VTK/Qt.

PubMed

Pengdong Xiao; Shuang Leng; Xiaodan Zhao; Hua Zou; Ru San Tan; Wong, Philip; Liang Zhong

2016-08-01

The quantitative measurement of the Atrioventricular Junction (AVJ) motion is an important index for ventricular functions of one cardiac cycle including systole and diastole. In this paper, a software tool that can conduct AVJ motion tracking from cardiovascular magnetic resonance (CMR) images is presented by using Insight Segmentation and Registration Toolkit (ITK), The Visualization Toolkit (VTK) and Qt. The software tool is written in C++ by using Visual Studio Community 2013 integrated development environment (IDE) containing both an editor and a Microsoft complier. The software package has been successfully implemented. From the software engineering practice, it is concluded that ITK, VTK, and Qt are very handy software systems to implement automatic image analysis functions for CMR images such as quantitative measure of motion by visual tracking.

A software platform for continuum modeling of ion channels based on unstructured mesh

NASA Astrophysics Data System (ADS)

Tu, B.; Bai, S. Y.; Chen, M. X.; Xie, Y.; Zhang, L. B.; Lu, B. Z.

2014-01-01

Most traditional continuum molecular modeling adopted finite difference or finite volume methods which were based on a structured mesh (grid). Unstructured meshes were only occasionally used, but an increased number of applications emerge in molecular simulations. To facilitate the continuum modeling of biomolecular systems based on unstructured meshes, we are developing a software platform with tools which are particularly beneficial to those approaches. This work describes the software system specifically for the simulation of a typical, complex molecular procedure: ion transport through a three-dimensional channel system that consists of a protein and a membrane. The platform contains three parts: a meshing tool chain for ion channel systems, a parallel finite element solver for the Poisson-Nernst-Planck equations describing the electrodiffusion process of ion transport, and a visualization program for continuum molecular modeling. The meshing tool chain in the platform, which consists of a set of mesh generation tools, is able to generate high-quality surface and volume meshes for ion channel systems. The parallel finite element solver in our platform is based on the parallel adaptive finite element package PHG which wass developed by one of the authors [1]. As a featured component of the platform, a new visualization program, VCMM, has specifically been developed for continuum molecular modeling with an emphasis on providing useful facilities for unstructured mesh-based methods and for their output analysis and visualization. VCMM provides a graphic user interface and consists of three modules: a molecular module, a meshing module and a numerical module. A demonstration of the platform is provided with a study of two real proteins, the connexin 26 and hemolysin ion channels.

Software Process Assurance for Complex Electronics

NASA Technical Reports Server (NTRS)

Plastow, Richard A.

2007-01-01

Complex Electronics (CE) now perform tasks that were previously handled in software, such as communication protocols. Many methods used to develop software bare a close resemblance to CE development. Field Programmable Gate Arrays (FPGAs) can have over a million logic gates while system-on-chip (SOC) devices can combine a microprocessor, input and output channels, and sometimes an FPGA for programmability. With this increased intricacy, the possibility of software-like bugs such as incorrect design, logic, and unexpected interactions within the logic is great. With CE devices obscuring the hardware/software boundary, we propose that mature software methodologies may be utilized with slight modifications in the development of these devices. Software Process Assurance for Complex Electronics (SPACE) is a research project that used standardized S/W Assurance/Engineering practices to provide an assurance framework for development activities. Tools such as checklists, best practices and techniques were used to detect missing requirements and bugs earlier in the development cycle creating a development process for CE that was more easily maintained, consistent and configurable based on the device used.

A Java-based tool for the design of classification microarrays.

PubMed

Meng, Da; Broschat, Shira L; Call, Douglas R

2008-08-04

Classification microarrays are used for purposes such as identifying strains of bacteria and determining genetic relationships to understand the epidemiology of an infectious disease. For these cases, mixed microarrays, which are composed of DNA from more than one organism, are more effective than conventional microarrays composed of DNA from a single organism. Selection of probes is a key factor in designing successful mixed microarrays because redundant sequences are inefficient and limited representation of diversity can restrict application of the microarray. We have developed a Java-based software tool, called PLASMID, for use in selecting the minimum set of probe sequences needed to classify different groups of plasmids or bacteria. The software program was successfully applied to several different sets of data. The utility of PLASMID was illustrated using existing mixed-plasmid microarray data as well as data from a virtual mixed-genome microarray constructed from different strains of Streptococcus. Moreover, use of data from expression microarray experiments demonstrated the generality of PLASMID. In this paper we describe a new software tool for selecting a set of probes for a classification microarray. While the tool was developed for the design of mixed microarrays-and mixed-plasmid microarrays in particular-it can also be used to design expression arrays. The user can choose from several clustering methods (including hierarchical, non-hierarchical, and a model-based genetic algorithm), several probe ranking methods, and several different display methods. A novel approach is used for probe redundancy reduction, and probe selection is accomplished via stepwise discriminant analysis. Data can be entered in different formats (including Excel and comma-delimited text), and dendrogram, heat map, and scatter plot images can be saved in several different formats (including jpeg and tiff). Weights generated using stepwise discriminant analysis can be stored for analysis of subsequent experimental data. Additionally, PLASMID can be used to construct virtual microarrays with genomes from public databases, which can then be used to identify an optimal set of probes.

SU-E-J-272: Auto-Segmentation of Regions with Differentiating CT Numbers for Treatment Response Assessment

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

Yang, C; Noid, G; Dalah, E

2015-06-15

Purpose: It has been reported recently that the change of CT number (CTN) during and after radiation therapy (RT) may be used to assess RT response. The purpose of this work is to develop a tool to automatically segment the regions with differentiating CTN and/or with change of CTN in a series of CTs. Methods: A software tool was developed to identify regions with differentiating CTN using K-mean Cluster of CT numbers and to automatically delineate these regions using convex hull enclosing method. Pre- and Post-RT CT, PET, or MRI images acquired for sample lung and pancreatic cancer cases weremore » used to test the software tool. K-mean cluster of CT numbers within the gross tumor volumes (GTVs) delineated based on PET SUV (standard uptake value of fludeoxyglucose) and/or MRI ADC (apparent diffusion coefficient) map was analyzed. The cluster centers with higher value were considered as active tumor volumes (ATV). The convex hull contours enclosing preset clusters were used to delineate these ATVs with color washed displays. The CTN defined ATVs were compared with the SUV- or ADC-defined ATVs. Results: CTN stability of the CT scanner used to acquire the CTs in this work is less than 1.5 Hounsfield Unit (HU) variation annually. K-mean cluster centers in the GTV have difference of ∼20 HU, much larger than variation due to CTN stability, for the lung cancer cases studied. The dice coefficient between the ATVs delineated based on convex hull enclosure of high CTN centers and the PET defined GTVs based on SUV cutoff value of 2.5 was 90(±5)%. Conclusion: A software tool was developed using K-mean cluster and convex hull contour to automatically segment high CTN regions which may not be identifiable using a simple threshold method. These CTN regions were reasonably overlapped with the PET or MRI defined GTVs.« less

Object-oriented design of medical imaging software.

PubMed

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

1994-01-01

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

Security Risks: Management and Mitigation in the Software Life Cycle

NASA Technical Reports Server (NTRS)

Gilliam, David P.

2004-01-01

A formal approach to managing and mitigating security risks in the software life cycle is requisite to developing software that has a higher degree of assurance that it is free of security defects which pose risk to the computing environment and the organization. Due to its criticality, security should be integrated as a formal approach in the software life cycle. Both a software security checklist and assessment tools should be incorporated into this life cycle process and integrated with a security risk assessment and mitigation tool. The current research at JPL addresses these areas through the development of a Sotfware Security Assessment Instrument (SSAI) and integrating it with a Defect Detection and Prevention (DDP) risk management tool.

Improving the Agency's Software Acquisition Capability

NASA Technical Reports Server (NTRS)

Hankinson, Allen

2003-01-01

External development of software has oftc n led to unsatisfactory results and great frustration for the assurE 7ce community. Contracts frequently omit critical assuranc 4 processes or the right to oversee software development activitie: At a time when NASA depends more and more on software to in plement critical system functions, combination of three factors ex; cerbate this problem: I ) the ever-increasing trend to acquire rather than develop software in-house, 2) the trend toward performance based contracts, and 3) acquisition vehicles that only state softwar 2 requirements while leaving development standards and assur! ince methodologies up to the contractor. We propose to identify specific methods at d tools that NASA projects can use to mitigate the adverse el ects of the three problems. TWO broad classes of methoddt ols will be explored. The first will be those that provide NASA p ojects with insight and oversight into contractors' activities. The st cond will be those that help projects objectively assess, and thus i nprwe, their software acquisition capability. Of particular interest is the Software Engineering Institute's (SEI) Software Acqt isition Capability Maturity Model (SA-CMMO).

A simplified close range photogrammetry method for soil erosion assessment

USDA-ARS?s Scientific Manuscript database

With the increased affordability of consumer grade cameras and the development of powerful image processing software, digital photogrammetry offers a competitive advantage as a tool for soil erosion estimation compared to other technologies. One bottleneck of digital photogrammetry is its dependency...

Program Office Guide to Ada. Edition 1

DTIC Science & Technology

1986-09-17

publication. MARK V. ZIEMBA , 2Lt, USAF Project Officer, Software Engineering Tools & Methods ARTHUR G. DECELLES, Capt, USAF Program Manager, Computer...UNLIMITED G3 SAME AS RPT D DTIC USERS 21 ABSTRACT SECURITY CLASSIFICATION UNCLASSIFIED 22a. NAME OF RESPONSIBLE INDIVIDUAL M.V. Ziemba

Methods, Knowledge Support, and Experimental Tools for Modeling

DTIC Science & Technology

2006-10-01

open source software entities: the PostgreSQL relational database management system (http://www.postgres.org), the Apache web server (http...past. The revision control system allows the program to capture disagreements, and allows users to explore the history of such disagreements by

Evaluating a digital ship design tool prototype: Designers' perceptions of novel ergonomics software.

PubMed

Mallam, Steven C; Lundh, Monica; MacKinnon, Scott N

2017-03-01

Computer-aided solutions are essential for naval architects to manage and optimize technical complexities when developing a ship's design. Although there are an array of software solutions aimed to optimize the human element in design, practical ergonomics methodologies and technological solutions have struggled to gain widespread application in ship design processes. This paper explores how a new ergonomics technology is perceived by naval architecture students using a mixed-methods framework. Thirteen Naval Architecture and Ocean Engineering Masters students participated in the study. Overall, results found participants perceived the software and its embedded ergonomics tools to benefit their design work, increasing their empathy and ability to understand the work environment and work demands end-users face. However, participant's questioned if ergonomics could be practically and efficiently implemented under real-world project constraints. This revealed underlying social biases and a fundamental lack of understanding in engineering postgraduate students regarding applied ergonomics in naval architecture. Copyright © 2016 Elsevier Ltd. All rights reserved.

Software Development Of XML Parser Based On Algebraic Tools

NASA Astrophysics Data System (ADS)

Georgiev, Bozhidar; Georgieva, Adriana

2011-12-01

In this paper, is presented one software development and implementation of an algebraic method for XML data processing, which accelerates XML parsing process. Therefore, the proposed in this article nontraditional approach for fast XML navigation with algebraic tools contributes to advanced efforts in the making of an easier user-friendly API for XML transformations. Here the proposed software for XML documents processing (parser) is easy to use and can manage files with strictly defined data structure. The purpose of the presented algorithm is to offer a new approach for search and restructuring hierarchical XML data. This approach permits fast XML documents processing, using algebraic model developed in details in previous works of the same authors. So proposed parsing mechanism is easy accessible to the web consumer who is able to control XML file processing, to search different elements (tags) in it, to delete and to add a new XML content as well. The presented various tests show higher rapidity and low consumption of resources in comparison with some existing commercial parsers.

Guidance, navigation, and control subsystem equipment selection algorithm using expert system methods

NASA Technical Reports Server (NTRS)

Allen, Cheryl L.

1991-01-01

Enhanced engineering tools can be obtained through the integration of expert system methodologies and existing design software. The application of these methodologies to the spacecraft design and cost model (SDCM) software provides an improved technique for the selection of hardware for unmanned spacecraft subsystem design. The knowledge engineering system (KES) expert system development tool was used to implement a smarter equipment section algorithm than that which is currently achievable through the use of a standard data base system. The guidance, navigation, and control subsystems of the SDCM software was chosen as the initial subsystem for implementation. The portions of the SDCM code which compute the selection criteria and constraints remain intact, and the expert system equipment selection algorithm is embedded within this existing code. The architecture of this new methodology is described and its implementation is reported. The project background and a brief overview of the expert system is described, and once the details of the design are characterized, an example of its implementation is demonstrated.

A workflow learning model to improve geovisual analytics utility

PubMed Central

Roth, Robert E; MacEachren, Alan M; McCabe, Craig A

2011-01-01

Introduction This paper describes the design and implementation of the G-EX Portal Learn Module, a web-based, geocollaborative application for organizing and distributing digital learning artifacts. G-EX falls into the broader context of geovisual analytics, a new research area with the goal of supporting visually-mediated reasoning about large, multivariate, spatiotemporal information. Because this information is unprecedented in amount and complexity, GIScientists are tasked with the development of new tools and techniques to make sense of it. Our research addresses the challenge of implementing these geovisual analytics tools and techniques in a useful manner. Objectives The objective of this paper is to develop and implement a method for improving the utility of geovisual analytics software. The success of software is measured by its usability (i.e., how easy the software is to use?) and utility (i.e., how useful the software is). The usability and utility of software can be improved by refining the software, increasing user knowledge about the software, or both. It is difficult to achieve transparent usability (i.e., software that is immediately usable without training) of geovisual analytics software because of the inherent complexity of the included tools and techniques. In these situations, improving user knowledge about the software through the provision of learning artifacts is as important, if not more so, than iterative refinement of the software itself. Therefore, our approach to improving utility is focused on educating the user. Methodology The research reported here was completed in two steps. First, we developed a model for learning about geovisual analytics software. Many existing digital learning models assist only with use of the software to complete a specific task and provide limited assistance with its actual application. To move beyond task-oriented learning about software use, we propose a process-oriented approach to learning based on the concept of scientific workflows. Second, we implemented an interface in the G-EX Portal Learn Module to demonstrate the workflow learning model. The workflow interface allows users to drag learning artifacts uploaded to the G-EX Portal onto a central whiteboard and then annotate the workflow using text and drawing tools. Once completed, users can visit the assembled workflow to get an idea of the kind, number, and scale of analysis steps, view individual learning artifacts associated with each node in the workflow, and ask questions about the overall workflow or individual learning artifacts through the associated forums. An example learning workflow in the domain of epidemiology is provided to demonstrate the effectiveness of the approach. Results/Conclusions In the context of geovisual analytics, GIScientists are not only responsible for developing software to facilitate visually-mediated reasoning about large and complex spatiotemporal information, but also for ensuring that this software works. The workflow learning model discussed in this paper and demonstrated in the G-EX Portal Learn Module is one approach to improving the utility of geovisual analytics software. While development of the G-EX Portal Learn Module is ongoing, we expect to release the G-EX Portal Learn Module by Summer 2009. PMID:21983545

A workflow learning model to improve geovisual analytics utility.

PubMed

Roth, Robert E; Maceachren, Alan M; McCabe, Craig A

2009-01-01

INTRODUCTION: This paper describes the design and implementation of the G-EX Portal Learn Module, a web-based, geocollaborative application for organizing and distributing digital learning artifacts. G-EX falls into the broader context of geovisual analytics, a new research area with the goal of supporting visually-mediated reasoning about large, multivariate, spatiotemporal information. Because this information is unprecedented in amount and complexity, GIScientists are tasked with the development of new tools and techniques to make sense of it. Our research addresses the challenge of implementing these geovisual analytics tools and techniques in a useful manner. OBJECTIVES: The objective of this paper is to develop and implement a method for improving the utility of geovisual analytics software. The success of software is measured by its usability (i.e., how easy the software is to use?) and utility (i.e., how useful the software is). The usability and utility of software can be improved by refining the software, increasing user knowledge about the software, or both. It is difficult to achieve transparent usability (i.e., software that is immediately usable without training) of geovisual analytics software because of the inherent complexity of the included tools and techniques. In these situations, improving user knowledge about the software through the provision of learning artifacts is as important, if not more so, than iterative refinement of the software itself. Therefore, our approach to improving utility is focused on educating the user. METHODOLOGY: The research reported here was completed in two steps. First, we developed a model for learning about geovisual analytics software. Many existing digital learning models assist only with use of the software to complete a specific task and provide limited assistance with its actual application. To move beyond task-oriented learning about software use, we propose a process-oriented approach to learning based on the concept of scientific workflows. Second, we implemented an interface in the G-EX Portal Learn Module to demonstrate the workflow learning model. The workflow interface allows users to drag learning artifacts uploaded to the G-EX Portal onto a central whiteboard and then annotate the workflow using text and drawing tools. Once completed, users can visit the assembled workflow to get an idea of the kind, number, and scale of analysis steps, view individual learning artifacts associated with each node in the workflow, and ask questions about the overall workflow or individual learning artifacts through the associated forums. An example learning workflow in the domain of epidemiology is provided to demonstrate the effectiveness of the approach. RESULTS/CONCLUSIONS: In the context of geovisual analytics, GIScientists are not only responsible for developing software to facilitate visually-mediated reasoning about large and complex spatiotemporal information, but also for ensuring that this software works. The workflow learning model discussed in this paper and demonstrated in the G-EX Portal Learn Module is one approach to improving the utility of geovisual analytics software. While development of the G-EX Portal Learn Module is ongoing, we expect to release the G-EX Portal Learn Module by Summer 2009.

The Knowledge-Based Software Assistant: Beyond CASE

NASA Technical Reports Server (NTRS)

Carozzoni, Joseph A.

1993-01-01

This paper will outline the similarities and differences between two paradigms of software development. Both support the whole software life cycle and provide automation for most of the software development process, but have different approaches. The CASE approach is based on a set of tools linked by a central data repository. This tool-based approach is data driven and views software development as a series of sequential steps, each resulting in a product. The Knowledge-Based Software Assistant (KBSA) approach, a radical departure from existing software development practices, is knowledge driven and centers around a formalized software development process. KBSA views software development as an incremental, iterative, and evolutionary process with development occurring at the specification level.

Methods and tools for profiling and control of distributed systems

NASA Astrophysics Data System (ADS)

Sukharev, R.; Lukyanchikov, O.; Nikulchev, E.; Biryukov, D.; Ryadchikov, I.

2018-02-01

This article is devoted to the topic of profiling and control of distributed systems. Distributed systems have a complex architecture, applications are distributed among various computing nodes, and many network operations are performed. Therefore, today it is important to develop methods and tools for profiling distributed systems. The article analyzes and standardizes methods for profiling distributed systems that focus on simulation to conduct experiments and build a graph model of the system. The theory of queueing networks is used for simulation modeling of distributed systems, receiving and processing user requests. To automate the above method of profiling distributed systems the software application was developed with a modular structure and similar to a SCADA-system.

Chipster: user-friendly analysis software for microarray and other high-throughput data.

PubMed

Kallio, M Aleksi; Tuimala, Jarno T; Hupponen, Taavi; Klemelä, Petri; Gentile, Massimiliano; Scheinin, Ilari; Koski, Mikko; Käki, Janne; Korpelainen, Eija I

2011-10-14

The growth of high-throughput technologies such as microarrays and next generation sequencing has been accompanied by active research in data analysis methodology, producing new analysis methods at a rapid pace. While most of the newly developed methods are freely available, their use requires substantial computational skills. In order to enable non-programming biologists to benefit from the method development in a timely manner, we have created the Chipster software. Chipster (http://chipster.csc.fi/) brings a powerful collection of data analysis methods within the reach of bioscientists via its intuitive graphical user interface. Users can analyze and integrate different data types such as gene expression, miRNA and aCGH. The analysis functionality is complemented with rich interactive visualizations, allowing users to select datapoints and create new gene lists based on these selections. Importantly, users can save the performed analysis steps as reusable, automatic workflows, which can also be shared with other users. Being a versatile and easily extendable platform, Chipster can be used for microarray, proteomics and sequencing data. In this article we describe its comprehensive collection of analysis and visualization tools for microarray data using three case studies. Chipster is a user-friendly analysis software for high-throughput data. Its intuitive graphical user interface enables biologists to access a powerful collection of data analysis and integration tools, and to visualize data interactively. Users can collaborate by sharing analysis sessions and workflows. Chipster is open source, and the server installation package is freely available.

Chipster: user-friendly analysis software for microarray and other high-throughput data

PubMed Central

2011-01-01

Background The growth of high-throughput technologies such as microarrays and next generation sequencing has been accompanied by active research in data analysis methodology, producing new analysis methods at a rapid pace. While most of the newly developed methods are freely available, their use requires substantial computational skills. In order to enable non-programming biologists to benefit from the method development in a timely manner, we have created the Chipster software. Results Chipster (http://chipster.csc.fi/) brings a powerful collection of data analysis methods within the reach of bioscientists via its intuitive graphical user interface. Users can analyze and integrate different data types such as gene expression, miRNA and aCGH. The analysis functionality is complemented with rich interactive visualizations, allowing users to select datapoints and create new gene lists based on these selections. Importantly, users can save the performed analysis steps as reusable, automatic workflows, which can also be shared with other users. Being a versatile and easily extendable platform, Chipster can be used for microarray, proteomics and sequencing data. In this article we describe its comprehensive collection of analysis and visualization tools for microarray data using three case studies. Conclusions Chipster is a user-friendly analysis software for high-throughput data. Its intuitive graphical user interface enables biologists to access a powerful collection of data analysis and integration tools, and to visualize data interactively. Users can collaborate by sharing analysis sessions and workflows. Chipster is open source, and the server installation package is freely available. PMID:21999641

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.

Implementation of Task-Tracking Software for Clinical IT Management.

PubMed

Purohit, Anne-Maria; Brutscheck, Clemens; Prokosch, Hans-Ulrich; Ganslandt, Thomas; Schneider, Martin

2017-01-01

Often in clinical IT departments, many different methods and IT systems are used for task-tracking and project organization. Based on managers' personal preferences and knowledge about project management methods, tools differ from team to team and even from employee to employee. This causes communication problems, especially when tasks need to be done in cooperation with different teams. Monitoring tasks and resources becomes impossible: there are no defined deliverables, which prevents reliable deadlines. Because of these problems, we implemented task-tracking software which is now in use across all seven teams at the University Hospital Erlangen. Over a period of seven months, a working group defined types of tasks (project, routine task, etc.), workflows, and views to monitor the tasks of the 7 divisions, 20 teams and 340 different IT services. The software has been in use since December 2016.

An Intracranial Electroencephalography (iEEG) Brain Function Mapping Tool with an Application to Epilepsy Surgery Evaluation.

PubMed

Wang, Yinghua; Yan, Jiaqing; Wen, Jianbin; Yu, Tao; Li, Xiaoli

2016-01-01

Before epilepsy surgeries, intracranial electroencephalography (iEEG) is often employed in function mapping and epileptogenic foci localization. Although the implanted electrodes provide crucial information for epileptogenic zone resection, a convenient clinical tool for electrode position registration and Brain Function Mapping (BFM) visualization is still lacking. In this study, we developed a BFM Tool, which facilitates electrode position registration and BFM visualization, with an application to epilepsy surgeries. The BFM Tool mainly utilizes electrode location registration and function mapping based on pre-defined brain models from other software. In addition, the electrode node and mapping properties, such as the node size/color, edge color/thickness, mapping method, can be adjusted easily using the setting panel. Moreover, users may manually import/export location and connectivity data to generate figures for further application. The role of this software is demonstrated by a clinical study of language area localization. The BFM Tool helps clinical doctors and researchers visualize implanted electrodes and brain functions in an easy, quick and flexible manner. Our tool provides convenient electrode registration, easy brain function visualization, and has good performance. It is clinical-oriented and is easy to deploy and use. The BFM tool is suitable for epilepsy and other clinical iEEG applications.

The Software Management Environment (SME)

NASA Technical Reports Server (NTRS)

Valett, Jon D.; Decker, William; Buell, John

1988-01-01

The Software Management Environment (SME) is a research effort designed to utilize the past experiences and results of the Software Engineering Laboratory (SEL) and to incorporate this knowledge into a tool for managing projects. SME provides the software development manager with the ability to observe, compare, predict, analyze, and control key software development parameters such as effort, reliability, and resource utilization. The major components of the SME, the architecture of the system, and examples of the functionality of the tool are discussed.

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

PubMed

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

2014-01-01

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

SU-E-J-199: A Software Tool for Quality Assurance of Online Replanning with MR-Linac

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

Chen, G; Ahunbay, E; Li, X

2015-06-15

Purpose: To develop a quality assurance software tool, ArtQA, capable of automatically checking radiation treatment plan parameters, verifying plan data transfer from treatment planning system (TPS) to record and verify (R&V) system, performing a secondary MU calculation considering the effect of magnetic field from MR-Linac, and verifying the delivery and plan consistency, for online replanning. Methods: ArtQA was developed by creating interfaces to TPS (e.g., Monaco, Elekta), R&V system (Mosaiq, Elekta), and secondary MU calculation system. The tool obtains plan parameters from the TPS via direct file reading, and retrieves plan data both transferred from TPS and recorded during themore » actual delivery in the R&V system database via open database connectivity and structured query language. By comparing beam/plan datasets in different systems, ArtQA detects and outputs discrepancies between TPS, R&V system and secondary MU calculation system, and delivery. To consider the effect of 1.5T transverse magnetic field from MR-Linac in the secondary MU calculation, a method based on modified Clarkson integration algorithm was developed and tested for a series of clinical situations. Results: ArtQA is capable of automatically checking plan integrity and logic consistency, detecting plan data transfer errors, performing secondary MU calculations with or without a transverse magnetic field, and verifying treatment delivery. The tool is efficient and effective for pre- and post-treatment QA checks of all available treatment parameters that may be impractical with the commonly-used visual inspection. Conclusion: The software tool ArtQA can be used for quick and automatic pre- and post-treatment QA check, eliminating human error associated with visual inspection. While this tool is developed for online replanning to be used on MR-Linac, where the QA needs to be performed rapidly as the patient is lying on the table waiting for the treatment, ArtQA can be used as a general QA tool in radiation oncology practice. This work is partially supported by Elekta Inc.« less

TU-FG-201-07: Development of SRS Conical Collimator Collision Prediction Software for Radiation Treatment Safety

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

Gutti, V; Morrow, A; Kim, S

Purpose: Stereotactic radiosurgery (SRS) treatments using conical collimators can potentially result in gantry collision with treatment table due to limited collision-clear spaces. An in-house software was developed to help the SRS treatment planner mitigate potential SRS conical collimator (Varian Medical System, Palo Alto, CA) collisions with the treatment table. This software was designed to remove treatment re-planning secondary to unexpected collisions. Methods: A BrainLAB SRS ICT Frameless Extension used for SRS treatments in our clinic was mathematically modelled using surface points registered to the 3D co-ordinate space of the couch extension. The surface points are transformed based on the treatmentmore » isocenter point and potential collisions are determined in 3D space for couch and gantry angle combinations. The distance between the SRS conical collimators and LINAC isocenter is known. The collision detection model was programmed in MATLAB (Mathwork, Natick, MA) to display graphical plots of the calculations, and the plotted data is used to avoid the gantry and couch angle combinations that would likely result in a collision. We have utilized the cone collision tool for 23 SRS cone treatment plans (8 retrospective and 15 prospective for 10 patients). Results: Twenty one plans strongly agreed with the software tool prediction for collision. However, in two plans, a collision was observed with a 0.5 cm margin when the software predicted no collision. Therefore, additional margins were added to the clearance criteria in the program to achieve a lower risk of actual collisions. Conclusion: Our in-house developed collision check software successfully avoided SRS cone re-planning by 91.3% due to a reduction in cone collisions with the treatment table. Future developments to our software will include a CT image data set based collision prediction model as well as a beam angle optimization tool to avoid normal critical tissues as well as previously treated lesions.« less

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

PubMed

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

2017-02-01

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

FFI: A software tool for ecological monitoring

Treesearch

Duncan C. Lutes; Nathan C. Benson; MaryBeth Keifer; John F. Caratti; S. Austin Streetman

2009-01-01

A new monitoring tool called FFI (FEAT/FIREMON Integrated) has been developed to assist managers with collection, storage and analysis of ecological information. The tool was developed through the complementary integration of two fire effects monitoring systems commonly used in the United States: FIREMON and the Fire Ecology Assessment Tool. FFI provides software...

SUNREL Related Links | Buildings | NREL

Science.gov Websites

SUNREL Related Links SUNREL Related Links DOE Simulation Software Tools Directory a directory of 301 building software tools for evaluation of energy efficiency, renewable energy, and sustainability in buildings. TREAT Software Program a computer program that uses SUNREL and is designed to provide

IUWare and Computing Tools: Indiana University's Approach to Low-Cost Software.

ERIC Educational Resources Information Center

Sheehan, Mark C.; Williams, James G.

1987-01-01

Describes strategies for providing low-cost microcomputer-based software for classroom use on college campuses. Highlights include descriptions of the software (IUWare and Computing Tools); computing center support; license policies; documentation; promotion; distribution; staff, faculty, and user training; problems; and future plans. (LRW)

Publishing Platform for Scientific Software - Lessons Learned

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

Design pattern mining using distributed learning automata and DNA sequence alignment.

PubMed

Esmaeilpour, Mansour; Naderifar, Vahideh; Shukur, Zarina

2014-01-01

Over the last decade, design patterns have been used extensively to generate reusable solutions to frequently encountered problems in software engineering and object oriented programming. A design pattern is a repeatable software design solution that provides a template for solving various instances of a general problem. This paper describes a new method for pattern mining, isolating design patterns and relationship between them; and a related tool, DLA-DNA for all implemented pattern and all projects used for evaluation. DLA-DNA achieves acceptable precision and recall instead of other evaluated tools based on distributed learning automata (DLA) and deoxyribonucleic acid (DNA) sequences alignment. The proposed method mines structural design patterns in the object oriented source code and extracts the strong and weak relationships between them, enabling analyzers and programmers to determine the dependency rate of each object, component, and other section of the code for parameter passing and modular programming. The proposed model can detect design patterns better that available other tools those are Pinot, PTIDEJ and DPJF; and the strengths of their relationships. The result demonstrate that whenever the source code is build standard and non-standard, based on the design patterns, then the result of the proposed method is near to DPJF and better that Pinot and PTIDEJ. The proposed model is tested on the several source codes and is compared with other related models and available tools those the results show the precision and recall of the proposed method, averagely 20% and 9.6% are more than Pinot, 27% and 31% are more than PTIDEJ and 3.3% and 2% are more than DPJF respectively. The primary idea of the proposed method is organized in two following steps: the first step, elemental design patterns are identified, while at the second step, is composed to recognize actual design patterns.

Finite Element Simulation of Temperature and Strain Distribution during Friction Stir Welding of AA2024 Aluminum Alloy

NASA Astrophysics Data System (ADS)

Jain, Rahul; Pal, Surjya Kanta; Singh, Shiv Brat

2017-02-01

Friction Stir Welding (FSW) is a solid state joining process and is handy for welding aluminum alloys. Finite Element Method (FEM) is an important tool to predict state variables of the process but numerical simulation of FSW is highly complex due to non-linear contact interactions between tool and work piece and interdependency of displacement and temperature. In the present work, a three dimensional coupled thermo-mechanical method based on Lagrangian implicit method is proposed to study the thermal history, strain distribution and thermo-mechanical process in butt welding of Aluminum alloy 2024 using DEFORM-3D software. Workpiece is defined as rigid-visco plastic material and sticking condition between tool and work piece is defined. Adaptive re-meshing is used to tackle high mesh distortion. Effect of tool rotational and welding speed on plastic strain is studied and insight is given on asymmetric nature of FSW process. Temperature distribution on the workpiece and tool is predicted and maximum temperature is found in workpiece top surface.

DECONV-TOOL: An IDL based deconvolution software package

NASA Technical Reports Server (NTRS)

Varosi, F.; Landsman, W. B.

1992-01-01

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

The Holistic Targeting (HOT) Methodology as the Means to Improve Information Operations (IO) Target Development and Prioritization

DTIC Science & Technology

2008-09-01

software facilitate targeting problem understanding and the network analysis tool, Palantir , as an efficient and tailored semi-automated means to...the use of compendium software facilitate targeting problem understanding and the network analysis tool, Palantir , as an efficient and tailored semi...OBJECTIVES USING COMPENDIUM SOFTWARE .....63 E. HOT TARGET PRIORITIZATION AND DEVELOPMENT USING PALANTIR SOFTWARE .................................69 1

Validation of Tendril TrueHome Using Software-to-Software Comparison

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

Maguire, Jeffrey B; Horowitz, Scott G; Moore, Nathan

This study performed comparative evaluation of EnergyPlus version 8.6 and Tendril TrueHome, two physics-based home energy simulation models, to identify differences in energy consumption predictions between the two programs and resolve discrepancies between them. EnergyPlus is considered a benchmark, best-in-class software tool for building energy simulation. This exercise sought to improve both software tools through additional evaluation/scrutiny.

Tool Use Within NASA Software Quality Assurance

NASA Technical Reports Server (NTRS)

Shigeta, Denise; Port, Dan; Nikora, Allen P.; Wilf, Joel

2013-01-01

As space mission software systems become larger and more complex, it is increasingly important for the software assurance effort to have the ability to effectively assess both the artifacts produced during software system development and the development process itself. Conceptually, assurance is a straightforward idea - it is the result of activities carried out by an organization independent of the software developers to better inform project management of potential technical and programmatic risks, and thus increase management's confidence in the decisions they ultimately make. In practice, effective assurance for large, complex systems often entails assessing large, complex software artifacts (e.g., requirements specifications, architectural descriptions) as well as substantial amounts of unstructured information (e.g., anomaly reports resulting from testing activities during development). In such an environment, assurance engineers can benefit greatly from appropriate tool support. In order to do so, an assurance organization will need accurate and timely information on the tool support available for various types of assurance activities. In this paper, we investigate the current use of tool support for assurance organizations within NASA, and describe on-going work at JPL for providing assurance organizations with the information about tools they need to use them effectively.

Software reengineering

NASA Technical Reports Server (NTRS)

Fridge, Ernest M., III

1991-01-01

Today's software systems generally use obsolete technology, are not integrated properly with other software systems, and are difficult and costly to maintain. The discipline of reverse engineering is becoming prominent as organizations try to move their systems up to more modern and maintainable technology in a cost effective manner. JSC created a significant set of tools to develop and maintain FORTRAN and C code during development of the Space Shuttle. This tool set forms the basis for an integrated environment to re-engineer existing code into modern software engineering structures which are then easier and less costly to maintain and which allow a fairly straightforward translation into other target languages. The environment will support these structures and practices even in areas where the language definition and compilers do not enforce good software engineering. The knowledge and data captured using the reverse engineering tools is passed to standard forward engineering tools to redesign or perform major upgrades to software systems in a much more cost effective manner than using older technologies. A beta vision of the environment was released in Mar. 1991. The commercial potential for such re-engineering tools is very great. CASE TRENDS magazine reported it to be the primary concern of over four hundred of the top MIS executives.

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

PubMed

Davis, Sean; Meltzer, Paul S

2007-07-15

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

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.

Runtime Performance Monitoring Tool for RTEMS System Software

NASA Astrophysics Data System (ADS)

Cho, B.; Kim, S.; Park, H.; Kim, H.; Choi, J.; Chae, D.; Lee, J.

2007-08-01

RTEMS is a commercial-grade real-time operating system that supports multi-processor computers. However, there are not many development tools for RTEMS. In this paper, we report new RTEMS-based runtime performance monitoring tool. We have implemented a light weight runtime monitoring task with an extension to the RTEMS APIs. Using our tool, software developers can verify various performance- related parameters during runtime. Our tool can be used during software development phase and in-orbit operation as well. Our implemented target agent is light weight and has small overhead using SpaceWire interface. Efforts to reduce overhead and to add other monitoring parameters are currently under research.

ELER software - a new tool for urban earthquake loss assessment

NASA Astrophysics Data System (ADS)

Hancilar, U.; Tuzun, C.; Yenidogan, C.; Erdik, M.

2010-12-01

Rapid loss estimation after potentially damaging earthquakes is critical for effective emergency response and public information. A methodology and software package, ELER-Earthquake Loss Estimation Routine, for rapid estimation of earthquake shaking and losses throughout the Euro-Mediterranean region was developed under the Joint Research Activity-3 (JRA3) of the EC FP6 Project entitled "Network of Research Infrastructures for European Seismology-NERIES". Recently, a new version (v2.0) of ELER software has been released. The multi-level methodology developed is capable of incorporating regional variability and uncertainty originating from ground motion predictions, fault finiteness, site modifications, inventory of physical and social elements subjected to earthquake hazard and the associated vulnerability relationships. Although primarily intended for quasi real-time estimation of earthquake shaking and losses, the routine is also equally capable of incorporating scenario-based earthquake loss assessments. This paper introduces the urban earthquake loss assessment module (Level 2) of the ELER software which makes use of the most detailed inventory databases of physical and social elements at risk in combination with the analytical vulnerability relationships and building damage-related casualty vulnerability models for the estimation of building damage and casualty distributions, respectively. Spectral capacity-based loss assessment methodology and its vital components are presented. The analysis methods of the Level 2 module, i.e. Capacity Spectrum Method (ATC-40, 1996), Modified Acceleration-Displacement Response Spectrum Method (FEMA 440, 2005), Reduction Factor Method (Fajfar, 2000) and Coefficient Method (ASCE 41-06, 2006), are applied to the selected building types for validation and verification purposes. The damage estimates are compared to the results obtained from the other studies available in the literature, i.e. SELENA v4.0 (Molina et al., 2008) and ATC-55 (Yang, 2005). An urban loss assessment exercise for a scenario earthquake for the city of Istanbul is conducted and physical and social losses are presented. Damage to the urban environment is compared to the results obtained from similar software, i.e. KOERILoss (KOERI, 2002) and DBELA (Crowley et al., 2004). The European rapid loss estimation tool is expected to help enable effective emergency response, on both local and global level, as well as public information.