Software Tool Issues

NASA Astrophysics Data System (ADS)

Hennell, Michael

This chapter relies on experience with tool development gained over the last thirty years. It shows that there are a large number of techniques that contribute to any successful project, and that formality is always the key: a modern software test tool is based on a firm mathematical foundation. After a brief introduction, Section 2 recalls and extends the terminology of Chapter 1. Section 3 discusses the the design of different sorts of static and dynamic analysis tools. Nine important issues to be taken into consideration when evaluating such tools are presented in Section 4. Section 5 investigates the interplay between testing and proof. In Section 6, we call for developers to take their own medicine and verify their tools. Finally, we conclude in Section 7 with a summary of our main messages, emphasising the important role of testing.

Software-Based Visual Loan Calculator For Banking Industry

NASA Astrophysics Data System (ADS)

Isizoh, A. N.; Anazia, A. E.; Okide, S. O. 3; Onyeyili, T. I.; Okwaraoka, C. A. P.

2012-03-01

industry is very necessary in modern day banking system using many design techniques for security reasons. This paper thus presents the software-based design and implementation of a Visual Loan calculator for banking industry using Visual Basic .Net (VB.Net). The fundamental approach to this is to develop a Graphical User Interface (GUI) using VB.Net operating tools, and then developing a working program which calculates the interest of any loan obtained. The VB.Net programming was done, implemented and the software proved satisfactory.

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.

Mathematical support for automated geometry analysis of lathe machining of oblique peakless round-nose tools

NASA Astrophysics Data System (ADS)

Filippov, A. V.; Tarasov, S. Yu; Podgornyh, O. A.; Shamarin, N. N.; Filippova, E. O.

2017-01-01

Automatization of engineering processes requires developing relevant mathematical support and a computer software. Analysis of metal cutting kinematics and tool geometry is a necessary key task at the preproduction stage. This paper is focused on developing a procedure for determining the geometry of oblique peakless round-nose tool lathe machining with the use of vector/matrix transformations. Such an approach allows integration into modern mathematical software packages in distinction to the traditional analytic description. Such an advantage is very promising for developing automated control of the preproduction process. A kinematic criterion for the applicable tool geometry has been developed from the results of this study. The effect of tool blade inclination and curvature on the geometry-dependent process parameters was evaluated.

A WebGL Tool for Visualizing the Topology of the Sun's Coronal Magnetic Field

NASA Astrophysics Data System (ADS)

Duffy, A.; Cheung, C.; DeRosa, M. L.

2012-12-01

We present a web-based, topology-viewing tool that allows users to visualize the geometry and topology of the Sun's 3D coronal magnetic field in an interactive manner. The tool is implemented using, open-source, mature, modern web technologies including WebGL, jQuery, HTML 5, and CSS 3, which are compatible with nearly all modern web browsers. As opposed to the traditional method of visualization, which involves the downloading and setup of various software packages-proprietary and otherwise-the tool presents a clean interface that allows the user to easily load and manipulate the model, while also offering great power to choose which topological features are displayed. The tool accepts data encoded in the JSON open format that has libraries available for nearly every major programming language, making it simple to generate the data.

A Roadmap to Continuous Integration for ATLAS Software Development

NASA Astrophysics Data System (ADS)

Elmsheuser, J.; Krasznahorkay, A.; Obreshkov, E.; Undrus, A.; ATLAS Collaboration

2017-10-01

The ATLAS software infrastructure facilitates efforts of more than 1000 developers working on the code base of 2200 packages with 4 million lines of C++ and 1.4 million lines of python code. The ATLAS offline code management system is the powerful, flexible framework for processing new package versions requests, probing code changes in the Nightly Build System, migration to new platforms and compilers, deployment of production releases for worldwide access and supporting physicists with tools and interfaces for efficient software use. It maintains multi-stream, parallel development environment with about 70 multi-platform branches of nightly releases and provides vast opportunities for testing new packages, for verifying patches to existing software and for migrating to new platforms and compilers. The system evolution is currently aimed on the adoption of modern continuous integration (CI) practices focused on building nightly releases early and often, with rigorous unit and integration testing. This paper describes the CI incorporation program for the ATLAS software infrastructure. It brings modern open source tools such as Jenkins and GitLab into the ATLAS Nightly System, rationalizes hardware resource allocation and administrative operations, provides improved feedback and means to fix broken builds promptly for developers. Once adopted, ATLAS CI practices will improve and accelerate innovation cycles and result in increased confidence in new software deployments. The paper reports the status of Jenkins integration with the ATLAS Nightly System as well as short and long term plans for the incorporation of CI practices.

Systems Engineering Building Advances Power Grid Research

ScienceCinema

Virden, Jud; Huang, Henry; Skare, Paul; Dagle, Jeff; Imhoff, Carl; Stoustrup, Jakob; Melton, Ron; Stiles, Dennis; Pratt, Rob

2018-01-16

Researchers and industry are now better equipped to tackle the nation’s most pressing energy challenges through PNNL’s new Systems Engineering Building – including challenges in grid modernization, buildings efficiency and renewable energy integration. This lab links real-time grid data, software platforms, specialized laboratories and advanced computing resources for the design and demonstration of new tools to modernize the grid and increase buildings energy efficiency.

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.

Improving Earth Science Metadata: Modernizing ncISO

NASA Astrophysics Data System (ADS)

O'Brien, K.; Schweitzer, R.; Neufeld, D.; Burger, E. F.; Signell, R. P.; Arms, S. C.; Wilcox, K.

2016-12-01

ncISO is a package of tools developed at NOAA's National Center for Environmental Information (NCEI) that facilitates the generation of ISO 19115-2 metadata from NetCDF data sources. The tool currently exists in two iterations: a command line utility and a web-accessible service within the THREDDS Data Server (TDS). Several projects, including NOAA's Unified Access Framework (UAF), depend upon ncISO to generate the ISO-compliant metadata from their data holdings and use the resulting information to populate discovery tools such as NCEI's ESRI Geoportal and NOAA's data.noaa.gov CKAN system. In addition to generating ISO 19115-2 metadata, the tool calculates a rubric score based on how well the dataset follows the Attribute Conventions for Dataset Discovery (ACDD). The result of this rubric calculation, along with information about what has been included and what is missing is displayed in an HTML document generated by the ncISO software package. Recently ncISO has fallen behind in terms of supporting updates to conventions such updates to the ACDD. With the blessing of the original programmer, NOAA's UAF has been working to modernize the ncISO software base. In addition to upgrading ncISO to utilize version1.3 of the ACDD, we have been working with partners at Unidata and IOOS to unify the tool's code base. In essence, we are merging the command line capabilities into the same software that will now be used by the TDS service, allowing easier updates when conventions such as ACDD are updated in the future. In this presentation, we will discuss the work the UAF project has done to support updated conventions within ncISO, as well as describe how the updated tool is helping to improve metadata throughout the earth and ocean sciences.

The Capability Portfolio Analysis Tool (CPAT): A Mixed Integer Linear Programming Formulation for Fleet Modernization Analysis (Version 2.0.2).

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

Waddell, Lucas; Muldoon, Frank; Henry, Stephen Michael

In order to effectively plan the management and modernization of their large and diverse fleets of vehicles, Program Executive Office Ground Combat Systems (PEO GCS) and Program Executive Office Combat Support and Combat Service Support (PEO CS&CSS) commis- sioned the development of a large-scale portfolio planning optimization tool. This software, the Capability Portfolio Analysis Tool (CPAT), creates a detailed schedule that optimally prioritizes the modernization or replacement of vehicles within the fleet - respecting numerous business rules associated with fleet structure, budgets, industrial base, research and testing, etc., while maximizing overall fleet performance through time. This paper contains a thor-more » ough documentation of the terminology, parameters, variables, and constraints that comprise the fleet management mixed integer linear programming (MILP) mathematical formulation. This paper, which is an update to the original CPAT formulation document published in 2015 (SAND2015-3487), covers the formulation of important new CPAT features.« less

"Extreme Programming" in a Bioinformatics Class

ERIC Educational Resources Information Center

Kelley, Scott; Alger, Christianna; Deutschman, Douglas

2009-01-01

The importance of Bioinformatics tools and methodology in modern biological research underscores the need for robust and effective courses at the college level. This paper describes such a course designed on the principles of cooperative learning based on a computer software industry production model called "Extreme Programming" (EP).…

ProteoWizard: open source software for rapid proteomics tools development.

PubMed

Kessner, Darren; Chambers, Matt; Burke, Robert; Agus, David; Mallick, Parag

2008-11-01

The ProteoWizard software project provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard proteomics and LCMS dataset computations. The library contains readers and writers of the mzML data format, which has been written using modern C++ techniques and design principles and supports a variety of platforms with native compilers. The software has been specifically released under the Apache v2 license to ensure it can be used in both academic and commercial projects. In addition to the library, we also introduce a rapidly growing set of companion tools whose implementation helps to illustrate the simplicity of developing applications on top of the ProteoWizard library. Cross-platform software that compiles using native compilers (i.e. GCC on Linux, MSVC on Windows and XCode on OSX) is available for download free of charge, at http://proteowizard.sourceforge.net. This website also provides code examples, and documentation. It is our hope the ProteoWizard project will become a standard platform for proteomics development; consequently, code use, contribution and further development are strongly encouraged.

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.

Instrument control software requirement specification for Extremely Large Telescopes

NASA Astrophysics Data System (ADS)

Young, Peter J.; Kiekebusch, Mario J.; Chiozzi, Gianluca

2010-07-01

Engineers in several observatories are now designing the next generation of optical telescopes, the Extremely Large Telescopes (ELT). These are very complex machines that will host sophisticated astronomical instruments to be used for a wide range of scientific studies. In order to carry out scientific observations, a software infrastructure is required to orchestrate the control of the multiple subsystems and functions. This paper will focus on describing the considerations, strategies and main issues related to the definition and analysis of the software requirements for the ELT's Instrument Control System using modern development processes and modelling tools like SysML.

Rethinking Technology-Enhanced Physics Teacher Education: From Theory to Practice

ERIC Educational Resources Information Center

Milner-Bolotin, Marina

2016-01-01

This article discusses how modern technology, such as electronic response systems, PeerWise system, data collection and analysis tools, computer simulations, and modeling software can be used in physics methods courses to promote teacher-candidates' professional competencies and their positive attitudes about mathematics and science education. We…

Robotics for Computer Scientists: What's the Big Idea?

ERIC Educational Resources Information Center

Touretzky, David S.

2013-01-01

Modern robots, like today's smartphones, are complex devices with intricate software systems. Introductory robot programming courses must evolve to reflect this reality, by teaching students to make use of the sophisticated tools their robots provide rather than reimplementing basic algorithms. This paper focuses on teaching with Tekkotsu, an open…

Using Modern And Inexpensive Tools In the Classroom To Teach Spectroscopy And To Do Exciting Citizen Science On Astronomical Objects

NASA Astrophysics Data System (ADS)

Field, T.

2014-12-01

Spectroscopy is a key tool used in modern astronomical research. But, it's always been a difficult topic to teach or practice because the expense and complexity of the available tools. Over the past few years, there's been somewhat of a revolution in this field as new technologies have applied. In this presentation we'll review some new spectroscopy tools that enable educators, students and citizen scientists to do exciting spectroscopic work. With the addition of a simple, inexpensive grating, it's now possible to capture scientifically significant spectra of astronomical objects with small (6") telescopes and even just a DSLR. See the tools that citizen scientists are using to contribute data to pro-am collaborations around the world. We'll also examine a simple, surprisingly inexpensive, tripod-mounted spectrometer that can be used in the classroom for demonstrations and hands-on labs with gas tubes and other light sources. Both of the above instruments use a software program named RSpec, which is state of the art software suite that is easy to learn and easy to use. In this presentation we'll see these devices in operation and discuss how they can be used by educators to dramatically improve their teaching of this topic. You'll see how these tools can eliminate the frustration of hand-held rainbow foil and plastic spectrometers. And we'll review some exciting examples of astronomical spectra being collected by amateurs and educators.

Atomdroid: a computational chemistry tool for mobile platforms.

PubMed

Feldt, Jonas; Mata, Ricardo A; Dieterich, Johannes M

2012-04-23

We present the implementation of a new molecular mechanics program designed for use in mobile platforms, the first specifically built for these devices. The software is designed to run on Android operating systems and is compatible with several modern tablet-PCs and smartphones available in the market. It includes molecular viewer/builder capabilities with integrated routines for geometry optimizations and Monte Carlo simulations. These functionalities allow it to work as a stand-alone tool. We discuss some particular development aspects, as well as the overall feasibility of using computational chemistry software packages in mobile platforms. Benchmark calculations show that through efficient implementation techniques even hand-held devices can be used to simulate midsized systems using force fields.

Using the Eclipse Parallel Tools Platform to Assist Earth Science Model Development and Optimization on High Performance Computers

NASA Astrophysics Data System (ADS)

Alameda, J. C.

2011-12-01

Development and optimization of computational science models, particularly on high performance computers, and with the advent of ubiquitous multicore processor systems, practically on every system, has been accomplished with basic software tools, typically, command-line based compilers, debuggers, performance tools that have not changed substantially from the days of serial and early vector computers. However, model complexity, including the complexity added by modern message passing libraries such as MPI, and the need for hybrid code models (such as openMP and MPI) to be able to take full advantage of high performance computers with an increasing core count per shared memory node, has made development and optimization of such codes an increasingly arduous task. Additional architectural developments, such as many-core processors, only complicate the situation further. In this paper, we describe how our NSF-funded project, "SI2-SSI: A Productive and Accessible Development Workbench for HPC Applications Using the Eclipse Parallel Tools Platform" (WHPC) seeks to improve the Eclipse Parallel Tools Platform, an environment designed to support scientific code development targeted at a diverse set of high performance computing systems. Our WHPC project to improve Eclipse PTP takes an application-centric view to improve PTP. We are using a set of scientific applications, each with a variety of challenges, and using PTP to drive further improvements to both the scientific application, as well as to understand shortcomings in Eclipse PTP from an application developer perspective, to drive our list of improvements we seek to make. We are also partnering with performance tool providers, to drive higher quality performance tool integration. We have partnered with the Cactus group at Louisiana State University to improve Eclipse's ability to work with computational frameworks and extremely complex build systems, as well as to develop educational materials to incorporate into computational science and engineering codes. Finally, we are partnering with the lead PTP developers at IBM, to ensure we are as effective as possible within the Eclipse community development. We are also conducting training and outreach to our user community, including conference BOF sessions, monthly user calls, and an annual user meeting, so that we can best inform the improvements we make to Eclipse PTP. With these activities we endeavor to encourage use of modern software engineering practices, as enabled through the Eclipse IDE, with computational science and engineering applications. These practices include proper use of source code repositories, tracking and rectifying issues, measuring and monitoring code performance changes against both optimizations as well as ever-changing software stacks and configurations on HPC systems, as well as ultimately encouraging development and maintenance of testing suites -- things that have become commonplace in many software endeavors, but have lagged in the development of science applications. We view that the challenge with the increased complexity of both HPC systems and science applications demands the use of better software engineering methods, preferably enabled by modern tools such as Eclipse PTP, to help the computational science community thrive as we evolve the HPC landscape.

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

Integrating Multimedia ICT Software in Language Curriculum: Students' Perception, Use, and Effectiveness

ERIC Educational Resources Information Center

Penner, Nikolai; Grodek, Elzbieta

2014-01-01

Information and Communication Technologies (ICT) constitute an integral part of the teaching and learning environment in present-day educational institutions and play an increasingly important role in the modern second language classroom. In this study, an online language learning tool "Tell Me More" (TMM) has been introduced as a…

Design and Implementation of a Modern Automatic Deformation Monitoring System

NASA Astrophysics Data System (ADS)

Engel, Philipp; Schweimler, Björn

2016-03-01

The deformation monitoring of structures and buildings is an important task field of modern engineering surveying, ensuring the standing and reliability of supervised objects over a long period. Several commercial hardware and software solutions for the realization of such monitoring measurements are available on the market. In addition to them, a research team at the University of Applied Sciences in Neubrandenburg (NUAS) is actively developing a software package for monitoring purposes in geodesy and geotechnics, which is distributed under an open source licence and free of charge. The task of managing an open source project is well-known in computer science, but it is fairly new in a geodetic context. This paper contributes to that issue by detailing applications, frameworks, and interfaces for the design and implementation of open hardware and software solutions for sensor control, sensor networks, and data management in automatic deformation monitoring. It will be discussed how the development effort of networked applications can be reduced by using free programming tools, cloud computing technologies, and rapid prototyping methods.

Hardware and software for automating the process of studying high-speed gas flows in wind tunnels of short-term action

NASA Astrophysics Data System (ADS)

Yakovlev, V. V.; Shakirov, S. R.; Gilyov, V. M.; Shpak, S. I.

2017-10-01

In this paper, we propose a variant of constructing automation systems for aerodynamic experiments on the basis of modern hardware-software means of domestic development. The structure of the universal control and data collection system for performing experiments in wind tunnels of continuous, periodic or short-term action is proposed. The proposed hardware and software development tools for ICT SB RAS and ITAM SB RAS, as well as subsystems based on them, can be widely applied to any scientific and experimental installations, as well as to the automation of technological processes in production.

Updates to FuncLab, a Matlab based GUI for handling receiver functions

NASA Astrophysics Data System (ADS)

Porritt, Robert W.; Miller, Meghan S.

2018-02-01

Receiver functions are a versatile tool commonly used in seismic imaging. Depending on how they are processed, they can be used to image discontinuity structure within the crust or mantle or they can be inverted for seismic velocity either directly or jointly with complementary datasets. However, modern studies generally require large datasets which can be challenging to handle; therefore, FuncLab was originally written as an interactive Matlab GUI to assist in handling these large datasets. This software uses a project database to allow interactive trace editing, data visualization, H-κ stacking for crustal thickness and Vp/Vs ratio, and common conversion point stacking while minimizing computational costs. Since its initial release, significant advances have been made in the implementation of web services and changes in the underlying Matlab platform have necessitated a significant revision to the software. Here, we present revisions to the software, including new features such as data downloading via irisFetch.m, receiver function calculations via processRFmatlab, on-the-fly cross-section tools, interface picking, and more. In the descriptions of the tools, we present its application to a test dataset in Michigan, Wisconsin, and neighboring areas following the passage of USArray Transportable Array. The software is made available online at https://robporritt.wordpress.com/software.

Living Color Frame System: PC graphics tool for data visualization

NASA Technical Reports Server (NTRS)

Truong, Long V.

1993-01-01

Living Color Frame System (LCFS) is a personal computer software tool for generating real-time graphics applications. It is highly applicable for a wide range of data visualization in virtual environment applications. Engineers often use computer graphics to enhance the interpretation of data under observation. These graphics become more complicated when 'run time' animations are required, such as found in many typical modern artificial intelligence and expert systems. Living Color Frame System solves many of these real-time graphics problems.

GeoGebra Materials for LMS Moodle Focused Monge on Projection

ERIC Educational Resources Information Center

Ferdiánová, Vera

2017-01-01

"The use of e-learning and modern technologies is an integral part of teaching descriptive geometry" (Rankowski and Minaruth, 1979). Teachers often create Flash animations, websites and other interactive materials for their students using special tools and software; e.g. Cabri, GeoGebra or Construct 3D (García et al, 2007). There is an…

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.

Leveraging e-Science infrastructure for electrochemical research.

PubMed

Peachey, Tom; Mashkina, Elena; Lee, Chong-Yong; Enticott, Colin; Abramson, David; Bond, Alan M; Elton, Darrell; Gavaghan, David J; Stevenson, Gareth P; Kennedy, Gareth F

2011-08-28

As in many scientific disciplines, modern chemistry involves a mix of experimentation and computer-supported theory. Historically, these skills have been provided by different groups, and range from traditional 'wet' laboratory science to advanced numerical simulation. Increasingly, progress is made by global collaborations, in which new theory may be developed in one part of the world and applied and tested in the laboratory elsewhere. e-Science, or cyber-infrastructure, underpins such collaborations by providing a unified platform for accessing scientific instruments, computers and data archives, and collaboration tools. In this paper we discuss the application of advanced e-Science software tools to electrochemistry research performed in three different laboratories--two at Monash University in Australia and one at the University of Oxford in the UK. We show that software tools that were originally developed for a range of application domains can be applied to electrochemical problems, in particular Fourier voltammetry. Moreover, we show that, by replacing ad-hoc manual processes with e-Science tools, we obtain more accurate solutions automatically.

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.

A software tool for automatic classification and segmentation of 2D/3D medical images

NASA Astrophysics Data System (ADS)

Strzelecki, Michal; Szczypinski, Piotr; Materka, Andrzej; Klepaczko, Artur

2013-02-01

Modern medical diagnosis utilizes techniques of visualization of human internal organs (CT, MRI) or of its metabolism (PET). However, evaluation of acquired images made by human experts is usually subjective and qualitative only. Quantitative analysis of MR data, including tissue classification and segmentation, is necessary to perform e.g. attenuation compensation, motion detection, and correction of partial volume effect in PET images, acquired with PET/MR scanners. This article presents briefly a MaZda software package, which supports 2D and 3D medical image analysis aiming at quantification of image texture. MaZda implements procedures for evaluation, selection and extraction of highly discriminative texture attributes combined with various classification, visualization and segmentation tools. Examples of MaZda application in medical studies are also provided.

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

PubMed

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

2014-01-01

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

Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2)

PubMed Central

Weber, Griffin; Mendis, Michael; Gainer, Vivian; Chueh, Henry C; Churchill, Susanne; Kohane, Isaac

2010-01-01

Informatics for Integrating Biology and the Bedside (i2b2) is one of seven projects sponsored by the NIH Roadmap National Centers for Biomedical Computing (http://www.ncbcs.org). Its mission is to provide clinical investigators with the tools necessary to integrate medical record and clinical research data in the genomics age, a software suite to construct and integrate the modern clinical research chart. i2b2 software may be used by an enterprise's research community to find sets of interesting patients from electronic patient medical record data, while preserving patient privacy through a query tool interface. Project-specific mini-databases (“data marts”) can be created from these sets to make highly detailed data available on these specific patients to the investigators on the i2b2 platform, as reviewed and restricted by the Institutional Review Board. The current version of this software has been released into the public domain and is available at the URL: http://www.i2b2.org/software. PMID:20190053

A generic testbed for the design of plasma spectrometer control software with application to the THOR-CSW solar wind instrument

NASA Astrophysics Data System (ADS)

De Keyser, Johan; Lavraud, Benoit; Neefs, Eddy; Berkenbosch, Sophie; Beeckman, Bram; Maggiolo, Romain; Gamby, Emmanuel; Fedorov, Andrei; Baruah, Rituparna; Wong, King-Wah; Amoros, Carine; Mathon, Romain; Génot, Vincent; Marcucci, Federica; Brienza, Daniele

2017-04-01

Modern plasma spectrometers require intelligent software that is able to exploit their capabilities to the fullest. While the low-level control of the instrument and basic tasks such as performing the basic measurement, temperature control, and production of housekeeping data are to be done by software that is executed on an FPGA and/or processor inside the instrument, higher level tasks such as control of measurement sequences, on-board moment calculation, beam tracking decisions, and data compression, may be performed by the instrument or in the payload data processing unit. Such design decisions, as well as an assessment of the workload on the different processing components, require early prototyping. We have developed a generic simulation testbed for the design of plasma spectrometer control software that allows an early evaluation of the level of resources that is needed at each level. Early prototyping can pinpoint bottlenecks in the design allowing timely remediation. We have applied this tool to the THOR Cold Solar Wind (CSW) plasma spectrometer. Some examples illustrating the usefulness of the tool are given.

Toward improved peptide feature detection in quantitative proteomics using stable isotope labeling.

PubMed

Nilse, Lars; Sigloch, Florian Christoph; Biniossek, Martin L; Schilling, Oliver

2015-08-01

Reliable detection of peptides in LC-MS data is a key algorithmic step in the analysis of quantitative proteomics experiments. While highly abundant peptides can be detected reliably by most modern software tools, there is much less agreement on medium and low-intensity peptides in a sample. The choice of software tools can have a big impact on the quantification of proteins, especially for proteins that appear in lower concentrations. However, in many experiments, it is precisely this region of less abundant but substantially regulated proteins that holds the biggest potential for discoveries. This is particularly true for discovery proteomics in the pharmacological sector with a specific interest in key regulatory proteins. In this viewpoint article, we discuss how the development of novel software algorithms allows us to study this region of the proteome with increased confidence. Reliable results are one of many aspects to be considered when deciding on a bioinformatics software platform. Deployment into existing IT infrastructures, compatibility with other software packages, scalability, automation, flexibility, and support need to be considered and are briefly addressed in this viewpoint article. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

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 Case Study in Flight Computer Software Redesign

NASA Astrophysics Data System (ADS)

Shimoni, R.; Ben-Zur, Y.

2004-06-01

Historically many real-time systems were developed using technologies that are now obsolete. There is a need for upgrading these systems. A good development process is essential to achieve a well-designed software product. We, at MLM, a subsidary of Israel Aircraft Industries, faced a similar situation in the Flight Mission Computer (Main Airborne Computer-MAC) of the SHAVIT launcher. It was necessary to upgrade the computer hardware and we decided to update the software as well. During the last two years, we have designed and implemented and new version of the MAC software, to be run on a new and stronger target platform. We undertook to create a new version of the MAC program using modern software development techniques. The process included Object-Oriented design using a CASE tool suitable for embedded real-time systems. We have partially implemented the ROPES development process. In this article we present the difficulties and challenges we faced in the software development process.

A Powerful, Cost Effective, Web Based Engineering Solution Supporting Conjunction Detection and Visual Analysis

NASA Astrophysics Data System (ADS)

Novak, Daniel M.; Biamonti, Davide; Gross, Jeremy; Milnes, Martin

2013-08-01

An innovative and visually appealing tool is presented for efficient all-vs-all conjunction analysis on a large catalogue of objects. The conjunction detection uses a nearest neighbour search algorithm, based on spatial binning and identification of pairs of objects in adjacent bins. This results in the fastest all vs all filtering the authors are aware of. The tool is constructed on a server-client architecture, where the server broadcasts to the client the conjunction data and ephemerides, while the client supports the user interface through a modern browser, without plug-in. In order to make the tool flexible and maintainable, Java software technologies were used on the server side, including Spring, Camel, ActiveMQ and CometD. The user interface and visualisation are based on the latest web technologies: HTML5, WebGL, THREE.js. Importance has been given on the ergonomics and visual appeal of the software. In fact certain design concepts have been borrowed from the gaming industry.

PIPER: Performance Insight for Programmers and Exascale Runtimes: Guiding the Development of the Exascale Software Stack

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

Mellor-Crummey, John

The PIPER project set out to develop methodologies and software for measurement, analysis, attribution, and presentation of performance data for extreme-scale systems. Goals of the project were to support analysis of massive multi-scale parallelism, heterogeneous architectures, multi-faceted performance concerns, and to support both post-mortem performance analysis to identify program features that contribute to problematic performance and on-line performance analysis to drive adaptation. This final report summarizes the research and development activity at Rice University as part of the PIPER project. Producing a complete suite of performance tools for exascale platforms during the course of this project was impossible since bothmore » hardware and software for exascale systems is still a moving target. For that reason, the project focused broadly on the development of new techniques for measurement and analysis of performance on modern parallel architectures, enhancements to HPCToolkit’s software infrastructure to support our research goals or use on sophisticated applications, engaging developers of multithreaded runtimes to explore how support for tools should be integrated into their designs, engaging operating system developers with feature requests for enhanced monitoring support, engaging vendors with requests that they add hardware measure- ment capabilities and software interfaces needed by tools as they design new components of HPC platforms including processors, accelerators and networks, and finally collaborations with partners interested in using HPCToolkit to analyze and tune scalable parallel applications.« less

Development of Fuel Shuffling Module for PHISICS

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

Allan Mabe; Andrea Alfonsi; Cristian Rabiti

2013-06-01

PHISICS (Parallel and Highly Innovative Simulation for the INL Code System) [4] code toolkit has been in development at the Idaho National Laboratory. This package is intended to provide a modern analysis tool for reactor physics investigation. It is designed with the mindset to maximize accuracy for a given availability of computational resources and to give state of the art tools to the modern nuclear engineer. This is obtained by implementing several different algorithms and meshing approaches among which the user will be able to choose, in order to optimize his computational resources and accuracy needs. The software is completelymore » modular in order to simplify the independent development of modules by different teams and future maintenance. The package is coupled with the thermo-hydraulic code RELAP5-3D [3]. In the following the structure of the different PHISICS modules is briefly recalled, focusing on the new shuffling module (SHUFFLE), object of this paper.« less

Open-source framework for documentation of scientific software written on MATLAB-compatible programming languages

NASA Astrophysics Data System (ADS)

Konnik, Mikhail V.; Welsh, James

2012-09-01

Numerical simulators for adaptive optics systems have become an essential tool for the research and development of the future advanced astronomical instruments. However, growing software code of the numerical simulator makes it difficult to continue to support the code itself. The problem of adequate documentation of the astronomical software for adaptive optics simulators may complicate the development since the documentation must contain up-to-date schemes and mathematical descriptions implemented in the software code. Although most modern programming environments like MATLAB or Octave have in-built documentation abilities, they are often insufficient for the description of a typical adaptive optics simulator code. This paper describes a general cross-platform framework for the documentation of scientific software using open-source tools such as LATEX, mercurial, Doxygen, and Perl. Using the Perl script that translates M-files MATLAB comments into C-like, one can use Doxygen to generate and update the documentation for the scientific source code. The documentation generated by this framework contains the current code description with mathematical formulas, images, and bibliographical references. A detailed description of the framework components is presented as well as the guidelines for the framework deployment. Examples of the code documentation for the scripts and functions of a MATLAB-based adaptive optics simulator are provided.

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

PubMed Central

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

2014-01-01

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

OASYS (OrAnge SYnchrotron Suite): an open-source graphical environment for x-ray virtual experiments

NASA Astrophysics Data System (ADS)

Rebuffi, Luca; Sanchez del Rio, Manuel

2017-08-01

The evolution of the hardware platforms, the modernization of the software tools, the access to the codes of a large number of young people and the popularization of the open source software for scientific applications drove us to design OASYS (ORange SYnchrotron Suite), a completely new graphical environment for modelling X-ray experiments. The implemented software architecture allows to obtain not only an intuitive and very-easy-to-use graphical interface, but also provides high flexibility and rapidity for interactive simulations, making configuration changes to quickly compare multiple beamline configurations. Its purpose is to integrate in a synergetic way the most powerful calculation engines available. OASYS integrates different simulation strategies via the implementation of adequate simulation tools for X-ray Optics (e.g. ray tracing and wave optics packages). It provides a language to make them to communicate by sending and receiving encapsulated data. Python has been chosen as main programming language, because of its universality and popularity in scientific computing. The software Orange, developed at the University of Ljubljana (SLO), is the high level workflow engine that provides the interaction with the user and communication mechanisms.

OpenCFU, a new free and open-source software to count cell colonies and other circular objects.

PubMed

Geissmann, Quentin

2013-01-01

Counting circular objects such as cell colonies is an important source of information for biologists. Although this task is often time-consuming and subjective, it is still predominantly performed manually. The aim of the present work is to provide a new tool to enumerate circular objects from digital pictures and video streams. Here, I demonstrate that the created program, OpenCFU, is very robust, accurate and fast. In addition, it provides control over the processing parameters and is implemented in an intuitive and modern interface. OpenCFU is a cross-platform and open-source software freely available at http://opencfu.sourceforge.net.

PEOPLE’S LIBERATION ARMY AFTER NEXT

DTIC Science & Technology

2000-08-01

machine tools and workforce training), and, above all, money (to support the modernization of Chinese factories and product l ines)—but also “software...shipbuilding capacity. This overcapacity is exacerbated by an endemic lack of sufficient capital. The government often does not have enough money to put...arms industries reportedly are among biggest money -losers.110 As a result, most SOEs are burdened with 30 considerable debt, much of which is

j5 DNA assembly design automation.

PubMed

Hillson, Nathan J

2014-01-01

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

Ada education in a software life-cycle context

NASA Technical Reports Server (NTRS)

Clough, Anne J.

1986-01-01

Some of the experience gained from a comprehensive educational program undertaken at The Charles Stark Draper Lab. to introduce the Ada language and to transition modern software engineering technology into the development of Ada and non-Ada applications is described. Initially, a core group, which included manager, engineers and programmers, received training in Ada. An Ada Office was established to assume the major responsibility for training, evaluation, acquisition and benchmarking of tools, and consultation on Ada projects. As a first step in this process, and in-house educational program was undertaken to introduce Ada to the Laboratory. Later, a software engineering course was added to the educational program as the need to address issues spanning the entire software life cycle became evident. Educational efforts to date are summarized, with an emphasis on the educational approach adopted. Finally, lessons learned in administering this program are addressed.

A Tool for Longitudinal Beam Dynamics in Synchrotrons

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

Ostiguy, J.-F.; Lebedev, V. A.

2017-05-01

A number of codes are available to simulate longitudinal dynamics in synchrotrons. Some established ones include TIBETAN, LONG1D, ESME and ORBIT. While they embody a wealth of accumulated wisdom and experience, most of these codes were written decades ago and to some extent they reflect the constraints of their time. As a result, there is an interest for updated tools taking better advantage of modern software and hardware capabilities. At Fermilab, the PIP-II project has provided the impetus for development of such a tool. In this contribution, we discuss design decisions and code architecture. A selection of test cases basedmore » on an initial prototype are also presented.« less

A Microarray Tool Provides Pathway and GO Term Analysis.

PubMed

Koch, Martin; Royer, Hans-Dieter; Wiese, Michael

2011-12-01

Analysis of gene expression profiles is no longer exclusively a task for bioinformatic experts. However, gaining statistically significant results is challenging and requires both biological knowledge and computational know-how. Here we present a novel, user-friendly microarray reporting tool called maRt. The software provides access to bioinformatic resources, like gene ontology terms and biological pathways by use of the DAVID and the BioMart web-service. Results are summarized in structured HTML reports, each presenting a different layer of information. In these report, contents of diverse sources are integrated and interlinked. To speed up processing, maRt takes advantage of the multi-core technology of modern desktop computers by using parallel processing. Since the software is built upon a RCP infrastructure it might be an outset for developers aiming to integrate novel R based applications. Installer, documentation and various kinds of tutorials are available under LGPL license at the website of our institute http://www.pharma.uni-bonn.de/www/mart. This software is free for academic use. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bringing Legacy Visualization Software to Modern Computing Devices via Application Streaming

NASA Astrophysics Data System (ADS)

Fisher, Ward

2014-05-01

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

A computer network with scada and case tools for on-line process control in greenhouses

NASA Astrophysics Data System (ADS)

Gieling, Th. H.; van Meurs, W. Th. M.; Janssen, H. J. J.

Climate control computers in greenhouses are used to control heating and ventilation, supply water and dilute and dispense nutrients. They integrate models into optimally controlled systems. This paper describes how information technology, as in use in other sectors of industry, is applied to greenhouse control. The introduction of modern software and hardware concepts in horticulture adds power and extra opportunities to climate control in greenhouses.

A computer network with SCADA and case tools for on-line process control in greenhouses.

PubMed

Gieling ThH; van Meurs WTh; Janssen, H J

1996-01-01

Climate control computers in greenhouses are used to control heating and ventilation, supply water and dilute and dispense nutrients. They integrate models into optimally controlled systems. This paper describes how information technology, as in use in other sectors of industry, is applied to greenhouse control. The introduction of modern software and hardware concepts in horticulture adds power and extra oppurtunities to climate contol in greenhouses.

Testing, Requirements, and Metrics

NASA Technical Reports Server (NTRS)

Rosenberg, Linda; Hyatt, Larry; Hammer, Theodore F.; Huffman, Lenore; Wilson, William

1998-01-01

The criticality of correct, complete, testable requirements is a fundamental tenet of software engineering. Also critical is complete requirements based testing of the final product. Modern tools for managing requirements allow new metrics to be used in support of both of these critical processes. Using these tools, potential problems with the quality of the requirements and the test plan can be identified early in the life cycle. Some of these quality factors include: ambiguous or incomplete requirements, poorly designed requirements databases, excessive or insufficient test cases, and incomplete linkage of tests to requirements. This paper discusses how metrics can be used to evaluate the quality of the requirements and test to avoid problems later. Requirements management and requirements based testing have always been critical in the implementation of high quality software systems. Recently, automated tools have become available to support requirements management. At NASA's Goddard Space Flight Center (GSFC), automated requirements management tools are being used on several large projects. The use of these tools opens the door to innovative uses of metrics in characterizing test plan quality and assessing overall testing risks. In support of these projects, the Software Assurance Technology Center (SATC) is working to develop and apply a metrics program that utilizes the information now available through the application of requirements management tools. Metrics based on this information provides real-time insight into the testing of requirements and these metrics assist the Project Quality Office in its testing oversight role. This paper discusses three facets of the SATC's efforts to evaluate the quality of the requirements and test plan early in the life cycle, thus preventing costly errors and time delays later.

Using McIDAS-V data analysis and visualization software as an educational tool for understanding the atmosphere

NASA Astrophysics Data System (ADS)

Achtor, T. H.; Rink, T.

2010-12-01

The University of Wisconsin’s Space Science and Engineering Center (SSEC) has been at the forefront in developing data analysis and visualization tools for environmental satellites and other geophysical data. The fifth generation of the Man-computer Interactive Data Access System (McIDAS-V) is Java-based, open-source, freely available software that operates on Linux, Macintosh and Windows systems. The software tools provide powerful new data manipulation and visualization capabilities that work with geophysical data in research, operational and educational environments. McIDAS-V provides unique capabilities to support innovative techniques for evaluating research results, teaching and training. McIDAS-V is based on three powerful software elements. VisAD is a Java library for building interactive, collaborative, 4 dimensional visualization and analysis tools. The Integrated Data Viewer (IDV) is a reference application based on the VisAD system and developed by the Unidata program that demonstrates the flexibility that is needed in this evolving environment, using a modern, object-oriented software design approach. The third tool, HYDRA, allows users to build, display and interrogate multi and hyperspectral environmental satellite data in powerful ways. The McIDAS-V software is being used for training and education in several settings. The McIDAS User Group provides training workshops at its annual meeting. Numerous online tutorials with training data sets have been developed to aid users in learning simple and more complex operations in McIDAS-V, all are available online. In a University of Wisconsin-Madison undergraduate course in Radar and Satellite Meteorology, McIDAS-V is used to create and deliver laboratory exercises using case study and real time data. At the high school level, McIDAS-V is used in several exercises in our annual Summer Workshop in Earth and Atmospheric Sciences to provide young scientists the opportunity to examine data with friendly and powerful tools. This presentation will describe the McIDAS-V software and demonstrate some of the capabilities of McIDAS-V to analyze and display many types of global data. The presentation will also focus on describing how McIDAS-V can be used as an educational window to examine global geophysical data. Consecutive polar orbiting passes of NASA MODIS and CALIPSO observations

NEURON and Python.

PubMed

Hines, Michael L; Davison, Andrew P; Muller, Eilif

2009-01-01

The NEURON simulation program now allows Python to be used, alone or in combination with NEURON's traditional Hoc interpreter. Adding Python to NEURON has the immediate benefit of making available a very extensive suite of analysis tools written for engineering and science. It also catalyzes NEURON software development by offering users a modern programming tool that is recognized for its flexibility and power to create and maintain complex programs. At the same time, nothing is lost because all existing models written in Hoc, including graphical user interface tools, continue to work without change and are also available within the Python context. An example of the benefits of Python availability is the use of the xml module in implementing NEURON's Import3D and CellBuild tools to read MorphML and NeuroML model specifications.

NEURON and Python

PubMed Central

Hines, Michael L.; Davison, Andrew P.; Muller, Eilif

2008-01-01

The NEURON simulation program now allows Python to be used, alone or in combination with NEURON's traditional Hoc interpreter. Adding Python to NEURON has the immediate benefit of making available a very extensive suite of analysis tools written for engineering and science. It also catalyzes NEURON software development by offering users a modern programming tool that is recognized for its flexibility and power to create and maintain complex programs. At the same time, nothing is lost because all existing models written in Hoc, including graphical user interface tools, continue to work without change and are also available within the Python context. An example of the benefits of Python availability is the use of the xml module in implementing NEURON's Import3D and CellBuild tools to read MorphML and NeuroML model specifications. PMID:19198661

Web-Based Environment for Maintaining Legacy Software

NASA Technical Reports Server (NTRS)

Tigges, Michael; Thompson, Nelson; Orr, Mark; Fox, Richard

2007-01-01

Advanced Tool Integration Environment (ATIE) is the name of both a software system and a Web-based environment created by the system for maintaining an archive of legacy software and expertise involved in developing the legacy software. ATIE can also be used in modifying legacy software and developing new software. The information that can be encapsulated in ATIE includes experts documentation, input and output data of tests cases, source code, and compilation scripts. All of this information is available within a common environment and retained in a database for ease of access and recovery by use of powerful search engines. ATIE also accommodates the embedment of supporting software that users require for their work, and even enables access to supporting commercial-off-the-shelf (COTS) software within the flow of the experts work. The flow of work can be captured by saving the sequence of computer programs that the expert uses. A user gains access to ATIE via a Web browser. A modern Web-based graphical user interface promotes efficiency in the retrieval, execution, and modification of legacy code. Thus, ATIE saves time and money in the support of new and pre-existing programs.

OpenCFU, a New Free and Open-Source Software to Count Cell Colonies and Other Circular Objects

PubMed Central

Geissmann, Quentin

2013-01-01

Counting circular objects such as cell colonies is an important source of information for biologists. Although this task is often time-consuming and subjective, it is still predominantly performed manually. The aim of the present work is to provide a new tool to enumerate circular objects from digital pictures and video streams. Here, I demonstrate that the created program, OpenCFU, is very robust, accurate and fast. In addition, it provides control over the processing parameters and is implemented in an intuitive and modern interface. OpenCFU is a cross-platform and open-source software freely available at http://opencfu.sourceforge.net. PMID:23457446

Atropos: specific, sensitive, and speedy trimming of sequencing reads.

PubMed

Didion, John P; Martin, Marcel; Collins, Francis S

2017-01-01

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves significant increases in trimming accuracy while remaining competitive in execution times. Furthermore, Atropos maintains high accuracy even when trimming data with elevated rates of sequencing errors. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of Illumina, ABI SOLiD, and other current-generation short-read sequencing datasets. Atropos is open source and free software written in Python (3.3+) and available at https://github.com/jdidion/atropos.

Atropos: specific, sensitive, and speedy trimming of sequencing reads

PubMed Central

Collins, Francis S.

2017-01-01

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves significant increases in trimming accuracy while remaining competitive in execution times. Furthermore, Atropos maintains high accuracy even when trimming data with elevated rates of sequencing errors. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of Illumina, ABI SOLiD, and other current-generation short-read sequencing datasets. Atropos is open source and free software written in Python (3.3+) and available at https://github.com/jdidion/atropos. PMID:28875074

Making software get along: integrating optical and mechanical design programs

NASA Astrophysics Data System (ADS)

Shackelford, Christie J.; Chinnock, Randal B.

2001-03-01

As modern optomechanical engineers, we have the good fortune of having very sophisticated software programs available to us. The current optical design, mechanical design, industrial design, and CAM programs are very powerful tools with some very desirable features. However, no one program can do everything necessary to complete an entire optomechanical system design. Each program has a unique set of features and benefits, and typically two or mo re will be used during the product development process. At a minimum, an optical design program and a mechanical CAD package will be employed. As we strive for efficient, cost-effective, and rapid progress in our development projects, we must use these programs to their full advantage, while keeping redundant tasks to a minimum. Together, these programs offer the promise of a `seamless' flow of data from concept all the way to the download of part designs directly to the machine shop for fabrication. In reality, transferring data from one software package to the next is often frustrating. Overcoming these problems takes some know-how, a bit of creativity, and a lot of persistence. This paper describes a complex optomechanical development effort in which a variety of software tools were used from the concept stage to prototyping. It will describe what software was used for each major design task, how we learned to use them together to best advantage, and how we overcame the frustrations of software that didn't get along.

DIC-CAM recipe for reverse engineering

NASA Astrophysics Data System (ADS)

Romero-Carrillo, P.; Lopez-Alba, E.; Dorado, R.; Diaz-Garrido, F. A.

2012-04-01

Reverse engineering (RE) tries to model and manufacture an object from measurements one of a reference object. Modern optical measurement systems and computer aided engineering software have improved reverse engineering procedures. We detail the main RE steps from 3D digitalization by Digital Image Correlation to manufacturing. The previous description is complemented with an application example, which portrays the performance of RE. The differences between original and manufactured objects are less than 2 mm (close to the tool radius).

Development of an Automated Modality-Independent Elastographic Image Analysis System for Tumor Screening

DTIC Science & Technology

2008-02-01

journal article. Didactic coursework requirements for the PhD degree have been completed at this time as well as successful presentation of the...Libraries", Modern Software Tools in Scientific Computing. Birkhauser Press, pp. 163-202, 1997. [5] Doyley MM, Weaver JB, Van Houten EEW, Kennedy FE...data from MR, x-ray computed tomography (CT) and digital photography have been used to successfully drive the algorithm in two-dimensional (2D) work

Static and Dynamic Verification of Critical Software for Space Applications

NASA Astrophysics Data System (ADS)

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

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

New advances in lower gastrointestinal bleeding management with embolotherapy

PubMed Central

Ierardi, Anna Maria; Urbano, Josè; De Marchi, Giuseppe; Micieli, Camilla; Duka, Ejona; Iacobellis, Francesca; Fontana, Federico

2016-01-01

Lower gastrointestinal bleeding (LGIB) is associated with high morbidity and mortality. Embolization is currently proposed as the first step in the treatment of acute, life-threatening LGIB, when endoscopic approach is not possible or is unsuccessful. Like most procedures performed in emergency setting, time represents a significant factor influencing outcome. Modern tools permit identifying and reaching the bleeding site faster than two-dimensional angiography. Non-selective cone-beam CT arteriography can identify a damaged vessel. Moreover, sophisticated software able to detect the vessel may facilitate direct placement of a microcatheter into the culprit vessel without the need for sequential angiography. A further important aspect is the use of an appropriate technique of embolization and a safe and effective embolic agent. Current evidence shows the use of detachable coils (with or without a triaxial system) and liquid embolics has proven advantages compared with other embolic agents. The present article analyses these modern tools, making embolization of acute LGIB safer and more effective. PMID:26764281

The CPAT 2.0.2 Domain Model - How CPAT 2.0.2 "Thinks" From an Analyst Perspective.

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

Waddell, Lucas; Muldoon, Frank; Melander, Darryl J.

To help effectively plan the management and modernization of their large and diverse fleets of vehicles, the Program Executive Office Ground Combat Systems (PEO GCS) and the Program Executive Office Combat Support and Combat Service Support (PEO CS &CSS) commissioned the development of a large - scale portfolio planning optimization tool. This software, the Capability Portfolio Analysis Tool (CPAT), creates a detailed schedule that optimally prioritizes the modernization or replacement of vehicles within the fleet - respecting numerous business rules associated with fleet structure, budgets, industrial base, research and testing, etc., while maximizing overall fleet performance through time. This reportmore » contains a description of the organizational fleet structure and a thorough explanation of the business rules that the CPAT formulation follows involving performance, scheduling, production, and budgets. This report, which is an update to the original CPAT domain model published in 2015 (SAND2015 - 4009), covers important new CPAT features. This page intentionally left blank« less

Mission Analysis, Operations, and Navigation Toolkit Environment (Monte) Version 040

NASA Technical Reports Server (NTRS)

Sunseri, Richard F.; Wu, Hsi-Cheng; Evans, Scott E.; Evans, James R.; Drain, Theodore R.; Guevara, Michelle M.

2012-01-01

Monte is a software set designed for use in mission design and spacecraft navigation operations. The system can process measurement data, design optimal trajectories and maneuvers, and do orbit determination, all in one application. For the first time, a single software set can be used for mission design and navigation operations. This eliminates problems due to different models and fidelities used in legacy mission design and navigation software. The unique features of Monte 040 include a blowdown thruster model for GRAIL (Gravity Recovery and Interior Laboratory) with associated pressure models, as well as an updated, optimalsearch capability (COSMIC) that facilitated mission design for ARTEMIS. Existing legacy software lacked the capabilities necessary for these two missions. There is also a mean orbital element propagator and an osculating to mean element converter that allows long-term orbital stability analysis for the first time in compiled code. The optimized trajectory search tool COSMIC allows users to place constraints and controls on their searches without any restrictions. Constraints may be user-defined and depend on trajectory information either forward or backwards in time. In addition, a long-term orbit stability analysis tool (morbiter) existed previously as a set of scripts on top of Monte. Monte is becoming the primary tool for navigation operations, a core competency at JPL. The mission design capabilities in Monte are becoming mature enough for use in project proposals as well as post-phase A mission design. Monte has three distinct advantages over existing software. First, it is being developed in a modern paradigm: object- oriented C++ and Python. Second, the software has been developed as a toolkit, which allows users to customize their own applications and allows the development team to implement requirements quickly, efficiently, and with minimal bugs. Finally, the software is managed in accordance with the CMMI (Capability Maturity Model Integration), where it has been ap praised at maturity level 3.

Ada software productivity prototypes: A case study

NASA Technical Reports Server (NTRS)

Hihn, Jairus M.; Habib-Agahi, Hamid; Malhotra, Shan

1988-01-01

A case study of the impact of Ada on a Command and Control project completed at the Jet Propulsion Laboratory (JPL) is given. The data for this study was collected as part of a general survey of software costs and productivity at JPL and other NASA sites. The task analyzed is a successful example of the use of rapid prototyping as applied to command and control for the U.S. Air Force and provides the U.S. Air Force Military Airlift Command with the ability to track aircraft, air crews and payloads worldwide. The task consists of a replicated database at several globally distributed sites. The local databases at each site can be updated within seconds after changes are entered at any one site. The system must be able to handle up to 400,000 activities per day. There are currently seven sites, each with a local area network of computers and a variety of user displays; the local area networks are tied together into a single wide area network. Using data obtained for eight modules, totaling approximately 500,000 source lines of code, researchers analyze the differences in productivities between subtasks. Factors considered are percentage of Ada used in coding, years of programmer experience, and the use of Ada tools and modern programming practices. The principle findings are the following. Productivity is very sensitive to programmer experience. The use of Ada software tools and the use of modern programming practices are important; without such use Ada is just a large complex language which can cause productivity to decrease. The impact of Ada on development effort phases is consistent with earlier reports at the project level but not at the module level.

Software ion scan functions in analysis of glycomic and lipidomic MS/MS datasets.

PubMed

Haramija, Marko

2018-03-01

Hardware ion scan functions unique to tandem mass spectrometry (MS/MS) mode of data acquisition, such as precursor ion scan (PIS) and neutral loss scan (NLS), are important for selective extraction of key structural data from complex MS/MS spectra. However, their software counterparts, software ion scan (SIS) functions, are still not regularly available. Software ion scan functions can be easily coded for additional functionalities, such as software multiple precursor ion scan, software no ion scan, and software variable ion scan functions. These are often necessary, since they allow more efficient analysis of complex MS/MS datasets, often encountered in glycomics and lipidomics. Software ion scan functions can be easily coded by using modern script languages and can be independent of instrument manufacturer. Here we demonstrate the utility of SIS functions on a medium-size glycomic MS/MS dataset. Knowledge of sample properties, as well as of diagnostic and conditional diagnostic ions crucial for data analysis, was needed. Based on the tables constructed with the output data from the SIS functions performed, a detailed analysis of a complex MS/MS glycomic dataset could be carried out in a quick, accurate, and efficient manner. Glycomic research is progressing slowly, and with respect to the MS experiments, one of the key obstacles for moving forward is the lack of appropriate bioinformatic tools necessary for fast analysis of glycomic MS/MS datasets. Adding novel SIS functionalities to the glycomic MS/MS toolbox has a potential to significantly speed up the glycomic data analysis process. Similar tools are useful for analysis of lipidomic MS/MS datasets as well, as will be discussed briefly. Copyright © 2017 John Wiley & Sons, Ltd.

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

Germain, Shawn

Nuclear Power Plant (NPP) refueling outages create some of the most challenging activities the utilities face in both tracking and coordinating thousands of activities in a short period of time. Other challenges, including nuclear safety concerns arising from atypical system configurations and resource allocation issues, can create delays and schedule overruns, driving up outage costs. Today the majority of the outage communication is done using processes that do not take advantage of advances in modern technologies that enable enhanced communication, collaboration and information sharing. Some of the common practices include: runners that deliver paper-based requests for approval, radios, telephones, desktopmore » computers, daily schedule printouts, and static whiteboards that are used to display information. Many gains have been made to reduce the challenges facing outage coordinators; however; new opportunities can be realized by utilizing modern technological advancements in communication and information tools that can enhance the collective situational awareness of plant personnel leading to improved decision-making. Ongoing research as part of the Light Water Reactor Sustainability Program (LWRS) has been targeting NPP outage improvement. As part of this research, various applications of collaborative software have been demonstrated through pilot project utility partnerships. Collaboration software can be utilized as part of the larger concept of Computer-Supported Cooperative Work (CSCW). Collaborative software can be used for emergent issue resolution, Outage Control Center (OCC) displays, and schedule monitoring. Use of collaboration software enables outage staff and subject matter experts (SMEs) to view and update critical outage information from any location on site or off.« less

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

PubMed

Koukouvaos, Charalambos; Kandris, Dionisis; Samarakou, Maria

2014-01-01

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

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

PubMed Central

Koukouvaos, Charalambos

2014-01-01

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

The GENIE Neutrino Monte Carlo Generator: Physics and User Manual

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

Andreopoulos, Costas; Barry, Christopher; Dytman, Steve

2015-10-20

GENIE is a suite of products for the experimental neutrino physics community. This suite includes i) a modern software framework for implementing neutrino event generators, a state-of-the-art comprehensive physics model and tools to support neutrino interaction simulation for realistic experimental setups (the Generator product), ii) extensive archives of neutrino, charged-lepton and hadron scattering data and software to produce a comprehensive set of data/MC comparisons (the Comparisons product), and iii) a generator tuning framework and fitting applications (the Tuning product). This book provides the definite guide for the GENIE Generator: It presents the software architecture and a detailed description of itsmore » physics model and official tunes. In addition, it provides a rich set of data/MC comparisons that characterise the physics performance of GENIE. Detailed step-by-step instructions on how to install and configure the Generator, run its applications and analyze its outputs are also included.« less

Bioinformatics.

PubMed

Moore, Jason H

2007-11-01

Bioinformatics is an interdisciplinary field that blends computer science and biostatistics with biological and biomedical sciences such as biochemistry, cell biology, developmental biology, genetics, genomics, and physiology. An important goal of bioinformatics is to facilitate the management, analysis, and interpretation of data from biological experiments and observational studies. The goal of this review is to introduce some of the important concepts in bioinformatics that must be considered when planning and executing a modern biological research study. We review database resources as well as data mining software tools.

Development of Modern Performance Assessment Tools and Capabilities for Underground Disposal of Transuranic Waste at WIPP

NASA Astrophysics Data System (ADS)

Zeitler, T.; Kirchner, T. B.; Hammond, G. E.; Park, H.

2014-12-01

The Waste Isolation Pilot Plant (WIPP) has been developed by the U.S. Department of Energy (DOE) for the geologic (deep underground) disposal of transuranic (TRU) waste. Containment of TRU waste at the WIPP is regulated by the U.S. Environmental Protection Agency (EPA). The DOE demonstrates compliance with the containment requirements by means of performance assessment (PA) calculations. WIPP PA calculations estimate the probability and consequence of potential radionuclide releases from the repository to the accessible environment for a regulatory period of 10,000 years after facility closure. The long-term performance of the repository is assessed using a suite of sophisticated computational codes. In a broad modernization effort, the DOE has overseen the transfer of these codes to modern hardware and software platforms. Additionally, there is a current effort to establish new performance assessment capabilities through the further development of the PFLOTRAN software, a state-of-the-art massively parallel subsurface flow and reactive transport code. Improvements to the current computational environment will result in greater detail in the final models due to the parallelization afforded by the modern code. Parallelization will allow for relatively faster calculations, as well as a move from a two-dimensional calculation grid to a three-dimensional grid. The result of the modernization effort will be a state-of-the-art subsurface flow and transport capability that will serve WIPP PA into the future. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. This research is funded by WIPP programs administered by the Office of Environmental Management (EM) of the U.S Department of Energy.

GIS Toolsets for Planetary Geomorphology and Landing-Site Analysis

NASA Astrophysics Data System (ADS)

Nass, Andrea; van Gasselt, Stephan

2015-04-01

Modern Geographic Information Systems (GIS) allow expert and lay users alike to load and position geographic data and perform simple to highly complex surface analyses. For many applications dedicated and ready-to-use GIS tools are available in standard software systems while other applications require the modular combination of available basic tools to answer more specific questions. This also applies to analyses in modern planetary geomorphology where many of such (basic) tools can be used to build complex analysis tools, e.g. in image- and terrain model analysis. Apart from the simple application of sets of different tools, many complex tasks require a more sophisticated design for storing and accessing data using databases (e.g. ArcHydro for hydrological data analysis). In planetary sciences, complex database-driven models are often required to efficiently analyse potential landings sites or store rover data, but also geologic mapping data can be efficiently stored and accessed using database models rather than stand-alone shapefiles. For landings-site analyses, relief and surface roughness estimates are two common concepts that are of particular interest and for both, a number of different definitions co-exist. We here present an advanced toolset for the analysis of image and terrain-model data with an emphasis on extraction of landing site characteristics using established criteria. We provide working examples and particularly focus on the concepts of terrain roughness as it is interpreted in geomorphology and engineering studies.

Investigation into the development of computer aided design software for space based sensors

NASA Technical Reports Server (NTRS)

Pender, C. W.; Clark, W. L.

1987-01-01

The described effort is phase one of the development of a Computer Aided Design (CAD) software to be used to perform radiometric sensor design. The software package will be referred to as SCAD and is directed toward the preliminary phase of the design of space based sensor system. The approach being followed is to develop a modern, graphic intensive, user friendly software package using existing software as building blocks. The emphasis will be directed toward the development of a shell containing menus, smart defaults, and interfaces, which can accommodate a wide variety of existing application software packages. The shell will offer expected utilities such as graphics, tailored menus, and a variety of drivers for I/O devices. Following the development of the shell, the development of SCAD is planned as chiefly selection and integration of appropriate building blocks. The phase one development activities have included: the selection of hardware which will be used with SCAD; the determination of the scope of SCAD; the preliminary evaluation of a number of software packages for applicability to SCAD; determination of a method for achieving required capabilities where voids exist; and then establishing a strategy for binding the software modules into an easy to use tool kit.

Customer-experienced rapid prototyping

NASA Astrophysics Data System (ADS)

Zhang, Lijuan; Zhang, Fu; Li, Anbo

2008-12-01

In order to describe accurately and comprehend quickly the perfect GIS requirements, this article will integrate the ideas of QFD (Quality Function Deployment) and UML (Unified Modeling Language), and analyze the deficiency of prototype development model, and will propose the idea of the Customer-Experienced Rapid Prototyping (CE-RP) and describe in detail the process and framework of the CE-RP, from the angle of the characteristics of Modern-GIS. The CE-RP is mainly composed of Customer Tool-Sets (CTS), Developer Tool-Sets (DTS) and Barrier-Free Semantic Interpreter (BF-SI) and performed by two roles of customer and developer. The main purpose of the CE-RP is to produce the unified and authorized requirements data models between customer and software developer.

Continuous integration and quality control for scientific software

NASA Astrophysics Data System (ADS)

Neidhardt, A.; Ettl, M.; Brisken, W.; Dassing, R.

2013-08-01

Modern software has to be stable, portable, fast and reliable. This is going to be also more and more important for scientific software. But this requires a sophisticated way to inspect, check and evaluate the quality of source code with a suitable, automated infrastructure. A centralized server with a software repository and a version control system is one essential part, to manage the code basis and to control the different development versions. While each project can be compiled separately, the whole code basis can also be compiled with one central “Makefile”. This is used to create automated, nightly builds. Additionally all sources are inspected automatically with static code analysis and inspection tools, which check well-none error situations, memory and resource leaks, performance issues, or style issues. In combination with an automatic documentation generator it is possible to create the developer documentation directly from the code and the inline comments. All reports and generated information are presented as HTML page on a Web server. Because this environment increased the stability and quality of the software of the Geodetic Observatory Wettzell tremendously, it is now also available for scientific communities. One regular customer is already the developer group of the DiFX software correlator project.

LiPD and CSciBox: A Case Study in Why Data Standards are Important for Paleoscience

NASA Astrophysics Data System (ADS)

Weiss, I.; Bradley, E.; McKay, N.; Emile-Geay, J.; de Vesine, L. R.; Anderson, K. A.; White, J. W. C.; Marchitto, T. M., Jr.

2016-12-01

CSciBox [1] is an integrated software system that helps geoscientists build and evaluate age models. Its user chooses from a number of built-in analysis tools, composing them into an analysis workflow and applying it to paleoclimate proxy datasets. CSciBox employs modern database technology to store both the data and the analysis results in an easily accessible and searchable form, and offers the user access to the computational toolbox, the data, and the results via a graphical user interface and a sophisticated plotter. Standards are a staple of modern life, and underlie any form of automation. Without data standards, it is difficult, if not impossible, to construct effective computer tools for paleoscience analysis. The LiPD (Linked Paleo Data) framework [2] enables the storage of both data and metadata in systematic, meaningful, machine-readable ways. LiPD has been a primary enabler of CSciBox's goals of usability, interoperability, and reproducibility. Building LiPD capabilities into CSciBox's importer, for instance, eliminated the need to ask the user about file formats, variable names, relationships between columns in the input file, etc. Building LiPD capabilities into the exporter facilitated the storage of complete details about the input data-provenance, preprocessing steps, etc.-as well as full descriptions of any analyses that were performed using the CSciBox tool, along with citations to appropriate references. This comprehensive collection of data and metadata, which is all linked together in a semantically meaningful, machine-readable way, not only completely documents the analyses and makes them reproducible. It also enables interoperability with any other software system that employs the LiPD standard. [1] www.cs.colorado.edu/ lizb/cscience.html[2] McKay & Emile-Geay, Climate of the Past 12:1093 (2016)

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

PubMed

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

2016-09-02

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

Modernization of the USGS Hawaiian Volcano Observatory Seismic Processing Infrastructure

NASA Astrophysics Data System (ADS)

Antolik, L.; Shiro, B.; Friberg, P. A.

2016-12-01

The USGS Hawaiian Volcano Observatory (HVO) operates a Tier 1 Advanced National Seismic System (ANSS) seismic network to monitor, characterize, and report on volcanic and earthquake activity in the State of Hawaii. Upgrades at the observatory since 2009 have improved the digital telemetry network, computing resources, and seismic data processing with the adoption of the ANSS Quake Management System (AQMS) system. HVO aims to build on these efforts by further modernizing its seismic processing infrastructure and strengthen its ability to meet ANSS performance standards. Most notably, this will also allow HVO to support redundant systems, both onsite and offsite, in order to provide better continuity of operation during intermittent power and network outages. We are in the process of implementing a number of upgrades and improvements on HVO's seismic processing infrastructure, including: 1) Virtualization of AQMS physical servers; 2) Migration of server operating systems from Solaris to Linux; 3) Consolidation of AQMS real-time and post-processing services to a single server; 4) Upgrading database from Oracle 10 to Oracle 12; and 5) Upgrading to the latest Earthworm and AQMS software. These improvements will make server administration more efficient, minimize hardware resources required by AQMS, simplify the Oracle replication setup, and provide better integration with HVO's existing state of health monitoring tools and backup system. Ultimately, it will provide HVO with the latest and most secure software available while making the software easier to deploy and support.

PICASSO: an end-to-end image simulation tool for space and airborne imaging systems

NASA Astrophysics Data System (ADS)

Cota, Steve A.; Bell, Jabin T.; Boucher, Richard H.; Dutton, Tracy E.; Florio, Chris J.; Franz, Geoffrey A.; Grycewicz, Thomas J.; Kalman, Linda S.; Keller, Robert A.; Lomheim, Terrence S.; Paulson, Diane B.; Willkinson, Timothy S.

2008-08-01

The design of any modern imaging system is the end result of many trade studies, each seeking to optimize image quality within real world constraints such as cost, schedule and overall risk. Image chain analysis - the prediction of image quality from fundamental design parameters - is an important part of this design process. At The Aerospace Corporation we have been using a variety of image chain analysis tools for many years, the Parameterized Image Chain Analysis & Simulation SOftware (PICASSO) among them. In this paper we describe our PICASSO tool, showing how, starting with a high quality input image and hypothetical design descriptions representative of the current state of the art in commercial imaging satellites, PICASSO can generate standard metrics of image quality in support of the decision processes of designers and program managers alike.

PICASSO: an end-to-end image simulation tool for space and airborne imaging systems

NASA Astrophysics Data System (ADS)

Cota, Stephen A.; Bell, Jabin T.; Boucher, Richard H.; Dutton, Tracy E.; Florio, Christopher J.; Franz, Geoffrey A.; Grycewicz, Thomas J.; Kalman, Linda S.; Keller, Robert A.; Lomheim, Terrence S.; Paulson, Diane B.; Wilkinson, Timothy S.

2010-06-01

The design of any modern imaging system is the end result of many trade studies, each seeking to optimize image quality within real world constraints such as cost, schedule and overall risk. Image chain analysis - the prediction of image quality from fundamental design parameters - is an important part of this design process. At The Aerospace Corporation we have been using a variety of image chain analysis tools for many years, the Parameterized Image Chain Analysis & Simulation SOftware (PICASSO) among them. In this paper we describe our PICASSO tool, showing how, starting with a high quality input image and hypothetical design descriptions representative of the current state of the art in commercial imaging satellites, PICASSO can generate standard metrics of image quality in support of the decision processes of designers and program managers alike.

Complexity: an internet resource for analysis of DNA sequence complexity

PubMed Central

Orlov, Y. L.; Potapov, V. N.

2004-01-01

The search for DNA regions with low complexity is one of the pivotal tasks of modern structural analysis of complete genomes. The low complexity may be preconditioned by strong inequality in nucleotide content (biased composition), by tandem or dispersed repeats or by palindrome-hairpin structures, as well as by a combination of all these factors. Several numerical measures of textual complexity, including combinatorial and linguistic ones, together with complexity estimation using a modified Lempel–Ziv algorithm, have been implemented in a software tool called ‘Complexity’ (http://wwwmgs.bionet.nsc.ru/mgs/programs/low_complexity/). The software enables a user to search for low-complexity regions in long sequences, e.g. complete bacterial genomes or eukaryotic chromosomes. In addition, it estimates the complexity of groups of aligned sequences. PMID:15215465

WinTRAX: A raytracing software package for the design of multipole focusing systems

NASA Astrophysics Data System (ADS)

Grime, G. W.

2013-07-01

The software package TRAX was a simulation tool for modelling the path of charged particles through linear cylindrical multipole fields described by analytical expressions and was a development of the earlier OXRAY program (Grime and Watt, 1983; Grime et al., 1982) [1,2]. In a 2005 comparison of raytracing software packages (Incerti et al., 2005) [3], TRAX/OXRAY was compared with Geant4 and Zgoubi and was found to give close agreement with the more modern codes. TRAX was a text-based program which was only available for operation in a now rare VMS workstation environment, so a new program, WinTRAX, has been developed for the Windows operating system. This implements the same basic computing strategy as TRAX, and key sections of the code are direct translations from FORTRAN to C++, but the Windows environment is exploited to make an intuitive graphical user interface which simplifies and enhances many operations including system definition and storage, optimisation, beam simulation (including with misaligned elements) and aberration coefficient determination. This paper describes the program and presents comparisons with other software and real installations.

Introducing the Computer to Family Practice

PubMed Central

Petreman, Mel

1984-01-01

The medical profession has been far more reluctant than the general business community to adopt the computer as a useful business tool. The experience of a group of five family physicians who have been using a computer since 1979 demonstrates that it is possible to achieve significant financial benefits, and to reduce the stress and workload of both physicians and office staff. The computerization of medical records, scheduling, and patient billing is discussed in detail. Physicians have controlled the paper load of the modern medical office by pioneering their own medical software system. PMID:21279036

System of HPC content archiving

NASA Astrophysics Data System (ADS)

Bogdanov, A.; Ivashchenko, A.

2017-12-01

This work is aimed to develop a system, that will effectively solve the problem of storing and analyzing files containing text data, by using modern software development tools, techniques and approaches. The main challenge of storing a large number of text documents defined at the problem formulation stage, have to be resolved with such functionality as full text search and document clustering depends on their contents. Main system features could be described with notions of distributed multilevel architecture, flexibility and interchangeability of components, achieved through the standard functionality incapsulation in independent executable modules.

Using the CAE technologies of engineering analysis for designing steam turbines at ZAO Ural Turbine Works

NASA Astrophysics Data System (ADS)

Goloshumova, V. N.; Kortenko, V. V.; Pokhoriler, V. L.; Kultyshev, A. Yu.; Ivanovskii, A. A.

2008-08-01

We describe the experience ZAO Ural Turbine Works specialists gained from mastering the series of CAD/CAE/CAM/PDM technologies, which are modern software tools of computer-aided engineering. We also present the results obtained from mathematical simulation of the process through which high-and intermediate-pressure rotors are heated for revealing the most thermally stressed zones, as well as the results from mathematical simulation of a new design of turbine cylinder shells for improving the maneuverability of these turbines.

Perspectives on bioanalytical mass spectrometry and automation in drug discovery.

PubMed

Janiszewski, John S; Liston, Theodore E; Cole, Mark J

2008-11-01

The use of high speed synthesis technologies has resulted in a steady increase in the number of new chemical entities active in the drug discovery research stream. Large organizations can have thousands of chemical entities in various stages of testing and evaluation across numerous projects on a weekly basis. Qualitative and quantitative measurements made using LC/MS are integrated throughout this process from early stage lead generation through candidate nomination. Nearly all analytical processes and procedures in modern research organizations are automated to some degree. This includes both hardware and software automation. In this review we discuss bioanalytical mass spectrometry and automation as components of the analytical chemistry infrastructure in pharma. Analytical chemists are presented as members of distinct groups with similar skillsets that build automated systems, manage test compounds, assays and reagents, and deliver data to project teams. The ADME-screening process in drug discovery is used as a model to highlight the relationships between analytical tasks in drug discovery. Emerging software and process automation tools are described that can potentially address gaps and link analytical chemistry related tasks. The role of analytical chemists and groups in modern 'industrialized' drug discovery is also discussed.

Constraints and Opportunities in GCM Model Development

NASA Technical Reports Server (NTRS)

Schmidt, Gavin; Clune, Thomas

2010-01-01

Over the past 30 years climate models have evolved from relatively simple representations of a few atmospheric processes to complex multi-disciplinary system models which incorporate physics from bottom of the ocean to the mesopause and are used for seasonal to multi-million year timescales. Computer infrastructure over that period has gone from punchcard mainframes to modern parallel clusters. Constraints of working within an ever evolving research code mean that most software changes must be incremental so as not to disrupt scientific throughput. Unfortunately, programming methodologies have generally not kept pace with these challenges, and existing implementations now present a heavy and growing burden on further model development as well as limiting flexibility and reliability. Opportunely, advances in software engineering from other disciplines (e.g. the commercial software industry) as well as new generations of powerful development tools can be incorporated by the model developers to incrementally and systematically improve underlying implementations and reverse the long term trend of increasing development overhead. However, these methodologies cannot be applied blindly, but rather must be carefully tailored to the unique characteristics of scientific software development. We will discuss the need for close integration of software engineers and climate scientists to find the optimal processes for climate modeling.

Implementation of the new hydrographic technologies for bottom topography and seafloor gas venting investigations in the russian northern seas

NASA Astrophysics Data System (ADS)

Koloskov, Evgenii

2017-04-01

The report examines modern hydrographic technologies for the Russian northern seas investigations. The new hydro acoustics methods for seabed study are discussed. It presents stages of seafloor relief studies in the Russian Arctic seas since the 1950s and the obtained results. At the beginning of the 21st century an entirely new phase of bathymetric investigations began with the use of Multibeam Echosounders (MB) and modern hydrographic software. The software tools to process and analyze the bathymetry, and more recently to characterize the seabed from the backscatter, are available in a majority of modern sonar systems. Besides the bathymetry and sonar data, modern MB can produce water column images. These hydrographic technologies provide the possibility to achieve a high level of the seafloor topography. The latest generation of hydrographic MB now has the ability to provide the water column images along with the seafloor. The gas seeps from multibeam water column data can be distantly discerned against the seabed relief background with the aid of the Fledermause software package ("FMMidwater" module). The ability to integrate the water column data with the seafoor and other information,in an integrated geospatial and temporal environment, enhanced the analysis and interpretation of the data which is essential for marine geological research and investigations. The modern hydrographic equipment presents the ability to integrate the MB digital relief models (DTM) and sub bottom profiler data. This provide the possibility to obtain not only the detailed seabed topography, but also the additional information concerning the structure of under bottom soil layers and presence of the endogenous objects in near bottom environment. The importance of the hydrographic software tools needed to process and analyze the bathymetry and water column data are emphasized. The practical importance of the water column and bottom profiler data processing for the submarine gas-hydrates survey is stated. The attention is paid to the implementation of the parametric sub bottom profilers - the low frequency sonar for the sea bottom vertical section investigation. The ability for the integrated presentation of the multibeam bathymetry and vertical curtains in the 3D environment are discussed. As an example of the modern swath survey results achieved with Kongsberg EM2040CD MB and hydrographic information technology QINSy/ Fledermause, are discussed and presented. This survey was performed for the RosNeft company in the Kara sea. Recommendations for the implementation of the multi beam echo sounder and parametric sub bottom profiler for the combined hydrographic and submarine gas-hydrates survey in the Russian northern seas are delivered.The gas-hydrate survey guidelines using MB and QINSy/Fledermause software are provided. The hydrographic software tools used to process and analyze the bathymetry can create the seafloor DTM with the high degree of resolution and provide 3D visualization.These new possibilities provide such realistic view of the sea bottom relief and environment that can be characterized as the marine landscapes. Thus it became possible to investigate the relief morphological peculiarities and obtain the information about the relief genesis. This opens the new opportunities for using the acoustic techniques for varies types of marine activity including the bottom environmental study. The appearance of the bottom thermokarst activity derived from the high resolution DTM generated from the real time MB data is presented. The bottom thermokarst provides the potential threat for underwater pipelines and other submarine communications. The arctic bottom relief peculiarities are also covered including grounded hummock traces and dome-shaped elevations. The investigation of such bottom land forms has become possible recently as the result of implementing the wide swath survey methods. Such unique relief features are in general related to seabed gas venting in the form of the submarine gas-hydrates seeps. The opportunities for investigation of the morphological relief peculiarities and getting the new information is mportant also for varies types of marine activity including the marine ecology study. The arctic sea specific microrelief images are provided to show the abnormality of the bottom surface. The main attention is paid to specific and bottom features such as trenches the grounded hummock traces and dome-shaped elevations of the Pingo-type-unique forms of microrelief usually confined to the bottom gas flow in the form of methane emissions. The attention is also paid to the consequences of the global climate change and its influence on the bottom sole. Key words: hydrographic technologies, hydro acoustics methods, swathe survey, sea bottom vertical section, submarine gas-hydrates, submarine permafrost, seafloor gas venting,multi beam echo sounder, parametric sub bottom profiler.

A Software Tool for Quantitative Seismicity Analysis - ZMAP

NASA Astrophysics Data System (ADS)

Wiemer, S.; Gerstenberger, M.

2001-12-01

Earthquake catalogs are probably the most basic product of seismology, and remain arguably the most useful for tectonic studies. Modern seismograph networks can locate up to 100,000 earthquakes annually, providing a continuous and sometime overwhelming stream of data. ZMAP is a set of tools driven by a graphical user interface (GUI), designed to help seismologists analyze catalog data. ZMAP is primarily a research tool suited to the evaluation of catalog quality and to addressing specific hypotheses; however, it can also be useful in routine network operations. Examples of ZMAP features include catalog quality assessment (artifacts, completeness, explosion contamination), interactive data exploration, mapping transients in seismicity (rate changes, b-values, p-values), fractal dimension analysis and stress tensor inversions. Roughly 100 scientists worldwide have used the software at least occasionally. About 30 peer-reviewed publications have made use of ZMAP. ZMAP code is open source, written in the commercial software language Matlab by the Mathworks, a widely used software in the natural sciences. ZMAP was first published in 1994, and has continued to grow over the past 7 years. Recently, we released ZMAP v.6. The poster will introduce the features of ZMAP. We will specifically focus on ZMAP features related to time-dependent probabilistic hazard assessment. We are currently implementing a ZMAP based system that computes probabilistic hazard maps, which combine the stationary background hazard as well as aftershock and foreshock hazard into a comprehensive time dependent probabilistic hazard map. These maps will be displayed in near real time on the Internet. This poster is also intended as a forum for ZMAP users to provide feedback and discuss the future of ZMAP.

Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.

PubMed

Waltemath, Dagmar; Adams, Richard; Bergmann, Frank T; Hucka, Michael; Kolpakov, Fedor; Miller, Andrew K; Moraru, Ion I; Nickerson, David; Sahle, Sven; Snoep, Jacky L; Le Novère, Nicolas

2011-12-15

The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined.

Personalized, Shareable Geoscience Dataspaces For Simplifying Data Management and Improving Reproducibility

NASA Astrophysics Data System (ADS)

Malik, T.; Foster, I.; Goodall, J. L.; Peckham, S. D.; Baker, J. B. H.; Gurnis, M.

2015-12-01

Research activities are iterative, collaborative, and now data- and compute-intensive. Such research activities mean that even the many researchers who work in small laboratories must often create, acquire, manage, and manipulate much diverse data and keep track of complex software. They face difficult data and software management challenges, and data sharing and reproducibility are neglected. There is signficant federal investment in powerful cyberinfrastructure, in part to lesson the burden associated with modern data- and compute-intensive research. Similarly, geoscience communities are establishing research repositories to facilitate data preservation. Yet we observe a large fraction of the geoscience community continues to struggle with data and software management. The reason, studies suggest, is not lack of awareness but rather that tools do not adequately support time-consuming data life cycle activities. Through NSF/EarthCube-funded GeoDataspace project, we are building personalized, shareable dataspaces that help scientists connect their individual or research group efforts with the community at large. The dataspaces provide a light-weight multiplatform research data management system with tools for recording research activities in what we call geounits, so that a geoscientist can at any time snapshot and preserve, both for their own use and to share with the community, all data and code required to understand and reproduce a study. A software-as-a-service (SaaS) deployment model enhances usability of core components, and integration with widely used software systems. In this talk we will present the open-source GeoDataspace project and demonstrate how it is enabling reproducibility across geoscience domains of hydrology, space science, and modeling toolkits.

FDT 2.0: Improving scalability of the fuzzy decision tree induction tool - integrating database storage.

PubMed

Durham, Erin-Elizabeth A; Yu, Xiaxia; Harrison, Robert W

2014-12-01

Effective machine-learning handles large datasets efficiently. One key feature of handling large data is the use of databases such as MySQL. The freeware fuzzy decision tree induction tool, FDT, is a scalable supervised-classification software tool implementing fuzzy decision trees. It is based on an optimized fuzzy ID3 (FID3) algorithm. FDT 2.0 improves upon FDT 1.0 by bridging the gap between data science and data engineering: it combines a robust decisioning tool with data retention for future decisions, so that the tool does not need to be recalibrated from scratch every time a new decision is required. In this paper we briefly review the analytical capabilities of the freeware FDT tool and its major features and functionalities; examples of large biological datasets from HIV, microRNAs and sRNAs are included. This work shows how to integrate fuzzy decision algorithms with modern database technology. In addition, we show that integrating the fuzzy decision tree induction tool with database storage allows for optimal user satisfaction in today's Data Analytics world.

Wireless local area network for the dental office.

PubMed

Mupparapu, Muralidhar

2004-01-01

Dental offices are no exception to the implementation of new and advanced technology, especially if it enhances productivity. In a rapidly transforming digital world, wireless technology has a special place, as it has truly "retired the wire" and contributed to the ease and efficient access to patient data and other software-based applications for diagnosis and treatment. If the office or the clinic is networked, access to patient management software, imaging software and treatment planning tools is enhanced. Access will be further enhanced and unrestricted if the entire network is wireless. As with any new, emerging technology, there will be issues that should be kept in mind before adapting to the wireless environment. Foremost is the network security involved in the installation and use of these wireless networks. This short, technical manuscript deals with standards and choices in wireless technology currently available for implementation within a dental office. The benefits of each network security protocol available to protect patient data and boost the efficiency of a modern dental office are discussed.

SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research.

PubMed

Yaniv, Ziv; Lowekamp, Bradley C; Johnson, Hans J; Beare, Richard

2018-06-01

Modern scientific endeavors increasingly require team collaborations to construct and interpret complex computational workflows. This work describes an image-analysis environment that supports the use of computational tools that facilitate reproducible research and support scientists with varying levels of software development skills. The Jupyter notebook web application is the basis of an environment that enables flexible, well-documented, and reproducible workflows via literate programming. Image-analysis software development is made accessible to scientists with varying levels of programming experience via the use of the SimpleITK toolkit, a simplified interface to the Insight Segmentation and Registration Toolkit. Additional features of the development environment include user friendly data sharing using online data repositories and a testing framework that facilitates code maintenance. SimpleITK provides a large number of examples illustrating educational and research-oriented image analysis workflows for free download from GitHub under an Apache 2.0 license: github.com/InsightSoftwareConsortium/SimpleITK-Notebooks .

TeraStitcher - A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images

PubMed Central

2012-01-01

Background Further advances in modern microscopy are leading to teravoxel-sized tiled 3D images at high resolution, thus increasing the dimension of the stitching problem of at least two orders of magnitude. The existing software solutions do not seem adequate to address the additional requirements arising from these datasets, such as the minimization of memory usage and the need to process just a small portion of data. Results We propose a free and fully automated 3D Stitching tool designed to match the special requirements coming out of teravoxel-sized tiled microscopy images that is able to stitch them in a reasonable time even on workstations with limited resources. The tool was tested on teravoxel-sized whole mouse brain images with micrometer resolution and it was also compared with the state-of-the-art stitching tools on megavoxel-sized publicy available datasets. This comparison confirmed that the solutions we adopted are suited for stitching very large images and also perform well on datasets with different characteristics. Indeed, some of the algorithms embedded in other stitching tools could be easily integrated in our framework if they turned out to be more effective on other classes of images. To this purpose, we designed a software architecture which separates the strategies that use efficiently memory resources from the algorithms which may depend on the characteristics of the acquired images. Conclusions TeraStitcher is a free tool that enables the stitching of Teravoxel-sized tiled microscopy images even on workstations with relatively limited resources of memory (<8 GB) and processing power. It exploits the knowledge of approximate tile positions and uses ad-hoc strategies and algorithms designed for such very large datasets. The produced images can be saved into a multiresolution representation to be efficiently retrieved and processed. We provide TeraStitcher both as standalone application and as plugin of the free software Vaa3D. PMID:23181553

Open Source Seismic Software in NOAA's Next Generation Tsunami Warning System

NASA Astrophysics Data System (ADS)

Hellman, S. B.; Baker, B. I.; Hagerty, M. T.; Leifer, J. M.; Lisowski, S.; Thies, D. A.; Donnelly, B. K.; Griffith, F. P.

2014-12-01

The Tsunami Information technology Modernization (TIM) is a project spearheaded by National Oceanic and Atmospheric Administration to update the United States' Tsunami Warning System software currently employed at the Pacific Tsunami Warning Center (Eva Beach, Hawaii) and the National Tsunami Warning Center (Palmer, Alaska). This entirely open source software project will integrate various seismic processing utilities with the National Weather Service Weather Forecast Office's core software, AWIPS2. For the real-time and near real-time seismic processing aspect of this project, NOAA has elected to integrate the open source portions of GFZ's SeisComP 3 (SC3) processing system into AWIPS2. To provide for better tsunami threat assessments we are developing open source tools for magnitude estimations (e.g., moment magnitude, energy magnitude, surface wave magnitude), detection of slow earthquakes with the Theta discriminant, moment tensor inversions (e.g. W-phase and teleseismic body waves), finite fault inversions, and array processing. With our reliance on common data formats such as QuakeML and seismic community standard messaging systems, all new facilities introduced into AWIPS2 and SC3 will be available as stand-alone tools or could be easily integrated into other real time seismic monitoring systems such as Earthworm, Antelope, etc. Additionally, we have developed a template based design paradigm so that the developer or scientist can efficiently create upgrades, replacements, and/or new metrics to the seismic data processing with only a cursory knowledge of the underlying SC3.

ITK: enabling reproducible research and open science

PubMed Central

McCormick, Matthew; Liu, Xiaoxiao; Jomier, Julien; Marion, Charles; Ibanez, Luis

2014-01-01

Reproducibility verification is essential to the practice of the scientific method. Researchers report their findings, which are strengthened as other independent groups in the scientific community share similar outcomes. In the many scientific fields where software has become a fundamental tool for capturing and analyzing data, this requirement of reproducibility implies that reliable and comprehensive software platforms and tools should be made available to the scientific community. The tools will empower them and the public to verify, through practice, the reproducibility of observations that are reported in the scientific literature. Medical image analysis is one of the fields in which the use of computational resources, both software and hardware, are an essential platform for performing experimental work. In this arena, the introduction of the Insight Toolkit (ITK) in 1999 has transformed the field and facilitates its progress by accelerating the rate at which algorithmic implementations are developed, tested, disseminated and improved. By building on the efficiency and quality of open source methodologies, ITK has provided the medical image community with an effective platform on which to build a daily workflow that incorporates the true scientific practices of reproducibility verification. This article describes the multiple tools, methodologies, and practices that the ITK community has adopted, refined, and followed during the past decade, in order to become one of the research communities with the most modern reproducibility verification infrastructure. For example, 207 contributors have created over 2400 unit tests that provide over 84% code line test coverage. The Insight Journal, an open publication journal associated with the toolkit, has seen over 360,000 publication downloads. The median normalized closeness centrality, a measure of knowledge flow, resulting from the distributed peer code review system was high, 0.46. PMID:24600387

ITK: enabling reproducible research and open science.

PubMed

McCormick, Matthew; Liu, Xiaoxiao; Jomier, Julien; Marion, Charles; Ibanez, Luis

2014-01-01

Reproducibility verification is essential to the practice of the scientific method. Researchers report their findings, which are strengthened as other independent groups in the scientific community share similar outcomes. In the many scientific fields where software has become a fundamental tool for capturing and analyzing data, this requirement of reproducibility implies that reliable and comprehensive software platforms and tools should be made available to the scientific community. The tools will empower them and the public to verify, through practice, the reproducibility of observations that are reported in the scientific literature. Medical image analysis is one of the fields in which the use of computational resources, both software and hardware, are an essential platform for performing experimental work. In this arena, the introduction of the Insight Toolkit (ITK) in 1999 has transformed the field and facilitates its progress by accelerating the rate at which algorithmic implementations are developed, tested, disseminated and improved. By building on the efficiency and quality of open source methodologies, ITK has provided the medical image community with an effective platform on which to build a daily workflow that incorporates the true scientific practices of reproducibility verification. This article describes the multiple tools, methodologies, and practices that the ITK community has adopted, refined, and followed during the past decade, in order to become one of the research communities with the most modern reproducibility verification infrastructure. For example, 207 contributors have created over 2400 unit tests that provide over 84% code line test coverage. The Insight Journal, an open publication journal associated with the toolkit, has seen over 360,000 publication downloads. The median normalized closeness centrality, a measure of knowledge flow, resulting from the distributed peer code review system was high, 0.46.

Analytical improvements of hybrid LC-MS/MS techniques for the efficient evaluation of emerging contaminants in river waters: a case study of the Henares River (Madrid, Spain).

PubMed

Pérez-Parada, Andrés; Gómez-Ramos, María del Mar; Martínez Bueno, María Jesús; Uclés, Samanta; Uclés, Ana; Fernández-Alba, Amadeo R

2012-02-01

Instrumental capabilities and software tools of modern hybrid mass spectrometry (MS) instruments such as high-resolution mass spectrometry (HRMS), quadrupole time-of-flight (QTOF), and quadrupole linear ion trap (QLIT) were experimentally investigated for the study of emerging contaminants in Henares River water samples. Automated screening and confirmatory capabilities of QTOF working in full-scan MS and tandem MS (MS/MS) were explored when dealing with real samples. Investigations on the effect of sensitivity and resolution power influence on mass accuracy were studied for the correct assignment of the amoxicillin transformation product 5(R) amoxicillin-diketopiperazine-2',5' as an example of a nontarget compound. On the other hand, a comparison of quantitative and qualitative strategies based on direct injection analysis and off-line solid-phase extraction sample treatment were assayed using two different QLIT instruments for a selected group of emerging contaminants when operating in selected reaction monitoring (SRM) and information-dependent acquisition (IDA) modes. Software-aided screening usually needs a further confirmatory step. Resolving power and MS/MS feature of QTOF showed to confirm/reject most findings in river water, although sensitivity-related limitations are usually found. Superior sensitivity of modern QLIT-MS/MS offered the possibility of direct injection analysis for proper quantitative study of a variety of contaminants, while it simultaneously reduced the matrix effect and increased the reliability of the results. Confirmation of ethylamphetamine, which lacks on a second SRM transition, was accomplished by using the IDA feature. Hybrid MS instruments equipped with high resolution and high sensitivity contributes to enlarge the scope of targeted analytes in river waters. However, in the tested instruments, there is a margin of improvement principally in required sensitivity and data treatment software tools devoted to reliable confirmation and improved automated data processing.

Valorisation of Como Historical Cadastral Maps Through Modern Web Geoservices

NASA Astrophysics Data System (ADS)

Brovelli, M. A.; Minghini, M.; Zamboni, G.

2012-07-01

Cartographic cultural heritage preserved in worldwide archives is often stored in the original paper version only, thus restricting both the chances of utilization and the range of possible users. The Web C.A.R.T.E. system addressed this issue with regard to the precious cadastral maps preserved at the State Archive of Como. Aim of the project was to improve the visibility and accessibility of this heritage using the latest free and open source tools for processing, cataloguing and web publishing the maps. The resulting architecture should therefore assist the State Archive of Como in managing its cartographic contents. After a pre-processing consisting of digitization and georeferencing steps, maps were provided with metadata, compiled according to the current Italian standards and managed through an ad hoc version of the GeoNetwork Opensource geocatalog software. A dedicated MapFish-based webGIS client, with an optimized version also for mobile platforms, was built for maps publication and 2D navigation. A module for 3D visualization of cadastral maps was finally developed using the NASA World Wind Virtual Globe. Thanks to a temporal slidebar, time was also included in the system producing a 4D Graphical User Interface. The overall architecture was totally built with free and open source software and allows a direct and intuitive consultation of historical maps. Besides the notable advantage of keeping original paper maps intact, the system greatly simplifies the work of the State Archive of Como common users and together widens the same range of users thanks to the modernization of map consultation tools.

Global Combat Support System-Marine Corps Proof-of-Concept for Dashboard Analytics

DTIC Science & Technology

2014-12-01

The core is modern, commercial-off-the-shelf enterprise resource planning ( ERP ) software (Oracle 11i e-Business Suite). GCSS-MCs design is focused...factor in the decision to implement this new software . GCSS-MC is the technology centerpiece of the Logistics Modernization (LogMod) Program...GCSS-MC is based on the implementation of Oracle e-Business Suite 11i as the core software package. This is the same infrastructure that Oracle

Physically Based Virtual Surgery Planning and Simulation Tools for Personal Health Care Systems

NASA Astrophysics Data System (ADS)

Dogan, Firat; Atilgan, Yasemin

The virtual surgery planning and simulation tools have gained a great deal of importance in the last decade in a consequence of increasing capacities at the information technology level. The modern hardware architectures, large scale database systems, grid based computer networks, agile development processes, better 3D visualization and all the other strong aspects of the information technology brings necessary instruments into almost every desk. The last decade’s special software and sophisticated super computer environments are now serving to individual needs inside “tiny smart boxes” for reasonable prices. However, resistance to learning new computerized environments, insufficient training and all the other old habits prevents effective utilization of IT resources by the specialists of the health sector. In this paper, all the aspects of the former and current developments in surgery planning and simulation related tools are presented, future directions and expectations are investigated for better electronic health care systems.

Enhancing Cassini Operations & Science Planning Tools

NASA Technical Reports Server (NTRS)

Castello, Jonathan

2012-01-01

The Cassini team uses a variety of software utilities as they manage and coordinate their mission to Saturn. Most of these tools have been unchanged for many years, and although stability is a virtue for long-lived space missions, there are some less-fragile tools that could greatly benefit from modern improvements. This report shall describe three such upgrades, including their architectural differences and their overall impact. Emphasis is placed on the motivation and rationale behind architectural choices rather than the final product, so as to illuminate the lessons learned and discoveries made.These three enhancements included developing a strategy for migrating Science Planning utilities to a new execution model, rewriting the team's internal portal for ease of use and maintenance, and developing a web-based agenda application for tracking the sequence of files being transmitted to the Cassini spacecraft. Of this set, the first two have been fully completed, while the agenda application is currently in the early prototype stage.

Systems Biology-Driven Hypotheses Tested In Vivo: The Need to Advancing Molecular Imaging Tools.

PubMed

Verma, Garima; Palombo, Alessandro; Grigioni, Mauro; La Monaca, Morena; D'Avenio, Giuseppe

2018-01-01

Processing and interpretation of biological images may provide invaluable insights on complex, living systems because images capture the overall dynamics as a "whole." Therefore, "extraction" of key, quantitative morphological parameters could be, at least in principle, helpful in building a reliable systems biology approach in understanding living objects. Molecular imaging tools for system biology models have attained widespread usage in modern experimental laboratories. Here, we provide an overview on advances in the computational technology and different instrumentations focused on molecular image processing and analysis. Quantitative data analysis through various open source software and algorithmic protocols will provide a novel approach for modeling the experimental research program. Besides this, we also highlight the predictable future trends regarding methods for automatically analyzing biological data. Such tools will be very useful to understand the detailed biological and mathematical expressions under in-silico system biology processes with modeling properties.

FTDD973: A multimedia knowledge-based system and methodology for operator training and diagnostics

NASA Technical Reports Server (NTRS)

Hekmatpour, Amir; Brown, Gary; Brault, Randy; Bowen, Greg

1993-01-01

FTDD973 (973 Fabricator Training, Documentation, and Diagnostics) is an interactive multimedia knowledge based system and methodology for computer-aided training and certification of operators, as well as tool and process diagnostics in IBM's CMOS SGP fabrication line (building 973). FTDD973 is an example of what can be achieved with modern multimedia workstations. Knowledge-based systems, hypertext, hypergraphics, high resolution images, audio, motion video, and animation are technologies that in synergy can be far more useful than each by itself. FTDD973's modular and object-oriented architecture is also an example of how improvements in software engineering are finally making it possible to combine many software modules into one application. FTDD973 is developed in ExperMedia/2; and OS/2 multimedia expert system shell for domain experts.

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

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

Post-Modern Software Development

NASA Technical Reports Server (NTRS)

Filman, Robert E.

2005-01-01

The history of software development includes elements of art, science, engineering, and fashion(though very little manufacturing). In all domains, old ideas give way or evolve to new ones: in the fine arts, the baroque gave way to rococo, romanticism, modernism, postmodernism, and so forth. What is the postmodern programming equivalent? That is, what comes after object orientation?

Teacher's Guide to SERAPHIM Software III. Modern Chemistry.

ERIC Educational Resources Information Center

Bogner, Donna J.

Designed to assist chemistry teachers in selecting appropriate software programs, this publication is the third in a series of six teacher's guides from Project SERAPHIM, a program sponsored by the National Science Foundation. This guide is keyed to the chapters of the text "Modern Chemistry." Program suggestions are arranged in the same…

Teacher's Guide to SERAPHIM Software IV Chemistry: A Modern Course.

ERIC Educational Resources Information Center

Bogner, Donna J.

Designed to assist chemistry teachers in selecting appropriate software programs, this publication is the fourth in a series of six teacher's guides from Project SERAPHIM, a program sponsored by the National Science Foundation. This guide is keyed to the chapters of the text "Chemistry: A Modern Course." Program suggestions are arranged…

Using ChEMBL web services for building applications and data processing workflows relevant to drug discovery.

PubMed

Nowotka, Michał M; Gaulton, Anna; Mendez, David; Bento, A Patricia; Hersey, Anne; Leach, Andrew

2017-08-01

ChEMBL is a manually curated database of bioactivity data on small drug-like molecules, used by drug discovery scientists. Among many access methods, a REST API provides programmatic access, allowing the remote retrieval of ChEMBL data and its integration into other applications. This approach allows scientists to move from a world where they go to the ChEMBL web site to search for relevant data, to one where ChEMBL data can be simply integrated into their everyday tools and work environment. Areas covered: This review highlights some of the audiences who may benefit from using the ChEMBL API, and the goals they can address, through the description of several use cases. The examples cover a team communication tool (Slack), a data analytics platform (KNIME), batch job management software (Luigi) and Rich Internet Applications. Expert opinion: The advent of web technologies, cloud computing and micro services oriented architectures have made REST APIs an essential ingredient of modern software development models. The widespread availability of tools consuming RESTful resources have made them useful for many groups of users. The ChEMBL API is a valuable resource of drug discovery bioactivity data for professional chemists, chemistry students, data scientists, scientific and web developers.

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

NASA Technical Reports Server (NTRS)

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

1990-01-01

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

Using a formal requirements management tool for system engineering: first results at ESO

NASA Astrophysics Data System (ADS)

Zamparelli, Michele

2006-06-01

The attention to proper requirement analysis and maintenance is growing in modern astronomical undertakings. The increasing degree of complexity that current and future generations of projects have reached requires substantial system engineering efforts and the usage of all available technology to keep project development under control. One such technology is a tool which helps managing relationships between deliverables at various development stages, and across functional subsystems and disciplines as different as software, mechanics, optics and electronics. The immediate benefits are traceability and the possibility to do impact analysis. An industrially proven tool for requirements management is presented together with the first results across some projects at ESO and a cost/benefit analysis of its usage. Experience gathered so far shows that the extensibility and configurability of the tool from one hand, and integration with common documentation formats and standards on the other, make it appear as a promising solution for even small scale system development.

Modular workcells: modern methods for laboratory automation.

PubMed

Felder, R A

1998-12-01

Laboratory automation is beginning to become an indispensable survival tool for laboratories facing difficult market competition. However, estimates suggest that only 8% of laboratories will be able to afford total laboratory automation systems. Therefore, automation vendors have developed alternative hardware configurations called 'modular automation', to fit the smaller laboratory. Modular automation consists of consolidated analyzers, integrated analyzers, modular workcells, and pre- and post-analytical automation. These terms will be defined in this paper. Using a modular automation model, the automated core laboratory will become a site where laboratory data is evaluated by trained professionals to provide diagnostic information to practising physicians. Modem software information management and process control tools will complement modular hardware. Proper standardization that will allow vendor-independent modular configurations will assure success of this revolutionary new technology.

Some Observations on the Current Status of Performing Finite Element Analyses

NASA Technical Reports Server (NTRS)

Raju, Ivatury S.; Knight, Norman F., Jr; Shivakumar, Kunigal N.

2015-01-01

Aerospace structures are complex high-performance structures. Advances in reliable and efficient computing and modeling tools are enabling analysts to consider complex configurations, build complex finite element models, and perform analysis rapidly. Many of the early career engineers of today are very proficient in the usage of modern computers, computing engines, complex software systems, and visualization tools. These young engineers are becoming increasingly efficient in building complex 3D models of complicated aerospace components. However, the current trends demonstrate blind acceptance of the results of the finite element analysis results. This paper is aimed at raising an awareness of this situation. Examples of the common encounters are presented. To overcome the current trends, some guidelines and suggestions for analysts, senior engineers, and educators are offered.

Applied mediation analyses: a review and tutorial.

PubMed

Lange, Theis; Hansen, Kim Wadt; Sørensen, Rikke; Galatius, Søren

2017-01-01

In recent years, mediation analysis has emerged as a powerful tool to disentangle causal pathways from an exposure/treatment to clinically relevant outcomes. Mediation analysis has been applied in scientific fields as diverse as labour market relations and randomized clinical trials of heart disease treatments. In parallel to these applications, the underlying mathematical theory and computer tools have been refined. This combined review and tutorial will introduce the reader to modern mediation analysis including: the mathematical framework; required assumptions; and software implementation in the R package medflex. All results are illustrated using a recent study on the causal pathways stemming from the early invasive treatment of acute coronary syndrome, for which the rich Danish population registers allow us to follow patients' medication use and more after being discharged from hospital.

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.

What precision-protein-tuning and nano-resolved single molecule sciences can do for each other.

PubMed

Milles, Sigrid; Lemke, Edward A

2013-01-01

While innovations in modern microscopy, spectroscopy, and nanoscopy techniques have made single molecule observation a standard in many laboratories, the actual design of meaningful fluorescence reporter systems now hinders major scientific breakthroughs. Even though the field of chemical biology is supercharging the fluorescence toolbox, surprisingly few strategies exist that make the transition from model systems to biologically relevant applications. At the same time, the number of microscopy techniques is growing dramatically. We explain our view on how the impact of modern technologies is influenced not only by further hard- and software developments, but also by the availability and suitability of protein-engineering tools. We identify how the largely independent research fields of chemical biology and fluorescence nanoscopy can influence each other to synergistically drive future technology that can visualize the localization, structure, and dynamics of molecular function without constraints. Copyright © 2013 WILEY Periodicals, Inc.

Reproducing the internal and external anatomy of fossil bones: Two new automatic digital tools.

PubMed

Profico, Antonio; Schlager, Stefan; Valoriani, Veronica; Buzi, Costantino; Melchionna, Marina; Veneziano, Alessio; Raia, Pasquale; Moggi-Cecchi, Jacopo; Manzi, Giorgio

2018-04-21

We present two new automatic tools, developed under the R environment, to reproduce the internal and external structures of bony elements. The first method, Computer-Aided Laser Scanner Emulator (CA-LSE), provides the reconstruction of the external portions of a 3D mesh by simulating the action of a laser scanner. The second method, Automatic Segmentation Tool for 3D objects (AST-3D), performs the digital reconstruction of anatomical cavities. We present the application of CA-LSE and AST-3D methods to different anatomical remains, highly variable in terms of shape, size and structure: a modern human skull, a malleus bone, and a Neanderthal deciduous tooth. Both methods are developed in the R environment and embedded in the packages "Arothron" and "Morpho," where both the codes and the data are fully available. The application of CA-LSE and AST-3D allows the isolation and manipulation of the internal and external components of the 3D virtual representation of complex bony elements. In particular, we present the output of the four case studies: a complete modern human endocast and the right maxillary sinus, the dental pulp of the Neanderthal tooth and the inner network of blood vessels of the malleus. Both methods demonstrated to be much faster, cheaper, and more accurate than other conventional approaches. The tools we presented are available as add-ons in existing software within the R platform. Because of ease of application, and unrestrained availability of the methods proposed, these tools can be widely used by paleoanthropologists, paleontologists and anatomists. © 2018 Wiley Periodicals, Inc.

Computer Simulation Performed for Columbia Project Cooling System

NASA Technical Reports Server (NTRS)

Ahmad, Jasim

2005-01-01

This demo shows a high-fidelity simulation of the air flow in the main computer room housing the Columbia (10,024 intel titanium processors) system. The simulation asseses the performance of the cooling system and identified deficiencies, and recommended modifications to eliminate them. It used two in house software packages on NAS supercomputers: Chimera Grid tools to generate a geometric model of the computer room, OVERFLOW-2 code for fluid and thermal simulation. This state-of-the-art technology can be easily extended to provide a general capability for air flow analyses on any modern computer room. Columbia_CFD_black.tiff

The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications

PubMed Central

Bare, J Christopher; Shannon, Paul T; Schmid, Amy K; Baliga, Nitin S

2007-01-01

Background Information resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between naming systems, or perform ongoing maintenance of local copies of public databases. Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data. Results The Firegoose, an extension to the Mozilla Firefox web browser, enables data transfer between web sites and desktop tools. As a component of the Gaggle integration framework, Firegoose can also exchange data with Cytoscape, the R statistical package, Multiexperiment Viewer (MeV), and several other popular desktop software tools. Firegoose adds the capability to easily use local data to query KEGG, EMBL STRING, DAVID, and other widely-used bioinformatics web sites. Query results from these web sites can be transferred to desktop tools for further analysis with a few clicks. Firegoose acquires data from the web by screen scraping, microformats, embedded XML, or web services. We define a microformat, which allows structured information compatible with the Gaggle to be embedded in HTML documents. We demonstrate the capabilities of this software by performing an analysis of the genes activated in the microbe Halobacterium salinarum NRC-1 in response to anaerobic environments. Starting with microarray data, we explore functions of differentially expressed genes by combining data from several public web resources and construct an integrated view of the cellular processes involved. Conclusion The Firegoose incorporates Mozilla Firefox into the Gaggle environment and enables interactive sharing of data between diverse web resources and desktop software tools without maintaining local copies. Additional web sites can be incorporated easily into the framework using the scripting platform of the Firefox browser. Performing data integration in the browser allows the excellent search and navigation capabilities of the browser to be used in combination with powerful desktop tools. PMID:18021453

The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications.

PubMed

Bare, J Christopher; Shannon, Paul T; Schmid, Amy K; Baliga, Nitin S

2007-11-19

Information resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between naming systems, or perform ongoing maintenance of local copies of public databases. Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data. The Firegoose, an extension to the Mozilla Firefox web browser, enables data transfer between web sites and desktop tools. As a component of the Gaggle integration framework, Firegoose can also exchange data with Cytoscape, the R statistical package, Multiexperiment Viewer (MeV), and several other popular desktop software tools. Firegoose adds the capability to easily use local data to query KEGG, EMBL STRING, DAVID, and other widely-used bioinformatics web sites. Query results from these web sites can be transferred to desktop tools for further analysis with a few clicks. Firegoose acquires data from the web by screen scraping, microformats, embedded XML, or web services. We define a microformat, which allows structured information compatible with the Gaggle to be embedded in HTML documents. We demonstrate the capabilities of this software by performing an analysis of the genes activated in the microbe Halobacterium salinarum NRC-1 in response to anaerobic environments. Starting with microarray data, we explore functions of differentially expressed genes by combining data from several public web resources and construct an integrated view of the cellular processes involved. The Firegoose incorporates Mozilla Firefox into the Gaggle environment and enables interactive sharing of data between diverse web resources and desktop software tools without maintaining local copies. Additional web sites can be incorporated easily into the framework using the scripting platform of the Firefox browser. Performing data integration in the browser allows the excellent search and navigation capabilities of the browser to be used in combination with powerful desktop tools.

Application of Neutron Tomography in Culture Heritage research.

PubMed

Mongy, T

2014-02-01

Neutron Tomography (NT) investigation of Culture Heritages (CH) is an efficient tool for understanding the culture of ancient civilizations. Neutron imaging (NI) is a-state-of-the-art non-destructive tool in the area of CH and plays an important role in the modern archeology. The NI technology can be widely utilized in the field of elemental analysis. At Egypt Second Research Reactor (ETRR-2), a collimated Neutron Radiography (NR) beam is employed for neutron imaging purposes. A digital CCD camera is utilized for recording the beam attenuation in the sample. This helps for the detection of hidden objects and characterization of material properties. Research activity can be extended to use computer software for quantitative neutron measurement. Development of image processing algorithms can be used to obtain high quality images. In this work, full description of ETRR-2 was introduced with up to date neutron imaging system as well. Tomographic investigation of a clay forged artifact represents CH object was studied by neutron imaging methods in order to obtain some hidden information and highlight some attractive quantitative measurements. Computer software was used for imaging processing and enhancement. Also the Astra Image 3.0 Pro software was employed for high precise measurements and imaging enhancement using advanced algorithms. This work increased the effective utilization of the ETRR-2 Neutron Radiography/Tomography (NR/T) technique in Culture Heritages activities. © 2013 Elsevier Ltd. All rights reserved.

Bim Automation: Advanced Modeling Generative Process for Complex Structures

NASA Astrophysics Data System (ADS)

Banfi, F.; Fai, S.; Brumana, R.

2017-08-01

The new paradigm of the complexity of modern and historic structures, which are characterised by complex forms, morphological and typological variables, is one of the greatest challenges for building information modelling (BIM). Generation of complex parametric models needs new scientific knowledge concerning new digital technologies. These elements are helpful to store a vast quantity of information during the life cycle of buildings (LCB). The latest developments of parametric applications do not provide advanced tools, resulting in time-consuming work for the generation of models. This paper presents a method capable of processing and creating complex parametric Building Information Models (BIM) with Non-Uniform to NURBS) with multiple levels of details (Mixed and ReverseLoD) based on accurate 3D photogrammetric and laser scanning surveys. Complex 3D elements are converted into parametric BIM software and finite element applications (BIM to FEA) using specific exchange formats and new modelling tools. The proposed approach has been applied to different case studies: the BIM of modern structure for the courtyard of West Block on Parliament Hill in Ottawa (Ontario) and the BIM of Masegra Castel in Sondrio (Italy), encouraging the dissemination and interaction of scientific results without losing information during the generative process.

WASP (Write a Scientific Paper) using Excel - 1: Data entry and validation.

PubMed

Grech, Victor

2018-02-01

Data collection for the purposes of analysis, after the planning and execution of a research study, commences with data input and validation. The process of data entry and analysis may appear daunting to the uninitiated, but as pointed out in the 1970s in a series of papers by British Medical Journal Deputy Editor TDV Swinscow, modern hardware and software (he was then referring to the availability of hand calculators) permits the performance of statistical testing outside a computer laboratory. In this day and age, modern software, such as the ubiquitous and almost universally familiar Microsoft Excel™ greatly facilitates this process. This first paper comprises the first of a collection of papers which will emulate Swinscow's series, in his own words, "addressed to readers who want to start at the beginning, not to those who are already skilled statisticians." These papers will have less focus on the actual arithmetic, and more emphasis on how to actually implement simple statistics, step by step, using Excel, thereby constituting the equivalent of Swinscow's papers in the personal computer age. Data entry can be facilitated by several underutilised features in Excel. This paper will explain Excel's little-known form function, data validation implementation at input stage, simple coding tips and data cleaning tools. Copyright © 2018 Elsevier B.V. All rights reserved.

The virtual digital nuclear power plant: A modern tool for supporting the lifecycle of VVER-based nuclear power units

NASA Astrophysics Data System (ADS)

Arkadov, G. V.; Zhukavin, A. P.; Kroshilin, A. E.; Parshikov, I. A.; Solov'ev, S. L.; Shishov, A. V.

2014-10-01

The article describes the "Virtual Digital VVER-Based Nuclear Power Plant" computerized system comprising a totality of verified initial data (sets of input data for a model intended for describing the behavior of nuclear power plant (NPP) systems in design and emergency modes of their operation) and a unified system of new-generation computation codes intended for carrying out coordinated computation of the variety of physical processes in the reactor core and NPP equipment. Experiments with the demonstration version of the "Virtual Digital VVER-Based NPP" computerized system has shown that it is in principle possible to set up a unified system of computation codes in a common software environment for carrying out interconnected calculations of various physical phenomena at NPPs constructed according to the standard AES-2006 project. With the full-scale version of the "Virtual Digital VVER-Based NPP" computerized system put in operation, the concerned engineering, design, construction, and operating organizations will have access to all necessary information relating to the NPP power unit project throughout its entire lifecycle. The domestically developed commercial-grade software product set to operate as an independently operating application to the project will bring about additional competitive advantages in the modern market of nuclear power technologies.

PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories.

PubMed

Hanson-Smith, Victor; Johnson, Alexander

2016-07-01

The method of phylogenetic ancestral sequence reconstruction is a powerful approach for studying evolutionary relationships among protein sequence, structure, and function. In particular, this approach allows investigators to (1) reconstruct and "resurrect" (that is, synthesize in vivo or in vitro) extinct proteins to study how they differ from modern proteins, (2) identify key amino acid changes that, over evolutionary timescales, have altered the function of the protein, and (3) order historical events in the evolution of protein function. Widespread use of this approach has been slow among molecular biologists, in part because the methods require significant computational expertise. Here we present PhyloBot, a web-based software tool that makes ancestral sequence reconstruction easy. Designed for non-experts, it integrates all the necessary software into a single user interface. Additionally, PhyloBot provides interactive tools to explore evolutionary trajectories between ancestors, enabling the rapid generation of hypotheses that can be tested using genetic or biochemical approaches. Early versions of this software were used in previous studies to discover genetic mechanisms underlying the functions of diverse protein families, including V-ATPase ion pumps, DNA-binding transcription regulators, and serine/threonine protein kinases. PhyloBot runs in a web browser, and is available at the following URL: http://www.phylobot.com. The software is implemented in Python using the Django web framework, and runs on elastic cloud computing resources from Amazon Web Services. Users can create and submit jobs on our free server (at the URL listed above), or use our open-source code to launch their own PhyloBot server.

PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories

PubMed Central

Hanson-Smith, Victor; Johnson, Alexander

2016-01-01

The method of phylogenetic ancestral sequence reconstruction is a powerful approach for studying evolutionary relationships among protein sequence, structure, and function. In particular, this approach allows investigators to (1) reconstruct and “resurrect” (that is, synthesize in vivo or in vitro) extinct proteins to study how they differ from modern proteins, (2) identify key amino acid changes that, over evolutionary timescales, have altered the function of the protein, and (3) order historical events in the evolution of protein function. Widespread use of this approach has been slow among molecular biologists, in part because the methods require significant computational expertise. Here we present PhyloBot, a web-based software tool that makes ancestral sequence reconstruction easy. Designed for non-experts, it integrates all the necessary software into a single user interface. Additionally, PhyloBot provides interactive tools to explore evolutionary trajectories between ancestors, enabling the rapid generation of hypotheses that can be tested using genetic or biochemical approaches. Early versions of this software were used in previous studies to discover genetic mechanisms underlying the functions of diverse protein families, including V-ATPase ion pumps, DNA-binding transcription regulators, and serine/threonine protein kinases. PhyloBot runs in a web browser, and is available at the following URL: http://www.phylobot.com. The software is implemented in Python using the Django web framework, and runs on elastic cloud computing resources from Amazon Web Services. Users can create and submit jobs on our free server (at the URL listed above), or use our open-source code to launch their own PhyloBot server. PMID:27472806

A Legal Perspective on Business: Modeling the Impact of Law

NASA Astrophysics Data System (ADS)

Ghanavati, Sepideh; Siena, Alberto; Perini, Anna; Amyot, Daniel; Peyton, Liam; Susi, Angelo

Modern goal-oriented requirements engineering frameworks use modeling as a means of better understanding a domain, leading to an overall improvement in the quality of the requirements. Regulations and laws impose additional context and constraints on software goals and can limit the satisfaction of stakeholder needs. Organizations and software developers need modeling tools that can properly address the potential deep impact legal issues can have on the effectiveness of business strategies. In this paper, we perform a preliminary study into the development of a modeling framework able to support the analysis of legal prescriptions alongside business strategies. We demonstrate, via an example drawn from a case study of the Health Insurance Portability and Accountability Act (HIPAA), how models of this law can be built with the GRL modeling language and how they can be evaluated as part of the business goal models.

Mercury BLASTP: Accelerating Protein Sequence Alignment

PubMed Central

Jacob, Arpith; Lancaster, Joseph; Buhler, Jeremy; Harris, Brandon; Chamberlain, Roger D.

2008-01-01

Large-scale protein sequence comparison is an important but compute-intensive task in molecular biology. BLASTP is the most popular tool for comparative analysis of protein sequences. In recent years, an exponential increase in the size of protein sequence databases has required either exponentially more running time or a cluster of machines to keep pace. To address this problem, we have designed and built a high-performance FPGA-accelerated version of BLASTP, Mercury BLASTP. In this paper, we describe the architecture of the portions of the application that are accelerated in the FPGA, and we also describe the integration of these FPGA-accelerated portions with the existing BLASTP software. We have implemented Mercury BLASTP on a commodity workstation with two Xilinx Virtex-II 6000 FPGAs. We show that the new design runs 11-15 times faster than software BLASTP on a modern CPU while delivering close to 99% identical results. PMID:19492068

Neandertals made the first specialized bone tools in Europe

PubMed Central

Soressi, Marie; McPherron, Shannon P.; Lenoir, Michel; Dogandžić, Tamara; Goldberg, Paul; Jacobs, Zenobia; Maigrot, Yolaine; Martisius, Naomi L.; Miller, Christopher E.; Rendu, William; Richards, Michael; Skinner, Matthew M.; Steele, Teresa E.; Talamo, Sahra; Texier, Jean-Pierre

2013-01-01

Modern humans replaced Neandertals ∼40,000 y ago. Close to the time of replacement, Neandertals show behaviors similar to those of the modern humans arriving into Europe, including the use of specialized bone tools, body ornaments, and small blades. It is highly debated whether these modern behaviors developed before or as a result of contact with modern humans. Here we report the identification of a type of specialized bone tool, lissoir, previously only associated with modern humans. The microwear preserved on one of these lissoir is consistent with the use of lissoir in modern times to obtain supple, lustrous, and more impermeable hides. These tools are from a Neandertal context proceeding the replacement period and are the oldest specialized bone tools in Europe. As such, they are either a demonstration of independent invention by Neandertals or an indication that modern humans started influencing European Neandertals much earlier than previously believed. Because these finds clearly predate the oldest known age for the use of similar objects in Europe by anatomically modern humans, they could also be evidence for cultural diffusion from Neandertals to modern humans. PMID:23940333

Modernized Approach for Generating Reproducible Heterogeneity Using Transmitted-Light for Flow Visualization Experiments

NASA Astrophysics Data System (ADS)

Jones, A. A.; Holt, R. M.

2017-12-01

Image capturing in flow experiments has been used for fluid mechanics research since the early 1970s. Interactions of fluid flow between the vadose zone and permanent water table are of great interest because this zone is responsible for all recharge waters, pollutant transport and irrigation efficiency for agriculture. Griffith, et al. (2011) developed an approach where constructed reproducible "geologically realistic" sand configurations are deposited in sandfilled experimental chambers for light-transmitted flow visualization experiments. This method creates reproducible, reverse graded, layered (stratified) thin-slab sand chambers for point source experiments visualizing multiphase flow through porous media. Reverse-graded stratification of sand chambers mimic many naturally occurring sedimentary deposits. Sandfilled chambers use light as nonintrusive tools for measuring water saturation in two-dimensions (2-D). Homogeneous and heterogeneous sand configurations can be produced to visualize the complex physics of the unsaturated zone. The experimental procedure developed by Griffith, et al. (2011) was designed using now outdated and obsolete equipment. We have modernized this approach with new Parker Deadel linear actuator and programed projects/code for multiple configurations. We have also updated the Roper CCD software and image processing software with the latest in industry standards. Modernization of transmitted-light source, robotic equipment, redesigned experimental chambers, and newly developed analytical procedures have greatly reduced time and cost per experiment. We have verified the ability of the new equipment to generate reproducible heterogeneous sand-filled chambers and demonstrated the functionality of the new equipment and procedures by reproducing several gravity-driven fingering experiments conducted by Griffith (2008).

CSciBox: An Intelligent Assistant for Dating Ice and Sediment Cores

NASA Astrophysics Data System (ADS)

Finlinson, K.; Bradley, E.; White, J. W. C.; Anderson, K. A.; Marchitto, T. M., Jr.; de Vesine, L. R.; Jones, T. R.; Lindsay, C. M.; Israelsen, B.

2015-12-01

CSciBox is an integrated software system for the construction and evaluation of age models of paleo-environmental archives. It incorporates a number of data-processing and visualization facilities, ranging from simple interpolation to reservoir-age correction and 14C calibration via the Calib algorithm, as well as a number of firn and ice-flow models. It employs modern database technology to store paleoclimate proxy data and analysis results in an easily accessible and searchable form, and offers the user access to those data and computational elements via a modern graphical user interface (GUI). In the case of truly large data or computations, CSciBox is parallelizable across modern multi-core processors, or clusters, or even the cloud. The code is open source and freely available on github, as are one-click installers for various versions of Windows and Mac OSX. The system's architecture allows users to incorporate their own software in the form of computational components that can be built smoothly into CSciBox workflows, taking advantage of CSciBox's GUI, data importing facilities, and plotting capabilities. To date, BACON and StratiCounter have been integrated into CSciBox as embedded components. The user can manipulate and compose all of these tools and facilities as she sees fit. Alternatively, she can employ CSciBox's automated reasoning engine, which uses artificial intelligence techniques to explore the gamut of age models and cross-dating scenarios automatically. The automated reasoning engine captures the knowledge of expert geoscientists, and can output a description of its reasoning.

Research on ARM Numerical Control System

NASA Astrophysics Data System (ADS)

Wei, Xu; JiHong, Chen

Computerized Numerical Control (CNC) machine tools is the foundation of modern manufacturing systems, whose advanced digital technology is the key to solve the problem of sustainable development of machine tool manufacturing industry. The paper is to design CNC system embedded on ARM and indicates the hardware design and the software systems supported. On the hardware side: the driving chip of the motor control unit, as the core of components, is MCX314AL of DSP motion control which is developed by NOVA Electronics Co., Ltd. of Japan. It make convenient to control machine because of its excellent performance, simple interface, easy programming. On the Software side, the uC/OS-2 is selected as the embedded operating system of the open source, which makes a detailed breakdown of the modules of the CNC system. Those priorities are designed according to their actual requirements. The ways of communication between the module and the interrupt response are so different that it guarantees real-time property and reliability of the numerical control system. Therefore, it not only meets the requirements of the current social precision machining, but has good man-machine interface and network support to facilitate a variety of craftsmen use.

DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs.

PubMed

Chodkiewicz, Michał L; Migacz, Szymon; Rudnicki, Witold; Makal, Anna; Kalinowski, Jarosław A; Moriarty, Nigel W; Grosse-Kunstleve, Ralf W; Afonine, Pavel V; Adams, Paul D; Dominiak, Paulina Maria

2018-02-01

It has been recently established that the accuracy of structural parameters from X-ray refinement of crystal structures can be improved by using a bank of aspherical pseudoatoms instead of the classical spherical model of atomic form factors. This comes, however, at the cost of increased complexity of the underlying calculations. In order to facilitate the adoption of this more advanced electron density model by the broader community of crystallographers, a new software implementation called DiSCaMB , 'densities in structural chemistry and molecular biology', has been developed. It addresses the challenge of providing for high performance on modern computing architectures. With parallelization options for both multi-core processors and graphics processing units (using CUDA), the library features calculation of X-ray scattering factors and their derivatives with respect to structural parameters, gives access to intermediate steps of the scattering factor calculations (thus allowing for experimentation with modifications of the underlying electron density model), and provides tools for basic structural crystallographic operations. Permissively (MIT) licensed, DiSCaMB is an open-source C++ library that can be embedded in both academic and commercial tools for X-ray structure refinement.

Novel Method of Storing and Reconstructing Events at Fermilab E-906/SeaQuest Using a MySQL Database

NASA Astrophysics Data System (ADS)

Hague, Tyler

2010-11-01

Fermilab E-906/SeaQuest is a fixed target experiment at Fermi National Accelerator Laboratory. We are investigating the antiquark asymmetry in the nucleon sea. By examining the ratio of the Drell- Yan cross sections of proton-proton and proton-deuterium collisions we can determine the asymmetry ratio. An essential feature in the development of the analysis software is to update the event reconstruction to modern software tools. We are doing this in a unique way by doing a majority of the calculations within an SQL database. Using a MySQL database allows us to take advantage of off-the-shelf software without sacrificing ROOT compatibility and avoid network bottlenecks with server-side data selection. Using our raw data we create stubs, or partial tracks, at each station which are pieced together to create full tracks. Our reconstruction process uses dynamically created SQL statements to analyze the data. These SQL statements create tables that contain the final reconstructed tracks as well as intermediate values. This poster will explain the reconstruction process and how it is being implemented.

Development of AN Open-Source Automatic Deformation Monitoring System for Geodetical and Geotechnical Measurements

NASA Astrophysics Data System (ADS)

Engel, P.; Schweimler, B.

2016-04-01

The deformation monitoring of structures and buildings is an important task field of modern engineering surveying, ensuring the standing and reliability of supervised objects over a long period. Several commercial hardware and software solutions for the realization of such monitoring measurements are available on the market. In addition to them, a research team at the Neubrandenburg University of Applied Sciences (NUAS) is actively developing a software package for monitoring purposes in geodesy and geotechnics, which is distributed under an open source licence and free of charge. The task of managing an open source project is well-known in computer science, but it is fairly new in a geodetic context. This paper contributes to that issue by detailing applications, frameworks, and interfaces for the design and implementation of open hardware and software solutions for sensor control, sensor networks, and data management in automatic deformation monitoring. It will be discussed how the development effort of networked applications can be reduced by using free programming tools, cloud computing technologies, and rapid prototyping methods.

The Role of Free/Libre and Open Source Software in Learning Health Systems.

PubMed

Paton, C; Karopka, T

2017-08-01

Objective: To give an overview of the role of Free/Libre and Open Source Software (FLOSS) in the context of secondary use of patient data to enable Learning Health Systems (LHSs). Methods: We conducted an environmental scan of the academic and grey literature utilising the MedFLOSS database of open source systems in healthcare to inform a discussion of the role of open source in developing LHSs that reuse patient data for research and quality improvement. Results: A wide range of FLOSS is identified that contributes to the information technology (IT) infrastructure of LHSs including operating systems, databases, frameworks, interoperability software, and mobile and web apps. The recent literature around the development and use of key clinical data management tools is also reviewed. Conclusions: FLOSS already plays a critical role in modern health IT infrastructure for the collection, storage, and analysis of patient data. The nature of FLOSS systems to be collaborative, modular, and modifiable may make open source approaches appropriate for building the digital infrastructure for a LHS. Georg Thieme Verlag KG Stuttgart.

Heterogeneous computing architecture for fast detection of SNP-SNP interactions.

PubMed

Sluga, Davor; Curk, Tomaz; Zupan, Blaz; Lotric, Uros

2014-06-25

The extent of data in a typical genome-wide association study (GWAS) poses considerable computational challenges to software tools for gene-gene interaction discovery. Exhaustive evaluation of all interactions among hundreds of thousands to millions of single nucleotide polymorphisms (SNPs) may require weeks or even months of computation. Massively parallel hardware within a modern Graphic Processing Unit (GPU) and Many Integrated Core (MIC) coprocessors can shorten the run time considerably. While the utility of GPU-based implementations in bioinformatics has been well studied, MIC architecture has been introduced only recently and may provide a number of comparative advantages that have yet to be explored and tested. We have developed a heterogeneous, GPU and Intel MIC-accelerated software module for SNP-SNP interaction discovery to replace the previously single-threaded computational core in the interactive web-based data exploration program SNPsyn. We report on differences between these two modern massively parallel architectures and their software environments. Their utility resulted in an order of magnitude shorter execution times when compared to the single-threaded CPU implementation. GPU implementation on a single Nvidia Tesla K20 runs twice as fast as that for the MIC architecture-based Xeon Phi P5110 coprocessor, but also requires considerably more programming effort. General purpose GPUs are a mature platform with large amounts of computing power capable of tackling inherently parallel problems, but can prove demanding for the programmer. On the other hand the new MIC architecture, albeit lacking in performance reduces the programming effort and makes it up with a more general architecture suitable for a wider range of problems.

Heterogeneous computing architecture for fast detection of SNP-SNP interactions

PubMed Central

2014-01-01

Background The extent of data in a typical genome-wide association study (GWAS) poses considerable computational challenges to software tools for gene-gene interaction discovery. Exhaustive evaluation of all interactions among hundreds of thousands to millions of single nucleotide polymorphisms (SNPs) may require weeks or even months of computation. Massively parallel hardware within a modern Graphic Processing Unit (GPU) and Many Integrated Core (MIC) coprocessors can shorten the run time considerably. While the utility of GPU-based implementations in bioinformatics has been well studied, MIC architecture has been introduced only recently and may provide a number of comparative advantages that have yet to be explored and tested. Results We have developed a heterogeneous, GPU and Intel MIC-accelerated software module for SNP-SNP interaction discovery to replace the previously single-threaded computational core in the interactive web-based data exploration program SNPsyn. We report on differences between these two modern massively parallel architectures and their software environments. Their utility resulted in an order of magnitude shorter execution times when compared to the single-threaded CPU implementation. GPU implementation on a single Nvidia Tesla K20 runs twice as fast as that for the MIC architecture-based Xeon Phi P5110 coprocessor, but also requires considerably more programming effort. Conclusions General purpose GPUs are a mature platform with large amounts of computing power capable of tackling inherently parallel problems, but can prove demanding for the programmer. On the other hand the new MIC architecture, albeit lacking in performance reduces the programming effort and makes it up with a more general architecture suitable for a wider range of problems. PMID:24964802

RELAP-7 Level 2 Milestone Report: Demonstration of a Steady State Single Phase PWR Simulation with RELAP-7

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

David Andrs; Ray Berry; Derek Gaston

The document contains the simulation results of a steady state model PWR problem with the RELAP-7 code. The RELAP-7 code is the next generation nuclear reactor system safety analysis code being developed at Idaho National Laboratory (INL). The code is based on INL's modern scientific software development framework - MOOSE (Multi-Physics Object-Oriented Simulation Environment). This report summarizes the initial results of simulating a model steady-state single phase PWR problem using the current version of the RELAP-7 code. The major purpose of this demonstration simulation is to show that RELAP-7 code can be rapidly developed to simulate single-phase reactor problems. RELAP-7more » is a new project started on October 1st, 2011. It will become the main reactor systems simulation toolkit for RISMC (Risk Informed Safety Margin Characterization) and the next generation tool in the RELAP reactor safety/systems analysis application series (the replacement for RELAP5). The key to the success of RELAP-7 is the simultaneous advancement of physical models, numerical methods, and software design while maintaining a solid user perspective. Physical models include both PDEs (Partial Differential Equations) and ODEs (Ordinary Differential Equations) and experimental based closure models. RELAP-7 will eventually utilize well posed governing equations for multiphase flow, which can be strictly verified. Closure models used in RELAP5 and newly developed models will be reviewed and selected to reflect the progress made during the past three decades. RELAP-7 uses modern numerical methods, which allow implicit time integration, higher order schemes in both time and space, and strongly coupled multi-physics simulations. RELAP-7 is written with object oriented programming language C++. Its development follows modern software design paradigms. The code is easy to read, develop, maintain, and couple with other codes. Most importantly, the modern software design allows the RELAP-7 code to evolve with time. RELAP-7 is a MOOSE-based application. MOOSE (Multiphysics Object-Oriented Simulation Environment) is a framework for solving computational engineering problems in a well-planned, managed, and coordinated way. By leveraging millions of lines of open source software packages, such as PETSC (a nonlinear solver developed at Argonne National Laboratory) and LibMesh (a Finite Element Analysis package developed at University of Texas), MOOSE significantly reduces the expense and time required to develop new applications. Numerical integration methods and mesh management for parallel computation are provided by MOOSE. Therefore RELAP-7 code developers only need to focus on physics and user experiences. By using the MOOSE development environment, RELAP-7 code is developed by following the same modern software design paradigms used for other MOOSE development efforts. There are currently over 20 different MOOSE based applications ranging from 3-D transient neutron transport, detailed 3-D transient fuel performance analysis, to long-term material aging. Multi-physics and multiple dimensional analyses capabilities can be obtained by coupling RELAP-7 and other MOOSE based applications and by leveraging with capabilities developed by other DOE programs. This allows restricting the focus of RELAP-7 to systems analysis-type simulations and gives priority to retain and significantly extend RELAP5's capabilities.« less

New media applications and their potential for the advancement of public perceptions of archaeoastronomy and for the testing of archaeoastronomical hypotheses.

NASA Astrophysics Data System (ADS)

MacDonald, J.

This paper looks at the use of astronomical programmes and the development of new media modeling techniques as a means to better understand archaeoastronomy. The paper also suggests that these new methods and technologies are a means of furthering the public perceptions of archaeoastronomy and the important role that 'astronomy' played in the history and development of human culture. This discussion is rooted in a computer simulation of Stonehenge and its land and skyscape. The integration of the astronomy software allows viewing horizon astronomical lignments in relation to digitally recreated Neolithic/Early Bronze Age (EBA) monumental architecture. This work shows how modern virtual modelling techniques can be a tool for testing archaeoastronomical hypotheses, as well as a demonstrative tool for teaching and promoting archaeoastronomy in mainstream media.

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

PubMed Central

2011-01-01

Background The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. Results In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. Conclusions With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined. PMID:22172142

LeaRN: A Collaborative Learning-Research Network for a WLCG Tier-3 Centre

NASA Astrophysics Data System (ADS)

Pérez Calle, Elio

2011-12-01

The Department of Modern Physics of the University of Science and Technology of China is hosting a Tier-3 centre for the ATLAS experiment. A interdisciplinary team of researchers, engineers and students are devoted to the task of receiving, storing and analysing the scientific data produced by the LHC. In order to achieve the highest performance and to develop a knowledge base shared by all members of the team, the research activities and their coordination are being supported by an array of computing systems. These systems have been designed to foster communication, collaboration and coordination among the members of the team, both face-to-face and remotely, and both in synchronous and asynchronous ways. The result is a collaborative learning-research network whose main objectives are awareness (to get shared knowledge about other's activities and therefore obtain synergies), articulation (to allow a project to be divided, work units to be assigned and then reintegrated) and adaptation (to adapt information technologies to the needs of the group). The main technologies involved are Communication Tools such as web publishing, revision control and wikis, Conferencing Tools such as forums, instant messaging and video conferencing and Coordination Tools, such as time management, project management and social networks. The software toolkit has been deployed by the members of the team and it has been based on free and open source software.

The NOD3 software package: A graphical user interface-supported reduction package for single-dish radio continuum and polarisation observations

NASA Astrophysics Data System (ADS)

Müller, Peter; Krause, Marita; Beck, Rainer; Schmidt, Philip

2017-10-01

Context. The venerable NOD2 data reduction software package for single-dish radio continuum observations, which was developed for use at the 100-m Effelsberg radio telescope, has been successfully applied over many decades. Modern computing facilities, however, call for a new design. Aims: We aim to develop an interactive software tool with a graphical user interface for the reduction of single-dish radio continuum maps. We make a special effort to reduce the distortions along the scanning direction (scanning effects) by combining maps scanned in orthogonal directions or dual- or multiple-horn observations that need to be processed in a restoration procedure. The package should also process polarisation data and offer the possibility to include special tasks written by the individual user. Methods: Based on the ideas of the NOD2 package we developed NOD3, which includes all necessary tasks from the raw maps to the final maps in total intensity and linear polarisation. Furthermore, plot routines and several methods for map analysis are available. The NOD3 package is written in Python, which allows the extension of the package via additional tasks. The required data format for the input maps is FITS. Results: The NOD3 package is a sophisticated tool to process and analyse maps from single-dish observations that are affected by scanning effects from clouds, receiver instabilities, or radio-frequency interference. The "basket-weaving" tool combines orthogonally scanned maps into a final map that is almost free of scanning effects. The new restoration tool for dual-beam observations reduces the noise by a factor of about two compared to the NOD2 version. Combining single-dish with interferometer data in the map plane ensures the full recovery of the total flux density. Conclusions: This software package is available under the open source license GPL for free use at other single-dish radio telescopes of the astronomical community. The NOD3 package is designed to be extendable to multi-channel data represented by data cubes in Stokes I, Q, and U.

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.

A new spatial multi-criteria decision support tool for site selection for implementation of managed aquifer recharge.

PubMed

Rahman, M Azizur; Rusteberg, Bernd; Gogu, R C; Lobo Ferreira, J P; Sauter, Martin

2012-05-30

This study reports the development of a new spatial multi-criteria decision analysis (SMCDA) software tool for selecting suitable sites for Managed Aquifer Recharge (MAR) systems. The new SMCDA software tool functions based on the combination of existing multi-criteria evaluation methods with modern decision analysis techniques. More specifically, non-compensatory screening, criteria standardization and weighting, and Analytical Hierarchy Process (AHP) have been combined with Weighted Linear Combination (WLC) and Ordered Weighted Averaging (OWA). This SMCDA tool may be implemented with a wide range of decision maker's preferences. The tool's user-friendly interface helps guide the decision maker through the sequential steps for site selection, those steps namely being constraint mapping, criteria hierarchy, criteria standardization and weighting, and criteria overlay. The tool offers some predetermined default criteria and standard methods to increase the trade-off between ease-of-use and efficiency. Integrated into ArcGIS, the tool has the advantage of using GIS tools for spatial analysis, and herein data may be processed and displayed. The tool is non-site specific, adaptive, and comprehensive, and may be applied to any type of site-selection problem. For demonstrating the robustness of the new tool, a case study was planned and executed at Algarve Region, Portugal. The efficiency of the SMCDA tool in the decision making process for selecting suitable sites for MAR was also demonstrated. Specific aspects of the tool such as built-in default criteria, explicit decision steps, and flexibility in choosing different options were key features, which benefited the study. The new SMCDA tool can be augmented by groundwater flow and transport modeling so as to achieve a more comprehensive approach to the selection process for the best locations of the MAR infiltration basins, as well as the locations of recovery wells and areas of groundwater protection. The new spatial multicriteria analysis tool has already been implemented within the GIS based Gabardine decision support system as an innovative MAR planning tool. Copyright © 2012 Elsevier Ltd. All rights reserved.

Putting Safety in the Software

NASA Technical Reports Server (NTRS)

Wetherholt, Martha S.; Berens, Kalynnda M.; Hardy, Sandra (Technical Monitor)

2001-01-01

Software is a vital component of nearly every piece of modern technology. It is not a 'sub-system', able to be separated out from the system as a whole, but a 'co-system' that controls, manipulates, or interacts with the hardware and with the end user. Software has its fingers into all the pieces of the pie. If that 'pie', the system, can lead to injury, death, loss of major equipment, or impact your business bottom line, then software safety becomes vitally important. Learning to think about software from a safety perspective is the focus of this paper. We want you to think of software as part of the safety critical system, a major part. This requires 'system thinking' - being able to grasp the whole picture. Software's contribution to modern technology is both good and potentially bad. Software allows more complex and useful devices to be built. It can also contribute to plane crashes and power outages. We want you to see software in a whole new light, see it as a contributor to system hazards, and also as a possible fix or mitigation to some of those hazards.

Bioboxes: standardised containers for interchangeable bioinformatics software.

PubMed

Belmann, Peter; Dröge, Johannes; Bremges, Andreas; McHardy, Alice C; Sczyrba, Alexander; Barton, Michael D

2015-01-01

Software is now both central and essential to modern biology, yet lack of availability, difficult installations, and complex user interfaces make software hard to obtain and use. Containerisation, as exemplified by the Docker platform, has the potential to solve the problems associated with sharing software. We propose bioboxes: containers with standardised interfaces to make bioinformatics software interchangeable.

Modern Physics Simulations

NASA Astrophysics Data System (ADS)

Brandt, Douglas; Hiller, John R.; Moloney, Michael J.

1995-10-01

The Consortium for Upper Level Physics Software (CUPS) has developed a comprehensive series of Nine Book/Software packages that Wiley will publish in FY `95 and `96. CUPS is an international group of 27 physicists, all with extensive backgrounds in the research, teaching, and development of instructional software. The project is being supported by the National Science Foundation (PHY-9014548), and it has received other support from the IBM Corp., Apple Computer Corp., and George Mason University. The Simulations being developed are: Astrophysics, Classical Mechanics, Electricity & Magnetism, Modern Physics, Nuclear and Particle Physics, Quantum Mechanics, Solid State, Thermal and Statistical, and Wave and Optics.

Advanced Scientific Computing Research Exascale Requirements Review. An Office of Science review sponsored by Advanced Scientific Computing Research, September 27-29, 2016, Rockville, Maryland

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

Almgren, Ann; DeMar, Phil; Vetter, Jeffrey

The widespread use of computing in the American economy would not be possible without a thoughtful, exploratory research and development (R&D) community pushing the performance edge of operating systems, computer languages, and software libraries. These are the tools and building blocks — the hammers, chisels, bricks, and mortar — of the smartphone, the cloud, and the computing services on which we rely. Engineers and scientists need ever-more specialized computing tools to discover new material properties for manufacturing, make energy generation safer and more efficient, and provide insight into the fundamentals of the universe, for example. The research division of themore » U.S. Department of Energy’s (DOE’s) Office of Advanced Scientific Computing and Research (ASCR Research) ensures that these tools and building blocks are being developed and honed to meet the extreme needs of modern science. See also http://exascaleage.org/ascr/ for additional information.« less

Highly scalable parallel processing of extracellular recordings of Multielectrode Arrays.

PubMed

Gehring, Tiago V; Vasilaki, Eleni; Giugliano, Michele

2015-01-01

Technological advances of Multielectrode Arrays (MEAs) used for multisite, parallel electrophysiological recordings, lead to an ever increasing amount of raw data being generated. Arrays with hundreds up to a few thousands of electrodes are slowly seeing widespread use and the expectation is that more sophisticated arrays will become available in the near future. In order to process the large data volumes resulting from MEA recordings there is a pressing need for new software tools able to process many data channels in parallel. Here we present a new tool for processing MEA data recordings that makes use of new programming paradigms and recent technology developments to unleash the power of modern highly parallel hardware, such as multi-core CPUs with vector instruction sets or GPGPUs. Our tool builds on and complements existing MEA data analysis packages. It shows high scalability and can be used to speed up some performance critical pre-processing steps such as data filtering and spike detection, helping to make the analysis of larger data sets tractable.

Romanian traditional motif - element of modernity in clothing

NASA Astrophysics Data System (ADS)

Doble, L.; Stan, O.; Suteu, M. D.; Albu, A.; Bohm, G.; Tsatsarou-Michalaki, A.; Gialinou, E.

2017-10-01

In this paper are presented the phases for improving from an aesthetic point of view a clothing item, the jacket respectively, with a straight cut for women using software design patterns, computerised graphics and textile different modern technologies including: industrial embroidery, digital printing, sublimation. In the first phase a documentation was prepared in the Ethnographic Museum of Transylvania from Cluj Napoca where more traditional motifs were selected specific to Transylvania etnographic region and were reintepreted and stylized whilst preserving the symbolism and color range specified to the area. For the styling phase was used CorelDraw vector graphics program that allows changing the shape, size and color of the drawings without affecting the identity of the pattern. In the patterns design phase Gemini CAD software was used and for the modeling and model development Optitex software was used. The part for garnishing the model was performed using Embrodery machine software reproducing the stylized motif identically. In order to obtain a significantly improved aesthetic look and an added artistic value the pattern chosen for the jacket was done using a combination of modern textile technologies. This has allowed the realization of a particular texture on the surface of the designed product, demonstrating that traditional patterns can be reintepreted in modern clothing

Lunar and Planetary Science XXXV: Image Processing and Earth Observations

NASA Technical Reports Server (NTRS)

2004-01-01

The titles in this section include: 1) Expansion in Geographic Information Services for PIGWAD; 2) Modernization of the Integrated Software for Imagers and Spectrometers; 3) Science-based Region-of-Interest Image Compression; 4) Topographic Analysis with a Stereo Matching Tool Kit; 5) Central Avra Valley Storage and Recovery Project (CAVSARP) Site, Tucson, Arizona: Floodwater and Soil Moisture Investigations with Extraterrestrial Applications; 6) ASE Floodwater Classifier Development for EO-1 HYPERION Imagery; 7) Autonomous Sciencecraft Experiment (ASE) Operations on EO-1 in 2004; 8) Autonomous Vegetation Cover Scene Classification of EO-1 Hyperion Hyperspectral Data; 9) Long-Term Continental Areal Reduction Produced by Tectonic Processes.

Space station data management system - A common GSE test interface for systems testing and verification

NASA Technical Reports Server (NTRS)

Martinez, Pedro A.; Dunn, Kevin W.

1987-01-01

This paper examines the fundamental problems and goals associated with test, verification, and flight-certification of man-rated distributed data systems. First, a summary of the characteristics of modern computer systems that affect the testing process is provided. Then, verification requirements are expressed in terms of an overall test philosophy for distributed computer systems. This test philosophy stems from previous experience that was gained with centralized systems (Apollo and the Space Shuttle), and deals directly with the new problems that verification of distributed systems may present. Finally, a description of potential hardware and software tools to help solve these problems is provided.

Computing Legacy Software Behavior to Understand Functionality and Security Properties: An IBM/370 Demonstration

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

Linger, Richard C; Pleszkoch, Mark G; Prowell, Stacy J

Organizations maintaining mainframe legacy software can benefit from code modernization and incorporation of security capabilities to address the current threat environment. Oak Ridge National Laboratory is developing the Hyperion system to compute the behavior of software as a means to gain understanding of software functionality and security properties. Computation of functionality is critical to revealing security attributes, which are in fact specialized functional behaviors of software. Oak Ridge is collaborating with MITRE Corporation to conduct a demonstration project to compute behavior of legacy IBM Assembly Language code for a federal agency. The ultimate goal is to understand functionality and securitymore » vulnerabilities as a basis for code modernization. This paper reports on the first phase, to define functional semantics for IBM Assembly instructions and conduct behavior computation experiments.« less

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

Evolution of the Space Shuttle Primary Avionics Software and Avionics for Shuttle Derived Launch Vehicles

NASA Technical Reports Server (NTRS)

Ferguson, Roscoe C.

2011-01-01

As a result of recommendation from the Augustine Panel, the direction for Human Space Flight has been altered from the original plan referred to as Constellation. NASA s Human Exploration Framework Team (HEFT) proposes the use of a Shuttle Derived Heavy Lift Launch Vehicle (SDLV) and an Orion derived spacecraft (salvaged from Constellation) to support a new flexible direction for space exploration. The SDLV must be developed within an environment of a constrained budget and a preferred fast development schedule. Thus, it has been proposed to utilize existing assets from the Shuttle Program to speed development at a lower cost. These existing assets should not only include structures such as external tanks or solid rockets, but also the Flight Software which has traditionally been a "long pole" in new development efforts. The avionics and software for the Space Shuttle was primarily developed in the 70 s and considered state of the art for that time. As one may argue that the existing avionics and flight software may be too outdated to support the new SDLV effort, this is a fallacy if they can be evolved over time into a "modern avionics" platform. The technology may be outdated, but the avionics concepts and flight software algorithms are not. The reuse of existing avionics and software also allows for the reuse of development, verification, and operations facilities. The keyword is evolve in that these assets can support the fast development of such a vehicle, but then be gradually evolved over time towards more modern platforms as budget and schedule permits. The "gold" of the flight software is the "control loop" algorithms of the vehicle. This is the Guidance, Navigation, and Control (GNC) software algorithms. This software is typically the most expensive to develop, test, and verify. Thus, the approach is to preserve the GNC flight software, while first evolving the supporting software (such as Command and Data Handling, Caution and Warning, Telemetry, etc.). This can be accomplished by gradually removing the "support software" from the legacy flight software leaving only the GNC algorithms. The "support software" could be re-developed for modern platforms, while leaving the GNC algorithms to execute on technology compatible with the legacy system. It is also possible to package the GNC algorithms into an emulated version of the original computer (via Field Programmable Gate Arrays or FPGAs), thus becoming a "GNC on a Chip" solution where it could live forever to be embedded in modern avionics platforms.

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.

Computational Software for Fitting Seismic Data to Epidemic-Type Aftershock Sequence Models

NASA Astrophysics Data System (ADS)

Chu, A.

2014-12-01

Modern earthquake catalogs are often analyzed using spatial-temporal point process models such as the epidemic-type aftershock sequence (ETAS) models of Ogata (1998). My work introduces software to implement two of ETAS models described in Ogata (1998). To find the Maximum-Likelihood Estimates (MLEs), my software provides estimates of the homogeneous background rate parameter and the temporal and spatial parameters that govern triggering effects by applying the Expectation-Maximization (EM) algorithm introduced in Veen and Schoenberg (2008). Despite other computer programs exist for similar data modeling purpose, using EM-algorithm has the benefits of stability and robustness (Veen and Schoenberg, 2008). Spatial shapes that are very long and narrow cause difficulties in optimization convergence and problems with flat or multi-modal log-likelihood functions encounter similar issues. My program uses a robust method to preset a parameter to overcome the non-convergence computational issue. In addition to model fitting, the software is equipped with useful tools for examining modeling fitting results, for example, visualization of estimated conditional intensity, and estimation of expected number of triggered aftershocks. A simulation generator is also given with flexible spatial shapes that may be defined by the user. This open-source software has a very simple user interface. The user may execute it on a local computer, and the program also has potential to be hosted online. Java language is used for the software's core computing part and an optional interface to the statistical package R is provided.

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.

bioboxes v510

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

Barton, Michael; Droge, Johannes; Belmann, Peter

2017-06-22

Software is now both central and essential to modern biology, yet lack of availability, difficult installations, and complex user interfaces make software hard to obtain and use. Containerisation, as exemplified by the Docker platform, has the potential to solve the problems associated with sharing software. The developers propose bioboxes: containers with standardised interfaces to make bioinformatics software interchangeable.

Implementation of Simple and Functional Web Applications at the Alaska Volcano Observatory Remote Sensing Group

NASA Astrophysics Data System (ADS)

Skoog, R. A.

2007-12-01

Web pages are ubiquitous and accessible, but when compared to stand-alone applications they are limited in capability. The Alaska Volcano Observatory (AVO) Remote Sensing Group has implemented web pages and supporting server software that provide relatively advanced features to any user able to meet basic requirements. Anyone in the world with access to a modern web browser (such as Mozilla Firefox 1.5 or Internet Explorer 6) and reasonable internet connection can fully use the tools, with no software installation or configuration. This allows faculty, staff and students at AVO to perform many aspects of volcano monitoring from home or the road as easily as from the office. Additionally, AVO collaborators such as the National Weather Service and the Anchorage Volcanic Ash Advisory Center are able to use these web tools to quickly assess volcanic events. Capabilities of this web software include (1) ability to obtain accurate measured remote sensing data values on an semi- quantitative compressed image of a large area, (2) to view any data from a wide time range of data swaths, (3) to view many different satellite remote sensing spectral bands and combinations, to adjust color range thresholds, (4) and to export to KML files which are viewable virtual globes such as Google Earth. The technologies behind this implementation are primarily Javascript, PHP, and MySQL which are free to use and well documented, in addition to Terascan, a commercial software package used to extract data from level-0 data files. These technologies will be presented in conjunction with the techniques used to combine them into the final product used by AVO and its collaborators for operational volcanic monitoring.

A measuring tool for tree-rings analysis

NASA Astrophysics Data System (ADS)

Shumilov, Oleg; Kanatjev, Alexander; Kasatkina, Elena

2013-04-01

A special tool has been created for the annual tree-ring widths measurement and analysis. It consists of professional scanner, computer system and software. This created complex in many aspects does not yield the similar systems (LINTAB, WinDENDRO), but in comparison to manual measurement systems, it offers a number of advantages: productivity gain, possibility of archiving the results of the measurements at any stage of the processing, operator comfort. It has been developed a new software, allowing processing of samples of different types (cores, saw cuts), including those which is difficult to process, having got a complex wood structure (inhomogeneity of growing in different directions, missed, light and false rings etc.). This software can analyze pictures made with optical scanners, analog or digital cameras. The complex software program was created on programming language C++, being compatible with modern operating systems like Windows X. Annual ring widths are measured along paths traced interactively. These paths can have any orientation and can be created so that ring widths are measured perpendicular to ring boundaries. A graphic of ring-widths in function of the year is displayed on a screen during the analysis and it can be used for visual and numerical cross-dating and comparison with other series or master-chronologies. Ring widths are saved to the text files in a special format, and those files are converted to the format accepted for data conservation in the International Tree-Ring Data Bank. The created complex is universal in application that will allow its use for decision of the different problems in biology and ecology. With help of this complex it has been reconstructed a long-term juniper (1328-2004) and pine (1445-2005) tree-ring chronologies on the base of samples collected at Kola Peninsula (northwestern Russia).

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.

75 FR 11914 - Chrysler, LLC, Mount Elliott Tool and Die, Including On-Site Leased Workers From Modern...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-12

... Elliott Tool and Die, Including On-Site Leased Workers From Modern Professional Services, TAC Automotive... on-site leased workers from Modern Professional Services, TAC Automotive, Syncreon, CSC, and Resource... subject firm. The workers are engaged in the production of automotive dies and tooling. New information...

Fault Tree Analysis Application for Safety and Reliability

NASA Technical Reports Server (NTRS)

Wallace, Dolores R.

2003-01-01

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

PINT, A Modern Software Package for Pulsar Timing

NASA Astrophysics Data System (ADS)

Luo, Jing; Ransom, Scott M.; Demorest, Paul; Ray, Paul S.; Stovall, Kevin; Jenet, Fredrick; Ellis, Justin; van Haasteren, Rutger; Bachetti, Matteo; NANOGrav PINT developer team

2018-01-01

Pulsar timing, first developed decades ago, has provided an extremely wide range of knowledge about our universe. It has been responsible for many important discoveries, such as the discovery of the first exoplanet and the orbital period decay of double neutron star systems. Currently pulsar timing is the leading technique for detecting low frequency (about 10^-9 Hertz) gravitational waves (GW) using an array of pulsars as the detectors. To achieve this goal, high precision pulsar timing data, at about nanoseconds level, is required. Most high precision pulsar timing data are analyzed using the widely adopted software TEMPO/TEMPO2. But for a robust and believable GW detection, it is important to have independent software that can cross-check the result. In this poster we present the new generation pulsar timing software PINT. This package will provide a robust system to cross check high-precision timing results, completely independent of TEMPO and TEMPO2. In addition, PINT is designed to be a package that is easy to extend and modify, through use of flexible code architecture and a modern programming language, Python, with modern technology and libraries.

A Parallel Numerical Micromagnetic Code Using FEniCS

NASA Astrophysics Data System (ADS)

Nagy, L.; Williams, W.; Mitchell, L.

2013-12-01

Many problems in the geosciences depend on understanding the ability of magnetic minerals to provide stable paleomagnetic recordings. Numerical micromagnetic modelling allows us to calculate the domain structures found in naturally occurring magnetic materials. However the computational cost rises exceedingly quickly with respect to the size and complexity of the geometries that we wish to model. This problem is compounded by the fact that the modern processor design no longer focuses on the speed at which calculations are performed, but rather on the number of computational units amongst which we may distribute our calculations. Consequently to better exploit modern computational resources our micromagnetic simulations must "go parallel". We present a parallel and scalable micromagnetics code written using FEniCS. FEniCS is a multinational collaboration involving several institutions (University of Cambridge, University of Chicago, The Simula Research Laboratory, etc.) that aims to provide a set of tools for writing scientific software; in particular software that employs the finite element method. The advantages of this approach are the leveraging of pre-existing projects from the world of scientific computing (PETSc, Trilinos, Metis/Parmetis, etc.) and exposing these so that researchers may pose problems in a manner closer to the mathematical language of their domain. Our code provides a scriptable interface (in Python) that allows users to not only run micromagnetic models in parallel, but also to perform pre/post processing of data.

Basin Assessment Spatial Planning Platform

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

The tool is intended to facilitate hydropower development and water resource planning by improving synthesis and interpretation of disparate spatial datasets that are considered in development actions (e.g., hydrological characteristics, environmentally and culturally sensitive areas, existing or proposed water power resources, climate-informed forecasts). The tool enables this capability by providing a unique framework for assimilating, relating, summarizing, and visualizing disparate spatial data through the use of spatial aggregation techniques, relational geodatabase platforms, and an interactive web-based Geographic Information Systems (GIS). Data are aggregated and related based on shared intersections with a common spatial unit; in this case, industry-standard hydrologic drainagemore » areas for the U.S. (National Hydrography Dataset) are used as the spatial unit to associate planning data. This process is performed using all available scalar delineations of drainage areas (i.e., region, sub-region, basin, sub-basin, watershed, sub-watershed, catchment) to create spatially hierarchical relationships among planning data and drainages. These entity-relationships are stored in a relational geodatabase that provides back-end structure to the web GIS and its widgets. The full technology stack was built using all open-source software in modern programming languages. Interactive widgets that function within the viewport are also compatible with all modern browsers.« less

Automated Comparative Metabolite Profiling of Large LC-ESIMS Data Sets in an ACD/MS Workbook Suite Add-in, and Data Clustering on a New Open-Source Web Platform FreeClust.

PubMed

Božičević, Alen; Dobrzyński, Maciej; De Bie, Hans; Gafner, Frank; Garo, Eliane; Hamburger, Matthias

2017-12-05

The technological development of LC-MS instrumentation has led to significant improvements of performance and sensitivity, enabling high-throughput analysis of complex samples, such as plant extracts. Most software suites allow preprocessing of LC-MS chromatograms to obtain comprehensive information on single constituents. However, more advanced processing needs, such as the systematic and unbiased comparative metabolite profiling of large numbers of complex LC-MS chromatograms remains a challenge. Currently, users have to rely on different tools to perform such data analyses. We developed a two-step protocol comprising a comparative metabolite profiling tool integrated in ACD/MS Workbook Suite, and a web platform developed in R language designed for clustering and visualization of chromatographic data. Initially, all relevant chromatographic and spectroscopic data (retention time, molecular ions with the respective ion abundance, and sample names) are automatically extracted and assembled in an Excel spreadsheet. The file is then loaded into an online web application that includes various statistical algorithms and provides the user with tools to compare and visualize the results in intuitive 2D heatmaps. We applied this workflow to LC-ESIMS profiles obtained from 69 honey samples. Within few hours of calculation with a standard PC, honey samples were preprocessed and organized in clusters based on their metabolite profile similarities, thereby highlighting the common metabolite patterns and distributions among samples. Implementation in the ACD/Laboratories software package enables ulterior integration of other analytical data, and in silico prediction tools for modern drug discovery.

JINR cloud infrastructure evolution

NASA Astrophysics Data System (ADS)

Baranov, A. V.; Balashov, N. A.; Kutovskiy, N. A.; Semenov, R. N.

2016-09-01

To fulfil JINR commitments in different national and international projects related to the use of modern information technologies such as cloud and grid computing as well as to provide a modern tool for JINR users for their scientific research a cloud infrastructure was deployed at Laboratory of Information Technologies of Joint Institute for Nuclear Research. OpenNebula software was chosen as a cloud platform. Initially it was set up in simple configuration with single front-end host and a few cloud nodes. Some custom development was done to tune JINR cloud installation to fit local needs: web form in the cloud web-interface for resources request, a menu item with cloud utilization statistics, user authentication via Kerberos, custom driver for OpenVZ containers. Because of high demand in that cloud service and its resources over-utilization it was re-designed to cover increasing users' needs in capacity, availability and reliability. Recently a new cloud instance has been deployed in high-availability configuration with distributed network file system and additional computing power.

Parallel Index and Query for Large Scale Data Analysis

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

Chou, Jerry; Wu, Kesheng; Ruebel, Oliver

2011-07-18

Modern scientific datasets present numerous data management and analysis challenges. State-of-the-art index and query technologies are critical for facilitating interactive exploration of large datasets, but numerous challenges remain in terms of designing a system for process- ing general scientific datasets. The system needs to be able to run on distributed multi-core platforms, efficiently utilize underlying I/O infrastructure, and scale to massive datasets. We present FastQuery, a novel software framework that address these challenges. FastQuery utilizes a state-of-the-art index and query technology (FastBit) and is designed to process mas- sive datasets on modern supercomputing platforms. We apply FastQuery to processing ofmore » a massive 50TB dataset generated by a large scale accelerator modeling code. We demonstrate the scalability of the tool to 11,520 cores. Motivated by the scientific need to search for inter- esting particles in this dataset, we use our framework to reduce search time from hours to tens of seconds.« less

Pycortex: an interactive surface visualizer for fMRI

PubMed Central

Gao, James S.; Huth, Alexander G.; Lescroart, Mark D.; Gallant, Jack L.

2015-01-01

Surface visualizations of fMRI provide a comprehensive view of cortical activity. However, surface visualizations are difficult to generate and most common visualization techniques rely on unnecessary interpolation which limits the fidelity of the resulting maps. Furthermore, it is difficult to understand the relationship between flattened cortical surfaces and the underlying 3D anatomy using tools available currently. To address these problems we have developed pycortex, a Python toolbox for interactive surface mapping and visualization. Pycortex exploits the power of modern graphics cards to sample volumetric data on a per-pixel basis, allowing dense and accurate mapping of the voxel grid across the surface. Anatomical and functional information can be projected onto the cortical surface. The surface can be inflated and flattened interactively, aiding interpretation of the correspondence between the anatomical surface and the flattened cortical sheet. The output of pycortex can be viewed using WebGL, a technology compatible with modern web browsers. This allows complex fMRI surface maps to be distributed broadly online without requiring installation of complex software. PMID:26483666

CIAO: A Modern Data Analysis System for X-Ray Astronomy

NASA Astrophysics Data System (ADS)

Fruscione, Antonella

2017-08-01

It is now eighteen years after launch and Chandra continues to produce spectacular results!A portion of the success is to be attributed to the data analysis software CIAO (Chandra Interactive Analysis of Observations) that the Chandra X-Ray Center (CXC) continues to improve and release year after year.CIAO is downloaded more than 1200 times a year and it is used by a wide variety of users around the world: from novice to experienced X-ray astronomers, high school, undergraduate and graduate students, archival users (many new to X-ray or Chandra data), users with extensive resources and others from smaller countries and institutions.The scientific goals and kinds of datasets and analysis cover a wide range: observations spanning from days to years, different instrument configurations and different kinds of targets, from pointlike stars and quasars, to fuzzy galaxies and clusters, to moving solar objects. These different needs and goals require a variety of specialized software and careful and detailed documentation which is what the CIAO software provides. In general, we strive to build a software system which is easy for beginners, yet powerful for advanced users.The complexity of the Chandra data require a flexible data analysis system which provides an environment where the users can apply our tools, but can also explore and construct their own applications. The main purpose of this talk is to present CIAO as a modern data analysis system for X-ray data analysis.CIAO has grown tremendously over the years and we will highlight (a) the most recent advancements with a particular emphasis on the newly developed high-level scripts which simplify the analysis steps for the most common cases making CIAO more accessible to all users - including beginners and users who are not X-ray astronomy specialists, (b) the python-based Sherpa modelling and fitting application and the new stand-alone version openly developed and distributed on Github and (c) progress on methods to characterize the Chandra PSF.

Optimizing Perioperative Decision Making: Improved Information for Clinical Workflow Planning

PubMed Central

Doebbeling, Bradley N.; Burton, Matthew M.; Wiebke, Eric A.; Miller, Spencer; Baxter, Laurence; Miller, Donald; Alvarez, Jorge; Pekny, Joseph

2012-01-01

Perioperative care is complex and involves multiple interconnected subsystems. Delayed starts, prolonged cases and overtime are common. Surgical procedures account for 40–70% of hospital revenues and 30–40% of total costs. Most planning and scheduling in healthcare is done without modern planning tools, which have potential for improving access by assisting in operations planning support. We identified key planning scenarios of interest to perioperative leaders, in order to examine the feasibility of applying combinatorial optimization software solving some of those planning issues in the operative setting. Perioperative leaders desire a broad range of tools for planning and assessing alternate solutions. Our modeled solutions generated feasible solutions that varied as expected, based on resource and policy assumptions and found better utilization of scarce resources. Combinatorial optimization modeling can effectively evaluate alternatives to support key decisions for planning clinical workflow and improving care efficiency and satisfaction. PMID:23304284

A case study for cloud based high throughput analysis of NGS data using the globus genomics system

DOE PAGES

Bhuvaneshwar, Krithika; Sulakhe, Dinanath; Gauba, Robinder; ...

2015-01-01

Next generation sequencing (NGS) technologies produce massive amounts of data requiring a powerful computational infrastructure, high quality bioinformatics software, and skilled personnel to operate the tools. We present a case study of a practical solution to this data management and analysis challenge that simplifies terabyte scale data handling and provides advanced tools for NGS data analysis. These capabilities are implemented using the “Globus Genomics” system, which is an enhanced Galaxy workflow system made available as a service that offers users the capability to process and transfer data easily, reliably and quickly to address end-to-end NGS analysis requirements. The Globus Genomicsmore » system is built on Amazon's cloud computing infrastructure. The system takes advantage of elastic scaling of compute resources to run multiple workflows in parallel and it also helps meet the scale-out analysis needs of modern translational genomics research.« less

Optimizing perioperative decision making: improved information for clinical workflow planning.

PubMed

Doebbeling, Bradley N; Burton, Matthew M; Wiebke, Eric A; Miller, Spencer; Baxter, Laurence; Miller, Donald; Alvarez, Jorge; Pekny, Joseph

2012-01-01

Perioperative care is complex and involves multiple interconnected subsystems. Delayed starts, prolonged cases and overtime are common. Surgical procedures account for 40-70% of hospital revenues and 30-40% of total costs. Most planning and scheduling in healthcare is done without modern planning tools, which have potential for improving access by assisting in operations planning support. We identified key planning scenarios of interest to perioperative leaders, in order to examine the feasibility of applying combinatorial optimization software solving some of those planning issues in the operative setting. Perioperative leaders desire a broad range of tools for planning and assessing alternate solutions. Our modeled solutions generated feasible solutions that varied as expected, based on resource and policy assumptions and found better utilization of scarce resources. Combinatorial optimization modeling can effectively evaluate alternatives to support key decisions for planning clinical workflow and improving care efficiency and satisfaction.

A case study for cloud based high throughput analysis of NGS data using the globus genomics system

PubMed Central

Bhuvaneshwar, Krithika; Sulakhe, Dinanath; Gauba, Robinder; Rodriguez, Alex; Madduri, Ravi; Dave, Utpal; Lacinski, Lukasz; Foster, Ian; Gusev, Yuriy; Madhavan, Subha

2014-01-01

Next generation sequencing (NGS) technologies produce massive amounts of data requiring a powerful computational infrastructure, high quality bioinformatics software, and skilled personnel to operate the tools. We present a case study of a practical solution to this data management and analysis challenge that simplifies terabyte scale data handling and provides advanced tools for NGS data analysis. These capabilities are implemented using the “Globus Genomics” system, which is an enhanced Galaxy workflow system made available as a service that offers users the capability to process and transfer data easily, reliably and quickly to address end-to-endNGS analysis requirements. The Globus Genomics system is built on Amazon 's cloud computing infrastructure. The system takes advantage of elastic scaling of compute resources to run multiple workflows in parallel and it also helps meet the scale-out analysis needs of modern translational genomics research. PMID:26925205

Principles of Metamorphic Petrology

NASA Astrophysics Data System (ADS)

Williams, Michael L.

2009-05-01

The field of metamorphic petrology has seen spectacular advances in the past decade, including new X-ray mapping techniques for characterizing metamorphic rocks and minerals, new internally consistent thermobarometers, new software for constructing and viewing phase diagrams, new methods to date metamorphic processes, and perhaps most significant, revised petrologic databases and the ability to calculate accurate phase diagrams and pseudosections. These tools and techniques provide new power and resolution for constraining pressure-temperature (P-T) histories and tectonic events. Two books have been fundamental for empowering petrologists and structural geologists during the past decade. Frank Spear's Metamorphic Phase Equilibria and Pressure-Temperature-Time Paths, published in 1993, builds on his seminal papers to provide a quantitative framework for P-T path analysis. Spear's book lays the foundation for modern quantitative metamorphic analysis. Cees Passchier and Rudolph Trouw's Microtectonics, published in 2005, with its superb photos and figures, provides the tools and the theory for interpreting deformation textures and inferring deformation processes.

Mac OS X for Astronomy

NASA Astrophysics Data System (ADS)

Pierfederici, F.; Pirzkal, N.; Hook, R. N.

Mac OS X is the new Unix based version of the Macintosh operating system. It combines a high performance DisplayPDF user interface with a standard BSD UNIX subsystem and provides users with simultaneous access to a broad range of applications which were not previously available on a single system such as Microsoft Office and Adobe Photoshop, as well as legacy X11-based scientific tools and packages like IRAF, SuperMongo, MIDAS, etc. The combination of a modern GUI layered on top of a familiar UNIX environment paves the way for new, more flexible and powerful astronomical tools to be developed while assuring compatibility with already existing, older programs. In this paper, we outline the strengths of the Mac OS X platform in a scientific environment, astronomy in particular, and point to the numerous astronomical software packages available for this platform; most notably the Scisoft collection which we have compiled.

The nuMOIRCS project: detector upgrade overview and early commissioning results

NASA Astrophysics Data System (ADS)

Walawender, Josh; Wung, Matthew; Fabricius, Maximilian; Tanaka, Ichi; Arimoto, Nobuo; Cook, David; Elms, Brian; Hashiba, Yasuhito; Hu, Yen-Sang; Iwata, Ikuru; Nishimura, Tetsuo; Omata, Koji; Takato, Naruhisa; Wang, Shiang-Yu; Weber, Mark

2016-08-01

In 2014 and 2015 the Multi-Object InfraRed Camera and Spectrograph (MOIRCS) instrument at the Subaru Telescope on Maunakea is underwent a significant modernization and upgrade project. We upgraded the two Hawaii2 detectors to Hawaii2-RG models, modernized the cryogenic temperature control system, and rewrote much of the instrument control software. The detector upgrade replaced the Hawaii2 detectors which use the Tohoku University Focal Plane Array Controller (TUFPAC) electronics with Hawaii2-RG detectors using SIDECAR ASIC (a fully integrated FPA controller system-on-a-chip) and a SAM interface card. We achieved an improvement in read noise by a factor of about 2 with this detector and electronics upgrade. The cryogenic temperature control upgrade focused on modernizing the components and making the procedures for warm up and cool down of the instrument safer. We have moved PID control loops out of the instrument control software and into Lakeshore model 336 cryogenic temperature controllers and have added interlocks on the warming systems to prevent overheating of the instrument. Much of the instrument control software has also been re-written. This was necessitated by the different interface to the detector electronics (ASIC and SAM vs. TUFPAC) and by the desire to modernize the interface to the telescope control software which has been updated to Subaru's "Gen2" system since the time of MOIRCS construction and first light. The new software is also designed to increase reliability of operation of the instrument, decrease overheads, and be easier for night time operators and support astronomers to use.

Modernizing Systems and Software: How Evolving Trends in Future Trends in Systems and Software Technology Bode Well for Advancing the Precision of Technology

DTIC Science & Technology

2009-04-23

of Code Need for increased functionality will be a forcing function to bring the fields of software and systems engineering... of Software-Intensive Systems is Increasing 3 How Evolving Trends in Systems and Software Technologies Bode Well for Advancing the Precision of ...Engineering in Continued Partnership 4 How Evolving Trends in Systems and Software Technologies Bode Well for Advancing the

The Generic Mapping Tools 6: Classic versus Modern Mode

NASA Astrophysics Data System (ADS)

Wessel, P.; Uieda, L.; Luis, J. M. F.; Scharroo, R.; Smith, W. H. F.; Wobbe, F.

2017-12-01

The Generic Mapping Tools (GMT; gmt.soest.hawaii.edu) is a 25-year old, mature open-source software package for the analysis and display of geoscience data (e.g., interpolate, filter, manipulate, project and plot temporal and spatial data). The GMT "toolbox" includes about 80 core and 40 supplemental modules sharing a common set of command options, file structures, and documentation. GMT5, when released in 2013, introduced an application programming interface (API) to allow programmatic access to GMT from other computing environments. Since then, we have released a GMT/MATLAB toolbox, an experimental GMT/Julia package, and will soon introduce a GMT/Python module. In developing these extensions, we wanted to simplify the GMT learning curve but quickly realized the main stumbling blocks to GMT command-line mastery would be ported to the external environments unless we introduced major changes. With thousands of GMT scripts already in use by scientists around the world, we were acutely aware of the need for backwards compatibility. Our solution, to be released as GMT 6, was to add a modern run mode that complements the classic mode offered so far. Modern mode completely eliminates the top three obstacles for new (and not so new) GMT users: (1) The responsibility to properly stack PostScript layers manually (i.e., the -O -K dance), (2) the responsibility of handling output redirection of PostScript (create versus append), and (3) the need to provide commands with repeated information about regions (-R) and projections (-J). Thus, modern mode results in shorter, simpler scripts with fewer pitfalls, without interfering with classic scripts. Our implementation adds five new commands that begin and end a modern session, simplify figure management, automate the conversion of PostScript to more suitable formats, automate region detection, and offer a new automated subplot environment for multi-panel illustrations. Here, we highlight the GMT modern mode and the simplifications it offers, both for command-line use and in external environments. GMT 6 is in beta mode but accessible from our repository. Numerous improvements have been added in addition to modern mode; we expect a formal release in early 2018. Publication partially supported by FCT project UID/GEO/50019/2013 - Instituto D. Luiz.

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

Ergonomics Perspective in Agricultural Research: A User-Centred Approach Using CAD and Digital Human Modeling (DHM) Technologies

NASA Astrophysics Data System (ADS)

Patel, Thaneswer; Sanjog, J.; Karmakar, Sougata

2016-09-01

Computer-aided Design (CAD) and Digital Human Modeling (DHM) (specialized CAD software for virtual human representation) technologies endow unique opportunities to incorporate human factors pro-actively in design development. Challenges of enhancing agricultural productivity through improvement of agricultural tools/machineries and better human-machine compatibility can be ensured by adoption of these modern technologies. Objectives of present work are to provide the detailed scenario of CAD and DHM applications in agricultural sector; and finding out means for wide adoption of these technologies for design and development of cost-effective, user-friendly, efficient and safe agricultural tools/equipment and operator's workplace. Extensive literature review has been conducted for systematic segregation and representation of available information towards drawing inferences. Although applications of various CAD software have momentum in agricultural research particularly for design and manufacturing of agricultural equipment/machinery, use of DHM is still at its infancy in this sector. Current review discusses about reasons of less adoption of these technologies in agricultural sector and steps to be taken for their wide adoption. It also suggests possible future research directions to come up with better ergonomic design strategies for improvement of agricultural equipment/machines and workstations through application of CAD and DHM.

Viewpoints: A High-Performance High-Dimensional Exploratory Data Analysis Tool

NASA Astrophysics Data System (ADS)

Gazis, P. R.; Levit, C.; Way, M. J.

2010-12-01

Scientific data sets continue to increase in both size and complexity. In the past, dedicated graphics systems at supercomputing centers were required to visualize large data sets, but as the price of commodity graphics hardware has dropped and its capability has increased, it is now possible, in principle, to view large complex data sets on a single workstation. To do this in practice, an investigator will need software that is written to take advantage of the relevant graphics hardware. The Viewpoints visualization package described herein is an example of such software. Viewpoints is an interactive tool for exploratory visual analysis of large high-dimensional (multivariate) data. It leverages the capabilities of modern graphics boards (GPUs) to run on a single workstation or laptop. Viewpoints is minimalist: it attempts to do a small set of useful things very well (or at least very quickly) in comparison with similar packages today. Its basic feature set includes linked scatter plots with brushing, dynamic histograms, normalization, and outlier detection/removal. Viewpoints was originally designed for astrophysicists, but it has since been used in a variety of fields that range from astronomy, quantum chemistry, fluid dynamics, machine learning, bioinformatics, and finance to information technology server log mining. In this article, we describe the Viewpoints package and show examples of its usage.

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.

Motions of Celestial Bodies; Computer simulations

NASA Astrophysics Data System (ADS)

Butikov, Eugene

2014-10-01

This book is written for a wide range of graduate and undergraduate students studying various courses in physics and astronomy. It is accompanied by the award winning educational software package 'Planets and Satellites' developed by the author. This text, together with the interactive software, is intended to help students learn and understand the fundamental concepts and the laws of physics as they apply to the fascinating world of the motions of natural and artificial celestial bodies. The primary aim of the book is the understanding of the foundations of classical and modern physics, while their application to celestial mechanics is used to illustrate these concepts. The simulation programs create vivid and lasting impressions of the investigated phenomena, and provide students and their instructors with a powerful tool which enables them to explore basic concepts that are difficult to study and teach in an abstract conventional manner. Students can work with the text and software at a pace they can enjoy, varying parameters of the simulated systems. Each section of the textbook is supplied with questions, exercises, and problems. Using some of the suggested simulation programs, students have an opportunity to perform interesting mini-research projects in physics and astronomy.

Estimating population diversity with CatchAll

PubMed Central

Bunge, John; Woodard, Linda; Böhning, Dankmar; Foster, James A.; Connolly, Sean; Allen, Heather K.

2012-01-01

Motivation: The massive data produced by next-generation sequencing require advanced statistical tools. We address estimating the total diversity or species richness in a population. To date, only relatively simple methods have been implemented in available software. There is a need for software employing modern, computationally intensive statistical analyses including error, goodness-of-fit and robustness assessments. Results: We present CatchAll, a fast, easy-to-use, platform-independent program that computes maximum likelihood estimates for finite-mixture models, weighted linear regression-based analyses and coverage-based non-parametric methods, along with outlier diagnostics. Given sample ‘frequency count’ data, CatchAll computes 12 different diversity estimates and applies a model-selection algorithm. CatchAll also derives discounted diversity estimates to adjust for possibly uncertain low-frequency counts. It is accompanied by an Excel-based graphics program. Availability: Free executable downloads for Linux, Windows and Mac OS, with manual and source code, at www.northeastern.edu/catchall. Contact: jab18@cornell.edu PMID:22333246

Exploiting current-generation graphics hardware for synthetic-scene generation

NASA Astrophysics Data System (ADS)

Tanner, Michael A.; Keen, Wayne A.

2010-04-01

Increasing seeker frame rate and pixel count, as well as the demand for higher levels of scene fidelity, have driven scene generation software for hardware-in-the-loop (HWIL) and software-in-the-loop (SWIL) testing to higher levels of parallelization. Because modern PC graphics cards provide multiple computational cores (240 shader cores for a current NVIDIA Corporation GeForce and Quadro cards), implementation of phenomenology codes on graphics processing units (GPUs) offers significant potential for simultaneous enhancement of simulation frame rate and fidelity. To take advantage of this potential requires algorithm implementation that is structured to minimize data transfers between the central processing unit (CPU) and the GPU. In this paper, preliminary methodologies developed at the Kinetic Hardware In-The-Loop Simulator (KHILS) will be presented. Included in this paper will be various language tradeoffs between conventional shader programming, Compute Unified Device Architecture (CUDA) and Open Computing Language (OpenCL), including performance trades and possible pathways for future tool development.

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.

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.

Interactive Visualization of Assessment Data: The Software Package Mondrian

ERIC Educational Resources Information Center

Unlu, Ali; Sargin, Anatol

2009-01-01

Mondrian is state-of-the-art statistical data visualization software featuring modern interactive visualization techniques for a wide range of data types. This article reviews the capabilities, functionality, and interactive properties of this software package. Key features of Mondrian are illustrated with data from the Programme for International…

Automated video surveillance: teaching an old dog new tricks

NASA Astrophysics Data System (ADS)

McLeod, Alastair

1993-12-01

The automated video surveillance market is booming with new players, new systems, new hardware and software, and an extended range of applications. This paper reviews available technology, and describes the features required for a good automated surveillance system. Both hardware and software are discussed. An overview of typical applications is also given. A shift towards PC-based hybrid systems, use of parallel processing, neural networks, and exploitation of modern telecomms are introduced, highlighting the evolution modern video surveillance systems.

Final Project Report: Data Locality Enhancement of Dynamic Simulations for Exascale Computing

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

Shen, Xipeng

The goal of this project is to develop a set of techniques and software tools to enhance the matching between memory accesses in dynamic simulations and the prominent features of modern and future manycore systems, alleviating the memory performance issues for exascale computing. In the first three years, the PI and his group have achieves some significant progress towards the goal, producing a set of novel techniques for improving the memory performance and data locality in manycore systems, yielding 18 conference and workshop papers and 4 journal papers and graduating 6 Ph.Ds. This report summarizes the research results of thismore » project through that period.« less

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.

Software attribute visualization for high integrity software

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

Pollock, G.M.

1998-03-01

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

An image-processing software package: UU and Fig for optical metrology applications

NASA Astrophysics Data System (ADS)

Chen, Lujie

2013-06-01

Modern optical metrology applications are largely supported by computational methods, such as phase shifting [1], Fourier Transform [2], digital image correlation [3], camera calibration [4], etc, in which image processing is a critical and indispensable component. While it is not too difficult to obtain a wide variety of image-processing programs from the internet; few are catered for the relatively special area of optical metrology. This paper introduces an image-processing software package: UU (data processing) and Fig (data rendering) that incorporates many useful functions to process optical metrological data. The cross-platform programs UU and Fig are developed based on wxWidgets. At the time of writing, it has been tested on Windows, Linux and Mac OS. The userinterface is designed to offer precise control of the underline processing procedures in a scientific manner. The data input/output mechanism is designed to accommodate diverse file formats and to facilitate the interaction with other independent programs. In terms of robustness, although the software was initially developed for personal use, it is comparably stable and accurate to most of the commercial software of similar nature. In addition to functions for optical metrology, the software package has a rich collection of useful tools in the following areas: real-time image streaming from USB and GigE cameras, computational geometry, computer vision, fitting of data, 3D image processing, vector image processing, precision device control (rotary stage, PZT stage, etc), point cloud to surface reconstruction, volume rendering, batch processing, etc. The software package is currently used in a number of universities for teaching and research.

Conversion of HSPF Legacy Model to a Platform-Independent, Open-Source Language

NASA Astrophysics Data System (ADS)

Heaphy, R. T.; Burke, M. P.; Love, J. T.

2015-12-01

Since its initial development over 30 years ago, the Hydrologic Simulation Program - FORTAN (HSPF) model has been used worldwide to support water quality planning and management. In the United States, HSPF receives widespread endorsement as a regulatory tool at all levels of government and is a core component of the EPA's Better Assessment Science Integrating Point and Nonpoint Sources (BASINS) system, which was developed to support nationwide Total Maximum Daily Load (TMDL) analysis. However, the model's legacy code and data management systems have limitations in their ability to integrate with modern software, hardware, and leverage parallel computing, which have left voids in optimization, pre-, and post-processing tools. Advances in technology and our scientific understanding of environmental processes that have occurred over the last 30 years mandate that upgrades be made to HSPF to allow it to evolve and continue to be a premiere tool for water resource planners. This work aims to mitigate the challenges currently facing HSPF through two primary tasks: (1) convert code to a modern widely accepted, open-source, high-performance computing (hpc) code; and (2) convert model input and output files to modern widely accepted, open-source, data model, library, and binary file format. Python was chosen as the new language for the code conversion. It is an interpreted, object-oriented, hpc code with dynamic semantics that has become one of the most popular open-source languages. While python code execution can be slow compared to compiled, statically typed programming languages, such as C and FORTRAN, the integration of Numba (a just-in-time specializing compiler) has allowed this challenge to be overcome. For the legacy model data management conversion, HDF5 was chosen to store the model input and output. The code conversion for HSPF's hydrologic and hydraulic modules has been completed. The converted code has been tested against HSPF's suite of "test" runs and shown good agreement and similar execution times while using the Numba compiler. Continued verification of the accuracy of the converted code against more complex legacy applications and improvement upon execution times by incorporating an intelligent network change detection tool is currently underway, and preliminary results will be presented.

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

Generating DEM from LIDAR data - comparison of available software tools

NASA Astrophysics Data System (ADS)

Korzeniowska, K.; Lacka, M.

2011-12-01

In recent years many software tools and applications have appeared that offer procedures, scripts and algorithms to process and visualize ALS data. This variety of software tools and of "point cloud" processing methods contributed to the aim of this study: to assess algorithms available in various software tools that are used to classify LIDAR "point cloud" data, through a careful examination of Digital Elevation Models (DEMs) generated from LIDAR data on a base of these algorithms. The works focused on the most important available software tools: both commercial and open source ones. Two sites in a mountain area were selected for the study. The area of each site is 0.645 sq km. DEMs generated with analysed software tools ware compared with a reference dataset, generated using manual methods to eliminate non ground points. Surfaces were analysed using raster analysis. Minimum, maximum and mean differences between reference DEM and DEMs generated with analysed software tools were calculated, together with Root Mean Square Error. Differences between DEMs were also examined visually using transects along the grid axes in the test sites.

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.

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

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

NASA Technical Reports Server (NTRS)

Campbell, Roy H.; Beckman-Davies, C. S.; Benzinger, L.; Beshers, G.; Laliberte, D.; Render, H.; Sum, R.; Smith, W.; Terwilliger, R.

1986-01-01

Research into software development is required to reduce its production cost and to improve its quality. Modern software systems, such as the embedded software required for NASA's space station initiative, stretch current software engineering techniques. The requirements to build large, reliable, and maintainable software systems increases with time. Much theoretical and practical research is in progress to improve software engineering techniques. One such technique is to build a software system or environment which directly supports the software engineering process, i.e., the SAGA project, comprising the research necessary to design and build a software development which automates the software engineering process. Progress under SAGA is described.

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

Using parallel computing for the display and simulation of the space debris environment

NASA Astrophysics Data System (ADS)

Möckel, M.; Wiedemann, C.; Flegel, S.; Gelhaus, J.; Vörsmann, P.; Klinkrad, H.; Krag, H.

2011-07-01

Parallelism is becoming the leading paradigm in today's computer architectures. In order to take full advantage of this development, new algorithms have to be specifically designed for parallel execution while many old ones have to be upgraded accordingly. One field in which parallel computing has been firmly established for many years is computer graphics. Calculating and displaying three-dimensional computer generated imagery in real time requires complex numerical operations to be performed at high speed on a large number of objects. Since most of these objects can be processed independently, parallel computing is applicable in this field. Modern graphics processing units (GPUs) have become capable of performing millions of matrix and vector operations per second on multiple objects simultaneously. As a side project, a software tool is currently being developed at the Institute of Aerospace Systems that provides an animated, three-dimensional visualization of both actual and simulated space debris objects. Due to the nature of these objects it is possible to process them individually and independently from each other. Therefore, an analytical orbit propagation algorithm has been implemented to run on a GPU. By taking advantage of all its processing power a huge performance increase, compared to its CPU-based counterpart, could be achieved. For several years efforts have been made to harness this computing power for applications other than computer graphics. Software tools for the simulation of space debris are among those that could profit from embracing parallelism. With recently emerged software development tools such as OpenCL it is possible to transfer the new algorithms used in the visualization outside the field of computer graphics and implement them, for example, into the space debris simulation environment. This way they can make use of parallel hardware such as GPUs and Multi-Core-CPUs for faster computation. In this paper the visualization software will be introduced, including a comparison between the serial and the parallel method of orbit propagation. Ways of how to use the benefits of the latter method for space debris simulation will be discussed. An introduction to OpenCL will be given as well as an exemplary algorithm from the field of space debris simulation.

Using parallel computing for the display and simulation of the space debris environment

NASA Astrophysics Data System (ADS)

Moeckel, Marek; Wiedemann, Carsten; Flegel, Sven Kevin; Gelhaus, Johannes; Klinkrad, Heiner; Krag, Holger; Voersmann, Peter

Parallelism is becoming the leading paradigm in today's computer architectures. In order to take full advantage of this development, new algorithms have to be specifically designed for parallel execution while many old ones have to be upgraded accordingly. One field in which parallel computing has been firmly established for many years is computer graphics. Calculating and displaying three-dimensional computer generated imagery in real time requires complex numerical operations to be performed at high speed on a large number of objects. Since most of these objects can be processed independently, parallel computing is applicable in this field. Modern graphics processing units (GPUs) have become capable of performing millions of matrix and vector operations per second on multiple objects simultaneously. As a side project, a software tool is currently being developed at the Institute of Aerospace Systems that provides an animated, three-dimensional visualization of both actual and simulated space debris objects. Due to the nature of these objects it is possible to process them individually and independently from each other. Therefore, an analytical orbit propagation algorithm has been implemented to run on a GPU. By taking advantage of all its processing power a huge performance increase, compared to its CPU-based counterpart, could be achieved. For several years efforts have been made to harness this computing power for applications other than computer graphics. Software tools for the simulation of space debris are among those that could profit from embracing parallelism. With recently emerged software development tools such as OpenCL it is possible to transfer the new algorithms used in the visualization outside the field of computer graphics and implement them, for example, into the space debris simulation environment. This way they can make use of parallel hardware such as GPUs and Multi-Core-CPUs for faster computation. In this paper the visualization software will be introduced, including a comparison between the serial and the parallel method of orbit propagation. Ways of how to use the benefits of the latter method for space debris simulation will be discussed. An introduction of OpenCL will be given as well as an exemplary algorithm from the field of space debris simulation.

Effective Tooling for Linked Data Publishing in Scientific Research

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

Purohit, Sumit; Smith, William P.; Chappell, Alan R.

Challenges that make it difficult to find, share, and combine published data, such as data heterogeneity and resource discovery, have led to increased adoption of semantic data standards and data publishing technologies. To make data more accessible, interconnected and discoverable, some domains are being encouraged to publish their data as Linked Data. Consequently, this trend greatly increases the amount of data that semantic web tools are required to process, store, and interconnect. In attempting to process and manipulate large data sets, tools–ranging from simple text editors to modern triplestores– eventually breakdown upon reaching undefined thresholds. This paper offers a systematicmore » approach that data publishers can use to categorize suitable tools to meet their data publishing needs. We present a real-world use case, the Resource Discovery for Extreme Scale Collaboration (RDESC), which features a scientific dataset(maximum size of 1.4 billion triples) used to evaluate a toolbox for data publishing in climate research. This paper also introduces a semantic data publishing software suite developed for the RDESC project.« less

Active Learning through Modeling: Introduction to Software Development in the Business Curriculum

ERIC Educational Resources Information Center

Roussev, Boris; Rousseva, Yvonna

2004-01-01

Modern software practices call for the active involvement of business people in the software process. Therefore, programming has become an indispensable part of the information systems component of the core curriculum at business schools. In this paper, we present a model-based approach to teaching introduction to programming to general business…

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

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

Myers, K; Bakic, P; Abbey, C

2014-06-15

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

DigitSeis: A New Digitization Software and its Application to the Harvard-Adam Dziewoński Observatory Collection

NASA Astrophysics Data System (ADS)

Bogiatzis, P.; Altoé, I. L.; Karamitrou, A.; Ishii, M.; Ishii, H.

2015-12-01

DigitSeis is a new open-source, interactive digitization software written in MATLAB that converts digital, raster images of analog seismograms to readily usable, discretized time series using image processing algorithms. DigitSeis automatically identifies and corrects for various geometrical distortions of seismogram images that are acquired through the original recording, storage, and scanning procedures. With human supervision, the software further identifies and classifies important features such as time marks and notes, corrects time-mark offsets from the main trace, and digitizes the combined trace with an analysis to obtain as accurate timing as possible. Although a large effort has been made to minimize the human input, DigitSeis provides interactive tools for challenging situations such as trace crossings and stains in the paper. The effectiveness of the software is demonstrated with the digitization of seismograms that are over half a century old from the Harvard-Adam Dziewoński observatory that is still in operation as a part of the Global Seismographic Network (station code HRV and network code IU). The spectral analysis of the digitized time series shows no spurious features that may be related to the occurrence of minute and hour marks. They also display signals associated with significant earthquakes, and a comparison of the spectrograms with modern recordings reveals similarities in the background noise.

Applying CASE Tools for On-Board Software Development

NASA Astrophysics Data System (ADS)

Brammer, U.; Hönle, A.

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

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

PubMed

Tenenhaus-Aziza, Fanny; Ellouze, Mariem

2015-02-01

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

Journal of Chemical Education: Software.

ERIC Educational Resources Information Center

Journal of Chemical Education, 1988

1988-01-01

Describes a chemistry software program that emulates a modern binary gradient HPLC system with reversed phase column behavior. Allows for solvent selection, adjustment of gradient program, column selection, detectory selection, handling of computer sample data, and sample preparation. (MVL)

Toolpack mathematical software development environment

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

Osterweil, L.

1982-07-21

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

Software development environments: Status and trends

NASA Technical Reports Server (NTRS)

Duffel, Larry E.

1988-01-01

Currently software engineers are the essential integrating factors tying several components together. The components consist of process, methods, computers, tools, support environments, and software engineers. The engineers today empower the tools versus the tools empowering the engineers. Some of the issues in software engineering are quality, managing the software engineering process, and productivity. A strategy to accomplish this is to promote the evolution of software engineering from an ad hoc, labor intensive activity to a managed, technology supported discipline. This strategy may be implemented by putting the process under management control, adopting appropriate methods, inserting the technology that provides automated support for the process and methods, collecting automated tools into an integrated environment and educating the personnel.

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

Prescott, Ryan; Marger, Bernard L.; Chiu, Ailsa

During the second iteration of the US NDC Modernization Elaboration phase (E2), the SNL US NDC Modernization project team completed follow-on COTS surveys & exploratory prototyping related to the Object Storage & Distribution (OSD) mechanism, and the processing control software infrastructure. This report summarizes the E2 prototyping work.

Current trends for customized biomedical software tools.

PubMed

Khan, Haseeb Ahmad

2017-01-01

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

Software management tools: Lessons learned from use

NASA Technical Reports Server (NTRS)

Reifer, D. J.; Valett, J.; Knight, J.; Wenneson, G.

1985-01-01

Experience in inserting software project planning tools into more than 100 projects producing mission critical software are discussed. The problems the software project manager faces are listed along with methods and tools available to handle them. Experience is reported with the Project Manager's Workstation (PMW) and the SoftCost-R cost estimating package. Finally, the results of a survey, which looked at what could be done in the future to overcome the problems experienced and build a set of truly useful tools, are presented.

A Quantitative Inquiry into Software Developers' Intentions to Use Agile Scrum Method

ERIC Educational Resources Information Center

Huq, M. Shamsul

2017-01-01

In recent years, organizations have shown increasing willingness to adopt agile scrum method (ASM) to meet the demand of modern-day software development; that is to deliver faster and better software, with a built-in flexibility to absorb last minute changes in requirements. This research study was undertaken to uncover the underlying factors that…

A Middleware Platform for Providing Mobile and Embedded Computing Instruction to Software Engineering Students

ERIC Educational Resources Information Center

Mattmann, C. A.; Medvidovic, N.; Malek, S.; Edwards, G.; Banerjee, S.

2012-01-01

As embedded software systems have grown in number, complexity, and importance in the modern world, a corresponding need to teach computer science students how to effectively engineer such systems has arisen. Embedded software systems, such as those that control cell phones, aircraft, and medical equipment, are subject to requirements and…

Perceptions of the Software Skills of Graduates by Employers in the Financial Services Industry

ERIC Educational Resources Information Center

Kyng, Tim; Tickle, Leonie; Wood, Leigh N.

2013-01-01

Software, particularly spreadsheet software, is ubiquitous in the financial services workplace. Yet little is known about the extent to which universities should, and do, prepare graduates for this aspect of the modern workplace. We have investigated this issue through a survey of financial services employers of graduates, the results of which are…

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.

Air Traffic Control: Immature Software Acquisition Processes Increase FAA System Acquisition Risks

DOT National Transportation Integrated Search

1997-03-01

The General Accounting Office (GAO) at the request of Congress reviewed (1) : the maturity of Federal Aviation Administration's (FAA's) Air Traffic Control : (ATC) modernization software acquisition processes, and (2) the steps/actions : FAA has unde...

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.

Towards a New Paradigm of Software Development: an Ambassador Driven Process in Distributed Software Companies

NASA Astrophysics Data System (ADS)

Kumlander, Deniss

The globalization of companies operations and competitor between software vendors demand improving quality of delivered software and decreasing the overall cost. The same in fact introduce a lot of problem into software development process as produce distributed organization breaking the co-location rule of modern software development methodologies. Here we propose a reformulation of the ambassador position increasing its productivity in order to bridge communication and workflow gap by managing the entire communication process rather than concentrating purely on the communication result.

Retraining the Modern Civil Engineer.

ERIC Educational Resources Information Center

Priscoli, Jerome Delli

1983-01-01

Discusses why modern engineering requires social science and the nature of planning. After these conceptional discussions, 12 practical tools which social science brings to engineering are reviewed. A tested approach to training engineers in these tools is then described. Tools include institutional analysis, policy profiling, and other impact…

ToxPredictor: a Toxicity Estimation Software Tool

EPA Science Inventory

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

Dynamic visualization techniques for high consequence software

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

Pollock, G.M.

1998-02-01

This report documents a prototype tool developed to investigate the use of visualization and virtual reality technologies for improving software surety confidence. The tool is utilized within the execution phase of the software life cycle. It provides a capability to monitor an executing program against prespecified requirements constraints provided in a program written in the requirements specification language SAGE. The resulting Software Attribute Visual Analysis Tool (SAVAnT) also provides a technique to assess the completeness of a software specification. The prototype tool is described along with the requirements constraint language after a brief literature review is presented. Examples of howmore » the tool can be used are also presented. In conclusion, the most significant advantage of this tool is to provide a first step in evaluating specification completeness, and to provide a more productive method for program comprehension and debugging. The expected payoff is increased software surety confidence, increased program comprehension, and reduced development and debugging time.« less

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.

Visual DMDX: A web-based authoring tool for DMDX, a Windows display program with millisecond accuracy.

PubMed

Garaizar, Pablo; Reips, Ulf-Dietrich

2015-09-01

DMDX is a software package for the experimental control and timing of stimulus display for Microsoft Windows systems. DMDX is reliable, flexible, millisecond accurate, and can be downloaded free of charge; therefore it has become very popular among experimental researchers. However, setting up a DMDX-based experiment is burdensome because of its command-based interface. Further, DMDX relies on RTF files in which parts of the stimuli, design, and procedure of an experiment are defined in a complicated (DMASTR-compatible) syntax. Other experiment software, such as E-Prime, Psychopy, and WEXTOR, became successful as a result of integrated visual authoring tools. Such an intuitive interface was lacking for DMDX. We therefore created and present here Visual DMDX (http://visualdmdx.com/), a HTML5-based web interface to set up experiments and export them to DMDX item files format in RTF. Visual DMDX offers most of the features available from the rich DMDX/DMASTR syntax, and it is a useful tool to support researchers who are new to DMDX. Both old and modern versions of DMDX syntax are supported. Further, with Visual DMDX, we go beyond DMDX by having added export to JSON (a versatile web format), easy backup, and a preview option for experiments. In two examples, one experiment each on lexical decision making and affective priming, we explain in a step-by-step fashion how to create experiments using Visual DMDX. We release Visual DMDX under an open-source license to foster collaboration in its continuous improvement.

Design and implementation of a general main axis controller for the ESO telescopes

NASA Astrophysics Data System (ADS)

Sandrock, Stefan; Di Lieto, Nicola; Pettazzi, Lorenzo; Erm, Toomas

2012-09-01

Most of the real-time control systems at the existing ESO telescopes were developed with "traditional" methods, using general purpose VMEbus electronics, and running applications that were coded by hand, mostly using the C programming language under VxWorks. As we are moving towards more modern design methods, we have explored a model-based design approach for real-time applications in the telescope area, and used the control algorithm of a standard telescope main axis as a first example. We wanted to have a clear work-flow that follows the "correct-by-construction" paradigm, where the implementation is testable in simulation on the development host, and where the testing time spent by debugging on target is minimized. It should respect the domains of control, electronics, and software engineers in the choice of tools. It should be a targetindependent approach so that the result could be deployed on various platforms. We have selected the Mathworks tools Simulink, Stateflow, and Embedded Coder for design and implementation, and LabVIEW with NI hardware for hardware-in-the-loop testing, all of which are widely used in industry. We describe how these tools have been used in order to model, simulate, and test the application. We also evaluate the benefits of this approach compared to the traditional method with respect to testing effort and maintainability. For a specific axis controller application we have successfully integrated the result into the legacy platform of the existing VLT software, as well as demonstrated how to use the same design for a new development with a completely different environment.

Agile Acceptance Test–Driven Development of Clinical Decision Support Advisories: Feasibility of Using Open Source Software

PubMed Central

Baldwin, Krystal L; Kannan, Vaishnavi; Flahaven, Emily L; Parks, Cassandra J; Ott, Jason M; Willett, Duwayne L

2018-01-01

Background Moving to electronic health records (EHRs) confers substantial benefits but risks unintended consequences. Modern EHRs consist of complex software code with extensive local configurability options, which can introduce defects. Defects in clinical decision support (CDS) tools are surprisingly common. Feasible approaches to prevent and detect defects in EHR configuration, including CDS tools, are needed. In complex software systems, use of test–driven development and automated regression testing promotes reliability. Test–driven development encourages modular, testable design and expanding regression test coverage. Automated regression test suites improve software quality, providing a “safety net” for future software modifications. Each automated acceptance test serves multiple purposes, as requirements (prior to build), acceptance testing (on completion of build), regression testing (once live), and “living” design documentation. Rapid-cycle development or “agile” methods are being successfully applied to CDS development. The agile practice of automated test–driven development is not widely adopted, perhaps because most EHR software code is vendor-developed. However, key CDS advisory configuration design decisions and rules stored in the EHR may prove amenable to automated testing as “executable requirements.” Objective We aimed to establish feasibility of acceptance test–driven development of clinical decision support advisories in a commonly used EHR, using an open source automated acceptance testing framework (FitNesse). Methods Acceptance tests were initially constructed as spreadsheet tables to facilitate clinical review. Each table specified one aspect of the CDS advisory’s expected behavior. Table contents were then imported into a test suite in FitNesse, which queried the EHR database to automate testing. Tests and corresponding CDS configuration were migrated together from the development environment to production, with tests becoming part of the production regression test suite. Results We used test–driven development to construct a new CDS tool advising Emergency Department nurses to perform a swallowing assessment prior to administering oral medication to a patient with suspected stroke. Test tables specified desired behavior for (1) applicable clinical settings, (2) triggering action, (3) rule logic, (4) user interface, and (5) system actions in response to user input. Automated test suite results for the “executable requirements” are shown prior to building the CDS alert, during build, and after successful build. Conclusions Automated acceptance test–driven development and continuous regression testing of CDS configuration in a commercial EHR proves feasible with open source software. Automated test–driven development offers one potential contribution to achieving high-reliability EHR configuration. Vetting acceptance tests with clinicians elicits their input on crucial configuration details early during initial CDS design and iteratively during rapid-cycle optimization. PMID:29653922

Agile Acceptance Test-Driven Development of Clinical Decision Support Advisories: Feasibility of Using Open Source Software.

PubMed

Basit, Mujeeb A; Baldwin, Krystal L; Kannan, Vaishnavi; Flahaven, Emily L; Parks, Cassandra J; Ott, Jason M; Willett, Duwayne L

2018-04-13

Moving to electronic health records (EHRs) confers substantial benefits but risks unintended consequences. Modern EHRs consist of complex software code with extensive local configurability options, which can introduce defects. Defects in clinical decision support (CDS) tools are surprisingly common. Feasible approaches to prevent and detect defects in EHR configuration, including CDS tools, are needed. In complex software systems, use of test-driven development and automated regression testing promotes reliability. Test-driven development encourages modular, testable design and expanding regression test coverage. Automated regression test suites improve software quality, providing a "safety net" for future software modifications. Each automated acceptance test serves multiple purposes, as requirements (prior to build), acceptance testing (on completion of build), regression testing (once live), and "living" design documentation. Rapid-cycle development or "agile" methods are being successfully applied to CDS development. The agile practice of automated test-driven development is not widely adopted, perhaps because most EHR software code is vendor-developed. However, key CDS advisory configuration design decisions and rules stored in the EHR may prove amenable to automated testing as "executable requirements." We aimed to establish feasibility of acceptance test-driven development of clinical decision support advisories in a commonly used EHR, using an open source automated acceptance testing framework (FitNesse). Acceptance tests were initially constructed as spreadsheet tables to facilitate clinical review. Each table specified one aspect of the CDS advisory's expected behavior. Table contents were then imported into a test suite in FitNesse, which queried the EHR database to automate testing. Tests and corresponding CDS configuration were migrated together from the development environment to production, with tests becoming part of the production regression test suite. We used test-driven development to construct a new CDS tool advising Emergency Department nurses to perform a swallowing assessment prior to administering oral medication to a patient with suspected stroke. Test tables specified desired behavior for (1) applicable clinical settings, (2) triggering action, (3) rule logic, (4) user interface, and (5) system actions in response to user input. Automated test suite results for the "executable requirements" are shown prior to building the CDS alert, during build, and after successful build. Automated acceptance test-driven development and continuous regression testing of CDS configuration in a commercial EHR proves feasible with open source software. Automated test-driven development offers one potential contribution to achieving high-reliability EHR configuration. Vetting acceptance tests with clinicians elicits their input on crucial configuration details early during initial CDS design and iteratively during rapid-cycle optimization. ©Mujeeb A Basit, Krystal L Baldwin, Vaishnavi Kannan, Emily L Flahaven, Cassandra J Parks, Jason M Ott, Duwayne L Willett. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 13.04.2018.

Error modelling of quantum Hall array resistance standards

NASA Astrophysics Data System (ADS)

Marzano, Martina; Oe, Takehiko; Ortolano, Massimo; Callegaro, Luca; Kaneko, Nobu-Hisa

2018-04-01

Quantum Hall array resistance standards (QHARSs) are integrated circuits composed of interconnected quantum Hall effect elements that allow the realization of virtually arbitrary resistance values. In recent years, techniques were presented to efficiently design QHARS networks. An open problem is that of the evaluation of the accuracy of a QHARS, which is affected by contact and wire resistances. In this work, we present a general and systematic procedure for the error modelling of QHARSs, which is based on modern circuit analysis techniques and Monte Carlo evaluation of the uncertainty. As a practical example, this method of analysis is applied to the characterization of a 1 MΩ QHARS developed by the National Metrology Institute of Japan. Software tools are provided to apply the procedure to other arrays.

Parallel-hierarchical processing and classification of laser beam profile images based on the GPU-oriented architecture

NASA Astrophysics Data System (ADS)

Yarovyi, Andrii A.; Timchenko, Leonid I.; Kozhemiako, Volodymyr P.; Kokriatskaia, Nataliya I.; Hamdi, Rami R.; Savchuk, Tamara O.; Kulyk, Oleksandr O.; Surtel, Wojciech; Amirgaliyev, Yedilkhan; Kashaganova, Gulzhan

2017-08-01

The paper deals with a problem of insufficient productivity of existing computer means for large image processing, which do not meet modern requirements posed by resource-intensive computing tasks of laser beam profiling. The research concentrated on one of the profiling problems, namely, real-time processing of spot images of the laser beam profile. Development of a theory of parallel-hierarchic transformation allowed to produce models for high-performance parallel-hierarchical processes, as well as algorithms and software for their implementation based on the GPU-oriented architecture using GPGPU technologies. The analyzed performance of suggested computerized tools for processing and classification of laser beam profile images allows to perform real-time processing of dynamic images of various sizes.

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.

Modernization of the Transonic Axial Compressor Test Rig

DTIC Science & Technology

2017-12-01

13. ABSTRACT (maximum 200 words) This work presents the design and simulation process of modernizing the Naval Postgraduate School’s transonic...fabricate the materials. Stiffness tests and modal analysis were conducted via Finite Element Analysis (FEA) software. This analysis was used to design ...work presents the design and simulation process of modernizing the Naval Postgraduate School’s transonic compressor test rig (TCR). The TCR, which

The importance of data curation on QSAR Modeling ...

EPA Pesticide Factsheets

During the last few decades many QSAR models and tools have been developed at the US EPA, including the widely used EPISuite. During this period the arsenal of computational capabilities supporting cheminformatics has broadened dramatically with multiple software packages. These modern tools allow for more advanced techniques in terms of chemical structure representation and storage, as well as enabling automated data-mining and standardization approaches to examine and fix data quality issues.This presentation will investigate the impact of data curation on the reliability of QSAR models being developed within the EPA‘s National Center for Computational Toxicology. As part of this work we have attempted to disentangle the influence of the quality versus quantity of data based on the Syracuse PHYSPROP database partly used by EPISuite software. We will review our automated approaches to examining key datasets related to the EPISuite data to validate across chemical structure representations (e.g., mol file and SMILES) and identifiers (chemical names and registry numbers) and approaches to standardize data into QSAR-ready formats prior to modeling procedures. Our efforts to quantify and segregate data into quality categories has allowed us to evaluate the resulting models that can be developed from these data slices and to quantify to what extent efforts developing high-quality datasets have the expected pay-off in terms of predicting performance. The most accur

ProteoSign: an end-user online differential proteomics statistical analysis platform.

PubMed

Efstathiou, Georgios; Antonakis, Andreas N; Pavlopoulos, Georgios A; Theodosiou, Theodosios; Divanach, Peter; Trudgian, David C; Thomas, Benjamin; Papanikolaou, Nikolas; Aivaliotis, Michalis; Acuto, Oreste; Iliopoulos, Ioannis

2017-07-03

Profiling of proteome dynamics is crucial for understanding cellular behavior in response to intrinsic and extrinsic stimuli and maintenance of homeostasis. Over the last 20 years, mass spectrometry (MS) has emerged as the most powerful tool for large-scale identification and characterization of proteins. Bottom-up proteomics, the most common MS-based proteomics approach, has always been challenging in terms of data management, processing, analysis and visualization, with modern instruments capable of producing several gigabytes of data out of a single experiment. Here, we present ProteoSign, a freely available web application, dedicated in allowing users to perform proteomics differential expression/abundance analysis in a user-friendly and self-explanatory way. Although several non-commercial standalone tools have been developed for post-quantification statistical analysis of proteomics data, most of them are not end-user appealing as they often require very stringent installation of programming environments, third-party software packages and sometimes further scripting or computer programming. To avoid this bottleneck, we have developed a user-friendly software platform accessible via a web interface in order to enable proteomics laboratories and core facilities to statistically analyse quantitative proteomics data sets in a resource-efficient manner. ProteoSign is available at http://bioinformatics.med.uoc.gr/ProteoSign and the source code at https://github.com/yorgodillo/ProteoSign. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

mzStudio: A Dynamic Digital Canvas for User-Driven Interrogation of Mass Spectrometry Data.

PubMed

Ficarro, Scott B; Alexander, William M; Marto, Jarrod A

2017-08-01

Although not yet truly 'comprehensive', modern mass spectrometry-based experiments can generate quantitative data for a meaningful fraction of the human proteome. Importantly for large-scale protein expression analysis, robust data pipelines are in place for identification of un-modified peptide sequences and aggregation of these data to protein-level quantification. However, interoperable software tools that enable scientists to computationally explore and document novel hypotheses for peptide sequence, modification status, or fragmentation behavior are not well-developed. Here, we introduce mzStudio, an open-source Python module built on our multiplierz project. This desktop application provides a highly-interactive graphical user interface (GUI) through which scientists can examine and annotate spectral features, re-search existing PSMs to test different modifications or new spectral matching algorithms, share results with colleagues, integrate other domain-specific software tools, and finally create publication-quality graphics. mzStudio leverages our common application programming interface (mzAPI) for access to native data files from multiple instrument platforms, including ion trap, quadrupole time-of-flight, Orbitrap, matrix-assisted laser desorption ionization, and triple quadrupole mass spectrometers and is compatible with several popular search engines including Mascot, Proteome Discoverer, X!Tandem, and Comet. The mzStudio toolkit enables researchers to create a digital provenance of data analytics and other evidence that support specific peptide sequence assignments.

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.'

American Meteorological Society (AMS) - The Modern Era Retrospective-Analysis for Research and Applications (MERRA) Data and Accessibility

NASA Technical Reports Server (NTRS)

daSilva, Arlindo

2009-01-01

The AM Short Course on The Modern Era Retrospective-analysis for Research and Applications (MERRA) data and accessibility will be held on January 11, 2009 preceding the 89th Annual Meeting in Phoenix, Arizona. Preliminary programs, registration, hotel, and general information will be posted on the AMS Web site in mid-September 2008. Retrospective-analyses (or reanalyses) have been established as an important tool in weather and climate research over the last decade. As computer power increases, the data assimilation and modeling systems improve and become more advanced, the input data quality increases and so reanalyses become more reliable. In 2008, NASA Global Modeling and Assimilation Office began producing a new reanalysis called the Modem Era Retrospective-analysis for Research and Applications (MERRA). The initial data from the reanalysis has been made available to the community and should be complete through 30 years (1979-present) by Fall of 2009. MERRA has taken advantage of the advancement of computing resources to provide users more data than previously available. The native spatial resolution is nominally 1/2 degrees and the surface two dimensional data are one hourly frequency. In addition to the meteorological analysis data, complete mass, energy and momentum budget data and also stratospheric data are provided. The eventual data holdings will exceed 150Tb. In order to facilitate user accessibility to the data, it will be stored in online hard drives (not tape storage) and available through several portals. Subsetting tools will also be available to allow users to tailor their data requests. The goals of this short course are to provide hands on users of reanalyses instruction on MERRA systems and also interactive experience with the online data and access tools. The course is intended for students and research scientists who will be actively interested in accessing and applying MERRA data in their weather, climate or applications work. The course has three parts. There will be an overview of the MERRA system, the validation of the system and the native data format. Second, Instructors will provide examples of weather and climate data analysis using various software packages (primarily GrADS) as well as the online access tools for subsetting and download, as well as visualization (e.g. Giovanni and Google Earth). This will also include examples on changing the data format to fit user's preferences and also to regrid the data for comparisons to other reanalyses and observational data. Lastly, there will he time set aside for participants to have hands on access to the data and software while interacting with the instructors and other developers. The course convener is Dr. Michael Bosilovich, NASA GSFC Global Modeling and Assimilation Office (GMAO). He will be joined by several GMAO, Goddard Earth Science Data and information Services Center (GES DISC) and Software Integration and Visualization Office (SIVO) staff.

Machine learning models for lipophilicity and their domain of applicability.

PubMed

Schroeter, Timon; Schwaighofer, Anton; Mika, Sebastian; Laak, Antonius Ter; Suelzle, Detlev; Ganzer, Ursula; Heinrich, Nikolaus; Müller, Klaus-Robert

2007-01-01

Unfavorable lipophilicity and water solubility cause many drug failures; therefore these properties have to be taken into account early on in lead discovery. Commercial tools for predicting lipophilicity usually have been trained on small and neutral molecules, and are thus often unable to accurately predict in-house data. Using a modern Bayesian machine learning algorithm--a Gaussian process model--this study constructs a log D7 model based on 14,556 drug discovery compounds of Bayer Schering Pharma. Performance is compared with support vector machines, decision trees, ridge regression, and four commercial tools. In a blind test on 7013 new measurements from the last months (including compounds from new projects) 81% were predicted correctly within 1 log unit, compared to only 44% achieved by commercial software. Additional evaluations using public data are presented. We consider error bars for each method (model based error bars, ensemble based, and distance based approaches), and investigate how well they quantify the domain of applicability of each model.

AUSPEX: a graphical tool for X-ray diffraction data analysis.

PubMed

Thorn, Andrea; Parkhurst, James; Emsley, Paul; Nicholls, Robert A; Vollmar, Melanie; Evans, Gwyndaf; Murshudov, Garib N

2017-09-01

In this paper, AUSPEX, a new software tool for experimental X-ray data analysis, is presented. Exploring the behaviour of diffraction intensities and the associated estimated uncertainties facilitates the discovery of underlying problems and can help users to improve their data acquisition and processing in order to obtain better structural models. The program enables users to inspect the distribution of observed intensities (or amplitudes) against resolution as well as the associated estimated uncertainties (sigmas). It is demonstrated how AUSPEX can be used to visually and automatically detect ice-ring artefacts in integrated X-ray diffraction data. Such artefacts can hamper structure determination, but may be difficult to identify from the raw diffraction images produced by modern pixel detectors. The analysis suggests that a significant portion of the data sets deposited in the PDB contain ice-ring artefacts. Furthermore, it is demonstrated how other problems in experimental X-ray data caused, for example, by scaling and data-conversion procedures can be detected by AUSPEX.

Telescience workstation

NASA Technical Reports Server (NTRS)

Brown, Robert L.; Doyle, Dee; Haines, Richard F.; Slocum, Michael

1989-01-01

As part of the Telescience Testbed Pilot Program, the Universities Space Research Association/ Research Institute for Advanced Computer Science (USRA/RIACS) proposed to support remote communication by providing a network of human/machine interfaces, computer resources, and experimental equipment which allows: remote science, collaboration, technical exchange, and multimedia communication. The telescience workstation is intended to provide a local computing environment for telescience. The purpose of the program are as follows: (1) to provide a suitable environment to integrate existing and new software for a telescience workstation; (2) to provide a suitable environment to develop new software in support of telescience activities; (3) to provide an interoperable environment so that a wide variety of workstations may be used in the telescience program; (4) to provide a supportive infrastructure and a common software base; and (5) to advance, apply, and evaluate the telescience technolgy base. A prototype telescience computing environment designed to bring practicing scientists in domains other than their computer science into a modern style of doing their computing was created and deployed. This environment, the Telescience Windowing Environment, Phase 1 (TeleWEn-1), met some, but not all of the goals stated above. The TeleWEn-1 provided a window-based workstation environment and a set of tools for text editing, document preparation, electronic mail, multimedia mail, raster manipulation, and system management.

Improvement of Computer Software Quality through Software Automated Tools.

DTIC Science & Technology

1986-08-31

requirement for increased emphasis on software quality assurance has lead to the creation of various methods of verification and validation. Experience...result was a vast array of methods , systems, languages and automated tools to assist in the process. Given that the primary role of quality assurance is...Unfortunately, there is no single method , tool or technique that can insure accurate, reliable and cost effective software. Therefore, government and industry

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.

BATS: a Bayesian user-friendly software for analyzing time series microarray experiments.

PubMed

Angelini, Claudia; Cutillo, Luisa; De Canditiis, Daniela; Mutarelli, Margherita; Pensky, Marianna

2008-10-06

Gene expression levels in a given cell can be influenced by different factors, namely pharmacological or medical treatments. The response to a given stimulus is usually different for different genes and may depend on time. One of the goals of modern molecular biology is the high-throughput identification of genes associated with a particular treatment or a biological process of interest. From methodological and computational point of view, analyzing high-dimensional time course microarray data requires very specific set of tools which are usually not included in standard software packages. Recently, the authors of this paper developed a fully Bayesian approach which allows one to identify differentially expressed genes in a 'one-sample' time-course microarray experiment, to rank them and to estimate their expression profiles. The method is based on explicit expressions for calculations and, hence, very computationally efficient. The software package BATS (Bayesian Analysis of Time Series) presented here implements the methodology described above. It allows an user to automatically identify and rank differentially expressed genes and to estimate their expression profiles when at least 5-6 time points are available. The package has a user-friendly interface. BATS successfully manages various technical difficulties which arise in time-course microarray experiments, such as a small number of observations, non-uniform sampling intervals and replicated or missing data. BATS is a free user-friendly software for the analysis of both simulated and real microarray time course experiments. The software, the user manual and a brief illustrative example are freely available online at the BATS website: http://www.na.iac.cnr.it/bats.

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.

Software Health Management: A Short Review of Challenges and Existing Techniques

NASA Technical Reports Server (NTRS)

Pipatsrisawat, Knot; Darwiche, Adnan; Mengshoel, Ole J.; Schumann, Johann

2009-01-01

Modern spacecraft (as well as most other complex mechanisms like aircraft, automobiles, and chemical plants) rely more and more on software, to a point where software failures have caused severe accidents and loss of missions. Software failures during a manned mission can cause loss of life, so there are severe requirements to make the software as safe and reliable as possible. Typically, verification and validation (V&V) has the task of making sure that all software errors are found before the software is deployed and that it always conforms to the requirements. Experience, however, shows that this gold standard of error-free software cannot be reached in practice. Even if the software alone is free of glitches, its interoperation with the hardware (e.g., with sensors or actuators) can cause problems. Unexpected operational conditions or changes in the environment may ultimately cause a software system to fail. Is there a way to surmount this problem? In most modern aircraft and many automobiles, hardware such as central electrical, mechanical, and hydraulic components are monitored by IVHM (Integrated Vehicle Health Management) systems. These systems can recognize, isolate, and identify faults and failures, both those that already occurred as well as imminent ones. With the help of diagnostics and prognostics, appropriate mitigation strategies can be selected (replacement or repair, switch to redundant systems, etc.). In this short paper, we discuss some challenges and promising techniques for software health management (SWHM). In particular, we identify unique challenges for preventing software failure in systems which involve both software and hardware components. We then present our classifications of techniques related to SWHM. These classifications are performed based on dimensions of interest to both developers and users of the techniques, and hopefully provide a map for dealing with software faults and failures.

Investigation of near-surface chemical, physical and mechanical properties of silicon carbide crystals and fibers modified by ion implantation

NASA Astrophysics Data System (ADS)

Spitznagel, J. A.; Wood, Susan

1988-08-01

The Software Engineering institute is a federally funded research and development center sponsored by the Department of Defense (DOD). It was chartered by the Undersecretary of Defense for Research and Engineering on June 15, 1984. The SEI was established and is operated by Carnegie Mellon University (CUM) under contract F19628-C-0003, which was competitively awarded on December 28, 1984, by the Air Force Electronic Systems Division. The mission of the SEI is to provide the means to bring the ablest minds and the most effective technology to bear on the rapid improvement of the quality of operational software in mission-critical computer systems; to accelerate the reduction to practice of modern software engineering techniques and methods; to promulgate the use of modern techniques and methods throughout the mission-critical systems community; and to establish standards of excellence for the practice of software engineering. This report provides a summary of the programs and projects, staff, facilities, and service accomplishments of the Software Engineering Institute during 1987.

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.

Evolution of the SOFIA tracking control system

NASA Astrophysics Data System (ADS)

Fiebig, Norbert; Jakob, Holger; Pfüller, Enrico; Röser, Hans-Peter; Wiedemann, Manuel; Wolf, Jürgen

2014-07-01

The airborne observatory SOFIA (Stratospheric Observatory for Infrared Astronomy) is undergoing a modernization of its tracking system. This included new, highly sensitive tracking cameras, control computers, filter wheels and other equipment, as well as a major redesign of the control software. The experiences along the migration path from an aged 19" VMbus based control system to the application of modern industrial PCs, from VxWorks real-time operating system to embedded Linux and a state of the art software architecture are presented. Further, the concept is presented to operate the new camera also as a scientific instrument, in parallel to tracking.

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…

PDS4: Current Status and Future Vision

NASA Astrophysics Data System (ADS)

Crichton, D. J.; Hughes, J. S.; Hardman, S. H.; Law, E. S.; Beebe, R. F.

2017-12-01

In 2010, the Planetary Data System began the largest standards and software upgrade in its history called "PDS4". PDS4 was architected with core principles, applying years of experience and lessons learned working with scientific data returned from robotic solar system missions. In addition to applying those lessons learned, the PDS team was able to take advantage of modern software and data architecture approaches and emerging information technologies which has enabled the capture, management, discovery, and distribution of data from planetary science archives world-wide. What has emerged is a foundational set of standards, services, and common tools to construct and enable interoperability of planetary science archives from distributed repositories. Early in the PDS4 development, PDS selected two missions as drivers to be used to validate the PDS4 approach: LADEE and MAVEN. Additionally, PDS partnered with international agencies to begin discussing the architecture, design, and implementation to ensure that PDS4 would be architected as a world-wide standard and platform for archive development and interoperability. Given the evolving requirements, an agile software development methodology known as the "Evolutionary Software Development Lifecycle" was chosen. This led to incremental releases of increasing capability over time which were matched against emerging mission and user needs. To date, PDS has now performed 16 releases of PDS4 with adoption of over 12 missions world-wide. PDS has also increased from approximately 200 TBs in 2010 to approximately 1.3 PBs of data today, bringing it into the era of big data. The development of PDS4 has not only focused on the construction of compatible archives, but also on increasing access and use of the data in the big data era. As PDS looks forward, it is focused on achieving the recommendations of the Planetary Science Decadal Survey (2013-2022): "support the ongoing effort to evolve the Planetary Data System to an effective online resource for the NASA and international communities". The foundation laid by the standards, software services, and tools positions PDS to develop and adopt new approaches and technologies to enable users to effectively search, extract, integrate, and analyze with the wealth of observational data across international boundaries.

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.

Infrastructure and the Virtual Observatory

NASA Astrophysics Data System (ADS)

Dowler, P.; Gaudet, S.; Schade, D.

2011-07-01

The modern data center is faced with architectural and software engineering challenges that grow along with the challenges facing observatories: massive data flow, distributed computing environments, and distributed teams collaborating on large and small projects. By using VO standards as key components of the infrastructure, projects can take advantage of a decade of intellectual investment by the IVOA community. By their nature, these standards are proven and tested designs that already exist. Adopting VO standards saves considerable design effort, allows projects to take advantage of open-source software and test suites to speed development, and enables the use of third party tools that understand the VO protocols. The evolving CADC architecture now makes heavy use of VO standards. We show examples of how these standards may be used directly, coupled with non-VO standards, or extended with custom capabilities to solve real problems and provide value to our users. In the end, we use VO services as major parts of the core infrastructure to reduce cost rather than as an extra layer with additional cost and we can deliver more general purpose and robust services to our user community.

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.

Development of a Radiation Dose Reporting Software for X-ray Computed Tomography (CT)

NASA Astrophysics Data System (ADS)

Ding, Aiping

X-ray computed tomography (CT) has experienced tremendous technological advances in recent years and has established itself as one of the most popular diagnostic imaging tools. While CT imaging clearly plays an invaluable role in modern medicine, its rapid adoption has resulted in a dramatic increase in the average medical radiation exposure to the worldwide and United States populations. Existing software tools for CT dose estimation and reporting are mostly based on patient phantoms that contain overly simplified anatomies insufficient in meeting the current and future needs. This dissertation describes the development of an easy-to-use software platform, “VirtualDose”, as a service to estimate and report the organ dose and effective dose values for patients undergoing the CT examinations. “VirtualDose” incorporates advanced models for the adult male and female, pregnant women, and children. To cover a large portion of the ignored obese patients that frequents the radiology clinics, a new set of obese male and female phantoms are also developed and applied to study the effects of the fat tissues on the CT radiation dose. Multi-detector CT scanners (MDCT) and clinical protocols, as well as the most recent effective dose algorithms from the International Commission on Radiological Protection (ICRP) Publication 103 are adopted in “VirtualDose” to keep pace with the MDCT development and regulatory requirements. A new MDCT scanner model with both body and head bowtie filter is developed to cover both the head and body scanning modes. This model was validated through the clinical measurements. A comprehensive slice-by-slice database is established by deriving the data from a larger number of single axial scans simulated on the patient phantoms using different CT bowtie filters, beam thicknesses, and different tube voltages in the Monte Carlo N-Particle Extended (MCNPX) code. When compared to the existing CT dose software packages, organ dose data in this software provides a better CT dose assessment by using anatomically realistic patient phantoms. All the related organ doses are incorporated into a standardized database compiled using Microsoft Structured Query Language (SQL) server 2008. Organ doses from contiguous axial or helical scans defined by a specific protocol can be rapidly obtained from the database. A next-generation software architecture and Active Server Pages (ASP) .NET framework are adopted to create a browser-hosted application to improve the user interactivity and reporting functionality including scanning parameter selection and organ dose reporting. “VirtualDose” has been developed as a web-based CT dose reporting platform to facilitate several important features including: (1) easy access via Internet; (2) no need for installation on the local computer; (3) a user-friendly, dynamic, browser-hosted graphical user interface; (4) use of advanced patient models for the adult male and female, pregnant women, children, and obese patient models; (5) adoption of modern CT scanners and protocols, as well as the most recent ICRP 103 effective dose algorithms; and (6) flexibility to manage and easily upgrade without impacting user’s usage.

Application of NX Siemens PLM software in educational process in preparing students of engineering branch

NASA Astrophysics Data System (ADS)

Sadchikova, G. M.

2017-01-01

This article discusses the results of the introduction of computer-aided design NX by Siemens Plm Software to the classes of a higher education institution. The necessity of application of modern information technologies in teaching students of engineering profile and selection of a software product is substantiated. The author describes stages of the software module study in relation to some specific courses, considers the features of NX software, which require the creation of standard and unified product databases. The article also gives examples of research carried out by the students with the various software modules.

Bayesian Software Health Management for Aircraft Guidance, Navigation, and Control

NASA Technical Reports Server (NTRS)

Schumann, Johann; Mbaya, Timmy; Menghoel, Ole

2011-01-01

Modern aircraft, both piloted fly-by-wire commercial aircraft as well as UAVs, more and more depend on highly complex safety critical software systems with many sensors and computer-controlled actuators. Despite careful design and V&V of the software, severe incidents have happened due to malfunctioning software. In this paper, we discuss the use of Bayesian networks (BNs) to monitor the health of the on-board software and sensor system, and to perform advanced on-board diagnostic reasoning. We will focus on the approach to develop reliable and robust health models for the combined software and sensor systems.

Reuseable Objects Software Environment (ROSE): Introduction to Air Force Software Reuse Workshop

NASA Technical Reports Server (NTRS)

Cottrell, William L.

1994-01-01

The Reusable Objects Software Environment (ROSE) is a common, consistent, consolidated implementation of software functionality using modern object oriented software engineering including designed-in reuse and adaptable requirements. ROSE is designed to minimize abstraction and reduce complexity. A planning model for the reverse engineering of selected objects through object oriented analysis is depicted. Dynamic and functional modeling are used to develop a system design, the object design, the language, and a database management system. The return on investment for a ROSE pilot program and timelines are charted.

A Multidimensional Software Engineering Course

ERIC Educational Resources Information Center

Barzilay, O.; Hazzan, O.; Yehudai, A.

2009-01-01

Software engineering (SE) is a multidimensional field that involves activities in various areas and disciplines, such as computer science, project management, and system engineering. Though modern SE curricula include designated courses that address these various subjects, an advanced summary course that synthesizes them is still missing. Such a…

Rearchitecting IT: Simplify. Simplify

ERIC Educational Resources Information Center

Panettieri, Joseph C.

2006-01-01

Simplifying and securing an IT infrastructure is not easy. It frequently requires rethinking years of hardware and software investments, and a gradual migration to modern systems. Even so, writes the author, universities can take six practical steps to success: (1) Audit software infrastructure; (2) Evaluate current applications; (3) Centralize…

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.

Cscibox: A Software System for Age-Model Construction and Evaluation

NASA Astrophysics Data System (ADS)

Bradley, E.; Anderson, K. A.; Marchitto, T. M., Jr.; de Vesine, L. R.; White, J. W. C.; Anderson, D. M.

2014-12-01

CSciBox is an integrated software system for the construction and evaluation of age models of paleo-environmetal archives, both directly dated and cross dated. The time has come to encourage cross-pollinization between earth science and computer science in dating paleorecords. This project addresses that need. The CSciBox code, which is being developed by a team of computer scientists and geoscientists, is open source and freely available on github. The system employs modern database technology to store paleoclimate proxy data and analysis results in an easily accessible and searchable form. This makes it possible to do analysis on the whole core at once, in an interactive fashion, or to tailor the analysis to a subset of the core without loading the entire data file. CSciBox provides a number of 'components' that perform the common steps in age-model construction and evaluation: calibrations, reservoir-age correction, interpolations, statistics, and so on. The user employs these components via a graphical user interface (GUI) to go from raw data to finished age model in a single tool: e.g., an IntCal09 calibration of 14C data from a marine sediment core, followed by a piecewise-linear interpolation. CSciBox's GUI supports plotting of any measurement in the core against any other measurement, or against any of the variables in the calculation of the age model-with or without explicit error representations. Using the GUI, CSciBox's user can import a new calibration curve or other background data set and define a new module that employs that information. Users can also incorporate other software (e.g., Calib, BACON) as 'plug ins.' In the case of truly large data or significant computational effort, CSciBox is parallelizable across modern multicore processors, or clusters, or even the cloud. The next generation of the CSciBox code, currently in the testing stages, includes an automated reasoning engine that supports a more-thorough exploration of plausible age models and cross-dating scenarios.

Modernizing Earth and Space Science Modeling Workflows in the Big Data Era

NASA Astrophysics Data System (ADS)

Kinter, J. L.; Feigelson, E.; Walker, R. J.; Tino, C.

2017-12-01

Modeling is a major aspect of the Earth and space science research. The development of numerical models of the Earth system, planetary systems or astrophysical systems is essential to linking theory with observations. Optimal use of observations that are quite expensive to obtain and maintain typically requires data assimilation that involves numerical models. In the Earth sciences, models of the physical climate system are typically used for data assimilation, climate projection, and inter-disciplinary research, spanning applications from analysis of multi-sensor data sets to decision-making in climate-sensitive sectors with applications to ecosystems, hazards, and various biogeochemical processes. In space physics, most models are from first principles, require considerable expertise to run and are frequently modified significantly for each case study. The volume and variety of model output data from modeling Earth and space systems are rapidly increasing and have reached a scale where human interaction with data is prohibitively inefficient. A major barrier to progress is that modeling workflows isn't deemed by practitioners to be a design problem. Existing workflows have been created by a slow accretion of software, typically based on undocumented, inflexible scripts haphazardly modified by a succession of scientists and students not trained in modern software engineering methods. As a result, existing modeling workflows suffer from an inability to onboard new datasets into models; an inability to keep pace with accelerating data production rates; and irreproducibility, among other problems. These factors are creating an untenable situation for those conducting and supporting Earth system and space science. Improving modeling workflows requires investments in hardware, software and human resources. This paper describes the critical path issues that must be targeted to accelerate modeling workflows, including script modularization, parallelization, and automation in the near term, and longer term investments in virtualized environments for improved scalability, tolerance for lossy data compression, novel data-centric memory and storage technologies, and tools for peer reviewing, preserving and sharing workflows, as well as fundamental statistical and machine learning algorithms.

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.

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...

Innovations for the future of pharmacovigilance.

PubMed

Almenoff, June S

2007-01-01

Post-marketing pharmacovigilance involves the review and management of safety information from many sources. Among these sources, spontaneous adverse event reporting systems are among the most challenging and resource-intensive to manage. Traditionally, efforts to monitor spontaneous adverse event reporting systems have focused on review of individual case reports. The science of pharmacovigilance could be enhanced with the availability of systems-based tools that facilitate analysis of aggregate data for purposes of signal detection, signal evaluation and knowledge management. GlaxoSmithKline (GSK) recently implemented Online Signal Management (OSM) as a data-driven framework for managing the pharmacovigilance of marketed products. This pioneering work builds upon the strong history GSK has of innovation in this area. OSM is a software application co-developed by GSK and Lincoln Technologies that integrates traditional pharmacovigilance methods with modern quantitative statistical methods and data visualisation tools. OSM enables the rapid identification of trends from the individual adverse event reports received by GSK. OSM also provides knowledge-management tools to ensure the successful tracking of emerging safety issues. GSK has developed standard procedures and 'best practices' around the use of OSM to ensure the systematic evaluation of complex safety datasets. In summary, the implementation of OSM provides new tools and efficient processes to advance the science of pharmacovigilance.

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.

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.

The Singing Rod (in the Modern Age)

ERIC Educational Resources Information Center

Lasby, B.; O'Meara, J. M.; Williams, M.

2014-01-01

This is a classic classroom demonstration of resonance, nodes, anti-nodes, and standing waves that has been described elsewhere. The modern age twist that we are advocating is the coupling of this classic demo with free (or relatively inexpensive) sound analysis software, thereby allowing for quantitative analysis of resonance while experimenting…

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

Ganalyzer: A Tool for Automatic Galaxy Image Analysis

NASA Astrophysics Data System (ADS)

Shamir, Lior

2011-08-01

We describe Ganalyzer, a model-based tool that can automatically analyze and classify galaxy images. Ganalyzer works by separating the galaxy pixels from the background pixels, finding the center and radius of the galaxy, generating the radial intensity plot, and then computing the slopes of the peaks detected in the radial intensity plot to measure the spirality of the galaxy and determine its morphological class. Unlike algorithms that are based on machine learning, Ganalyzer is based on measuring the spirality of the galaxy, a task that is difficult to perform manually, and in many cases can provide a more accurate analysis compared to manual observation. Ganalyzer is simple to use, and can be easily embedded into other image analysis applications. Another advantage is its speed, which allows it to analyze ~10,000,000 galaxy images in five days using a standard modern desktop computer. These capabilities can make Ganalyzer a useful tool in analyzing large data sets of galaxy images collected by autonomous sky surveys such as SDSS, LSST, or DES. The software is available for free download at http://vfacstaff.ltu.edu/lshamir/downloads/ganalyzer, and the data used in the experiment are available at http://vfacstaff.ltu.edu/lshamir/downloads/ganalyzer/GalaxyImages.zip.

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

Williams, Edward J., Jr.; Henry, Karen Lynne

Sandia National Laboratories develops technologies to: (1) sustain, modernize, and protect our nuclear arsenal (2) Prevent the spread of weapons of mass destruction; (3) Provide new capabilities to our armed forces; (4) Protect our national infrastructure; (5) Ensure the stability of our nation's energy and water supplies; and (6) Defend our nation against terrorist threats. We identified the need for a single overarching Integrated Workplace Management System (IWMS) that would enable us to focus on customer missions and improve FMOC processes. Our team selected highly configurable commercial-off-the-shelf (COTS) software with out-of-the-box workflow processes that integrate strategic planning, project management, facilitymore » assessments, and space management, and can interface with existing systems, such as Oracle, PeopleSoft, Maximo, Bentley, and FileNet. We selected the Integrated Workplace Management System (IWMS) from Tririga, Inc. Facility Management System (FMS) Benefits are: (1) Create a single reliable source for facility data; (2) Improve transparency with oversight organizations; (3) Streamline FMOC business processes with a single, integrated facility-management tool; (4) Give customers simple tools and real-time information; (5) Reduce indirect costs; (6) Replace approximately 30 FMOC systems and 60 homegrown tools (such as Microsoft Access databases); and (7) Integrate with FIMS.« less

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.

Computer implemented method, and apparatus for controlling a hand-held tool

NASA Technical Reports Server (NTRS)

Wagner, Kenneth William (Inventor); Taylor, James Clayton (Inventor)

1999-01-01

The invention described here in is a computer-implemented method and apparatus for controlling a hand-held tool. In particular, the control of a hand held tool is for the purpose of controlling the speed of a fastener interface mechanism and the torque applied to fasteners by the fastener interface mechanism of the hand-held tool and monitoring the operating parameters of the tool. The control is embodied in intool software embedded on a processor within the tool which also communicates with remote software. An operator can run the tool, or through the interaction of both software, operate the tool from a remote location, analyze data from a performance history recorded by the tool, and select various torque and speed parameters for each fastener.

Lessons learned applying CASE methods/tools to Ada software development projects

NASA Technical Reports Server (NTRS)

Blumberg, Maurice H.; Randall, Richard L.

1993-01-01

This paper describes the lessons learned from introducing CASE methods/tools into organizations and applying them to actual Ada software development projects. This paper will be useful to any organization planning to introduce a software engineering environment (SEE) or evolving an existing one. It contains management level lessons learned, as well as lessons learned in using specific SEE tools/methods. The experiences presented are from Alpha Test projects established under the STARS (Software Technology for Adaptable and Reliable Systems) project. They reflect the front end efforts by those projects to understand the tools/methods, initial experiences in their introduction and use, and later experiences in the use of specific tools/methods and the introduction of new ones.

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.

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.

Industrial Inspection with Open Eyes: Advance with Machine Vision Technology

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

Liu, Zheng; Ukida, H.; Niel, Kurt

Machine vision systems have evolved significantly with the technology advances to tackle the challenges from modern manufacturing industry. A wide range of industrial inspection applications for quality control are benefiting from visual information captured by different types of cameras variously configured in a machine vision system. This chapter screens the state of the art in machine vision technologies in the light of hardware, software tools, and major algorithm advances for industrial inspection. The inspection beyond visual spectrum offers a significant complementary to the visual inspection. The combination with multiple technologies makes it possible for the inspection to achieve a bettermore » performance and efficiency in varied applications. The diversity of the applications demonstrates the great potential of machine vision systems for industry.« less

Glycoprotein Enrichment Analytical Techniques: Advantages and Disadvantages.

PubMed

Zhu, R; Zacharias, L; Wooding, K M; Peng, W; Mechref, Y

2017-01-01

Protein glycosylation is one of the most important posttranslational modifications. Numerous biological functions are related to protein glycosylation. However, analytical challenges remain in the glycoprotein analysis. To overcome the challenges associated with glycoprotein analysis, many analytical techniques were developed in recent years. Enrichment methods were used to improve the sensitivity of detection, while HPLC and mass spectrometry methods were developed to facilitate the separation of glycopeptides/proteins and enhance detection, respectively. Fragmentation techniques applied in modern mass spectrometers allow the structural interpretation of glycopeptides/proteins, while automated software tools started replacing manual processing to improve the reliability and throughput of the analysis. In this chapter, the current methodologies of glycoprotein analysis were discussed. Multiple analytical techniques are compared, and advantages and disadvantages of each technique are highlighted. © 2017 Elsevier Inc. All rights reserved.

CHAPTER 7: Glycoprotein Enrichment Analytical Techniques: Advantages and Disadvantages

PubMed Central

Zhu, Rui; Zacharias, Lauren; Wooding, Kerry M.; Peng, Wenjing; Mechref, Yehia

2017-01-01

Protein glycosylation is one of the most important posttranslational modifications. Numerous biological functions are related to protein glycosylation. However, analytical challenges remain in the glycoprotein analysis. To overcome the challenges associated with glycoprotein analysis, many analytical techniques were developed in recent years. Enrichment methods were used to improve the sensitivity of detection while HPLC and mass spectrometry methods were developed to facilitate the separation of glycopeptides/proteins and enhance detection, respectively. Fragmentation techniques applied in modern mass spectrometers allow the structural interpretation of glycopeptides/proteins while automated software tools started replacing manual processing to improve the reliability and throughout of the analysis. In this chapter, the current methodologies of glycoprotein analysis were discussed. Multiple analytical techniques are compared, and advantages and disadvantages of each technique are highlighted. PMID:28109440

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 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

General Purpose Data-Driven Monitoring for Space Operations

NASA Technical Reports Server (NTRS)

Iverson, David L.; Martin, Rodney A.; Schwabacher, Mark A.; Spirkovska, Liljana; Taylor, William McCaa; Castle, Joseph P.; Mackey, Ryan M.

2009-01-01

As modern space propulsion and exploration systems improve in capability and efficiency, their designs are becoming increasingly sophisticated and complex. Determining the health state of these systems, using traditional parameter limit checking, model-based, or rule-based methods, is becoming more difficult as the number of sensors and component interactions grow. Data-driven monitoring techniques have been developed to address these issues by analyzing system operations data to automatically characterize normal system behavior. System health can be monitored by comparing real-time operating data with these nominal characterizations, providing detection of anomalous data signatures indicative of system faults or failures. The Inductive Monitoring System (IMS) is a data-driven system health monitoring software tool that has been successfully applied to several aerospace applications. IMS uses a data mining technique called clustering to analyze archived system data and characterize normal interactions between parameters. The scope of IMS based data-driven monitoring applications continues to expand with current development activities. Successful IMS deployment in the International Space Station (ISS) flight control room to monitor ISS attitude control systems has led to applications in other ISS flight control disciplines, such as thermal control. It has also generated interest in data-driven monitoring capability for Constellation, NASA's program to replace the Space Shuttle with new launch vehicles and spacecraft capable of returning astronauts to the moon, and then on to Mars. Several projects are currently underway to evaluate and mature the IMS technology and complementary tools for use in the Constellation program. These include an experiment on board the Air Force TacSat-3 satellite, and ground systems monitoring for NASA's Ares I-X and Ares I launch vehicles. The TacSat-3 Vehicle System Management (TVSM) project is a software experiment to integrate fault and anomaly detection algorithms and diagnosis tools with executive and adaptive planning functions contained in the flight software on-board the Air Force Research Laboratory TacSat-3 satellite. The TVSM software package will be uploaded after launch to monitor spacecraft subsystems such as power and guidance, navigation, and control (GN&C). It will analyze data in real-time to demonstrate detection of faults and unusual conditions, diagnose problems, and react to threats to spacecraft health and mission goals. The experiment will demonstrate the feasibility and effectiveness of integrated system health management (ISHM) technologies with both ground and on-board experiments.

Let's Scrum! Learning Digital Media Collaboratively

ERIC Educational Resources Information Center

Wilson, Daniel G.; Brown, Joshua; Burke, Adam A.

2013-01-01

The changing landscape of digital media and software development has immense impact on society, not only through consumer use of the products, but also in the way these technologies are developed. Modern software and media-development companies are using collaborative methods to develop innovative and useful products. Technology and engineering…

Real Time Network Monitoring and Reporting System

ERIC Educational Resources Information Center

Massengale, Ricky L., Sr.

2009-01-01

With the ability of modern system developers to develop intelligent programs that allows machines to learn, modify and evolve themselves, current trends of reactionary methods to detect and eradicate malicious software code from infected machines is proving to be too costly. Addressing malicious software after an attack is the current methodology…

MIRO and IRbase: IT Tools for the Epidemiological Monitoring of Insecticide Resistance in Mosquito Disease Vectors

PubMed Central

Dialynas, Emmanuel; Topalis, Pantelis; Vontas, John; Louis, Christos

2009-01-01

Background Monitoring of insect vector populations with respect to their susceptibility to one or more insecticides is a crucial element of the strategies used for the control of arthropod-borne diseases. This management task can nowadays be achieved more efficiently when assisted by IT (Information Technology) tools, ranging from modern integrated databases to GIS (Geographic Information System). Here we describe an application ontology that we developed de novo, and a specially designed database that, based on this ontology, can be used for the purpose of controlling mosquitoes and, thus, the diseases that they transmit. Methodology/Principal Findings The ontology, named MIRO for Mosquito Insecticide Resistance Ontology, developed using the OBO-Edit software, describes all pertinent aspects of insecticide resistance, including specific methodology and mode of action. MIRO, then, forms the basis for the design and development of a dedicated database, IRbase, constructed using open source software, which can be used to retrieve data on mosquito populations in a temporally and spatially separate way, as well as to map the output using a Google Earth interface. The dependency of the database on the MIRO allows for a rational and efficient hierarchical search possibility. Conclusions/Significance The fact that the MIRO complies with the rules set forward by the OBO (Open Biomedical Ontologies) Foundry introduces cross-referencing with other biomedical ontologies and, thus, both MIRO and IRbase are suitable as parts of future comprehensive surveillance tools and decision support systems that will be used for the control of vector-borne diseases. MIRO is downloadable from and IRbase is accessible at VectorBase, the NIAID-sponsored open access database for arthropod vectors of disease. PMID:19547750

StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics

PubMed Central

Ramirez-Gonzalez, Ricardo H.; Leggett, Richard M.; Waite, Darren; Thanki, Anil; Drou, Nizar; Caccamo, Mario; Davey, Robert

2014-01-01

Modern sequencing platforms generate enormous quantities of data in ever-decreasing amounts of time. Additionally, techniques such as multiplex sequencing allow one run to contain hundreds of different samples. With such data comes a significant challenge to understand its quality and to understand how the quality and yield are changing across instruments and over time. As well as the desire to understand historical data, sequencing centres often have a duty to provide clear summaries of individual run performance to collaborators or customers. We present StatsDB, an open-source software package for storage and analysis of next generation sequencing run metrics. The system has been designed for incorporation into a primary analysis pipeline, either at the programmatic level or via integration into existing user interfaces. Statistics are stored in an SQL database and APIs provide the ability to store and access the data while abstracting the underlying database design. This abstraction allows simpler, wider querying across multiple fields than is possible by the manual steps and calculation required to dissect individual reports, e.g. ”provide metrics about nucleotide bias in libraries using adaptor barcode X, across all runs on sequencer A, within the last month”. The software is supplied with modules for storage of statistics from FastQC, a commonly used tool for analysis of sequence reads, but the open nature of the database schema means it can be easily adapted to other tools. Currently at The Genome Analysis Centre (TGAC), reports are accessed through our LIMS system or through a standalone GUI tool, but the API and supplied examples make it easy to develop custom reports and to interface with other packages. PMID:24627795

Modernized build and test infrastructure for control software at ESO: highly flexible building, testing, and automatic quality practices for telescope control software

NASA Astrophysics Data System (ADS)

Pellegrin, F.; Jeram, B.; Haucke, J.; Feyrin, S.

2016-07-01

The paper describes the introduction of a new automatized build and test infrastructure, based on the open-source software Jenkins1, into the ESO Very Large Telescope control software to replace the preexisting in-house solution. A brief introduction to software quality practices is given, a description of the previous solution, the limitations of it and new upcoming requirements. Modifications required to adapt the new system are described, how these were implemented to current software and the results obtained. An overview on how the new system may be used in future projects is also presented.

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.

Software reengineering

NASA Technical Reports Server (NTRS)

Fridge, Ernest M., III

1991-01-01

Programs in use today generally have all of the function and information processing capabilities required to do their specified job. However, older programs usually use obsolete technology, are not integrated properly with other programs, and are difficult to maintain. Reengineering is becoming a prominent discipline as organizations try to move their systems to more modern and maintainable technologies. The Johnson Space Center (JSC) Software Technology Branch (STB) is researching and developing a system to support reengineering older FORTRAN programs into more maintainable forms that can also be more readily translated to a modern languages such as FORTRAN 8x, Ada, or C. This activity has led to the development of maintenance strategies for design recovery and reengineering. These strategies include a set of standards, methodologies, and the concepts for a software environment to support design recovery and reengineering. A brief description of the problem being addressed and the approach that is being taken by the STB toward providing an economic solution to the problem is provided. A statement of the maintenance problems, the benefits and drawbacks of three alternative solutions, and a brief history of the STB experience in software reengineering are followed by the STB new FORTRAN standards, methodology, and the concepts for a software environment.

The Value of Open Source Software Tools in Qualitative Research

ERIC Educational Resources Information Center

Greenberg, Gary

2011-01-01

In an era of global networks, researchers using qualitative methods must consider the impact of any software they use on the sharing of data and findings. In this essay, I identify researchers' main areas of concern regarding the use of qualitative software packages for research. I then examine how open source software tools, wherein the publisher…

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.…

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

NASA Technical Reports Server (NTRS)

Campbell, R. H.; Badger, W.; Beckman, C. S.; Beshers, G.; Hammerslag, D.; Kimball, J.; Kirslis, P. A.; Render, H.; Richards, P.; Terwilliger, R.

1984-01-01

The project to automate the management of software production systems is described. 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. Several major components of the SAGA system are completed to prototype form. The construction methods are described.

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…

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.

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.

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

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.

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.

SSAGES: Software Suite for Advanced General Ensemble Simulations

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

Sidky, Hythem; Colón, Yamil J.; Helfferich, Julian

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods, and that facilitates implementation of new techniquesmore » as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite.« less

The Planning and Scheduling of HST: Improvements and Enhancements since Launch

NASA Astrophysics Data System (ADS)

Taylor, D. K.; Chance, D. R.; Jordan, I. J. E.; Patterson, A. P.; Stanley, M.; Taylor, D. C.

2001-12-01

The planning and scheduling (P&S) systems used in operating the Hubble Space Telescope (HST) have undergone such substantial and pervasive re-engineering that today they dimly resemble those used when HST was launched. Processes (i.e., software, procedures, networking, etc.) which allow program implementation, the generation of a Long Range Plan (LRP), and the scheduling of science and mission activities have improved drastically in nearly 12 years, resulting in a consistently high observing efficiency, a stable LRP that principal investigators can use, exceptionally clean command loads uplinked to the spacecraft, and the capability of a very fast response time due to onboard anomalies or targets of opportunity. In this presentation we describe many of the systems which comprise the P&S ("front-end") system for HST, how and why they were improved, and what benefits have been realized by either the HST user community or the STScI staff. The systems include the Guide Star System, the Remote Proposal Submission System - 2 (RPS2), Artificial Intelligence (AI) planning tools such as Spike, and the science and mission scheduling software. We also describe how using modern software languages such as Python and better development practices allow STScI staff to do more with HST (e.g., to handle much more science data when ACS is installed) without increasing the cost to HST operations.

Porting and redesign of Geotool software system to Qt

NASA Astrophysics Data System (ADS)

Miljanovic Tamarit, V.; Carneiro, L.; Henson, I. H.; Tomuta, E.

2016-12-01

Geotool is a software system that allows a user to interactively display and process seismoacoustic data from International Monitoring System (IMS) station. Geotool can be used to perform a number of analysis and review tasks, including data I/O, waveform filtering, quality control, component rotation, amplitude and arrival measurement and review, array beamforming, correlation, Fourier analysis, FK analysis, event review and location, particle motion visualization, polarization analysis, instrument response convolution/deconvolution, real-time display, signal to noise measurement, spectrogram, and travel time model display. The Geotool program was originally written in C using the X11/Xt/Motif libraries for graphics. It was later ported to C++. Now the program is being ported to the Qt graphics system to be more compatible with the other software in the International Data Centre (IDC). Along with this port, a redesign of the architecture is underway to achieve a separation between user interface, control, and data model elements, in line with design patterns such as Model-View-Controller. Qt is a cross-platform application framework that will allow geotool to easily run on Linux, Mac, and Windows. The Qt environment includes modern libraries and user interfaces for standard utilities such as file and database access, printing, and inter-process communications. The Qt Widgets for Technical Applications library (QWT) provides tools for displaying standard data analysis graphics.

SSAGES: Software Suite for Advanced General Ensemble Simulations.

PubMed

Sidky, Hythem; Colón, Yamil J; Helfferich, Julian; Sikora, Benjamin J; Bezik, Cody; Chu, Weiwei; Giberti, Federico; Guo, Ashley Z; Jiang, Xikai; Lequieu, Joshua; Li, Jiyuan; Moller, Joshua; Quevillon, Michael J; Rahimi, Mohammad; Ramezani-Dakhel, Hadi; Rathee, Vikramjit S; Reid, Daniel R; Sevgen, Emre; Thapar, Vikram; Webb, Michael A; Whitmer, Jonathan K; de Pablo, Juan J

2018-01-28

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques-including adaptive biasing force, string methods, and forward flux sampling-that extract meaningful free energy and transition path data from all-atom and coarse-grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite. The code may be found at: https://github.com/MICCoM/SSAGES-public.

SSAGES: Software Suite for Advanced General Ensemble Simulations

NASA Astrophysics Data System (ADS)

Sidky, Hythem; Colón, Yamil J.; Helfferich, Julian; Sikora, Benjamin J.; Bezik, Cody; Chu, Weiwei; Giberti, Federico; Guo, Ashley Z.; Jiang, Xikai; Lequieu, Joshua; Li, Jiyuan; Moller, Joshua; Quevillon, Michael J.; Rahimi, Mohammad; Ramezani-Dakhel, Hadi; Rathee, Vikramjit S.; Reid, Daniel R.; Sevgen, Emre; Thapar, Vikram; Webb, Michael A.; Whitmer, Jonathan K.; de Pablo, Juan J.

2018-01-01

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse-grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite. The code may be found at: https://github.com/MICCoM/SSAGES-public.

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.

Modern Material Analysis Instruments Add a New Dimension to Materials Characterization and Failure Analysis

NASA Technical Reports Server (NTRS)

Panda, Binayak

2009-01-01

Modern analytical tools can yield invaluable results during materials characterization and failure analysis. Scanning electron microscopes (SEMs) provide significant analytical capabilities, including angstrom-level resolution. These systems can be equipped with a silicon drift detector (SDD) for very fast yet precise analytical mapping of phases, as well as electron back-scattered diffraction (EBSD) units to map grain orientations, chambers that admit large samples, variable pressure for wet samples, and quantitative analysis software to examine phases. Advanced solid-state electronics have also improved surface and bulk analysis instruments: Secondary ion mass spectroscopy (SIMS) can quantitatively determine and map light elements such as hydrogen, lithium, and boron - with their isotopes. Its high sensitivity detects impurities at parts per billion (ppb) levels. X-ray photo-electron spectroscopy (XPS) can determine oxidation states of elements, as well as identifying polymers and measuring film thicknesses on coated composites. This technique is also known as electron spectroscopy for chemical analysis (ESCA). Scanning Auger electron spectroscopy (SAM) combines surface sensitivity, spatial lateral resolution (10 nm), and depth profiling capabilities to describe elemental compositions of near and below surface regions down to the chemical state of an atom.

An Overview of Cloud Implementation in the Manufacturing Process Life Cycle

NASA Astrophysics Data System (ADS)

Kassim, Noordiana; Yusof, Yusri; Hakim Mohamad, Mahmod Abd; Omar, Abdul Halim; Roslan, Rosfuzah; Aryanie Bahrudin, Ida; Ali, Mohd Hatta Mohamed

2017-08-01

The advancement of information and communication technology (ICT) has changed the structure and functions of various sectors and it has also started to play a significant role in modern manufacturing in terms of computerized machining and cloud manufacturing. It is important for industries to keep up with the current trend of ICT for them to be able survive and be competitive. Cloud manufacturing is an approach that wanted to realize a real-world manufacturing processes that will apply the basic concept from the field of Cloud computing to the manufacturing domain called Cloud-based manufacturing (CBM) or cloud manufacturing (CM). Cloud manufacturing has been recognized as a new paradigm for manufacturing businesses. In cloud manufacturing, manufacturing companies need to support flexible and scalable business processes in the shop floor as well as the software itself. This paper provides an insight or overview on the implementation of cloud manufacturing in the modern manufacturing processes and at the same times analyses the requirements needed regarding process enactment for Cloud manufacturing and at the same time proposing a STEP-NC concept that can function as a tool to support the cloud manufacturing concept.

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.

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.

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.

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2016-11-01

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

Development of an irrigation scheduling software based on model predicted crop water stress

USDA-ARS?s Scientific Manuscript database

Modern irrigation scheduling methods are generally based on sensor-monitored soil moisture regimes rather than crop water stress which is difficult to measure in real-time, but can be computed using agricultural system models. In this study, an irrigation scheduling software based on RZWQM2 model pr...

How In-Service Teachers Develop Electronic Lessons

ERIC Educational Resources Information Center

Zsoldos-Marchis, Iuliana

2014-01-01

Computer assisted teaching (CAL) is considered to be a modern teaching method, but it is not widely used by teachers because lack of technology and adequate educational softwares in schools; or lack of teachers' knowledge on methodology and computer use. In order to select the most efficient educational software for their class, teachers should…

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

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.

SNAPSHOT: A MODERN, SUSTAINABLE HOLDUP MEASUREMENT SYSTEM

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

Rowe, Nathan C; Younkin, James R; Smith, Steven E

2016-01-01

SNAPSHOT is a software platform designed to eventually replace Holdup Measurement System 4 (HMS 4), which is the current state-of-the-art for acquisition and analysis of nondestructive assay measurement data for in situ nuclear materials, holdup, in support of criticality safety and material control and accounting. HMS 4 is over 10 years old and is currently unsustainable due to hardware and software incompatibilities that have arisen from advances in detector electronics, primarily updates to multi-channel analyzers (MCAs), and both computer and handheld operating systems. SNAPSHOT is a complete redesign of HMS 4 that addresses the issue of compatibility with modern MCAsmore » and operating systems and that is designed with a flexible architecture to support long-term sustainability. It also provides an updated and more user friendly interface and is being developed under an NQA 1 software quality assurance (SQA) program to facilitate site acceptance for safety-related applications. This paper provides an overview of the SNAPSHOT project including details of the software development process, the SQA program, and the architecture designed to support sustainability.« less

GraphCrunch 2: Software tool for network modeling, alignment and clustering.

PubMed

Kuchaiev, Oleksii; Stevanović, Aleksandar; Hayes, Wayne; Pržulj, Nataša

2011-01-19

Recent advancements in experimental biotechnology have produced large amounts of protein-protein interaction (PPI) data. The topology of PPI networks is believed to have a strong link to their function. Hence, the abundance of PPI data for many organisms stimulates the development of computational techniques for the modeling, comparison, alignment, and clustering of networks. In addition, finding representative models for PPI networks will improve our understanding of the cell just as a model of gravity has helped us understand planetary motion. To decide if a model is representative, we need quantitative comparisons of model networks to real ones. However, exact network comparison is computationally intractable and therefore several heuristics have been used instead. Some of these heuristics are easily computable "network properties," such as the degree distribution, or the clustering coefficient. An important special case of network comparison is the network alignment problem. Analogous to sequence alignment, this problem asks to find the "best" mapping between regions in two networks. It is expected that network alignment might have as strong an impact on our understanding of biology as sequence alignment has had. Topology-based clustering of nodes in PPI networks is another example of an important network analysis problem that can uncover relationships between interaction patterns and phenotype. We introduce the GraphCrunch 2 software tool, which addresses these problems. It is a significant extension of GraphCrunch which implements the most popular random network models and compares them with the data networks with respect to many network properties. Also, GraphCrunch 2 implements the GRAph ALigner algorithm ("GRAAL") for purely topological network alignment. GRAAL can align any pair of networks and exposes large, dense, contiguous regions of topological and functional similarities far larger than any other existing tool. Finally, GraphCruch 2 implements an algorithm for clustering nodes within a network based solely on their topological similarities. Using GraphCrunch 2, we demonstrate that eukaryotic and viral PPI networks may belong to different graph model families and show that topology-based clustering can reveal important functional similarities between proteins within yeast and human PPI networks. GraphCrunch 2 is a software tool that implements the latest research on biological network analysis. It parallelizes computationally intensive tasks to fully utilize the potential of modern multi-core CPUs. It is open-source and freely available for research use. It runs under the Windows and Linux platforms.

WebViz: A web browser based application for collaborative analysis of 3D data

NASA Astrophysics Data System (ADS)

Ruegg, C. S.

2011-12-01

In the age of high speed Internet where people can interact instantly, scientific tools have lacked technology which can incorporate this concept of communication using the web. To solve this issue a web application for geological studies has been created, tentatively titled WebViz. This web application utilizes tools provided by Google Web Toolkit to create an AJAX web application capable of features found in non web based software. Using these tools, a web application can be created to act as piece of software from anywhere in the globe with a reasonably speedy Internet connection. An application of this technology can be seen with data regarding the recent tsunami from the major japan earthquakes. After constructing the appropriate data to fit a computer render software called HVR, WebViz can request images of the tsunami data and display it to anyone who has access to the application. This convenience alone makes WebViz a viable solution, but the option to interact with this data with others around the world causes WebViz to be taken as a serious computational tool. WebViz also can be used on any javascript enabled browser such as those found on modern tablets and smart phones over a fast wireless connection. Due to the fact that WebViz's current state is built using Google Web Toolkit the portability of the application is in it's most efficient form. Though many developers have been involved with the project, each person has contributed to increase the usability and speed of the application. In the project's most recent form a dramatic speed increase has been designed as well as a more efficient user interface. The speed increase has been informally noticed in recent uses of the application in China and Australia with the hosting server being located at the University of Minnesota. The user interface has been improved to not only look better but the functionality has been improved. Major functions of the application are rotating the 3D object using buttons. These buttons have been replaced with a new layout that is easier to understand the function and is also easy to use with mobile devices. With these new changes, WebViz is easier to control and use for general use.

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.

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.

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.

Performing Quantitative Imaging Acquisition, Analysis and Visualization Using the Best of Open Source and Commercial Software Solutions.

PubMed

Shenoy, Shailesh M

2016-07-01

A challenge in any imaging laboratory, especially one that uses modern techniques, is to achieve a sustainable and productive balance between using open source and commercial software to perform quantitative image acquisition, analysis and visualization. In addition to considering the expense of software licensing, one must consider factors such as the quality and usefulness of the software's support, training and documentation. Also, one must consider the reproducibility with which multiple people generate results using the same software to perform the same analysis, how one may distribute their methods to the community using the software and the potential for achieving automation to improve productivity.

GEAS Spectroscopy Tools for Authentic Research Investigations in the Classroom

NASA Astrophysics Data System (ADS)

Rector, Travis A.; Vogt, Nicole P.

2018-06-01

Spectroscopy is one of the most powerful tools that astronomers use to study the universe. However relatively few resources are available that enable undergraduates to explore astronomical spectra interactively. We present web-based applications which guide students through the analysis of real spectra of stars, galaxies, and quasars. The tools are written in HTML5 and function in all modern web browsers on computers and tablets. No software needs to be installed nor do any datasets need to be downloaded, enabling students to use the tools in or outside of class (e.g., for online classes).Approachable GUIs allow students to analyze spectra in the same manner as professional astronomers. The stellar spectroscopy tool can fit a continuum with a blackbody and identify spectral features, as well as fit line profiles and determine equivalent widths. The galaxy and AGN tools can also measure redshifts and calcium break strengths. The tools provide access to an archive of hundreds of spectra obtained with the optical telescopes at Kitt Peak National Observatory. It is also possible to load your own spectra or to query the Sloan Digital Sky Survey (SDSS) database.We have also developed curricula to investigate these topics: spectral classification, variable stars, redshift, and AGN classification. We will present the functionality of the tools and describe the associated curriculum. The tools are part of the General Education Astronomy Source (GEAS) project based at New Mexico State University, with support from the National Science Foundation (NSF, AST-0349155) and the National Aeronautics and Space Administration (NASA, NNX09AV36G). Curriculum development was supported by the NSF (DUE-0618849 and DUE-0920293).

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)

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.

Advances in molecular labeling, high throughput imaging and machine intelligence portend powerful functional cellular biochemistry tools.

PubMed

Price, Jeffrey H; Goodacre, Angela; Hahn, Klaus; Hodgson, Louis; Hunter, Edward A; Krajewski, Stanislaw; Murphy, Robert F; Rabinovich, Andrew; Reed, John C; Heynen, Susanne

2002-01-01

Cellular behavior is complex. Successfully understanding systems at ever-increasing complexity is fundamental to advances in modern science and unraveling the functional details of cellular behavior is no exception. We present a collection of prospectives to provide a glimpse of the techniques that will aid in collecting, managing and utilizing information on complex cellular processes via molecular imaging tools. These include: 1) visualizing intracellular protein activity with fluorescent markers, 2) high throughput (and automated) imaging of multilabeled cells in statistically significant numbers, and 3) machine intelligence to analyze subcellular image localization and pattern. Although not addressed here, the importance of combining cell-image-based information with detailed molecular structure and ligand-receptor binding models cannot be overlooked. Advanced molecular imaging techniques have the potential to impact cellular diagnostics for cancer screening, clinical correlations of tissue molecular patterns for cancer biology, and cellular molecular interactions for accelerating drug discovery. The goal of finally understanding all cellular components and behaviors will be achieved by advances in both instrumentation engineering (software and hardware) and molecular biochemistry. Copyright 2002 Wiley-Liss, Inc.

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.

ImagePy: an open-source, Python-based and platform-independent software package for boimage analysis.

PubMed

Wang, Anliang; Yan, Xiaolong; Wei, Zhijun

2018-04-27

This note presents the design of a scalable software package named ImagePy for analysing biological images. Our contribution is concentrated on facilitating extensibility and interoperability of the software through decoupling the data model from the user interface. Especially with assistance from the Python ecosystem, this software framework makes modern computer algorithms easier to be applied in bioimage analysis. ImagePy is free and open source software, with documentation and code available at https://github.com/Image-Py/imagepy under the BSD license. It has been tested on the Windows, Mac and Linux operating systems. wzjdlut@dlut.edu.cn or yxdragon@imagepy.org.

Scalability and Validation of Big Data Bioinformatics Software.

PubMed

Yang, Andrian; Troup, Michael; Ho, Joshua W K

2017-01-01

This review examines two important aspects that are central to modern big data bioinformatics analysis - software scalability and validity. We argue that not only are the issues of scalability and validation common to all big data bioinformatics analyses, they can be tackled by conceptually related methodological approaches, namely divide-and-conquer (scalability) and multiple executions (validation). Scalability is defined as the ability for a program to scale based on workload. It has always been an important consideration when developing bioinformatics algorithms and programs. Nonetheless the surge of volume and variety of biological and biomedical data has posed new challenges. We discuss how modern cloud computing and big data programming frameworks such as MapReduce and Spark are being used to effectively implement divide-and-conquer in a distributed computing environment. Validation of software is another important issue in big data bioinformatics that is often ignored. Software validation is the process of determining whether the program under test fulfils the task for which it was designed. Determining the correctness of the computational output of big data bioinformatics software is especially difficult due to the large input space and complex algorithms involved. We discuss how state-of-the-art software testing techniques that are based on the idea of multiple executions, such as metamorphic testing, can be used to implement an effective bioinformatics quality assurance strategy. We hope this review will raise awareness of these critical issues in bioinformatics.

Use of Software Tools in Teaching Relational Database Design.

ERIC Educational Resources Information Center

McIntyre, D. R.; And Others

1995-01-01

Discusses the use of state-of-the-art software tools in teaching a graduate, advanced, relational database design course. Results indicated a positive student response to the prototype of expert systems software and a willingness to utilize this new technology both in their studies and in future work applications. (JKP)

Analyzing the Core Flight Software (CFS) with SAVE

NASA Technical Reports Server (NTRS)

Ganesan, Dharmalingam; Lindvall, Mikael; McComas, David

2008-01-01

This viewgraph presentation describes the SAVE tool and it's application to Core Flight Software (CFS). The contents include: 1) Fraunhofer-a short intro; 2) Context of this Collaboration; 3) CFS-Core Flight Software?; 4) The SAVE Tool; 5) Applying SAVE to CFS -A few example analyses; and 6) Goals.

Designing and Using Software Tools for Educational Purposes: FLAT, a Case Study

ERIC Educational Resources Information Center

Castro-Schez, J. J.; del Castillo, E.; Hortolano, J.; Rodriguez, A.

2009-01-01

Educational software tools are considered to enrich teaching strategies, providing a more compelling means of exploration and feedback than traditional blackboard methods. Moreover, software simulators provide a more motivating link between theory and practice than pencil-paper methods, encouraging active and discovery learning in the students.…

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

ERIC Educational Resources Information Center

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

2017-01-01

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

Introducing the CUAHSI Hydrologic Information System Desktop Application (HydroDesktop) and Open Development Community

NASA Astrophysics Data System (ADS)

Ames, D.; Kadlec, J.; Horsburgh, J. S.; Maidment, D. R.

2009-12-01

The Consortium of Universities for the Advancement of Hydrologic Sciences (CUAHSI) Hydrologic Information System (HIS) project includes extensive development of data storage and delivery tools and standards including WaterML (a language for sharing hydrologic data sets via web services); and HIS Server (a software tool set for delivering WaterML from a server); These and other CUASHI HIS tools have been under development and deployment for several years and together, present a relatively complete software “stack” to support the consistent storage and delivery of hydrologic and other environmental observation data. This presentation describes the development of a new HIS software tool called “HydroDesktop” and the development of an online open source software development community to update and maintain the software. HydroDesktop is a local (i.e. not server-based) client side software tool that ultimately will run on multiple operating systems and will provide a highly usable level of access to HIS services. The software provides many key capabilities including data query, map-based visualization, data download, local data maintenance, editing, graphing, data export to selected model-specific data formats, linkage with integrated modeling systems such as OpenMI, and ultimately upload to HIS servers from the local desktop software. As the software is presently in the early stages of development, this presentation will focus on design approach and paradigm and is viewed as an opportunity to encourage participation in the open development community. Indeed, recognizing the value of community based code development as a means of ensuring end-user adoption, this project has adopted an “iterative” or “spiral” software development approach which will be described in this presentation.

Final Technical Report - Center for Technology for Advanced Scientific Component Software (TASCS)

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

Sussman, Alan

2014-10-21

This is a final technical report for the University of Maryland work in the SciDAC Center for Technology for Advanced Scientific Component Software (TASCS). The Maryland work focused on software tools for coupling parallel software components built using the Common Component Architecture (CCA) APIs. Those tools are based on the Maryland InterComm software framework that has been used in multiple computational science applications to build large-scale simulations of complex physical systems that employ multiple separately developed codes.

Bildung as a Powerful Tool in Modern University Teaching

ERIC Educational Resources Information Center

Olesen, Mogens Noergaard

2009-01-01

In this paper we will demonstrate how powerful "Bildung" is as a tool in modern university teaching. The concept of "Bildung" was originally introduced by the German philosopher Immanuel Kant (Kant 1787, 1798, 1804) and the Prussian lawyer and politician Wilhelm von Humboldt (Humboldt 1792, Bohlin 2008). From 1810…

New in protein structure and function annotation: hotspots, single nucleotide polymorphisms and the 'Deep Web'.

PubMed

Bromberg, Yana; Yachdav, Guy; Ofran, Yanay; Schneider, Reinhard; Rost, Burkhard

2009-05-01

The rapidly increasing quantity of protein sequence data continues to widen the gap between available sequences and annotations. Comparative modeling suggests some aspects of the 3D structures of approximately half of all known proteins; homology- and network-based inferences annotate some aspect of function for a similar fraction of the proteome. For most known protein sequences, however, there is detailed knowledge about neither their function nor their structure. Comprehensive efforts towards the expert curation of sequence annotations have failed to meet the demand of the rapidly increasing number of available sequences. Only the automated prediction of protein function in the absence of homology can close the gap between available sequences and annotations in the foreseeable future. This review focuses on two novel methods for automated annotation, and briefly presents an outlook on how modern web software may revolutionize the field of protein sequence annotation. First, predictions of protein binding sites and functional hotspots, and the evolution of these into the most successful type of prediction of protein function from sequence will be discussed. Second, a new tool, comprehensive in silico mutagenesis, which contributes important novel predictions of function and at the same time prepares for the onset of the next sequencing revolution, will be described. While these two new sub-fields of protein prediction represent the breakthroughs that have been achieved methodologically, it will then be argued that a different development might further change the way biomedical researchers benefit from annotations: modern web software can connect the worldwide web in any browser with the 'Deep Web' (ie, proprietary data resources). The availability of this direct connection, and the resulting access to a wealth of data, may impact drug discovery and development more than any existing method that contributes to protein annotation.

DCMS: A data analytics and management system for molecular simulation.

PubMed

Kumar, Anand; Grupcev, Vladimir; Berrada, Meryem; Fogarty, Joseph C; Tu, Yi-Cheng; Zhu, Xingquan; Pandit, Sagar A; Xia, Yuni

Molecular Simulation (MS) is a powerful tool for studying physical/chemical features of large systems and has seen applications in many scientific and engineering domains. During the simulation process, the experiments generate a very large number of atoms and intend to observe their spatial and temporal relationships for scientific analysis. The sheer data volumes and their intensive interactions impose significant challenges for data accessing, managing, and analysis. To date, existing MS software systems fall short on storage and handling of MS data, mainly because of the missing of a platform to support applications that involve intensive data access and analytical process. In this paper, we present the database-centric molecular simulation (DCMS) system our team developed in the past few years. The main idea behind DCMS is to store MS data in a relational database management system (DBMS) to take advantage of the declarative query interface ( i.e. , SQL), data access methods, query processing, and optimization mechanisms of modern DBMSs. A unique challenge is to handle the analytical queries that are often compute-intensive. For that, we developed novel indexing and query processing strategies (including algorithms running on modern co-processors) as integrated components of the DBMS. As a result, researchers can upload and analyze their data using efficient functions implemented inside the DBMS. Index structures are generated to store analysis results that may be interesting to other users, so that the results are readily available without duplicating the analysis. We have developed a prototype of DCMS based on the PostgreSQL system and experiments using real MS data and workload show that DCMS significantly outperforms existing MS software systems. We also used it as a platform to test other data management issues such as security and compression.

SAM Theory Manual

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

Hu, Rui

The System Analysis Module (SAM) is an advanced and modern system analysis tool being developed at Argonne National Laboratory under the U.S. DOE Office of Nuclear Energy’s Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. SAM development aims for advances in physical modeling, numerical methods, and software engineering to enhance its user experience and usability for reactor transient analyses. To facilitate the code development, SAM utilizes an object-oriented application framework (MOOSE), and its underlying meshing and finite-element library (libMesh) and linear and non-linear solvers (PETSc), to leverage modern advanced software environments and numerical methods. SAM focuses on modeling advanced reactormore » concepts such as SFRs (sodium fast reactors), LFRs (lead-cooled fast reactors), and FHRs (fluoride-salt-cooled high temperature reactors) or MSRs (molten salt reactors). These advanced concepts are distinguished from light-water reactors in their use of single-phase, low-pressure, high-temperature, and low Prandtl number (sodium and lead) coolants. As a new code development, the initial effort has been focused on modeling and simulation capabilities of heat transfer and single-phase fluid dynamics responses in Sodium-cooled Fast Reactor (SFR) systems. The system-level simulation capabilities of fluid flow and heat transfer in general engineering systems and typical SFRs have been verified and validated. This document provides the theoretical and technical basis of the code to help users understand the underlying physical models (such as governing equations, closure models, and component models), system modeling approaches, numerical discretization and solution methods, and the overall capabilities in SAM. As the code is still under ongoing development, this SAM Theory Manual will be updated periodically to keep it consistent with the state of the development.« less

Computer Synthesis Approaches of Hyperboloid Gear Drives with Linear Contact

NASA Astrophysics Data System (ADS)

Abadjiev, Valentin; Kawasaki, Haruhisa

2014-09-01

The computer design has improved forming different type software for scientific researches in the field of gearing theory as well as performing an adequate scientific support of the gear drives manufacture. Here are attached computer programs that are based on mathematical models as a result of scientific researches. The modern gear transmissions require the construction of new mathematical approaches to their geometric, technological and strength analysis. The process of optimization, synthesis and design is based on adequate iteration procedures to find out an optimal solution by varying definite parameters. The study is dedicated to accepted methodology in the creation of soft- ware for the synthesis of a class high reduction hyperboloid gears - Spiroid and Helicon ones (Spiroid and Helicon are trademarks registered by the Illinois Tool Works, Chicago, Ill). The developed basic computer products belong to software, based on original mathematical models. They are based on the two mathematical models for the synthesis: "upon a pitch contact point" and "upon a mesh region". Computer programs are worked out on the basis of the described mathematical models, and the relations between them are shown. The application of the shown approaches to the synthesis of commented gear drives is illustrated.

High-throughput bioinformatics with the Cyrille2 pipeline system

PubMed Central

Fiers, Mark WEJ; van der Burgt, Ate; Datema, Erwin; de Groot, Joost CW; van Ham, Roeland CHJ

2008-01-01

Background Modern omics research involves the application of high-throughput technologies that generate vast volumes of data. These data need to be pre-processed, analyzed and integrated with existing knowledge through the use of diverse sets of software tools, models and databases. The analyses are often interdependent and chained together to form complex workflows or pipelines. Given the volume of the data used and the multitude of computational resources available, specialized pipeline software is required to make high-throughput analysis of large-scale omics datasets feasible. Results We have developed a generic pipeline system called Cyrille2. The system is modular in design and consists of three functionally distinct parts: 1) a web based, graphical user interface (GUI) that enables a pipeline operator to manage the system; 2) the Scheduler, which forms the functional core of the system and which tracks what data enters the system and determines what jobs must be scheduled for execution, and; 3) the Executor, which searches for scheduled jobs and executes these on a compute cluster. Conclusion The Cyrille2 system is an extensible, modular system, implementing the stated requirements. Cyrille2 enables easy creation and execution of high throughput, flexible bioinformatics pipelines. PMID:18269742

OrthoANI: An improved algorithm and software for calculating average nucleotide identity.

PubMed

Lee, Imchang; Ouk Kim, Yeong; Park, Sang-Cheol; Chun, Jongsik

2016-02-01

Species demarcation in Bacteria and Archaea is mainly based on overall genome relatedness, which serves a framework for modern microbiology. Current practice for obtaining these measures between two strains is shifting from experimentally determined similarity obtained by DNA-DNA hybridization (DDH) to genome-sequence-based similarity. Average nucleotide identity (ANI) is a simple algorithm that mimics DDH. Like DDH, ANI values between two genome sequences may be different from each other when reciprocal calculations are compared. We compared 63 690 pairs of genome sequences and found that the differences in reciprocal ANI values are significantly high, exceeding 1 % in some cases. To resolve this problem of not being symmetrical, a new algorithm, named OrthoANI, was developed to accommodate the concept of orthology for which both genome sequences were fragmented and only orthologous fragment pairs taken into consideration for calculating nucleotide identities. OrthoANI is highly correlated with ANI (using BLASTn) and the former showed approximately 0.1 % higher values than the latter. In conclusion, OrthoANI provides a more robust and faster means of calculating average nucleotide identity for taxonomic purposes. The standalone software tools are freely available at http://www.ezbiocloud.net/sw/oat.

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

PubMed

Hannisdal, E

1996-01-01

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

BiNA: A Visual Analytics Tool for Biological Network Data

PubMed Central

Gerasch, Andreas; Faber, Daniel; Küntzer, Jan; Niermann, Peter; Kohlbacher, Oliver; Lenhof, Hans-Peter; Kaufmann, Michael

2014-01-01

Interactive visual analysis of biological high-throughput data in the context of the underlying networks is an essential task in modern biomedicine with applications ranging from metabolic engineering to personalized medicine. The complexity and heterogeneity of data sets require flexible software architectures for data analysis. Concise and easily readable graphical representation of data and interactive navigation of large data sets are essential in this context. We present BiNA - the Biological Network Analyzer - a flexible open-source software for analyzing and visualizing biological networks. Highly configurable visualization styles for regulatory and metabolic network data offer sophisticated drawings and intuitive navigation and exploration techniques using hierarchical graph concepts. The generic projection and analysis framework provides powerful functionalities for visual analyses of high-throughput omics data in the context of networks, in particular for the differential analysis and the analysis of time series data. A direct interface to an underlying data warehouse provides fast access to a wide range of semantically integrated biological network databases. A plugin system allows simple customization and integration of new analysis algorithms or visual representations. BiNA is available under the 3-clause BSD license at http://bina.unipax.info/. PMID:24551056

An Adaptable Seismic Data Format for Modern Scientific Workflows

NASA Astrophysics Data System (ADS)

Smith, J. A.; Bozdag, E.; Krischer, L.; Lefebvre, M.; Lei, W.; Podhorszki, N.; Tromp, J.

2013-12-01

Data storage, exchange, and access play a critical role in modern seismology. Current seismic data formats, such as SEED, SAC, and SEG-Y, were designed with specific applications in mind and are frequently a major bottleneck in implementing efficient workflows. We propose a new modern parallel format that can be adapted for a variety of seismic workflows. The Adaptable Seismic Data Format (ASDF) features high-performance parallel read and write support and the ability to store an arbitrary number of traces of varying sizes. Provenance information is stored inside the file so that users know the origin of the data as well as the precise operations that have been applied to the waveforms. The design of the new format is based on several real-world use cases, including earthquake seismology and seismic interferometry. The metadata is based on the proven XML schemas StationXML and QuakeML. Existing time-series analysis tool-kits are easily interfaced with this new format so that seismologists can use robust, previously developed software packages, such as ObsPy and the SAC library. ADIOS, netCDF4, and HDF5 can be used as the underlying container format. At Princeton University, we have chosen to use ADIOS as the container format because it has shown superior scalability for certain applications, such as dealing with big data on HPC systems. In the context of high-performance computing, we have implemented ASDF into the global adjoint tomography workflow on Oak Ridge National Laboratory's supercomputer Titan.

Extending the knowledge in histochemistry and cell biology.

PubMed

Heupel, Wolfgang-Moritz; Drenckhahn, Detlev

2010-01-01

Central to modern Histochemistry and Cell Biology stands the need for visualization of cellular and molecular processes. In the past several years, a variety of techniques has been achieved bridging traditional light microscopy, fluorescence microscopy and electron microscopy with powerful software-based post-processing and computer modeling. Researchers now have various tools available to investigate problems of interest from bird's- up to worm's-eye of view, focusing on tissues, cells, proteins or finally single molecules. Applications of new approaches in combination with well-established traditional techniques of mRNA, DNA or protein analysis have led to enlightening and prudent studies which have paved the way toward a better understanding of not only physiological but also pathological processes in the field of cell biology. This review is intended to summarize articles standing for the progress made in "histo-biochemical" techniques and their manifold applications.

Additive manufacturing technology in reconstructive surgery.

PubMed

Fuller, Scott C; Moore, Michael G

2016-10-01

Technological advances have been part and parcel of modern reconstructive surgery, in that practitioners of this discipline are continually looking for innovative ways to perfect their craft and improve patient outcomes. We are currently in a technological climate wherein advances in computers, imaging, and science have coalesced with resulting innovative breakthroughs that are not merely limited to improved outcomes and enhanced patient care, but may provide novel approaches to training the next generation of reconstructive surgeons. New developments in software and modeling platforms, imaging modalities, tissue engineering, additive manufacturing, and customization of implants are poised to revolutionize the field of reconstructive surgery. The interface between technological advances and reconstructive surgery continues to expand. Additive manufacturing techniques continue to evolve in an effort to improve patient outcomes, decrease operative time, and serve as instructional tools for the training of reconstructive surgeons.

Visualization of LC-MS/MS proteomics data in MaxQuant.

PubMed

Tyanova, Stefka; Temu, Tikira; Carlson, Arthur; Sinitcyn, Pavel; Mann, Matthias; Cox, Juergen

2015-04-01

Modern software platforms enable the analysis of shotgun proteomics data in an automated fashion resulting in high quality identification and quantification results. Additional understanding of the underlying data can be gained with the help of advanced visualization tools that allow for easy navigation through large LC-MS/MS datasets potentially consisting of terabytes of raw data. The updated MaxQuant version has a map navigation component that steers the users through mass and retention time-dependent mass spectrometric signals. It can be used to monitor a peptide feature used in label-free quantification over many LC-MS runs and visualize it with advanced 3D graphic models. An expert annotation system aids the interpretation of the MS/MS spectra used for the identification of these peptide features. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Big data analytics for early detection of breast cancer based on machine learning

NASA Astrophysics Data System (ADS)

Ivanova, Desislava

2017-12-01

This paper presents the concept and the modern advances in personalized medicine that rely on technology and review the existing tools for early detection of breast cancer. The breast cancer types and distribution worldwide is discussed. It is spent time to explain the importance of identifying the normality and to specify the main classes in breast cancer, benign or malignant. The main purpose of the paper is to propose a conceptual model for early detection of breast cancer based on machine learning for processing and analysis of medical big dataand further knowledge discovery for personalized treatment. The proposed conceptual model is realized by using Naive Bayes classifier. The software is written in python programming language and for the experiments the Wisconsin breast cancer database is used. Finally, the experimental results are presented and discussed.

User experience integrated life-style cloud-based medical application.

PubMed

Serban, Alexandru; Lupşe, Oana Sorina; Stoicu-Tivadar, Lăcrămioara

2015-01-01

Having a modern application capable to automatically collect and process data from users, based on information and lifestyle answers is one of current challenges for researchers and medical science. The purpose of the current study is to integrate user experience design (UXD) in a cloud-based medical application to improve patient safety, quality of care and organizational efficiency. The process consists of collecting traditional and new data from patients and users using online questionnaires. A questionnaire dynamically asks questions about the user's current diet and lifestyle. After the user will introduce the data, the application will formulate a presumptive nutritional plan and will suggest different medical recommendations regarding a healthy lifestyle, and calculates a risk factor for diseases. This software application, by design and usability will be an efficient tool dedicated for fitness, nutrition and health professionals.

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

Science.gov Websites

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

Computer-Aided Process and Tools for Mobile Software Acquisition

DTIC Science & Technology

2013-04-01

Software Acquisition Christopher Bonine , Man-Tak Shing, and Thomas W. Otani Naval Postgraduate School Published April 1, 2013 Approved for public...ManTech International Corporation Computer-Aided Process and Tools for Mobile Software Acquisition Christopher Bonine , Man-Tak Shing, and Thomas W. Otani...Mobile Software Acquisition Christopher Bonine — Bonine is a lieutenant in the United States Navy. He is currently assigned to the Navy Cyber Defense

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.

Airplane numerical simulation for the rapid prototyping process

NASA Astrophysics Data System (ADS)

Roysdon, Paul F.

Airplane Numerical Simulation for the Rapid Prototyping Process is a comprehensive research investigation into the most up-to-date methods for airplane development and design. Uses of modern engineering software tools, like MatLab and Excel, are presented with examples of batch and optimization algorithms which combine the computing power of MatLab with robust aerodynamic tools like XFOIL and AVL. The resulting data is demonstrated in the development and use of a full non-linear six-degrees-of-freedom simulator. The applications for this numerical tool-box vary from un-manned aerial vehicles to first-order analysis of manned aircraft. A Blended-Wing-Body airplane is used for the analysis to demonstrate the flexibility of the code from classic wing-and-tail configurations to less common configurations like the blended-wing-body. This configuration has been shown to have superior aerodynamic performance -- in contrast to their classic wing-and-tube fuselage counterparts -- and have reduced sensitivity to aerodynamic flutter as well as potential for increased engine noise abatement. Of course without a classic tail elevator to damp the nose up pitching moment, and the vertical tail rudder to damp the yaw and possible rolling aerodynamics, the challenges in lateral roll and yaw stability, as well as pitching moment are not insignificant. This thesis work applies the tools necessary to perform the airplane development and optimization on a rapid basis, demonstrating the strength of this tool through examples and comparison of the results to similar airplane performance characteristics published in literature.

Gene Unprediction with Spurio: A tool to identify spurious protein sequences.

PubMed

Höps, Wolfram; Jeffryes, Matt; Bateman, Alex

2018-01-01

We now have access to the sequences of tens of millions of proteins. These protein sequences are essential for modern molecular biology and computational biology. The vast majority of protein sequences are derived from gene prediction tools and have no experimental supporting evidence for their translation.  Despite the increasing accuracy of gene prediction tools there likely exists a large number of spurious protein predictions in the sequence databases.  We have developed the Spurio tool to help identify spurious protein predictions in prokaryotes.  Spurio searches the query protein sequence against a prokaryotic nucleotide database using tblastn and identifies homologous sequences. The tblastn matches are used to score the query sequence's likelihood of being a spurious protein prediction using a Gaussian process model. The most informative feature is the appearance of stop codons within the presumed translation of homologous DNA sequences. Benchmarking shows that the Spurio tool is able to distinguish spurious from true proteins. However, transposon proteins are prone to be predicted as spurious because of the frequency of degraded homologs found in the DNA sequence databases. Our initial experiments suggest that less than 1% of the proteins in the UniProtKB sequence database are likely to be spurious and that Spurio is able to identify over 60 times more spurious proteins than the AntiFam resource. The Spurio software and source code is available under an MIT license at the following URL: https://bitbucket.org/bateman-group/spurio.

Interactive metagenomic visualization in a Web browser.

PubMed

Ondov, Brian D; Bergman, Nicholas H; Phillippy, Adam M

2011-09-30

A critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. The inherent uncertainty in assignments to these groups makes it important to consider both their hierarchical contexts and their prediction confidence. The current tools for visualizing metagenomic data, however, omit or distort quantitative hierarchical relationships and lack the facility for displaying secondary variables. Here we present Krona, a new visualization tool that allows intuitive exploration of relative abundances and confidences within the complex hierarchies of metagenomic classifications. Krona combines a variant of radial, space-filling displays with parametric coloring and interactive polar-coordinate zooming. The HTML5 and JavaScript implementation enables fully interactive charts that can be explored with any modern Web browser, without the need for installed software or plug-ins. This Web-based architecture also allows each chart to be an independent document, making them easy to share via e-mail or post to a standard Web server. To illustrate Krona's utility, we describe its application to various metagenomic data sets and its compatibility with popular metagenomic analysis tools. Krona is both a powerful metagenomic visualization tool and a demonstration of the potential of HTML5 for highly accessible bioinformatic visualizations. Its rich and interactive displays facilitate more informed interpretations of metagenomic analyses, while its implementation as a browser-based application makes it extremely portable and easily adopted into existing analysis packages. Both the Krona rendering code and conversion tools are freely available under a BSD open-source license, and available from: http://krona.sourceforge.net.

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

PubMed

Lee, Kuo-Wei; Lee, Ying-Chu

2012-01-01

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

SU-F-J-72: A Clinical Usable Integrated Contouring Quality Evaluation Software for Radiotherapy

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

Jiang, S; Dolly, S; Cai, B

Purpose: To introduce the Auto Contour Evaluation (ACE) software, which is the clinical usable, user friendly, efficient and all-in-one toolbox for automatically identify common contouring errors in radiotherapy treatment planning using supervised machine learning techniques. Methods: ACE is developed with C# using Microsoft .Net framework and Windows Presentation Foundation (WPF) for elegant GUI design and smooth GUI transition animations through the integration of graphics engines and high dots per inch (DPI) settings on modern high resolution monitors. The industrial standard software design pattern, Model-View-ViewModel (MVVM) pattern, is chosen to be the major architecture of ACE for neat coding structure, deepmore » modularization, easy maintainability and seamless communication with other clinical software. ACE consists of 1) a patient data importing module integrated with clinical patient database server, 2) a 2D DICOM image and RT structure simultaneously displaying module, 3) a 3D RT structure visualization module using Visualization Toolkit or VTK library and 4) a contour evaluation module using supervised pattern recognition algorithms to detect contouring errors and display detection results. ACE relies on supervised learning algorithms to handle all image processing and data processing jobs. Implementations of related algorithms are powered by Accord.Net scientific computing library for better efficiency and effectiveness. Results: ACE can take patient’s CT images and RT structures from commercial treatment planning software via direct user input or from patients’ database. All functionalities including 2D and 3D image visualization and RT contours error detection have been demonstrated with real clinical patient cases. Conclusion: ACE implements supervised learning algorithms and combines image processing and graphical visualization modules for RT contours verification. ACE has great potential for automated radiotherapy contouring quality verification. Structured with MVVM pattern, it is highly maintainable and extensible, and support smooth connections with other clinical software tools.« less

Planetary Geologic Mapping Handbook - 2010. Appendix

NASA Technical Reports Server (NTRS)

Tanaka, K. L.; Skinner, J. A., Jr.; Hare, T. M.

2010-01-01

Geologic maps present, in an historical context, fundamental syntheses of interpretations of the materials, landforms, structures, and processes that characterize planetary surfaces and shallow subsurfaces. Such maps also provide a contextual framework for summarizing and evaluating thematic research for a given region or body. In planetary exploration, for example, geologic maps are used for specialized investigations such as targeting regions of interest for data collection and for characterizing sites for landed missions. Whereas most modern terrestrial geologic maps are constructed from regional views provided by remote sensing data and supplemented in detail by field-based observations and measurements, planetary maps have been largely based on analyses of orbital photography. For planetary bodies in particular, geologic maps commonly represent a snapshot of a surface, because they are based on available information at a time when new data are still being acquired. Thus the field of planetary geologic mapping has been evolving rapidly to embrace the use of new data and modern technology and to accommodate the growing needs of planetary exploration. Planetary geologic maps have been published by the U.S. Geological Survey (USGS) since 1962. Over this time, numerous maps of several planetary bodies have been prepared at a variety of scales and projections using the best available image and topographic bases. Early geologic map bases commonly consisted of hand-mosaicked photographs or airbrushed shaded-relief views and geologic linework was manually drafted using mylar bases and ink drafting pens. Map publishing required a tedious process of scribing, color peel-coat preparation, typesetting, and photo-laboratory work. Beginning in the 1990s, inexpensive computing, display capability and user-friendly illustration software allowed maps to be drawn using digital tools rather than pen and ink, and mylar bases became obsolete. Terrestrial geologic maps published by the USGS now are primarily digital products using geographic information system (GIS) software and file formats. GIS mapping tools permit easy spatial comparison, generation, importation, manipulation, and analysis of multiple raster image, gridded, and vector data sets. GIS software has also permitted the development of projectspecific tools and the sharing of geospatial products among researchers. GIS approaches are now being used in planetary geologic mapping as well. Guidelines or handbooks on techniques in planetary geologic mapping have been developed periodically. As records of the heritage of mapping methods and data, these remain extremely useful guides. However, many of the fundamental aspects of earlier mapping handbooks have evolved significantly, and a comprehensive review of currently accepted mapping methodologies is now warranted. As documented in this handbook, such a review incorporates additional guidelines developed in recent years for planetary geologic mapping by the NASA Planetary Geology and Geophysics (PGG) Program's Planetary Cartography and Geologic Mapping Working Group's (PCGMWG) Geologic Mapping Subcommittee (GEMS) on the selection and use of map bases as well as map preparation, review, publication, and distribution. In light of the current boom in planetary exploration and the ongoing rapid evolution of available data for planetary mapping, this handbook is especially timely.

Use of NMR and NMR Prediction Software to Identify Components in Red Bull Energy Drinks

ERIC Educational Resources Information Center

Simpson, Andre J.; Shirzadi, Azadeh; Burrow, Timothy E.; Dicks, Andrew P.; Lefebvre, Brent; Corrin, Tricia

2009-01-01

A laboratory experiment designed as part of an upper-level undergraduate analytical chemistry course is described. Students investigate two popular soft drinks (Red Bull Energy Drink and sugar-free Red Bull Energy Drink) by NMR spectroscopy. With assistance of modern NMR prediction software they identify and quantify major components in each…

The GenABEL Project for statistical genomics.

PubMed

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

2016-01-01

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

20 CFR 619.1 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-04-01

... inquiries and responses between SWAs. Major IT Modernization Project means conversion, re-engineering..., or upgrading software libraries, protocols, or hardware platform and infrastructure. These are...

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.

Machine Tool Software

NASA Technical Reports Server (NTRS)

1988-01-01

A NASA-developed software package has played a part in technical education of students who major in Mechanical Engineering Technology at William Rainey Harper College. Professor Hack has been using (APT) Automatically Programmed Tool Software since 1969 in his CAD/CAM Computer Aided Design and Manufacturing curriculum. Professor Hack teaches the use of APT programming languages for control of metal cutting machines. Machine tool instructions are geometry definitions written in APT Language to constitute a "part program." The part program is processed by the machine tool. CAD/CAM students go from writing a program to cutting steel in the course of a semester.

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

NASA Technical Reports Server (NTRS)

Ramakrishnan, Sudhakar

1995-01-01

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

USER'S GUIDE: Strategic Waste Minimization Initiative (SWAMI) Version 2.0 - A Software Tool to Aid in Process Analysis for Pollution Prevention

EPA Science Inventory

The Strategic WAste Minimization Initiative (SWAMI) Software, Version 2.0 is a tool for using process analysis for identifying waste minimization opportunities within an industrial setting. The software requires user-supplied information for process definition, as well as materia...

76 FR 5832 - International Business Machines (IBM), Software Group Business Unit, Optim Data Studio Tools QA...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-02

... DEPARTMENT OF LABOR Employment and Training Administration [TA-W-74,554] International Business Machines (IBM), Software Group Business Unit, Optim Data Studio Tools QA, San Jose, CA; Notice of... determination of the TAA petition filed on behalf of workers at International Business Machines (IBM), Software...

An Overview of Public Access Computer Software Management Tools for Libraries

ERIC Educational Resources Information Center

Wayne, Richard

2004-01-01

An IT decision maker gives an overview of public access PC software that's useful in controlling session length and scheduling, Internet access, print output, security, and the latest headaches: spyware and adware. In this article, the author describes a representative sample of software tools in several important categories such as setup…

A Multifaceted Approach to Modernizing NASA's Advanced Multi-Mission Operations System (AMMOS) System Architecture

NASA Technical Reports Server (NTRS)

Estefan, Jeff A.; Giovannoni, Brian J.

2014-01-01

The Advanced Multi-Mission Operations Systems (AMMOS) is NASA's premier space mission operations product line offering for use in deep-space robotic and astrophysics missions. The general approach to AMMOS modernization over the course of its 29-year history exemplifies a continual, evolutionary approach with periods of sponsor investment peaks and valleys in between. Today, the Multimission Ground Systems and Services (MGSS) office-the program office that manages the AMMOS for NASA-actively pursues modernization initiatives and continues to evolve the AMMOS by incorporating enhanced capabilities and newer technologies into its end-user tool and service offerings. Despite the myriad of modernization investments that have been made over the evolutionary course of the AMMOS, pain points remain. These pain points, based on interviews with numerous flight project mission operations personnel, can be classified principally into two major categories: 1) information-related issues, and 2) process-related issues. By information-related issues, we mean pain points associated with the management and flow of MOS data across the various system interfaces. By process-related issues, we mean pain points associated with the MOS activities performed by mission operators (i.e., humans) and supporting software infrastructure used in support of those activities. In this paper, three foundational concepts-Timeline, Closed Loop Control, and Separation of Concerns-collectively form the basis for expressing a set of core architectural tenets that provides a multifaceted approach to AMMOS system architecture modernization intended to address the information- and process-related issues. Each of these architectural tenets will be further explored in this paper. Ultimately, we envision the application of these core tenets resulting in a unified vision of a future-state architecture for the AMMOS-one that is intended to result in a highly adaptable, highly efficient, and highly cost-effective set of multimission MOS products and services.

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.

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

PubMed Central

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

2018-01-01

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

Software tool for data mining and its applications

NASA Astrophysics Data System (ADS)

Yang, Jie; Ye, Chenzhou; Chen, Nianyi

2002-03-01

A software tool for data mining is introduced, which integrates pattern recognition (PCA, Fisher, clustering, hyperenvelop, regression), artificial intelligence (knowledge representation, decision trees), statistical learning (rough set, support vector machine), computational intelligence (neural network, genetic algorithm, fuzzy systems). It consists of nine function models: pattern recognition, decision trees, association rule, fuzzy rule, neural network, genetic algorithm, Hyper Envelop, support vector machine, visualization. The principle and knowledge representation of some function models of data mining are described. The software tool of data mining is realized by Visual C++ under Windows 2000. Nonmonotony in data mining is dealt with by concept hierarchy and layered mining. The software tool of data mining has satisfactorily applied in the prediction of regularities of the formation of ternary intermetallic compounds in alloy systems, and diagnosis of brain glioma.

A digital flight control system verification laboratory

NASA Technical Reports Server (NTRS)

De Feo, P.; Saib, S.

1982-01-01

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

Management of an affiliated Physics Residency Program using a commercial software tool.

PubMed

Zacarias, Albert S; Mills, Michael D

2010-06-01

A review of commercially available allied health educational management software tools was performed to evaluate their capacity to manage program data associated with a CAMPEP-accredited Therapy Physics Residency Program. Features of these software tools include: a) didactic course reporting and organization, b) competency reporting by topic, category and didactic course, c) student time management and accounting, and d) student patient case reporting by topic, category and course. The software package includes features for recording school administrative information; setting up lists of courses, faculty, clinical sites, categories, competencies, and time logs; and the inclusion of standardized external documents. There are provisions for developing evaluation and survey instruments. The mentors and program may be evaluated by residents, and residents may be evaluated by faculty members using this feature. Competency documentation includes the time spent on the problem or with the patient, time spent with the mentor, date of the competency, and approval by the mentor and program director. Course documentation includes course and lecture title, lecturer, topic information, date of lecture and approval by the Program Director. These software tools have the facility to include multiple clinical sites, with local subadministrators having the ability to approve competencies and attendance at clinical conferences. In total, these software tools have the capability of managing all components of a CAMPEP-accredited residency program. The application database lends the software to the support of multiple affiliated clinical sites within a single residency program. Such tools are a critical and necessary component if the medical physics profession is to meet the projected needs for qualified medical physicists in future years.

Simulation supported POD for RT test case-concept and modeling

NASA Astrophysics Data System (ADS)

Gollwitzer, C.; Bellon, C.; Deresch, A.; Ewert, U.; Jaenisch, G.-R.; Zscherpel, U.; Mistral, Q.

2012-05-01

Within the framework of the European project PICASSO, the radiographic simulator aRTist (analytical Radiographic Testing inspection simulation tool) developed by BAM has been extended for reliability assessment of film and digital radiography. NDT of safety relevant components of aerospace industry requires the proof of probability of detection (POD) of the inspection. Modeling tools can reduce the expense of such extended, time consuming NDT trials, if the result of simulation fits to the experiment. Our analytic simulation tool consists of three modules for the description of the radiation source, the interaction of radiation with test pieces and flaws, and the detection process with special focus on film and digital industrial radiography. It features high processing speed with near-interactive frame rates and a high level of realism. A concept has been developed as well as a software extension for reliability investigations, completed by a user interface for planning automatic simulations with varying parameters and defects. Furthermore, an automatic image analysis procedure is included to evaluate the defect visibility. The radiographic modeling from 3D CAD of aero engine components and quality test samples are compared as a precondition for real trials. This enables the evaluation and optimization of film replacement for application of modern digital equipment for economical NDT and defined POD.

Fiji: an open-source platform for biological-image analysis.

PubMed

Schindelin, Johannes; Arganda-Carreras, Ignacio; Frise, Erwin; Kaynig, Verena; Longair, Mark; Pietzsch, Tobias; Preibisch, Stephan; Rueden, Curtis; Saalfeld, Stephan; Schmid, Benjamin; Tinevez, Jean-Yves; White, Daniel James; Hartenstein, Volker; Eliceiri, Kevin; Tomancak, Pavel; Cardona, Albert

2012-06-28

Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

The VLBI Data Analysis Software νSolve: Development Progress and Plans for the Future

NASA Astrophysics Data System (ADS)

Bolotin, S.; Baver, K.; Gipson, J.; Gordon, D.; MacMillan, D.

2014-12-01

The program νSolve is a part of the CALC/SOLVE VLBI data analysis system. It is a replacement for interactive SOLVE, the part of CALC/SOLVE that is used for preliminary data analysis of new VLBI sessions. νSolve is completely new software. It is written in C++ and has a modern graphical user interface. In this article we present the capabilities of the software, its current status, and our plans for future development.

Shortcomings of existing systems for registration and legal protection of software products and possible ways to overcome them

NASA Astrophysics Data System (ADS)

Liapidevskiy, A. V.; Petrov, A. S.; Zhmud, V. A.; Sherubneva, I. G.

2018-05-01

The paper reveals the shortcomings of the existing system of registration and legal protection of software products. The system has too many disadvantages and shortcomings. Explanatory examples are given. Possible ways of overcoming these shortcomings are discussed. The paper also gives possible prospects for the use of new digital technologies. Also in the paper, the information is provided about the modern software components for protecting intellectual property rights of State corporations

Integrated Software Health Management for Aircraft GN and C

NASA Technical Reports Server (NTRS)

Schumann, Johann; Mengshoel, Ole

2011-01-01

Modern aircraft rely heavily on dependable operation of many safety-critical software components. Despite careful design, verification and validation (V&V), on-board software can fail with disastrous consequences if it encounters problematic software/hardware interaction or must operate in an unexpected environment. We are using a Bayesian approach to monitor the software and its behavior during operation and provide up-to-date information about the health of the software and its components. The powerful reasoning mechanism provided by our model-based Bayesian approach makes reliable diagnosis of the root causes possible and minimizes the number of false alarms. Compilation of the Bayesian model into compact arithmetic circuits makes SWHM feasible even on platforms with limited CPU power. We show initial results of SWHM on a small simulator of an embedded aircraft software system, where software and sensor faults can be injected.

PopED lite: An optimal design software for preclinical pharmacokinetic and pharmacodynamic studies.

PubMed

Aoki, Yasunori; Sundqvist, Monika; Hooker, Andrew C; Gennemark, Peter

2016-04-01

Optimal experimental design approaches are seldom used in preclinical drug discovery. The objective is to develop an optimal design software tool specifically designed for preclinical applications in order to increase the efficiency of drug discovery in vivo studies. Several realistic experimental design case studies were collected and many preclinical experimental teams were consulted to determine the design goal of the software tool. The tool obtains an optimized experimental design by solving a constrained optimization problem, where each experimental design is evaluated using some function of the Fisher Information Matrix. The software was implemented in C++ using the Qt framework to assure a responsive user-software interaction through a rich graphical user interface, and at the same time, achieving the desired computational speed. In addition, a discrete global optimization algorithm was developed and implemented. The software design goals were simplicity, speed and intuition. Based on these design goals, we have developed the publicly available software PopED lite (http://www.bluetree.me/PopED_lite). Optimization computation was on average, over 14 test problems, 30 times faster in PopED lite compared to an already existing optimal design software tool. PopED lite is now used in real drug discovery projects and a few of these case studies are presented in this paper. PopED lite is designed to be simple, fast and intuitive. Simple, to give many users access to basic optimal design calculations. Fast, to fit a short design-execution cycle and allow interactive experimental design (test one design, discuss proposed design, test another design, etc). Intuitive, so that the input to and output from the software tool can easily be understood by users without knowledge of the theory of optimal design. In this way, PopED lite is highly useful in practice and complements existing tools. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Coordinating the Complexity of Tools, Tasks, and Users: On Theory-Based Approaches to Authoring Tool Usability

ERIC Educational Resources Information Center

Murray, Tom

2016-01-01

Intelligent Tutoring Systems authoring tools are highly complex educational software applications used to produce highly complex software applications (i.e. ITSs). How should our assumptions about the target users (authors) impact the design of authoring tools? In this article I first reflect on the factors leading to my original 1999 article on…

Software analysis handbook: Software complexity analysis and software reliability estimation and prediction

NASA Technical Reports Server (NTRS)

Lee, Alice T.; Gunn, Todd; Pham, Tuan; Ricaldi, Ron

1994-01-01

This handbook documents the three software analysis processes the Space Station Software Analysis team uses to assess space station software, including their backgrounds, theories, tools, and analysis procedures. Potential applications of these analysis results are also presented. The first section describes how software complexity analysis provides quantitative information on code, such as code structure and risk areas, throughout the software life cycle. Software complexity analysis allows an analyst to understand the software structure, identify critical software components, assess risk areas within a software system, identify testing deficiencies, and recommend program improvements. Performing this type of analysis during the early design phases of software development can positively affect the process, and may prevent later, much larger, difficulties. The second section describes how software reliability estimation and prediction analysis, or software reliability, provides a quantitative means to measure the probability of failure-free operation of a computer program, and describes the two tools used by JSC to determine failure rates and design tradeoffs between reliability, costs, performance, and schedule.

Software Tools for Developing and Simulating the NASA LaRC CMF Motion Base

NASA Technical Reports Server (NTRS)

Bryant, Richard B., Jr.; Carrelli, David J.

2006-01-01

The NASA Langley Research Center (LaRC) Cockpit Motion Facility (CMF) motion base has provided many design and analysis challenges. In the process of addressing these challenges, a comprehensive suite of software tools was developed. The software tools development began with a detailed MATLAB/Simulink model of the motion base which was used primarily for safety loads prediction, design of the closed loop compensator and development of the motion base safety systems1. A Simulink model of the digital control law, from which a portion of the embedded code is directly generated, was later added to this model to form a closed loop system model. Concurrently, software that runs on a PC was created to display and record motion base parameters. It includes a user interface for controlling time history displays, strip chart displays, data storage, and initializing of function generators used during motion base testing. Finally, a software tool was developed for kinematic analysis and prediction of mechanical clearances for the motion system. These tools work together in an integrated package to support normal operations of the motion base, simulate the end to end operation of the motion base system providing facilities for software-in-the-loop testing, mechanical geometry and sensor data visualizations, and function generator setup and evaluation.

Framework Support For Knowledge-Based Software Development

NASA Astrophysics Data System (ADS)

Huseth, Steve

1988-03-01

The advent of personal engineering workstations has brought substantial information processing power to the individual programmer. Advanced tools and environment capabilities supporting the software lifecycle are just beginning to become generally available. However, many of these tools are addressing only part of the software development problem by focusing on rapid construction of self-contained programs by a small group of talented engineers. Additional capabilities are required to support the development of large programming systems where a high degree of coordination and communication is required among large numbers of software engineers, hardware engineers, and managers. A major player in realizing these capabilities is the framework supporting the software development environment. In this paper we discuss our research toward a Knowledge-Based Software Assistant (KBSA) framework. We propose the development of an advanced framework containing a distributed knowledge base that can support the data representation needs of tools, provide environmental support for the formalization and control of the software development process, and offer a highly interactive and consistent user interface.

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.

Pre- and Post-Processing Tools to Streamline the CFD Process

NASA Technical Reports Server (NTRS)

Dorney, Suzanne Miller

2002-01-01

This viewgraph presentation provides information on software development tools to facilitate the use of CFD (Computational Fluid Dynamics) codes. The specific CFD codes FDNS and CORSAIR are profiled, and uses for software development tools with these codes during pre-processing, interim-processing, and post-processing are explained.

A NASA-wide approach toward cost-effective, high-quality software through reuse

NASA Technical Reports Server (NTRS)

Scheper, Charlotte O. (Editor); Smith, Kathryn A. (Editor)

1993-01-01

NASA Langley Research Center sponsored the second Workshop on NASA Research in Software Reuse on May 5-6, 1992 at the Research Triangle Park, North Carolina. The workshop was hosted by the Research Triangle Institute. Participants came from the three NASA centers, four NASA contractor companies, two research institutes and the Air Force's Rome Laboratory. The purpose of the workshop was to exchange information on software reuse tool development, particularly with respect to tool needs, requirements, and effectiveness. The participants presented the software reuse activities and tools being developed and used by their individual centers and programs. These programs address a wide range of reuse issues. The group also developed a mission and goals for software reuse within NASA. This publication summarizes the presentations and the issues discussed during the workshop.

Automated Translation of Safety Critical Application Software Specifications into PLC Ladder Logic

NASA Technical Reports Server (NTRS)

Leucht, Kurt W.; Semmel, Glenn S.

2008-01-01

The numerous benefits of automatic application code generation are widely accepted within the software engineering community. A few of these benefits include raising the abstraction level of application programming, shorter product development time, lower maintenance costs, and increased code quality and consistency. Surprisingly, code generation concepts have not yet found wide acceptance and use in the field of programmable logic controller (PLC) software development. Software engineers at the NASA Kennedy Space Center (KSC) recognized the need for PLC code generation while developing their new ground checkout and launch processing system. They developed a process and a prototype software tool that automatically translates a high-level representation or specification of safety critical application software into ladder logic that executes on a PLC. This process and tool are expected to increase the reliability of the PLC code over that which is written manually, and may even lower life-cycle costs and shorten the development schedule of the new control system at KSC. This paper examines the problem domain and discusses the process and software tool that were prototyped by the KSC software engineers.

Formal verification of medical monitoring software using Z language: a representative sample.

PubMed

Babamir, Seyed Morteza; Borhani, Mehdi

2012-08-01

Medical monitoring systems are useful aids assisting physicians in keeping patients under constant surveillance; however, taking sound decision by the systems is a physician concern. As a result, verification of the systems behavior in monitoring patients is a matter of significant. The patient monitoring is undertaken by software in modern medical systems; so, software verification of modern medial systems have been noticed. Such verification can be achieved by the Formal Languages having mathematical foundations. Among others, the Z language is a suitable formal language has been used to formal verification of systems. This study aims to present a constructive method to verify a representative sample of a medical system by which the system is visually specified and formally verified against patient constraints stated in Z Language. Exploiting our past experience in formal modeling Continuous Infusion Insulin Pump (CIIP), we think of the CIIP system as a representative sample of medical systems in proposing our present study. The system is responsible for monitoring diabetic's blood sugar.

Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform.

PubMed

List, Markus

2017-06-10

Docker virtualization allows for software tools to be executed in an isolated and controlled environment referred to as a container. In Docker containers, dependencies are provided exactly as intended by the developer and, consequently, they simplify the distribution of scientific software and foster reproducible research. The Docker paradigm is that each container encapsulates one particular software tool. However, to analyze complex biomedical data sets, it is often necessary to combine several software tools into elaborate workflows. To address this challenge, several Docker containers need to be instantiated and properly integrated, which complicates the software deployment process unnecessarily. Here, we demonstrate how an extension to Docker, Docker compose, can be used to mitigate these problems by providing a unified setup routine that deploys several tools in an integrated fashion. We demonstrate the power of this approach by example of a Docker compose setup for a drug target screening platform consisting of five integrated web applications and shared infrastructure, deployable in just two lines of codes.

Capturing Your Students' Attention is Easier with this Month's Software Selections. Blue Ribbon Reviews

ERIC Educational Resources Information Center

Lindroth, Linda

2005-01-01

This article describes new presentation tools and game shows that can make the classroom into a learning stage. RM Easiteach Studio, a presentation software from RM Educational Software, provides teaching tools for use on any interactive whiteboard. Classroom Jeopardy[R] from Educational Insights includes a scoreboard/base control unit, three…

Using Academia-Industry Partnerships to Enhance Software Verification & Validation Education via Active Learning Tools

ERIC Educational Resources Information Center

Acharya, Sushil; Manohar, Priyadarshan; Wu, Peter; Schilling, Walter

2017-01-01

Imparting real world experiences in a software verification and validation (SV&V) course is often a challenge due to the lack of effective active learning tools. This pedagogical requirement is important because graduates are expected to develop software that meets rigorous quality standards in functional and application domains. Realizing the…

Research flight software engineering and MUST, an integrated system of support tools

NASA Technical Reports Server (NTRS)

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

1977-01-01

Consideration is given to software development to support NASA flight research. The Multipurpose User-Oriented Software Technology (MUST) program, designed to integrate digital systems into flight research, is discussed. Particular attention is given to the program's special interactive user interface, subroutine library, assemblers, compiler, automatic documentation tools, and test and simulation subsystems.

Automated data collection in single particle electron microscopy

PubMed Central

Tan, Yong Zi; Cheng, Anchi; Potter, Clinton S.; Carragher, Bridget

2016-01-01

Automated data collection is an integral part of modern workflows in single particle electron microscopy (EM) research. This review surveys the software packages available for automated single particle EM data collection. The degree of automation at each stage of data collection is evaluated, and the capabilities of the software packages are described. Finally, future trends in automation are discussed. PMID:26671944

Software engineering activities at SEI (Software Engineering Institute)

NASA Technical Reports Server (NTRS)

Chittister, Clyde

1990-01-01

Prototyping was shown to ease system specification and implementation, especially in the area of user interfaces. Other prototyping approaches do not allow for the evolution of the prototype into a production system or support maintenance after the system is fielded. A set of goals is presented for a modern user interface environment and Serpent, a prototype implementation that achieves these goals, is described.

Training, Quality Assurance Factors, and Tools Investigation: a Work Report and Suggestions on Software Quality Assurance

NASA Technical Reports Server (NTRS)

Lee, Pen-Nan

1991-01-01

Previously, several research tasks have been conducted, some observations were obtained, and several possible suggestions have been contemplated involving software quality assurance engineering at NASA Johnson. These research tasks are briefly described. Also, a brief discussion is given on the role of software quality assurance in software engineering along with some observations and suggestions. A brief discussion on a training program for software quality assurance engineers is provided. A list of assurance factors as well as quality factors are also included. Finally, a process model which can be used for searching and collecting software quality assurance tools is presented.

A high order approach to flight software development and testing

NASA Technical Reports Server (NTRS)

Steinbacher, J.

1981-01-01

The use of a software development facility is discussed as a means of producing a reliable and maintainable ECS software system, and as a means of providing efficient use of the ECS hardware test facility. Principles applied to software design are given, including modularity, abstraction, hiding, and uniformity. The general objectives of each phase of the software life cycle are also given, including testing, maintenance, code development, and requirement specifications. Software development facility tools are summarized, and tool deficiencies recognized in the code development and testing phases are considered. Due to limited lab resources, the functional simulation capabilities may be indispensable in the testing phase.

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.

Efficient analysis of large-scale genome-wide data with two R packages: bigstatsr and bigsnpr.

PubMed

Privé, Florian; Aschard, Hugues; Ziyatdinov, Andrey; Blum, Michael G B

2017-03-30

Genome-wide datasets produced for association studies have dramatically increased in size over the past few years, with modern datasets commonly including millions of variants measured in dozens of thousands of individuals. This increase in data size is a major challenge severely slowing down genomic analyses, leading to some software becoming obsolete and researchers having limited access to diverse analysis tools. Here we present two R packages, bigstatsr and bigsnpr, allowing for the analysis of large scale genomic data to be performed within R. To address large data size, the packages use memory-mapping for accessing data matrices stored on disk instead of in RAM. To perform data pre-processing and data analysis, the packages integrate most of the tools that are commonly used, either through transparent system calls to existing software, or through updated or improved implementation of existing methods. In particular, the packages implement fast and accurate computations of principal component analysis and association studies, functions to remove SNPs in linkage disequilibrium and algorithms to learn polygenic risk scores on millions of SNPs. We illustrate applications of the two R packages by analyzing a case-control genomic dataset for celiac disease, performing an association study and computing Polygenic Risk Scores. Finally, we demonstrate the scalability of the R packages by analyzing a simulated genome-wide dataset including 500,000 individuals and 1 million markers on a single desktop computer. https://privefl.github.io/bigstatsr/ & https://privefl.github.io/bigsnpr/. florian.prive@univ-grenoble-alpes.fr & michael.blum@univ-grenoble-alpes.fr. Supplementary materials are available at Bioinformatics online.

Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web.

PubMed

Miller, Chase A; Anthony, Jon; Meyer, Michelle M; Marth, Gabor

2013-02-01

High-throughput biological research requires simultaneous visualization as well as analysis of genomic data, e.g. read alignments, variant calls and genomic annotations. Traditionally, such integrative analysis required desktop applications operating on locally stored data. Many current terabyte-size datasets generated by large public consortia projects, however, are already only feasibly stored at specialist genome analysis centers. As even small laboratories can afford very large datasets, local storage and analysis are becoming increasingly limiting, and it is likely that most such datasets will soon be stored remotely, e.g. in the cloud. These developments will require web-based tools that enable users to access, analyze and view vast remotely stored data with a level of sophistication and interactivity that approximates desktop applications. As rapidly dropping cost enables researchers to collect data intended to answer questions in very specialized contexts, developers must also provide software libraries that empower users to implement customized data analyses and data views for their particular application. Such specialized, yet lightweight, applications would empower scientists to better answer specific biological questions than possible with general-purpose genome browsers currently available. Using recent advances in core web technologies (HTML5), we developed Scribl, a flexible genomic visualization library specifically targeting coordinate-based data such as genomic features, DNA sequence and genetic variants. Scribl simplifies the development of sophisticated web-based graphical tools that approach the dynamism and interactivity of desktop applications. Software is freely available online at http://chmille4.github.com/Scribl/ and is implemented in JavaScript with all modern browsers supported.

Software tool for physics chart checks.

PubMed

Li, H Harold; Wu, Yu; Yang, Deshan; Mutic, Sasa

2014-01-01

Physics chart check has long been a central quality assurance (QC) measure in radiation oncology. The purpose of this work is to describe a software tool that aims to accomplish simplification, standardization, automation, and forced functions in the process. Nationally recognized guidelines, including American College of Radiology and American Society for Radiation Oncology guidelines and technical standards, and the American Association of Physicists in Medicine Task Group reports were identified, studied, and summarized. Meanwhile, the reported events related to physics chart check service were analyzed using an event reporting and learning system. A number of shortfalls in the chart check process were identified. To address these problems, a software tool was designed and developed under Microsoft. Net in C# to hardwire as many components as possible at each stage of the process. The software consists of the following 4 independent modules: (1) chart check management; (2) pretreatment and during treatment chart check assistant; (3) posttreatment chart check assistant; and (4) quarterly peer-review management. The users were a large group of physicists in the author's radiation oncology clinic. During over 1 year of use the tool has proven very helpful in chart checking management, communication, documentation, and maintaining consistency. The software tool presented in this work aims to assist physicists at each stage of the physics chart check process. The software tool is potentially useful for any radiation oncology clinics that are either in the process of pursuing or maintaining the American College of Radiology accreditation.

The GenABEL Project for statistical genomics

PubMed Central

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

2016-01-01

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

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

Virtual Reality as Innovative Approach to the Interior Designing

NASA Astrophysics Data System (ADS)

Kaleja, Pavol; Kozlovská, Mária

2017-06-01

We can observe significant potential of information and communication technologies (ICT) in interior designing field, by development of software and hardware virtual reality tools. Using ICT tools offer realistic perception of proposal in its initial idea (the study). A group of real-time visualization, supported by hardware tools like Oculus Rift HTC Vive, provides free walkthrough and movement in virtual interior with the possibility of virtual designing. By improving of ICT software tools for designing in virtual reality we can achieve still more realistic virtual environment. The contribution presented proposal of an innovative approach of interior designing in virtual reality, using the latest software and hardware ICT virtual reality technologies

ReGaTE: Registration of Galaxy Tools in Elixir

PubMed Central

Mareuil, Fabien; Deveaud, Eric; Kalaš, Matúš; Soranzo, Nicola; van den Beek, Marius; Grüning, Björn; Ison, Jon; Ménager, Hervé

2017-01-01

Abstract Background: Bioinformaticians routinely use multiple software tools and data sources in their day-to-day work and have been guided in their choices by a number of cataloguing initiatives. The ELIXIR Tools and Data Services Registry (bio.tools) aims to provide a central information point, independent of any specific scientific scope within bioinformatics or technological implementation. Meanwhile, efforts to integrate bioinformatics software in workbench and workflow environments have accelerated to enable the design, automation, and reproducibility of bioinformatics experiments. One such popular environment is the Galaxy framework, with currently more than 80 publicly available Galaxy servers around the world. In the context of a generic registry for bioinformatics software, such as bio.tools, Galaxy instances constitute a major source of valuable content. Yet there has been, to date, no convenient mechanism to register such services en masse. Findings: We present ReGaTE (Registration of Galaxy Tools in Elixir), a software utility that automates the process of registering the services available in a Galaxy instance. This utility uses the BioBlend application program interface to extract service metadata from a Galaxy server, enhance the metadata with the scientific information required by bio.tools, and push it to the registry. Conclusions: ReGaTE provides a fast and convenient way to publish Galaxy services in bio.tools. By doing so, service providers may increase the visibility of their services while enriching the software discovery function that bio.tools provides for its users. The source code of ReGaTE is freely available on Github at https://github.com/C3BI-pasteur-fr/ReGaTE. PMID:28402416

Supporting geoscience with graphical-user-interface Internet tools for the Macintosh

NASA Astrophysics Data System (ADS)

Robin, Bernard

1995-07-01

This paper describes a suite of Macintosh graphical-user-interface (GUI) software programs that can be used in conjunction with the Internet to support geoscience education. These software programs allow science educators to access and retrieve a large body of resources from an increasing number of network sites, taking advantage of the intuitive, simple-to-use Macintosh operating system. With these tools, educators easily can locate, download, and exchange not only text files but also sound resources, video movie clips, and software application files from their desktop computers. Another major advantage of these software tools is that they are available at no cost and may be distributed freely. The following GUI software tools are described including examples of how they can be used in an educational setting: ∗ Eudora—an e-mail program ∗ NewsWatcher—a newsreader ∗ TurboGopher—a Gopher program ∗ Fetch—a software application for easy File Transfer Protocol (FTP) ∗ NCSA Mosaic—a worldwide hypertext browsing program. An explosive growth of online archives currently is underway as new electronic sites are being added continuously to the Internet. Many of these resources may be of interest to science educators who learn they can share not only ASCII text files, but also graphic image files, sound resources, QuickTime movie clips, and hypermedia projects with colleagues from locations around the world. These powerful, yet simple to learn GUI software tools are providing a revolution in how knowledge can be accessed, retrieved, and shared.

Making Research Fly in Schools: "Drosophila" as a Powerful Modern Tool for Teaching Biology

ERIC Educational Resources Information Center

Harbottle, Jennifer; Strangward, Patrick; Alnuamaani, Catherine; Lawes, Surita; Patel, Sanjai; Prokop, Andreas

2016-01-01

The "droso4schools" project aims to introduce the fruit fly "Drosophila" as a powerful modern teaching tool to convey curriculum-relevant specifications in biology lessons. Flies are easy and cheap to breed and have been at the forefront of biology research for a century, providing unique conceptual understanding of biology and…

The Pathway Tools software.

PubMed

Karp, Peter D; Paley, Suzanne; Romero, Pedro

2002-01-01

Bioinformatics requires reusable software tools for creating model-organism databases (MODs). The Pathway Tools is a reusable, production-quality software environment for creating a type of MOD called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc (see http://ecocyc.org) integrates our evolving understanding of the genes, proteins, metabolic network, and genetic network of an organism. This paper provides an overview of the four main components of the Pathway Tools: The PathoLogic component supports creation of new PGDBs from the annotated genome of an organism. The Pathway/Genome Navigator provides query, visualization, and Web-publishing services for PGDBs. The Pathway/Genome Editors support interactive updating of PGDBs. The Pathway Tools ontology defines the schema of PGDBs. The Pathway Tools makes use of the Ocelot object database system for data management services for PGDBs. The Pathway Tools has been used to build PGDBs for 13 organisms within SRI and by external users.

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.

Methods for transition toward computer assisted cognitive examination.

PubMed

Jurica, P; Valenzi, S; Struzik, Z R; Cichocki, A

2015-01-01

We present a software framework which enables the extension of current methods for the assessment of cognitive fitness using recent technological advances. Screening for cognitive impairment is becoming more important as the world's population grows older. Current methods could be enhanced by use of computers. Introduction of new methods to clinics requires basic tools for collection and communication of collected data. To develop tools that, with minimal interference, offer new opportunities for the enhancement of the current interview based cognitive examinations. We suggest methods and discuss process by which established cognitive tests can be adapted for data collection through digitization by pen enabled tablets. We discuss a number of methods for evaluation of collected data, which promise to increase the resolution and objectivity of the common scoring strategy based on visual inspection. By involving computers in the roles of both instructing and scoring, we aim to increase the precision and reproducibility of cognitive examination. The tools provided in Python framework CogExTools available at http://bsp. brain.riken.jp/cogextools/ enable the design, application and evaluation of screening tests for assessment of cognitive impairment. The toolbox is a research platform; it represents a foundation for further collaborative development by the wider research community and enthusiasts. It is free to download and use, and open-source. We introduce a set of open-source tools that facilitate the design and development of new cognitive tests for modern technology. We provide these tools in order to enable the adaptation of technology for cognitive examination in clinical settings. The tools provide the first step in a possible transition toward standardized mental state examination using computers.

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.

Social Software in Academia

ERIC Educational Resources Information Center

Bryant, Todd

2006-01-01

Considerable buzz has appeared on the Internet over a group of new tools labeled social software. These tools can expand discussion beyond the classroom and provide new ways for students to collaborate and communicate within their class or around the world. Dickinson College has implemented two of the best-known tools, the wiki and the blog, in…

CrossTalk: The Journal of Defense Software Engineering. Volume 18, Number 4

DTIC Science & Technology

2005-04-01

older automated cost- estimating tools are no longer being actively marketed but are still in use such as CheckPoint, COCOMO, ESTIMACS, REVIC, and SPQR ...estimation tools: SPQR /20, Checkpoint, and Knowl- edgePlan. These software estimation tools pioneered the use of function point metrics for sizing and

The Implications of Cognitive Psychology for Computer-Based Learning Tools.

ERIC Educational Resources Information Center

Kozma, Robert B.

1987-01-01

Defines cognitive computer tools as software programs that use the control capabilities of computers to amplify, extend, or enhance human cognition; suggests seven ways in which computers can aid learning; and describes the "Learning Tool," a software package for the Apple Macintosh microcomputer that is designed to aid learning of…

New software tools for enhanced precision in robot-assisted laser phonomicrosurgery.

PubMed

Dagnino, Giulio; Mattos, Leonardo S; Caldwell, Darwin G

2012-01-01

This paper describes a new software package created to enhance precision during robot-assisted laser phonomicrosurgery procedures. The new software is composed of three tools for camera calibration, automatic tumor segmentation, and laser tracking. These were designed and developed to improve the outcome of this demanding microsurgical technique, and were tested herein to produce quantitative performance data. The experimental setup was based on the motorized laser micromanipulator created by Istituto Italiano di Tecnologia and the experimental protocols followed are fully described in this paper. The results show the new tools are robust and effective: The camera calibration tool reduced residual errors (RMSE) to 0.009 ± 0.002 mm under 40× microscope magnification; the automatic tumor segmentation tool resulted in deep lesion segmentations comparable to manual segmentations (RMSE= 0.160 ± 0.028 mm under 40× magnification); and the laser tracker tool proved to be reliable even during cutting procedures (RMSE= 0.073 ± 0.023 mm under 40× magnification). These results demonstrate the new software package can provide excellent improvements to the previous microsurgical system, leading to important enhancements in surgical outcome.

Giving pandas ROOT to chew on: experiences with the XENON1T Dark Matter experiment

NASA Astrophysics Data System (ADS)

Remenska, D.; Tunnell, C.; Aalbers, J.; Verhoeven, S.; Maassen, J.; Templon, J.

2017-10-01

In preparation for the XENON1T Dark Matter data acquisition, we have prototyped and implemented a new computing model. The XENON signal and data processing software is developed fully in Python 3, and makes extensive use of generic scientific data analysis libraries, such as the SciPy stack. A certain tension between modern “Big Data” solutions and existing HEP frameworks is typically experienced in smaller particle physics experiments. ROOT is still the “standard” data format in our field, defined by large experiments (ATLAS, CMS). To ease the transition, our computing model caters to both analysis paradigms, leaving the choice of using ROOT-specific C++ libraries, or alternatively, Python and its data analytics tools, as a front-end choice of developing physics algorithms. We present our path on harmonizing these two ecosystems, which allowed us to use off-the-shelf software libraries (e.g., NumPy, SciPy, scikit-learn, matplotlib) and lower the cost of development and maintenance. To analyse the data, our software allows researchers to easily create “mini-trees” small, tabular ROOT structures for Python analysis, which can be read directly into pandas DataFrame structures. One of our goals was making ROOT available as a cross-platform binary for an easy installation from the Anaconda Cloud (without going through the “dependency hell”). In addition to helping us discover dark matter interactions, lowering this barrier helps shift the particle physics toward non-domain-specific code.

NSTX-U Control System Upgrades

DOE PAGES

Erickson, K. G.; Gates, D. A.; Gerhardt, S. P.; ...

2014-06-01

The National Spherical Tokamak Experiment (NSTX) is undergoing a wealth of upgrades (NSTX-U). These upgrades, especially including an elongated pulse length, require broad changes to the control system that has served NSTX well. A new fiber serial Front Panel Data Port input and output (I/O) stream will supersede the aging copper parallel version. Driver support for the new I/O and cyber security concerns require updating the operating system from Redhat Enterprise Linux (RHEL) v4 to RedHawk (based on RHEL) v6. While the basic control system continues to use the General Atomics Plasma Control System (GA PCS), the effort to forwardmore » port the entire software package to run under 64-bit Linux instead of 32-bit Linux included PCS modifications subsequently shared with GA and other PCS users. Software updates focused on three key areas: (1) code modernization through coding standards (C99/C11), (2) code portability and maintainability through use of the GA PCS code generator, and (3) support of 64-bit platforms. Central to the control system upgrade is the use of a complete real time (RT) Linux platform provided by Concurrent Computer Corporation, consisting of a computer (iHawk), an operating system and drivers (RedHawk), and RT tools (NightStar). Strong vendor support coupled with an extensive RT toolset influenced this decision. The new real-time Linux platform, I/O, and software engineering will foster enhanced capability and performance for NSTX-U plasma control.« less

ASKI: A modular toolbox for scattering-integral-based seismic full waveform inversion and sensitivity analysis utilizing external forward codes

NASA Astrophysics Data System (ADS)

Schumacher, Florian; Friederich, Wolfgang

Due to increasing computational resources, the development of new numerically demanding methods and software for imaging Earth's interior remains of high interest in Earth sciences. Here, we give a description from a user's and programmer's perspective of the highly modular, flexible and extendable software package ASKI-Analysis of Sensitivity and Kernel Inversion-recently developed for iterative scattering-integral-based seismic full waveform inversion. In ASKI, the three fundamental steps of solving the seismic forward problem, computing waveform sensitivity kernels and deriving a model update are solved by independent software programs that interact via file output/input only. Furthermore, the spatial discretizations of the model space used for solving the seismic forward problem and for deriving model updates, respectively, are kept completely independent. For this reason, ASKI does not contain a specific forward solver but instead provides a general interface to established community wave propagation codes. Moreover, the third fundamental step of deriving a model update can be repeated at relatively low costs applying different kinds of model regularization or re-selecting/weighting the inverted dataset without need to re-solve the forward problem or re-compute the kernels. Additionally, ASKI offers the user sensitivity and resolution analysis tools based on the full sensitivity matrix and allows to compose customized workflows in a consistent computational environment. ASKI is written in modern Fortran and Python, it is well documented and freely available under terms of the GNU General Public License (http://www.rub.de/aski).

High-performance coupled poro-hydro-mechanical models to resolve fluid escape pipes

NASA Astrophysics Data System (ADS)

Räss, Ludovic; Makhnenko, Roman; Podladchikov, Yury

2017-04-01

Field observations and laboratory experiments exhibit inelastic deformation features arising in many coupled settings relevant to geo-applications. These irreversible deformations and their specific patterns suggest a rather ductile or brittle mechanism, such as viscous creep or micro cracks, taking place on both geological (long) and human (short) timescales. In order to understand the underlying mechanisms responsible for these deformation features, there is a current need to accurately resolve the non-linearities inherent to strongly coupled physical processes. Among the large variety of modelling tools and softwares available nowadays in the community, very few are capable to efficiently solve coupled systems with high accuracy in both space and time and run efficiently on modern hardware. Here, we propose a robust framework to solve coupled multi-physics hydro-mechanical processes on very high spatial and temporal resolution in both two and three dimensions. Our software relies on the Finite-Difference Method and a pseudo-transient scheme is used to converge to the implicit solution of the system of poro-visco-elasto-plastic equations at each physical time step. The rheology including viscosity estimates for major reservoir rock types is inferred from novel lab experiments and confirms the ease of flow of sedimentary rocks. Our results propose a physical mechanism responsible for the generation of high permeability pathways in fluid saturated porous media and predict their propagation in rates observable on operational timescales. Finally, our software scales linearly on more than 5000 GPUs.

The advanced magnetovision system for Smart application

NASA Astrophysics Data System (ADS)

Kaleta, Jerzy; Wiewiórski, Przemyslaw; Lewandowski, Daniel

2010-04-01

An original method, measurement devices and software tool for examination of magneto-mechanical phenomena in wide range of SMART applications is proposed. In many Hi-End market constructions it is necessary to carry out examinations of mechanical and magnetic properties simultaneously. Technological processes of fabrication of modern materials (for example cutting, premagnetisation and prestress) and advanced concept of using SMART structures involves the design of next generation system for optimization of electric and magnetic field distribution. The original fast and higher than million point static resolution scanner with mulitsensor probes has been constructed to measure full components of the magnetic field intensity vector H, and to visualize them into end user acceptable variant. The scanner has also the capability to acquire electric potentials on surface to work with magneto-piezo devices. Advanced electronic subsystems have been applied for processing of results in the Magscaner Vison System and the corresponding software - Maglab has been also evaluated. The Dipole Contour Method (DCM) is provided for modeling different states between magnetic and electric coupled materials and to visually explain the information of the experimental data. Dedicated software collaborating with industrial parametric systems CAD. Measurement technique consists of acquiring a cloud of points similarly as in tomography, 3D visualisation. The actually carried verification of abilities of 3D digitizer will enable inspection of SMART actuators with the cylindrical form, pellets with miniature sizes designed for oscillations dampers in various construction, for example in vehicle industry.

New hardware and software platform for experiments on a HUBER-5042 X-ray diffractometer with a DISPLEX DE-202 helium cryostat in the temperature range of 20-300 K

NASA Astrophysics Data System (ADS)

Dudka, A. P.; Antipin, A. M.; Verin, I. A.

2017-09-01

Huber-5042 diffractometer with a closed-cycle Displex DE-202 helium cryostat is a unique scientific instrument for carrying out X-ray diffraction experiments when studying the single crystal structure in the temperature range of 20-300 K. To make the service life longer and develop new experimental techniques, the diffractometer control is transferred to a new hardware and software platform. To this end, a modern computer; a new detector reader unit; and new control interfaces for stepper motors, temperature controller, and cryostat vacuum pumping system are used. The system for cooling the X-ray tube, the high-voltage generator, and the helium compressor and pump for maintaining the desired vacuum in the cryostat are replaced. The system for controlling the primary beam shutter is upgraded. A biological shielding is installed. The new program tools, which use the Linux Ubuntu operating system and SPEC constructor, include a set of drivers for control units through the aforementioned interfaces. A program for searching reflections from a sample using fast continuous scanning and a priori information about crystal is written. Thus, the software package for carrying out the complete cycle of precise diffraction experiment (from determining the crystal unit cell to calculating the integral reflection intensities) is upgraded. High quality of the experimental data obtained on this equipment is confirmed in a number of studies in the temperature range from 20 to 300 K.

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

PubMed Central

Ahmed, Zeeshan; Zeeshan, Saman; Dandekar, Thomas

2014-01-01

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

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

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

PubMed

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

2014-02-01

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

Perceptions of the software skills of graduates by employers in the financial services industry

NASA Astrophysics Data System (ADS)

Kyng, Tim; Tickle, Leonie; Wood, Leigh N.

2013-12-01

Software, particularly spreadsheet software, is ubiquitous in the financial services workplace. Yet little is known about the extent to which universities should, and do, prepare graduates for this aspect of the modern workplace. We have investigated this issue through a survey of financial services employers of graduates, the results of which are reported in this paper, as well as surveys of university graduates and academics, reported previously. Financial services employers rate software skills as important, would like their employees to be more highly skilled in the use of such software, and tend to prefer 'on-the-job' training rather than university training for statistical, database and specialized actuarial/financial software. There is a perception among graduates that employers do not provide adequate formal workplace training in the use of technical software.

Modernization of software quality assurance

NASA Technical Reports Server (NTRS)

Bhaumik, Gokul

1988-01-01

The customers satisfaction depends not only on functional performance, it also depends on the quality characteristics of the software products. An examination of this quality aspect of software products will provide a clear, well defined framework for quality assurance functions, which improve the life-cycle activities of software development. Software developers must be aware of the following aspects which have been expressed by many quality experts: quality cannot be added on; the level of quality built into a program is a function of the quality attributes employed during the development process; and finally, quality must be managed. These concepts have guided our development of the following definition for a Software Quality Assurance function: Software Quality Assurance is a formal, planned approach of actions designed to evaluate the degree of an identifiable set of quality attributes present in all software systems and their products. This paper is an explanation of how this definition was developed and how it is used.

RELAP-7 Software Verification and Validation Plan

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

Smith, Curtis L.; Choi, Yong-Joon; Zou, Ling

This INL plan comprehensively describes the software for RELAP-7 and documents the software, interface, and software design requirements for the application. The plan also describes the testing-based software verification and validation (SV&V) process—a set of specially designed software models used to test RELAP-7. The RELAP-7 (Reactor Excursion and Leak Analysis Program) code is a nuclear reactor system safety analysis code being developed at Idaho National Laboratory (INL). The code is based on the INL’s modern scientific software development framework – MOOSE (Multi-Physics Object-Oriented Simulation Environment). The overall design goal of RELAP-7 is to take advantage of the previous thirty yearsmore » of advancements in computer architecture, software design, numerical integration methods, and physical models. The end result will be a reactor systems analysis capability that retains and improves upon RELAP5’s capability and extends the analysis capability for all reactor system simulation scenarios.« less

Computer software.

PubMed

Rosenthal, L E

1986-10-01

Software is the component in a computer system that permits the hardware to perform the various functions that a computer system is capable of doing. The history of software and its development can be traced to the early nineteenth century. All computer systems are designed to utilize the "stored program concept" as first developed by Charles Babbage in the 1850s. The concept was lost until the mid-1940s, when modern computers made their appearance. Today, because of the complex and myriad tasks that a computer system can perform, there has been a differentiation of types of software. There is software designed to perform specific business applications. There is software that controls the overall operation of a computer system. And there is software that is designed to carry out specialized tasks. Regardless of types, software is the most critical component of any computer system. Without it, all one has is a collection of circuits, transistors, and silicone chips.

The Toxicity Estimation Software Tool (T.E.S.T.)

EPA Science Inventory

The Toxicity Estimation Software Tool (T.E.S.T.) has been developed to estimate toxicological values for aquatic and mammalian species considering acute and chronic endpoints for screening purposes within TSCA and REACH programs.

A Tale of Two Cultures: Cross Cultural Comparison in Learning the Prezi Presentation Software Tool in the US and Norway

ERIC Educational Resources Information Center

Brock, Sabra; Brodahl, Cornelia

2013-01-01

Presentation software is an important tool for both student and professorial communicators. PowerPoint has been the standard since it was introduced in 1990. However, new "improved" software platforms are emerging. Prezi is one of these, claiming to remedy the linear thinking that underlies PowerPoint by creating one canvas and…

Role of the Educator in Social Software Initiatives in Further and Higher Education: A Conceptualisation and Research Agenda

ERIC Educational Resources Information Center

Minocha, Shailey; Schroeder, Andreas; Schneider, Christoph

2011-01-01

Higher and further education institutions are increasingly using social software tools to support teaching and learning. A growing body of research investigates the diversity of tools and their range of contributions. However, little research has focused on investigating the role of the educator in the context of a social software initiative, even…

ISWHM: Tools and Techniques for Software and System Health Management

NASA Technical Reports Server (NTRS)

Schumann, Johann; Mengshoel, Ole J.; Darwiche, Adnan

2010-01-01

This presentation presents status and results of research on Software Health Management done within the NRA "ISWHM: Tools and Techniques for Software and System Health Management." Topics include: Ingredients of a Guidance, Navigation, and Control System (GN and C); Selected GN and C Testbed example; Health Management of major ingredients; ISWHM testbed architecture; and Conclusions and next Steps.

Planning for land use and conservation: Assessing GIS-based conservation software for land use planning

Treesearch

Rob Baldwin; Ryan Scherzinger; Don Lipscomb; Miranda Mockrin; Susan Stein

2014-01-01

Recent advances in planning and ecological software make it possible to conduct highly technical analyses to prioritize conservation investments and inform local land use planning. We review these tools, termed conservation planning tools, and assess the knowledge of a key set of potential users: the land use planning community. We grouped several conservation software...

Report on Automated Semantic Analysis of Scientific and Engineering Codes

NASA Technical Reports Server (NTRS)

Stewart. Maark E. M.; Follen, Greg (Technical Monitor)

2001-01-01

The loss of the Mars Climate Orbiter due to a software error reveals what insiders know: software development is difficult and risky because, in part, current practices do not readily handle the complex details of software. Yet, for scientific software development the MCO mishap represents the tip of the iceberg; few errors are so public, and many errors are avoided with a combination of expertise, care, and testing during development and modification. Further, this effort consumes valuable time and resources even when hardware costs and execution time continually decrease. Software development could use better tools! This lack of tools has motivated the semantic analysis work explained in this report. However, this work has a distinguishing emphasis; the tool focuses on automated recognition of the fundamental mathematical and physical meaning of scientific code. Further, its comprehension is measured by quantitatively evaluating overall recognition with practical codes. This emphasis is necessary if software errors-like the MCO error-are to be quickly and inexpensively avoided in the future. This report evaluates the progress made with this problem. It presents recommendations, describes the approach, the tool's status, the challenges, related research, and a development strategy.

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

ObsPy: A Python toolbox for seismology - Current state, applications, and ecosystem around it

NASA Astrophysics Data System (ADS)

Lecocq, Thomas; Megies, Tobias; Krischer, Lion; Sales de Andrade, Elliott; Barsch, Robert; Beyreuther, Moritz

2016-04-01

ObsPy (http://www.obspy.org) is a community-driven, open-source project offering a bridge for seismology into the scientific Python ecosystem. It provides * read and write support for essentially all commonly used waveform, station, and event metadata formats with a unified interface, * a comprehensive signal processing toolbox tuned to the needs of seismologists, * integrated access to all large data centers, web services and databases, and * convenient wrappers to third party codes like libmseed and evalresp. Python, in contrast to many other languages and tools, is simple enough to enable an exploratory and interactive coding style desired by many scientists. At the same time it is a full-fledged programming language usable by software engineers to build complex and large programs. This combination makes it very suitable for use in seismology where research code often has to be translated to stable and production ready environments. It furthermore offers many freely available high quality scientific modules covering most needs in developing scientific software. ObsPy has been in constant development for more than 5 years and nowadays enjoys a large rate of adoption in the community with thousands of users. Successful applications include time-dependent and rotational seismology, big data processing, event relocations, and synthetic studies about attenuation kernels and full-waveform inversions to name a few examples. Additionally it sparked the development of several more specialized packages slowly building a modern seismological ecosystem around it. This contribution will give a short introduction and overview of ObsPy and highlight a number of use cases and software built around it. We will furthermore discuss the issue of sustainability of scientific software.

ObsPy: A Python toolbox for seismology - Current state, applications, and ecosystem around it

NASA Astrophysics Data System (ADS)

Krischer, L.; Megies, T.; Sales de Andrade, E.; Barsch, R.; Beyreuther, M.

2015-12-01

ObsPy (http://www.obspy.org) is a community-driven, open-source project offering a bridge for seismology into the scientific Python ecosystem. It provides read and write support for essentially all commonly used waveform, station, and event metadata formats with a unified interface, a comprehensive signal processing toolbox tuned to the needs of seismologists, integrated access to all large data centers, web services and databases, and convenient wrappers to third party codes like libmseed and evalresp. Python, in contrast to many other languages and tools, is simple enough to enable an exploratory and interactive coding style desired by many scientists. At the same time it is a full-fledged programming language usable by software engineers to build complex and large programs. This combination makes it very suitable for use in seismology where research code often has to be translated to stable and production ready environments. It furthermore offers many freely available high quality scientific modules covering most needs in developing scientific software.ObsPy has been in constant development for more than 5 years and nowadays enjoys a large rate of adoption in the community with thousands of users. Successful applications include time-dependent and rotational seismology, big data processing, event relocations, and synthetic studies about attenuation kernels and full-waveform inversions to name a few examples. Additionally it sparked the development of several more specialized packages slowly building a modern seismological ecosystem around it.This contribution will give a short introduction and overview of ObsPy and highlight a number of us cases and software built around it. We will furthermore discuss the issue of sustainability of scientific software.

Architecture for autonomy

NASA Astrophysics Data System (ADS)

Broten, Gregory S.; Monckton, Simon P.; Collier, Jack; Giesbrecht, Jared

2006-05-01

In 2002 Defence R&D Canada changed research direction from pure tele-operated land vehicles to general autonomy for land, air, and sea craft. The unique constraints of the military environment coupled with the complexity of autonomous systems drove DRDC to carefully plan a research and development infrastructure that would provide state of the art tools without restricting research scope. DRDC's long term objectives for its autonomy program address disparate unmanned ground vehicle (UGV), unattended ground sensor (UGS), air (UAV), and subsea and surface (UUV and USV) vehicles operating together with minimal human oversight. Individually, these systems will range in complexity from simple reconnaissance mini-UAVs streaming video to sophisticated autonomous combat UGVs exploiting embedded and remote sensing. Together, these systems can provide low risk, long endurance, battlefield services assuming they can communicate and cooperate with manned and unmanned systems. A key enabling technology for this new research is a software architecture capable of meeting both DRDC's current and future requirements. DRDC built upon recent advances in the computing science field while developing its software architecture know as the Architecture for Autonomy (AFA). Although a well established practice in computing science, frameworks have only recently entered common use by unmanned vehicles. For industry and government, the complexity, cost, and time to re-implement stable systems often exceeds the perceived benefits of adopting a modern software infrastructure. Thus, most persevere with legacy software, adapting and modifying software when and wherever possible or necessary -- adopting strategic software frameworks only when no justifiable legacy exists. Conversely, academic programs with short one or two year projects frequently exploit strategic software frameworks but with little enduring impact. The open-source movement radically changes this picture. Academic frameworks, open to public scrutiny and modification, now rival commercial frameworks in both quality and economic impact. Further, industry now realizes that open source frameworks can reduce cost and risk of systems engineering. This paper describes the Architecture for Autonomy implemented by DRDC and how this architecture meets DRDC's current needs. It also presents an argument for why this architecture should also satisfy DRDC's future requirements as well.

A Vision on the Status and Evolution of HEP Physics Software Tools

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

Canal, P.; Elvira, D.; Hatcher, R.

2013-07-28

This paper represents the vision of the members of the Fermilab Scientific Computing Division's Computational Physics Department (SCD-CPD) on the status and the evolution of various HEP software tools such as the Geant4 detector simulation toolkit, the Pythia and GENIE physics generators, and the ROOT data analysis framework. The goal of this paper is to contribute ideas to the Snowmass 2013 process toward the composition of a unified document on the current status and potential evolution of the physics software tools which are essential to HEP.

Artificial intelligence and expert systems in-flight software testing

NASA Technical Reports Server (NTRS)

Demasie, M. P.; Muratore, J. F.

1991-01-01

The authors discuss the introduction of advanced information systems technologies such as artificial intelligence, expert systems, and advanced human-computer interfaces directly into Space Shuttle software engineering. The reconfiguration automation project (RAP) was initiated to coordinate this move towards 1990s software technology. The idea behind RAP is to automate several phases of the flight software testing procedure and to introduce AI and ES into space shuttle flight software testing. In the first phase of RAP, conventional tools to automate regression testing have already been developed or acquired. There are currently three tools in use.

OEXP Analysis Tools Workshop

NASA Technical Reports Server (NTRS)

Garrett, L. Bernard; Wright, Robert L.; Badi, Deborah; Findlay, John T.

1988-01-01

This publication summarizes the software needs and available analysis tools presented at the OEXP Analysis Tools Workshop held at the NASA Langley Research Center, Hampton, Virginia on June 21 to 22, 1988. The objective of the workshop was to identify available spacecraft system (and subsystem) analysis and engineering design tools, and mission planning and analysis software that could be used for various NASA Office of Exploration (code Z) studies, specifically lunar and Mars missions.

Computer Forensics Education - the Open Source Approach

NASA Astrophysics Data System (ADS)

Huebner, Ewa; Bem, Derek; Cheung, Hon

In this chapter we discuss the application of the open source software tools in computer forensics education at tertiary level. We argue that open source tools are more suitable than commercial tools, as they provide the opportunity for students to gain in-depth understanding and appreciation of the computer forensic process as opposed to familiarity with one software product, however complex and multi-functional. With the access to all source programs the students become more than just the consumers of the tools as future forensic investigators. They can also examine the code, understand the relationship between the binary images and relevant data structures, and in the process gain necessary background to become the future creators of new and improved forensic software tools. As a case study we present an advanced subject, Computer Forensics Workshop, which we designed for the Bachelor's degree in computer science at the University of Western Sydney. We based all laboratory work and the main take-home project in this subject on open source software tools. We found that without exception more than one suitable tool can be found to cover each topic in the curriculum adequately. We argue that this approach prepares students better for forensic field work, as they gain confidence to use a variety of tools, not just a single product they are familiar with.

Nuclear and Particle Physics Simulations: The Consortium of Upper-Level Physics Software

NASA Astrophysics Data System (ADS)

Bigelow, Roberta; Moloney, Michael J.; Philpott, John; Rothberg, Joseph

1995-06-01

The Consortium for Upper Level Physics Software (CUPS) has developed a comprehensive series of Nine Book/Software packages that Wiley will publish in FY `95 and `96. CUPS is an international group of 27 physicists, all with extensive backgrounds in the research, teaching, and development of instructional software. The project is being supported by the National Science Foundation (PHY-9014548), and it has received other support from the IBM Corp., Apple Computer Corp., and George Mason University. The Simulations being developed are: Astrophysics, Classical Mechanics, Electricity & Magnetism, Modern Physics, Nuclear and Particle Physics, Quantum Mechanics, Solid State, Thermal and Statistical, and Wave and Optics.

The use of applied software for the professional training of students studying humanities

NASA Astrophysics Data System (ADS)

Sadchikova, A. S.; Rodin, M. M.

2017-01-01

Research practice is an integral part of humanities students' training process. In this regard the training process is to include modern information techniques of the training process of students studying humanities. This paper examines the most popular applied software products used for data processing in social science. For testing purposes we selected the most commonly preferred professional packages: MS Excel, IBM SPSS Statistics, STATISTICA, STADIA. Moreover the article contains testing results of a specialized software Prikladnoy Sotsiolog that is applicable for the preparation stage of the research. The specialised software were tested during one term in groups of students studying humanities.