iStethoscope: a demonstration of the use of mobile devices for auscultation.

PubMed

Bentley, Peter J

2015-01-01

iStethoscope Pro is the first piece of software (an "App") produced for iOS devices, which enabled users to exploit their smartphones, music players, or tablets as stethoscopes. The software exploits the built-in microphone (and supports externally added microphones) and performs real-time amplification and filtering to enable heart sounds to be heard with high fidelity. The software also enables the heart sounds to be recorded, analyzed using a spectrogram, and to be transmitted to others via e-mail. This chapter describes the motivation, functionality, and results from this work.

The Five 'R's' for Developing Trusted Software Frameworks to increase confidence in, and maximise reuse of, Open Source Software.

NASA Astrophysics Data System (ADS)

Fraser, Ryan; Gross, Lutz; Wyborn, Lesley; Evans, Ben; Klump, Jens

2015-04-01

Recent investments in HPC, cloud and Petascale data stores, have dramatically increased the scale and resolution that earth science challenges can now be tackled. These new infrastructures are highly parallelised and to fully utilise them and access the large volumes of earth science data now available, a new approach to software stack engineering needs to be developed. The size, complexity and cost of the new infrastructures mean any software deployed has to be reliable, trusted and reusable. Increasingly software is available via open source repositories, but these usually only enable code to be discovered and downloaded. As a user it is hard for a scientist to judge the suitability and quality of individual codes: rarely is there information on how and where codes can be run, what the critical dependencies are, and in particular, on the version requirements and licensing of the underlying software stack. A trusted software framework is proposed to enable reliable software to be discovered, accessed and then deployed on multiple hardware environments. More specifically, this framework will enable those who generate the software, and those who fund the development of software, to gain credit for the effort, IP, time and dollars spent, and facilitate quantification of the impact of individual codes. For scientific users, the framework delivers reviewed and benchmarked scientific software with mechanisms to reproduce results. The trusted framework will have five separate, but connected components: Register, Review, Reference, Run, and Repeat. 1) The Register component will facilitate discovery of relevant software from multiple open source code repositories. The registration process of the code should include information about licensing, hardware environments it can be run on, define appropriate validation (testing) procedures and list the critical dependencies. 2) The Review component is targeting on the verification of the software typically against a set of benchmark cases. This will be achieved by linking the code in the software framework to peer review forums such as Mozilla Science or appropriate Journals (e.g. Geoscientific Model Development Journal) to assist users to know which codes to trust. 3) Referencing will be accomplished by linking the Software Framework to groups such as Figshare or ImpactStory that help disseminate and measure the impact of scientific research, including program code. 4) The Run component will draw on information supplied in the registration process, benchmark cases described in the review and relevant information to instantiate the scientific code on the selected environment. 5) The Repeat component will tap into existing Provenance Workflow engines that will automatically capture information that relate to a particular run of that software, including identification of all input and output artefacts, and all elements and transactions within that workflow. The proposed trusted software framework will enable users to rapidly discover and access reliable code, reduce the time to deploy it and greatly facilitate sharing, reuse and reinstallation of code. Properly designed it could enable an ability to scale out to massively parallel systems and be accessed nationally/ internationally for multiple use cases, including Supercomputer centres, cloud facilities, and local computers.

Chipster: user-friendly analysis software for microarray and other high-throughput data.

PubMed

Kallio, M Aleksi; Tuimala, Jarno T; Hupponen, Taavi; Klemelä, Petri; Gentile, Massimiliano; Scheinin, Ilari; Koski, Mikko; Käki, Janne; Korpelainen, Eija I

2011-10-14

The growth of high-throughput technologies such as microarrays and next generation sequencing has been accompanied by active research in data analysis methodology, producing new analysis methods at a rapid pace. While most of the newly developed methods are freely available, their use requires substantial computational skills. In order to enable non-programming biologists to benefit from the method development in a timely manner, we have created the Chipster software. Chipster (http://chipster.csc.fi/) brings a powerful collection of data analysis methods within the reach of bioscientists via its intuitive graphical user interface. Users can analyze and integrate different data types such as gene expression, miRNA and aCGH. The analysis functionality is complemented with rich interactive visualizations, allowing users to select datapoints and create new gene lists based on these selections. Importantly, users can save the performed analysis steps as reusable, automatic workflows, which can also be shared with other users. Being a versatile and easily extendable platform, Chipster can be used for microarray, proteomics and sequencing data. In this article we describe its comprehensive collection of analysis and visualization tools for microarray data using three case studies. Chipster is a user-friendly analysis software for high-throughput data. Its intuitive graphical user interface enables biologists to access a powerful collection of data analysis and integration tools, and to visualize data interactively. Users can collaborate by sharing analysis sessions and workflows. Chipster is open source, and the server installation package is freely available.

Chipster: user-friendly analysis software for microarray and other high-throughput data

PubMed Central

2011-01-01

Background The growth of high-throughput technologies such as microarrays and next generation sequencing has been accompanied by active research in data analysis methodology, producing new analysis methods at a rapid pace. While most of the newly developed methods are freely available, their use requires substantial computational skills. In order to enable non-programming biologists to benefit from the method development in a timely manner, we have created the Chipster software. Results Chipster (http://chipster.csc.fi/) brings a powerful collection of data analysis methods within the reach of bioscientists via its intuitive graphical user interface. Users can analyze and integrate different data types such as gene expression, miRNA and aCGH. The analysis functionality is complemented with rich interactive visualizations, allowing users to select datapoints and create new gene lists based on these selections. Importantly, users can save the performed analysis steps as reusable, automatic workflows, which can also be shared with other users. Being a versatile and easily extendable platform, Chipster can be used for microarray, proteomics and sequencing data. In this article we describe its comprehensive collection of analysis and visualization tools for microarray data using three case studies. Conclusions Chipster is a user-friendly analysis software for high-throughput data. Its intuitive graphical user interface enables biologists to access a powerful collection of data analysis and integration tools, and to visualize data interactively. Users can collaborate by sharing analysis sessions and workflows. Chipster is open source, and the server installation package is freely available. PMID:21999641

Evaluation of interaction dynamics of concurrent processes

NASA Astrophysics Data System (ADS)

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

2017-03-01

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

Graphics Software For VT Terminals

NASA Technical Reports Server (NTRS)

Wang, Caroline

1991-01-01

VTGRAPH graphics software tool for DEC/VT computer terminal or terminals compatible with it, widely used by government and industry. Callable in FORTRAN or C language, library program enabling user to cope with many computer environments in which VT terminals used for window management and graphic systems. Provides PLOT10-like package plus color or shade capability for VT240, VT241, and VT300 terminals. User can easily design more-friendly user-interface programs and design PLOT10 programs on VT terminals with different computer systems. Requires ReGis graphics set terminal and FORTRAN compiler.

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

NASA Technical Reports Server (NTRS)

Ryan, Shannon; Christiansen, Erie

2010-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Pathogen metadata platform: software for accessing and analyzing pathogen strain information.

PubMed

Chang, Wenling E; Peterson, Matthew W; Garay, Christopher D; Korves, Tonia

2016-09-15

Pathogen metadata includes information about where and when a pathogen was collected and the type of environment it came from. Along with genomic nucleotide sequence data, this metadata is growing rapidly and becoming a valuable resource not only for research but for biosurveillance and public health. However, current freely available tools for analyzing this data are geared towards bioinformaticians and/or do not provide summaries and visualizations needed to readily interpret results. We designed a platform to easily access and summarize data about pathogen samples. The software includes a PostgreSQL database that captures metadata useful for disease outbreak investigations, and scripts for downloading and parsing data from NCBI BioSample and BioProject into the database. The software provides a user interface to query metadata and obtain standardized results in an exportable, tab-delimited format. To visually summarize results, the user interface provides a 2D histogram for user-selected metadata types and mapping of geolocated entries. The software is built on the LabKey data platform, an open-source data management platform, which enables developers to add functionalities. We demonstrate the use of the software in querying for a pathogen serovar and for genome sequence identifiers. This software enables users to create a local database for pathogen metadata, populate it with data from NCBI, easily query the data, and obtain visual summaries. Some of the components, such as the database, are modular and can be incorporated into other data platforms. The source code is freely available for download at https://github.com/wchangmitre/bioattribution .

Framework for End-User Programming of Cross-Smart Space Applications

PubMed Central

Palviainen, Marko; Kuusijärvi, Jarkko; Ovaska, Eila

2012-01-01

Cross-smart space applications are specific types of software services that enable users to share information, monitor the physical and logical surroundings and control it in a way that is meaningful for the user's situation. For developing cross-smart space applications, this paper makes two main contributions: it introduces (i) a component design and scripting method for end-user programming of cross-smart space applications and (ii) a backend framework of components that interwork to support the brunt of the RDFScript translation, and the use and execution of ontology models. Before end-user programming activities, the software professionals must develop easy-to-apply Driver components for the APIs of existing software systems. Thereafter, end-users are able to create applications from the commands of the Driver components with the help of the provided toolset. The paper also introduces the reference implementation of the framework, tools for the Driver component development and end-user programming of cross-smart space applications and the first evaluation results on their application. PMID:23202169

Visualizer: 3D Gridded Data Visualization Software for Geoscience Education and Research

NASA Astrophysics Data System (ADS)

Harwood, C.; Billen, M. I.; Kreylos, O.; Jadamec, M.; Sumner, D. Y.; Kellogg, L. H.; Hamann, B.

2008-12-01

In both research and education learning is an interactive and iterative process of exploring and analyzing data or model results. However, visualization software often presents challenges on the path to learning because it assumes the user already knows the locations and types of features of interest, instead of enabling flexible and intuitive examination of results. We present examples of research and teaching using the software, Visualizer, specifically designed to create an effective and intuitive environment for interactive, scientific analysis of 3D gridded data. Visualizer runs in a range of 3D virtual reality environments (e.g., GeoWall, ImmersaDesk, or CAVE), but also provides a similar level of real-time interactivity on a desktop computer. When using Visualizer in a 3D-enabled environment, the software allows the user to interact with the data images as real objects, grabbing, rotating or walking around the data to gain insight and perspective. On the desktop, simple features, such as a set of cross-bars marking the plane of the screen, provide extra 3D spatial cues that allow the user to more quickly understand geometric relationships within the data. This platform portability allows the user to more easily integrate research results into classroom demonstrations and exercises, while the interactivity provides an engaging environment for self-directed and inquiry-based learning by students. Visualizer software is freely available for download (www.keckcaves.org) and runs on Mac OSX and Linux platforms.

Generic Software Architecture for Prognostics (GSAP) User Guide

NASA Technical Reports Server (NTRS)

Teubert, Christopher Allen; Daigle, Matthew John; Watkins, Jason; Sankararaman, Shankar; Goebel, Kai

2016-01-01

The Generic Software Architecture for Prognostics (GSAP) is a framework for applying prognostics. It makes applying prognostics easier by implementing many of the common elements across prognostic applications. The standard interface enables reuse of prognostic algorithms and models across systems using the GSAP framework.

LK Scripting Language

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

The LK scripting language is a simple and fast computer programming language designed for easy integration with existing software to enable automation of tasks. The LK language is used by NREL’s System Advisor Model (SAM), the SAM Software Development Kit (SDK), and SolTrace products. LK is easy extensible and adaptable to new software due to its small footprint and is designed to be statically linked into other software. It is written in standard C++, is cross-platform (Windows, Linux, and OSX), and includes optional portions that enable direct integration with graphical user interfaces written in the open source C++ wxWidgets Versionmore » 3.0+ toolkit.« less

A New User Interface for On-Demand Customizable Data Products for Sensors in a SensorWeb

NASA Technical Reports Server (NTRS)

Mandl, Daniel; Cappelaere, Pat; Frye, Stuart; Sohlberg, Rob; Ly, Vuong; Chien, Steve; Sullivan, Don

2011-01-01

A SensorWeb is a set of sensors, which can consist of ground, airborne and space-based sensors interoperating in an automated or autonomous collaborative manner. The NASA SensorWeb toolbox, developed at NASA/GSFC in collaboration with NASA/JPL, NASA/Ames and other partners, is a set of software and standards that (1) enables users to create virtual private networks of sensors over open networks; (2) provides the capability to orchestrate their actions; (3) provides the capability to customize the output data products and (4) enables automated delivery of the data products to the users desktop. A recent addition to the SensorWeb Toolbox is a new user interface, together with web services co-resident with the sensors, to enable rapid creation, loading and execution of new algorithms for processing sensor data. The web service along with the user interface follows the Open Geospatial Consortium (OGC) standard called Web Coverage Processing Service (WCPS). This presentation will detail the prototype that was built and how the WCPS was tested against a HyspIRI flight testbed and an elastic computation cloud on the ground with EO-1 data. HyspIRI is a future NASA decadal mission. The elastic computation cloud stores EO-1 data and runs software similar to Amazon online shopping.

Development of a Common User Interface for the Launch Decision Support System

NASA Technical Reports Server (NTRS)

Scholtz, Jean C.

1991-01-01

The Launch Decision Support System (LDSS) is software to be used by the NASA Test Director (NTD) in the firing room during countdown. This software is designed to assist the NTD with time management, that is, when to resume from a hold condition. This software will assist the NTD in making and evaluating alternate plans and will keep him advised of the existing situation. As such, the interface to this software must be designed to provide the maximum amount of information in the clearest fashion and in a timely manner. This research involves applying user interface guidelines to a mature prototype of LDSS and developing displays that will enable the users to easily and efficiently obtain information from the LDSS displays. This research also extends previous work on organizing and prioritizing human-computer interaction knowledge.

Calypso: a user-friendly web-server for mining and visualizing microbiome-environment interactions.

PubMed

Zakrzewski, Martha; Proietti, Carla; Ellis, Jonathan J; Hasan, Shihab; Brion, Marie-Jo; Berger, Bernard; Krause, Lutz

2017-03-01

Calypso is an easy-to-use online software suite that allows non-expert users to mine, interpret and compare taxonomic information from metagenomic or 16S rDNA datasets. Calypso has a focus on multivariate statistical approaches that can identify complex environment-microbiome associations. The software enables quantitative visualizations, statistical testing, multivariate analysis, supervised learning, factor analysis, multivariable regression, network analysis and diversity estimates. Comprehensive help pages, tutorials and videos are provided via a wiki page. The web-interface is accessible via http://cgenome.net/calypso/ . The software is programmed in Java, PERL and R and the source code is available from Zenodo ( https://zenodo.org/record/50931 ). The software is freely available for non-commercial users. l.krause@uq.edu.au. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

SIMPAVE : towards building interactive simulations for planning pavement construction

DOT National Transportation Integrated Search

2007-04-01

The goal of this project is to produce a software simulation that enables a user to manage a road construction project from the hot mix asphalt plant operation to the finished paved road. Throughout the simulation, the user is provided with the resou...

NavMol 3.0: enabling the representation of metabolic reactions by blind users.

PubMed

Binev, Yuri; Peixoto, Daniela; Pereira, Florbela; Rodrigues, Ian; Cavaco, Sofia; Lobo, Ana M; Aires-de-Sousa, João

2018-01-01

The representation of metabolic reactions strongly relies on visualization, which is a major barrier for blind users. The NavMol software renders the communication and interpretation of molecular structures and reactions accessible by integrating chemoinformatics and assistive technology. NavMol 3.0 provides a molecular editor for metabolic reactions. The user can start with templates of reactions and build from such cores. Atom-to-atom mapping enables changes in the reactants to be reflected in the products (and vice-versa) and the reaction centres to be automatically identified. Blind users can easily interact with the software using the keyboard and text-to-speech technology. NavMol 3.0 is free and open source under the GNU general public license (GPLv3), and can be downloaded at http://sourceforge.net/projects/navmol as a JAR file. joao@airesdesousa.com. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

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.

Web servers and services for electrostatics calculations with APBS and PDB2PQR

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

Unni, Samir; Huang, Yong; Hanson, Robert M.

APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but it also increases the availability of electrostatics calculations on portable computing platforms. Users can access this new functionality in two ways. First, an Opal-enabled version of APBS is provided in currentmore » distributions, available freely on the web. Second, we have extended the PDB2PQR web server to provide an interface for the setup, execution, and visualization electrostatics potentials as calculated by APBS. This web interface also uses the Opal framework which ensures the scalability needed to support the large APBS user community. Both of these resources are available from the APBS/PDB2PQR website: http://www.poissonboltzmann.org/.« less

Web servers and services for electrostatics calculations with APBS and PDB2PQR

PubMed Central

Unni, Samir; Huang, Yong; Hanson, Robert; Tobias, Malcolm; Krishnan, Sriram; Li, Wilfred W.; Nielsen, Jens E.; Baker, Nathan A.

2011-01-01

APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a Web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but it also increases the availability of electrostatics calculations on portable computing platforms. Users can access this new functionality in two ways. First, an Opal-enabled version of APBS is provided in current distributions, available freely on the web. Second, we have extended the PDB2PQR web server to provide an interface for the setup, execution, and visualization electrostatics potentials as calculated by APBS. This web interface also uses the Opal framework which ensures the scalability needed to support the large APBS user community. Both of these resources are available from the APBS/PDB2PQR website: http://www.poissonboltzmann.org/. PMID:21425296

Improving Airline Safety

NASA Technical Reports Server (NTRS)

1998-01-01

Under a NASA-Ames Space Act Agreement, Coryphaeus Software and Simauthor, Inc., developed an Aviation Performance Measuring System (APMS). This software, developed for the aerospace and airline industry, enables the replay of Digital Flight Data Recorder (DFDR) data in a flexible, user-configurable, real-time, high fidelity 3D (three dimensional) environment.

Towards Context-Aware and User-Centered Analysis in Assistive Environments: A Methodology and a Software Tool.

PubMed

Fontecha, Jesús; Hervás, Ramón; Mondéjar, Tania; González, Iván; Bravo, José

2015-10-01

One of the main challenges on Ambient Assisted Living (AAL) is to reach an appropriate acceptance level of the assistive systems, as well as to analyze and monitor end user tasks in a feasible and efficient way. The development and evaluation of AAL solutions based on user-centered perspective help to achive these goals. In this work, we have designed a methodology to integrate and develop analytics user-centered tools into assistive systems. An analysis software tool gathers information of end users from adapted psychological questionnaires and naturalistic observation of their own context. The aim is to enable an in-deep analysis focused on improving the life quality of elderly people and their caregivers.

An electronic registry for physiotherapists in Belgium.

PubMed

Buyl, Ronald; Nyssen, Marc

2008-01-01

This paper describes the results of the KINELECTRICS project. Since more and more clinical documents are stored and transmitted in an electronic way, the aim of this project was to design an electronic version of the registry that contains all acts of physiotherapists. The solution we present here, not only meets all legal constraints, but also enables to verify the traceability and inalterability of the generated documents, by means of SHA-256 codes. The proposed structure, using XML technology can also form a basis for the development of tools that can be used by the controlling authorities. By means of a certification procedure for software systems, we succeeded in developing a user friendly system that enables end-users that use a quality labeled software package, to automatically produce all the legally necessary documents concerning the registry. Moreover, we hope that this development will be an incentive for non-users to start working in an electronic way.

An Enhanced Z39.50 Gateway to the WorldWideWeb.

ERIC Educational Resources Information Center

Cunningham, David; Sloan, Stephen

1994-01-01

Describes how a university library uses the WorldWideWeb (WWW) to enable users to access resources mounted on a local Z39.50 server and to order prints from articles stored on a CD-ROM jukebox. The software used in the construction of the system, necessary modifications to the software, and software ordering information are covered. (KRN)

From expert-derived user needs to user-perceived ease of use and usefulness: a two-phase mixed-methods evaluation framework.

PubMed

Boland, Mary Regina; Rusanov, Alexander; So, Yat; Lopez-Jimenez, Carlos; Busacca, Linda; Steinman, Richard C; Bakken, Suzanne; Bigger, J Thomas; Weng, Chunhua

2014-12-01

Underspecified user needs and frequent lack of a gold standard reference are typical barriers to technology evaluation. To address this problem, this paper presents a two-phase evaluation framework involving usability experts (phase 1) and end-users (phase 2). In phase 1, a cross-system functionality alignment between expert-derived user needs and system functions was performed to inform the choice of "the best available" comparison system to enable a cognitive walkthrough in phase 1 and a comparative effectiveness evaluation in phase 2. During phase 2, five quantitative and qualitative evaluation methods are mixed to assess usability: time-motion analysis, software log, questionnaires - System Usability Scale and the Unified Theory of Acceptance of Use of Technology, think-aloud protocols, and unstructured interviews. Each method contributes data for a unique measure (e.g., time motion analysis contributes task-completion-time; software log contributes action transition frequency). The measures are triangulated to yield complementary insights regarding user-perceived ease-of-use, functionality integration, anxiety during use, and workflow impact. To illustrate its use, we applied this framework in a formative evaluation of a software called Integrated Model for Patient Care and Clinical Trials (IMPACT). We conclude that this mixed-methods evaluation framework enables an integrated assessment of user needs satisfaction and user-perceived usefulness and usability of a novel design. This evaluation framework effectively bridges the gap between co-evolving user needs and technology designs during iterative prototyping and is particularly useful when it is difficult for users to articulate their needs for technology support due to the lack of a baseline. Copyright © 2013 Elsevier Inc. All rights reserved.

Web-Based Software for Managing Research

NASA Technical Reports Server (NTRS)

Hoadley, Sherwood T.; Ingraldi, Anthony M.; Gough, Kerry M.; Fox, Charles; Cronin, Catherine K.; Hagemann, Andrew G.; Kemmerly, Guy T.; Goodman, Wesley L.

2007-01-01

aeroCOMPASS is a software system, originally designed to aid in the management of wind tunnels at Langley Research Center, that could be adapted to provide similar aid to other enterprises in which research is performed in common laboratory facilities by users who may be geographically dispersed. Included in aeroCOMPASS is Web-interface software that provides a single, convenient portal to a set of project- and test-related software tools and other application programs. The heart of aeroCOMPASS is a user-oriented document-management software subsystem that enables geographically dispersed users to easily share and manage a variety of documents. A principle of "write once, read many" is implemented throughout aeroCOMPASS to eliminate the need for multiple entry of the same information. The Web framework of aeroCOMPASS provides links to client-side application programs that are fully integrated with databases and server-side application programs. Other subsystems of aeroCOMPASS include ones for reserving hardware, tracking of requests and feedback from users, generating interactive notes, administration of a customer-satisfaction questionnaire, managing execution of tests, managing archives of metadata about tests, planning tests, and providing online help and instruction for users.

The cloud services innovation platform- enabling service-based environmental modelling using infrastructure-as-a-service cloud computing

USDA-ARS?s Scientific Manuscript database

Service oriented architectures allow modelling engines to be hosted over the Internet abstracting physical hardware configuration and software deployments from model users. Many existing environmental models are deployed as desktop applications running on user's personal computers (PCs). Migration ...

Software Tools Streamline Project Management

NASA Technical Reports Server (NTRS)

2009-01-01

Three innovative software inventions from Ames Research Center (NETMARK, Program Management Tool, and Query-Based Document Management) are finding their way into NASA missions as well as industry applications. The first, NETMARK, is a program that enables integrated searching of data stored in a variety of databases and documents, meaning that users no longer have to look in several places for related information. NETMARK allows users to search and query information across all of these sources in one step. This cross-cutting capability in information analysis has exponentially reduced the amount of time needed to mine data from days or weeks to mere seconds. NETMARK has been used widely throughout NASA, enabling this automatic integration of information across many documents and databases. NASA projects that use NETMARK include the internal reporting system and project performance dashboard, Erasmus, NASA s enterprise management tool, which enhances organizational collaboration and information sharing through document routing and review; the Integrated Financial Management Program; International Space Station Knowledge Management; Mishap and Anomaly Information Reporting System; and management of the Mars Exploration Rovers. Approximately $1 billion worth of NASA s projects are currently managed using Program Management Tool (PMT), which is based on NETMARK. PMT is a comprehensive, Web-enabled application tool used to assist program and project managers within NASA enterprises in monitoring, disseminating, and tracking the progress of program and project milestones and other relevant resources. The PMT consists of an integrated knowledge repository built upon advanced enterprise-wide database integration techniques and the latest Web-enabled technologies. The current system is in a pilot operational mode allowing users to automatically manage, track, define, update, and view customizable milestone objectives and goals. The third software invention, Query-Based Document Management (QBDM) is a tool that enables content or context searches, either simple or hierarchical, across a variety of databases. The system enables users to specify notification subscriptions where they associate "contexts of interest" and "events of interest" to one or more documents or collection(s) of documents. Based on these subscriptions, users receive notification when the events of interest occur within the contexts of interest for associated document or collection(s) of documents. Users can also associate at least one notification time as part of the notification subscription, with at least one option for the time period of notifications.

Draper Station Analysis Tool

NASA Technical Reports Server (NTRS)

Bedrossian, Nazareth; Jang, Jiann-Woei; McCants, Edward; Omohundro, Zachary; Ring, Tom; Templeton, Jeremy; Zoss, Jeremy; Wallace, Jonathan; Ziegler, Philip

2011-01-01

Draper Station Analysis Tool (DSAT) is a computer program, built on commercially available software, for simulating and analyzing complex dynamic systems. Heretofore used in designing and verifying guidance, navigation, and control systems of the International Space Station, DSAT has a modular architecture that lends itself to modification for application to spacecraft or terrestrial systems. DSAT consists of user-interface, data-structures, simulation-generation, analysis, plotting, documentation, and help components. DSAT automates the construction of simulations and the process of analysis. DSAT provides a graphical user interface (GUI), plus a Web-enabled interface, similar to the GUI, that enables a remotely located user to gain access to the full capabilities of DSAT via the Internet and Webbrowser software. Data structures are used to define the GUI, the Web-enabled interface, simulations, and analyses. Three data structures define the type of analysis to be performed: closed-loop simulation, frequency response, and/or stability margins. DSAT can be executed on almost any workstation, desktop, or laptop computer. DSAT provides better than an order of magnitude improvement in cost, schedule, and risk assessment for simulation based design and verification of complex dynamic systems.

Viewing ISS Data in Real Time via the Internet

NASA Technical Reports Server (NTRS)

Myers, Gerry; Chamberlain, Jim

2004-01-01

EZStream is a computer program that enables authorized users at diverse terrestrial locations to view, in real time, data generated by scientific payloads aboard the International Space Station (ISS). The only computation/communication resource needed for use of EZStream is a computer equipped with standard Web-browser software and a connection to the Internet. EZStream runs in conjunction with the TReK software, described in a prior NASA Tech Briefs article, that coordinates multiple streams of data for the ground communication system of the ISS. EZStream includes server components that interact with TReK within the ISS ground communication system and client components that reside in the users' remote computers. Once an authorized client has logged in, a server component of EZStream pulls the requested data from a TReK application-program interface and sends the data to the client. Future EZStream enhancements will include (1) extensions that enable the server to receive and process arbitrary data streams on its own and (2) a Web-based graphical-user-interface-building subprogram that enables a client who lacks programming expertise to create customized display Web pages.

Software Tool Integrating Data Flow Diagrams and Petri Nets

NASA Technical Reports Server (NTRS)

Thronesbery, Carroll; Tavana, Madjid

2010-01-01

Data Flow Diagram - Petri Net (DFPN) is a software tool for analyzing other software to be developed. The full name of this program reflects its design, which combines the benefit of data-flow diagrams (which are typically favored by software analysts) with the power and precision of Petri-net models, without requiring specialized Petri-net training. (A Petri net is a particular type of directed graph, a description of which would exceed the scope of this article.) DFPN assists a software analyst in drawing and specifying a data-flow diagram, then translates the diagram into a Petri net, then enables graphical tracing of execution paths through the Petri net for verification, by the end user, of the properties of the software to be developed. In comparison with prior means of verifying the properties of software to be developed, DFPN makes verification by the end user more nearly certain, thereby making it easier to identify and correct misconceptions earlier in the development process, when correction is less expensive. After the verification by the end user, DFPN generates a printable system specification in the form of descriptions of processes and data.

Enhancement/upgrade of Engine Structures Technology Best Estimator (EST/BEST) Software System

NASA Technical Reports Server (NTRS)

Shah, Ashwin

2003-01-01

This report describes the work performed during the contract period and the capabilities included in the EST/BEST software system. The developed EST/BEST software system includes the integrated NESSUS, IPACS, COBSTRAN, and ALCCA computer codes required to perform the engine cycle mission and component structural analysis. Also, the interactive input generator for NESSUS, IPACS, and COBSTRAN computer codes have been developed and integrated with the EST/BEST software system. The input generator allows the user to create input from scratch as well as edit existing input files interactively. Since it has been integrated with the EST/BEST software system, it enables the user to modify EST/BEST generated files and perform the analysis to evaluate the benefits. Appendix A gives details of how to use the newly added features in the EST/BEST software system.

Technology for Manufacturing Efficiency

NASA Technical Reports Server (NTRS)

1995-01-01

The Ground Processing Scheduling System (GPSS) was developed by Ames Research Center, Kennedy Space Center and divisions of the Lockheed Company to maintain the scheduling for preparing a Space Shuttle Orbiter for a mission. Red Pepper Software Company, now part of PeopleSoft, Inc., commercialized the software as their ResponseAgent product line. The software enables users to monitor manufacturing variables, report issues and develop solutions to existing problems.

Enabling a systems biology knowledgebase with gaggle and firegoose

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

Baliga, Nitin S.

The overall goal of this project was to extend the existing Gaggle and Firegoose systems to develop an open-source technology that runs over the web and links desktop applications with many databases and software applications. This technology would enable researchers to incorporate workflows for data analysis that can be executed from this interface to other online applications. The four specific aims were to (1) provide one-click mapping of genes, proteins, and complexes across databases and species; (2) enable multiple simultaneous workflows; (3) expand sophisticated data analysis for online resources; and enhance open-source development of the Gaggle-Firegoose infrastructure. Gaggle is anmore » open-source Java software system that integrates existing bioinformatics programs and data sources into a user-friendly, extensible environment to allow interactive exploration, visualization, and analysis of systems biology data. Firegoose is an extension to the Mozilla Firefox web browser that enables data transfer between websites and desktop tools including Gaggle. In the last phase of this funding period, we have made substantial progress on development and application of the Gaggle integration framework. We implemented the workspace to the Network Portal. Users can capture data from Firegoose and save them to the workspace. Users can create workflows to start multiple software components programmatically and pass data between them. Results of analysis can be saved to the cloud so that they can be easily restored on any machine. We also developed the Gaggle Chrome Goose, a plugin for the Google Chrome browser in tandem with an opencpu server in the Amazon EC2 cloud. This allows users to interactively perform data analysis on a single web page using the R packages deployed on the opencpu server. The cloud-based framework facilitates collaboration between researchers from multiple organizations. We have made a number of enhancements to the cmonkey2 application to enable and improve the integration within different environments, and we have created a new tools pipeline for generating EGRIN2 models in a largely automated way.« less

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

PubMed

Jha, Ashish Kumar

2015-01-01

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

NASA Meteoroid Engineering Model Release 2.0

NASA Technical Reports Server (NTRS)

Moorhead, A. V.; Koehler, H. M.; Cooke, W. J.

2015-01-01

The Meteoroid Engineering Model release 2.0 (MEMR2) software is NASA's most current and accurate model of the meteoroid environment. It enables the user to generate a trajectory-specific meteoroid environment for spacecraft traveling within the inner solar system. In addition to the total meteoroid flux, MEMR2 provides the user with meteoroid directionality and velocity information. Users have the ability to make a number of analysis and output choices that tailor the resulting environment to their needs. This Technical Memorandum outlines the history of MEMR2, the meteoroid environment it describes, and makes recommendations for the correct use of the software and interpretation of its results.

Building a Generic Virtual Research Environment Framework for Multiple Earth and Space Science Domains and a Diversity of Users.

NASA Astrophysics Data System (ADS)

Wyborn, L. A.; Fraser, R.; Evans, B. J. K.; Friedrich, C.; Klump, J. F.; Lescinsky, D. T.

2017-12-01

Virtual Research Environments (VREs) are now part of academic infrastructures. Online research workflows can be orchestrated whereby data can be accessed from multiple external repositories with processing taking place on public or private clouds, and centralised supercomputers using a mixture of user codes, and well-used community software and libraries. VREs enable distributed members of research teams to actively work together to share data, models, tools, software, workflows, best practices, infrastructures, etc. These environments and their components are increasingly able to support the needs of undergraduate teaching. External to the research sector, they can also be reused by citizen scientists, and be repurposed for industry users to help accelerate the diffusion and hence enable the translation of research innovations. The Virtual Geophysics Laboratory (VGL) in Australia was started in 2012, built using a collaboration between CSIRO, the National Computational Infrastructure (NCI) and Geoscience Australia, with support funding from the Australian Government Department of Education. VGL comprises three main modules that provide an interface to enable users to first select their required data; to choose a tool to process that data; and then access compute infrastructure for execution. VGL was initially built to enable a specific set of researchers in government agencies access to specific data sets and a limited number of tools. Over the years it has evolved into a multi-purpose Earth science platform with access to an increased variety of data (e.g., Natural Hazards, Geochemistry), a broader range of software packages, and an increasing diversity of compute infrastructures. This expansion has been possible because of the approach to loosely couple data, tools and compute resources via interfaces that are built on international standards and accessed as network-enabled services wherever possible. Built originally for researchers that were not fussy about general usability, increasing emphasis on User Interfaces (UIs) and stability will lead to increased uptake in the education and industry sectors. Simultaneously, improvements are being added to facilitate access to data and tools by experienced researchers who want direct access to both data and flexible workflows.

TLM-Tracker: software for cell segmentation, tracking and lineage analysis in time-lapse microscopy movies.

PubMed

Klein, Johannes; Leupold, Stefan; Biegler, Ilona; Biedendieck, Rebekka; Münch, Richard; Jahn, Dieter

2012-09-01

Time-lapse imaging in combination with fluorescence microscopy techniques enable the investigation of gene regulatory circuits and uncovered phenomena like culture heterogeneity. In this context, computational image processing for the analysis of single cell behaviour plays an increasing role in systems biology and mathematical modelling approaches. Consequently, we developed a software package with graphical user interface for the analysis of single bacterial cell behaviour. A new software called TLM-Tracker allows for the flexible and user-friendly interpretation for the segmentation, tracking and lineage analysis of microbial cells in time-lapse movies. The software package, including manual, tutorial video and examples, is available as Matlab code or executable binaries at http://www.tlmtracker.tu-bs.de.

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.

Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows.

PubMed

Specht, Michael; Kuhlgert, Sebastian; Fufezan, Christian; Hippler, Michael

2011-04-15

We present Proteomatic, an operating system independent and user-friendly platform that enables the construction and execution of MS/MS data evaluation pipelines using free and commercial software. Required external programs such as for peptide identification are downloaded automatically in the case of free software. Due to a strict separation of functionality and presentation, and support for multiple scripting languages, new processing steps can be added easily. Proteomatic is implemented in C++/Qt, scripts are implemented in Ruby, Python and PHP. All source code is released under the LGPL. Source code and installers for Windows, Mac OS X, and Linux are freely available at http://www.proteomatic.org. michael.specht@uni-muenster.de Supplementary data are available at Bioinformatics online.

e-Stars Template Builder

NASA Technical Reports Server (NTRS)

Cox, Brian

2003-01-01

e-Stars Template Builder is a computer program that implements a concept of enabling users to rapidly gain access to information on projects of NASA's Jet Propulsion Laboratory. The information about a given project is not stored in a data base, but rather, in a network that follows the project as it develops. e-Stars Template Builder resides on a server computer, using Practical Extraction and Reporting Language (PERL) scripts to create what are called "e-STARS node templates," which are software constructs that allow for project-specific configurations. The software resides on the server and does not require specific software on the user machine except for an Internet browser. A user's computer need not be equipped with special software (other than an Internet-browser program). e-Stars Template Builder is compatible with Windows, Macintosh, and UNIX operating systems. A user invokes e-Stars Template Builder from a browser window. Operations that can be performed by the user include the creation of child processes and the addition of links and descriptions of documentation to existing pages or nodes. By means of this addition of "child processes" of nodes, a network that reflects the development of a project is generated.

Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories.

PubMed

Cardoso, João G R; Jensen, Kristian; Lieven, Christian; Lærke Hansen, Anne Sofie; Galkina, Svetlana; Beber, Moritz; Özdemir, Emre; Herrgård, Markus J; Redestig, Henning; Sonnenschein, Nikolaus

2018-04-20

Computational systems biology methods enable rational design of cell factories on a genome-scale and thus accelerate the engineering of cells for the production of valuable chemicals and proteins. Unfortunately, the majority of these methods' implementations are either not published, rely on proprietary software, or do not provide documented interfaces, which has precluded their mainstream adoption in the field. In this work we present cameo, a platform-independent software that enables in silico design of cell factories and targets both experienced modelers as well as users new to the field. It is written in Python and implements state-of-the-art methods for enumerating and prioritizing knockout, knock-in, overexpression, and down-regulation strategies and combinations thereof. Cameo is an open source software project and is freely available under the Apache License 2.0. A dedicated Web site including documentation, examples, and installation instructions can be found at http://cameo.bio . Users can also give cameo a try at http://try.cameo.bio .

Embedded Web Technology: Internet Technology Applied to Real-Time System Control

NASA Technical Reports Server (NTRS)

Daniele, Carl J.

1998-01-01

The NASA Lewis Research Center is developing software tools to bridge the gap between the traditionally non-real-time Internet technology and the real-time, embedded-controls environment for space applications. Internet technology has been expanding at a phenomenal rate. The simple World Wide Web browsers (such as earlier versions of Netscape, Mosaic, and Internet Explorer) that resided on personal computers just a few years ago only enabled users to log into and view a remote computer site. With current browsers, users not only view but also interact with remote sites. In addition, the technology now supports numerous computer platforms (PC's, MAC's, and Unix platforms), thereby providing platform independence.In contrast, the development of software to interact with a microprocessor (embedded controller) that is used to monitor and control a space experiment has generally been a unique development effort. For each experiment, a specific graphical user interface (GUI) has been developed. This procedure works well for a single-user environment. However, the interface for the International Space Station (ISS) Fluids and Combustion Facility will have to enable scientists throughout the world and astronauts onboard the ISS, using different computer platforms, to interact with their experiments in the Fluids and Combustion Facility. Developing a specific GUI for all these users would be cost prohibitive. An innovative solution to this requirement, developed at Lewis, is to use Internet technology, where the general problem of platform independence has already been partially solved, and to leverage this expanding technology as new products are developed. This approach led to the development of the Embedded Web Technology (EWT) program at Lewis, which has the potential to significantly reduce software development costs for both flight and ground software.

Program For Generating Interactive Displays

NASA Technical Reports Server (NTRS)

Costenbader, Jay; Moleski, Walt; Szczur, Martha; Howell, David; Engelberg, Norm; Li, Tin P.; Misra, Dharitri; Miller, Philip; Neve, Leif; Wolf, Karl;

Geospatial-enabled Data Exploration and Computation through Data Infrastructure Building Blocks

NASA Astrophysics Data System (ADS)

Song, C. X.; Biehl, L. L.; Merwade, V.; Villoria, N.

2015-12-01

Geospatial data are present everywhere today with the proliferation of location-aware computing devices and sensors. This is especially true in the scientific community where large amounts of data are driving research and education activities in many domains. Collaboration over geospatial data, for example, in modeling, data analysis and visualization, must still overcome the barriers of specialized software and expertise among other challenges. The GABBs project aims at enabling broader access to geospatial data exploration and computation by developing spatial data infrastructure building blocks that leverage capabilities of end-to-end application service and virtualized computing framework in HUBzero. Funded by NSF Data Infrastructure Building Blocks (DIBBS) initiative, GABBs provides a geospatial data architecture that integrates spatial data management, mapping and visualization and will make it available as open source. The outcome of the project will enable users to rapidly create tools and share geospatial data and tools on the web for interactive exploration of data without requiring significant software development skills, GIS expertise or IT administrative privileges. This presentation will describe the development of geospatial data infrastructure building blocks and the scientific use cases that help drive the software development, as well as seek feedback from the user communities.

Simulation Control Graphical User Interface Logging Report

NASA Technical Reports Server (NTRS)

Hewling, Karl B., Jr.

2012-01-01

One of the many tasks of my project was to revise the code of the Simulation Control Graphical User Interface (SIM GUI) to enable logging functionality to a file. I was also tasked with developing a script that directed the startup and initialization flow of the various LCS software components. This makes sure that a software component will not spin up until all the appropriate dependencies have been configured properly. Also I was able to assist hardware modelers in verifying the configuration of models after they have been upgraded to a new software version. I developed some code that analyzes the MDL files to determine if any error were generated due to the upgrade process. Another one of the projects assigned to me was supporting the End-to-End Hardware/Software Daily Tag-up meeting.

Tools of the Courseware Trade: A Comparison of ToolBook 1.0 and HyperCard 2.0.

ERIC Educational Resources Information Center

Brader, Lorinda L.

1990-01-01

Compares two authoring tools that were developed to enable users without programing experience to create and modify software. HyperCard, designed for Macintosh microcomputers, and ToolBook, for microcomputers that run on MS-DOS, are compared in the areas of programing languages, graphics and printing capabilities, user interface, system…

Software For Computing Reliability Of Other Software

NASA Technical Reports Server (NTRS)

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

1995-01-01

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

Problem-Solving Software

NASA Technical Reports Server (NTRS)

1992-01-01

CBR Express software solves problems by adapting sorted solutions to new problems specified by a user. It is applicable to a wide range of situations. The technology was originally developed by Inference Corporation for Johnson Space Center's Advanced Software Development Workstation. The project focused on the reuse of software designs, and Inference used CBR as part of the ACCESS prototype software. The commercial CBR Express is used as a "help desk" for customer support, enabling reuse of existing information when necessary. It has been adopted by several companies, among them American Airlines, which uses it to solve reservation system software problems.

Collaboration using open standards and open source software (examples of DIAS/CEOS Water Portal)

NASA Astrophysics Data System (ADS)

Miura, S.; Sekioka, S.; Kuroiwa, K.; Kudo, Y.

2015-12-01

The DIAS/CEOS Water Portal is a part of the DIAS (Data Integration and Analysis System, http://www.editoria.u-tokyo.ac.jp/projects/dias/?locale=en_US) systems for data distribution for users including, but not limited to, scientists, decision makers and officers like river administrators. One of the functions of this portal is to enable one-stop search and access variable water related data archived multiple data centers located all over the world. This portal itself does not store data. Instead, according to requests made by users on the web page, it retrieves data from distributed data centers on-the-fly and lets them download and see rendered images/plots. Our system mainly relies on the open source software GI-cat (http://essi-lab.eu/do/view/GIcat) and open standards such as OGC-CSW, Opensearch and OPeNDAP protocol to enable the above functions. Details on how it works will be introduced during the presentation. Although some data centers have unique meta data format and/or data search protocols, our portal's brokering function enables users to search across various data centers at one time. And this portal is also connected to other data brokering systems, including GEOSS DAB (Discovery and Access Broker). As a result, users can search over thousands of datasets, millions of files at one time. Users can access the DIAS/CEOS Water Portal system at http://waterportal.ceos.org/.

Fuzzy Logic Engine

NASA Technical Reports Server (NTRS)

Howard, Ayanna

2005-01-01

The Fuzzy Logic Engine is a software package that enables users to embed fuzzy-logic modules into their application programs. Fuzzy logic is useful as a means of formulating human expert knowledge and translating it into software to solve problems. Fuzzy logic provides flexibility for modeling relationships between input and output information and is distinguished by its robustness with respect to noise and variations in system parameters. In addition, linguistic fuzzy sets and conditional statements allow systems to make decisions based on imprecise and incomplete information. The user of the Fuzzy Logic Engine need not be an expert in fuzzy logic: it suffices to have a basic understanding of how linguistic rules can be applied to the user's problem. The Fuzzy Logic Engine is divided into two modules: (1) a graphical-interface software tool for creating linguistic fuzzy sets and conditional statements and (2) a fuzzy-logic software library for embedding fuzzy processing capability into current application programs. The graphical- interface tool was developed using the Tcl/Tk programming language. The fuzzy-logic software library was written in the C programming language.

One-Click Data Analysis Software for Science Operations

NASA Astrophysics Data System (ADS)

Navarro, Vicente

2015-12-01

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

Science Gateways, Scientific Workflows and Open Community Software

NASA Astrophysics Data System (ADS)

Pierce, M. E.; Marru, S.

2014-12-01

Science gateways and scientific workflows occupy different ends of the spectrum of user-focused cyberinfrastructure. Gateways, sometimes called science portals, provide a way for enabling large numbers of users to take advantage of advanced computing resources (supercomputers, advanced storage systems, science clouds) by providing Web and desktop interfaces and supporting services. Scientific workflows, at the other end of the spectrum, support advanced usage of cyberinfrastructure that enable "power users" to undertake computational experiments that are not easily done through the usual mechanisms (managing simulations across multiple sites, for example). Despite these different target communities, gateways and workflows share many similarities and can potentially be accommodated by the same software system. For example, pipelines to process InSAR imagery sets or to datamine GPS time series data are workflows. The results and the ability to make downstream products may be made available through a gateway, and power users may want to provide their own custom pipelines. In this abstract, we discuss our efforts to build an open source software system, Apache Airavata, that can accommodate both gateway and workflow use cases. Our approach is general, and we have applied the software to problems in a number of scientific domains. In this talk, we discuss our applications to usage scenarios specific to earth science, focusing on earthquake physics examples drawn from the QuakSim.org and GeoGateway.org efforts. We also examine the role of the Apache Software Foundation's open community model as a way to build up common commmunity codes that do not depend upon a single "owner" to sustain. Pushing beyond open source software, we also see the need to provide gateways and workflow systems as cloud services. These services centralize operations, provide well-defined programming interfaces, scale elastically, and have global-scale fault tolerance. We discuss our work providing Apache Airavata as a hosted service to provide these features.

State criminal justice telecommunications (STACOM). Volume 4: Network design software user's guide

NASA Technical Reports Server (NTRS)

Lee, J. J.

1977-01-01

A user's guide to the network design program is presented. The program is written in FORTRAN V and implemented on a UNIVAC 1108 computer under the EXEC-8 operating system which enables the user to construct least-cost network topologies for criminal justice digital telecommunications networks. A complete description of program features, inputs, processing logic, and outputs is presented, and a sample run and a program listing are included.

Simplified programming and control of automated radiosynthesizers through unit operations.

PubMed

Claggett, Shane B; Quinn, Kevin M; Lazari, Mark; Moore, Melissa D; van Dam, R Michael

2013-07-15

Many automated radiosynthesizers for producing positron emission tomography (PET) probes provide a means for the operator to create custom synthesis programs. The programming interfaces are typically designed with the engineer rather than the radiochemist in mind, requiring lengthy programs to be created from sequences of low-level, non-intuitive hardware operations. In some cases, the user is even responsible for adding steps to update the graphical representation of the system. In light of these unnecessarily complex approaches, we have created software to perform radiochemistry on the ELIXYS radiosynthesizer with the goal of being intuitive and easy to use. Radiochemists were consulted, and a wide range of radiosyntheses were analyzed to determine a comprehensive set of basic chemistry unit operations. Based around these operations, we created a software control system with a client-server architecture. In an attempt to maximize flexibility, the client software was designed to run on a variety of portable multi-touch devices. The software was used to create programs for the synthesis of several 18F-labeled probes on the ELIXYS radiosynthesizer, with [18F]FDG detailed here. To gauge the user-friendliness of the software, program lengths were compared to those from other systems. A small sample group with no prior radiosynthesizer experience was tasked with creating and running a simple protocol. The software was successfully used to synthesize several 18F-labeled PET probes, including [18F]FDG, with synthesis times and yields comparable to literature reports. The resulting programs were significantly shorter and easier to debug than programs from other systems. The sample group of naive users created and ran a simple protocol within a couple of hours, revealing a very short learning curve. The client-server architecture provided reliability, enabling continuity of the synthesis run even if the computer running the client software failed. The architecture enabled a single user to control the hardware while others observed the run in progress or created programs for other probes. We developed a novel unit operation-based software interface to control automated radiosynthesizers that reduced the program length and complexity and also exhibited a short learning curve. The client-server architecture provided robustness and flexibility.

Simplified programming and control of automated radiosynthesizers through unit operations

PubMed Central

2013-01-01

Background Many automated radiosynthesizers for producing positron emission tomography (PET) probes provide a means for the operator to create custom synthesis programs. The programming interfaces are typically designed with the engineer rather than the radiochemist in mind, requiring lengthy programs to be created from sequences of low-level, non-intuitive hardware operations. In some cases, the user is even responsible for adding steps to update the graphical representation of the system. In light of these unnecessarily complex approaches, we have created software to perform radiochemistry on the ELIXYS radiosynthesizer with the goal of being intuitive and easy to use. Methods Radiochemists were consulted, and a wide range of radiosyntheses were analyzed to determine a comprehensive set of basic chemistry unit operations. Based around these operations, we created a software control system with a client–server architecture. In an attempt to maximize flexibility, the client software was designed to run on a variety of portable multi-touch devices. The software was used to create programs for the synthesis of several 18F-labeled probes on the ELIXYS radiosynthesizer, with [18F]FDG detailed here. To gauge the user-friendliness of the software, program lengths were compared to those from other systems. A small sample group with no prior radiosynthesizer experience was tasked with creating and running a simple protocol. Results The software was successfully used to synthesize several 18F-labeled PET probes, including [18F]FDG, with synthesis times and yields comparable to literature reports. The resulting programs were significantly shorter and easier to debug than programs from other systems. The sample group of naive users created and ran a simple protocol within a couple of hours, revealing a very short learning curve. The client–server architecture provided reliability, enabling continuity of the synthesis run even if the computer running the client software failed. The architecture enabled a single user to control the hardware while others observed the run in progress or created programs for other probes. Conclusions We developed a novel unit operation-based software interface to control automated radiosynthesizers that reduced the program length and complexity and also exhibited a short learning curve. The client–server architecture provided robustness and flexibility. PMID:23855995

DA+ data acquisition and analysis software at the Swiss Light Source macromolecular crystallography beamlines.

PubMed

Wojdyla, Justyna Aleksandra; Kaminski, Jakub W; Panepucci, Ezequiel; Ebner, Simon; Wang, Xiaoqiang; Gabadinho, Jose; Wang, Meitian

2018-01-01

Data acquisition software is an essential component of modern macromolecular crystallography (MX) beamlines, enabling efficient use of beam time at synchrotron facilities. Developed at the Paul Scherrer Institute, the DA+ data acquisition software is implemented at all three Swiss Light Source (SLS) MX beamlines. DA+ consists of distributed services and components written in Python and Java, which communicate via messaging and streaming technologies. The major components of DA+ are the user interface, acquisition engine, online processing and database. Immediate data quality feedback is achieved with distributed automatic data analysis routines. The software architecture enables exploration of the full potential of the latest instrumentation at the SLS MX beamlines, such as the SmarGon goniometer and the EIGER X 16M detector, and development of new data collection methods.

Climate tools in mainstream Linux distributions

NASA Astrophysics Data System (ADS)

McKinstry, Alastair

2015-04-01

Debian/meterology is a project to integrate climate tools and analysis software into the mainstream Debian/Ubuntu Linux distributions. This work describes lessons learnt, and recommends practices for scientific software to be adopted and maintained in OS distributions. In addition to standard analysis tools (cdo,, grads, ferret, metview, ncl, etc.), software used by the Earth System Grid Federation was chosen for integraion, to enable ESGF portals to be built on this base; however exposing scientific codes via web APIs enables security weaknesses, normally ignorable, to be exposed. How tools are hardened, and what changes are required to handle security upgrades, are described. Secondly, to enable libraries and components (e.g. Python modules) to be integrated requires planning by writers: it is not sufficient to assume users can upgrade their code when you make incompatible changes. Here, practices are recommended to enable upgrades and co-installability of C, C++, Fortran and Python codes. Finally, software packages such as NetCDF and HDF5 can be built in multiple configurations. Tools may then expect incompatible versions of these libraries (e.g. serial and parallel) to be simultaneously available; how this was solved in Debian using "pkg-config" and shared library interfaces is described, and best practices for software writers to enable this are summarised.

User interface design principles for the SSM/PMAD automated power system

NASA Technical Reports Server (NTRS)

Jakstas, Laura M.; Myers, Chris J.

1991-01-01

Martin Marietta has developed a user interface for the space station module power management and distribution (SSM/PMAD) automated power system testbed which provides human access to the functionality of the power system, as well as exemplifying current techniques in user interface design. The testbed user interface was designed to enable an engineer to operate the system easily without having significant knowledge of computer systems, as well as provide an environment in which the engineer can monitor and interact with the SSM/PMAD system hardware. The design of the interface supports a global view of the most important data from the various hardware and software components, as well as enabling the user to obtain additional or more detailed data when needed. The components and representations of the SSM/PMAD testbed user interface are examined. An engineer's interactions with the system are also described.

An Intuitive Dashboard for Bayesian Network Inference

NASA Astrophysics Data System (ADS)

Reddy, Vikas; Charisse Farr, Anna; Wu, Paul; Mengersen, Kerrie; Yarlagadda, Prasad K. D. V.

2014-03-01

Current Bayesian network software packages provide good graphical interface for users who design and develop Bayesian networks for various applications. However, the intended end-users of these networks may not necessarily find such an interface appealing and at times it could be overwhelming, particularly when the number of nodes in the network is large. To circumvent this problem, this paper presents an intuitive dashboard, which provides an additional layer of abstraction, enabling the end-users to easily perform inferences over the Bayesian networks. Unlike most software packages, which display the nodes and arcs of the network, the developed tool organises the nodes based on the cause-and-effect relationship, making the user-interaction more intuitive and friendly. In addition to performing various types of inferences, the users can conveniently use the tool to verify the behaviour of the developed Bayesian network. The tool has been developed using QT and SMILE libraries in C++.

An Open-source Toolbox for Analysing and Processing PhysioNet Databases in MATLAB and Octave.

PubMed

Silva, Ikaro; Moody, George B

The WaveForm DataBase (WFDB) Toolbox for MATLAB/Octave enables integrated access to PhysioNet's software and databases. Using the WFDB Toolbox for MATLAB/Octave, users have access to over 50 physiological databases in PhysioNet. The toolbox provides access over 4 TB of biomedical signals including ECG, EEG, EMG, and PLETH. Additionally, most signals are accompanied by metadata such as medical annotations of clinical events: arrhythmias, sleep stages, seizures, hypotensive episodes, etc. Users of this toolbox should easily be able to reproduce, validate, and compare results published based on PhysioNet's software and databases.

CASL Dakota Capabilities Summary

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

Adams, Brian M.; Simmons, Chris; Williams, Brian J.

2017-10-10

The Dakota software project serves the mission of Sandia National Laboratories and supports a worldwide user community by delivering state-of-the-art research and robust, usable software for optimization and uncertainty quantification. These capabilities enable advanced exploration and riskinformed prediction with a wide range of computational science and engineering models. Dakota is the verification and validation (V&V) / uncertainty quantification (UQ) software delivery vehicle for CASL, allowing analysts across focus areas to apply these capabilities to myriad nuclear engineering analyses.

Proceedings of the 1977 MACSYMA users' conference (NASA)

NASA Technical Reports Server (NTRS)

1977-01-01

The MACSYMA program for symbolic and algebraic manipulation enables exact, symbolic mathematical computations to be performed on a computer. This program is rather large, and various approaches to the hardware and software problems are examined.

AceTree: a major update and case study in the long term maintenance of open-source scientific software.

PubMed

Katzman, Braden; Tang, Doris; Santella, Anthony; Bao, Zhirong

2018-04-04

AceTree, a software application first released in 2006, facilitates exploration, curation and editing of tracked C. elegans nuclei in 4-dimensional (4D) fluorescence microscopy datasets. Since its initial release, AceTree has been continuously used to interact with, edit and interpret C. elegans lineage data. In its 11 year lifetime, AceTree has been periodically updated to meet the technical and research demands of its community of users. This paper presents the newest iteration of AceTree which contains extensive updates, demonstrates the new applicability of AceTree in other developmental contexts, and presents its evolutionary software development paradigm as a viable model for maintaining scientific software. Large scale updates have been made to the user interface for an improved user experience. Tools have been grouped according to functionality and obsolete methods have been removed. Internal requirements have been changed that enable greater flexibility of use both in C. elegans contexts and in other model organisms. Additionally, the original 3-dimensional (3D) viewing window has been completely reimplemented. The new window provides a new suite of tools for data exploration. By responding to technical advancements and research demands, AceTree has remained a useful tool for scientific research for over a decade. The updates made to the codebase have extended AceTree's applicability beyond its initial use in C. elegans and enabled its usage with other model organisms. The evolution of AceTree demonstrates a viable model for maintaining scientific software over long periods of time.

Teaching with Real-time Earthquake Data in jAmaSeis

NASA Astrophysics Data System (ADS)

Bravo, T. K.; Coleman, B.; Taber, J.

2011-12-01

Earthquakes can capture the attention of students and inspire them to explore the Earth. The Incorporated Research Institutions in Seismology (IRIS) and Moravian College are collaborating to develop cross-platform software (jAmaSeis) that enables students to access real-time earthquake waveform data. Users can record their own data from several different types of educational seismometers, and they can obtain data in real-time from other jAmaseis users nationwide. Additionally, the ability to stream data from the IRIS Data Management Center (DMC) is under development. Once real-time data is obtained, users of jAmaseis can study seismological concepts in the classroom. The user interface of the software is carefully designed to lead students through the steps to interrogate seismic data following a large earthquake. Users can process data to determine characteristics of seismograms such as time of occurrence, distance from the epicenter to the station, magnitude, and location (via triangulation). Along the way, the software provides graphical clues to assist student interpretations. In addition to the inherent pedagogical features of the software, IRIS provides pre-packaged data and instructional activities to help students learn the analysis steps. After using these activities, students can apply their skills to interpret seismic waves from their own real-time data.

Software as a service approach to sensor simulation software deployment

NASA Astrophysics Data System (ADS)

Webster, Steven; Miller, Gordon; Mayott, Gregory

2012-05-01

Traditionally, military simulation has been problem domain specific. Executing an exercise currently requires multiple simulation software providers to specialize, deploy, and configure their respective implementations, integrate the collection of software to achieve a specific system behavior, and then execute for the purpose at hand. This approach leads to rigid system integrations which require simulation expertise for each deployment due to changes in location, hardware, and software. Our alternative is Software as a Service (SaaS) predicated on the virtualization of Night Vision Electronic Sensors (NVESD) sensor simulations as an exemplary case. Management middleware elements layer self provisioning, configuration, and integration services onto the virtualized sensors to present a system of services at run time. Given an Infrastructure as a Service (IaaS) environment, enabled and managed system of simulations yields a durable SaaS delivery without requiring user simulation expertise. Persistent SaaS simulations would provide on demand availability to connected users, decrease integration costs and timelines, and benefit the domain community from immediate deployment of lessons learned.

A Digital Repository and Execution Platform for Interactive Scholarly Publications in Neuroscience.

PubMed

Hodge, Victoria; Jessop, Mark; Fletcher, Martyn; Weeks, Michael; Turner, Aaron; Jackson, Tom; Ingram, Colin; Smith, Leslie; Austin, Jim

2016-01-01

The CARMEN Virtual Laboratory (VL) is a cloud-based platform which allows neuroscientists to store, share, develop, execute, reproduce and publicise their work. This paper describes new functionality in the CARMEN VL: an interactive publications repository. This new facility allows users to link data and software to publications. This enables other users to examine data and software associated with the publication and execute the associated software within the VL using the same data as the authors used in the publication. The cloud-based architecture and SaaS (Software as a Service) framework allows vast data sets to be uploaded and analysed using software services. Thus, this new interactive publications facility allows others to build on research results through reuse. This aligns with recent developments by funding agencies, institutions, and publishers with a move to open access research. Open access provides reproducibility and verification of research resources and results. Publications and their associated data and software will be assured of long-term preservation and curation in the repository. Further, analysing research data and the evaluations described in publications frequently requires a number of execution stages many of which are iterative. The VL provides a scientific workflow environment to combine software services into a processing tree. These workflows can also be associated with publications and executed by users. The VL also provides a secure environment where users can decide the access rights for each resource to ensure copyright and privacy restrictions are met.

A Flexible Evolvable Architecture for Constellation Mission Systems User Applications

NASA Technical Reports Server (NTRS)

Trimble, Jay P.; Crocker, Alan R.

2008-01-01

While simulating a complex set of repair tasks to be performed by EVA crewmembers on an upcoming mission, flight controllers and astronauts determine that the repair will take much longer than originally anticipated. All equipment in the vicinity of the worksite must be powered off to maintain a safe environment for the astronauts. Because heater power will be unavailable, several critical components will now be at risk of freezing and permanent damage. If an impending thermal violation is detected, Mission Control will have very limited time to react. Therefore, flight controllers must not only modify their procedures to account for these risks, they must also incorporate into their displays outputs from thermal models, alternate temperature measurements, new alarm limits, and emergency power-on commands to enable the detection and response to freezing conditions. Current software for mission control systems makes scenarios like this difficult to address. Given the time frame for modifying software, operations teams are left with labor-intensive operational workarounds as their only options. NASA Ames Research Center (ARC) and NASA Johnson Space Center (JSC) are collaborating on the development of a flexible software system for mission operations that will enable greater user flexibility than has been available to date. Using composable software, end users in the scenario described above could recompose procedures and command and control displays to allow flight controllers to monitor temperature measurements, identify time-critical conditions, and execute the procedures required to respond to these conditions before flight hardware is permanently damaged.

Enable Web-Based Tracking and Guiding by Integrating Location-Awareness with the World Wide Web

ERIC Educational Resources Information Center

Zhou, Rui

2008-01-01

Purpose: The aim of this research is to enable web-based tracking and guiding by integrating location-awareness with the Worldwide Web so that the users can use various location-based applications without installing extra software. Design/methodology/approach: The concept of web-based tracking and guiding is introduced and the relevant issues are…

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.

ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level

PubMed Central

Rocca-Serra, Philippe; Brandizi, Marco; Maguire, Eamonn; Sklyar, Nataliya; Taylor, Chris; Begley, Kimberly; Field, Dawn; Harris, Stephen; Hide, Winston; Hofmann, Oliver; Neumann, Steffen; Sterk, Peter; Tong, Weida; Sansone, Susanna-Assunta

2010-01-01

Summary: The first open source software suite for experimentalists and curators that (i) assists in the annotation and local management of experimental metadata from high-throughput studies employing one or a combination of omics and other technologies; (ii) empowers users to uptake community-defined checklists and ontologies; and (iii) facilitates submission to international public repositories. Availability and Implementation: Software, documentation, case studies and implementations at http://www.isa-tools.org Contact: isatools@googlegroups.com PMID:20679334

KCNSC Automated RAIL

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

Branson, Donald

The KCNSC Automated RAIL (Rolling Action Item List) system provides an electronic platform to manage and escalate rolling action items within an business and manufacturing environment at Honeywell. The software enables a tiered approach to issue management where issues are escalated up a management chain based on team input and compared to business metrics. The software manages action items at different levels of the organization and allows all users to discuss action items concurrently. In addition, the software drives accountability through timely emails and proper visibility during team meetings.

DA+ data acquisition and analysis software at the Swiss Light Source macromolecular crystallography beamlines

PubMed Central

Wojdyla, Justyna Aleksandra; Kaminski, Jakub W.; Ebner, Simon; Wang, Xiaoqiang; Gabadinho, Jose; Wang, Meitian

2018-01-01

Data acquisition software is an essential component of modern macromolecular crystallography (MX) beamlines, enabling efficient use of beam time at synchrotron facilities. Developed at the Paul Scherrer Institute, the DA+ data acquisition software is implemented at all three Swiss Light Source (SLS) MX beamlines. DA+ consists of distributed services and components written in Python and Java, which communicate via messaging and streaming technologies. The major components of DA+ are the user interface, acquisition engine, online processing and database. Immediate data quality feedback is achieved with distributed automatic data analysis routines. The software architecture enables exploration of the full potential of the latest instrumentation at the SLS MX beamlines, such as the SmarGon goniometer and the EIGER X 16M detector, and development of new data collection methods. PMID:29271779

OntoSoft: A Software Registry for Geosciences

NASA Astrophysics Data System (ADS)

Garijo, D.; Gil, Y.

2017-12-01

The goal of the EarthCube OntoSoft project is to enable the creation of an ecosystem for software stewardship in geosciences that will empower scientists to manage their software as valuable scientific assets. By sharing software metadata in OntoSoft, scientists enable broader access to that software by other scientists, software professionals, students, and decision makers. Our work to date includes: 1) an ontology for describing scientific software metadata, 2) a distributed scientific software repository that contains more than 750 entries that can be searched and compared across metadata fields, 3) an intelligent user interface that guides scientists to publish software and allows them to crowdsource its corresponding metadata. We have also developed a training program where scientists learn to describe and cite software in their papers in addition to data and provenance, and we are using OntoSoft to show them the benefits of publishing their software metadata. This training program is part of a Geoscience Papers of the Future Initiative, where scientists are reflecting on their current practices, benefits and effort for sharing software and data. This journal paper can be submitted to a Special Section of the AGU Earth and Space Science Journal.

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.

Simulating Technology Processes to Foster Learning.

ERIC Educational Resources Information Center

Krumholtz, Nira

1998-01-01

Based on a spiral model of technology evolution, elementary students used LOGO computer software to become both developers and users of technology. The computerized environment enabled 87% to reach intuitive understanding of physical concepts; 24% expressed more formal scientific understanding. (SK)

Agricultural Conservation Planning Toolbox User's Manual

USDA-ARS?s Scientific Manuscript database

Agricultural Conservation Planning Framework (ACPF) comprises an approach for applying concepts of precision conservation to watershed planning in agricultural landscapes. To enable application of this approach, USDA/ARS has developed a set of Geographic Information System (GIS) based software tools...

Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results.

PubMed

Dai, Yilin; Guo, Ling; Li, Meng; Chen, Yi-Bu

2012-06-08

Microarray data analysis presents a significant challenge to researchers who are unable to use the powerful Bioconductor and its numerous tools due to their lack of knowledge of R language. Among the few existing software programs that offer a graphic user interface to Bioconductor packages, none have implemented a comprehensive strategy to address the accuracy and reliability issue of microarray data analysis due to the well known probe design problems associated with many widely used microarray chips. There is also a lack of tools that would expedite the functional analysis of microarray results. We present Microarray Я US, an R-based graphical user interface that implements over a dozen popular Bioconductor packages to offer researchers a streamlined workflow for routine differential microarray expression data analysis without the need to learn R language. In order to enable a more accurate analysis and interpretation of microarray data, we incorporated the latest custom probe re-definition and re-annotation for Affymetrix and Illumina chips. A versatile microarray results output utility tool was also implemented for easy and fast generation of input files for over 20 of the most widely used functional analysis software programs. Coupled with a well-designed user interface, Microarray Я US leverages cutting edge Bioconductor packages for researchers with no knowledge in R language. It also enables a more reliable and accurate microarray data analysis and expedites downstream functional analysis of microarray results.

Release of the gPhoton Database of GALEX Photon Events

NASA Astrophysics Data System (ADS)

Fleming, Scott W.; Million, Chase; Shiao, Bernie; Tucker, Michael; Loyd, R. O. Parke

2016-01-01

The GALEX spacecraft surveyed much of the sky in two ultraviolet bands between 2003 and 2013 with non-integrating microchannel plate detectors. The Mikulski Archive for Space Telescopes (MAST) has made more than one trillion photon events observed by the spacecraft available, stored as a 130 TB database, along with an open-source, python-based software package to query this database and create calibrated lightcurves or images from these data at user-defined spatial and temporal scales. In particular, MAST users can now conduct photometry at the intra-visit level (timescales of seconds and minutes). The software, along with the fully populated database, was officially released in Aug. 2015, and improvements to both software functionality and data calibration are ongoing. We summarize the current calibration status of the gPhoton software, along with examples of early science enabled by gPhoton that include stellar flares, AGN, white dwarfs, exoplanet hosts, novae, and nearby galaxies.

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.

Ergatis: a web interface and scalable software system for bioinformatics workflows

PubMed Central

Orvis, Joshua; Crabtree, Jonathan; Galens, Kevin; Gussman, Aaron; Inman, Jason M.; Lee, Eduardo; Nampally, Sreenath; Riley, David; Sundaram, Jaideep P.; Felix, Victor; Whitty, Brett; Mahurkar, Anup; Wortman, Jennifer; White, Owen; Angiuoli, Samuel V.

2010-01-01

Motivation: The growth of sequence data has been accompanied by an increasing need to analyze data on distributed computer clusters. The use of these systems for routine analysis requires scalable and robust software for data management of large datasets. Software is also needed to simplify data management and make large-scale bioinformatics analysis accessible and reproducible to a wide class of target users. Results: We have developed a workflow management system named Ergatis that enables users to build, execute and monitor pipelines for computational analysis of genomics data. Ergatis contains preconfigured components and template pipelines for a number of common bioinformatics tasks such as prokaryotic genome annotation and genome comparisons. Outputs from many of these components can be loaded into a Chado relational database. Ergatis was designed to be accessible to a broad class of users and provides a user friendly, web-based interface. Ergatis supports high-throughput batch processing on distributed compute clusters and has been used for data management in a number of genome annotation and comparative genomics projects. Availability: Ergatis is an open-source project and is freely available at http://ergatis.sourceforge.net Contact: jorvis@users.sourceforge.net PMID:20413634

Recent developments in the CCP-EM software suite.

PubMed

Burnley, Tom; Palmer, Colin M; Winn, Martyn

2017-06-01

As part of its remit to provide computational support to the cryo-EM community, the Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) has produced a software framework which enables easy access to a range of programs and utilities. The resulting software suite incorporates contributions from different collaborators by encapsulating them in Python task wrappers, which are then made accessible via a user-friendly graphical user interface as well as a command-line interface suitable for scripting. The framework includes tools for project and data management. An overview of the design of the framework is given, together with a survey of the functionality at different levels. The current CCP-EM suite has particular strength in the building and refinement of atomic models into cryo-EM reconstructions, which is described in detail.

Recent developments in the CCP-EM software suite

PubMed Central

Burnley, Tom

2017-01-01

As part of its remit to provide computational support to the cryo-EM community, the Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) has produced a software framework which enables easy access to a range of programs and utilities. The resulting software suite incorporates contributions from different collaborators by encapsulating them in Python task wrappers, which are then made accessible via a user-friendly graphical user interface as well as a command-line interface suitable for scripting. The framework includes tools for project and data management. An overview of the design of the framework is given, together with a survey of the functionality at different levels. The current CCP-EM suite has particular strength in the building and refinement of atomic models into cryo-EM reconstructions, which is described in detail. PMID:28580908

Tools and Approaches for the Construction of Knowledge Models from the Neuroscientific Literature

PubMed Central

Burns, Gully A. P. C.; Khan, Arshad M.; Ghandeharizadeh, Shahram; O’Neill, Mark A.; Chen, Yi-Shin

2015-01-01

Within this paper, we describe a neuroinformatics project (called “NeuroScholar,” http://www.neuroscholar.org/) that enables researchers to examine, manage, manipulate, and use the information contained within the published neuroscientific literature. The project is built within a multi-level, multi-component framework constructed with the use of software engineering methods that themselves provide code-building functionality for neuroinformaticians. We describe the different software layers of the system. First, we present a hypothetical usage scenario illustrating how NeuroScholar permits users to address large-scale questions in a way that would otherwise be impossible. We do this by applying NeuroScholar to a “real-world” neuroscience question: How is stress-related information processed in the brain? We then explain how the overall design of NeuroScholar enables the system to work and illustrate different components of the user interface. We then describe the knowledge management strategy we use to store interpretations. Finally, we describe the software engineering framework we have devised (called the “View-Primitive-Data Model framework,” [VPDMf]) to provide an open-source, accelerated software development environment for the project. We believe that NeuroScholar will be useful to experimental neuroscientists by helping them interact with the primary neuroscientific literature in a meaningful way, and to neuroinformaticians by providing them with useful, affordable software engineering tools. PMID:15055395

Research on Spoken Dialogue Systems

NASA Technical Reports Server (NTRS)

Aist, Gregory; Hieronymus, James; Dowding, John; Hockey, Beth Ann; Rayner, Manny; Chatzichrisafis, Nikos; Farrell, Kim; Renders, Jean-Michel

2010-01-01

Research in the field of spoken dialogue systems has been performed with the goal of making such systems more robust and easier to use in demanding situations. The term "spoken dialogue systems" signifies unified software systems containing speech-recognition, speech-synthesis, dialogue management, and ancillary components that enable human users to communicate, using natural spoken language or nearly natural prescribed spoken language, with other software systems that provide information and/or services.

Software Helps Retrieve Information Relevant to the User

NASA Technical Reports Server (NTRS)

Mathe, Natalie; Chen, James

2003-01-01

The Adaptive Indexing and Retrieval Agent (ARNIE) is a code library, designed to be used by an application program, that assists human users in retrieving desired information in a hypertext setting. Using ARNIE, the program implements a computational model for interactively learning what information each human user considers relevant in context. The model, called a "relevance network," incrementally adapts retrieved information to users individual profiles on the basis of feedback from the users regarding specific queries. The model also generalizes such knowledge for subsequent derivation of relevant references for similar queries and profiles, thereby, assisting users in filtering information by relevance. ARNIE thus enables users to categorize and share information of interest in various contexts. ARNIE encodes the relevance and structure of information in a neural network dynamically configured with a genetic algorithm. ARNIE maintains an internal database, wherein it saves associations, and from which it returns associated items in response to a query. A C++ compiler for a platform on which ARNIE will be utilized is necessary for creating the ARNIE library but is not necessary for the execution of the software.

Math Description Engine Software Development Kit

NASA Technical Reports Server (NTRS)

Shelton, Robert O.; Smith, Stephanie L.; Dexter, Dan E.; Hodgson, Terry R.

2010-01-01

The Math Description Engine Software Development Kit (MDE SDK) can be used by software developers to make computer-rendered graphs more accessible to blind and visually-impaired users. The MDE SDK generates alternative graph descriptions in two forms: textual descriptions and non-verbal sound renderings, or sonification. It also enables display of an animated trace of a graph sonification on a visual graph component, with color and line-thickness options for users having low vision or color-related impairments. A set of accessible graphical user interface widgets is provided for operation by end users and for control of accessible graph displays. Version 1.0 of the MDE SDK generates text descriptions for 2D graphs commonly seen in math and science curriculum (and practice). The mathematically rich text descriptions can also serve as a virtual math and science assistant for blind and sighted users, making graphs more accessible for everyone. The MDE SDK has a simple application programming interface (API) that makes it easy for programmers and Web-site developers to make graphs accessible with just a few lines of code. The source code is written in Java for cross-platform compatibility and to take advantage of Java s built-in support for building accessible software application interfaces. Compiled-library and NASA Open Source versions are available with API documentation and Programmer s Guide at http:/ / prim e.jsc.n asa. gov.

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

PubMed

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

2014-12-01

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

Analyzing Dynamics of Cooperating Spacecraft

NASA Technical Reports Server (NTRS)

Hughes, Stephen P.; Folta, David C.; Conway, Darrel J.

2004-01-01

A software library has been developed to enable high-fidelity computational simulation of the dynamics of multiple spacecraft distributed over a region of outer space and acting with a common purpose. All of the modeling capabilities afforded by this software are available independently in other, separate software systems, but have not previously been brought together in a single system. A user can choose among several dynamical models, many high-fidelity environment models, and several numerical-integration schemes. The user can select whether to use models that assume weak coupling between spacecraft, or strong coupling in the case of feedback control or tethering of spacecraft to each other. For weak coupling, spacecraft orbits are propagated independently, and are synchronized in time by controlling the step size of the integration. For strong coupling, the orbits are integrated simultaneously. Among the integration schemes that the user can choose are Runge-Kutta Verner, Prince-Dormand, Adams-Bashforth-Moulton, and Bulirsh- Stoer. Comparisons of performance are included for both the weak- and strongcoupling dynamical models for all of the numerical integrators.

Definition and testing of the hydrologic component of the pilot land data system

NASA Technical Reports Server (NTRS)

Ragan, Robert M.; Sircar, Jayanta K.

1987-01-01

The specific aim was to develop within the Pilot Land Data System (PLDS) software design environment, an easily implementable and user friendly geometric correction procedure to readily enable the georeferencing of imagery data from the Advanced Very High Resolution Radiometer (AVHRR) onboard the NOAA series spacecraft. A software subsystem was developed within the guidelines set by the PLDS development environment utilizing NASA Goddard Space Flight Center (GSFC) Image Analysis Facility's (IAF's) Land Analysis Software (LAS) coding standards. The IAS current program development environment, the Transportable Applications Executive (TAE), operates under a VAX VMS operating system and was used as the user interface. A brief overview of the ICARUS algorithm that was implemented in the set of functions developed, is provided. The functional specifications decription is provided, and a list of the individual programs and directory names containing the source and executables installed in the IAF system are listed. A user guide is provided for the LAS system documentation format for the three functions developed.

Digital Multicasting of Multiple Audio Streams

NASA Technical Reports Server (NTRS)

Macha, Mitchell; Bullock, John

2007-01-01

The Mission Control Center Voice Over Internet Protocol (MCC VOIP) system (see figure) comprises hardware and software that effect simultaneous, nearly real-time transmission of as many as 14 different audio streams to authorized listeners via the MCC intranet and/or the Internet. The original version of the MCC VOIP system was conceived to enable flight-support personnel located in offices outside a spacecraft mission control center to monitor audio loops within the mission control center. Different versions of the MCC VOIP system could be used for a variety of public and commercial purposes - for example, to enable members of the general public to monitor one or more NASA audio streams through their home computers, to enable air-traffic supervisors to monitor communication between airline pilots and air-traffic controllers in training, and to monitor conferences among brokers in a stock exchange. At the transmitting end, the audio-distribution process begins with feeding the audio signals to analog-to-digital converters. The resulting digital streams are sent through the MCC intranet, using a user datagram protocol (UDP), to a server that converts them to encrypted data packets. The encrypted data packets are then routed to the personal computers of authorized users by use of multicasting techniques. The total data-processing load on the portion of the system upstream of and including the encryption server is the total load imposed by all of the audio streams being encoded, regardless of the number of the listeners or the number of streams being monitored concurrently by the listeners. The personal computer of a user authorized to listen is equipped with special- purpose MCC audio-player software. When the user launches the program, the user is prompted to provide identification and a password. In one of two access- control provisions, the program is hard-coded to validate the user s identity and password against a list maintained on a domain-controller computer at the MCC. In the other access-control provision, the program verifies that the user is authorized to have access to the audio streams. Once both access-control checks are completed, the audio software presents a graphical display that includes audiostream-selection buttons and volume-control sliders. The user can select all or any subset of the available audio streams and can adjust the volume of each stream independently of that of the other streams. The audio-player program spawns a "read" process for the selected stream(s). The spawned process sends, to the router(s), a "multicast-join" request for the selected streams. The router(s) responds to the request by sending the encrypted multicast packets to the spawned process. The spawned process receives the encrypted multicast packets and sends a decryption packet to audio-driver software. As the volume or muting features are changed by the user, interrupts are sent to the spawned process to change the corresponding attributes sent to the audio-driver software. The total latency of this system - that is, the total time from the origination of the audio signals to generation of sound at a listener s computer - lies between four and six seconds.

Enhanced CARES Software Enables Improved Ceramic Life Prediction

NASA Technical Reports Server (NTRS)

Janosik, Lesley A.

1997-01-01

The NASA Lewis Research Center has developed award-winning software that enables American industry to establish the reliability and life of brittle material (e.g., ceramic, intermetallic, graphite) structures in a wide variety of 21st century applications. The CARES (Ceramics Analysis and Reliability Evaluation of Structures) series of software is successfully used by numerous engineers in industrial, academic, and government organizations as an essential element of the structural design and material selection processes. The latest version of this software, CARES/Life, provides a general- purpose design tool that predicts the probability of failure of a ceramic component as a function of its time in service. CARES/Life was recently enhanced by adding new modules designed to improve functionality and user-friendliness. In addition, a beta version of the newly-developed CARES/Creep program (for determining the creep life of monolithic ceramic components) has just been released to selected organizations.

Solving Equations of Multibody Dynamics

NASA Technical Reports Server (NTRS)

Jain, Abhinandan; Lim, Christopher

2007-01-01

Darts++ is a computer program for solving the equations of motion of a multibody system or of a multibody model of a dynamic system. It is intended especially for use in dynamical simulations performed in designing and analyzing, and developing software for the control of, complex mechanical systems. Darts++ is based on the Spatial-Operator- Algebra formulation for multibody dynamics. This software reads a description of a multibody system from a model data file, then constructs and implements an efficient algorithm that solves the dynamical equations of the system. The efficiency and, hence, the computational speed is sufficient to make Darts++ suitable for use in realtime closed-loop simulations. Darts++ features an object-oriented software architecture that enables reconfiguration of system topology at run time; in contrast, in related prior software, system topology is fixed during initialization. Darts++ provides an interface to scripting languages, including Tcl and Python, that enable the user to configure and interact with simulation objects at run time.

SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing.

PubMed

Sato, Yukuto; Kojima, Kaname; Nariai, Naoki; Yamaguchi-Kabata, Yumi; Kawai, Yosuke; Takahashi, Mamoru; Mimori, Takahiro; Nagasaki, Masao

2014-08-08

Next-generation sequencers (NGSs) have become one of the main tools for current biology. To obtain useful insights from the NGS data, it is essential to control low-quality portions of the data affected by technical errors such as air bubbles in sequencing fluidics. We develop a software SUGAR (subtile-based GUI-assisted refiner) which can handle ultra-high-throughput data with user-friendly graphical user interface (GUI) and interactive analysis capability. The SUGAR generates high-resolution quality heatmaps of the flowcell, enabling users to find possible signals of technical errors during the sequencing. The sequencing data generated from the error-affected regions of a flowcell can be selectively removed by automated analysis or GUI-assisted operations implemented in the SUGAR. The automated data-cleaning function based on sequence read quality (Phred) scores was applied to a public whole human genome sequencing data and we proved the overall mapping quality was improved. The detailed data evaluation and cleaning enabled by SUGAR would reduce technical problems in sequence read mapping, improving subsequent variant analysis that require high-quality sequence data and mapping results. Therefore, the software will be especially useful to control the quality of variant calls to the low population cells, e.g., cancers, in a sample with technical errors of sequencing procedures.

JAva GUi for Applied Research (JAGUAR) v 3.0

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

JAGUAR is a Java software tool for automatically rendering a graphical user interface (GUI) from a structured input specification. It is designed as a plug-in to the Eclipse workbench to enable users to create, edit, and externally execute analysis application input decks and then view the results. JAGUAR serves as a GUI for Sandia's DAKOTA software toolkit for optimization and uncertainty quantification. It will include problem (input deck)set-up, option specification, analysis execution, and results visualization. Through the use of wizards, templates, and views, JAGUAR helps uses navigate the complexity of DAKOTA's complete input specification. JAGUAR is implemented in Java, leveragingmore » Eclipse extension points and Eclipse user interface. JAGUAR parses a DAKOTA NIDR input specification and presents the user with linked graphical and plain text representations of problem set-up and option specification for DAKOTA studies. After the data has been input by the user, JAGUAR generates one or more input files for DAKOTA, executes DAKOTA, and captures and interprets the results« less

Web-based interactive visualization in a Grid-enabled neuroimaging application using HTML5.

PubMed

Siewert, René; Specovius, Svenja; Wu, Jie; Krefting, Dagmar

2012-01-01

Interactive visualization and correction of intermediate results are required in many medical image analysis pipelines. To allow certain interaction in the remote execution of compute- and data-intensive applications, new features of HTML5 are used. They allow for transparent integration of user interaction into Grid- or Cloud-enabled scientific workflows. Both 2D and 3D visualization and data manipulation can be performed through a scientific gateway without the need to install specific software or web browser plugins. The possibilities of web-based visualization are presented along the FreeSurfer-pipeline, a popular compute- and data-intensive software tool for quantitative neuroimaging.

Phisherman v 1.0

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

Phisherman is an online software tool that was created to help experimenters study phishing. It can potentially be re-purposed to run other human studies. Phisherman enables studies to be run online, so that users can participate from their own computers. This means that experimenters can get data from subjects in their natural settings. Alternatively, an experimenter can also run the app online in a lab-based setting, if that is desired. The software enables the online deployment of a study that is comprised of three main parts: (1) a consent page, (2) a survey, and (3) an identification task, with instruction/transitionmore » screens between each part, allowing the experimenter to provide the user with instructions and messages. Upon logging in, the subject is taken to the permission page, where they agree to or do not agree to take part in the study. If the subject agrees to participate, then the software randomly chooses between doing the survey first (and identification task second) or the identification task first (and survey second). This is to balance possible order effects in the data. Procedurally, in the identification task, the software shows the stimuli to the subject, and asks if she thinks it is a phish (yes/no) and how confident she is about her answer. The subject is given 5 levels of certainty to select from, labeled "low" (1), to "medium" (3), to "high" (5), with the option of picking a level between low and medium (2), and between medium and high (4). After selecting his/her confidence level, then the "Next" button activates, allowing a user to move to the next email. The software saves a given subject's progress in the identification task, so that she may log in and out of the site. The consent page is a space for the experimenter to provide the subject with human studies board /internal review board information, and to formally consent to participate in the study. The survey is a space for the experimenter to provide questions and spaces for the users to input answers (allowing both multiple-choice and free-answer options). Phisherman includes administrative pages for managing the stimuli and users. This includes a tool for the experimenter to create, preview, edit, delete (if desired), and manage stimuli (emails). The stimuli may include pictures (uploaded to an appropriate folder) and links, for realism. The software includes a safety feature that prevents the user from going to any link location or opening a file/image. Instead of re-directing the subject's browser, the software provides a pop-up box with the URL location of where the user would have gone. Another administrative page may be used to create fake subject accounts for testing the software prior to deployment, as well as to delete subject accounts when necessary. Data from the experiment can be downloaded from another administrative page.« less

System for Secure Integration of Aviation Data

NASA Technical Reports Server (NTRS)

Kulkarni, Deepak; Wang, Yao; Keller, Rich; Chidester, Tom; Statler, Irving; Lynch, Bob; Patel, Hemil; Windrem, May; Lawrence, Bob

2007-01-01

The Aviation Data Integration System (ADIS) of Ames Research Center has been established to promote analysis of aviation data by airlines and other interested users for purposes of enhancing the quality (especially safety) of flight operations. The ADIS is a system of computer hardware and software for collecting, integrating, and disseminating aviation data pertaining to flights and specified flight events that involve one or more airline(s). The ADIS is secure in the sense that care is taken to ensure the integrity of sources of collected data and to verify the authorizations of requesters to receive data. Most importantly, the ADIS removes a disincentive to collection and exchange of useful data by providing for automatic removal of information that could be used to identify specific flights and crewmembers. Such information, denoted sensitive information, includes flight data (here signifying data collected by sensors aboard an aircraft during flight), weather data for a specified route on a specified date, date and time, and any other information traceable to a specific flight. The removal of information that could be used to perform such tracing is called "deidentification." Airlines are often reluctant to keep flight data in identifiable form because of concerns about loss of anonymity. Hence, one of the things needed to promote retention and analysis of aviation data is an automated means of de-identification of archived flight data to enable integration of flight data with non-flight aviation data while preserving anonymity. Preferably, such an automated means would enable end users of the data to continue to use pre-existing data-analysis software to identify anomalies in flight data without identifying a specific anomalous flight. It would then also be possible to perform statistical analyses of integrated data. These needs are satisfied by the ADIS, which enables an end user to request aviation data associated with de-identified flight data. The ADIS includes client software integrated with other software running on flight-operations quality-assurance (FOQA) computers for purposes of analyzing data to study specified types of events or exceedences (departures of flight parameters from normal ranges). In addition to ADIS client software, ADIS includes server hardware and software that provide services to the ADIS clients via the Internet (see figure). The ADIS server receives and integrates flight and non-flight data pertaining to flights from multiple sources. The server accepts data updates from authorized sources only and responds to requests from authorized users only. In order to satisfy security requirements established by the airlines, (1) an ADIS client must not be accessible from the Internet by an unauthorized user and (2) non-flight data as airport terminal information system (ATIS) and weather data must be displayed without any identifying flight information. ADIS hardware and software architecture as well as encryption and data display scheme are designed to meet these requirements. When a user requests one or more selected aviation data characteristics associated with an event (e.g., a collision, near miss, equipment malfunction, or exceedence), the ADIS client augments the request with date and time information from encrypted files and submits the augmented request to the server. Once the user s authorization has been verified, the server returns the requested information in de-identified form.

NERSC News

Science.gov Websites

Performance Data, Analytics & Services Job Logs & Statistics Training & Tutorials Software Outages NERSC Training Spectrum Scale User Group Meeting Live Status Now Computing Queue Look MOTD » Deep Learning at 15 PFlops Enables Training for Extreme Weather Identification at Scale March 29, 2018

External Data and Attribute Hyperlink Programs for Promis*e(Registered Trademark)

NASA Technical Reports Server (NTRS)

Derengowski, Rich; Gruel, Andrew

2001-01-01

External Data and Attribute Hyperlink are computer programs that can be added to Promis*e(trademark) which is a commercial software system that automates routine tasks in the design (including drawing schematic diagrams) of electrical control systems. The programs were developed under the Stennis Space Center's (SSC) Dual Use Technology Development Program to provide capabilities for SSC's BMCS configuration management system which uses Promis*e(trademark). The External Data program enables the storage and management of information in an external database linked to a drawing. Changes can be made either in the database or on the drawing. Information that originates outside Promis*e(trademark) can be stored in custom fields that can be added to the database. Although this information is not available in Promis*e(trademark) printed drawings, it can be associated with symbols in the drawings, and can be retrieved through the drawings when the software is running. The Attribute Hyperlink program enables the addition of hyperlink information as attributes of symbols. This program enables the formation of a direct hyperlink between a schematic diagram and an Internet site or a file on a compact disk, on the user's hard drive, or on another computer on a network to which the user's computer is connected. The user can then obtain information directly related to the part (e.g., maintenance, or troubleshooting information) associated with the hyperlink.

PixelLearn

NASA Technical Reports Server (NTRS)

Mazzoni, Dominic; Wagstaff, Kiri; Bornstein, Benjamin; Tang, Nghia; Roden, Joseph

2006-01-01

PixelLearn is an integrated user-interface computer program for classifying pixels in scientific images. Heretofore, training a machine-learning algorithm to classify pixels in images has been tedious and difficult. PixelLearn provides a graphical user interface that makes it faster and more intuitive, leading to more interactive exploration of image data sets. PixelLearn also provides image-enhancement controls to make it easier to see subtle details in images. PixelLearn opens images or sets of images in a variety of common scientific file formats and enables the user to interact with several supervised or unsupervised machine-learning pixel-classifying algorithms while the user continues to browse through the images. The machinelearning algorithms in PixelLearn use advanced clustering and classification methods that enable accuracy much higher than is achievable by most other software previously available for this purpose. PixelLearn is written in portable C++ and runs natively on computers running Linux, Windows, or Mac OS X.

A Full-Featured User Friendly CO 2-EOR and Sequestration Planning Software

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

Savage, Bill

A Full-Featured, User Friendly CO 2-EOR and Sequestration Planning Software This project addressed the development of an integrated software solution that includes a graphical user interface, numerical simulation, visualization tools and optimization processes for reservoir simulation modeling of CO 2-EOR. The objective was to assist the industry in the development of domestic energy resources by expanding the application of CO 2-EOR technologies, and ultimately to maximize the CO 2} sequestration capacity of the U.S. The software resulted in a field-ready application for the industry to address the current CO 2-EOR technologies. The software has been made available to the publicmore » without restrictions and with user friendly operating documentation and tutorials. The software (executable only) can be downloaded from NITEC’s website at www.nitecllc.com. This integrated solution enables the design, optimization and operation of CO 2-EOR processes for small and mid-sized operators, who currently cannot afford the expensive, time intensive solutions that the major oil companies enjoy. Based on one estimate, small oil fields comprise 30% of the of total economic resource potential for the application of CO 2-EOR processes in the U.S. This corresponds to 21.7 billion barrels of incremental, technically recoverable oil using the current “best practices”, and 31.9 billion barrels using “next-generation” CO 2-EOR techniques. The project included a Case Study of a prospective CO 2-EOR candidate field in Wyoming by a small independent, Linc Energy Petroleum Wyoming, Inc. NITEC LLC has an established track record of developing innovative and user friendly software. The Principle Investigator is an experienced manager and engineer with expertise in software development, numerical techniques, and GUI applications. Unique, presently-proprietary NITEC technologies have been integrated into this application to further its ease of use and technical functionality.« less

Datalist: A Value Added Service to Enable Easy Data Selection

NASA Technical Reports Server (NTRS)

Li, Angela; Hegde, Mahabaleshwa; Bryant, Keith; Seiler, Edward; Shie, Chung-Lin; Teng, William; Liu, Zhong; Hearty, Thomas; Shen, Suhung; Kempler, Steven;

Web-based software tool for constraint-based design specification of synthetic biological systems.

PubMed

Oberortner, Ernst; Densmore, Douglas

2015-06-19

miniEugene provides computational support for solving combinatorial design problems, enabling users to specify and enumerate designs for novel biological systems based on sets of biological constraints. This technical note presents a brief tutorial for biologists and software engineers in the field of synthetic biology on how to use miniEugene. After reading this technical note, users should know which biological constraints are available in miniEugene, understand the syntax and semantics of these constraints, and be able to follow a step-by-step guide to specify the design of a classical synthetic biological system-the genetic toggle switch.1 We also provide links and references to more information on the miniEugene web application and the integration of the miniEugene software library into sophisticated Computer-Aided Design (CAD) tools for synthetic biology ( www.eugenecad.org ).

JPSS Science Data Services for the Direct Readout Community

NASA Technical Reports Server (NTRS)

Chander, Gyanesh; Lutz, Bob

2014-01-01

The Suomi National Polar-orbiting Partnership (S-NPP) and Joint Polar Satellite System (JPSS) High Rate Data (HRD) link provides Direct Broadcast data to users in real-time, utilizing their own remote field terminals. The Field Terminal Support (FTS) provides the resources needed to support the Direct Readout communities by providing software, documentation, and periodic updates to enable them to produce data products from SNPP and JPSS. The FTS distribution server will also provide the necessary ancillary and auxiliary data needed for processing the broadcasts, as well as making orbital data available to assist in locating the satellites of interest. In addition, the FTS provides development support for the algorithm and software through GSFC Direct Readout Laboratory (DRL) International Polar Orbiter Processing Package (IPOPP) and University of Wisconsin (UWISC) Community Satellite Processing Package (CSPP), to enable users to integrate the algorithms into their remote terminals. The support the JPSS Program provides to the institutions developing and maintaining these two software packages, will demonstrate the ability to produce ready-to-use products from the HRD link and provide risk reduction effort at a minimal cost. This paper discusses the key functions and system architecture of FTS.

Airborne Doppler Wind Lidar Post Data Processing Software DAPS-LV

NASA Technical Reports Server (NTRS)

Kavaya, Michael J. (Inventor); Beyon, Jeffrey Y. (Inventor); Koch, Grady J. (Inventor)

2015-01-01

Systems, methods, and devices of the present invention enable post processing of airborne Doppler wind LIDAR data. In an embodiment, airborne Doppler wind LIDAR data software written in LabVIEW may be provided and may run two versions of different airborne wind profiling algorithms. A first algorithm may be the Airborne Wind Profiling Algorithm for Doppler Wind LIDAR ("APOLO") using airborne wind LIDAR data from two orthogonal directions to estimate wind parameters, and a second algorithm may be a five direction based method using pseudo inverse functions to estimate wind parameters. The various embodiments may enable wind profiles to be compared using different algorithms, may enable wind profile data for long haul color displays to be generated, may display long haul color displays, and/or may enable archiving of data at user-selectable altitudes over a long observation period for data distribution and population.

The SHIP: A SIP to HTTP Interaction Protocol

NASA Astrophysics Data System (ADS)

Zeiß, Joachim; Gabner, Rene; Bessler, Sandford; Happenhofer, Marco

IMS is capable of providing a wide range of services. As a result, terminal software becomes more and more complex to deliver network intelligence to user applications. Currently mobile terminal software needs to be permanently updated so that the latest network services and functionality can be delivered to the user. In the Internet, browser based user interfaces assure that an interface is made available to the user which offers the latest services in the net immediately. Our approach combines the benefits of the Session Initiation Protocol (SIP) and those of the HTTP protocol to bring the same type of user interfacing to IMS. SIP (IMS) realizes authentication, session management, charging and Quality of Service (QoS), HTTP provides access to Internet services and allows the user interface of an application to run on a mobile terminal while processing and orchestration is done on the server. A SHIP enabled IMS client only needs to handle data transport and session management via SIP, HTTP and RTP and render streaming media, HTML and Javascript. SHIP allows new kinds of applications, which combine audio, video and data within a single multimedia session.

Maneuver Automation Software

NASA Technical Reports Server (NTRS)

Uffelman, Hal; Goodson, Troy; Pellegrin, Michael; Stavert, Lynn; Burk, Thomas; Beach, David; Signorelli, Joel; Jones, Jeremy; Hahn, Yungsun; Attiyah, Ahlam;

Lab Streaming Layer Enabled Myo Data Collection Software User Manual

DTIC Science & Technology

2017-06-07

time - series data over a local network. LSL handles the networking, time -synchronization, (near-) real- time access as well as, optionally, the... series data collection (e.g., brain activity, heart activity, muscle activity) using the LSL application programming interface (API). Time -synchronized...saved to a single extensible data format (XDF) file. Once the time - series data are collected in a Lab Recorder XDF file, users will be able to query

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

PubMed

Harshbarger, Jayson; Kratz, Anton; Carninci, Piero

2017-01-07

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

Crowdsourcing Based 3d Modeling

NASA Astrophysics Data System (ADS)

Somogyi, A.; Barsi, A.; Molnar, B.; Lovas, T.

2016-06-01

Web-based photo albums that support organizing and viewing the users' images are widely used. These services provide a convenient solution for storing, editing and sharing images. In many cases, the users attach geotags to the images in order to enable using them e.g. in location based applications on social networks. Our paper discusses a procedure that collects open access images from a site frequently visited by tourists. Geotagged pictures showing the image of a sight or tourist attraction are selected and processed in photogrammetric processing software that produces the 3D model of the captured object. For the particular investigation we selected three attractions in Budapest. To assess the geometrical accuracy, we used laser scanner and DSLR as well as smart phone photography to derive reference values to enable verifying the spatial model obtained from the web-album images. The investigation shows how detailed and accurate models could be derived applying photogrammetric processing software, simply by using images of the community, without visiting the site.

DSN Array Simulator

NASA Technical Reports Server (NTRS)

Tikidjian, Raffi; Mackey, Ryan

2008-01-01

The DSN Array Simulator (wherein 'DSN' signifies NASA's Deep Space Network) is an updated version of software previously denoted the DSN Receive Array Technology Assessment Simulation. This software (see figure) is used for computational modeling of a proposed DSN facility comprising user-defined arrays of antennas and transmitting and receiving equipment for microwave communication with spacecraft on interplanetary missions. The simulation includes variations in spacecraft tracked and communication demand changes for up to several decades of future operation. Such modeling is performed to estimate facility performance, evaluate requirements that govern facility design, and evaluate proposed improvements in hardware and/or software. The updated version of this software affords enhanced capability for characterizing facility performance against user-defined mission sets. The software includes a Monte Carlo simulation component that enables rapid generation of key mission-set metrics (e.g., numbers of links, data rates, and date volumes), and statistical distributions thereof as functions of time. The updated version also offers expanded capability for mixed-asset network modeling--for example, for running scenarios that involve user-definable mixtures of antennas having different diameters (in contradistinction to a fixed number of antennas having the same fixed diameter). The improved version also affords greater simulation fidelity, sufficient for validation by comparison with actual DSN operations and analytically predictable performance metrics.

Remote Sensing Image Analysis Without Expert Knowledge - A Web-Based Classification Tool On Top of Taverna Workflow Management System

NASA Astrophysics Data System (ADS)

Selsam, Peter; Schwartze, Christian

2016-10-01

Providing software solutions via internet has been known for quite some time and is now an increasing trend marketed as "software as a service". A lot of business units accept the new methods and streamlined IT strategies by offering web-based infrastructures for external software usage - but geospatial applications featuring very specialized services or functionalities on demand are still rare. Originally applied in desktop environments, the ILMSimage tool for remote sensing image analysis and classification was modified in its communicating structures and enabled for running on a high-power server and benefiting from Tavema software. On top, a GIS-like and web-based user interface guides the user through the different steps in ILMSimage. ILMSimage combines object oriented image segmentation with pattern recognition features. Basic image elements form a construction set to model for large image objects with diverse and complex appearance. There is no need for the user to set up detailed object definitions. Training is done by delineating one or more typical examples (templates) of the desired object using a simple vector polygon. The template can be large and does not need to be homogeneous. The template is completely independent from the segmentation. The object definition is done completely by the software.

Collaborative Planning of Robotic Exploration

NASA Technical Reports Server (NTRS)

Norris, Jeffrey; Backes, Paul; Powell, Mark; Vona, Marsette; Steinke, Robert

2004-01-01

The Science Activity Planner (SAP) software system includes an uplink-planning component, which enables collaborative planning of activities to be undertaken by an exploratory robot on a remote planet or on Earth. Included in the uplink-planning component is the SAP-Uplink Browser, which enables users to load multiple spacecraft activity plans into a single window, compare them, and merge them. The uplink-planning component includes a subcomponent that implements the Rover Markup Language Activity Planning format (RML-AP), based on the Extensible Markup Language (XML) format that enables the representation, within a single document, of planned spacecraft and robotic activities together with the scientific reasons for the activities. Each such document is highly parseable and can be validated easily. Another subcomponent of the uplink-planning component is the Activity Dictionary Markup Language (ADML), which eliminates the need for two mission activity dictionaries - one in a human-readable format and one in a machine-readable format. Style sheets that have been developed along with the ADML format enable users to edit one dictionary in a user-friendly environment without compromising

The SeaDAS Processing and Analysis System: SeaWiFS, MODIS, and Beyond

NASA Astrophysics Data System (ADS)

MacDonald, M. D.; Ruebens, M.; Wang, L.; Franz, B. A.

2005-12-01

The SeaWiFS Data Analysis System (SeaDAS) is a comprehensive software package for the processing, display, and analysis of ocean data from a variety of satellite sensors. Continuous development and user support by programmers and scientists for more than a decade has helped to make SeaDAS the most widely used software package in the world for ocean color applications, with a growing base of users from the land and sea surface temperature community. Full processing support for past (CZCS, OCTS, MOS) and present (SeaWiFS, MODIS) sensors, and anticipated support for future missions such as NPP/VIIRS, enables end users to reproduce the standard ocean archive product suite distributed by NASA's Ocean Biology Processing Group (OBPG), as well as a variety of evaluation and intermediate ocean, land, and atmospheric products. Availability of the processing algorithm source codes and a software build environment also provide users with the tools to implement custom algorithms. Recent SeaDAS enhancements include synchronization of MODIS processing with the latest code and calibration updates from the MODIS Calibration Support Team (MCST), support for all levels of MODIS processing including Direct Broadcast, a port to the Macintosh OS X operating system, release of the display/analysis-only SeaDAS-Lite, and an extremely active web-based user support forum.

Development and use of mathematical models and software frameworks for integrated analysis of agricultural systems and associated water use impacts

USGS Publications Warehouse

Fowler, K. R.; Jenkins, E.W.; Parno, M.; Chrispell, J.C.; Colón, A. I.; Hanson, Randall T.

2016-01-01

The development of appropriate water management strategies requires, in part, a methodology for quantifying and evaluating the impact of water policy decisions on regional stakeholders. In this work, we describe the framework we are developing to enhance the body of resources available to policy makers, farmers, and other community members in their e orts to understand, quantify, and assess the often competing objectives water consumers have with respect to usage. The foundation for the framework is the construction of a simulation-based optimization software tool using two existing software packages. In particular, we couple a robust optimization software suite (DAKOTA) with the USGS MF-OWHM water management simulation tool to provide a flexible software environment that will enable the evaluation of one or multiple (possibly competing) user-defined (or stakeholder) objectives. We introduce the individual software components and outline the communication strategy we defined for the coupled development. We present numerical results for case studies related to crop portfolio management with several defined objectives. The objectives are not optimally satisfied for any single user class, demonstrating the capability of the software tool to aid in the evaluation of a variety of competing interests.

Video-Game-Like Engine for Depicting Spacecraft Trajectories

NASA Technical Reports Server (NTRS)

Upchurch, Paul R.

2009-01-01

GoView is a video-game-like software engine, written in the C and C++ computing languages, that enables real-time, three-dimensional (3D)-appearing visual representation of spacecraft and trajectories (1) from any perspective; (2) at any spatial scale from spacecraft to Solar-system dimensions; (3) in user-selectable time scales; (4) in the past, present, and/or future; (5) with varying speeds; and (6) forward or backward in time. GoView constructs an interactive 3D world by use of spacecraft-mission data from pre-existing engineering software tools. GoView can also be used to produce distributable application programs for depicting NASA orbital missions on personal computers running the Windows XP, Mac OsX, and Linux operating systems. GoView enables seamless rendering of Cartesian coordinate spaces with programmable graphics hardware, whereas prior programs for depicting spacecraft trajectories variously require non-Cartesian coordinates and/or are not compatible with programmable hardware. GoView incorporates an algorithm for nonlinear interpolation between arbitrary reference frames, whereas the prior programs are restricted to special classes of inertial and non-inertial reference frames. Finally, whereas the prior programs present complex user interfaces requiring hours of training, the GoView interface provides guidance, enabling use without any training.

A Formal Approach to Domain-Oriented Software Design Environments

NASA Technical Reports Server (NTRS)

Lowry, Michael; Philpot, Andrew; Pressburger, Thomas; Underwood, Ian; Lum, Henry, Jr. (Technical Monitor)

1994-01-01

This paper describes a formal approach to domain-oriented software design environments, based on declarative domain theories, formal specifications, and deductive program synthesis. A declarative domain theory defines the semantics of a domain-oriented specification language and its relationship to implementation-level subroutines. Formal specification development and reuse is made accessible to end-users through an intuitive graphical interface that guides them in creating diagrams denoting formal specifications. The diagrams also serve to document the specifications. Deductive program synthesis ensures that end-user specifications are correctly implemented. AMPHION has been applied to the domain of solar system kinematics through the development of a declarative domain theory, which includes an axiomatization of JPL's SPICELIB subroutine library. Testing over six months with planetary scientists indicates that AMPHION's interactive specification acquisition paradigm enables users to develop, modify, and reuse specifications at least an order of magnitude more rapidly than manual program development. Furthermore, AMPHION synthesizes one to two page programs consisting of calls to SPICELIB subroutines from these specifications in just a few minutes. Test results obtained by metering AMPHION's deductive program synthesis component are examined. AMPHION has been installed at JPL and is currently undergoing further refinement in preparation for distribution to hundreds of SPICELIB users worldwide. Current work to support end-user customization of AMPHION's specification acquisition subsystem is briefly discussed, as well as future work to enable domain-expert creation of new AMPHION applications through development of suitable domain theories.

Co-streaming classes: a follow-up study in improving the user experience to better reach users.

PubMed

Hayes, Barrie E; Handler, Lara J; Main, Lindsey R

2011-01-01

Co-streaming classes have enabled library staff to extend open classes to distance education students and other users. Student evaluations showed that the model could be improved. Two areas required attention: audio problems experienced by online participants and staff teaching methods. Staff tested equipment and adjusted software configuration to improve user experience. Staff training increased familiarity with specialized teaching techniques and troubleshooting procedures. Technology testing and staff training were completed, and best practices were developed and applied. Class evaluations indicate improvements in classroom experience. Future plans include expanding co-streaming to more classes and on-going data collection, evaluation, and improvement of classes.

Bio-Docklets: virtualization containers for single-step execution of NGS pipelines.

PubMed

Kim, Baekdoo; Ali, Thahmina; Lijeron, Carlos; Afgan, Enis; Krampis, Konstantinos

2017-08-01

Processing of next-generation sequencing (NGS) data requires significant technical skills, involving installation, configuration, and execution of bioinformatics data pipelines, in addition to specialized postanalysis visualization and data mining software. In order to address some of these challenges, developers have leveraged virtualization containers toward seamless deployment of preconfigured bioinformatics software and pipelines on any computational platform. We present an approach for abstracting the complex data operations of multistep, bioinformatics pipelines for NGS data analysis. As examples, we have deployed 2 pipelines for RNA sequencing and chromatin immunoprecipitation sequencing, preconfigured within Docker virtualization containers we call Bio-Docklets. Each Bio-Docklet exposes a single data input and output endpoint and from a user perspective, running the pipelines as simply as running a single bioinformatics tool. This is achieved using a "meta-script" that automatically starts the Bio-Docklets and controls the pipeline execution through the BioBlend software library and the Galaxy Application Programming Interface. The pipeline output is postprocessed by integration with the Visual Omics Explorer framework, providing interactive data visualizations that users can access through a web browser. Our goal is to enable easy access to NGS data analysis pipelines for nonbioinformatics experts on any computing environment, whether a laboratory workstation, university computer cluster, or a cloud service provider. Beyond end users, the Bio-Docklets also enables developers to programmatically deploy and run a large number of pipeline instances for concurrent analysis of multiple datasets. © The Authors 2017. Published by Oxford University Press.

Bio-Docklets: virtualization containers for single-step execution of NGS pipelines

PubMed Central

Kim, Baekdoo; Ali, Thahmina; Lijeron, Carlos; Afgan, Enis

2017-01-01

Abstract Processing of next-generation sequencing (NGS) data requires significant technical skills, involving installation, configuration, and execution of bioinformatics data pipelines, in addition to specialized postanalysis visualization and data mining software. In order to address some of these challenges, developers have leveraged virtualization containers toward seamless deployment of preconfigured bioinformatics software and pipelines on any computational platform. We present an approach for abstracting the complex data operations of multistep, bioinformatics pipelines for NGS data analysis. As examples, we have deployed 2 pipelines for RNA sequencing and chromatin immunoprecipitation sequencing, preconfigured within Docker virtualization containers we call Bio-Docklets. Each Bio-Docklet exposes a single data input and output endpoint and from a user perspective, running the pipelines as simply as running a single bioinformatics tool. This is achieved using a “meta-script” that automatically starts the Bio-Docklets and controls the pipeline execution through the BioBlend software library and the Galaxy Application Programming Interface. The pipeline output is postprocessed by integration with the Visual Omics Explorer framework, providing interactive data visualizations that users can access through a web browser. Our goal is to enable easy access to NGS data analysis pipelines for nonbioinformatics experts on any computing environment, whether a laboratory workstation, university computer cluster, or a cloud service provider. Beyond end users, the Bio-Docklets also enables developers to programmatically deploy and run a large number of pipeline instances for concurrent analysis of multiple datasets. PMID:28854616

Multiuser Collaboration with Networked Mobile Devices

NASA Technical Reports Server (NTRS)

Tso, Kam S.; Tai, Ann T.; Deng, Yong M.; Becks, Paul G.

2006-01-01

In this paper we describe a multiuser collaboration infrastructure that enables multiple mission scientists to remotely and collaboratively interact with visualization and planning software, using wireless networked personal digital assistants(PDAs) and other mobile devices. During ground operations of planetary rover and lander missions, scientists need to meet daily to review downlinked data and plan science activities. For example, scientists use the Science Activity Planner (SAP) in the Mars Exploration Rover (MER) mission to visualize downlinked data and plan rover activities during the science meetings [1]. Computer displays are projected onto large screens in the meeting room to enable the scientists to view and discuss downlinked images and data displayed by SAP and other software applications. However, only one person can interact with the software applications because input to the computer is limited to a single mouse and keyboard. As a result, the scientists have to verbally express their intentions, such as selecting a target at a particular location on the Mars terrain image, to that person in order to interact with the applications. This constrains communication and limits the returns of science planning. Furthermore, ground operations for Mars missions are fundamentally constrained by the short turnaround time for science and engineering teams to process and analyze data, plan the next uplink, generate command sequences, and transmit the uplink to the vehicle [2]. Therefore, improving ground operations is crucial to the success of Mars missions. The multiuser collaboration infrastructure enables users to control software applications remotely and collaboratively using mobile devices. The infrastructure includes (1) human-computer interaction techniques to provide natural, fast, and accurate inputs, (2) a communications protocol to ensure reliable and efficient coordination of the input devices and host computers, (3) an application-independent middleware that maintains the states, sessions, and interactions of individual users of the software applications, (4) an application programming interface to enable tight integration of applications and the middleware. The infrastructure is able to support any software applications running under the Windows or Unix platforms. The resulting technologies not only are applicable to NASA mission operations, but also useful in other situations such as design reviews, brainstorming sessions, and business meetings, as they can benefit from having the participants concurrently interact with the software applications (e.g., presentation applications and CAD design tools) to illustrate their ideas and provide inputs.

Sharing Research Models: Using Software Engineering Practices for Facilitation

PubMed Central

Bryant, Stephanie P.; Solano, Eric; Cantor, Susanna; Cooley, Philip C.; Wagener, Diane K.

2011-01-01

Increasingly, researchers are turning to computational models to understand the interplay of important variables on systems’ behaviors. Although researchers may develop models that meet the needs of their investigation, application limitations—such as nonintuitive user interface features and data input specifications—may limit the sharing of these tools with other research groups. By removing these barriers, other research groups that perform related work can leverage these work products to expedite their own investigations. The use of software engineering practices can enable managed application production and shared research artifacts among multiple research groups by promoting consistent models, reducing redundant effort, encouraging rigorous peer review, and facilitating research collaborations that are supported by a common toolset. This report discusses three established software engineering practices— the iterative software development process, object-oriented methodology, and Unified Modeling Language—and the applicability of these practices to computational model development. Our efforts to modify the MIDAS TranStat application to make it more user-friendly are presented as an example of how computational models that are based on research and developed using software engineering practices can benefit a broader audience of researchers. PMID:21687780

Software Verification of Orion Cockpit Displays

NASA Technical Reports Server (NTRS)

Biswas, M. A. Rafe; Garcia, Samuel; Prado, Matthew; Hossain, Sadad; Souris, Matthew; Morin, Lee

2017-01-01

NASA's latest spacecraft Orion is in the development process of taking humans deeper into space. Orion is equipped with three main displays to monitor and control the spacecraft. To ensure the software behind the glass displays operates without faults, rigorous testing is needed. To conduct such testing, the Rapid Prototyping Lab at NASA's Johnson Space Center along with the University of Texas at Tyler employed a software verification tool, EggPlant Functional by TestPlant. It is an image based test automation tool that allows users to create scripts to verify the functionality within a program. A set of edge key framework and Common EggPlant Functions were developed to enable creation of scripts in an efficient fashion. This framework standardized the way to code and to simulate user inputs in the verification process. Moreover, the Common EggPlant Functions can be used repeatedly in verification of different displays.

A Database-Based and Web-Based Meta-CASE System

NASA Astrophysics Data System (ADS)

Eessaar, Erki; Sgirka, Rünno

Each Computer Aided Software Engineering (CASE) system provides support to a software process or specific tasks or activities that are part of a software process. Each meta-CASE system allows us to create new CASE systems. The creators of a new CASE system have to specify abstract syntax of the language that is used in the system and functionality as well as non-functional properties of the new system. Many meta-CASE systems record their data directly in files. In this paper, we introduce a meta-CASE system, the enabling technology of which is an object-relational database system (ORDBMS). The system allows users to manage specifications of languages and create models by using these languages. The system has web-based and form-based user interface. We have created a proof-of-concept prototype of the system by using PostgreSQL ORDBMS and PHP scripting language.

Representation of Ice Geometry by Parametric Functions: Construction of Approximating NURBS Curves and Quantification of Ice Roughness--Year 1: Approximating NURBS Curves

NASA Technical Reports Server (NTRS)

Dill, Loren H.; Choo, Yung K. (Technical Monitor)

2004-01-01

Software was developed to construct approximating NURBS curves for iced airfoil geometries. Users specify a tolerance that determines the extent to which the approximating curve follows the rough ice. The user can therefore smooth the ice geometry in a controlled manner, thereby enabling the generation of grids suitable for numerical aerodynamic simulations. Ultimately, this ability to smooth the ice geometry will permit studies of the effects of smoothing upon the aerodynamics of iced airfoils. The software was applied to several different types of iced airfoil data collected in the Icing Research Tunnel at NASA Glenn Research Center, and in all cases was found to efficiently generate suitable approximating NURBS curves. This method is an improvement over the current "control point formulation" of Smaggice (v.1.2). In this report, we present the relevant theory of approximating NURBS curves and discuss typical results of the software.

Security System Software

NASA Technical Reports Server (NTRS)

1993-01-01

C Language Integration Production System (CLIPS), a NASA-developed expert systems program, has enabled a security systems manufacturer to design a new generation of hardware. C.CURESystem 1 Plus, manufactured by Software House, is a software based system that is used with a variety of access control hardware at installations around the world. Users can manage large amounts of information, solve unique security problems and control entry and time scheduling. CLIPS acts as an information management tool when accessed by C.CURESystem 1 Plus. It asks questions about the hardware and when given the answer, recommends possible quick solutions by non-expert persons.

IBM NJE protocol emulator for VAX/VMS

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

Engert, D.E.

1981-01-01

Communications software has been written at Argonne National Laboratory to enable a VAX/VMS system to participate as an end-node in a standard IBM network by emulating the Network Job Entry (NJE) protocol. NJE is actually a collection of programs that support job networking for the operating systems used on most large IBM-compatible computers (e.g., VM/370, MVS with JES2 or JES3, SVS, MVT with ASP or HASP). Files received by the VAX can be printed or saved in user-selected disk files. Files sent to the network can be routed to any node in the network for printing, punching, or job submission,more » as well as to a VM/370 user's virtual reader. Files sent from the VAX are queued and transmitted asynchronously to allow users to perform other work while files are awaiting transmission. No changes are required to the IBM software.« less

Enabling Creative Learning Design through Semantic Technologies

ERIC Educational Resources Information Center

Charlton, Patricia; Magoulas, George; Laurillard, Diana

2012-01-01

The paper advocates an approach to learning design that considers it as creating digital artefacts that can be extended, modified and used for different purposes. This is realised through an "act becoming artefact" cycle, where users' actions in the authors' software environment, named Learning Designer, are automatically interpreted on…

Software Framework for Advanced Power Plant Simulations

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

John Widmann; Sorin Munteanu; Aseem Jain

2010-08-01

This report summarizes the work accomplished during the Phase II development effort of the Advanced Process Engineering Co-Simulator (APECS). The objective of the project is to develop the tools to efficiently combine high-fidelity computational fluid dynamics (CFD) models with process modeling software. During the course of the project, a robust integration controller was developed that can be used in any CAPE-OPEN compliant process modeling environment. The controller mediates the exchange of information between the process modeling software and the CFD software. Several approaches to reducing the time disparity between CFD simulations and process modeling have been investigated and implemented. Thesemore » include enabling the CFD models to be run on a remote cluster and enabling multiple CFD models to be run simultaneously. Furthermore, computationally fast reduced-order models (ROMs) have been developed that can be 'trained' using the results from CFD simulations and then used directly within flowsheets. Unit operation models (both CFD and ROMs) can be uploaded to a model database and shared between multiple users.« less

Web Implementation of Quality Assurance (QA) for X-ray Units in Balkanic Medical Institutions.

PubMed

Urošević, Vlade; Ristić, Olga; Milošević, Danijela; Košutić, Duško

2015-08-01

Diagnostic radiology is the major contributor to the total dose of the population from all artificial sources. In order to reduce radiation exposure and optimize diagnostic x-ray image quality, it is necessary to increase the quality and efficiency of quality assurance (QA) and audit programs. This work presents a web application providing completely new QA solutions for x-ray modalities and facilities. The software gives complete online information (using European standards) with which the corresponding institutions and individuals can evaluate and control a facility's Radiation Safety and QA program. The software enables storage of all data in one place and sharing the same information (data), regardless of whether the measured data is used by an individual user or by an authorized institution. The software overcomes the distance and time separation of institutions and individuals who take part in QA. Upgrading the software will enable assessment of the medical exposure level to ionizing radiation.

Program Helps Simulate Neural Networks

NASA Technical Reports Server (NTRS)

Villarreal, James; Mcintire, Gary

1993-01-01

Neural Network Environment on Transputer System (NNETS) computer program provides users high degree of flexibility in creating and manipulating wide variety of neural-network topologies at processing speeds not found in conventional computing environments. Supports back-propagation and back-propagation-related algorithms. Back-propagation algorithm used is implementation of Rumelhart's generalized delta rule. NNETS developed on INMOS Transputer(R). Predefines back-propagation network, Jordan network, and reinforcement network to assist users in learning and defining own networks. Also enables users to configure other neural-network paradigms from NNETS basic architecture. Small portion of software written in OCCAM(R) language.

Orchestrating high-throughput genomic analysis with Bioconductor

PubMed Central

Huber, Wolfgang; Carey, Vincent J.; Gentleman, Robert; Anders, Simon; Carlson, Marc; Carvalho, Benilton S.; Bravo, Hector Corrada; Davis, Sean; Gatto, Laurent; Girke, Thomas; Gottardo, Raphael; Hahne, Florian; Hansen, Kasper D.; Irizarry, Rafael A.; Lawrence, Michael; Love, Michael I.; MacDonald, James; Obenchain, Valerie; Oleś, Andrzej K.; Pagès, Hervé; Reyes, Alejandro; Shannon, Paul; Smyth, Gordon K.; Tenenbaum, Dan; Waldron, Levi; Morgan, Martin

2015-01-01

Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors. PMID:25633503

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)

Benefits of Matching Domain Structure for Planning Software: The Right Stuff

NASA Technical Reports Server (NTRS)

Billman, Dorrit Owen; Arsintescu, Lucica; Feary, Michael S.; Lee, Jessica Chia-Rong; Smith, Asha Halima; Tiwary, Rachna

2011-01-01

We investigated the role of domain structure in software design. We compared 2 planning applications, for a Mission Control group (International Space Station), and measured users speed and accuracy. Based on our needs analysis, we identified domain structure and used this to develop new prototype software that matched domain structure better than the legacy system. We took a high-fidelity analog of the natural task into the laboratory and found (large) periformance differences, favoring the system that matched domain structure. Our task design enabled us to attribute better periormance to better match of domain structure. We ran through the whole development cycle, in miniature, from needs analysis through design, development, and evaluation. Doing so enabled inferences not just about the particular systems compared, but also provided evidence for the viability of the design process (particularly needs analysis) that we are exploring.

The EPOS e-Infrastructure

NASA Astrophysics Data System (ADS)

Jeffery, Keith; Bailo, Daniele

2014-05-01

The European Plate Observing System (EPOS) is integrating geoscientific information concerning earth movements in Europe. We are approaching the end of the PP (Preparatory Project) phase and in October 2014 expect to continue with the full project within ESFRI (European Strategic Framework for Research Infrastructures). The key aspects of EPOS concern providing services to allow homogeneous access by end-users over heterogeneous data, software, facilities, equipment and services. The e-infrastructure of EPOS is the heart of the project since it integrates the work on organisational, legal, economic and scientific aspects. Following the creation of an inventory of relevant organisations, persons, facilities, equipment, services, datasets and software (RIDE) the scale of integration required became apparent. The EPOS e-infrastructure architecture has been developed systematically based on recorded primary (user) requirements and secondary (interoperation with other systems) requirements through Strawman, Woodman and Ironman phases with the specification - and developed confirmatory prototypes - becoming more precise and progressively moving from paper to implemented system. The EPOS architecture is based on global core services (Integrated Core Services - ICS) which access thematic nodes (domain-specific European-wide collections, called thematic Core Services - TCS), national nodes and specific institutional nodes. The key aspect is the metadata catalog. In one dimension this is described in 3 levels: (1) discovery metadata using well-known and commonly used standards such as DC (Dublin Core) to enable users (via an intelligent user interface) to search for objects within the EPOS environment relevant to their needs; (2) contextual metadata providing the context of the object described in the catalog to enable a user or the system to determine the relevance of the discovered object(s) to their requirement - the context includes projects, funding, organisations involved, persons involved, related publications, facilities, equipment and others, and utilises CERIF (Common European Research Information Format) standard (see www.eurocris.org); (3) detailed metadata which is specific to a domain or to a particular object and includes the schema describing the object to processing software. The other dimension of the metadata concerns the objects described. These are classified into users, services (including software), data and resources (computing, data storage, instruments and scientific equipment). An alternative architecture has been considered: using brokering. This technique has been used especially in North America geoscience projects to interoperate datasets. The technique involves writing software to interconvert between any two node datasets. Given n nodes this implies writing n*(n-1) convertors. EPOS Working Group 7 (e-infrastructures and virtual community) which deals with the design and implementation of a prototype of the EPOS services, chose to use an approach which endows the system with an extreme flexibility and sustainability. It is called the Metadata Catalogue approach. With the use of the catalogue the EPOS system can: 1. interoperate with software, services, users, organisations, facilities, equipment etc. as well as datasets; 2. avoid to write n*(n-1) software convertors and generate as much as possible, through the information contained in the catalogue only n convertors. This is a huge saving - especially in maintenance as the datasets (or other node resources) evolve. We are working on (semi-) automation of convertor generation by metadata mapping - this is leading-edge computer science research; 3. make large use of contextual metadata which enable a user or a machine to: (i) improve discovery of resources at nodes; (ii) improve precision and recall in search; (iii) drive the systems for identification, authentication, authorisation, security and privacy recording the relevant attributes of the node resources and of the user; (iv) manage provenance and long-term digital preservation; The linkage between the Integrated Services, which provide the integration of data and services, with the diverse Thematic Services Nodes is provided by means of a compatibility layer, which includes the aforementioned metadata catalogue. This layer provides 'connectors' to make local data, software and services available through the EPOS Integrated Services layer. In conclusion, we believe the EPOS e-infrastructure architecture is fit for purpose including long-term sustainability and pan-European access to data and services.

GPFrontend and GPGraphics: graphical analysis tools for genetic association studies.

PubMed

Uebe, Steffen; Pasutto, Francesca; Krumbiegel, Mandy; Schanze, Denny; Ekici, Arif B; Reis, André

2010-09-21

Most software packages for whole genome association studies are non-graphical, purely text based programs originally designed to run with UNIX-like operating systems. Graphical output is often not intended or supposed to be performed with other command line tools, e.g. gnuplot. Using the Microsoft .NET 2.0 platform and Visual Studio 2005, we have created a graphical software package to analyze data from microarray whole genome association studies, both for a DNA-pooling based approach as well as regular single sample data. Part of this package was made to integrate with GenePool 0.8.2, a previously existing software suite for GNU/Linux systems, which we have modified to run in a Microsoft Windows environment. Further modifications cause it to generate some additional data. This enables GenePool to interact with the .NET parts created by us. The programs we developed are GPFrontend, a graphical user interface and frontend to use GenePool and create metadata files for it, and GPGraphics, a program to further analyze and graphically evaluate output of different WGA analysis programs, among them also GenePool. Our programs enable regular MS Windows users without much experience in bioinformatics to easily visualize whole genome data from a variety of sources.

SimPhospho: a software tool enabling confident phosphosite assignment.

PubMed

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

2018-03-27

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

Aviation Safety Simulation Model

NASA Technical Reports Server (NTRS)

Houser, Scott; Yackovetsky, Robert (Technical Monitor)

2001-01-01

The Aviation Safety Simulation Model is a software tool that enables users to configure a terrain, a flight path, and an aircraft and simulate the aircraft's flight along the path. The simulation monitors the aircraft's proximity to terrain obstructions, and reports when the aircraft violates accepted minimum distances from an obstruction. This model design facilitates future enhancements to address other flight safety issues, particularly air and runway traffic scenarios. This report shows the user how to build a simulation scenario and run it. It also explains the model's output.

Generalizing the extensibility of a dynamic geometry software

NASA Astrophysics Data System (ADS)

Herceg, Đorđe; Radaković, Davorka; Herceg, Dejana

2012-09-01

Plug-and-play visual components in a Dynamic Geometry Software (DGS) enable development of visually attractive, rich and highly interactive dynamic drawings. We are developing SLGeometry, a DGS that contains a custom programming language, a computer algebra system (CAS engine) and a graphics subsystem. The basic extensibility framework on SLGeometry supports dynamic addition of new functions from attribute annotated classes that implement runtime metadata registration in code. We present a general plug-in framework for dynamic importing of arbitrary Silverlight user interface (UI) controls into SLGeometry at runtime. The CAS engine maintains a metadata storage that describes each imported visual component and enables two-way communication between the expressions stored in the engine and the UI controls on the screen.

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

PubMed

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

2017-05-01

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

Transportable Applications Environment Plus, Version 5.1

NASA Technical Reports Server (NTRS)

1994-01-01

Transportable Applications Environment Plus (TAE+) computer program providing integrated, portable programming environment for developing and running application programs based on interactive windows, text, and graphical objects. Enables both programmers and nonprogrammers to construct own custom application interfaces easily and to move interfaces and application programs to different computers. Used to define corporate user interface, with noticeable improvements in application developer's and end user's learning curves. Main components are; WorkBench, What You See Is What You Get (WYSIWYG) software tool for design and layout of user interface; and WPT (Window Programming Tools) Package, set of callable subroutines controlling user interface of application program. WorkBench and WPT's written in C++, and remaining code written in C.

Power User Interface

NASA Technical Reports Server (NTRS)

Pfister, Robin; McMahon, Joe

2006-01-01

Power User Interface 5.0 (PUI) is a system of middleware, written for expert users in the Earth-science community, PUI enables expedited ordering of data granules on the basis of specific granule-identifying information that the users already know or can assemble. PUI also enables expert users to perform quick searches for orderablegranule information for use in preparing orders. PUI 5.0 is available in two versions (note: PUI 6.0 has command-line mode only): a Web-based application program and a UNIX command-line- mode client program. Both versions include modules that perform data-granule-ordering functions in conjunction with external systems. The Web-based version works with Earth Observing System Clearing House (ECHO) metadata catalog and order-entry services and with an open-source order-service broker server component, called the Mercury Shopping Cart, that is provided separately by Oak Ridge National Laboratory through the Department of Energy. The command-line version works with the ECHO metadata and order-entry process service. Both versions of PUI ultimately use ECHO to process an order to be sent to a data provider. Ordered data are provided through means outside the PUI software system.

An open-architecture approach to defect analysis software for mask inspection systems

NASA Astrophysics Data System (ADS)

Pereira, Mark; Pai, Ravi R.; Reddy, Murali Mohan; Krishna, Ravi M.

2009-04-01

Industry data suggests that Mask Inspection represents the second biggest component of Mask Cost and Mask Turn Around Time (TAT). Ever decreasing defect size targets lead to more sensitive mask inspection across the chip, thus generating too many defects. Hence, more operator time is being spent in analyzing and disposition of defects. Also, the fact that multiple Mask Inspection Systems and Defect Analysis strategies would typically be in use in a Mask Shop or a Wafer Foundry further complicates the situation. In this scenario, there is a need for a versatile, user friendly and extensible Defect Analysis software that reduces operator analysis time and enables correct classification and disposition of mask defects by providing intuitive visual and analysis aids. We propose a new vendor-neutral defect analysis software, NxDAT, based on an open architecture. The open architecture of NxDAT makes it easily extensible to support defect analysis for mask inspection systems from different vendors. The capability to load results from mask inspection systems from different vendors either directly or through a common interface enables the functionality of establishing correlation between inspections carried out by mask inspection systems from different vendors. This capability of NxDAT enhances the effectiveness of defect analysis as it directly addresses the real-life scenario where multiple types of mask inspection systems from different vendors co-exist in mask shops or wafer foundries. The open architecture also potentially enables loading wafer inspection results as well as loading data from other related tools such as Review Tools, Repair Tools, CD-SEM tools etc, and correlating them with the corresponding mask inspection results. A unique concept of Plug-In interface to NxDAT further enhances the openness of the architecture of NxDAT by enabling end-users to add their own proprietary defect analysis and image processing algorithms. The plug-in interface makes it possible for the end-users to make use of their collected knowledge through the years of experience in mask inspection process by encapsulating the knowledge into software utilities and plugging them into NxDAT. The plug-in interface is designed with the intent of enabling the pro-active mask defect analysis teams to build competitive differentiation into their defect analysis process while protecting their knowledge internally within their company. By providing interface with all major standard layout and mask data formats, NxDAT enables correlation of defect data on reticles with design and mask databases, further extending the effectiveness of defect analysis for D2DB inspection. NxDAT also includes many other advanced features for easy and fast navigation, visual display of defects, defect selection, multi-tier classification, defect clustering and gridding, sophisticated CD and contact measurement analysis, repeatability analysis such as adder analysis, defect trend, capture rate etc.

User Guidelines and Best Practices for CASL VUQ Analysis Using Dakota.

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

Adams, Brian M.; Coleman, Kayla; Hooper, Russell

2016-11-01

Sandia's Dakota software (available at http://dakota.sandia.gov) supports science and engineering transformation through advanced exploration of simulations. Specifically it manages and analyzes ensembles of simulations to provide broader and deeper perspective for analysts and decision makers. This enables them to enhance understanding of risk, improve products, and assess simulation credibility.

Implementation guide for turbidity threshold sampling: principles, procedures, and analysis

Treesearch

Jack Lewis; Rand Eads

2009-01-01

Turbidity Threshold Sampling uses real-time turbidity and river stage information to automatically collect water quality samples for estimating suspended sediment loads. The system uses a programmable data logger in conjunction with a stage measurement device, a turbidity sensor, and a pumping sampler. Specialized software enables the user to control the sampling...

Enhanced, Partially Redundant Emergency Notification System

NASA Technical Reports Server (NTRS)

Pounds, Clark D.

2005-01-01

The Johnson Space Center Emergency Notification System (JENS) software utilizes pre-existing computation and communication infrastructure to augment a prior variable-tone, siren-based, outdoor alarm system, in order to enhance the ability to give notice of emergencies to employees working in multiple buildings. The JENS software includes a component that implements an administrative Web site. Administrators can grant and deny access to the administrative site and to an originator Web site that enables authorized individuals to quickly compose and issue alarms. The originator site also facilitates maintenance and review of alarms already issued. A custom client/server application program enables an originator to notify every user who is logged in on a Microsoft Windows-based desktop computer by means of a pop-up message that interrupts, but does not disrupt, the user s work. Alternatively or in addition, the originator can send an alarm message to recipients on an e-mail distribution list and/or can post the notice on an internal Web site. An alarm message can consist of (1) text describing the emergency and suggesting a course of action and (2) a replica of the corresponding audible outdoor alarm.

a Low-Cost and Lightweight 3d Interactive Real Estate-Purposed Indoor Virtual Reality Application

NASA Astrophysics Data System (ADS)

Ozacar, K.; Ortakci, Y.; Kahraman, I.; Durgut, R.; Karas, I. R.

2017-11-01

Interactive 3D architectural indoor design have been more popular after it benefited from Virtual Reality (VR) technologies. VR brings computer-generated 3D content to real life scale and enable users to observe immersive indoor environments so that users can directly modify it. This opportunity enables buyers to purchase a property off-the-plan cheaper through virtual models. Instead of showing property through 2D plan or renders, this visualized interior architecture of an on-sale unbuilt property is demonstrated beforehand so that the investors have an impression as if they were in the physical building. However, current applications either use highly resource consuming software, or are non-interactive, or requires specialist to create such environments. In this study, we have created a real-estate purposed low-cost high quality fully interactive VR application that provides a realistic interior architecture of the property by using free and lightweight software: Sweet Home 3D and Unity. A preliminary study showed that participants generally liked proposed real estate-purposed VR application, and it satisfied the expectation of the property buyers.

THE VIRTUAL INSTRUMENT: SUPPORT FOR GRID-ENABLED MCELL SIMULATIONS

PubMed Central

Casanova, Henri; Berman, Francine; Bartol, Thomas; Gokcay, Erhan; Sejnowski, Terry; Birnbaum, Adam; Dongarra, Jack; Miller, Michelle; Ellisman, Mark; Faerman, Marcio; Obertelli, Graziano; Wolski, Rich; Pomerantz, Stuart; Stiles, Joel

2010-01-01

Ensembles of widely distributed, heterogeneous resources, or Grids, have emerged as popular platforms for large-scale scientific applications. In this paper we present the Virtual Instrument project, which provides an integrated application execution environment that enables end-users to run and interact with running scientific simulations on Grids. This work is performed in the specific context of MCell, a computational biology application. While MCell provides the basis for running simulations, its capabilities are currently limited in terms of scale, ease-of-use, and interactivity. These limitations preclude usage scenarios that are critical for scientific advances. Our goal is to create a scientific “Virtual Instrument” from MCell by allowing its users to transparently access Grid resources while being able to steer running simulations. In this paper, we motivate the Virtual Instrument project and discuss a number of relevant issues and accomplishments in the area of Grid software development and application scheduling. We then describe our software design and report on the current implementation. We verify and evaluate our design via experiments with MCell on a real-world Grid testbed. PMID:20689618

MODFLOW-CDSS, a version of MODFLOW-2005 with modifications for Colorado Decision Support Systems

USGS Publications Warehouse

Banta, Edward R.

2011-01-01

MODFLOW-CDSS is a three-dimensional, finite-difference groundwater-flow model based on MODFLOW-2005, with two modifications. The first modification is the introduction of a Partition Stress Boundaries capability, which enables the user to partition a selected subset of MODFLOW's stress-boundary packages, with each partition defined by a separate input file. Volumetric water-budget components of each partition are tracked and listed separately in the volumetric water-budget tables. The second modification enables the user to specify that execution of a simulation should continue despite failure of the solver to satisfy convergence criteria. This modification is particularly intended to be used in conjunction with automated model-analysis software; its use is not recommended for other purposes.

Geodetic Strain Analysis Tool

NASA Technical Reports Server (NTRS)

Kedar, Sharon; Baxter, Sean C.; Parker, Jay W.; Webb, Frank H.; Owen, Susan E.; Sibthorpe, Anthony J.; Dong, Danan

2011-01-01

A geodetic software analysis tool enables the user to analyze 2D crustal strain from geodetic ground motion, and create models of crustal deformation using a graphical interface. Users can use any geodetic measurements of ground motion and derive the 2D crustal strain interactively. This software also provides a forward-modeling tool that calculates a geodetic velocity and strain field for a given fault model, and lets the user compare the modeled strain field with the strain field obtained from the user s data. Users may change parameters on-the-fly and obtain a real-time recalculation of the resulting strain field. Four data products are computed: maximum shear, dilatation, shear angle, and principal components. The current view and data dependencies are processed first. The remaining data products and views are then computed in a round-robin fashion to anticipate view changes. When an analysis or display parameter is changed, the affected data products and views are invalidated and progressively re-displayed as available. This software is designed to facilitate the derivation of the strain fields from the GPS and strain meter data that sample it to facilitate the understanding of the strengths and weaknesses of the strain field derivation from continuous GPS (CGPS) and other geodetic data from a variety of tectonic settings, to converge on the "best practices" strain derivation strategy for the Solid Earth Science ESDR System (SESES) project given the CGPS station distribution in the western U.S., and to provide SESES users with a scientific and educational tool to explore the strain field on their own with user-defined parameters.

Seamless transitions from early prototypes to mature operational software - A technology that enables the process for planning and scheduling applications

NASA Technical Reports Server (NTRS)

Hornstein, Rhoda S.; Wunderlich, Dana A.; Willoughby, John K.

1992-01-01

New and innovative software technology is presented that provides a cost effective bridge for smoothly transitioning prototype software, in the field of planning and scheduling, into an operational environment. Specifically, this technology mixes the flexibility and human design efficiency of dynamic data typing with the rigor and run-time efficiencies of static data typing. This new technology provides a very valuable tool for conducting the extensive, up-front system prototyping that leads to specifying the correct system and producing a reliable, efficient version that will be operationally effective and will be accepted by the intended users.

RGG: A general GUI Framework for R scripts

PubMed Central

Visne, Ilhami; Dilaveroglu, Erkan; Vierlinger, Klemens; Lauss, Martin; Yildiz, Ahmet; Weinhaeusel, Andreas; Noehammer, Christa; Leisch, Friedrich; Kriegner, Albert

2009-01-01

Background R is the leading open source statistics software with a vast number of biostatistical and bioinformatical analysis packages. To exploit the advantages of R, extensive scripting/programming skills are required. Results We have developed a software tool called R GUI Generator (RGG) which enables the easy generation of Graphical User Interfaces (GUIs) for the programming language R by adding a few Extensible Markup Language (XML) – tags. RGG consists of an XML-based GUI definition language and a Java-based GUI engine. GUIs are generated in runtime from defined GUI tags that are embedded into the R script. User-GUI input is returned to the R code and replaces the XML-tags. RGG files can be developed using any text editor. The current version of RGG is available as a stand-alone software (RGGRunner) and as a plug-in for JGR. Conclusion RGG is a general GUI framework for R that has the potential to introduce R statistics (R packages, built-in functions and scripts) to users with limited programming skills and helps to bridge the gap between R developers and GUI-dependent users. RGG aims to abstract the GUI development from individual GUI toolkits by using an XML-based GUI definition language. Thus RGG can be easily integrated in any software. The RGG project further includes the development of a web-based repository for RGG-GUIs. RGG is an open source project licensed under the Lesser General Public License (LGPL) and can be downloaded freely at PMID:19254356

Proactive Security Testing and Fuzzing

NASA Astrophysics Data System (ADS)

Takanen, Ari

Software is bound to have security critical flaws, and no testing or code auditing can ensure that software is flaw-less. But software security testing requirements have improved radically during the past years, largely due to criticism from security conscious consumers and Enterprise customers. Whereas in the past, security flaws were taken for granted (and patches were quietly and humbly installed), they now are probably one of the most common reasons why people switch vendors or software providers. The maintenance costs from security updates often add to become one of the biggest cost items to large Enterprise users. Fortunately test automation techniques have also improved. Techniques like model-based testing (MBT) enable efficient generation of security tests that reach good confidence levels in discovering zero-day mistakes in software. This technique is called fuzzing.

User Interface Technology for Formal Specification Development

NASA Technical Reports Server (NTRS)

Lowry, Michael; Philpot, Andrew; Pressburger, Thomas; Underwood, Ian; Lum, Henry, Jr. (Technical Monitor)

1994-01-01

Formal specification development and modification are an essential component of the knowledge-based software life cycle. User interface technology is needed to empower end-users to create their own formal specifications. This paper describes the advanced user interface for AMPHION1 a knowledge-based software engineering system that targets scientific subroutine libraries. AMPHION is a generic, domain-independent architecture that is specialized to an application domain through a declarative domain theory. Formal specification development and reuse is made accessible to end-users through an intuitive graphical interface that provides semantic guidance in creating diagrams denoting formal specifications in an application domain. The diagrams also serve to document the specifications. Automatic deductive program synthesis ensures that end-user specifications are correctly implemented. The tables that drive AMPHION's user interface are automatically compiled from a domain theory; portions of the interface can be customized by the end-user. The user interface facilitates formal specification development by hiding syntactic details, such as logical notation. It also turns some of the barriers for end-user specification development associated with strongly typed formal languages into active sources of guidance, without restricting advanced users. The interface is especially suited for specification modification. AMPHION has been applied to the domain of solar system kinematics through the development of a declarative domain theory. Testing over six months with planetary scientists indicates that AMPHION's interactive specification acquisition paradigm enables users to develop, modify, and reuse specifications at least an order of magnitude more rapidly than manual program development.

Applications of artificial intelligence to space station and automated software techniques: High level robot command language

NASA Technical Reports Server (NTRS)

Mckee, James W.

1989-01-01

The objective is to develop a system that will allow a person not necessarily skilled in the art of programming robots to quickly and naturally create the necessary data and commands to enable a robot to perform a desired task. The system will use a menu driven graphical user interface. This interface will allow the user to input data to select objects to be moved. There will be an imbedded expert system to process the knowledge about objects and the robot to determine how they are to be moved. There will be automatic path planning to avoid obstacles in the work space and to create a near optimum path. The system will contain the software to generate the required robot instructions.

An intelligent maximum permissible exposure meter for safety assessments of laser radiation

NASA Astrophysics Data System (ADS)

Corder, D. A.; Evans, D. R.; Tyrer, J. R.

1996-09-01

There is frequently a need to make laser power or energy density measurements when determining whether radiation from a laser system exceeds the Maximum Permissible Exposure (MPE) as defined in BS EN 60825. This can be achieved using standard commercially available laser power or energy measurement equipment, but some of these have shortcomings when used in this application. Calculations must be performed by the user to compare the measured value to the MPE. The measurement and calculation procedure appears complex to the nonexpert who may be performing the assessment. A novel approach is described which uses purpose designed hardware and software to simplify the process. The hardware is optimized for measuring the relatively low powers associated with MPEs. The software runs on a Psion Series 3a palmtop computer. This reduces the cost and size of the system yet allows graphical and numerical presentation of data. Data output to other software running on PCs is also possible, enabling the instrument to be used as part of a quality system. Throughout the measurement process the opportunity for user error has been minimized by the hardware and software design.

BioSPICE: access to the most current computational tools for biologists.

PubMed

Garvey, Thomas D; Lincoln, Patrick; Pedersen, Charles John; Martin, David; Johnson, Mark

2003-01-01

The goal of the BioSPICE program is to create a framework that provides biologists access to the most current computational tools. At the program midpoint, the BioSPICE member community has produced a software system that comprises contributions from approximately 20 participating laboratories integrated under the BioSPICE Dashboard and a methodology for continued software integration. These contributed software modules are the BioSPICE Dashboard, a graphical environment that combines Open Agent Architecture and NetBeans software technologies in a coherent, biologist-friendly user interface. The current Dashboard permits data sources, models, simulation engines, and output displays provided by different investigators and running on different machines to work together across a distributed, heterogeneous network. Among several other features, the Dashboard enables users to create graphical workflows by configuring and connecting available BioSPICE components. Anticipated future enhancements to BioSPICE include a notebook capability that will permit researchers to browse and compile data to support model building, a biological model repository, and tools to support the development, control, and data reduction of wet-lab experiments. In addition to the BioSPICE software products, a project website supports information exchange and community building.

Section 508 Electronic Information Accessibility Requirements for Software Development

NASA Technical Reports Server (NTRS)

Ellis, Rebecca

2014-01-01

Section 508 Subpart B 1194.21 outlines requirements for operating system and software development in order to create a product that is accessible to users with various disabilities. This portion of Section 508 contains a variety of standards to enable those using assistive technology and with visual, hearing, cognitive and motor difficulties to access all information provided in software. The focus on requirements was limited to the Microsoft Windows® operating system as it is the predominant operating system used at this center. Compliance with this portion of the requirements can be obtained by integrating the requirements into the software development cycle early and by remediating issues in legacy software if possible. There are certain circumstances with software that may arise necessitating an exemption from these requirements, such as design or engineering software using dynamically changing graphics or numbers to convey information. These exceptions can be discussed with the Section 508 Coordinator and another method of accommodation used.

Addressing hypertext design and conversion issues

NASA Technical Reports Server (NTRS)

Glusko, Robert J.

1990-01-01

Hypertext is a network of information units connected by relational links. A hypertext system is a configuration of hardware and software that presents a hypertext to users and allows them to manage and access the information that it contains. Hypertext is also a user interface concept that closely supports the ways that people use printed information. Hypertext concepts encourage modularity and the elimination of redundancy in data bases because information can be stored only once but viewed in any appropriate context. Hypertext is such a hot idea because it is an enabling technology in that workstations and personal computers finally provide enough local processing power for hypertext user interfaces.

Brain Computer Interface on Track to Home.

PubMed

Miralles, Felip; Vargiu, Eloisa; Dauwalder, Stefan; Solà, Marc; Müller-Putz, Gernot; Wriessnegger, Selina C; Pinegger, Andreas; Kübler, Andrea; Halder, Sebastian; Käthner, Ivo; Martin, Suzanne; Daly, Jean; Armstrong, Elaine; Guger, Christoph; Hintermüller, Christoph; Lowish, Hannah

2015-01-01

The novel BackHome system offers individuals with disabilities a range of useful services available via brain-computer interfaces (BCIs), to help restore their independence. This is the time such technology is ready to be deployed in the real world, that is, at the target end users' home. This has been achieved by the development of practical electrodes, easy to use software, and delivering telemonitoring and home support capabilities which have been conceived, implemented, and tested within a user-centred design approach. The final BackHome system is the result of a 3-year long process involving extensive user engagement to maximize effectiveness, reliability, robustness, and ease of use of a home based BCI system. The system is comprised of ergonomic and hassle-free BCI equipment; one-click software services for Smart Home control, cognitive stimulation, and web browsing; and remote telemonitoring and home support tools to enable independent home use for nonexpert caregivers and users. BackHome aims to successfully bring BCIs to the home of people with limited mobility to restore their independence and ultimately improve their quality of life.

Brain Computer Interface on Track to Home

PubMed Central

Miralles, Felip; Dauwalder, Stefan; Müller-Putz, Gernot; Wriessnegger, Selina C.; Pinegger, Andreas; Kübler, Andrea; Halder, Sebastian; Käthner, Ivo; Guger, Christoph; Lowish, Hannah

2015-01-01

The novel BackHome system offers individuals with disabilities a range of useful services available via brain-computer interfaces (BCIs), to help restore their independence. This is the time such technology is ready to be deployed in the real world, that is, at the target end users' home. This has been achieved by the development of practical electrodes, easy to use software, and delivering telemonitoring and home support capabilities which have been conceived, implemented, and tested within a user-centred design approach. The final BackHome system is the result of a 3-year long process involving extensive user engagement to maximize effectiveness, reliability, robustness, and ease of use of a home based BCI system. The system is comprised of ergonomic and hassle-free BCI equipment; one-click software services for Smart Home control, cognitive stimulation, and web browsing; and remote telemonitoring and home support tools to enable independent home use for nonexpert caregivers and users. BackHome aims to successfully bring BCIs to the home of people with limited mobility to restore their independence and ultimately improve their quality of life. PMID:26167530

A user-friendly software package to ease the use of VIC hydrologic model for practitioners

NASA Astrophysics Data System (ADS)

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

2016-12-01

The VIC (Variable Infiltration Capacity) hydrologic and river routing model simulates the water and energy fluxes that occur near the land surface and provides users with useful information regarding the quantity and timing of available water at points of interest within the basin. However, despite its popularity (proved by numerous applications in the literature), its wider adoption is hampered by the considerable effort required to prepare model inputs; e.g., input files storing spatial information related to watershed topography, soil properties, and land cover. This study presents a user-friendly software package (named VIC Setup Toolkit) developed within the MATLAB (matrix laboratory) framework and accessible through an intuitive graphical user interface. The VIC Setup Toolkit enables users to navigate the model building process confidently through prompts and automation, with an intention to promote the use of the model for both practical and academic purposes. The automated processes include watershed delineation, climate and geographical input set-up, model parameter calibration, graph generation and output evaluation. We demonstrate the package's usefulness in various case studies with the American River, Oklahoma River, Feather River and Zambezi River basins.

Making Temporal Search More Central in Spatial Data Infrastructures

NASA Astrophysics Data System (ADS)

Corti, P.; Lewis, B.

2017-10-01

A temporally enabled Spatial Data Infrastructure (SDI) is a framework of geospatial data, metadata, users, and tools intended to provide an efficient and flexible way to use spatial information which includes the historical dimension. One of the key software components of an SDI is the catalogue service which is needed to discover, query, and manage the metadata. A search engine is a software system capable of supporting fast and reliable search, which may use any means necessary to get users to the resources they need quickly and efficiently. These techniques may include features such as full text search, natural language processing, weighted results, temporal search based on enrichment, visualization of patterns in distributions of results in time and space using temporal and spatial faceting, and many others. In this paper we will focus on the temporal aspects of search which include temporal enrichment using a time miner - a software engine able to search for date components within a larger block of text, the storage of time ranges in the search engine, handling historical dates, and the use of temporal histograms in the user interface to display the temporal distribution of search results.

A software controllable modular RF signal generator with multichannel transmission capabilities.

PubMed

Shaw, Z; Feilner, W; Esser, B; Dickens, J C; Neuber, A A

2017-09-01

A software controllable system which generates and transmits user defined RF signals is discussed. The system is implemented with multiple, modular transmitting channels that allow the user to easily replace parts such as amplifiers or antennas. Each channel is comprised of a data pattern generator (DPG), a digital to analog converter (DAC), a power amplifier, and a transmitting antenna. All channels are controlled through a host PC and synchronized through a master clock signal provided to each DAC by an external clock source. Signals to be transmitted are generated through the DPG control software on the PC or can be created by the user in a numerical computing environment. Three experiments are discussed using a two- and four-channel antenna array incorporating Chebyshev tapered TEM horn antennas. Transmitting distinct sets of nonperiodic bipolar impulses through each of the antennas in the array enabled synthesizing a sinusoidal signal of specific frequency in free space. Opposite to the standard phased array approach, each antenna radiates a distinctly different signal rather than the same signal simply phase shifted. The presented approach may be employed as a physical layer of encryption dependent on the position of the receiving antenna.

Automation and hypermedia technology applications

NASA Technical Reports Server (NTRS)

Jupin, Joseph H.; Ng, Edward W.; James, Mark L.

1993-01-01

This paper represents a progress report on HyLite (Hypermedia Library technology): a research and development activity to produce a versatile system as part of NASA's technology thrusts in automation, information sciences, and communications. HyLite can be used as a system or tool to facilitate the creation and maintenance of large distributed electronic libraries. The contents of such a library may be software components, hardware parts or designs, scientific data sets or databases, configuration management information, etc. Proliferation of computer use has made the diversity and quantity of information too large for any single user to sort, process, and utilize effectively. In response to this information deluge, we have created HyLite to enable the user to process relevant information into a more efficient organization for presentation, retrieval, and readability. To accomplish this end, we have incorporated various AI techniques into the HyLite hypermedia engine to facilitate parameters and properties of the system. The proposed techniques include intelligent searching tools for the libraries, intelligent retrievals, and navigational assistance based on user histories. HyLite itself is based on an earlier project, the Encyclopedia of Software Components (ESC) which used hypermedia to facilitate and encourage software reuse.

IDL Object Oriented Software for Hinode/XRT Image Analysis

NASA Astrophysics Data System (ADS)

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

2008-09-01

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

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

PubMed

Kumar, Sudhir; Stecher, Glen; Li, Michael; Knyaz, Christina; Tamura, Koichiro

2018-06-01

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

Automated Test for NASA CFS

NASA Technical Reports Server (NTRS)

McComas, David C.; Strege, Susanne L.; Carpenter, Paul B. Hartman, Randy

2015-01-01

The core Flight System (cFS) is a flight software (FSW) product line developed by the Flight Software Systems Branch (FSSB) at NASA's Goddard Space Flight Center (GSFC). The cFS uses compile-time configuration parameters to implement variable requirements to enable portability across embedded computing platforms and to implement different end-user functional needs. The verification and validation of these requirements is proving to be a significant challenge. This paper describes the challenges facing the cFS and the results of a pilot effort to apply EXB Solution's testing approach to the cFS applications.

Practical uses of SPFIT

NASA Astrophysics Data System (ADS)

Drouin, Brian J.

2017-10-01

Over twenty-five years ago, Herb Pickett introduced his quantum-mechanical fitting programs to the spectroscopic community. The utility and flexibility of the software has enabled a whole generation of spectroscopists to analyze both simple and complex spectra without having to write and compile their own code. Last year Stewart Novick provided a primer for the coming generation of users. This follow-on work will serve as a guide to intermediate and advanced usage of the software. It is meant to be used in concert with the online documentation as well as the spectral line catalog archive.

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

Chen, Yixing; Zhang, Jianshun; Pelken, Michael

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

Improved Open-Microphone Speech Recognition

NASA Astrophysics Data System (ADS)

Abrash, Victor

2002-12-01

Many current and future NASA missions make extreme demands on mission personnel both in terms of work load and in performing under difficult environmental conditions. In situations where hands are impeded or needed for other tasks, eyes are busy attending to the environment, or tasks are sufficiently complex that ease of use of the interface becomes critical, spoken natural language dialog systems offer unique input and output modalities that can improve efficiency and safety. They also offer new capabilities that would not otherwise be available. For example, many NASA applications require astronauts to use computers in micro-gravity or while wearing space suits. Under these circumstances, command and control systems that allow users to issue commands or enter data in hands-and eyes-busy situations become critical. Speech recognition technology designed for current commercial applications limits the performance of the open-ended state-of-the-art dialog systems being developed at NASA. For example, today's recognition systems typically listen to user input only during short segments of the dialog, and user input outside of these short time windows is lost. Mistakes detecting the start and end times of user utterances can lead to mistakes in the recognition output, and the dialog system as a whole has no way to recover from this, or any other, recognition error. Systems also often require the user to signal when that user is going to speak, which is impractical in a hands-free environment, or only allow a system-initiated dialog requiring the user to speak immediately following a system prompt. In this project, SRI has developed software to enable speech recognition in a hands-free, open-microphone environment, eliminating the need for a push-to-talk button or other signaling mechanism. The software continuously captures a user's speech and makes it available to one or more recognizers. By constantly monitoring and storing the audio stream, it provides the spoken dialog manager extra flexibility to recognize the signal with no audio gaps between recognition requests, as well as to rerecognize portions of the signal, or to rerecognize speech with different grammars, acoustic models, recognizers, start times, and so on. SRI expects that this new open-mic functionality will enable NASA to develop better error-correction mechanisms for spoken dialog systems, and may also enable new interaction strategies.

Improved Open-Microphone Speech Recognition

NASA Technical Reports Server (NTRS)

Abrash, Victor

2002-01-01

Many current and future NASA missions make extreme demands on mission personnel both in terms of work load and in performing under difficult environmental conditions. In situations where hands are impeded or needed for other tasks, eyes are busy attending to the environment, or tasks are sufficiently complex that ease of use of the interface becomes critical, spoken natural language dialog systems offer unique input and output modalities that can improve efficiency and safety. They also offer new capabilities that would not otherwise be available. For example, many NASA applications require astronauts to use computers in micro-gravity or while wearing space suits. Under these circumstances, command and control systems that allow users to issue commands or enter data in hands-and eyes-busy situations become critical. Speech recognition technology designed for current commercial applications limits the performance of the open-ended state-of-the-art dialog systems being developed at NASA. For example, today's recognition systems typically listen to user input only during short segments of the dialog, and user input outside of these short time windows is lost. Mistakes detecting the start and end times of user utterances can lead to mistakes in the recognition output, and the dialog system as a whole has no way to recover from this, or any other, recognition error. Systems also often require the user to signal when that user is going to speak, which is impractical in a hands-free environment, or only allow a system-initiated dialog requiring the user to speak immediately following a system prompt. In this project, SRI has developed software to enable speech recognition in a hands-free, open-microphone environment, eliminating the need for a push-to-talk button or other signaling mechanism. The software continuously captures a user's speech and makes it available to one or more recognizers. By constantly monitoring and storing the audio stream, it provides the spoken dialog manager extra flexibility to recognize the signal with no audio gaps between recognition requests, as well as to rerecognize portions of the signal, or to rerecognize speech with different grammars, acoustic models, recognizers, start times, and so on. SRI expects that this new open-mic functionality will enable NASA to develop better error-correction mechanisms for spoken dialog systems, and may also enable new interaction strategies.

cisTEM, user-friendly software for single-particle image processing.

PubMed

Grant, Timothy; Rohou, Alexis; Grigorieff, Nikolaus

2018-03-07

We have developed new open-source software called cis TEM (computational imaging system for transmission electron microscopy) for the processing of data for high-resolution electron cryo-microscopy and single-particle averaging. cis TEM features a graphical user interface that is used to submit jobs, monitor their progress, and display results. It implements a full processing pipeline including movie processing, image defocus determination, automatic particle picking, 2D classification, ab-initio 3D map generation from random parameters, 3D classification, and high-resolution refinement and reconstruction. Some of these steps implement newly-developed algorithms; others were adapted from previously published algorithms. The software is optimized to enable processing of typical datasets (2000 micrographs, 200 k - 300 k particles) on a high-end, CPU-based workstation in half a day or less, comparable to GPU-accelerated processing. Jobs can also be scheduled on large computer clusters using flexible run profiles that can be adapted for most computing environments. cis TEM is available for download from cistem.org. © 2018, Grant et al.

Onyx-Advanced Aeropropulsion Simulation Framework Created

NASA Technical Reports Server (NTRS)

Reed, John A.

2001-01-01

The Numerical Propulsion System Simulation (NPSS) project at the NASA Glenn Research Center is developing a new software environment for analyzing and designing aircraft engines and, eventually, space transportation systems. Its purpose is to dramatically reduce the time, effort, and expense necessary to design and test jet engines by creating sophisticated computer simulations of an aerospace object or system (refs. 1 and 2). Through a university grant as part of that effort, researchers at the University of Toledo have developed Onyx, an extensible Java-based (Sun Micro-systems, Inc.), objectoriented simulation framework, to investigate how advanced software design techniques can be successfully applied to aeropropulsion system simulation (refs. 3 and 4). The design of Onyx's architecture enables users to customize and extend the framework to add new functionality or adapt simulation behavior as required. It exploits object-oriented technologies, such as design patterns, domain frameworks, and software components, to develop a modular system in which users can dynamically replace components with others having different functionality.

cisTEM, user-friendly software for single-particle image processing

PubMed Central

2018-01-01

We have developed new open-source software called cisTEM (computational imaging system for transmission electron microscopy) for the processing of data for high-resolution electron cryo-microscopy and single-particle averaging. cisTEM features a graphical user interface that is used to submit jobs, monitor their progress, and display results. It implements a full processing pipeline including movie processing, image defocus determination, automatic particle picking, 2D classification, ab-initio 3D map generation from random parameters, 3D classification, and high-resolution refinement and reconstruction. Some of these steps implement newly-developed algorithms; others were adapted from previously published algorithms. The software is optimized to enable processing of typical datasets (2000 micrographs, 200 k – 300 k particles) on a high-end, CPU-based workstation in half a day or less, comparable to GPU-accelerated processing. Jobs can also be scheduled on large computer clusters using flexible run profiles that can be adapted for most computing environments. cisTEM is available for download from cistem.org. PMID:29513216

Real-Time Spatio-Temporal Twice Whitening for MIMO Energy Detector

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

Humble, Travis S; Mitra, Pramita; Barhen, Jacob

2010-01-01

While many techniques exist for local spectrum sensing of a primary user, each represents a computationally demanding task to secondary user receivers. In software-defined radio, computational complexity lengthens the time for a cognitive radio to recognize changes in the transmission environment. This complexity is even more significant for spatially multiplexed receivers, e.g., in SIMO and MIMO, where the spatio-temporal data sets grow in size with the number of antennae. Limits on power and space for the processor hardware further constrain SDR performance. In this report, we discuss improvements in spatio-temporal twice whitening (STTW) for real-time local spectrum sensing by demonstratingmore » a form of STTW well suited for MIMO environments. We implement STTW on the Coherent Logix hx3100 processor, a multicore processor intended for low-power, high-throughput software-defined signal processing. These results demonstrate how coupling the novel capabilities of emerging multicore processors with algorithmic advances can enable real-time, software-defined processing of large spatio-temporal data sets.« less

Development of fuel oil management system software: Phase 1, Tank management module. Final report

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

Lange, H.B.; Baker, J.P.; Allen, D.

1992-01-01

The Fuel Oil Management System (FOMS) is a micro-computer based software system being developed to assist electric utilities that use residual fuel oils with oil purchase and end-use decisions. The Tank Management Module (TMM) is the first FOMS module to be produced. TMM enables the user to follow the mixing status of oils contained in a number of oil storage tanks. The software contains a computational model of residual fuel oil mixing which addresses mixing that occurs as one oil is added to another in a storage tank and also purposeful mixing of the tank by propellers, recirculation or convection.Themore » model also addresses the potential for sludge formation due to incompatibility of oils being mixed. Part 1 of the report presents a technical description of the mixing model and a description of its development. Steps followed in developing the mixing model included: (1) definition of ranges of oil properties and tank design factors used by utilities; (2) review and adaption of prior applicable work; (3) laboratory development; and (4) field verification. Also, a brief laboratory program was devoted to exploring the suitability of suggested methods for predicting viscosities, flash points and pour points of oil mixtures. Part 2 of the report presents a functional description of the TMM software and a description of its development. The software development program consisted of the following steps: (1) on-site interviews at utilities to prioritize needs and characterize user environments; (2) construction of the user interface; and (3) field testing the software.« less

Development of fuel oil management system software: Phase 1, Tank management module

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

Lange, H.B.; Baker, J.P.; Allen, D.

1992-01-01

The Fuel Oil Management System (FOMS) is a micro-computer based software system being developed to assist electric utilities that use residual fuel oils with oil purchase and end-use decisions. The Tank Management Module (TMM) is the first FOMS module to be produced. TMM enables the user to follow the mixing status of oils contained in a number of oil storage tanks. The software contains a computational model of residual fuel oil mixing which addresses mixing that occurs as one oil is added to another in a storage tank and also purposeful mixing of the tank by propellers, recirculation or convection.Themore » model also addresses the potential for sludge formation due to incompatibility of oils being mixed. Part 1 of the report presents a technical description of the mixing model and a description of its development. Steps followed in developing the mixing model included: (1) definition of ranges of oil properties and tank design factors used by utilities; (2) review and adaption of prior applicable work; (3) laboratory development; and (4) field verification. Also, a brief laboratory program was devoted to exploring the suitability of suggested methods for predicting viscosities, flash points and pour points of oil mixtures. Part 2 of the report presents a functional description of the TMM software and a description of its development. The software development program consisted of the following steps: (1) on-site interviews at utilities to prioritize needs and characterize user environments; (2) construction of the user interface; and (3) field testing the software.« less

The 4MOST facility control software

NASA Astrophysics Data System (ADS)

Pramskiy, Alexander; Mandel, Holger; Rothmaier, Florian; Stilz, Ingo; Winkler, Roland; Hahn, Thomas

2016-07-01

The 4-m Multi-Object Spectrographic Telescope (4MOST) is one high-resolution (R 18000) and two lowresolution (R fi 5000) spectrographs covering the wavelength range between 390 and 950 nm. The spectrographs will be installed on ESO VISTA telescope and will be fed by approximately 2400 fibres. The instrument is capable to simultaneously obtain spectra of about 2400 objects distributed over an hexagonal field-of-view of four square degrees. This paper aims at giving an overview of the control software design, which is based on the standard ESO VLT software architecture and customised to fit the needs of the 4MOST instrument. In particular, the facility control software is intended to arrange the precise positioning of the fibres, to schedule and observe many surveys in parallel, and to combine the output from the three spectrographs. Moreover, 4MOST's software will include user-friendly graphical user interfaces that enable users to interact with the facility control system and to monitor all data-taking and calibration tasks of the instrument. A secondary guiding system will be implemented to correct for any fibre exure and thus to improve 4MOST's guiding performance. The large amount of fibres requires the custom design of data exchange to avoid performance issues. The observation sequences are designed to use spectrographs in parallel with synchronous points for data exchange between subsystems. In order to control hardware devices, Programmable Logic Controller (PLC) components will be used, the new standard for future instruments at ESO.

DRIFTER Web App Development Support

NASA Technical Reports Server (NTRS)

Davis, Derrick D.; Armstrong, Curtis D.

2015-01-01

During my 2015 internship at Stennis Space Center (SSC) I supported the development of a web based tool to enable user interaction with a low-cost environmental monitoring buoy called the DRIFTER. DRIFTERs are designed by SSC's Applied Science and Technology Projects branch and are used to measure parameters such as water temperature and salinity. Data collected by the buoys help verify measurements by NASA satellites, which contributes to NASA's mission to advance understanding of the Earth by developing technologies to improve the quality of life on or home planet. My main objective during this internship was to support the development of the DRIFTER by writing web-based software that allows the public to view and access data collected by the buoys. In addition, this software would enable DRIFTER owners to configure and control the devices.

Basic Training

ERIC Educational Resources Information Center

Branzburg, Jeffrey

2006-01-01

In April 2006, Apple released a beta version of Boot Camp, a free software product that enables the installation of Windows XP (Home Edition or Professional with Service Pack 2) on an Intel-based Mac. (A beta version is not the final version, but it is ready for end users to try and test.) Essentially, Boot Camp splits your Mac into two hard…

DEVELOPMENT OF QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIPS (QSARS) TO PREDICT TOXICITY FOR A VARIETY OF HUMAN AND ECOLOGICAL ENDPOINTS

EPA Science Inventory

A web accessible software tool is being developed to predict the toxicity of unknown chemicals for a wide variety of endpoints. The tool will enable a user to easily predict the toxicity of a query compound by simply entering its structure in a 2-dimensional (2-D) chemical sketc...

Process and information integration via hypermedia

NASA Technical Reports Server (NTRS)

Hammen, David G.; Labasse, Daniel L.; Myers, Robert M.

1990-01-01

Success stories for advanced automation prototypes abound in the literature but the deployments of practical large systems are few in number. There are several factors that militate against the maturation of such prototypes into products. Here, the integration of advanced automation software into large systems is discussed. Advanced automation systems tend to be specific applications that need to be integrated and aggregated into larger systems. Systems integration can be achieved by providing expert user-developers with verified tools to efficiently create small systems that interface to large systems through standard interfaces. The use of hypermedia as such a tool in the context of the ground control centers that support Shuttle and space station operations is explored. Hypermedia can be an integrating platform for data, conventional software, and advanced automation software, enabling data integration through the display of diverse types of information and through the creation of associative links between chunks of information. Further, hypermedia enables process integration through graphical invoking of system functions. Through analysis and examples, researchers illustrate how diverse information and processing paradigms can be integrated into a single software platform.

The ESGF Software Stack: a Configurable and Extensible Framework for Enabling Access to Geospatial Data

NASA Astrophysics Data System (ADS)

Cinquini, L.; Bell, G. M.; Williams, D.; Harney, J.

2012-12-01

The Earth System Grid Federation (ESGF) is a multi-agency, international collaboration that aims at developing state-of-the-art services for the management and access of Earth system data. ESGF is currently used to serve the totality of the model output used for the forthcoming IPCC 5th assessment report on climate change, as well as supporting observational and reanalysis datasets. Also, it is been adopted by several other projects that focus on global, regional and local climate modeling. The ESGF software stack is composed of several modular applications that cover related but disjoint areas of functionality: data publishing, data search and discovery, data access, user management, security, and federation. Overall, the ESGF infrastructure offers a configurable end-to-end solution to the problem of enabling web-based access to large amounts of geospatial data. This talk will present the architectural and configuration options that are available to a data provider leveraging ESGF to serve their data: which services to expose, how to scale to larger data collections, how to establish access control, how to customize the user interface, and others. Additionally, the framework provides extension points that allow each site to plug in custom functionality such as crawling of specific metadata repositories, exposing domain-specific analysis and visualization services, developing custom access clients that interact with the system APIs. These configuration and extension capabilities are based on simple but effective domain-specific object models, that underpin the software applications: the data model, the security model, and the federation model. The ESGF software stack is developed collaboratively by software engineers at many institutions around the world, and is made freely available to the community under an open source license to promote adoption, reuse, inspection and continuous improvement.

Instrumentino: An Open-Source Software for Scientific Instruments.

PubMed

Koenka, Israel Joel; Sáiz, Jorge; Hauser, Peter C

2015-01-01

Scientists often need to build dedicated computer-controlled experimental systems. For this purpose, it is becoming common to employ open-source microcontroller platforms, such as the Arduino. These boards and associated integrated software development environments provide affordable yet powerful solutions for the implementation of hardware control of transducers and acquisition of signals from detectors and sensors. It is, however, a challenge to write programs that allow interactive use of such arrangements from a personal computer. This task is particularly complex if some of the included hardware components are connected directly to the computer and not via the microcontroller. A graphical user interface framework, Instrumentino, was therefore developed to allow the creation of control programs for complex systems with minimal programming effort. By writing a single code file, a powerful custom user interface is generated, which enables the automatic running of elaborate operation sequences and observation of acquired experimental data in real time. The framework, which is written in Python, allows extension by users, and is made available as an open source project.

Activity Catalog Tool (ACT) user manual, version 2.0

NASA Technical Reports Server (NTRS)

Segal, Leon D.; Andre, Anthony D.

1994-01-01

This report comprises the user manual for version 2.0 of the Activity Catalog Tool (ACT) software program, developed by Leon D. Segal and Anthony D. Andre in cooperation with NASA Ames Aerospace Human Factors Research Division, FLR branch. ACT is a software tool for recording and analyzing sequences of activity over time that runs on the Macintosh platform. It was designed as an aid for professionals who are interested in observing and understanding human behavior in field settings, or from video or audio recordings of the same. Specifically, the program is aimed at two primary areas of interest: human-machine interactions and interactions between humans. The program provides a means by which an observer can record an observed sequence of events, logging such parameters as frequency and duration of particular events. The program goes further by providing the user with a quantified description of the observed sequence, through application of a basic set of statistical routines, and enables merging and appending of several files and more extensive analysis of the resultant data.

The National Solar Permitting Database

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

Gunderson, Renic

"The soft costs of solar — costs not associated with hardware — remain stubbornly high. Among the biggest soft costs are those associated with inefficiencies in local permitting and inspection. A study by the National Renewable Energy Laboratory and Lawrence Berkeley National Laboratory estimates that these costs add an average of $0.22/W per residential installation. This project helps reduce non-hardware/balance of system (BOS) costs by creating and maintaining a free and available site of permitting requirements and solar system verification software that installers can use to reduce time, capital, and resource investments in tracking permitting requirements. Software tools to identifymore » best permitting practices can enable government stakeholders to optimize their permitting process and remove superfluous costs and requirements. Like ""a Wikipedia for solar permitting"", users can add, edit, delete, and update information for a given jurisdiction. We incentivize this crowdsourcing approach by recognizing users for their contributions in the form of SEO benefits to their company or organization by linking back to users' websites."« less

TADPLOT program, version 2.0: User's guide

NASA Technical Reports Server (NTRS)

Hammond, Dana P.

1991-01-01

The TADPLOT Program, Version 2.0 is described. The TADPLOT program is a software package coordinated by a single, easy-to-use interface, enabling the researcher to access several standard file formats, selectively collect specific subsets of data, and create full-featured publication and viewgraph quality plots. The user-interface was designed to be independent from any file format, yet provide capabilities to accommodate highly specialized data queries. Integrated with an applications software network, data can be assessed, collected, and viewed quickly and easily. Since the commands are data independent, subsequent modifications to the file format will be transparent, while additional file formats can be integrated with minimal impact on the user-interface. The graphical capabilities are independent of the method of data collection; thus, the data specification and subsequent plotting can be modified and upgraded as separate functional components. The graphics kernel selected adheres to the full functional specifications of the CORE standard. Both interface and postprocessing capabilities are fully integrated into TADPLOT.

Write, read and answer emails with a dry 'n' wireless brain-computer interface system.

PubMed

Pinegger, Andreas; Deckert, Lisa; Halder, Sebastian; Barry, Norbert; Faller, Josef; Käthner, Ivo; Hintermüller, Christoph; Wriessnegger, Selina C; Kübler, Andrea; Müller-Putz, Gernot R

2014-01-01

Brain-computer interface (BCI) users can control very complex applications such as multimedia players or even web browsers. Therefore, different biosignal acquisition systems are available to noninvasively measure the electrical activity of the brain, the electroencephalogram (EEG). To make BCIs more practical, hardware and software are nowadays designed more user centered and user friendly. In this paper we evaluated one of the latest innovations in the area of BCI: A wireless EEG amplifier with dry electrode technology combined with a web browser which enables BCI users to use standard webmail. With this system ten volunteers performed a daily life task: Write, read and answer an email. Experimental results of this study demonstrate the power of the introduced BCI system.

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.

PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis.

PubMed

Scheltema, Richard A; Jankevics, Andris; Jansen, Ritsert C; Swertz, Morris A; Breitling, Rainer

2011-04-01

The recent proliferation of high-resolution mass spectrometers has generated a wealth of new data analysis methods. However, flexible integration of these methods into configurations best suited to the research question is hampered by heterogeneous file formats and monolithic software development. The mzXML, mzData, and mzML file formats have enabled uniform access to unprocessed raw data. In this paper we present our efforts to produce an equally simple and powerful format, PeakML, to uniformly exchange processed intermediary and result data. To demonstrate the versatility of PeakML, we have developed an open source Java toolkit for processing, filtering, and annotating mass spectra in a customizable pipeline (mzMatch), as well as a user-friendly data visualization environment (PeakML Viewer). The PeakML format in particular enables the flexible exchange of processed data between software created by different groups or companies, as we illustrate by providing a PeakML-based integration of the widely used XCMS package with mzMatch data processing tools. As an added advantage, downstream analysis can benefit from direct access to the full mass trace information underlying summarized mass spectrometry results, providing the user with the means to rapidly verify results. The PeakML/mzMatch software is freely available at http://mzmatch.sourceforge.net, with documentation, tutorials, and a community forum.

Development of Hardware-in-the-Loop Simulation Based on Gazebo and Pixhawk for Unmanned Aerial Vehicles

NASA Astrophysics Data System (ADS)

Nguyen, Khoa Dang; Ha, Cheolkeun

2018-04-01

Hardware-in-the-loop simulation (HILS) is well known as an effective approach in the design of unmanned aerial vehicles (UAV) systems, enabling engineers to test the control algorithm on a hardware board with a UAV model on the software. Performance of HILS is determined by performances of the control algorithm, the developed model, and the signal transfer between the hardware and software. The result of HILS is degraded if any signal could not be transferred to the correct destination. Therefore, this paper aims to develop a middleware software to secure communications in HILS system for testing the operation of a quad-rotor UAV. In our HILS, the Gazebo software is used to generate a nonlinear six-degrees-of-freedom (6DOF) model, sensor model, and 3D visualization for the quad-rotor UAV. Meanwhile, the flight control algorithm is designed and implemented on the Pixhawk hardware. New middleware software, referred to as the control application software (CAS), is proposed to ensure the connection and data transfer between Gazebo and Pixhawk using the multithread structure in Qt Creator. The CAS provides a graphical user interface (GUI), allowing the user to monitor the status of packet transfer, and perform the flight control commands and the real-time tuning parameters for the quad-rotor UAV. Numerical implementations have been performed to prove the effectiveness of the middleware software CAS suggested in this paper.

Open-Source Software in Computational Research: A Case Study

DOE PAGES

Syamlal, Madhava; O'Brien, Thomas J.; Benyahia, Sofiane; ...

2008-01-01

A case study of open-source (OS) development of the computational research software MFIX, used for multiphase computational fluid dynamics simulations, is presented here. The verification and validation steps required for constructing modern computational software and the advantages of OS development in those steps are discussed. The infrastructure used for enabling the OS development of MFIX is described. The impact of OS development on computational research and education in gas-solids flow, as well as the dissemination of information to other areas such as geophysical and volcanology research, is demonstrated. This study shows that the advantages of OS development were realized inmore » the case of MFIX: verification by many users, which enhances software quality; the use of software as a means for accumulating and exchanging information; the facilitation of peer review of the results of computational research.« less

Agile data management for curation of genomes to watershed datasets

NASA Astrophysics Data System (ADS)

Varadharajan, C.; Agarwal, D.; Faybishenko, B.; Versteeg, R.

2015-12-01

A software platform is being developed for data management and assimilation [DMA] as part of the U.S. Department of Energy's Genomes to Watershed Sustainable Systems Science Focus Area 2.0. The DMA components and capabilities are driven by the project science priorities and the development is based on agile development techniques. The goal of the DMA software platform is to enable users to integrate and synthesize diverse and disparate field, laboratory, and simulation datasets, including geological, geochemical, geophysical, microbiological, hydrological, and meteorological data across a range of spatial and temporal scales. The DMA objectives are (a) developing an integrated interface to the datasets, (b) storing field monitoring data, laboratory analytical results of water and sediments samples collected into a database, (c) providing automated QA/QC analysis of data and (d) working with data providers to modify high-priority field and laboratory data collection and reporting procedures as needed. The first three objectives are driven by user needs, while the last objective is driven by data management needs. The project needs and priorities are reassessed regularly with the users. After each user session we identify development priorities to match the identified user priorities. For instance, data QA/QC and collection activities have focused on the data and products needed for on-going scientific analyses (e.g. water level and geochemistry). We have also developed, tested and released a broker and portal that integrates diverse datasets from two different databases used for curation of project data. The development of the user interface was based on a user-centered design process involving several user interviews and constant interaction with data providers. The initial version focuses on the most requested feature - i.e. finding the data needed for analyses through an intuitive interface. Once the data is found, the user can immediately plot and download data through the portal. The resulting product has an interface that is more intuitive and presents the highest priority datasets that are needed by the users. Our agile approach has enabled us to build a system that is keeping pace with the science needs while utilizing limited resources.

Space Images for NASA JPL Android Version

NASA Technical Reports Server (NTRS)

Nelson, Jon D.; Gutheinz, Sandy C.; Strom, Joshua R.; Arca, Jeremy M.; Perez, Martin; Boggs, Karen; Stanboli, Alice

2013-01-01

This software addresses the demand for easily accessible NASA JPL images and videos by providing a user friendly and simple graphical user interface that can be run via the Android platform from any location where Internet connection is available. This app is complementary to the iPhone version of the application. A backend infrastructure stores, tracks, and retrieves space images from the JPL Photojournal and Institutional Communications Web server, and catalogs the information into a streamlined rating infrastructure. This system consists of four distinguishing components: image repository, database, server-side logic, and Android mobile application. The image repository contains images from various JPL flight projects. The database stores the image information as well as the user rating. The server-side logic retrieves the image information from the database and categorizes each image for display. The Android mobile application is an interfacing delivery system that retrieves the image information from the server for each Android mobile device user. Also created is a reporting and tracking system for charting and monitoring usage. Unlike other Android mobile image applications, this system uses the latest emerging technologies to produce image listings based directly on user input. This allows for countless combinations of images returned. The backend infrastructure uses industry-standard coding and database methods, enabling future software improvement and technology updates. The flexibility of the system design framework permits multiple levels of display possibilities and provides integration capabilities. Unique features of the software include image/video retrieval from a selected set of categories, image Web links that can be shared among e-mail users, sharing to Facebook/Twitter, marking as user's favorites, and image metadata searchable for instant results.

JHelioviewer: Open-Source Software for Discovery and Image Access in the Petabyte Age

NASA Astrophysics Data System (ADS)

Mueller, D.; Dimitoglou, G.; Garcia Ortiz, J.; Langenberg, M.; Nuhn, M.; Dau, A.; Pagel, S.; Schmidt, L.; Hughitt, V. K.; Ireland, J.; Fleck, B.

2011-12-01

The unprecedented torrent of data returned by the Solar Dynamics Observatory is both a blessing and a barrier: a blessing for making available data with significantly higher spatial and temporal resolution, but a barrier for scientists to access, browse and analyze them. With such staggering data volume, the data is accessible only from a few repositories and users have to deal with data sets effectively immobile and practically difficult to download. From a scientist's perspective this poses three challenges: accessing, browsing and finding interesting data while avoiding the proverbial search for a needle in a haystack. To address these challenges, we have developed JHelioviewer, an open-source visualization software that lets users browse large data volumes both as still images and movies. We did so by deploying an efficient image encoding, storage, and dissemination solution using the JPEG 2000 standard. This solution enables users to access remote images at different resolution levels as a single data stream. Users can view, manipulate, pan, zoom, and overlay JPEG 2000 compressed data quickly, without severe network bandwidth penalties. Besides viewing data, the browser provides third-party metadata and event catalog integration to quickly locate data of interest, as well as an interface to the Virtual Solar Observatory to download science-quality data. As part of the ESA/NASA Helioviewer Project, JHelioviewer offers intuitive ways to browse large amounts of heterogeneous data remotely and provides an extensible and customizable open-source platform for the scientific community. In addition, the easy-to-use graphical user interface enables the general public and educators to access, enjoy and reuse data from space missions without barriers.

Planning of electroporation-based treatments using Web-based treatment-planning software.

PubMed

Pavliha, Denis; Kos, Bor; Marčan, Marija; Zupanič, Anže; Serša, Gregor; Miklavčič, Damijan

2013-11-01

Electroporation-based treatment combining high-voltage electric pulses and poorly permanent cytotoxic drugs, i.e., electrochemotherapy (ECT), is currently used for treating superficial tumor nodules by following standard operating procedures. Besides ECT, another electroporation-based treatment, nonthermal irreversible electroporation (N-TIRE), is also efficient at ablating deep-seated tumors. To perform ECT or N-TIRE of deep-seated tumors, following standard operating procedures is not sufficient and patient-specific treatment planning is required for successful treatment. Treatment planning is required because of the use of individual long-needle electrodes and the diverse shape, size and location of deep-seated tumors. Many institutions that already perform ECT of superficial metastases could benefit from treatment-planning software that would enable the preparation of patient-specific treatment plans. To this end, we have developed a Web-based treatment-planning software for planning electroporation-based treatments that does not require prior engineering knowledge from the user (e.g., the clinician). The software includes algorithms for automatic tissue segmentation and, after segmentation, generation of a 3D model of the tissue. The procedure allows the user to define how the electrodes will be inserted. Finally, electric field distribution is computed, the position of electrodes and the voltage to be applied are optimized using the 3D model and a downloadable treatment plan is made available to the user.

BEST Winery Guidebook: Benchmarking and Energy and Water SavingsTool for the Wine Industry

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

Galitsky, Christina; Worrell, Ernst; Radspieler, Anthony

2005-10-15

Not all industrial facilities have the staff or the opportunity to perform a detailed audit of their operations. The lack of knowledge of energy efficiency opportunities provides an important barrier to improving efficiency. Benchmarking has demonstrated to help energy users understand energy use and the potential for energy efficiency improvement, reducing the information barrier. In California, the wine making industry is not only one of the economic pillars of the economy; it is also a large energy consumer, with a considerable potential for energy-efficiency improvement. Lawrence Berkeley National Laboratory and Fetzer Vineyards developed an integrated benchmarking and self-assessment tool formore » the California wine industry called ''BEST''(Benchmarking and Energy and water Savings Tool) Winery. BEST Winery enables a winery to compare its energy efficiency to a best practice winery, accounting for differences in product mix and other characteristics of the winery. The tool enables the user to evaluate the impact of implementing energy and water efficiency measures. The tool facilitates strategic planning of efficiency measures, based on the estimated impact of the measures, their costs and savings. BEST Winery is available as a software tool in an Excel environment. This report serves as background material, documenting assumptions and information on the included energy and water efficiency measures. It also serves as a user guide for the software package.« less

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

PubMed Central

2011-01-01

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

Water Quality Analysis Tool (WQAT) | Science Inventory | US ...

EPA Pesticide Factsheets

The purpose of the Water Quality Analysis Tool (WQAT) software is to provide a means for analyzing and producing useful remotely sensed data products for an entire estuary, a particular point or area of interest (AOI or POI) in estuaries, or water bodies of interest where pre-processed and geographically gridded remotely sensed images are available. A graphical user interface (GUI), was created to enable the user to select and display imagery from a variety of remote sensing data sources. The user can select a date (or date range) and location to extract pixels from the remotely sensed imagery. The GUI is used to obtain all available pixel values (i.e. pixel from all available bands of all available satellites) for a given location on a given date and time. The resultant data set can be analyzed or saved to a file for future use. The WQAT software provides users with a way to establish algorithms between remote sensing reflectance (Rrs) and any available in situ parameters, as well as statistical and regression analysis. The combined data sets can be used to improve water quality research and studies. Satellites provide spatially synoptic data at high frequency (daily to weekly). These characteristics are desirable for supplementing existing water quality observations and for providing information for large aquatic ecosystems that are historically under-sampled by field programs. Thus, the Water Quality Assessment Tool (WQAT) software tool was developed to suppo

A gesture-controlled projection display for CT-guided interventions.

PubMed

Mewes, A; Saalfeld, P; Riabikin, O; Skalej, M; Hansen, C

2016-01-01

The interaction with interventional imaging systems within a sterile environment is a challenging task for physicians. Direct physician-machine interaction during an intervention is rather limited because of sterility and workspace restrictions. We present a gesture-controlled projection display that enables a direct and natural physician-machine interaction during computed tomography (CT)-based interventions. Therefore, a graphical user interface is projected on a radiation shield located in front of the physician. Hand gestures in front of this display are captured and classified using a leap motion controller. We propose a gesture set to control basic functions of intervention software such as gestures for 2D image exploration, 3D object manipulation and selection. Our methods were evaluated in a clinically oriented user study with 12 participants. The results of the performed user study confirm that the display and the underlying interaction concept are accepted by clinical users. The recognition of the gestures is robust, although there is potential for improvements. The gesture training times are less than 10 min, but vary heavily between the participants of the study. The developed gestures are connected logically to the intervention software and intuitive to use. The proposed gesture-controlled projection display counters current thinking, namely it gives the radiologist complete control of the intervention software. It opens new possibilities for direct physician-machine interaction during CT-based interventions and is well suited to become an integral part of future interventional suites.

P-MartCancer–Interactive Online Software to Enable Analysis of Shotgun Cancer Proteomic Datasets

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

Webb-Robertson, Bobbie-Jo M.; Bramer, Lisa M.; Jensen, Jeffrey L.

P-MartCancer is a new interactive web-based software environment that enables biomedical and biological scientists to perform in-depth analyses of global proteomics data without requiring direct interaction with the data or with statistical software. P-MartCancer offers a series of statistical modules associated with quality assessment, peptide and protein statistics, protein quantification and exploratory data analyses driven by the user via customized workflows and interactive visualization. Currently, P-MartCancer offers access to multiple cancer proteomic datasets generated through the Clinical Proteomics Tumor Analysis Consortium (CPTAC) at the peptide, gene and protein levels. P-MartCancer is deployed using Azure technologies (http://pmart.labworks.org/cptac.html), the web-service is alternativelymore » available via Docker Hub (https://hub.docker.com/r/pnnl/pmart-web/) and many statistical functions can be utilized directly from an R package available on GitHub (https://github.com/pmartR).« less

Algorithm-Based Fault Tolerance for Numerical Subroutines

NASA Technical Reports Server (NTRS)

Tumon, Michael; Granat, Robert; Lou, John

2007-01-01

A software library implements a new methodology of detecting faults in numerical subroutines, thus enabling application programs that contain the subroutines to recover transparently from single-event upsets. The software library in question is fault-detecting middleware that is wrapped around the numericalsubroutines. Conventional serial versions (based on LAPACK and FFTW) and a parallel version (based on ScaLAPACK) exist. The source code of the application program that contains the numerical subroutines is not modified, and the middleware is transparent to the user. The methodology used is a type of algorithm- based fault tolerance (ABFT). In ABFT, a checksum is computed before a computation and compared with the checksum of the computational result; an error is declared if the difference between the checksums exceeds some threshold. Novel normalization methods are used in the checksum comparison to ensure correct fault detections independent of algorithm inputs. In tests of this software reported in the peer-reviewed literature, this library was shown to enable detection of 99.9 percent of significant faults while generating no false alarms.

A cloud-based semantic wiki for user training in healthcare process management.

PubMed

Papakonstantinou, D; Poulymenopoulou, M; Malamateniou, F; Vassilacopoulos, G

2011-01-01

Successful healthcare process design requires active participation of users who are familiar with the cooperative and collaborative nature of healthcare delivery, expressed in terms of healthcare processes. Hence, a reusable, flexible, agile and adaptable training material is needed with the objective to enable users instill their knowledge and expertise in healthcare process management and (re)configuration activities. To this end, social software, such as a wiki, could be used as it supports cooperation and collaboration anytime, anywhere and combined with semantic web technology that enables structuring pieces of information for easy retrieval, reuse and exchange between different systems and tools. In this paper a semantic wiki is presented as a means for developing training material for healthcare providers regarding healthcare process management. The semantic wiki should act as a collective online memory containing training material that is accessible to authorized users, thus enhancing the training process with collaboration and cooperation capabilities. It is proposed that the wiki is stored in a secure virtual private cloud that is accessible from anywhere, be it an excessively open environment, while meeting the requirements of redundancy, high performance and autoscaling.

Genetic Constructor: An Online DNA Design Platform.

PubMed

Bates, Maxwell; Lachoff, Joe; Meech, Duncan; Zulkower, Valentin; Moisy, Anaïs; Luo, Yisha; Tekotte, Hille; Franziska Scheitz, Cornelia Johanna; Khilari, Rupal; Mazzoldi, Florencio; Chandran, Deepak; Groban, Eli

2017-12-15

Genetic Constructor is a cloud Computer Aided Design (CAD) application developed to support synthetic biologists from design intent through DNA fabrication and experiment iteration. The platform allows users to design, manage, and navigate complex DNA constructs and libraries, using a new visual language that focuses on functional parts abstracted from sequence. Features like combinatorial libraries and automated primer design allow the user to separate design from construction by focusing on functional intent, and design constraints aid iterative refinement of designs. A plugin architecture enables contributions from scientists and coders to leverage existing powerful software and connect to DNA foundries. The software is easily accessible and platform agnostic, free for academics, and available in an open-source community edition. Genetic Constructor seeks to democratize DNA design, manufacture, and access to tools and services from the synthetic biology community.

CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentation

PubMed Central

2013-01-01

The application of fluorescence microscopy in cell biology often generates a huge amount of imaging data. Automated whole cell segmentation of such data enables the detection and analysis of individual cells, where a manual delineation is often time consuming, or practically not feasible. Furthermore, compared to manual analysis, automation normally has a higher degree of reproducibility. CellSegm, the software presented in this work, is a Matlab based command line software toolbox providing an automated whole cell segmentation of images showing surface stained cells, acquired by fluorescence microscopy. It has options for both fully automated and semi-automated cell segmentation. Major algorithmic steps are: (i) smoothing, (ii) Hessian-based ridge enhancement, (iii) marker-controlled watershed segmentation, and (iv) feature-based classfication of cell candidates. Using a wide selection of image recordings and code snippets, we demonstrate that CellSegm has the ability to detect various types of surface stained cells in 3D. After detection and outlining of individual cells, the cell candidates can be subject to software based analysis, specified and programmed by the end-user, or they can be analyzed by other software tools. A segmentation of tissue samples with appropriate characteristics is also shown to be resolvable in CellSegm. The command-line interface of CellSegm facilitates scripting of the separate tools, all implemented in Matlab, offering a high degree of flexibility and tailored workflows for the end-user. The modularity and scripting capabilities of CellSegm enable automated workflows and quantitative analysis of microscopic data, suited for high-throughput image based screening. PMID:23938087

CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentation.

PubMed

Hodneland, Erlend; Kögel, Tanja; Frei, Dominik Michael; Gerdes, Hans-Hermann; Lundervold, Arvid

2013-08-09

: The application of fluorescence microscopy in cell biology often generates a huge amount of imaging data. Automated whole cell segmentation of such data enables the detection and analysis of individual cells, where a manual delineation is often time consuming, or practically not feasible. Furthermore, compared to manual analysis, automation normally has a higher degree of reproducibility. CellSegm, the software presented in this work, is a Matlab based command line software toolbox providing an automated whole cell segmentation of images showing surface stained cells, acquired by fluorescence microscopy. It has options for both fully automated and semi-automated cell segmentation. Major algorithmic steps are: (i) smoothing, (ii) Hessian-based ridge enhancement, (iii) marker-controlled watershed segmentation, and (iv) feature-based classfication of cell candidates. Using a wide selection of image recordings and code snippets, we demonstrate that CellSegm has the ability to detect various types of surface stained cells in 3D. After detection and outlining of individual cells, the cell candidates can be subject to software based analysis, specified and programmed by the end-user, or they can be analyzed by other software tools. A segmentation of tissue samples with appropriate characteristics is also shown to be resolvable in CellSegm. The command-line interface of CellSegm facilitates scripting of the separate tools, all implemented in Matlab, offering a high degree of flexibility and tailored workflows for the end-user. The modularity and scripting capabilities of CellSegm enable automated workflows and quantitative analysis of microscopic data, suited for high-throughput image based screening.

From a paper-based to an electronic registry in physiotherapy.

PubMed

Buyl, Ronald; Nyssen, Marc

2008-01-01

During the past decade the healthcare industry has evolved from paper-based storage of clinical data into the digital era. Electronic healthcare records play a crucial role to meet the growing need for integrated data-storage and data communication. In this context a new law was issued in Belgium on December 7th, 2005, which requires physiotherapists (but also nurses and speech therapists) to keep an electronic version of the registry. This (electronic) registry contains all physiotherapeutic acts, starting from January 1, 2007. Up until that day, a paper version of the registry had to be created every month.This article describes the development of an electronic version of the registry that not only meets all legal constraints, but also enables to verify the traceability and inalterability of the generated documents, by means of SHA-256 codes. One of the major concerns of the process was that the rationale behind the electronic registry would conform well to the common practice of the physiotherapist. Therefore we opted for a periodic recording of a standardized "image" of the controllable data, in the patient database of the software-system, into the XML registry messages. The proposed XSLT schema can also form a basis for the development of tools that can be used by the controlling authorities. Hopefully the electronic registry for physiotherapists will be a first step towards the future development of a fully integrated electronic physiotherapy record.By means of a certification procedure for the software systems, we succeeded in developing a user friendly system that enables end-users that use a quality labeled software package, to automatically produce all the legally necessary documents concerning the registry. Moreover, we hope that this development will be an incentive for non-users to start working in an electronic way.

The Nuclear Energy Advanced Modeling and Simulation Safeguards and Separations Reprocessing Plant Toolkit

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

McCaskey, Alex; Billings, Jay Jay; de Almeida, Valmor F

2011-08-01

This report details the progress made in the development of the Reprocessing Plant Toolkit (RPTk) for the DOE Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. RPTk is an ongoing development effort intended to provide users with an extensible, integrated, and scalable software framework for the modeling and simulation of spent nuclear fuel reprocessing plants by enabling the insertion and coupling of user-developed physicochemical modules of variable fidelity. The NEAMS Safeguards and Separations IPSC (SafeSeps) and the Enabling Computational Technologies (ECT) supporting program element have partnered to release an initial version of the RPTk with a focus on software usabilitymore » and utility. RPTk implements a data flow architecture that is the source of the system's extensibility and scalability. Data flows through physicochemical modules sequentially, with each module importing data, evolving it, and exporting the updated data to the next downstream module. This is accomplished through various architectural abstractions designed to give RPTk true plug-and-play capabilities. A simple application of this architecture, as well as RPTk data flow and evolution, is demonstrated in Section 6 with an application consisting of two coupled physicochemical modules. The remaining sections describe this ongoing work in full, from system vision and design inception to full implementation. Section 3 describes the relevant software development processes used by the RPTk development team. These processes allow the team to manage system complexity and ensure stakeholder satisfaction. This section also details the work done on the RPTk ``black box'' and ``white box'' models, with a special focus on the separation of concerns between the RPTk user interface and application runtime. Section 4 and 5 discuss that application runtime component in more detail, and describe the dependencies, behavior, and rigorous testing of its constituent components.« less

InSAR Scientific Computing Environment

NASA Astrophysics Data System (ADS)

Gurrola, E. M.; Rosen, P. A.; Sacco, G.; Zebker, H. A.; Simons, M.; Sandwell, D. T.

2010-12-01

The InSAR Scientific Computing Environment (ISCE) is a software development effort in its second year within the NASA Advanced Information Systems and Technology program. The ISCE will provide a new computing environment for geodetic image processing for InSAR sensors that will enable scientists to reduce measurements directly from radar satellites and aircraft to new geophysical products without first requiring them to develop detailed expertise in radar processing methods. The environment can serve as the core of a centralized processing center to bring Level-0 raw radar data up to Level-3 data products, but is adaptable to alternative processing approaches for science users interested in new and different ways to exploit mission data. The NRC Decadal Survey-recommended DESDynI mission will deliver data of unprecedented quantity and quality, making possible global-scale studies in climate research, natural hazards, and Earth's ecosystem. The InSAR Scientific Computing Environment is planned to become a key element in processing DESDynI data into higher level data products and it is expected to enable a new class of analyses that take greater advantage of the long time and large spatial scales of these new data, than current approaches. At the core of ISCE is both legacy processing software from the JPL/Caltech ROI_PAC repeat-pass interferometry package as well as a new InSAR processing package containing more efficient and more accurate processing algorithms being developed at Stanford for this project that is based on experience gained in developing processors for missions such as SRTM and UAVSAR. Around the core InSAR processing programs we are building object-oriented wrappers to enable their incorporation into a more modern, flexible, extensible software package that is informed by modern programming methods, including rigorous componentization of processing codes, abstraction and generalization of data models, and a robust, intuitive user interface with graduated exposure to the levels of sophistication, allowing novices to apply it readily for common tasks and experienced users to mine data with great facility and flexibility. The environment is designed to easily allow user contributions, enabling an open source community to extend the framework into the indefinite future. In this paper we briefly describe both the legacy and the new core processing algorithms and their integration into the new computing environment. We describe the ISCE component and application architecture and the features that permit the desired flexibility, extensibility and ease-of-use. We summarize the state of progress of the environment and the plans for completion of the environment and for its future introduction into the radar processing community.

Arrowland v1.0

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

BIRKEL, GARRETT; GARCIA MARTIN, HECTOR; MORRELL, WILLIAM

"Arrowland" is a web-based software application primarily for mapping, integrating and visualizing a variety of metabolism data of living organisms, including but not limited to metabolomics, proteomics, transcriptomics and fluxomics. This software application makes multi-omics data analysis intuitive and interactive. It improves data sharing and communication by enabling users to visualize their omics data using a web browser (on a PC or mobile device). It increases user's productivity by simplifying multi-omics data analysis using well developed maps as a guide. Users using this tool can gain insights into their data sets that would be difficult or even impossible to teasemore » out by looking at raw number, or using their currently existing toolchains to generate static single-use maps. Arrowland helps users save time by visualizing relative changes in different conditions or over time, and helps users to produce more significant insights faster. Preexisting maps decrease the learning curve for beginners in the omics field. Sets of multi-omics data are presented in the browser, as a two-dimensional flowchart resembling a map, with varying levels of detail information, based on the scaling of the map. Users can pan and zoom to explore different maps, compare maps, upload their own research data sets onto desired maps, alter map appearance in ways that facilitate interpretation, visualization and analysis of the given data, and export data, reports and actionable items to help the user initiative.« less

Distributing Data to Hand-Held Devices in a Wireless Network

NASA Technical Reports Server (NTRS)

Hodges, Mark; Simmons, Layne

2008-01-01

ADROIT is a developmental computer program for real-time distribution of complex data streams for display on Web-enabled, portable terminals held by members of an operational team of a spacecraft-command-and-control center who may be located away from the center. Examples of such terminals include personal data assistants, laptop computers, and cellular telephones. ADROIT would make it unnecessary to equip each terminal with platform- specific software for access to the data streams or with software that implements the information-sharing protocol used to deliver telemetry data to clients in the center. ADROIT is a combination of middleware plus software specific to the center. (Middleware enables one application program to communicate with another by performing such functions as conversion, translation, consolidation, and/or integration.) ADROIT translates a data stream (voice, video, or alphanumerical data) from the center into Extensible Markup Language, effectuates a subscription process to determine who gets what data when, and presents the data to each user in real time. Thus, ADROIT is expected to enable distribution of operations and to reduce the cost of operations by reducing the number of persons required to be in the center.

OpenSatKit Enables Quick Startup for CubeSat Missions

NASA Technical Reports Server (NTRS)

McComas, David; Melton, Ryan

2017-01-01

The software required to develop, integrate, and operate a spacecraft is substantial regardless of whether its a large or small satellite. Even getting started can be a monumental task. To solve this problem, NASAs Core Flight System (cFS), NASA's 42 spacecraft dynamics simulator, and Ball Aerospaces COSMOS ground system have been integrated together into a kit called OpenSatKit that provides a complete and open source software solution for starting a new satellite mission. Users can have a working system with flight software, dynamics simulation, and a ground command and control system up and running within hours.Every satellite mission requires three primary categories of software to function. The first is Flight Software (FSW) which provides the onboard control of the satellites and its payload(s). NASA's cFS provides a great platform for developing this software. Second, while developing a satellite on earth, it is necessary to simulate the satellites orbit, attitude, and actuators, to ensure that the systems that control these aspects will work correctly in the real environment. NASAs 42 simulator provides these functionalities. Finally, the ground has to be able to communicate with the satellite, monitor its performance and health, and display its data. Additionally, test scripts have to be written to verify the system on the ground. Ball Aerospace's COSMOS command and control system provides this functionality. Once the OpenSatKit is up and running, the next step is to customize the platform and get it running on the end target. Starting from a fully working system makes porting the cFS from Linux to a users platform much easier. An example Raspberry Pi target is included in the kit so users can gain experience working with a low cost hardware target. All users can benefit from OpenSatKit but the greatest impact and benefits will be to SmallSat missions with constrained budgets and small software teams. This paper describes OpenSatKits system design, the steps necessary to run the system to target the Raspberry Pi, and future plans. OpenSatKit is a free fully functional spacecraft software system that we hope will greatly benefit the SmallSat community.

The Australian SKA Pathfinder: operations management and user engagement

NASA Astrophysics Data System (ADS)

Harvey-Smith, Lisa

2016-07-01

This paper describes the science operations model for the Australian Square Kilometre Array Pathfinder (ASKAP) telescope. ASKAP is a radio interferometer currently being commissioned in Western Australia. It will be operated by a dedicated team of observatory staff with the support of telescope monitoring, control and scheduling software. These tools, as well as the proposal tools and data archive will enable the telescope to operate with little direct input from the astronomy user. The paper also discusses how close engagement with the telescope user community has been maintained throughout the ASKAP construction and commissioning phase, leading to positive outcomes including early input into the design of telescope systems and a vibrant early science program.

2001 Industry Studies: Information

DTIC Science & Technology

2001-01-01

increasingly demand communications, computers, and software for use in the Internet , intranets, and extranets. Information technology (IT) - enabled...As the number of Internet users increases, so does the demand for the rapid deployment of information and telecommunication technologies . The key...proliferation has become uncontrollable. Only then will the US maintain the lead in the IT market . 13 ESSAYS ON MAJOR ISSUES ISSUE: THE INFORMATION TECHNOLOGY

Pathway collages: personalized multi-pathway diagrams.

PubMed

Paley, Suzanne; O'Maille, Paul E; Weaver, Daniel; Karp, Peter D

2016-12-13

Metabolic pathway diagrams are a classical way of visualizing a linked cascade of biochemical reactions. However, to understand some biochemical situations, viewing a single pathway is insufficient, whereas viewing the entire metabolic network results in information overload. How do we enable scientists to rapidly construct personalized multi-pathway diagrams that depict a desired collection of interacting pathways that emphasize particular pathway interactions? We define software for constructing personalized multi-pathway diagrams called pathway-collages using a combination of manual and automatic layouts. The user specifies a set of pathways of interest for the collage from a Pathway/Genome Database. Layouts for the individual pathways are generated by the Pathway Tools software, and are sent to a Javascript Pathway Collage application implemented using Cytoscape.js. That application allows the user to re-position pathways; define connections between pathways; change visual style parameters; and paint metabolomics, gene expression, and reaction flux data onto the collage to obtain a desired multi-pathway diagram. We demonstrate the use of pathway collages in two application areas: a metabolomics study of pathogen drug response, and an Escherichia coli metabolic model. Pathway collages enable facile construction of personalized multi-pathway diagrams.

Web Program for Development of GUIs for Cluster Computers

NASA Technical Reports Server (NTRS)

Czikmantory, Akos; Cwik, Thomas; Klimeck, Gerhard; Hua, Hook; Oyafuso, Fabiano; Vinyard, Edward

2003-01-01

WIGLAF (a Web Interface Generator and Legacy Application Facade) is a computer program that provides a Web-based, distributed, graphical-user-interface (GUI) framework that can be adapted to any of a broad range of application programs, written in any programming language, that are executed remotely on any cluster computer system. WIGLAF enables the rapid development of a GUI for controlling and monitoring a specific application program running on the cluster and for transferring data to and from the application program. The only prerequisite for the execution of WIGLAF is a Web-browser program on a user's personal computer connected with the cluster via the Internet. WIGLAF has a client/server architecture: The server component is executed on the cluster system, where it controls the application program and serves data to the client component. The client component is an applet that runs in the Web browser. WIGLAF utilizes the Extensible Markup Language to hold all data associated with the application software, Java to enable platform-independent execution on the cluster system and the display of a GUI generator through the browser, and the Java Remote Method Invocation software package to provide simple, effective client/server networking.

Enhanced International Space Station Ku-Band Telemetry Service

NASA Technical Reports Server (NTRS)

Cecil, Andrew J.; Pitts, R. Lee; Welch, Steven J.; Bryan, Jason D.

2014-01-01

The International Space Station (ISS) is in an operational configuration. To fully utilize the ISS and take advantage of the modern protocols and updated Ku-band access, the Huntsville Operations Support Center (HOSC) has designed an approach to extend the Kuband forward link access for payload investigators to their on-orbit payloads. This dramatically increases the ground to ISS communications for those users. This access also enables the ISS flight controllers operating in the Payload Operations and Integration Center to have more direct control over the systems they are responsible for managing and operating. To extend the Ku-band forward link to the payload user community the development of a new command server is necessary. The HOSC subsystems were updated to process the Internet Protocol Encapsulated packets, enable users to use the service based on their approved services, and perform network address translation to insure that the packets are forwarded from the user to the correct payload repeating that process in reverse from ISS to the payload user. This paper presents the architecture, implementation, and lessons learned. This will include the integration of COTS hardware and software as well as how the device is incorporated into the operational mission of the ISS. Thus, this paper also discusses how this technology can be applicable to payload users of the ISS.

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.

APT: what it has enabled us to do

NASA Astrophysics Data System (ADS)

Blacker, Brett S.; Golombek, Daniel

2004-09-01

With the development and operations deployment of the Astronomer's Proposal Tool (APT), Hubble Space Telescope (HST) proposers have been provided with an integrated toolset for Phase I and Phase II. This toolset consists of editors for filling out proposal information, an Orbit Planner for determining observation feasibility, a Visit Planner for determining schedulability, diagnostic and reporting tools and an integrated Visual Target Tuner (VTT) for viewing exposure specifications. The VTT can also overlay HST"s field of view on user-selected Flexible Image Transport System (FITS) images, perform bright object checks and query the HST archive. In addition to these direct benefits for the HST user, STScI"s internal Phase I process has been able to take advantage of the APT products. APT has enabled a substantial streamlining of the process and software processing tools, which enabled a compression by three months of the Phase I to Phase II schedule, allowing to schedule observations earlier and thus further benefiting HST observers. Some of the improvements to our process include: creating a compact disk (CD) of Phase I products; being able to print all proposals on the day of the deadline; link the proposal in Portable Document Format (PDF) with a database, and being able to run all Phase I software on a single platform. In this paper we will discuss the operational results of using APT for HST's Cycles 12 and 13 Phase I process and will show the improvements for the users and the overall process that is allowing STScI to obtain scientific results with HST three months earlier than in previous years. We will also show how APT can be and is being used for multiple missions.

Unified Software Solution for Efficient SPR Data Analysis in Drug Research

PubMed Central

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

2016-01-01

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

Development of a Remote Accessibility Assessment System through three-dimensional reconstruction technology.

PubMed

Kim, Jong Bae; Brienza, David M

2006-01-01

A Remote Accessibility Assessment System (RAAS) that uses three-dimensional (3-D) reconstruction technology is being developed; it enables clinicians to assess the wheelchair accessibility of users' built environments from a remote location. The RAAS uses commercial software to construct 3-D virtualized environments from photographs. We developed custom screening algorithms and instruments for analyzing accessibility. Characteristics of the camera and 3-D reconstruction software chosen for the system significantly affect its overall reliability. In this study, we performed an accuracy assessment to verify that commercial hardware and software can construct accurate 3-D models by analyzing the accuracy of dimensional measurements in a virtual environment and a comparison of dimensional measurements from 3-D models created with four cameras/settings. Based on these two analyses, we were able to specify a consumer-grade digital camera and PhotoModeler (EOS Systems, Inc, Vancouver, Canada) software for this system. Finally, we performed a feasibility analysis of the system in an actual environment to evaluate its ability to assess the accessibility of a wheelchair user's typical built environment. The field test resulted in an accurate accessibility assessment and thus validated our system.

Netlib services and resources

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

Browne, S.V.; Green, S.C.; Moore, K.

1994-04-01

The Netlib repository, maintained by the University of Tennessee and Oak Ridge National Laboratory, contains freely available software, documents, and databases of interest to the numerical, scientific computing, and other communities. This report includes both the Netlib User`s Guide and the Netlib System Manager`s Guide, and contains information about Netlib`s databases, interfaces, and system implementation. The Netlib repository`s databases include the Performance Database, the Conferences Database, and the NA-NET mail forwarding and Whitepages Databases. A variety of user interfaces enable users to access the Netlib repository in the manner most convenient and compatible with their networking capabilities. These interfaces includemore » the Netlib email interface, the Xnetlib X Windows client, the netlibget command-line TCP/IP client, anonymous FTP, anonymous RCP, and gopher.« less

Opacplot2: Enabling tabulated EoS and opacity compatibility for HEDLP simulations with the FLASH code

NASA Astrophysics Data System (ADS)

Laune, Jordan; Tzeferacos, Petros; Feister, Scott; Fatenejad, Milad; Yurchak, Roman; Flocke, Norbert; Weide, Klaus; Lamb, Donald

2017-10-01

Thermodynamic and opacity properties of materials are necessary to accurately simulate laser-driven laboratory experiments. Such data are compiled in tabular format since the thermodynamic range that needs to be covered cannot be described with one single theoretical model. Moreover, tabulated data can be made available prior to runtime, reducing both compute cost and code complexity. This approach is employed by the FLASH code. Equation of state (EoS) and opacity data comes in various formats, matrix-layouts, and file-structures. We discuss recent developments on opacplot2, an open-source Python module that manipulates tabulated EoS and opacity data. We present software that builds upon opacplot2 and enables easy-to-use conversion of different table formats into the IONMIX format, the native tabular input used by FLASH. Our work enables FLASH users to take advantage of a wider range of accurate EoS and opacity tables in simulating HELP experiments at the National Laser User Facilities.

Multi-focus and multi-level techniques for visualization and analysis of networks with thematic data

NASA Astrophysics Data System (ADS)

Cossalter, Michele; Mengshoel, Ole J.; Selker, Ted

2013-01-01

Information-rich data sets bring several challenges in the areas of visualization and analysis, even when associated with node-link network visualizations. This paper presents an integration of multi-focus and multi-level techniques that enable interactive, multi-step comparisons in node-link networks. We describe NetEx, a visualization tool that enables users to simultaneously explore different parts of a network and its thematic data, such as time series or conditional probability tables. NetEx, implemented as a Cytoscape plug-in, has been applied to the analysis of electrical power networks, Bayesian networks, and the Enron e-mail repository. In this paper we briefly discuss visualization and analysis of the Enron social network, but focus on data from an electrical power network. Specifically, we demonstrate how NetEx supports the analytical task of electrical power system fault diagnosis. Results from a user study with 25 subjects suggest that NetEx enables more accurate isolation of complex faults compared to an especially designed software tool.

HashDist: Reproducible, Relocatable, Customizable, Cross-Platform Software Stacks for Open Hydrological Science

NASA Astrophysics Data System (ADS)

Ahmadia, A. J.; Kees, C. E.

2014-12-01

Developing scientific software is a continuous balance between not reinventing the wheel and getting fragile codes to interoperate with one another. Binary software distributions such as Anaconda provide a robust starting point for many scientific software packages, but this solution alone is insufficient for many scientific software developers. HashDist provides a critical component of the development workflow, enabling highly customizable, source-driven, and reproducible builds for scientific software stacks, available from both the IPython Notebook and the command line. To address these issues, the Coastal and Hydraulics Laboratory at the US Army Engineer Research and Development Center has funded the development of HashDist in collaboration with Simula Research Laboratories and the University of Texas at Austin. HashDist is motivated by a functional approach to package build management, and features intelligent caching of sources and builds, parametrized build specifications, and the ability to interoperate with system compilers and packages. HashDist enables the easy specification of "software stacks", which allow both the novice user to install a default environment and the advanced user to configure every aspect of their build in a modular fashion. As an advanced feature, HashDist builds can be made relocatable, allowing the easy redistribution of binaries on all three major operating systems as well as cloud, and supercomputing platforms. As a final benefit, all HashDist builds are reproducible, with a build hash specifying exactly how each component of the software stack was installed. This talk discusses the role of HashDist in the hydrological sciences, including its use by the Coastal and Hydraulics Laboratory in the development and deployment of the Proteus Toolkit as well as the Rapid Operational Access and Maneuver Support project. We demonstrate HashDist in action, and show how it can effectively support development, deployment, teaching, and reproducibility for scientists working in the hydrological sciences. The HashDist documentation is available from: http://hashdist.readthedocs.org/en/latest/ HashDist is currently hosted at: https://github.com/hashdist/hashdist

Software for Automated Reading of STEP Files by I-DEAS(trademark)

NASA Technical Reports Server (NTRS)

Pinedo, John

2003-01-01

A program called "readstep" enables the I-DEAS(tm) computer-aided-design (CAD) software to automatically read Standard for the Exchange of Product Model Data (STEP) files. (The STEP format is one of several used to transfer data between dissimilar CAD programs.) Prior to the development of "readstep," it was necessary to read STEP files into I-DEAS(tm) one at a time in a slow process that required repeated intervention by the user. In operation, "readstep" prompts the user for the location of the desired STEP files and the names of the I-DEAS(tm) project and model file, then generates an I-DEAS(tm) program file called "readstep.prg" and two Unix shell programs called "runner" and "controller." The program "runner" runs I-DEAS(tm) sessions that execute readstep.prg, while "controller" controls the execution of "runner" and edits readstep.prg if necessary. The user sets "runner" and "controller" into execution simultaneously, and then no further intervention by the user is required. When "runner" has finished, the user should see only parts from successfully read STEP files present in the model file. STEP files that could not be read successfully (e.g., because of format errors) should be regenerated before attempting to read them again.

LabVIEW Serial Driver Software for an Electronic Load

NASA Technical Reports Server (NTRS)

Scullin, Vincent; Garcia, Christopher

2003-01-01

A LabVIEW-language computer program enables monitoring and control of a Transistor Devices, Inc., Dynaload WCL232 (or equivalent) electronic load via an RS-232 serial communication link between the electronic load and a remote personal computer. (The electronic load can operate at constant voltage, current, power consumption, or resistance.) The program generates a graphical user interface (GUI) at the computer that looks and acts like the front panel of the electronic load. Once the electronic load has been placed in remote-control mode, this program first queries the electronic load for the present values of all its operational and limit settings, and then drops into a cycle in which it reports the instantaneous voltage, current, and power values in displays that resemble those on the electronic load while monitoring the GUI images of pushbuttons for control actions by the user. By means of the pushbutton images and associated prompts, the user can perform such operations as changing limit values, the operating mode, or the set point. The benefit of this software is that it relieves the user of the need to learn one method for operating the electronic load locally and another method for operating it remotely via a personal computer.

PeptideDepot: flexible relational database for visual analysis of quantitative proteomic data and integration of existing protein information.

PubMed

Yu, Kebing; Salomon, Arthur R

2009-12-01

Recently, dramatic progress has been achieved in expanding the sensitivity, resolution, mass accuracy, and scan rate of mass spectrometers able to fragment and identify peptides through MS/MS. Unfortunately, this enhanced ability to acquire proteomic data has not been accompanied by a concomitant increase in the availability of flexible tools allowing users to rapidly assimilate, explore, and analyze this data and adapt to various experimental workflows with minimal user intervention. Here we fill this critical gap by providing a flexible relational database called PeptideDepot for organization of expansive proteomic data sets, collation of proteomic data with available protein information resources, and visual comparison of multiple quantitative proteomic experiments. Our software design, built upon the synergistic combination of a MySQL database for safe warehousing of proteomic data with a FileMaker-driven graphical user interface for flexible adaptation to diverse workflows, enables proteomic end-users to directly tailor the presentation of proteomic data to the unique analysis requirements of the individual proteomics lab. PeptideDepot may be deployed as an independent software tool or integrated directly with our high throughput autonomous proteomic pipeline used in the automated acquisition and post-acquisition analysis of proteomic data.

A Visual Basic program for analyzing oedometer test results and evaluating intergranular void ratio

NASA Astrophysics Data System (ADS)

Monkul, M. Murat; Önal, Okan

2006-06-01

A visual basic program (POCI) is proposed and explained in order to analyze oedometer test results. Oedometer test results have vital importance from geotechnical point of view, since settlement requirements usually control the design of foundations. The software POCI is developed in order perform the necessary calculations for convential oedometer test. The change of global void ratio and stress-strain characteristics can be observed both numerically and graphically. It enables the users to calculate some parameters such as coefficient of consolidation, compression index, recompression index, and preconsolidation pressure depending on the type and stress history of the soil. Moreover, it adopts the concept of intergranular void ratio which may be important especially in the compression behavior of sandy soils. POCI shows the variation of intergranular void ratio and also enables the users to calculate granular compression index.

A voxel visualization and analysis system based on AutoCAD

NASA Astrophysics Data System (ADS)

Marschallinger, Robert

1996-05-01

A collection of AutoLISP programs is presented which enable the visualization and analysis of voxel models by AutoCAD rel. 12/rel. 13. The programs serve as an interactive, graphical front end for manipulating the results of three-dimensional modeling software producing block estimation data. ASCII data files describing geometry and attributes per estimation block are imported and stored as a voxel array. Each voxel may contain multiple attributes, therefore different parameters may be incorporated in one voxel array. Voxel classification is implemented on a layer basis providing flexible treatment of voxel classes such as recoloring, peeling, or volumetry. A versatile clipping tool enables slicing voxel arrays according to combinations of three perpendicular clipping planes. The programs feature an up-to-date, graphical user interface for user-friendly operation by non AutoCAD specialists.

eLoom and Flatland: specification, simulation and visualization engines for the study of arbitrary hierarchical neural architectures.

PubMed

Caudell, Thomas P; Xiao, Yunhai; Healy, Michael J

2003-01-01

eLoom is an open source graph simulation software tool, developed at the University of New Mexico (UNM), that enables users to specify and simulate neural network models. Its specification language and libraries enables users to construct and simulate arbitrary, potentially hierarchical network structures on serial and parallel processing systems. In addition, eLoom is integrated with UNM's Flatland, an open source virtual environments development tool to provide real-time visualizations of the network structure and activity. Visualization is a useful method for understanding both learning and computation in artificial neural networks. Through 3D animated pictorially representations of the state and flow of information in the network, a better understanding of network functionality is achieved. ART-1, LAPART-II, MLP, and SOM neural networks are presented to illustrate eLoom and Flatland's capabilities.

GenoMatrix: A Software Package for Pedigree-Based and Genomic Prediction Analyses on Complex Traits.

PubMed

Nazarian, Alireza; Gezan, Salvador Alejandro

2016-07-01

Genomic and pedigree-based best linear unbiased prediction methodologies (G-BLUP and P-BLUP) have proven themselves efficient for partitioning the phenotypic variance of complex traits into its components, estimating the individuals' genetic merits, and predicting unobserved (or yet-to-be observed) phenotypes in many species and fields of study. The GenoMatrix software, presented here, is a user-friendly package to facilitate the process of using genome-wide marker data and parentage information for G-BLUP and P-BLUP analyses on complex traits. It provides users with a collection of applications which help them on a set of tasks from performing quality control on data to constructing and manipulating the genomic and pedigree-based relationship matrices and obtaining their inverses. Such matrices will be then used in downstream analyses by other statistical packages. The package also enables users to obtain predicted values for unobserved individuals based on the genetic values of observed related individuals. GenoMatrix is available to the research community as a Windows 64bit executable and can be downloaded free of charge at: http://compbio.ufl.edu/software/genomatrix/. © The American Genetic Association. 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

PRISE2: software for designing sequence-selective PCR primers and probes.

PubMed

Huang, Yu-Ting; Yang, Jiue-in; Chrobak, Marek; Borneman, James

2014-09-25

PRISE2 is a new software tool for designing sequence-selective PCR primers and probes. To achieve high level of selectivity, PRISE2 allows the user to specify a collection of target sequences that the primers are supposed to amplify, as well as non-target sequences that should not be amplified. The program emphasizes primer selectivity on the 3' end, which is crucial for selective amplification of conserved sequences such as rRNA genes. In PRISE2, users can specify desired properties of primers, including length, GC content, and others. They can interactively manipulate the list of candidate primers, to choose primer pairs that are best suited for their needs. A similar process is used to add probes to selected primer pairs. More advanced features include, for example, the capability to define a custom mismatch penalty function. PRISE2 is equipped with a graphical, user-friendly interface, and it runs on Windows, Macintosh or Linux machines. PRISE2 has been tested on two very similar strains of the fungus Dactylella oviparasitica, and it was able to create highly selective primers and probes for each of them, demonstrating the ability to create useful sequence-selective assays. PRISE2 is a user-friendly, interactive software package that can be used to design high-quality selective primers for PCR experiments. In addition to choosing primers, users have an option to add a probe to any selected primer pair, enabling design of Taqman and other primer-probe based assays. PRISE2 can also be used to design probes for FISH and other hybridization-based assays.

ConfocalVR: Immersive Visualization Applied to Confocal Microscopy.

PubMed

Stefani, Caroline; Lacy-Hulbert, Adam; Skillman, Thomas

2018-06-24

ConfocalVR is a virtual reality (VR) application created to improve the ability of researchers to study the complexity of cell architecture. Confocal microscopes take pictures of fluorescently labeled proteins or molecules at different focal planes to create a stack of 2D images throughout the specimen. Current software applications reconstruct the 3D image and render it as a 2D projection onto a computer screen where users need to rotate the image to expose the full 3D structure. This process is mentally taxing, breaks down if you stop the rotation, and does not take advantage of the eye's full field of view. ConfocalVR exploits consumer-grade virtual reality (VR) systems to fully immerse the user in the 3D cellular image. In this virtual environment the user can: 1) adjust image viewing parameters without leaving the virtual space, 2) reach out and grab the image to quickly rotate and scale the image to focus on key features, and 3) interact with other users in a shared virtual space enabling real-time collaborative exploration and discussion. We found that immersive VR technology allows the user to rapidly understand cellular architecture and protein or molecule distribution. We note that it is impossible to understand the value of immersive visualization without experiencing it first hand, so we encourage readers to get access to a VR system, download this software, and evaluate it for yourself. The ConfocalVR software is available for download at http://www.confocalvr.com, and is free for nonprofits. Copyright © 2018. Published by Elsevier Ltd.

Scalable web services for the PSIPRED Protein Analysis Workbench.

PubMed

Buchan, Daniel W A; Minneci, Federico; Nugent, Tim C O; Bryson, Kevin; Jones, David T

2013-07-01

Here, we present the new UCL Bioinformatics Group's PSIPRED Protein Analysis Workbench. The Workbench unites all of our previously available analysis methods into a single web-based framework. The new web portal provides a greatly streamlined user interface with a number of new features to allow users to better explore their results. We offer a number of additional services to enable computationally scalable execution of our prediction methods; these include SOAP and XML-RPC web server access and new HADOOP packages. All software and services are available via the UCL Bioinformatics Group website at http://bioinf.cs.ucl.ac.uk/.

Logical optimization for database uniformization

NASA Technical Reports Server (NTRS)

Grant, J.

1984-01-01

Data base uniformization refers to the building of a common user interface facility to support uniform access to any or all of a collection of distributed heterogeneous data bases. Such a system should enable a user, situated anywhere along a set of distributed data bases, to access all of the information in the data bases without having to learn the various data manipulation languages. Furthermore, such a system should leave intact the component data bases, and in particular, their already existing software. A survey of various aspects of the data bases uniformization problem and a proposed solution are presented.

Diamond Eye: a distributed architecture for image data mining

NASA Astrophysics Data System (ADS)

Burl, Michael C.; Fowlkes, Charless; Roden, Joe; Stechert, Andre; Mukhtar, Saleem

1999-02-01

Diamond Eye is a distributed software architecture, which enables users (scientists) to analyze large image collections by interacting with one or more custom data mining servers via a Java applet interface. Each server is coupled with an object-oriented database and a computational engine, such as a network of high-performance workstations. The database provides persistent storage and supports querying of the 'mined' information. The computational engine provides parallel execution of expensive image processing, object recognition, and query-by-content operations. Key benefits of the Diamond Eye architecture are: (1) the design promotes trial evaluation of advanced data mining and machine learning techniques by potential new users (all that is required is to point a web browser to the appropriate URL), (2) software infrastructure that is common across a range of science mining applications is factored out and reused, and (3) the system facilitates closer collaborations between algorithm developers and domain experts.

PredGuid+A: Orion Entry Guidance Modified for Aerocapture

NASA Technical Reports Server (NTRS)

Lafleur, Jarret

2013-01-01

PredGuid+A software was developed to enable a unique numerical predictor-corrector aerocapture guidance capability that builds on heritage Orion entry guidance algorithms. The software can be used for both planetary entry and aerocapture applications. Furthermore, PredGuid+A implements a new Delta-V minimization guidance option that can take the place of traditional targeting guidance and can result in substantial propellant savings. PredGuid+A allows the user to set a mode flag and input a target orbit's apoapsis and periapsis. Using bank angle control, the guidance will then guide the vehicle to the appropriate post-aerocapture orbit using one of two algorithms: Apoapsis Targeting or Delta-V Minimization (as chosen by the user). Recently, the PredGuid guidance algorithm was adapted for use in skip-entry scenarios for NASA's Orion multi-purpose crew vehicle (MPCV). To leverage flight heritage, most of Orion's entry guidance routines are adapted from the Apollo program.

Programmable ubiquitous telerobotic devices

NASA Astrophysics Data System (ADS)

Doherty, Michael; Greene, Matthew; Keaton, David; Och, Christian; Seidl, Matthew L.; Waite, William; Zorn, Benjamin G.

1997-12-01

We are investigating a field of research that we call ubiquitous telepresence, which involves the design and implementation of low-cost robotic devices that can be programmed and operated from anywhere on the Internet. These devices, which we call ubots, can be used for academic purposes (e.g., a biologist could remote conduct a population survey), commercial purposes (e.g., a house could be shown remotely by a real-estate agent), and for recreation and education (e.g., someone could tour a museum remotely). We anticipate that such devices will become increasingly common due to recent changes in hardware and software technology. In particular, current hardware technology enables such devices to be constructed very cheaply (less than $500), and current software and network technology allows highly portable code to be written and downloaded across the Internet. In this paper, we present our prototype system architecture, and the ubot implementation we have constructed based on it. The hardware technology we use is the handy board, a 6811-based controller board with digital and analog inputs and outputs. Our software includes a network layer based on TCP/IP and software layers written in Java. Our software enables users across the Internet to program the behavior of the vehicle and to receive image feedback from a camera mounted on it.

Processing LiDAR Data to Predict Natural Hazards

NASA Technical Reports Server (NTRS)

Fairweather, Ian; Crabtree, Robert; Hager, Stacey

2008-01-01

ELF-Base and ELF-Hazards (wherein 'ELF' signifies 'Extract LiDAR Features' and 'LiDAR' signifies 'light detection and ranging') are developmental software modules for processing remote-sensing LiDAR data to identify past natural hazards (principally, landslides) and predict future ones. ELF-Base processes raw LiDAR data, including LiDAR intensity data that are often ignored in other software, to create digital terrain models (DTMs) and digital feature models (DFMs) with sub-meter accuracy. ELF-Hazards fuses raw LiDAR data, data from multispectral and hyperspectral optical images, and DTMs and DFMs generated by ELF-Base to generate hazard risk maps. Advanced algorithms in these software modules include line-enhancement and edge-detection algorithms, surface-characterization algorithms, and algorithms that implement innovative data-fusion techniques. The line-extraction and edge-detection algorithms enable users to locate such features as faults and landslide headwall scarps. Also implemented in this software are improved methodologies for identification and mapping of past landslide events by use of (1) accurate, ELF-derived surface characterizations and (2) three LiDAR/optical-data-fusion techniques: post-classification data fusion, maximum-likelihood estimation modeling, and hierarchical within-class discrimination. This software is expected to enable faster, more accurate forecasting of natural hazards than has previously been possible.

Advanced Structural Optimization Under Consideration of Cost Tracking

NASA Astrophysics Data System (ADS)

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

2014-06-01

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

Ground control station software design for micro aerial vehicles

NASA Astrophysics Data System (ADS)

Walendziuk, Wojciech; Oldziej, Daniel; Binczyk, Dawid Przemyslaw; Slowik, Maciej

2017-08-01

This article describes the process of designing the equipment part and the software of a ground control station used for configuring and operating micro unmanned aerial vehicles (UAV). All the works were conducted on a quadrocopter model being a commonly accessible commercial construction. This article contains a characteristics of the research object, the basics of operating the micro aerial vehicles (MAV) and presents components of the ground control station model. It also describes the communication standards for the purpose of building a model of the station. Further part of the work concerns the software of the product - the GIMSO application (Generally Interactive Station for Mobile Objects), which enables the user to manage the actions and communication and control processes from the UAV. The process of creating the software and the field tests of a station model are also presented in the article.

OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets.

PubMed

Perez-Riverol, Yasset; Ternent, Tobias; Koch, Maximilian; Barsnes, Harald; Vrousgou, Olga; Jupp, Simon; Vizcaíno, Juan Antonio

2017-10-01

The availability of user-friendly software to annotate biological datasets and experimental details is becoming essential in data management practices, both in local storage systems and in public databases. The Ontology Lookup Service (OLS, http://www.ebi.ac.uk/ols) is a popular centralized service to query, browse and navigate biomedical ontologies and controlled vocabularies. Recently, the OLS framework has been completely redeveloped (version 3.0), including enhancements in the data model, like the added support for Web Ontology Language based ontologies, among many other improvements. However, the new OLS is not backwards compatible and new software tools are needed to enable access to this widely used framework now that the previous version is no longer available. We here present the OLS Client as a free, open-source Java library to retrieve information from the new version of the OLS. It enables rapid tool creation by providing a robust, pluggable programming interface and common data model to programmatically access the OLS. The library has already been integrated and is routinely used by several bioinformatics resources and related data annotation tools. Secondly, we also introduce an updated version of the OLS Dialog (version 2.0), a Java graphical user interface that can be easily plugged into Java desktop applications to access the OLS. The software and related documentation are freely available at https://github.com/PRIDE-Utilities/ols-client and https://github.com/PRIDE-Toolsuite/ols-dialog. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

CB-EMIS CELL PHONE CLIENT

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

Lurie, Gordon

2007-01-02

The cell phone software allows any Java enabled cell phone to view sensor and meteorological data via an internet connection using a secure connection to the CB-EMIS Web Service. Users with appropriate privileges can monitor the state of the sensors and perform simple maintenance tasks remotely. All sensitive data is downloaded from the web service, thus protecting sensitive data in the event a cell phone is lost.

Web-based Tool Suite for Plasmasphere Information Discovery

NASA Astrophysics Data System (ADS)

Newman, T. S.; Wang, C.; Gallagher, D. L.

2005-12-01

A suite of tools that enable discovery of terrestrial plasmasphere characteristics from NASA IMAGE Extreme Ultra Violet (EUV) images is described. The tool suite is web-accessible, allowing easy remote access without the need for any software installation on the user's computer. The features supported by the tool include reconstruction of the plasmasphere plasma density distribution from a short sequence of EUV images, semi-automated selection of the plasmapause boundary in an EUV image, and mapping of the selected boundary to the geomagnetic equatorial plane. EUV image upload and result download is also supported. The tool suite's plasmapause mapping feature is achieved via the Roelof and Skinner (2000) Edge Algorithm. The plasma density reconstruction is achieved through a tomographic technique that exploits physical constraints to allow for a moderate resolution result. The tool suite's software architecture uses Java Server Pages (JSP) and Java Applets on the front side for user-software interaction and Java Servlets on the server side for task execution. The compute-intensive components of the tool suite are implemented in C++ and invoked by the server via Java Native Interface (JNI).

Information and communication systems for the assistance of carers based on ACTION.

PubMed

Kraner, M; Emery, D; Cvetkovic, S R; Procter, P; Smythe, C

1999-01-01

Recent advances in telecommunication technologies allow the design of information and communication systems for people who are caring for others in the home as family members or as professionals in the health or community centres. The present paper analyses and classifies the information flow and maps it to an information life cycle, which governs the design of the deployed hardware, software and the data-structure. This is based on the initial findings of ACTION (assisting carers using telematics interventions to meet older persons' needs) a European Union funded project. The proposed information architecture discusses different designs such as centralized or decentralized Web and Client server solutions. A user interface is developed reflecting the special requirements of the targeted user group, which influences the functionality and design of the software, data architecture and the integrated communication system using video-conferencing. ACTION has engineered a system using plain Web technology based on HTML, extended with JavaScript and ActiveX and a software switch enabling the integration of different types of videoconferencing and other applications providing manufacturer independence.

MATtrack: A MATLAB-Based Quantitative Image Analysis Platform for Investigating Real-Time Photo-Converted Fluorescent Signals in Live Cells.

PubMed

Courtney, Jane; Woods, Elena; Scholz, Dimitri; Hall, William W; Gautier, Virginie W

2015-01-01

We introduce here MATtrack, an open source MATLAB-based computational platform developed to process multi-Tiff files produced by a photo-conversion time lapse protocol for live cell fluorescent microscopy. MATtrack automatically performs a series of steps required for image processing, including extraction and import of numerical values from Multi-Tiff files, red/green image classification using gating parameters, noise filtering, background extraction, contrast stretching and temporal smoothing. MATtrack also integrates a series of algorithms for quantitative image analysis enabling the construction of mean and standard deviation images, clustering and classification of subcellular regions and injection point approximation. In addition, MATtrack features a simple user interface, which enables monitoring of Fluorescent Signal Intensity in multiple Regions of Interest, over time. The latter encapsulates a region growing method to automatically delineate the contours of Regions of Interest selected by the user, and performs background and regional Average Fluorescence Tracking, and automatic plotting. Finally, MATtrack computes convenient visualization and exploration tools including a migration map, which provides an overview of the protein intracellular trajectories and accumulation areas. In conclusion, MATtrack is an open source MATLAB-based software package tailored to facilitate the analysis and visualization of large data files derived from real-time live cell fluorescent microscopy using photoconvertible proteins. It is flexible, user friendly, compatible with Windows, Mac, and Linux, and a wide range of data acquisition software. MATtrack is freely available for download at eleceng.dit.ie/courtney/MATtrack.zip.

MATtrack: A MATLAB-Based Quantitative Image Analysis Platform for Investigating Real-Time Photo-Converted Fluorescent Signals in Live Cells

PubMed Central

Courtney, Jane; Woods, Elena; Scholz, Dimitri; Hall, William W.; Gautier, Virginie W.

2015-01-01

We introduce here MATtrack, an open source MATLAB-based computational platform developed to process multi-Tiff files produced by a photo-conversion time lapse protocol for live cell fluorescent microscopy. MATtrack automatically performs a series of steps required for image processing, including extraction and import of numerical values from Multi-Tiff files, red/green image classification using gating parameters, noise filtering, background extraction, contrast stretching and temporal smoothing. MATtrack also integrates a series of algorithms for quantitative image analysis enabling the construction of mean and standard deviation images, clustering and classification of subcellular regions and injection point approximation. In addition, MATtrack features a simple user interface, which enables monitoring of Fluorescent Signal Intensity in multiple Regions of Interest, over time. The latter encapsulates a region growing method to automatically delineate the contours of Regions of Interest selected by the user, and performs background and regional Average Fluorescence Tracking, and automatic plotting. Finally, MATtrack computes convenient visualization and exploration tools including a migration map, which provides an overview of the protein intracellular trajectories and accumulation areas. In conclusion, MATtrack is an open source MATLAB-based software package tailored to facilitate the analysis and visualization of large data files derived from real-time live cell fluorescent microscopy using photoconvertible proteins. It is flexible, user friendly, compatible with Windows, Mac, and Linux, and a wide range of data acquisition software. MATtrack is freely available for download at eleceng.dit.ie/courtney/MATtrack.zip. PMID:26485569

A User-Friendly DNA Modeling Software for the Interpretation of Cryo-Electron Microscopy Data.

PubMed

Larivière, Damien; Galindo-Murillo, Rodrigo; Fourmentin, Eric; Hornus, Samuel; Lévy, Bruno; Papillon, Julie; Ménétret, Jean-François; Lamour, Valérie

2017-01-01

The structural modeling of a macromolecular machine is like a "Lego" approach that is challenged when blocks, like proteins imported from the Protein Data Bank, are to be assembled with an element adopting a serpentine shape, such as DNA templates. DNA must then be built ex nihilo, but modeling approaches are either not user-friendly or very long and fastidious. In this method chapter we show how to use GraphiteLifeExplorer, a software with a simple graphical user interface that enables the sketching of free forms of DNA, of any length, at the atomic scale, as fast as drawing a line on a sheet of paper. We took as an example the nucleoprotein complex of DNA gyrase, a bacterial topoisomerase whose structure has been determined using cryo-electron microscopy (Cryo-EM). Using GraphiteLifeExplorer, we could model in one go a 155 bp long and twisted DNA duplex that wraps around DNA gyrase in the cryo-EM map, improving the quality and interpretation of the final model compared to the initially published data.

Providing Assistive Technology Applications as a Service Through Cloud Computing.

PubMed

Mulfari, Davide; Celesti, Antonio; Villari, Massimo; Puliafito, Antonio

2015-01-01

Users with disabilities interact with Personal Computers (PCs) using Assistive Technology (AT) software solutions. Such applications run on a PC that a person with a disability commonly uses. However the configuration of AT applications is not trivial at all, especially whenever the user needs to work on a PC that does not allow him/her to rely on his / her AT tools (e.g., at work, at university, in an Internet point). In this paper, we discuss how cloud computing provides a valid technological solution to enhance such a scenario.With the emergence of cloud computing, many applications are executed on top of virtual machines (VMs). Virtualization allows us to achieve a software implementation of a real computer able to execute a standard operating system and any kind of application. In this paper we propose to build personalized VMs running AT programs and settings. By using the remote desktop technology, our solution enables users to control their customized virtual desktop environment by means of an HTML5-based web interface running on any computer equipped with a browser, whenever they are.

Power API Prototype

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

2014-12-04

The software serves two purposes. The first purpose of the software is to prototype the Sandia High Performance Computing Power Application Programming Interface Specification effort. The specification can be found at http://powerapi.sandia.gov . Prototypes of the specification were developed in parallel with the development of the specification. Release of the prototype will be instructive to anyone who intends to implement the specification. More specifically, our vendor collaborators will benefit from the availability of the prototype. The second is in direct support of the PowerInsight power measurement device, which was co-developed with Penguin Computing. The software provides a cluster wide measurementmore » capability enabled by the PowerInsight device. The software can be used by anyone who purchases a PowerInsight device. The software will allow the user to easily collect power and energy information of a node that is instrumented with PowerInsight. The software can also be used as an example prototype implementation of the High Performance Computing Power Application Programming Interface Specification.« less

Simulation Enabled Safeguards Assessment Methodology

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

Robert Bean; Trond Bjornard; Thomas Larson

2007-09-01

It is expected that nuclear energy will be a significant component of future supplies. New facilities, operating under a strengthened international nonproliferation regime will be needed. There is good reason to believe virtual engineering applied to the facility design, as well as to the safeguards system design will reduce total project cost and improve efficiency in the design cycle. Simulation Enabled Safeguards Assessment MEthodology (SESAME) has been developed as a software package to provide this capability for nuclear reprocessing facilities. The software architecture is specifically designed for distributed computing, collaborative design efforts, and modular construction to allow step improvements inmore » functionality. Drag and drop wireframe construction allows the user to select the desired components from a component warehouse, render the system for 3D visualization, and, linked to a set of physics libraries and/or computational codes, conduct process evaluations of the system they have designed.« less

P-MartCancer-Interactive Online Software to Enable Analysis of Shotgun Cancer Proteomic Datasets.

PubMed

Webb-Robertson, Bobbie-Jo M; Bramer, Lisa M; Jensen, Jeffrey L; Kobold, Markus A; Stratton, Kelly G; White, Amanda M; Rodland, Karin D

2017-11-01

P-MartCancer is an interactive web-based software environment that enables statistical analyses of peptide or protein data, quantitated from mass spectrometry-based global proteomics experiments, without requiring in-depth knowledge of statistical programming. P-MartCancer offers a series of statistical modules associated with quality assessment, peptide and protein statistics, protein quantification, and exploratory data analyses driven by the user via customized workflows and interactive visualization. Currently, P-MartCancer offers access and the capability to analyze multiple cancer proteomic datasets generated through the Clinical Proteomics Tumor Analysis Consortium at the peptide, gene, and protein levels. P-MartCancer is deployed as a web service (https://pmart.labworks.org/cptac.html), alternatively available via Docker Hub (https://hub.docker.com/r/pnnl/pmart-web/). Cancer Res; 77(21); e47-50. ©2017 AACR . ©2017 American Association for Cancer Research.

The Nuclear Energy Advanced Modeling and Simulation Enabling Computational Technologies FY09 Report

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

Diachin, L F; Garaizar, F X; Henson, V E

2009-10-12

In this document we report on the status of the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Enabling Computational Technologies (ECT) effort. In particular, we provide the context for ECT In the broader NEAMS program and describe the three pillars of the ECT effort, namely, (1) tools and libraries, (2) software quality assurance, and (3) computational facility (computers, storage, etc) needs. We report on our FY09 deliverables to determine the needs of the integrated performance and safety codes (IPSCs) in these three areas and lay out the general plan for software quality assurance to meet the requirements of DOE andmore » the DOE Advanced Fuel Cycle Initiative (AFCI). We conclude with a brief description of our interactions with the Idaho National Laboratory computer center to determine what is needed to expand their role as a NEAMS user facility.« less

MiRTE: Mixed Reality Triage and Evacuation game for Mass Casualty information systems design, testing and training.

PubMed

Yu, Xunyi; Ganz, Aura

2011-01-01

In this paper we introduce a Mixed Reality Triage and Evacuation game, MiRTE, that is used in the development, testing and training of Mass Casualty Incident (MCI) information systems for first responders. Using the Source game engine from Valve software, MiRTE creates immersive virtual environments to simulate various incident scenarios, and enables interactions between multiple players/first responders. What distinguishes it from a pure computer simulation game is that it can interface with external mass casualty incident management systems, such as DIORAMA. The game will enable system developers to specify technical requirements of underlying technology, and test different alternatives of design. After the information system hardware and software are completed, the game can simulate various algorithms such as localization technologies, and interface with an actual user interface on PCs and Smartphones. We implemented and tested the game with the DIORAMA system.

Cafe: A Generic Configurable Customizable Composite Cloud Application Framework

NASA Astrophysics Data System (ADS)

Mietzner, Ralph; Unger, Tobias; Leymann, Frank

In this paper we present Cafe (Composite Application Framework) an approach to describe configurable composite service-oriented applications and to automatically provision them across different providers. Cafe enables independent software vendors to describe their composite service-oriented applications and the components that are used to assemble them. Components can be internal to the application or external and can be deployed in any of the delivery models present in the cloud. The components are annotated with requirements for the infrastructure they later need to be run on. Providers on the other hand advertise their infrastructure services by describing them as infrastructure capabilities. The separation of software vendors and providers enables end users and providers to follow a best-of-breed strategy by combining arbitrary applications with arbitrary providers. We show how such applications can be automatically provisioned and present an architecture and a prototype that implements the concepts.

Open-source, community-driven microfluidics with Metafluidics.

PubMed

Kong, David S; Thorsen, Todd A; Babb, Jonathan; Wick, Scott T; Gam, Jeremy J; Weiss, Ron; Carr, Peter A

2017-06-07

Microfluidic devices have the potential to automate and miniaturize biological experiments, but open-source sharing of device designs has lagged behind sharing of other resources such as software. Synthetic biologists have used microfluidics for DNA assembly, cell-free expression, and cell culture, but a combination of expense, device complexity, and reliance on custom set-ups hampers their widespread adoption. We present Metafluidics, an open-source, community-driven repository that hosts digital design files, assembly specifications, and open-source software to enable users to build, configure, and operate a microfluidic device. We use Metafluidics to share designs and fabrication instructions for both a microfluidic ring-mixer device and a 32-channel tabletop microfluidic controller. This device and controller are applied to build genetic circuits using standard DNA assembly methods including ligation, Gateway, Gibson, and Golden Gate. Metafluidics is intended to enable a broad community of engineers, DIY enthusiasts, and other nontraditional participants with limited fabrication skills to contribute to microfluidic research.

MOtoNMS: A MATLAB toolbox to process motion data for neuromusculoskeletal modeling and simulation.

PubMed

Mantoan, Alice; Pizzolato, Claudio; Sartori, Massimo; Sawacha, Zimi; Cobelli, Claudio; Reggiani, Monica

2015-01-01

Neuromusculoskeletal modeling and simulation enable investigation of the neuromusculoskeletal system and its role in human movement dynamics. These methods are progressively introduced into daily clinical practice. However, a major factor limiting this translation is the lack of robust tools for the pre-processing of experimental movement data for their use in neuromusculoskeletal modeling software. This paper presents MOtoNMS (matlab MOtion data elaboration TOolbox for NeuroMusculoSkeletal applications), a toolbox freely available to the community, that aims to fill this lack. MOtoNMS processes experimental data from different motion analysis devices and generates input data for neuromusculoskeletal modeling and simulation software, such as OpenSim and CEINMS (Calibrated EMG-Informed NMS Modelling Toolbox). MOtoNMS implements commonly required processing steps and its generic architecture simplifies the integration of new user-defined processing components. MOtoNMS allows users to setup their laboratory configurations and processing procedures through user-friendly graphical interfaces, without requiring advanced computer skills. Finally, configuration choices can be stored enabling the full reproduction of the processing steps. MOtoNMS is released under GNU General Public License and it is available at the SimTK website and from the GitHub repository. Motion data collected at four institutions demonstrate that, despite differences in laboratory instrumentation and procedures, MOtoNMS succeeds in processing data and producing consistent inputs for OpenSim and CEINMS. MOtoNMS fills the gap between motion analysis and neuromusculoskeletal modeling and simulation. Its support to several devices, a complete implementation of the pre-processing procedures, its simple extensibility, the available user interfaces, and its free availability can boost the translation of neuromusculoskeletal methods in daily and clinical practice.

Genes2WordCloud: a quick way to identify biological themes from gene lists and free text.

PubMed

Baroukh, Caroline; Jenkins, Sherry L; Dannenfelser, Ruth; Ma'ayan, Avi

2011-10-13

Word-clouds recently emerged on the web as a solution for quickly summarizing text by maximizing the display of most relevant terms about a specific topic in the minimum amount of space. As biologists are faced with the daunting amount of new research data commonly presented in textual formats, word-clouds can be used to summarize and represent biological and/or biomedical content for various applications. Genes2WordCloud is a web application that enables users to quickly identify biological themes from gene lists and research relevant text by constructing and displaying word-clouds. It provides users with several different options and ideas for the sources that can be used to generate a word-cloud. Different options for rendering and coloring the word-clouds give users the flexibility to quickly generate customized word-clouds of their choice. Genes2WordCloud is a word-cloud generator and a word-cloud viewer that is based on WordCram implemented using Java, Processing, AJAX, mySQL, and PHP. Text is fetched from several sources and then processed to extract the most relevant terms with their computed weights based on word frequencies. Genes2WordCloud is freely available for use online; it is open source software and is available for installation on any web-site along with supporting documentation at http://www.maayanlab.net/G2W. Genes2WordCloud provides a useful way to summarize and visualize large amounts of textual biological data or to find biological themes from several different sources. The open source availability of the software enables users to implement customized word-clouds on their own web-sites and desktop applications.

Genes2WordCloud: a quick way to identify biological themes from gene lists and free text

PubMed Central

2011-01-01

Background Word-clouds recently emerged on the web as a solution for quickly summarizing text by maximizing the display of most relevant terms about a specific topic in the minimum amount of space. As biologists are faced with the daunting amount of new research data commonly presented in textual formats, word-clouds can be used to summarize and represent biological and/or biomedical content for various applications. Results Genes2WordCloud is a web application that enables users to quickly identify biological themes from gene lists and research relevant text by constructing and displaying word-clouds. It provides users with several different options and ideas for the sources that can be used to generate a word-cloud. Different options for rendering and coloring the word-clouds give users the flexibility to quickly generate customized word-clouds of their choice. Methods Genes2WordCloud is a word-cloud generator and a word-cloud viewer that is based on WordCram implemented using Java, Processing, AJAX, mySQL, and PHP. Text is fetched from several sources and then processed to extract the most relevant terms with their computed weights based on word frequencies. Genes2WordCloud is freely available for use online; it is open source software and is available for installation on any web-site along with supporting documentation at http://www.maayanlab.net/G2W. Conclusions Genes2WordCloud provides a useful way to summarize and visualize large amounts of textual biological data or to find biological themes from several different sources. The open source availability of the software enables users to implement customized word-clouds on their own web-sites and desktop applications. PMID:21995939

Magic star puzzle for educational mathematics

NASA Astrophysics Data System (ADS)

Gan, Yee Siang; Fong, Wan Heng; Sarmin, Nor Haniza

2013-04-01

One of the interesting fields in recreational mathematics is the magic number arrangement. There are different kinds of arrays in the arrangement for a group of numbers. In particular, one of the arrays in magic number arrangement is called magic star. In fact, magic star involves combinatorics that contributes to geometrical analysis and number theory. Hence, magic star is suitable to be introduced as educational mathematics to cultivate interest in different area of mathematics. To obtain the solutions of normal magic stars of order six, the possible sets of numbers for every line in a magic star have been considered. Previously, the calculation for obtaining the solutions has been done manually which is time-consuming. Therefore, a programming code to generate all the fundamental solutions for normal magic star of order six without including the properties of rotation and reflection has been done. In this puzzle, a magic star puzzle is created by using Matlab software, which enables a user to verify the entries for the cells of magic star of order six. Moreover, it is also user-friendly as it provides interactive commands on the inputs given by the user, which enables the user to detect the incorrect inputs. In addition, user can also choose to view all the fundamental solutions as generated by the programming code.

Software-codec-based full motion video conferencing on the PC using visual pattern image sequence coding

NASA Astrophysics Data System (ADS)

Barnett, Barry S.; Bovik, Alan C.

1995-04-01

This paper presents a real time full motion video conferencing system based on the Visual Pattern Image Sequence Coding (VPISC) software codec. The prototype system hardware is comprised of two personal computers, two camcorders, two frame grabbers, and an ethernet connection. The prototype system software has a simple structure. It runs under the Disk Operating System, and includes a user interface, a video I/O interface, an event driven network interface, and a free running or frame synchronous video codec that also acts as the controller for the video and network interfaces. Two video coders have been tested in this system. Simple implementations of Visual Pattern Image Coding and VPISC have both proven to support full motion video conferencing with good visual quality. Future work will concentrate on expanding this prototype to support the motion compensated version of VPISC, as well as encompassing point-to-point modem I/O and multiple network protocols. The application will be ported to multiple hardware platforms and operating systems. The motivation for developing this prototype system is to demonstrate the practicality of software based real time video codecs. Furthermore, software video codecs are not only cheaper, but are more flexible system solutions because they enable different computer platforms to exchange encoded video information without requiring on-board protocol compatible video codex hardware. Software based solutions enable true low cost video conferencing that fits the `open systems' model of interoperability that is so important for building portable hardware and software applications.

Database Organisation in a Web-Enabled Free and Open-Source Software (foss) Environment for Spatio-Temporal Landslide Modelling

NASA Astrophysics Data System (ADS)

Das, I.; Oberai, K.; Sarathi Roy, P.

2012-07-01

Landslides exhibit themselves in different mass movement processes and are considered among the most complex natural hazards occurring on the earth surface. Making landslide database available online via WWW (World Wide Web) promotes the spreading and reaching out of the landslide information to all the stakeholders. The aim of this research is to present a comprehensive database for generating landslide hazard scenario with the help of available historic records of landslides and geo-environmental factors and make them available over the Web using geospatial Free & Open Source Software (FOSS). FOSS reduces the cost of the project drastically as proprietary software's are very costly. Landslide data generated for the period 1982 to 2009 were compiled along the national highway road corridor in Indian Himalayas. All the geo-environmental datasets along with the landslide susceptibility map were served through WEBGIS client interface. Open source University of Minnesota (UMN) mapserver was used as GIS server software for developing web enabled landslide geospatial database. PHP/Mapscript server-side application serve as a front-end application and PostgreSQL with PostGIS extension serve as a backend application for the web enabled landslide spatio-temporal databases. This dynamic virtual visualization process through a web platform brings an insight into the understanding of the landslides and the resulting damage closer to the affected people and user community. The landslide susceptibility dataset is also made available as an Open Geospatial Consortium (OGC) Web Feature Service (WFS) which can be accessed through any OGC compliant open source or proprietary GIS Software.

SensorWeb 3G: Extending On-Orbit Sensor Capabilities to Enable Near Realtime User Configurability

NASA Technical Reports Server (NTRS)

Mandl, Daniel; Cappelaere, Pat; Frye, Stuart; Sohlberg, Rob; Ly, Vuong; Chien, Steve; Tran, Daniel; Davies, Ashley; Sullivan, Don; Ames, Troy;

Linear Quadratic Gaussian Controller Design Using a Graphical User Interface: Application to the Beam-Waveguide Antennas

NASA Astrophysics Data System (ADS)

Maneri, E.; Gawronski, W.

1999-10-01

The linear quadratic Gaussian (LQG) design algorithms described in [2] and [5] have been used in the controller design of JPL's beam-waveguide [5] and 70-m [6] antennas. This algorithm significantly improves tracking precision in a windy environment. This article describes the graphical user interface (GUI) software for the design LQG controllers. It consists of two parts: the basic LQG design and the fine-tuning of the basic design using a constrained optimization algorithm. The presented GUI was developed to simplify the design process, to make the design process user-friendly, and to enable design of an LQG controller for one with a limited control engineering background. The user is asked to manipulate the GUI sliders and radio buttons to watch the antenna performance. Simple rules are given at the GUI display.

Enabling Discoveries in Earth Sciences Through the Geosciences Network (GEON)

NASA Astrophysics Data System (ADS)

Seber, D.; Baru, C.; Memon, A.; Lin, K.; Youn, C.

2005-12-01

Taking advantage of the state-of-the-art information technology resources GEON researchers are building a cyberinfrastructure designed to enable data sharing, semantic data integration, high-end computations and 4D visualization in easy-to-use web-based environments. The GEON Network currently allows users to search and register Earth science resources such as data sets (GIS layers, GMT files, geoTIFF images, ASCII files, relational databases etc), software applications or ontologies. Portal based access mechanisms enable developers to built dynamic user interfaces to conduct advanced processing and modeling efforts across distributed computers and supercomputers. Researchers and educators can access the networked resources through the GEON portal and its portlets that were developed to conduct better and more comprehensive science and educational studies. For example, the SYNSEIS portlet in GEON enables users to access in near-real time seismic waveforms from the IRIS Data Management Center, easily build a 3D geologic model within the area of the seismic station(s) and the epicenter and perform a 3D synthetic seismogram analysis to understand the lithospheric structure and earthquake source parameters for any given earthquake in the US. Similarly, GEON's workbench area enables users to create their own work environment and copy, visualize and analyze any data sets within the network, and create subsets of the data sets for their own purposes. Since all these resources are built as part of a Service-oriented Architecture (SOA), they are also used in other development platforms. One such platform is Kepler Workflow system which can access web service based resources and provides users with graphical programming interfaces to build a model to conduct computations and/or visualization efforts using the networked resources. Developments in the area of semantic integration of the networked datasets continue to advance and prototype studies can be accessed via the GEON portal at www.geongrid.org

CILogon: An Integrated Identity and Access Management Platform for Science

NASA Astrophysics Data System (ADS)

Basney, J.

2016-12-01

When scientists work together, they use web sites and other software to share their ideas and data. To ensure the integrity of their work, these systems require the scientists to log in and verify that they are part of the team working on a particular science problem. Too often, the identity and access verification process is a stumbling block for the scientists. Scientific research projects are forced to invest time and effort into developing and supporting Identity and Access Management (IAM) services, distracting them from the core goals of their research collaboration. CILogon provides an IAM platform that enables scientists to work together to meet their IAM needs more effectively so they can allocate more time and effort to their core mission of scientific research. The CILogon platform enables federated identity management and collaborative organization management. Federated identity management enables researchers to use their home organization identities to access cyberinfrastructure, rather than requiring yet another username and password to log on. Collaborative organization management enables research projects to define user groups for authorization to collaboration platforms (e.g., wikis, mailing lists, and domain applications). CILogon's IAM platform serves the unique needs of research collaborations, namely the need to dynamically form collaboration groups across organizations and countries, sharing access to data, instruments, compute clusters, and other resources to enable scientific discovery. CILogon provides a software-as-a-service platform to ease integration with cyberinfrastructure, while making all software components publicly available under open source licenses to enable re-use. Figure 1 illustrates the components and interfaces of this platform. CILogon has been operational since 2010 and has been used by over 7,000 researchers from more than 170 identity providers to access cyberinfrastructure including Globus, LIGO, Open Science Grid, SeedMe, and XSEDE. The "CILogon 2.0" platform, launched in 2016, adds support for virtual organization (VO) membership management, identity linking, international collaborations, and standard integration protocols, through integration with the Internet2 COmanage collaboration software.

Bigger data, collaborative tools and the future of predictive drug discovery

NASA Astrophysics Data System (ADS)

Ekins, Sean; Clark, Alex M.; Swamidass, S. Joshua; Litterman, Nadia; Williams, Antony J.

2014-10-01

Over the past decade we have seen a growth in the provision of chemistry data and cheminformatics tools as either free websites or software as a service commercial offerings. These have transformed how we find molecule-related data and use such tools in our research. There have also been efforts to improve collaboration between researchers either openly or through secure transactions using commercial tools. A major challenge in the future will be how such databases and software approaches handle larger amounts of data as it accumulates from high throughput screening and enables the user to draw insights, enable predictions and move projects forward. We now discuss how information from some drug discovery datasets can be made more accessible and how privacy of data should not overwhelm the desire to share it at an appropriate time with collaborators. We also discuss additional software tools that could be made available and provide our thoughts on the future of predictive drug discovery in this age of big data. We use some examples from our own research on neglected diseases, collaborations, mobile apps and algorithm development to illustrate these ideas.

Simple Web-based interactive key development software (WEBiKEY) and an example key for Kuruna (Poaceae: Bambusoideae).

PubMed

Attigala, Lakshmi; De Silva, Nuwan I; Clark, Lynn G

2016-04-01

Programs that are user-friendly and freely available for developing Web-based interactive keys are scarce and most of the well-structured applications are relatively expensive. WEBiKEY was developed to enable researchers to easily develop their own Web-based interactive keys with fewer resources. A Web-based multiaccess identification tool (WEBiKEY) was developed that uses freely available Microsoft ASP.NET technologies and an SQL Server database for Windows-based hosting environments. WEBiKEY was tested for its usability with a sample data set, the temperate woody bamboo genus Kuruna (Poaceae). WEBiKEY is freely available to the public and can be used to develop Web-based interactive keys for any group of species. The interactive key we developed for Kuruna using WEBiKEY enables users to visually inspect characteristics of Kuruna and identify an unknown specimen as one of seven possible species in the genus.

A Bookmarking Service for Organizing and Sharing URLs

NASA Technical Reports Server (NTRS)

Keller, Richard M.; Wolfe, Shawn R.; Chen, James R.; Mathe, Nathalie; Rabinowitz, Joshua L.

1997-01-01

Web browser bookmarking facilities predominate as the method of choice for managing URLs. In this paper, we describe some deficiencies of current bookmarking schemes, and examine an alternative to current approaches. We present WebTagger(TM), an implemented prototype of a personal bookmarking service that provides both individuals and groups with a customizable means of organizing and accessing Web-based information resources. In addition, the service enables users to supply feedback on the utility of these resources relative to their information needs, and provides dynamically-updated ranking of resources based on incremental user feedback. Individuals may access the service from anywhere on the Internet, and require no special software. This service greatly simplifies the process of sharing URLs within groups, in comparison with manual methods involving email. The underlying bookmark organization scheme is more natural and flexible than current hierarchical schemes supported by the major Web browsers, and enables rapid access to stored bookmarks.

Portable open-path optical remote sensing (ORS) Fourier transform infrared (FTIR) instrumentation miniaturization and software for point and click real-time analysis

NASA Astrophysics Data System (ADS)

Zemek, Peter G.; Plowman, Steven V.

2010-04-01

Advances in hardware have miniaturized the emissions spectrometer and associated optics, rendering them easily deployed in the field. Such systems are also suitable for vehicle mounting, and can provide high quality data and concentration information in minutes. Advances in software have accompanied this hardware evolution, enabling the development of portable point-and-click OP-FTIR systems that weigh less than 16 lbs. These systems are ideal for first-responders, military, law enforcement, forensics, and screening applications using optical remote sensing (ORS) methodologies. With canned methods and interchangeable detectors, the new generation of OP-FTIR technology is coupled to the latest forward reference-type model software to provide point-and-click technology. These software models have been established for some time. However, refined user-friendly models that use active, passive, and solar occultation methodologies now allow the user to quickly field-screen and quantify plumes, fence-lines, and combustion incident scenarios in high-temporal-resolution. Synthetic background generation is now redundant as the models use highly accurate instrument line shape (ILS) convolutions and several other parameters, in conjunction with radiative transfer model databases to model a single calibration spectrum to collected sample spectra. Data retrievals are performed directly on single beam spectra using non-linear classical least squares (NLCLS). Typically, the Hitran line database is used to generate the initial calibration spectrum contained within the software.

Advances in the REDCAT software package

PubMed Central

2013-01-01

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

Managing Content in a Matter of Minutes

NASA Technical Reports Server (NTRS)

2004-01-01

NASA software created to help scientists expeditiously search and organize their research documents is now aiding compliance personnel, law enforcement investigators, and the general public in their efforts to search, store, manage, and retrieve documents more efficiently. Developed at Ames Research Center, NETMARK software was designed to manipulate vast amounts of unstructured and semi-structured NASA documents. NETMARK is both a relational and object-oriented technology built on an Oracle enterprise-wide database. To ensure easy user access, Ames constructed NETMARK as a Web-enabled platform utilizing the latest in Internet technology. One of the significant benefits of the program was its ability to store and manage mission-critical data.

Data from fitting Gaussian process models to various data sets using eight Gaussian process software packages.

PubMed

Erickson, Collin B; Ankenman, Bruce E; Sanchez, Susan M

2018-06-01

This data article provides the summary data from tests comparing various Gaussian process software packages. Each spreadsheet represents a single function or type of function using a particular input sample size. In each spreadsheet, a row gives the results for a particular replication using a single package. Within each spreadsheet there are the results from eight Gaussian process model-fitting packages on five replicates of the surface. There is also one spreadsheet comparing the results from two packages performing stochastic kriging. These data enable comparisons between the packages to determine which package will give users the best results.

XaNSoNS: GPU-accelerated simulator of diffraction patterns of nanoparticles

NASA Astrophysics Data System (ADS)

Neverov, V. S.

XaNSoNS is an open source software with GPU support, which simulates X-ray and neutron 1D (or 2D) diffraction patterns and pair-distribution functions (PDF) for amorphous or crystalline nanoparticles (up to ∼107 atoms) of heterogeneous structural content. Among the multiple parameters of the structure the user may specify atomic displacements, site occupancies, molecular displacements and molecular rotations. The software uses general equations nonspecific to crystalline structures to calculate the scattering intensity. It supports four major standards of parallel computing: MPI, OpenMP, Nvidia CUDA and OpenCL, enabling it to run on various architectures, from CPU-based HPCs to consumer-level GPUs.

Automated response matching for organic scintillation detector arrays

NASA Astrophysics Data System (ADS)

Aspinall, M. D.; Joyce, M. J.; Cave, F. D.; Plenteda, R.; Tomanin, A.

2017-07-01

This paper identifies a digitizer technology with unique features that facilitates feedback control for the realization of a software-based technique for automatically calibrating detector responses. Three such auto-calibration techniques have been developed and are described along with an explanation of the main configuration settings and potential pitfalls. Automating this process increases repeatability, simplifies user operation, enables remote and periodic system calibration where consistency across detectors' responses are critical.

Rebuilding the NAVSEA Early Stage Ship Design Environment

DTIC Science & Technology

2010-04-01

rules -of- thumb to base these crucial decisions upon. With High Performance Computing (HPC) as an enabler, the vision is to explore all downstream...the results of the analysis back into LEAPS. Another software development worthy of discussion here is Intelligent Ship Arrangements ( ISA ), which...constraints and rules set by the users ahead of time. When used in a systematic and stochastic way, and when integrated using LEAPS, having this

Experiment Software and Projects on the Web with VISPA

NASA Astrophysics Data System (ADS)

Erdmann, M.; Fischer, B.; Fischer, R.; Geiser, E.; Glaser, C.; Müller, G.; Rieger, M.; Urban, M.; von Cube, R. F.; Welling, C.

2017-10-01

The Visual Physics Analysis (VISPA) project defines a toolbox for accessing software via the web. It is based on latest web technologies and provides a powerful extension mechanism that enables to interface a wide range of applications. Beyond basic applications such as a code editor, a file browser, or a terminal, it meets the demands of sophisticated experiment-specific use cases that focus on physics data analyses and typically require a high degree of interactivity. As an example, we developed a data inspector that is capable of browsing interactively through event content of several data formats, e.g., MiniAOD which is utilized by the CMS collaboration. The VISPA extension mechanism can also be used to embed external web-based applications that benefit from dynamic allocation of user-defined computing resources via SSH. For example, by wrapping the JSROOT project, ROOT files located on any remote machine can be inspected directly through a VISPA server instance. We introduced domains that combine groups of users and role-based permissions. Thereby, tailored projects are enabled, e.g. for teaching where access to student’s homework is restricted to a team of tutors, or for experiment-specific data that may only be accessible for members of the collaboration. We present the extension mechanism including corresponding applications and give an outlook onto the new permission system.

WinClastour—a Visual Basic program for tourmaline formula calculation and classification

NASA Astrophysics Data System (ADS)

Yavuz, Fuat; Yavuz, Vural; Sasmaz, Ahmet

2006-10-01

WinClastour is a Microsoft ® Visual Basic 6.0 program that enables the user to enter and calculate structural formulae of tourmaline analyses obtained both by the electron-microprobe or wet-chemical analyses. It is developed to predict cation site-allocations at the different structural positions, as well as to estimate mole percent of the end-members of the calcic-, alkali-, and X-site vacant group tourmalines. Using the different normalization schemes, such as 24.5 oxygens, 31 anions, 15 cations ( T+ Z+ Y), and 6 silicons, the present program classifies tourmaline data based on the classification scheme proposed by Hawthorne and Henry [1999. Classification of the minerals of the tourmaline group. European Journal of Mineralogy 11, 201-215]. The present program also enables the user Al-Mg disorder between Y and Z sites. WinClastour stores all the calculated results in a comma-delimited ASCII file format. Hence, output of the program can be displayed and processed by any other software for general data manipulation and graphing purposes. The compiled program code together with a test data file and related graphic files, which are designed to produce a high-quality printout from the Grapher program of Golden Software, is approximately 3 Mb as a self-extracting setup file.

The social disutility of software ownership.

PubMed

Douglas, David M

2011-09-01

Software ownership allows the owner to restrict the distribution of software and to prevent others from reading the software's source code and building upon it. However, free software is released to users under software licenses that give them the right to read the source code, modify it, reuse it, and distribute the software to others. Proponents of free software such as Richard M. Stallman and Eben Moglen argue that the social disutility of software ownership is a sufficient justification for prohibiting it. This social disutility includes the social instability of disregarding laws and agreements covering software use and distribution, inequality of software access, and the inability to help others by sharing software with them. Here I consider these and other social disutility claims against withholding specific software rights from users, in particular, the rights to read the source code, duplicate, distribute, modify, imitate, and reuse portions of the software within new programs. I find that generally while withholding these rights from software users does cause some degree of social disutility, only the rights to duplicate, modify and imitate cannot legitimately be denied to users on this basis. The social disutility of withholding the rights to distribute the software, read its source code and reuse portions of it in new programs is insufficient to prohibit software owners from denying them to users. A compromise between the software owner and user can minimise the social disutility of withholding these particular rights from users. However, the social disutility caused by software patents is sufficient for rejecting such patents as they restrict the methods of reducing social disutility possible with other forms of software ownership.

Prowess - A Software Model for the Ooty Wide Field Array

NASA Astrophysics Data System (ADS)

Marthi, Visweshwar Ram

2017-03-01

One of the scientific objectives of the Ooty Wide Field Array (OWFA) is to observe the redshifted H i emission from z ˜ 3.35. Although predictions spell out optimistic outcomes in reasonable integration times, these studies were based purely on analytical assumptions, without accounting for limiting systematics. A software model for OWFA has been developed with a view to understanding the instrument-induced systematics, by describing a complete software model for the instrument. This model has been implemented through a suite of programs, together called Prowess, which has been conceived with the dual role of an emulator as well as observatory data analysis software. The programming philosophy followed in building Prowess enables a general user to define an own set of functions and add new functionality. This paper describes a co-ordinate system suitable for OWFA in which the baselines are defined. The foregrounds are simulated from their angular power spectra. The visibilities are then computed from the foregrounds. These visibilities are then used for further processing, such as calibration and power spectrum estimation. The package allows for rich visualization features in multiple output formats in an interactive fashion, giving the user an intuitive feel for the data. Prowess has been extensively used for numerical predictions of the foregrounds for the OWFA H i experiment.

Common Data Models and Efficient Reproducible Workflows for Distributed Ocean Model Skill Assessment

NASA Astrophysics Data System (ADS)

Signell, R. P.; Snowden, D. P.; Howlett, E.; Fernandes, F. A.

2014-12-01

Model skill assessment requires discovery, access, analysis, and visualization of information from both sensors and models, and traditionally has been possible only by a few experts. The US Integrated Ocean Observing System (US-IOOS) consists of 17 Federal Agencies and 11 Regional Associations that produce data from various sensors and numerical models; exactly the information required for model skill assessment. US-IOOS is seeking to develop documented skill assessment workflows that are standardized, efficient, and reproducible so that a much wider community can participate in the use and assessment of model results. Standardization requires common data models for observational and model data. US-IOOS relies on the CF Conventions for observations and structured grid data, and on the UGRID Conventions for unstructured (e.g. triangular) grid data. This allows applications to obtain only the data they require in a uniform and parsimonious way using web services: OPeNDAP for model output and OGC Sensor Observation Service (SOS) for observed data. Reproducibility is enabled with IPython Notebooks shared on GitHub (http://github.com/ioos). These capture the entire skill assessment workflow, including user input, search, access, analysis, and visualization, ensuring that workflows are self-documenting and reproducible by anyone, using free software. Python packages for common data models are Pyugrid and the British Met Office Iris package. Python packages required to run the workflows (pyugrid, pyoos, and the British Met Office Iris package) are also available on GitHub and on Binstar.org so that users can run scenarios using the free Anaconda Python distribution. Hosted services such as Wakari enable anyone to reproduce these workflows for free, without installing any software locally, using just their web browser. We are also experimenting with Wakari Enterprise, which allows multi-user access from a web browser to an IPython Server running where large quantities of model output reside, increasing the efficiency. The open development and distribution of these workflows, and the software on which they depend, is an educational resource for those new to the field and a center of focus where practitioners can contribute new software and ideas.

'Tagger' - a Mac OS X Interactive Graphical Application for Data Inference and Analysis of N-Dimensional Datasets in the Natural Physical Sciences.

NASA Astrophysics Data System (ADS)

Morse, P. E.; Reading, A. M.; Lueg, C.

2014-12-01

Pattern-recognition in scientific data is not only a computational problem but a human-observer problem as well. Human observation of - and interaction with - data visualization software can augment, select, interrupt and modify computational routines and facilitate processes of pattern and significant feature recognition for subsequent human analysis, machine learning, expert and artificial intelligence systems.'Tagger' is a Mac OS X interactive data visualisation tool that facilitates Human-Computer interaction for the recognition of patterns and significant structures. It is a graphical application developed using the Quartz Composer framework. 'Tagger' follows a Model-View-Controller (MVC) software architecture: the application problem domain (the model) is to facilitate novel ways of abstractly representing data to a human interlocutor, presenting these via different viewer modalities (e.g. chart representations, particle systems, parametric geometry) to the user (View) and enabling interaction with the data (Controller) via a variety of Human Interface Devices (HID). The software enables the user to create an arbitrary array of tags that may be appended to the visualised data, which are then saved into output files as forms of semantic metadata. Three fundamental problems that are not strongly supported by conventional scientific visualisation software are addressed:1] How to visually animate data over time, 2] How to rapidly deploy unconventional parametrically driven data visualisations, 3] How to construct and explore novel interaction models that capture the activity of the end-user as semantic metadata that can be used to computationally enhance subsequent interrogation. Saved tagged data files may be loaded into Tagger, so that tags may be tagged, if desired. Recursion opens up the possibility of refining or overlapping different types of tags, tagging a variety of different POIs or types of events, and of capturing different types of specialist observations of important or noticeable events. Other visualisations and modes of interaction will also be demonstrated, with the aim of discovering knowledge in large datasets in the natural, physical sciences. Fig.1 Wave height data from an oceanographic Wave Rider Buoy. Colors/radii are driven by wave height data.

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

PubMed

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

2018-01-01

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

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.

Translator for Optimizing Fluid-Handling Components

NASA Technical Reports Server (NTRS)

Landon, Mark; Perry, Ernest

2007-01-01

A software interface has been devised to facilitate optimization of the shapes of valves, elbows, fittings, and other components used to handle fluids under extreme conditions. This software interface translates data files generated by PLOT3D (a NASA grid-based plotting-and- data-display program) and by computational fluid dynamics (CFD) software into a format in which the files can be read by Sculptor, which is a shape-deformation- and-optimization program. Sculptor enables the user to interactively, smoothly, and arbitrarily deform the surfaces and volumes in two- and three-dimensional CFD models. Sculptor also includes design-optimization algorithms that can be used in conjunction with the arbitrary-shape-deformation components to perform automatic shape optimization. In the optimization process, the output of the CFD software is used as feedback while the optimizer strives to satisfy design criteria that could include, for example, improved values of pressure loss, velocity, flow quality, mass flow, etc.

IBM system/360 assembly language interval arithmetic software

NASA Technical Reports Server (NTRS)

Phillips, E. J.

1972-01-01

Computer software designed to perform interval arithmetic is described. An interval is defined as the set of all real numbers between two given numbers including or excluding one or both endpoints. Interval arithmetic consists of the various elementary arithmetic operations defined on the set of all intervals, such as interval addition, subtraction, union, etc. One of the main applications of interval arithmetic is in the area of error analysis of computer calculations. For example, it has been used sucessfully to compute bounds on sounding errors in the solution of linear algebraic systems, error bounds in numerical solutions of ordinary differential equations, as well as integral equations and boundary value problems. The described software enables users to implement algorithms of the type described in references efficiently on the IBM 360 system.

OIPAV: an integrated software system for ophthalmic image processing, analysis and visualization

NASA Astrophysics Data System (ADS)

Zhang, Lichun; Xiang, Dehui; Jin, Chao; Shi, Fei; Yu, Kai; Chen, Xinjian

2018-03-01

OIPAV (Ophthalmic Images Processing, Analysis and Visualization) is a cross-platform software which is specially oriented to ophthalmic images. It provides a wide range of functionalities including data I/O, image processing, interaction, ophthalmic diseases detection, data analysis and visualization to help researchers and clinicians deal with various ophthalmic images such as optical coherence tomography (OCT) images and color photo of fundus, etc. It enables users to easily access to different ophthalmic image data manufactured from different imaging devices, facilitate workflows of processing ophthalmic images and improve quantitative evaluations. In this paper, we will present the system design and functional modules of the platform and demonstrate various applications. With a satisfying function scalability and expandability, we believe that the software can be widely applied in ophthalmology field.

Software for Tracking Costs of Mars Projects

NASA Technical Reports Server (NTRS)

Wong, Alvin; Warfield, Keith

2003-01-01

The Mars Cost Tracking Model is a computer program that administers a system set up for tracking the costs of future NASA projects that pertain to Mars. Previously, no such tracking system existed, and documentation was written in a variety of formats and scattered in various places. It was difficult to justify costs or even track the history of costs of a spacecraft mission to Mars. The present software enables users to maintain all cost-model definitions, documentation, and justifications of cost estimates in one computer system that is accessible via the Internet. The software provides sign-off safeguards to ensure the reliability of information entered into the system. This system may eventually be used to track the costs of projects other than only those that pertain to Mars.

ICAROUS - Integrated Configurable Algorithms for Reliable Operations Of Unmanned Systems

NASA Technical Reports Server (NTRS)

Consiglio, María; Muñoz, César; Hagen, George; Narkawicz, Anthony; Balachandran, Swee

2016-01-01

NASA's Unmanned Aerial System (UAS) Traffic Management (UTM) project aims at enabling near-term, safe operations of small UAS vehicles in uncontrolled airspace, i.e., Class G airspace. A far-term goal of UTM research and development is to accommodate the expected rise in small UAS traffic density throughout the National Airspace System (NAS) at low altitudes for beyond visual line-of-sight operations. This paper describes a new capability referred to as ICAROUS (Integrated Configurable Algorithms for Reliable Operations of Unmanned Systems), which is being developed under the UTM project. ICAROUS is a software architecture comprised of highly assured algorithms for building safety-centric, autonomous, unmanned aircraft applications. Central to the development of the ICAROUS algorithms is the use of well-established formal methods to guarantee higher levels of safety assurance by monitoring and bounding the behavior of autonomous systems. The core autonomy-enabling capabilities in ICAROUS include constraint conformance monitoring and contingency control functions. ICAROUS also provides a highly configurable user interface that enables the modular integration of mission-specific software components.

ICAROUS: Integrated Configurable Architecture for Unmanned Systems

NASA Technical Reports Server (NTRS)

Consiglio, Maria C.

2016-01-01

NASA's Unmanned Aerial System (UAS) Traffic Management (UTM) project aims at enabling near-term, safe operations of small UAS vehicles in uncontrolled airspace, i.e., Class G airspace. A far-term goal of UTM research and development is to accommodate the expected rise in small UAS traffic density throughout the National Airspace System (NAS) at low altitudes for beyond visual line-of-sight operations. This video describes a new capability referred to as ICAROUS (Integrated Configurable Algorithms for Reliable Operations of Unmanned Systems), which is being developed under the auspices of the UTM project. ICAROUS is a software architecture comprised of highly assured algorithms for building safety-centric, autonomous, unmanned aircraft applications. Central to the development of the ICAROUS algorithms is the use of well-established formal methods to guarantee higher levels of safety assurance by monitoring and bounding the behavior of autonomous systems. The core autonomy-enabling capabilities in ICAROUS include constraint conformance monitoring and autonomous detect and avoid functions. ICAROUS also provides a highly configurable user interface that enables the modular integration of mission-specific software components.

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.

ABrox-A user-friendly Python module for approximate Bayesian computation with a focus on model comparison.

PubMed

Mertens, Ulf Kai; Voss, Andreas; Radev, Stefan

2018-01-01

We give an overview of the basic principles of approximate Bayesian computation (ABC), a class of stochastic methods that enable flexible and likelihood-free model comparison and parameter estimation. Our new open-source software called ABrox is used to illustrate ABC for model comparison on two prominent statistical tests, the two-sample t-test and the Levene-Test. We further highlight the flexibility of ABC compared to classical Bayesian hypothesis testing by computing an approximate Bayes factor for two multinomial processing tree models. Last but not least, throughout the paper, we introduce ABrox using the accompanied graphical user interface.

The PyRosetta Toolkit: a graphical user interface for the Rosetta software suite.

PubMed

Adolf-Bryfogle, Jared; Dunbrack, Roland L

2013-01-01

The Rosetta Molecular Modeling suite is a command-line-only collection of applications that enable high-resolution modeling and design of proteins and other molecules. Although extremely useful, Rosetta can be difficult to learn for scientists with little computational or programming experience. To that end, we have created a Graphical User Interface (GUI) for Rosetta, called the PyRosetta Toolkit, for creating and running protocols in Rosetta for common molecular modeling and protein design tasks and for analyzing the results of Rosetta calculations. The program is highly extensible so that developers can add new protocols and analysis tools to the PyRosetta Toolkit GUI.

Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform

PubMed Central

2013-01-01

Background Immunoassays that employ multiplexed bead arrays produce high information content per sample. Such assays are now frequently used to evaluate humoral responses in clinical trials. Integrated software is needed for the analysis, quality control, and secure sharing of the high volume of data produced by such multiplexed assays. Software that facilitates data exchange and provides flexibility to perform customized analyses (including multiple curve fits and visualizations of assay performance over time) could increase scientists’ capacity to use these immunoassays to evaluate human clinical trials. Results The HIV Vaccine Trials Network and the Statistical Center for HIV/AIDS Research and Prevention collaborated with LabKey Software to enhance the open source LabKey Server platform to facilitate workflows for multiplexed bead assays. This system now supports the management, analysis, quality control, and secure sharing of data from multiplexed immunoassays that leverage Luminex xMAP® technology. These assays may be custom or kit-based. Newly added features enable labs to: (i) import run data from spreadsheets output by Bio-Plex Manager™ software; (ii) customize data processing, curve fits, and algorithms through scripts written in common languages, such as R; (iii) select script-defined calculation options through a graphical user interface; (iv) collect custom metadata for each titration, analyte, run and batch of runs; (v) calculate dose–response curves for titrations; (vi) interpolate unknown concentrations from curves for titrated standards; (vii) flag run data for exclusion from analysis; (viii) track quality control metrics across runs using Levey-Jennings plots; and (ix) automatically flag outliers based on expected values. Existing system features allow researchers to analyze, integrate, visualize, export and securely share their data, as well as to construct custom user interfaces and workflows. Conclusions Unlike other tools tailored for Luminex immunoassays, LabKey Server allows labs to customize their Luminex analyses using scripting while still presenting users with a single, graphical interface for processing and analyzing data. The LabKey Server system also stands out among Luminex tools for enabling smooth, secure transfer of data, quality control information, and analyses between collaborators. LabKey Server and its Luminex features are freely available as open source software at http://www.labkey.com under the Apache 2.0 license. PMID:23631706

Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform.

PubMed

Eckels, Josh; Nathe, Cory; Nelson, Elizabeth K; Shoemaker, Sara G; Nostrand, Elizabeth Van; Yates, Nicole L; Ashley, Vicki C; Harris, Linda J; Bollenbeck, Mark; Fong, Youyi; Tomaras, Georgia D; Piehler, Britt

2013-04-30

Immunoassays that employ multiplexed bead arrays produce high information content per sample. Such assays are now frequently used to evaluate humoral responses in clinical trials. Integrated software is needed for the analysis, quality control, and secure sharing of the high volume of data produced by such multiplexed assays. Software that facilitates data exchange and provides flexibility to perform customized analyses (including multiple curve fits and visualizations of assay performance over time) could increase scientists' capacity to use these immunoassays to evaluate human clinical trials. The HIV Vaccine Trials Network and the Statistical Center for HIV/AIDS Research and Prevention collaborated with LabKey Software to enhance the open source LabKey Server platform to facilitate workflows for multiplexed bead assays. This system now supports the management, analysis, quality control, and secure sharing of data from multiplexed immunoassays that leverage Luminex xMAP® technology. These assays may be custom or kit-based. Newly added features enable labs to: (i) import run data from spreadsheets output by Bio-Plex Manager™ software; (ii) customize data processing, curve fits, and algorithms through scripts written in common languages, such as R; (iii) select script-defined calculation options through a graphical user interface; (iv) collect custom metadata for each titration, analyte, run and batch of runs; (v) calculate dose-response curves for titrations; (vi) interpolate unknown concentrations from curves for titrated standards; (vii) flag run data for exclusion from analysis; (viii) track quality control metrics across runs using Levey-Jennings plots; and (ix) automatically flag outliers based on expected values. Existing system features allow researchers to analyze, integrate, visualize, export and securely share their data, as well as to construct custom user interfaces and workflows. Unlike other tools tailored for Luminex immunoassays, LabKey Server allows labs to customize their Luminex analyses using scripting while still presenting users with a single, graphical interface for processing and analyzing data. The LabKey Server system also stands out among Luminex tools for enabling smooth, secure transfer of data, quality control information, and analyses between collaborators. LabKey Server and its Luminex features are freely available as open source software at http://www.labkey.com under the Apache 2.0 license.

Information management and analysis system for groundwater data in Thailand

NASA Astrophysics Data System (ADS)

Gill, D.; Luckananurung, P.

1992-01-01

The Ground Water Division of the Thai Department of Mineral Resources maintains a large archive of groundwater data with information on some 50,000 water wells. Each well file contains information on well location, well completion, borehole geology, water levels, water quality, and pumping tests. In order to enable efficient use of this information a computer-based system for information management and analysis was created. The project was sponsored by the United Nations Development Program and the Thai Department of Mineral Resources. The system was designed to serve users who lack prior training in automated data processing. Access is through a friendly user/system dialogue. Tasks are segmented into a number of logical steps, each of which is managed by a separate screen. Selective retrieval is possible by four different methods of area definition and by compliance with user-specified constraints on any combination of database variables. The main types of outputs are: (1) files of retrieved data, screened according to users' specifications; (2) an assortment of pre-formatted reports; (3) computed geochemical parameters and various diagrams of water chemistry derived therefrom; (4) bivariate scatter diagrams and linear regression analysis; (5) posting of data and computed results on maps; and (6) hydraulic aquifer characteristics as computed from pumping tests. Data are entered directly from formatted screens. Most records can be copied directly from hand-written documents. The database-management program performs data integrity checks in real time, enabling corrections at the time of input. The system software can be grouped into: (1) database administration and maintenance—these functions are carried out by the SIR/DBMS software package; (2) user communication interface for task definition and execution control—the interface is written in the operating system command language (VMS/DCL) and in FORTRAN 77; and (3) scientific data-processing programs, written in FORTRAN 77. The system was implemented on a DEC MicroVAX II computer.

Identification of MS-Cleavable and Non-Cleavable Chemically Crosslinked Peptides with MetaMorpheus.

PubMed

Lu, Lei; Millikin, Robert J; Solntsev, Stefan K; Rolfs, Zach; Scalf, Mark; Shortreed, Michael R; Smith, Lloyd M

2018-05-25

Protein chemical crosslinking combined with mass spectrometry has become an important technique for the analysis of protein structure and protein-protein interactions. A variety of crosslinkers are well developed, but reliable, rapid, and user-friendly tools for large-scale analysis of crosslinked proteins are still in need. Here we report MetaMorpheusXL, a new search module within the MetaMorpheus software suite that identifies both MS-cleavable and non-cleavable crosslinked peptides in MS data. MetaMorpheusXL identifies MS-cleavable crosslinked peptides with an ion-indexing algorithm, which enables an efficient large database search. The identification does not require the presence of signature fragment ions, an advantage compared to similar programs such as XlinkX. One complication associated with the need for signature ions from cleavable crosslinkers such as DSSO (disuccinimidyl sulfoxide) is the requirement for multiple fragmentation types and energy combinations, which is not necessary for MetaMorpheusXL. The ability to perform proteome-wide analysis is another advantage of MetaMorpheusXl compared to such programs as MeroX and DXMSMS. MetaMorpheusXL is also faster than other currently available MS-cleavable crosslink search software programs. It is imbedded in MetaMorpheus, an open-source and freely available software suite that provides a reliable, fast, user-friendly graphical user interface that is readily accessible to researchers.

Multi-Mission Automated Task Invocation Subsystem

NASA Technical Reports Server (NTRS)

Cheng, Cecilia S.; Patel, Rajesh R.; Sayfi, Elias M.; Lee, Hyun H.

2009-01-01

Multi-Mission Automated Task Invocation Subsystem (MATIS) is software that establishes a distributed data-processing framework for automated generation of instrument data products from a spacecraft mission. Each mission may set up a set of MATIS servers for processing its data products. MATIS embodies lessons learned in experience with prior instrument- data-product-generation software. MATIS is an event-driven workflow manager that interprets project-specific, user-defined rules for managing processes. It executes programs in response to specific events under specific conditions according to the rules. Because requirements of different missions are too diverse to be satisfied by one program, MATIS accommodates plug-in programs. MATIS is flexible in that users can control such processing parameters as how many pipelines to run and on which computing machines to run them. MATIS has a fail-safe capability. At each step, MATIS captures and retains pertinent information needed to complete the step and start the next step. In the event of a restart, this information is retrieved so that processing can be resumed appropriately. At this writing, it is planned to develop a graphical user interface (GUI) for monitoring and controlling a product generation engine in MATIS. The GUI would enable users to schedule multiple processes and manage the data products produced in the processes. Although MATIS was initially designed for instrument data product generation,

PeptideDepot: Flexible Relational Database for Visual Analysis of Quantitative Proteomic Data and Integration of Existing Protein Information

PubMed Central

Yu, Kebing; Salomon, Arthur R.

2010-01-01

Recently, dramatic progress has been achieved in expanding the sensitivity, resolution, mass accuracy, and scan rate of mass spectrometers able to fragment and identify peptides through tandem mass spectrometry (MS/MS). Unfortunately, this enhanced ability to acquire proteomic data has not been accompanied by a concomitant increase in the availability of flexible tools allowing users to rapidly assimilate, explore, and analyze this data and adapt to a variety of experimental workflows with minimal user intervention. Here we fill this critical gap by providing a flexible relational database called PeptideDepot for organization of expansive proteomic data sets, collation of proteomic data with available protein information resources, and visual comparison of multiple quantitative proteomic experiments. Our software design, built upon the synergistic combination of a MySQL database for safe warehousing of proteomic data with a FileMaker-driven graphical user interface for flexible adaptation to diverse workflows, enables proteomic end-users to directly tailor the presentation of proteomic data to the unique analysis requirements of the individual proteomics lab. PeptideDepot may be deployed as an independent software tool or integrated directly with our High Throughput Autonomous Proteomic Pipeline (HTAPP) used in the automated acquisition and post-acquisition analysis of proteomic data. PMID:19834895

Micromechanics-Based Structural Analysis (FEAMAC) and Multiscale Visualization within Abaqus/CAE Environment

NASA Technical Reports Server (NTRS)

Arnold, Steven M.; Bednarcyk, Brett A.; Hussain, Aquila; Katiyar, Vivek

2010-01-01

A unified framework is presented that enables coupled multiscale analysis of composite structures and associated graphical pre- and postprocessing within the Abaqus/CAE environment. The recently developed, free, Finite Element Analysis--Micromechanics Analysis Code (FEAMAC) software couples NASA's Micromechanics Analysis Code with Generalized Method of Cells (MAC/GMC) with Abaqus/Standard and Abaqus/Explicit to perform micromechanics based FEA such that the nonlinear composite material response at each integration point is modeled at each increment by MAC/GMC. The Graphical User Interfaces (FEAMAC-Pre and FEAMAC-Post), developed through collaboration between SIMULIA Erie and the NASA Glenn Research Center, enable users to employ a new FEAMAC module within Abaqus/CAE that provides access to the composite microscale. FEA IAC-Pre is used to define and store constituent material properties, set-up and store composite repeating unit cells, and assign composite materials as sections with all data being stored within the CAE database. Likewise FEAMAC-Post enables multiscale field quantity visualization (contour plots, X-Y plots), with point and click access to the microscale i.e., fiber and matrix fields).

A generic open-source software framework supporting scenario simulations in bioterrorist crises.

PubMed

Falenski, Alexander; Filter, Matthias; Thöns, Christian; Weiser, Armin A; Wigger, Jan-Frederik; Davis, Matthew; Douglas, Judith V; Edlund, Stefan; Hu, Kun; Kaufman, James H; Appel, Bernd; Käsbohrer, Annemarie

2013-09-01

Since the 2001 anthrax attack in the United States, awareness of threats originating from bioterrorism has grown. This led internationally to increased research efforts to improve knowledge of and approaches to protecting human and animal populations against the threat from such attacks. A collaborative effort in this context is the extension of the open-source Spatiotemporal Epidemiological Modeler (STEM) simulation and modeling software for agro- or bioterrorist crisis scenarios. STEM, originally designed to enable community-driven public health disease models and simulations, was extended with new features that enable integration of proprietary data as well as visualization of agent spread along supply and production chains. STEM now provides a fully developed open-source software infrastructure supporting critical modeling tasks such as ad hoc model generation, parameter estimation, simulation of scenario evolution, estimation of effects of mitigation or management measures, and documentation. This open-source software resource can be used free of charge. Additionally, STEM provides critical features like built-in worldwide data on administrative boundaries, transportation networks, or environmental conditions (eg, rainfall, temperature, elevation, vegetation). Users can easily combine their own confidential data with built-in public data to create customized models of desired resolution. STEM also supports collaborative and joint efforts in crisis situations by extended import and export functionalities. In this article we demonstrate specifically those new software features implemented to accomplish STEM application in agro- or bioterrorist crisis scenarios.

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

PubMed Central

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

2016-01-01

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

A Concept for the One Degree Imager (ODI) Data Reduction Pipeline and Archiving System

NASA Astrophysics Data System (ADS)

Knezek, Patricia; Stobie, B.; Michael, S.; Valdes, F.; Marru, S.; Henschel, R.; Pierce, M.

2010-05-01

The One Degree Imager (ODI), currently being built by the WIYN Observatory, will provide tremendous possibilities for conducting diverse scientific programs. ODI will be a complex instrument, using non-conventional Orthogonal Transfer Array (OTA) detectors. Due to its large field of view, small pixel size, use of OTA technology, and expected frequent use, ODI will produce vast amounts of astronomical data. If ODI is to achieve its full potential, a data reduction pipeline must be developed. Long-term archiving must also be incorporated into the pipeline system to ensure the continued value of ODI data. This paper presents a concept for an ODI data reduction pipeline and archiving system. To limit costs and development time, our plan leverages existing software and hardware, including existing pipeline software, Science Gateways, Computational Grid & Cloud Technology, Indiana University's Data Capacitor and Massive Data Storage System, and TeraGrid compute resources. Existing pipeline software will be augmented to add functionality required to meet challenges specific to ODI, enhance end-user control, and enable the execution of the pipeline on grid resources including national grid resources such as the TeraGrid and Open Science Grid. The planned system offers consistent standard reductions and end-user flexibility when working with images beyond the initial instrument signature removal. It also gives end-users access to computational and storage resources far beyond what are typically available at most institutions. Overall, the proposed system provides a wide array of software tools and the necessary hardware resources to use them effectively.

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

PubMed

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

2017-07-15

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

BioShaDock: a community driven bioinformatics shared Docker-based tools registry

PubMed Central

Moreews, François; Sallou, Olivier; Ménager, Hervé; Le bras, Yvan; Monjeaud, Cyril; Blanchet, Christophe; Collin, Olivier

2015-01-01

Linux container technologies, as represented by Docker, provide an alternative to complex and time-consuming installation processes needed for scientific software. The ease of deployment and the process isolation they enable, as well as the reproducibility they permit across environments and versions, are among the qualities that make them interesting candidates for the construction of bioinformatic infrastructures, at any scale from single workstations to high throughput computing architectures. The Docker Hub is a public registry which can be used to distribute bioinformatic software as Docker images. However, its lack of curation and its genericity make it difficult for a bioinformatics user to find the most appropriate images needed. BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images. It provides a number of improvements over the base Docker registry on authentication and permissions management, that enable its integration in existing bioinformatic infrastructures such as computing platforms. The metadata associated with the registered images are domain-centric, including for instance concepts defined in the EDAM ontology, a shared and structured vocabulary of commonly used terms in bioinformatics. The registry also includes user defined tags to facilitate its discovery, as well as a link to the tool description in the ELIXIR registry if it already exists. If it does not, the BioShaDock registry will synchronize with the registry to create a new description in the Elixir registry, based on the BioShaDock entry metadata. This link will help users get more information on the tool such as its EDAM operations, input and output types. This allows integration with the ELIXIR Tools and Data Services Registry, thus providing the appropriate visibility of such images to the bioinformatics community. PMID:26913191

BioShaDock: a community driven bioinformatics shared Docker-based tools registry.

PubMed

Moreews, François; Sallou, Olivier; Ménager, Hervé; Le Bras, Yvan; Monjeaud, Cyril; Blanchet, Christophe; Collin, Olivier

2015-01-01

Linux container technologies, as represented by Docker, provide an alternative to complex and time-consuming installation processes needed for scientific software. The ease of deployment and the process isolation they enable, as well as the reproducibility they permit across environments and versions, are among the qualities that make them interesting candidates for the construction of bioinformatic infrastructures, at any scale from single workstations to high throughput computing architectures. The Docker Hub is a public registry which can be used to distribute bioinformatic software as Docker images. However, its lack of curation and its genericity make it difficult for a bioinformatics user to find the most appropriate images needed. BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images. It provides a number of improvements over the base Docker registry on authentication and permissions management, that enable its integration in existing bioinformatic infrastructures such as computing platforms. The metadata associated with the registered images are domain-centric, including for instance concepts defined in the EDAM ontology, a shared and structured vocabulary of commonly used terms in bioinformatics. The registry also includes user defined tags to facilitate its discovery, as well as a link to the tool description in the ELIXIR registry if it already exists. If it does not, the BioShaDock registry will synchronize with the registry to create a new description in the Elixir registry, based on the BioShaDock entry metadata. This link will help users get more information on the tool such as its EDAM operations, input and output types. This allows integration with the ELIXIR Tools and Data Services Registry, thus providing the appropriate visibility of such images to the bioinformatics community.

Support Vector Machine algorithm for regression and classification

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

Yu, Chenggang; Zavaljevski, Nela

2001-08-01

The software is an implementation of the Support Vector Machine (SVM) algorithm that was invented and developed by Vladimir Vapnik and his co-workers at AT&T Bell Laboratories. The specific implementation reported here is an Active Set method for solving a quadratic optimization problem that forms the major part of any SVM program. The implementation is tuned to specific constraints generated in the SVM learning. Thus, it is more efficient than general-purpose quadratic optimization programs. A decomposition method has been implemented in the software that enables processing large data sets. The size of the learning data is virtually unlimited by themore » capacity of the computer physical memory. The software is flexible and extensible. Two upper bounds are implemented to regulate the SVM learning for classification, which allow users to adjust the false positive and false negative rates. The software can be used either as a standalone, general-purpose SVM regression or classification program, or be embedded into a larger software system.« less

STRS Radio Service Software for NASA's SCaN Testbed

NASA Technical Reports Server (NTRS)

Mortensen, Dale J.; Bishop, Daniel Wayne; Chelmins, David T.

2012-01-01

NASAs Space Communication and Navigation(SCaN) Testbed was launched to the International Space Station in 2012. The objective is to promote new software defined radio technologies and associated software application reuse, enabled by this first flight of NASAs Space Telecommunications Radio System(STRS) architecture standard. Pre-launch testing with the testbeds software defined radios was performed as part of system integration. Radio services for the JPL SDR were developed during system integration to allow the waveform application to operate properly in the space environment, especially considering thermal effects. These services include receiver gain control, frequency offset, IQ modulator balance, and transmit level control. Development, integration, and environmental testing of the radio services will be described. The added software allows the waveform application to operate properly in the space environment, and can be reused by future experimenters testing different waveform applications. Integrating such services with the platform provided STRS operating environment will attract more users, and these services are candidates for interface standardization via STRS.

STRS Radio Service Software for NASA's SCaN Testbed

NASA Technical Reports Server (NTRS)

Mortensen, Dale J.; Bishop, Daniel Wayne; Chelmins, David T.

2013-01-01

NASA's Space Communication and Navigation(SCaN) Testbed was launched to the International Space Station in 2012. The objective is to promote new software defined radio technologies and associated software application reuse, enabled by this first flight of NASA's Space Telecommunications Radio System (STRS) architecture standard. Pre-launch testing with the testbed's software defined radios was performed as part of system integration. Radio services for the JPL SDR were developed during system integration to allow the waveform application to operate properly in the space environment, especially considering thermal effects. These services include receiver gain control, frequency offset, IQ modulator balance, and transmit level control. Development, integration, and environmental testing of the radio services will be described. The added software allows the waveform application to operate properly in the space environment, and can be reused by future experimenters testing different waveform applications. Integrating such services with the platform provided STRS operating environment will attract more users, and these services are candidates for interface standardization via STRS.

PSAMM: A Portable System for the Analysis of Metabolic Models

PubMed Central

Steffensen, Jon Lund; Dufault-Thompson, Keith; Zhang, Ying

2016-01-01

The genome-scale models of metabolic networks have been broadly applied in phenotype prediction, evolutionary reconstruction, community functional analysis, and metabolic engineering. Despite the development of tools that support individual steps along the modeling procedure, it is still difficult to associate mathematical simulation results with the annotation and biological interpretation of metabolic models. In order to solve this problem, here we developed a Portable System for the Analysis of Metabolic Models (PSAMM), a new open-source software package that supports the integration of heterogeneous metadata in model annotations and provides a user-friendly interface for the analysis of metabolic models. PSAMM is independent of paid software environments like MATLAB, and all its dependencies are freely available for academic users. Compared to existing tools, PSAMM significantly reduced the running time of constraint-based analysis and enabled flexible settings of simulation parameters using simple one-line commands. The integration of heterogeneous, model-specific annotation information in PSAMM is achieved with a novel format of YAML-based model representation, which has several advantages, such as providing a modular organization of model components and simulation settings, enabling model version tracking, and permitting the integration of multiple simulation problems. PSAMM also includes a number of quality checking procedures to examine stoichiometric balance and to identify blocked reactions. Applying PSAMM to 57 models collected from current literature, we demonstrated how the software can be used for managing and simulating metabolic models. We identified a number of common inconsistencies in existing models and constructed an updated model repository to document the resolution of these inconsistencies. PMID:26828591

Image-based mobile service: automatic text extraction and translation

NASA Astrophysics Data System (ADS)

Berclaz, Jérôme; Bhatti, Nina; Simske, Steven J.; Schettino, John C.

2010-01-01

We present a new mobile service for the translation of text from images taken by consumer-grade cell-phone cameras. Such capability represents a new paradigm for users where a simple image provides the basis for a service. The ubiquity and ease of use of cell-phone cameras enables acquisition and transmission of images anywhere and at any time a user wishes, delivering rapid and accurate translation over the phone's MMS and SMS facilities. Target text is extracted completely automatically, requiring no bounding box delineation or related user intervention. The service uses localization, binarization, text deskewing, and optical character recognition (OCR) in its analysis. Once the text is translated, an SMS message is sent to the user with the result. Further novelties include that no software installation is required on the handset, any service provider or camera phone can be used, and the entire service is implemented on the server side.

Lipid Informed Quantitation and Identification

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

Kevin Crowell, PNNL

2014-07-21

LIQUID (Lipid Informed Quantitation and Identification) is a software program that has been developed to enable users to conduct both informed and high-throughput global liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based lipidomics analysis. This newly designed desktop application can quickly identify and quantify lipids from LC-MS/MS datasets while providing a friendly graphical user interface for users to fully explore the data. Informed data analysis simply involves the user specifying an electrospray ionization mode, lipid common name (i.e. PE(16:0/18:2)), and associated charge carrier. A stemplot of the isotopic profile and a line plot of the extracted ion chromatogram are also provided to showmore » the MS-level evidence of the identified lipid. In addition to plots, other information such as intensity, mass measurement error, and elution time are also provided. Typically, a global analysis for 15,000 lipid targets« less

The U. S. Geological Survey, Digital Spectral Library: Version 1 (0.2 to 3.0um)

USGS Publications Warehouse

Clark, Roger N.; Swayze, Gregg A.; Gallagher, Andrea J.; King, Trude V.V.; Calvin, Wendy M.

1993-01-01

We have developed a digital reflectance spectral library, with management and spectral analysis software. The library includes 498 spectra of 444 samples (some samples include a series of grain sizes) measured from approximately 0.2 to 3.0 um . The spectral resolution (Full Width Half Maximum) of the reflectance data is <= 4 nm in the visible (0.2-0.8 um) and <= 10 nm in the NIR (0.8-2.35 um). All spectra were corrected to absolute reflectance using an NIST Halon standard. Library management software lets users search on parameters (e.g. chemical formulae, chemical analyses, purity of samples, mineral groups, etc.) as well as spectral features. Minerals from borate, carbonate, chloride, element, halide, hydroxide, nitrate, oxide, phosphate, sulfate, sulfide, sulfosalt, and the silicate (cyclosilicate, inosilicate, nesosilicate, phyllosilicate, sorosilicate, and tectosilicate) classes are represented. X-Ray and chemical analyses are tabulated for many of the entries, and all samples have been evaluated for spectral purity. The library also contains end and intermediate members for the olivine, garnet, scapolite, montmorillonite, muscovite, jarosite, and alunite solid-solution series. We have included representative spectra of H2O ice, kerogen, ammonium-bearing minerals, rare-earth oxides, desert varnish coatings, kaolinite crystallinity series, kaolinite-smectite series, zeolite series, and an extensive evaporite series. Because of the importance of vegetation to climate-change studies we have include 17 spectra of tree leaves, bushes, and grasses. The library and software are available as a series of U.S.G.S. Open File reports. PC user software is available to convert the binary data to ascii files (a separate U.S.G.S. open file report). Additionally, a binary data files are on line at the U.S.G.S. in Denver for anonymous ftp to users on the Internet. The library search software enables a user to search on documentation parameters as well as spectral features. The analysis system includes general spectral analysis routines, plotting packages, radiative transfer software for computing intimate mixtures, routines to derive optical constants from reflectance spectra, tools to analyze spectral features, and the capability to access imaging spectrometer data cubes for spectral analysis. Users may build customized libraries (at specific wavelengths and spectral resolution) for their own instruments using the library software. We are currently extending spectral coverage to 150 um. The libraries (original and convolved) will be made available in the future on a CD-ROM.

Requirements Engineering in Building Climate Science Software

NASA Astrophysics Data System (ADS)

Batcheller, Archer L.

Software has an important role in supporting scientific work. This dissertation studies teams that build scientific software, focusing on the way that they determine what the software should do. These requirements engineering processes are investigated through three case studies of climate science software projects. The Earth System Modeling Framework assists modeling applications, the Earth System Grid distributes data via a web portal, and the NCAR (National Center for Atmospheric Research) Command Language is used to convert, analyze and visualize data. Document analysis, observation, and interviews were used to investigate the requirements-related work. The first research question is about how and why stakeholders engage in a project, and what they do for the project. Two key findings arise. First, user counts are a vital measure of project success, which makes adoption important and makes counting tricky and political. Second, despite the importance of quantities of users, a few particular "power users" develop a relationship with the software developers and play a special role in providing feedback to the software team and integrating the system into user practice. The second research question focuses on how project objectives are articulated and how they are put into practice. The team seeks to both build a software system according to product requirements but also to conduct their work according to process requirements such as user support. Support provides essential communication between users and developers that assists with refining and identifying requirements for the software. It also helps users to learn and apply the software to their real needs. User support is a vital activity for scientific software teams aspiring to create infrastructure. The third research question is about how change in scientific practice and knowledge leads to changes in the software, and vice versa. The "thickness" of a layer of software infrastructure impacts whether the software team or users have control and responsibility for making changes in response to new scientific ideas. Thick infrastructure provides more functionality for users, but gives them less control of it. The stability of infrastructure trades off against the responsiveness that the infrastructure can have to user needs.

The Human-Robot Interaction Operating System

NASA Technical Reports Server (NTRS)

Fong, Terrence; Kunz, Clayton; Hiatt, Laura M.; Bugajska, Magda

2006-01-01

In order for humans and robots to work effectively together, they need to be able to converse about abilities, goals and achievements. Thus, we are developing an interaction infrastructure called the "Human-Robot Interaction Operating System" (HRI/OS). The HRI/OS provides a structured software framework for building human-robot teams, supports a variety of user interfaces, enables humans and robots to engage in task-oriented dialogue, and facilitates integration of robots through an extensible API.

Using the Global Forest Products Model (GFPM version 2012)

Treesearch

Joseph Buongiorno; Shushuai Zhu

2012-01-01

The purpose of this manual is to enable users of the Global Forest Products Model to: • Install and run the GFPM software • Understand the input data • Change the input data to explore different scenarios • Interpret the output The GFPM is an economic model of global production, consumption and trade of forest products (Buongiorno et al. 2003). The GFPM2012 has data...

Web-based spatial analysis with the ILWIS open source GIS software and satellite images from GEONETCast

NASA Astrophysics Data System (ADS)

Lemmens, R.; Maathuis, B.; Mannaerts, C.; Foerster, T.; Schaeffer, B.; Wytzisk, A.

2009-12-01

This paper involves easy accessible integrated web-based analysis of satellite images with a plug-in based open source software. The paper is targeted to both users and developers of geospatial software. Guided by a use case scenario, we describe the ILWIS software and its toolbox to access satellite images through the GEONETCast broadcasting system. The last two decades have shown a major shift from stand-alone software systems to networked ones, often client/server applications using distributed geo-(web-)services. This allows organisations to combine without much effort their own data with remotely available data and processing functionality. Key to this integrated spatial data analysis is a low-cost access to data from within a user-friendly and flexible software. Web-based open source software solutions are more often a powerful option for developing countries. The Integrated Land and Water Information System (ILWIS) is a PC-based GIS & Remote Sensing software, comprising a complete package of image processing, spatial analysis and digital mapping and was developed as commercial software from the early nineties onwards. Recent project efforts have migrated ILWIS into a modular, plug-in-based open source software, and provide web-service support for OGC-based web mapping and processing. The core objective of the ILWIS Open source project is to provide a maintainable framework for researchers and software developers to implement training components, scientific toolboxes and (web-) services. The latest plug-ins have been developed for multi-criteria decision making, water resources analysis and spatial statistics analysis. The development of this framework is done since 2007 in the context of 52°North, which is an open initiative that advances the development of cutting edge open source geospatial software, using the GPL license. GEONETCast, as part of the emerging Global Earth Observation System of Systems (GEOSS), puts essential environmental data at the fingertips of users around the globe. This user-friendly and low-cost information dissemination provides global information as a basis for decision-making in a number of critical areas, including public health, energy, agriculture, weather, water, climate, natural disasters and ecosystems. GEONETCast makes available satellite images via Digital Video Broadcast (DVB) technology. An OGC WMS interface and plug-ins which convert GEONETCast data streams allow an ILWIS user to integrate various distributed data sources with data locally stored on his machine. Our paper describes a use case in which ILWIS is used with GEONETCast satellite imagery for decision making processes in Ghana. We also explain how the ILWIS software can be extended with additional functionality by means of building plug-ins and unfold our plans to implement other OGC standards, such as WCS and WPS in the same context. Especially, the latter one can be seen as a major step forward in terms of moving well-proven desktop based processing functionality to the web. This enables the embedding of ILWIS functionality in Spatial Data Infrastructures or even the execution in scalable and on-demand cloud computing environments.

An Earthquake Shake Map Routine with Low Cost Accelerometers: Preliminary Results

NASA Astrophysics Data System (ADS)

Alcik, H. A.; Tanircan, G.; Kaya, Y.

2015-12-01

Vast amounts of high quality strong motion data are indispensable inputs of the analyses in the field of geotechnical and earthquake engineering however, high cost of installation of the strong motion systems constitutes the biggest obstacle for worldwide dissemination. In recent years, MEMS based (micro-electro-mechanical systems) accelerometers have been used in seismological research-oriented studies as well as earthquake engineering oriented projects basically due to precision obtained in downsized instruments. In this research our primary goal is to ensure the usage of these low-cost instruments in the creation of shake-maps immediately after a strong earthquake. Second goal is to develop software that will automatically process the real-time data coming from the rapid response network and create shake-map. For those purposes, four MEMS sensors have been set up to deliver real-time data. Data transmission is done through 3G modems. A subroutine was coded in assembler language and embedded into the operating system of each instrument to create MiniSEED files with packages of 1-second instead of 512-byte packages.The Matlab-based software calculates the strong motion (SM) parameters at every second, and they are compared with the user-defined thresholds. A voting system embedded in the software captures the event if the total vote exceeds the threshold. The user interface of the software enables users to monitor the calculated SM parameters either in a table or in a graph (Figure 1). A small scale and affordable rapid response network is created using four MEMS sensors, and the functionality of the software has been tested and validated using shake table tests. The entire system is tested together with a reference sensor under real strong ground motion recordings as well as series of sine waves with varying amplitude and frequency. The successful realization of this software allowed us to set up a test network at Tekirdağ Province, the closest coastal point to the moderate size earthquake activities in the Marmara Sea, Turkey.

Web survey data collection and retrieval to plan teleradiology implementation

NASA Astrophysics Data System (ADS)

Alaoui, Adil; Collmann, Jeff R.; Johnson, Jeffrey A.; Lindisch, David; Nguyen, Dan; Mun, Seong K.

2003-05-01

This case study details the experience of system engineers of the Imaging Science and Information Systems Center, Georgetown University Medical Center (ISIS) and radiologists from the department of Radiology in the implementation of a new Teleradiology system. The Teleradiology system enables radiologists to view medical images from remote sites under those circumstances where a resident radiologist needs assistance in evaluating the images after hours and during weekends; it also enables clinicians access to patients" medical images from different workstations within the hospital. The Implementation of the Teleradiology project was preceded by an evaluation phase to perform testing, gather users feedback using a web site and collect information that helped eliminate system bugs, complete recommendations regarding minimum hardware configuration and bandwidth and enhance system"s functions, this phase included a survey-based system assessment of computer configurations, Internet connections, problem identification, and recommendations for improvement, and a testing period with 2 radiologists and ISIS engineers; The second phase was designed to launch the system and make it available to all attending radiologists in the department. To accomplish the first phase of the project a web site was designed and ASP pages were created to enable users to securely logon and enter feedback and recommendations into an SQL database. This efficient, accurate data flow alleviated networking, software and hardware problems. Corrective recommendations were immediately forwarded to the software vendor. The vendor responded with software updates that better met the needs of the radiologists. The ISIS Center completed recommendations for minimum hardware and bandwidth requirements. This experience illustrates that the approach used in collecting the data and facilitating the teamwork between the system engineers and radiologists was instrumental in the project"s success. Major problems with the Teleradiology system were discovered and remedied early by linking the actual practice experience of the physicians to the system improvements.

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

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

Software Defined Cyberinfrastructure

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

Foster, Ian; Blaiszik, Ben; Chard, Kyle

Within and across thousands of science labs, researchers and students struggle to manage data produced in experiments, simulations, and analyses. Largely manual research data lifecycle management processes mean that much time is wasted, research results are often irreproducible, and data sharing and reuse remain rare. In response, we propose a new approach to data lifecycle management in which researchers are empowered to define the actions to be performed at individual storage systems when data are created or modified: actions such as analysis, transformation, copying, and publication. We term this approach software-defined cyberinfrastructure because users can implement powerful data management policiesmore » by deploying rules to local storage systems, much as software-defined networking allows users to configure networks by deploying rules to switches.We argue that this approach can enable a new class of responsive distributed storage infrastructure that will accelerate research innovation by allowing any researcher to associate data workflows with data sources, whether local or remote, for such purposes as data ingest, characterization, indexing, and sharing. We report on early experiments with this approach in the context of experimental science, in which a simple if-trigger-then-action (IFTA) notation is used to define rules.« less

Battery Data MI Importer Template Quick Start Guide

NASA Technical Reports Server (NTRS)

Levinson, Laurie H.

2017-01-01

In order to ensure the persistent availability and reliability of test data generated over the course of the project, the M-SHELLS Project has decided to store acquired test data, as well as associated pedigree information, in the Granta Materials Intelligence (MI) database. To facilitate that effort, an importer template and associated graphical user interface (GUI) software have been developed, with this guide providing the operating instructions for their use. The template and automation software GUI are contained in the BatteryDataImporter.xlsm Excel workbook, and are to be used to import M-SHELLS summary, or pedigree, data and the associated raw test data results into an importer template-based file, formatted in such a way as to be ready for immediate upload to the Test Data: Battery Performance table of the Granta MI database. The provided GUI enables the user to select the appropriate summary data file(s), with each file containing the required information to identify any associated raw test data file(s) to be processed. In addition to describing the setup and operation of the importer template and GUI software, this guide also provides instructions for uploading processed data to the database and for viewing the data following upload.

The CARMEN software as a service infrastructure.

PubMed

Weeks, Michael; Jessop, Mark; Fletcher, Martyn; Hodge, Victoria; Jackson, Tom; Austin, Jim

2013-01-28

The CARMEN platform allows neuroscientists to share data, metadata, services and workflows, and to execute these services and workflows remotely via a Web portal. This paper describes how we implemented a service-based infrastructure into the CARMEN Virtual Laboratory. A Software as a Service framework was developed to allow generic new and legacy code to be deployed as services on a heterogeneous execution framework. Users can submit analysis code typically written in Matlab, Python, C/C++ and R as non-interactive standalone command-line applications and wrap them as services in a form suitable for deployment on the platform. The CARMEN Service Builder tool enables neuroscientists to quickly wrap their analysis software for deployment to the CARMEN platform, as a service without knowledge of the service framework or the CARMEN system. A metadata schema describes each service in terms of both system and user requirements. The search functionality allows services to be quickly discovered from the many services available. Within the platform, services may be combined into more complicated analyses using the workflow tool. CARMEN and the service infrastructure are targeted towards the neuroscience community; however, it is a generic platform, and can be targeted towards any discipline.

Dynamic optical resource allocation for mobile core networks with software defined elastic optical networking.

PubMed

Zhao, Yongli; Chen, Zhendong; Zhang, Jie; Wang, Xinbo

2016-07-25

Driven by the forthcoming of 5G mobile communications, the all-IP architecture of mobile core networks, i.e. evolved packet core (EPC) proposed by 3GPP, has been greatly challenged by the users' demands for higher data rate and more reliable end-to-end connection, as well as operators' demands for low operational cost. These challenges can be potentially met by software defined optical networking (SDON), which enables dynamic resource allocation according to the users' requirement. In this article, a novel network architecture for mobile core network is proposed based on SDON. A software defined network (SDN) controller is designed to realize the coordinated control over different entities in EPC networks. We analyze the requirement of EPC-lightpath (EPCL) in data plane and propose an optical switch load balancing (OSLB) algorithm for resource allocation in optical layer. The procedure of establishment and adjustment of EPCLs is demonstrated on a SDON-based EPC testbed with extended OpenFlow protocol. We also evaluate the OSLB algorithm through simulation in terms of bandwidth blocking ratio, traffic load distribution, and resource utilization ratio compared with link-based load balancing (LLB) and MinHops algorithms.

State-Chart Autocoder

NASA Technical Reports Server (NTRS)

Clark, Kenneth; Watney, Garth; Murray, Alexander; Benowitz, Edward

2007-01-01

A computer program translates Unified Modeling Language (UML) representations of state charts into source code in the C, C++, and Python computing languages. ( State charts signifies graphical descriptions of states and state transitions of a spacecraft or other complex system.) The UML representations constituting the input to this program are generated by using a UML-compliant graphical design program to draw the state charts. The generated source code is consistent with the "quantum programming" approach, which is so named because it involves discrete states and state transitions that have features in common with states and state transitions in quantum mechanics. Quantum programming enables efficient implementation of state charts, suitable for real-time embedded flight software. In addition to source code, the autocoder program generates a graphical-user-interface (GUI) program that, in turn, generates a display of state transitions in response to events triggered by the user. The GUI program is wrapped around, and can be used to exercise the state-chart behavior of, the generated source code. Once the expected state-chart behavior is confirmed, the generated source code can be augmented with a software interface to the rest of the software with which the source code is required to interact.

Applications of Sentinel-2 data for agriculture and forest monitoring using the absolute difference (ZABUD) index derived from the AgroEye software (ESA)

NASA Astrophysics Data System (ADS)

de Kok, R.; WeŻyk, P.; PapieŻ, M.; Migo, L.

2017-10-01

To convince new users of the advantages of the Sentinel_2 sensor, a simplification of classic remote sensing tools allows to create a platform of communication among domain specialists of agricultural analysis, visual image interpreters and remote sensing programmers. An index value, known in the remote sensing user domain as "Zabud" was selected to represent, in color, the essentials of a time series analysis. The color index used in a color atlas offers a working platform for an agricultural field control. This creates a database of test and training areas that enables rapid anomaly detection in the agricultural domain. The use cases and simplifications now function as an introduction to Sentinel_2 based remote sensing, in an area that before relies on VHR imagery and aerial data, to serve mainly the visual interpretation. The database extension with detected anomalies allows developers of open source software to design solutions for further agricultural control with remote sensing.

MetaPathways v2.5: quantitative functional, taxonomic and usability improvements.

PubMed

Konwar, Kishori M; Hanson, Niels W; Bhatia, Maya P; Kim, Dongjae; Wu, Shang-Ju; Hahn, Aria S; Morgan-Lang, Connor; Cheung, Hiu Kan; Hallam, Steven J

2015-10-15

Next-generation sequencing is producing vast amounts of sequence information from natural and engineered ecosystems. Although this data deluge has an enormous potential to transform our lives, knowledge creation and translation need software applications that scale with increasing data processing and analysis requirements. Here, we present improvements to MetaPathways, an annotation and analysis pipeline for environmental sequence information that expedites this transformation. We specifically address pathway prediction hazards through integration of a weighted taxonomic distance and enable quantitative comparison of assembled annotations through a normalized read-mapping measure. Additionally, we improve LAST homology searches through BLAST-equivalent E-values and output formats that are natively compatible with prevailing software applications. Finally, an updated graphical user interface allows for keyword annotation query and projection onto user-defined functional gene hierarchies, including the Carbohydrate-Active Enzyme database. MetaPathways v2.5 is available on GitHub: http://github.com/hallamlab/metapathways2. shallam@mail.ubc.ca Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

NJE; VAX-VMS IBM NJE network protocol emulator. [DEC VAX11/780; VAX-11 FORTRAN 77 (99%) and MACRO-11 (1%)

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

Engert, D.E.; Raffenetti, C.

NJE is communications software developed to enable a VAX VMS system to participate as an end-node in a standard IBM network by emulating the Network Job Entry (NJE) protocol. NJE supports job networking for the operating systems used on most large IBM-compatible computers (e.g., VM/370, MVS with JES2 or JES3, SVS, MVT with ASP or HASP). Files received by the VAX can be printed or saved in user-selected disk files. Files sent to the network can be routed to any network node for printing, punching, or job submission, or to a VM/370 user's virtual reader. Files sent from the VAXmore » are queued and transmitted asynchronously. No changes are required to the IBM software.DEC VAX11/780; VAX-11 FORTRAN 77 (99%) and MACRO-11 (1%); VMS 2.5; VAX11/780 with DUP-11 UNIBUS interface and 9600 baud synchronous modem..« less

REACH: Real-Time Data Awareness in Multi-Spacecraft Missions

NASA Technical Reports Server (NTRS)

Maks, Lori; Coleman, Jason; Hennessy, Joseph F. (Technical Monitor)

2002-01-01

NASA's Advanced Architectures and Automation Branch at the Goddard Space Flight Center (Code 588) saw the potential to reduce the cost of constellation missions by creating new user interfaces to the ground system health-and-safety data. The goal is to enable a small Flight Operations Team (FOT) to remain aware and responsive to the increased amount of ground system information in a multi-spacecraft environment. Rather than abandon the tried and true, these interfaces were developed to run alongside existing ground system software to provide additional support to the FOT. These new user interfaces have been combined in a tool called REACH. REACH-the Real-time Evaluation and Analysis of Consolidated Health-is a software product that uses advanced visualization techniques to make spacecraft anomalies easy to spot, no matter how many spacecraft are in the constellation. REACH reads numerous real-time streams of data from the ground system(s) and displays synthesized information to the FOT such that anomalies are easy to pick out and investigate.

A web-oriented software for the optimization of pooled experiments in NGS for detection of rare mutations.

PubMed

Evangelista, Daniela; Zuccaro, Antonio; Lančinskas, Algirdas; Žilinskas, Julius; Guarracino, Mario R

2016-02-17

The cost per patient of next generation sequencing for detection of rare mutations may be significantly reduced using pooled experiments. Recently, some techniques have been proposed for the planning of pooled experiments and for the optimal allocation of patients into pools. However, the lack of a user friendly resource for planning the design of pooled experiments forces the scientists to do frequent, complex and long computations. OPENDoRM is a powerful collection of novel mathematical algorithms usable via an intuitive graphical user interface. It enables researchers to speed up the planning of their routine experiments, as well as, to support scientists without specific bioinformatics expertises. Users can automatically carry out analysis in terms of costs associated with the optimal allocation of patients in pools. They are also able to choose between three distinct pooling mathematical methods, each of which also suggests the optimal configuration for the submitted experiment. Importantly, in order to keep track of the performed experiments, users can save and export the results of their experiments in standard tabular and charts contents. OPENDoRM is a freely available web-oriented application for the planning of pooled NGS experiments, available at: http://www-labgtp.na.icar.cnr.it/OPENDoRM. Its easy and intuitive graphical user interface enables researchers to plan theirs experiments using novel algorithms, and to interactively visualize the results.

Toward an automated parallel computing environment for geosciences

NASA Astrophysics Data System (ADS)

Zhang, Huai; Liu, Mian; Shi, Yaolin; Yuen, David A.; Yan, Zhenzhen; Liang, Guoping

2007-08-01

Software for geodynamic modeling has not kept up with the fast growing computing hardware and network resources. In the past decade supercomputing power has become available to most researchers in the form of affordable Beowulf clusters and other parallel computer platforms. However, to take full advantage of such computing power requires developing parallel algorithms and associated software, a task that is often too daunting for geoscience modelers whose main expertise is in geosciences. We introduce here an automated parallel computing environment built on open-source algorithms and libraries. Users interact with this computing environment by specifying the partial differential equations, solvers, and model-specific properties using an English-like modeling language in the input files. The system then automatically generates the finite element codes that can be run on distributed or shared memory parallel machines. This system is dynamic and flexible, allowing users to address different problems in geosciences. It is capable of providing web-based services, enabling users to generate source codes online. This unique feature will facilitate high-performance computing to be integrated with distributed data grids in the emerging cyber-infrastructures for geosciences. In this paper we discuss the principles of this automated modeling environment and provide examples to demonstrate its versatility.

The development of a clinical outcomes survey research application: Assessment Center.

PubMed

Gershon, Richard; Rothrock, Nan E; Hanrahan, Rachel T; Jansky, Liz J; Harniss, Mark; Riley, William

2010-06-01

The National Institutes of Health sponsored Patient-Reported Outcome Measurement Information System (PROMIS) aimed to create item banks and computerized adaptive tests (CATs) across multiple domains for individuals with a range of chronic diseases. Web-based software was created to enable a researcher to create study-specific Websites that could administer PROMIS CATs and other instruments to research participants or clinical samples. This paper outlines the process used to develop a user-friendly, free, Web-based resource (Assessment Center) for storage, retrieval, organization, sharing, and administration of patient-reported outcomes (PRO) instruments. Joint Application Design (JAD) sessions were conducted with representatives from numerous institutions in order to supply a general wish list of features. Use Cases were then written to ensure that end user expectations matched programmer specifications. Program development included daily programmer "scrum" sessions, weekly Usability Acceptability Testing (UAT) and continuous Quality Assurance (QA) activities pre- and post-release. Assessment Center includes features that promote instrument development including item histories, data management, and storage of statistical analysis results. This case study of software development highlights the collection and incorporation of user input throughout the development process. Potential future applications of Assessment Center in clinical research are discussed.

The SCEC/UseIT Intern Program: Creating Open-Source Visualization Software Using Diverse Resources

NASA Astrophysics Data System (ADS)

Francoeur, H.; Callaghan, S.; Perry, S.; Jordan, T.

2004-12-01

The Southern California Earthquake Center undergraduate IT intern program (SCEC UseIT) conducts IT research to benefit collaborative earth science research. Through this program, interns have developed real-time, interactive, 3D visualization software using open-source tools. Dubbed LA3D, a distribution of this software is now in use by the seismic community. LA3D enables the user to interactively view Southern California datasets and models of importance to earthquake scientists, such as faults, earthquakes, fault blocks, digital elevation models, and seismic hazard maps. LA3D is now being extended to support visualizations anywhere on the planet. The new software, called SCEC-VIDEO (Virtual Interactive Display of Earth Objects), makes use of a modular, plugin-based software architecture which supports easy development and integration of new data sets. Currently SCEC-VIDEO is in beta testing, with a full open-source release slated for the future. Both LA3D and SCEC-VIDEO were developed using a wide variety of software technologies. These, which included relational databases, web services, software management technologies, and 3-D graphics in Java, were necessary to integrate the heterogeneous array of data sources which comprise our software. Currently the interns are working to integrate new technologies and larger data sets to increase software functionality and value. In addition, both LA3D and SCEC-VIDEO allow the user to script and create movies. Thus program interns with computer science backgrounds have been writing software while interns with other interests, such as cinema, geology, and education, have been making movies that have proved of great use in scientific talks, media interviews, and education. Thus, SCEC UseIT incorporates a wide variety of scientific and human resources to create products of value to the scientific and outreach communities. The program plans to continue with its interdisciplinary approach, increasing the relevance of the software and expanding its use in the scientific community.

Wildlife in the cloud: a new approach for engaging stakeholders in wildlife management.

PubMed

Chapron, Guillaume

2015-11-01

Research in wildlife management increasingly relies on quantitative population models. However, a remaining challenge is to have end-users, who are often alienated by mathematics, benefiting from this research. I propose a new approach, 'wildlife in the cloud,' to enable active learning by practitioners from cloud-based ecological models whose complexity remains invisible to the user. I argue that this concept carries the potential to overcome limitations of desktop-based software and allows new understandings of human-wildlife systems. This concept is illustrated by presenting an online decision-support tool for moose management in areas with predators in Sweden. The tool takes the form of a user-friendly cloud-app through which users can compare the effects of alternative management decisions, and may feed into adjustment of their hunting strategy. I explain how the dynamic nature of cloud-apps opens the door to different ways of learning, informed by ecological models that can benefit both users and researchers.

Teaching Human Poses Interactively to a Social Robot

PubMed Central

Gonzalez-Pacheco, Victor; Malfaz, Maria; Fernandez, Fernando; Salichs, Miguel A.

2013-01-01

The main activity of social robots is to interact with people. In order to do that, the robot must be able to understand what the user is saying or doing. Typically, this capability consists of pre-programmed behaviors or is acquired through controlled learning processes, which are executed before the social interaction begins. This paper presents a software architecture that enables a robot to learn poses in a similar way as people do. That is, hearing its teacher's explanations and acquiring new knowledge in real time. The architecture leans on two main components: an RGB-D (Red-, Green-, Blue- Depth) -based visual system, which gathers the user examples, and an Automatic Speech Recognition (ASR) system, which processes the speech describing those examples. The robot is able to naturally learn the poses the teacher is showing to it by maintaining a natural interaction with the teacher. We evaluate our system with 24 users who teach the robot a predetermined set of poses. The experimental results show that, with a few training examples, the system reaches high accuracy and robustness. This method shows how to combine data from the visual and auditory systems for the acquisition of new knowledge in a natural manner. Such a natural way of training enables robots to learn from users, even if they are not experts in robotics. PMID:24048336

SOURCE EXPLORER: Towards Web Browser Based Tools for Astronomical Source Visualization and Analysis

NASA Astrophysics Data System (ADS)

Young, M. D.; Hayashi, S.; Gopu, A.

2014-05-01

As a new generation of large format, high-resolution imagers come online (ODI, DECAM, LSST, etc.) we are faced with the daunting prospect of astronomical images containing upwards of hundreds of thousands of identifiable sources. Visualizing and interacting with such large datasets using traditional astronomical tools appears to be unfeasible, and a new approach is required. We present here a method for the display and analysis of arbitrarily large source datasets using dynamically scaling levels of detail, enabling scientists to rapidly move from large-scale spatial overviews down to the level of individual sources and everything in-between. Based on the recognized standards of HTML5+JavaScript, we enable observers and archival users to interact with their images and sources from any modern computer without having to install specialized software. We demonstrate the ability to produce large-scale source lists from the images themselves, as well as overlaying data from publicly available source ( 2MASS, GALEX, SDSS, etc.) or user provided source lists. A high-availability cluster of computational nodes allows us to produce these source maps on demand and customized based on user input. User-generated source lists and maps are persistent across sessions and are available for further plotting, analysis, refinement, and culling.

Teaching human poses interactively to a social robot.

PubMed

Gonzalez-Pacheco, Victor; Malfaz, Maria; Fernandez, Fernando; Salichs, Miguel A

2013-09-17

The main activity of social robots is to interact with people. In order to do that, the robot must be able to understand what the user is saying or doing. Typically, this capability consists of pre-programmed behaviors or is acquired through controlled learning processes, which are executed before the social interaction begins. This paper presents a software architecture that enables a robot to learn poses in a similar way as people do. That is, hearing its teacher's explanations and acquiring new knowledge in real time. The architecture leans on two main components: an RGB-D (Red-, Green-, Blue- Depth) -based visual system, which gathers the user examples, and an Automatic Speech Recognition (ASR) system, which processes the speech describing those examples. The robot is able to naturally learn the poses the teacher is showing to it by maintaining a natural interaction with the teacher. We evaluate our system with 24 users who teach the robot a predetermined set of poses. The experimental results show that, with a few training examples, the system reaches high accuracy and robustness. This method shows how to combine data from the visual and auditory systems for the acquisition of new knowledge in a natural manner. Such a natural way of training enables robots to learn from users, even if they are not experts in robotics.

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

Chamana, Manohar; Prabakar, Kumaraguru; Palmintier, Bryan

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

Another Program For Generating Interactive Graphics

NASA Technical Reports Server (NTRS)

Costenbader, Jay; Moleski, Walt; Szczur, Martha; Howell, David; Engelberg, Norm; Li, Tin P.; Misra, Dharitri; Miller, Philip; Neve, Leif; Wolf, Karl;

Academic portfolio in the digital era: organizing and maintaining a portfolio using reference managers.

PubMed

Bhargava, Puneet; Patel, Vatsal B; Iyer, Ramesh S; Moshiri, Mariam; Robinson, Tracy J; Lall, Chandana; Heller, Matthew T

2015-02-01

The academic portfolio has become an integral part of the promotions process. Creating and maintaining an academic portfolio in paper-based or web-based formats can be a cumbersome and time-consuming task. In this article, we describe an alternative way to efficiently organize an academic portfolio using a reference manager software, and discuss some of the afforded advantages. The reference manager software Papers (Mekentosj, Amsterdam, The Netherlands) was used to create an academic portfolio. The article outlines the key steps in creating and maintaining a digital academic portfolio. Using reference manager software (Papers), we created an academic portfolio that allows the user to digitally organize clinical, teaching, and research accomplishments in an indexed library enabling efficient updating, rapid retrieval, and easy sharing. To our knowledge, this is the first digital portfolio of its kind.

Negotiation and Decision Making with Collaborative Software: How MarineMap 'Changed the Game' in California's Marine Life Protected Act Initiative.

PubMed

Cravens, Amanda E

2016-02-01

Environmental managers and planners have become increasingly enthusiastic about the potential of decision support tools (DSTs) to improve environmental decision-making processes as information technology transforms many aspects of daily life. Discussions about DSTs, however, rarely recognize the range of ways software can influence users' negotiation, problem-solving, or decision-making strategies and incentives, in part because there are few empirical studies of completed processes that used technology. This mixed-methods study-which draws on data from approximately 60 semi-structured interviews and an online survey--examines how one geospatial DST influenced participants' experiences during a multi-year marine planning process in California. Results suggest that DSTs can facilitate communication by creating a common language, help users understand the geography and scientific criteria in play during the process, aid stakeholders in identifying shared or diverging interests, and facilitate joint problem solving. The same design features that enabled the tool to aid in decision making, however, also presented surprising challenges in certain circumstances by, for example, making it difficult for participants to discuss information that was not spatially represented on the map-based interface. The study also highlights the importance of the social context in which software is developed and implemented, suggesting that the relationship between the software development team and other participants may be as important as technical software design in shaping how DSTs add value. The paper concludes with considerations to inform the future use of DSTs in environmental decision-making processes.

Negotiation and Decision Making with Collaborative Software: How MarineMap `Changed the Game' in California's Marine Life Protected Act Initiative

NASA Astrophysics Data System (ADS)

Cravens, Amanda E.

2016-02-01

Environmental managers and planners have become increasingly enthusiastic about the potential of decision support tools (DSTs) to improve environmental decision-making processes as information technology transforms many aspects of daily life. Discussions about DSTs, however, rarely recognize the range of ways software can influence users' negotiation, problem-solving, or decision-making strategies and incentives, in part because there are few empirical studies of completed processes that used technology. This mixed-methods study—which draws on data from approximately 60 semi-structured interviews and an online survey—examines how one geospatial DST influenced participants' experiences during a multi-year marine planning process in California. Results suggest that DSTs can facilitate communication by creating a common language, help users understand the geography and scientific criteria in play during the process, aid stakeholders in identifying shared or diverging interests, and facilitate joint problem solving. The same design features that enabled the tool to aid in decision making, however, also presented surprising challenges in certain circumstances by, for example, making it difficult for participants to discuss information that was not spatially represented on the map-based interface. The study also highlights the importance of the social context in which software is developed and implemented, suggesting that the relationship between the software development team and other participants may be as important as technical software design in shaping how DSTs add value. The paper concludes with considerations to inform the future use of DSTs in environmental decision-making processes.

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

NASA Technical Reports Server (NTRS)

Chase, A.

2003-01-01

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

GABBs: Cyberinfrastructure for Self-Service Geospatial Data Exploration, Computation, and Sharing

NASA Astrophysics Data System (ADS)

Song, C. X.; Zhao, L.; Biehl, L. L.; Merwade, V.; Villoria, N.

2016-12-01

Geospatial data are present everywhere today with the proliferation of location-aware computing devices. This is especially true in the scientific community where large amounts of data are driving research and education activities in many domains. Collaboration over geospatial data, for example, in modeling, data analysis and visualization, must still overcome the barriers of specialized software and expertise among other challenges. In addressing these needs, the Geospatial data Analysis Building Blocks (GABBs) project aims at building geospatial modeling, data analysis and visualization capabilities in an open source web platform, HUBzero. Funded by NSF's Data Infrastructure Building Blocks initiative, GABBs is creating a geospatial data architecture that integrates spatial data management, mapping and visualization, and interfaces in the HUBzero platform for scientific collaborations. The geo-rendering enabled Rappture toolkit, a generic Python mapping library, geospatial data exploration and publication tools, and an integrated online geospatial data management solution are among the software building blocks from the project. The GABBS software will be available through Amazon's AWS Marketplace VM images and open source. Hosting services are also available to the user community. The outcome of the project will enable researchers and educators to self-manage their scientific data, rapidly create GIS-enable tools, share geospatial data and tools on the web, and build dynamic workflows connecting data and tools, all without requiring significant software development skills, GIS expertise or IT administrative privileges. This presentation will describe the GABBs architecture, toolkits and libraries, and showcase the scientific use cases that utilize GABBs capabilities, as well as the challenges and solutions for GABBs to interoperate with other cyberinfrastructure platforms.

Dedicated computer system AOTK for image processing and analysis of horse navicular bone

NASA Astrophysics Data System (ADS)

Zaborowicz, M.; Fojud, A.; Koszela, K.; Mueller, W.; Górna, K.; Okoń, P.; Piekarska-Boniecka, H.

2017-07-01

The aim of the research was made the dedicated application AOTK (pol. Analiza Obrazu Trzeszczki Kopytowej) for image processing and analysis of horse navicular bone. The application was produced by using specialized software like Visual Studio 2013 and the .NET platform. To implement algorithms of image processing and analysis were used libraries of Aforge.NET. Implemented algorithms enabling accurate extraction of the characteristics of navicular bones and saving data to external files. Implemented in AOTK modules allowing the calculations of distance selected by user, preliminary assessment of conservation of structure of the examined objects. The application interface is designed in a way that ensures user the best possible view of the analyzed images.

ProteoCloud: a full-featured open source proteomics cloud computing pipeline.

PubMed

Muth, Thilo; Peters, Julian; Blackburn, Jonathan; Rapp, Erdmann; Martens, Lennart

2013-08-02

We here present the ProteoCloud pipeline, a freely available, full-featured cloud-based platform to perform computationally intensive, exhaustive searches in a cloud environment using five different peptide identification algorithms. ProteoCloud is entirely open source, and is built around an easy to use and cross-platform software client with a rich graphical user interface. This client allows full control of the number of cloud instances to initiate and of the spectra to assign for identification. It also enables the user to track progress, and to visualize and interpret the results in detail. Source code, binaries and documentation are all available at http://proteocloud.googlecode.com. Copyright © 2012 Elsevier B.V. All rights reserved.

Mechanical System Analysis/Design Tool (MSAT) Quick Guide

NASA Technical Reports Server (NTRS)

Lee, HauHua; Kolb, Mark; Madelone, Jack

1998-01-01

MSAT is a unique multi-component multi-disciplinary tool that organizes design analysis tasks around object-oriented representations of configuration components, analysis programs and modules, and data transfer links between them. This creative modular architecture enables rapid generation of input stream for trade-off studies of various engine configurations. The data transfer links automatically transport output from one application as relevant input to the next application once the sequence is set up by the user. The computations are managed via constraint propagation - the constraints supplied by the user as part of any optimization module. The software can be used in the preliminary design stage as well as during the detail design of product development process.

A web-based solution for 3D medical image visualization

NASA Astrophysics Data System (ADS)

Hou, Xiaoshuai; Sun, Jianyong; Zhang, Jianguo

2015-03-01

In this presentation, we present a web-based 3D medical image visualization solution which enables interactive large medical image data processing and visualization over the web platform. To improve the efficiency of our solution, we adopt GPU accelerated techniques to process images on the server side while rapidly transferring images to the HTML5 supported web browser on the client side. Compared to traditional local visualization solution, our solution doesn't require the users to install extra software or download the whole volume dataset from PACS server. By designing this web-based solution, it is feasible for users to access the 3D medical image visualization service wherever the internet is available.

High-quality remote interactive imaging in the operating theatre

NASA Astrophysics Data System (ADS)

Grimstead, Ian J.; Avis, Nick J.; Evans, Peter L.; Bocca, Alan

2009-02-01

We present a high-quality display system that enables the remote access within an operating theatre of high-end medical imaging and surgical planning software. Currently, surgeons often use printouts from such software for reference during surgery; our system enables surgeons to access and review patient data in a sterile environment, viewing real-time renderings of MRI & CT data as required. Once calibrated, our system displays shades of grey in Operating Room lighting conditions (removing any gamma correction artefacts). Our system does not require any expensive display hardware, is unobtrusive to the remote workstation and works with any application without requiring additional software licenses. To extend the native 256 levels of grey supported by a standard LCD monitor, we have used the concept of "PseudoGrey" where slightly off-white shades of grey are used to extend the intensity range from 256 to 1,785 shades of grey. Remote access is facilitated by a customized version of UltraVNC, which corrects remote shades of grey for display in the Operating Room. The system is successfully deployed at Morriston Hospital, Swansea, UK, and is in daily use during Maxillofacial surgery. More formal user trials and quantitative assessments are being planned for the future.

Bigger Data, Collaborative Tools and the Future of Predictive Drug Discovery

PubMed Central

Clark, Alex M.; Swamidass, S. Joshua; Litterman, Nadia; Williams, Antony J.

2014-01-01

Over the past decade we have seen a growth in the provision of chemistry data and cheminformatics tools as either free websites or software as a service (SaaS) commercial offerings. These have transformed how we find molecule-related data and use such tools in our research. There have also been efforts to improve collaboration between researchers either openly or through secure transactions using commercial tools. A major challenge in the future will be how such databases and software approaches handle larger amounts of data as it accumulates from high throughput screening and enables the user to draw insights, enable predictions and move projects forward. We now discuss how information from some drug discovery datasets can be made more accessible and how privacy of data should not overwhelm the desire to share it at an appropriate time with collaborators. We also discuss additional software tools that could be made available and provide our thoughts on the future of predictive drug discovery in this age of big data. We use some examples from our own research on neglected diseases, collaborations, mobile apps and algorithm development to illustrate these ideas. PMID:24943138

Argonne Leadership Computing Facility 2011 annual report : Shaping future supercomputing.

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

Papka, M.; Messina, P.; Coffey, R.

The ALCF's Early Science Program aims to prepare key applications for the architecture and scale of Mira and to solidify libraries and infrastructure that will pave the way for other future production applications. Two billion core-hours have been allocated to 16 Early Science projects on Mira. The projects, in addition to promising delivery of exciting new science, are all based on state-of-the-art, petascale, parallel applications. The project teams, in collaboration with ALCF staff and IBM, have undertaken intensive efforts to adapt their software to take advantage of Mira's Blue Gene/Q architecture, which, in a number of ways, is a precursormore » to future high-performance-computing architecture. The Argonne Leadership Computing Facility (ALCF) enables transformative science that solves some of the most difficult challenges in biology, chemistry, energy, climate, materials, physics, and other scientific realms. Users partnering with ALCF staff have reached research milestones previously unattainable, due to the ALCF's world-class supercomputing resources and expertise in computation science. In 2011, the ALCF's commitment to providing outstanding science and leadership-class resources was honored with several prestigious awards. Research on multiscale brain blood flow simulations was named a Gordon Bell Prize finalist. Intrepid, the ALCF's BG/P system, ranked No. 1 on the Graph 500 list for the second consecutive year. The next-generation BG/Q prototype again topped the Green500 list. Skilled experts at the ALCF enable researchers to conduct breakthrough science on the Blue Gene system in key ways. The Catalyst Team matches project PIs with experienced computational scientists to maximize and accelerate research in their specific scientific domains. The Performance Engineering Team facilitates the effective use of applications on the Blue Gene system by assessing and improving the algorithms used by applications and the techniques used to implement those algorithms. The Data Analytics and Visualization Team lends expertise in tools and methods for high-performance, post-processing of large datasets, interactive data exploration, batch visualization, and production visualization. The Operations Team ensures that system hardware and software work reliably and optimally; system tools are matched to the unique system architectures and scale of ALCF resources; the entire system software stack works smoothly together; and I/O performance issues, bug fixes, and requests for system software are addressed. The User Services and Outreach Team offers frontline services and support to existing and potential ALCF users. The team also provides marketing and outreach to users, DOE, and the broader community.« less

The key image and case log application: new radiology software for teaching file creation and case logging that incorporates elements of a social network.

PubMed

Rowe, Steven P; Siddiqui, Adeel; Bonekamp, David

2014-07-01

To create novel radiology key image software that is easy to use for novice users, incorporates elements adapted from social networking Web sites, facilitates resident and fellow education, and can serve as the engine for departmental sharing of interesting cases and follow-up studies. Using open-source programming languages and software, radiology key image software (the key image and case log application, KICLA) was developed. This system uses a lightweight interface with the institutional picture archiving and communications systems and enables the storage of key images, image series, and cine clips. It was designed to operate with minimal disruption to the radiologists' daily workflow. Many features of the user interface have been inspired by social networking Web sites, including image organization into private or public folders, flexible sharing with other users, and integration of departmental teaching files into the system. We also review the performance, usage, and acceptance of this novel system. KICLA was implemented at our institution and achieved widespread popularity among radiologists. A large number of key images have been transmitted to the system since it became available. After this early experience period, the most commonly encountered radiologic modalities are represented. A survey distributed to users revealed that most of the respondents found the system easy to use (89%) and fast at allowing them to record interesting cases (100%). Hundred percent of respondents also stated that they would recommend a system such as KICLA to their colleagues. The system described herein represents a significant upgrade to the Digital Imaging and Communications in Medicine teaching file paradigm with efforts made to maximize its ease of use and inclusion of characteristics inspired by social networking Web sites that allow the system additional functionality such as individual case logging. Copyright © 2014 AUR. Published by Elsevier Inc. All rights reserved.

The Digital Shoreline Analysis System (DSAS) Version 4.0 - An ArcGIS extension for calculating shoreline change

USGS Publications Warehouse

Thieler, E. Robert; Himmelstoss, Emily A.; Zichichi, Jessica L.; Ergul, Ayhan

2009-01-01

The Digital Shoreline Analysis System (DSAS) version 4.0 is a software extension to ESRI ArcGIS v.9.2 and above that enables a user to calculate shoreline rate-of-change statistics from multiple historic shoreline positions. A user-friendly interface of simple buttons and menus guides the user through the major steps of shoreline change analysis. Components of the extension and user guide include (1) instruction on the proper way to define a reference baseline for measurements, (2) automated and manual generation of measurement transects and metadata based on user-specified parameters, and (3) output of calculated rates of shoreline change and other statistical information. DSAS computes shoreline rates of change using four different methods: (1) endpoint rate, (2) simple linear regression, (3) weighted linear regression, and (4) least median of squares. The standard error, correlation coefficient, and confidence interval are also computed for the simple and weighted linear-regression methods. The results of all rate calculations are output to a table that can be linked to the transect file by a common attribute field. DSAS is intended to facilitate the shoreline change-calculation process and to provide rate-of-change information and the statistical data necessary to establish the reliability of the calculated results. The software is also suitable for any generic application that calculates positional change over time, such as assessing rates of change of glacier limits in sequential aerial photos, river edge boundaries, land-cover changes, and so on.

Small PACS implementation using publicly available software

NASA Astrophysics Data System (ADS)

Passadore, Diego J.; Isoardi, Roberto A.; Gonzalez Nicolini, Federico J.; Ariza, P. P.; Novas, C. V.; Omati, S. A.

1998-07-01

Building cost effective PACS solutions is a main concern in developing countries. Hardware and software components are generally much more expensive than in developed countries and also more tightened financial constraints are the main reasons contributing to a slow rate of implementation of PACS. The extensive use of Internet for sharing resources and information has brought a broad number of freely available software packages to an ever-increasing number of users. In the field of medical imaging is possible to find image format conversion packages, DICOM compliant servers for all kinds of service classes, databases, web servers, image visualization, manipulation and analysis tools, etc. This paper describes a PACS implementation for review and storage built on freely available software. It currently integrates four diagnostic modalities (PET, CT, MR and NM), a Radiotherapy Treatment Planning workstation and several computers in a local area network, for image storage, database management and image review, processing and analysis. It also includes a web-based application that allows remote users to query the archive for studies from any workstation and to view the corresponding images and reports. We conclude that the advantage of using this approach is twofold. It allows a full understanding of all the issues involved in the implementation of a PACS and also contributes to keep costs down while enabling the development of a functional system for storage, distribution and review that can prove to be helpful for radiologists and referring physicians.

PLEXOS Input Data Generator

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

The PLEXOS Input Data Generator (PIDG) is a tool that enables PLEXOS users to better version their data, automate data processing, collaborate in developing inputs, and transfer data between different production cost modeling and other power systems analysis software. PIDG can process data that is in a generalized format from multiple input sources, including CSV files, PostgreSQL databases, and PSS/E .raw files and write it to an Excel file that can be imported into PLEXOS with only limited manual intervention.

Small Business Innovations

NASA Technical Reports Server (NTRS)

1992-01-01

The purpose of QASE RT is to enable system analysts and software engineers to evaluate performance and reliability implications of design alternatives. The program resulted from two Small Business Innovation Research (SBIR) projects. After receiving a description of the system architecture and workload from the user, QASE RT translates the system description into simulation models and executes them. Simulation provides detailed performance evaluation. The results of the evaluations are service and response times, offered load and device utilizations and functional availability.

The T.M.R. Data Dictionary: A Management Tool for Data Base Design

PubMed Central

Ostrowski, Maureen; Bernes, Marshall R.

1984-01-01

In January 1981, a dictionary-driven ambulatory care information system known as TMR (The Medical Record) was installed at a large private medical group practice in Los Angeles. TMR's data dictionary has enabled the medical group to adapt the software to meet changing user needs largely without programming support. For top management, the dictionary is also a tool for navigating through the system's complexity and assuring the integrity of management goals.

Systems Architecture for Fully Autonomous Space Missions

NASA Technical Reports Server (NTRS)

Esper, Jamie; Schnurr, R.; VanSteenberg, M.; Brumfield, Mark (Technical Monitor)

2002-01-01

The NASA Goddard Space Flight Center is working to develop a revolutionary new system architecture concept in support of fully autonomous missions. As part of GSFC's contribution to the New Millenium Program (NMP) Space Technology 7 Autonomy and on-Board Processing (ST7-A) Concept Definition Study, the system incorporates the latest commercial Internet and software development ideas and extends them into NASA ground and space segment architectures. The unique challenges facing the exploration of remote and inaccessible locales and the need to incorporate corresponding autonomy technologies within reasonable cost necessitate the re-thinking of traditional mission architectures. A measure of the resiliency of this architecture in its application to a broad range of future autonomy missions will depend on its effectiveness in leveraging from commercial tools developed for the personal computer and Internet markets. Specialized test stations and supporting software come to past as spacecraft take advantage of the extensive tools and research investments of billion-dollar commercial ventures. The projected improvements of the Internet and supporting infrastructure go hand-in-hand with market pressures that provide continuity in research. By taking advantage of consumer-oriented methods and processes, space-flight missions will continue to leverage on investments tailored to provide better services at reduced cost. The application of ground and space segment architectures each based on Local Area Networks (LAN), the use of personal computer-based operating systems, and the execution of activities and operations through a Wide Area Network (Internet) enable a revolution in spacecraft mission formulation, implementation, and flight operations. Hardware and software design, development, integration, test, and flight operations are all tied-in closely to a common thread that enables the smooth transitioning between program phases. The application of commercial software development techniques lays the foundation for delivery of product-oriented flight software modules and models. Software can then be readily applied to support the on-board autonomy required for mission self-management. An on-board intelligent system, based on advanced scripting languages, facilitates the mission autonomy required to offload ground system resources, and enables the spacecraft to manage itself safely through an efficient and effective process of reactive planning, science data acquisition, synthesis, and transmission to the ground. Autonomous ground systems in turn coordinate and support schedule contact times with the spacecraft. Specific autonomy software modules on-board include mission and science planners, instrument and subsystem control, and fault tolerance response software, all residing within a distributed computing environment supported through the flight LAN. Autonomy also requires the minimization of human intervention between users on the ground and the spacecraft, and hence calls for the elimination of the traditional operations control center as a funnel for data manipulation. Basic goal-oriented commands are sent directly from the user to the spacecraft through a distributed internet-based payload operations "center". The ensuing architecture calls for the use of spacecraft as point extensions on the Internet. This paper will detail the system architecture implementation chosen to enable cost-effective autonomous missions with applicability to a broad range of conditions. It will define the structure needed for implementation of such missions, including software and hardware infrastructures. The overall architecture is then laid out as a common thread in the mission life cycle from formulation through implementation and flight operations.

Smart energy management system

NASA Astrophysics Data System (ADS)

Desai, Aniruddha; Singh, Jugdutt

2010-04-01

Peak and average energy usage in domestic and industrial environments is growing rapidly and absence of detailed energy consumption metrics is making systematic reduction of energy usage very difficult. Smart energy management system aims at providing a cost-effective solution for managing soaring energy consumption and its impact on green house gas emissions and climate change. The solution is based on seamless integration of existing wired and wireless communication technologies combined with smart context-aware software which offers a complete solution for automation of energy measurement and device control. The persuasive software presents users with easy-to-assimilate visual cues identifying problem areas and time periods and encourages a behavioural change to conserve energy. The system allows analysis of real-time/statistical consumption data with the ability to drill down into detailed analysis of power consumption, CO2 emissions and cost. The system generates intelligent projections and suggests potential methods (e.g. reducing standby, tuning heating/cooling temperature, etc.) of reducing energy consumption. The user interface is accessible using web enabled devices such as PDAs, PCs, etc. or using SMS, email, and instant messaging. Successful real-world trial of the system has demonstrated the potential to save 20 to 30% energy consumption on an average. Low cost of deployment and the ability to easily manage consumption from various web enabled devices offers gives this system a high penetration and impact capability offering a sustainable solution to act on climate change today.

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.

Moving Ahead With Eye Power

NASA Technical Reports Server (NTRS)

2002-01-01

NASA's Jet Propulsion Laboratory's collaborated with LC Technologies, Inc., to improve LCT's Eyegaze Communication System, an eye tracker that enables people with severe cerebral palsy, muscular dystrophy, multiple sclerosis, strokes, brain injuries, spinal cord injuries, and ALS (amyotrophic lateral sclerosis) to communicate and control their environment using their eye movements. To operate the system, the user sits in front of the computer monitor while the camera focuses on one eye. By looking at control keys on the monitor for a fraction of a second, the user can 'talk' with speech synthesis, type, operate a telephone, access the Internet and e-mail, and run computer software. Nothing is attached to the user's head or body, and the improved size and portability allow the system to be mounted on a wheelchair. LCT and JPL are working on several other areas of improvement that have commercial add-on potential.

A Coupled Simulation Architecture for Agent-Based/Geohydrological Modelling

NASA Astrophysics Data System (ADS)

Jaxa-Rozen, M.

2016-12-01

The quantitative modelling of social-ecological systems can provide useful insights into the interplay between social and environmental processes, and their impact on emergent system dynamics. However, such models should acknowledge the complexity and uncertainty of both of the underlying subsystems. For instance, the agent-based models which are increasingly popular for groundwater management studies can be made more useful by directly accounting for the hydrological processes which drive environmental outcomes. Conversely, conventional environmental models can benefit from an agent-based depiction of the feedbacks and heuristics which influence the decisions of groundwater users. From this perspective, this work describes a Python-based software architecture which couples the popular NetLogo agent-based platform with the MODFLOW/SEAWAT geohydrological modelling environment. This approach enables users to implement agent-based models in NetLogo's user-friendly platform, while benefiting from the full capabilities of MODFLOW/SEAWAT packages or reusing existing geohydrological models. The software architecture is based on the pyNetLogo connector, which provides an interface between the NetLogo agent-based modelling software and the Python programming language. This functionality is then extended and combined with Python's object-oriented features, to design a simulation architecture which couples NetLogo with MODFLOW/SEAWAT through the FloPy library (Bakker et al., 2016). The Python programming language also provides access to a range of external packages which can be used for testing and analysing the coupled models, which is illustrated for an application of Aquifer Thermal Energy Storage (ATES).

JAMI: a Java library for molecular interactions and data interoperability.

PubMed

Sivade Dumousseau, M; Koch, M; Shrivastava, A; Alonso-López, D; De Las Rivas, J; Del-Toro, N; Combe, C W; Meldal, B H M; Heimbach, J; Rappsilber, J; Sullivan, J; Yehudi, Y; Orchard, S

2018-04-11

A number of different molecular interactions data download formats now exist, designed to allow access to these valuable data by diverse user groups. These formats include the PSI-XML and MITAB standard interchange formats developed by Molecular Interaction workgroup of the HUPO-PSI in addition to other, use-specific downloads produced by other resources. The onus is currently on the user to ensure that a piece of software is capable of read/writing all necessary versions of each format. This problem may increase, as data providers strive to meet ever more sophisticated user demands and data types. A collaboration between EMBL-EBI and the University of Cambridge has produced JAMI, a single library to unify standard molecular interaction data formats such as PSI-MI XML and PSI-MITAB. The JAMI free, open-source library enables the development of molecular interaction computational tools and pipelines without the need to produce different versions of software to read different versions of the data formats. Software and tools developed on top of the JAMI framework are able to integrate and support both PSI-MI XML and PSI-MITAB. The use of JAMI avoids the requirement to chain conversions between formats in order to reach a desired output format and prevents code and unit test duplication as the code becomes more modular. JAMI's model interfaces are abstracted from the underlying format, hiding the complexity and requirements of each data format from developers using JAMI as a library.

Participatory interaction design in user requirements specification in healthcare.

PubMed

Martikainen, Susanna; Ikävalko, Pauliina; Korpela, Mikko

2010-01-01

Healthcare information systems are accused of poor usability even in the popular media in Finland. Doctors especially have been very critical and actively expressed their opinions in public. User involvement and user-centered design methods are seen as the key solution to usability problems. In this paper we describe a research case where participatory methods were experimented within healthcare information systems development in medicinal care in a hospital. The study was part of a larger research project on Activity-driven Information Systems Development in healthcare. The study started by finding out about and modeling the present state of medicinal care in the hospital. After that it was important to define and model the goal state. The goal state, facilitated by the would-be software package, was modeled with the help of user interface drawings as one way of prototyping. Traditional usability methods were extended during the study. According to the health professionals' feedback, the use of participatory and user-centered interaction design methods, particularly user interface drawings enabled them to describe their requirements and create common understanding with the system developers.

Software Supports Distributed Operations via the Internet

NASA Technical Reports Server (NTRS)

Norris, Jeffrey; Backers, Paul; Steinke, Robert

2003-01-01

Multi-mission Encrypted Communication System (MECS) is a computer program that enables authorized, geographically dispersed users to gain secure access to a common set of data files via the Internet. MECS is compatible with legacy application programs and a variety of operating systems. The MECS architecture is centered around maintaining consistent replicas of data files cached on remote computers. MECS monitors these files and, whenever one is changed, the changed file is committed to a master database as soon as network connectivity makes it possible to do so. MECS provides subscriptions for remote users to automatically receive new data as they are generated. Remote users can be producers as well as consumers of data. Whereas a prior program that provides some of the same services treats disconnection of a user from the network of users as an error from which recovery must be effected, MECS treats disconnection as a nominal state of the network: This leads to a different design that is more efficient for serving many users, each of whom typically connects and disconnects frequently and wants only a small fraction of the data at any given time.

SPICE Module for the Satellite Orbit Analysis Program (SOAP)

NASA Technical Reports Server (NTRS)

Coggi, John; Carnright, Robert; Hildebrand, Claude

2008-01-01

A SPICE module for the Satellite Orbit Analysis Program (SOAP) precisely represents complex motion and maneuvers in an interactive, 3D animated environment with support for user-defined quantitative outputs. (SPICE stands for Spacecraft, Planet, Instrument, Camera-matrix, and Events). This module enables the SOAP software to exploit NASA mission ephemeris represented in the JPL Ancillary Information Facility (NAIF) SPICE formats. Ephemeris types supported include position, velocity, and orientation for spacecraft and planetary bodies including the Sun, planets, natural satellites, comets, and asteroids. Entire missions can now be imported into SOAP for 3D visualization, playback, and analysis. The SOAP analysis and display features can now leverage detailed mission files to offer the analyst both a numerically correct and aesthetically pleasing combination of results that can be varied to study many hypothetical scenarios. The software provides a modeling and simulation environment that can encompass a broad variety of problems using orbital prediction. For example, ground coverage analysis, communications analysis, power and thermal analysis, and 3D visualization that provide the user with insight into complex geometric relations are included. The SOAP SPICE module allows distributed science and engineering teams to share common mission models of known pedigree, which greatly reduces duplication of effort and the potential for error. The use of the software spans all phases of the space system lifecycle, from the study of future concepts to operations and anomaly analysis. It allows SOAP software to correctly position and orient all of the principal bodies of the Solar System within a single simulation session along with multiple spacecraft trajectories and the orientation of mission payloads. In addition to the 3D visualization, the user can define numeric variables and x-y plots to quantitatively assess metrics of interest.

It’s about time: How do sky surveys manage uncertainty about scientific needs many years into the future

NASA Astrophysics Data System (ADS)

Darch, Peter T.; Sands, Ashley E.

2016-06-01

Sky surveys, such as the Sloan Digital Sky Survey (SDSS) and the Large Synoptic Survey Telescope (LSST), generate data on an unprecedented scale. While many scientific projects span a few years from conception to completion, sky surveys are typically on the scale of decades. This paper focuses on critical challenges arising from long timescales, and how sky surveys address these challenges.We present findings from a study of LSST, comprising interviews (n=58) and observation. Conceived in the 1990s, the LSST Corporation was formed in 2003, and construction began in 2014. LSST will commence data collection operations in 2022 for ten years.One challenge arising from this long timescale is uncertainty about future needs of the astronomers who will use these data many years hence. Sources of uncertainty include scientific questions to be posed, astronomical phenomena to be studied, and tools and practices these astronomers will have at their disposal. These uncertainties are magnified by the rapid technological and scientific developments anticipated between now and the start of LSST operations.LSST is implementing a range of strategies to address these challenges. Some strategies involve delaying resolution of uncertainty, placing this resolution in the hands of future data users. Other strategies aim to reduce uncertainty by shaping astronomers’ data analysis practices so that these practices will integrate well with LSST once operations begin.One approach that exemplifies both types of strategy is the decision to make LSST data management software open source, even now as it is being developed. This policy will enable future data users to adapt this software to evolving needs. In addition, LSST intends for astronomers to start using this software well in advance of 2022, thereby embedding LSST software and data analysis approaches in the practices of astronomers.These findings strengthen arguments for making the software supporting sky surveys available as open source. Such arguments usually focus on reuse potential of software, and enhancing replicability of analyses. In this case, however, open source software also promises to mitigate the critical challenge of anticipating the needs of future data users.

Second generation registry framework.

PubMed

Bellgard, Matthew I; Render, Lee; Radochonski, Maciej; Hunter, Adam

2014-01-01

Information management systems are essential to capture data be it for public health and human disease, sustainable agriculture, or plant and animal biosecurity. In public health, the term patient registry is often used to describe information management systems that are used to record and track phenotypic data of patients. Appropriate design, implementation and deployment of patient registries enables rapid decision making and ongoing data mining ultimately leading to improved patient outcomes. A major bottleneck encountered is the static nature of these registries. That is, software developers are required to work with stakeholders to determine requirements, design the system, implement the required data fields and functionality for each patient registry. Additionally, software developer time is required for ongoing maintenance and customisation. It is desirable to deploy a sophisticated registry framework that can allow scientists and registry curators possessing standard computing skills to dynamically construct a complete patient registry from scratch and customise it for their specific needs with little or no need to engage a software developer at any stage. This paper introduces our second generation open source registry framework which builds on our previous rare disease registry framework (RDRF). This second generation RDRF is a new approach as it empowers registry administrators to construct one or more patient registries without software developer effort. New data elements for a diverse range of phenotypic and genotypic measurements can be defined at any time. Defined data elements can then be utilised in any of the created registries. Fine grained, multi-level user and workgroup access can be applied to each data element to ensure appropriate access and data privacy. We introduce the concept of derived data elements to assist the data element standards communities on how they might be best categorised. We introduce the second generation RDRF that enables the user-driven dynamic creation of patient registries. We believe this second generation RDRF is a novel approach to patient registry design, implementation and deployment and a significant advance on existing registry systems.

Second generation registry framework

PubMed Central

2014-01-01

Background Information management systems are essential to capture data be it for public health and human disease, sustainable agriculture, or plant and animal biosecurity. In public health, the term patient registry is often used to describe information management systems that are used to record and track phenotypic data of patients. Appropriate design, implementation and deployment of patient registries enables rapid decision making and ongoing data mining ultimately leading to improved patient outcomes. A major bottleneck encountered is the static nature of these registries. That is, software developers are required to work with stakeholders to determine requirements, design the system, implement the required data fields and functionality for each patient registry. Additionally, software developer time is required for ongoing maintenance and customisation. It is desirable to deploy a sophisticated registry framework that can allow scientists and registry curators possessing standard computing skills to dynamically construct a complete patient registry from scratch and customise it for their specific needs with little or no need to engage a software developer at any stage. Results This paper introduces our second generation open source registry framework which builds on our previous rare disease registry framework (RDRF). This second generation RDRF is a new approach as it empowers registry administrators to construct one or more patient registries without software developer effort. New data elements for a diverse range of phenotypic and genotypic measurements can be defined at any time. Defined data elements can then be utilised in any of the created registries. Fine grained, multi-level user and workgroup access can be applied to each data element to ensure appropriate access and data privacy. We introduce the concept of derived data elements to assist the data element standards communities on how they might be best categorised. Conclusions We introduce the second generation RDRF that enables the user-driven dynamic creation of patient registries. We believe this second generation RDRF is a novel approach to patient registry design, implementation and deployment and a significant advance on existing registry systems. PMID:24982690

AF-GEOSPACE Version 2.1

NASA Astrophysics Data System (ADS)

Hilmer, R. V.; Ginet, G. P.; Hall, T.; Holeman, E.; Madden, D.; Tautz, M.; Roth, C.

2004-05-01

AF-GEOSpace is a graphics-intensive software program with space environment models and applications developed and distributed by the Space Weather Center of Excellence at AFRL. A review of current (Version 2.0) and planned (Version 2.1) AF-GEOSpace capabilities will be given. A wide range of physical domains is represented enabling the software to address such things as solar disturbance propagation, radiation belt configuration, and ionospheric auroral particle precipitation and scintillation. The software is currently being used to aid with the design, operation, and simulation of a wide variety of communications, navigation, and surveillance systems. Building on the success of previous releases, AF-GEOSpace has become a platform for the rapid prototyping of automated operational and simulation space weather visualization products and helps with a variety of tasks, including: orbit specification for radiation hazard avoidance; satellite design assessment and post-event anomaly analysis; solar disturbance effects forecasting; frequency and antenna management for radar and HF communications; determination of link outage regions for active ionospheric conditions; scientific model validation and comparison, physics research, and education. Version 2.0 provided a simplified graphical user interface, improved science and application modules, and significantly enhanced graphical performance. Common input data archive sets, application modules, and 1-D, 2-D, and 3-D visualization tools are provided to all models. Dynamic capabilities permit multiple environments to be generated at user-specified time intervals while animation tools enable displays such as satellite orbits and environment data together as a function of time. Building on the existing Version 2.0 software architecture, AF-GEOSpace Version 2.1 is currently under development and will include a host of new modules to provide, for example, geosynchronous charged particle fluxes, neutral atmosphere densities, cosmic ray cutoff maps, low-altitude trapped proton belt specification, and meteor shower/storm fluxes with spacecraft impact probabilities. AF-GEOSpace Version 2.1 is being developed for Windows NT/2000/XP and Linux systems.

Simple Web-based interactive key development software (WEBiKEY) and an example key for Kuruna (Poaceae: Bambusoideae)1

PubMed Central

Attigala, Lakshmi; De Silva, Nuwan I.; Clark, Lynn G.

2016-01-01

Premise of the study: Programs that are user-friendly and freely available for developing Web-based interactive keys are scarce and most of the well-structured applications are relatively expensive. WEBiKEY was developed to enable researchers to easily develop their own Web-based interactive keys with fewer resources. Methods and Results: A Web-based multiaccess identification tool (WEBiKEY) was developed that uses freely available Microsoft ASP.NET technologies and an SQL Server database for Windows-based hosting environments. WEBiKEY was tested for its usability with a sample data set, the temperate woody bamboo genus Kuruna (Poaceae). Conclusions: WEBiKEY is freely available to the public and can be used to develop Web-based interactive keys for any group of species. The interactive key we developed for Kuruna using WEBiKEY enables users to visually inspect characteristics of Kuruna and identify an unknown specimen as one of seven possible species in the genus. PMID:27144109

Improving the Accessibility and Use of NASA Earth Science Data

NASA Technical Reports Server (NTRS)

Tisdale, Matthew; Tisdale, Brian

2015-01-01

Many of the NASA Langley Atmospheric Science Data Center (ASDC) Distributed Active Archive Center (DAAC) multidimensional tropospheric and atmospheric chemistry data products are stored in HDF4, HDF5 or NetCDF format, which traditionally have been difficult to analyze and visualize with geospatial tools. With the rising demand from the diverse end-user communities for geospatial tools to handle multidimensional products, several applications, such as ArcGIS, have refined their software. Many geospatial applications now have new functionalities that enable the end user to: Store, serve, and perform analysis on each individual variable, its time dimension, and vertical dimension. Use NetCDF, GRIB, and HDF raster data formats across applications directly. Publish output within REST image services or WMS for time and space enabled web application development. During this webinar, participants will learn how to leverage geospatial applications such as ArcGIS, OPeNDAP and ncWMS in the production of Earth science information, and in increasing data accessibility and usability.

Institutional Transformation 2.5 Building Module Help Manual.

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

Villa, Daniel

The Institutional Transformation (IX) building module is a software tool developed at Sandia National Laboratories to evaluate energy conservation measures (ECMs) on hundreds of DOE-2 building energy models simultaneously. In IX, ECMs can be designed through parameterizing DOE-2 building models and doing further processing via visual basic for applications subroutines. IX provides the functionality to handle multiple building models for different years, which enables incrementally changing a site of hundreds of buildings over time. It also enables evaluation of the effects of changing climate, comparisons between data and modeling results, and energy use of centralized utility buildings (CUBs). IX consistsmore » of a Microsoft Excel(r) user interface, Microsoft Access(r) database, and Microsoft Excel(r) CUB build utility whose functionalities are described in detail in this report. In addition to descriptions of the user interfaces, descriptions of every ECM already designed in IX is included. SAND2016-8983 IX 2.5 Help Manual« less

The Virtual Solar Observatory: What Are We Up To Now?

NASA Technical Reports Server (NTRS)

Gurman, J. B.; Hill, F.; Suarez-Sola, F.; Bogart, R.; Amezcua, A.; Martens, P.; Hourcle, J.; Hughitt, K.; Davey, A.

2012-01-01

In the nearly ten years of a functional Virtual Solar Observatory (VSO), http://virtualsolar.org/ we have made it possible to query and access sixty-seven distinct solar data products and several event lists from nine spacecraft and fifteen observatories or observing networks. We have used existing VSO technology, and developed new software, for a distributed network of sites caching and serving SDO HMI and/ or AlA data. We have also developed an application programming interface (API) that has enabled VSO search and data access capabilities in IDL, Python, and Java. We also have quite a bit of work yet to do, including completion of the implementation of access to SDO EVE data, and access to some nineteen other data sets from space- and ground-based observatories. In addition, we have been developing a new graphic user interface that will enable the saving of user interface and search preferences. We solicit advice from the community input prioritizing our task list, and adding to it

Development of the ARISTOTLE webware for cloud-based rarefied gas flow modeling

NASA Astrophysics Data System (ADS)

Deschenes, Timothy R.; Grot, Jonathan; Cline, Jason A.

2016-11-01

Rarefied gas dynamics are important for a wide variety of applications. An improvement in the ability of general users to predict these gas flows will enable optimization of current, and discovery of future processes. Despite this potential, most rarefied simulation software is designed by and for experts in the community. This has resulted in low adoption of the methods outside of the immediate RGD community. This paper outlines an ongoing effort to create a rarefied gas dynamics simulation tool that can be used by a general audience. The tool leverages a direct simulation Monte Carlo (DSMC) library that is available to the entire community and a web-based simulation process that will enable all users to take advantage of high performance computing capabilities. First, the DSMC library and simulation architecture are described. Then the DSMC library is used to predict a number of representative transient gas flows that are applicable to the rarefied gas dynamics community. The paper closes with a summary and future direction.

CellShape: A user-friendly image analysis tool for quantitative visualization of bacterial cell factories inside.

PubMed

Goñi-Moreno, Ángel; Kim, Juhyun; de Lorenzo, Víctor

2017-02-01

Visualization of the intracellular constituents of individual bacteria while performing as live biocatalysts is in principle doable through more or less sophisticated fluorescence microscopy. Unfortunately, rigorous quantitation of the wealth of data embodied in the resulting images requires bioinformatic tools that are not widely extended within the community-let alone that they are often subject to licensing that impedes software reuse. In this context we have developed CellShape, a user-friendly platform for image analysis with subpixel precision and double-threshold segmentation system for quantification of fluorescent signals stemming from single-cells. CellShape is entirely coded in Python, a free, open-source programming language with widespread community support. For a developer, CellShape enhances extensibility (ease of software improvements) by acting as an interface to access and use existing Python modules; for an end-user, CellShape presents standalone executable files ready to open without installation. We have adopted this platform to analyse with an unprecedented detail the tridimensional distribution of the constituents of the gene expression flow (DNA, RNA polymerase, mRNA and ribosomal proteins) in individual cells of the industrial platform strain Pseudomonas putida KT2440. While the CellShape first release version (v0.8) is readily operational, users and/or developers are enabled to expand the platform further. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A DICOM based radiotherapy plan database for research collaboration and reporting

NASA Astrophysics Data System (ADS)

Westberg, J.; Krogh, S.; Brink, C.; Vogelius, I. R.

2014-03-01

Purpose: To create a central radiotherapy (RT) plan database for dose analysis and reporting, capable of calculating and presenting statistics on user defined patient groups. The goal is to facilitate multi-center research studies with easy and secure access to RT plans and statistics on protocol compliance. Methods: RT institutions are able to send data to the central database using DICOM communications on a secure computer network. The central system is composed of a number of DICOM servers, an SQL database and in-house developed software services to process the incoming data. A web site within the secure network allows the user to manage their submitted data. Results: The RT plan database has been developed in Microsoft .NET and users are able to send DICOM data between RT centers in Denmark. Dose-volume histogram (DVH) calculations performed by the system are comparable to those of conventional RT software. A permission system was implemented to ensure access control and easy, yet secure, data sharing across centers. The reports contain DVH statistics for structures in user defined patient groups. The system currently contains over 2200 patients in 14 collaborations. Conclusions: A central RT plan repository for use in multi-center trials and quality assurance was created. The system provides an attractive alternative to dummy runs by enabling continuous monitoring of protocol conformity and plan metrics in a trial.

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

Bridge, Pete, E-mail: pete.bridge@qut.edu.au; Gunn, Therese; Kastanis, Lazaros

A novel realistic 3D virtual reality (VR) application has been developed to allow medical imaging students at Queensland University of Technology to practice radiographic techniques independently outside the usual radiography laboratory. A flexible agile development methodology was used to create the software rapidly and effectively. A 3D gaming environment and realistic models were used to engender presence in the software while tutor-determined gold standards enabled students to compare their performance and learn in a problem-based learning pedagogy. Students reported high levels of satisfaction and perceived value and the software enabled up to 40 concurrent users to prepare for clinical practice.more » Student feedback also indicated that they found 3D to be of limited value in the desktop version compared to the usual 2D approach. A randomised comparison between groups receiving software-based and traditional practice measured performance in a formative role play with real equipment. The results of this work indicated superior performance with the equipment for the VR trained students (P = 0.0366) and confirmed the value of VR for enhancing 3D equipment-based problem-solving skills. Students practising projection techniques virtually performed better at role play assessments than students practising in a traditional radiography laboratory only. The application particularly helped with 3D equipment configuration, suggesting that teaching 3D problem solving is an ideal use of such medical equipment simulators. Ongoing development work aims to establish the role of VR software in preparing students for clinical practice with a range of medical imaging equipment.« less

An expert system based software sizing tool, phase 2

NASA Technical Reports Server (NTRS)

Friedlander, David

1990-01-01

A software tool was developed for predicting the size of a future computer program at an early stage in its development. The system is intended to enable a user who is not expert in Software Engineering to estimate software size in lines of source code with an accuracy similar to that of an expert, based on the program's functional specifications. The project was planned as a knowledge based system with a field prototype as the goal of Phase 2 and a commercial system planned for Phase 3. The researchers used techniques from Artificial Intelligence and knowledge from human experts and existing software from NASA's COSMIC database. They devised a classification scheme for the software specifications, and a small set of generic software components that represent complexity and apply to large classes of programs. The specifications are converted to generic components by a set of rules and the generic components are input to a nonlinear sizing function which makes the final prediction. The system developed for this project predicted code sizes from the database with a bias factor of 1.06 and a fluctuation factor of 1.77, an accuracy similar to that of human experts but without their significant optimistic bias.

Sequence Polishing Library (SPL) v10.0

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

Oberortner, Ernst

The Sequence Polishing Library (SPL) is a suite of software tools in order to automate "Design for Synthesis and Assembly" workflows. Specifically: The SPL "Converter" tool converts files among the following sequence data exchange formats: CSV, FASTA, GenBank, and Synthetic Biology Open Language (SBOL); The SPL "Juggler" tool optimizes the codon usages of DNA coding sequences according to an optimization strategy, a user-specific codon usage table and genetic code. In addition, the SPL "Juggler" can translate amino acid sequences into DNA sequences.:The SPL "Polisher" verifies NA sequences against DNA synthesis constraints, such as GC content, repeating k-mers, and restriction sites.more » In case of violations, the "Polisher" reports the violations in a comprehensive manner. The "Polisher" tool can also modify the violating regions according to an optimization strategy, a user-specific codon usage table and genetic code;The SPL "Partitioner" decomposes large DNA sequences into smaller building blocks with partial overlaps that enable an efficient assembly. The "Partitioner" enables the user to configure the characteristics of the overlaps, which are mostly determined by the utilized assembly protocol, such as length, GC content, or melting temperature.« less

Earth Observing System Data Gateway

NASA Technical Reports Server (NTRS)

Pfister, Robin; McMahon, Joe; Amrhein, James; Sefert, Ed; Marsans, Lorena; Solomon, Mark; Nestler, Mark

2006-01-01

The Earth Observing System Data Gateway (EDG) software provides a "one-stop-shopping" standard interface for exploring and ordering Earth-science data stored at geographically distributed sites. EDG enables a user to do the following: 1) Search for data according to high-level criteria (e.g., geographic location, time, or satellite that acquired the data); 2) Browse the results of a search, viewing thumbnail sketches of data that satisfy the user s criteria; and 3) Order selected data for delivery to a specified address on a chosen medium (e.g., compact disk or magnetic tape). EDG consists of (1) a component that implements a high-level client/server protocol, and (2) a collection of C-language libraries that implement the passing of protocol messages between an EDG client and one or more EDG servers. EDG servers are located at sites usually called "Distributed Active Archive Centers" (DAACs). Each DAAC may allow access to many individual data items, called "granules" (e.g., single Landsat images). Related granules are grouped into collections called "data sets." EDG enables a user to send a search query to multiple DAACs simultaneously, inspect the resulting information, select browseable granules, and then order selected data from the different sites in a seamless fashion.

Expressions Module for the Satellite Orbit Analysis Program

NASA Technical Reports Server (NTRS)

Edmonds, Karina

2008-01-01

The Expressions Module is a software module that has been incorporated into the Satellite Orbit Analysis Program (SOAP). The module includes an expressions- parser submodule built on top of an analytical system, enabling the user to define logical and numerical variables and constants. The variables can capture output from SOAP orbital-prediction and geometric-engine computations. The module can combine variables and constants with built-in logical operators (such as Boolean AND, OR, and NOT), relational operators (such as >, <, or =), and mathematical operators (such as addition, subtraction, multiplication, division, modulus, exponentiation, differentiation, and integration). Parentheses can be used to specify precedence of operations. The module contains a library of mathematical functions and operations, including logarithms, trigonometric functions, Bessel functions, minimum/ maximum operations, and floating- point-to-integer conversions. The module supports combinations of time, distance, and angular units and has a dimensional- analysis component that checks for correct usage of units. A parser based on the Flex language and the Bison program looks for and indicates errors in syntax. SOAP expressions can be built using other expressions as arguments, thus enabling the user to build analytical trees. A graphical user interface facilitates use.

A client/server system for Internet access to biomedical text/image databanks.

PubMed

Thoma, G R; Long, L R; Berman, L E

1996-01-01

Internet access to mixed text/image databanks is finding application in the medical world. An example is a database of medical X-rays and associated data consisting of demographic, socioeconomic, physician's exam, medical laboratory and other information collected as part of a nationwide health survey conducted by the government. Another example is a collection of digitized cryosection images, CT and MR taken of cadavers as part of the National Library of Medicine's Visible Human Project. In both cases, the challenge is to provide access to both the image and the associated text for a wide end user community to create atlases, conduct epidemiological studies, to develop image-specific algorithms for compression, enhancement and other types of image processing, among many other applications. The databanks mentioned above are being created in prototype form. This paper describes the prototype system developed for the archiving of the data and the client software to enable a broad range of end users to access the archive, retrieve text and image data, display the data and manipulate the images. System design considerations include; data organization in a relational database management system with object-oriented extensions; a hierarchical organization of the image data by different resolution levels for different user classes; client design based on common hardware and software platforms incorporating SQL search capability, X Window, Motif and TAE (a development environment supporting rapid prototyping and management of graphic-oriented user interfaces); potential to include ultra high resolution display monitors as a user option; intuitive user interface paradigm for building complex queries; and contrast enhancement, magnification and mensuration tools for better viewing by the user.

Fast interactive exploration of 4D MRI flow data

NASA Astrophysics Data System (ADS)

Hennemuth, A.; Friman, O.; Schumann, C.; Bock, J.; Drexl, J.; Huellebrand, M.; Markl, M.; Peitgen, H.-O.

2011-03-01

1- or 2-directional MRI blood flow mapping sequences are an integral part of standard MR protocols for diagnosis and therapy control in heart diseases. Recent progress in rapid MRI has made it possible to acquire volumetric, 3-directional cine images in reasonable scan time. In addition to flow and velocity measurements relative to arbitrarily oriented image planes, the analysis of 3-dimensional trajectories enables the visualization of flow patterns, local features of flow trajectories or possible paths into specific regions. The anatomical and functional information allows for advanced hemodynamic analysis in different application areas like stroke risk assessment, congenital and acquired heart disease, aneurysms or abdominal collaterals and cranial blood flow. The complexity of the 4D MRI flow datasets and the flow related image analysis tasks makes the development of fast comprehensive data exploration software for advanced flow analysis a challenging task. Most existing tools address only individual aspects of the analysis pipeline such as pre-processing, quantification or visualization, or are difficult to use for clinicians. The goal of the presented work is to provide a software solution that supports the whole image analysis pipeline and enables data exploration with fast intuitive interaction and visualization methods. The implemented methods facilitate the segmentation and inspection of different vascular systems. Arbitrary 2- or 3-dimensional regions for quantitative analysis and particle tracing can be defined interactively. Synchronized views of animated 3D path lines, 2D velocity or flow overlays and flow curves offer a detailed insight into local hemodynamics. The application of the analysis pipeline is shown for 6 cases from clinical practice, illustrating the usefulness for different clinical questions. Initial user tests show that the software is intuitive to learn and even inexperienced users achieve good results within reasonable processing times.

OpenTopography: Addressing Big Data Challenges Using Cloud Computing, HPC, and Data Analytics

NASA Astrophysics Data System (ADS)

Crosby, C. J.; Nandigam, V.; Phan, M.; Youn, C.; Baru, C.; Arrowsmith, R.

2014-12-01

OpenTopography (OT) is a geoinformatics-based data facility initiated in 2009 for democratizing access to high-resolution topographic data, derived products, and tools. Hosted at the San Diego Supercomputer Center (SDSC), OT utilizes cyberinfrastructure, including large-scale data management, high-performance computing, and service-oriented architectures to provide efficient Web based access to large, high-resolution topographic datasets. OT collocates data with processing tools to enable users to quickly access custom data and derived products for their application. OT's ongoing R&D efforts aim to solve emerging technical challenges associated with exponential growth in data, higher order data products, as well as user base. Optimization of data management strategies can be informed by a comprehensive set of OT user access metrics that allows us to better understand usage patterns with respect to the data. By analyzing the spatiotemporal access patterns within the datasets, we can map areas of the data archive that are highly active (hot) versus the ones that are rarely accessed (cold). This enables us to architect a tiered storage environment consisting of high performance disk storage (SSD) for the hot areas and less expensive slower disk for the cold ones, thereby optimizing price to performance. From a compute perspective, OT is looking at cloud based solutions such as the Microsoft Azure platform to handle sudden increases in load. An OT virtual machine image in Microsoft's VM Depot can be invoked and deployed quickly in response to increased system demand. OT has also integrated SDSC HPC systems like the Gordon supercomputer into our infrastructure tier to enable compute intensive workloads like parallel computation of hydrologic routing on high resolution topography. This capability also allows OT to scale to HPC resources during high loads to meet user demand and provide more efficient processing. With a growing user base and maturing scientific user community comes new requests for algorithms and processing capabilities. To address this demand, OT is developing an extensible service based architecture for integrating community-developed software. This "plugable" approach to Web service deployment will enable new processing and analysis tools to run collocated with OT hosted data.

New generation of exploration tools: interactive modeling software and microcomputers

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

Krajewski, S.A.

1986-08-01

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

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

PubMed Central

2018-01-01

Bugs and vulnerabilities in binary executables threaten cyber security. Current discovery methods, like fuzz testing, symbolic execution and manual analysis, both have advantages and disadvantages when exercising the deeper code area in binary executables to find more bugs. In this paper, we designed and implemented a hybrid automatic bug finding tool—Ffuzz—on top of fuzz testing and selective symbolic execution. It targets full system software stack testing including both the user space and kernel space. Combining these two mainstream techniques enables us to achieve higher coverage and avoid getting stuck both in fuzz testing and symbolic execution. We also proposed two key optimizations to improve the efficiency of full system testing. We evaluated the efficiency and effectiveness of our method on real-world binary software and 844 memory corruption vulnerable programs in the Juliet test suite. The results show that Ffuzz can discover software bugs in the full system software stack effectively and efficiently. PMID:29791469

Design and implementation of Skype USB user gateway software

NASA Astrophysics Data System (ADS)

Qi, Yang

2017-08-01

With the widespread application of VoIP, the client with private protocol becomes more and more popular. Skype is one of the representatives. How to connect Skype with PSTN just by Skype client has gradually become hot. This paper design and implement the software based on a kind of USB User Gateway. With the software Skype user can freely communicate with PSTN phone. FSM is designed as the core of the software, and Skype control is separated by the USB Gateway control. In this way, the communication becomes more flexible and efficient. In the actual user testing, the software obtains good results.

Preoperative Planning of Orthopedic Procedures using Digitalized Software Systems.

PubMed

Steinberg, Ely L; Segev, Eitan; Drexler, Michael; Ben-Tov, Tomer; Nimrod, Snir

2016-06-01

The progression from standard celluloid films to digitalized technology led to the development of new software programs to fulfill the needs of preoperative planning. We describe here preoperative digitalized programs and the variety of conditions for which those programs can be used to facilitate preparation for surgery. A PubMed search using the keywords "digitalized software programs," "preoperative planning" and "total joint arthroplasty" was performed for all studies regarding preoperative planning of orthopedic procedures that were published from 1989 to 2014 in English. Digitalized software programs are enabled to import and export all picture archiving communication system (PACS) files (i.e., X-rays, computerized tomograms, magnetic resonance images) from either the local working station or from any remote PACS. Two-dimension (2D) and 3D CT scans were found to be reliable tools with a high preoperative predicting accuracy for implants. The short learning curve, user-friendly features, accurate prediction of implant size, decreased implant stocks and low-cost maintenance makes digitalized software programs an attractive tool in preoperative planning of total joint replacement, fracture fixation, limb deformity repair and pediatric skeletal disorders.

Software to Facilitate Remote Sensing Data Access for Disease Early Warning Systems

PubMed Central

Liu, Yi; Hu, Jiameng; Snell-Feikema, Isaiah; VanBemmel, Michael S.; Lamsal, Aashis; Wimberly, Michael C.

2015-01-01

Satellite remote sensing produces an abundance of environmental data that can be used in the study of human health. To support the development of early warning systems for mosquito-borne diseases, we developed an open-source, client based software application to enable the Epidemiological Applications of Spatial Technologies (EASTWeb). Two major design decisions were full automation of the discovery, retrieval and processing of remote sensing data from multiple sources, and making the system easily modifiable in response to changes in data availability and user needs. Key innovations that helped to achieve these goals were the implementation of a software framework for data downloading and the design of a scheduler that tracks the complex dependencies among multiple data processing tasks and makes the system resilient to external errors. EASTWeb has been successfully applied to support forecasting of West Nile virus outbreaks in the United States and malaria epidemics in the Ethiopian highlands. PMID:26644779

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

PubMed

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

2016-08-30

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

Internet-Based Software Tools for Analysis and Processing of LIDAR Point Cloud Data via the OpenTopography Portal

NASA Astrophysics Data System (ADS)

Nandigam, V.; Crosby, C. J.; Baru, C.; Arrowsmith, R.

2009-12-01

LIDAR is an excellent example of the new generation of powerful remote sensing data now available to Earth science researchers. Capable of producing digital elevation models (DEMs) more than an order of magnitude higher resolution than those currently available, LIDAR data allows earth scientists to study the processes that contribute to landscape evolution at resolutions not previously possible, yet essential for their appropriate representation. Along with these high-resolution datasets comes an increase in the volume and complexity of data that the user must efficiently manage and process in order for it to be scientifically useful. Although there are expensive commercial LIDAR software applications available, processing and analysis of these datasets are typically computationally inefficient on the conventional hardware and software that is currently available to most of the Earth science community. We have designed and implemented an Internet-based system, the OpenTopography Portal, that provides integrated access to high-resolution LIDAR data as well as web-based tools for processing of these datasets. By using remote data storage and high performance compute resources, the OpenTopography Portal attempts to simplify data access and standard LIDAR processing tasks for the Earth Science community. The OpenTopography Portal allows users to access massive amounts of raw point cloud LIDAR data as well as a suite of DEM generation tools to enable users to generate custom digital elevation models to best fit their science applications. The Cyberinfrastructure software tools for processing the data are freely available via the portal and conveniently integrated with the data selection in a single user-friendly interface. The ability to run these tools on powerful Cyberinfrastructure resources instead of their own labs provides a huge advantage in terms of performance and compute power. The system also encourages users to explore data processing methods and the variations in algorithm parameters since all of the processing is done remotely and numerous jobs can be submitted in sequence. The web-based software also eliminates the need for users to deal with the hassles and costs associated with software installation and licensing while providing adequate disk space for storage and personal job archival capability. Although currently limited to data access and DEM generation tasks, the OpenTopography system is modular in design and can be modified to accommodate new processing tools as they become available. We are currently exploring implementation of higher-level DEM analysis tasks in OpenTopography, since such processing is often computationally intensive and thus lends itself to utilization of cyberinfrastructure. Products derived from OpenTopography processing are available in a variety of formats ranging from simple Google Earth visualizations of LIDAR-derived hillshades to various GIS-compatible grid formats. To serve community users less interested in data processing, OpenTopography also hosts 1 km^2 digital elevation model tiles as well as Google Earth image overlays for a synoptic view of the data.

Programming Makes Software; Support Makes Users

NASA Astrophysics Data System (ADS)

Batcheller, A. L.

2010-12-01

Skilled software engineers may build fantastic software for climate modeling, yet fail to achieve their project’s objectives. Software support and related activities are just as critical as writing software. This study followed three different software projects in the climate sciences, using interviews, observation, and document analysis to examine the value added by support work. Supporting the project and interacting with users was a key task for software developers, who often spent 50% of their time on it. Such support work most often involved replying to questions on an email list, but also included talking to users on teleconference calls and in person. Software support increased adoption by building the software’s reputation and showing individuals how the software can meet their needs. In the process of providing support, developers often learned new of requirements as users reported features they desire and bugs they found. As software matures and gains widespread use, support work often increases. In fact, such increases can be one signal that the software has achieved broad acceptance. Maturing projects also find demand for instructional classes, online tutorials and detailed examples of how to use the software. The importance of support highlights the fact that building software systems involves both social and technical aspects. Yes, we need to build the software, but we also need to “build” the users and practices that can take advantage of it.

MiMiR – an integrated platform for microarray data sharing, mining and analysis

PubMed Central

Tomlinson, Chris; Thimma, Manjula; Alexandrakis, Stelios; Castillo, Tito; Dennis, Jayne L; Brooks, Anthony; Bradley, Thomas; Turnbull, Carly; Blaveri, Ekaterini; Barton, Geraint; Chiba, Norie; Maratou, Klio; Soutter, Pat; Aitman, Tim; Game, Laurence

2008-01-01

Background Despite considerable efforts within the microarray community for standardising data format, content and description, microarray technologies present major challenges in managing, sharing, analysing and re-using the large amount of data generated locally or internationally. Additionally, it is recognised that inconsistent and low quality experimental annotation in public data repositories significantly compromises the re-use of microarray data for meta-analysis. MiMiR, the Microarray data Mining Resource was designed to tackle some of these limitations and challenges. Here we present new software components and enhancements to the original infrastructure that increase accessibility, utility and opportunities for large scale mining of experimental and clinical data. Results A user friendly Online Annotation Tool allows researchers to submit detailed experimental information via the web at the time of data generation rather than at the time of publication. This ensures the easy access and high accuracy of meta-data collected. Experiments are programmatically built in the MiMiR database from the submitted information and details are systematically curated and further annotated by a team of trained annotators using a new Curation and Annotation Tool. Clinical information can be annotated and coded with a clinical Data Mapping Tool within an appropriate ethical framework. Users can visualise experimental annotation, assess data quality, download and share data via a web-based experiment browser called MiMiR Online. All requests to access data in MiMiR are routed through a sophisticated middleware security layer thereby allowing secure data access and sharing amongst MiMiR registered users prior to publication. Data in MiMiR can be mined and analysed using the integrated EMAAS open source analysis web portal or via export of data and meta-data into Rosetta Resolver data analysis package. Conclusion The new MiMiR suite of software enables systematic and effective capture of extensive experimental and clinical information with the highest MIAME score, and secure data sharing prior to publication. MiMiR currently contains more than 150 experiments corresponding to over 3000 hybridisations and supports the Microarray Centre's large microarray user community and two international consortia. The MiMiR flexible and scalable hardware and software architecture enables secure warehousing of thousands of datasets, including clinical studies, from microarray and potentially other -omics technologies. PMID:18801157

Mapping and Modeling Web Portal to Advance Global Monitoring and Climate Research

NASA Astrophysics Data System (ADS)

Chang, G.; Malhotra, S.; Bui, B.; Sadaqathulla, S.; Goodale, C. E.; Ramirez, P.; Kim, R. M.; Rodriguez, L.; Law, E.

2011-12-01

Today, the principal investigators of NASA Earth Science missions develop their own software to manipulate, visualize, and analyze the data collected from Earth, space, and airborne observation instruments. There is very little, if any, collaboration among these principal investigators due to the lack of collaborative tools, which would allow these scientists to share data and results. At NASA's Jet Propulsion Laboratory (JPL), under the Lunar Mapping and Modeling Project (LMMP), we have built a web portal that exposes a set of common services to users to allow search, visualization, subset, and download lunar science data. Users also have access to a set of tools that visualize, analyze and annotate the data. These services are developed according to industry standards for data access and manipulation, such REST and Open Geospatial Consortium (OGC) web services. As a result, users can access the datasets through custom written applications or off-the-shelf applications such as Google Earth. Even though it's currently used to store and process lunar data, this web portal infrastructure has been designed to support other solar system bodies such as asteroids and planets, including Earth. The infrastructure uses a combination of custom, commercial, and open-source software as well as off-the-shelf hardware and pay-by-use cloud computing services. The use of standardized web service interfaces facilitates platform and application-independent access to the services and data. For instance, we have software clients for the LMMP portal that provide a rich browsing and analysis experience from a variety of platforms including iOS and Android mobile platforms and large screen multi-touch displays with 3-D terrain viewing functions. The service-oriented architecture and design principles utilized in the implementation of the portal lends itself to be reusable and scalable and could naturally be extended to include a collaborative environment that enables scientists and principal investigators to share their research and analysis seamlessly. In addition, this extension will allow users to easily share their tools and data, and to enrich their mapping and analysis experiences. In this talk, we will describe the advanced data management and portal technologies used to power this collaborative environment. We will further illustrate how this environment can enable, enhance and advance global monitoring and climate research.

MiMiR--an integrated platform for microarray data sharing, mining and analysis.

PubMed

Tomlinson, Chris; Thimma, Manjula; Alexandrakis, Stelios; Castillo, Tito; Dennis, Jayne L; Brooks, Anthony; Bradley, Thomas; Turnbull, Carly; Blaveri, Ekaterini; Barton, Geraint; Chiba, Norie; Maratou, Klio; Soutter, Pat; Aitman, Tim; Game, Laurence

2008-09-18

Despite considerable efforts within the microarray community for standardising data format, content and description, microarray technologies present major challenges in managing, sharing, analysing and re-using the large amount of data generated locally or internationally. Additionally, it is recognised that inconsistent and low quality experimental annotation in public data repositories significantly compromises the re-use of microarray data for meta-analysis. MiMiR, the Microarray data Mining Resource was designed to tackle some of these limitations and challenges. Here we present new software components and enhancements to the original infrastructure that increase accessibility, utility and opportunities for large scale mining of experimental and clinical data. A user friendly Online Annotation Tool allows researchers to submit detailed experimental information via the web at the time of data generation rather than at the time of publication. This ensures the easy access and high accuracy of meta-data collected. Experiments are programmatically built in the MiMiR database from the submitted information and details are systematically curated and further annotated by a team of trained annotators using a new Curation and Annotation Tool. Clinical information can be annotated and coded with a clinical Data Mapping Tool within an appropriate ethical framework. Users can visualise experimental annotation, assess data quality, download and share data via a web-based experiment browser called MiMiR Online. All requests to access data in MiMiR are routed through a sophisticated middleware security layer thereby allowing secure data access and sharing amongst MiMiR registered users prior to publication. Data in MiMiR can be mined and analysed using the integrated EMAAS open source analysis web portal or via export of data and meta-data into Rosetta Resolver data analysis package. The new MiMiR suite of software enables systematic and effective capture of extensive experimental and clinical information with the highest MIAME score, and secure data sharing prior to publication. MiMiR currently contains more than 150 experiments corresponding to over 3000 hybridisations and supports the Microarray Centre's large microarray user community and two international consortia. The MiMiR flexible and scalable hardware and software architecture enables secure warehousing of thousands of datasets, including clinical studies, from microarray and potentially other -omics technologies.

SimulatorToFMU v0.1

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

Nouidui, Thierry; Wetter, Michael

SimulatorToFMU is a software package written in Python which allows users to export a memoryless Python-driven simulation program or script as a Functional Mock-up Unit (FMU) for model exchange or co-simulation.In CyDER (Cyber Physical Co-simulation Platform for Distributed Energy Resources in Smart Grids), SimulatorToFMU will allow exporting OPAL-RT as an FMU. This will enable OPAL-RT to be linked to CYMDIST and GridDyn FMUs through a standardized open source interface.

Managing Data From Signal-Propagation Experiments

NASA Technical Reports Server (NTRS)

Kantak, A. V.

1989-01-01

Computer programs generate characteristic plots from amplitudes and phases. Software system enables minicomputer to process data on amplitudes and phases of signals received during experiments in ground-mobile/satellite radio propagation. Takes advantage of file-handling capabilities of UNIX operating system and C programming language. Interacts with user, under whose guidance programs in FORTRAN language generate plots of spectra or other curves of types commonly used to characterize signals. FORTRAN programs used to process file-handling outputs into any of several useful forms.

The fast azimuthal integration Python library: pyFAI.

PubMed

Ashiotis, Giannis; Deschildre, Aurore; Nawaz, Zubair; Wright, Jonathan P; Karkoulis, Dimitrios; Picca, Frédéric Emmanuel; Kieffer, Jérôme

2015-04-01

pyFAI is an open-source software package designed to perform azimuthal integration and, correspondingly, two-dimensional regrouping on area-detector frames for small- and wide-angle X-ray scattering experiments. It is written in Python (with binary submodules for improved performance), a language widely accepted and used by the scientific community today, which enables users to easily incorporate the pyFAI library into their processing pipeline. This article focuses on recent work, especially the ease of calibration, its accuracy and the execution speed for integration.

Managing Information On Technical Requirements

NASA Technical Reports Server (NTRS)

Mauldin, Lemuel E., III; Hammond, Dana P.

1993-01-01

Technical Requirements Analysis and Control Systems/Initial Operating Capability (TRACS/IOC) computer program provides supplemental software tools for analysis, control, and interchange of project requirements so qualified project members have access to pertinent project information, even if in different locations. Enables users to analyze and control requirements, serves as focal point for project requirements, and integrates system supporting efficient and consistent operations. TRACS/IOC is HyperCard stack for use on Macintosh computers running HyperCard 1.2 or later and Oracle 1.2 or later.

SOFA & astrometry

NASA Astrophysics Data System (ADS)

Hohenkerk, C.

2015-08-01

The International Astronomical Union's (IAU) Standards of Fundamental Astronomy (SOFA) software library has in the last year introduced a tranche of 32 new routines dealing with the subject area "astrometry". This poster provides a guide to enable users to get to grips easily with the various routines for the transformations between ICRS, ICRS astrometric, GCRS, Celestial Intermediate and observed positions of stars, together with their underlying routines for proper motion, parallax, aberration, light deflection and refraction. A summary of the current status of SOFA is also included.

An Interdisciplinary Approach Between Medical Informatics and Social Sciences to Transdisciplinary Requirements Engineering for an Integrated Care Setting.

PubMed

Vielhauer, Jan; Böckmann, Britta

2017-01-01

Requirements engineering of software products for elderly people faces some special challenges to ensure a maximum of user acceptance. Within the scope of a research project, a web-based platform and a mobile app are approached to enable people to live in their own home as long as possible. This paper is about a developed method of interdisciplinary requirements engineering by a team of social scientists in cooperation with computer scientists.

Neural-Network-Development Program

NASA Technical Reports Server (NTRS)

Phillips, Todd A.

1993-01-01

NETS, software tool for development and evaluation of neural networks, provides simulation of neural-network algorithms plus computing environment for development of such algorithms. Uses back-propagation learning method for all of networks it creates. Enables user to customize patterns of connections between layers of network. Also provides features for saving, during learning process, values of weights, providing more-precise control over learning process. Written in ANSI standard C language. Machine-independent version (MSC-21588) includes only code for command-line-interface version of NETS 3.0.

Data-Base Software For Tracking Technological Developments

NASA Technical Reports Server (NTRS)

Aliberti, James A.; Wright, Simon; Monteith, Steve K.

1996-01-01

Technology Tracking System (TechTracS) computer program developed for use in storing and retrieving information on technology and related patent information developed under auspices of NASA Headquarters and NASA's field centers. Contents of data base include multiple scanned still images and quick-time movies as well as text. TechTracS includes word-processing, report-editing, chart-and-graph-editing, and search-editing subprograms. Extensive keyword searching capabilities enable rapid location of technologies, innovators, and companies. System performs routine functions automatically and serves multiple users.

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

DTIC Science & Technology

2013-12-01

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

Wind Wake Watcher v. 1.0

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

Martin, Shawn

This software enables the user to produce Google Earth visualizations of turbine wake effects for wind farms. The visualizations are based on computations of statistical quantities that vary with wind direction and help quantify the effects on power production of upwind turbines on turbines in their wakes. The results of the software are plot images and kml files that can be loaded into Google Earth. The statistics computed are described in greater detail in the paper: S. Martin, C. H. Westergaard, and J. White (2016), Visualizing Wind Farm Wakes Using SCADA Data, in Wither Turbulence and Big Data in themore » 21st Century? Eds. A. Pollard, L. Castillo, L. Danaila, and M. Glauser. Springer, pgs. 231-254.« less

Workstation-Based Simulation for Rapid Prototyping and Piloted Evaluation of Control System Designs

NASA Technical Reports Server (NTRS)

Mansur, M. Hossein; Colbourne, Jason D.; Chang, Yu-Kuang; Aiken, Edwin W. (Technical Monitor)

1998-01-01

The development and optimization of flight control systems for modem fixed- and rotary-. wing aircraft consume a significant portion of the overall time and cost of aircraft development. Substantial savings can be achieved if the time required to develop and flight test the control system, and the cost, is reduced. To bring about such reductions, software tools such as Matlab/Simulink are being used to readily implement block diagrams and rapidly evaluate the expected responses of the completed system. Moreover, tools such as CONDUIT (CONtrol Designer's Unified InTerface) have been developed that enable the controls engineers to optimize their control laws and ensure that all the relevant quantitative criteria are satisfied, all within a fully interactive, user friendly, unified software environment.

Distributed nuclear medicine applications using World Wide Web and Java technology.

PubMed

Knoll, P; Höll, K; Mirzaei, S; Koriska, K; Köhn, H

2000-01-01

At present, medical applications applying World Wide Web (WWW) technology are mainly used to view static images and to retrieve some information. The Java platform is a relative new way of computing, especially designed for network computing and distributed applications which enables interactive connection between user and information via the WWW. The Java 2 Software Development Kit (SDK) including Java2D API, Java Remote Method Invocation (RMI) technology, Object Serialization and the Java Advanced Imaging (JAI) extension was used to achieve a robust, platform independent and network centric solution. Medical image processing software based on this technology is presented and adequate performance capability of Java is demonstrated by an iterative reconstruction algorithm for single photon emission computerized tomography (SPECT).

CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures.

PubMed

Kozlikova, Barbora; Sebestova, Eva; Sustr, Vilem; Brezovsky, Jan; Strnad, Ondrej; Daniel, Lukas; Bednar, David; Pavelka, Antonin; Manak, Martin; Bezdeka, Martin; Benes, Petr; Kotry, Matus; Gora, Artur; Damborsky, Jiri; Sochor, Jiri

2014-09-15

The transport of ligands, ions or solvent molecules into proteins with buried binding sites or through the membrane is enabled by protein tunnels and channels. CAVER Analyst is a software tool for calculation, analysis and real-time visualization of access tunnels and channels in static and dynamic protein structures. It provides an intuitive graphic user interface for setting up the calculation and interactive exploration of identified tunnels/channels and their characteristics. CAVER Analyst is a multi-platform software written in JAVA. Binaries and documentation are freely available for non-commercial use at http://www.caver.cz. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

NASA Orbital Debris Engineering Model ORDEM2008 (Beta Version)

NASA Technical Reports Server (NTRS)

Stansbery, Eugene G.; Krisko, Paula H.

2009-01-01

This is an interim document intended to accompany the beta-release of the ORDEM2008 model. As such it provides the user with a guide for its use, a list of its capabilities, a brief summary of model development, and appendices included to educate the user as to typical runtimes for different orbit configurations. More detailed documentation will be delivered with the final product. ORDEM2008 supersedes NASA's previous model - ORDEM2000. The availability of new sensor and in situ data, the re-analysis of older data, and the development of new analytical techniques, has enabled the construction of this more comprehensive and sophisticated model. Integrated with the software is an upgraded graphical user interface (GUI), which uses project-oriented organization and provides the user with graphical representations of numerous output data products. These range from the conventional average debris size vs. flux magnitude for chosen analysis orbits, to the more complex color-contoured two-dimensional (2-D) directional flux diagrams in terms of local spacecraft pitch and yaw.

Modelling parallel programs and multiprocessor architectures with AXE

NASA Technical Reports Server (NTRS)

Yan, Jerry C.; Fineman, Charles E.

1991-01-01

AXE, An Experimental Environment for Parallel Systems, was designed to model and simulate for parallel systems at the process level. It provides an integrated environment for specifying computation models, multiprocessor architectures, data collection, and performance visualization. AXE is being used at NASA-Ames for developing resource management strategies, parallel problem formulation, multiprocessor architectures, and operating system issues related to the High Performance Computing and Communications Program. AXE's simple, structured user-interface enables the user to model parallel programs and machines precisely and efficiently. Its quick turn-around time keeps the user interested and productive. AXE models multicomputers. The user may easily modify various architectural parameters including the number of sites, connection topologies, and overhead for operating system activities. Parallel computations in AXE are represented as collections of autonomous computing objects known as players. Their use and behavior is described. Performance data of the multiprocessor model can be observed on a color screen. These include CPU and message routing bottlenecks, and the dynamic status of the software.

Software for Remote Monitoring of Space-Station Payloads

NASA Technical Reports Server (NTRS)

Schneider, Michelle; Lippincott, Jeff; Chubb, Steve; Whitaker, Jimmy; Gillis, Robert; Sellers, Donna; Sims, Chris; Rice, James

2003-01-01

Telescience Resource Kit (TReK) is a suite of application programs that enable geographically dispersed users to monitor scientific payloads aboard the International Space Station (ISS). TReK provides local ground support services that can simultaneously receive, process, record, playback, and display data from multiple sources. TReK also provides interfaces to use the remote services provided by the Payload Operations Integration Center which manages all ISS payloads. An application programming interface (API) allows for payload users to gain access to all data processed by TReK and allows payload-specific tools and programs to be built or integrated with TReK. Used in conjunction with other ISS-provided tools, TReK provides the ability to integrate payloads with the operational ground system early in the lifecycle. This reduces the potential for operational problems and provides "cradle-to-grave" end-to-end operations. TReK contains user guides and self-paced tutorials along with training applications to allow the user to become familiar with the system.

Application and Evaluation of Interactive 3D PDF for Presenting and Sharing Planning Results for Liver Surgery in Clinical Routine

PubMed Central

Newe, Axel; Becker, Linda; Schenk, Andrea

2014-01-01

Background & Objectives The Portable Document Format (PDF) is the de-facto standard for the exchange of electronic documents. It is platform-independent, suitable for the exchange of medical data, and allows for the embedding of three-dimensional (3D) surface mesh models. In this article, we present the first clinical routine application of interactive 3D surface mesh models which have been integrated into PDF files for the presentation and the exchange of Computer Assisted Surgery Planning (CASP) results in liver surgery. We aimed to prove the feasibility of applying 3D PDF in medical reporting and investigated the user experience with this new technology. Methods We developed an interactive 3D PDF report document format and implemented a software tool to create these reports automatically. After more than 1000 liver CASP cases that have been reported in clinical routine using our 3D PDF report, an international user survey was carried out online to evaluate the user experience. Results Our solution enables the user to interactively explore the anatomical configuration and to have different analyses and various resection proposals displayed within a 3D PDF document covering only a single page that acts more like a software application than like a typical PDF file (“PDF App”). The new 3D PDF report offers many advantages over the previous solutions. According to the results of the online survey, the users have assessed the pragmatic quality (functionality, usability, perspicuity, efficiency) as well as the hedonic quality (attractiveness, novelty) very positively. Conclusion The usage of 3D PDF for reporting and sharing CASP results is feasible and well accepted by the target audience. Using interactive PDF with embedded 3D models is an enabler for presenting and exchanging complex medical information in an easy and platform-independent way. Medical staff as well as patients can benefit from the possibilities provided by 3D PDF. Our results open the door for a wider use of this new technology, since the basic idea can and should be applied for many medical disciplines and use cases. PMID:25551375

Application and evaluation of interactive 3D PDF for presenting and sharing planning results for liver surgery in clinical routine.

PubMed

Newe, Axel; Becker, Linda; Schenk, Andrea

2014-01-01

The Portable Document Format (PDF) is the de-facto standard for the exchange of electronic documents. It is platform-independent, suitable for the exchange of medical data, and allows for the embedding of three-dimensional (3D) surface mesh models. In this article, we present the first clinical routine application of interactive 3D surface mesh models which have been integrated into PDF files for the presentation and the exchange of Computer Assisted Surgery Planning (CASP) results in liver surgery. We aimed to prove the feasibility of applying 3D PDF in medical reporting and investigated the user experience with this new technology. We developed an interactive 3D PDF report document format and implemented a software tool to create these reports automatically. After more than 1000 liver CASP cases that have been reported in clinical routine using our 3D PDF report, an international user survey was carried out online to evaluate the user experience. Our solution enables the user to interactively explore the anatomical configuration and to have different analyses and various resection proposals displayed within a 3D PDF document covering only a single page that acts more like a software application than like a typical PDF file ("PDF App"). The new 3D PDF report offers many advantages over the previous solutions. According to the results of the online survey, the users have assessed the pragmatic quality (functionality, usability, perspicuity, efficiency) as well as the hedonic quality (attractiveness, novelty) very positively. The usage of 3D PDF for reporting and sharing CASP results is feasible and well accepted by the target audience. Using interactive PDF with embedded 3D models is an enabler for presenting and exchanging complex medical information in an easy and platform-independent way. Medical staff as well as patients can benefit from the possibilities provided by 3D PDF. Our results open the door for a wider use of this new technology, since the basic idea can and should be applied for many medical disciplines and use cases.

CognitionMaster: an object-based image analysis framework

PubMed Central

2013-01-01

Background Automated image analysis methods are becoming more and more important to extract and quantify image features in microscopy-based biomedical studies and several commercial or open-source tools are available. However, most of the approaches rely on pixel-wise operations, a concept that has limitations when high-level object features and relationships between objects are studied and if user-interactivity on the object-level is desired. Results In this paper we present an open-source software that facilitates the analysis of content features and object relationships by using objects as basic processing unit instead of individual pixels. Our approach enables also users without programming knowledge to compose “analysis pipelines“ that exploit the object-level approach. We demonstrate the design and use of example pipelines for the immunohistochemistry-based cell proliferation quantification in breast cancer and two-photon fluorescence microscopy data about bone-osteoclast interaction, which underline the advantages of the object-based concept. Conclusions We introduce an open source software system that offers object-based image analysis. The object-based concept allows for a straight-forward development of object-related interactive or fully automated image analysis solutions. The presented software may therefore serve as a basis for various applications in the field of digital image analysis. PMID:23445542

Trust-Based and Context-Aware Authentication in a Software Architecture for Context and Proximity-Aware Services

NASA Astrophysics Data System (ADS)

Lenzini, Gabriele

We describe an existing software architecture for context and proximity aware services that enables trust-based and context-aware authentication. A service is proximity aware when it automatically detects the presence of entities in its proximity. Authentication is context-aware when it uses contextual information to discern among different identities and to evaluate to which extent they are authentic. The software architecture that we describe here is functioning in our Institute: It manages a sensor network to detect the presence and location of users and their devices. A context manager is responsible to merge the different sources of contextual information, to solve potential contradictions, and to determine the level of authentication of the identity of the person approaching one of the services offered in the coffee-break corners of our Institute. In our solution for context-aware authentication, sensors are managed as if they were recommenders having subjective belief, disbelief, and uncertainty (i.e., trust) on the position and identity of users. A sensor’s subjective trust depends on what it has been sensing in the environment. We discuss the results of an array of simulations that we conducted to validate our concept of trust-based and context-aware authentication. We use Subjective Logic to manage trust.

Web-Based Real-Time Emergency Monitoring

NASA Technical Reports Server (NTRS)

Harvey, Craig A.; Lawhead, Joel

2007-01-01

The Web-based Real-Time Asset Monitoring (RAM) module for emergency operations and facility management enables emergency personnel in federal agencies and local and state governments to monitor and analyze data in the event of a natural disaster or other crisis that threatens a large number of people and property. The software can manage many disparate sources of data within a facility, city, or county. It was developed on industry-standard Geo- Spatial software and is compliant with open GIS standards. RAM View can function as a standalone system, or as an integrated plugin module to Emergency Operations Center (EOC) software suites such as REACT (Real-time Emergency Action Coordination Tool), thus ensuring the widest possible distribution among potential users. RAM has the ability to monitor various data sources, including streaming data. Many disparate systems are included in the initial suite of supported hardware systems, such as mobile GPS units, ambient measurements of temperature, moisture and chemical agents, flow meters, air quality, asset location, and meteorological conditions. RAM View displays real-time data streams such as gauge heights from the U.S. Geological Survey gauging stations, flood crests from the National Weather Service, and meteorological data from numerous sources. Data points are clearly visible on the map interface, and attributes as specified in the user requirements can be viewed and queried.

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

NASA Technical Reports Server (NTRS)

Cheng, U.

1989-01-01

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

PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination.

PubMed

Lee, Woonghee; Stark, Jaime L; Markley, John L

2014-11-01

Peak-picking Of Noe Data Enabled by Restriction Of Shift Assignments-Client Server (PONDEROSA-C/S) builds on the original PONDEROSA software (Lee et al. in Bioinformatics 27:1727-1728. doi: 10.1093/bioinformatics/btr200, 2011) and includes improved features for structure calculation and refinement. PONDEROSA-C/S consists of three programs: Ponderosa Server, Ponderosa Client, and Ponderosa Analyzer. PONDEROSA-C/S takes as input the protein sequence, a list of assigned chemical shifts, and nuclear Overhauser data sets ((13)C- and/or (15)N-NOESY). The output is a set of assigned NOEs and 3D structural models for the protein. Ponderosa Analyzer supports the visualization, validation, and refinement of the results from Ponderosa Server. These tools enable semi-automated NMR-based structure determination of proteins in a rapid and robust fashion. We present examples showing the use of PONDEROSA-C/S in solving structures of four proteins: two that enable comparison with the original PONDEROSA package, and two from the Critical Assessment of automated Structure Determination by NMR (Rosato et al. in Nat Methods 6:625-626. doi: 10.1038/nmeth0909-625 , 2009) competition. The software package can be downloaded freely in binary format from http://pine.nmrfam.wisc.edu/download_packages.html. Registered users of the National Magnetic Resonance Facility at Madison can submit jobs to the PONDEROSA-C/S server at http://ponderosa.nmrfam.wisc.edu, where instructions, tutorials, and instructions can be found. Structures are normally returned within 1-2 days.

SU-F-T-94: Plan2pdf - a Software Tool for Automatic Plan Report for Philips Pinnacle TPS

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

Wu, C

Purpose: To implement an automatic electronic PDF plan reporting tool for Philips Pinnacle treatment planning system (TPS) Methods: An electronic treatment plan reporting software is developed by us to enable fully automatic PDF report from Pinnacle TPS to external EMR programs such as MOSAIQ. The tool is named “plan2pdf”. plan2pdf is implemented using Pinnacle scripts, Java and UNIX shell scripts, without any external program needed. plan2pdf supports full auto-mode and manual mode reporting. In full auto-mode, with a single mouse click, plan2pdf will generate a detailed Pinnacle plan report in PDF format, which includes customizable cover page, Pinnacle plan summary,more » orthogonal views through each plan POI and maximum dose point, DRR for each beam, serial transverse views captured throughout the dose grid at a user specified interval, DVH and scorecard windows. The final PDF report is also automatically bookmarked for each section above for convenient plan review. The final PDF report can either be saved on a user specified folder on Pinnacle, or it can be automatically exported to an EMR import folder via a user configured FTP service. In manual capture mode, plan2pdf allows users to capture any Pinnacle plan by full screen, individual window or rectangular ROI drawn on screen. Furthermore, to avoid possible patients’ plan mix-up during auto-mode reporting, a user conflict check feature is included in plan2pdf: it prompts user to wait if another patient is being exported by plan2pdf by another user. Results: plan2pdf is tested extensively and successfully at our institution consists of 5 centers, 15 dosimetrists and 10 physicists, running Pinnacle version 9.10 on Enterprise servers. Conclusion: plan2pdf provides a highly efficient, user friendly and clinical proven platform for all Philips Pinnacle users, to generate a detailed plan report in PDF format for external EMR systems.« less

Dataworks for GNSS: Software for Supporting Data Sharing and Federation of Geodetic Networks

NASA Astrophysics Data System (ADS)

Boler, F. M.; Meertens, C. M.; Miller, M. M.; Wier, S.; Rost, M.; Matykiewicz, J.

2015-12-01

Continuously-operating Global Navigation Satellite System (GNSS) networks are increasingly being installed globally for a wide variety of science and societal applications. GNSS enables Earth science research in areas including tectonic plate interactions, crustal deformation in response to loading by tectonics, magmatism, water and ice, and the dynamics of water - and thereby energy transfer - in the atmosphere at regional scale. The many individual scientists and organizations that set up GNSS stations globally are often open to sharing data, but lack the resources or expertise to deploy systems and software to manage and curate data and metadata and provide user tools that would support data sharing. UNAVCO previously gained experience in facilitating data sharing through the NASA-supported development of the Geodesy Seamless Archive Centers (GSAC) open source software. GSAC provides web interfaces and simple web services for data and metadata discovery and access, supports federation of multiple data centers, and simplifies transfer of data and metadata to long-term archives. The NSF supported the dissemination of GSAC to multiple European data centers forming the European Plate Observing System. To expand upon GSAC to provide end-to-end, instrument-to-distribution capability, UNAVCO developed Dataworks for GNSS with NSF funding to the COCONet project, and deployed this software on systems that are now operating as Regional GNSS Data Centers as part of the NSF-funded TLALOCNet and COCONet projects. Dataworks consists of software modules written in Python and Java for data acquisition, management and sharing. There are modules for GNSS receiver control and data download, a database schema for metadata, tools for metadata handling, ingest software to manage file metadata, data file management scripts, GSAC, scripts for mirroring station data and metadata from partner GSACs, and extensive software and operator documentation. UNAVCO plans to provide a cloud VM image of Dataworks that would allow standing up a Dataworks-enabled GNSS data center without requiring upfront investment in server hardware. By enabling data creators to organize their data and metadata for sharing, Dataworks helps scientists expand their data curation awareness and responsibility, and enhances data access for all.

Share Data with OPeNDAP Hyrax: New Features and Improvements

NASA Technical Reports Server (NTRS)

Gallagher, James

2016-01-01

During the upcoming Summer 2016 meeting of the ESIP Federation (July 19-22), OpenDAP will hold a Developers and Users Workshop. While a broad set of topics will be covered, a key focus is capitalizing on recent EOSDIS-sponsored advances in Hyrax, OPeNDAPs own software for server-side realization of the DAP2 and DAP4 protocols. These Hyrax advances are as important to data users as to data providers, and the workshop will include hands-on experiences of value to both. Specifically, a balanced set of presentations and hands-on tutorials will address advances in 1. server installation, 2. server configuration, 3. Hyrax aggregation capabilities, 4. support for data-access from clients that are HTTP-based, JSON-based or OGC-compliant (especially WCS and WMS), 5. support for DAP4,6.use and extension of server-side computational capabilities, and7.several performance-affecting matters. Topics 2 through 7 will be relevant to data consumers, data providers and notably, due to the open-source nature of all OPeNDAP software to developers wishing to extend Hyrax, to build compatible clients and servers, and/or to employ Hyrax as middleware that enables interoperability across a variety of end-user and source-data contexts. A session for contributed talks will elaborate the topics listed above and embrace additional ones.

Implementation of GenePattern within the Stanford Microarray Database.

PubMed

Hubble, Jeremy; Demeter, Janos; Jin, Heng; Mao, Maria; Nitzberg, Michael; Reddy, T B K; Wymore, Farrell; Zachariah, Zachariah K; Sherlock, Gavin; Ball, Catherine A

2009-01-01

Hundreds of researchers across the world use the Stanford Microarray Database (SMD; http://smd.stanford.edu/) to store, annotate, view, analyze and share microarray data. In addition to providing registered users at Stanford access to their own data, SMD also provides access to public data, and tools with which to analyze those data, to any public user anywhere in the world. Previously, the addition of new microarray data analysis tools to SMD has been limited by available engineering resources, and in addition, the existing suite of tools did not provide a simple way to design, execute and share analysis pipelines, or to document such pipelines for the purposes of publication. To address this, we have incorporated the GenePattern software package directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. In this article, we describe our implementation of the GenePattern microarray analysis software package into the SMD code base. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability.

BRepertoire: a user-friendly web server for analysing antibody repertoire data.

PubMed

Margreitter, Christian; Lu, Hui-Chun; Townsend, Catherine; Stewart, Alexander; Dunn-Walters, Deborah K; Fraternali, Franca

2018-04-14

Antibody repertoire analysis by high throughput sequencing is now widely used, but a persisting challenge is enabling immunologists to explore their data to discover discriminating repertoire features for their own particular investigations. Computational methods are necessary for large-scale evaluation of antibody properties. We have developed BRepertoire, a suite of user-friendly web-based software tools for large-scale statistical analyses of repertoire data. The software is able to use data preprocessed by IMGT, and performs statistical and comparative analyses with versatile plotting options. BRepertoire has been designed to operate in various modes, for example analysing sequence-specific V(D)J gene usage, discerning physico-chemical properties of the CDR regions and clustering of clonotypes. Those analyses are performed on the fly by a number of R packages and are deployed by a shiny web platform. The user can download the analysed data in different table formats and save the generated plots as image files ready for publication. We believe BRepertoire to be a versatile analytical tool that complements experimental studies of immune repertoires. To illustrate the server's functionality, we show use cases including differential gene usage in a vaccination dataset and analysis of CDR3H properties in old and young individuals. The server is accessible under http://mabra.biomed.kcl.ac.uk/BRepertoire.

The development of a clinical outcomes survey research application: Assessment CenterSM

PubMed Central

Rothrock, Nan E.; Hanrahan, Rachel T.; Jansky, Liz J.; Harniss, Mark; Riley, William

2013-01-01

Introduction The National Institutes of Health sponsored Patient-Reported Outcome Measurement Information System (PROMIS) aimed to create item banks and computerized adaptive tests (CATs) across multiple domains for individuals with a range of chronic diseases. Purpose Web-based software was created to enable a researcher to create study-specific Websites that could administer PROMIS CATs and other instruments to research participants or clinical samples. This paper outlines the process used to develop a user-friendly, free, Web-based resource (Assessment CenterSM) for storage, retrieval, organization, sharing, and administration of patient-reported outcomes (PRO) instruments. Methods Joint Application Design (JAD) sessions were conducted with representatives from numerous institutions in order to supply a general wish list of features. Use Cases were then written to ensure that end user expectations matched programmer specifications. Program development included daily programmer “scrum” sessions, weekly Usability Acceptability Testing (UAT) and continuous Quality Assurance (QA) activities pre- and post-release. Results Assessment Center includes features that promote instrument development including item histories, data management, and storage of statistical analysis results. Conclusions This case study of software development highlights the collection and incorporation of user input throughout the development process. Potential future applications of Assessment Center in clinical research are discussed. PMID:20306332

Flexible software platform for fast-scan cyclic voltammetry data acquisition and analysis.

PubMed

Bucher, Elizabeth S; Brooks, Kenneth; Verber, Matthew D; Keithley, Richard B; Owesson-White, Catarina; Carroll, Susan; Takmakov, Pavel; McKinney, Collin J; Wightman, R Mark

2013-11-05

Over the last several decades, fast-scan cyclic voltammetry (FSCV) has proved to be a valuable analytical tool for the real-time measurement of neurotransmitter dynamics in vitro and in vivo. Indeed, FSCV has found application in a wide variety of disciplines including electrochemistry, neurobiology, and behavioral psychology. The maturation of FSCV as an in vivo technique led users to pose increasingly complex questions that require a more sophisticated experimental design. To accommodate recent and future advances in FSCV application, our lab has developed High Definition Cyclic Voltammetry (HDCV). HDCV is an electrochemical software suite that includes data acquisition and analysis programs. The data collection program delivers greater experimental flexibility and better user feedback through live displays. It supports experiments involving multiple electrodes with customized waveforms. It is compatible with transistor-transistor logic-based systems that are used for monitoring animal behavior, and it enables simultaneous recording of electrochemical and electrophysiological data. HDCV analysis streamlines data processing with superior filtering options, seamlessly manages behavioral events, and integrates chemometric processing. Furthermore, analysis is capable of handling single files collected over extended periods of time, allowing the user to consider biological events on both subsecond and multiminute time scales. Here we describe and demonstrate the utility of HDCV for in vivo experiments.

Service-Oriented Architecture for NVO and TeraGrid Computing

NASA Technical Reports Server (NTRS)

Jacob, Joseph; Miller, Craig; Williams, Roy; Steenberg, Conrad; Graham, Matthew

2008-01-01

The National Virtual Observatory (NVO) Extensible Secure Scalable Service Infrastructure (NESSSI) is a Web service architecture and software framework that enables Web-based astronomical data publishing and processing on grid computers such as the National Science Foundation's TeraGrid. Characteristics of this architecture include the following: (1) Services are created, managed, and upgraded by their developers, who are trusted users of computing platforms on which the services are deployed. (2) Service jobs can be initiated by means of Java or Python client programs run on a command line or with Web portals. (3) Access is granted within a graduated security scheme in which the size of a job that can be initiated depends on the level of authentication of the user.

VitaPad: visualization tools for the analysis of pathway data.

PubMed

Holford, Matthew; Li, Naixin; Nadkarni, Prakash; Zhao, Hongyu

2005-04-15

Packages that support the creation of pathway diagrams are limited by their inability to be readily extended to new classes of pathway-related data. VitaPad is a cross-platform application that enables users to create and modify biological pathway diagrams and incorporate microarray data with them. It improves on existing software in the following areas: (i) It can create diagrams dynamically through graph layout algorithms. (ii) It is open-source and uses an open XML format to store data, allowing for easy extension or integration with other tools. (iii) It features a cutting-edge user interface with intuitive controls, high-resolution graphics and fully customizable appearance. http://bioinformatics.med.yale.edu matthew.holford@yale.edu; hongyu.zhao@yale.edu.

Real time speech formant analyzer and display

DOEpatents

Holland, George E.; Struve, Walter S.; Homer, John F.

1987-01-01

A speech analyzer for interpretation of sound includes a sound input which converts the sound into a signal representing the sound. The signal is passed through a plurality of frequency pass filters to derive a plurality of frequency formants. These formants are converted to voltage signals by frequency-to-voltage converters and then are prepared for visual display in continuous real time. Parameters from the inputted sound are also derived and displayed. The display may then be interpreted by the user. The preferred embodiment includes a microprocessor which is interfaced with a television set for displaying of the sound formants. The microprocessor software enables the sound analyzer to present a variety of display modes for interpretive and therapeutic used by the user.

Real time speech formant analyzer and display

DOEpatents

Holland, G.E.; Struve, W.S.; Homer, J.F.

1987-02-03

A speech analyzer for interpretation of sound includes a sound input which converts the sound into a signal representing the sound. The signal is passed through a plurality of frequency pass filters to derive a plurality of frequency formants. These formants are converted to voltage signals by frequency-to-voltage converters and then are prepared for visual display in continuous real time. Parameters from the inputted sound are also derived and displayed. The display may then be interpreted by the user. The preferred embodiment includes a microprocessor which is interfaced with a television set for displaying of the sound formants. The microprocessor software enables the sound analyzer to present a variety of display modes for interpretive and therapeutic used by the user. 19 figs.

Giovanni - The Bridge Between Data and Science

NASA Technical Reports Server (NTRS)

Liu, Zhong; Acker, James

2017-01-01

This article describes new features in the Geospatial Interactive Online Visualization ANd aNalysis Infrastructure (Giovanni), a user-friendly online tool that enables visualization, analysis, and assessment of NASA Earth science data sets without downloading data and software. Since the satellite era began, data collected from Earth-observing satellites have been widely used in research and applications; however, using satellite-based data sets can still be a challenge to many. To facilitate data access and evaluation, as well as scientific exploration and discovery, the NASA Goddard Earth Sciences (GES) Data and Information Services Center (DISC) has developed Giovanni for a wide range of users around the world. This article describes the latest capabilities of Giovanni with examples, and discusses future plans for this innovative system.

A Scientific Software Product Line for the Bioinformatics domain.

PubMed

Costa, Gabriella Castro B; Braga, Regina; David, José Maria N; Campos, Fernanda

2015-08-01

Most specialized users (scientists) that use bioinformatics applications do not have suitable training on software development. Software Product Line (SPL) employs the concept of reuse considering that it is defined as a set of systems that are developed from a common set of base artifacts. In some contexts, such as in bioinformatics applications, it is advantageous to develop a collection of related software products, using SPL approach. If software products are similar enough, there is the possibility of predicting their commonalities, differences and then reuse these common features to support the development of new applications in the bioinformatics area. This paper presents the PL-Science approach which considers the context of SPL and ontology in order to assist scientists to define a scientific experiment, and to specify a workflow that encompasses bioinformatics applications of a given experiment. This paper also focuses on the use of ontologies to enable the use of Software Product Line in biological domains. In the context of this paper, Scientific Software Product Line (SSPL) differs from the Software Product Line due to the fact that SSPL uses an abstract scientific workflow model. This workflow is defined according to a scientific domain and using this abstract workflow model the products (scientific applications/algorithms) are instantiated. Through the use of ontology as a knowledge representation model, we can provide domain restrictions as well as add semantic aspects in order to facilitate the selection and organization of bioinformatics workflows in a Scientific Software Product Line. The use of ontologies enables not only the expression of formal restrictions but also the inferences on these restrictions, considering that a scientific domain needs a formal specification. This paper presents the development of the PL-Science approach, encompassing a methodology and an infrastructure, and also presents an approach evaluation. This evaluation presents case studies in bioinformatics, which were conducted in two renowned research institutions in Brazil. Copyright © 2015 Elsevier Inc. All rights reserved.

Mercury: Reusable software application for Metadata Management, Data Discovery and Access

NASA Astrophysics Data System (ADS)

Devarakonda, Ranjeet; Palanisamy, Giri; Green, James; Wilson, Bruce E.

2009-12-01

Mercury is a federated metadata harvesting, data discovery and access tool based on both open source packages and custom developed software. It was originally developed for NASA, and the Mercury development consortium now includes funding from NASA, USGS, and DOE. Mercury is itself a reusable toolset for metadata, with current use in 12 different projects. Mercury also supports the reuse of metadata by enabling searching across a range of metadata specification and standards including XML, Z39.50, FGDC, Dublin-Core, Darwin-Core, EML, and ISO-19115. Mercury provides a single portal to information contained in distributed data management systems. It collects metadata and key data from contributing project servers distributed around the world and builds a centralized index. The Mercury search interfaces then allow the users to perform simple, fielded, spatial and temporal searches across these metadata sources. One of the major goals of the recent redesign of Mercury was to improve the software reusability across the projects which currently fund the continuing development of Mercury. These projects span a range of land, atmosphere, and ocean ecological communities and have a number of common needs for metadata searches, but they also have a number of needs specific to one or a few projects To balance these common and project-specific needs, Mercury’s architecture includes three major reusable components; a harvester engine, an indexing system and a user interface component. The harvester engine is responsible for harvesting metadata records from various distributed servers around the USA and around the world. The harvester software was packaged in such a way that all the Mercury projects will use the same harvester scripts but each project will be driven by a set of configuration files. The harvested files are then passed to the Indexing system, where each of the fields in these structured metadata records are indexed properly, so that the query engine can perform simple, keyword, spatial and temporal searches across these metadata sources. The search user interface software has two API categories; a common core API which is used by all the Mercury user interfaces for querying the index and a customized API for project specific user interfaces. For our work in producing a reusable, portable, robust, feature-rich application, Mercury received a 2008 NASA Earth Science Data Systems Software Reuse Working Group Peer-Recognition Software Reuse Award. The new Mercury system is based on a Service Oriented Architecture and effectively reuses components for various services such as Thesaurus Service, Gazetteer Web Service and UDDI Directory Services. The software also provides various search services including: RSS, Geo-RSS, OpenSearch, Web Services and Portlets, integrated shopping cart to order datasets from various data centers (ORNL DAAC, NSIDC) and integrated visualization tools. Other features include: Filtering and dynamic sorting of search results, book-markable search results, save, retrieve, and modify search criteria.

Software Repository

NASA Technical Reports Server (NTRS)

Merwarth, P., D.

1983-01-01

The Common Software Module Repository (CSMR) is computerized library system with high product and service visibility to potential users. Online capabilities of system allow both librarian and user to interact with library. Librarian is responsible for maintaining information in CSMR library. User searches library to locate software modules that meet his or her current needs.

DIY-style GIS service in mobile navigation system integrated with web and wireless GIS

NASA Astrophysics Data System (ADS)

Yan, Yongbin; Wu, Jianping; Fan, Caiyou; Wang, Minqi; Dai, Sheng

2007-06-01

Mobile navigation system based on handheld device can not only provide basic GIS services, but also enable these GIS services to be provided without location limit, to be more instantly interacted between users and devices. However, we still see that most navigation systems have common defects on user experience like limited map format, few map resources, and unable location share. To overcome the above defects, we propose DIY-style GIS service which provide users a more free software environment and allow uses to customize their GIS services. These services include defining geographical coordinate system of maps which helps to hugely enlarge the map source, editing vector feature, related property information and hotlink images, customizing covered area of download map via General Packet Radio Service (GPRS), and sharing users' location information via SMS (Short Message Service) which establishes the communication between users who needs GIS services. The paper introduces the integration of web and wireless GIS service in a mobile navigation system and presents an implementation sample of a DIY-Style GIS service in a mobile navigation system.

Accelerating Science with the NERSC Burst Buffer Early User Program

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

Bhimji, Wahid; Bard, Debbie; Romanus, Melissa

NVRAM-based Burst Buffers are an important part of the emerging HPC storage landscape. The National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory recently installed one of the first Burst Buffer systems as part of its new Cori supercomputer, collaborating with Cray on the development of the DataWarp software. NERSC has a diverse user base comprised of over 6500 users in 700 different projects spanning a wide variety of scientific computing applications. The use-cases of the Burst Buffer at NERSC are therefore also considerable and diverse. We describe here performance measurements and lessons learned from the Burstmore » Buffer Early User Program at NERSC, which selected a number of research projects to gain early access to the Burst Buffer and exercise its capability to enable new scientific advancements. To the best of our knowledge this is the first time a Burst Buffer has been stressed at scale by diverse, real user workloads and therefore these lessons will be of considerable benefit to shaping the developing use of Burst Buffers at HPC centers.« less

Sharing data for public health research by members of an international online diabetes social network.

PubMed

Weitzman, Elissa R; Adida, Ben; Kelemen, Skyler; Mandl, Kenneth D

2011-04-27

Surveillance and response to diabetes may be accelerated through engaging online diabetes social networks (SNs) in consented research. We tested the willingness of an online diabetes community to share data for public health research by providing members with a privacy-preserving social networking software application for rapid temporal-geographic surveillance of glycemic control. SN-mediated collection of cross-sectional, member-reported data from an international online diabetes SN entered into a software application we made available in a "Facebook-like" environment to enable reporting, charting and optional sharing of recent hemoglobin A1c values through a geographic display. Self-enrollment by 17% (n = 1,136) of n = 6,500 active members representing 32 countries and 50 US states. Data were current with 83.1% of most recent A1c values reported obtained within the past 90 days. Sharing was high with 81.4% of users permitting data donation to the community display. 34.1% of users also displayed their A1cs on their SN profile page. Users selecting the most permissive sharing options had a lower average A1c (6.8%) than users not sharing with the community (7.1%, p = .038). 95% of users permitted re-contact. Unadjusted aggregate A1c reported by US users closely resembled aggregate 2007-2008 NHANES estimates (respectively, 6.9% and 6.9%, p = 0.85). Success within an early adopter community demonstrates that online SNs may comprise efficient platforms for bidirectional communication with and data acquisition from disease populations. Advancing this model for cohort and translational science and for use as a complementary surveillance approach will require understanding of inherent selection and publication (sharing) biases in the data and a technology model that supports autonomy, anonymity and privacy.

Software Piracy, Ethics, and the Academician.

ERIC Educational Resources Information Center

Bassler, Richard A.

The numerous software programs available for easy, low-cost copying raise ethical questions. The problem can be examined from the viewpoints of software users, teachers, authors, vendors, and distributors. Software users might hesitate to purchase or use software which prevents the making of back-up copies for program protection. Teachers in…

Software Engineering Laboratory (SEL) data base reporting software user's guide and system description. Volume 1: Introduction and user's guide

NASA Technical Reports Server (NTRS)

1983-01-01

Reporting software programs provide formatted listings and summary reports of the Software Engineering Laboratory (SEL) data base contents. The operating procedures and system information for 18 different reporting software programs are described. Sample output reports from each program are provided.

Multi-microphone adaptive array augmented with visual cueing.

PubMed

Gibson, Paul L; Hedin, Dan S; Davies-Venn, Evelyn E; Nelson, Peggy; Kramer, Kevin

2012-01-01

We present the development of an audiovisual array that enables hearing aid users to converse with multiple speakers in reverberant environments with significant speech babble noise where their hearing aids do not function well. The system concept consists of a smartphone, a smartphone accessory, and a smartphone software application. The smartphone accessory concept is a multi-microphone audiovisual array in a form factor that allows attachment to the back of the smartphone. The accessory will also contain a lower power radio by which it can transmit audio signals to compatible hearing aids. The smartphone software application concept will use the smartphone's built in camera to acquire images and perform real-time face detection using the built-in face detection support of the smartphone. The audiovisual beamforming algorithm uses the location of talking targets to improve the signal to noise ratio and consequently improve the user's speech intelligibility. Since the proposed array system leverages a handheld consumer electronic device, it will be portable and low cost. A PC based experimental system was developed to demonstrate the feasibility of an audiovisual multi-microphone array and these results are presented.

Automated CFD Parameter Studies on Distributed Parallel Computers

NASA Technical Reports Server (NTRS)

Rogers, Stuart E.; Aftosmis, Michael; Pandya, Shishir; Tejnil, Edward; Ahmad, Jasim; Kwak, Dochan (Technical Monitor)

2002-01-01

The objective of the current work is to build a prototype software system which will automated the process of running CFD jobs on Information Power Grid (IPG) resources. This system should remove the need for user monitoring and intervention of every single CFD job. It should enable the use of many different computers to populate a massive run matrix in the shortest time possible. Such a software system has been developed, and is known as the AeroDB script system. The approach taken for the development of AeroDB was to build several discrete modules. These include a database, a job-launcher module, a run-manager module to monitor each individual job, and a web-based user portal for monitoring of the progress of the parameter study. The details of the design of AeroDB are presented in the following section. The following section provides the results of a parameter study which was performed using AeroDB for the analysis of a reusable launch vehicle (RLV). The paper concludes with a section on the lessons learned in this effort, and ideas for future work in this area.

Use of Mapping and Spatial and Space-Time Modeling Approaches in Operational Control of Aedes aegypti and Dengue

PubMed Central

Eisen, Lars; Lozano-Fuentes, Saul

2009-01-01

The aims of this review paper are to 1) provide an overview of how mapping and spatial and space-time modeling approaches have been used to date to visualize and analyze mosquito vector and epidemiologic data for dengue; and 2) discuss the potential for these approaches to be included as routine activities in operational vector and dengue control programs. Geographical information system (GIS) software are becoming more user-friendly and now are complemented by free mapping software that provide access to satellite imagery and basic feature-making tools and have the capacity to generate static maps as well as dynamic time-series maps. Our challenge is now to move beyond the research arena by transferring mapping and GIS technologies and spatial statistical analysis techniques in user-friendly packages to operational vector and dengue control programs. This will enable control programs to, for example, generate risk maps for exposure to dengue virus, develop Priority Area Classifications for vector control, and explore socioeconomic associations with dengue risk. PMID:19399163

Document Concurrence System

NASA Technical Reports Server (NTRS)

Muhsin, Mansour; Walters, Ian

2004-01-01

The Document Concurrence System is a combination of software modules for routing users expressions of concurrence with documents. This system enables determination of the current status of concurrences and eliminates the need for the prior practice of manually delivering paper documents to all persons whose approvals were required. This system runs on a server, and participants gain access via personal computers equipped with Web-browser and electronic-mail software. A user can begin a concurrence routing process by logging onto an administration module, naming the approvers and stating the sequence for routing among them, and attaching documents. The server then sends a message to the first person on the list. Upon concurrence by the first person, the system sends a message to the second person, and so forth. A person on the list indicates approval, places the documents on hold, or indicates disapproval, via a Web-based module. When the last person on the list has concurred, a message is sent to the initiator, who can then finalize the process through the administration module. A background process running on the server identifies concurrence processes that are overdue and sends reminders to the appropriate persons.

Utilizing AI in Temporal, Spatial, and Resource Scheduling

NASA Technical Reports Server (NTRS)

Stottler, Richard; Kalton, Annaka; Bell, Aaron

2006-01-01

Aurora is a software system enabling the rapid, easy solution of complex scheduling problems involving spatial and temporal constraints among operations and scarce resources (such as equipment, workspace, and human experts). Although developed for use in the International Space Station Processing Facility, Aurora is flexible enough that it can be easily customized for application to other scheduling domains and adapted as the requirements change or become more precisely known over time. Aurora s scheduling module utilizes artificial-intelligence (AI) techniques to make scheduling decisions on the basis of domain knowledge, including knowledge of constraints and their relative importance, interdependencies among operations, and possibly frequent changes in governing schedule requirements. Unlike many other scheduling software systems, Aurora focuses on resource requirements and temporal scheduling in combination. For example, Aurora can accommodate a domain requirement to schedule two subsequent operations to locations adjacent to a shared resource. The graphical interface allows the user to quickly visualize the schedule and perform changes reflecting additional knowledge or alterations in the situation. For example, the user might drag the activity corresponding to the start of operations to reflect a late delivery.

Analyzing Spacecraft Telecommunication Systems

NASA Technical Reports Server (NTRS)

Kordon, Mark; Hanks, David; Gladden, Roy; Wood, Eric

2004-01-01

Multi-Mission Telecom Analysis Tool (MMTAT) is a C-language computer program for analyzing proposed spacecraft telecommunication systems. MMTAT utilizes parameterized input and computational models that can be run on standard desktop computers to perform fast and accurate analyses of telecommunication links. MMTAT is easy to use and can easily be integrated with other software applications and run as part of almost any computational simulation. It is distributed as either a stand-alone application program with a graphical user interface or a linkable library with a well-defined set of application programming interface (API) calls. As a stand-alone program, MMTAT provides both textual and graphical output. The graphs make it possible to understand, quickly and easily, how telecommunication performance varies with variations in input parameters. A delimited text file that can be read by any spreadsheet program is generated at the end of each run. The API in the linkable-library form of MMTAT enables the user to control simulation software and to change parameters during a simulation run. Results can be retrieved either at the end of a run or by use of a function call at any time step.

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.

A novel software architecture for the provision of context-aware semantic transport information.

PubMed

Moreno, Asier; Perallos, Asier; López-de-Ipiña, Diego; Onieva, Enrique; Salaberria, Itziar; Masegosa, Antonio D

2015-05-26

The effectiveness of Intelligent Transportation Systems depends largely on the ability to integrate information from diverse sources and the suitability of this information for the specific user. This paper describes a new approach for the management and exchange of this information, related to multimodal transportation. A novel software architecture is presented, with particular emphasis on the design of the data model and the enablement of services for information retrieval, thereby obtaining a semantic model for the representation of transport information. The publication of transport data as semantic information is established through the development of a Multimodal Transport Ontology (MTO) and the design of a distributed architecture allowing dynamic integration of transport data. The advantages afforded by the proposed system due to the use of Linked Open Data and a distributed architecture are stated, comparing it with other existing solutions. The adequacy of the information generated in regard to the specific user's context is also addressed. Finally, a working solution of a semantic trip planner using actual transport data and running on the proposed architecture is presented, as a demonstration and validation of the system.

Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh.

PubMed

Rizk, Aurélien; Paul, Grégory; Incardona, Pietro; Bugarski, Milica; Mansouri, Maysam; Niemann, Axel; Ziegler, Urs; Berger, Philipp; Sbalzarini, Ivo F

2014-03-01

Detection and quantification of fluorescently labeled molecules in subcellular compartments is a key step in the analysis of many cell biological processes. Pixel-wise colocalization analyses, however, are not always suitable, because they do not provide object-specific information, and they are vulnerable to noise and background fluorescence. Here we present a versatile protocol for a method named 'Squassh' (segmentation and quantification of subcellular shapes), which is used for detecting, delineating and quantifying subcellular structures in fluorescence microscopy images. The workflow is implemented in freely available, user-friendly software. It works on both 2D and 3D images, accounts for the microscope optics and for uneven image background, computes cell masks and provides subpixel accuracy. The Squassh software enables both colocalization and shape analyses. The protocol can be applied in batch, on desktop computers or computer clusters, and it usually requires <1 min and <5 min for 2D and 3D images, respectively. Basic computer-user skills and some experience with fluorescence microscopy are recommended to successfully use the protocol.

Internationalization of healthcare applications: a generic approach for PACS workstations.

PubMed

Hussein, R; Engelmann, U; Schroeter, A; Meinzer, H P

2004-01-01

Along with the revolution of information technology and the increasing use of computers world-wide, software providers recognize the emerging need for internationalized, or global, software applications. The importance of internationalization comes from its benefits such as addressing a broader audience, making the software applications more accessible, easier to use, more flexible to support and providing users with more consistent information. In addition, some governmental agencies, e.g., in Spain, accept only fully localized software. Although the healthcare communication standards, namely, Digital Imaging and Communication in Medicine (DICOM) and Health Level Seven (HL7) support wide areas of internationalization, most of the implementers are still protective about supporting the complex languages. This paper describes a generic internationalization approach for Picture Archiving and Communication System (PACS) workstations. The Unicode standard is used to internationalize the application user interface. An encoding converter was developed to encode and decode the data between the rendering module (in Unicode encoding) and the DICOM data (in ISO 8859 encoding). An integration gateway was required to integrate the internationalized PACS components with the different PACS installations. To introduce a pragmatic example, the described approach was applied to the CHILI PACS workstation. The approach has enabled the application to handle the different internationalization aspects transparently, such as supporting complex languages, switching between different languages at runtime, and supporting multilingual clinical reports. In the healthcare enterprises, internationalized applications play an essential role in supporting a seamless flow of information between the heterogeneous multivendor information systems.

A repository based on a dynamically extensible data model supporting multidisciplinary research in neuroscience.

PubMed

Corradi, Luca; Porro, Ivan; Schenone, Andrea; Momeni, Parastoo; Ferrari, Raffaele; Nobili, Flavio; Ferrara, Michela; Arnulfo, Gabriele; Fato, Marco M

2012-10-08

Robust, extensible and distributed databases integrating clinical, imaging and molecular data represent a substantial challenge for modern neuroscience. It is even more difficult to provide extensible software environments able to effectively target the rapidly changing data requirements and structures of research experiments. There is an increasing request from the neuroscience community for software tools addressing technical challenges about: (i) supporting researchers in the medical field to carry out data analysis using integrated bioinformatics services and tools; (ii) handling multimodal/multiscale data and metadata, enabling the injection of several different data types according to structured schemas; (iii) providing high extensibility, in order to address different requirements deriving from a large variety of applications simply through a user runtime configuration. A dynamically extensible data structure supporting collaborative multidisciplinary research projects in neuroscience has been defined and implemented. We have considered extensibility issues from two different points of view. First, the improvement of data flexibility has been taken into account. This has been done through the development of a methodology for the dynamic creation and use of data types and related metadata, based on the definition of "meta" data model. This way, users are not constrainted to a set of predefined data and the model can be easily extensible and applicable to different contexts. Second, users have been enabled to easily customize and extend the experimental procedures in order to track each step of acquisition or analysis. This has been achieved through a process-event data structure, a multipurpose taxonomic schema composed by two generic main objects: events and processes. Then, a repository has been built based on such data model and structure, and deployed on distributed resources thanks to a Grid-based approach. Finally, data integration aspects have been addressed by providing the repository application with an efficient dynamic interface designed to enable the user to both easily query the data depending on defined datatypes and view all the data of every patient in an integrated and simple way. The results of our work have been twofold. First, a dynamically extensible data model has been implemented and tested based on a "meta" data-model enabling users to define their own data types independently from the application context. This data model has allowed users to dynamically include additional data types without the need of rebuilding the underlying database. Then a complex process-event data structure has been built, based on this data model, describing patient-centered diagnostic processes and merging information from data and metadata. Second, a repository implementing such a data structure has been deployed on a distributed Data Grid in order to provide scalability both in terms of data input and data storage and to exploit distributed data and computational approaches in order to share resources more efficiently. Moreover, data managing has been made possible through a friendly web interface. The driving principle of not being forced to preconfigured data types has been satisfied. It is up to users to dynamically configure the data model for the given experiment or data acquisition program, thus making it potentially suitable for customized applications. Based on such repository, data managing has been made possible through a friendly web interface. The driving principle of not being forced to preconfigured data types has been satisfied. It is up to users to dynamically configure the data model for the given experiment or data acquisition program, thus making it potentially suitable for customized applications.

A repository based on a dynamically extensible data model supporting multidisciplinary research in neuroscience

PubMed Central

2012-01-01

Background Robust, extensible and distributed databases integrating clinical, imaging and molecular data represent a substantial challenge for modern neuroscience. It is even more difficult to provide extensible software environments able to effectively target the rapidly changing data requirements and structures of research experiments. There is an increasing request from the neuroscience community for software tools addressing technical challenges about: (i) supporting researchers in the medical field to carry out data analysis using integrated bioinformatics services and tools; (ii) handling multimodal/multiscale data and metadata, enabling the injection of several different data types according to structured schemas; (iii) providing high extensibility, in order to address different requirements deriving from a large variety of applications simply through a user runtime configuration. Methods A dynamically extensible data structure supporting collaborative multidisciplinary research projects in neuroscience has been defined and implemented. We have considered extensibility issues from two different points of view. First, the improvement of data flexibility has been taken into account. This has been done through the development of a methodology for the dynamic creation and use of data types and related metadata, based on the definition of “meta” data model. This way, users are not constrainted to a set of predefined data and the model can be easily extensible and applicable to different contexts. Second, users have been enabled to easily customize and extend the experimental procedures in order to track each step of acquisition or analysis. This has been achieved through a process-event data structure, a multipurpose taxonomic schema composed by two generic main objects: events and processes. Then, a repository has been built based on such data model and structure, and deployed on distributed resources thanks to a Grid-based approach. Finally, data integration aspects have been addressed by providing the repository application with an efficient dynamic interface designed to enable the user to both easily query the data depending on defined datatypes and view all the data of every patient in an integrated and simple way. Results The results of our work have been twofold. First, a dynamically extensible data model has been implemented and tested based on a “meta” data-model enabling users to define their own data types independently from the application context. This data model has allowed users to dynamically include additional data types without the need of rebuilding the underlying database. Then a complex process-event data structure has been built, based on this data model, describing patient-centered diagnostic processes and merging information from data and metadata. Second, a repository implementing such a data structure has been deployed on a distributed Data Grid in order to provide scalability both in terms of data input and data storage and to exploit distributed data and computational approaches in order to share resources more efficiently. Moreover, data managing has been made possible through a friendly web interface. The driving principle of not being forced to preconfigured data types has been satisfied. It is up to users to dynamically configure the data model for the given experiment or data acquisition program, thus making it potentially suitable for customized applications. Conclusions Based on such repository, data managing has been made possible through a friendly web interface. The driving principle of not being forced to preconfigured data types has been satisfied. It is up to users to dynamically configure the data model for the given experiment or data acquisition program, thus making it potentially suitable for customized applications. PMID:23043673

Accounting for Uncertainties in Strengths of SiC MEMS Parts

NASA Technical Reports Server (NTRS)

Nemeth, Noel; Evans, Laura; Beheim, Glen; Trapp, Mark; Jadaan, Osama; Sharpe, William N., Jr.

2007-01-01

A methodology has been devised for accounting for uncertainties in the strengths of silicon carbide structural components of microelectromechanical systems (MEMS). The methodology enables prediction of the probabilistic strengths of complexly shaped MEMS parts using data from tests of simple specimens. This methodology is intended to serve as a part of a rational basis for designing SiC MEMS, supplementing methodologies that have been borrowed from the art of designing macroscopic brittle material structures. The need for this or a similar methodology arises as a consequence of the fundamental nature of MEMS and the brittle silicon-based materials of which they are typically fabricated. When tested to fracture, MEMS and structural components thereof show wide part-to-part scatter in strength. The methodology involves the use of the Ceramics Analysis and Reliability Evaluation of Structures Life (CARES/Life) software in conjunction with the ANSYS Probabilistic Design System (PDS) software to simulate or predict the strength responses of brittle material components while simultaneously accounting for the effects of variability of geometrical features on the strength responses. As such, the methodology involves the use of an extended version of the ANSYS/CARES/PDS software system described in Probabilistic Prediction of Lifetimes of Ceramic Parts (LEW-17682-1/4-1), Software Tech Briefs supplement to NASA Tech Briefs, Vol. 30, No. 9 (September 2006), page 10. The ANSYS PDS software enables the ANSYS finite-element-analysis program to account for uncertainty in the design-and analysis process. The ANSYS PDS software accounts for uncertainty in material properties, dimensions, and loading by assigning probabilistic distributions to user-specified model parameters and performing simulations using various sampling techniques.

Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment.

PubMed

Bohler, Anwesha; Eijssen, Lars M T; van Iersel, Martijn P; Leemans, Christ; Willighagen, Egon L; Kutmon, Martina; Jaillard, Magali; Evelo, Chris T

2015-08-23

Biological pathways are descriptive diagrams of biological processes widely used for functional analysis of differentially expressed genes or proteins. Primary data analysis, such as quality control, normalisation, and statistical analysis, is often performed in scripting languages like R, Perl, and Python. Subsequent pathway analysis is usually performed using dedicated external applications. Workflows involving manual use of multiple environments are time consuming and error prone. Therefore, tools are needed that enable pathway analysis directly within the same scripting languages used for primary data analyses. Existing tools have limited capability in terms of available pathway content, pathway editing and visualisation options, and export file formats. Consequently, making the full-fledged pathway analysis tool PathVisio available from various scripting languages will benefit researchers. We developed PathVisioRPC, an XMLRPC interface for the pathway analysis software PathVisio. PathVisioRPC enables creating and editing biological pathways, visualising data on pathways, performing pathway statistics, and exporting results in several image formats in multiple programming environments. We demonstrate PathVisioRPC functionalities using examples in Python. Subsequently, we analyse a publicly available NCBI GEO gene expression dataset studying tumour bearing mice treated with cyclophosphamide in R. The R scripts demonstrate how calls to existing R packages for data processing and calls to PathVisioRPC can directly work together. To further support R users, we have created RPathVisio simplifying the use of PathVisioRPC in this environment. We have also created a pathway module for the microarray data analysis portal ArrayAnalysis.org that calls the PathVisioRPC interface to perform pathway analysis. This module allows users to use PathVisio functionality online without having to download and install the software and exemplifies how the PathVisioRPC interface can be used by data analysis pipelines for functional analysis of processed genomics data. PathVisioRPC enables data visualisation and pathway analysis directly from within various analytical environments used for preliminary analyses. It supports the use of existing pathways from WikiPathways or pathways created using the RPC itself. It also enables automation of tasks performed using PathVisio, making it useful to PathVisio users performing repeated visualisation and analysis tasks. PathVisioRPC is freely available for academic and commercial use at http://projects.bigcat.unimaas.nl/pathvisiorpc.

Smart Interpretation - Application of Machine Learning in Geological Interpretation of AEM Data

NASA Astrophysics Data System (ADS)

Bach, T.; Gulbrandsen, M. L.; Jacobsen, R.; Pallesen, T. M.; Jørgensen, F.; Høyer, A. S.; Hansen, T. M.

2015-12-01

When using airborne geophysical measurements in e.g. groundwater mapping, an overwhelming amount of data is collected. Increasingly larger survey areas, denser data collection and limited resources, combines to an increasing problem of building geological models that use all the available data in a manner that is consistent with the geologists knowledge about the geology of the survey area. In the ERGO project, funded by The Danish National Advanced Technology Foundation, we address this problem, by developing new, usable tools, enabling the geologist utilize her geological knowledge directly in the interpretation of the AEM data, and thereby handle the large amount of data, In the project we have developed the mathematical basis for capturing geological expertise in a statistical model. Based on this, we have implemented new algorithms that have been operationalized and embedded in user friendly software. In this software, the machine learning algorithm, Smart Interpretation, enables the geologist to use the system as an assistant in the geological modelling process. As the software 'learns' the geology from the geologist, the system suggest new modelling features in the data. In this presentation we demonstrate the application of the results from the ERGO project, including the proposed modelling workflow utilized on a variety of data examples.

Towards Model-Driven End-User Development in CALL

ERIC Educational Resources Information Center

Farmer, Rod; Gruba, Paul

2006-01-01

The purpose of this article is to introduce end-user development (EUD) processes to the CALL software development community. EUD refers to the active participation of end-users, as non-professional developers, in the software development life cycle. Unlike formal software engineering approaches, the focus in EUD on means/ends development is…

EASEE: an open architecture approach for modeling battlespace signal and sensor phenomenology

NASA Astrophysics Data System (ADS)

Waldrop, Lauren E.; Wilson, D. Keith; Ekegren, Michael T.; Borden, Christian T.

2017-04-01

Open architecture in the context of defense applications encourages collaboration across government agencies and academia. This paper describes a success story in the implementation of an open architecture framework that fosters transparency and modularity in the context of Environmental Awareness for Sensor and Emitter Employment (EASEE), a complex physics-based software package for modeling the effects of terrain and atmospheric conditions on signal propagation and sensor performance. Among the highlighted features in this paper are: (1) a code refactorization to separate sensitive parts of EASEE, thus allowing collaborators the opportunity to view and interact with non-sensitive parts of the EASEE framework with the end goal of supporting collaborative innovation, (2) a data exchange and validation effort to enable the dynamic addition of signatures within EASEE thus supporting a modular notion that components can be easily added or removed to the software without requiring recompilation by developers, and (3) a flexible and extensible XML interface, which aids in decoupling graphical user interfaces from EASEE's calculation engine, and thus encourages adaptability to many different defense applications. In addition to the outlined points above, this paper also addresses EASEE's ability to interface with both proprietary systems such as ArcGIS. A specific use case regarding the implementation of an ArcGIS toolbar that leverages EASEE's XML interface and enables users to set up an EASEE-compliant configuration for probability of detection or optimal sensor placement calculations in various modalities is discussed as well.

Enabling Web-Based GIS Tools for Internet and Mobile Devices To Improve and Expand NASA Data Accessibility and Analysis Functionality for the Renewable Energy and Agricultural Applications

NASA Astrophysics Data System (ADS)

Ross, A.; Stackhouse, P. W.; Tisdale, B.; Tisdale, M.; Chandler, W.; Hoell, J. M., Jr.; Kusterer, J.

2014-12-01

The NASA Langley Research Center Science Directorate and Atmospheric Science Data Center have initiated a pilot program to utilize Geographic Information System (GIS) tools that enable, generate and store climatological averages using spatial queries and calculations in a spatial database resulting in greater accessibility of data for government agencies, industry and private sector individuals. The major objectives of this effort include the 1) Processing and reformulation of current data to be consistent with ESRI and openGIS tools, 2) Develop functions to improve capability and analysis that produce "on-the-fly" data products, extending these past the single location to regional and global scales. 3) Update the current web sites to enable both web-based and mobile application displays for optimization on mobile platforms, 4) Interact with user communities in government and industry to test formats and usage of optimization, and 5) develop a series of metrics that allow for monitoring of progressive performance. Significant project results will include the the development of Open Geospatial Consortium (OGC) compliant web services (WMS, WCS, WFS, WPS) that serve renewable energy and agricultural application products to users using GIS software and tools. Each data product and OGC service will be registered within ECHO, the Common Metadata Repository, the Geospatial Platform, and Data.gov to ensure the data are easily discoverable and provide data users with enhanced access to SSE data, parameters, services, and applications. This effort supports cross agency, cross organization, and interoperability of SSE data products and services by collaborating with DOI, NRCan, NREL, NCAR, and HOMER for requirements vetting and test bed users before making available to the wider public.

The development and evaluation of a medical imaging training immersive environment

PubMed Central

Bridge, Pete; Gunn, Therese; Kastanis, Lazaros; Pack, Darren; Rowntree, Pamela; Starkey, Debbie; Mahoney, Gaynor; Berry, Clare; Braithwaite, Vicki; Wilson-Stewart, Kelly

2014-01-01

Introduction A novel realistic 3D virtual reality (VR) application has been developed to allow medical imaging students at Queensland University of Technology to practice radiographic techniques independently outside the usual radiography laboratory. Methods A flexible agile development methodology was used to create the software rapidly and effectively. A 3D gaming environment and realistic models were used to engender presence in the software while tutor-determined gold standards enabled students to compare their performance and learn in a problem-based learning pedagogy. Results Students reported high levels of satisfaction and perceived value and the software enabled up to 40 concurrent users to prepare for clinical practice. Student feedback also indicated that they found 3D to be of limited value in the desktop version compared to the usual 2D approach. A randomised comparison between groups receiving software-based and traditional practice measured performance in a formative role play with real equipment. The results of this work indicated superior performance with the equipment for the VR trained students (P = 0.0366) and confirmed the value of VR for enhancing 3D equipment-based problem-solving skills. Conclusions Students practising projection techniques virtually performed better at role play assessments than students practising in a traditional radiography laboratory only. The application particularly helped with 3D equipment configuration, suggesting that teaching 3D problem solving is an ideal use of such medical equipment simulators. Ongoing development work aims to establish the role of VR software in preparing students for clinical practice with a range of medical imaging equipment. PMID:26229652

The Logical Extension

NASA Technical Reports Server (NTRS)

2003-01-01

The same software controlling autonomous and crew-assisted operations for the International Space Station (ISS) is enabling commercial enterprises to integrate and automate manual operations, also known as decision logic, in real time across complex and disparate networked applications, databases, servers, and other devices, all with quantifiable business benefits. Auspice Corporation, of Framingham, Massachusetts, developed the Auspice TLX (The Logical Extension) software platform to effectively mimic the human decision-making process. Auspice TLX automates operations across extended enterprise systems, where any given infrastructure can include thousands of computers, servers, switches, and modems that are connected, and therefore, dependent upon each other. The concept behind the Auspice software spawned from a computer program originally developed in 1981 by Cambridge, Massachusetts-based Draper Laboratory for simulating tasks performed by astronauts aboard the Space Shuttle. At the time, the Space Shuttle Program was dependent upon paper-based procedures for its manned space missions, which typically averaged 2 weeks in duration. As the Shuttle Program progressed, NASA began increasing the length of manned missions in preparation for a more permanent space habitat. Acknowledging the need to relinquish paper-based procedures in favor of an electronic processing format to properly monitor and manage the complexities of these longer missions, NASA realized that Draper's task simulation software could be applied to its vision of year-round space occupancy. In 1992, Draper was awarded a NASA contract to build User Interface Language software to enable autonomous operations of a multitude of functions on Space Station Freedom (the station was redesigned in 1993 and converted into the international venture known today as the ISS)

VisBOL: Web-Based Tools for Synthetic Biology Design Visualization.

PubMed

McLaughlin, James Alastair; Pocock, Matthew; Mısırlı, Göksel; Madsen, Curtis; Wipat, Anil

2016-08-19

VisBOL is a Web-based application that allows the rendering of genetic circuit designs, enabling synthetic biologists to visually convey designs in SBOL visual format. VisBOL designs can be exported to formats including PNG and SVG images to be embedded in Web pages, presentations and publications. The VisBOL tool enables the automated generation of visualizations from designs specified using the Synthetic Biology Open Language (SBOL) version 2.0, as well as a range of well-known bioinformatics formats including GenBank and Pigeoncad notation. VisBOL is provided both as a user accessible Web site and as an open-source (BSD) JavaScript library that can be used to embed diagrams within other content and software.

Security Protection on Trust Delegated Data in Public Mobile Networks

NASA Astrophysics Data System (ADS)

Weerasinghe, Dasun; Rajarajan, Muttukrishnan; Rakocevic, Veselin

This paper provides detailed solutions for trust delegation and security protection for medical records in public mobile communication networks. The solutions presented in this paper enable the development of software for mobile devices that can be used by emergency medical units in urgent need of sensitive personal information about unconscious patients. In today's world, technical improvements in mobile communication systems mean that users can expect to have access to data at any time regardless of their location. This paper presents a token-based procedure for the data security at a mobile device and delegation of trust between a requesting mobile unit and secure medical data storage. The data security at the mobile device is enabled using identity based key generation methodology.

GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases.

PubMed

Zhu, Lihua Julie; Lawrence, Michael; Gupta, Ankit; Pagès, Hervé; Kucukural, Alper; Garber, Manuel; Wolfe, Scot A

2017-05-15

Genome editing technologies developed around the CRISPR-Cas9 nuclease system have facilitated the investigation of a broad range of biological questions. These nucleases also hold tremendous promise for treating a variety of genetic disorders. In the context of their therapeutic application, it is important to identify the spectrum of genomic sequences that are cleaved by a candidate nuclease when programmed with a particular guide RNA, as well as the cleavage efficiency of these sites. Powerful new experimental approaches, such as GUIDE-seq, facilitate the sensitive, unbiased genome-wide detection of nuclease cleavage sites within the genome. Flexible bioinformatics analysis tools for processing GUIDE-seq data are needed. Here, we describe an open source, open development software suite, GUIDEseq, for GUIDE-seq data analysis and annotation as a Bioconductor package in R. The GUIDEseq package provides a flexible platform with more than 60 adjustable parameters for the analysis of datasets associated with custom nuclease applications. These parameters allow data analysis to be tailored to different nuclease platforms with different length and complexity in their guide and PAM recognition sequences or their DNA cleavage position. They also enable users to customize sequence aggregation criteria, and vary peak calling thresholds that can influence the number of potential off-target sites recovered. GUIDEseq also annotates potential off-target sites that overlap with genes based on genome annotation information, as these may be the most important off-target sites for further characterization. In addition, GUIDEseq enables the comparison and visualization of off-target site overlap between different datasets for a rapid comparison of different nuclease configurations or experimental conditions. For each identified off-target, the GUIDEseq package outputs mapped GUIDE-Seq read count as well as cleavage score from a user specified off-target cleavage score prediction algorithm permitting the identification of genomic sequences with unexpected cleavage activity. The GUIDEseq package enables analysis of GUIDE-data from various nuclease platforms for any species with a defined genomic sequence. This software package has been used successfully to analyze several GUIDE-seq datasets. The software, source code and documentation are freely available at http://www.bioconductor.org/packages/release/bioc/html/GUIDEseq.html .

Software Prototyping: Designing Systems for Users.

ERIC Educational Resources Information Center

Spies, Phyllis Bova

1983-01-01

Reports on major change in computer software development process--the prototype model, i.e., implementation of skeletal system that is enhanced during interaction with users. Expensive and unreliable software, software design errors, traditional development approach, resources required for prototyping, success stories, and systems designer's role…

JHelioviewer: Open-Source Software for Discovery and Image Access in the Petabyte Age (Invited)

NASA Astrophysics Data System (ADS)

Mueller, D.; Dimitoglou, G.; Langenberg, M.; Pagel, S.; Dau, A.; Nuhn, M.; Garcia Ortiz, J. P.; Dietert, H.; Schmidt, L.; Hughitt, V. K.; Ireland, J.; Fleck, B.

2010-12-01

The unprecedented torrent of data returned by the Solar Dynamics Observatory is both a blessing and a barrier: a blessing for making available data with significantly higher spatial and temporal resolution, but a barrier for scientists to access, browse and analyze them. With such staggering data volume, the data is bound to be accessible only from a few repositories and users will have to deal with data sets effectively immobile and practically difficult to download. From a scientist's perspective this poses three challenges: accessing, browsing and finding interesting data while avoiding the proverbial search for a needle in a haystack. To address these challenges, we have developed JHelioviewer, an open-source visualization software that lets users browse large data volumes both as still images and movies. We did so by deploying an efficient image encoding, storage, and dissemination solution using the JPEG 2000 standard. This solution enables users to access remote images at different resolution levels as a single data stream. Users can view, manipulate, pan, zoom, and overlay JPEG 2000 compressed data quickly, without severe network bandwidth penalties. Besides viewing data, the browser provides third-party metadata and event catalog integration to quickly locate data of interest, as well as an interface to the Virtual Solar Observatory to download science-quality data. As part of the Helioviewer Project, JHelioviewer offers intuitive ways to browse large amounts of heterogeneous data remotely and provides an extensible and customizable open-source platform for the scientific community.

Earth Science Data Education through Cooking Up Recipes

NASA Astrophysics Data System (ADS)

Weigel, A. M.; Maskey, M.; Smith, T.; Conover, H.

2016-12-01

One of the major challenges in Earth science research and applications is understanding and applying the proper methods, tools, and software for using scientific data. These techniques are often difficult and time consuming to identify, requiring novel users to conduct extensive research, take classes, and reach out for assistance, thus hindering scientific discovery and real-world applications. To address these challenges, the Global Hydrology Resource Center (GHRC) DAAC has developed a series of data recipes that novel users such as students, decision makers, and general Earth scientists can leverage to learn how to use Earth science datasets. Once the data recipe content had been finalized, GHRC computer and Earth scientists collaborated with a web and graphic designer to ensure the content is both attractively presented to data users, and clearly communicated to promote the education and use of Earth science data. The completed data recipes include, but are not limited to, tutorials, iPython Notebooks, resources, and tools necessary for addressing key difficulties in data use across a broad user base. These recipes enable non-traditional users to learn how to use data, but also curates and communicates common methods and approaches that may be difficult and time consuming for these users to identify.

UWB Tracking Software Development

NASA Technical Reports Server (NTRS)

Gross, Julia; Arndt, Dickey; Ngo, Phong; Phan, Chau; Dusl, John; Ni, Jianjun; Rafford, Melinda

2006-01-01

An Ultra-Wideband (UWB) two-cluster Angle of Arrival (AOA) tracking prototype system is currently being developed and tested at NASA Johnson Space Center for space exploration applications. This talk discusses the software development efforts for this UWB two-cluster AOA tracking system. The role the software plays in this system is to take waveform data from two UWB radio receivers as an input, feed this input into an AOA tracking algorithm, and generate the target position as an output. The architecture of the software (Input/Output Interface and Algorithm Core) will be introduced in this talk. The development of this software has three phases. In Phase I, the software is mostly Matlab driven and calls C++ socket functions to provide the communication links to the radios. This is beneficial in the early stage when it is necessary to frequently test changes in the algorithm. Phase II of the development is to have the software mostly C++ driven and call a Matlab function for the AOA tracking algorithm. This is beneficial in order to send the tracking results to other systems and also to improve the tracking update rate of the system. The third phase is part of future work and is to have the software completely C++ driven with a graphics user interface. This software design enables the fine resolution tracking of the UWB two-cluster AOA tracking system.

NMRbox: A Resource for Biomolecular NMR Computation.

PubMed

Maciejewski, Mark W; Schuyler, Adam D; Gryk, Michael R; Moraru, Ion I; Romero, Pedro R; Ulrich, Eldon L; Eghbalnia, Hamid R; Livny, Miron; Delaglio, Frank; Hoch, Jeffrey C

2017-04-25

Advances in computation have been enabling many recent advances in biomolecular applications of NMR. Due to the wide diversity of applications of NMR, the number and variety of software packages for processing and analyzing NMR data is quite large, with labs relying on dozens, if not hundreds of software packages. Discovery, acquisition, installation, and maintenance of all these packages is a burdensome task. Because the majority of software packages originate in academic labs, persistence of the software is compromised when developers graduate, funding ceases, or investigators turn to other projects. To simplify access to and use of biomolecular NMR software, foster persistence, and enhance reproducibility of computational workflows, we have developed NMRbox, a shared resource for NMR software and computation. NMRbox employs virtualization to provide a comprehensive software environment preconfigured with hundreds of software packages, available as a downloadable virtual machine or as a Platform-as-a-Service supported by a dedicated compute cloud. Ongoing development includes a metadata harvester to regularize, annotate, and preserve workflows and facilitate and enhance data depositions to BioMagResBank, and tools for Bayesian inference to enhance the robustness and extensibility of computational analyses. In addition to facilitating use and preservation of the rich and dynamic software environment for biomolecular NMR, NMRbox fosters the development and deployment of a new class of metasoftware packages. NMRbox is freely available to not-for-profit users. Copyright © 2017 Biophysical Society. All rights reserved.

Encyclopedia of software components

NASA Technical Reports Server (NTRS)

Vanwarren, Lloyd (Inventor); Beckman, Brian C. (Inventor)

1991-01-01

Intelligent browsing through a collection of reusable software components is facilitated with a computer having a video monitor and a user input interface such as a keyboard or a mouse for transmitting user selections, by presenting a picture of encyclopedia volumes with respective visible labels referring to types of software, in accordance with a metaphor in which each volume includes a page having a list of general topics under the software type of the volume and pages having lists of software components for each one of the generic topics, altering the picture to open one of the volumes in response to an initial user selection specifying the one volume to display on the monitor a picture of the page thereof having the list of general topics and altering the picture to display the page thereof having a list of software components under one of the general topics in response to a next user selection specifying the one general topic, and then presenting a picture of a set of different informative plates depicting different types of information about one of the software components in response to a further user selection specifying the one component.

Encyclopedia of Software Components

NASA Technical Reports Server (NTRS)

Warren, Lloyd V. (Inventor); Beckman, Brian C. (Inventor)

1997-01-01

Intelligent browsing through a collection of reusable software components is facilitated with a computer having a video monitor and a user input interface such as a keyboard or a mouse for transmitting user selections, by presenting a picture of encyclopedia volumes with respective visible labels referring to types of software, in accordance with a metaphor in which each volume includes a page having a list of general topics under the software type of the volume and pages having lists of software components for each one of the generic topics, altering the picture to open one of the volumes in response to an initial user selection specifying the one volume to display on the monitor a picture of the page thereof having the list of general topics and altering the picture to display the page thereof having a list of software components under one of the general topics in response to a next user selection specifying the one general topic, and then presenting a picture of a set of different informative plates depicting different types of information about one of the software components in response to a further user selection specifying the one component.

PLUME-FEATHER, Referencing and Finding Software for Research and Education

NASA Astrophysics Data System (ADS)

Bénassy, O.; Caron, C.; Ferret-Canape, C.; Cheylus, A.; Courcelle, E.; Dantec, C.; Dayre, P.; Dostes, T.; Durand, A.; Facq, A.; Gambini, G.; Geahchan, E.; Helft, C.; Hoffmann, D.; Ingarao, M.; Joly, P.; Kieffer, J.; Larré, J.-M.; Libes, M.; Morris, F.; Parmentier, H.; Pérochon, L.; Porte, O.; Romier, G.; Rousse, D.; Tournoy, R.; Valeins, H.

2014-06-01

PLUME-FEATHER is a non-profit project created to Promote economicaL, Useful and Maintained softwarEFor theHigher Education And THE Research communities. The site references software, mainly Free/Libre Open Source Software (FLOSS) from French universities and national research organisations, (CNRS, INRA...), laboratories or departments as well as other FLOSS software used and evaluated by users within these institutions. Each software is represented by a reference card, which describes origin, aim, installation, cost (if applicable) and user experience from the point of view of an academic user for academic users. Presently over 1000 programs are referenced on PLUME by more than 900 contributors. Although the server is maintained by a French institution, it is open to international contributions in the academic domain. All contained and validated contents are visible to anonymous public, whereas (presently more than 2000) registered users can contribute, starting with comments on single software reference cards up to help with the organisation and presentation of the referenced software products. The project has been presented to the HEP community in 2012 for the first time [1]. This is an update of the status and a call for (further) contributions.

Cloud Computing for the Grid: GridControl: A Software Platform to Support the Smart Grid

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

None

GENI Project: Cornell University is creating a new software platform for grid operators called GridControl that will utilize cloud computing to more efficiently control the grid. In a cloud computing system, there are minimal hardware and software demands on users. The user can tap into a network of computers that is housed elsewhere (the cloud) and the network runs computer applications for the user. The user only needs interface software to access all of the cloud’s data resources, which can be as simple as a web browser. Cloud computing can reduce costs, facilitate innovation through sharing, empower users, and improvemore » the overall reliability of a dispersed system. Cornell’s GridControl will focus on 4 elements: delivering the state of the grid to users quickly and reliably; building networked, scalable grid-control software; tailoring services to emerging smart grid uses; and simulating smart grid behavior under various conditions.« less

Advanced software development workstation project ACCESS user's guide

NASA Technical Reports Server (NTRS)

1990-01-01

ACCESS is a knowledge based software information system designed to assist the user in modifying retrieved software to satisfy user specifications. A user's guide is presented for the knowledge engineer who wishes to create for ACCESS a knowledge base consisting of representations of objects in some software system. This knowledge is accessible to an end user who wishes to use the catalogued software objects to create a new application program or an input stream for an existing system. The application specific portion of an ACCESS knowledge base consists of a taxonomy of object classes, as well as instances of these classes. All objects in the knowledge base are stored in an associative memory. ACCESS provides a standard interface for the end user to browse and modify objects. In addition, the interface can be customized by the addition of application specific data entry forms and by specification of display order for the taxonomy and object attributes. These customization options are described.

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.

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

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

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

Chamana, Manohar; Prabakar, Kumaraguru; Palmintier, Bryan

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