Colossal Tooling Design: 3D Simulation for Ergonomic Analysis

NASA Technical Reports Server (NTRS)

Hunter, Steve L.; Dischinger, Charles; Thomas, Robert E.; Babai, Majid

2003-01-01

The application of high-level 3D simulation software to the design phase of colossal mandrel tooling for composite aerospace fuel tanks was accomplished to discover and resolve safety and human engineering problems. The analyses were conducted to determine safety, ergonomic and human engineering aspects of the disassembly process of the fuel tank composite shell mandrel. Three-dimensional graphics high-level software, incorporating various ergonomic analysis algorithms, was utilized to determine if the process was within safety and health boundaries for the workers carrying out these tasks. In addition, the graphical software was extremely helpful in the identification of material handling equipment and devices for the mandrel tooling assembly/disassembly process.

Incorporating biological information in sparse principal component analysis with application to genomic data.

PubMed

Li, Ziyi; Safo, Sandra E; Long, Qi

2017-07-11

Sparse principal component analysis (PCA) is a popular tool for dimensionality reduction, pattern recognition, and visualization of high dimensional data. It has been recognized that complex biological mechanisms occur through concerted relationships of multiple genes working in networks that are often represented by graphs. Recent work has shown that incorporating such biological information improves feature selection and prediction performance in regression analysis, but there has been limited work on extending this approach to PCA. In this article, we propose two new sparse PCA methods called Fused and Grouped sparse PCA that enable incorporation of prior biological information in variable selection. Our simulation studies suggest that, compared to existing sparse PCA methods, the proposed methods achieve higher sensitivity and specificity when the graph structure is correctly specified, and are fairly robust to misspecified graph structures. Application to a glioblastoma gene expression dataset identified pathways that are suggested in the literature to be related with glioblastoma. The proposed sparse PCA methods Fused and Grouped sparse PCA can effectively incorporate prior biological information in variable selection, leading to improved feature selection and more interpretable principal component loadings and potentially providing insights on molecular underpinnings of complex diseases.

Microscopy image segmentation tool: Robust image data analysis

NASA Astrophysics Data System (ADS)

Valmianski, Ilya; Monton, Carlos; Schuller, Ivan K.

2014-03-01

We present a software package called Microscopy Image Segmentation Tool (MIST). MIST is designed for analysis of microscopy images which contain large collections of small regions of interest (ROIs). Originally developed for analysis of porous anodic alumina scanning electron images, MIST capabilities have been expanded to allow use in a large variety of problems including analysis of biological tissue, inorganic and organic film grain structure, as well as nano- and meso-scopic structures. MIST provides a robust segmentation algorithm for the ROIs, includes many useful analysis capabilities, and is highly flexible allowing incorporation of specialized user developed analysis. We describe the unique advantages MIST has over existing analysis software. In addition, we present a number of diverse applications to scanning electron microscopy, atomic force microscopy, magnetic force microscopy, scanning tunneling microscopy, and fluorescent confocal laser scanning microscopy.

MIRO: A debugging tool for CLIPS incorporating historical Rete networks

NASA Technical Reports Server (NTRS)

Tuttle, Sharon M.; Eick, Christoph F.

1994-01-01

At the last CLIPS conference, we discussed our ideas for adding a temporal dimension to the Rete network used to implement CLIPS. The resulting historical Rete network could then be used to store 'historical' information about a run of a CLIPS program, to aid in debugging. MIRO, a debugging tool for CLIPS built on top of CLIPS, incorporates such a historical Rete network and uses it to support its prototype question-answering capability. By enabling CLIPS users to directly ask debugging-related questions about the history of a program run, we hope to reduce the amount of single-stepping and program tracing required to debug a CLIPS program. In this paper, we briefly describe MIRO's architecture and implementation, and the current question-types that MIRO supports. These question-types are further illustrated using an example, and the benefits of the debugging tool are discussed. We also present empirical results that measure the run-time and partial storage overhead of MIRO, and discuss how MIRO may also be used to study various efficiency aspects of CLIPS programs.

Incorporating parametric uncertainty into population viability analysis models

USGS Publications Warehouse

McGowan, Conor P.; Runge, Michael C.; Larson, Michael A.

2011-01-01

Uncertainty in parameter estimates from sampling variation or expert judgment can introduce substantial uncertainty into ecological predictions based on those estimates. However, in standard population viability analyses, one of the most widely used tools for managing plant, fish and wildlife populations, parametric uncertainty is often ignored in or discarded from model projections. We present a method for explicitly incorporating this source of uncertainty into population models to fully account for risk in management and decision contexts. Our method involves a two-step simulation process where parametric uncertainty is incorporated into the replication loop of the model and temporal variance is incorporated into the loop for time steps in the model. Using the piping plover, a federally threatened shorebird in the USA and Canada, as an example, we compare abundance projections and extinction probabilities from simulations that exclude and include parametric uncertainty. Although final abundance was very low for all sets of simulations, estimated extinction risk was much greater for the simulation that incorporated parametric uncertainty in the replication loop. Decisions about species conservation (e.g., listing, delisting, and jeopardy) might differ greatly depending on the treatment of parametric uncertainty in population models.

Data and Tools | Energy Analysis | NREL

Science.gov Websites

and Tools Energy Analysis Data and Tools NREL develops energy analysis data and tools to assess collections. Data Products Technology and Performance Analysis Tools Energy Systems Analysis Tools Economic and Financial Analysis Tools

OEXP Analysis Tools Workshop

NASA Technical Reports Server (NTRS)

Garrett, L. Bernard; Wright, Robert L.; Badi, Deborah; Findlay, John T.

1988-01-01

This publication summarizes the software needs and available analysis tools presented at the OEXP Analysis Tools Workshop held at the NASA Langley Research Center, Hampton, Virginia on June 21 to 22, 1988. The objective of the workshop was to identify available spacecraft system (and subsystem) analysis and engineering design tools, and mission planning and analysis software that could be used for various NASA Office of Exploration (code Z) studies, specifically lunar and Mars missions.

Systemic safety project selection tool.

DOT National Transportation Integrated Search

2013-07-01

"The Systemic Safety Project Selection Tool presents a process for incorporating systemic safety planning into traditional safety management processes. The Systemic Tool provides a step-by-step process for conducting systemic safety analysis; conside...

Incorporating psychological influences in probabilistic cost analysis

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

Kujawski, Edouard; Alvaro, Mariana; Edwards, William

2004-01-08

Today's typical probabilistic cost analysis assumes an ''ideal'' project that is devoid of the human and organizational considerations that heavily influence the success and cost of real-world projects. In the real world ''Money Allocated Is Money Spent'' (MAIMS principle); cost underruns are rarely available to protect against cost overruns while task overruns are passed on to the total project cost. Realistic cost estimates therefore require a modified probabilistic cost analysis that simultaneously models the cost management strategy including budget allocation. Psychological influences such as overconfidence in assessing uncertainties and dependencies among cost elements and risks are other important considerations thatmore » are generally not addressed. It should then be no surprise that actual project costs often exceed the initial estimates and are delivered late and/or with a reduced scope. This paper presents a practical probabilistic cost analysis model that incorporates recent findings in human behavior and judgment under uncertainty, dependencies among cost elements, the MAIMS principle, and project management practices. Uncertain cost elements are elicited from experts using the direct fractile assessment method and fitted with three-parameter Weibull distributions. The full correlation matrix is specified in terms of two parameters that characterize correlations among cost elements in the same and in different subsystems. The analysis is readily implemented using standard Monte Carlo simulation tools such as {at}Risk and Crystal Ball{reg_sign}. The analysis of a representative design and engineering project substantiates that today's typical probabilistic cost analysis is likely to severely underestimate project cost for probability of success values of importance to contractors and procuring activities. The proposed approach provides a framework for developing a viable cost management strategy for allocating baseline budgets and contingencies

The Challenge of Multiple Perspectives: Multiple Solution Tasks for Students Incorporating Diverse Tools and Representation Systems

ERIC Educational Resources Information Center

Kordaki, Maria

2015-01-01

This study focuses on the role of multiple solution tasks (MST) incorporating multiple learning tools and representation systems (MTRS) in encouraging each student to develop multiple perspectives on the learning concepts under study and creativity of thought. Specifically, two types of MST were used, namely tasks that allowed and demanded…

Oscillation Baselining and Analysis Tool

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

PNNL developed a new tool for oscillation analysis and baselining. This tool has been developed under a new DOE Grid Modernization Laboratory Consortium (GMLC) Project (GM0072 - “Suite of open-source applications and models for advanced synchrophasor analysis”) and it is based on the open platform for PMU analysis. The Oscillation Baselining and Analysis Tool (OBAT) performs the oscillation analysis and identifies modes of oscillations (frequency, damping, energy, and shape). The tool also does oscillation event baselining (fining correlation between oscillations characteristics and system operating conditions).

ISHM Decision Analysis Tool: Operations Concept

NASA Technical Reports Server (NTRS)

2006-01-01

The state-of-the-practice Shuttle caution and warning system warns the crew of conditions that may create a hazard to orbiter operations and/or crew. Depending on the severity of the alarm, the crew is alerted with a combination of sirens, tones, annunciator lights, or fault messages. The combination of anomalies (and hence alarms) indicates the problem. Even with much training, determining what problem a particular combination represents is not trivial. In many situations, an automated diagnosis system can help the crew more easily determine an underlying root cause. Due to limitations of diagnosis systems,however, it is not always possible to explain a set of alarms with a single root cause. Rather, the system generates a set of hypotheses that the crew can select from. The ISHM Decision Analysis Tool (IDAT) assists with this task. It presents the crew relevant information that could help them resolve the ambiguity of multiple root causes and determine a method for mitigating the problem. IDAT follows graphical user interface design guidelines and incorporates a decision analysis system. I describe both of these aspects.

State Analysis Database Tool

NASA Technical Reports Server (NTRS)

Rasmussen, Robert; Bennett, Matthew

2006-01-01

The State Analysis Database Tool software establishes a productive environment for collaboration among software and system engineers engaged in the development of complex interacting systems. The tool embodies State Analysis, a model-based system engineering methodology founded on a state-based control architecture (see figure). A state represents a momentary condition of an evolving system, and a model may describe how a state evolves and is affected by other states. The State Analysis methodology is a process for capturing system and software requirements in the form of explicit models and states, and defining goal-based operational plans consistent with the models. Requirements, models, and operational concerns have traditionally been documented in a variety of system engineering artifacts that address different aspects of a mission s lifecycle. In State Analysis, requirements, models, and operations information are State Analysis artifacts that are consistent and stored in a State Analysis Database. The tool includes a back-end database, a multi-platform front-end client, and Web-based administrative functions. The tool is structured to prompt an engineer to follow the State Analysis methodology, to encourage state discovery and model description, and to make software requirements and operations plans consistent with model descriptions.

BFPTool: a software tool for analysis of Biomembrane Force Probe experiments.

PubMed

Šmít, Daniel; Fouquet, Coralie; Doulazmi, Mohamed; Pincet, Frédéric; Trembleau, Alain; Zapotocky, Martin

2017-01-01

The Biomembrane Force Probe is an approachable experimental technique commonly used for single-molecule force spectroscopy and experiments on biological interfaces. The technique operates in the range of forces from 0.1 pN to 1000 pN. Experiments are typically repeated many times, conditions are often not optimal, the captured video can be unstable and lose focus; this makes efficient analysis challenging, while out-of-the-box non-proprietary solutions are not freely available. This dedicated tool was developed to integrate and simplify the image processing and analysis of videomicroscopy recordings from BFP experiments. A novel processing feature, allowing the tracking of the pipette, was incorporated to address a limitation of preceding methods. Emphasis was placed on versatility and comprehensible user interface implemented in a graphical form. An integrated analytical tool was implemented to provide a faster, simpler and more convenient way to process and analyse BFP experiments.

Economic Consequence Analysis of Disasters: The ECAT Software Tool

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

Rose, Adam; Prager, Fynn; Chen, Zhenhua

This study develops a methodology for rapidly obtaining approximate estimates of the economic consequences from numerous natural, man-made and technological threats. This software tool is intended for use by various decision makers and analysts to obtain estimates rapidly. It is programmed in Excel and Visual Basic for Applications (VBA) to facilitate its use. This tool is called E-CAT (Economic Consequence Analysis Tool) and accounts for the cumulative direct and indirect impacts (including resilience and behavioral factors that significantly affect base estimates) on the U.S. economy. E-CAT is intended to be a major step toward advancing the current state of economicmore » consequence analysis (ECA) and also contributing to and developing interest in further research into complex but rapid turnaround approaches. The essence of the methodology involves running numerous simulations in a computable general equilibrium (CGE) model for each threat, yielding synthetic data for the estimation of a single regression equation based on the identification of key explanatory variables (threat characteristics and background conditions). This transforms the results of a complex model, which is beyond the reach of most users, into a "reduced form" model that is readily comprehensible. Functionality has been built into E-CAT so that its users can switch various consequence categories on and off in order to create customized profiles of economic consequences of numerous risk events. E-CAT incorporates uncertainty on both the input and output side in the course of the analysis.« less

Development of a site analysis tool for distributed wind projects

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

Shaw, Shawn

The Cadmus Group, Inc., in collaboration with the National Renewable Energy Laboratory (NREL) and Encraft, was awarded a grant from the Department of Energy (DOE) to develop a site analysis tool for distributed wind technologies. As the principal investigator for this project, Mr. Shawn Shaw was responsible for overall project management, direction, and technical approach. The product resulting from this project is the Distributed Wind Site Analysis Tool (DSAT), a software tool for analyzing proposed sites for distributed wind technology (DWT) systems. This user-friendly tool supports the long-term growth and stability of the DWT market by providing reliable, realistic estimatesmore » of site and system energy output and feasibility. DSAT-which is accessible online and requires no purchase or download of software-is available in two account types; Standard: This free account allows the user to analyze a limited number of sites and to produce a system performance report for each; and Professional: For a small annual fee users can analyze an unlimited number of sites, produce system performance reports, and generate other customizable reports containing key information such as visual influence and wind resources. The tool’s interactive maps allow users to create site models that incorporate the obstructions and terrain types present. Users can generate site reports immediately after entering the requisite site information. Ideally, this tool also educates users regarding good site selection and effective evaluation practices.« less

An Observation Analysis Tool for time-series analysis and sensor management in the FREEWAT GIS environment for water resources management

NASA Astrophysics Data System (ADS)

Cannata, Massimiliano; Neumann, Jakob; Cardoso, Mirko; Rossetto, Rudy; Foglia, Laura; Borsi, Iacopo

2017-04-01

In situ time-series are an important aspect of environmental modelling, especially with the advancement of numerical simulation techniques and increased model complexity. In order to make use of the increasing data available through the requirements of the EU Water Framework Directive, the FREEWAT GIS environment incorporates the newly developed Observation Analysis Tool for time-series analysis. The tool is used to import time-series data into QGIS from local CSV files, online sensors using the istSOS service, or MODFLOW model result files and enables visualisation, pre-processing of data for model development, and post-processing of model results. OAT can be used as a pre-processor for calibration observations, integrating the creation of observations for calibration directly from sensor time-series. The tool consists in an expandable Python library of processing methods and an interface integrated in the QGIS FREEWAT plug-in which includes a large number of modelling capabilities, data management tools and calibration capacity.

The Environment-Power System Analysis Tool development program. [for spacecraft power supplies

NASA Technical Reports Server (NTRS)

Jongeward, Gary A.; Kuharski, Robert A.; Kennedy, Eric M.; Wilcox, Katherine G.; Stevens, N. John; Putnam, Rand M.; Roche, James C.

1989-01-01

The Environment Power System Analysis Tool (EPSAT) is being developed to provide engineers with the ability to assess the effects of a broad range of environmental interactions on space power systems. A unique user-interface-data-dictionary code architecture oversees a collection of existing and future environmental modeling codes (e.g., neutral density) and physical interaction models (e.g., sheath ionization). The user-interface presents the engineer with tables, graphs, and plots which, under supervision of the data dictionary, are automatically updated in response to parameter change. EPSAT thus provides the engineer with a comprehensive and responsive environmental assessment tool and the scientist with a framework into which new environmental or physical models can be easily incorporated.

Incorporating ICT Tools in an Active Engagement Strategy-Based Classroom to Promote Learning Awareness and Self-Monitoring

ERIC Educational Resources Information Center

Kean, Ang Chooi; Embi, Mohamed Amin; Yunus, Melor Md

2012-01-01

The paper examines the influence of incorporating information and communication technology (ICT) tools to help learners to promote learning awareness and self-monitoring skills. An open-ended online questionnaire survey was administered to 15 course participants at the conclusion of the course. The data were analysed on the basis of the percentage…

Higher Education Faculty Utilization of Online Technological Tools: A Multilevel Analysis

ERIC Educational Resources Information Center

Jackson, Brianne L.

2017-01-01

As online learning and the use of online technological tools in higher education continues to grow exponentially, higher education faculty are expected to incorporate these tools into their instruction. However, many faculty members are reluctant to embrace such tools, for a variety of professional and personal reasons. This study employs survey…

Economic and Financial Analysis Tools | Energy Analysis | NREL

Science.gov Websites

Economic and Financial Analysis Tools Economic and Financial Analysis Tools Use these economic and . Job and Economic Development Impact (JEDI) Model Use these easy-to-use, spreadsheet-based tools to analyze the economic impacts of constructing and operating power generation and biofuel plants at the

RSAT: regulatory sequence analysis tools.

PubMed

Thomas-Chollier, Morgane; Sand, Olivier; Turatsinze, Jean-Valéry; Janky, Rekin's; Defrance, Matthieu; Vervisch, Eric; Brohée, Sylvain; van Helden, Jacques

2008-07-01

The regulatory sequence analysis tools (RSAT, http://rsat.ulb.ac.be/rsat/) is a software suite that integrates a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences. The suite includes programs for sequence retrieval, pattern discovery, phylogenetic footprint detection, pattern matching, genome scanning and feature map drawing. Random controls can be performed with random gene selections or by generating random sequences according to a variety of background models (Bernoulli, Markov). Beyond the original word-based pattern-discovery tools (oligo-analysis and dyad-analysis), we recently added a battery of tools for matrix-based detection of cis-acting elements, with some original features (adaptive background models, Markov-chain estimation of P-values) that do not exist in other matrix-based scanning tools. The web server offers an intuitive interface, where each program can be accessed either separately or connected to the other tools. In addition, the tools are now available as web services, enabling their integration in programmatic workflows. Genomes are regularly updated from various genome repositories (NCBI and EnsEMBL) and 682 organisms are currently supported. Since 1998, the tools have been used by several hundreds of researchers from all over the world. Several predictions made with RSAT were validated experimentally and published.

Analysis Tools for CFD Multigrid Solvers

NASA Technical Reports Server (NTRS)

Mineck, Raymond E.; Thomas, James L.; Diskin, Boris

2004-01-01

Analysis tools are needed to guide the development and evaluate the performance of multigrid solvers for the fluid flow equations. Classical analysis tools, such as local mode analysis, often fail to accurately predict performance. Two-grid analysis tools, herein referred to as Idealized Coarse Grid and Idealized Relaxation iterations, have been developed and evaluated within a pilot multigrid solver. These new tools are applicable to general systems of equations and/or discretizations and point to problem areas within an existing multigrid solver. Idealized Relaxation and Idealized Coarse Grid are applied in developing textbook-efficient multigrid solvers for incompressible stagnation flow problems.

Extended Testability Analysis Tool

NASA Technical Reports Server (NTRS)

Melcher, Kevin; Maul, William A.; Fulton, Christopher

2012-01-01

The Extended Testability Analysis (ETA) Tool is a software application that supports fault management (FM) by performing testability analyses on the fault propagation model of a given system. Fault management includes the prevention of faults through robust design margins and quality assurance methods, or the mitigation of system failures. Fault management requires an understanding of the system design and operation, potential failure mechanisms within the system, and the propagation of those potential failures through the system. The purpose of the ETA Tool software is to process the testability analysis results from a commercial software program called TEAMS Designer in order to provide a detailed set of diagnostic assessment reports. The ETA Tool is a command-line process with several user-selectable report output options. The ETA Tool also extends the COTS testability analysis and enables variation studies with sensor sensitivity impacts on system diagnostics and component isolation using a single testability output. The ETA Tool can also provide extended analyses from a single set of testability output files. The following analysis reports are available to the user: (1) the Detectability Report provides a breakdown of how each tested failure mode was detected, (2) the Test Utilization Report identifies all the failure modes that each test detects, (3) the Failure Mode Isolation Report demonstrates the system s ability to discriminate between failure modes, (4) the Component Isolation Report demonstrates the system s ability to discriminate between failure modes relative to the components containing the failure modes, (5) the Sensor Sensor Sensitivity Analysis Report shows the diagnostic impact due to loss of sensor information, and (6) the Effect Mapping Report identifies failure modes that result in specified system-level effects.

Channel CAT: A Tactical Link Analysis Tool

DTIC Science & Technology

1997-09-01

NAVAL POSTGRADUATE SCHOOL Monterey, California THESIS CHANNEL CAT : A TACTICAL LINK ANALYSIS TOOL by Michael Glenn Coleman September 1997 Thesis...REPORT TYPE AND DATES COVERED September 1997 Master’s Thesis 4. TITLE AND SUBTITLE CHANNEL CAT : A TACTICAL LINK ANALYSIS TOOL 5. FUNDING NUMBERS 6...tool, the Channel Capacity Analysis Tool (Channel CAT ), designed to provide an automated tool for the anlysis of design decisions in developing client

Incorporating Experience Curves in Appliance Standards Analysis

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

Garbesi, Karina; Chan, Peter; Greenblatt, Jeffery

2011-10-31

The technical analyses in support of U.S. energy conservation standards for residential appliances and commercial equipment have typically assumed that manufacturing costs and retail prices remain constant during the projected 30-year analysis period. There is, however, considerable evidence that this assumption does not reflect real market prices. Costs and prices generally fall in relation to cumulative production, a phenomenon known as experience and modeled by a fairly robust empirical experience curve. Using price data from the Bureau of Labor Statistics, and shipment data obtained as part of the standards analysis process, we present U.S. experience curves for room air conditioners,more » clothes dryers, central air conditioners, furnaces, and refrigerators and freezers. These allow us to develop more representative appliance price projections than the assumption-based approach of constant prices. These experience curves were incorporated into recent energy conservation standards for these products. The impact on the national modeling can be significant, often increasing the net present value of potential standard levels in the analysis. In some cases a previously cost-negative potential standard level demonstrates a benefit when incorporating experience. These results imply that past energy conservation standards analyses may have undervalued the economic benefits of potential standard levels.« less

Opportunities and Strategies to Incorporate Ecosystem Services Knowledge and Decision Support Tools into Planning and Decision Making in Hawai`i

NASA Astrophysics Data System (ADS)

Bremer, Leah L.; Delevaux, Jade M. S.; Leary, James J. K.; J. Cox, Linda; Oleson, Kirsten L. L.

2015-04-01

Incorporating ecosystem services into management decisions is a promising means to link conservation and human well-being. Nonetheless, planning and management in Hawai`i, a state with highly valued natural capital, has yet to broadly utilize an ecosystem service approach. We conducted a stakeholder assessment, based on semi-structured interviews, with terrestrial ( n = 26) and marine ( n = 27) natural resource managers across the State of Hawai`i to understand the current use of ecosystem services (ES) knowledge and decision support tools and whether, how, and under what contexts, further development would potentially be useful. We found that ES knowledge and tools customized to Hawai`i could be useful for communication and outreach, justifying management decisions, and spatial planning. Greater incorporation of this approach is clearly desired and has a strong potential to contribute to more sustainable decision making and planning in Hawai`i and other oceanic island systems. However, the unique biophysical, socio-economic, and cultural context of Hawai`i, and other island systems, will require substantial adaptation of existing ES tools. Based on our findings, we identified four key opportunities for the use of ES knowledge and tools in Hawai`i: (1) linking native forest protection to watershed health; (2) supporting sustainable agriculture; (3) facilitating ridge-to-reef management; and (4) supporting statewide terrestrial and marine spatial planning. Given the interest expressed by natural resource managers, we envision broad adoption of ES knowledge and decision support tools if knowledge and tools are tailored to the Hawaiian context and coupled with adequate outreach and training.

Opportunities and strategies to incorporate ecosystem services knowledge and decision support tools into planning and decision making in Hawai'i.

PubMed

Bremer, Leah L; Delevaux, Jade M S; Leary, James J K; J Cox, Linda; Oleson, Kirsten L L

2015-04-01

Incorporating ecosystem services into management decisions is a promising means to link conservation and human well-being. Nonetheless, planning and management in Hawai'i, a state with highly valued natural capital, has yet to broadly utilize an ecosystem service approach. We conducted a stakeholder assessment, based on semi-structured interviews, with terrestrial (n = 26) and marine (n = 27) natural resource managers across the State of Hawai'i to understand the current use of ecosystem services (ES) knowledge and decision support tools and whether, how, and under what contexts, further development would potentially be useful. We found that ES knowledge and tools customized to Hawai'i could be useful for communication and outreach, justifying management decisions, and spatial planning. Greater incorporation of this approach is clearly desired and has a strong potential to contribute to more sustainable decision making and planning in Hawai'i and other oceanic island systems. However, the unique biophysical, socio-economic, and cultural context of Hawai'i, and other island systems, will require substantial adaptation of existing ES tools. Based on our findings, we identified four key opportunities for the use of ES knowledge and tools in Hawai'i: (1) linking native forest protection to watershed health; (2) supporting sustainable agriculture; (3) facilitating ridge-to-reef management; and (4) supporting statewide terrestrial and marine spatial planning. Given the interest expressed by natural resource managers, we envision broad adoption of ES knowledge and decision support tools if knowledge and tools are tailored to the Hawaiian context and coupled with adequate outreach and training.

Systematic Omics Analysis Review (SOAR) Tool to Support Risk Assessment

PubMed Central

McConnell, Emma R.; Bell, Shannon M.; Cote, Ila; Wang, Rong-Lin; Perkins, Edward J.; Garcia-Reyero, Natàlia; Gong, Ping; Burgoon, Lyle D.

2014-01-01

Environmental health risk assessors are challenged to understand and incorporate new data streams as the field of toxicology continues to adopt new molecular and systems biology technologies. Systematic screening reviews can help risk assessors and assessment teams determine which studies to consider for inclusion in a human health assessment. A tool for systematic reviews should be standardized and transparent in order to consistently determine which studies meet minimum quality criteria prior to performing in-depth analyses of the data. The Systematic Omics Analysis Review (SOAR) tool is focused on assisting risk assessment support teams in performing systematic reviews of transcriptomic studies. SOAR is a spreadsheet tool of 35 objective questions developed by domain experts, focused on transcriptomic microarray studies, and including four main topics: test system, test substance, experimental design, and microarray data. The tool will be used as a guide to identify studies that meet basic published quality criteria, such as those defined by the Minimum Information About a Microarray Experiment standard and the Toxicological Data Reliability Assessment Tool. Seven scientists were recruited to test the tool by using it to independently rate 15 published manuscripts that study chemical exposures with microarrays. Using their feedback, questions were weighted based on importance of the information and a suitability cutoff was set for each of the four topic sections. The final validation resulted in 100% agreement between the users on four separate manuscripts, showing that the SOAR tool may be used to facilitate the standardized and transparent screening of microarray literature for environmental human health risk assessment. PMID:25531884

Macro Analysis Tool - MAT

EPA Science Inventory

This product is an easy-to-use Excel-based macro analysis tool (MAT) for performing comparisons of air sensor data with reference data and interpreting the results. This tool tackles one of the biggest hurdles in citizen-led community air monitoring projects – working with ...

[3H]Leucine incorporation method as a tool to measure secondary production by periphytic bacteria associated to the roots of floating aquatic macrophyte.

PubMed

Miranda, M R; Guimarães, J R D; Coelho-Souza, A S

2007-10-01

The present study assessed the application of [(3)H]Leucine incorporation into protein by periphytic bacteria associated with the roots of the floating aquatic macrophyte Eichornia crassipes. Basic assumptions underlying the method, such as linearity of leucine incorporation, saturation level of incorporation rates, incorporation into other macromolecules, specificity of incorporation for bacterial assemblages and [(3)H]Leucine degradation during samples storage were tested, and two procedures for extracting the incorporated leucine were compared. Both methods gave the same results, however, the hot TCA extraction method was less time consuming than the alkaline extraction method. Incorporation of [(3)H]Leucine was linear for up to 40 min. Saturation concentration of [(3)H]Leucine incorporation into protein was 1500 nM. An experiment with prokaryotic and eukaryotic inhibitors showed no significant [(3)H]Leucine incorporation into eukaryotes even in high leucine concentrations. No significant amounts of radiolabel were incorporated into other macromolecules. The maximum time of sample storage after the incubation is 15 days. The leucine incorporation method can be a reliable tool to measure bacterial production in the periphyton root-associated bacteria.

Spectral Analysis Tool 6.2 for Windows

NASA Technical Reports Server (NTRS)

Morgan, Feiming; Sue, Miles; Peng, Ted; Tan, Harry; Liang, Robert; Kinman, Peter

2006-01-01

Spectral Analysis Tool 6.2 is the latest version of a computer program that assists in analysis of interference between radio signals of the types most commonly used in Earth/spacecraft radio communications. [An earlier version was reported in Software for Analyzing Earth/Spacecraft Radio Interference (NPO-20422), NASA Tech Briefs, Vol. 25, No. 4 (April 2001), page 52.] SAT 6.2 calculates signal spectra, bandwidths, and interference effects for several families of modulation schemes. Several types of filters can be modeled, and the program calculates and displays signal spectra after filtering by any of the modeled filters. The program accommodates two simultaneous signals: a desired signal and an interferer. The interference-to-signal power ratio can be calculated for the filtered desired and interfering signals. Bandwidth-occupancy and link-budget calculators are included for the user s convenience. SAT 6.2 has a new software structure and provides a new user interface that is both intuitive and convenient. SAT 6.2 incorporates multi-tasking, multi-threaded execution, virtual memory management, and a dynamic link library. SAT 6.2 is designed for use on 32- bit computers employing Microsoft Windows operating systems.

PAINT: a promoter analysis and interaction network generation tool for gene regulatory network identification.

PubMed

Vadigepalli, Rajanikanth; Chakravarthula, Praveen; Zak, Daniel E; Schwaber, James S; Gonye, Gregory E

2003-01-01

We have developed a bioinformatics tool named PAINT that automates the promoter analysis of a given set of genes for the presence of transcription factor binding sites. Based on coincidence of regulatory sites, this tool produces an interaction matrix that represents a candidate transcriptional regulatory network. This tool currently consists of (1) a database of promoter sequences of known or predicted genes in the Ensembl annotated mouse genome database, (2) various modules that can retrieve and process the promoter sequences for binding sites of known transcription factors, and (3) modules for visualization and analysis of the resulting set of candidate network connections. This information provides a substantially pruned list of genes and transcription factors that can be examined in detail in further experimental studies on gene regulation. Also, the candidate network can be incorporated into network identification methods in the form of constraints on feasible structures in order to render the algorithms tractable for large-scale systems. The tool can also produce output in various formats suitable for use in external visualization and analysis software. In this manuscript, PAINT is demonstrated in two case studies involving analysis of differentially regulated genes chosen from two microarray data sets. The first set is from a neuroblastoma N1E-115 cell differentiation experiment, and the second set is from neuroblastoma N1E-115 cells at different time intervals following exposure to neuropeptide angiotensin II. PAINT is available for use as an agent in BioSPICE simulation and analysis framework (www.biospice.org), and can also be accessed via a WWW interface at www.dbi.tju.edu/dbi/tools/paint/.

Building energy analysis tool

DOEpatents

Brackney, Larry; Parker, Andrew; Long, Nicholas; Metzger, Ian; Dean, Jesse; Lisell, Lars

2016-04-12

A building energy analysis system includes a building component library configured to store a plurality of building components, a modeling tool configured to access the building component library and create a building model of a building under analysis using building spatial data and using selected building components of the plurality of building components stored in the building component library, a building analysis engine configured to operate the building model and generate a baseline energy model of the building under analysis and further configured to apply one or more energy conservation measures to the baseline energy model in order to generate one or more corresponding optimized energy models, and a recommendation tool configured to assess the one or more optimized energy models against the baseline energy model and generate recommendations for substitute building components or modifications.

A decision-making tool for incorporating sustainability measures into pavement design : research project capsule.

DOT National Transportation Integrated Search

2016-10-01

The objective of the proposed study is to conceive and develop a decision-making tool : for evaluating sustainability of pavement designs based on a cradle-to-grave analysis. : This tool will utilize EPDs to enhance the reliability of the assessment ...

Tomato Expression Database (TED): a suite of data presentation and analysis tools

PubMed Central

Fei, Zhangjun; Tang, Xuemei; Alba, Rob; Giovannoni, James

2006-01-01

The Tomato Expression Database (TED) includes three integrated components. The Tomato Microarray Data Warehouse serves as a central repository for raw gene expression data derived from the public tomato cDNA microarray. In addition to expression data, TED stores experimental design and array information in compliance with the MIAME guidelines and provides web interfaces for researchers to retrieve data for their own analysis and use. The Tomato Microarray Expression Database contains normalized and processed microarray data for ten time points with nine pair-wise comparisons during fruit development and ripening in a normal tomato variety and nearly isogenic single gene mutants impacting fruit development and ripening. Finally, the Tomato Digital Expression Database contains raw and normalized digital expression (EST abundance) data derived from analysis of the complete public tomato EST collection containing >150 000 ESTs derived from 27 different non-normalized EST libraries. This last component also includes tools for the comparison of tomato and Arabidopsis digital expression data. A set of query interfaces and analysis, and visualization tools have been developed and incorporated into TED, which aid users in identifying and deciphering biologically important information from our datasets. TED can be accessed at . PMID:16381976

Tomato Expression Database (TED): a suite of data presentation and analysis tools.

PubMed

Fei, Zhangjun; Tang, Xuemei; Alba, Rob; Giovannoni, James

2006-01-01

The Tomato Expression Database (TED) includes three integrated components. The Tomato Microarray Data Warehouse serves as a central repository for raw gene expression data derived from the public tomato cDNA microarray. In addition to expression data, TED stores experimental design and array information in compliance with the MIAME guidelines and provides web interfaces for researchers to retrieve data for their own analysis and use. The Tomato Microarray Expression Database contains normalized and processed microarray data for ten time points with nine pair-wise comparisons during fruit development and ripening in a normal tomato variety and nearly isogenic single gene mutants impacting fruit development and ripening. Finally, the Tomato Digital Expression Database contains raw and normalized digital expression (EST abundance) data derived from analysis of the complete public tomato EST collection containing >150,000 ESTs derived from 27 different non-normalized EST libraries. This last component also includes tools for the comparison of tomato and Arabidopsis digital expression data. A set of query interfaces and analysis, and visualization tools have been developed and incorporated into TED, which aid users in identifying and deciphering biologically important information from our datasets. TED can be accessed at http://ted.bti.cornell.edu.

Environmental Tools and Radiological Assessment

EPA Science Inventory

This presentation details two tools (SADA and FRAMES) available for use in environmental assessments of chemicals that can also be used for radiological assessments of the environment. Spatial Analysis and Decision Assistance (SADA) is a Windows freeware program that incorporate...

Multi-mission telecom analysis tool

NASA Technical Reports Server (NTRS)

Hanks, D.; Kordon, M.; Baker, J.

2002-01-01

In the early formulation phase of a mission it is critically important to have fast, easy to use, easy to integrate space vehicle subsystem analysis tools so that engineers can rapidly perform trade studies not only by themselves but in coordination with other subsystem engineers as well. The Multi-Mission Telecom Analysis Tool (MMTAT) is designed for just this purpose.

Ultra-scale Visualization Climate Data Analysis Tools (UV-CDAT)

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

Williams, Dean N.; Silva, Claudio

2013-09-30

For the past three years, a large analysis and visualization effort—funded by the Department of Energy’s Office of Biological and Environmental Research (BER), the National Aeronautics and Space Administration (NASA), and the National Oceanic and Atmospheric Administration (NOAA)—has brought together a wide variety of industry-standard scientific computing libraries and applications to create Ultra-scale Visualization Climate Data Analysis Tools (UV-CDAT) to serve the global climate simulation and observational research communities. To support interactive analysis and visualization, all components connect through a provenance application–programming interface to capture meaningful history and workflow. Components can be loosely coupled into the framework for fast integrationmore » or tightly coupled for greater system functionality and communication with other components. The overarching goal of UV-CDAT is to provide a new paradigm for access to and analysis of massive, distributed scientific data collections by leveraging distributed data architectures located throughout the world. The UV-CDAT framework addresses challenges in analysis and visualization and incorporates new opportunities, including parallelism for better efficiency, higher speed, and more accurate scientific inferences. Today, it provides more than 600 users access to more analysis and visualization products than any other single source.« less

Mars Reconnaissance Orbiter Uplink Analysis Tool

NASA Technical Reports Server (NTRS)

Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; Hwang, Pauline

2008-01-01

This software analyzes Mars Reconnaissance Orbiter (MRO) orbital geometry with respect to Mars Exploration Rover (MER) contact windows, and is the first tool of its kind designed specifically to support MRO-MER interface coordination. Prior to this automated tool, this analysis was done manually with Excel and the UNIX command line. In total, the process would take approximately 30 minutes for each analysis. The current automated analysis takes less than 30 seconds. This tool resides on the flight machine and uses a PHP interface that does the entire analysis of the input files and takes into account one-way light time from another input file. Input flies are copied over to the proper directories and are dynamically read into the tool s interface. The user can then choose the corresponding input files based on the time frame desired for analysis. After submission of the Web form, the tool merges the two files into a single, time-ordered listing of events for both spacecraft. The times are converted to the same reference time (Earth Transmit Time) by reading in a light time file and performing the calculations necessary to shift the time formats. The program also has the ability to vary the size of the keep-out window on the main page of the analysis tool by inputting a custom time for padding each MRO event time. The parameters on the form are read in and passed to the second page for analysis. Everything is fully coded in PHP and can be accessed by anyone with access to the machine via Web page. This uplink tool will continue to be used for the duration of the MER mission's needs for X-band uplinks. Future missions also can use the tools to check overflight times as well as potential site observation times. Adaptation of the input files to the proper format, and the window keep-out times, would allow for other analyses. Any operations task that uses the idea of keep-out windows will have a use for this program.

From Numerical Problem Solving to Model-Based Experimentation Incorporating Computer-Based Tools of Various Scales into the ChE Curriculum

ERIC Educational Resources Information Center

Shacham, Mordechai; Cutlip, Michael B.; Brauner, Neima

2009-01-01

A continuing challenge to the undergraduate chemical engineering curriculum is the time-effective incorporation and use of computer-based tools throughout the educational program. Computing skills in academia and industry require some proficiency in programming and effective use of software packages for solving 1) single-model, single-algorithm…

Regulatory sequence analysis tools.

PubMed

van Helden, Jacques

2003-07-01

The web resource Regulatory Sequence Analysis Tools (RSAT) (http://rsat.ulb.ac.be/rsat) offers a collection of software tools dedicated to the prediction of regulatory sites in non-coding DNA sequences. These tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Alternative formats are supported for the representation of regulatory motifs (strings or position-specific scoring matrices) and several algorithms are proposed for pattern discovery. RSAT currently holds >100 fully sequenced genomes and these data are regularly updated from GenBank.

43 CFR 46.135 - Incorporation of referenced documents into NEPA analysis.

Code of Federal Regulations, 2012 CFR

2012-10-01

... the analysis at hand. (b) Citations of specific information or analysis from other source documents... NEPA analysis. 46.135 Section 46.135 Public Lands: Interior Office of the Secretary of the Interior... Quality § 46.135 Incorporation of referenced documents into NEPA analysis. (a) The Responsible Official...

43 CFR 46.135 - Incorporation of referenced documents into NEPA analysis.

Code of Federal Regulations, 2011 CFR

2011-10-01

... the analysis at hand. (b) Citations of specific information or analysis from other source documents... NEPA analysis. 46.135 Section 46.135 Public Lands: Interior Office of the Secretary of the Interior... Quality § 46.135 Incorporation of referenced documents into NEPA analysis. (a) The Responsible Official...

43 CFR 46.135 - Incorporation of referenced documents into NEPA analysis.

Code of Federal Regulations, 2014 CFR

2014-10-01

... the analysis at hand. (b) Citations of specific information or analysis from other source documents... NEPA analysis. 46.135 Section 46.135 Public Lands: Interior Office of the Secretary of the Interior... Quality § 46.135 Incorporation of referenced documents into NEPA analysis. (a) The Responsible Official...

43 CFR 46.135 - Incorporation of referenced documents into NEPA analysis.

Code of Federal Regulations, 2010 CFR

2010-10-01

... the analysis at hand. (b) Citations of specific information or analysis from other source documents... NEPA analysis. 46.135 Section 46.135 Public Lands: Interior Office of the Secretary of the Interior... Quality § 46.135 Incorporation of referenced documents into NEPA analysis. (a) The Responsible Official...

43 CFR 46.135 - Incorporation of referenced documents into NEPA analysis.

Code of Federal Regulations, 2013 CFR

2013-10-01

... the analysis at hand. (b) Citations of specific information or analysis from other source documents... NEPA analysis. 46.135 Section 46.135 Public Lands: Interior Office of the Secretary of the Interior... Quality § 46.135 Incorporation of referenced documents into NEPA analysis. (a) The Responsible Official...

WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data

PubMed Central

Yi, Ming; Horton, Jay D; Cohen, Jonathan C; Hobbs, Helen H; Stephens, Robert M

2006-01-01

Background Analysis of High Throughput (HTP) Data such as microarray and proteomics data has provided a powerful methodology to study patterns of gene regulation at genome scale. A major unresolved problem in the post-genomic era is to assemble the large amounts of data generated into a meaningful biological context. We have developed a comprehensive software tool, WholePathwayScope (WPS), for deriving biological insights from analysis of HTP data. Result WPS extracts gene lists with shared biological themes through color cue templates. WPS statistically evaluates global functional category enrichment of gene lists and pathway-level pattern enrichment of data. WPS incorporates well-known biological pathways from KEGG (Kyoto Encyclopedia of Genes and Genomes) and Biocarta, GO (Gene Ontology) terms as well as user-defined pathways or relevant gene clusters or groups, and explores gene-term relationships within the derived gene-term association networks (GTANs). WPS simultaneously compares multiple datasets within biological contexts either as pathways or as association networks. WPS also integrates Genetic Association Database and Partial MedGene Database for disease-association information. We have used this program to analyze and compare microarray and proteomics datasets derived from a variety of biological systems. Application examples demonstrated the capacity of WPS to significantly facilitate the analysis of HTP data for integrative discovery. Conclusion This tool represents a pathway-based platform for discovery integration to maximize analysis power. The tool is freely available at . PMID:16423281

Integrating Reliability Analysis with a Performance Tool

NASA Technical Reports Server (NTRS)

Nicol, David M.; Palumbo, Daniel L.; Ulrey, Michael

1995-01-01

A large number of commercial simulation tools support performance oriented studies of complex computer and communication systems. Reliability of these systems, when desired, must be obtained by remodeling the system in a different tool. This has obvious drawbacks: (1) substantial extra effort is required to create the reliability model; (2) through modeling error the reliability model may not reflect precisely the same system as the performance model; (3) as the performance model evolves one must continuously reevaluate the validity of assumptions made in that model. In this paper we describe an approach, and a tool that implements this approach, for integrating a reliability analysis engine into a production quality simulation based performance modeling tool, and for modeling within such an integrated tool. The integrated tool allows one to use the same modeling formalisms to conduct both performance and reliability studies. We describe how the reliability analysis engine is integrated into the performance tool, describe the extensions made to the performance tool to support the reliability analysis, and consider the tool's performance.

Interactive, open source, travel time scenario modelling: tools to facilitate participation in health service access analysis.

PubMed

Fisher, Rohan; Lassa, Jonatan

2017-04-18

Modelling travel time to services has become a common public health tool for planning service provision but the usefulness of these analyses is constrained by the availability of accurate input data and limitations inherent in the assumptions and parameterisation. This is particularly an issue in the developing world where access to basic data is limited and travel is often complex and multi-modal. Improving the accuracy and relevance in this context requires greater accessibility to, and flexibility in, travel time modelling tools to facilitate the incorporation of local knowledge and the rapid exploration of multiple travel scenarios. The aim of this work was to develop simple open source, adaptable, interactive travel time modelling tools to allow greater access to and participation in service access analysis. Described are three interconnected applications designed to reduce some of the barriers to the more wide-spread use of GIS analysis of service access and allow for complex spatial and temporal variations in service availability. These applications are an open source GIS tool-kit and two geo-simulation models. The development of these tools was guided by health service issues from a developing world context but they present a general approach to enabling greater access to and flexibility in health access modelling. The tools demonstrate a method that substantially simplifies the process for conducting travel time assessments and demonstrate a dynamic, interactive approach in an open source GIS format. In addition this paper provides examples from empirical experience where these tools have informed better policy and planning. Travel and health service access is complex and cannot be reduced to a few static modeled outputs. The approaches described in this paper use a unique set of tools to explore this complexity, promote discussion and build understanding with the goal of producing better planning outcomes. The accessible, flexible, interactive and

NASA's Aeroacoustic Tools and Methods for Analysis of Aircraft Noise

NASA Technical Reports Server (NTRS)

Rizzi, Stephen A.; Lopes, Leonard V.; Burley, Casey L.

2015-01-01

Aircraft community noise is a significant concern due to continued growth in air traffic, increasingly stringent environmental goals, and operational limitations imposed by airport authorities. The ability to quantify aircraft noise at the source and ultimately at observers is required to develop low noise aircraft designs and flight procedures. Predicting noise at the source, accounting for scattering and propagation through the atmosphere to the observer, and assessing the perception and impact on a community requires physics-based aeroacoustics tools. Along with the analyses for aero-performance, weights and fuel burn, these tools can provide the acoustic component for aircraft MDAO (Multidisciplinary Design Analysis and Optimization). Over the last decade significant progress has been made in advancing the aeroacoustic tools such that acoustic analyses can now be performed during the design process. One major and enabling advance has been the development of the system noise framework known as Aircraft NOise Prediction Program2 (ANOPP2). ANOPP2 is NASA's aeroacoustic toolset and is designed to facilitate the combination of acoustic approaches of varying fidelity for the analysis of noise from conventional and unconventional aircraft. The toolset includes a framework that integrates noise prediction and propagation methods into a unified system for use within general aircraft analysis software. This includes acoustic analyses, signal processing and interfaces that allow for the assessment of perception of noise on a community. ANOPP2's capability to incorporate medium fidelity shielding predictions and wind tunnel experiments into a design environment is presented. An assessment of noise from a conventional and Hybrid Wing Body (HWB) aircraft using medium fidelity scattering methods combined with noise measurements from a model-scale HWB recently placed in NASA's 14x22 wind tunnel are presented. The results are in the form of community noise metrics and

The Complexity Analysis Tool

DTIC Science & Technology

1988-10-01

overview of the complexity analysis tool ( CAT ), an automated tool which will analyze mission critical computer resources (MCCR) software. CAT is based...84 MAR UNCLASSIFIED SECURITY CLASSIFICATION OF THIS PAGE 19. ABSTRACT: (cont) CAT automates the metric for BASIC (HP-71), ATLAS (EQUATE), Ada (subset...UNIX 5.2). CAT analyzes source code and computes complexity on a module basis. CAT also generates graphic representations of the logic flow paths and

Multi-mission space vehicle subsystem analysis tools

NASA Technical Reports Server (NTRS)

Kordon, M.; Wood, E.

2003-01-01

Spacecraft engineers often rely on specialized simulation tools to facilitate the analysis, design and operation of space systems. Unfortunately these tools are often designed for one phase of a single mission and cannot be easily adapted to other phases or other misions. The Multi-Mission Pace Vehicle Susbsystem Analysis Tools are designed to provide a solution to this problem.

CRITICA: coding region identification tool invoking comparative analysis

NASA Technical Reports Server (NTRS)

Badger, J. H.; Olsen, G. J.; Woese, C. R. (Principal Investigator)

1999-01-01

Gene recognition is essential to understanding existing and future DNA sequence data. CRITICA (Coding Region Identification Tool Invoking Comparative Analysis) is a suite of programs for identifying likely protein-coding sequences in DNA by combining comparative analysis of DNA sequences with more common noncomparative methods. In the comparative component of the analysis, regions of DNA are aligned with related sequences from the DNA databases; if the translation of the aligned sequences has greater amino acid identity than expected for the observed percentage nucleotide identity, this is interpreted as evidence for coding. CRITICA also incorporates noncomparative information derived from the relative frequencies of hexanucleotides in coding frames versus other contexts (i.e., dicodon bias). The dicodon usage information is derived by iterative analysis of the data, such that CRITICA is not dependent on the existence or accuracy of coding sequence annotations in the databases. This independence makes the method particularly well suited for the analysis of novel genomes. CRITICA was tested by analyzing the available Salmonella typhimurium DNA sequences. Its predictions were compared with the DNA sequence annotations and with the predictions of GenMark. CRITICA proved to be more accurate than GenMark, and moreover, many of its predictions that would seem to be errors instead reflect problems in the sequence databases. The source code of CRITICA is freely available by anonymous FTP (rdp.life.uiuc.edu in/pub/critica) and on the World Wide Web (http:/(/)rdpwww.life.uiuc.edu).

Paediatric Automatic Phonological Analysis Tools (APAT).

PubMed

Saraiva, Daniela; Lousada, Marisa; Hall, Andreia; Jesus, Luis M T

2017-12-01

To develop the pediatric Automatic Phonological Analysis Tools (APAT) and to estimate inter and intrajudge reliability, content validity, and concurrent validity. The APAT were constructed using Excel spreadsheets with formulas. The tools were presented to an expert panel for content validation. The corpus used in the Portuguese standardized test Teste Fonético-Fonológico - ALPE produced by 24 children with phonological delay or phonological disorder was recorded, transcribed, and then inserted into the APAT. Reliability and validity of APAT were analyzed. The APAT present strong inter- and intrajudge reliability (>97%). The content validity was also analyzed (ICC = 0.71), and concurrent validity revealed strong correlations between computerized and manual (traditional) methods. The development of these tools contributes to fill existing gaps in clinical practice and research, since previously there were no valid and reliable tools/instruments for automatic phonological analysis, which allowed the analysis of different corpora.

Incorporating Basic Optical Microscopy in the Instrumental Analysis Laboratory

ERIC Educational Resources Information Center

Flowers, Paul A.

2011-01-01

A simple and versatile approach to incorporating basic optical microscopy in the undergraduate instrumental analysis laboratory is described. Attaching a miniature CCD spectrometer to the video port of a standard compound microscope yields a visible microspectrophotometer suitable for student investigations of fundamental spectrometry concepts,…

d-Omix: a mixer of generic protein domain analysis tools.

PubMed

Wichadakul, Duangdao; Numnark, Somrak; Ingsriswang, Supawadee

2009-07-01

Domain combination provides important clues to the roles of protein domains in protein function, interaction and evolution. We have developed a web server d-Omix (a Mixer of Protein Domain Analysis Tools) aiming as a unified platform to analyze, compare and visualize protein data sets in various aspects of protein domain combinations. With InterProScan files for protein sets of interest provided by users, the server incorporates four services for domain analyses. First, it constructs protein phylogenetic tree based on a distance matrix calculated from protein domain architectures (DAs), allowing the comparison with a sequence-based tree. Second, it calculates and visualizes the versatility, abundance and co-presence of protein domains via a domain graph. Third, it compares the similarity of proteins based on DA alignment. Fourth, it builds a putative protein network derived from domain-domain interactions from DOMINE. Users may select a variety of input data files and flexibly choose domain search tools (e.g. hmmpfam, superfamily) for a specific analysis. Results from the d-Omix could be interactively explored and exported into various formats such as SVG, JPG, BMP and CSV. Users with only protein sequences could prepare an InterProScan file using a service provided by the server as well. The d-Omix web server is freely available at http://www.biotec.or.th/isl/Domix.

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

PubMed

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

2015-09-01

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

FSSC Science Tools: Pulsar Analysis

NASA Technical Reports Server (NTRS)

Thompson, Dave

2010-01-01

This slide presentation reviews the typical pulsar analysis, giving tips for screening of the data, the use of time series analysis, and utility tools. Specific information about analyzing Vela data is reviewed.

Contamination Analysis Tools

NASA Technical Reports Server (NTRS)

Brieda, Lubos

2015-01-01

This talk presents 3 different tools developed recently for contamination analysis:HTML QCM analyzer: runs in a web browser, and allows for data analysis of QCM log filesJava RGA extractor: can load in multiple SRS.ana files and extract pressure vs. time dataC++ Contamination Simulation code: 3D particle tracing code for modeling transport of dust particulates and molecules. Uses residence time to determine if molecules stick. Particulates can be sampled from IEST-STD-1246 and be accelerated by aerodynamic forces.

Incorporating Online Tools in Tertiary Education

ERIC Educational Resources Information Center

Steenkamp, Leon P.; Rudman, Riaan J.

2013-01-01

Students currently studying at tertiary institutions have developed a set of attitudes and aptitudes as a result of growing up in an IT and media-rich environment. These attitudes and aptitudes influence how they learn and in order to be effective, lecturers must adapt to address their learning preferences and use the online teaching tools that…

Analysis and design of friction stir welding tool

NASA Astrophysics Data System (ADS)

Jagadeesha, C. B.

2016-12-01

Since its inception no one has done analysis and design of FSW tool. Initial dimensions of FSW tool are decided by educated guess. Optimum stresses on tool pin have been determined at optimized parameters for bead on plate welding on AZ31B-O Mg alloy plate. Fatigue analysis showed that the chosen FSW tool for the welding experiment has not ∞ life and it has determined that the life of FSW tool is 2.66×105 cycles or revolutions. So one can conclude that any arbitrarily decided FSW tool generally has finite life and cannot be used for ∞ life. In general, one can determine the suitability of tool and its material to be used in FSW of the given workpiece materials in advance by this analysis in terms of fatigue life of the tool.

A look-ahead probabilistic contingency analysis framework incorporating smart sampling techniques

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

Chen, Yousu; Etingov, Pavel V.; Ren, Huiying

2016-07-18

This paper describes a framework of incorporating smart sampling techniques in a probabilistic look-ahead contingency analysis application. The predictive probabilistic contingency analysis helps to reflect the impact of uncertainties caused by variable generation and load on potential violations of transmission limits.

Ion Beam Analysis Of Nitrogen Incorporated Ultrananocrystalline Diamond (UNCD) Thin Films

NASA Astrophysics Data System (ADS)

AlFaify, S.; Garratt, E.; Dissanayake, A.; Mancini, D. C.; Kayani, A.

2011-06-01

Determination of the elemental composition is important to correlate the properties of nitrogen incorporated Ultrananocrystalline Diamond (UNCD) thin films with their growth conditions. Films were deposited by CVD deposition technology and nitrogen incorporation was introduced by diluting the growth Ar/CH4 plasma with N2 gas. Deposition of UNCD thin films was carried out on tungsten (˜15 nm) coated Si substrates with varying concentrations of N2 diluted to the growth plasma. Scanning electron microscopy (SEM) and Raman spectroscopy (RS) were used to confirm the characteristic morphology of the UNCD film and its dominant sp3 bonding respectively. The deposited films were smooth on the submicron scale with the RMS roughness value of 2.9-5.1 nm. Reflectometry spectroscopy analysis (RES) technique was used to measure the films thicknesses. To obtain the elemental composition of the UNCD thin films, Rutherford Backscattering Spectrometry (RBS), Non-Rutherford Backscattering Spectrometry (NRBS), Elastic Recoil Detection Analysis (ERDA) and Nuclear Reaction Analysis (NRA) were performed. Deposited UNCD films contained less than 5 at.% of H while N content incorporated in the films was estimated to be lower than 1 at.%. The intermixing region between the substrate and the film was found to be negligible. Moreover, amorphous phase as determined by Raman analysis was found to be increasing for the sample deposited with N2.

Grid Stiffened Structure Analysis Tool

NASA Technical Reports Server (NTRS)

1999-01-01

The Grid Stiffened Analysis Tool contract is contract performed by Boeing under NASA purchase order H30249D. The contract calls for a "best effort" study comprised of two tasks: (1) Create documentation for a composite grid-stiffened structure analysis tool, in the form of a Microsoft EXCEL spread sheet, that was developed by originally at Stanford University and later further developed by the Air Force, and (2) Write a program that functions as a NASTRAN pre-processor to generate an FEM code for grid-stiffened structure. In performing this contract, Task 1 was given higher priority because it enables NASA to make efficient use of a unique tool they already have; Task 2 was proposed by Boeing because it also would be beneficial to the analysis of composite grid-stiffened structures, specifically in generating models for preliminary design studies. The contract is now complete, this package includes copies of the user's documentation for Task 1 and a CD ROM & diskette with an electronic copy of the user's documentation and an updated version of the "GRID 99" spreadsheet.

Navigating freely-available software tools for metabolomics analysis.

PubMed

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

2017-01-01

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

Analysis Tools (AT)

Treesearch

Larry J. Gangi

2006-01-01

The FIREMON Analysis Tools program is designed to let the user perform grouped or ungrouped summary calculations of single measurement plot data, or statistical comparisons of grouped or ungrouped plot data taken at different sampling periods. The program allows the user to create reports and graphs, save and print them, or cut and paste them into a word processor....

Surface analysis of stone and bone tools

NASA Astrophysics Data System (ADS)

Stemp, W. James; Watson, Adam S.; Evans, Adrian A.

2016-03-01

Microwear (use-wear) analysis is a powerful method for identifying tool use that archaeologists and anthropologists employ to determine the activities undertaken by both humans and their hominin ancestors. Knowledge of tool use allows for more accurate and detailed reconstructions of past behavior, particularly in relation to subsistence practices, economic activities, conflict and ritual. It can also be used to document changes in these activities over time, in different locations, and by different members of society, in terms of gender and status, for example. Both stone and bone tools have been analyzed using a variety of techniques that focus on the observation, documentation and interpretation of wear traces. Traditionally, microwear analysis relied on the qualitative assessment of wear features using microscopes and often included comparisons between replicated tools used experimentally and the recovered artifacts, as well as functional analogies dependent upon modern implements and those used by indigenous peoples from various places around the world. Determination of tool use has also relied on the recovery and analysis of both organic and inorganic residues of past worked materials that survived in and on artifact surfaces. To determine tool use and better understand the mechanics of wear formation, particularly on stone and bone, archaeologists and anthropologists have increasingly turned to surface metrology and tribology to assist them in their research. This paper provides a history of the development of traditional microwear analysis in archaeology and anthropology and also explores the introduction and adoption of more modern methods and technologies for documenting and identifying wear on stone and bone tools, specifically those developed for the engineering sciences to study surface structures on micro- and nanoscales. The current state of microwear analysis is discussed as are the future directions in the study of microwear on stone and bone tools.

Multi-criteria development and incorporation into decision tools for health technology adoption.

PubMed

Poulin, Paule; Austen, Lea; Scott, Catherine M; Waddell, Cameron D; Dixon, Elijah; Poulin, Michelle; Lafrenière, René

2013-01-01

When introducing new health technologies, decision makers must integrate research evidence with local operational management information to guide decisions about whether and under what conditions the technology will be used. Multi-criteria decision analysis can support the adoption or prioritization of health interventions by using criteria to explicitly articulate the health organization's needs, limitations, and values in addition to evaluating evidence for safety and effectiveness. This paper seeks to describe the development of a framework to create agreed-upon criteria and decision tools to enhance a pre-existing local health technology assessment (HTA) decision support program. The authors compiled a list of published criteria from the literature, consulted with experts to refine the criteria list, and used a modified Delphi process with a group of key stakeholders to review, modify, and validate each criterion. In a workshop setting, the criteria were used to create decision tools. A set of user-validated criteria for new health technology evaluation and adoption was developed and integrated into the local HTA decision support program. Technology evaluation and decision guideline tools were created using these criteria to ensure that the decision process is systematic, consistent, and transparent. This framework can be used by others to develop decision-making criteria and tools to enhance similar technology adoption programs. The development of clear, user-validated criteria for evaluating new technologies adds a critical element to improve decision-making on technology adoption, and the decision tools ensure consistency, transparency, and real-world relevance.

Design and Analysis Tools for Supersonic Inlets

NASA Technical Reports Server (NTRS)

Slater, John W.; Folk, Thomas C.

2009-01-01

Computational tools are being developed for the design and analysis of supersonic inlets. The objective is to update existing tools and provide design and low-order aerodynamic analysis capability for advanced inlet concepts. The Inlet Tools effort includes aspects of creating an electronic database of inlet design information, a document describing inlet design and analysis methods, a geometry model for describing the shape of inlets, and computer tools that implement the geometry model and methods. The geometry model has a set of basic inlet shapes that include pitot, two-dimensional, axisymmetric, and stream-traced inlet shapes. The inlet model divides the inlet flow field into parts that facilitate the design and analysis methods. The inlet geometry model constructs the inlet surfaces through the generation and transformation of planar entities based on key inlet design factors. Future efforts will focus on developing the inlet geometry model, the inlet design and analysis methods, a Fortran 95 code to implement the model and methods. Other computational platforms, such as Java, will also be explored.

Portfolio: a prototype workstation for development and evaluation of tools for analysis and management of digital portal images.

PubMed

Boxwala, A A; Chaney, E L; Fritsch, D S; Friedman, C P; Rosenman, J G

1998-09-01

The purpose of this investigation was to design and implement a prototype physician workstation, called PortFolio, as a platform for developing and evaluating, by means of controlled observer studies, user interfaces and interactive tools for analyzing and managing digital portal images. The first observer study was designed to measure physician acceptance of workstation technology, as an alternative to a view box, for inspection and analysis of portal images for detection of treatment setup errors. The observer study was conducted in a controlled experimental setting to evaluate physician acceptance of the prototype workstation technology exemplified by PortFolio. PortFolio incorporates a windows user interface, a compact kit of carefully selected image analysis tools, and an object-oriented data base infrastructure. The kit evaluated in the observer study included tools for contrast enhancement, registration, and multimodal image visualization. Acceptance was measured in the context of performing portal image analysis in a structured protocol designed to simulate clinical practice. The acceptability and usage patterns were measured from semistructured questionnaires and logs of user interactions. Radiation oncologists, the subjects for this study, perceived the tools in PortFolio to be acceptable clinical aids. Concerns were expressed regarding user efficiency, particularly with respect to the image registration tools. The results of our observer study indicate that workstation technology is acceptable to radiation oncologists as an alternative to a view box for clinical detection of setup errors from digital portal images. Improvements in implementation, including more tools and a greater degree of automation in the image analysis tasks, are needed to make PortFolio more clinically practical.

Debugging and Performance Analysis Software Tools for Peregrine System |

Science.gov Websites

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

Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes.

PubMed

Niu, Sheng-Yong; Yang, Jinyu; McDermaid, Adam; Zhao, Jing; Kang, Yu; Ma, Qin

2017-05-08

Metagenomic and metatranscriptomic sequencing approaches are more frequently being used to link microbiota to important diseases and ecological changes. Many analyses have been used to compare the taxonomic and functional profiles of microbiota across habitats or individuals. While a large portion of metagenomic analyses focus on species-level profiling, some studies use strain-level metagenomic analyses to investigate the relationship between specific strains and certain circumstances. Metatranscriptomic analysis provides another important insight into activities of genes by examining gene expression levels of microbiota. Hence, combining metagenomic and metatranscriptomic analyses will help understand the activity or enrichment of a given gene set, such as drug-resistant genes among microbiome samples. Here, we summarize existing bioinformatics tools of metagenomic and metatranscriptomic data analysis, the purpose of which is to assist researchers in deciding the appropriate tools for their microbiome studies. Additionally, we propose an Integrated Meta-Function mapping pipeline to incorporate various reference databases and accelerate functional gene mapping procedures for both metagenomic and metatranscriptomic analyses. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A Comparison of Satellite Conjunction Analysis Screening Tools

DTIC Science & Technology

2011-09-01

visualization tool. Version 13.1.4 for Linux was tested. The SOAP conjunction analysis function does not have the capacity to perform the large...was examined by SOAP to confirm the conjunction. STK Advanced CAT STK Advanced CAT (Conjunction Analysis Tools) is an add-on module for the STK ...run with each tool. When attempting to perform the seven day all vs all analysis with STK Advanced CAT, the program consistently crashed during report

The environment power system analysis tool development program

NASA Technical Reports Server (NTRS)

Jongeward, Gary A.; Kuharski, Robert A.; Kennedy, Eric M.; Stevens, N. John; Putnam, Rand M.; Roche, James C.; Wilcox, Katherine G.

1990-01-01

The Environment Power System Analysis Tool (EPSAT) is being developed to provide space power system design engineers with an analysis tool for determining system performance of power systems in both naturally occurring and self-induced environments. The program is producing an easy to use computer aided engineering (CAE) tool general enough to provide a vehicle for technology transfer from space scientists and engineers to power system design engineers. The results of the project after two years of a three year development program are given. The EPSAT approach separates the CAE tool into three distinct functional units: a modern user interface to present information, a data dictionary interpreter to coordinate analysis; and a data base for storing system designs and results of analysis.

msBiodat analysis tool, big data analysis for high-throughput experiments.

PubMed

Muñoz-Torres, Pau M; Rokć, Filip; Belužic, Robert; Grbeša, Ivana; Vugrek, Oliver

2016-01-01

Mass spectrometry (MS) are a group of a high-throughput techniques used to increase knowledge about biomolecules. They produce a large amount of data which is presented as a list of hundreds or thousands of proteins. Filtering those data efficiently is the first step for extracting biologically relevant information. The filtering may increase interest by merging previous data with the data obtained from public databases, resulting in an accurate list of proteins which meet the predetermined conditions. In this article we present msBiodat Analysis Tool, a web-based application thought to approach proteomics to the big data analysis. With this tool, researchers can easily select the most relevant information from their MS experiments using an easy-to-use web interface. An interesting feature of msBiodat analysis tool is the possibility of selecting proteins by its annotation on Gene Ontology using its Gene Id, ensembl or UniProt codes. The msBiodat analysis tool is a web-based application that allows researchers with any programming experience to deal with efficient database querying advantages. Its versatility and user-friendly interface makes easy to perform fast and accurate data screening by using complex queries. Once the analysis is finished, the result is delivered by e-mail. msBiodat analysis tool is freely available at http://msbiodata.irb.hr.

Analytical Tools for Affordability Analysis

DTIC Science & Technology

2015-05-01

function (Womer)  Unit cost as a function of learning and rate  Learning with forgetting (Benkard)  Learning depreciates over time  Discretionary...Analytical Tools for Affordability Analysis David Tate Cost Analysis and Research Division Institute for Defense Analyses Report Documentation...ES) Institute for Defense Analyses, Cost Analysis and Research Division,4850 Mark Center Drive,Alexandria,VA,22311-1882 8. PERFORMING ORGANIZATION

RADC SCAT automated sneak circuit analysis tool

NASA Astrophysics Data System (ADS)

Depalma, Edward L.

The sneak circuit analysis tool (SCAT) provides a PC-based system for real-time identification (during the design phase) of sneak paths and design concerns. The tool utilizes an expert system shell to assist the analyst so that prior experience with sneak analysis is not necessary for performance. Both sneak circuits and design concerns are targeted by this tool, with both digital and analog circuits being examined. SCAT focuses the analysis at the assembly level, rather than the entire system, so that most sneak problems can be identified and corrected by the responsible design engineer in a timely manner. The SCAT program identifies the sneak circuits to the designer, who then decides what course of action is necessary.

Analysis of Ten Reverse Engineering Tools

NASA Astrophysics Data System (ADS)

Koskinen, Jussi; Lehmonen, Tero

Reverse engineering tools can be used in satisfying the information needs of software maintainers. Especially in case of maintaining large-scale legacy systems tool support is essential. Reverse engineering tools provide various kinds of capabilities to provide the needed information to the tool user. In this paper we analyze the provided capabilities in terms of four aspects: provided data structures, visualization mechanisms, information request specification mechanisms, and navigation features. We provide a compact analysis of ten representative reverse engineering tools for supporting C, C++ or Java: Eclipse Java Development Tools, Wind River Workbench (for C and C++), Understand (for C++), Imagix 4D, Creole, Javadoc, Javasrc, Source Navigator, Doxygen, and HyperSoft. The results of the study supplement the earlier findings in this important area.

Advanced Launch Technology Life Cycle Analysis Using the Architectural Comparison Tool (ACT)

NASA Technical Reports Server (NTRS)

McCleskey, Carey M.

2015-01-01

Life cycle technology impact comparisons for nanolauncher technology concepts were performed using an Affordability Comparison Tool (ACT) prototype. Examined are cost drivers and whether technology investments can dramatically affect the life cycle characteristics. Primary among the selected applications was the prospect of improving nanolauncher systems. As a result, findings and conclusions are documented for ways of creating more productive and affordable nanolauncher systems; e.g., an Express Lane-Flex Lane concept is forwarded, and the beneficial effect of incorporating advanced integrated avionics is explored. Also, a Functional Systems Breakdown Structure (F-SBS) was developed to derive consistent definitions of the flight and ground systems for both system performance and life cycle analysis. Further, a comprehensive catalog of ground segment functions was created.

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

NASA Technical Reports Server (NTRS)

Maul, William A.; Fulton, Christopher E.

2011-01-01

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

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.

Stable-isotope analysis: a neglected tool for placing parasites in food webs.

PubMed

Sabadel, A J M; Stumbo, A D; MacLeod, C D

2018-02-28

Parasites are often overlooked in the construction of food webs, despite their ubiquitous presence in almost every type of ecosystem. Researchers who do recognize their importance often struggle to include parasites using classical food-web theory, mainly due to the parasites' multiple hosts and life stages. A novel approach using compound-specific stable-isotope analysis promises to provide considerable insight into the energetic exchanges of parasite and host, which may solve some of the issues inherent in incorporating parasites using a classical approach. Understanding the role of parasites within food webs, and tracing the associated biomass transfers, are crucial to constructing new models that will expand our knowledge of food webs. This mini-review focuses on stable-isotope studies published in the past decade, and introduces compound-specific stable-isotope analysis as a powerful, but underutilized, newly developed tool that may answer many unresolved questions regarding the role of parasites in food webs.

Physical Education Curriculum Analysis Tool (PECAT)

ERIC Educational Resources Information Center

Lee, Sarah M.; Wechsler, Howell

2006-01-01

The Physical Education Curriculum Analysis Tool (PECAT) will help school districts conduct a clear, complete, and consistent analysis of written physical education curricula, based upon national physical education standards. The PECAT is customizable to include local standards. The results from the analysis can help school districts enhance…

Decision Analysis Tools for Volcano Observatories

NASA Astrophysics Data System (ADS)

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

2005-12-01

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

COASTAL INVERTEBRATES AND FISHES: HOW WILL THEY BE AFFECTED BY CHANGING ENVIRONMENTAL CONDITIONS- INCORPORATING CLIMATE SCENARIOS INTO THE COASTAL BIODIVERSITY RISK ANALYSIS TOOL (CBRAT)

EPA Science Inventory

The Coastal Biodiversity Risk Analysis Tool (CBRAT) is a public website that functions as an ecoinformatics platform to synthesize biogeographical distributions, abundances, life history attributes, and environmental tolerances for near-coastal invertebrates and fishes on a broad...

Hydrogen Financial Analysis Scenario Tool (H2FAST). Web Tool User's Manual

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

Bush, B.; Penev, M.; Melaina, M.

The Hydrogen Financial Analysis Scenario Tool (H2FAST) provides a quick and convenient indepth financial analysis for hydrogen fueling stations. This manual describes how to use the H2FAST web tool, which is one of three H2FAST formats developed by the National Renewable Energy Laboratory (NREL). Although all of the formats are based on the same financial computations and conform to generally accepted accounting principles (FASAB 2014, Investopedia 2014), each format provides a different level of complexity and user interactivity.

Failure environment analysis tool applications

NASA Astrophysics Data System (ADS)

Pack, Ginger L.; Wadsworth, David B.

1993-02-01

Understanding risks and avoiding failure are daily concerns for the women and men of NASA. Although NASA's mission propels us to push the limits of technology, and though the risks are considerable, the NASA community has instilled within, the determination to preserve the integrity of the systems upon which our mission and, our employees lives and well-being depend. One of the ways this is being done is by expanding and improving the tools used to perform risk assessment. The Failure Environment Analysis Tool (FEAT) was developed to help engineers and analysts more thoroughly and reliably conduct risk assessment and failure analysis. FEAT accomplishes this by providing answers to questions regarding what might have caused a particular failure; or, conversely, what effect the occurrence of a failure might have on an entire system. Additionally, FEAT can determine what common causes could have resulted in other combinations of failures. FEAT will even help determine the vulnerability of a system to failures, in light of reduced capability. FEAT also is useful in training personnel who must develop an understanding of particular systems. FEAT facilitates training on system behavior, by providing an automated environment in which to conduct 'what-if' evaluation. These types of analyses make FEAT a valuable tool for engineers and operations personnel in the design, analysis, and operation of NASA space systems.

Failure environment analysis tool applications

NASA Technical Reports Server (NTRS)

Pack, Ginger L.; Wadsworth, David B.

1993-01-01

Understanding risks and avoiding failure are daily concerns for the women and men of NASA. Although NASA's mission propels us to push the limits of technology, and though the risks are considerable, the NASA community has instilled within, the determination to preserve the integrity of the systems upon which our mission and, our employees lives and well-being depend. One of the ways this is being done is by expanding and improving the tools used to perform risk assessment. The Failure Environment Analysis Tool (FEAT) was developed to help engineers and analysts more thoroughly and reliably conduct risk assessment and failure analysis. FEAT accomplishes this by providing answers to questions regarding what might have caused a particular failure; or, conversely, what effect the occurrence of a failure might have on an entire system. Additionally, FEAT can determine what common causes could have resulted in other combinations of failures. FEAT will even help determine the vulnerability of a system to failures, in light of reduced capability. FEAT also is useful in training personnel who must develop an understanding of particular systems. FEAT facilitates training on system behavior, by providing an automated environment in which to conduct 'what-if' evaluation. These types of analyses make FEAT a valuable tool for engineers and operations personnel in the design, analysis, and operation of NASA space systems.

Failure environment analysis tool applications

NASA Technical Reports Server (NTRS)

Pack, Ginger L.; Wadsworth, David B.

1994-01-01

Understanding risks and avoiding failure are daily concerns for the women and men of NASA. Although NASA's mission propels us to push the limits of technology, and though the risks are considerable, the NASA community has instilled within it, the determination to preserve the integrity of the systems upon which our mission and, our employees lives and well-being depend. One of the ways this is being done is by expanding and improving the tools used to perform risk assessment. The Failure Environment Analysis Tool (FEAT) was developed to help engineers and analysts more thoroughly and reliably conduct risk assessment and failure analysis. FEAT accomplishes this by providing answers to questions regarding what might have caused a particular failure; or, conversely, what effect the occurrence of a failure might have on an entire system. Additionally, FEAT can determine what common causes could have resulted in other combinations of failures. FEAT will even help determine the vulnerability of a system to failures, in light of reduced capability. FEAT also is useful in training personnel who must develop an understanding of particular systems. FEAT facilitates training on system behavior, by providing an automated environment in which to conduct 'what-if' evaluation. These types of analyses make FEAT a valuable tool for engineers and operations personnel in the design, analysis, and operation of NASA space systems.

A Data-Driven Framework for Incorporating New Tools for ...

EPA Pesticide Factsheets

This talk was given during the “Exposure-Based Toxicity Testing” session at the annual meeting of the International Society for Exposure Science. It provided an update on the state of the science and tools that may be employed in risk-based prioritization efforts. It outlined knowledge gained from the data provided using these high-throughput tools to assess chemical bioactivity and to predict chemical exposures and also identified future needs. It provided an opportunity to showcase ongoing research efforts within the National Exposure Research Laboratory and the National Center for Computational Toxicology within the Office of Research and Development to an international audience. The National Exposure Research Laboratory (NERL) Computational Exposure Division (CED) develops and evaluates data, decision-support tools, and models to be applied to media-specific or receptor-specific problem areas. CED uses modeling-based approaches to characterize exposures, evaluate fate and transport, and support environmental diagnostics/forensics with input from multiple data sources. It also develops media- and receptor-specific models, process models, and decision support tools for use both within and outside of EPA.

Tool for Rapid Analysis of Monte Carlo Simulations

NASA Technical Reports Server (NTRS)

Restrepo, Carolina; McCall, Kurt E.; Hurtado, John E.

2013-01-01

Designing a spacecraft, or any other complex engineering system, requires extensive simulation and analysis work. Oftentimes, the large amounts of simulation data generated are very difficult and time consuming to analyze, with the added risk of overlooking potentially critical problems in the design. The authors have developed a generic data analysis tool that can quickly sort through large data sets and point an analyst to the areas in the data set that cause specific types of failures. The first version of this tool was a serial code and the current version is a parallel code, which has greatly increased the analysis capabilities. This paper describes the new implementation of this analysis tool on a graphical processing unit, and presents analysis results for NASA's Orion Monte Carlo data to demonstrate its capabilities.

Nutrition screening tools: an analysis of the evidence.

PubMed

Skipper, Annalynn; Ferguson, Maree; Thompson, Kyle; Castellanos, Victoria H; Porcari, Judy

2012-05-01

In response to questions about tools for nutrition screening, an evidence analysis project was developed to identify the most valid and reliable nutrition screening tools for use in acute care and hospital-based ambulatory care settings. An oversight group defined nutrition screening and literature search criteria. A trained analyst conducted structured searches of the literature for studies of nutrition screening tools according to predetermined criteria. Eleven nutrition screening tools designed to detect undernutrition in patients in acute care and hospital-based ambulatory care were identified. Trained analysts evaluated articles for quality using criteria specified by the American Dietetic Association's Evidence Analysis Library. Members of the oversight group assigned quality grades to the tools based on the quality of the supporting evidence, including reliability and validity data. One tool, the NRS-2002, received a grade I, and 4 tools-the Simple Two-Part Tool, the Mini-Nutritional Assessment-Short Form (MNA-SF), the Malnutrition Screening Tool (MST), and Malnutrition Universal Screening Tool (MUST)-received a grade II. The MST was the only tool shown to be both valid and reliable for identifying undernutrition in the settings studied. Thus, validated nutrition screening tools that are simple and easy to use are available for application in acute care and hospital-based ambulatory care settings.

AQME: A forensic mitochondrial DNA analysis tool for next-generation sequencing data.

PubMed

Sturk-Andreaggi, Kimberly; Peck, Michelle A; Boysen, Cecilie; Dekker, Patrick; McMahon, Timothy P; Marshall, Charla K

2017-11-01

The feasibility of generating mitochondrial DNA (mtDNA) data has expanded considerably with the advent of next-generation sequencing (NGS), specifically in the generation of entire mtDNA genome (mitogenome) sequences. However, the analysis of these data has emerged as the greatest challenge to implementation in forensics. To address this need, a custom toolkit for use in the CLC Genomics Workbench (QIAGEN, Hilden, Germany) was developed through a collaborative effort between the Armed Forces Medical Examiner System - Armed Forces DNA Identification Laboratory (AFMES-AFDIL) and QIAGEN Bioinformatics. The AFDIL-QIAGEN mtDNA Expert, or AQME, generates an editable mtDNA profile that employs forensic conventions and includes the interpretation range required for mtDNA data reporting. AQME also integrates an mtDNA haplogroup estimate into the analysis workflow, which provides the analyst with phylogenetic nomenclature guidance and a profile quality check without the use of an external tool. Supplemental AQME outputs such as nucleotide-per-position metrics, configurable export files, and an audit trail are produced to assist the analyst during review. AQME is applied to standard CLC outputs and thus can be incorporated into any mtDNA bioinformatics pipeline within CLC regardless of sample type, library preparation or NGS platform. An evaluation of AQME was performed to demonstrate its functionality and reliability for the analysis of mitogenome NGS data. The study analyzed Illumina mitogenome data from 21 samples (including associated controls) of varying quality and sample preparations with the AQME toolkit. A total of 211 tool edits were automatically applied to 130 of the 698 total variants reported in an effort to adhere to forensic nomenclature. Although additional manual edits were required for three samples, supplemental tools such as mtDNA haplogroup estimation assisted in identifying and guiding these necessary modifications to the AQME-generated profile. Along

The genetic incorporation of p-azidomethyl-l-phenylalanine into proteins in yeast.

PubMed

Supekova, Lubica; Zambaldo, Claudio; Choi, Seihyun; Lim, Reyna; Luo, Xiaozhou; Kazane, Stephanie A; Young, Travis S; Schultz, Peter G

2018-05-15

The noncanonical amino acid p-azidomethyl-l-phenylalanine can be genetically incorporated into proteins in bacteria, and has been used both as a spectroscopic probe and for the selective modification of proteins by alkynes using click chemistry. Here we report identification of Escherichia coli tyrosyl tRNA synthetase mutants that allow incorporation of p-azidomethyl-l-phenylalanine into proteins in yeast. When expressed together with the cognate E. coli tRNA CUA Tyr , the new mutant tyrosyl tRNA synthetases directed robust incorporation of p-azidomethyl-l-phenylalanine into a model protein, human superoxide dismutase, in response to the UAG amber nonsense codon. Mass spectrometry analysis of purified superoxide dismutase proteins confirmed the efficient site-specific incorporation of p-azidomethyl-l-phenylalanine. This work provides an additional tool for the selective modification of proteins in eukaryotic cells. Copyright © 2018 Elsevier Ltd. All rights reserved.

General Mission Analysis Tool (GMAT) User's Guide (Draft)

NASA Technical Reports Server (NTRS)

Hughes, Steven P.

2007-01-01

4The General Mission Analysis Tool (GMAT) is a space trajectory optimization and mission analysis system. This document is a draft of the users guide for the tool. Included in the guide is information about Configuring Objects/Resources, Object Fields: Quick Look-up Tables, and Commands and Events.

Interchange Safety Analysis Tool (ISAT) : user manual

DOT National Transportation Integrated Search

2007-06-01

This User Manual describes the usage and operation of the spreadsheet-based Interchange Safety Analysis Tool (ISAT). ISAT provides design and safety engineers with an automated tool for assessing the safety effects of geometric design and traffic con...

Lifecycle Industry GreenHouse gas, Technology and Energy through the Use Phase (LIGHTEnUP) – Analysis Tool User’s Guide

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

Morrow, William R.; Shehabi, Arman; Smith, Sarah

The LIGHTEnUP Analysis Tool (Lifecycle Industry GreenHouse gas, Technology and Energy through the Use Phase) has been developed for The United States Department of Energy’s (U.S. DOE) Advanced Manufacturing Office (AMO) to forecast both the manufacturing sector and product life-cycle energy consumption implications of manufactured products across the U.S. economy. The tool architecture incorporates publicly available historic and projection datasets of U.S. economy-wide energy use including manufacturing, buildings operations, electricity generation and transportation. The tool requires minimal inputs to define alternate scenarios to business-as-usual projection data. The tool is not an optimization or equilibrium model and therefore does not selectmore » technologies or deployment scenarios endogenously. Instead, inputs are developed exogenous to the tool by the user to reflect detailed engineering calculations, future targets and goals, or creative insights. The tool projects the scenario’s energy, CO 2 emissions, and energy expenditure (i.e., economic spending to purchase energy) implications and provides documentation to communicate results. The tool provides a transparent and uniform system of comparing manufacturing and use-phase impacts of technologies. The tool allows the user to create multiple scenarios that can reflect a range of possible future outcomes. However, reasonable scenarios require careful attention to assumptions and details about the future. This tool is part of an emerging set of AMO’s life cycle analysis (LCA) tool such as the Material Flows the Industry (MFI) tool, and the Additive Manufacturing LCA tool.« less

Performance Analysis of GYRO: A Tool Evaluation

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

Worley, P.; Roth, P.; Candy, J.

2005-06-26

The performance of the Eulerian gyrokinetic-Maxwell solver code GYRO is analyzed on five high performance computing systems. First, a manual approach is taken, using custom scripts to analyze the output of embedded wall clock timers, floating point operation counts collected using hardware performance counters, and traces of user and communication events collected using the profiling interface to Message Passing Interface (MPI) libraries. Parts of the analysis are then repeated or extended using a number of sophisticated performance analysis tools: IPM, KOJAK, SvPablo, TAU, and the PMaC modeling tool suite. The paper briefly discusses what has been discovered via this manualmore » analysis process, what performance analyses are inconvenient or infeasible to attempt manually, and to what extent the tools show promise in accelerating or significantly extending the manual performance analyses.« less

Sustainability Tools Inventory - Initial Gaps Analysis | Science ...

EPA Pesticide Factsheets

This report identifies a suite of tools that address a comprehensive set of community sustainability concerns. The objective is to discover whether "gaps" exist in the tool suite’s analytic capabilities. These tools address activities that significantly influence resource consumption, waste generation, and hazard generation including air pollution and greenhouse gases. In addition, the tools have been evaluated using four screening criteria: relevance to community decision making, tools in an appropriate developmental stage, tools that may be transferrable to situations useful for communities, and tools with requiring skill levels appropriate to communities. This document provides an initial gap analysis in the area of community sustainability decision support tools. It provides a reference to communities for existing decision support tools, and a set of gaps for those wishing to develop additional needed tools to help communities to achieve sustainability. It contributes to SHC 1.61.4

SECIMTools: a suite of metabolomics data analysis tools.

PubMed

Kirpich, Alexander S; Ibarra, Miguel; Moskalenko, Oleksandr; Fear, Justin M; Gerken, Joseph; Mi, Xinlei; Ashrafi, Ali; Morse, Alison M; McIntyre, Lauren M

2018-04-20

Metabolomics has the promise to transform the area of personalized medicine with the rapid development of high throughput technology for untargeted analysis of metabolites. Open access, easy to use, analytic tools that are broadly accessible to the biological community need to be developed. While technology used in metabolomics varies, most metabolomics studies have a set of features identified. Galaxy is an open access platform that enables scientists at all levels to interact with big data. Galaxy promotes reproducibility by saving histories and enabling the sharing workflows among scientists. SECIMTools (SouthEast Center for Integrated Metabolomics) is a set of Python applications that are available both as standalone tools and wrapped for use in Galaxy. The suite includes a comprehensive set of quality control metrics (retention time window evaluation and various peak evaluation tools), visualization techniques (hierarchical cluster heatmap, principal component analysis, modular modularity clustering), basic statistical analysis methods (partial least squares - discriminant analysis, analysis of variance, t-test, Kruskal-Wallis non-parametric test), advanced classification methods (random forest, support vector machines), and advanced variable selection tools (least absolute shrinkage and selection operator LASSO and Elastic Net). SECIMTools leverages the Galaxy platform and enables integrated workflows for metabolomics data analysis made from building blocks designed for easy use and interpretability. Standard data formats and a set of utilities allow arbitrary linkages between tools to encourage novel workflow designs. The Galaxy framework enables future data integration for metabolomics studies with other omics data.

Post-Flight Data Analysis Tool

NASA Technical Reports Server (NTRS)

George, Marina

2018-01-01

A software tool that facilitates the retrieval and analysis of post-flight data. This allows our team and other teams to effectively and efficiently analyze and evaluate post-flight data in order to certify commercial providers.

Dynamic Hurricane Data Analysis Tool

NASA Technical Reports Server (NTRS)

Knosp, Brian W.; Li, Peggy; Vu, Quoc A.

2009-01-01

A dynamic hurricane data analysis tool allows users of the JPL Tropical Cyclone Information System (TCIS) to analyze data over a Web medium. The TCIS software is described in the previous article, Tropical Cyclone Information System (TCIS) (NPO-45748). This tool interfaces with the TCIS database to pull in data from several different atmospheric and oceanic data sets, both observed by instruments. Users can use this information to generate histograms, maps, and profile plots for specific storms. The tool also displays statistical values for the user-selected parameter for the mean, standard deviation, median, minimum, and maximum values. There is little wait time, allowing for fast data plots over date and spatial ranges. Users may also zoom-in for a closer look at a particular spatial range. This is version 1 of the software. Researchers will use the data and tools on the TCIS to understand hurricane processes, improve hurricane forecast models and identify what types of measurements the next generation of instruments will need to collect.

DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures.

PubMed

Mazandu, Gaston K; Mulder, Nicola J

2013-09-25

The use of Gene Ontology (GO) data in protein analyses have largely contributed to the improved outcomes of these analyses. Several GO semantic similarity measures have been proposed in recent years and provide tools that allow the integration of biological knowledge embedded in the GO structure into different biological analyses. There is a need for a unified tool that provides the scientific community with the opportunity to explore these different GO similarity measure approaches and their biological applications. We have developed DaGO-Fun, an online tool available at http://web.cbio.uct.ac.za/ITGOM, which incorporates many different GO similarity measures for exploring, analyzing and comparing GO terms and proteins within the context of GO. It uses GO data and UniProt proteins with their GO annotations as provided by the Gene Ontology Annotation (GOA) project to precompute GO term information content (IC), enabling rapid response to user queries. The DaGO-Fun online tool presents the advantage of integrating all the relevant IC-based GO similarity measures, including topology- and annotation-based approaches to facilitate effective exploration of these measures, thus enabling users to choose the most relevant approach for their application. Furthermore, this tool includes several biological applications related to GO semantic similarity scores, including the retrieval of genes based on their GO annotations, the clustering of functionally related genes within a set, and term enrichment analysis.

Vehicle Technology Simulation and Analysis Tools | Transportation Research

Science.gov Websites

| NREL Vehicle Technology Simulation and Analysis Tools Vehicle Technology Simulation and vehicle technologies with the potential to achieve significant fuel savings and emission reductions. NREL : Automotive Deployment Options Projection Tool The ADOPT modeling tool estimates vehicle technology

ROCKETSHIP: a flexible and modular software tool for the planning, processing and analysis of dynamic MRI studies.

PubMed

Barnes, Samuel R; Ng, Thomas S C; Santa-Maria, Naomi; Montagne, Axel; Zlokovic, Berislav V; Jacobs, Russell E

2015-06-16

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is a promising technique to characterize pathology and evaluate treatment response. However, analysis of DCE-MRI data is complex and benefits from concurrent analysis of multiple kinetic models and parameters. Few software tools are currently available that specifically focuses on DCE-MRI analysis with multiple kinetic models. Here, we developed ROCKETSHIP, an open-source, flexible and modular software for DCE-MRI analysis. ROCKETSHIP incorporates analyses with multiple kinetic models, including data-driven nested model analysis. ROCKETSHIP was implemented using the MATLAB programming language. Robustness of the software to provide reliable fits using multiple kinetic models is demonstrated using simulated data. Simulations also demonstrate the utility of the data-driven nested model analysis. Applicability of ROCKETSHIP for both preclinical and clinical studies is shown using DCE-MRI studies of the human brain and a murine tumor model. A DCE-MRI software suite was implemented and tested using simulations. Its applicability to both preclinical and clinical datasets is shown. ROCKETSHIP was designed to be easily accessible for the beginner, but flexible enough for changes or additions to be made by the advanced user as well. The availability of a flexible analysis tool will aid future studies using DCE-MRI. A public release of ROCKETSHIP is available at https://github.com/petmri/ROCKETSHIP .

Analysis Tool Web Services from the EMBL-EBI.

PubMed

McWilliam, Hamish; Li, Weizhong; Uludag, Mahmut; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Cowley, Andrew Peter; Lopez, Rodrigo

2013-07-01

Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods.

Analysis Tool Web Services from the EMBL-EBI

PubMed Central

McWilliam, Hamish; Li, Weizhong; Uludag, Mahmut; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Cowley, Andrew Peter; Lopez, Rodrigo

2013-01-01

Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods. PMID:23671338

methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data.

PubMed

Kishore, Kamal; de Pretis, Stefano; Lister, Ryan; Morelli, Marco J; Bianchi, Valerio; Amati, Bruno; Ecker, Joseph R; Pelizzola, Mattia

2015-09-29

Numerous methods are available to profile several epigenetic marks, providing data with different genome coverage and resolution. Large epigenomic datasets are then generated, and often combined with other high-throughput data, including RNA-seq, ChIP-seq for transcription factors (TFs) binding and DNase-seq experiments. Despite the numerous computational tools covering specific steps in the analysis of large-scale epigenomics data, comprehensive software solutions for their integrative analysis are still missing. Multiple tools must be identified and combined to jointly analyze histone marks, TFs binding and other -omics data together with DNA methylation data, complicating the analysis of these data and their integration with publicly available datasets. To overcome the burden of integrating various data types with multiple tools, we developed two companion R/Bioconductor packages. The former, methylPipe, is tailored to the analysis of high- or low-resolution DNA methylomes in several species, accommodating (hydroxy-)methyl-cytosines in both CpG and non-CpG sequence context. The analysis of multiple whole-genome bisulfite sequencing experiments is supported, while maintaining the ability of integrating targeted genomic data. The latter, compEpiTools, seamlessly incorporates the results obtained with methylPipe and supports their integration with other epigenomics data. It provides a number of methods to score these data in regions of interest, leading to the identification of enhancers, lncRNAs, and RNAPII stalling/elongation dynamics. Moreover, it allows a fast and comprehensive annotation of the resulting genomic regions, and the association of the corresponding genes with non-redundant GeneOntology terms. Finally, the package includes a flexible method based on heatmaps for the integration of various data types, combining annotation tracks with continuous or categorical data tracks. methylPipe and compEpiTools provide a comprehensive Bioconductor

Building and evaluating an informatics tool to facilitate analysis of a biomedical literature search service in an academic medical center library.

PubMed

Hinton, Elizabeth G; Oelschlegel, Sandra; Vaughn, Cynthia J; Lindsay, J Michael; Hurst, Sachiko M; Earl, Martha

2013-01-01

This study utilizes an informatics tool to analyze a robust literature search service in an academic medical center library. Structured interviews with librarians were conducted focusing on the benefits of such a tool, expectations for performance, and visual layout preferences. The resulting application utilizes Microsoft SQL Server and .Net Framework 3.5 technologies, allowing for the use of a web interface. Customer tables and MeSH terms are included. The National Library of Medicine MeSH database and entry terms for each heading are incorporated, resulting in functionality similar to searching the MeSH database through PubMed. Data reports will facilitate analysis of the search service.

RSAT 2015: Regulatory Sequence Analysis Tools

PubMed Central

Medina-Rivera, Alejandra; Defrance, Matthieu; Sand, Olivier; Herrmann, Carl; Castro-Mondragon, Jaime A.; Delerce, Jeremy; Jaeger, Sébastien; Blanchet, Christophe; Vincens, Pierre; Caron, Christophe; Staines, Daniel M.; Contreras-Moreira, Bruno; Artufel, Marie; Charbonnier-Khamvongsa, Lucie; Hernandez, Céline; Thieffry, Denis; Thomas-Chollier, Morgane; van Helden, Jacques

2015-01-01

RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative genomics and (iv) analysis of regulatory variations. Nine new programs have been added to the 43 described in the 2011 NAR Web Software Issue, including a tool to extract sequences from a list of coordinates (fetch-sequences from UCSC), novel programs dedicated to the analysis of regulatory variants from GWAS or population genomics (retrieve-variation-seq and variation-scan), a program to cluster motifs and visualize the similarities as trees (matrix-clustering). To deal with the drastic increase of sequenced genomes, RSAT public sites have been reorganized into taxon-specific servers. The suite is well-documented with tutorials and published protocols. The software suite is available through Web sites, SOAP/WSDL Web services, virtual machines and stand-alone programs at http://www.rsat.eu/. PMID:25904632

Cytoscape: the network visualization tool for GenomeSpace workflows.

PubMed

Demchak, Barry; Hull, Tim; Reich, Michael; Liefeld, Ted; Smoot, Michael; Ideker, Trey; Mesirov, Jill P

2014-01-01

Modern genomic analysis often requires workflows incorporating multiple best-of-breed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded over 850 times since the release of its first version in September, 2013.

Cytoscape: the network visualization tool for GenomeSpace workflows

PubMed Central

Demchak, Barry; Hull, Tim; Reich, Michael; Liefeld, Ted; Smoot, Michael; Ideker, Trey; Mesirov, Jill P.

2014-01-01

Modern genomic analysis often requires workflows incorporating multiple best-of-breed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded over 850 times since the release of its first version in September, 2013. PMID:25165537

Tool for Rapid Analysis of Monte Carlo Simulations

NASA Technical Reports Server (NTRS)

Restrepo, Carolina; McCall, Kurt E.; Hurtado, John E.

2011-01-01

Designing a spacecraft, or any other complex engineering system, requires extensive simulation and analysis work. Oftentimes, the large amounts of simulation data generated are very di cult and time consuming to analyze, with the added risk of overlooking potentially critical problems in the design. The authors have developed a generic data analysis tool that can quickly sort through large data sets and point an analyst to the areas in the data set that cause specific types of failures. The Tool for Rapid Analysis of Monte Carlo simulations (TRAM) has been used in recent design and analysis work for the Orion vehicle, greatly decreasing the time it takes to evaluate performance requirements. A previous version of this tool was developed to automatically identify driving design variables in Monte Carlo data sets. This paper describes a new, parallel version, of TRAM implemented on a graphical processing unit, and presents analysis results for NASA's Orion Monte Carlo data to demonstrate its capabilities.

An Integrated Tool for System Analysis of Sample Return Vehicles

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.; Maddock, Robert W.; Winski, Richard G.

2012-01-01

The next important step in space exploration is the return of sample materials from extraterrestrial locations to Earth for analysis. Most mission concepts that return sample material to Earth share one common element: an Earth entry vehicle. The analysis and design of entry vehicles is multidisciplinary in nature, requiring the application of mass sizing, flight mechanics, aerodynamics, aerothermodynamics, thermal analysis, structural analysis, and impact analysis tools. Integration of a multidisciplinary problem is a challenging task; the execution process and data transfer among disciplines should be automated and consistent. This paper describes an integrated analysis tool for the design and sizing of an Earth entry vehicle. The current tool includes the following disciplines: mass sizing, flight mechanics, aerodynamics, aerothermodynamics, and impact analysis tools. Python and Java languages are used for integration. Results are presented and compared with the results from previous studies.

Transmission Planning Analysis Tool

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

2015-06-23

Developed to solve specific problem: Assist transmission planning for regional transfers in interconnected power systems. This work was originated in a study for the U.S. Department of State, to recommend transmission reinforcements for the Central American regional system that interconnects 6 countries. Transmission planning analysis is currently performed by engineers with domainspecific and systemspecific knowledge without a unique methodology. The software codes of this disclosure assists engineers by defining systematic analysis procedures to help identify weak points and make decisions on transmission planning of regional interconnected power systems. Transmission Planning Analysis Tool groups PSS/E results of multiple AC contingency analysismore » and voltage stability analysis and QV analysis of many scenarios of study and arrange them in a systematic way to aid power system planning engineers or transmission operators in effective decision]making process or in the off]line study environment.« less

Challenges Facing Design and Analysis Tools

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr.; Broduer, Steve (Technical Monitor)

2001-01-01

The design and analysis of future aerospace systems will strongly rely on advanced engineering analysis tools used in combination with risk mitigation procedures. The implications of such a trend place increased demands on these tools to assess off-nominal conditions, residual strength, damage propagation, and extreme loading conditions in order to understand and quantify these effects as they affect mission success. Advances in computer hardware such as CPU processing speed, memory, secondary storage, and visualization provide significant resources for the engineer to exploit in engineering design. The challenges facing design and analysis tools fall into three primary areas. The first area involves mechanics needs such as constitutive modeling, contact and penetration simulation, crack growth prediction, damage initiation and progression prediction, transient dynamics and deployment simulations, and solution algorithms. The second area involves computational needs such as fast, robust solvers, adaptivity for model and solution strategies, control processes for concurrent, distributed computing for uncertainty assessments, and immersive technology. Traditional finite element codes still require fast direct solvers which when coupled to current CPU power enables new insight as a result of high-fidelity modeling. The third area involves decision making by the analyst. This area involves the integration and interrogation of vast amounts of information - some global in character while local details are critical and often drive the design. The proposed presentation will describe and illustrate these areas using composite structures, energy-absorbing structures, and inflatable space structures. While certain engineering approximations within the finite element model may be adequate for global response prediction, they generally are inadequate in a design setting or when local response prediction is critical. Pitfalls to be avoided and trends for emerging analysis tools

Using Kepler for Tool Integration in Microarray Analysis Workflows.

PubMed

Gan, Zhuohui; Stowe, Jennifer C; Altintas, Ilkay; McCulloch, Andrew D; Zambon, Alexander C

Increasing numbers of genomic technologies are leading to massive amounts of genomic data, all of which requires complex analysis. More and more bioinformatics analysis tools are being developed by scientist to simplify these analyses. However, different pipelines have been developed using different software environments. This makes integrations of these diverse bioinformatics tools difficult. Kepler provides an open source environment to integrate these disparate packages. Using Kepler, we integrated several external tools including Bioconductor packages, AltAnalyze, a python-based open source tool, and R-based comparison tool to build an automated workflow to meta-analyze both online and local microarray data. The automated workflow connects the integrated tools seamlessly, delivers data flow between the tools smoothly, and hence improves efficiency and accuracy of complex data analyses. Our workflow exemplifies the usage of Kepler as a scientific workflow platform for bioinformatics pipelines.

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.

Bayesian road safety analysis: incorporation of past evidence and effect of hyper-prior choice.

PubMed

Miranda-Moreno, Luis F; Heydari, Shahram; Lord, Dominique; Fu, Liping

2013-09-01

This paper aims to address two related issues when applying hierarchical Bayesian models for road safety analysis, namely: (a) how to incorporate available information from previous studies or past experiences in the (hyper) prior distributions for model parameters and (b) what are the potential benefits of incorporating past evidence on the results of a road safety analysis when working with scarce accident data (i.e., when calibrating models with crash datasets characterized by a very low average number of accidents and a small number of sites). A simulation framework was developed to evaluate the performance of alternative hyper-priors including informative and non-informative Gamma, Pareto, as well as Uniform distributions. Based on this simulation framework, different data scenarios (i.e., number of observations and years of data) were defined and tested using crash data collected at 3-legged rural intersections in California and crash data collected for rural 4-lane highway segments in Texas. This study shows how the accuracy of model parameter estimates (inverse dispersion parameter) is considerably improved when incorporating past evidence, in particular when working with the small number of observations and crash data with low mean. The results also illustrates that when the sample size (more than 100 sites) and the number of years of crash data is relatively large, neither the incorporation of past experience nor the choice of the hyper-prior distribution may affect the final results of a traffic safety analysis. As a potential solution to the problem of low sample mean and small sample size, this paper suggests some practical guidance on how to incorporate past evidence into informative hyper-priors. By combining evidence from past studies and data available, the model parameter estimates can significantly be improved. The effect of prior choice seems to be less important on the hotspot identification. The results show the benefits of incorporating prior

Common Bolted Joint Analysis Tool

NASA Technical Reports Server (NTRS)

Imtiaz, Kauser

2011-01-01

Common Bolted Joint Analysis Tool (comBAT) is an Excel/VB-based bolted joint analysis/optimization program that lays out a systematic foundation for an inexperienced or seasoned analyst to determine fastener size, material, and assembly torque for a given design. Analysts are able to perform numerous what-if scenarios within minutes to arrive at an optimal solution. The program evaluates input design parameters, performs joint assembly checks, and steps through numerous calculations to arrive at several key margins of safety for each member in a joint. It also checks for joint gapping, provides fatigue calculations, and generates joint diagrams for a visual reference. Optimum fastener size and material, as well as correct torque, can then be provided. Analysis methodology, equations, and guidelines are provided throughout the solution sequence so that this program does not become a "black box:" for the analyst. There are built-in databases that reduce the legwork required by the analyst. Each step is clearly identified and results are provided in number format, as well as color-coded spelled-out words to draw user attention. The three key features of the software are robust technical content, innovative and user friendly I/O, and a large database. The program addresses every aspect of bolted joint analysis and proves to be an instructional tool at the same time. It saves analysis time, has intelligent messaging features, and catches operator errors in real time.

RSAT 2015: Regulatory Sequence Analysis Tools.

PubMed

Medina-Rivera, Alejandra; Defrance, Matthieu; Sand, Olivier; Herrmann, Carl; Castro-Mondragon, Jaime A; Delerce, Jeremy; Jaeger, Sébastien; Blanchet, Christophe; Vincens, Pierre; Caron, Christophe; Staines, Daniel M; Contreras-Moreira, Bruno; Artufel, Marie; Charbonnier-Khamvongsa, Lucie; Hernandez, Céline; Thieffry, Denis; Thomas-Chollier, Morgane; van Helden, Jacques

2015-07-01

RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative genomics and (iv) analysis of regulatory variations. Nine new programs have been added to the 43 described in the 2011 NAR Web Software Issue, including a tool to extract sequences from a list of coordinates (fetch-sequences from UCSC), novel programs dedicated to the analysis of regulatory variants from GWAS or population genomics (retrieve-variation-seq and variation-scan), a program to cluster motifs and visualize the similarities as trees (matrix-clustering). To deal with the drastic increase of sequenced genomes, RSAT public sites have been reorganized into taxon-specific servers. The suite is well-documented with tutorials and published protocols. The software suite is available through Web sites, SOAP/WSDL Web services, virtual machines and stand-alone programs at http://www.rsat.eu/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures

PubMed Central

2013-01-01

Background The use of Gene Ontology (GO) data in protein analyses have largely contributed to the improved outcomes of these analyses. Several GO semantic similarity measures have been proposed in recent years and provide tools that allow the integration of biological knowledge embedded in the GO structure into different biological analyses. There is a need for a unified tool that provides the scientific community with the opportunity to explore these different GO similarity measure approaches and their biological applications. Results We have developed DaGO-Fun, an online tool available at http://web.cbio.uct.ac.za/ITGOM, which incorporates many different GO similarity measures for exploring, analyzing and comparing GO terms and proteins within the context of GO. It uses GO data and UniProt proteins with their GO annotations as provided by the Gene Ontology Annotation (GOA) project to precompute GO term information content (IC), enabling rapid response to user queries. Conclusions The DaGO-Fun online tool presents the advantage of integrating all the relevant IC-based GO similarity measures, including topology- and annotation-based approaches to facilitate effective exploration of these measures, thus enabling users to choose the most relevant approach for their application. Furthermore, this tool includes several biological applications related to GO semantic similarity scores, including the retrieval of genes based on their GO annotations, the clustering of functionally related genes within a set, and term enrichment analysis. PMID:24067102

VStar: Variable star data visualization and analysis tool

NASA Astrophysics Data System (ADS)

VStar Team

2014-07-01

VStar is a multi-platform, easy-to-use variable star data visualization and analysis tool. Data for a star can be read from the AAVSO (American Association of Variable Star Observers) database or from CSV and TSV files. VStar displays light curves and phase plots, can produce a mean curve, and analyzes time-frequency with Weighted Wavelet Z-Transform. It offers tools for period analysis, filtering, and other functions.

Water Quality Analysis Tool (WQAT)

EPA Science Inventory

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-pro...

Tools for Large-Scale Mobile Malware Analysis

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

Bierma, Michael

Analyzing mobile applications for malicious behavior is an important area of re- search, and is made di cult, in part, by the increasingly large number of appli- cations available for the major operating systems. There are currently over 1.2 million apps available in both the Google Play and Apple App stores (the respec- tive o cial marketplaces for the Android and iOS operating systems)[1, 2]. Our research provides two large-scale analysis tools to aid in the detection and analysis of mobile malware. The rst tool we present, Andlantis, is a scalable dynamic analysis system capa- ble of processing over 3000more » Android applications per hour. Traditionally, Android dynamic analysis techniques have been relatively limited in scale due to the compu- tational resources required to emulate the full Android system to achieve accurate execution. Andlantis is the most scalable Android dynamic analysis framework to date, and is able to collect valuable forensic data, which helps reverse-engineers and malware researchers identify and understand anomalous application behavior. We discuss the results of running 1261 malware samples through the system, and provide examples of malware analysis performed with the resulting data. While techniques exist to perform static analysis on a large number of appli- cations, large-scale analysis of iOS applications has been relatively small scale due to the closed nature of the iOS ecosystem, and the di culty of acquiring appli- cations for analysis. The second tool we present, iClone, addresses the challenges associated with iOS research in order to detect application clones within a dataset of over 20,000 iOS applications.« less

Spreadsheet-based engine data analysis tool - user's guide.

DOT National Transportation Integrated Search

2016-07-01

This record refers to both the spreadsheet tool - Fleet Equipment Performance Measurement Preventive Maintenance Model: Spreadsheet-Based Engine Data Analysis Tool, http://ntl.bts.gov/lib/60000/60000/60007/0-6626-P1_Final.xlsm - and its accompanying ...

Spacecraft Electrical Power System (EPS) generic analysis tools and techniques

NASA Technical Reports Server (NTRS)

Morris, Gladys M.; Sheppard, Mark A.

1992-01-01

An overview is provided of the analysis tools and techiques used in modeling the Space Station Freedom electrical power system, as well as future space vehicle power systems. The analysis capabilities of the Electrical Power System (EPS) are described and the EPS analysis tools are surveyed.

Open Source Tools for Seismicity Analysis

NASA Astrophysics Data System (ADS)

Powers, P.

2010-12-01

The spatio-temporal analysis of seismicity plays an important role in earthquake forecasting and is integral to research on earthquake interactions and triggering. For instance, the third version of the Uniform California Earthquake Rupture Forecast (UCERF), currently under development, will use Epidemic Type Aftershock Sequences (ETAS) as a model for earthquake triggering. UCERF will be a "living" model and therefore requires robust, tested, and well-documented ETAS algorithms to ensure transparency and reproducibility. Likewise, as earthquake aftershock sequences unfold, real-time access to high quality hypocenter data makes it possible to monitor the temporal variability of statistical properties such as the parameters of the Omori Law and the Gutenberg Richter b-value. Such statistical properties are valuable as they provide a measure of how much a particular sequence deviates from expected behavior and can be used when assigning probabilities of aftershock occurrence. To address these demands and provide public access to standard methods employed in statistical seismology, we present well-documented, open-source JavaScript and Java software libraries for the on- and off-line analysis of seismicity. The Javascript classes facilitate web-based asynchronous access to earthquake catalog data and provide a framework for in-browser display, analysis, and manipulation of catalog statistics; implementations of this framework will be made available on the USGS Earthquake Hazards website. The Java classes, in addition to providing tools for seismicity analysis, provide tools for modeling seismicity and generating synthetic catalogs. These tools are extensible and will be released as part of the open-source OpenSHA Commons library.

A Vision for Incorporating Environmental Effects into Nitrogen Management Decision Support Tools for U.S. Maize Production

PubMed Central

Banger, Kamaljit; Yuan, Mingwei; Wang, Junming; Nafziger, Emerson D.; Pittelkow, Cameron M.

2017-01-01

Meeting crop nitrogen (N) demand while minimizing N losses to the environment has proven difficult despite significant field research and modeling efforts. To improve N management, several real-time N management tools have been developed with a primary focus on enhancing crop production. However, no coordinated effort exists to simultaneously address sustainability concerns related to N losses at field- and regional-scales. In this perspective, we highlight the opportunity for incorporating environmental effects into N management decision support tools for United States maize production systems by integrating publicly available crop models with grower-entered management information and gridded soil and climate data in a geospatial framework specifically designed to quantify environmental and crop production tradeoffs. To facilitate advances in this area, we assess the capability of existing crop models to provide in-season N recommendations while estimating N leaching and nitrous oxide emissions, discuss several considerations for initial framework development, and highlight important challenges related to improving the accuracy of crop model predictions. Such a framework would benefit the development of regional sustainable intensification strategies by enabling the identification of N loss hotspots which could be used to implement spatially explicit mitigation efforts in relation to current environmental quality goals and real-time weather conditions. Nevertheless, we argue that this long-term vision can only be realized by leveraging a variety of existing research efforts to overcome challenges related to improving model structure, accessing field data to enhance model performance, and addressing the numerous social difficulties in delivery and adoption of such tool by stakeholders. PMID:28804490

A Vision for Incorporating Environmental Effects into Nitrogen Management Decision Support Tools for U.S. Maize Production.

PubMed

Banger, Kamaljit; Yuan, Mingwei; Wang, Junming; Nafziger, Emerson D; Pittelkow, Cameron M

2017-01-01

Meeting crop nitrogen (N) demand while minimizing N losses to the environment has proven difficult despite significant field research and modeling efforts. To improve N management, several real-time N management tools have been developed with a primary focus on enhancing crop production. However, no coordinated effort exists to simultaneously address sustainability concerns related to N losses at field- and regional-scales. In this perspective, we highlight the opportunity for incorporating environmental effects into N management decision support tools for United States maize production systems by integrating publicly available crop models with grower-entered management information and gridded soil and climate data in a geospatial framework specifically designed to quantify environmental and crop production tradeoffs. To facilitate advances in this area, we assess the capability of existing crop models to provide in-season N recommendations while estimating N leaching and nitrous oxide emissions, discuss several considerations for initial framework development, and highlight important challenges related to improving the accuracy of crop model predictions. Such a framework would benefit the development of regional sustainable intensification strategies by enabling the identification of N loss hotspots which could be used to implement spatially explicit mitigation efforts in relation to current environmental quality goals and real-time weather conditions. Nevertheless, we argue that this long-term vision can only be realized by leveraging a variety of existing research efforts to overcome challenges related to improving model structure, accessing field data to enhance model performance, and addressing the numerous social difficulties in delivery and adoption of such tool by stakeholders.

Structured Analysis and the Data Flow Diagram: Tools for Library Analysis.

ERIC Educational Resources Information Center

Carlson, David H.

1986-01-01

This article discusses tools developed to aid the systems analysis process (program evaluation and review technique, Gantt charts, organizational charts, decision tables, flowcharts, hierarchy plus input-process-output). Similarities and differences among techniques, library applications of analysis, structured systems analysis, and the data flow…

General Mission Analysis Tool (GMAT) Mathematical Specifications

NASA Technical Reports Server (NTRS)

Hughes, Steve

2007-01-01

The General Mission Analysis Tool (GMAT) is a space trajectory optimization and mission analysis system developed by NASA and private industry in the spirit of the NASA Mission. GMAT contains new technology and is a testbed for future technology development.

Deliberate teaching tools for clinical teaching encounters: A critical scoping review and thematic analysis to establish definitional clarity.

PubMed

Sidhu, Navdeep S; Edwards, Morgan

2018-04-27

We conducted a scoping review of tools designed to add structure to clinical teaching, with a thematic analysis to establish definitional clarity. Six thousand and forty nine citations were screened, 434 reviewed for eligibility, and 230 identified as meeting study inclusion criteria. Eighty-nine names and 51 definitions were identified. Based on a post facto thematic analysis, we propose that these tools be named "deliberate teaching tools" (DTTs) and defined as "frameworks that enable clinicians to have a purposeful and considered approach to teaching encounters by incorporating elements identified with good teaching practice." We identified 46 DTTs in the literature, with 38 (82.6%) originally described for the medical setting. Forty justification articles consisted of 16 feedback surveys, 13 controlled trials, seven pre-post intervention studies with no control group, and four observation studies. Current evidence of efficacy is not entirely conclusive, and many studies contain methodology flaws. Forty-nine clarification articles comprised 12 systematic reviews and 37 narrative reviews. The most number of DTTs described by any review was four. A common design theme was identified in approximately three-quarters of DTTs. Applicability of DTTs to specific alternate settings should be considered in context, and appropriately designed justification studies are warranted to demonstrate efficacy.

A Multidimensional Analysis Tool for Visualizing Online Interactions

ERIC Educational Resources Information Center

Kim, Minjeong; Lee, Eunchul

2012-01-01

This study proposes and verifies the performance of an analysis tool for visualizing online interactions. A review of the most widely used methods for analyzing online interactions, including quantitative analysis, content analysis, and social network analysis methods, indicates these analysis methods have some limitations resulting from their…

Charming the Snake: Student Experiences with Python Programming as a Data Analysis Tool

NASA Astrophysics Data System (ADS)

Booker, Melissa; Ivers, C. B.; Piper, M.; Powers, L.; Ali, B.

2014-01-01

During the past year, twelve high school students and one undergraduate student participated in the NASA/IPAC Teacher Archive Research Program (NITARP) alongside three high school educators and one informal educator, gaining experience in using Python as a tool for analyzing the vast amount of photometry data available from the Herschel and Spitzer telescopes in the NGC 281 region. Use of Python appeared to produce two main positive gains: (1) a gain in student ability to successfully write and execute Python programs for the bulk analysis of data, and (2) a change in their perceptions of the utility of computer programming and of the students’ abilities to use programming to solve problems. We outline the trials, tribulations, successes, and failures of the teachers and students through this learning exercise and provide some recommendations for incorporating programming in scientific learning.

Designed tools for analysis of lithography patterns and nanostructures

NASA Astrophysics Data System (ADS)

Dervillé, Alexandre; Baderot, Julien; Bernard, Guilhem; Foucher, Johann; Grönqvist, Hanna; Labrosse, Aurélien; Martinez, Sergio; Zimmermann, Yann

2017-03-01

We introduce a set of designed tools for the analysis of lithography patterns and nano structures. The classical metrological analysis of these objects has the drawbacks of being time consuming, requiring manual tuning and lacking robustness and user friendliness. With the goal of improving the current situation, we propose new image processing tools at different levels: semi automatic, automatic and machine-learning enhanced tools. The complete set of tools has been integrated into a software platform designed to transform the lab into a virtual fab. The underlying idea is to master nano processes at the research and development level by accelerating the access to knowledge and hence speed up the implementation in product lines.

Analysis Tools in Geant4 10.2 and 10.3

NASA Astrophysics Data System (ADS)

Hřivnáčová, I.; Barrand, G.

2017-10-01

A new analysis category based on g4tools was added in Geant4 release 9.5 (2011). The aim was to provide users with a lightweight analysis tool available as part of the Geant4 installation without the need to link to an external analysis package. It has progressively been included in all Geant4 examples. Frequent questions in the Geant4 users forum show its increasing popularity in the Geant4 users community. In this presentation, we will give a brief overview of g4tools and the analysis category. We report on new developments since our CHEP 2013 contribution as well as mention upcoming new features.

Development of guidance for states transitioning to new safety analysis tools

NASA Astrophysics Data System (ADS)

Alluri, Priyanka

With about 125 people dying on US roads each day, the US Department of Transportation heightened the awareness of critical safety issues with the passage of SAFETEA-LU (Safe Accountable Flexible Efficient Transportation Equity Act---a Legacy for Users) legislation in 2005. The legislation required each of the states to develop a Strategic Highway Safety Plan (SHSP) and incorporate data-driven approaches to prioritize and evaluate program outcomes: Failure to do so resulted in funding sanctioning. In conjunction with the legislation, research efforts have also been progressing toward the development of new safety analysis tools such as IHSDM (Interactive Highway Safety Design Model), SafetyAnalyst, and HSM (Highway Safety Manual). These software and analysis tools are comparatively more advanced in statistical theory and level of accuracy, and have a tendency to be more data intensive. A review of the 2009 five-percent reports and excerpts from the nationwide survey revealed astonishing facts about the continuing use of traditional methods including crash frequencies and rates for site selection and prioritization. The intense data requirements and statistical complexity of advanced safety tools are considered as a hindrance to their adoption. In this context, this research aims at identifying the data requirements and data availability for SafetyAnalyst and HSM by working with both the tools. This research sets the stage for working with the Empirical Bayes approach by highlighting some of the biases and issues associated with the traditional methods of selecting projects such as greater emphasis on traffic volume and regression-to-mean phenomena. Further, the not-so-obvious issue with shorter segment lengths, which effect the results independent of the methods used, is also discussed. The more reliable and statistically acceptable Empirical Bayes methodology requires safety performance functions (SPFs), regression equations predicting the relation between crashes

A Software Tool for Integrated Optical Design Analysis

NASA Technical Reports Server (NTRS)

Moore, Jim; Troy, Ed; DePlachett, Charles; Montgomery, Edward (Technical Monitor)

2001-01-01

Design of large precision optical systems requires multi-disciplinary analysis, modeling, and design. Thermal, structural and optical characteristics of the hardware must be accurately understood in order to design a system capable of accomplishing the performance requirements. The interactions between each of the disciplines become stronger as systems are designed lighter weight for space applications. This coupling dictates a concurrent engineering design approach. In the past, integrated modeling tools have been developed that attempt to integrate all of the complex analysis within the framework of a single model. This often results in modeling simplifications and it requires engineering specialist to learn new applications. The software described in this presentation addresses the concurrent engineering task using a different approach. The software tool, Integrated Optical Design Analysis (IODA), uses data fusion technology to enable a cross discipline team of engineering experts to concurrently design an optical system using their standard validated engineering design tools.

Traffic analysis toolbox volume XI : weather and traffic analysis, modeling and simulation.

DOT National Transportation Integrated Search

2010-12-01

This document presents a weather module for the traffic analysis tools program. It provides traffic engineers, transportation modelers and decisions makers with a guide that can incorporate weather impacts into transportation system analysis and mode...

LinkedIn as a Learning Tool in Business Education

ERIC Educational Resources Information Center

Cooper, Brett; Naatus, Mary Kate

2014-01-01

This article summarizes the existing research on social media as a learning tool in higher education and adds to the literature on incorporating social media tools into collegiate business education by suggesting specific course content areas of business where LinkedIn exercises and training can be incorporated. LinkedIn as a classroom tool cannot…

Applying AI tools to operational space environmental analysis

NASA Technical Reports Server (NTRS)

Krajnak, Mike; Jesse, Lisa; Mucks, John

1995-01-01

The U.S. Air Force and National Oceanic Atmospheric Agency (NOAA) space environmental operations centers are facing increasingly complex challenges meeting the needs of their growing user community. These centers provide current space environmental information and short term forecasts of geomagnetic activity. Recent advances in modeling and data access have provided sophisticated tools for making accurate and timely forecasts, but have introduced new problems associated with handling and analyzing large quantities of complex data. AI (Artificial Intelligence) techniques have been considered as potential solutions to some of these problems. Fielding AI systems has proven more difficult than expected, in part because of operational constraints. Using systems which have been demonstrated successfully in the operational environment will provide a basis for a useful data fusion and analysis capability. Our approach uses a general purpose AI system already in operational use within the military intelligence community, called the Temporal Analysis System (TAS). TAS is an operational suite of tools supporting data processing, data visualization, historical analysis, situation assessment and predictive analysis. TAS includes expert system tools to analyze incoming events for indications of particular situations and predicts future activity. The expert system operates on a knowledge base of temporal patterns encoded using a knowledge representation called Temporal Transition Models (TTM's) and an event database maintained by the other TAS tools. The system also includes a robust knowledge acquisition and maintenance tool for creating TTM's using a graphical specification language. The ability to manipulate TTM's in a graphical format gives non-computer specialists an intuitive way of accessing and editing the knowledge base. To support space environmental analyses, we used TAS's ability to define domain specific event analysis abstractions. The prototype system defines

Integrative analysis of transcriptomic and metabolomic data via sparse canonical correlation analysis with incorporation of biological information.

PubMed

Safo, Sandra E; Li, Shuzhao; Long, Qi

2018-03-01

Integrative analysis of high dimensional omics data is becoming increasingly popular. At the same time, incorporating known functional relationships among variables in analysis of omics data has been shown to help elucidate underlying mechanisms for complex diseases. In this article, our goal is to assess association between transcriptomic and metabolomic data from a Predictive Health Institute (PHI) study that includes healthy adults at a high risk of developing cardiovascular diseases. Adopting a strategy that is both data-driven and knowledge-based, we develop statistical methods for sparse canonical correlation analysis (CCA) with incorporation of known biological information. Our proposed methods use prior network structural information among genes and among metabolites to guide selection of relevant genes and metabolites in sparse CCA, providing insight on the molecular underpinning of cardiovascular disease. Our simulations demonstrate that the structured sparse CCA methods outperform several existing sparse CCA methods in selecting relevant genes and metabolites when structural information is informative and are robust to mis-specified structural information. Our analysis of the PHI study reveals that a number of gene and metabolic pathways including some known to be associated with cardiovascular diseases are enriched in the set of genes and metabolites selected by our proposed approach. © 2017, The International Biometric Society.

RSAT 2018: regulatory sequence analysis tools 20th anniversary.

PubMed

Nguyen, Nga Thi Thuy; Contreras-Moreira, Bruno; Castro-Mondragon, Jaime A; Santana-Garcia, Walter; Ossio, Raul; Robles-Espinoza, Carla Daniela; Bahin, Mathieu; Collombet, Samuel; Vincens, Pierre; Thieffry, Denis; van Helden, Jacques; Medina-Rivera, Alejandra; Thomas-Chollier, Morgane

2018-05-02

RSAT (Regulatory Sequence Analysis Tools) is a suite of modular tools for the detection and the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, including from genome-wide datasets like ChIP-seq/ATAC-seq, (ii) motif scanning, (iii) motif analysis (quality assessment, comparisons and clustering), (iv) analysis of regulatory variations, (v) comparative genomics. Six public servers jointly support 10 000 genomes from all kingdoms. Six novel or refactored programs have been added since the 2015 NAR Web Software Issue, including updated programs to analyse regulatory variants (retrieve-variation-seq, variation-scan, convert-variations), along with tools to extract sequences from a list of coordinates (retrieve-seq-bed), to select motifs from motif collections (retrieve-matrix), and to extract orthologs based on Ensembl Compara (get-orthologs-compara). Three use cases illustrate the integration of new and refactored tools to the suite. This Anniversary update gives a 20-year perspective on the software suite. RSAT is well-documented and available through Web sites, SOAP/WSDL (Simple Object Access Protocol/Web Services Description Language) web services, virtual machines and stand-alone programs at http://www.rsat.eu/.

IPMP Global Fit - A one-step direct data analysis tool for predictive microbiology.

PubMed

Huang, Lihan

2017-12-04

The objective of this work is to develop and validate a unified optimization algorithm for performing one-step global regression analysis of isothermal growth and survival curves for determination of kinetic parameters in predictive microbiology. The algorithm is incorporated with user-friendly graphical interfaces (GUIs) to develop a data analysis tool, the USDA IPMP-Global Fit. The GUIs are designed to guide the users to easily navigate through the data analysis process and properly select the initial parameters for different combinations of mathematical models. The software is developed for one-step kinetic analysis to directly construct tertiary models by minimizing the global error between the experimental observations and mathematical models. The current version of the software is specifically designed for constructing tertiary models with time and temperature as the independent model parameters in the package. The software is tested with a total of 9 different combinations of primary and secondary models for growth and survival of various microorganisms. The results of data analysis show that this software provides accurate estimates of kinetic parameters. In addition, it can be used to improve the experimental design and data collection for more accurate estimation of kinetic parameters. IPMP-Global Fit can be used in combination with the regular USDA-IPMP for solving the inverse problems and developing tertiary models in predictive microbiology. Published by Elsevier B.V.

Tools for T-RFLP data analysis using Excel.

PubMed

Fredriksson, Nils Johan; Hermansson, Malte; Wilén, Britt-Marie

2014-11-08

Terminal restriction fragment length polymorphism (T-RFLP) analysis is a DNA-fingerprinting method that can be used for comparisons of the microbial community composition in a large number of samples. There is no consensus on how T-RFLP data should be treated and analyzed before comparisons between samples are made, and several different approaches have been proposed in the literature. The analysis of T-RFLP data can be cumbersome and time-consuming, and for large datasets manual data analysis is not feasible. The currently available tools for automated T-RFLP analysis, although valuable, offer little flexibility, and few, if any, options regarding what methods to use. To enable comparisons and combinations of different data treatment methods an analysis template and an extensive collection of macros for T-RFLP data analysis using Microsoft Excel were developed. The Tools for T-RFLP data analysis template provides procedures for the analysis of large T-RFLP datasets including application of a noise baseline threshold and setting of the analysis range, normalization and alignment of replicate profiles, generation of consensus profiles, normalization and alignment of consensus profiles and final analysis of the samples including calculation of association coefficients and diversity index. The procedures are designed so that in all analysis steps, from the initial preparation of the data to the final comparison of the samples, there are various different options available. The parameters regarding analysis range, noise baseline, T-RF alignment and generation of consensus profiles are all given by the user and several different methods are available for normalization of the T-RF profiles. In each step, the user can also choose to base the calculations on either peak height data or peak area data. The Tools for T-RFLP data analysis template enables an objective and flexible analysis of large T-RFLP datasets in a widely used spreadsheet application.

LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights

PubMed Central

Dong, Xinran; Hao, Yun; Wang, Xiao; Tian, Weidong

2016-01-01

Pathway or gene set over-representation analysis (ORA) has become a routine task in functional genomics studies. However, currently widely used ORA tools employ statistical methods such as Fisher’s exact test that reduce a pathway into a list of genes, ignoring the constitutive functional non-equivalent roles of genes and the complex gene-gene interactions. Here, we develop a novel method named LEGO (functional Link Enrichment of Gene Ontology or gene sets) that takes into consideration these two types of information by incorporating network-based gene weights in ORA analysis. In three benchmarks, LEGO achieves better performance than Fisher and three other network-based methods. To further evaluate LEGO’s usefulness, we compare LEGO with five gene expression-based and three pathway topology-based methods using a benchmark of 34 disease gene expression datasets compiled by a recent publication, and show that LEGO is among the top-ranked methods in terms of both sensitivity and prioritization for detecting target KEGG pathways. In addition, we develop a cluster-and-filter approach to reduce the redundancy among the enriched gene sets, making the results more interpretable to biologists. Finally, we apply LEGO to two lists of autism genes, and identify relevant gene sets to autism that could not be found by Fisher. PMID:26750448

LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights.

PubMed

Dong, Xinran; Hao, Yun; Wang, Xiao; Tian, Weidong

2016-01-11

Pathway or gene set over-representation analysis (ORA) has become a routine task in functional genomics studies. However, currently widely used ORA tools employ statistical methods such as Fisher's exact test that reduce a pathway into a list of genes, ignoring the constitutive functional non-equivalent roles of genes and the complex gene-gene interactions. Here, we develop a novel method named LEGO (functional Link Enrichment of Gene Ontology or gene sets) that takes into consideration these two types of information by incorporating network-based gene weights in ORA analysis. In three benchmarks, LEGO achieves better performance than Fisher and three other network-based methods. To further evaluate LEGO's usefulness, we compare LEGO with five gene expression-based and three pathway topology-based methods using a benchmark of 34 disease gene expression datasets compiled by a recent publication, and show that LEGO is among the top-ranked methods in terms of both sensitivity and prioritization for detecting target KEGG pathways. In addition, we develop a cluster-and-filter approach to reduce the redundancy among the enriched gene sets, making the results more interpretable to biologists. Finally, we apply LEGO to two lists of autism genes, and identify relevant gene sets to autism that could not be found by Fisher.

System Analysis Applied to Autonomy: Application to High-Altitude Long-Endurance Remotely Operated Aircraft

NASA Technical Reports Server (NTRS)

Young, Larry A.; Yetter, Jeffrey A.; Guynn, Mark D.

2006-01-01

Maturation of intelligent systems technologies and their incorporation into aerial platforms are dictating the development of new analysis tools and incorporation of such tools into existing system analysis methodologies in order to fully capture the trade-offs of autonomy on vehicle and mission success. A first-order "system analysis of autonomy" methodology is outlined in this paper. Further, this analysis methodology is subsequently applied to notional high-altitude long-endurance (HALE) aerial vehicle missions.

Rapid Modeling and Analysis Tools: Evolution, Status, Needs and Directions

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr.; Stone, Thomas J.; Ransom, Jonathan B. (Technical Monitor)

2002-01-01

Advanced aerospace systems are becoming increasingly more complex, and customers are demanding lower cost, higher performance, and high reliability. Increased demands are placed on the design engineers to collaborate and integrate design needs and objectives early in the design process to minimize risks that may occur later in the design development stage. High performance systems require better understanding of system sensitivities much earlier in the design process to meet these goals. The knowledge, skills, intuition, and experience of an individual design engineer will need to be extended significantly for the next generation of aerospace system designs. Then a collaborative effort involving the designer, rapid and reliable analysis tools and virtual experts will result in advanced aerospace systems that are safe, reliable, and efficient. This paper discusses the evolution, status, needs and directions for rapid modeling and analysis tools for structural analysis. First, the evolution of computerized design and analysis tools is briefly described. Next, the status of representative design and analysis tools is described along with a brief statement on their functionality. Then technology advancements to achieve rapid modeling and analysis are identified. Finally, potential future directions including possible prototype configurations are proposed.

Dipole estimation errors due to not incorporating anisotropic conductivities in realistic head models for EEG source analysis

NASA Astrophysics Data System (ADS)

Hallez, Hans; Staelens, Steven; Lemahieu, Ignace

2009-10-01

EEG source analysis is a valuable tool for brain functionality research and for diagnosing neurological disorders, such as epilepsy. It requires a geometrical representation of the human head or a head model, which is often modeled as an isotropic conductor. However, it is known that some brain tissues, such as the skull or white matter, have an anisotropic conductivity. Many studies reported that the anisotropic conductivities have an influence on the calculated electrode potentials. However, few studies have assessed the influence of anisotropic conductivities on the dipole estimations. In this study, we want to determine the dipole estimation errors due to not taking into account the anisotropic conductivities of the skull and/or brain tissues. Therefore, head models are constructed with the same geometry, but with an anisotropically conducting skull and/or brain tissue compartment. These head models are used in simulation studies where the dipole location and orientation error is calculated due to neglecting anisotropic conductivities of the skull and brain tissue. Results show that not taking into account the anisotropic conductivities of the skull yields a dipole location error between 2 and 25 mm, with an average of 10 mm. When the anisotropic conductivities of the brain tissues are neglected, the dipole location error ranges between 0 and 5 mm. In this case, the average dipole location error was 2.3 mm. In all simulations, the dipole orientation error was smaller than 10°. We can conclude that the anisotropic conductivities of the skull have to be incorporated to improve the accuracy of EEG source analysis. The results of the simulation, as presented here, also suggest that incorporation of the anisotropic conductivities of brain tissues is not necessary. However, more studies are needed to confirm these suggestions.

Porcupine: A visual pipeline tool for neuroimaging analysis

PubMed Central

Snoek, Lukas; Knapen, Tomas

2018-01-01

The field of neuroimaging is rapidly adopting a more reproducible approach to data acquisition and analysis. Data structures and formats are being standardised and data analyses are getting more automated. However, as data analysis becomes more complicated, researchers often have to write longer analysis scripts, spanning different tools across multiple programming languages. This makes it more difficult to share or recreate code, reducing the reproducibility of the analysis. We present a tool, Porcupine, that constructs one’s analysis visually and automatically produces analysis code. The graphical representation improves understanding of the performed analysis, while retaining the flexibility of modifying the produced code manually to custom needs. Not only does Porcupine produce the analysis code, it also creates a shareable environment for running the code in the form of a Docker image. Together, this forms a reproducible way of constructing, visualising and sharing one’s analysis. Currently, Porcupine links to Nipype functionalities, which in turn accesses most standard neuroimaging analysis tools. Our goal is to release researchers from the constraints of specific implementation details, thereby freeing them to think about novel and creative ways to solve a given problem. Porcupine improves the overview researchers have of their processing pipelines, and facilitates both the development and communication of their work. This will reduce the threshold at which less expert users can generate reusable pipelines. With Porcupine, we bridge the gap between a conceptual and an implementational level of analysis and make it easier for researchers to create reproducible and shareable science. We provide a wide range of examples and documentation, as well as installer files for all platforms on our website: https://timvanmourik.github.io/Porcupine. Porcupine is free, open source, and released under the GNU General Public License v3.0. PMID:29746461

Enhancement of bronze alloy surface properties by FSP second-phase particle incorporation

DOE PAGES

Ajayi, O. O.; Lorenzo-Martin, Cinta

2017-06-15

This study presents results of an experimental study to evaluate friction stir processing (FSP) with and without hard second-phase particle incorporation as a means to enhance surface properties and wear performance of C86300 manganese bronze alloy. FSP of flat bronze alloy specimens was conducted with hardened H-13 tool steel to create a 3-mm-thick processed surface layer. The process was also used to incorporate B 4C particles, thereby creating a metal-matrix composite layer on the alloy surface. FSP alone was observed to produce substantial reduction in grain size (from an initial value of 350 mu m to 1-5 μm). FSP withoutmore » particle incorporation resulted in modest surface hardening due to grain refinement and dispersion hardening. Under lubricated contact in block-on-ring testing with a hardened steel counter face, FSP produced substantial reduction (about 3X) in bronze wear after polishing of processing surface roughening. FSP with hard B 4C second-phase particle incorporation further reduced wear by up to 20X. The improvement in wear behavior is attributed to grain refinement and load shielding by second-phase particles, as determined by wear mechanism analysis.« less

The prevention of mother-to-child transmission of HIV cascade analysis tool: supporting health managers to improve facility-level service delivery.

PubMed

Gimbel, Sarah; Voss, Joachim; Mercer, Mary Anne; Zierler, Brenda; Gloyd, Stephen; Coutinho, Maria de Joana; Floriano, Florencia; Cuembelo, Maria de Fatima; Einberg, Jennifer; Sherr, Kenneth

2014-10-21

The objective of the prevention of Mother-to-Child Transmission (pMTCT) cascade analysis tool is to provide frontline health managers at the facility level with the means to rapidly, independently and quantitatively track patient flows through the pMTCT cascade, and readily identify priority areas for clinic-level improvement interventions. Over a period of six months, five experienced maternal-child health managers and researchers iteratively adapted and tested this systems analysis tool for pMTCT services. They prioritized components of the pMTCT cascade for inclusion, disseminated multiple versions to 27 health managers and piloted it in five facilities. Process mapping techniques were used to chart PMTCT cascade steps in these five facilities, to document antenatal care attendance, HIV testing and counseling, provision of prophylactic anti-retrovirals, safe delivery, safe infant feeding, infant follow-up including HIV testing, and family planning, in order to obtain site-specific knowledge of service delivery. Seven pMTCT cascade steps were included in the Excel-based final tool. Prevalence calculations were incorporated as sub-headings under relevant steps. Cells not requiring data inputs were locked, wording was simplified and stepwise drop-offs and maximization functions were included at key steps along the cascade. While the drop off function allows health workers to rapidly assess how many patients were lost at each step, the maximization function details the additional people served if only one step improves to 100% capacity while others stay constant. Our experience suggests that adaptation of a cascade analysis tool for facility-level pMTCT services is feasible and appropriate as a starting point for discussions of where to implement improvement strategies. The resulting tool facilitates the engagement of frontline health workers and managers who fill out, interpret, apply the tool, and then follow up with quality improvement activities. Research on

Tool Efficiency Analysis model research in SEMI industry

NASA Astrophysics Data System (ADS)

Lei, Ma; Nana, Zhang; Zhongqiu, Zhang

2018-06-01

One of the key goals in SEMI industry is to improve equipment through put and ensure equipment production efficiency maximization. This paper is based on SEMI standards in semiconductor equipment control, defines the transaction rules between different tool states, and presents a TEA system model which is to analysis tool performance automatically based on finite state machine. The system was applied to fab tools and verified its effectiveness successfully, and obtained the parameter values used to measure the equipment performance, also including the advices of improvement.

Incorporation of a health economic modelling tool into public health commissioning: Evidence use in a politicised context.

PubMed

Sanders, Tom; Grove, Amy; Salway, Sarah; Hampshaw, Susan; Goyder, Elizabeth

2017-08-01

This paper explores how commissioners working in an English local government authority (LA) viewed a health economic decision tool for planning services in relation to diabetes. We conducted 15 interviews and 2 focus groups between July 2015 and February 2016, with commissioners (including public health managers, data analysts and council members). Two overlapping themes were identified explaining the obstacles and enablers of using such a tool in commissioning: a) evidence cultures, and b) system interdependency. The former highlighted the diverse evidence cultures present in the LA with politicians influenced by the 'soft' social care agendas affecting their local population and treating local opinion as evidence, whilst public health managers prioritised the scientific view of evidence informed by research. System interdependency further complicated the decision making process by recognizing interlinking with departments and other disease groups. To achieve legitimacy within the commissioning arena health economic modelling needs to function effectively in a highly politicised environment where decisions are made not only on the basis of research evidence, but on grounds of 'soft' data, personal opinion and intelligence. In this context decisions become politicised, with multiple opinions seeking a voice. The way that such decisions are negotiated and which ones establish authority is of importance. We analyse the data using Larson's (1990) discursive field concept to show how the tool becomes an object of research push and pull likely to be used instrumentally by stakeholders to advance specific agendas, not a means of informing complex decisions. In conclusion, LA decision making is underpinned by a transactional business ethic which is a further potential 'pull' mechanism for the incorporation of health economic modelling in local commissioning. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Common features of microRNA target prediction tools

PubMed Central

Peterson, Sarah M.; Thompson, Jeffrey A.; Ufkin, Melanie L.; Sathyanarayana, Pradeep; Liaw, Lucy; Congdon, Clare Bates

2014-01-01

The human genome encodes for over 1800 microRNAs (miRNAs), which are short non-coding RNA molecules that function to regulate gene expression post-transcriptionally. Due to the potential for one miRNA to target multiple gene transcripts, miRNAs are recognized as a major mechanism to regulate gene expression and mRNA translation. Computational prediction of miRNA targets is a critical initial step in identifying miRNA:mRNA target interactions for experimental validation. The available tools for miRNA target prediction encompass a range of different computational approaches, from the modeling of physical interactions to the incorporation of machine learning. This review provides an overview of the major computational approaches to miRNA target prediction. Our discussion highlights three tools for their ease of use, reliance on relatively updated versions of miRBase, and range of capabilities, and these are DIANA-microT-CDS, miRanda-mirSVR, and TargetScan. In comparison across all miRNA target prediction tools, four main aspects of the miRNA:mRNA target interaction emerge as common features on which most target prediction is based: seed match, conservation, free energy, and site accessibility. This review explains these features and identifies how they are incorporated into currently available target prediction tools. MiRNA target prediction is a dynamic field with increasing attention on development of new analysis tools. This review attempts to provide a comprehensive assessment of these tools in a manner that is accessible across disciplines. Understanding the basis of these prediction methodologies will aid in user selection of the appropriate tools and interpretation of the tool output. PMID:24600468

Common features of microRNA target prediction tools.

PubMed

Peterson, Sarah M; Thompson, Jeffrey A; Ufkin, Melanie L; Sathyanarayana, Pradeep; Liaw, Lucy; Congdon, Clare Bates

2014-01-01

The human genome encodes for over 1800 microRNAs (miRNAs), which are short non-coding RNA molecules that function to regulate gene expression post-transcriptionally. Due to the potential for one miRNA to target multiple gene transcripts, miRNAs are recognized as a major mechanism to regulate gene expression and mRNA translation. Computational prediction of miRNA targets is a critical initial step in identifying miRNA:mRNA target interactions for experimental validation. The available tools for miRNA target prediction encompass a range of different computational approaches, from the modeling of physical interactions to the incorporation of machine learning. This review provides an overview of the major computational approaches to miRNA target prediction. Our discussion highlights three tools for their ease of use, reliance on relatively updated versions of miRBase, and range of capabilities, and these are DIANA-microT-CDS, miRanda-mirSVR, and TargetScan. In comparison across all miRNA target prediction tools, four main aspects of the miRNA:mRNA target interaction emerge as common features on which most target prediction is based: seed match, conservation, free energy, and site accessibility. This review explains these features and identifies how they are incorporated into currently available target prediction tools. MiRNA target prediction is a dynamic field with increasing attention on development of new analysis tools. This review attempts to provide a comprehensive assessment of these tools in a manner that is accessible across disciplines. Understanding the basis of these prediction methodologies will aid in user selection of the appropriate tools and interpretation of the tool output.

New Tools for Sea Ice Data Analysis and Visualization: NSIDC's Arctic Sea Ice News and Analysis

NASA Astrophysics Data System (ADS)

Vizcarra, N.; Stroeve, J.; Beam, K.; Beitler, J.; Brandt, M.; Kovarik, J.; Savoie, M. H.; Skaug, M.; Stafford, T.

2017-12-01

Arctic sea ice has long been recognized as a sensitive climate indicator and has undergone a dramatic decline over the past thirty years. Antarctic sea ice continues to be an intriguing and active field of research. The National Snow and Ice Data Center's Arctic Sea Ice News & Analysis (ASINA) offers researchers and the public a transparent view of sea ice data and analysis. We have released a new set of tools for sea ice analysis and visualization. In addition to Charctic, our interactive sea ice extent graph, the new Sea Ice Data and Analysis Tools page provides access to Arctic and Antarctic sea ice data organized in seven different data workbooks, updated daily or monthly. An interactive tool lets scientists, or the public, quickly compare changes in ice extent and location. Another tool allows users to map trends, anomalies, and means for user-defined time periods. Animations of September Arctic and Antarctic monthly average sea ice extent and concentration may also be accessed from this page. Our tools help the NSIDC scientists monitor and understand sea ice conditions in near real time. They also allow the public to easily interact with and explore sea ice data. Technical innovations in our data center helped NSIDC quickly build these tools and more easily maintain them. The tools were made publicly accessible to meet the desire from the public and members of the media to access the numbers and calculations that power our visualizations and analysis. This poster explores these tools and how other researchers, the media, and the general public are using them.

Data Analysis with Graphical Models: Software Tools

NASA Technical Reports Server (NTRS)

Buntine, Wray L.

1994-01-01

Probabilistic graphical models (directed and undirected Markov fields, and combined in chain graphs) are used widely in expert systems, image processing and other areas as a framework for representing and reasoning with probabilities. They come with corresponding algorithms for performing probabilistic inference. This paper discusses an extension to these models by Spiegelhalter and Gilks, plates, used to graphically model the notion of a sample. This offers a graphical specification language for representing data analysis problems. When combined with general methods for statistical inference, this also offers a unifying framework for prototyping and/or generating data analysis algorithms from graphical specifications. This paper outlines the framework and then presents some basic tools for the task: a graphical version of the Pitman-Koopman Theorem for the exponential family, problem decomposition, and the calculation of exact Bayes factors. Other tools already developed, such as automatic differentiation, Gibbs sampling, and use of the EM algorithm, make this a broad basis for the generation of data analysis software.

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.

Lightweight Object Oriented Structure analysis: Tools for building Tools to Analyze Molecular Dynamics Simulations

PubMed Central

Romo, Tod D.; Leioatts, Nicholas; Grossfield, Alan

2014-01-01

LOOS (Lightweight Object-Oriented Structure-analysis) is a C++ library designed to facilitate making novel tools for analyzing molecular dynamics simulations by abstracting out the repetitive tasks, allowing developers to focus on the scientifically relevant part of the problem. LOOS supports input using the native file formats of most common biomolecular simulation packages, including CHARMM, NAMD, Amber, Tinker, and Gromacs. A dynamic atom selection language based on the C expression syntax is included and is easily accessible to the tool-writer. In addition, LOOS is bundled with over 120 pre-built tools, including suites of tools for analyzing simulation convergence, 3D histograms, and elastic network models. Through modern C++ design, LOOS is both simple to develop with (requiring knowledge of only 4 core classes and a few utility functions) and is easily extensible. A python interface to the core classes is also provided, further facilitating tool development. PMID:25327784

DIY Solar Market Analysis Webinar Series: Top Solar Tools | State, Local,

Science.gov Websites

and Tribal Governments | NREL DIY Solar Market Analysis Webinar Series: Top Solar Tools DIY Solar Market Analysis Webinar Series: Top Solar Tools Wednesday, May 14, 2014 As part of a Do-It -Yourself Solar Market Analysis summer series, NREL's Solar Technical Assistance Team (STAT) presented a

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database.

PubMed

Zappia, Luke; Phipson, Belinda; Oshlack, Alicia

2018-06-25

As single-cell RNA-sequencing (scRNA-seq) datasets have become more widespread the number of tools designed to analyse these data has dramatically increased. Navigating the vast sea of tools now available is becoming increasingly challenging for researchers. In order to better facilitate selection of appropriate analysis tools we have created the scRNA-tools database (www.scRNA-tools.org) to catalogue and curate analysis tools as they become available. Our database collects a range of information on each scRNA-seq analysis tool and categorises them according to the analysis tasks they perform. Exploration of this database gives insights into the areas of rapid development of analysis methods for scRNA-seq data. We see that many tools perform tasks specific to scRNA-seq analysis, particularly clustering and ordering of cells. We also find that the scRNA-seq community embraces an open-source and open-science approach, with most tools available under open-source licenses and preprints being extensively used as a means to describe methods. The scRNA-tools database provides a valuable resource for researchers embarking on scRNA-seq analysis and records the growth of the field over time.

Sensitivity Analysis of Weather Variables on Offsite Consequence Analysis Tools in South Korea and the United States.

PubMed

Kim, Min-Uk; Moon, Kyong Whan; Sohn, Jong-Ryeul; Byeon, Sang-Hoon

2018-05-18

We studied sensitive weather variables for consequence analysis, in the case of chemical leaks on the user side of offsite consequence analysis (OCA) tools. We used OCA tools Korea Offsite Risk Assessment (KORA) and Areal Location of Hazardous Atmospheres (ALOHA) in South Korea and the United States, respectively. The chemicals used for this analysis were 28% ammonia (NH₃), 35% hydrogen chloride (HCl), 50% hydrofluoric acid (HF), and 69% nitric acid (HNO₃). The accident scenarios were based on leakage accidents in storage tanks. The weather variables were air temperature, wind speed, humidity, and atmospheric stability. Sensitivity analysis was performed using the Statistical Package for the Social Sciences (SPSS) program for dummy regression analysis. Sensitivity analysis showed that impact distance was not sensitive to humidity. Impact distance was most sensitive to atmospheric stability, and was also more sensitive to air temperature than wind speed, according to both the KORA and ALOHA tools. Moreover, the weather variables were more sensitive in rural conditions than in urban conditions, with the ALOHA tool being more influenced by weather variables than the KORA tool. Therefore, if using the ALOHA tool instead of the KORA tool in rural conditions, users should be careful not to cause any differences in impact distance due to input errors of weather variables, with the most sensitive one being atmospheric stability.

Analysis of Alternatives for Risk Assessment Methodologies and Tools

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

Nachtigal, Noel M.; Fruetel, Julia A.; Gleason, Nathaniel J.

The purpose of this document is to provide a basic overview and understanding of risk assessment methodologies and tools from the literature and to assess the suitability of these methodologies and tools for cyber risk assessment. Sandia National Laboratories (SNL) performed this review in support of risk modeling activities performed for the Stakeholder Engagement and Cyber Infrastructure Resilience (SECIR) division of the Department of Homeland Security (DHS) Office of Cybersecurity and Communications (CS&C). The set of methodologies and tools covered in this document is not intended to be exhaustive; instead, it focuses on those that are commonly used in themore » risk assessment community. The classification of methodologies and tools was performed by a group of analysts with experience in risk analysis and cybersecurity, and the resulting analysis of alternatives has been tailored to address the needs of a cyber risk assessment.« less

Improvements to Integrated Tradespace Analysis of Communications Architectures (ITACA) Network Loading Analysis Tool

NASA Technical Reports Server (NTRS)

Lee, Nathaniel; Welch, Bryan W.

2018-01-01

NASA's SCENIC project aims to simplify and reduce the cost of space mission planning by replicating the analysis capabilities of commercially licensed software which are integrated with relevant analysis parameters specific to SCaN assets and SCaN supported user missions. SCENIC differs from current tools that perform similar analyses in that it 1) does not require any licensing fees, 2) will provide an all-in-one package for various analysis capabilities that normally requires add-ons or multiple tools to complete. As part of SCENIC's capabilities, the ITACA network loading analysis tool will be responsible for assessing the loading on a given network architecture and generating a network service schedule. ITACA will allow users to evaluate the quality of service of a given network architecture and determine whether or not the architecture will satisfy the mission's requirements. ITACA is currently under development, and the following improvements were made during the fall of 2017: optimization of runtime, augmentation of network asset pre-service configuration time, augmentation of Brent's method of root finding, augmentation of network asset FOV restrictions, augmentation of mission lifetimes, and the integration of a SCaN link budget calculation tool. The improvements resulted in (a) 25% reduction in runtime, (b) more accurate contact window predictions when compared to STK(Registered Trademark) contact window predictions, and (c) increased fidelity through the use of specific SCaN asset parameters.

CMM Data Analysis Tool

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

Due to the increase in the use of Coordinate Measuring Machines (CMMs) to measure fine details and complex geometries in manufacturing, many programs have been made to compile and analyze the data. These programs typically require extensive setup to determine the expected results in order to not only track the pass/fail of a dimension, but also to use statistical process control (SPC). These extra steps and setup times have been addressed through the CMM Data Analysis Tool, which only requires the output of the CMM to provide both pass/fail analysis on all parts run to the same inspection program asmore » well as provide graphs which help visualize where the part measures within the allowed tolerances. This provides feedback not only to the customer for approval of a part during development, but also to machining process engineers to identify when any dimension is drifting towards an out of tolerance condition during production. This program can handle hundreds of parts with complex dimensions and will provide an analysis within minutes.« less

Elementary Mode Analysis: A Useful Metabolic Pathway Analysis Tool for Characterizing Cellular Metabolism

PubMed Central

Trinh, Cong T.; Wlaschin, Aaron; Srienc, Friedrich

2010-01-01

Elementary Mode Analysis is a useful Metabolic Pathway Analysis tool to identify the structure of a metabolic network that links the cellular phenotype to the corresponding genotype. The analysis can decompose the intricate metabolic network comprised of highly interconnected reactions into uniquely organized pathways. These pathways consisting of a minimal set of enzymes that can support steady state operation of cellular metabolism represent independent cellular physiological states. Such pathway definition provides a rigorous basis to systematically characterize cellular phenotypes, metabolic network regulation, robustness, and fragility that facilitate understanding of cell physiology and implementation of metabolic engineering strategies. This mini-review aims to overview the development and application of elementary mode analysis as a metabolic pathway analysis tool in studying cell physiology and as a basis of metabolic engineering. PMID:19015845

Network Analysis Tools: from biological networks to clusters and pathways.

PubMed

Brohée, Sylvain; Faust, Karoline; Lima-Mendez, Gipsi; Vanderstocken, Gilles; van Helden, Jacques

2008-01-01

Network Analysis Tools (NeAT) is a suite of computer tools that integrate various algorithms for the analysis of biological networks: comparison between graphs, between clusters, or between graphs and clusters; network randomization; analysis of degree distribution; network-based clustering and path finding. The tools are interconnected to enable a stepwise analysis of the network through a complete analytical workflow. In this protocol, we present a typical case of utilization, where the tasks above are combined to decipher a protein-protein interaction network retrieved from the STRING database. The results returned by NeAT are typically subnetworks, networks enriched with additional information (i.e., clusters or paths) or tables displaying statistics. Typical networks comprising several thousands of nodes and arcs can be analyzed within a few minutes. The complete protocol can be read and executed in approximately 1 h.

SATRAT: Staphylococcus aureus transcript regulatory network analysis tool.

PubMed

Gopal, Tamilselvi; Nagarajan, Vijayaraj; Elasri, Mohamed O

2015-01-01

Staphylococcus aureus is a commensal organism that primarily colonizes the nose of healthy individuals. S. aureus causes a spectrum of infections that range from skin and soft-tissue infections to fatal invasive diseases. S. aureus uses a large number of virulence factors that are regulated in a coordinated fashion. The complex regulatory mechanisms have been investigated in numerous high-throughput experiments. Access to this data is critical to studying this pathogen. Previously, we developed a compilation of microarray experimental data to enable researchers to search, browse, compare, and contrast transcript profiles. We have substantially updated this database and have built a novel exploratory tool-SATRAT-the S. aureus transcript regulatory network analysis tool, based on the updated database. This tool is capable of performing deep searches using a query and generating an interactive regulatory network based on associations among the regulators of any query gene. We believe this integrated regulatory network analysis tool would help researchers explore the missing links and identify novel pathways that regulate virulence in S. aureus. Also, the data model and the network generation code used to build this resource is open sourced, enabling researchers to build similar resources for other bacterial systems.

Issues and approach to develop validated analysis tools for hypersonic flows: One perspective

NASA Technical Reports Server (NTRS)

Deiwert, George S.

1993-01-01

Critical issues concerning the modeling of low density hypervelocity flows where thermochemical nonequilibrium effects are pronounced are discussed. Emphasis is on the development of validated analysis tools, and the activity in the NASA Ames Research Center's Aerothermodynamics Branch is described. Inherent in the process is a strong synergism between ground test and real gas computational fluid dynamics (CFD). Approaches to develop and/or enhance phenomenological models and incorporate them into computational flowfield simulation codes are discussed. These models were partially validated with experimental data for flows where the gas temperature is raised (compressive flows). Expanding flows, where temperatures drop, however, exhibit somewhat different behavior. Experimental data for these expanding flow conditions is sparse and reliance must be made on intuition and guidance from computational chemistry to model transport processes under these conditions. Ground based experimental studies used to provide necessary data for model development and validation are described. Included are the performance characteristics of high enthalpy flow facilities, such as shock tubes and ballistic ranges.

Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations.

PubMed

Romo, Tod D; Leioatts, Nicholas; Grossfield, Alan

2014-12-15

LOOS (Lightweight Object Oriented Structure-analysis) is a C++ library designed to facilitate making novel tools for analyzing molecular dynamics simulations by abstracting out the repetitive tasks, allowing developers to focus on the scientifically relevant part of the problem. LOOS supports input using the native file formats of most common biomolecular simulation packages, including CHARMM, NAMD, Amber, Tinker, and Gromacs. A dynamic atom selection language based on the C expression syntax is included and is easily accessible to the tool-writer. In addition, LOOS is bundled with over 140 prebuilt tools, including suites of tools for analyzing simulation convergence, three-dimensional histograms, and elastic network models. Through modern C++ design, LOOS is both simple to develop with (requiring knowledge of only four core classes and a few utility functions) and is easily extensible. A python interface to the core classes is also provided, further facilitating tool development. © 2014 Wiley Periodicals, Inc.

On the next generation of reliability analysis tools

NASA Technical Reports Server (NTRS)

Babcock, Philip S., IV; Leong, Frank; Gai, Eli

1987-01-01

The current generation of reliability analysis tools concentrates on improving the efficiency of the description and solution of the fault-handling processes and providing a solution algorithm for the full system model. The tools have improved user efficiency in these areas to the extent that the problem of constructing the fault-occurrence model is now the major analysis bottleneck. For the next generation of reliability tools, it is proposed that techniques be developed to improve the efficiency of the fault-occurrence model generation and input. Further, the goal is to provide an environment permitting a user to provide a top-down design description of the system from which a Markov reliability model is automatically constructed. Thus, the user is relieved of the tedious and error-prone process of model construction, permitting an efficient exploration of the design space, and an independent validation of the system's operation is obtained. An additional benefit of automating the model construction process is the opportunity to reduce the specialized knowledge required. Hence, the user need only be an expert in the system he is analyzing; the expertise in reliability analysis techniques is supplied.

DIY Solar Market Analysis Webinar Series: Community Solar Scenario Tool |

Science.gov Websites

State, Local, and Tribal Governments | NREL Webinar Series: Community Solar Scenario Tool DIY Solar Market Analysis Webinar Series: Community Solar Scenario Tool Wednesday, August 13, 2014 As part ) presented a live webinar titled, "Community Solar Scenario Tool: Planning for a fruitful solar garden

A reliability analysis tool for SpaceWire network

NASA Astrophysics Data System (ADS)

Zhou, Qiang; Zhu, Longjiang; Fei, Haidong; Wang, Xingyou

2017-04-01

A SpaceWire is a standard for on-board satellite networks as the basis for future data-handling architectures. It is becoming more and more popular in space applications due to its technical advantages, including reliability, low power and fault protection, etc. High reliability is the vital issue for spacecraft. Therefore, it is very important to analyze and improve the reliability performance of the SpaceWire network. This paper deals with the problem of reliability modeling and analysis with SpaceWire network. According to the function division of distributed network, a reliability analysis method based on a task is proposed, the reliability analysis of every task can lead to the system reliability matrix, the reliability result of the network system can be deduced by integrating these entire reliability indexes in the matrix. With the method, we develop a reliability analysis tool for SpaceWire Network based on VC, where the computation schemes for reliability matrix and the multi-path-task reliability are also implemented. By using this tool, we analyze several cases on typical architectures. And the analytic results indicate that redundancy architecture has better reliability performance than basic one. In practical, the dual redundancy scheme has been adopted for some key unit, to improve the reliability index of the system or task. Finally, this reliability analysis tool will has a directive influence on both task division and topology selection in the phase of SpaceWire network system design.

Incorporation of lean methodology into pharmacy residency programs.

PubMed

John, Natalie; Snider, Holly; Edgerton, Lisa; Whalin, Laurie

2017-03-15

The implementation of lean methodology into pharmacy residency programs at a community teaching hospital is described. New Hanover Regional Medical Center, a community teaching hospital in southeastern North Carolina, fully adopted a lean culture in 2010. Given the success of lean strategies organizationally, this methodology was used to assist with the evaluation and development of its pharmacy residency programs in 2014. Lean tools and activities have also been incorporated into residency requirements and rotation learning activities. The majority of lean events correspond to the required competency areas evaluating leadership and management, teaching, and education. These events have included participation in and facilitation of various lean problem-solving and communication tools. The application of the 4 rules of lean has resulted in enhanced management of the programs and provides a set of tools by which continual quality improvement can be ensured. Regular communication and direct involvement of all invested parties have been critical in developing and sustaining new improvements. In addition to program enhancements, lean methodology offers novel methods by which residents may be incorporated into leadership activities. The incorporation of lean methodology into pharmacy residency programs has translated into a variety of realized and potential benefits for the programs, the preceptors and residents, and the health system. Specific areas of growth have included quality-improvement processes, the expansion of leadership opportunities for residents, and improved communication among program directors, preceptors, and residents. Copyright © 2017 by the American Society of Health-System Pharmacists, Inc. All rights reserved.

MetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models

DOE PAGES

Aurich, Maike K.; Fleming, Ronan M. T.; Thiele, Ines

2016-08-03

Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Previous work, by us and others, revealed the potential of analyzing extracellular metabolomic data in the context of the metabolic model using constraint-based modeling. With the MetaboTools, we make our methods available to the broader scientific community. The MetaboTools consist of a protocol, a toolbox, and tutorials of two use cases. The protocol describes, in a step-wise manner, the workflow of data integration, and computational analysis. The MetaboTools comprise the Matlab code required to complete the workflow described in the protocol. Tutorialsmore » explain the computational steps for integration of two different data sets and demonstrate a comprehensive set of methods for the computational analysis of metabolic models and stratification thereof into different phenotypes. The presented workflow supports integrative analysis of multiple omics data sets. Importantly, all analysis tools can be applied to metabolic models without performing the entire workflow. Taken together, the MetaboTools constitute a comprehensive guide to the intra-model analysis of extracellular metabolomic data from microbial, plant, or human cells. In conclusion, this computational modeling resource offers a broad set of computational analysis tools for a wide biomedical and non-biomedical research community.« less

FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data.

PubMed

DeTomaso, David; Yosef, Nir

2016-08-23

A key challenge in the emerging field of single-cell RNA-Seq is to characterize phenotypic diversity between cells and visualize this information in an informative manner. A common technique when dealing with high-dimensional data is to project the data to 2 or 3 dimensions for visualization. However, there are a variety of methods to achieve this result and once projected, it can be difficult to ascribe biological significance to the observed features. Additionally, when analyzing single-cell data, the relationship between cells can be obscured by technical confounders such as variable gene capture rates. To aid in the analysis and interpretation of single-cell RNA-Seq data, we have developed FastProject, a software tool which analyzes a gene expression matrix and produces a dynamic output report in which two-dimensional projections of the data can be explored. Annotated gene sets (referred to as gene 'signatures') are incorporated so that features in the projections can be understood in relation to the biological processes they might represent. FastProject provides a novel method of scoring each cell against a gene signature so as to minimize the effect of missed transcripts as well as a method to rank signature-projection pairings so that meaningful associations can be quickly identified. Additionally, FastProject is written with a modular architecture and designed to serve as a platform for incorporating and comparing new projection methods and gene selection algorithms. Here we present FastProject, a software package for two-dimensional visualization of single cell data, which utilizes a plethora of projection methods and provides a way to systematically investigate the biological relevance of these low dimensional representations by incorporating domain knowledge.

Multi-Spacecraft Analysis with Generic Visualization Tools

NASA Astrophysics Data System (ADS)

Mukherjee, J.; Vela, L.; Gonzalez, C.; Jeffers, S.

2010-12-01

To handle the needs of scientists today and in the future, software tools are going to have to take better advantage of the currently available hardware. Specifically, computing power, memory, and disk space have become cheaper, while bandwidth has become more expensive due to the explosion of online applications. To overcome these limitations, we have enhanced our Southwest Data Display and Analysis System (SDDAS) to take better advantage of the hardware by utilizing threads and data caching. Furthermore, the system was enhanced to support a framework for adding data formats and data visualization methods without costly rewrites. Visualization tools can speed analysis of many common scientific tasks and we will present a suite of tools that encompass the entire process of retrieving data from multiple data stores to common visualizations of the data. The goals for the end user are ease of use and interactivity with the data and the resulting plots. The data can be simultaneously plotted in a variety of formats and/or time and spatial resolutions. The software will allow one to slice and separate data to achieve other visualizations. Furthermore, one can interact with the data using the GUI or through an embedded language based on the Lua scripting language. The data presented will be primarily from the Cluster and Mars Express missions; however, the tools are data type agnostic and can be used for virtually any type of data.

Statistical methods for the forensic analysis of striated tool marks

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

Hoeksema, Amy Beth

In forensics, fingerprints can be used to uniquely identify suspects in a crime. Similarly, a tool mark left at a crime scene can be used to identify the tool that was used. However, the current practice of identifying matching tool marks involves visual inspection of marks by forensic experts which can be a very subjective process. As a result, declared matches are often successfully challenged in court, so law enforcement agencies are particularly interested in encouraging research in more objective approaches. Our analysis is based on comparisons of profilometry data, essentially depth contours of a tool mark surface taken alongmore » a linear path. In current practice, for stronger support of a match or non-match, multiple marks are made in the lab under the same conditions by the suspect tool. We propose the use of a likelihood ratio test to analyze the difference between a sample of comparisons of lab tool marks to a field tool mark, against a sample of comparisons of two lab tool marks. Chumbley et al. (2010) point out that the angle of incidence between the tool and the marked surface can have a substantial impact on the tool mark and on the effectiveness of both manual and algorithmic matching procedures. To better address this problem, we describe how the analysis can be enhanced to model the effect of tool angle and allow for angle estimation for a tool mark left at a crime scene. With sufficient development, such methods may lead to more defensible forensic analyses.« less

Surface Analysis Cluster Tool | Materials Science | NREL

Science.gov Websites

spectroscopic ellipsometry during film deposition. The cluster tool can be used to study the effect of various prior to analysis. Here we illustrate the surface cleaning effect of an aqueous ammonia treatment on a

Application of stable isotope tools for evaluating natural and stimulated biodegradation of organic pollutants in field studies.

PubMed

Fischer, Anko; Manefield, Mike; Bombach, Petra

2016-10-01

Stable isotope tools are increasingly applied for in-depth evaluation of biodegradation of organic pollutants at contaminated field sites. They can be divided into three methods i) determination of changes in natural abundance of stable isotopes using compound-specific stable isotope analysis (CSIA), ii) detection of incorporation of stable-isotope label from a stable-isotope labelled target compound into degradation and/or mineralisation products and iii) determination of stable-isotope label incorporation into biomarkers using stable isotope probing (SIP). Stable isotope tools have been applied as key monitoring tools for multiple-line-of-evidence-approaches (MLEA) for sensitive evaluation of pollutant biodegradation. This review highlights the application of CSIA, SIP and MLEA including stable isotope tools for assessing natural and stimulated biodegradation of organic pollutants in field studies dealing with soil and groundwater contaminations. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

PubMed

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

2014-09-01

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

Designing an Exploratory Text Analysis Tool for Humanities and Social Sciences Research

ERIC Educational Resources Information Center

Shrikumar, Aditi

2013-01-01

This dissertation presents a new tool for exploratory text analysis that attempts to improve the experience of navigating and exploring text and its metadata. The design of the tool was motivated by the unmet need for text analysis tools in the humanities and social sciences. In these fields, it is common for scholars to have hundreds or thousands…

The Development of a Humanitarian Health Ethics Analysis Tool.

PubMed

Fraser, Veronique; Hunt, Matthew R; de Laat, Sonya; Schwartz, Lisa

2015-08-01

Introduction Health care workers (HCWs) who participate in humanitarian aid work experience a range of ethical challenges in providing care and assistance to communities affected by war, disaster, or extreme poverty. Although there is increasing discussion of ethics in humanitarian health care practice and policy, there are very few resources available for humanitarian workers seeking ethical guidance in the field. To address this knowledge gap, a Humanitarian Health Ethics Analysis Tool (HHEAT) was developed and tested as an action-oriented resource to support humanitarian workers in ethical decision making. While ethical analysis tools increasingly have become prevalent in a variety of practice contexts over the past two decades, very few of these tools have undergone a process of empirical validation to assess their usefulness for practitioners. A qualitative study consisting of a series of six case-analysis sessions with 16 humanitarian HCWs was conducted to evaluate and refine the HHEAT. Participant feedback inspired the creation of a simplified and shortened version of the tool and prompted the development of an accompanying handbook. The study generated preliminary insight into the ethical deliberation processes of humanitarian health workers and highlighted different types of ethics support that humanitarian workers might find helpful in supporting the decision-making process.

Incorporating scale into digital terrain analysis

NASA Astrophysics Data System (ADS)

Dragut, L. D.; Eisank, C.; Strasser, T.

2009-04-01

Digital Elevation Models (DEMs) and their derived terrain attributes are commonly used in soil-landscape modeling. Process-based terrain attributes meaningful to the soil properties of interest are sought to be produced through digital terrain analysis. Typically, the standard 3 X 3 window-based algorithms are used for this purpose, thus tying the scale of resulting layers to the spatial resolution of the available DEM. But this is likely to induce mismatches between scale domains of terrain information and soil properties of interest, which further propagate biases in soil-landscape modeling. We have started developing a procedure to incorporate scale into digital terrain analysis for terrain-based environmental modeling (Drăguţ et al., in press). The workflow was exemplified on crop yield data. Terrain information was generalized into successive scale levels with focal statistics on increasing neighborhood size. The degree of association between each terrain derivative and crop yield values was established iteratively for all scale levels through correlation analysis. The first peak of correlation indicated the scale level to be further retained. While in a standard 3 X 3 window-based analysis mean curvature was one of the poorest correlated terrain attribute, after generalization it turned into the best correlated variable. To illustrate the importance of scale, we compared the regression results of unfiltered and filtered mean curvature vs. crop yield. The comparison shows an improvement of R squared from a value of 0.01 when the curvature was not filtered, to 0.16 when the curvature was filtered within 55 X 55 m neighborhood size. This indicates the optimum size of curvature information (scale) that influences soil fertility. We further used these results in an object-based image analysis environment to create terrain objects containing aggregated values of both terrain derivatives and crop yield. Hence, we introduce terrain segmentation as an alternative

Applications of a broad-spectrum tool for conservation and fisheries analysis: aquatic gap analysis

USGS Publications Warehouse

McKenna, James E.; Steen, Paul J.; Lyons, John; Stewart, Jana S.

2009-01-01

Natural resources support all of our social and economic activities, as well as our biological existence. Humans have little control over most of the physical, biological, and sociological conditions dictating the status and capacity of natural resources in any particular area. However, the most rapid and threatening influences on natural resources typically are anthropogenic overuse and degradation. In addition, living natural resources (i.e., organisms) do not respect political boundaries, but are aware of their optimal habitat and environmental conditions. Most organisms have wider spatial ranges than the jurisdictional boundaries of environmental agencies that deal with them; even within those jurisdictions, information is patchy and disconnected. Planning and projecting effects of ecological management are difficult, because many organisms, habitat conditions, and interactions are involved. Conservation and responsible resource use involves wise management and manipulation of the aspects of the environment and biological communities that can be effectively changed. Tools and data sets that provide new insights and analysis capabilities can enhance the ability of resource managers to make wise decisions and plan effective, long-term management strategies. Aquatic gap analysis has been developed to provide those benefits. Gap analysis is more than just the assessment of the match or mis-match (i.e., gaps) between habitats of ecological value and areas with an appropriate level of environmental protection (e.g., refuges, parks, preserves), as the name suggests. Rather, a Gap Analysis project is a process which leads to an organized database of georeferenced information and previously available tools to examine conservation and other ecological issues; it provides a geographic analysis platform that serves as a foundation for aquatic ecological studies. This analytical tool box allows one to conduct assessments of all habitat elements within an area of interest

Developing a tool to support diagnostic delivery of dementia.

PubMed

Bennett, Claire E; De Boos, Danielle; Moghaddam, Nima G

2018-01-01

It is increasingly recognised that there are challenges affecting the current delivery of dementia diagnoses. Steps are required to address this. Current good practice guidelines provide insufficient direction and interventions from other healthcare settings do not appear to fully translate to dementia care settings. This project has taken a sequential two-phase design to developing a tool specific to dementia diagnostic delivery. Interviews with 14 participants explored good diagnostic delivery. Thematic analysis produced key themes (overcoming barriers, navigation of multiple journeys and completing overt and covert tasks) that were used to inform the design of a tool for use by clinicians, patients and companions. The tool was evaluated for acceptability in focused group discussions with 13 participants, which indicated a desire to use the tool and that it could encourage good practice. Adaptations were highlighted and incorporated to improve acceptability. Future research is now required to further evaluate the tool.

Thermal Management Tools for Propulsion System Trade Studies and Analysis

NASA Technical Reports Server (NTRS)

McCarthy, Kevin; Hodge, Ernie

2011-01-01

Energy-related subsystems in modern aircraft are more tightly coupled with less design margin. These subsystems include thermal management subsystems, vehicle electric power generation and distribution, aircraft engines, and flight control. Tighter coupling, lower design margins, and higher system complexity all make preliminary trade studies difficult. A suite of thermal management analysis tools has been developed to facilitate trade studies during preliminary design of air-vehicle propulsion systems. Simulink blocksets (from MathWorks) for developing quasi-steady-state and transient system models of aircraft thermal management systems and related energy systems have been developed. These blocksets extend the Simulink modeling environment in the thermal sciences and aircraft systems disciplines. The blocksets include blocks for modeling aircraft system heat loads, heat exchangers, pumps, reservoirs, fuel tanks, and other components at varying levels of model fidelity. The blocksets have been applied in a first-principles, physics-based modeling and simulation architecture for rapid prototyping of aircraft thermal management and related systems. They have been applied in representative modern aircraft thermal management system studies. The modeling and simulation architecture has also been used to conduct trade studies in a vehicle level model that incorporates coupling effects among the aircraft mission, engine cycle, fuel, and multi-phase heat-transfer materials.

Development and phytochemical content analysis of bun incorporated with Kappaphycus Alvarezii seaweed powder

NASA Astrophysics Data System (ADS)

Sasue, Anita; Kasim, Zalifah Mohd

2016-11-01

Consumer awareness of the importance of functional foods has greatly grown in the past years. Functional foods with elevated levels of antioxidants are of high demand because of its associated health benefits. As bread is a common component in our daily diet, it may be convenient food to deliver antioxidants at a high concentration. The main approach of this study is to incorporate Kappaphycus alvarezii seaweed powder (SWP) and white flour in the bun formulation in order to develop seaweed bun with higher level of phytochemicals. The fresh Kappaphycus alvarezii seaweeds were washed, soaked in distilled water overnight, dried in a cabinet dryer at 40°C for 24 hours and ground into fine powder using universal miller. There were five different percentages of SWP incorporated into bun that were formulation A - control (0% SWP), B (3% SWP), C (6% SWP), D (9% SWP) and E (12% SWP). All the samples were undergone texture, total phenolic content and DPPH analysis. Seaweed concentration had most significant effect on phytochemical constituents of the bun with TPC (35.07 GAE, mg/100g) and DPPH activity (49.02%) maximized when 12% SWP was incorporated into the flour (P<0.05). The incorporation of the SWP also gives significant effects towards the texture of the bun where the bun becomes harder and denser as compared to the control.

Multi-national, multi-lingual, multi-professional CATs: (Curriculum Analysis Tools).

PubMed

Eisner, J

1995-01-01

A consortium of dental schools and allied dental programs was established in 1991 with the expressed purpose of creating a curriculum database program that was end-user modifiable [1]. In April of 1994, a beta version (Beta 2.5 written in FoxPro(TM) 2.5) of the software CATs, an acronym for Curriculum Analysis Tools, was released for use by over 30 of the consortium's 60 member institutions, while the remainder either waited for the Macintosh (TM) or Windows (TM) versions of the program or were simply not ready to begin an institutional curriculum analysis project. Shortly after this release, the design specifications were rewritten based on a thorough critique of the Beta 2.5 design and coding structures and user feedback. The result was Beta 3.0 which has been designed to accommodate any health professions curriculum, in any country that uses English or French as one of its languages. Given the program's extensive use of screen generation tools, it was quite easy to offer screen displays in a second language. As more languages become available as part of the Unified Medical Language System, used to document curriculum content, the program's design will allow their incorporation. When the software arrives at a new institution, the choice of language and health profession will have been preselected, leaving the Curriculum Database Manager to identify the country where the member institution is located. With these 'macro' end-user decisions completed, the database manager can turn to a more specific set of end-user questions including: 1) will the curriculum view selected for analysis be created by the course directors (provider entry of structured course outlines) or by the students (consumer entry of class session summaries)?; 2) which elements within the provided course outline or class session modules will be used?; 3) which, if any, internal curriculum validation measures will be included?; and 4) which, if any, external validation measures will be included

Stability analysis using SDSA tool

NASA Astrophysics Data System (ADS)

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

2011-11-01

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

Incorporating Handling Qualities Analysis into Rotorcraft Conceptual Design

NASA Technical Reports Server (NTRS)

Lawrence, Ben

2014-01-01

This paper describes the initial development of a framework to incorporate handling qualities analyses into a rotorcraft conceptual design process. In particular, the paper describes how rotorcraft conceptual design level data can be used to generate flight dynamics models for handling qualities analyses. Also, methods are described that couple a basic stability augmentation system to the rotorcraft flight dynamics model to extend analysis to beyond that of the bare airframe. A methodology for calculating the handling qualities characteristics of the flight dynamics models and for comparing the results to ADS-33E criteria is described. Preliminary results from the application of the handling qualities analysis for variations in key rotorcraft design parameters of main rotor radius, blade chord, hub stiffness and flap moment of inertia are shown. Varying relationships, with counteracting trends for different handling qualities criteria and different flight speeds are exhibited, with the action of the control system playing a complex part in the outcomes. Overall, the paper demonstrates how a broad array of technical issues across flight dynamics stability and control, simulation and modeling, control law design and handling qualities testing and evaluation had to be confronted to implement even a moderately comprehensive handling qualities analysis of relatively low fidelity models. A key outstanding issue is to how to 'close the loop' with an overall design process, and options for the exploration of how to feedback handling qualities results to a conceptual design process are proposed for future work.

ISSARS Aerosol Database : an Incorporation of Atmospheric Particles into a Universal Tool to Simulate Remote Sensing Instruments

NASA Technical Reports Server (NTRS)

Goetz, Michael B.

2011-01-01

The Instrument Simulator Suite for Atmospheric Remote Sensing (ISSARS) entered its third and final year of development with an overall goal of providing a unified tool to simulate active and passive space borne atmospheric remote sensing instruments. These simulations focus on the atmosphere ranging from UV to microwaves. ISSARS handles all assumptions and uses various models on scattering and microphysics to fill the gaps left unspecified by the atmospheric models to create each instrument's measurements. This will help benefit mission design and reduce mission cost, create efficient implementation of multi-instrument/platform Observing System Simulation Experiments (OSSE), and improve existing models as well as new advanced models in development. In this effort, various aerosol particles are incorporated into the system, and a simulation of input wavelength and spectral refractive indices related to each spherical test particle(s) generate its scattering properties and phase functions. These atmospheric particles being integrated into the system comprise the ones observed by the Multi-angle Imaging SpectroRadiometer(MISR) and by the Multiangle SpectroPolarimetric Imager(MSPI). In addition, a complex scattering database generated by Prof. Ping Yang (Texas A&M) is also incorporated into this aerosol database. Future development with a radiative transfer code will generate a series of results that can be validated with results obtained by the MISR and MSPI instruments; nevertheless, test cases are simulated to determine the validity of various plugin libraries used to determine or gather the scattering properties of particles studied by MISR and MSPI, or within the Single-scattering properties of tri-axial ellipsoidal mineral dust particles database created by Prof. Ping Yang.

Electromechanical hand incorporates touch sensors and trigger function

NASA Technical Reports Server (NTRS)

Dane, D. H.

1970-01-01

Electromechanical hand incorporates touch sensors, concealed fingers, and a structure that allows the hand to hold a tool on a flat surface. The hands can be mounted on most types of existing manipulators either directly or by means of modified mounting brackets.

Rapid Benefit Indicators (RBI) Spatial Analysis Tools

EPA Science Inventory

The Rapid Benefit Indicators (RBI) approach consists of five steps and is outlined in Assessing the Benefits of Wetland Restoration - A Rapid Benefits Indicators Approach for Decision Makers. This spatial analysis tool is intended to be used to analyze existing spatial informatio...

Flow Analysis Tool White Paper

NASA Technical Reports Server (NTRS)

Boscia, Nichole K.

2012-01-01

Faster networks are continually being built to accommodate larger data transfers. While it is intuitive to think that implementing faster networks will result in higher throughput rates, this is often not the case. There are many elements involved in data transfer, many of which are beyond the scope of the network itself. Although networks may get bigger and support faster technologies, the presence of other legacy components, such as older application software or kernel parameters, can often cause bottlenecks. Engineers must be able to identify when data flows are reaching a bottleneck that is not imposed by the network and then troubleshoot it using the tools available to them. The current best practice is to collect as much information as possible on the network traffic flows so that analysis is quick and easy. Unfortunately, no single method of collecting this information can sufficiently capture the whole endto- end picture. This becomes even more of a hurdle when large, multi-user systems are involved. In order to capture all the necessary information, multiple data sources are required. This paper presents a method for developing a flow analysis tool to effectively collect network flow data from multiple sources and provide that information to engineers in a clear, concise way for analysis. The purpose of this method is to collect enough information to quickly (and automatically) identify poorly performing flows along with the cause of the problem. The method involves the development of a set of database tables that can be populated with flow data from multiple sources, along with an easyto- use, web-based front-end interface to help network engineers access, organize, analyze, and manage all the information.

General Mission Analysis Tool (GMAT)

NASA Technical Reports Server (NTRS)

Hughes, Steven P.

2007-01-01

The General Mission Analysis Tool (GMAT) is a space trajectory optimization and mission analysis system developed by NASA and private industry in the spirit of the NASA Mission. GMAT contains new technology and is a testbed for future technology development. The goal of the GMAT project is to develop new space trajectory optimization and mission design technology by working inclusively with ordinary people, universities, businesses, and other government organizations, and to share that technology in an open and unhindered way. GMAT is a free and open source software system licensed under the NASA Open Source Agreement: free for anyone to use in development of new mission concepts or to improve current missions, freely available in source code form for enhancement or further technology development.

Incorporating unnatural amino acids to engineer biocatalysts for industrial bioprocess applications.

PubMed

Ravikumar, Yuvaraj; Nadarajan, Saravanan Prabhu; Hyeon Yoo, Tae; Lee, Chong-Soon; Yun, Hyungdon

2015-12-01

The bioprocess engineering with biocatalysts broadly spans its development and actual application of enzymes in an industrial context. Recently, both the use of bioprocess engineering and the development and employment of enzyme engineering techniques have been increasing rapidly. Importantly, engineering techniques that incorporate unnatural amino acids (UAAs) in vivo has begun to produce enzymes with greater stability and altered catalytic properties. Despite the growth of this technique, its potential value in bioprocess applications remains to be fully exploited. In this review, we explore the methodologies involved in UAA incorporation as well as ways to synthesize these UAAs. In addition, we summarize recent efforts to increase the yield of UAA engineered proteins in Escherichia coli and also the application of this tool in enzyme engineering. Furthermore, this protein engineering tool based on the incorporation of UAA can be used to develop immobilized enzymes that are ideal for bioprocess applications. Considering the potential of this tool and by exploiting these engineered enzymes, we expect the field of bioprocess engineering to open up new opportunities for biocatalysis in the near future. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Quality Assessment Tool for Non-Specialist Users of Regression Analysis

ERIC Educational Resources Information Center

Argyrous, George

2015-01-01

This paper illustrates the use of a quality assessment tool for regression analysis. It is designed for non-specialist "consumers" of evidence, such as policy makers. The tool provides a series of questions such consumers of evidence can ask to interrogate regression analysis, and is illustrated with reference to a recent study published…

Pre-Steady-State Kinetic Analysis of Single-Nucleotide Incorporation by DNA Polymerases

PubMed Central

Su, Yan; Guengerich, F. Peter

2016-01-01

Pre-steady-state kinetic analysis is a powerful and widely used method to obtain multiple kinetic parameters. This protocol provides a step-by-step procedure for pre-steady-state kinetic analysis of single-nucleotide incorporation by a DNA polymerase. It describes the experimental details of DNA substrate annealing, reaction mixture preparation, handling of the RQF-3 rapid quench-flow instrument, denaturing polyacrylamide DNA gel preparation, electrophoresis, quantitation, and data analysis. The core and unique part of this protocol is the rationale for preparation of the reaction mixture (the ratio of the polymerase to the DNA substrate) and methods for conducting pre-steady-state assays on an RQF-3 rapid quench-flow instrument, as well as data interpretation after analysis. In addition, the methods for the DNA substrate annealing and DNA polyacrylamide gel preparation, electrophoresis, quantitation and analysis are suitable for use in other studies. PMID:27248785

Development of a User Interface for a Regression Analysis Software Tool

NASA Technical Reports Server (NTRS)

Ulbrich, Norbert Manfred; Volden, Thomas R.

2010-01-01

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

A comparative analysis of Patient-Reported Expanded Disability Status Scale tools.

PubMed

Collins, Christian DE; Ivry, Ben; Bowen, James D; Cheng, Eric M; Dobson, Ruth; Goodin, Douglas S; Lechner-Scott, Jeannette; Kappos, Ludwig; Galea, Ian

2016-09-01

Patient-Reported Expanded Disability Status Scale (PREDSS) tools are an attractive alternative to the Expanded Disability Status Scale (EDSS) during long term or geographically challenging studies, or in pressured clinical service environments. Because the studies reporting these tools have used different metrics to compare the PREDSS and EDSS, we undertook an individual patient data level analysis of all available tools. Spearman's rho and the Bland-Altman method were used to assess correlation and agreement respectively. A systematic search for validated PREDSS tools covering the full EDSS range identified eight such tools. Individual patient data were available for five PREDSS tools. Excellent correlation was observed between EDSS and PREDSS with all tools. A higher level of agreement was observed with increasing levels of disability. In all tools, the 95% limits of agreement were greater than the minimum EDSS difference considered to be clinically significant. However, the intra-class coefficient was greater than that reported for EDSS raters of mixed seniority. The visual functional system was identified as the most significant predictor of the PREDSS-EDSS difference. This analysis will (1) enable researchers and service providers to make an informed choice of PREDSS tool, depending on their individual requirements, and (2) facilitate improvement of current PREDSS tools. © The Author(s), 2015.

Bioimpedance Harmonic Analysis as a Diagnostic Tool to Assess Regional Circulation and Neural Activity

NASA Astrophysics Data System (ADS)

Mudraya, I. S.; Revenko, S. V.; Khodyreva, L. A.; Markosyan, T. G.; Dudareva, A. A.; Ibragimov, A. R.; Romich, V. V.; Kirpatovsky, V. I.

2013-04-01

The novel technique based on harmonic analysis of bioimpedance microvariations with original hard- and software complex incorporating a high-resolution impedance converter was used to assess the neural activity and circulation in human urinary bladder and penis in patients with pelvic pain, erectile dysfunction, and overactive bladder. The therapeutic effects of shock wave therapy and Botulinum toxin detrusor injections were evaluated quantitatively according to the spectral peaks at low 0.1 Hz frequency (M for Mayer wave), respiratory (R) and cardiac (C) rhythms with their harmonics. Enhanced baseline regional neural activity identified according to M and R peaks was found to be presumably sympathetic in pelvic pain patients, and parasympathetic - in patients with overactive bladder. Total pulsatile activity and pulsatile resonances found in the bladder as well as in the penile spectrum characterised regional circulation and vascular tone. The abnormal spectral parameters characteristic of the patients with genitourinary diseases shifted to the norm in the cases of efficient therapy. Bioimpedance harmonic analysis seems to be a potent tool to assess regional peculiarities of circulatory and autonomic nervous activity in the course of patient treatment.

MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling.

PubMed

Piro, Vitor C; Matschkowski, Marcel; Renard, Bernhard Y

2017-08-14

Many metagenome analysis tools are presently available to classify sequences and profile environmental samples. In particular, taxonomic profiling and binning methods are commonly used for such tasks. Tools available among these two categories make use of several techniques, e.g., read mapping, k-mer alignment, and composition analysis. Variations on the construction of the corresponding reference sequence databases are also common. In addition, different tools provide good results in different datasets and configurations. All this variation creates a complicated scenario to researchers to decide which methods to use. Installation, configuration and execution can also be difficult especially when dealing with multiple datasets and tools. We propose MetaMeta: a pipeline to execute and integrate results from metagenome analysis tools. MetaMeta provides an easy workflow to run multiple tools with multiple samples, producing a single enhanced output profile for each sample. MetaMeta includes a database generation, pre-processing, execution, and integration steps, allowing easy execution and parallelization. The integration relies on the co-occurrence of organisms from different methods as the main feature to improve community profiling while accounting for differences in their databases. In a controlled case with simulated and real data, we show that the integrated profiles of MetaMeta overcome the best single profile. Using the same input data, it provides more sensitive and reliable results with the presence of each organism being supported by several methods. MetaMeta uses Snakemake and has six pre-configured tools, all available at BioConda channel for easy installation (conda install -c bioconda metameta). The MetaMeta pipeline is open-source and can be downloaded at: https://gitlab.com/rki_bioinformatics .

Aeroelastic Ground Wind Loads Analysis Tool for Launch Vehicles

NASA Technical Reports Server (NTRS)

Ivanco, Thomas G.

2016-01-01

Launch vehicles are exposed to ground winds during rollout and on the launch pad that can induce static and dynamic loads. Of particular concern are the dynamic loads caused by vortex shedding from nearly-cylindrical structures. When the frequency of vortex shedding nears that of a lowly-damped structural mode, the dynamic loads can be more than an order of magnitude greater than mean drag loads. Accurately predicting vehicle response to vortex shedding during the design and analysis cycles is difficult and typically exceeds the practical capabilities of modern computational fluid dynamics codes. Therefore, mitigating the ground wind loads risk typically requires wind-tunnel tests of dynamically-scaled models that are time consuming and expensive to conduct. In recent years, NASA has developed a ground wind loads analysis tool for launch vehicles to fill this analytical capability gap in order to provide predictions for prelaunch static and dynamic loads. This paper includes a background of the ground wind loads problem and the current state-of-the-art. It then discusses the history and significance of the analysis tool and the methodology used to develop it. Finally, results of the analysis tool are compared to wind-tunnel and full-scale data of various geometries and Reynolds numbers.

CoryneBase: Corynebacterium Genomic Resources and Analysis Tools at Your Fingertips

PubMed Central

Tan, Mui Fern; Jakubovics, Nick S.; Wee, Wei Yee; Mutha, Naresh V. R.; Wong, Guat Jah; Ang, Mia Yang; Yazdi, Amir Hessam; Choo, Siew Woh

2014-01-01

Corynebacteria are used for a wide variety of industrial purposes but some species are associated with human diseases. With increasing number of corynebacterial genomes having been sequenced, comparative analysis of these strains may provide better understanding of their biology, phylogeny, virulence and taxonomy that may lead to the discoveries of beneficial industrial strains or contribute to better management of diseases. To facilitate the ongoing research of corynebacteria, a specialized central repository and analysis platform for the corynebacterial research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. Here we present CoryneBase, a genomic database for Corynebacterium with diverse functionality for the analysis of genomes aimed to provide: (1) annotated genome sequences of Corynebacterium where 165,918 coding sequences and 4,180 RNAs can be found in 27 species; (2) access to comprehensive Corynebacterium data through the use of advanced web technologies for interactive web interfaces; and (3) advanced bioinformatic analysis tools consisting of standard BLAST for homology search, VFDB BLAST for sequence homology search against the Virulence Factor Database (VFDB), Pairwise Genome Comparison (PGC) tool for comparative genomic analysis, and a newly designed Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomic analysis. CoryneBase offers the access of a range of Corynebacterium genomic resources as well as analysis tools for comparative genomics and pathogenomics. It is publicly available at http://corynebacterium.um.edu.my/. PMID:24466021

Panning for the gold in health research: incorporating studies' methodological quality in meta-analysis.

PubMed

Johnson, Blair T; Low, Robert E; MacDonald, Hayley V

2015-01-01

Systematic reviews now routinely assess methodological quality to gauge the validity of the included studies and of the synthesis as a whole. Although trends from higher quality studies should be clearer, it is uncertain how often meta-analyses incorporate methodological quality in models of study results either as predictors, or, more interestingly, in interactions with theoretical moderators. We survey 200 meta-analyses in three health promotion domains to examine when and how meta-analyses incorporate methodological quality. Although methodological quality assessments commonly appear in contemporary meta-analyses (usually as scales), they are rarely incorporated in analyses, and still more rarely analysed in interaction with theoretical determinants of the success of health promotions. The few meta-analyses (2.5%) that did include such an interaction analysis showed that moderator results remained significant in higher quality studies or were present only among higher quality studies. We describe how to model quality interactively with theoretically derived moderators and discuss strengths and weaknesses of this approach and in relation to current meta-analytic practice. In large literatures exhibiting heterogeneous effects, meta-analyses can incorporate methodological quality and generate conclusions that enable greater confidence not only about the substantive phenomenon but also about the role that methodological quality itself plays.

Code Analysis and Refactoring with Clang Tools, Version 0.1

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

Kelley, Timothy M.

2016-12-23

Code Analysis and Refactoring with Clang Tools is a small set of example code that demonstrates techniques for applying tools distributed with the open source Clang compiler. Examples include analyzing where variables are used and replacing old data structures with standard structures.

Paramedir: A Tool for Programmable Performance Analysis

NASA Technical Reports Server (NTRS)

Jost, Gabriele; Labarta, Jesus; Gimenez, Judit

2004-01-01

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

Integrated multidisciplinary analysis tool IMAT users' guide

NASA Technical Reports Server (NTRS)

Meissner, Frances T. (Editor)

1988-01-01

The Integrated Multidisciplinary Analysis Tool (IMAT) is a computer software system developed at Langley Research Center. IMAT provides researchers and analysts with an efficient capability to analyze satellite controls systems influenced by structural dynamics. Using a menu-driven executive system, IMAT leads the user through the program options. IMAT links a relational database manager to commercial and in-house structural and controls analysis codes. This paper describes the IMAT software system and how to use it.

Advanced Vibration Analysis Tool Developed for Robust Engine Rotor Designs

NASA Technical Reports Server (NTRS)

Min, James B.

2005-01-01

The primary objective of this research program is to develop vibration analysis tools, design tools, and design strategies to significantly improve the safety and robustness of turbine engine rotors. Bladed disks in turbine engines always feature small, random blade-to-blade differences, or mistuning. Mistuning can lead to a dramatic increase in blade forced-response amplitudes and stresses. Ultimately, this results in high-cycle fatigue, which is a major safety and cost concern. In this research program, the necessary steps will be taken to transform a state-of-the-art vibration analysis tool, the Turbo- Reduce forced-response prediction code, into an effective design tool by enhancing and extending the underlying modeling and analysis methods. Furthermore, novel techniques will be developed to assess the safety of a given design. In particular, a procedure will be established for using natural-frequency curve veerings to identify ranges of operating conditions (rotational speeds and engine orders) in which there is a great risk that the rotor blades will suffer high stresses. This work also will aid statistical studies of the forced response by reducing the necessary number of simulations. Finally, new strategies for improving the design of rotors will be pursued.

Analysis and control on changeable wheel tool system of hybrid grinding and polishing machine tool for blade finishing

NASA Astrophysics Data System (ADS)

He, Qiuwei; Lv, Xingming; Wang, Xin; Qu, Xingtian; Zhao, Ji

2017-01-01

Blade is the key component in the energy power equipment of turbine, aircraft engines and so on. Researches on the process and equipment for blade finishing become one of important and difficult point. To control precisely tool system of developed hybrid grinding and polishing machine tool for blade finishing, the tool system with changeable wheel for belt polishing is analyzed in this paper. Firstly, the belt length and wrap angle of each wheel in different position of tension wheel swing angle in the process of changing wheel is analyzed. The reasonable belt length is calculated by using MATLAB, and relationships between wrap angle of each wheel and cylinder expansion amount of contact wheel are obtained. Then, the control system for changeable wheel tool structure is developed. Lastly, the surface roughness of blade finishing is verified by experiments. Theoretical analysis and experimental results show that reasonable belt length and wheel wrap angle can be obtained by proposed analysis method, the changeable wheel tool system can be controlled precisely, and the surface roughness of blade after grinding meets the design requirements.

Standardizing Exoplanet Analysis with the Exoplanet Characterization Tool Kit (ExoCTK)

NASA Astrophysics Data System (ADS)

Fowler, Julia; Stevenson, Kevin B.; Lewis, Nikole K.; Fraine, Jonathan D.; Pueyo, Laurent; Bruno, Giovanni; Filippazzo, Joe; Hill, Matthew; Batalha, Natasha; Wakeford, Hannah; Bushra, Rafia

2018-06-01

Exoplanet characterization depends critically on analysis tools, models, and spectral libraries that are constantly under development and have no single source nor sense of unified style or methods. The complexity of spectroscopic analysis and initial time commitment required to become competitive is prohibitive to new researchers entering the field, as well as a remaining obstacle for established groups hoping to contribute in a comparable manner to their peers. As a solution, we are developing an open-source, modular data analysis package in Python and a publicly facing web interface including tools that address atmospheric characterization, transit observation planning with JWST, JWST corongraphy simulations, limb darkening, forward modeling, and data reduction, as well as libraries of stellar, planet, and opacity models. The foundation of these software tools and libraries exist within pockets of the exoplanet community, but our project will gather these seedling tools and grow a robust, uniform, and well-maintained exoplanet characterization toolkit.

Big Data Geo-Analytical Tool Development for Spatial Analysis Uncertainty Visualization and Quantification Needs

NASA Astrophysics Data System (ADS)

Rose, K.; Bauer, J. R.; Baker, D. V.

2015-12-01

As big data computing capabilities are increasingly paired with spatial analytical tools and approaches, there is a need to ensure uncertainty associated with the datasets used in these analyses is adequately incorporated and portrayed in results. Often the products of spatial analyses, big data and otherwise, are developed using discontinuous, sparse, and often point-driven data to represent continuous phenomena. Results from these analyses are generally presented without clear explanations of the uncertainty associated with the interpolated values. The Variable Grid Method (VGM) offers users with a flexible approach designed for application to a variety of analyses where users there is a need to study, evaluate, and analyze spatial trends and patterns while maintaining connection to and communicating the uncertainty in the underlying spatial datasets. The VGM outputs a simultaneous visualization representative of the spatial data analyses and quantification of underlying uncertainties, which can be calculated using data related to sample density, sample variance, interpolation error, uncertainty calculated from multiple simulations. In this presentation we will show how we are utilizing Hadoop to store and perform spatial analysis through the development of custom Spark and MapReduce applications that incorporate ESRI Hadoop libraries. The team will present custom 'Big Data' geospatial applications that run on the Hadoop cluster and integrate with ESRI ArcMap with the team's probabilistic VGM approach. The VGM-Hadoop tool has been specially built as a multi-step MapReduce application running on the Hadoop cluster for the purpose of data reduction. This reduction is accomplished by generating multi-resolution, non-overlapping, attributed topology that is then further processed using ESRI's geostatistical analyst to convey a probabilistic model of a chosen study region. Finally, we will share our approach for implementation of data reduction and topology generation

High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis.

PubMed

Simonyan, Vahan; Mazumder, Raja

2014-09-30

The High-performance Integrated Virtual Environment (HIVE) is a high-throughput cloud-based infrastructure developed for the storage and analysis of genomic and associated biological data. HIVE consists of a web-accessible interface for authorized users to deposit, retrieve, share, annotate, compute and visualize Next-generation Sequencing (NGS) data in a scalable and highly efficient fashion. The platform contains a distributed storage library and a distributed computational powerhouse linked seamlessly. Resources available through the interface include algorithms, tools and applications developed exclusively for the HIVE platform, as well as commonly used external tools adapted to operate within the parallel architecture of the system. HIVE is composed of a flexible infrastructure, which allows for simple implementation of new algorithms and tools. Currently, available HIVE tools include sequence alignment and nucleotide variation profiling tools, metagenomic analyzers, phylogenetic tree-building tools using NGS data, clone discovery algorithms, and recombination analysis algorithms. In addition to tools, HIVE also provides knowledgebases that can be used in conjunction with the tools for NGS sequence and metadata analysis.

High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis

PubMed Central

Simonyan, Vahan; Mazumder, Raja

2014-01-01

The High-performance Integrated Virtual Environment (HIVE) is a high-throughput cloud-based infrastructure developed for the storage and analysis of genomic and associated biological data. HIVE consists of a web-accessible interface for authorized users to deposit, retrieve, share, annotate, compute and visualize Next-generation Sequencing (NGS) data in a scalable and highly efficient fashion. The platform contains a distributed storage library and a distributed computational powerhouse linked seamlessly. Resources available through the interface include algorithms, tools and applications developed exclusively for the HIVE platform, as well as commonly used external tools adapted to operate within the parallel architecture of the system. HIVE is composed of a flexible infrastructure, which allows for simple implementation of new algorithms and tools. Currently, available HIVE tools include sequence alignment and nucleotide variation profiling tools, metagenomic analyzers, phylogenetic tree-building tools using NGS data, clone discovery algorithms, and recombination analysis algorithms. In addition to tools, HIVE also provides knowledgebases that can be used in conjunction with the tools for NGS sequence and metadata analysis. PMID:25271953

Modeling Tools for Propulsion Analysis and Computational Fluid Dynamics on the Internet

NASA Technical Reports Server (NTRS)

Muss, J. A.; Johnson, C. W.; Gotchy, M. B.

2000-01-01

The existing RocketWeb(TradeMark) Internet Analysis System (httr)://www.iohnsonrockets.com/rocketweb) provides an integrated set of advanced analysis tools that can be securely accessed over the Internet. Since these tools consist of both batch and interactive analysis codes, the system includes convenient methods for creating input files and evaluating the resulting data. The RocketWeb(TradeMark) system also contains many features that permit data sharing which, when further developed, will facilitate real-time, geographically diverse, collaborative engineering within a designated work group. Adding work group management functionality while simultaneously extending and integrating the system's set of design and analysis tools will create a system providing rigorous, controlled design development, reducing design cycle time and cost.

SADA: A FREEWARE DECISION SUPPORT TOOL INTEGRATING GIS, SAMPLE DESIGN, SPATIAL MODELING AND RISK ASSESSMENT (SLIDE PRESENTATION)

EPA Science Inventory

Spatial Analysis and Decision Assistance (SADA) is a Windows freeware program that incorporates tools from environmental assessment into an effective problem-solving environment. SADA was developed by the Institute for Environmental Modeling at the University of Tennessee and inc...

Genetic incorporation of recycled unnatural amino acids.

PubMed

Ko, Wooseok; Kim, Sanggil; Jo, Kyubong; Lee, Hyun Soo

2016-02-01

The genetic incorporation of unnatural amino acids (UAAs) into proteins has been a useful tool for protein engineering. However, most UAAs are expensive, and the method requires a high concentration of UAAs, which has been a drawback of the technology, especially for large-scale applications. To address this problem, a method to recycle cultured UAAs was developed. The method is based on recycling a culture medium containing the UAA, in which some of essential nutrients were resupplemented after each culture cycle, and induction of protein expression was controlled with glucose. Under optimal conditions, five UAAs were recycled for up to seven rounds of expression without a decrease in expression level, cell density, or incorporation fidelity. This method can generally be applied to other UAAs; therefore, it is useful for reducing the cost of UAAs for genetic incorporation and helpful for expanding the use of the technology to industrial applications.

SNP_tools: A compact tool package for analysis and conversion of genotype data for MS-Excel

PubMed Central

Chen, Bowang; Wilkening, Stefan; Drechsel, Marion; Hemminki, Kari

2009-01-01

Background Single nucleotide polymorphism (SNP) genotyping is a major activity in biomedical research. Scientists prefer to have a facile access to the results which may require conversions between data formats. First hand SNP data is often entered in or saved in the MS-Excel format, but this software lacks genetic and epidemiological related functions. A general tool to do basic genetic and epidemiological analysis and data conversion for MS-Excel is needed. Findings The SNP_tools package is prepared as an add-in for MS-Excel. The code is written in Visual Basic for Application, embedded in the Microsoft Office package. This add-in is an easy to use tool for users with basic computer knowledge (and requirements for basic statistical analysis). Conclusion Our implementation for Microsoft Excel 2000-2007 in Microsoft Windows 2000, XP, Vista and Windows 7 beta can handle files in different formats and converts them into other formats. It is a free software. PMID:19852806

SNP_tools: A compact tool package for analysis and conversion of genotype data for MS-Excel.

PubMed

Chen, Bowang; Wilkening, Stefan; Drechsel, Marion; Hemminki, Kari

2009-10-23

Single nucleotide polymorphism (SNP) genotyping is a major activity in biomedical research. Scientists prefer to have a facile access to the results which may require conversions between data formats. First hand SNP data is often entered in or saved in the MS-Excel format, but this software lacks genetic and epidemiological related functions. A general tool to do basic genetic and epidemiological analysis and data conversion for MS-Excel is needed. The SNP_tools package is prepared as an add-in for MS-Excel. The code is written in Visual Basic for Application, embedded in the Microsoft Office package. This add-in is an easy to use tool for users with basic computer knowledge (and requirements for basic statistical analysis). Our implementation for Microsoft Excel 2000-2007 in Microsoft Windows 2000, XP, Vista and Windows 7 beta can handle files in different formats and converts them into other formats. It is a free software.

Issues and approach to develop validated analysis tools for hypersonic flows: One perspective

NASA Technical Reports Server (NTRS)

Deiwert, George S.

1992-01-01

Critical issues concerning the modeling of low-density hypervelocity flows where thermochemical nonequilibrium effects are pronounced are discussed. Emphasis is on the development of validated analysis tools. A description of the activity in the Ames Research Center's Aerothermodynamics Branch is also given. Inherent in the process is a strong synergism between ground test and real-gas computational fluid dynamics (CFD). Approaches to develop and/or enhance phenomenological models and incorporate them into computational flow-field simulation codes are discussed. These models have been partially validated with experimental data for flows where the gas temperature is raised (compressive flows). Expanding flows, where temperatures drop, however, exhibit somewhat different behavior. Experimental data for these expanding flow conditions are sparse; reliance must be made on intuition and guidance from computational chemistry to model transport processes under these conditions. Ground-based experimental studies used to provide necessary data for model development and validation are described. Included are the performance characteristics of high-enthalpy flow facilities, such as shock tubes and ballistic ranges.

Scoring Tools for the Analysis of Infant Respiratory Inductive Plethysmography Signals.

PubMed

Robles-Rubio, Carlos Alejandro; Bertolizio, Gianluca; Brown, Karen A; Kearney, Robert E

2015-01-01

Infants recovering from anesthesia are at risk of life threatening Postoperative Apnea (POA). POA events are rare, and so the study of POA requires the analysis of long cardiorespiratory records. Manual scoring is the preferred method of analysis for these data, but it is limited by low intra- and inter-scorer repeatability. Furthermore, recommended scoring rules do not provide a comprehensive description of the respiratory patterns. This work describes a set of manual scoring tools that address these limitations. These tools include: (i) a set of definitions and scoring rules for 6 mutually exclusive, unique patterns that fully characterize infant respiratory inductive plethysmography (RIP) signals; (ii) RIPScore, a graphical, manual scoring software to apply these rules to infant data; (iii) a library of data segments representing each of the 6 patterns; (iv) a fully automated, interactive formal training protocol to standardize the analysis and establish intra- and inter-scorer repeatability; and (v) a quality control method to monitor scorer ongoing performance over time. To evaluate these tools, three scorers from varied backgrounds were recruited and trained to reach a performance level similar to that of an expert. These scorers used RIPScore to analyze data from infants at risk of POA in two separate, independent instances. Scorers performed with high accuracy and consistency, analyzed data efficiently, had very good intra- and inter-scorer repeatability, and exhibited only minor confusion between patterns. These results indicate that our tools represent an excellent method for the analysis of respiratory patterns in long data records. Although the tools were developed for the study of POA, their use extends to any study of respiratory patterns using RIP (e.g., sleep apnea, extubation readiness). Moreover, by establishing and monitoring scorer repeatability, our tools enable the analysis of large data sets by multiple scorers, which is essential for

Incorporating nuclear vibrational energies into the "atom in molecules" analysis: An analytical study

NASA Astrophysics Data System (ADS)

Gharabaghi, Masumeh; Shahbazian, Shant

2017-04-01

The quantum theory of atoms in molecules (QTAIM) is based on the clamped nucleus paradigm and solely working with the electronic wavefunctions, so does not include nuclear vibrations in the AIM analysis. On the other hand, the recently extended version of the QTAIM, called the multi-component QTAIM (MC-QTAIM), incorporates both electrons and quantum nuclei, i.e., those nuclei treated as quantum waves instead of clamped point charges, into the AIM analysis using non-adiabatic wavefunctions. Thus, the MC-QTAIM is the natural framework to incorporate the role of nuclear vibrations into the AIM analysis. In this study, within the context of the MC-QTAIM, the formalism of including nuclear vibrational energy in the atomic basin energy is developed in detail and its contribution is derived analytically using the recently proposed non-adiabatic Hartree product nuclear wavefunction. It is demonstrated that within the context of this wavefunction, the quantum nuclei may be conceived pseudo-adiabatically as quantum oscillators and both isotropic harmonic and anisotropic anharmonic oscillator models are used to compute the zero-point nuclear vibrational energy contribution to the basin energies explicitly. Inspired by the results gained within the context of the MC-QTAIM analysis, a heuristic approach is proposed within the context of the QTAIM to include nuclear vibrational energy in the basin energy from the vibrational wavefunction derived adiabatically. The explicit calculation of the basin contribution of the zero-point vibrational energy using the uncoupled harmonic oscillator model leads to results consistent with those derived from the MC-QTAIM.

Incorporating nuclear vibrational energies into the "atom in molecules" analysis: An analytical study.

PubMed

Gharabaghi, Masumeh; Shahbazian, Shant

2017-04-21

The quantum theory of atoms in molecules (QTAIM) is based on the clamped nucleus paradigm and solely working with the electronic wavefunctions, so does not include nuclear vibrations in the AIM analysis. On the other hand, the recently extended version of the QTAIM, called the multi-component QTAIM (MC-QTAIM), incorporates both electrons and quantum nuclei, i.e., those nuclei treated as quantum waves instead of clamped point charges, into the AIM analysis using non-adiabatic wavefunctions. Thus, the MC-QTAIM is the natural framework to incorporate the role of nuclear vibrations into the AIM analysis. In this study, within the context of the MC-QTAIM, the formalism of including nuclear vibrational energy in the atomic basin energy is developed in detail and its contribution is derived analytically using the recently proposed non-adiabatic Hartree product nuclear wavefunction. It is demonstrated that within the context of this wavefunction, the quantum nuclei may be conceived pseudo-adiabatically as quantum oscillators and both isotropic harmonic and anisotropic anharmonic oscillator models are used to compute the zero-point nuclear vibrational energy contribution to the basin energies explicitly. Inspired by the results gained within the context of the MC-QTAIM analysis, a heuristic approach is proposed within the context of the QTAIM to include nuclear vibrational energy in the basin energy from the vibrational wavefunction derived adiabatically. The explicit calculation of the basin contribution of the zero-point vibrational energy using the uncoupled harmonic oscillator model leads to results consistent with those derived from the MC-QTAIM.

Extravehicular Activity System Sizing Analysis Tool (EVAS_SAT)

NASA Technical Reports Server (NTRS)

Brown, Cheryl B.; Conger, Bruce C.; Miranda, Bruno M.; Bue, Grant C.; Rouen, Michael N.

2007-01-01

An effort was initiated by NASA/JSC in 2001 to develop an Extravehicular Activity System Sizing Analysis Tool (EVAS_SAT) for the sizing of Extravehicular Activity System (EVAS) architecture and studies. Its intent was to support space suit development efforts and to aid in conceptual designs for future human exploration missions. Its basis was the Life Support Options Performance Program (LSOPP), a spacesuit and portable life support system (PLSS) sizing program developed for NASA/JSC circa 1990. EVAS_SAT estimates the mass, power, and volume characteristics for user-defined EVAS architectures, including Suit Systems, Airlock Systems, Tools and Translation Aids, and Vehicle Support equipment. The tool has undergone annual changes and has been updated as new data have become available. Certain sizing algorithms have been developed based on industry standards, while others are based on the LSOPP sizing routines. The sizing algorithms used by EVAS_SAT are preliminary. Because EVAS_SAT was designed for use by members of the EVA community, subsystem familiarity on the part of the intended user group and in the analysis of results is assumed. The current EVAS_SAT is operated within Microsoft Excel 2003 using a Visual Basic interface system.

Predicting performance with traffic analysis tools : final report.

DOT National Transportation Integrated Search

2008-03-01

This document provides insights into the common pitfalls and challenges associated with use of traffic analysis tools for predicting future performance of a transportation facility. It provides five in-depth case studies that demonstrate common ways ...

VARS-TOOL: A Comprehensive, Efficient, and Robust Sensitivity Analysis Toolbox

NASA Astrophysics Data System (ADS)

Razavi, S.; Sheikholeslami, R.; Haghnegahdar, A.; Esfahbod, B.

2016-12-01

VARS-TOOL is an advanced sensitivity and uncertainty analysis toolbox, applicable to the full range of computer simulation models, including Earth and Environmental Systems Models (EESMs). The toolbox was developed originally around VARS (Variogram Analysis of Response Surfaces), which is a general framework for Global Sensitivity Analysis (GSA) that utilizes the variogram/covariogram concept to characterize the full spectrum of sensitivity-related information, thereby providing a comprehensive set of "global" sensitivity metrics with minimal computational cost. VARS-TOOL is unique in that, with a single sample set (set of simulation model runs), it generates simultaneously three philosophically different families of global sensitivity metrics, including (1) variogram-based metrics called IVARS (Integrated Variogram Across a Range of Scales - VARS approach), (2) variance-based total-order effects (Sobol approach), and (3) derivative-based elementary effects (Morris approach). VARS-TOOL is also enabled with two novel features; the first one being a sequential sampling algorithm, called Progressive Latin Hypercube Sampling (PLHS), which allows progressively increasing the sample size for GSA while maintaining the required sample distributional properties. The second feature is a "grouping strategy" that adaptively groups the model parameters based on their sensitivity or functioning to maximize the reliability of GSA results. These features in conjunction with bootstrapping enable the user to monitor the stability, robustness, and convergence of GSA with the increase in sample size for any given case study. VARS-TOOL has been shown to achieve robust and stable results within 1-2 orders of magnitude smaller sample sizes (fewer model runs) than alternative tools. VARS-TOOL, available in MATLAB and Python, is under continuous development and new capabilities and features are forthcoming.

Incorporation of Data Analysis throughout the ChE Curriculum Made Easy with DataFit

ERIC Educational Resources Information Center

Brenner, James R.

2007-01-01

At Florida Tech, we have incorporated DataFit from Oakdale Engineering throughout the entire curriculum, beginning with ChE 1102, an eight-week, one-day-per-week, two-hour, one-credit-hour, second-semester Introduction to Chemical Engineering course in a hands-on computer classroom. Our experience is that students retain data analysis concepts…

Analysis Tools for Next-Generation Hadron Spectroscopy Experiments

NASA Astrophysics Data System (ADS)

Battaglieri, M.; Briscoe, B. J.; Celentano, A.; Chung, S.-U.; D'Angelo, A.; De Vita, R.; Döring, M.; Dudek, J.; Eidelman, S.; Fegan, S.; Ferretti, J.; Filippi, A.; Fox, G.; Galata, G.; García-Tecocoatzi, H.; Glazier, D. I.; Grube, B.; Hanhart, C.; Hoferichter, M.; Hughes, S. M.; Ireland, D. G.; Ketzer, B.; Klein, F. J.; Kubis, B.; Liu, B.; Masjuan, P.; Mathieu, V.; McKinnon, B.; Mitchel, R.; Nerling, F.; Paul, S.; Peláez, J. R.; Rademacker, J.; Rizzo, A.; Salgado, C.; Santopinto, E.; Sarantsev, A. V.; Sato, T.; Schlüter, T.; [Silva]da Silva, M. L. L.; Stankovic, I.; Strakovsky, I.; Szczepaniak, A.; Vassallo, A.; Walford, N. K.; Watts, D. P.; Zana, L.

The series of workshops on New Partial-Wave Analysis Tools for Next-Generation Hadron Spectroscopy Experiments was initiated with the ATHOS 2012 meeting, which took place in Camogli, Italy, June 20-22, 2012. It was followed by ATHOS 2013 in Kloster Seeon near Munich, Germany, May 21-24, 2013. The third, ATHOS3, meeting is planned for April 13-17, 2015 at The George Washington University Virginia Science and Technology Campus, USA. The workshops focus on the development of amplitude analysis tools for meson and baryon spectroscopy, and complement other programs in hadron spectroscopy organized in the recent past including the INT-JLab Workshop on Hadron Spectroscopy in Seattle in 2009, the International Workshop on Amplitude Analysis in Hadron Spectroscopy at the ECT*-Trento in 2011, the School on Amplitude Analysis in Modern Physics in Bad Honnef in 2011, the Jefferson Lab Advanced Study Institute Summer School in 2012, and the School on Concepts of Modern Amplitude Analysis Techniques in Flecken-Zechlin near Berlin in September 2013. The aim of this document is to summarize the discussions that took place at the ATHOS 2012 and ATHOS 2013 meetings. We do not attempt a comprehensive review of the field of amplitude analysis, but offer a collection of thoughts that we hope may lay the ground for such a document.

Analysis Tools for Next-Generation Hadron Spectroscopy Experiments

DOE PAGES

Battaglieri, Marco; Briscoe, William; Celentano, Andrea; ...

2015-01-01

The series of workshops on New Partial-Wave Analysis Tools for Next-Generation Hadron Spectroscopy Experiments was initiated with the ATHOS 2012 meeting, which took place in Camogli, Italy, June 20-22, 2012. It was followed by ATHOS 2013 in Kloster Seeon near Munich, Germany, May 21-24, 2013. The third, ATHOS3, meeting is planned for April 13-17, 2015 at The George Washington University Virginia Science and Technology Campus, USA. The workshops focus on the development of amplitude analysis tools for meson and baryon spectroscopy, and complement other programs in hadron spectroscopy organized in the recent past including the INT-JLab Workshop on Hadron Spectroscopymore » in Seattle in 2009, the International Workshop on Amplitude Analysis in Hadron Spectroscopy at the ECT*-Trento in 2011, the School on Amplitude Analysis in Modern Physics in Bad Honnef in 2011, the Jefferson Lab Advanced Study Institute Summer School in 2012, and the School on Concepts of Modern Amplitude Analysis Techniques in Flecken-Zechlin near Berlin in September 2013. The aim of this document is to summarize the discussions that took place at the ATHOS 2012 and ATHOS 2013 meetings. We do not attempt a comprehensive review of the field of amplitude analysis, but offer a collection of thoughts that we hope may lay the ground for such a document.« less

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

NASA Technical Reports Server (NTRS)

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

2004-01-01

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

Tool Support for Parametric Analysis of Large Software Simulation Systems

NASA Technical Reports Server (NTRS)

Schumann, Johann; Gundy-Burlet, Karen; Pasareanu, Corina; Menzies, Tim; Barrett, Tony

2008-01-01

The analysis of large and complex parameterized software systems, e.g., systems simulation in aerospace, is very complicated and time-consuming due to the large parameter space, and the complex, highly coupled nonlinear nature of the different system components. Thus, such systems are generally validated only in regions local to anticipated operating points rather than through characterization of the entire feasible operational envelope of the system. We have addressed the factors deterring such an analysis with a tool to support envelope assessment: we utilize a combination of advanced Monte Carlo generation with n-factor combinatorial parameter variations to limit the number of cases, but still explore important interactions in the parameter space in a systematic fashion. Additional test-cases, automatically generated from models (e.g., UML, Simulink, Stateflow) improve the coverage. The distributed test runs of the software system produce vast amounts of data, making manual analysis impossible. Our tool automatically analyzes the generated data through a combination of unsupervised Bayesian clustering techniques (AutoBayes) and supervised learning of critical parameter ranges using the treatment learner TAR3. The tool has been developed around the Trick simulation environment, which is widely used within NASA. We will present this tool with a GN&C (Guidance, Navigation and Control) simulation of a small satellite system.

Incorporating Wind Excerpts in the School Band Curriculum

ERIC Educational Resources Information Center

Bruns, Robert

2010-01-01

Professional musicians and college students commonly study orchestral excerpts, but a similar practice has yet to be implemented in the band field. Due to their widespread use in orchestral auditions, excerpts have been incorporated as a tool for musical development. Many college professors regularly assign excerpt study as part of their…

Multi-body Dynamic Contact Analysis Tool for Transmission Design

DTIC Science & Technology

2003-04-01

frequencies were computed in COSMIC NASTRAN, and were validated against the published experimental modal analysis [17]. • Using assumed time domain... modal superposition. • Results from the structural analysis (mode shapes or forced response) were converted into IDEAS universal format (dataset 55...ARMY RESEARCH LABORATORY Multi-body Dynamic Contact Analysis Tool for Transmission Design SBIR Phase II Final Report by

Making Culturally Responsive Mathematics Teaching Explicit: A Lesson Analysis Tool

ERIC Educational Resources Information Center

Aguirre, Julia M.; Zavala, Maria del Rosario

2013-01-01

In the United States, there is a need for pedagogical tools that help teachers develop essential pedagogical content knowledge and practices to meet the mathematical education needs of a growing culturally and linguistically diverse student population. In this article, we introduce an innovative lesson analysis tool that focuses on integrating…

New Tools in Orthology Analysis: A Brief Review of Promising Perspectives

PubMed Central

Nichio, Bruno T. L.; Marchaukoski, Jeroniza Nunes; Raittz, Roberto Tadeu

2017-01-01

Nowadays defying homology relationships among sequences is essential for biological research. Within homology the analysis of orthologs sequences is of great importance for computational biology, annotation of genomes and for phylogenetic inference. Since 2007, with the increase in the number of new sequences being deposited in large biological databases, researchers have begun to analyse computerized methodologies and tools aimed at selecting the most promising ones in the prediction of orthologous groups. Literature in this field of research describes the problems that the majority of available tools show, such as those encountered in accuracy, time required for analysis (especially in light of the increasing volume of data being submitted, which require faster techniques) and the automatization of the process without requiring manual intervention. Conducting our search through BMC, Google Scholar, NCBI PubMed, and Expasy, we examined more than 600 articles pursuing the most recent techniques and tools developed to solve most the problems still existing in orthology detection. We listed the main computational tools created and developed between 2011 and 2017, taking into consideration the differences in the type of orthology analysis, outlining the main features of each tool and pointing to the problems that each one tries to address. We also observed that several tools still use as their main algorithm the BLAST “all-against-all” methodology, which entails some limitations, such as limited number of queries, computational cost, and high processing time to complete the analysis. However, new promising tools are being developed, like OrthoVenn (which uses the Venn diagram to show the relationship of ortholog groups generated by its algorithm); or proteinOrtho (which improves the accuracy of ortholog groups); or ReMark (tackling the integration of the pipeline to turn the entry process automatic); or OrthAgogue (using algorithms developed to minimize processing

New Tools in Orthology Analysis: A Brief Review of Promising Perspectives.

PubMed

Nichio, Bruno T L; Marchaukoski, Jeroniza Nunes; Raittz, Roberto Tadeu

2017-01-01

Nowadays defying homology relationships among sequences is essential for biological research. Within homology the analysis of orthologs sequences is of great importance for computational biology, annotation of genomes and for phylogenetic inference. Since 2007, with the increase in the number of new sequences being deposited in large biological databases, researchers have begun to analyse computerized methodologies and tools aimed at selecting the most promising ones in the prediction of orthologous groups. Literature in this field of research describes the problems that the majority of available tools show, such as those encountered in accuracy, time required for analysis (especially in light of the increasing volume of data being submitted, which require faster techniques) and the automatization of the process without requiring manual intervention. Conducting our search through BMC, Google Scholar, NCBI PubMed, and Expasy, we examined more than 600 articles pursuing the most recent techniques and tools developed to solve most the problems still existing in orthology detection. We listed the main computational tools created and developed between 2011 and 2017, taking into consideration the differences in the type of orthology analysis, outlining the main features of each tool and pointing to the problems that each one tries to address. We also observed that several tools still use as their main algorithm the BLAST "all-against-all" methodology, which entails some limitations, such as limited number of queries, computational cost, and high processing time to complete the analysis. However, new promising tools are being developed, like OrthoVenn (which uses the Venn diagram to show the relationship of ortholog groups generated by its algorithm); or proteinOrtho (which improves the accuracy of ortholog groups); or ReMark (tackling the integration of the pipeline to turn the entry process automatic); or OrthAgogue (using algorithms developed to minimize processing

Interactive Graphics Tools for Analysis of MOLA and Other Data

NASA Technical Reports Server (NTRS)

Frey, H.; Roark, J.; Sakimoto, S.

2000-01-01

We have developed several interactive analysis tools based on the IDL programming language for the analysis of Mars Orbiting Laser Altimeter (MOLA) profile and gridded data which are available to the general community.

OpenMSI Arrayed Analysis Tools v2.0

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

BOWEN, BENJAMIN; RUEBEL, OLIVER; DE ROND, TRISTAN

2017-02-07

Mass spectrometry imaging (MSI) enables high-resolution spatial mapping of biomolecules in samples and is a valuable tool for the analysis of tissues from plants and animals, microbial interactions, high-throughput screening, drug metabolism, and a host of other applications. This is accomplished by desorbing molecules from the surface on spatially defined locations, using a laser or ion beam. These ions are analyzed by a mass spectrometry and collected into a MSI 'image', a dataset containing unique mass spectra from the sampled spatial locations. MSI is used in a diverse and increasing number of biological applications. The OpenMSI Arrayed Analysis Tool (OMAAT)more » is a new software method that addresses the challenges of analyzing spatially defined samples in large MSI datasets, by providing support for automatic sample position optimization and ion selection.« less

RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis.

PubMed

Afzal, Muhammad; Shahid, Ahmad Ali; Shehzadi, Abida; Nadeem, Shahid; Husnain, Tayyab

2012-01-01

RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available. http://www.cemb.edu.pk/sw.html RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language.

RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis

PubMed Central

Afzal, Muhammad; Shahid, Ahmad Ali; Shehzadi, Abida; Nadeem, Shahid; Husnain, Tayyab

2012-01-01

RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available. Availability http://www.cemb.edu.pk/sw.html Abbreviations RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language. PMID:23055611

Incorporating INTERACT II Clinical Decision Support Tools into Nursing Home Health Information Technology

PubMed Central

Handler, Steven M.; Sharkey, Siobhan S.; Hudak, Sandra; Ouslander, Joseph G.

2012-01-01

A substantial reduction in hospitalization rates has been associated with the implementation of the Interventions to Reduce Acute Care Transfers (INTERACT) quality improvement intervention using the accompanying paper-based clinical practice tools (INTERACT II). There is significant potential to further increase the impact of INTERACT by integrating INTERACT II tools into nursing home (NH) health information technology (HIT) via standalone or integrated clinical decision support (CDS) systems. This article highlights the process of translating INTERACT II tools from paper to NH HIT. The authors believe that widespread dissemination and integration of INTERACT II CDS tools into various NH HIT products could lead to sustainable improvement in resident and clinician process and outcome measures, including enhanced interclinician communication and a reduction in potentially avoidable hospitalizations. PMID:22267955

Audio signal analysis for tool wear monitoring in sheet metal stamping

NASA Astrophysics Data System (ADS)

Ubhayaratne, Indivarie; Pereira, Michael P.; Xiang, Yong; Rolfe, Bernard F.

2017-02-01

Stamping tool wear can significantly degrade product quality, and hence, online tool condition monitoring is a timely need in many manufacturing industries. Even though a large amount of research has been conducted employing different sensor signals, there is still an unmet demand for a low-cost easy to set up condition monitoring system. Audio signal analysis is a simple method that has the potential to meet this demand, but has not been previously used for stamping process monitoring. Hence, this paper studies the existence and the significance of the correlation between emitted sound signals and the wear state of sheet metal stamping tools. The corrupting sources generated by the tooling of the stamping press and surrounding machinery have higher amplitudes compared to that of the sound emitted by the stamping operation itself. Therefore, a newly developed semi-blind signal extraction technique was employed as a pre-processing technique to mitigate the contribution of these corrupting sources. The spectral analysis results of the raw and extracted signals demonstrate a significant qualitative relationship between wear progression and the emitted sound signature. This study lays the basis for employing low-cost audio signal analysis in the development of a real-time industrial tool condition monitoring system.

Modelling the exposure to chemicals for risk assessment: a comprehensive library of multimedia and PBPK models for integration, prediction, uncertainty and sensitivity analysis - the MERLIN-Expo tool.

PubMed

Ciffroy, P; Alfonso, B; Altenpohl, A; Banjac, Z; Bierkens, J; Brochot, C; Critto, A; De Wilde, T; Fait, G; Fierens, T; Garratt, J; Giubilato, E; Grange, E; Johansson, E; Radomyski, A; Reschwann, K; Suciu, N; Tanaka, T; Tediosi, A; Van Holderbeke, M; Verdonck, F

2016-10-15

MERLIN-Expo is a library of models that was developed in the frame of the FP7 EU project 4FUN in order to provide an integrated assessment tool for state-of-the-art exposure assessment for environment, biota and humans, allowing the detection of scientific uncertainties at each step of the exposure process. This paper describes the main features of the MERLIN-Expo tool. The main challenges in exposure modelling that MERLIN-Expo has tackled are: (i) the integration of multimedia (MM) models simulating the fate of chemicals in environmental media, and of physiologically based pharmacokinetic (PBPK) models simulating the fate of chemicals in human body. MERLIN-Expo thus allows the determination of internal effective chemical concentrations; (ii) the incorporation of a set of functionalities for uncertainty/sensitivity analysis, from screening to variance-based approaches. The availability of such tools for uncertainty and sensitivity analysis aimed to facilitate the incorporation of such issues in future decision making; (iii) the integration of human and wildlife biota targets with common fate modelling in the environment. MERLIN-Expo is composed of a library of fate models dedicated to non biological receptor media (surface waters, soils, outdoor air), biological media of concern for humans (several cultivated crops, mammals, milk, fish), as well as wildlife biota (primary producers in rivers, invertebrates, fish) and humans. These models can be linked together to create flexible scenarios relevant for both human and wildlife biota exposure. Standardized documentation for each model and training material were prepared to support an accurate use of the tool by end-users. One of the objectives of the 4FUN project was also to increase the confidence in the applicability of the MERLIN-Expo tool through targeted realistic case studies. In particular, we aimed at demonstrating the feasibility of building complex realistic exposure scenarios and the accuracy of the

Incorporating Probability Models of Complex Test Structures to Perform Technology Independent FPGA Single Event Upset Analysis

NASA Technical Reports Server (NTRS)

Berg, M. D.; Kim, H. S.; Friendlich, M. A.; Perez, C. E.; Seidlick, C. M.; LaBel, K. A.

2011-01-01

We present SEU test and analysis of the Microsemi ProASIC3 FPGA. SEU Probability models are incorporated for device evaluation. Included is a comparison to the RTAXS FPGA illustrating the effectiveness of the overall testing methodology.

[Factor Analysis: Principles to Evaluate Measurement Tools for Mental Health].

PubMed

Campo-Arias, Adalberto; Herazo, Edwin; Oviedo, Heidi Celina

2012-09-01

The validation of a measurement tool in mental health is a complex process that usually starts by estimating reliability, to later approach its validity. Factor analysis is a way to know the number of dimensions, domains or factors of a measuring tool, generally related to the construct validity of the scale. The analysis could be exploratory or confirmatory, and helps in the selection of the items with better performance. For an acceptable factor analysis, it is necessary to follow some steps and recommendations, conduct some statistical tests, and rely on a proper sample of participants. Copyright © 2012 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

Software Construction and Analysis Tools for Future Space Missions

NASA Technical Reports Server (NTRS)

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

2002-01-01

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

Lightweight Low Force Rotary Percussive Coring Tool for Planetary Applications

NASA Technical Reports Server (NTRS)

Hironaka, Ross; Stanley, Scott

2010-01-01

A prototype low-force rotary-percussive rock coring tool for use in acquiring samples for geological surveys in future planetary missions was developed. The coring tool could eventually enable a lightweight robotic system to operate from a relatively small (less than 200 kg) mobile or fixed platform to acquire and cache Mars or other planetary rock samples for eventual return to Earth for analysis. To gain insight needed to design an integrated coring tool, the coring ability of commercially available coring bits was evaluated for effectiveness of varying key parameters: weight-on-bit, rotation speed, percussive rate and force. Trade studies were performed for different methods of breaking a core at its base and for retaining the core in a sleeve to facilitate sample transfer. This led to a custom coring tool design which incorporated coring, core breakage, core retention, and core extraction functions. The coring tool was tested on several types of rock and demonstrated the overall feasibility of this approach for robotic rock sample acquisition.

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

PubMed Central

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

2008-01-01

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

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

PubMed

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

2008-08-15

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

The NOAA Local Climate Analysis Tool - An Application in Support of a Weather Ready Nation

NASA Astrophysics Data System (ADS)

Timofeyeva, M. M.; Horsfall, F. M.

2012-12-01

Citizens across the U.S., including decision makers from the local to the national level, have a multitude of questions about climate, such as the current state and how that state fits into the historical context, and more importantly, how climate will impact them, especially with regard to linkages to extreme weather events. Developing answers to these types of questions for locations has typically required extensive work to gather data, conduct analyses, and generate relevant explanations and graphics. Too frequently providers don't have ready access to or knowledge of reliable, trusted data sets, nor sound, scientifically accepted analysis techniques such that they can provide a rapid response to queries they receive. In order to support National Weather Service (NWS) local office forecasters with information they need to deliver timely responses to climate-related questions from their customers, we have developed the Local Climate Analysis Tool (LCAT). LCAT uses the principles of artificial intelligence to respond to queries, in particular, through use of machine technology that responds intelligently to input from users. A user translates customer questions into primary variables and issues and LCAT pulls the most relevant data and analysis techniques to provide information back to the user, who in turn responds to their customer. Most responses take on the order of 10 seconds, which includes providing statistics, graphical displays of information, translations for users, metadata, and a summary of the user request to LCAT. Applications in Phase I of LCAT, which is targeted for the NWS field offices, include Climate Change Impacts, Climate Variability Impacts, Drought Analysis and Impacts, Water Resources Applications, Attribution of Extreme Events, and analysis techniques such as time series analysis, trend analysis, compositing, and correlation and regression techniques. Data accessed by LCAT are homogenized historical COOP and Climate Prediction Center

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

NASA Technical Reports Server (NTRS)

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

2017-01-01

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

Incorporation of tracers and dazomet by rotary tillers and a spading machine

Treesearch

J. Juzwik; D. L. Stenlund; R.R. Allmaras; S. M. Copeland; R. E. McRoberts

1997-01-01

Soil fumigant efficacy in forest-tree and ornamental nurseries depends on the tillage tool used for incorporation. Maximum depth and uniformity of incorporation of surface applied materials by three rotary tillers and a spading machine were compared in a loamy sand nursery using ceramic-sphere tracers (1-3 mm diameter) and dazomet (tetrahydro-3,5,dimethyl-2H-1,3,5-...

Errata: Response Analysis and Error Diagnosis Tools.

ERIC Educational Resources Information Center

Hart, Robert S.

This guide to ERRATA, a set of HyperCard-based tools for response analysis and error diagnosis in language testing, is intended as a user manual and general reference and designed to be used with the software (not included here). It has three parts. The first is a brief survey of computational techniques available for dealing with student test…

Overview of the Development for a Suite of Low-Thrust Trajectory Analysis Tools

NASA Technical Reports Server (NTRS)

Kos, Larry D.; Polsgrove, Tara; Hopkins, Randall; Thomas, Dan; Sims, Jon A.

2006-01-01

A NASA intercenter team has developed a suite of low-thrust trajectory analysis tools to make a significant improvement in three major facets of low-thrust trajectory and mission analysis. These are: 1) ease of use, 2) ability to more robustly converge to solutions, and 3) higher fidelity modeling and accuracy of results. Due mostly to the short duration of the development, the team concluded that a suite of tools was preferred over having one integrated tool. This tool-suite, their characteristics, and their applicability will be described. Trajectory analysts can read this paper and determine which tool is most appropriate for their problem.

Design and analysis of lifting tool assemblies to lift different engine block

NASA Astrophysics Data System (ADS)

Sawant, Arpana; Deshmukh, Nilaj N.; Chauhan, Santosh; Dabhadkar, Mandar; Deore, Rupali

2017-07-01

Engines block are required to be lifted from one place to another while they are being processed. The human effort required for this purpose is more and also the engine block may get damaged if it is not handled properly. There is a need for designing a proper lifting tool which will be able to conveniently lift the engine block and place it at the desired position without any accident and damage to the engine block. In the present study lifting tool assemblies are designed and analyzed in such way that it may lift different categories of engine blocks. The lifting tool assembly consists of lifting plate, lifting ring, cap screws and washers. A parametric model and assembly of Lifting tool is done in 3D modelling software CREO 2.0 and analysis is carried out in ANSYS Workbench 16.0. A test block of weight equivalent to that of an engine block is considered for the purpose of analysis. In the preliminary study, without washer the stresses obtained on the lifting tool were more than the safety margin. In the present design, washers were used with appropriate dimensions which helps to bring down the stresses on the lifting tool within the safety margin. Analysis is carried out to verify that tool design meets the ASME BTH-1 required safety margin.

Generic trending and analysis system

NASA Technical Reports Server (NTRS)

Keehan, Lori; Reese, Jay

1994-01-01

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

Upgrade of DRAMA-ESA's Space Debris Mitigation Analysis Tool Suite

NASA Astrophysics Data System (ADS)

Gelhaus, Johannes; Sanchez-Ortiz, Noelia; Braun, Vitali; Kebschull, Christopher; de Oliveira, Joaquim Correia; Dominguez-Gonzalez, Raul; Wiedemann, Carsten; Krag, Holger; Vorsmann, Peter

2013-08-01

One decade ago ESA started the dev elopment of the first version of the software tool called DRAMA (Debris Risk Assessment and Mitigation Analysis) to enable ESA space programs to assess their compliance with the recommendations in the European Code of Conduct for Space Debris Mitigation. This tool was maintained, upgraded and extended during the last year and is now a combination of five individual tools, each addressing a different aspect of debris mitigation. This paper gives an overview of the new DRAMA software in general. Both, the main tools ARES, OSCAR, MIDAS, CROC and SARA will be discussed and the environment used by DRAMA will be explained shortly.

TACIT: An open-source text analysis, crawling, and interpretation tool.

PubMed

Dehghani, Morteza; Johnson, Kate M; Garten, Justin; Boghrati, Reihane; Hoover, Joe; Balasubramanian, Vijayan; Singh, Anurag; Shankar, Yuvarani; Pulickal, Linda; Rajkumar, Aswin; Parmar, Niki Jitendra

2017-04-01

As human activity and interaction increasingly take place online, the digital residues of these activities provide a valuable window into a range of psychological and social processes. A great deal of progress has been made toward utilizing these opportunities; however, the complexity of managing and analyzing the quantities of data currently available has limited both the types of analysis used and the number of researchers able to make use of these data. Although fields such as computer science have developed a range of techniques and methods for handling these difficulties, making use of those tools has often required specialized knowledge and programming experience. The Text Analysis, Crawling, and Interpretation Tool (TACIT) is designed to bridge this gap by providing an intuitive tool and interface for making use of state-of-the-art methods in text analysis and large-scale data management. Furthermore, TACIT is implemented as an open, extensible, plugin-driven architecture, which will allow other researchers to extend and expand these capabilities as new methods become available.

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.

Computational Tools and Facilities for the Next-Generation Analysis and Design Environment

NASA Technical Reports Server (NTRS)

Noor, Ahmed K. (Compiler); Malone, John B. (Compiler)

1997-01-01

This document contains presentations from the joint UVA/NASA Workshop on Computational Tools and Facilities for the Next-Generation Analysis and Design Environment held at the Virginia Consortium of Engineering and Science Universities in Hampton, Virginia on September 17-18, 1996. The presentations focused on the computational tools and facilities for analysis and design of engineering systems, including, real-time simulations, immersive systems, collaborative engineering environment, Web-based tools and interactive media for technical training. Workshop attendees represented NASA, commercial software developers, the aerospace industry, government labs, and academia. The workshop objectives were to assess the level of maturity of a number of computational tools and facilities and their potential for application to the next-generation integrated design environment.

Transportation systems safety hazard analysis tool (SafetyHAT) user guide (version 1.0)

DOT National Transportation Integrated Search

2014-03-24

This is a user guide for the transportation system Safety Hazard Analysis Tool (SafetyHAT) Version 1.0. SafetyHAT is a software tool that facilitates System Theoretic Process Analysis (STPA.) This user guide provides instructions on how to download, ...

Integrated Modeling Tools for Thermal Analysis and Applications

NASA Technical Reports Server (NTRS)

Milman, Mark H.; Needels, Laura; Papalexandris, Miltiadis

1999-01-01

Integrated modeling of spacecraft systems is a rapidly evolving area in which multidisciplinary models are developed to design and analyze spacecraft configurations. These models are especially important in the early design stages where rapid trades between subsystems can substantially impact design decisions. Integrated modeling is one of the cornerstones of two of NASA's planned missions in the Origins Program -- the Next Generation Space Telescope (NGST) and the Space Interferometry Mission (SIM). Common modeling tools for control design and opto-mechanical analysis have recently emerged and are becoming increasingly widely used. A discipline that has been somewhat less integrated, but is nevertheless of critical concern for high precision optical instruments, is thermal analysis and design. A major factor contributing to this mild estrangement is that the modeling philosophies and objectives for structural and thermal systems typically do not coincide. Consequently the tools that are used in these discplines suffer a degree of incompatibility, each having developed along their own evolutionary path. Although standard thermal tools have worked relatively well in the past. integration with other disciplines requires revisiting modeling assumptions and solution methods. Over the past several years we have been developing a MATLAB based integrated modeling tool called IMOS (Integrated Modeling of Optical Systems) which integrates many aspects of structural, optical, control and dynamical analysis disciplines. Recent efforts have included developing a thermal modeling and analysis capability, which is the subject of this article. Currently, the IMOS thermal suite contains steady state and transient heat equation solvers, and the ability to set up the linear conduction network from an IMOS finite element model. The IMOS code generates linear conduction elements associated with plates and beams/rods of the thermal network directly from the finite element structural

Aeroelastic Analysis of Helicopter Rotor Blades Incorporating Anisotropic Piezoelectric Twist Actuation

NASA Technical Reports Server (NTRS)

Wilkie, W. Keats; Belvin, W. Keith; Park, K. C.

1996-01-01

A simple aeroelastic analysis of a helicopter rotor blade incorporating embedded piezoelectric fiber composite, interdigitated electrode blade twist actuators is described. The analysis consists of a linear torsion and flapwise bending model coupled with a nonlinear ONERA based unsteady aerodynamics model. A modified Galerkin procedure is performed upon the rotor blade partial differential equations of motion to develop a system of ordinary differential equations suitable for dynamics simulation using numerical integration. The twist actuation responses for three conceptual fullscale blade designs with realistic constraints on blade mass are numerically evaluated using the analysis. Numerical results indicate that useful amplitudes of nonresonant elastic twist, on the order of one to two degrees, are achievable under one-g hovering flight conditions for interdigitated electrode poling configurations. Twist actuation for the interdigitated electrode blades is also compared with the twist actuation of a conventionally poled piezoelectric fiber composite blade. Elastic twist produced using the interdigitated electrode actuators was found to be four to five times larger than that obtained with the conventionally poled actuators.

Multi-criteria decision analysis tools for prioritising emerging or re-emerging infectious diseases associated with climate change in Canada.

PubMed

Cox, Ruth; Sanchez, Javier; Revie, Crawford W

2013-01-01

Global climate change is known to result in the emergence or re-emergence of some infectious diseases. Reliable methods to identify the infectious diseases of humans and animals and that are most likely to be influenced by climate are therefore required. Since different priorities will affect the decision to address a particular pathogen threat, decision makers need a standardised method of prioritisation. Ranking methods and Multi-Criteria Decision approaches provide such a standardised method and were employed here to design two different pathogen prioritisation tools. The opinion of 64 experts was elicited to assess the importance of 40 criteria that could be used to prioritise emerging infectious diseases of humans and animals in Canada. A weight was calculated for each criterion according to the expert opinion. Attributes were defined for each criterion as a transparent and repeatable method of measurement. Two different Multi-Criteria Decision Analysis tools were tested, both of which used an additive aggregation approach. These were an Excel spreadsheet tool and a tool developed in software 'M-MACBETH'. The tools were trialed on nine 'test' pathogens. Two different methods of criteria weighting were compared, one using fixed weighting values, the other using probability distributions to account for uncertainty and variation in expert opinion. The ranking of the nine pathogens varied according to the weighting method that was used. In both tools, using both weighting methods, the diseases that tended to rank the highest were West Nile virus, Giardiasis and Chagas, while Coccidioidomycosis tended to rank the lowest. Both tools are a simple and user friendly approach to prioritising pathogens according to climate change by including explicit scoring of 40 criteria and incorporating weighting methods based on expert opinion. They provide a dynamic interactive method that can help to identify pathogens for which a full risk assessment should be pursued.

Multi-Criteria Decision Analysis Tools for Prioritising Emerging or Re-Emerging Infectious Diseases Associated with Climate Change in Canada

PubMed Central

Cox, Ruth; Sanchez, Javier; Revie, Crawford W.

2013-01-01

Global climate change is known to result in the emergence or re-emergence of some infectious diseases. Reliable methods to identify the infectious diseases of humans and animals and that are most likely to be influenced by climate are therefore required. Since different priorities will affect the decision to address a particular pathogen threat, decision makers need a standardised method of prioritisation. Ranking methods and Multi-Criteria Decision approaches provide such a standardised method and were employed here to design two different pathogen prioritisation tools. The opinion of 64 experts was elicited to assess the importance of 40 criteria that could be used to prioritise emerging infectious diseases of humans and animals in Canada. A weight was calculated for each criterion according to the expert opinion. Attributes were defined for each criterion as a transparent and repeatable method of measurement. Two different Multi-Criteria Decision Analysis tools were tested, both of which used an additive aggregation approach. These were an Excel spreadsheet tool and a tool developed in software ‘M-MACBETH’. The tools were trialed on nine ‘test’ pathogens. Two different methods of criteria weighting were compared, one using fixed weighting values, the other using probability distributions to account for uncertainty and variation in expert opinion. The ranking of the nine pathogens varied according to the weighting method that was used. In both tools, using both weighting methods, the diseases that tended to rank the highest were West Nile virus, Giardiasis and Chagas, while Coccidioidomycosis tended to rank the lowest. Both tools are a simple and user friendly approach to prioritising pathogens according to climate change by including explicit scoring of 40 criteria and incorporating weighting methods based on expert opinion. They provide a dynamic interactive method that can help to identify pathogens for which a full risk assessment should be pursued

Evaluation of an open source tool for indexing and searching enterprise radiology and pathology reports

NASA Astrophysics Data System (ADS)

Kim, Woojin; Boonn, William

2010-03-01

Data mining of existing radiology and pathology reports within an enterprise health system can be used for clinical decision support, research, education, as well as operational analyses. In our health system, the database of radiology and pathology reports exceeds 13 million entries combined. We are building a web-based tool to allow search and data analysis of these combined databases using freely available and open source tools. This presentation will compare performance of an open source full-text indexing tool to MySQL's full-text indexing and searching and describe implementation procedures to incorporate these capabilities into a radiology-pathology search engine.

Scheduling Results for the THEMIS Observation Scheduling Tool

NASA Technical Reports Server (NTRS)

Mclaren, David; Rabideau, Gregg; Chien, Steve; Knight, Russell; Anwar, Sadaat; Mehall, Greg; Christensen, Philip

2011-01-01

We describe a scheduling system intended to assist in the development of instrument data acquisitions for the THEMIS instrument, onboard the Mars Odyssey spacecraft, and compare results from multiple scheduling algorithms. This tool creates observations of both (a) targeted geographical regions of interest and (b) general mapping observations, while respecting spacecraft constraints such as data volume, observation timing, visibility, lighting, season, and science priorities. This tool therefore must address both geometric and state/timing/resource constraints. We describe a tool that maps geometric polygon overlap constraints to set covering constraints using a grid-based approach. These set covering constraints are then incorporated into a greedy optimization scheduling algorithm incorporating operations constraints to generate feasible schedules. The resultant tool generates schedules of hundreds of observations per week out of potential thousands of observations. This tool is currently under evaluation by the THEMIS observation planning team at Arizona State University.

EZ and GOSSIP, two new VO compliant tools for spectral analysis

NASA Astrophysics Data System (ADS)

Franzetti, P.; Garill, B.; Fumana, M.; Paioro, L.; Scodeggio, M.; Paltani, S.; Scaramella, R.

2008-10-01

We present EZ and GOSSIP, two new VO compliant tools dedicated to spectral analysis. EZ is a tool to perform automatic redshift measurement; GOSSIP is a tool created to perform the SED fitting procedure in a simple, user friendly and efficient way. These two tools have been developed by the PANDORA Group at INAF-IASF (Milano); EZ has been developed in collaboration with Osservatorio Monte Porzio (Roma) and Integral Science Data Center (Geneve). EZ is released to the astronomical community; GOSSIP is currently in beta-testing.

The Precision Formation Flying Integrated Analysis Tool (PFFIAT)

NASA Technical Reports Server (NTRS)

Stoneking, Eric; Lyon, Richard G.; Sears, Edie; Lu, Victor

2004-01-01

Several space missions presently in the concept phase (e.g. Stellar Imager, Submillimeter Probe of Evolutionary Cosmic Structure, Terrestrial Planet Finder) plan to use multiple spacecraft flying in precise formation to synthesize unprecedently large aperture optical systems. These architectures present challenges to the attitude and position determination and control system; optical performance is directly coupled to spacecraft pointing with typical control requirements being on the scale of milliarcseconds and nanometers. To investigate control strategies, rejection of environmental disturbances, and sensor and actuator requirements, a capability is needed to model both the dynamical and optical behavior of such a distributed telescope system. This paper describes work ongoing at NASA Goddard Space Flight Center toward the integration of a set of optical analysis tools (Optical System Characterization and Analysis Research software, or OSCAR) with the Formation Flying Test Bed (FFTB). The resulting system is called the Precision Formation Flying Integrated Analysis Tool (PFFIAT), and it provides the capability to simulate closed-loop control of optical systems composed of elements mounted on multiple spacecraft. The attitude and translation spacecraft dynamics are simulated in the FFTB, including effects of the space environment (e.g. solar radiation pressure, differential orbital motion). The resulting optical configuration is then processed by OSCAR to determine an optical image. From this image, wavefront sensing (e.g. phase retrieval) techniques are being developed to derive attitude and position errors. These error signals will be fed back to the spacecraft control systems, completing the control loop. A simple case study is presented to demonstrate the present capabilities of the tool.

The Precision Formation Flying Integrated Analysis Tool (PFFIAT)

NASA Technical Reports Server (NTRS)

Stoneking, Eric; Lyon, Richard G.; Sears, Edie; Lu, Victor

2004-01-01

Several space missions presently in the concept phase (e.g. Stellar Imager, Sub- millimeter Probe of Evolutionary Cosmic Structure, Terrestrial Planet Finder) plan to use multiple spacecraft flying in precise formation to synthesize unprecedently large aperture optical systems. These architectures present challenges to the attitude and position determination and control system; optical performance is directly coupled to spacecraft pointing with typical control requirements being on the scale of milliarcseconds and nanometers. To investigate control strategies, rejection of environmental disturbances, and sensor and actuator requirements, a capability is needed to model both the dynamical and optical behavior of such a distributed telescope system. This paper describes work ongoing at NASA Goddard Space Flight Center toward the integration of a set of optical analysis tools (Optical System Characterization and Analysis Research software, or OSCAR) with the Formation J?lying Test Bed (FFTB). The resulting system is called the Precision Formation Flying Integrated Analysis Tool (PFFIAT), and it provides the capability to simulate closed-loop control of optical systems composed of elements mounted on multiple spacecraft. The attitude and translation spacecraft dynamics are simulated in the FFTB, including effects of the space environment (e.g. solar radiation pressure, differential orbital motion). The resulting optical configuration is then processed by OSCAR to determine an optical image. From this image, wavefront sensing (e.g. phase retrieval) techniques are being developed to derive attitude and position errors. These error signals will be fed back to the spacecraft control systems, completing the control loop. A simple case study is presented to demonstrate the present capabilities of the tool.

Incorporating Eco-Evolutionary Processes into Population Models:Design and Applications

EPA Science Inventory

Eco-evolutionary population models are powerful new tools for exploring howevolutionary processes influence plant and animal population dynamics andvice-versa. The need to manage for climate change and other dynamicdisturbance regimes is creating a demand for the incorporation of...

A Registry for Planetary Data Tools and Services

NASA Astrophysics Data System (ADS)

Hardman, S.; Cayanan, M.; Hughes, J. S.; Joyner, R.; Crichton, D.; Law, E.

2018-04-01

The PDS Engineering Node has upgraded a prototype Tool Registry developed by the International Planetary Data Alliance to increase the visibility and enhance functionality along with incorporating the registered tools into PDS data search results.

Development of a decision support tool for seasonal water supply management incorporating system uncertainties and operational constraints

NASA Astrophysics Data System (ADS)

Wang, H.; Asefa, T.

2017-12-01

A real-time decision support tool (DST) for water supply system would consider system uncertainties, e.g., uncertain streamflow and demand, as well as operational constraints and infrastructure outage (e.g., pump station shutdown, an offline reservoir due to maintenance). Such DST is often used by water managers for resource allocation and delivery for customers. Although most seasonal DST used by water managers recognize those system uncertainties and operational constraints, most use only historical information or assume deterministic outlook of water supply systems. This study presents a seasonal DST that incorporates rainfall/streamflow uncertainties, seasonal demand outlook and system operational constraints. Large scale climate-information is captured through a rainfall simulator driven by a Bayesian non-homogeneous Markov Chain Monte Carlo model that allows non-stationary transition probabilities contingent on Nino 3.4 index. An ad-hoc seasonal demand forecasting model considers weather conditions explicitly and socio-economic factors implicitly. Latin Hypercube sampling is employed to effectively sample probability density functions of flow and demand. Seasonal system operation is modelled as a mixed-integer optimization problem that aims at minimizing operational costs. It embeds the flexibility of modifying operational rules at different components, e.g., surface water treatment plants, desalination facilities, and groundwater pumping stations. The proposed framework is illustrated at a wholesale water supplier in Southeastern United States, Tampa Bay Water. The use of the tool is demonstrated in proving operational guidance in a typical drawdown and refill cycle of a regional reservoir. The DST provided: 1) probabilistic outlook of reservoir storage and chance of a successful refill by the end of rainy season; 2) operational expectations for large infrastructures (e.g., high service pumps and booster stations) throughout the season. Other potential use

MEETING IN CHICAGO: SADA: A FREEWARE DECISION SUPPORT TOOL INTEGRATING GIS, SAMPLE DESIGN, SPATIAL MODELING, AND ENVIRONMENTAL RISK ASSESSMENT

EPA Science Inventory

Spatial Analysis and Decision Assistance (SADA) is a Windows freeware program that incorporates tools from environmental assessment into an effective problem-solving environment. SADA was developed by the Institute for Environmental Modeling at the University of Tennessee and inc...

MEETING IN CZECH REPUBLIC: SADA: A FREEWARE DECISION SUPPORT TOOL INTEGRATING GIS, SAMPLE DESIGN, SPATIAL MODELING, AND RISK ASSESSMENT

EPA Science Inventory

Spatial Analysis and Decision Assistance (SADA) is a Windows freeware program that incorporates tools from environmental assessment into an effective problem-solving environment. SADA was developed by the Institute for Environmental Modeling at the University of Tennessee and inc...

Managing complex research datasets using electronic tools: a meta-analysis exemplar.

PubMed

Brown, Sharon A; Martin, Ellen E; Garcia, Theresa J; Winter, Mary A; García, Alexandra A; Brown, Adama; Cuevas, Heather E; Sumlin, Lisa L

2013-06-01

Meta-analyses of broad scope and complexity require investigators to organize many study documents and manage communication among several research staff. Commercially available electronic tools, for example, EndNote, Adobe Acrobat Pro, Blackboard, Excel, and IBM SPSS Statistics (SPSS), are useful for organizing and tracking the meta-analytic process as well as enhancing communication among research team members. The purpose of this article is to describe the electronic processes designed, using commercially available software, for an extensive, quantitative model-testing meta-analysis. Specific electronic tools improved the efficiency of (a) locating and screening studies, (b) screening and organizing studies and other project documents, (c) extracting data from primary studies, (d) checking data accuracy and analyses, and (e) communication among team members. The major limitation in designing and implementing a fully electronic system for meta-analysis was the requisite upfront time to decide on which electronic tools to use, determine how these tools would be used, develop clear guidelines for their use, and train members of the research team. The electronic process described here has been useful in streamlining the process of conducting this complex meta-analysis and enhancing communication and sharing documents among research team members.

Ramping and Uncertainty Prediction Tool - Analysis and Visualization of Wind Generation Impact on Electrical Grid

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

Etingov, Pavel; Makarov, PNNL Yuri; Subbarao, PNNL Kris

RUT software is designed for use by the Balancing Authorities to predict and display additional requirements caused by the variability and uncertainty in load and generation. The prediction is made for the next operating hours as well as for the next day. The tool predicts possible deficiencies in generation capability and ramping capability. This deficiency of balancing resources can cause serious risks to power system stability and also impact real-time market energy prices. The tool dynamically and adaptively correlates changing system conditions with the additional balancing needs triggered by the interplay between forecasted and actual load and output of variablemore » resources. The assessment is performed using a specially developed probabilistic algorithm incorporating multiple sources of uncertainty including wind, solar and load forecast errors. The tool evaluates required generation for a worst case scenario, with a user-specified confidence level.« less

Capturing district nursing through a knowledge-based electronic caseload analysis tool (eCAT).

PubMed

Kane, Kay

2014-03-01

The Electronic Caseload Analysis Tool (eCAT) is a knowledge-based software tool to assist the caseload analysis process. The tool provides a wide range of graphical reports, along with an integrated clinical advisor, to assist district nurses, team leaders, operational and strategic managers with caseload analysis by describing, comparing and benchmarking district nursing practice in the context of population need, staff resources, and service structure. District nurses and clinical lead nurses in Northern Ireland developed the tool, along with academic colleagues from the University of Ulster, working in partnership with a leading software company. The aim was to use the eCAT tool to identify the nursing need of local populations, along with the variances in district nursing practice, and match the workforce accordingly. This article reviews the literature, describes the eCAT solution and discusses the impact of eCAT on nursing practice, staff allocation, service delivery and workforce planning, using fictitious exemplars and a post-implementation evaluation from the trusts.

Design of a Syntax Validation Tool for Requirements Analysis Using Structured Analysis and Design Technique (SADT)

DTIC Science & Technology

1988-09-01

analysis phase of the software life cycle (16:1-1). While editing a SADT diagram, the tool should be able to check whether or not structured analysis...diag-ams are valid for the SADT’s syntax, produce error messages, do error recovery, and perform editing suggestions. Thus, this tool must have the...directed editors are editors which use the syn- tax of the programming language while editing a program. While text editors treat programs as text, syntax

DEVELOPING NEW TOOLS FOR POLICY ANALYSIS

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

Donovan, Richard L.; Schwartz, Michael J.; Selby, Kevin B.

2010-08-11

For the past three years, the Office of Security Policy has been aggressively pursuing substantial improvements in the U. S. Department of Energy (DOE) regulations and directives related to safeguards and security (S&S). An initial effort focused on areas where specific improvements could be made. This revision was completed during 2009 with the publication of a number of revised manuals. Developing these revisions involved more than 100 experts in the various disciplines involved, yet the changes made were only those that could be identified and agreed upon based largely on expert opinion. The next phase of changes will be moremore » analytically based. A thorough review of the entire (S&S) directives set will be conducted using software tools to analyze the present directives with a view toward 1) identifying areas of positive synergism among topical areas, 2) identifying areas of unnecessary duplication within and among topical areas, and 3) identifying requirements that are less than effective in achieving the intended protection goals. This paper will describe the software tools available and in development that will be used in this effort. Some examples of the output of the tools will be included, as will a short discussion of the follow-on analysis that will be performed when these outputs are available to policy analysts.« less

PySCeSToolbox: a collection of metabolic pathway analysis tools.

PubMed

Christensen, Carl D; Hofmeyr, Jan-Hendrik S; Rohwer, Johann M

2018-01-01

PySCeSToolbox is an extension to the Python Simulator for Cellular Systems (PySCeS) that includes tools for performing generalized supply-demand analysis, symbolic metabolic control analysis, and a framework for investigating the kinetic and thermodynamic aspects of enzyme-catalyzed reactions. Each tool addresses a different aspect of metabolic behaviour, control, and regulation; the tools complement each other and can be used in conjunction to better understand higher level system behaviour. PySCeSToolbox is available on Linux, Mac OS X and Windows. It is licensed under the BSD 3-clause licence. Code, setup instructions and a link to documentation can be found at https://github.com/PySCeS/PyscesToolbox. jr@sun.ac.za. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Development of a task analysis tool to facilitate user interface design

NASA Technical Reports Server (NTRS)

Scholtz, Jean C.

1992-01-01

A good user interface is one that facilitates the user in carrying out his task. Such interfaces are difficult and costly to produce. The most important aspect in producing a good interface is the ability to communicate to the software designers what the user's task is. The Task Analysis Tool is a system for cooperative task analysis and specification of the user interface requirements. This tool is intended to serve as a guide to development of initial prototypes for user feedback.

Use of New Communication Technologies to Change NASA Safety Culture: Incorporating the Use of Blogs as a Fundamental Communications Tool

NASA Astrophysics Data System (ADS)

Huls, Dale Thomas

2005-12-01

Blogs are an increasingly dominant new communication function on the internet. The power of this technology has forced media, corporations and government organizations to begin to incorporate blogging into their normal business practices. Blogs could be a key component to overcoming NASA's "silent safety culture." As a communications tool, blogs are used to establish trust primarily through the use of a personal voice style of writing. Dissenting voices can be raised and thoroughly vetted via a diversity of participation and experience without peer pressure or fear of retribution. Furthermore, the benefits of blogging as a technical resource to enhance safety are also discussed. The speed and self-vetting nature of blogging can allow managers and decision-makers to make more informed and therefore potentially better decisions with regard to technical and safety issues. Consequently, it is recommended that NASA utilize this new technology as an agent for cultural change.

Microgrid Analysis Tools Summary

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

Jimenez, Antonio; Haase, Scott G; Mathur, Shivani

2018-03-05

The over-arching goal of the Alaska Microgrid Partnership is to reduce the use of total imported fuel into communities to secure all energy services by at least 50% in Alaska's remote microgrids without increasing system life cycle costs while also improving overall system reliability, security, and resilience. One goal of the Alaska Microgrid Partnership is to investigate whether a combination of energy efficiency and high-contribution (from renewable energy) power systems can reduce total imported energy usage by 50% while reducing life cycle costs and improving reliability and resiliency. This presentation provides an overview of the following four renewable energy optimizationmore » tools. Information is from respective tool websites, tool developers, and author experience. Distributed Energy Resources Customer Adoption Model (DER-CAM) Microgrid Design Toolkit (MDT) Renewable Energy Optimization (REopt) Tool Hybrid Optimization Model for Electric Renewables (HOMER).« less

R-based Tool for a Pairwise Structure-activity Relationship Analysis.

PubMed

Klimenko, Kyrylo

2018-04-01

The Structure-Activity Relationship analysis is a complex process that can be enhanced by computational techniques. This article describes a simple tool for SAR analysis that has a graphic user interface and a flexible approach towards the input of molecular data. The application allows calculating molecular similarity represented by Tanimoto index & Euclid distance, as well as, determining activity cliffs by means of Structure-Activity Landscape Index. The calculation is performed in a pairwise manner either for the reference compound and other compounds or for all possible pairs in the data set. The results of SAR analysis are visualized using two types of plot. The application capability is demonstrated by the analysis of a set of COX2 inhibitors with respect to Isoxicam. This tool is available online: it includes manual and input file examples. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Efficacy of antimicrobial agents incorporated in orthodontic bonding systems: a systematic review and meta-analysis.

PubMed

de Almeida, C M; da Rosa, W L O; Meereis, C T W; de Almeida, S M; Ribeiro, J S; da Silva, A F; Lund, Rafael Guerra

2018-06-01

The purpose of this study was to evaluate the efficacy of orthodontic bonding systems containing different antimicrobial agents, as well as the influence of antimicrobial agent incorporation in the bonding properties of these materials. Eight databases were searched: PubMed (Medline), Web of Science, Scopus, Lilacs, Ibecs, BBO, Scielo and Google Scholar. Any study that evaluated antimicrobial activity in experimental or commercial orthodontic bonding systems was included. Data were tabulated independently and in duplicated by two authors on pre-designed data collection form. The global analysis was carried out using a random-effects model, and pooled-effect estimates were obtained by comparing the standardised mean difference of each antimicrobial orthodontic adhesive with the respective control group. A p-value < .05 was considered as statistically significant. Thirty-two studies were included in the qualitative analysis; of these, 22 studies were included in the meta-analysis. Antimicrobial agents such as silver nanoparticles, benzalkonium chloride, chlorhexidine, triclosan, cetylpyridinium chloride, Galla chinensis extract, acid ursolic, dimethylaminododecyl methacrylate, dimethylaminohexadecyl methacrylate, 2-methacryloyloxyethyl phosphorylcholine, 1,3,5-triacryloylhexahydro-1,3,5-triazine, zinc oxide and titanium oxide have been incorporated into orthodontic bonding systems. The antimicrobial agent incorporation in orthodontic bonding systems showed higher antimicrobial activity than the control group in agar diffusion (overall standardised mean difference: 3.71; 95% CI 2.98 to 4.43) and optical density tests (0.41; 95% CI -0.05 to 0.86) (p < .05). However, for biofilm, the materials did not present antimicrobial activity (6.78; 95% CI 4.78 to 8.77). Regarding bond strength, the global analysis showed antimicrobial orthodontic bonding systems were statistically similar to the control. Although there is evidence of antibacterial activity from in vitro

CloudMan as a platform for tool, data, and analysis distribution.

PubMed

Afgan, Enis; Chapman, Brad; Taylor, James

2012-11-27

Cloud computing provides an infrastructure that facilitates large scale computational analysis in a scalable, democratized fashion, However, in this context it is difficult to ensure sharing of an analysis environment and associated data in a scalable and precisely reproducible way. CloudMan (usecloudman.org) enables individual researchers to easily deploy, customize, and share their entire cloud analysis environment, including data, tools, and configurations. With the enabled customization and sharing of instances, CloudMan can be used as a platform for collaboration. The presented solution improves accessibility of cloud resources, tools, and data to the level of an individual researcher and contributes toward reproducibility and transparency of research solutions.

Open source tools for ATR development and performance evaluation

NASA Astrophysics Data System (ADS)

Baumann, James M.; Dilsavor, Ronald L.; Stubbles, James; Mossing, John C.

2002-07-01

Early in almost every engineering project, a decision must be made about tools; should I buy off-the-shelf tools or should I develop my own. Either choice can involve significant cost and risk. Off-the-shelf tools may be readily available, but they can be expensive to purchase and to maintain licenses, and may not be flexible enough to satisfy all project requirements. On the other hand, developing new tools permits great flexibility, but it can be time- (and budget-) consuming, and the end product still may not work as intended. Open source software has the advantages of both approaches without many of the pitfalls. This paper examines the concept of open source software, including its history, unique culture, and informal yet closely followed conventions. These characteristics influence the quality and quantity of software available, and ultimately its suitability for serious ATR development work. We give an example where Python, an open source scripting language, and OpenEV, a viewing and analysis tool for geospatial data, have been incorporated into ATR performance evaluation projects. While this case highlights the successful use of open source tools, we also offer important insight into risks associated with this approach.

Virtual tool mark generation for efficient striation analysis in forensic science

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

Ekstrand, Laura

In 2009, a National Academy of Sciences report called for investigation into the scienti c basis behind tool mark comparisons (National Academy of Sciences, 2009). Answering this call, Chumbley et al. (2010) attempted to prove or disprove the hypothesis that tool marks are unique to a single tool. They developed a statistical algorithm that could, in most cases, discern matching and non-matching tool marks made at di erent angles by sequentially numbered screwdriver tips. Moreover, in the cases where the algorithm misinterpreted a pair of marks, an experienced forensics examiner could discern the correct outcome. While this research served tomore » con rm the basic assumptions behind tool mark analysis, it also suggested that statistical analysis software could help to reduce the examiner's workload. This led to a new tool mark analysis approach, introduced in this thesis, that relies on 3D scans of screwdriver tip and marked plate surfaces at the micrometer scale from an optical microscope. These scans are carefully cleaned to remove noise from the data acquisition process and assigned a coordinate system that mathematically de nes angles and twists in a natural way. The marking process is then simulated by using a 3D graphics software package to impart rotations to the tip and take the projection of the tip's geometry in the direction of tool travel. The edge of this projection, retrieved from the 3D graphics software, becomes a virtual tool mark. Using this method, virtual marks are made at increments of 5 and compared to a scan of the evidence mark. The previously developed statistical package from Chumbley et al. (2010) performs the comparison, comparing the similarity of the geometry of both marks to the similarity that would occur due to random chance. The resulting statistical measure of the likelihood of the match informs the examiner of the angle of the best matching virtual mark, allowing the examiner to focus his/her mark analysis on a smaller range

A Meta-analysis Method to Advance Design of Technology-Based Learning Tool: Combining Qualitative and Quantitative Research to Understand Learning in Relation to Different Technology Features

NASA Astrophysics Data System (ADS)

Zhang, Lin

2014-02-01

Educators design and create various technology tools to scaffold students' learning. As more and more technology designs are incorporated into learning, growing attention has been paid to the study of technology-based learning tool. This paper discusses the emerging issues, such as how can learning effectiveness be understood in relation to different technology features? And how can pieces of qualitative and quantitative results be integrated to achieve a broader understanding of technology designs? To address these issues, this paper proposes a meta-analysis method. Detailed explanations about the structure of the methodology and its scientific mechanism are provided for discussions and suggestions. This paper ends with an in-depth discussion on the concerns and questions that educational researchers might raise, such as how this methodology takes care of learning contexts.

A Comparative Analysis of Life-Cycle Assessment Tools for ...

EPA Pesticide Factsheets

We identified and evaluated five life-cycle assessment tools that community decision makers can use to assess the environmental and economic impacts of end-of-life (EOL) materials management options. The tools evaluated in this report are waste reduction mode (WARM), municipal solid waste-decision support tool (MSW-DST), solid waste optimization life-cycle framework (SWOLF), environmental assessment system for environmental technologies (EASETECH), and waste and resources assessment for the environment (WRATE). WARM, MSW-DST, and SWOLF were developed for US-specific materials management strategies, while WRATE and EASETECH were developed for European-specific conditions. All of the tools (with the exception of WARM) allow specification of a wide variety of parameters (e.g., materials composition and energy mix) to a varying degree, thus allowing users to model specific EOL materials management methods even outside the geographical domain they are originally intended for. The flexibility to accept user-specified input for a large number of parameters increases the level of complexity and the skill set needed for using these tools. The tools were evaluated and compared based on a series of criteria, including general tool features, the scope of the analysis (e.g., materials and processes included), and the impact categories analyzed (e.g., climate change, acidification). A series of scenarios representing materials management problems currently relevant to c

Tools for observational gait analysis in patients with stroke: a systematic review.

PubMed

Ferrarello, Francesco; Bianchi, Valeria Anna Maria; Baccini, Marco; Rubbieri, Gaia; Mossello, Enrico; Cavallini, Maria Chiara; Marchionni, Niccolò; Di Bari, Mauro

2013-12-01

Stroke severely affects walking ability, and assessment of gait kinematics is important in defining diagnosis, planning treatment, and evaluating interventions in stroke rehabilitation. Although observational gait analysis is the most common approach to evaluate gait kinematics, tools useful for this purpose have received little attention in the scientific literature and have not been thoroughly reviewed. The aims of this systematic review were to identify tools proposed to conduct observational gait analysis in adults with a stroke, to summarize evidence concerning their quality, and to assess their implementation in rehabilitation research and clinical practice. An extensive search was performed of original articles reporting on visual/observational tools developed to investigate gait kinematics in adults with a stroke. Two reviewers independently selected studies, extracted data, assessed quality of the included studies, and scored the metric properties and clinical utility of each tool. Rigor in reporting metric properties and dissemination of the tools also was evaluated. Five tools were identified, not all of which had been tested adequately for their metric properties. Evaluation of content validity was partially satisfactory. Reliability was poorly investigated in all but one tool. Concurrent validity and sensitivity to change were shown for 3 and 2 tools, respectively. Overall, adequate levels of quality were rarely reached. The dissemination of the tools was poor. Based on critical appraisal, the Gait Assessment and Intervention Tool shows a good level of quality, and its use in stroke rehabilitation is recommended. Rigorous studies are needed for the other tools in order to establish their usefulness.

Image edge detection based tool condition monitoring with morphological component analysis.

PubMed

Yu, Xiaolong; Lin, Xin; Dai, Yiquan; Zhu, Kunpeng

2017-07-01

The measurement and monitoring of tool condition are keys to the product precision in the automated manufacturing. To meet the need, this study proposes a novel tool wear monitoring approach based on the monitored image edge detection. Image edge detection has been a fundamental tool to obtain features of images. This approach extracts the tool edge with morphological component analysis. Through the decomposition of original tool wear image, the approach reduces the influence of texture and noise for edge measurement. Based on the target image sparse representation and edge detection, the approach could accurately extract the tool wear edge with continuous and complete contour, and is convenient in charactering tool conditions. Compared to the celebrated algorithms developed in the literature, this approach improves the integrity and connectivity of edges, and the results have shown that it achieves better geometry accuracy and lower error rate in the estimation of tool conditions. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Analysis of the electromagnetic wave resistivity tool in deviated well drilling

NASA Astrophysics Data System (ADS)

Zhang, Yumei; Xu, Lijun; Cao, Zhang

2014-04-01

Electromagnetic wave resistivity (EWR) tools are used to provide real-time measurements of resistivity in the formation around the tool in Logging While Drilling (LWD). In this paper, the acquired resistivity information in the formation is analyzed to extract more information, including dipping angle and azimuth direction of the drill. A finite element (FM) model of EWR tool working in layered earth formations is established. Numerical analysis and FM simulations are employed to analyze the amplitude ratio and phase difference between the voltages measured at the two receivers of the EWR tool in deviated well drilling.

Application of modern tools and techniques to maximize engineering productivity in the development of orbital operations plans for the space station progrm

NASA Technical Reports Server (NTRS)

Manford, J. S.; Bennett, G. R.

1985-01-01

The Space Station Program will incorporate analysis of operations constraints and considerations in the early design phases to avoid the need for later modifications to the Space Station for operations. The application of modern tools and administrative techniques to minimize the cost of performing effective orbital operations planning and design analysis in the preliminary design phase of the Space Station Program is discussed. Tools and techniques discussed include: approach for rigorous analysis of operations functions, use of the resources of a large computer network, and providing for efficient research and access to information.

PATHA: Performance Analysis Tool for HPC Applications

DOE PAGES

Yoo, Wucherl; Koo, Michelle; Cao, Yi; ...

2016-02-18

Large science projects rely on complex workflows to analyze terabytes or petabytes of data. These jobs are often running over thousands of CPU cores and simultaneously performing data accesses, data movements, and computation. It is difficult to identify bottlenecks or to debug the performance issues in these large workflows. In order to address these challenges, we have developed Performance Analysis Tool for HPC Applications (PATHA) using the state-of-art open source big data processing tools. Our framework can ingest system logs to extract key performance measures, and apply the most sophisticated statistical tools and data mining methods on the performance data.more » Furthermore, it utilizes an efficient data processing engine to allow users to interactively analyze a large amount of different types of logs and measurements. To illustrate the functionality of PATHA, we conduct a case study on the workflows from an astronomy project known as the Palomar Transient Factory (PTF). This study processed 1.6 TB of system logs collected on the NERSC supercomputer Edison. Using PATHA, we were able to identify performance bottlenecks, which reside in three tasks of PTF workflow with the dependency on the density of celestial objects.« less

The Adversarial Route Analysis Tool: A Web Application

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

Casson, William H. Jr.

2012-08-02

The Adversarial Route Analysis Tool is a type of Google maps for adversaries. It's a web-based Geospatial application similar to Google Maps. It helps the U.S. government plan operations that predict where an adversary might be. It's easily accessible and maintainble and it's simple to use without much training.

An Online Image Analysis Tool for Science Education

ERIC Educational Resources Information Center

Raeside, L.; Busschots, B.; Waddington, S.; Keating, J. G.

2008-01-01

This paper describes an online image analysis tool developed as part of an iterative, user-centered development of an online Virtual Learning Environment (VLE) called the Education through Virtual Experience (EVE) Portal. The VLE provides a Web portal through which schoolchildren and their teachers create scientific proposals, retrieve images and…

Managing complex research datasets using electronic tools: A meta-analysis exemplar

PubMed Central

Brown, Sharon A.; Martin, Ellen E.; Garcia, Theresa J.; Winter, Mary A.; García, Alexandra A.; Brown, Adama; Cuevas, Heather E.; Sumlin, Lisa L.

2013-01-01

Meta-analyses of broad scope and complexity require investigators to organize many study documents and manage communication among several research staff. Commercially available electronic tools, e.g., EndNote, Adobe Acrobat Pro, Blackboard, Excel, and IBM SPSS Statistics (SPSS), are useful for organizing and tracking the meta-analytic process, as well as enhancing communication among research team members. The purpose of this paper is to describe the electronic processes we designed, using commercially available software, for an extensive quantitative model-testing meta-analysis we are conducting. Specific electronic tools improved the efficiency of (a) locating and screening studies, (b) screening and organizing studies and other project documents, (c) extracting data from primary studies, (d) checking data accuracy and analyses, and (e) communication among team members. The major limitation in designing and implementing a fully electronic system for meta-analysis was the requisite upfront time to: decide on which electronic tools to use, determine how these tools would be employed, develop clear guidelines for their use, and train members of the research team. The electronic process described here has been useful in streamlining the process of conducting this complex meta-analysis and enhancing communication and sharing documents among research team members. PMID:23681256

Biofuel transportation analysis tool : description, methodology, and demonstration scenarios

DOT National Transportation Integrated Search

2014-01-01

This report describes a Biofuel Transportation Analysis Tool (BTAT), developed by the U.S. Department of Transportation (DOT) Volpe National Transportation Systems Center (Volpe) in support of the Department of Defense (DOD) Office of Naval Research ...

Improved Data Analysis Tools for the Thermal Emission Spectrometer

NASA Astrophysics Data System (ADS)

Rodriguez, K.; Laura, J.; Fergason, R.; Bogle, R.

2017-06-01

We plan to stand up three different database systems for testing of a new datastore for MGS TES data allowing for more accessible tools supporting high throughput data analysis on the high-dimensionality hyperspectral data set.

Capitalizing on App Development Tools and Technologies

ERIC Educational Resources Information Center

Luterbach, Kenneth J.; Hubbell, Kenneth R.

2015-01-01

Instructional developers and others creating apps must choose from a wide variety of app development tools and technologies. Some app development tools have incorporated visual programming features, which enable some drag and drop coding and contextual programming. While those features help novices begin programming with greater ease, questions…

Incorporating travel-time reliability into the congestion management process : a primer.

DOT National Transportation Integrated Search

2015-02-01

This primer explains the value of incorporating travel-time reliability into the Congestion Management Process (CMP) : and identifies the most current tools available to assist with this effort. It draws from applied research and best practices : fro...

Simulation Tools for Forest Health Analysis: An Application in the Red River Watershed, Idaho

Treesearch

Andrew J. McMahan; Eric L. Smith

2006-01-01

Software tools for landscape analyses--including FVS model extensions, and a number of FVS-related pre- and post-processing “tools”--are presented, using an analysis in the Red River Watershed, Nez Perce National Forest as an example. We present (1) a discussion of pre-simulation data analysis; (2) the Physiographic Information Extraction System (PIES), a tool that can...

Separation analysis, a tool for analyzing multigrid algorithms

NASA Technical Reports Server (NTRS)

Costiner, Sorin; Taasan, Shlomo

1995-01-01

The separation of vectors by multigrid (MG) algorithms is applied to the study of convergence and to the prediction of the performance of MG algorithms. The separation operator for a two level cycle algorithm is derived. It is used to analyze the efficiency of the cycle when mixing of eigenvectors occurs. In particular cases the separation analysis reduces to Fourier type analysis. The separation operator of a two level cycle for a Schridubger eigenvalue problem, is derived and analyzed in a Fourier basis. Separation analysis gives information on how to choose performance relaxations and inter-level transfers. Separation analysis is a tool for analyzing and designing algorithms, and for optimizing their performance.

Discovery and New Frontiers Project Budget Analysis Tool

NASA Technical Reports Server (NTRS)

Newhouse, Marilyn E.

2011-01-01

The Discovery and New Frontiers (D&NF) programs are multi-project, uncoupled programs that currently comprise 13 missions in phases A through F. The ability to fly frequent science missions to explore the solar system is the primary measure of program success. The program office uses a Budget Analysis Tool to perform "what-if" analyses and compare mission scenarios to the current program budget, and rapidly forecast the programs ability to meet their launch rate requirements. The tool allows the user to specify the total mission cost (fixed year), mission development and operations profile by phase (percent total mission cost and duration), launch vehicle, and launch date for multiple missions. The tool automatically applies inflation and rolls up the total program costs (in real year dollars) for comparison against available program budget. Thus, the tool allows the user to rapidly and easily explore a variety of launch rates and analyze the effect of changes in future mission or launch vehicle costs, the differing development profiles or operational durations of a future mission, or a replan of a current mission on the overall program budget. Because the tool also reports average monthly costs for the specified mission profile, the development or operations cost profile can easily be validate against program experience for similar missions. While specifically designed for predicting overall program budgets for programs that develop and operate multiple missions concurrently, the basic concept of the tool (rolling up multiple, independently-budget lines) could easily be adapted to other applications.

FORENSIC ANALYSIS OF WINDOW’S® VIRTUAL MEMORY INCORPORATING THE SYSTEM’S PAGEFILE COUNTERINTELLIGENCE THROUGH MALICIOUS CODE ANALYSIS

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

Jared Stimson

FORENSIC ANALYSIS OF WINDOW’S® VIRTUAL MEMORY INCORPORATING THE SYSTEM’S PAGEFILE Computer Forensics is concerned with the use of computer investigation and analysis techniques in order to collect evidence suitable for presentation in court. The examination of volatile memory is a relatively new but important area in computer forensics. More recently criminals are becoming more forensically aware and are now able to compromise computers without accessing the hard disk of the target computer. This means that traditional incident response practice of pulling the plug will destroy the only evidence of the crime. While some techniques are available for acquiring the contentsmore » of main memory, few exist which can analyze these data in a meaningful way. One reason for this is how memory is managed by the operating system. Data belonging to one process can be distributed arbitrarily across physical memory or the hard disk, making it very difficult to recover useful information. This report will focus on how these disparate sources of information can be combined to give a single, contiguous address space for each process. Using address translation a tool is developed to reconstruct the virtual address space of a process by combining a physical memory dump with the page-file on the hard disk. COUNTERINTELLIGENCE THROUGH MALICIOUS CODE ANALYSIS As computer network technology continues to grow so does the reliance on this technology for everyday business functionality. To appeal to customers and employees alike, businesses are seeking an increased online prescience, and to increase productivity the same businesses are computerizing their day-to-day operations. The combination of a publicly accessible interface to the businesses network, and the increase in the amount of intellectual property present on these networks presents serious risks. All of this intellectual property now faces constant attacks from a wide variety of malicious software that is intended to

Incorporating Functional Imaging Information into rpFNA Analysis for Breast Cancer Detection in High Risk Women

DTIC Science & Technology

2010-03-01

TITLE: INCORPORATING FUNCTIONAL IMAGING INFORMATION TO rpFNA ANALYSIS FOR BREAST CANCER DETECTION IN HIGH-RISK WOMEN PRINCIPAL INVESTIGATOR...Imaging Information into rpFNA 5a. CONTRACT NUMBER Analysis for Breast Cancer Detection in High Risk Women 5b. GRANT NUMBER W81XWH-08-1-0192 5c...results of random periareolar fine needle aspiration (rpFNA) in women at high risk for breast cancer. In this second year of work, efforts have been

A population MRI brain template and analysis tools for the macaque.

PubMed

Seidlitz, Jakob; Sponheim, Caleb; Glen, Daniel; Ye, Frank Q; Saleem, Kadharbatcha S; Leopold, David A; Ungerleider, Leslie; Messinger, Adam

2018-04-15

The use of standard anatomical templates is common in human neuroimaging, as it facilitates data analysis and comparison across subjects and studies. For non-human primates, previous in vivo templates have lacked sufficient contrast to reliably validate known anatomical brain regions and have not provided tools for automated single-subject processing. Here we present the "National Institute of Mental Health Macaque Template", or NMT for short. The NMT is a high-resolution in vivo MRI template of the average macaque brain generated from 31 subjects, as well as a neuroimaging tool for improved data analysis and visualization. From the NMT volume, we generated maps of tissue segmentation and cortical thickness. Surface reconstructions and transformations to previously published digital brain atlases are also provided. We further provide an analysis pipeline using the NMT that automates and standardizes the time-consuming processes of brain extraction, tissue segmentation, and morphometric feature estimation for anatomical scans of individual subjects. The NMT and associated tools thus provide a common platform for precise single-subject data analysis and for characterizations of neuroimaging results across subjects and studies. Copyright © 2017 ElsevierCompany. All rights reserved.

Virtual Tool Mark Generation for Efficient Striation Analysis

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

Ekstrand, Laura; Zhang, Song; Grieve, Taylor

2014-02-16

This study introduces a tool mark analysis approach based upon 3D scans of screwdriver tip and marked plate surfaces at the micrometer scale from an optical microscope. An open-source 3D graphics software package is utilized to simulate the marking process as the projection of the tip's geometry in the direction of tool travel. The edge of this projection becomes a virtual tool mark that is compared to cross-sections of the marked plate geometry using the statistical likelihood algorithm introduced by Chumbley et al. In a study with both sides of six screwdriver tips and 34 corresponding marks, the method distinguishedmore » known matches from known nonmatches with zero false-positive matches and two false-negative matches. For matches, it could predict the correct marking angle within ±5–10°. Individual comparisons could be made in seconds on a desktop computer, suggesting that the method could save time for examiners.« less

Design and Application of the Exploration Maintainability Analysis Tool

NASA Technical Reports Server (NTRS)

Stromgren, Chel; Terry, Michelle; Crillo, William; Goodliff, Kandyce; Maxwell, Andrew

2012-01-01

Conducting human exploration missions beyond Low Earth Orbit (LEO) will present unique challenges in the areas of supportability and maintainability. The durations of proposed missions can be relatively long and re-supply of logistics, including maintenance and repair items, will be limited or non-existent. In addition, mass and volume constraints in the transportation system will limit the total amount of logistics that can be flown along with the crew. These constraints will require that new strategies be developed with regards to how spacecraft systems are designed and maintained. NASA is currently developing Design Reference Missions (DRMs) as an initial step in defining future human missions. These DRMs establish destinations and concepts of operation for future missions, and begin to define technology and capability requirements. Because of the unique supportability challenges, historical supportability data and models are not directly applicable for establishing requirements for beyond LEO missions. However, supportability requirements could have a major impact on the development of the DRMs. The mass, volume, and crew resources required to support the mission could all be first order drivers in the design of missions, elements, and operations. Therefore, there is a need for enhanced analysis capabilities to more accurately establish mass, volume, and time requirements for supporting beyond LEO missions. Additionally, as new technologies and operations are proposed to reduce these requirements, it is necessary to have accurate tools to evaluate the efficacy of those approaches. In order to improve the analysis of supportability requirements for beyond LEO missions, the Space Missions Analysis Branch at the NASA Langley Research Center is developing the Exploration Maintainability Analysis Tool (EMAT). This tool is a probabilistic simulator that evaluates the need for repair and maintenance activities during space missions and the logistics and crew

CALS Database Usage and Analysis Tool Study

DTIC Science & Technology

1991-09-01

inference aggregation and cardinality aggregation as two distinct aspects of the aggregation problem. The paper develops the concept of a semantic...aggregation, cardinality aggregation I " CALS Database Usage Analysis Tool Study * Bibliography * Page 7 i NIDX - An Expert System for Real-Time...1989 IEEE Symposium on Research in Security and Privacy, Oakland, CA, May 1989. [21 Baur, D.S.; Eichelman, F.R. 1I; Herrera , R.M.; Irgon, A.E

Trajectory design strategies that incorporate invariant manifolds and swingby

NASA Technical Reports Server (NTRS)

Guzman, J. J.; Cooley, D. S.; Howell, K. C.; Folta, D. C.

1998-01-01

Libration point orbits serve as excellent platforms for scientific investigations involving the Sun as well as planetary environments. Trajectory design in support of such missions is increasingly challenging as more complex missions are envisioned in the next few decades. Software tools for trajectory design in this regime must be further developed to incorporate better understanding of the solution space and, thus, improve the efficiency and expand the capabilities of current approaches. Only recently applied to trajectory design, dynamical systems theory now offers new insights into the natural dynamics associated with the multi-body problem. The goal of this effort is the blending of analysis from dynamical systems theory with the well established NASA Goddard software program SWINGBY to enhance and expand the capabilities for mission design. Basic knowledge concerning the solution space is improved as well.

NeedATool: A Needlet Analysis Tool for Cosmological Data Processing

NASA Astrophysics Data System (ADS)

Pietrobon, Davide; Balbi, Amedeo; Cabella, Paolo; Gorski, Krzysztof M.

2010-11-01

We introduce NeedATool (Needlet Analysis Tool), a software for data analysis based on needlets, a wavelet rendition which is powerful for the analysis of fields defined on a sphere. Needlets have been applied successfully to the treatment of astrophysical and cosmological observations, and in particular to the analysis of cosmic microwave background (CMB) data. Usually, such analyses are performed in real space as well as in its dual domain, the harmonic one. Both spaces have advantages and disadvantages: for example, in pixel space it is easier to deal with partial sky coverage and experimental noise; in the harmonic domain, beam treatment and comparison with theoretical predictions are more effective. During the last decade, however, wavelets have emerged as a useful tool for CMB data analysis, since they allow us to combine most of the advantages of the two spaces, one of the main reasons being their sharp localization. In this paper, we outline the analytical properties of needlets and discuss the main features of the numerical code, which should be a valuable addition to the CMB analyst's toolbox.

Mindfulness: An Underused Tool for Deepening Music Understanding

ERIC Educational Resources Information Center

Falter, H. Ellie

2016-01-01

Music teachers aim to deepen their students' music understanding. An underused tool for doing so is incorporating mindful practice into music teaching. Through discussing research, examples from the classroom, and steps for incorporating mindful practices in lesson planning, the author hopes to illustrate its potential benefits and set music…

Gene Ontology-Based Analysis of Zebrafish Omics Data Using the Web Tool Comparative Gene Ontology.

PubMed

Ebrahimie, Esmaeil; Fruzangohar, Mario; Moussavi Nik, Seyyed Hani; Newman, Morgan

2017-10-01

Gene Ontology (GO) analysis is a powerful tool in systems biology, which uses a defined nomenclature to annotate genes/proteins within three categories: "Molecular Function," "Biological Process," and "Cellular Component." GO analysis can assist in revealing functional mechanisms underlying observed patterns in transcriptomic, genomic, and proteomic data. The already extensive and increasing use of zebrafish for modeling genetic and other diseases highlights the need to develop a GO analytical tool for this organism. The web tool Comparative GO was originally developed for GO analysis of bacterial data in 2013 ( www.comparativego.com ). We have now upgraded and elaborated this web tool for analysis of zebrafish genetic data using GOs and annotations from the Gene Ontology Consortium.

Prototype Development of a Tradespace Analysis Tool for Spaceflight Medical Resources.

PubMed

Antonsen, Erik L; Mulcahy, Robert A; Rubin, David; Blue, Rebecca S; Canga, Michael A; Shah, Ronak

2018-02-01

The provision of medical care in exploration-class spaceflight is limited by mass, volume, and power constraints, as well as limitations of available skillsets of crewmembers. A quantitative means of exploring the risks and benefits of inclusion or exclusion of onboard medical capabilities may help to inform the development of an appropriate medical system. A pilot project was designed to demonstrate the utility of an early tradespace analysis tool for identifying high-priority resources geared toward properly equipping an exploration mission medical system. Physician subject matter experts identified resources, tools, and skillsets required, as well as associated criticality scores of the same, to meet terrestrial, U.S.-specific ideal medical solutions for conditions concerning for exploration-class spaceflight. A database of diagnostic and treatment actions and resources was created based on this input and weighed against the probabilities of mission-specific medical events to help identify common and critical elements needed in a future exploration medical capability. Analysis of repository data demonstrates the utility of a quantitative method of comparing various medical resources and skillsets for future missions. Directed database queries can provide detailed comparative estimates concerning likelihood of resource utilization within a given mission and the weighted utility of tangible and intangible resources. This prototype tool demonstrates one quantitative approach to the complex needs and limitations of an exploration medical system. While this early version identified areas for refinement in future version development, more robust analysis tools may help to inform the development of a comprehensive medical system for future exploration missions.Antonsen EL, Mulcahy RA, Rubin D, Blue RS, Canga MA, Shah R. Prototype development of a tradespace analysis tool for spaceflight medical resources. Aerosp Med Hum Perform. 2018; 89(2):108-114.

CloudMan as a platform for tool, data, and analysis distribution

PubMed Central

2012-01-01

Background Cloud computing provides an infrastructure that facilitates large scale computational analysis in a scalable, democratized fashion, However, in this context it is difficult to ensure sharing of an analysis environment and associated data in a scalable and precisely reproducible way. Results CloudMan (usecloudman.org) enables individual researchers to easily deploy, customize, and share their entire cloud analysis environment, including data, tools, and configurations. Conclusions With the enabled customization and sharing of instances, CloudMan can be used as a platform for collaboration. The presented solution improves accessibility of cloud resources, tools, and data to the level of an individual researcher and contributes toward reproducibility and transparency of research solutions. PMID:23181507

HISTORICAL ANALYSIS OF ECOLOGICAL EFFECTS: A USEFUL EDUCATIONAL TOOL

EPA Science Inventory

An historical analysis that presents the ecological consequences of development can be a valuable educational tool for citizens, students, and environmental managers. In highly impacted areas, the cumulative impacts of multiple stressors can result in complex environmental condit...

Cataract Surgery Tool

NASA Technical Reports Server (NTRS)

1977-01-01

The NASA-McGannon cataract surgery tool is a tiny cutter-pump which liquefies and pumps the cataract lens material from the eye. Inserted through a small incision in the cornea, the tool can be used on the hardest cataract lens. The cutter is driven by a turbine which operates at about 200,000 revolutions per minute. Incorporated in the mechanism are two passages for saline solutions, one to maintain constant pressure within the eye, the other for removal of the fragmented lens material and fluids. Three years of effort have produced a design, now being clinically evaluated, with excellent potential for improved cataract surgery. The use of this tool is expected to reduce the patient's hospital stay and recovery period significantly.

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

NASA Astrophysics Data System (ADS)

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

2014-05-01

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

Principles and tools for collaborative entity-based intelligence analysis.

PubMed

Bier, Eric A; Card, Stuart K; Bodnar, John W

2010-01-01

Software tools that make it easier for analysts to collaborate as a natural part of their work will lead to better analysis that is informed by more perspectives. We are interested to know if software tools can be designed that support collaboration even as they allow analysts to find documents and organize information (including evidence, schemas, and hypotheses). We have modified the Entity Workspace system, described previously, to test such designs. We have evaluated the resulting design in both a laboratory study and a study where it is situated with an analysis team. In both cases, effects on collaboration appear to be positive. Key aspects of the design include an evidence notebook optimized for organizing entities (rather than text characters), information structures that can be collapsed and expanded, visualization of evidence that emphasizes events and documents (rather than emphasizing the entity graph), and a notification system that finds entities of mutual interest to multiple analysts. Long-term tests suggest that this approach can support both top-down and bottom-up styles of analysis.

RdTools: An Open Source Python Library for PV Degradation Analysis

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

Deceglie, Michael G; Jordan, Dirk; Nag, Ambarish

RdTools is a set of Python tools for analysis of photovoltaic data. In particular, PV production data is evaluated over several years to obtain rates of performance degradation over time. Rdtools can handle both high frequency (hourly or better) or low frequency (daily, weekly, etc.) datasets. Best results are obtained with higher frequency data.

Integrated Analysis Tools for Determination of Structural Integrity and Durability of High temperature Polymer Matrix Composites

DTIC Science & Technology

2008-08-18

fidelity will be used to reduce the massive experimental testing and associated time required for qualification of new materials. Tools and...develping a model of the thermo-oxidative process for polymer systems, that incorporates the effects of reaction rates, Fickian diffusion, time varying...degradation processes. Year: 2005 Month: 12 Not required at this time . AIR FORCE OFFICE OF SCIENTIFIC KESEARCH 04 SEP 2008 Page 2 of 2 DTIC Data

Agricultural Body-Building: Incorporations of Gender, Body and Work

ERIC Educational Resources Information Center

Brandth, Berit

2006-01-01

This paper is concerned with gendered embodiment of agricultural work, particularly the connection between women's gender identity and the body at work. Focussing on how the body enters into relations with the tools of work, four processes are identified by which women's bodies, work and machinery are incorporated into each other and give each…

Introduction, comparison, and validation of Meta‐Essentials: A free and simple tool for meta‐analysis

PubMed Central

van Rhee, Henk; Hak, Tony

2017-01-01

We present a new tool for meta‐analysis, Meta‐Essentials, which is free of charge and easy to use. In this paper, we introduce the tool and compare its features to other tools for meta‐analysis. We also provide detailed information on the validation of the tool. Although free of charge and simple, Meta‐Essentials automatically calculates effect sizes from a wide range of statistics and can be used for a wide range of meta‐analysis applications, including subgroup analysis, moderator analysis, and publication bias analyses. The confidence interval of the overall effect is automatically based on the Knapp‐Hartung adjustment of the DerSimonian‐Laird estimator. However, more advanced meta‐analysis methods such as meta‐analytical structural equation modelling and meta‐regression with multiple covariates are not available. In summary, Meta‐Essentials may prove a valuable resource for meta‐analysts, including researchers, teachers, and students. PMID:28801932

Cognitive mapping tools: review and risk management needs.

PubMed

Wood, Matthew D; Bostrom, Ann; Bridges, Todd; Linkov, Igor

2012-08-01

Risk managers are increasingly interested in incorporating stakeholder beliefs and other human factors into the planning process. Effective risk assessment and management requires understanding perceptions and beliefs of involved stakeholders, and how these beliefs give rise to actions that influence risk management decisions. Formal analyses of risk manager and stakeholder cognitions represent an important first step. Techniques for diagramming stakeholder mental models provide one tool for risk managers to better understand stakeholder beliefs and perceptions concerning risk, and to leverage this new understanding in developing risk management strategies. This article reviews three methodologies for assessing and diagramming stakeholder mental models--decision-analysis-based mental modeling, concept mapping, and semantic web analysis--and assesses them with regard to their ability to address risk manager needs. © 2012 Society for Risk Analysis.

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

Ganalyzer: A tool for automatic galaxy image analysis

NASA Astrophysics Data System (ADS)

Shamir, Lior

2011-05-01

Ganalyzer is a model-based tool that automatically analyzes and classifies galaxy images. Ganalyzer works by separating the galaxy pixels from the background pixels, finding the center and radius of the galaxy, generating the radial intensity plot, and then computing the slopes of the peaks detected in the radial intensity plot to measure the spirality of the galaxy and determine its morphological class. Unlike algorithms that are based on machine learning, Ganalyzer is based on measuring the spirality of the galaxy, a task that is difficult to perform manually, and in many cases can provide a more accurate analysis compared to manual observation. Ganalyzer is simple to use, and can be easily embedded into other image analysis applications. Another advantage is its speed, which allows it to analyze ~10,000,000 galaxy images in five days using a standard modern desktop computer. These capabilities can make Ganalyzer a useful tool in analyzing large datasets of galaxy images collected by autonomous sky surveys such as SDSS, LSST or DES.

TOOL ASSEMBLY WITH BI-DIRECTIONAL BEARING

DOEpatents

Longhurst, G.E.

1961-07-11

A two-direction motion bearing which is incorporated in a refueling nuclear fuel element trsnsfer tool assembly is described. A plurality of bi- directional bearing assembliesare fixed equi-distantly about the circumference of the transfer tool assembly to provide the tool assembly with a bearing surface- for both axial and rotational motion. Each bi-directional bearing assembly contains a plurality of circumferentially bulged rollers mounted in a unique arrangement which will provide a bearing surface for rotational movement of the tool assembly within a bore. The bi-direc tional bearing assembly itself is capable of rational motion and thus provides for longitudinal movement of the tool assembly.

A comprehensive comparison of tools for differential ChIP-seq analysis

PubMed Central

Steinhauser, Sebastian; Kurzawa, Nils; Eils, Roland

2016-01-01

ChIP-seq has become a widely adopted genomic assay in recent years to determine binding sites for transcription factors or enrichments for specific histone modifications. Beside detection of enriched or bound regions, an important question is to determine differences between conditions. While this is a common analysis for gene expression, for which a large number of computational approaches have been validated, the same question for ChIP-seq is particularly challenging owing to the complexity of ChIP-seq data in terms of noisiness and variability. Many different tools have been developed and published in recent years. However, a comprehensive comparison and review of these tools is still missing. Here, we have reviewed 14 tools, which have been developed to determine differential enrichment between two conditions. They differ in their algorithmic setups, and also in the range of applicability. Hence, we have benchmarked these tools on real data sets for transcription factors and histone modifications, as well as on simulated data sets to quantitatively evaluate their performance. Overall, there is a great variety in the type of signal detected by these tools with a surprisingly low level of agreement. Depending on the type of analysis performed, the choice of method will crucially impact the outcome. PMID:26764273

Federal metering data analysis needs and existing tools

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

Henderson, Jordan W.; Fowler, Kimberly M.

2015-07-01

Agencies have been working to improve their metering data collection, management, and analysis efforts over the last decade (since EPAct 2005) and will continue to address these challenges as new requirements and data needs come into place. Unfortunately there is no “one-size-fits-all” solution. As agencies continue to expand their capabilities to use metered consumption data to reducing resource use and improve operations, the hope is that shared knowledge will empower others to follow suit. This paper discusses the Federal metering data analysis needs and some existing tools.

Documentary analysis as an assessment tool.

PubMed

Lawson, Lauren V

2018-05-29

Documentary analysis of existing information, such as newspaper articles, is an identified method for use in an assessment to provide a descriptive explanation of existing problems or assets. The intention of this case study is to explore the effectiveness of documentary analysis of newspaper articles as a tool to inform an assessment of factors influencing the implementation of a medical respite for the homeless. Two questions framed the assessment; (a) What was occurring or might occur that will affect the development of a medical respite; and (b) What opportunities or threats are generated as a result? Articles from two local newspapers identified themes related to the three external forces of change that impact medical respites; (a) funding; (b) community resistance; and (c) the health care system. Three themes emerged: a) uncertain funding; b) neighborhood resistance, and c) improved access to healthcare would result from the Affordable Care Act. Use of documentary analysis of newspaper articles provided applicable content for the assessment. Themes from the assessment informed strategic planning, such as addressing potential neighborhood resistance. © 2018 Wiley Periodicals, Inc.

Minimally invasive surgical video analysis: a powerful tool for surgical training and navigation.

PubMed

Sánchez-González, P; Oropesa, I; Gómez, E J

2013-01-01

Analysis of minimally invasive surgical videos is a powerful tool to drive new solutions for achieving reproducible training programs, objective and transparent assessment systems and navigation tools to assist surgeons and improve patient safety. This paper presents how video analysis contributes to the development of new cognitive and motor training and assessment programs as well as new paradigms for image-guided surgery.

Introduction, comparison, and validation of Meta-Essentials: A free and simple tool for meta-analysis.

PubMed

Suurmond, Robert; van Rhee, Henk; Hak, Tony

2017-12-01

We present a new tool for meta-analysis, Meta-Essentials, which is free of charge and easy to use. In this paper, we introduce the tool and compare its features to other tools for meta-analysis. We also provide detailed information on the validation of the tool. Although free of charge and simple, Meta-Essentials automatically calculates effect sizes from a wide range of statistics and can be used for a wide range of meta-analysis applications, including subgroup analysis, moderator analysis, and publication bias analyses. The confidence interval of the overall effect is automatically based on the Knapp-Hartung adjustment of the DerSimonian-Laird estimator. However, more advanced meta-analysis methods such as meta-analytical structural equation modelling and meta-regression with multiple covariates are not available. In summary, Meta-Essentials may prove a valuable resource for meta-analysts, including researchers, teachers, and students. © 2017 The Authors. Research Synthesis Methods published by John Wiley & Sons Ltd.

Just tooling around: Experiences with arctools

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

Tuttle, M.A.

1994-06-01

The three US Department of Energy (DOE) Installations on the Oak Ridge Reservation (Oak Ridge National Laboratory, Y-12 and K-25) were established during World War II as part of the Manhattan Project to build ``the bomb.`` In later years, the work at these facilities involved nuclear energy research, defense-related activities, and uranium enrichment, resulting in the generation of radioactive material and other toxic by-products. Work is now in progress to identify and clean up the environmental contamination from these and other wastes. Martin Marietta Energy Systems, Inc., which manages the Oak Ridge sites as well as DOE installations at Portsmouth,more » Ohio and Paducah, Kentucky, has been charged with creating and maintaining a comprehensive environmental information system in order to comply with the Federal Facility Agreement (FFA) for the Oak Ridge Reservation and the State of Tennessee Oversight Agreement between the US Department of Energy and the State of Tennessee. As a result, the Oak Ridge Environmental Information System (OREIS) was conceived and is currently being implemented. The tools chosen for the OREIS system are Oracle for the relational database, SAS for data analysis and graphical representation, and Arc/INFO and ArcView for the spatial analysis and display component. Within the broad scope of ESRI`s Arc/Info software, ArcTools was chosen as the graphic user interface for inclusion of Arc/Info into OREIS. The purpose of this paper is to examine in the advantages and disadvantages of incorporating ArcTools for the presentation of Arc/INFO in the OREIS system. The immediate and mid-term development goals of the OREIS system as they relate to ArcTools will be presented. A general discussion of our experiences with the ArcTools product is also included.« less

Multispectral analysis tools can increase utility of RGB color images in histology

NASA Astrophysics Data System (ADS)

Fereidouni, Farzad; Griffin, Croix; Todd, Austin; Levenson, Richard

2018-04-01

Multispectral imaging (MSI) is increasingly finding application in the study and characterization of biological specimens. However, the methods typically used come with challenges on both the acquisition and the analysis front. MSI can be slow and photon-inefficient, leading to long imaging times and possible phototoxicity and photobleaching. The resulting datasets can be large and complex, prompting the development of a number of mathematical approaches for segmentation and signal unmixing. We show that under certain circumstances, just three spectral channels provided by standard color cameras, coupled with multispectral analysis tools, including a more recent spectral phasor approach, can efficiently provide useful insights. These findings are supported with a mathematical model relating spectral bandwidth and spectral channel number to achievable spectral accuracy. The utility of 3-band RGB and MSI analysis tools are demonstrated on images acquired using brightfield and fluorescence techniques, as well as a novel microscopy approach employing UV-surface excitation. Supervised linear unmixing, automated non-negative matrix factorization and phasor analysis tools all provide useful results, with phasors generating particularly helpful spectral display plots for sample exploration.

Knickpoint finder: A software tool that improves neotectonic analysis

NASA Astrophysics Data System (ADS)

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

2015-03-01

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

Toxic release consequence analysis tool (TORCAT) for inherently safer design plant.

PubMed

Shariff, Azmi Mohd; Zaini, Dzulkarnain

2010-10-15

Many major accidents due to toxic release in the past have caused many fatalities such as the tragedy of MIC release in Bhopal, India (1984). One of the approaches is to use inherently safer design technique that utilizes inherent safety principle to eliminate or minimize accidents rather than to control the hazard. This technique is best implemented in preliminary design stage where the consequence of toxic release can be evaluated and necessary design improvements can be implemented to eliminate or minimize the accidents to as low as reasonably practicable (ALARP) without resorting to costly protective system. However, currently there is no commercial tool available that has such capability. This paper reports on the preliminary findings on the development of a prototype tool for consequence analysis and design improvement via inherent safety principle by utilizing an integrated process design simulator with toxic release consequence analysis model. The consequence analysis based on the worst-case scenarios during process flowsheeting stage were conducted as case studies. The preliminary finding shows that toxic release consequences analysis tool (TORCAT) has capability to eliminate or minimize the potential toxic release accidents by adopting the inherent safety principle early in preliminary design stage. 2010 Elsevier B.V. All rights reserved.

Design Package for Fuel Retrieval System Fuel Handling Tool Modification

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

TEDESCHI, D.J.

This design package documents design, fabrication, and testing of new stinger tool design. Future revisions will document further development of the stinger tool and incorporate various developmental stages, and final test results.

High-Performance Data Analysis Tools for Sun-Earth Connection Missions

NASA Technical Reports Server (NTRS)

Messmer, Peter

2011-01-01

The data analysis tool of choice for many Sun-Earth Connection missions is the Interactive Data Language (IDL) by ITT VIS. The increasing amount of data produced by these missions and the increasing complexity of image processing algorithms requires access to higher computing power. Parallel computing is a cost-effective way to increase the speed of computation, but algorithms oftentimes have to be modified to take advantage of parallel systems. Enhancing IDL to work on clusters gives scientists access to increased performance in a familiar programming environment. The goal of this project was to enable IDL applications to benefit from both computing clusters as well as graphics processing units (GPUs) for accelerating data analysis tasks. The tool suite developed in this project enables scientists now to solve demanding data analysis problems in IDL that previously required specialized software, and it allows them to be solved orders of magnitude faster than on conventional PCs. The tool suite consists of three components: (1) TaskDL, a software tool that simplifies the creation and management of task farms, collections of tasks that can be processed independently and require only small amounts of data communication; (2) mpiDL, a tool that allows IDL developers to use the Message Passing Interface (MPI) inside IDL for problems that require large amounts of data to be exchanged among multiple processors; and (3) GPULib, a tool that simplifies the use of GPUs as mathematical coprocessors from within IDL. mpiDL is unique in its support for the full MPI standard and its support of a broad range of MPI implementations. GPULib is unique in enabling users to take advantage of an inexpensive piece of hardware, possibly already installed in their computer, and achieve orders of magnitude faster execution time for numerically complex algorithms. TaskDL enables the simple setup and management of task farms on compute clusters. The products developed in this project have the

Analysis of design tool attributes with regards to sustainability benefits

NASA Astrophysics Data System (ADS)

Zain, S.; Ismail, A. F.; Ahmad, Z.; Adesta, E. Y. T.

2018-01-01

The trend of global manufacturing competitiveness has shown a significant shift from profit and customer driven business to a more harmonious sustainability paradigm. This new direction, which emphasises the interests of three pillars of sustainability, i.e., social, economic and environment dimensions, has changed the ways products are designed. As a result, the roles of design tools in the product development stage of manufacturing in adapting to the new strategy are vital and increasingly challenging. The aim of this paper is to review the literature on the attributes of design tools with regards to the sustainability perspective. Four well-established design tools are selected, namely Quality Function Deployment (QFD), Failure Mode and Element Analysis (FMEA), Design for Six Sigma (DFSS) and Design for Environment (DfE). By analysing previous studies, the main attributes of each design tool and its benefits with respect to each sustainability dimension throughout four stages of product lifecycle are discussed. From this study, it is learnt that each of the design tools contributes to the three pillars of sustainability either directly or indirectly, but they are unbalanced and not holistic. Therefore, the prospective of improving and optimising the design tools is projected, and the possibility of collaboration between the different tools is discussed.

Providing web-based tools for time series access and analysis

NASA Astrophysics Data System (ADS)

Eberle, Jonas; Hüttich, Christian; Schmullius, Christiane

2014-05-01

Time series information is widely used in environmental change analyses and is also an essential information for stakeholders and governmental agencies. However, a challenging issue is the processing of raw data and the execution of time series analysis. In most cases, data has to be found, downloaded, processed and even converted in the correct data format prior to executing time series analysis tools. Data has to be prepared to use it in different existing software packages. Several packages like TIMESAT (Jönnson & Eklundh, 2004) for phenological studies, BFAST (Verbesselt et al., 2010) for breakpoint detection, and GreenBrown (Forkel et al., 2013) for trend calculations are provided as open-source software and can be executed from the command line. This is needed if data pre-processing and time series analysis is being automated. To bring both parts, automated data access and data analysis, together, a web-based system was developed to provide access to satellite based time series data and access to above mentioned analysis tools. Users of the web portal are able to specify a point or a polygon and an available dataset (e.g., Vegetation Indices and Land Surface Temperature datasets from NASA MODIS). The data is then being processed and provided as a time series CSV file. Afterwards the user can select an analysis tool that is being executed on the server. The final data (CSV, plot images, GeoTIFFs) is visualized in the web portal and can be downloaded for further usage. As a first use case, we built up a complimentary web-based system with NASA MODIS products for Germany and parts of Siberia based on the Earth Observation Monitor (www.earth-observation-monitor.net). The aim of this work is to make time series analysis with existing tools as easy as possible that users can focus on the interpretation of the results. References: Jönnson, P. and L. Eklundh (2004). TIMESAT - a program for analysing time-series of satellite sensor data. Computers and Geosciences 30

Incorporating spatial context into the analysis of salmonid habitat relations: Chapter 18

USGS Publications Warehouse

Torgersen, Christian E.; Baxter, Colden V.; Ebersole, J.L.; Gresswell, Bob; Church, Michael; Biron, Pascale M.; Roy, Andre G.

2012-01-01

In this response to the chapter by Lapointe (this volume), we discuss the question of why it is so difficult to predict salmonid-habitat relations in gravel-bed rivers and streams. We acknowledge that this cannot be an exhaustive treatment of the subject and, thus, identify what we believe are several key issues that demonstrate the necessity of incorporating spatial context into the analysis of fish-habitat data. Our emphasis is on spatial context (i.e., scale and location), but it is important to note that the same principles may be applied with some modification to temporal context, which is beyond the scope of this chapter.

Incorporating twitter-based human activity information in spatial analysis of crashes in urban areas.

PubMed

Bao, Jie; Liu, Pan; Yu, Hao; Xu, Chengcheng

2017-09-01

The primary objective of this study was to investigate how to incorporate human activity information in spatial analysis of crashes in urban areas using Twitter check-in data. This study used the data collected from the City of Los Angeles in the United States to illustrate the procedure. The following five types of data were collected: crash data, human activity data, traditional traffic exposure variables, road network attributes and social-demographic data. A web crawler by Python was developed to collect the venue type information from the Twitter check-in data automatically. The human activities were classified into seven categories by the obtained venue types. The collected data were aggregated into 896 Traffic Analysis Zones (TAZ). Geographically weighted regression (GWR) models were developed to establish a relationship between the crash counts reported in a TAZ and various contributing factors. Comparative analyses were conducted to compare the performance of GWR models which considered traditional traffic exposure variables only, Twitter-based human activity variables only, and both traditional traffic exposure and Twitter-based human activity variables. The model specification results suggested that human activity variables significantly affected the crash counts in a TAZ. The results of comparative analyses suggested that the models which considered both traditional traffic exposure and human activity variables had the best goodness-of-fit in terms of the highest R 2 and lowest AICc values. The finding seems to confirm the benefits of incorporating human activity information in spatial analysis of crashes using Twitter check-in data. Copyright © 2017 Elsevier Ltd. All rights reserved.

Hurricane Data Analysis Tool

NASA Technical Reports Server (NTRS)

Liu, Zhong; Ostrenga, Dana; Leptoukh, Gregory

2011-01-01

In order to facilitate Earth science data access, the NASA Goddard Earth Sciences Data Information Services Center (GES DISC) has developed a web prototype, the Hurricane Data Analysis Tool (HDAT; URL: http://disc.gsfc.nasa.gov/HDAT), to allow users to conduct online visualization and analysis of several remote sensing and model datasets for educational activities and studies of tropical cyclones and other weather phenomena. With a web browser and few mouse clicks, users can have a full access to terabytes of data and generate 2-D or time-series plots and animation without downloading any software and data. HDAT includes data from the NASA Tropical Rainfall Measuring Mission (TRMM), the NASA Quick Scatterometer(QuikSCAT) and NECP Reanalysis, and the NCEP/CPC half-hourly, 4-km Global (60 N - 60 S) IR Dataset. The GES DISC archives TRMM data. The daily global rainfall product derived from the 3-hourly multi-satellite precipitation product (3B42 V6) is available in HDAT. The TRMM Microwave Imager (TMI) sea surface temperature from the Remote Sensing Systems is in HDAT as well. The NASA QuikSCAT ocean surface wind and the NCEP Reanalysis provide ocean surface and atmospheric conditions, respectively. The global merged IR product, also known as, the NCEP/CPC half-hourly, 4-km Global (60 N -60 S) IR Dataset, is one of TRMM ancillary datasets. They are globally-merged pixel-resolution IR brightness temperature data (equivalent blackbody temperatures), merged from all available geostationary satellites (GOES-8/10, METEOSAT-7/5 & GMS). The GES DISC has collected over 10 years of the data beginning from February of 2000. This high temporal resolution (every 30 minutes) dataset not only provides additional background information to TRMM and other satellite missions, but also allows observing a wide range of meteorological phenomena from space, such as, hurricanes, typhoons, tropical cyclones, mesoscale convection system, etc. Basic functions include selection of area of

Introducing New Learning Tools into a Standard Classroom: A Multi-Tool Approach to Integrating Fuel-Cell Concepts into Introductory College Chemistry

ERIC Educational Resources Information Center

D'Amato, Matthew J.; Lux, Kenneth W.; Walz, Kenneth A.; Kerby, Holly Walter; Anderegg, Barbara

2007-01-01

A multi-tool approach incorporating traditional lectures, multimedia learning objects, and a laboratory activity were introduced as the concepts surrounding hydrogen fuel-cell technology in college chemistry courses. The new tools are adaptable, facilitating use in different educational environments and address variety of learning styles to…

A prediction tool incorporating the biomarker S-100B for patient selection for completion lymph node dissection in stage III melanoma.

PubMed

Damude, S; Wevers, K P; Murali, R; Kruijff, S; Hoekstra, H J; Bastiaannet, E

2017-09-01

Completion lymph node dissection (CLND) in sentinel node (SN)-positive melanoma patients is accompanied with morbidity, while about 80% yield no additional metastases in non-sentinel nodes (NSNs). A prediction tool for NSN involvement could be of assistance in patient selection for CLND. This study investigated which parameters predict NSN-positivity, and whether the biomarker S-100B improves the accuracy of a prediction model. Recorded clinicopathologic factors were tested for their association with NSN-positivity in 110 SN-positive patients who underwent CLND. A prediction model was developed with multivariable logistic regression, incorporating all predictive factors. Five models were compared for their predictive power by calculating the Area Under the Curve (AUC). A weighted risk score, 'S-100B Non-Sentinel Node Risk Score' (SN-SNORS), was derived for the model with the highest AUC. Besides, a nomogram was developed as visual representation. NSN-positivity was present in 24 (21.8%) patients. Sex, ulceration, number of harvested SNs, number of positive SNs, and S-100B value were independently associated with NSN-positivity. The AUC for the model including all these factors was 0.78 (95%CI 0.69-0.88). SN-SNORS was the sum of scores for the five parameters. Scores of ≤9.5, 10-11.5, and ≥12 were associated with low (0%), intermediate (21.0%) and high (43.2%) risk of NSN involvement. A prediction tool based on five parameters, including the biomarker S-100B, showed accurate risk stratification for NSN-involvement in SN-positive melanoma patients. If validated in future studies, this tool could help to identify patients with low risk for NSN-involvement. Copyright © 2017 Elsevier Ltd, BASO ~ The Association for Cancer Surgery, and the European Society of Surgical Oncology. All rights reserved.

Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis

DOE PAGES

Pavlopoulos, Georgios A.; Paez-Espino, David; Kyrpides, Nikos C.; ...

2017-07-18

Gene expression, signal transduction, protein/chemical interactions, biomedical literature cooccurrences, and other concepts are often captured in biological network representations where nodes represent a certain bioentity and edges the connections between them. While many tools to manipulate, visualize, and interactively explore such networks already exist, only few of them can scale up and follow today’s indisputable information growth. In this review, we shortly list a catalog of available network visualization tools and, from a user-experience point of view, we identify four candidate tools suitable for larger-scale network analysis, visualization, and exploration. Lastly, we comment on their strengths and their weaknesses andmore » empirically discuss their scalability, user friendliness, and postvisualization capabilities.« less

Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis

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

Pavlopoulos, Georgios A.; Paez-Espino, David; Kyrpides, Nikos C.

Gene expression, signal transduction, protein/chemical interactions, biomedical literature cooccurrences, and other concepts are often captured in biological network representations where nodes represent a certain bioentity and edges the connections between them. While many tools to manipulate, visualize, and interactively explore such networks already exist, only few of them can scale up and follow today’s indisputable information growth. In this review, we shortly list a catalog of available network visualization tools and, from a user-experience point of view, we identify four candidate tools suitable for larger-scale network analysis, visualization, and exploration. Lastly, we comment on their strengths and their weaknesses andmore » empirically discuss their scalability, user friendliness, and postvisualization capabilities.« less

Incorporating Descriptive Assessment Results into the Design of a Functional Analysis: A Case Example Involving a Preschooler's Hand Mouthing

ERIC Educational Resources Information Center

Tiger, Jeffrey H.; Hanley, Gregory P.; Bessette, Kimberly K.

2006-01-01

Functional analysis methodology has become the hallmark of behavioral assessment, yielding a determination of behavioral function in roughly 96% of the cases published (Hanley, Iwata, & McCord, 2003). Some authors have suggested that incorporating the results of a descriptive assessment into the design of a functional analysis may be useful in…

Aerospace Power Systems Design and Analysis (APSDA) Tool

NASA Technical Reports Server (NTRS)

Truong, Long V.

1998-01-01

The conceptual design of space and/or planetary electrical power systems has required considerable effort. Traditionally, in the early stages of the design cycle (conceptual design), the researchers have had to thoroughly study and analyze tradeoffs between system components, hardware architectures, and operating parameters (such as frequencies) to optimize system mass, efficiency, reliability, and cost. This process could take anywhere from several months to several years (as for the former Space Station Freedom), depending on the scale of the system. Although there are many sophisticated commercial software design tools for personal computers (PC's), none of them can support or provide total system design. To meet this need, researchers at the NASA Lewis Research Center cooperated with Professor George Kusic from the University of Pittsburgh to develop a new tool to help project managers and design engineers choose the best system parameters as quickly as possible in the early design stages (in days instead of months). It is called the Aerospace Power Systems Design and Analysis (APSDA) Tool. By using this tool, users can obtain desirable system design and operating parameters such as system weight, electrical distribution efficiency, bus power, and electrical load schedule. With APSDA, a large-scale specific power system was designed in a matter of days. It is an excellent tool to help designers make tradeoffs between system components, hardware architectures, and operation parameters in the early stages of the design cycle. user interface. It operates on any PC running the MS-DOS (Microsoft Corp.) operating system, version 5.0 or later. A color monitor (EGA or VGA) and two-button mouse are required. The APSDA tool was presented at the 30th Intersociety Energy Conversion Engineering Conference (IECEC) and is being beta tested at several NASA centers. Beta test packages are available for evaluation by contacting the author.

Analysis tools for discovering strong parity violation at hadron colliders

NASA Astrophysics Data System (ADS)

Backović, Mihailo; Ralston, John P.

2011-07-01

Several arguments suggest parity violation may be observable in high energy strong interactions. We introduce new analysis tools to describe the azimuthal dependence of multiparticle distributions, or “azimuthal flow.” Analysis uses the representations of the orthogonal group O(2) and dihedral groups DN necessary to define parity completely in two dimensions. Classification finds that collective angles used in event-by-event statistics represent inequivalent tensor observables that cannot generally be represented by a single “reaction plane.” Many new parity-violating observables exist that have never been measured, while many parity-conserving observables formerly lumped together are now distinguished. We use the concept of “event-shape sorting” to suggest separating right- and left-handed events, and we discuss the effects of transverse and longitudinal spin. The analysis tools are statistically robust, and can be applied equally to low or high multiplicity events at the Tevatron, RHIC or RHIC Spin, and the LHC.

Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses

PubMed Central

Torre, Denis; Krawczuk, Patrycja; Jagodnik, Kathleen M.; Lachmann, Alexander; Wang, Zichen; Wang, Lily; Kuleshov, Maxim V.; Ma’ayan, Avi

2018-01-01

Biomedical data repositories such as the Gene Expression Omnibus (GEO) enable the search and discovery of relevant biomedical digital data objects. Similarly, resources such as OMICtools, index bioinformatics tools that can extract knowledge from these digital data objects. However, systematic access to pre-generated ‘canned’ analyses applied by bioinformatics tools to biomedical digital data objects is currently not available. Datasets2Tools is a repository indexing 31,473 canned bioinformatics analyses applied to 6,431 datasets. The Datasets2Tools repository also contains the indexing of 4,901 published bioinformatics software tools, and all the analyzed datasets. Datasets2Tools enables users to rapidly find datasets, tools, and canned analyses through an intuitive web interface, a Google Chrome extension, and an API. Furthermore, Datasets2Tools provides a platform for contributing canned analyses, datasets, and tools, as well as evaluating these digital objects according to their compliance with the findable, accessible, interoperable, and reusable (FAIR) principles. By incorporating community engagement, Datasets2Tools promotes sharing of digital resources to stimulate the extraction of knowledge from biomedical research data. Datasets2Tools is freely available from: http://amp.pharm.mssm.edu/datasets2tools. PMID:29485625

Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses.

PubMed

Torre, Denis; Krawczuk, Patrycja; Jagodnik, Kathleen M; Lachmann, Alexander; Wang, Zichen; Wang, Lily; Kuleshov, Maxim V; Ma'ayan, Avi

2018-02-27

Biomedical data repositories such as the Gene Expression Omnibus (GEO) enable the search and discovery of relevant biomedical digital data objects. Similarly, resources such as OMICtools, index bioinformatics tools that can extract knowledge from these digital data objects. However, systematic access to pre-generated 'canned' analyses applied by bioinformatics tools to biomedical digital data objects is currently not available. Datasets2Tools is a repository indexing 31,473 canned bioinformatics analyses applied to 6,431 datasets. The Datasets2Tools repository also contains the indexing of 4,901 published bioinformatics software tools, and all the analyzed datasets. Datasets2Tools enables users to rapidly find datasets, tools, and canned analyses through an intuitive web interface, a Google Chrome extension, and an API. Furthermore, Datasets2Tools provides a platform for contributing canned analyses, datasets, and tools, as well as evaluating these digital objects according to their compliance with the findable, accessible, interoperable, and reusable (FAIR) principles. By incorporating community engagement, Datasets2Tools promotes sharing of digital resources to stimulate the extraction of knowledge from biomedical research data. Datasets2Tools is freely available from: http://amp.pharm.mssm.edu/datasets2tools.

MetaGenyo: a web tool for meta-analysis of genetic association studies.

PubMed

Martorell-Marugan, Jordi; Toro-Dominguez, Daniel; Alarcon-Riquelme, Marta E; Carmona-Saez, Pedro

2017-12-16

Genetic association studies (GAS) aims to evaluate the association between genetic variants and phenotypes. In the last few years, the number of this type of study has increased exponentially, but the results are not always reproducible due to experimental designs, low sample sizes and other methodological errors. In this field, meta-analysis techniques are becoming very popular tools to combine results across studies to increase statistical power and to resolve discrepancies in genetic association studies. A meta-analysis summarizes research findings, increases statistical power and enables the identification of genuine associations between genotypes and phenotypes. Meta-analysis techniques are increasingly used in GAS, but it is also increasing the amount of published meta-analysis containing different errors. Although there are several software packages that implement meta-analysis, none of them are specifically designed for genetic association studies and in most cases their use requires advanced programming or scripting expertise. We have developed MetaGenyo, a web tool for meta-analysis in GAS. MetaGenyo implements a complete and comprehensive workflow that can be executed in an easy-to-use environment without programming knowledge. MetaGenyo has been developed to guide users through the main steps of a GAS meta-analysis, covering Hardy-Weinberg test, statistical association for different genetic models, analysis of heterogeneity, testing for publication bias, subgroup analysis and robustness testing of the results. MetaGenyo is a useful tool to conduct comprehensive genetic association meta-analysis. The application is freely available at http://bioinfo.genyo.es/metagenyo/ .

THE SMALL BODY GEOPHYSICAL ANALYSIS TOOL

NASA Astrophysics Data System (ADS)

Bercovici, Benjamin; McMahon, Jay

2017-10-01

The Small Body Geophysical Analysis Tool (SBGAT) that we are developing aims at providing scientists and mission designers with a comprehensive, easy to use, open-source analysis tool. SBGAT is meant for seamless generation of valuable simulated data originating from small bodies shape models, combined with advanced shape-modification properties.The current status of SBGAT is as follows:The modular software architecture that was specified in the original SBGAT proposal was implemented in the form of two distinct packages: a dynamic library SBGAT Core containing the data structure and algorithm backbone of SBGAT, and SBGAT Gui which wraps the former inside a VTK, Qt user interface to facilitate user/data interaction. This modular development facilitates maintenance and addi- tion of new features. Note that SBGAT Core can be utilized independently from SBGAT Gui.SBGAT is presently being hosted on a GitHub repository owned by SBGAT’s main developer. This repository is public and can be accessed at https://github.com/bbercovici/SBGAT. Along with the commented code, one can find the code documentation at https://bbercovici.github.io/sbgat-doc/index.html. This code documentation is constently updated in order to reflect new functionalities.SBGAT’s user’s manual is available at https://github.com/bbercovici/SBGAT/wiki. This document contains a comprehensive tutorial indicating how to retrieve, compile and run SBGAT from scratch.Some of the upcoming development goals are listed hereafter. First, SBGAT's dynamics module will be extented: the PGM algorithm is the only type of analysis method currently implemented. Future work will therefore consists in broadening SBGAT’s capabilities with the Spherical Harmonics Expansion of the gravity field and the calculation of YORP coefficients. Second, synthetic measurements will soon be available within SBGAT. The software should be able to generate synthetic observations of different type (radar, lightcurve, point clouds

Irena : tool suite for modeling and analysis of small-angle scattering.

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

Ilavsky, J.; Jemian, P.

2009-04-01

Irena, a tool suite for analysis of both X-ray and neutron small-angle scattering (SAS) data within the commercial Igor Pro application, brings together a comprehensive suite of tools useful for investigations in materials science, physics, chemistry, polymer science and other fields. In addition to Guinier and Porod fits, the suite combines a variety of advanced SAS data evaluation tools for the modeling of size distribution in the dilute limit using maximum entropy and other methods, dilute limit small-angle scattering from multiple non-interacting populations of scatterers, the pair-distance distribution function, a unified fit, the Debye-Bueche model, the reflectivity (X-ray and neutron)more » using Parratt's formalism, and small-angle diffraction. There are also a number of support tools, such as a data import/export tool supporting a broad sampling of common data formats, a data modification tool, a presentation-quality graphics tool optimized for small-angle scattering data, and a neutron and X-ray scattering contrast calculator. These tools are brought together into one suite with consistent interfaces and functionality. The suite allows robust automated note recording and saving of parameters during export.« less

Incorporation of Solar-Induced Chlorophyll Fluorescence into the Breathing Earth System Simulator (BESS)

NASA Astrophysics Data System (ADS)

Dechant, B.; Ryu, Y.; Jiang, C.; Yang, K.

2017-12-01

Solar-induced chlorophyll fluorescence (SIF) is rapidly becoming an important tool to remotely estimate terrestrial gross primary productivity (GPP) at large spatial scales. Many findings, however, are based on empirical relationships between SIF and GPP that have been found to be dependent on plant functional types. Therefore, combining model-based analysis with observations is crucial to improve our understanding of SIF-GPP relationships. So far, most model-based results were based on SCOPE, a complex ecophysiological model with explicit description of canopy layers and a large number of parameters that may not be easily obtained reliably on large scales. Here, we report on our efforts to incorporate SIF into a two-big leaf (sun and shade) process-based model that is suitable for obtaining its inputs entirely from satellite products. We examine if the SIF-GPP relationships are consistent with the findings from SCOPE simulations and investigate if incorporation of the SIF signal into BESS can help improve GPP estimation. A case study in a rice paddy is presented.

General Mission Analysis Tool (GMAT)

NASA Technical Reports Server (NTRS)

Hughes, Steven P. (Compiler)

2016-01-01

This is a software tutorial and presentation demonstrating the application of the General Mission Analysis Tool (GMAT) to the critical design phase of NASA missions. The demonstration discusses GMAT basics, then presents a detailed example of GMAT application to the Transiting Exoplanet Survey Satellite (TESS) mission. Other examples include OSIRIS-Rex. This talk is a combination of existing presentations; a GMAT basics and overview, and technical presentations from the TESS and OSIRIS-REx projects on their application of GMAT to critical mission design. The GMAT basics slides are taken from the open source training material. The OSIRIS-REx slides are from a previous conference presentation. The TESS slides are a streamlined version of the CDR package provided by the project with SBU and ITAR data removed by the TESS project.

General Mission Analysis Tool (GMAT) Architectural Specification. Draft

NASA Technical Reports Server (NTRS)

Hughes, Steven P.; Conway, Darrel, J.

2007-01-01

Early in 2002, Goddard Space Flight Center (GSFC) began to identify requirements for the flight dynamics software needed to fly upcoming missions that use formations of spacecraft to collect data. These requirements ranged from low level modeling features to large scale interoperability requirements. In 2003 we began work on a system designed to meet these requirement; this system is GMAT. The General Mission Analysis Tool (GMAT) is a general purpose flight dynamics modeling tool built on open source principles. The GMAT code is written in C++, and uses modern C++ constructs extensively. GMAT can be run through either a fully functional Graphical User Interface (GUI) or as a command line program with minimal user feedback. The system is built and runs on Microsoft Windows, Linux, and Macintosh OS X platforms. The GMAT GUI is written using wxWidgets, a cross platform library of components that streamlines the development and extension of the user interface Flight dynamics modeling is performed in GMAT by building components that represent the players in the analysis problem that is being modeled. These components interact through the sequential execution of instructions, embodied in the GMAT Mission Sequence. A typical Mission Sequence will model the trajectories of a set of spacecraft evolving over time, calculating relevant parameters during this propagation, and maneuvering individual spacecraft to maintain a set of mission constraints as established by the mission analyst. All of the elements used in GMAT for mission analysis can be viewed in the GMAT GUI or through a custom scripting language. Analysis problems modeled in GMAT are saved as script files, and these files can be read into GMAT. When a script is read into the GMAT GUI, the corresponding user interface elements are constructed in the GMAT GUI. The GMAT system was developed from the ground up to run in a platform agnostic environment. The source code compiles on numerous different platforms, and is

Semantic integration of gene expression analysis tools and data sources using software connectors

PubMed Central

2013-01-01

Background The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heteregeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data. Results We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data. Conclusions The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools

Semantic integration of gene expression analysis tools and data sources using software connectors.

PubMed

Miyazaki, Flávia A; Guardia, Gabriela D A; Vêncio, Ricardo Z N; de Farias, Cléver R G

2013-10-25

The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heterogeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data. We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data. The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools and data sources. The

Scalability Analysis of Gleipnir: A Memory Tracing and Profiling Tool, on Titan

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

Janjusic, Tommy; Kartsaklis, Christos; Wang, Dali

2013-01-01

Application performance is hindered by a variety of factors but most notably driven by the well know CPU-memory speed gap (also known as the memory wall). Understanding application s memory behavior is key if we are trying to optimize performance. Understanding application performance properties is facilitated with various performance profiling tools. The scope of profiling tools varies in complexity, ease of deployment, profiling performance, and the detail of profiled information. Specifically, using profiling tools for performance analysis is a common task when optimizing and understanding scientific applications on complex and large scale systems such as Cray s XK7. This papermore » describes the performance characteristics of using Gleipnir, a memory tracing tool, on the Titan Cray XK7 system when instrumenting large applications such as the Community Earth System Model. Gleipnir is a memory tracing tool built as a plug-in tool for the Valgrind instrumentation framework. The goal of Gleipnir is to provide fine-grained trace information. The generated traces are a stream of executed memory transactions mapped to internal structures per process, thread, function, and finally the data structure or variable. Our focus was to expose tool performance characteristics when using Gleipnir with a combination of an external tools such as a cache simulator, Gl CSim, to characterize the tool s overall performance. In this paper we describe our experience with deploying Gleipnir on the Titan Cray XK7 system, report on the tool s ease-of-use, and analyze run-time performance characteristics under various workloads. While all performance aspects are important we mainly focus on I/O characteristics analysis due to the emphasis on the tools output which are trace-files. Moreover, the tool is dependent on the run-time system to provide the necessary infrastructure to expose low level system detail; therefore, we also discuss any theoretical benefits that can be achieved if

Incorporating Measurement Non-Equivalence in a Cross-Study Latent Growth Curve Analysis

PubMed Central

Flora, David B.; Curran, Patrick J.; Hussong, Andrea M.; Edwards, Michael C.

2009-01-01

A large literature emphasizes the importance of testing for measurement equivalence in scales that may be used as observed variables in structural equation modeling applications. When the same construct is measured across more than one developmental period, as in a longitudinal study, it can be especially critical to establish measurement equivalence, or invariance, across the developmental periods. Similarly, when data from more than one study are combined into a single analysis, it is again important to assess measurement equivalence across the data sources. Yet, how to incorporate non-equivalence when it is discovered is not well described for applied researchers. Here, we present an item response theory approach that can be used to create scale scores from measures while explicitly accounting for non-equivalence. We demonstrate these methods in the context of a latent curve analysis in which data from two separate studies are combined to create a single longitudinal model spanning several developmental periods. PMID:19890440

Incorporating molecular and functional context into the analysis and prioritization of human variants associated with cancer

PubMed Central

Peterson, Thomas A; Nehrt, Nathan L; Park, DoHwan

2012-01-01

Background and objective With recent breakthroughs in high-throughput sequencing, identifying deleterious mutations is one of the key challenges for personalized medicine. At the gene and protein level, it has proven difficult to determine the impact of previously unknown variants. A statistical method has been developed to assess the significance of disease mutation clusters on protein domains by incorporating domain functional annotations to assist in the functional characterization of novel variants. Methods Disease mutations aggregated from multiple databases were mapped to domains, and were classified as either cancer- or non-cancer-related. The statistical method for identifying significantly disease-associated domain positions was applied to both sets of mutations and to randomly generated mutation sets for comparison. To leverage the known function of protein domain regions, the method optionally distributes significant scores to associated functional feature positions. Results Most disease mutations are localized within protein domains and display a tendency to cluster at individual domain positions. The method identified significant disease mutation hotspots in both the cancer and non-cancer datasets. The domain significance scores (DS-scores) for cancer form a bimodal distribution with hotspots in oncogenes forming a second peak at higher DS-scores than non-cancer, and hotspots in tumor suppressors have scores more similar to non-cancers. In addition, on an independent mutation benchmarking set, the DS-score method identified mutations known to alter protein function with very high precision. Conclusion By aggregating mutations with known disease association at the domain level, the method was able to discover domain positions enriched with multiple occurrences of deleterious mutations while incorporating relevant functional annotations. The method can be incorporated into translational bioinformatics tools to characterize rare and novel variants within

Hydrogen Financial Analysis Scenario Tool (H2FAST); NREL (National Renewable Energy Laboratory)

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

Melaina, Marc

This presentation describes the Hydrogen Financial Analysis Scenario Tool, H2FAST, and provides an overview of each of the three H2FAST formats: the H2FAST web tool, the H2FAST Excel spreadsheet, and the H2FAST Business Case Scenario (BCS) tool. Examples are presented to illustrate the types of questions that H2FAST can help answer.

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

ERIC Educational Resources Information Center

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

2017-01-01

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

Syntheses and characterization of liposome-incorporated adamantyl aminoguanidines.

PubMed

Šekutor, Marina; Štimac, Adela; Mlinarić-Majerski, Kata; Frkanec, Ruža

2014-08-21

A series of mono and bis-aminoguanidinium adamantane derivatives has been synthesized and incorporated into liposomes. They combine two biomedically significant molecules, the adamantane moiety and the guanidinium group. The adamantane moiety possesses the membrane compatible features while the cationic guanidinium subunit was recognized as a favourable structural feature for binding to complementary molecules comprising phosphate groups. The liposome formulations of adamantyl aminoguanidines were characterized and it was shown that the entrapment efficiency of the examined compounds is significant. In addition, it was demonstrated that liposomes with incorporated adamantyl aminoguanidines effectively recognized the complementary liposomes via the phosphate group. These results indicate that adamantane derivatives bearing guanidinium groups might be versatile tools for biomedical application, from studies of molecular recognition processes to usage in drug formulation and cell targeting.

Building a Community Infrastructure for Scalable On-Line Performance Analysis Tools around Open|Speedshop

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

Miller, Barton

2014-06-30

Peta-scale computing environments pose significant challenges for both system and application developers and addressing them required more than simply scaling up existing tera-scale solutions. Performance analysis tools play an important role in gaining this understanding, but previous monolithic tools with fixed feature sets have not sufficed. Instead, this project worked on the design, implementation, and evaluation of a general, flexible tool infrastructure supporting the construction of performance tools as “pipelines” of high-quality tool building blocks. These tool building blocks provide common performance tool functionality, and are designed for scalability, lightweight data acquisition and analysis, and interoperability. For this project, wemore » built on Open|SpeedShop, a modular and extensible open source performance analysis tool set. The design and implementation of such a general and reusable infrastructure targeted for petascale systems required us to address several challenging research issues. All components needed to be designed for scale, a task made more difficult by the need to provide general modules. The infrastructure needed to support online data aggregation to cope with the large amounts of performance and debugging data. We needed to be able to map any combination of tool components to each target architecture. And we needed to design interoperable tool APIs and workflows that were concrete enough to support the required functionality, yet provide the necessary flexibility to address a wide range of tools. A major result of this project is the ability to use this scalable infrastructure to quickly create tools that match with a machine architecture and a performance problem that needs to be understood. Another benefit is the ability for application engineers to use the highly scalable, interoperable version of Open|SpeedShop, which are reassembled from the tool building blocks into a flexible, multi-user interface set of tools

A web-based tool for groundwater mapping and drought analysis

NASA Astrophysics Data System (ADS)

Christensen, S.; Burns, M.; Jones, N.; Strassberg, G.

2012-12-01

In 2011-2012, the state of Texas saw the worst one-year drought on record. Fluctuations in gravity measured by GRACE satellites indicate that as much as 100 cubic kilometers of water was lost during this period. Much of this came from reservoirs and shallow soil moisture, but a significant amount came from aquifers. In response to this crisis, a Texas Drought Technology Steering Committee (TDTSC) consisting of academics and water managers was formed to develop new tools and strategies to assist the state in monitoring, predicting, and responding to drought events. In this presentation, we describe one of the tools that was developed as part of this effort. When analyzing the impact of drought on groundwater levels, it is fairly common to examine time series data at selected monitoring wells. However, accurately assessing impacts and trends requires both spatial and temporal analysis involving the development of detailed water level maps at various scales. Creating such maps in a flexible and rapid fashion is critical for effective drought analysis, but can be challenging due to the massive amounts of data involved and the processing required to generate such maps. Furthermore, wells are typically not sampled at the same points in time, and so developing a water table map for a particular date requires both spatial and temporal interpolation of water elevations. To address this challenge, a Cloud-based water level mapping system was developed for the state of Texas. The system is based on the Texas Water Development Board (TWDB) groundwater database, but can be adapted to use other databases as well. The system involves a set of ArcGIS workflows running on a server with a web-based front end and a Google Earth plug-in. A temporal interpolation geoprocessing tool was developed to estimate the piezometric heads for all wells in a given region at a specific date using a regression analysis. This interpolation tool is coupled with other geoprocessing tools to filter

Aviation System Analysis Capability Executive Assistant Analyses

NASA Technical Reports Server (NTRS)

Roberts, Eileen; Kostiuk, Peter

1999-01-01

This document describes the analyses that may be incorporated into the Aviation System Analysis Capability Executive Assistant. The document will be used as a discussion tool to enable NASA and other integrated aviation system entities to evaluate, discuss, and prioritize analyses.

Extending the Virtual Solar Observatory (VSO) to Incorporate Data Analysis Capabilities (III)

NASA Astrophysics Data System (ADS)

Csillaghy, A.; Etesi, L.; Dennis, B.; Zarro, D.; Schwartz, R.; Tolbert, K.

2008-12-01

We will present a progress report on our activities to extend the data analysis capabilities of the VSO. Our efforts to date have focused on three areas: 1. Extending the data retrieval capabilities by developing a centralized data processing server. The server is built with Java, IDL (Interactive Data Language), and the SSW (Solar SoftWare) package with all SSW-related instrument libraries and required calibration data. When a user requests VSO data that requires preprocessing, the data are transparently sent to the server, processed, and returned to the user's IDL session for viewing and analysis. It is possible to have any Java or IDL client connect to the server. An IDL prototype for preparing and calibrating SOHO/EIT data wll be demonstrated. 2. Improving the solar data search in SHOW SYNOP, a graphical user tool connected to VSO in IDL. We introduce the Java-IDL interface that allows a flexible dynamic, and extendable way of searching the VSO, where all the communication with VSO are managed dynamically by standard Java tools. 3. Improving image overlay capability to support coregistration of solar disk observations obtained from different orbital view angles, position angles, and distances - such as from the twin STEREO spacecraft.

Measuring laboratory-based influenza surveillance capacity: development of the 'International Influenza Laboratory Capacity Review' Tool.

PubMed

Muir-Paulik, S A; Johnson, L E A; Kennedy, P; Aden, T; Villanueva, J; Reisdorf, E; Humes, R; Moen, A C

2016-01-01

The 2005 International Health Regulations (IHR 2005) emphasized the importance of laboratory capacity to detect emerging diseases including novel influenza viruses. To support IHR 2005 requirements and the need to enhance influenza laboratory surveillance capacity, the Association of Public Health Laboratories (APHL) and the Centers for Disease Control and Prevention (CDC) Influenza Division developed the International Influenza Laboratory Capacity Review (Tool). Data from 37 assessments were reviewed and analyzed to verify that the quantitative analysis results accurately depicted a laboratory's capacity and capabilities. Subject matter experts in influenza and laboratory practice used an iterative approach to develop the Tool incorporating feedback and lessons learnt through piloting and implementation. To systematically analyze assessment data, a quantitative framework for analysis was added to the Tool. The review indicated that changes in scores consistently reflected enhanced or decreased capacity. The review process also validated the utility of adding a quantitative analysis component to the assessments and the benefit of establishing a baseline from which to compare future assessments in a standardized way. Use of the Tool has provided APHL, CDC and each assessed laboratory with a standardized analysis of the laboratory's capacity. The information generated is used to improve laboratory systems for laboratory testing and enhance influenza surveillance globally. We describe the development of the Tool and lessons learnt. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Breads enriched with guava flour as a tool for studying the incorporation of phenolic compounds in bread melanoidins.

PubMed

Alves, Genilton; Perrone, Daniel

2015-10-15

In the present study we aimed at studying, for the first time, the incorporation of phenolic compounds into bread melanoidins. Fermentation significantly affected the phenolics profile of bread doughs. Melanoidins contents continuously increased from 24.1 mg/g to 71.9 mg/g during baking, but their molecular weight decreased at the beginning of the process and increased thereafter. Enrichment of white wheat bread with guava flour increased the incorporation of phenolic compounds up to 2.4-fold. Most phenolic compounds showed higher incorporation than release rates during baking, leading to increases from 3.3- to 13.3-fold in total melanoidin-bound phenolics. Incorporation patterns suggested that phenolic hydroxyls, but not glycosidic bonds of melanoidin-bound phenolics are cleaved during thermal processing. Antioxidant capacity of bread melanoidins increased due to enrichment with guava flour and increasing baking periods and was partially attributed to bound phenolics. Moreover, FRAP assay was more sensitive to measure this parameter than TEAC assay. Copyright © 2015 Elsevier Ltd. All rights reserved.

Incorporating ethical principles into clinical research protocols: a tool for protocol writers and ethics committees

PubMed Central

Li, Rebecca H; Wacholtz, Mary C; Barnes, Mark; Boggs, Liam; Callery-D'Amico, Susan; Davis, Amy; Digilova, Alla; Forster, David; Heffernan, Kate; Luthin, Maeve; Lynch, Holly Fernandez; McNair, Lindsay; Miller, Jennifer E; Murphy, Jacquelyn; Van Campen, Luann; Wilenzick, Mark; Wolf, Delia; Woolston, Cris; Aldinger, Carmen; Bierer, Barbara E

2016-01-01

A novel Protocol Ethics Tool Kit (‘Ethics Tool Kit’) has been developed by a multi-stakeholder group of the Multi-Regional Clinical Trials Center of Brigham and Women's Hospital and Harvard. The purpose of the Ethics Tool Kit is to facilitate effective recognition, consideration and deliberation of critical ethical issues in clinical trial protocols. The Ethics Tool Kit may be used by investigators and sponsors to develop a dedicated Ethics Section within a protocol to improve the consistency and transparency between clinical trial protocols and research ethics committee reviews. It may also streamline ethics review and may facilitate and expedite the review process by anticipating the concerns of ethics committee reviewers. Specific attention was given to issues arising in multinational settings. With the use of this Tool Kit, researchers have the opportunity to address critical research ethics issues proactively, potentially speeding the time and easing the process to final protocol approval. PMID:26811365

A Meta-Analysis Method to Advance Design of Technology-Based Learning Tool: Combining Qualitative and Quantitative Research to Understand Learning in Relation to Different Technology Features

ERIC Educational Resources Information Center

Zhang, Lin

2014-01-01

Educators design and create various technology tools to scaffold students' learning. As more and more technology designs are incorporated into learning, growing attention has been paid to the study of technology-based learning tool. This paper discusses the emerging issues, such as how can learning effectiveness be understood in relation to…

A Revenue Planning Tool for Charter School Operators

ERIC Educational Resources Information Center

Keller, Eric; Hayes, Cheryl D.

2009-01-01

This revenue planning tool aims to help charter school operators develop a sound revenue base that can meet their school's current and future funding needs. It helps identify and assess potential public (federal, state, and local) and private funding sources. The tool incorporates a four-step revenue planning process which includes: (1)…

State Wildlife Action Plans as Tools for Adapting to a Continuously Changing Climate

NASA Astrophysics Data System (ADS)

Metivier, D. W.; Yocum, H.; Ray, A. J.

2015-12-01

Public land management plans are potentially powerful policies for building sustainability and adaptive capacity. Land managers are recognizing the need to respond to numerous climate change impacts on natural and human systems. For the first time, in 2015, the federal government required each state to incorporate climate change into their State Wildlife Action Plans (SWAP) as a condition for funding. As important land management tools, SWAPs have the potential to guide state agencies in shaping and implementing practices for climate change adaptation. Intended to be revised every ten years, SWAPs can change as conditions and understanding of climate change evolves. This study asks what practices are states using to integrate climate change, and how does this vary between states? To answer this question, we conducted a broad analysis among seven states (CO, MT, NE, ND, SD, UT, WY) and a more in-depth analysis of four states (CO, ND, SD, WY). We use seven key factors that represent best practices for incorporating climate change identified in the literature. These best practices are species prioritization, key habitats, threats, monitoring, partnerships and participation, identification of management options, and implementation of management options. The in-depth analysis focuses on how states are using climate change information for specific habitats addressed in the plans. We find that states are integrating climate change in many different ways, showing varying degrees of sophistication and preparedness. We summarize different practices and highlight opportunities to improve the effectiveness of plans through: communication tools across state lines and stakeholders, explicit targeting of key habitats, enforcement and monitoring progress and success, and conducting vulnerability analyses that incorporate topics beyond climate and include other drivers, trajectories, and implications of historic and future land-use change.

Decision Matrices: Tools to Enhance Middle School Engineering Instruction

ERIC Educational Resources Information Center

Gonczi, Amanda L.; Bergman, Brenda G.; Huntoon, Jackie; Allen, Robin; McIntyre, Barb; Turner, Sheri; Davis, Jen; Handler, Rob

2017-01-01

Decision matrices are valuable engineering tools. They allow engineers to objectively examine solution options. Decision matrices can be incorporated in K-12 classrooms to support authentic engineering instruction. In this article we provide examples of how decision matrices have been incorporated into 6th and 7th grade classrooms as part of an…

Tools for Data Analysis in the Middle School Classroom: A Teacher Professional Development Program

NASA Astrophysics Data System (ADS)

Ledley, T. S.; Haddad, N.; McAuliffe, C.; Dahlman, L.

2006-12-01

In order for students to learn how to engage with scientific data to answer questions about the real world, it is imperative that their teachers are 1) comfortable with the data and the tools used to analyze it, and 2) feel prepared to support their students in this complex endeavor. TERC's Tools for Data Analysis in the Middle School Classroom (DataTools) professional development program, funded by NSF's ITEST program, prepares middle school teachers to integrate Web-based scientific data and analysis tools into their existing curricula. This 13-month program supports teachers in using a set of freely or commonly available tools with a wide range of data. It also gives them an opportunity to practice teaching these skills to students before teaching in their own classrooms. The ultimate goal of the program is to increase the number of middle school students who work directly with scientific data, who use the tools of technology to import, manipulate, visualize and analyze the data, who come to understand the power of data-based arguments, and who will consider pursuing a career in technical and scientific fields. In this session, we will describe the elements of the DataTools program and the Earth Exploration Toolbook (EET, http://serc.carleton.edu/eet), a Web-based resource that supports Earth system education for teachers and students in grades 6 through 16. The EET provides essential support to DataTools teachers as they use it to learn to locate and download Web-based data and use data analysis tools. We will also share what we have learned during the first year of this three-year program.

Analysis of effects of impurities intentionally incorporated into silicon

NASA Technical Reports Server (NTRS)

Uno, F.

1977-01-01

A methodology was developed and implemented to allow silicon samples containing intentionally incorporated impurities to be fabricated into finished solar cells under carefully controlled conditions. The electrical and spectral properties were then measured for each group processed.

System analysis tools for an ELT at ESO

NASA Astrophysics Data System (ADS)

Mueller, Michael; Koch, Franz

2006-06-01

Engineering of complex, large scale systems like the ELT designs currently investigated and developed in Europe and Northern America require powerful and sophisticated tools within specific technical disciplines such as mechanics, optics and control engineering. However, even analyzing a certain component of the telescope like the telescope structure necessitates a system approach to evaluate the structural effects onto the optical performance. This paper shows several software tools developed by the European Southern Observatory (ESO) which focus onto the system approach in the analyses: Using modal results of a finite element analysis the SMI-toolbox allows an easy generation of structural models with different sizes and levels of accuracy for the control design and closed-loop simulations. The optical modeling code BeamWarrior was developed by ESO and Astrium GmbH, Germany) especially for integrated modeling and interfering with a structural model. Within BeamWarrior displacements and deformations can be applied in an arbitrary coordinate system, and hence also in the global coordinates of the FE model avoiding error prone transformations. In addition to this, a sparse state space model object was developed for Matlab to gain in computational efficiency and reduced memory requirements due to the sparsity pattern of both the structural models and the control architecture. As one result these tools allow building an integrated model in order to reliably simulate interactions, cross-coupling effects, system responses, and to evaluate global performance. In order to evaluate disturbance effects on the optical performance in openloop more efficiently, an optical evaluation toolbox was built in the FE software ANSYS which performs Zernike decomposition and best-fit computation of the deformations directly in the FE analysis.

A learning tool for optical and microwave satellite image processing and analysis

NASA Astrophysics Data System (ADS)

Dashondhi, Gaurav K.; Mohanty, Jyotirmoy; Eeti, Laxmi N.; Bhattacharya, Avik; De, Shaunak; Buddhiraju, Krishna M.

2016-04-01

This paper presents a self-learning tool, which contains a number of virtual experiments for processing and analysis of Optical/Infrared and Synthetic Aperture Radar (SAR) images. The tool is named Virtual Satellite Image Processing and Analysis Lab (v-SIPLAB) Experiments that are included in Learning Tool are related to: Optical/Infrared - Image and Edge enhancement, smoothing, PCT, vegetation indices, Mathematical Morphology, Accuracy Assessment, Supervised/Unsupervised classification etc.; Basic SAR - Parameter extraction and range spectrum estimation, Range compression, Doppler centroid estimation, Azimuth reference function generation and compression, Multilooking, image enhancement, texture analysis, edge and detection. etc.; SAR Interferometry - BaseLine Calculation, Extraction of single look SAR images, Registration, Resampling, and Interferogram generation; SAR Polarimetry - Conversion of AirSAR or Radarsat data to S2/C3/T3 matrix, Speckle Filtering, Power/Intensity image generation, Decomposition of S2/C3/T3, Classification of S2/C3/T3 using Wishart Classifier [3]. A professional quality polarimetric SAR software can be found at [8], a part of whose functionality can be found in our system. The learning tool also contains other modules, besides executable software experiments, such as aim, theory, procedure, interpretation, quizzes, link to additional reading material and user feedback. Students can have understanding of Optical and SAR remotely sensed images through discussion of basic principles and supported by structured procedure for running and interpreting the experiments. Quizzes for self-assessment and a provision for online feedback are also being provided to make this Learning tool self-contained. One can download results after performing experiments.

The Tracking Meteogram, an AWIPS II Tool for Time-Series Analysis

NASA Technical Reports Server (NTRS)

Burks, Jason Eric; Sperow, Ken

2015-01-01

A new tool has been developed for the National Weather Service (NWS) Advanced Weather Interactive Processing System (AWIPS) II through collaboration between NASA's Short-term Prediction Research and Transition (SPoRT) and the NWS Meteorological Development Laboratory (MDL). Referred to as the "Tracking Meteogram", the tool aids NWS forecasters in assessing meteorological parameters associated with moving phenomena. The tool aids forecasters in severe weather situations by providing valuable satellite and radar derived trends such as cloud top cooling rates, radial velocity couplets, reflectivity, and information from ground-based lightning networks. The Tracking Meteogram tool also aids in synoptic and mesoscale analysis by tracking parameters such as the deepening of surface low pressure systems, changes in surface or upper air temperature, and other properties. The tool provides a valuable new functionality and demonstrates the flexibility and extensibility of the NWS AWIPS II architecture. In 2014, the operational impact of the tool was formally evaluated through participation in the NOAA/NWS Operations Proving Ground (OPG), a risk reduction activity to assess performance and operational impact of new forecasting concepts, tools, and applications. Performance of the Tracking Meteogram Tool during the OPG assessment confirmed that it will be a valuable asset to the operational forecasters. This presentation reviews development of the Tracking Meteogram tool, performance and feedback acquired during the OPG activity, and future goals for continued support and extension to other application areas.

Storytelling: a leadership and educational tool.

PubMed

Kowalski, Karren

2015-06-01

A powerful tool that leaders and educators can use to engage the listeners-both staff and learners-is storytelling. Stories demonstrate important points, valuable lessons, and the behaviors that are preferred by the leader. Copyright 2015, SLACK Incorporated.

An Automated Data Analysis Tool for Livestock Market Data

ERIC Educational Resources Information Center

Williams, Galen S.; Raper, Kellie Curry

2011-01-01

This article describes an automated data analysis tool that allows Oklahoma Cooperative Extension Service educators to disseminate results in a timely manner. Primary data collected at Oklahoma Quality Beef Network (OQBN) certified calf auctions across the state results in a large amount of data per sale site. Sale summaries for an individual sale…

An evaluation of the accuracy and speed of metagenome analysis tools

PubMed Central

Lindgreen, Stinus; Adair, Karen L.; Gardner, Paul P.

2016-01-01

Metagenome studies are becoming increasingly widespread, yielding important insights into microbial communities covering diverse environments from terrestrial and aquatic ecosystems to human skin and gut. With the advent of high-throughput sequencing platforms, the use of large scale shotgun sequencing approaches is now commonplace. However, a thorough independent benchmark comparing state-of-the-art metagenome analysis tools is lacking. Here, we present a benchmark where the most widely used tools are tested on complex, realistic data sets. Our results clearly show that the most widely used tools are not necessarily the most accurate, that the most accurate tool is not necessarily the most time consuming, and that there is a high degree of variability between available tools. These findings are important as the conclusions of any metagenomics study are affected by errors in the predicted community composition and functional capacity. Data sets and results are freely available from http://www.ucbioinformatics.org/metabenchmark.html PMID:26778510

ISAC: A tool for aeroservoelastic modeling and analysis