deepTools: a flexible platform for exploring deep-sequencing data.

PubMed

Ramírez, Fidel; Dündar, Friederike; Diehl, Sarah; Grüning, Björn A; Manke, Thomas

2014-07-01

We present a Galaxy based web server for processing and visualizing deeply sequenced data. The web server's core functionality consists of a suite of newly developed tools, called deepTools, that enable users with little bioinformatic background to explore the results of their sequencing experiments in a standardized setting. Users can upload pre-processed files with continuous data in standard formats and generate heatmaps and summary plots in a straight-forward, yet highly customizable manner. In addition, we offer several tools for the analysis of files containing aligned reads and enable efficient and reproducible generation of normalized coverage files. As a modular and open-source platform, deepTools can easily be expanded and customized to future demands and developments. The deepTools webserver is freely available at http://deeptools.ie-freiburg.mpg.de and is accompanied by extensive documentation and tutorials aimed at conveying the principles of deep-sequencing data analysis. The web server can be used without registration. deepTools can be installed locally either stand-alone or as part of Galaxy. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

ScienceOrganizer System and Interface Summary

NASA Technical Reports Server (NTRS)

Keller, Richard M.; Norvig, Peter (Technical Monitor)

2001-01-01

ScienceOrganizer is a specialized knowledge management tool designed to enhance the information storage, organization, and access capabilities of distributed NASA science teams. Users access ScienceOrganizer through an intuitive Web-based interface that enables them to upload, download, and organize project information - including data, documents, images, and scientific records associated with laboratory and field experiments. Information in ScienceOrganizer is "threaded", or interlinked, to enable users to locate, track, and organize interrelated pieces of scientific data. Linkages capture important semantic relationships among information resources in the repository, and these assist users in navigating through the information related to their projects.

Spaceflight Operations Services Grid (SOSG) Prototype Implementation and Feasibility Study

NASA Technical Reports Server (NTRS)

Bradford, Robert N.; Thigpen, William W.; Lisotta, Anthony J.; Redman, Sandra

2004-01-01

Science Operations Services Grid is focusing on building a prototype grid-based environment that incorporates existing and new spaceflight services to enable current and future NASA programs with cost savings and new and evolvable methods to conduct science in a distributed environment. The Science Operations Services Grid (SOSG) will provide a distributed environment for widely disparate organizations to conduct their systems and processes in a more efficient and cost effective manner. These organizations include those that: 1) engage in space-based science and operations, 2) develop space-based systems and processes, and 3) conduct scientific research, bringing together disparate scientific disciplines like geology and oceanography to create new information. In addition educational outreach will be significantly enhanced by providing to schools the same tools used by NASA with the ability of the schools to actively participate on many levels in the science generated by NASA from space and on the ground. The services range from voice, video and telemetry processing and display to data mining, high level processing and visualization tools all accessible from a single portal. In this environment, users would not require high end systems or processes at their home locations to use these services. Also, the user would need to know minimal details about the applications in order to utilize the services. In addition, security at all levels is an underlying goal of the project. The Science Operations Services Grid will focus on four tools that are currently used by the ISS Payload community along with nine more that are new to the community. Under the prototype four Grid virtual organizations PO) will be developed to represent four types of users. They are a Payload (experimenters) VO, a Flight Controllers VO, an Engineering and Science Collaborators VO and an Education and Public Outreach VO. The User-based services will be implemented to replicate the operational voice, video, telemetry and commanding systems. Once the User-based services are in place, they will be analyzed to establish feasibility for Grid enabling. If feasible then each User-based service will be Grid enabled. The remaining non-Grid services if not already Web enabled will be so enabled. In the end, four portals will be developed one for each VO. Each portal will contain the appropriate User-based services required for that VO to operate.

Teaching Tectonics to Undergraduates with Web GIS

NASA Astrophysics Data System (ADS)

Anastasio, D. J.; Bodzin, A.; Sahagian, D. L.; Rutzmoser, S.

2013-12-01

Geospatial reasoning skills provide a means for manipulating, interpreting, and explaining structured information and are involved in higher-order cognitive processes that include problem solving and decision-making. Appropriately designed tools, technologies, and curriculum can support spatial learning. We present Web-based visualization and analysis tools developed with Javascript APIs to enhance tectonic curricula while promoting geospatial thinking and scientific inquiry. The Web GIS interface integrates graphics, multimedia, and animations that allow users to explore and discover geospatial patterns that are not easily recognized. Features include a swipe tool that enables users to see underneath layers, query tools useful in exploration of earthquake and volcano data sets, a subduction and elevation profile tool which facilitates visualization between map and cross-sectional views, drafting tools, a location function, and interactive image dragging functionality on the Web GIS. The Web GIS platform is independent and can be implemented on tablets or computers. The GIS tool set enables learners to view, manipulate, and analyze rich data sets from local to global scales, including such data as geology, population, heat flow, land cover, seismic hazards, fault zones, continental boundaries, and elevation using two- and three- dimensional visualization and analytical software. Coverages which allow users to explore plate boundaries and global heat flow processes aided learning in a Lehigh University Earth and environmental science Structural Geology and Tectonics class and are freely available on the Web.

Online educational tools developed by Heart improve the knowledge and skills of hospital doctors in cardiology

PubMed Central

Walsh, Kieran; Rafiq, Isma; Hall, Roger

2007-01-01

We conducted this study to find out if online learning packages in cardiology enabled users to increase their knowledge and skills. We also looked at how acceptable users found these packages. The journal Heart in association with BMJ Learning produced a series of modules on common cardiology problems. The modules involved a pre‐test, a number of interactive cases and a post‐test. A total of 1786 users completed these modules. Doing the modules enabled users to improve their score from the pre‐test to the post‐test by a significant amount (p<0.001). Feedback to the modules was very positive. PMID:17621623

Service composition towards increasing end-user accessibility.

PubMed

Kaklanis, Nikolaos; Votis, Konstantinos; Tzovaras, Dimitrios

2015-01-01

This paper presents the Cloud4all Service Synthesizer Tool, a framework that enables efficient orchestration of accessibility services, as well as their combination into complex forms, providing more advanced functionalities towards increasing the accessibility of end-users with various types of functional limitations. The supported services are described formally within an ontology, enabling, thus, semantic service composition. The proposed service composition approach is based on semantic matching between services specifications on the one hand and user needs/preferences and current context of use on the other hand. The use of automatic composition of accessibility services can significantly enhance end-users' accessibility, especially in cases where assistive solutions are not available in their device.

Droplet Digital™ PCR Next-Generation Sequencing Library QC Assay.

PubMed

Heredia, Nicholas J

2018-01-01

Digital PCR is a valuable tool to quantify next-generation sequencing (NGS) libraries precisely and accurately. Accurately quantifying NGS libraries enable accurate loading of the libraries on to the sequencer and thus improve sequencing performance by reducing under and overloading error. Accurate quantification also benefits users by enabling uniform loading of indexed/barcoded libraries which in turn greatly improves sequencing uniformity of the indexed/barcoded samples. The advantages gained by employing the Droplet Digital PCR (ddPCR™) library QC assay includes the precise and accurate quantification in addition to size quality assessment, enabling users to QC their sequencing libraries with confidence.

Visualizing Dataflow Graphs of Deep Learning Models in TensorFlow.

PubMed

Wongsuphasawat, Kanit; Smilkov, Daniel; Wexler, James; Wilson, Jimbo; Mane, Dandelion; Fritz, Doug; Krishnan, Dilip; Viegas, Fernanda B; Wattenberg, Martin

2018-01-01

We present a design study of the TensorFlow Graph Visualizer, part of the TensorFlow machine intelligence platform. This tool helps users understand complex machine learning architectures by visualizing their underlying dataflow graphs. The tool works by applying a series of graph transformations that enable standard layout techniques to produce a legible interactive diagram. To declutter the graph, we decouple non-critical nodes from the layout. To provide an overview, we build a clustered graph using the hierarchical structure annotated in the source code. To support exploration of nested structure on demand, we perform edge bundling to enable stable and responsive cluster expansion. Finally, we detect and highlight repeated structures to emphasize a model's modular composition. To demonstrate the utility of the visualizer, we describe example usage scenarios and report user feedback. Overall, users find the visualizer useful for understanding, debugging, and sharing the structures of their models.

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.

Sequence Polishing Library (SPL) v10.0

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

Oberortner, Ernst

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

An Intuitive Dashboard for Bayesian Network Inference

NASA Astrophysics Data System (ADS)

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

2014-03-01

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

ReactPRED: a tool to predict and analyze biochemical reactions.

PubMed

Sivakumar, Tadi Venkata; Giri, Varun; Park, Jin Hwan; Kim, Tae Yong; Bhaduri, Anirban

2016-11-15

Biochemical pathways engineering is often used to synthesize or degrade target chemicals. In silico screening of the biochemical transformation space allows predicting feasible reactions, constituting these pathways. Current enabling tools are customized to predict reactions based on pre-defined biochemical transformations or reaction rule sets. Reaction rule sets are usually curated manually and tailored to specific applications. They are not exhaustive. In addition, current systems are incapable of regulating and refining data with an aim to tune specificity and sensitivity. A robust and flexible tool that allows automated reaction rule set creation along with regulated pathway prediction and analyses is a need. ReactPRED aims to address the same. ReactPRED is an open source flexible and customizable tool enabling users to predict biochemical reactions and pathways. The tool allows automated reaction rule creation from a user defined reaction set. Additionally, reaction rule degree and rule tolerance features allow refinement of predicted data. It is available as a flexible graphical user interface and a console application. ReactPRED is available at: https://sourceforge.net/projects/reactpred/ CONTACT: anirban.b@samsung.com or ty76.kim@samsung.comSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A Fast, Minimalist Search Tool for Remote Sensing Data

NASA Astrophysics Data System (ADS)

Lynnes, C. S.; Macharrie, P. G.; Elkins, M.; Joshi, T.; Fenichel, L. H.

2005-12-01

We present a tool that emphasizes speed and simplicity in searching remotely sensed Earth Science data. The tool, nicknamed "Mirador" (Spanish for a scenic overlook), provides only four freetext search form fields, for Keywords, Location, Data Start and Data Stop. This contrasts with many current Earth Science search tools that offer highly structured interfaces in order to ensure precise, non-zero results. The disadvantages of the structured approach lie in its complexity and resultant learning curve, as well as the time it takes to formulate and execute the search, thus discouraging iterative discovery. On the other hand, the success of the basic Google search interface shows that many users are willing to forgo high search precision if the search process is fast enough to enable rapid iteration. Therefore, we employ several methods to increase the speed of search formulation and execution. Search formulation is expedited by the minimalist search form, with only one required field. Also, a gazetteer enables the use of geographic terms as shorthand for latitude/longitude coordinates. The search execution is accelerated by initially presenting dataset results (returned from a Google Mini appliance) with an estimated number of "hits" for each dataset based on the user's space-time constraints. The more costly file-level search is executed against a PostGres database only when the user "drills down", and then covering only the fraction of the time period needed to return the next page of results. The simplicity of the search form makes the tool easy to learn and use, and the speed of the searches enables an iterative form of data discovery.

imDEV: a graphical user interface to R multivariate analysis tools in Microsoft Excel

USDA-ARS?s Scientific Manuscript database

Interactive modules for data exploration and visualization (imDEV) is a Microsoft Excel spreadsheet embedded application providing an integrated environment for the analysis of omics data sets with a user-friendly interface. Individual modules were designed to provide toolsets to enable interactive ...

Enabling Web-Based GIS Tools for Internet and Mobile Devices To Improve and Expand NASA Data Accessibility and Analysis Functionality for the Renewable Energy and Agricultural Applications

NASA Astrophysics Data System (ADS)

Ross, A.; Stackhouse, P. W.; Tisdale, B.; Tisdale, M.; Chandler, W.; Hoell, J. M., Jr.; Kusterer, J.

2014-12-01

The NASA Langley Research Center Science Directorate and Atmospheric Science Data Center have initiated a pilot program to utilize Geographic Information System (GIS) tools that enable, generate and store climatological averages using spatial queries and calculations in a spatial database resulting in greater accessibility of data for government agencies, industry and private sector individuals. The major objectives of this effort include the 1) Processing and reformulation of current data to be consistent with ESRI and openGIS tools, 2) Develop functions to improve capability and analysis that produce "on-the-fly" data products, extending these past the single location to regional and global scales. 3) Update the current web sites to enable both web-based and mobile application displays for optimization on mobile platforms, 4) Interact with user communities in government and industry to test formats and usage of optimization, and 5) develop a series of metrics that allow for monitoring of progressive performance. Significant project results will include the the development of Open Geospatial Consortium (OGC) compliant web services (WMS, WCS, WFS, WPS) that serve renewable energy and agricultural application products to users using GIS software and tools. Each data product and OGC service will be registered within ECHO, the Common Metadata Repository, the Geospatial Platform, and Data.gov to ensure the data are easily discoverable and provide data users with enhanced access to SSE data, parameters, services, and applications. This effort supports cross agency, cross organization, and interoperability of SSE data products and services by collaborating with DOI, NRCan, NREL, NCAR, and HOMER for requirements vetting and test bed users before making available to the wider public.

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

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

Galitsky, Christina; Worrell, Ernst; Radspieler, Anthony

2005-10-15

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

Transportable Applications Environment Plus, Version 5.1

NASA Technical Reports Server (NTRS)

1994-01-01

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

Web-Based Architecture to Enable Compute-Intensive CAD Tools and Multi-user Synchronization in Teleradiology

NASA Astrophysics Data System (ADS)

Mehta, Neville; Kompalli, Suryaprakash; Chaudhary, Vipin

Teleradiology is the electronic transmission of radiological patient images, such as x-rays, CT, or MR across multiple locations. The goal could be interpretation, consultation, or medical records keeping. Information technology solutions have enabled electronic records and their associated benefits are evident in health care today. However, salient aspects of collaborative interfaces, and computer assisted diagnostic (CAD) tools are yet to be integrated into workflow designs. The Computer Assisted Diagnostics and Interventions (CADI) group at the University at Buffalo has developed an architecture that facilitates web-enabled use of CAD tools, along with the novel concept of synchronized collaboration. The architecture can support multiple teleradiology applications and case studies are presented here.

Interoperable Solar Data and Metadata via LISIRD 3

NASA Astrophysics Data System (ADS)

Wilson, A.; Lindholm, D. M.; Pankratz, C. K.; Snow, M. A.; Woods, T. N.

2015-12-01

LISIRD 3 is a major upgrade of the LASP Interactive Solar Irradiance Data Center (LISIRD), which serves several dozen space based solar irradiance and related data products to the public. Through interactive plots, LISIRD 3 provides data browsing supported by data subsetting and aggregation. Incorporating a semantically enabled metadata repository, LISIRD 3 users see current, vetted, consistent information about the datasets offered. Users can now also search for datasets based on metadata fields such as dataset type and/or spectral or temporal range. This semantic database enables metadata browsing, so users can discover the relationships between datasets, instruments, spacecraft, mission and PI. The database also enables creation and publication of metadata records in a variety of formats, such as SPASE or ISO, making these datasets more discoverable. The database also enables the possibility of a public SPARQL endpoint, making the metadata browsable in an automated fashion. LISIRD 3's data access middleware, LaTiS, provides dynamic, on demand reformatting of data and timestamps, subsetting and aggregation, and other server side functionality via a RESTful OPeNDAP compliant API, enabling interoperability between LASP datasets and many common tools. LISIRD 3's templated front end design, coupled with the uniform data interface offered by LaTiS, allows easy integration of new datasets. Consequently the number and variety of datasets offered by LISIRD has grown to encompass several dozen, with many more to come. This poster will discuss design and implementation of LISIRD 3, including tools used, capabilities enabled, and issues encountered.

EpiHosp: A web-based visualization tool enabling the exploratory analysis of complications of implantable medical devices from a nationwide hospital database.

PubMed

Ficheur, Grégoire; Ferreira Careira, Lionel; Beuscart, Régis; Chazard, Emmanuel

2015-01-01

Administrative data can be used for the surveillance of the outcomes of implantable medical devices (IMDs). The objective of this work is to build a web-based tool allowing for an exploratory analysis of time-dependent events that may occur after the implementation of an IMD. This tool should enable a pharmacoepidemiologist to explore on the fly the relationship between a given IMD and a potential outcome. This tool mine the French nationwide database of inpatient stays from 2008 to 2013. The data are preprocessed in order to optimize the queries. A web tool is developed in PHP, MySQL and Javascript. The user selects one or a group of IMD from a tree, and can filter the results using years and hospital names. Four result pages describe the selected inpatient stays: (1) temporal and demographic description, (2) a description of the geographical location of the hospital, (3) a description of the geographical place of residence of the patient and (4) a table showing the rehospitalization reasons by decreasing order of frequency. Then, the user can select one readmission reason and display dynamically the probability of readmission by mean of a Kaplan-Meier curve with confidence intervals. This tool enables to dynamically monitor the occurrence of time-dependent complications of IMD.

Distributed Observer Network (DON), Version 3.0, User's Guide

NASA Technical Reports Server (NTRS)

Mazzone, Rebecca A.; Conroy, Michael P.

2015-01-01

The Distributed Observer Network (DON) is a data presentation tool developed by the National Aeronautics and Space Administration (NASA) to distribute and publish simulation results. Leveraging the display capabilities inherent in modern gaming technology, DON places users in a fully navigable 3-D environment containing graphical models and allows the users to observe how those models evolve and interact over time in a given scenario. Each scenario is driven with data that has been generated by authoritative NASA simulation tools and exported in accordance with a published data interface specification. This decoupling of the data from the source tool enables DON to faithfully display a simulator's results and ensure that every simulation stakeholder will view the exact same information every time.

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

Enabling Rapid Naval Architecture Design Space Exploration

NASA Technical Reports Server (NTRS)

Mueller, Michael A.; Dufresne, Stephane; Balestrini-Robinson, Santiago; Mavris, Dimitri

2011-01-01

Well accepted conceptual ship design tools can be used to explore a design space, but more precise results can be found using detailed models in full-feature computer aided design programs. However, defining a detailed model can be a time intensive task and hence there is an incentive for time sensitive projects to use conceptual design tools to explore the design space. In this project, the combination of advanced aerospace systems design methods and an accepted conceptual design tool facilitates the creation of a tool that enables the user to not only visualize ship geometry but also determine design feasibility and estimate the performance of a design.

An overview of the NASA Langley Atmospheric Data Center: Online tools to effectively disseminate Earth science data products

NASA Astrophysics Data System (ADS)

Parker, L.; Dye, R. A.; Perez, J.; Rinsland, P.

2012-12-01

Over the past decade the Atmospheric Science Data Center (ASDC) at NASA Langley Research Center has archived and distributed a variety of satellite mission and aircraft campaign data sets. These datasets posed unique challenges to the user community at large due to the sheer volume and variety of the data and the lack of intuitive features in the order tools available to the investigator. Some of these data sets also lack sufficient metadata to provide rudimentary data discovery. To meet the needs of emerging users, the ASDC addressed issues in data discovery and delivery through the use of standards in data and access methods, and distribution through appropriate portals. The ASDC is currently undergoing a refresh of its webpages and Ordering Tools that will leverage updated collection level metadata in an effort to enhance the user experience. The ASDC is now providing search and subset capability to key mission satellite data sets. The ASDC has collaborated with Science Teams to accommodate prospective science users in the climate and modeling communities. The ASDC is using a common framework that enables more rapid development and deployment of search and subset tools that provide enhanced access features for the user community. Features of the Search and Subset web application enables a more sophisticated approach to selecting and ordering data subsets by parameter, date, time, and geographic area. The ASDC has also applied key practices from satellite missions to the multi-campaign aircraft missions executed for Earth Venture-1 and MEaSUReS

Preservice Teachers' Perception and Use of Personal Learning Environments (PLEs)

ERIC Educational Resources Information Center

Sahin, Sami; Uluyol, Çelebi

2016-01-01

Personal learning environments (PLEs) are Web 2.0 tools and services by which users' access, construct, manage, and share educational contents in order to meet their learning needs. These environments enable users to manage their learning according to their own personal preferences. They further promote socialization and collaboration with their…

PLOT3D Export Tool for Tecplot

NASA Technical Reports Server (NTRS)

Alter, Stephen

2010-01-01

The PLOT3D export tool for Tecplot solves the problem of modified data being impossible to output for use by another computational science solver. The PLOT3D Exporter add-on enables the use of the most commonly available visualization tools to engineers for output of a standard format. The exportation of PLOT3D data from Tecplot has far reaching effects because it allows for grid and solution manipulation within a graphical user interface (GUI) that is easily customized with macro language-based and user-developed GUIs. The add-on also enables the use of Tecplot as an interpolation tool for solution conversion between different grids of different types. This one add-on enhances the functionality of Tecplot so significantly, it offers the ability to incorporate Tecplot into a general suite of tools for computational science applications as a 3D graphics engine for visualization of all data. Within the PLOT3D Export Add-on are several functions that enhance the operations and effectiveness of the add-on. Unlike Tecplot output functions, the PLOT3D Export Add-on enables the use of the zone selection dialog in Tecplot to choose which zones are to be written by offering three distinct options - output of active, inactive, or all zones (grid blocks). As the user modifies the zones to output with the zone selection dialog, the zones to be written are similarly updated. This enables the use of Tecplot to create multiple configurations of a geometry being analyzed. For example, if an aircraft is loaded with multiple deflections of flaps, by activating and deactivating different zones for a specific flap setting, new specific configurations of that aircraft can be easily generated by only writing out specific zones. Thus, if ten flap settings are loaded into Tecplot, the PLOT3D Export software can output ten different configurations, one for each flap setting.

A web-based data visualization tool for the MIMIC-II database.

PubMed

Lee, Joon; Ribey, Evan; Wallace, James R

2016-02-04

Although MIMIC-II, a public intensive care database, has been recognized as an invaluable resource for many medical researchers worldwide, becoming a proficient MIMIC-II researcher requires knowledge of SQL programming and an understanding of the MIMIC-II database schema. These are challenging requirements especially for health researchers and clinicians who may have limited computer proficiency. In order to overcome this challenge, our objective was to create an interactive, web-based MIMIC-II data visualization tool that first-time MIMIC-II users can easily use to explore the database. The tool offers two main features: Explore and Compare. The Explore feature enables the user to select a patient cohort within MIMIC-II and visualize the distributions of various administrative, demographic, and clinical variables within the selected cohort. The Compare feature enables the user to select two patient cohorts and visually compare them with respect to a variety of variables. The tool is also helpful to experienced MIMIC-II researchers who can use it to substantially accelerate the cumbersome and time-consuming steps of writing SQL queries and manually visualizing extracted data. Any interested researcher can use the MIMIC-II data visualization tool for free to quickly and conveniently conduct a preliminary investigation on MIMIC-II with a few mouse clicks. Researchers can also use the tool to learn the characteristics of the MIMIC-II patients. Since it is still impossible to conduct multivariable regression inside the tool, future work includes adding analytics capabilities. Also, the next version of the tool will aim to utilize MIMIC-III which contains more data.

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

PubMed

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

2011-10-14

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

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

PubMed Central

2011-01-01

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

A parallel coordinates style interface for exploratory volume visualization.

PubMed

Tory, Melanie; Potts, Simeon; Möller, Torsten

2005-01-01

We present a user interface, based on parallel coordinates, that facilitates exploration of volume data. By explicitly representing the visualization parameter space, the interface provides an overview of rendering options and enables users to easily explore different parameters. Rendered images are stored in an integrated history bar that facilitates backtracking to previous visualization options. Initial usability testing showed clear agreement between users and experts of various backgrounds (usability, graphic design, volume visualization, and medical physics) that the proposed user interface is a valuable data exploration tool.

The fast encryption package

NASA Technical Reports Server (NTRS)

Bishop, Matt

1988-01-01

The organization of some tools to help improve passwork security at a UNIX-based site is described along with how to install and use them. These tools and their associated library enable a site to force users to pick reasonably safe passwords (safe being site configurable) and to enable site management to try to crack existing passworks. The library contains various versions of a very fast implementation of the Data Encryption Standard and of the one-way encryption functions used to encryp the password.

An online database for plant image analysis software tools.

PubMed

Lobet, Guillaume; Draye, Xavier; Périlleux, Claire

2013-10-09

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

iTesla Power Systems Library (iPSL): A Modelica library for phasor time-domain simulations

NASA Astrophysics Data System (ADS)

Vanfretti, L.; Rabuzin, T.; Baudette, M.; Murad, M.

The iTesla Power Systems Library (iPSL) is a Modelica package providing a set of power system components for phasor time-domain modeling and simulation. The Modelica language provides a systematic approach to develop models using a formal mathematical description, that uniquely specifies the physical behavior of a component or the entire system. Furthermore, the standardized specification of the Modelica language (Modelica Association [1]) enables unambiguous model exchange by allowing any Modelica-compliant tool to utilize the models for simulation and their analyses without the need of a specific model transformation tool. As the Modelica language is being developed with open specifications, any tool that implements these requirements can be utilized. This gives users the freedom of choosing an Integrated Development Environment (IDE) of their choice. Furthermore, any integration solver can be implemented within a Modelica tool to simulate Modelica models. Additionally, Modelica is an object-oriented language, enabling code factorization and model re-use to improve the readability of a library by structuring it with object-oriented hierarchy. The developed library is released under an open source license to enable a wider distribution and let the user customize it to their specific needs. This paper describes the iPSL and provides illustrative application examples.

Impact and User Satisfaction of a Clinical Information Portal Embedded in an Electronic Health Record

PubMed Central

Tannery, Nancy H; Epstein, Barbara A; Wessel, Charles B; Yarger, Frances; LaDue, John; Klem, Mary Lou

2011-01-01

In 2008, a clinical information tool was developed and embedded in the electronic health record system of an academic medical center. In 2009, the initial information tool, Clinical-e, was superseded by a portal called Clinical Focus, with a single search box enabling a federated search of selected online information resources. To measure the usefulness and impact of Clinical Focus, a survey was used to gather feedback about users' experience with this clinical resource. The survey determined what type of clinicians were using this tool and assessed user satisfaction and perceived impact on patient care decision making. Initial survey results suggest the majority of respondents found Clinical Focus easy to navigate, the content easy to read, and the retrieved information relevant and complete. The majority would recommend Clinical Focus to their colleagues. Results indicate that this tool is a promising area for future development. PMID:22016670

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

NASA Astrophysics Data System (ADS)

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

2013-01-01

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

Supervised learning of tools for content-based search of image databases

NASA Astrophysics Data System (ADS)

Delanoy, Richard L.

1996-03-01

A computer environment, called the Toolkit for Image Mining (TIM), is being developed with the goal of enabling users with diverse interests and varied computer skills to create search tools for content-based image retrieval and other pattern matching tasks. Search tools are generated using a simple paradigm of supervised learning that is based on the user pointing at mistakes of classification made by the current search tool. As mistakes are identified, a learning algorithm uses the identified mistakes to build up a model of the user's intentions, construct a new search tool, apply the search tool to a test image, display the match results as feedback to the user, and accept new inputs from the user. Search tools are constructed in the form of functional templates, which are generalized matched filters capable of knowledge- based image processing. The ability of this system to learn the user's intentions from experience contrasts with other existing approaches to content-based image retrieval that base searches on the characteristics of a single input example or on a predefined and semantically- constrained textual query. Currently, TIM is capable of learning spectral and textural patterns, but should be adaptable to the learning of shapes, as well. Possible applications of TIM include not only content-based image retrieval, but also quantitative image analysis, the generation of metadata for annotating images, data prioritization or data reduction in bandwidth-limited situations, and the construction of components for larger, more complex computer vision algorithms.

Indentured Parts List Maintenance and Part Assembly Capture Tool - IMPACT

NASA Technical Reports Server (NTRS)

Jain, Bobby; Morris, Jill; Sharpe, Kelly

2004-01-01

Johnson Space Center's (JSC's) indentured parts list (IPL) maintenance and parts assembly capture tool (IMPACT) is an easy-to-use graphical interface for viewing and maintaining the complex assembly hierarchies of large databases. IMPACT, already in use at JSC to support the International Space Station (ISS), queries, updates, modifies, and views data in IPL and associated resource data, functions that it can also perform, with modification, for any large commercial database. By enabling its users to efficiently view and manipulate IPL hierarchical data, IMPACT performs a function unlike that of any other tool. Through IMPACT, users will achieve results quickly, efficiently, and cost effectively.

Evaluating service user pedagogy in UK higher education: Validating the Huddersfield Service User Pedagogy Scale.

PubMed

Tobbell, Jane; Boduszek, Daniel; Kola-Palmer, Susanna; Vaughan, Joanne; Hargreaves, Janet

2018-04-01

There is global recognition that the inclusion of service users in the education of health and social care students in higher education can lead to more compassionate professional identities which will enable better decision making. However, to date there is no systematic tool to explore learning and service user involvement in the curriculum. To generate and validate a psychometric instrument which will allow educators to evaluate service user pedagogy. Construction and validation of a new scale. 365 undergraduate students from health and social care departments in two universities. A two correlated factor scale. Factor 1 - perceived presence of service users in the taught curriculum and factor 2 - professionals and service users working together (correlation between factor 1 and factor 2 - r = 0.32). The Huddersfield Service User Pedagogy Scale provides a valid instrument for educators to evaluate student learning. In addition, the tool can contribute to student reflections on their shifting professional identities as they progress through their studies. Copyright © 2018 Elsevier Ltd. All rights reserved.

A quality assessment tool for markup-based clinical guidelines.

PubMed

Shalom, Erez; Shahar, Yuval; Taieb-Maimon, Meirav; Lunenfeld, Eitan

2008-11-06

We introduce a tool for quality assessment of procedural and declarative knowledge. We developed this tool for evaluating the specification of mark-up-based clinical GLs. Using this graphical tool, the expert physician and knowledge engineer collaborate to perform scoring, using pre-defined scoring scale, each of the knowledge roles of the mark-ups, comparing it to a gold standard. The tool enables scoring the mark-ups simultaneously at different sites by different users at different locations.

GenomeGems: evaluation of genetic variability from deep sequencing data

PubMed Central

2012-01-01

Background Detection of disease-causing mutations using Deep Sequencing technologies possesses great challenges. In particular, organizing the great amount of sequences generated so that mutations, which might possibly be biologically relevant, are easily identified is a difficult task. Yet, for this assignment only limited automatic accessible tools exist. Findings We developed GenomeGems to gap this need by enabling the user to view and compare Single Nucleotide Polymorphisms (SNPs) from multiple datasets and to load the data onto the UCSC Genome Browser for an expanded and familiar visualization. As such, via automatic, clear and accessible presentation of processed Deep Sequencing data, our tool aims to facilitate ranking of genomic SNP calling. GenomeGems runs on a local Personal Computer (PC) and is freely available at http://www.tau.ac.il/~nshomron/GenomeGems. Conclusions GenomeGems enables researchers to identify potential disease-causing SNPs in an efficient manner. This enables rapid turnover of information and leads to further experimental SNP validation. The tool allows the user to compare and visualize SNPs from multiple experiments and to easily load SNP data onto the UCSC Genome browser for further detailed information. PMID:22748151

The Teaching of Critical Thinking Skills by Academic Librarians.

ERIC Educational Resources Information Center

Goetzfridt, Nicholas J.

Teaching critical thinking is a relatively new dimension of bibliographic instruction (BI) in the academic environment. It marks a departure from the teaching of "user skills" in which the primary concern is enabling library patrons to determine the appropriateness of reference tools and to use those tools effectively. This report assembles a…

Promoting scientific collaboration and research through integrated social networking capabilities within the OpenTopography Portal

NASA Astrophysics Data System (ADS)

Nandigam, V.; Crosby, C. J.; Baru, C.

2009-04-01

LiDAR (Light Distance And Ranging) topography data offer earth scientists the opportunity to study the earth's surface at very high resolutions. As a result, the popularity of these data is growing dramatically. However, the management, distribution, and analysis of community LiDAR data sets is a challenge due to their massive size (multi-billion point, mutli-terabyte). We have also found that many earth science users of these data sets lack the computing resources and expertise required to process these data. We have developed the OpenTopography Portal to democratize access to these large and computationally challenging data sets. The OpenTopography Portal uses cyberinfrastructure technology developed by the GEON project to provide access to LiDAR data in a variety of formats. LiDAR data products available range from simple Google Earth visualizations of LiDAR-derived hillshades to 1 km2 tiles of standard digital elevation model (DEM) products as well as LiDAR point cloud data and user generated custom-DEMs. We have found that the wide spectrum of LiDAR users have variable scientific applications, computing resources and technical experience and thus require a data system with multiple distribution mechanisms and platforms to serve a broader range of user communities. Because the volume of LiDAR topography data available is rapidly expanding, and data analysis techniques are evolving, there is a need for the user community to be able to communicate and interact to share knowledge and experiences. To address this need, the OpenTopography Portal enables social networking capabilities through a variety of collaboration tools, web 2.0 technologies and customized usage pattern tracking. Fundamentally, these tools offer users the ability to communicate, to access and share documents, participate in discussions, and to keep up to date on upcoming events and emerging technologies. The OpenTopography portal achieves the social networking capabilities by integrating various software technologies and platforms. These include the Expression Engine Content Management System (CMS) that comes with pre-packaged collaboration tools like blogs and wikis, the Gridsphere portal framework that contains the primary GEON LiDAR System portlet with user job monitoring capabilities and a java web based discussion forum (Jforums) application all seamlessly integrated under one portal. The OpenTopography Portal also provides integrated authentication mechanism between the various CMS collaboration tools and the core gridsphere based portlets. The integration of these various technologies allows for enhanced user interaction capabilities within the portal. By integrating popular collaboration tools like discussion forums and blogs we can promote conversation and openness among users. The ability to ask question and share expertise in forum discussions allows users to easily find information and interact with users facing similar challenges. The OpenTopography Blog enables our domain experts to post ideas, news items, commentary, and other resources in order to foster discussion and information sharing. The content management capabilities of the portal allow for easy updates to information in the form of publications, documents, and news articles. Access to the most current information fosters better decision-making. As has become the standard for web 2.0 technologies, the OpenTopography Portal is fully RSS enabled to allow users of the portal to keep track of news items, forum discussions, blog updates, and system outages. We are currently exploring how the information captured by user and job monitoring components of the Gridsphere based GEON LiDAR System can be harnessed to provide a recommender system that will help users to identify appropriate processing parameters and to locate related documents and data. By seamlessly integrating the various platforms and technologies under one single portal, we can take advantage of popular online collaboration tools that are either stand alone or software platform restricted. The availability of these collaboration tools along with the data will foster more community interaction and increase the strength and vibrancy of the LiDAR topography user community.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

The Australian SKA Pathfinder: operations management and user engagement

NASA Astrophysics Data System (ADS)

Harvey-Smith, Lisa

2016-07-01

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

Planetary Surface Visualization and Analytics

NASA Astrophysics Data System (ADS)

Law, E. S.; Solar System Treks Team

2018-04-01

An introduction and update of the Solar System Treks Project which provides a suite of interactive visualization and analysis tools to enable users (engineers, scientists, public) to access large amounts of mapped planetary data products.

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

PubMed

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

2003-01-01

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

Gradually including potential users: A tool to counter design exclusions.

PubMed

Zitkus, Emilene; Langdon, Patrick; Clarkson, P John

2018-01-01

The paper describes an iterative development process used to understand the suitability of different inclusive design evaluation tools applied into design practices. At the end of this process, a tool named Inclusive Design Advisor was developed, combining data related to design features of small appliances with ergonomic task demands, anthropometric data and exclusion data. When auditing a new design the tool examines the exclusion that each design feature can cause, followed by objective recommendations directly related to its features. Interactively, it allows designers or clients to balance design changes with the exclusion caused. It presents the type of information that enables designers and clients to discuss user needs and make more inclusive design decisions. Copyright © 2017. Published by Elsevier Ltd.

Knob manager (KM) operators guide

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

NONE

1993-10-08

KM, Knob Manager, is a tool which enables the user to use the SUNDIALS knob box to adjust the settings of the control system. The followings are some features of KM: dynamic knob assignments with the user friendly interface; user-defined gain for individual knob; graphical displays for operating range and status of each process variable is assigned; backup and restore one or multiple process variable; save current settings to a file and recall the settings from that file in future.

Self-enforcing Private Inference Control

NASA Astrophysics Data System (ADS)

Yang, Yanjiang; Li, Yingjiu; Weng, Jian; Zhou, Jianying; Bao, Feng

Private inference control enables simultaneous enforcement of inference control and protection of users' query privacy. Private inference control is a useful tool for database applications, especially when users are increasingly concerned about individual privacy nowadays. However, protection of query privacy on top of inference control is a double-edged sword: without letting the database server know the content of user queries, users can easily launch DoS attacks. To assuage DoS attacks in private inference control, we propose the concept of self-enforcing private inference control, whose intuition is to force users to only make inference-free queries by enforcing inference control themselves; otherwise, penalty will inflict upon the violating users.

Protecting count queries in study design

PubMed Central

Sarwate, Anand D; Boxwala, Aziz A

2012-01-01

Objective Today's clinical research institutions provide tools for researchers to query their data warehouses for counts of patients. To protect patient privacy, counts are perturbed before reporting; this compromises their utility for increased privacy. The goal of this study is to extend current query answer systems to guarantee a quantifiable level of privacy and allow users to tailor perturbations to maximize the usefulness according to their needs. Methods A perturbation mechanism was designed in which users are given options with respect to scale and direction of the perturbation. The mechanism translates the true count, user preferences, and a privacy level within administrator-specified bounds into a probability distribution from which the perturbed count is drawn. Results Users can significantly impact the scale and direction of the count perturbation and can receive more accurate final cohort estimates. Strong and semantically meaningful differential privacy is guaranteed, providing for a unified privacy accounting system that can support role-based trust levels. This study provides an open source web-enabled tool to investigate visually and numerically the interaction between system parameters, including required privacy level and user preference settings. Conclusions Quantifying privacy allows system administrators to provide users with a privacy budget and to monitor its expenditure, enabling users to control the inevitable loss of utility. While current measures of privacy are conservative, this system can take advantage of future advances in privacy measurement. The system provides new ways of trading off privacy and utility that are not provided in current study design systems. PMID:22511018

Protecting count queries in study design.

PubMed

Vinterbo, Staal A; Sarwate, Anand D; Boxwala, Aziz A

2012-01-01

Today's clinical research institutions provide tools for researchers to query their data warehouses for counts of patients. To protect patient privacy, counts are perturbed before reporting; this compromises their utility for increased privacy. The goal of this study is to extend current query answer systems to guarantee a quantifiable level of privacy and allow users to tailor perturbations to maximize the usefulness according to their needs. A perturbation mechanism was designed in which users are given options with respect to scale and direction of the perturbation. The mechanism translates the true count, user preferences, and a privacy level within administrator-specified bounds into a probability distribution from which the perturbed count is drawn. Users can significantly impact the scale and direction of the count perturbation and can receive more accurate final cohort estimates. Strong and semantically meaningful differential privacy is guaranteed, providing for a unified privacy accounting system that can support role-based trust levels. This study provides an open source web-enabled tool to investigate visually and numerically the interaction between system parameters, including required privacy level and user preference settings. Quantifying privacy allows system administrators to provide users with a privacy budget and to monitor its expenditure, enabling users to control the inevitable loss of utility. While current measures of privacy are conservative, this system can take advantage of future advances in privacy measurement. The system provides new ways of trading off privacy and utility that are not provided in current study design systems.

Enhancing User Customization through Novel Software Architecture for Utility Scale Solar Siting Software

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

Brant Peery; Sam Alessi; Randy Lee

2014-06-01

There is a need for a spatial decision support application that allows users to create customized metrics for comparing proposed locations of a new solar installation. This document discusses how PVMapper was designed to overcome the customization problem through the development of loosely coupled spatial and decision components in a JavaScript plugin architecture. This allows the user to easily add functionality and data to the system. The paper also explains how PVMapper provides the user with a dynamic and customizable decision tool that enables them to visually modify the formulas that are used in the decision algorithms that convert datamore » to comparable metrics. The technologies that make up the presentation and calculation software stack are outlined. This document also explains the architecture that allows the tool to grow through custom plugins created by the software users. Some discussion is given on the difficulties encountered while designing the system.« less

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

EPA Science Inventory

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

An Interactive Mobile Lecturing Model: Enhancing Student Engagement with Face-to-Face Sessions

ERIC Educational Resources Information Center

Boyinbode, Olutayo; Ng'ambi, Dick; Bagula, Antoine

2013-01-01

Although use of podcasts and vodcasts are increasingly becoming popular in higher education, their use is usually unidirectional and therefore replicates the transmission mode of traditional face-to-face lectures. In this paper, the authors propose a tool, MOBILect, a mobile lecturing tool that enables users to comment on lecture vodcasts using…

What matters to users of services? An explorative study to promote shared decision making in health care

PubMed Central

Padgett, Kath; Rhodes, Christine; Lumb, Maureen; Morris, Penny; Sherwin, Sue; Symons, Jools; Tate, Joannie; Townend, Ken

2012-01-01

Abstract Background  Involving service users and carers in decisions about their health care is a key feature of health‐care practice. Professional health and social care students need to develop skills and attributes to best enable this to happen. Aims  The aims were to explore service user and carer perceptions of behaviours, attributes and context required to enable shared decision making; to compare these perceptions to those of students and academic staff with a view to utilizing the findings to inform the development of student assessment tools. Methods  A mixed methods approach was used including action learning groups (ALG) and an iterative process alongside a modified Delphi survey. Participants  The ALGs were from an existing service user and carer network. The survey was sent to sixty students, sixty academics and 30 service users from 16 different professional disciplines, spanning four Universities in England. Results  The collaborative enquiry process and survey identified general agreement that being open and honest, listening, showing respect, giving time and being up to date were important. The qualitative findings identified that individual interpretation was a key factor. An unexpected result was an insight into possible insecurities of students. Conclusions  The findings indicate that distilling rich qualitative information into a format for student assessment tools could be problematic as the individual context could be lost, it is therefore proposed that the information could be better used as a learning rather than assessment tool. Several of those involved identified how they valued the process and found it beneficial. PMID:22390320

What matters to users of services? An explorative study to promote shared decision making in health care.

PubMed

Padgett, Kath; Rhodes, Christine; Lumb, Maureen; Morris, Penny; Sherwin, Sue; Symons, Jools; Tate, Joannie; Townend, Ken

2014-06-01

Involving service users and carers in decisions about their health care is a key feature of health-care practice. Professional health and social care students need to develop skills and attributes to best enable this to happen. The aims were to explore service user and carer perceptions of behaviours, attributes and context required to enable shared decision making; to compare these perceptions to those of students and academic staff with a view to utilizing the findings to inform the development of student assessment tools. A mixed methods approach was used including action learning groups (ALG) and an iterative process alongside a modified Delphi survey. The ALGs were from an existing service user and carer network. The survey was sent to sixty students, sixty academics and 30 service users from 16 different professional disciplines, spanning four Universities in England. The collaborative enquiry process and survey identified general agreement that being open and honest, listening, showing respect, giving time and being up to date were important. The qualitative findings identified that individual interpretation was a key factor. An unexpected result was an insight into possible insecurities of students. The findings indicate that distilling rich qualitative information into a format for student assessment tools could be problematic as the individual context could be lost, it is therefore proposed that the information could be better used as a learning rather than assessment tool. Several of those involved identified how they valued the process and found it beneficial. © 2012 John Wiley & Sons Ltd.

Simulation of streamflows and basin-wide hydrologic variables over several climate-change scenarios, Methow River basin, Washington

USGS Publications Warehouse

Voss, Frank D.; Mastin, Mark C.

2012-01-01

A database was developed to automate model execution and to provide users with Internet access to voluminous data products ranging from summary figures to model output timeseries. Database-enabled Internet tools were developed to allow users to create interactive graphs of output results based on their analysis needs. For example, users were able to create graphs by selecting time intervals, greenhouse gas emission scenarios, general circulation models, and specific hydrologic variables.

Making Interoperability Easier with the NASA Metadata Management Tool

NASA Astrophysics Data System (ADS)

Shum, D.; Reese, M.; Pilone, D.; Mitchell, A. E.

2016-12-01

ISO 19115 has enabled interoperability amongst tools, yet many users find it hard to build ISO metadata for their collections because it can be large and overly flexible for their needs. The Metadata Management Tool (MMT), part of NASA's Earth Observing System Data and Information System (EOSDIS), offers users a modern, easy to use browser based tool to develop ISO compliant metadata. Through a simplified UI experience, metadata curators can create and edit collections without any understanding of the complex ISO-19115 format, while still generating compliant metadata. The MMT is also able to assess the completeness of collection level metadata by evaluating it against a variety of metadata standards. The tool provides users with clear guidance as to how to change their metadata in order to improve their quality and compliance. It is based on NASA's Unified Metadata Model for Collections (UMM-C) which is a simpler metadata model which can be cleanly mapped to ISO 19115. This allows metadata authors and curators to meet ISO compliance requirements faster and more accurately. The MMT and UMM-C have been developed in an agile fashion, with recurring end user tests and reviews to continually refine the tool, the model and the ISO mappings. This process is allowing for continual improvement and evolution to meet the community's needs.

Metabolome searcher: a high throughput tool for metabolite identification and metabolic pathway mapping directly from mass spectrometry and using genome restriction.

PubMed

Dhanasekaran, A Ranjitha; Pearson, Jon L; Ganesan, Balasubramanian; Weimer, Bart C

2015-02-25

Mass spectrometric analysis of microbial metabolism provides a long list of possible compounds. Restricting the identification of the possible compounds to those produced by the specific organism would benefit the identification process. Currently, identification of mass spectrometry (MS) data is commonly done using empirically derived compound databases. Unfortunately, most databases contain relatively few compounds, leaving long lists of unidentified molecules. Incorporating genome-encoded metabolism enables MS output identification that may not be included in databases. Using an organism's genome as a database restricts metabolite identification to only those compounds that the organism can produce. To address the challenge of metabolomic analysis from MS data, a web-based application to directly search genome-constructed metabolic databases was developed. The user query returns a genome-restricted list of possible compound identifications along with the putative metabolic pathways based on the name, formula, SMILES structure, and the compound mass as defined by the user. Multiple queries can be done simultaneously by submitting a text file created by the user or obtained from the MS analysis software. The user can also provide parameters specific to the experiment's MS analysis conditions, such as mass deviation, adducts, and detection mode during the query so as to provide additional levels of evidence to produce the tentative identification. The query results are provided as an HTML page and downloadable text file of possible compounds that are restricted to a specific genome. Hyperlinks provided in the HTML file connect the user to the curated metabolic databases housed in ProCyc, a Pathway Tools platform, as well as the KEGG Pathway database for visualization and metabolic pathway analysis. Metabolome Searcher, a web-based tool, facilitates putative compound identification of MS output based on genome-restricted metabolic capability. This enables researchers to rapidly extend the possible identifications of large data sets for metabolites that are not in compound databases. Putative compound names with their associated metabolic pathways from metabolomics data sets are returned to the user for additional biological interpretation and visualization. This novel approach enables compound identification by restricting the possible masses to those encoded in the genome.

Advancements in Large-Scale Data/Metadata Management for Scientific Data.

NASA Astrophysics Data System (ADS)

Guntupally, K.; Devarakonda, R.; Palanisamy, G.; Frame, M. T.

2017-12-01

Scientific data often comes with complex and diverse metadata which are critical for data discovery and users. The Online Metadata Editor (OME) tool, which was developed by an Oak Ridge National Laboratory team, effectively manages diverse scientific datasets across several federal data centers, such as DOE's Atmospheric Radiation Measurement (ARM) Data Center and USGS's Core Science Analytics, Synthesis, and Libraries (CSAS&L) project. This presentation will focus mainly on recent developments and future strategies for refining OME tool within these centers. The ARM OME is a standard based tool (https://www.archive.arm.gov/armome) that allows scientists to create and maintain metadata about their data products. The tool has been improved with new workflows that help metadata coordinators and submitting investigators to submit and review their data more efficiently. The ARM Data Center's newly upgraded Data Discovery Tool (http://www.archive.arm.gov/discovery) uses rich metadata generated by the OME to enable search and discovery of thousands of datasets, while also providing a citation generator and modern order-delivery techniques like Globus (using GridFTP), Dropbox and THREDDS. The Data Discovery Tool also supports incremental indexing, which allows users to find new data as and when they are added. The USGS CSAS&L search catalog employs a custom version of the OME (https://www1.usgs.gov/csas/ome), which has been upgraded with high-level Federal Geographic Data Committee (FGDC) validations and the ability to reserve and mint Digital Object Identifiers (DOIs). The USGS's Science Data Catalog (SDC) (https://data.usgs.gov/datacatalog) allows users to discover a myriad of science data holdings through a web portal. Recent major upgrades to the SDC and ARM Data Discovery Tool include improved harvesting performance and migration using new search software, such as Apache Solr 6.0 for serving up data/metadata to scientific communities. Our presentation will highlight the future enhancements of these tools which enable users to retrieve fast search results, along with parallelizing the retrieval process from online and High Performance Storage Systems. In addition, these improvements to the tools will support additional metadata formats like the Large-Eddy Simulation (LES) ARM Symbiotic and Observation (LASSO) bundle data.

Tools in Support of Planning for Weather and Climate Extremes

NASA Astrophysics Data System (ADS)

Done, J.; Bruyere, C. L.; Hauser, R.; Holland, G. J.; Tye, M. R.

2016-12-01

A major limitation to planning for weather and climate extremes is the lack of maintained and readily available tools that can provide robust and well-communicated predictions and advice on their impacts. The National Center for Atmospheric Research is facilitating a collaborative international program to develop and support such tools within its Capacity Center for Climate and Weather Extremes aimed at improving community resilience planning and reducing weather and climate impacts. A Global Risk, Resilience and Impacts Toolbox is in development and will provide: A portable web-based interface to process work requests from a variety of users and locations; A sophisticated framework that enables specialized community tools to access a comprehensive database (public and private) of geo-located hazard, vulnerability, exposure, and loss data; A community development toolkit that enables and encourages community tool developments geared towards specific user man­agement and planning needs, and A comprehensive community sup­port facilitated by NCAR utilizing tutorials and a help desk. A number of applications are in development, built off the latest climate science, and in collaboration with private industry and local and state governments. Example applications will be described, including a hurricane damage tool in collaboration with the reinsurance sector, and a weather management tool for the construction industry. These examples will serve as starting points to discuss the broader potential of the toolbox.

Enabling a systems biology knowledgebase with gaggle and firegoose

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

Baliga, Nitin S.

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

Bringing your tools to CyVerse Discovery Environment using Docker

PubMed Central

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

2016-01-01

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

Bringing your tools to CyVerse Discovery Environment using Docker.

PubMed

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

2016-01-01

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

Climate tools in mainstream Linux distributions

NASA Astrophysics Data System (ADS)

McKinstry, Alastair

2015-04-01

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

Agricultural Conservation Planning Toolbox User's Manual

USDA-ARS?s Scientific Manuscript database

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

Lunar and Vesta Web Portals

NASA Astrophysics Data System (ADS)

Law, E.; JPL Luna Mapping; Modeling Project Team

2015-06-01

The Lunar Mapping and Modeling Project offers Lunar Mapping and Modeling Portal (http://lmmp.nasa.gov) and Vesta Trek Portal (http://vestatrek.jpl.nasa.gov) providing interactive visualization and analysis tools to enable users to access mapped Lunar and Vesta data products.

Web-based metabolic network visualization with a zooming user interface

PubMed Central

2011-01-01

Background Displaying complex metabolic-map diagrams, for Web browsers, and allowing users to interact with them for querying and overlaying expression data over them is challenging. Description We present a Web-based metabolic-map diagram, which can be interactively explored by the user, called the Cellular Overview. The main characteristic of this application is the zooming user interface enabling the user to focus on appropriate granularities of the network at will. Various searching commands are available to visually highlight sets of reactions, pathways, enzymes, metabolites, and so on. Expression data from single or multiple experiments can be overlaid on the diagram, which we call the Omics Viewer capability. The application provides Web services to highlight the diagram and to invoke the Omics Viewer. This application is entirely written in JavaScript for the client browsers and connect to a Pathway Tools Web server to retrieve data and diagrams. It uses the OpenLayers library to display tiled diagrams. Conclusions This new online tool is capable of displaying large and complex metabolic-map diagrams in a very interactive manner. This application is available as part of the Pathway Tools software that powers multiple metabolic databases including Biocyc.org: The Cellular Overview is accessible under the Tools menu. PMID:21595965

An Interactive, Integrated, Instructional Pathway to the LEAD Science Gateway

NASA Astrophysics Data System (ADS)

Yalda, S.; Clark, R.; Davis, L.; Wiziecki, E. N.

2008-12-01

Linked Environments for Atmospheric Discovery (LEAD) is a bold and revolutionary paradigm that through a Web-based Service Oriented Architecture (SOA) exposes the user to a rich environment of data, models, data mining and visualization and analysis tools, enabling the user to ask science questions of applications while the complexity of the software and middleware managing these applications is hidden from the user. From its inception in 2003, LEAD has championed goals that have context for the future of weather and related research and education. LEAD espouses to lowering the barrier for using complex end-to-end weather technologies by a) democratizing the availability of advanced weather technologies, b) empowering the user of these technologies to tackle a variety of problems, and c) facilitating learning and understanding. LEAD, as it exists today, is poised to enable a diverse community of scientists, educators, students, and operational practitioners. The project has been informed by atmospheric and computer scientists, educators, and educational consultants who, in search of new knowledge, understanding, ideas, and learning methodologies, seek easy access to new capabilities that allow for user-directed and interactive query and acquisition, simulation, assimilation, data mining, computational modeling, and visualization. As one component of the total LEAD effort, the LEAD education team has designed interactive, integrated, instructional pathways within a set of learning modules (LEAD-to-Learn) to facilitate, enhance, and enable the use of the LEAD gateway in the classroom. The LEAD education initiative focuses on the means to integrate data, tools, and services used by researchers into undergraduate meteorology education in order to provide an authentic and contextualized environment for teaching and learning. Educators, educational specialists, and students from meteorology and computer science backgrounds have collaborated on the design and development of learning materials, as well as new tools and features, to enhance the appearance and use of the LEAD portal gateway and its underlying cyberinfrastructure in an educational setting. The development of educational materials has centered on promoting the accessibility and use of meteorological data and analysis tools through the LEAD portal by providing instructional materials, additional custom designed tools that build off of Unidata's Integrated Data Viewer (IDV) (e.g. IDV Basic and NCDestroyer), and an interactive component that takes the user through specific tasks utilizing multiple tools. In fact, select improvements to parameter lists and domain subsetting have inspired IDV developers to incorporate changes in IDV revisions that are now available to the entire community. This collection of materials, demonstrations, interactive guides, student exercises, and customized tools, which are now available to the educator and student through the LEAD portal gateway, can serve as an instructional pathway for a set of guided, phenomenon-based exercises (e.g. fronts, lake-effect snows, etc.). This paper will provide an overview of the LEAD education and outreach efforts with a focus on the design of Web-based educational materials and instructional approaches for user interaction with the LEAD portal gateway and the underlying cyberinfrastructure, and will encourage educators, especially those involved in undergraduate meteorology education, to begin incorporating these capabilities into their course materials.

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

NASA Astrophysics Data System (ADS)

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

2014-05-01

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

Haptic feedback improves surgeons' user experience and fracture reduction in facial trauma simulation.

PubMed

Girod, Sabine; Schvartzman, Sara C; Gaudilliere, Dyani; Salisbury, Kenneth; Silva, Rebeka

2016-01-01

Computer-assisted surgical (CAS) planning tools are available for craniofacial surgery, but are usually based on computer-aided design (CAD) tools that lack the ability to detect the collision of virtual objects (i.e., fractured bone segments). We developed a CAS system featuring a sense of touch (haptic) that enables surgeons to physically interact with individual, patient-specific anatomy and immerse in a three-dimensional virtual environment. In this study, we evaluated initial user experience with our novel system compared to an existing CAD system. Ten surgery resident trainees received a brief verbal introduction to both the haptic and CAD systems. Users simulated mandibular fracture reduction in three clinical cases within a 15 min time limit for each system and completed a questionnaire to assess their subjective experience. We compared standard landmarks and linear and angular measurements between the simulated results and the actual surgical outcome and found that haptic simulation results were not significantly different from actual postoperative outcomes. In contrast, CAD results significantly differed from both the haptic simulation and actual postoperative results. In addition to enabling a more accurate fracture repair, the haptic system provided a better user experience than the CAD system in terms of intuitiveness and self-reported quality of repair.

Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data.

PubMed

Dunn, Joshua G; Weissman, Jonathan S

2016-11-22

Next-generation sequencing (NGS) informs many biological questions with unprecedented depth and nucleotide resolution. These assays have created a need for analytical tools that enable users to manipulate data nucleotide-by-nucleotide robustly and easily. Furthermore, because many NGS assays encode information jointly within multiple properties of read alignments - for example, in ribosome profiling, the locations of ribosomes are jointly encoded in alignment coordinates and length - analytical tools are often required to extract the biological meaning from the alignments before analysis. Many assay-specific pipelines exist for this purpose, but there remains a need for user-friendly, generalized, nucleotide-resolution tools that are not limited to specific experimental regimes or analytical workflows. Plastid is a Python library designed specifically for nucleotide-resolution analysis of genomics and NGS data. As such, Plastid is designed to extract assay-specific information from read alignments while retaining generality and extensibility to novel NGS assays. Plastid represents NGS and other biological data as arrays of values associated with genomic or transcriptomic positions, and contains configurable tools to convert data from a variety of sources to such arrays. Plastid also includes numerous tools to manipulate even discontinuous genomic features, such as spliced transcripts, with nucleotide precision. Plastid automatically handles conversion between genomic and feature-centric coordinates, accounting for splicing and strand, freeing users of burdensome accounting. Finally, Plastid's data models use consistent and familiar biological idioms, enabling even beginners to develop sophisticated analytical workflows with minimal effort. Plastid is a versatile toolkit that has been used to analyze data from multiple NGS assays, including RNA-seq, ribosome profiling, and DMS-seq. It forms the genomic engine of our ORF annotation tool, ORF-RATER, and is readily adapted to novel NGS assays. Examples, tutorials, and extensive documentation can be found at https://plastid.readthedocs.io .

The NCAR Research Data Archive's Hybrid Approach for Data Discovery and Access

NASA Astrophysics Data System (ADS)

Schuster, D.; Worley, S. J.

2013-12-01

The NCAR Research Data Archive (RDA http://rda.ucar.edu) maintains a variety of data discovery and access capabilities for it's 600+ dataset collections to support the varying needs of a diverse user community. In-house developed and standards-based community tools offer services to more than 10,000 users annually. By number of users the largest group is external and access the RDA through web based protocols; the internal NCAR HPC users are fewer in number, but typically access more data volume. This paper will detail the data discovery and access services maintained by the RDA to support both user groups, and show metrics that illustrate how the community is using the services. The distributed search capability enabled by standards-based community tools, such as Geoportal and an OAI-PMH access point that serves multiple metadata standards, provide pathways for external users to initially discover RDA holdings. From here, in-house developed web interfaces leverage primary discovery level metadata databases that support keyword and faceted searches. Internal NCAR HPC users, or those familiar with the RDA, may go directly to the dataset collection of interest and refine their search based on rich file collection metadata. Multiple levels of metadata have proven to be invaluable for discovery within terabyte-sized archives composed of many atmospheric or oceanic levels, hundreds of parameters, and often numerous grid and time resolutions. Once users find the data they want, their access needs may vary as well. A THREDDS data server running on targeted dataset collections enables remote file access through OPENDAP and other web based protocols primarily for external users. In-house developed tools give all users the capability to submit data subset extraction and format conversion requests through scalable, HPC based delayed mode batch processing. Users can monitor their RDA-based data processing progress and receive instructions on how to access the data when it is ready. External users are provided with RDA server generated scripts to download the resulting request output. Similarly they can download native dataset collection files or partial files using Wget or cURL based scripts supplied by the RDA server. Internal users can access the resulting request output or native dataset collection files directly from centralized file systems.

ProphTools: general prioritization tools for heterogeneous biological networks.

PubMed

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

2017-12-01

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

MemAxes: Visualization and Analytics for Characterizing Complex Memory Performance Behaviors.

PubMed

Gimenez, Alfredo; Gamblin, Todd; Jusufi, Ilir; Bhatele, Abhinav; Schulz, Martin; Bremer, Peer-Timo; Hamann, Bernd

2018-07-01

Memory performance is often a major bottleneck for high-performance computing (HPC) applications. Deepening memory hierarchies, complex memory management, and non-uniform access times have made memory performance behavior difficult to characterize, and users require novel, sophisticated tools to analyze and optimize this aspect of their codes. Existing tools target only specific factors of memory performance, such as hardware layout, allocations, or access instructions. However, today's tools do not suffice to characterize the complex relationships between these factors. Further, they require advanced expertise to be used effectively. We present MemAxes, a tool based on a novel approach for analytic-driven visualization of memory performance data. MemAxes uniquely allows users to analyze the different aspects related to memory performance by providing multiple visual contexts for a centralized dataset. We define mappings of sampled memory access data to new and existing visual metaphors, each of which enabling a user to perform different analysis tasks. We present methods to guide user interaction by scoring subsets of the data based on known performance problems. This scoring is used to provide visual cues and automatically extract clusters of interest. We designed MemAxes in collaboration with experts in HPC and demonstrate its effectiveness in case studies.

AutoCellSeg: robust automatic colony forming unit (CFU)/cell analysis using adaptive image segmentation and easy-to-use post-editing techniques.

PubMed

Khan, Arif Ul Maula; Torelli, Angelo; Wolf, Ivo; Gretz, Norbert

2018-05-08

In biological assays, automated cell/colony segmentation and counting is imperative owing to huge image sets. Problems occurring due to drifting image acquisition conditions, background noise and high variation in colony features in experiments demand a user-friendly, adaptive and robust image processing/analysis method. We present AutoCellSeg (based on MATLAB) that implements a supervised automatic and robust image segmentation method. AutoCellSeg utilizes multi-thresholding aided by a feedback-based watershed algorithm taking segmentation plausibility criteria into account. It is usable in different operation modes and intuitively enables the user to select object features interactively for supervised image segmentation method. It allows the user to correct results with a graphical interface. This publicly available tool outperforms tools like OpenCFU and CellProfiler in terms of accuracy and provides many additional useful features for end-users.

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.

Graphics Software For VT Terminals

NASA Technical Reports Server (NTRS)

Wang, Caroline

1991-01-01

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

A tool for exploring space-time patterns: an animation user research.

PubMed

Ogao, Patrick J

2006-08-29

Ever since Dr. John Snow (1813-1854) used a case map to identify water well as the source of a cholera outbreak in London in the 1800s, the use of spatio-temporal maps have become vital tools in a wide range of disease mapping and control initiatives. The increasing use of spatio-temporal maps in these life-threatening sectors warrants that they are accurate, and easy to interpret to enable prompt decision making by health experts. Similar spatio-temporal maps are observed in urban growth and census mapping--all critical aspects a of a country's socio-economic development. In this paper, a user test research was carried out to determine the effectiveness of spatio-temporal maps (animation) in exploring geospatial structures encompassing disease, urban and census mapping. Three types of animation were used, namely; passive, interactive and inference-based animation, with the key differences between them being on the level of interactivity and complementary domain knowledge that each offers to the user. Passive animation maintains the view only status. The user has no control over its contents and dynamic variables. Interactive animation provides users with the basic media player controls, navigation and orientation tools. Inference-based animation incorporates these interactive capabilities together with a complementary automated intelligent view that alerts users to interesting patterns, trends or anomalies that may be inherent in the data sets. The test focussed on the role of animation passive and interactive capabilities in exploring space-time patterns by engaging test-subjects in thinking aloud evaluation protocol. The test subjects were selected from a geoinformatics (map reading, interpretation and analysis abilities) background. Every test-subject used each of the three types of animation and their performances for each session assessed. The results show that interactivity in animation is a preferred exploratory tool in identifying, interpreting and providing explanations about observed geospatial phenomena. Also, exploring geospatial data structures using animation is best achieved using provocative interactive tools such as was seen with the inference-based animation. The visual methods employed using the three types of animation are all related and together these patterns confirm the exploratory cognitive structure and processes for visualization tools. The generic types of animation as defined in this paper play a crucial role in facilitating the visualization of geospatial data. These animations can be created and their contents defined based on the user's presentational and exploratory needs. For highly explorative tasks, maintaining a link between the data sets and the animation is crucial to enabling a rich and effective knowledge discovery environment.

A tool for exploring space-time patterns : an animation user research

PubMed Central

Ogao, Patrick J

2006-01-01

Background Ever since Dr. John Snow (1813–1854) used a case map to identify water well as the source of a cholera outbreak in London in the 1800s, the use of spatio-temporal maps have become vital tools in a wide range of disease mapping and control initiatives. The increasing use of spatio-temporal maps in these life-threatening sectors warrants that they are accurate, and easy to interpret to enable prompt decision making by health experts. Similar spatio-temporal maps are observed in urban growth and census mapping – all critical aspects a of a country's socio-economic development. In this paper, a user test research was carried out to determine the effectiveness of spatio-temporal maps (animation) in exploring geospatial structures encompassing disease, urban and census mapping. Results Three types of animation were used, namely; passive, interactive and inference-based animation, with the key differences between them being on the level of interactivity and complementary domain knowledge that each offers to the user. Passive animation maintains the view only status. The user has no control over its contents and dynamic variables. Interactive animation provides users with the basic media player controls, navigation and orientation tools. Inference-based animation incorporates these interactive capabilities together with a complementary automated intelligent view that alerts users to interesting patterns, trends or anomalies that may be inherent in the data sets. The test focussed on the role of animation passive and interactive capabilities in exploring space-time patterns by engaging test-subjects in thinking aloud evaluation protocol. The test subjects were selected from a geoinformatics (map reading, interpretation and analysis abilities) background. Every test-subject used each of the three types of animation and their performances for each session assessed. The results show that interactivity in animation is a preferred exploratory tool in identifying, interpreting and providing explanations about observed geospatial phenomena. Also, exploring geospatial data structures using animation is best achieved using provocative interactive tools such as was seen with the inference-based animation. The visual methods employed using the three types of animation are all related and together these patterns confirm the exploratory cognitive structure and processes for visualization tools. Conclusion The generic types of animation as defined in this paper play a crucial role in facilitating the visualization of geospatial data. These animations can be created and their contents defined based on the user's presentational and exploratory needs. For highly explorative tasks, maintaining a link between the data sets and the animation is crucial to enabling a rich and effective knowledge discovery environment. PMID:16938138

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics

PubMed Central

Brusniak, Mi-Youn; Bodenmiller, Bernd; Campbell, David; Cooke, Kelly; Eddes, James; Garbutt, Andrew; Lau, Hollis; Letarte, Simon; Mueller, Lukas N; Sharma, Vagisha; Vitek, Olga; Zhang, Ning; Aebersold, Ruedi; Watts, Julian D

2008-01-01

Background Quantitative proteomics holds great promise for identifying proteins that are differentially abundant between populations representing different physiological or disease states. A range of computational tools is now available for both isotopically labeled and label-free liquid chromatography mass spectrometry (LC-MS) based quantitative proteomics. However, they are generally not comparable to each other in terms of functionality, user interfaces, information input/output, and do not readily facilitate appropriate statistical data analysis. These limitations, along with the array of choices, present a daunting prospect for biologists, and other researchers not trained in bioinformatics, who wish to use LC-MS-based quantitative proteomics. Results We have developed Corra, a computational framework and tools for discovery-based LC-MS proteomics. Corra extends and adapts existing algorithms used for LC-MS-based proteomics, and statistical algorithms, originally developed for microarray data analyses, appropriate for LC-MS data analysis. Corra also adapts software engineering technologies (e.g. Google Web Toolkit, distributed processing) so that computationally intense data processing and statistical analyses can run on a remote server, while the user controls and manages the process from their own computer via a simple web interface. Corra also allows the user to output significantly differentially abundant LC-MS-detected peptide features in a form compatible with subsequent sequence identification via tandem mass spectrometry (MS/MS). We present two case studies to illustrate the application of Corra to commonly performed LC-MS-based biological workflows: a pilot biomarker discovery study of glycoproteins isolated from human plasma samples relevant to type 2 diabetes, and a study in yeast to identify in vivo targets of the protein kinase Ark1 via phosphopeptide profiling. Conclusion The Corra computational framework leverages computational innovation to enable biologists or other researchers to process, analyze and visualize LC-MS data with what would otherwise be a complex and not user-friendly suite of tools. Corra enables appropriate statistical analyses, with controlled false-discovery rates, ultimately to inform subsequent targeted identification of differentially abundant peptides by MS/MS. For the user not trained in bioinformatics, Corra represents a complete, customizable, free and open source computational platform enabling LC-MS-based proteomic workflows, and as such, addresses an unmet need in the LC-MS proteomics field. PMID:19087345

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

PubMed

Chapron, Guillaume

2015-11-01

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

CRISPR Primer Designer: Design primers for knockout and chromosome imaging CRISPR-Cas system.

PubMed

Yan, Meng; Zhou, Shi-Rong; Xue, Hong-Wei

2015-07-01

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated system enables biologists to edit genomes precisely and provides a powerful tool for perturbing endogenous gene regulation, modulation of epigenetic markers, and genome architecture. However, there are concerns about the specificity of the system, especially the usages of knocking out a gene. Previous designing tools either were mostly built-in websites or ran as command-line programs, and none of them ran locally and acquired a user-friendly interface. In addition, with the development of CRISPR-derived systems, such as chromosome imaging, there were still no tools helping users to generate specific end-user spacers. We herein present CRISPR Primer Designer for researchers to design primers for CRISPR applications. The program has a user-friendly interface, can analyze the BLAST results by using multiple parameters, score for each candidate spacer, and generate the primers when using a certain plasmid. In addition, CRISPR Primer Designer runs locally and can be used to search spacer clusters, and exports primers for the CRISPR-Cas system-based chromosome imaging system. © 2014 Institute of Botany, Chinese Academy of Sciences.

HiRel: Hybrid Automated Reliability Predictor (HARP) integrated reliability tool system, (version 7.0). Volume 3: HARP Graphics Oriented (GO) input user's guide

NASA Technical Reports Server (NTRS)

Bavuso, Salvatore J.; Rothmann, Elizabeth; Mittal, Nitin; Koppen, Sandra Howell

1994-01-01

The Hybrid Automated Reliability Predictor (HARP) integrated Reliability (HiRel) tool system for reliability/availability prediction offers a toolbox of integrated reliability/availability programs that can be used to customize the user's application in a workstation or nonworkstation environment. HiRel consists of interactive graphical input/output programs and four reliability/availability modeling engines that provide analytical and simulative solutions to a wide host of highly reliable fault-tolerant system architectures and is also applicable to electronic systems in general. The tool system was designed at the outset to be compatible with most computing platforms and operating systems, and some programs have been beta tested within the aerospace community for over 8 years. This document is a user's guide for the HiRel graphical preprocessor Graphics Oriented (GO) program. GO is a graphical user interface for the HARP engine that enables the drawing of reliability/availability models on a monitor. A mouse is used to select fault tree gates or Markov graphical symbols from a menu for drawing.

Developing A Web-based User Interface for Semantic Information Retrieval

NASA Technical Reports Server (NTRS)

Berrios, Daniel C.; Keller, Richard M.

2003-01-01

While there are now a number of languages and frameworks that enable computer-based systems to search stored data semantically, the optimal design for effective user interfaces for such systems is still uncle ar. Such interfaces should mask unnecessary query detail from users, yet still allow them to build queries of arbitrary complexity without significant restrictions. We developed a user interface supporting s emantic query generation for Semanticorganizer, a tool used by scient ists and engineers at NASA to construct networks of knowledge and dat a. Through this interface users can select node types, node attribute s and node links to build ad-hoc semantic queries for searching the S emanticOrganizer network.

Coastal On-line Assessment and Synthesis Tool 2.0

NASA Technical Reports Server (NTRS)

Brown, Richard; Navard, Andrew; Nguyen, Beth

2011-01-01

COAST (Coastal On-line Assessment and Synthesis Tool) is a 3D, open-source Earth data browser developed by leveraging and enhancing previous NASA open-source tools. These tools use satellite imagery and elevation data in a way that allows any user to zoom from orbit view down into any place on Earth, and enables the user to experience Earth terrain in a visually rich 3D view. The benefits associated with taking advantage of an open-source geo-browser are that it is free, extensible, and offers a worldwide developer community that is available to provide additional development and improvement potential. What makes COAST unique is that it simplifies the process of locating and accessing data sources, and allows a user to combine them into a multi-layered and/or multi-temporal visual analytical look into possible data interrelationships and coeffectors for coastal environment phenomenology. COAST provides users with new data visual analytic capabilities. COAST has been upgraded to maximize use of open-source data access, viewing, and data manipulation software tools. The COAST 2.0 toolset has been developed to increase access to a larger realm of the most commonly implemented data formats used by the coastal science community. New and enhanced functionalities that upgrade COAST to COAST 2.0 include the development of the Temporal Visualization Tool (TVT) plug-in, the Recursive Online Remote Data-Data Mapper (RECORD-DM) utility, the Import Data Tool (IDT), and the Add Points Tool (APT). With these improvements, users can integrate their own data with other data sources, and visualize the resulting layers of different data types (such as spatial and spectral, for simultaneous visual analysis), and visualize temporal changes in areas of interest.

A multimedia comprehensive informatics system with decision support tools for a multi-site collaboration research of stroke rehabilitation

NASA Astrophysics Data System (ADS)

Wang, Ximing; Documet, Jorge; Garrison, Kathleen A.; Winstein, Carolee J.; Liu, Brent

2012-02-01

Stroke is a major cause of adult disability. The Interdisciplinary Comprehensive Arm Rehabilitation Evaluation (I-CARE) clinical trial aims to evaluate a therapy for arm rehabilitation after stroke. A primary outcome measure is correlative analysis between stroke lesion characteristics and standard measures of rehabilitation progress, from data collected at seven research facilities across the country. Sharing and communication of brain imaging and behavioral data is thus a challenge for collaboration. A solution is proposed as a web-based system with tools supporting imaging and informatics related data. In this system, users may upload anonymized brain images through a secure internet connection and the system will sort the imaging data for storage in a centralized database. Users may utilize an annotation tool to mark up images. In addition to imaging informatics, electronic data forms, for example, clinical data forms, are also integrated. Clinical information is processed and stored in the database to enable future data mining related development. Tele-consultation is facilitated through the development of a thin-client image viewing application. For convenience, the system supports access through desktop PC, laptops, and iPAD. Thus, clinicians may enter data directly into the system via iPAD while working with participants in the study. Overall, this comprehensive imaging informatics system enables users to collect, organize and analyze stroke cases efficiently.

Automated Test Case Generation for an Autopilot Requirement Prototype

NASA Technical Reports Server (NTRS)

Giannakopoulou, Dimitra; Rungta, Neha; Feary, Michael

2011-01-01

Designing safety-critical automation with robust human interaction is a difficult task that is susceptible to a number of known Human-Automation Interaction (HAI) vulnerabilities. It is therefore essential to develop automated tools that provide support both in the design and rapid evaluation of such automation. The Automation Design and Evaluation Prototyping Toolset (ADEPT) enables the rapid development of an executable specification for automation behavior and user interaction. ADEPT supports a number of analysis capabilities, thus enabling the detection of HAI vulnerabilities early in the design process, when modifications are less costly. In this paper, we advocate the introduction of a new capability to model-based prototyping tools such as ADEPT. The new capability is based on symbolic execution that allows us to automatically generate quality test suites based on the system design. Symbolic execution is used to generate both user input and test oracles user input drives the testing of the system implementation, and test oracles ensure that the system behaves as designed. We present early results in the context of a component in the Autopilot system modeled in ADEPT, and discuss the challenges of test case generation in the HAI domain.

Enabling Interoperability and Servicing Multiple User Segments Through Web Services, Standards, and Data Tools

NASA Astrophysics Data System (ADS)

Palanisamy, Giriprakash; Wilson, Bruce E.; Cook, Robert B.; Lenhardt, Chris W.; Santhana Vannan, Suresh; Pan, Jerry; McMurry, Ben F.; Devarakonda, Ranjeet

2010-12-01

The Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC) is one of the science-oriented data centers in EOSDIS, aligned primarily with terrestrial ecology. The ORNL DAAC archives and serves data from NASA-funded field campaigns (such as BOREAS, FIFE, and LBA), regional and global data sets relevant to biogeochemical cycles, land validation studies for remote sensing, and source code for some terrestrial ecology models. Users of the ORNL DAAC include field ecologists, remote sensing scientists, modelers at various scales, synthesis scientific groups, a range of educational users (particularly baccalaureate and graduate instruction), and decision support analysts. It is clear that the wide range of users served by the ORNL DAAC have differing needs and differing capabilities for accessing and using data. It is also not possible for the ORNL DAAC, or the other data centers in EDSS to develop all of the tools and interfaces to support even most of the potential uses of data directly. As is typical of Information Technology to support a research enterprise, the user needs will continue to evolve rapidly over time and users themselves cannot predict future needs, as those needs depend on the results of current investigation. The ORNL DAAC is addressing these needs by targeted implementation of web services and tools which can be consumed by other applications, so that a modeler can retrieve data in netCDF format with the Climate Forecasting convention and a field ecologist can retrieve subsets of that same data in a comma separated value format, suitable for use in Excel or R. Tools such as our MODIS Subsetting capability, the Spatial Data Access Tool (SDAT; based on OGC web services), and OPeNDAP-compliant servers such as THREDDS particularly enable such diverse means of access. We also seek interoperability of metadata, recognizing that terrestrial ecology is a field where there are a very large number of relevant data repositories. ORNL DAAC metadata is published to several metadata repositories using the Open Archive Initiative Protocol for Metadata Handling (OAI-PMH), to increase the chances that users can find data holdings relevant to their particular scientific problem. ORNL also seeks to leverage technology across these various data projects and encourage standardization of processes and technical architecture. This standardization is behind current efforts involving the use of Drupal and Fedora Commons. This poster describes the current and planned approaches that the ORNL DAAC is taking to enable cost-effective interoperability among data centers, both across the NASA EOSDIS data centers and across the international spectrum of terrestrial ecology-related data centers. The poster will highlight the standards that we are currently using across data formats, metadata formats, and data protocols. References: [1]Devarakonda R., et al. Mercury: reusable metadata management, data discovery and access system. Earth Science Informatics (2010), 3(1): 87-94. [2]Devarakonda R., et al. Data sharing and retrieval using OAI-PMH. Earth Science Informatics (2011), 4(1): 1-5.

APT: what it has enabled us to do

NASA Astrophysics Data System (ADS)

Blacker, Brett S.; Golombek, Daniel

2004-09-01

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

Tools for discovering and accessing Great Lakes scientific data

USGS Publications Warehouse

Lucido, Jessica M.; Bruce, Jennifer L.

2015-01-01

The USGS strives to develop data products that are easy to find, easy to understand, and easy to use through Web-accessible tools that allow users to learn about the breadth and scope of GLRI activities being undertaken by the USGS and its partners. By creating tools that enable data to be shared and reused more easily, the USGS can encourage collaboration and assist the GL community in finding, interpreting, and understanding the information created during GLRI science activities.

Approaching Suspicious Substances Safely

NASA Technical Reports Server (NTRS)

2004-01-01

A mineral identification tool that was developed for NASA's Mars Rover Technology Development program is now serving as a powerful tool for U.S. law enforcement agencies and military personnel to identify suspicious liquid and solid substances. The tool can measure unknown substances through glass and plastic packaging materials with the RamanProbe(TradeMark) focused fiber-optic probe. The probe length can be extended up to 200 meters to enable users to analyze potentially dangerous substances at a safe distance. In many cases, the spectrometer and personnel are kept in a safe zone while the probe is positioned next to the sample being analyzed. Being able to identify chemicals in remote locations also saves users time and labor, since otherwise the samples would need to be collected, transported, and prepared prior to measurement in the laboratory.

Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud

PubMed Central

Afgan, Enis; Sloggett, Clare; Goonasekera, Nuwan; Makunin, Igor; Benson, Derek; Crowe, Mark; Gladman, Simon; Kowsar, Yousef; Pheasant, Michael; Horst, Ron; Lonie, Andrew

2015-01-01

Background Analyzing high throughput genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation. A computational platform enabling best practice genomics analysis ideally meets a number of requirements, including: a wide range of analysis and visualisation tools, closely linked to large user and reference data sets; workflow platform(s) enabling accessible, reproducible, portable analyses, through a flexible set of interfaces; highly available, scalable computational resources; and flexibility and versatility in the use of these resources to meet demands and expertise of a variety of users. Access to an appropriate computational platform can be a significant barrier to researchers, as establishing such a platform requires a large upfront investment in hardware, experience, and expertise. Results We designed and implemented the Genomics Virtual Laboratory (GVL) as a middleware layer of machine images, cloud management tools, and online services that enable researchers to build arbitrarily sized compute clusters on demand, pre-populated with fully configured bioinformatics tools, reference datasets and workflow and visualisation options. The platform is flexible in that users can conduct analyses through web-based (Galaxy, RStudio, IPython Notebook) or command-line interfaces, and add/remove compute nodes and data resources as required. Best-practice tutorials and protocols provide a path from introductory training to practice. The GVL is available on the OpenStack-based Australian Research Cloud (http://nectar.org.au) and the Amazon Web Services cloud. The principles, implementation and build process are designed to be cloud-agnostic. Conclusions This paper provides a blueprint for the design and implementation of a cloud-based Genomics Virtual Laboratory. We discuss scope, design considerations and technical and logistical constraints, and explore the value added to the research community through the suite of services and resources provided by our implementation. PMID:26501966

Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud.

PubMed

Afgan, Enis; Sloggett, Clare; Goonasekera, Nuwan; Makunin, Igor; Benson, Derek; Crowe, Mark; Gladman, Simon; Kowsar, Yousef; Pheasant, Michael; Horst, Ron; Lonie, Andrew

2015-01-01

Analyzing high throughput genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation. A computational platform enabling best practice genomics analysis ideally meets a number of requirements, including: a wide range of analysis and visualisation tools, closely linked to large user and reference data sets; workflow platform(s) enabling accessible, reproducible, portable analyses, through a flexible set of interfaces; highly available, scalable computational resources; and flexibility and versatility in the use of these resources to meet demands and expertise of a variety of users. Access to an appropriate computational platform can be a significant barrier to researchers, as establishing such a platform requires a large upfront investment in hardware, experience, and expertise. We designed and implemented the Genomics Virtual Laboratory (GVL) as a middleware layer of machine images, cloud management tools, and online services that enable researchers to build arbitrarily sized compute clusters on demand, pre-populated with fully configured bioinformatics tools, reference datasets and workflow and visualisation options. The platform is flexible in that users can conduct analyses through web-based (Galaxy, RStudio, IPython Notebook) or command-line interfaces, and add/remove compute nodes and data resources as required. Best-practice tutorials and protocols provide a path from introductory training to practice. The GVL is available on the OpenStack-based Australian Research Cloud (http://nectar.org.au) and the Amazon Web Services cloud. The principles, implementation and build process are designed to be cloud-agnostic. This paper provides a blueprint for the design and implementation of a cloud-based Genomics Virtual Laboratory. We discuss scope, design considerations and technical and logistical constraints, and explore the value added to the research community through the suite of services and resources provided by our implementation.

Interactive Learning Modules: Enabling Near Real-Time Oceanographic Data Use In Undergraduate Education

NASA Astrophysics Data System (ADS)

Kilb, D. L.; Fundis, A. T.; Risien, C. M.

2012-12-01

The focus of the Education and Public Engagement (EPE) component of the NSF's Ocean Observatories Initiative (OOI) is to provide a new layer of cyber-interactivity for undergraduate educators to bring near real-time data from the global ocean into learning environments. To accomplish this, we are designing six online services including: 1) visualization tools, 2) a lesson builder, 3) a concept map builder, 4) educational web services (middleware), 5) collaboration tools and 6) an educational resource database. Here, we report on our Fall 2012 release that includes the first four of these services: 1) Interactive visualization tools allow users to interactively select data of interest, display the data in various views (e.g., maps, time-series and scatter plots) and obtain statistical measures such as mean, standard deviation and a regression line fit to select data. Specific visualization tools include a tool to compare different months of data, a time series explorer tool to investigate the temporal evolution of select data parameters (e.g., sea water temperature or salinity), a glider profile tool that displays ocean glider tracks and associated transects, and a data comparison tool that allows users to view the data either in scatter plot view comparing one parameter with another, or in time series view. 2) Our interactive lesson builder tool allows users to develop a library of online lesson units, which are collaboratively editable and sharable and provides starter templates designed from learning theory knowledge. 3) Our interactive concept map tool allows the user to build and use concept maps, a graphical interface to map the connection between concepts and ideas. This tool also provides semantic-based recommendations, and allows for embedding of associated resources such as movies, images and blogs. 4) Education web services (middleware) will provide an educational resource database API.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Activity Catalog Tool (ACT) user manual, version 2.0

NASA Technical Reports Server (NTRS)

Segal, Leon D.; Andre, Anthony D.

1994-01-01

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

Integrating management tools and concepts to develop an estuarine planning support system: A case study of the Humber Estuary, Eastern England.

PubMed

Lonsdale, Jemma-Anne; Weston, Keith; Barnard, Steve; Boyes, Suzanne J; Elliott, Michael

2015-11-15

Estuaries are important because of their multiple uses and users which often makes them challenging to manage since management must strike a balance between the needs of users, the estuaries' ecological and economic value and the context of multiple legislative drivers. To facilitate management we have therefore developed an Estuarine Planning Support System (EPSS) framework using the Humber Estuary, Eastern England, as a case study which integrates the current legislation tools and concepts. This integrated EPSS framework is an improvement on previous approaches for assessing cumulative impacts as it takes into account legislative drivers, management tools and other mechanisms for controlling plans/projects specific to the estuary. It therefore enables managers and users to assess and address both the current state and the way in which a new industrial, port or urban development could impact an estuary in an accessible and understandable framework. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

BIDDSAT: visualizing the content of biodiversity data publishers in the Global Biodiversity Information Facility network.

PubMed

Otegui, Javier; Ariño, Arturo H

2012-08-15

In any data quality workflow, data publishers must become aware of issues in their data so these can be corrected. User feedback mechanisms provide one avenue, while global assessments of datasets provide another. To date, there is no publicly available tool to allow both biodiversity data institutions sharing their data through the Global Biodiversity Information Facility network and its potential users to assess datasets as a whole. Contributing to bridge this gap both for publishers and users, we introduce BIoDiversity DataSets Assessment Tool, an online tool that enables selected diagnostic visualizations on the content of data publishers and/or their individual collections. The online application is accessible at http://www.unav.es/unzyec/mzna/biddsat/ and is supported by all major browsers. The source code is licensed under the GNU GPLv3 license (http://www.gnu.org/licenses/gpl-3.0.txt) and is available at https://github.com/jotegui/BIDDSAT.

Prosthetic Tool For Holding Small Ferromagnetic Parts

NASA Technical Reports Server (NTRS)

Norton, William E.; Carden, James R.; Belcher, Jewell G., Jr.; Vest, Thomas W.

1995-01-01

Tool attached to prosthetic hand or arm enables user to hold nails, screws, nuts, rivets, and other small ferromagnetic objects on small magnetic tip. Device adjusted to hold nail or screw at proper angle for hammering or for use of screwdriver, respectively. Includes base connector with threaded outer surface and lower male member inserted in standard spring-action, quick-connect/quick-disconnect wrist adapter on prosthetic hand or arm.

FINAL REPORT FOR VERIFICATION OF THE METAL FINISHING FACILITY POLLUTION PREVENTION TOOL (MFFPPT)

EPA Science Inventory

The United States Environmental Protection Agency (USEPA) has prepared a computer process simulation package for the metal finishing industry that enables users to predict process outputs based upon process inputs and other operating conditions. This report documents the developm...

Improving the Accessibility and Use of NASA Earth Science Data

NASA Technical Reports Server (NTRS)

Tisdale, Matthew; Tisdale, Brian

2015-01-01

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

A PICKSC Science Gateway for enabling the common plasma physicist to run kinetic software

NASA Astrophysics Data System (ADS)

Hu, Q.; Winjum, B. J.; Zonca, A.; Youn, C.; Tsung, F. S.; Mori, W. B.

2017-10-01

Computer simulations offer tremendous opportunities for studying plasmas, ranging from simulations for students that illuminate fundamental educational concepts to research-level simulations that advance scientific knowledge. Nevertheless, there is a significant hurdle to using simulation tools. Users must navigate codes and software libraries, determine how to wrangle output into meaningful plots, and oftentimes confront a significant cyberinfrastructure with powerful computational resources. Science gateways offer a Web-based environment to run simulations without needing to learn or manage the underlying software and computing cyberinfrastructure. We discuss our progress on creating a Science Gateway for the Particle-in-Cell and Kinetic Simulation Software Center that enables users to easily run and analyze kinetic simulations with our software. We envision that this technology could benefit a wide range of plasma physicists, both in the use of our simulation tools as well as in its adaptation for running other plasma simulation software. Supported by NSF under Grant ACI-1339893 and by the UCLA Institute for Digital Research and Education.

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

NASA Astrophysics Data System (ADS)

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

2016-11-01

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

proBAMconvert: A Conversion Tool for proBAM/proBed.

PubMed

Olexiouk, Volodimir; Menschaert, Gerben

2017-07-07

The introduction of new standard formats, proBAM and proBed, improves the integration of genomics and proteomics information, thus aiding proteogenomics applications. These novel formats enable peptide spectrum matches (PSM) to be stored, inspected, and analyzed within the context of the genome. However, an easy-to-use and transparent tool to convert mass spectrometry identification files to these new formats is indispensable. proBAMconvert enables the conversion of common identification file formats (mzIdentML, mzTab, and pepXML) to proBAM/proBed using an intuitive interface. Furthermore, ProBAMconvert enables information to be output both at the PSM and peptide levels and has a command line interface next to the graphical user interface. Detailed documentation and a completely worked-out tutorial is available at http://probam.biobix.be .

PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data.

PubMed

Anslan, Sten; Bahram, Mohammad; Hiiesalu, Indrek; Tedersoo, Leho

2017-11-01

High-throughput sequencing methods have become a routine analysis tool in environmental sciences as well as in public and private sector. These methods provide vast amount of data, which need to be analysed in several steps. Although the bioinformatics may be applied using several public tools, many analytical pipelines allow too few options for the optimal analysis for more complicated or customized designs. Here, we introduce PipeCraft, a flexible and handy bioinformatics pipeline with a user-friendly graphical interface that links several public tools for analysing amplicon sequencing data. Users are able to customize the pipeline by selecting the most suitable tools and options to process raw sequences from Illumina, Pacific Biosciences, Ion Torrent and Roche 454 sequencing platforms. We described the design and options of PipeCraft and evaluated its performance by analysing the data sets from three different sequencing platforms. We demonstrated that PipeCraft is able to process large data sets within 24 hr. The graphical user interface and the automated links between various bioinformatics tools enable easy customization of the workflow. All analytical steps and options are recorded in log files and are easily traceable. © 2017 John Wiley & Sons Ltd.

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.

Web Audio/Video Streaming Tool

NASA Technical Reports Server (NTRS)

Guruvadoo, Eranna K.

2003-01-01

In order to promote NASA-wide educational outreach program to educate and inform the public of space exploration, NASA, at Kennedy Space Center, is seeking efficient ways to add more contents to the web by streaming audio/video files. This project proposes a high level overview of a framework for the creation, management, and scheduling of audio/video assets over the web. To support short-term goals, the prototype of a web-based tool is designed and demonstrated to automate the process of streaming audio/video files. The tool provides web-enabled users interfaces to manage video assets, create publishable schedules of video assets for streaming, and schedule the streaming events. These operations are performed on user-defined and system-derived metadata of audio/video assets stored in a relational database while the assets reside on separate repository. The prototype tool is designed using ColdFusion 5.0.

Unified User Interface to Support Effective and Intuitive Data Discovery, Dissemination, and Analysis at NASA GES DISC

NASA Technical Reports Server (NTRS)

Petrenko, M.; Hegde, M.; Bryant, K.; Johnson, J. E.; Ritrivi, A.; Shen, S.; Volmer, B.; Pham, L. B.

2015-01-01

Goddard Earth Sciences Data and Information Services Center (GES DISC) has been providing access to scientific data sets since 1990s. Beginning as one of the first Earth Observing System Data and Information System (EOSDIS) archive centers, GES DISC has evolved to offer a wide range of science-enabling services. With a growing understanding of needs and goals of its science users, GES DISC continues to improve and expand on its broad set of data discovery and access tools, sub-setting services, and visualization tools. Nonetheless, the multitude of the available tools, a partial overlap of functionality, and independent and uncoupled interfaces employed by these tools often leave the end users confused as of what tools or services are the most appropriate for a task at hand. As a result, some the services remain underutilized or largely unknown to the users, significantly reducing the availability of the data and leading to a great loss of scientific productivity. In order to improve the accessibility of GES DISC tools and services, we have designed and implemented UUI, the Unified User Interface. UUI seeks to provide a simple, unified, and intuitive one-stop shop experience for the key services available at GES DISC, including sub-setting (Simple Subset Wizard), granule file search (Mirador), plotting (Giovanni), and other services. In this poster, we will discuss the main lessons, obstacles, and insights encountered while designing the UUI experience. We will also present the architecture and technology behind UUI, including NodeJS, Angular, and Mongo DB, as well as speculate on the future of the tool at GES DISC as well as in a broader context of the Space Science Informatics.

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

Judd, Kathleen S.; Judd, Chaeli; Engel-Cox, Jill A.

This report presents the results of the Gulf of Mexico Regional Collaborative (GoMRC), a year-long project funded by NASA. The GoMRC project was organized around end user outreach activities, a science applications team, and a team for information technology (IT) development. Key outcomes are summarized below for each of these areas. End User Outreach; Successfully engaged federal and state end users in project planning and feedback; With end user input, defined needs and system functional requirements; Conducted demonstration to End User Advisory Committee on July 9, 2007 and presented at Gulf of Mexico Alliance (GOMA) meeting of Habitat Identification committee;more » Conducted significant engagement of other end user groups, such as the National Estuary Programs (NEP), in the Fall of 2007; Established partnership with SERVIR and Harmful Algal Blooms Observing System (HABSOS) programs and initiated plan to extend HABs monitoring and prediction capabilities to the southern Gulf; Established a science and technology working group with Mexican institutions centered in the State of Veracruz. Key team members include the Federal Commission for the Protection Against Sanitary Risks (COFEPRIS), the Ecological Institute (INECOL) a unit of the National Council for science and technology (CONACYT), the Veracruz Aquarium (NOAA’s first international Coastal Ecology Learning Center) and the State of Veracruz. The Mexican Navy (critical to coastal studies in the Southern Gulf) and other national and regional entities have also been engaged; and Training on use of SERVIR portal planned for Fall 2007 in Veracruz, Mexico Science Applications; Worked with regional scientists to produce conceptual models of submerged aquatic vegetation (SAV) ecosystems; Built a logical framework and tool for ontological modeling of SAV and HABs; Created online guidance for SAV restoration planning; Created model runs which link potential future land use trends, runoff and SAV viability; Analyzed SAV cover change at five other bays in the Gulf of Mexico to demonstrate extensibility of the analytical tools; and Initiated development of a conceptual model for understanding the causes and effects of HABs in the Gulf of Mexico IT Tool Development; Established a website with the GoMRC web-based tools at www.gomrc.org; Completed development of an ArcGIS-based decision support tool for SAV restoration prioritization decisions, and demonstrated its use in Mobile Bay; Developed a web-based application, called Conceptual Model Explorer (CME), that enables non-GIS users to employ the prioritization model for SAV restoration; Created CME tool enabling scientists to view existing, and create new, ecosystem conceptual models which can be used to document cause-effect relationships within coastal ecosystems, and offer guidance on management solutions; Adapted the science-driven advanced web search engine, Noesis, to focus on an initial set of coastal and marine resource issues, including SAV and HABs; Incorporated map visualization tools with initial data layers related to coastal wetlands and SAVs; and Supported development of a SERVIR portal for data management and visualization in the southern Gulf of Mexico, as well as training of end users in Mexican Gulf States.« less

Biomedical image analysis and processing in clouds

NASA Astrophysics Data System (ADS)

Bednarz, Tomasz; Szul, Piotr; Arzhaeva, Yulia; Wang, Dadong; Burdett, Neil; Khassapov, Alex; Chen, Shiping; Vallotton, Pascal; Lagerstrom, Ryan; Gureyev, Tim; Taylor, John

2013-10-01

Cloud-based Image Analysis and Processing Toolbox project runs on the Australian National eResearch Collaboration Tools and Resources (NeCTAR) cloud infrastructure and allows access to biomedical image processing and analysis services to researchers via remotely accessible user interfaces. By providing user-friendly access to cloud computing resources and new workflow-based interfaces, our solution enables researchers to carry out various challenging image analysis and reconstruction tasks. Several case studies will be presented during the conference.

An electronic registry for physiotherapists in Belgium.

PubMed

Buyl, Ronald; Nyssen, Marc

2008-01-01

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

Translating research into practice through user-centered design: An application for osteoarthritis healthcare planning.

PubMed

Carr, Eloise Cj; Babione, Julie N; Marshall, Deborah

2017-08-01

To identify the needs and requirements of the end users, to inform the development of a user-interface to translate an existing evidence-based decision support tool into a practical and usable interface for health service planning for osteoarthritis (OA) care. We used a user-centered design (UCD) approach that emphasized the role of the end-users and is well-suited to knowledge translation (KT). The first phase used a needs assessment focus group (n=8) and interviews (n=5) with target users (health care planners) within a provincial health care organization. The second phase used a participatory design approach, with two small group sessions (n=6) to explore workflow, thought processes, and needs of intended users. The needs assessment identified five design recommendations: ensuring the user-interface supports the target user group, allowing for user-directed data explorations, input parameter flexibility, clear presentation, and provision of relevant definitions. The second phase identified workflow insights from a proposed scenario. Graphs, the need for a visual overview of the data, and interactivity were key considerations to aid in meaningful use of the model and knowledge translation. A UCD approach is well suited to identify health care planners' requirements when using a decision support tool to improve health service planning and management of OA. We believe this is one of the first applications to be used in planning for health service delivery. We identified specific design recommendations that will increase user acceptability and uptake of the user-interface and underlying decision support tool in practice. Our approach demonstrated how UCD can be used to enable knowledge translation. Copyright © 2017 Elsevier B.V. All rights reserved.

Keys to success of a community of clinical practice in primary care: a qualitative evaluation of the ECOPIH project.

PubMed

Lacasta Tintorer, David; Manresa Domínguez, Josep Maria; Pujol-Rivera, Enriqueta; Flayeh Beneyto, Souhel; Mundet Tuduri, Xavier; Saigí-Rubió, Francesc

2018-05-09

The current reality of primary care (PC) makes it essential to have telemedicine systems available to facilitate communication between care levels. Communities of practice have great potential in terms of care and education, and that is why the Online Communication Tool between Primary and Hospital Care was created. This tool enables PC and non-GP specialist care (SC) professionals to raise clinical cases for consultation and to share information. The objective of this article is to explore healthcare professionals' views on communities of clinical practice (CoCPs) and the changes that need to be made in an uncontrolled real-life setting after more than two years of use. A descriptive-interpretative qualitative study was conducted on a total of 29 healthcare professionals who were users and non-users of a CoCP using 2 focus groups, 3 triangular groups and 5 individual interviews. There were 18 women, 21 physicians and 8 nurses. Of the interviewees, 21 were PC professionals, 24 were users of a CoCP and 7 held managerial positions. For a system of communication between PC and SC to become a tool that is habitually used and very useful, the interviewees considered that it would have to be able to find quick, effective solutions to the queries raised, based on up-to-date information that is directly applicable to daily clinical practice. Contact should be virtual - and probably collaborative - via a platform integrated into their habitual workstations and led by PC professionals. Organisational changes should be implemented to enable users to have more time in their working day to spend on the tool, and professionals should have a proactive attitude in order to make the most if its potential. It is also important to make certain technological changes, basically aimed at improving the tool's accessibility, by integrating it into habitual clinical workstations. The collaborative tool that provides reliable, up-to-date information that is highly transferrable to clinical practice is valued for its effectiveness, efficiency and educational capacity. In order to make the most of its potential in terms of care and education, organisational changes and techniques are required to foster greater use.

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.

PubMed

Afgan, Enis; Baker, Dannon; Batut, Bérénice; van den Beek, Marius; Bouvier, Dave; Cech, Martin; Chilton, John; Clements, Dave; Coraor, Nate; Grüning, Björn A; Guerler, Aysam; Hillman-Jackson, Jennifer; Hiltemann, Saskia; Jalili, Vahid; Rasche, Helena; Soranzo, Nicola; Goecks, Jeremy; Taylor, James; Nekrutenko, Anton; Blankenberg, Daniel

2018-05-22

Galaxy (homepage: https://galaxyproject.org, main public server: https://usegalaxy.org) is a web-based scientific analysis platform used by tens of thousands of scientists across the world to analyze large biomedical datasets such as those found in genomics, proteomics, metabolomics and imaging. Started in 2005, Galaxy continues to focus on three key challenges of data-driven biomedical science: making analyses accessible to all researchers, ensuring analyses are completely reproducible, and making it simple to communicate analyses so that they can be reused and extended. During the last two years, the Galaxy team and the open-source community around Galaxy have made substantial improvements to Galaxy's core framework, user interface, tools, and training materials. Framework and user interface improvements now enable Galaxy to be used for analyzing tens of thousands of datasets, and >5500 tools are now available from the Galaxy ToolShed. The Galaxy community has led an effort to create numerous high-quality tutorials focused on common types of genomic analyses. The Galaxy developer and user communities continue to grow and be integral to Galaxy's development. The number of Galaxy public servers, developers contributing to the Galaxy framework and its tools, and users of the main Galaxy server have all increased substantially.

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

Mechanical System Analysis/Design Tool (MSAT) Quick Guide

NASA Technical Reports Server (NTRS)

Lee, HauHua; Kolb, Mark; Madelone, Jack

1998-01-01

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

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.

STITCHER 2.0: primer design for overlapping PCR applications.

PubMed

O'Halloran, Damien M; Uriagereka-Herburger, Isabel; Bode, Katrin

2017-03-30

Overlapping polymerase chain reaction (PCR) is a common technique used by researchers in very diverse fields that enables the user to 'stitch' individual pieces of DNA together. Previously, we have reported a web based tool called STITCHER that provides a platform for researchers to automate the design of primers for overlapping PCR applications. Here we present STITCHER 2.0, which represents a substantial update to STITCHER. STITCHER 2.0 is a newly designed web tool that automates the design of primers for overlapping PCR. Unlike STITCHER, STITCHER 2.0 considers diverse algorithmic parameters, and returns multiple result files that include a facility for the user to draw their own primers as well as comprehensive visual guides to the user's input, output, and designed primers. These result files provide greater control and insight during experimental design and troubleshooting. STITCHER 2.0 is freely available to all users without signup or login requirements and can be accessed at the following webpage: www.ohalloranlab.net/STITCHER2.html.

Software for Remote Monitoring of Space-Station Payloads

NASA Technical Reports Server (NTRS)

Schneider, Michelle; Lippincott, Jeff; Chubb, Steve; Whitaker, Jimmy; Gillis, Robert; Sellers, Donna; Sims, Chris; Rice, James

2003-01-01

Telescience Resource Kit (TReK) is a suite of application programs that enable geographically dispersed users to monitor scientific payloads aboard the International Space Station (ISS). TReK provides local ground support services that can simultaneously receive, process, record, playback, and display data from multiple sources. TReK also provides interfaces to use the remote services provided by the Payload Operations Integration Center which manages all ISS payloads. An application programming interface (API) allows for payload users to gain access to all data processed by TReK and allows payload-specific tools and programs to be built or integrated with TReK. Used in conjunction with other ISS-provided tools, TReK provides the ability to integrate payloads with the operational ground system early in the lifecycle. This reduces the potential for operational problems and provides "cradle-to-grave" end-to-end operations. TReK contains user guides and self-paced tutorials along with training applications to allow the user to become familiar with the system.

ESA Earth Observation Ground Segment Evolution Strategy

NASA Astrophysics Data System (ADS)

Benveniste, J.; Albani, M.; Laur, H.

2016-12-01

One of the key elements driving the evolution of EO Ground Segments, in particular in Europe, has been to enable the creation of added value from EO data and products. This requires the ability to constantly adapt and improve the service to a user base expanding far beyond the `traditional' EO user community of remote sensing specialists. Citizen scientists, the general public, media and educational actors form another user group that is expected to grow. Technological advances, Open Data policies, including those implemented by ESA and the EU, as well as an increasing number of satellites in operations (e.g. Copernicus Sentinels) have led to an enormous increase in available data volumes. At the same time, even with modern network and data handling services, fewer users can afford to bulk-download and consider all potentially relevant data and associated knowledge. The "EO Innovation Europe" concept is being implemented in Europe in coordination between the European Commission, ESA and other European Space Agencies, and industry. This concept is encapsulated in the main ideas of "Bringing the User to the Data" and "Connecting the Users" to complement the traditional one-to-one "data delivery" approach of the past. Both ideas are aiming to better "empower the users" and to create a "sustainable system of interconnected EO Exploitation Platforms", with the objective to enable large scale exploitation of European EO data assets for stimulating innovation and to maximize their impact. These interoperable/interconnected platforms are virtual environments in which the users - individually or collaboratively - have access to the required data sources and processing tools, as opposed to downloading and handling the data `at home'. EO-Innovation Europe has been structured around three elements: an enabling element (acting as a back office), a stimulating element and an outreach element (acting as a front office). Within the enabling element, a "mutualisation" of efforts and funding between public institutions should prevent an unnecessary duplication of investments for enabling infrastructures in Europe and will stimulate the existence of many exploitation platforms or value-adding add-ons funded by different public and private entities in the outreach element (front office).

Web-based Tool Suite for Plasmasphere Information Discovery

NASA Astrophysics Data System (ADS)

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

2005-12-01

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

Contributions of Traditional Web 1.0 Tools e.g. Email and Web 2.0 Tools e.g. Weblog towards Knowledge Management

ERIC Educational Resources Information Center

Dehinbo, Johnson

2010-01-01

The use of email utilizes the power of Web 1.0 to enable users to access their email from any computer and mobile devices that is connected to the Internet making email valuable in acquiring and transferring knowledge. But the advent of Web 2.0 and social networking seems to indicate certain limitations of email. The use of social networking seems…

GenePattern | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

GenePattern is a genomic analysis platform that provides access to hundreds of tools for the analysis and visualization of multiple data types. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. A new GenePattern Notebook environment allows users to combine GenePattern analyses with text, graphics, and code to create complete reproducible research narratives.

Web tools for large-scale 3D biological images and atlases

PubMed Central

2012-01-01

Background Large-scale volumetric biomedical image data of three or more dimensions are a significant challenge for distributed browsing and visualisation. Many images now exceed 10GB which for most users is too large to handle in terms of computer RAM and network bandwidth. This is aggravated when users need to access tens or hundreds of such images from an archive. Here we solve the problem for 2D section views through archive data delivering compressed tiled images enabling users to browse through very-large volume data in the context of a standard web-browser. The system provides an interactive visualisation for grey-level and colour 3D images including multiple image layers and spatial-data overlay. Results The standard Internet Imaging Protocol (IIP) has been extended to enable arbitrary 2D sectioning of 3D data as well a multi-layered images and indexed overlays. The extended protocol is termed IIP3D and we have implemented a matching server to deliver the protocol and a series of Ajax/Javascript client codes that will run in an Internet browser. We have tested the server software on a low-cost linux-based server for image volumes up to 135GB and 64 simultaneous users. The section views are delivered with response times independent of scale and orientation. The exemplar client provided multi-layer image views with user-controlled colour-filtering and overlays. Conclusions Interactive browsing of arbitrary sections through large biomedical-image volumes is made possible by use of an extended internet protocol and efficient server-based image tiling. The tools open the possibility of enabling fast access to large image archives without the requirement of whole image download and client computers with very large memory configurations. The system was demonstrated using a range of medical and biomedical image data extending up to 135GB for a single image volume. PMID:22676296

A NEO population generation and observation simulation software tool

NASA Astrophysics Data System (ADS)

Müller, Sven; Gelhaus, Johannes; Hahn, Gerhard; Franco, Raffaella

One of the main targets of ESA's Space Situational Awareness (SSA) program is to build a wide knowledge base about objects that can potentially harm Earth (Near-Earth Objects, NEOs). An important part of this effort is to create the Small Bodies Data Centre (SBDC) which is going to aggregate measurement data from a fully-integrated NEO observation sensor network. Until this network is developed, artificial NEO measurement data is needed in order to validate SBDC algorithms. Moreover, to establish a functioning NEO observation sensor network, it has to be determined where to place sensors, what technical requirements have to be met in order to be able to detect NEOs and which observation strategies work the best. Because of this, a sensor simulation software was needed. This paper presents a software tool which allows users to create and analyse NEO populations and to simulate and analyse population observations. It is a console program written in Fortran and comes with a Graphical User Interface (GUI) written in Java and C. The tool can be distinguished into the components ``Population Generator'' and ``Observation Simulator''. The Population Generator component is responsible for generating and analysing a NEO population. Users can choose between creating fictitious (random) and synthetic populations. The latter are based on one of two models describing the orbital and size distribution of observed NEOs: The existing socalled ``Bottke Model'' (Bottke et al. 2000, 2002) and the new ``Granvik Model'' (Granvik et al. 2014, in preparation) which has been developed in parallel to the tool. Generated populations can be analysed by defining 2D, 3D and scatter plots using various NEO attributes. As a result, the tool creates the appropiate files for the plotting tool ``gnuplot''. The tool's Observation Simulator component yields the Observation Simulation and Observation Analysis functions. Users can define sensor systems using ground- or space-based locations as well as optical or radar sensors and simulate observation campaigns. The tool outputs field-of-view crossings and actual detections of the selected NEO population objects. Using the Observation Analysis users are able to process and plot the results of the Observation Simulation. In order to enable end-users to handle the tool in a user-intuitive and comfortable way, a GUI has been created based on the modular Eclipse Rich Client Platform (RCP) technology. Through the GUI users can easily enter input data for the tool, execute it and view its output data in a clear way. Additionally, the GUI runs gnuplot to create plot pictures and presents them to the user. Furthermore, users can create projects to organise executions of the tool.

BioWord: A sequence manipulation suite for Microsoft Word

PubMed Central

2012-01-01

Background The ability to manipulate, edit and process DNA and protein sequences has rapidly become a necessary skill for practicing biologists across a wide swath of disciplines. In spite of this, most everyday sequence manipulation tools are distributed across several programs and web servers, sometimes requiring installation and typically involving frequent switching between applications. To address this problem, here we have developed BioWord, a macro-enabled self-installing template for Microsoft Word documents that integrates an extensive suite of DNA and protein sequence manipulation tools. Results BioWord is distributed as a single macro-enabled template that self-installs with a single click. After installation, BioWord will open as a tab in the Office ribbon. Biologists can then easily manipulate DNA and protein sequences using a familiar interface and minimize the need to switch between applications. Beyond simple sequence manipulation, BioWord integrates functionality ranging from dyad search and consensus logos to motif discovery and pair-wise alignment. Written in Visual Basic for Applications (VBA) as an open source, object-oriented project, BioWord allows users with varying programming experience to expand and customize the program to better meet their own needs. Conclusions BioWord integrates a powerful set of tools for biological sequence manipulation within a handy, user-friendly tab in a widely used word processing software package. The use of a simple scripting language and an object-oriented scheme facilitates customization by users and provides a very accessible educational platform for introducing students to basic bioinformatics algorithms. PMID:22676326

BioWord: a sequence manipulation suite for Microsoft Word.

PubMed

Anzaldi, Laura J; Muñoz-Fernández, Daniel; Erill, Ivan

2012-06-07

The ability to manipulate, edit and process DNA and protein sequences has rapidly become a necessary skill for practicing biologists across a wide swath of disciplines. In spite of this, most everyday sequence manipulation tools are distributed across several programs and web servers, sometimes requiring installation and typically involving frequent switching between applications. To address this problem, here we have developed BioWord, a macro-enabled self-installing template for Microsoft Word documents that integrates an extensive suite of DNA and protein sequence manipulation tools. BioWord is distributed as a single macro-enabled template that self-installs with a single click. After installation, BioWord will open as a tab in the Office ribbon. Biologists can then easily manipulate DNA and protein sequences using a familiar interface and minimize the need to switch between applications. Beyond simple sequence manipulation, BioWord integrates functionality ranging from dyad search and consensus logos to motif discovery and pair-wise alignment. Written in Visual Basic for Applications (VBA) as an open source, object-oriented project, BioWord allows users with varying programming experience to expand and customize the program to better meet their own needs. BioWord integrates a powerful set of tools for biological sequence manipulation within a handy, user-friendly tab in a widely used word processing software package. The use of a simple scripting language and an object-oriented scheme facilitates customization by users and provides a very accessible educational platform for introducing students to basic bioinformatics algorithms.

Aviation Safety Simulation Model

NASA Technical Reports Server (NTRS)

Houser, Scott; Yackovetsky, Robert (Technical Monitor)

2001-01-01

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

Batch Proving and Proof Scripting in PVS

NASA Technical Reports Server (NTRS)

Munoz, Cesar A.

2007-01-01

The batch execution modes of PVS are powerful, but highly technical, features of the system that are mostly accessible to expert users. This paper presents a PVS tool, called ProofLite, that extends the theorem prover interface with a batch proving utility and a proof scripting notation. ProofLite enables a semi-literate proving style where specification and proof scripts reside in the same file. The goal of ProofLite is to provide batch proving and proof scripting capabilities to regular, non-expert, users of PVS.

The Geospatial Web and Local Geographical Education

ERIC Educational Resources Information Center

Harris, Trevor M.; Rouse, L. Jesse; Bergeron, Susan J.

2010-01-01

Recent innovations in the Geospatial Web represent a paradigm shift in Web mapping by enabling educators to explore geography in the classroom by dynamically using a rapidly growing suite of impressive online geospatial tools. Coupled with access to spatial data repositories and User-Generated Content, the Geospatial Web provides a powerful…

Integration of Open Educational Resources in Undergraduate Chemistry Teaching--A Mapping Tool and Lecturers' Considerations

ERIC Educational Resources Information Center

Feldman-Maggor, Yael; Rom, Amira; Tuvi-Arad, Inbal

2016-01-01

This study examines chemistry lecturers' considerations for using open educational resources (OER) in their teaching. Recent technological developments provide innovative approaches for teaching chemistry and visualizing chemical phenomena. End users' improved ability to upload information online enables integration of various pedagogical models…

Netmeld v. 1.0

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

BERG, MICHAEL; RILEY, MARSHALL

System assessments typically yield large quantities of data from disparate sources for an analyst to scrutinize for issues. Netmeld is used to parse input from different file formats, store the data in a common format, allow users to easily query it, and enable analysts to tie different analysis tools together using a common back-end.

Processing MPI Datatypes Outside MPI

NASA Astrophysics Data System (ADS)

Ross, Robert; Latham, Robert; Gropp, William; Lusk, Ewing; Thakur, Rajeev

The MPI datatype functionality provides a powerful tool for describing structured memory and file regions in parallel applications, enabling noncontiguous data to be operated on by MPI communication and I/O routines. However, no facilities are provided by the MPI standard to allow users to efficiently manipulate MPI datatypes in their own codes.

A new forecast presentation tool for offshore contractors

NASA Astrophysics Data System (ADS)

Jørgensen, M.

2009-09-01

Contractors working off shore are often very sensitive to both sea and weather conditions, and it's essential that they have easy access to reliable information on coming conditions to enable planning of when to start or shut down offshore operations to avoid loss of life and materials. Danish Meteorological Institute, DMI, recently, in cooperation with business partners in the field, developed a new application to accommodate that need. The "Marine Forecast Service” is a browser based forecast presentation tool. It provides an interface for the user to enable easy and quick access to all relevant meteorological and oceanographic forecasts and observations for a given area of interest. Each customer gains access to the application via a standard login/password procedure. Once logged in, the user can inspect animated forecast maps of parameters like wind, gust, wave height, swell and current among others. Supplementing the general maps, the user can choose to look at forecast graphs for each of the locations where the user is running operations. These forecast graphs can also be overlaid with the user's own in situ observations, if such exist. Furthermore, the data from the graphs can be exported as data files that the customer can use in his own applications as he desires. As part of the application, a forecaster's view on the current and near future weather situation is presented to the user as well, adding further value to the information presented through maps and graphs. Among other features of the product, animated radar and satellite images could be mentioned. And finally the application provides the possibility of a "second opinion” through traditional weather charts from another recognized provider of weather forecasts. The presentation will provide more detailed insights into the contents of the applications as well as some of the experiences with the product.

From Management to Negotiation: Technical and Institutional Innovations for Integrated Water Resource Management in the Upper Comoé River Basin, Burkina Faso

NASA Astrophysics Data System (ADS)

Roncoli, Carla; Kirshen, Paul; Etkin, Derek; Sanon, Moussa; Somé, Léopold; Dembélé, Youssouf; Sanfo, Bienvenue J.; Zoungrana, Jacqueline; Hoogenboom, Gerrit

2009-10-01

This study focuses on the potential role of technical and institutional innovations for improving water management in a multi-user context in Burkina Faso. We focus on a system centered on three reservoirs that capture the waters of the Upper Comoé River Basin and servicing a diversity of users, including a sugar manufacturing company, a urban water supply utility, a farmer cooperative, and other downstream users. Due to variable and declining rainfall and expanding users’ needs, drastic fluctuations in water supply and demand occur during each dry season. A decision support tool was developed through participatory research to enable users to assess the impact of alternative release and diversion schedules on deficits faced by each user. The tool is meant to be applied in the context of consultative planning by a local user committee that has been created by a new national integrated water management policy. We contend that both solid science and good governance are instrumental in realizing efficient and equitable water management and adaptation to climate variability and change. But, while modeling tools and negotiation platforms may assist users in managing climate risk, they also introduce additional uncertainties into the deliberative process. It is therefore imperative to understand how these technological and institutional innovations frame water use issues and decisions to ensure that such framing is consistent with the goals of integrated water resource management.

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements.

PubMed

Mi, Huaiyu; Huang, Xiaosong; Muruganujan, Anushya; Tang, Haiming; Mills, Caitlin; Kang, Diane; Thomas, Paul D

2017-01-04

The PANTHER database (Protein ANalysis THrough Evolutionary Relationships, http://pantherdb.org) contains comprehensive information on the evolution and function of protein-coding genes from 104 completely sequenced genomes. PANTHER software tools allow users to classify new protein sequences, and to analyze gene lists obtained from large-scale genomics experiments. In the past year, major improvements include a large expansion of classification information available in PANTHER, as well as significant enhancements to the analysis tools. Protein subfamily functional classifications have more than doubled due to progress of the Gene Ontology Phylogenetic Annotation Project. For human genes (as well as a few other organisms), PANTHER now also supports enrichment analysis using pathway classifications from the Reactome resource. The gene list enrichment tools include a new 'hierarchical view' of results, enabling users to leverage the structure of the classifications/ontologies; the tools also allow users to upload genetic variant data directly, rather than requiring prior conversion to a gene list. The updated coding single-nucleotide polymorphisms (SNP) scoring tool uses an improved algorithm. The hidden Markov model (HMM) search tools now use HMMER3, dramatically reducing search times and improving accuracy of E-value statistics. Finally, the PANTHER Tree-Attribute Viewer has been implemented in JavaScript, with new views for exploring protein sequence evolution. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Interactive access to LP DAAC satellite data archives through a combination of open-source and custom middleware web services

USGS Publications Warehouse

Davis, Brian N.; Werpy, Jason; Friesz, Aaron M.; Impecoven, Kevin; Quenzer, Robert; Maiersperger, Tom; Meyer, David J.

2015-01-01

Current methods of searching for and retrieving data from satellite land remote sensing archives do not allow for interactive information extraction. Instead, Earth science data users are required to download files over low-bandwidth networks to local workstations and process data before science questions can be addressed. New methods of extracting information from data archives need to become more interactive to meet user demands for deriving increasingly complex information from rapidly expanding archives. Moving the tools required for processing data to computer systems of data providers, and away from systems of the data consumer, can improve turnaround times for data processing workflows. The implementation of middleware services was used to provide interactive access to archive data. The goal of this middleware services development is to enable Earth science data users to access remote sensing archives for immediate answers to science questions instead of links to large volumes of data to download and process. Exposing data and metadata to web-based services enables machine-driven queries and data interaction. Also, product quality information can be integrated to enable additional filtering and sub-setting. Only the reduced content required to complete an analysis is then transferred to the user.

Interactive computation of coverage regions for indoor wireless communication

NASA Astrophysics Data System (ADS)

Abbott, A. Lynn; Bhat, Nitin; Rappaport, Theodore S.

1995-12-01

This paper describes a system which assists in the strategic placement of rf base stations within buildings. Known as the site modeling tool (SMT), this system allows the user to display graphical floor plans and to select base station transceiver parameters, including location and orientation, interactively. The system then computes and highlights estimated coverage regions for each transceiver, enabling the user to assess the total coverage within the building. For single-floor operation, the user can choose between distance-dependent and partition- dependent path-loss models. Similar path-loss models are also available for the case of multiple floors. This paper describes the method used by the system to estimate coverage for both directional and omnidirectional antennas. The site modeling tool is intended to be simple to use by individuals who are not experts at wireless communication system design, and is expected to be very useful in the specification of indoor wireless systems.

Eureka-DMA: an easy-to-operate graphical user interface for fast comprehensive investigation and analysis of DNA microarray data.

PubMed

Abelson, Sagi

2014-02-24

In the past decade, the field of molecular biology has become increasingly quantitative; rapid development of new technologies enables researchers to investigate and address fundamental issues quickly and in an efficient manner which were once impossible. Among these technologies, DNA microarray provides methodology for many applications such as gene discovery, diseases diagnosis, drug development and toxicological research and it has been used increasingly since it first emerged. Multiple tools have been developed to interpret the high-throughput data produced by microarrays. However, many times, less consideration has been given to the fact that an extensive and effective interpretation requires close interplay between the bioinformaticians who analyze the data and the biologists who generate it. To bridge this gap and to simplify the usability of such tools we developed Eureka-DMA - an easy-to-operate graphical user interface that allows bioinformaticians and bench-biologists alike to initiate analyses as well as to investigate the data produced by DNA microarrays. In this paper, we describe Eureka-DMA, a user-friendly software that comprises a set of methods for the interpretation of gene expression arrays. Eureka-DMA includes methods for the identification of genes with differential expression between conditions; it searches for enriched pathways and gene ontology terms and combines them with other relevant features. It thus enables the full understanding of the data for following testing as well as generating new hypotheses. Here we show two analyses, demonstrating examples of how Eureka-DMA can be used and its capability to produce relevant and reliable results. We have integrated several elementary expression analysis tools to provide a unified interface for their implementation. Eureka-DMA's simple graphical user interface provides effective and efficient framework in which the investigator has the full set of tools for the visualization and interpretation of the data with the option of exporting the analysis results for later use in other platforms. Eureka-DMA is freely available for academic users and can be downloaded at http://blue-meduza.org/Eureka-DMA.

Earth Science Data Education through Cooking Up Recipes

NASA Astrophysics Data System (ADS)

Weigel, A. M.; Maskey, M.; Smith, T.; Conover, H.

2016-12-01

One of the major challenges in Earth science research and applications is understanding and applying the proper methods, tools, and software for using scientific data. These techniques are often difficult and time consuming to identify, requiring novel users to conduct extensive research, take classes, and reach out for assistance, thus hindering scientific discovery and real-world applications. To address these challenges, the Global Hydrology Resource Center (GHRC) DAAC has developed a series of data recipes that novel users such as students, decision makers, and general Earth scientists can leverage to learn how to use Earth science datasets. Once the data recipe content had been finalized, GHRC computer and Earth scientists collaborated with a web and graphic designer to ensure the content is both attractively presented to data users, and clearly communicated to promote the education and use of Earth science data. The completed data recipes include, but are not limited to, tutorials, iPython Notebooks, resources, and tools necessary for addressing key difficulties in data use across a broad user base. These recipes enable non-traditional users to learn how to use data, but also curates and communicates common methods and approaches that may be difficult and time consuming for these users to identify.

Collaboration tools and techniques for large model datasets

USGS Publications Warehouse

Signell, R.P.; Carniel, S.; Chiggiato, J.; Janekovic, I.; Pullen, J.; Sherwood, C.R.

2008-01-01

In MREA and many other marine applications, it is common to have multiple models running with different grids, run by different institutions. Techniques and tools are described for low-bandwidth delivery of data from large multidimensional datasets, such as those from meteorological and oceanographic models, directly into generic analysis and visualization tools. Output is stored using the NetCDF CF Metadata Conventions, and then delivered to collaborators over the web via OPeNDAP. OPeNDAP datasets served by different institutions are then organized via THREDDS catalogs. Tools and procedures are then used which enable scientists to explore data on the original model grids using tools they are familiar with. It is also low-bandwidth, enabling users to extract just the data they require, an important feature for access from ship or remote areas. The entire implementation is simple enough to be handled by modelers working with their webmasters - no advanced programming support is necessary. ?? 2007 Elsevier B.V. All rights reserved.

The Cluster Science Archive: from Time Period to Physics Based Search

NASA Astrophysics Data System (ADS)

Masson, A.; Escoubet, C. P.; Laakso, H. E.; Perry, C. H.

2015-12-01

Since 2000, the Cluster spacecraft relay the most detailed information on how the solar wind affects our geospace in three dimensions. Science output from Cluster is a leap forward in our knowledge of space plasma physics: the science behind space weather. It has been key in improving the modeling of the magnetosphere and understanding its various physical processes. Cluster data have enabled the publication of more than 2000 refereed papers and counting. This substantial scientific return is often attributed to the online availability of the Cluster data archive, now called the Cluster Science Archive (CSA). It is being developed by the ESAC Science Data Center (ESDC) team and maintained alongside other science ESA archives at ESAC (ESA Space Astronomy Center, Madrid, Spain). CSA is a public archive, which contains the entire set of Cluster high-resolution data, and other related products in a standard format and with a complete set of metadata. Since May 2015, it also contains data from the CNSA/ESA Double Star mission (2003-2008), a mission operated in conjunction with Cluster. The total amount of data format now exceeds 100 TB. Accessing CSA requires to be registered to enable user profiles and CSA accounts more than 1,500 users. CSA provides unique tools for visualizing its data including - on-demand particle distribution functions visualization - fast data browsing with more than 15TB of pre-generated plots - inventory plots It also offers command line capabilities (e.g. data access via Matlab or IDL softwares, data streaming). Despite its reliability, users can only request data for a specific time period while scientists often focus on specific regions or data signatures. For these reasons, a data-mining tool is being developed to do just that. It offers an interface to select data based not only on a time period but on various criteria including: key physical parameters, regions of space and spacecraft constellation geometry. The output of this tool is a list of time periods that fits the criteria imposed by the user. Such a list enables to download any bunch of datasets for all these time periods in one go. We propose to present the state of development of this tool and interact with the scientific community to better fit its needs.

ClimatePipes: User-Friendly Data Access, Manipulation, Analysis & Visualization of Community Climate Models

NASA Astrophysics Data System (ADS)

Chaudhary, A.; DeMarle, D.; Burnett, B.; Harris, C.; Silva, W.; Osmari, D.; Geveci, B.; Silva, C.; Doutriaux, C.; Williams, D. N.

2013-12-01

The impact of climate change will resonate through a broad range of fields including public health, infrastructure, water resources, and many others. Long-term coordinated planning, funding, and action are required for climate change adaptation and mitigation. Unfortunately, widespread use of climate data (simulated and observed) in non-climate science communities is impeded by factors such as large data size, lack of adequate metadata, poor documentation, and lack of sufficient computational and visualization resources. We present ClimatePipes to address many of these challenges by creating an open source platform that provides state-of-the-art, user-friendly data access, analysis, and visualization for climate and other relevant geospatial datasets, making the climate data available to non-researchers, decision-makers, and other stakeholders. The overarching goals of ClimatePipes are: - Enable users to explore real-world questions related to climate change. - Provide tools for data access, analysis, and visualization. - Facilitate collaboration by enabling users to share datasets, workflows, and visualization. ClimatePipes uses a web-based application platform for its widespread support on mainstream operating systems, ease-of-use, and inherent collaboration support. The front-end of ClimatePipes uses HTML5 (WebGL, Canvas2D, CSS3) to deliver state-of-the-art visualization and to provide a best-in-class user experience. The back-end of the ClimatePipes is built around Python using the Visualization Toolkit (VTK, http://vtk.org), Climate Data Analysis Tools (CDAT, http://uv-cdat.llnl.gov), and other climate and geospatial data processing tools such as GDAL and PROJ4. ClimatePipes web-interface to query and access data from remote sources (such as ESGF). Shown in the figure is climate data layer from ESGF on top of map data layer from OpenStreetMap. The ClimatePipes workflow editor provides flexibility and fine grained control, and uses the VisTrails (http://www.vistrails.org) workflow engine in the backend.

Scientists and Public: Is the Information Flow Direction Starting to Change?

NASA Astrophysics Data System (ADS)

Diaz-Doce, D.; Bee, E. J.; Bell, P. D.; Marchant, A. P.; Reay, S.; Richardson, S. L.; Shelley, W. A.

2014-12-01

Over half of the population of the UK own a smartphone, and about the same number of people uses social media such as Twitter. For the British Geological Survey (BGS) this means millions of potential reporters of real-time events and in-the-field data capturers, creating a new source of scientific information that could help to better understand and predict natural processes. BGS first started collecting citizen data, using crowd-sourcing, through websites and smartphone apps focused on gathering geological related information (e.g. mySoil and myVolcano). These tools ask volunteers to follow a guided form where they can upload data related to geology and geological events; including location, description, measurements, photos, videos, or even instructions on sending physical samples. This information is used to augment existing data collections. Social media provides a different channel for gathering useful scientific information from the public. BGS is starting to explore this route with the release of GeoSocial-Aurora , a web mapping tool that searches for tweets related to aurora sightings and locates them as markers on a map. Users are actively encouraged to contribute by sending tweets about aurora sightings in a specific format, which contains the #BGSaurora hashtag, the location of the sighting, and any comments or pictures. The tool harvests these tweets through the Twitter REST API and places them on the map, enabling the user to generate clusters and heatmaps. GeoSocial-Aurora provides scientists with a potential tool for gathering useful data for scientific analysis. It collects actual aurora sighting locations, enabling users to check where the aurora is taking place in real time. This may, in time, help scientists to improve future predictions of when and where auroras are visible.

Local Debonding and Fiber Breakage in Composite Materials Modeled Accurately

NASA Technical Reports Server (NTRS)

Bednarcyk, Brett A.; Arnold, Steven M.

2001-01-01

A prerequisite for full utilization of composite materials in aerospace components is accurate design and life prediction tools that enable the assessment of component performance and reliability. Such tools assist both structural analysts, who design and optimize structures composed of composite materials, and materials scientists who design and optimize the composite materials themselves. NASA Glenn Research Center's Micromechanics Analysis Code with Generalized Method of Cells (MAC/GMC) software package (http://www.grc.nasa.gov/WWW/LPB/mac) addresses this need for composite design and life prediction tools by providing a widely applicable and accurate approach to modeling composite materials. Furthermore, MAC/GMC serves as a platform for incorporating new local models and capabilities that are under development at NASA, thus enabling these new capabilities to progress rapidly to a stage in which they can be employed by the code's end users.

Collaborative Web-Enabled GeoAnalytics Applied to OECD Regional Data

NASA Astrophysics Data System (ADS)

Jern, Mikael

Recent advances in web-enabled graphics technologies have the potential to make a dramatic impact on developing collaborative geovisual analytics (GeoAnalytics). In this paper, tools are introduced that help establish progress initiatives at international and sub-national levels aimed at measuring and collaborating, through statistical indicators, economic, social and environmental developments and to engage both statisticians and the public in such activities. Given this global dimension of such a task, the “dream” of building a repository of progress indicators, where experts and public users can use GeoAnalytics collaborative tools to compare situations for two or more countries, regions or local communities, could be accomplished. While the benefits of GeoAnalytics tools are many, it remains a challenge to adapt these dynamic visual tools to the Internet. For example, dynamic web-enabled animation that enables statisticians to explore temporal, spatial and multivariate demographics data from multiple perspectives, discover interesting relationships, share their incremental discoveries with colleagues and finally communicate selected relevant knowledge to the public. These discoveries often emerge through the diverse backgrounds and experiences of expert domains and are precious in a creative analytics reasoning process. In this context, we introduce a demonstrator “OECD eXplorer”, a customized tool for interactively analyzing, and collaborating gained insights and discoveries based on a novel story mechanism that capture, re-use and share task-related explorative events.

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

PubMed Central

Ostrowski, Maureen; Bernes, Marshall R.

1984-01-01

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

[Web TV, a tool favouring collaboration for quality care].

PubMed

Decobert, Jean-Pierre; Weill, Stéphanie

The Web TV of the EPSM Lille-Métropole is an innovative communication tool in mental health. Aiming to change the image of psychiatry among users as well as professionals, these programmes, posted online, enable viewers to see the care provided by mental health professionals. They are also an opportunity for those involved to get to know each other better to improve the way they work together. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Implementation of GenePattern within the Stanford Microarray Database.

PubMed

Hubble, Jeremy; Demeter, Janos; Jin, Heng; Mao, Maria; Nitzberg, Michael; Reddy, T B K; Wymore, Farrell; Zachariah, Zachariah K; Sherlock, Gavin; Ball, Catherine A

2009-01-01

Hundreds of researchers across the world use the Stanford Microarray Database (SMD; http://smd.stanford.edu/) to store, annotate, view, analyze and share microarray data. In addition to providing registered users at Stanford access to their own data, SMD also provides access to public data, and tools with which to analyze those data, to any public user anywhere in the world. Previously, the addition of new microarray data analysis tools to SMD has been limited by available engineering resources, and in addition, the existing suite of tools did not provide a simple way to design, execute and share analysis pipelines, or to document such pipelines for the purposes of publication. To address this, we have incorporated the GenePattern software package directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. In this article, we describe our implementation of the GenePattern microarray analysis software package into the SMD code base. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability.

Next generation tools for genomic data generation, distribution, and visualization

PubMed Central

2010-01-01

Background With the rapidly falling cost and availability of high throughput sequencing and microarray technologies, the bottleneck for effectively using genomic analysis in the laboratory and clinic is shifting to one of effectively managing, analyzing, and sharing genomic data. Results Here we present three open-source, platform independent, software tools for generating, analyzing, distributing, and visualizing genomic data. These include a next generation sequencing/microarray LIMS and analysis project center (GNomEx); an application for annotating and programmatically distributing genomic data using the community vetted DAS/2 data exchange protocol (GenoPub); and a standalone Java Swing application (GWrap) that makes cutting edge command line analysis tools available to those who prefer graphical user interfaces. Both GNomEx and GenoPub use the rich client Flex/Flash web browser interface to interact with Java classes and a relational database on a remote server. Both employ a public-private user-group security model enabling controlled distribution of patient and unpublished data alongside public resources. As such, they function as genomic data repositories that can be accessed manually or programmatically through DAS/2-enabled client applications such as the Integrated Genome Browser. Conclusions These tools have gained wide use in our core facilities, research laboratories and clinics and are freely available for non-profit use. See http://sourceforge.net/projects/gnomex/, http://sourceforge.net/projects/genoviz/, and http://sourceforge.net/projects/useq. PMID:20828407

Improving Patient Experience and Primary Care Quality for Patients With Complex Chronic Disease Using the Electronic Patient-Reported Outcomes Tool: Adopting Qualitative Methods Into a User-Centered Design Approach.

PubMed

Steele Gray, Carolyn; Khan, Anum Irfan; Kuluski, Kerry; McKillop, Ian; Sharpe, Sarah; Bierman, Arlene S; Lyons, Renee F; Cott, Cheryl

2016-02-18

Many mHealth technologies do not meet the needs of patients with complex chronic disease and disabilities (CCDDs) who are among the highest users of health systems worldwide. Furthermore, many of the development methodologies used in the creation of mHealth and eHealth technologies lack the ability to embrace users with CCDD in the specification process. This paper describes how we adopted and modified development techniques to create the electronic Patient-Reported Outcomes (ePRO) tool, a patient-centered mHealth solution to help improve primary health care for patients experiencing CCDD. This paper describes the design and development approach, specifically the process of incorporating qualitative research methods into user-centered design approaches to create the ePRO tool. Key lessons learned are offered as a guide for other eHealth and mHealth research and technology developers working with complex patient populations and their primary health care providers. Guided by user-centered design principles, interpretive descriptive qualitative research methods were adopted to capture user experiences through interviews and working groups. Consistent with interpretive descriptive methods, an iterative analysis technique was used to generate findings, which were then organized in relation to the tool design and function to help systematically inform modifications to the tool. User feedback captured and analyzed through this method was used to challenge the design and inform the iterative development of the tool. Interviews with primary health care providers (n=7) and content experts (n=6), and four focus groups with patients and carers (n=14) along with a PICK analysis-Possible, Implementable, (to be) Challenged, (to be) Killed-guided development of the first prototype. The initial prototype was presented in three design working groups with patients/carers (n=5), providers (n=6), and experts (n=5). Working group findings were broken down into categories of what works and what does not work to inform modifications to the prototype. This latter phase led to a major shift in the purpose and design of the prototype, validating the importance of using iterative codesign processes. Interpretive descriptive methods allow for an understanding of user experiences of patients with CCDD, their carers, and primary care providers. Qualitative methods help to capture and interpret user needs, and identify contextual barriers and enablers to tool adoption, informing a redesign to better suit the needs of this diverse user group. This study illustrates the value of adopting interpretive descriptive methods into user-centered mHealth tool design and can also serve to inform the design of other eHealth technologies. Our approach is particularly useful in requirements determination when developing for a complex user group and their health care providers.

Information Management Workflow and Tools Enabling Multiscale Modeling Within ICME Paradigm

NASA Technical Reports Server (NTRS)

Arnold, Steven M.; Bednarcyk, Brett A.; Austin, Nic; Terentjev, Igor; Cebon, Dave; Marsden, Will

2016-01-01

With the increased emphasis on reducing the cost and time to market of new materials, the need for analytical tools that enable the virtual design and optimization of materials throughout their processing - internal structure - property - performance envelope, along with the capturing and storing of the associated material and model information across its lifecycle, has become critical. This need is also fueled by the demands for higher efficiency in material testing; consistency, quality and traceability of data; product design; engineering analysis; as well as control of access to proprietary or sensitive information. Fortunately, material information management systems and physics-based multiscale modeling methods have kept pace with the growing user demands. Herein, recent efforts to establish workflow for and demonstrate a unique set of web application tools for linking NASA GRC's Integrated Computational Materials Engineering (ICME) Granta MI database schema and NASA GRC's Integrated multiscale Micromechanics Analysis Code (ImMAC) software toolset are presented. The goal is to enable seamless coupling between both test data and simulation data, which is captured and tracked automatically within Granta MI®, with full model pedigree information. These tools, and this type of linkage, are foundational to realizing the full potential of ICME, in which materials processing, microstructure, properties, and performance are coupled to enable application-driven design and optimization of materials and structures.

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.

Strategies to explore functional genomics data sets in NCBI's GEO database.

PubMed

Wilhite, Stephen E; Barrett, Tanya

2012-01-01

The Gene Expression Omnibus (GEO) database is a major repository that stores high-throughput functional genomics data sets that are generated using both microarray-based and sequence-based technologies. Data sets are submitted to GEO primarily by researchers who are publishing their results in journals that require original data to be made freely available for review and analysis. In addition to serving as a public archive for these data, GEO has a suite of tools that allow users to identify, analyze, and visualize data relevant to their specific interests. These tools include sample comparison applications, gene expression profile charts, data set clusters, genome browser tracks, and a powerful search engine that enables users to construct complex queries.

Strategies to Explore Functional Genomics Data Sets in NCBI’s GEO Database

PubMed Central

Wilhite, Stephen E.; Barrett, Tanya

2012-01-01

The Gene Expression Omnibus (GEO) database is a major repository that stores high-throughput functional genomics data sets that are generated using both microarray-based and sequence-based technologies. Data sets are submitted to GEO primarily by researchers who are publishing their results in journals that require original data to be made freely available for review and analysis. In addition to serving as a public archive for these data, GEO has a suite of tools that allow users to identify, analyze and visualize data relevant to their specific interests. These tools include sample comparison applications, gene expression profile charts, data set clusters, genome browser tracks, and a powerful search engine that enables users to construct complex queries. PMID:22130872

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

PubMed

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

2011-01-01

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

PeptideNavigator: An interactive tool for exploring large and complex data sets generated during peptide-based drug design projects.

PubMed

Diller, Kyle I; Bayden, Alexander S; Audie, Joseph; Diller, David J

2018-01-01

There is growing interest in peptide-based drug design and discovery. Due to their relatively large size, polymeric nature, and chemical complexity, the design of peptide-based drugs presents an interesting "big data" challenge. Here, we describe an interactive computational environment, PeptideNavigator, for naturally exploring the tremendous amount of information generated during a peptide drug design project. The purpose of PeptideNavigator is the presentation of large and complex experimental and computational data sets, particularly 3D data, so as to enable multidisciplinary scientists to make optimal decisions during a peptide drug discovery project. PeptideNavigator provides users with numerous viewing options, such as scatter plots, sequence views, and sequence frequency diagrams. These views allow for the collective visualization and exploration of many peptides and their properties, ultimately enabling the user to focus on a small number of peptides of interest. To drill down into the details of individual peptides, PeptideNavigator provides users with a Ramachandran plot viewer and a fully featured 3D visualization tool. Each view is linked, allowing the user to seamlessly navigate from collective views of large peptide data sets to the details of individual peptides with promising property profiles. Two case studies, based on MHC-1A activating peptides and MDM2 scaffold design, are presented to demonstrate the utility of PeptideNavigator in the context of disparate peptide-design projects. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

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

NASA Astrophysics Data System (ADS)

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

2009-04-01

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

Information transfer satellite concept study. Volume 4: computer manual

NASA Technical Reports Server (NTRS)

Bergin, P.; Kincade, C.; Kurpiewski, D.; Leinhaupel, F.; Millican, F.; Onstad, R.

1971-01-01

The Satellite Telecommunications Analysis and Modeling Program (STAMP) provides the user with a flexible and comprehensive tool for the analysis of ITS system requirements. While obtaining minimum cost design points, the program enables the user to perform studies over a wide range of user requirements and parametric demands. The program utilizes a total system approach wherein the ground uplink and downlink, the spacecraft, and the launch vehicle are simultaneously synthesized. A steepest descent algorithm is employed to determine the minimum total system cost design subject to the fixed user requirements and imposed constraints. In the process of converging to the solution, the pertinent subsystem tradeoffs are resolved. This report documents STAMP through a technical analysis and a description of the principal techniques employed in the program.

Pins and posters: Paradigms for content publication on situated displays.

PubMed

José, Rui; Pinto, Hélder; Silva, Bruno; Melro, Ana

2013-01-01

Public-display systems are still far from being a medium for meeting people's diverse communication goals. Moving toward open displays will require publication paradigms that can overcome the challenges of meaningful engagement and enable users to fully understand and control the publication process. The metaphors of pins and posters have inspired two complementary paradigms for public displays. Researchers implemented these paradigms in the Instant Places system, which they deployed on 10 displays in diverse urban locations for six months. They collected user and system data regarding the users' practices. The findings improve the understanding of what might drive user-generated content in networks of urban displays. Such knowledge can inform the design of tools and procedures for situated publication in public displays.

The I4 Online Query Tool for Earth Observations Data

NASA Technical Reports Server (NTRS)

Stefanov, William L.; Vanderbloemen, Lisa A.; Lawrence, Samuel J.

2015-01-01

The NASA Earth Observation System Data and Information System (EOSDIS) delivers an average of 22 terabytes per day of data collected by orbital and airborne sensor systems to end users through an integrated online search environment (the Reverb/ECHO system). Earth observations data collected by sensors on the International Space Station (ISS) are not currently included in the EOSDIS system, and are only accessible through various individual online locations. This increases the effort required by end users to query multiple datasets, and limits the opportunity for data discovery and innovations in analysis. The Earth Science and Remote Sensing Unit of the Exploration Integration and Science Directorate at NASA Johnson Space Center has collaborated with the School of Earth and Space Exploration at Arizona State University (ASU) to develop the ISS Instrument Integration Implementation (I4) data query tool to provide end users a clean, simple online interface for querying both current and historical ISS Earth Observations data. The I4 interface is based on the Lunaserv and Lunaserv Global Explorer (LGE) open-source software packages developed at ASU for query of lunar datasets. In order to avoid mirroring existing databases - and the need to continually sync/update those mirrors - our design philosophy is for the I4 tool to be a pure query engine only. Once an end user identifies a specific scene or scenes of interest, I4 transparently takes the user to the appropriate online location to download the data. The tool consists of two public-facing web interfaces. The Map Tool provides a graphic geobrowser environment where the end user can navigate to an area of interest and select single or multiple datasets to query. The Map Tool displays active image footprints for the selected datasets (Figure 1). Selecting a footprint will open a pop-up window that includes a browse image and a link to available image metadata, along with a link to the online location to order or download the actual data. Search results are either delivered in the form of browse images linked to the appropriate online database, similar to the Map Tool, or they may be transferred within the I4 environment for display as footprints in the Map Tool. Datasets searchable through I4 (http://eol.jsc.nasa.gov/I4_tool) currently include: Crew Earth Observations (CEO) cataloged and uncataloged handheld astronaut photography; Sally Ride EarthKAM; Hyperspectral Imager for the Coastal Ocean (HICO); and the ISS SERVIR Environmental Research and Visualization System (ISERV). The ISS is a unique platform in that it will have multiple users over its lifetime, and that no single remote sensing system has a permanent internal or external berth. The open source I4 tool is designed to enable straightforward addition of new datasets as they become available such as ISS-RapidSCAT, Cloud Aerosol Transport System (CATS), and the High Definition Earth Viewing (HDEV) system. Data from other sensor systems, such as those operated by the ISS International Partners or under the auspices of the US National Laboratory program, can also be added to I4 provided sufficient access to enable searching of data or metadata is available. Commercial providers of remotely sensed data from the ISS may be particularly interested in I4 as an additional means of directing potential customers and clients to their products.

User Oriented Techniques to Support Interaction and Decision Making with Large Educational Databases

ERIC Educational Resources Information Center

Hartley, Roger; Almuhaidib, Saud M. Y.

2007-01-01

Information Technology is developing rapidly and providing policy/decision makers with large amounts of information that require processing and analysis. Decision support systems (DSS) aim to provide tools that not only help such analyses, but enable the decision maker to experiment and simulate the effects of different policies and selection…

Investigating the Role of Minecraft in Educational Learning Environments

ERIC Educational Resources Information Center

Callaghan, Noelene

2016-01-01

This research paper identifies the way in which Minecraft Edu can be used to contribute to the teaching and learning of secondary students via a multiple case research study. Minecraft Edu is recognised as a gamification tool that enables its users to create and evaluate project-based learning activities within a classroom context. Learning…

Maximizing Access Technology Tools for the Library of the Future

ERIC Educational Resources Information Center

Pearson, Waynn

2003-01-01

The renovated Cerritos Public Library is a unique blending of traditional and hightech features. One of the key principles in its planning and design was to enable a range of convenient access services. This article summarizes the process of building this library and how it has been received by users. (Contains 5 figures.)

Scripting for Collaborative Search Computer-Supported Classroom Activities

ERIC Educational Resources Information Center

Verdugo, Renato; Barros, Leonardo; Albornoz, Daniela; Nussbaum, Miguel; McFarlane, Angela

2014-01-01

Searching online is one of the most powerful resources today's students have for accessing information. Searching in groups is a daily practice across multiple contexts; however, the tools we use for searching online do not enable collaborative practices and traditional search models consider a single user navigating online in solitary. This paper…

Fast simulation tool for ultraviolet radiation at the earth's surface

NASA Astrophysics Data System (ADS)

Engelsen, Ola; Kylling, Arve

2005-04-01

FastRT is a fast, yet accurate, UV simulation tool that computes downward surface UV doses, UV indices, and irradiances in the spectral range 290 to 400 nm with a resolution as small as 0.05 nm. It computes a full UV spectrum within a few milliseconds on a standard PC, and enables the user to convolve the spectrum with user-defined and built-in spectral response functions including the International Commission on Illumination (CIE) erythemal response function used for UV index calculations. The program accounts for the main radiative input parameters, i.e., instrumental characteristics, solar zenith angle, ozone column, aerosol loading, clouds, surface albedo, and surface altitude. FastRT is based on look-up tables of carefully selected entries of atmospheric transmittances and spherical albedos, and exploits the smoothness of these quantities with respect to atmospheric, surface, geometrical, and spectral parameters. An interactive site, http://nadir.nilu.no/~olaeng/fastrt/fastrt.html, enables the public to run the FastRT program with most input options. This page also contains updated information about FastRT and links to freely downloadable source codes and binaries.

Mindtagger: A Demonstration of Data Labeling in Knowledge Base Construction.

PubMed

Shin, Jaeho; Ré, Christopher; Cafarella, Michael

2015-08-01

End-to-end knowledge base construction systems using statistical inference are enabling more people to automatically extract high-quality domain-specific information from unstructured data. As a result of deploying DeepDive framework across several domains, we found new challenges in debugging and improving such end-to-end systems to construct high-quality knowledge bases. DeepDive has an iterative development cycle in which users improve the data. To help our users, we needed to develop principles for analyzing the system's error as well as provide tooling for inspecting and labeling various data products of the system. We created guidelines for error analysis modeled after our colleagues' best practices, in which data labeling plays a critical role in every step of the analysis. To enable more productive and systematic data labeling, we created Mindtagger, a versatile tool that can be configured to support a wide range of tasks. In this demonstration, we show in detail what data labeling tasks are modeled in our error analysis guidelines and how each of them is performed using Mindtagger.

Service-based analysis of biological pathways

PubMed Central

Zheng, George; Bouguettaya, Athman

2009-01-01

Background Computer-based pathway discovery is concerned with two important objectives: pathway identification and analysis. Conventional mining and modeling approaches aimed at pathway discovery are often effective at achieving either objective, but not both. Such limitations can be effectively tackled leveraging a Web service-based modeling and mining approach. Results Inspired by molecular recognitions and drug discovery processes, we developed a Web service mining tool, named PathExplorer, to discover potentially interesting biological pathways linking service models of biological processes. The tool uses an innovative approach to identify useful pathways based on graph-based hints and service-based simulation verifying user's hypotheses. Conclusion Web service modeling of biological processes allows the easy access and invocation of these processes on the Web. Web service mining techniques described in this paper enable the discovery of biological pathways linking these process service models. Algorithms presented in this paper for automatically highlighting interesting subgraph within an identified pathway network enable the user to formulate hypothesis, which can be tested out using our simulation algorithm that are also described in this paper. PMID:19796403

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.

Supporting Snow Research: SnowEx Data and Services at the NASA National Snow and Ice Data Center DAAC

NASA Astrophysics Data System (ADS)

Leon, A.; Tanner, S.; Deems, J. S.

2017-12-01

The National Snow and Ice Data Center Distributed Active Archive Center (NSIDC DAAC), part of the Cooperative Institute for Research in Environmental Sciences (CIRES) at the University of Colorado Boulder, will archive and distribute all primary data sets collected during the NASA SnowEx campaigns. NSIDC DAAC's overarching goal for SnowEx data management is to steward the diverse SnowEx data sets to provide a reliable long-term archive, to enable effective data discovery, retrieval, and usage, and to support end user engagement. This goal will be achieved though coordination and collaboration with SnowEx project management and investigators. NSIDC DAAC's core functions for SnowEx data management include: Data Creation: Advise investigators on data formats and structure as well as metadata creation and content to enable preservation, usability, and discoverability. Data Documentation: Develop comprehensive data set documentation describing the instruments, data collection and derivation methods, and data file contents. Data Distribution: Provide discovery and access through NSIDC and NASA data portals to make SnowEx data available to a broad user community Data & User Support: Assist user communities with the selection and usage of SnowEx data products. In an effort to educate and broaden the SnowEx user community, we will present an overview of the SnowEx data products, tools, and services which will be available at the NSIDC DAAC. We hope to gain further insight into how the DAAC can enable the user community to seamlessly and effectively utilize SnowEx data in their research and applications.

Clinical benchmarking enabled by the digital health record.

PubMed

Ricciardi, T N; Masarie, F E; Middleton, B

2001-01-01

Office-based physicians are often ill equipped to report aggregate information about their patients and practice of medicine, since their practices have relied upon paper records for the management of clinical information. Physicians who do not have access to large-scale information technology support can now benefit from low-cost clinical documentation and reporting tools. We developed a hosted clinical data mart for users of a web-enabled charting tool, targeting the solo or small group practice. The system uses secure Java Server Pages with a dashboard-like menu to provide point-and-click access to simple reports such as case mix, medications, utilization, productivity, and patient demographics in its first release. The system automatically normalizes user-entered clinical terms to enhance the quality of structured data. Individual providers benefit from rapid patient identification for disease management, quality of care self-assessments, drug recalls, and compliance with clinical guidelines. The system provides knowledge integration by linking to trusted sources of online medical information in context. Information derived from the clinical record is clinically more accurate than billing data. Provider self-assessment and benchmarking empowers physicians, who may resent "being profiled" by external entities. In contrast to large-scale data warehouse projects, the current system delivers immediate value to individual physicians who choose an electronic clinical documentation tool.

RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement.

PubMed

Sandhu, Maninder; Sureshkumar, V; Prakash, Chandra; Dixit, Rekha; Solanke, Amolkumar U; Sharma, Tilak Raj; Mohapatra, Trilochan; S V, Amitha Mithra

2017-09-30

Genome-wide microarray has enabled development of robust databases for functional genomics studies in rice. However, such databases do not directly cater to the needs of breeders. Here, we have attempted to develop a web interface which combines the information from functional genomic studies across different genetic backgrounds with DNA markers so that they can be readily deployed in crop improvement. In the current version of the database, we have included drought and salinity stress studies since these two are the major abiotic stresses in rice. RiceMetaSys, a user-friendly and freely available web interface provides comprehensive information on salt responsive genes (SRGs) and drought responsive genes (DRGs) across genotypes, crop development stages and tissues, identified from multiple microarray datasets. 'Physical position search' is an attractive tool for those using QTL based approach for dissecting tolerance to salt and drought stress since it can provide the list of SRGs and DRGs in any physical interval. To identify robust candidate genes for use in crop improvement, the 'common genes across varieties' search tool is useful. Graphical visualization of expression profiles across genes and rice genotypes has been enabled to facilitate the user and to make the comparisons more impactful. Simple Sequence Repeat (SSR) search in the SRGs and DRGs is a valuable tool for fine mapping and marker assisted selection since it provides primers for survey of polymorphism. An external link to intron specific markers is also provided for this purpose. Bulk retrieval of data without any limit has been enabled in case of locus and SSR search. The aim of this database is to facilitate users with a simple and straight-forward search options for identification of robust candidate genes from among thousands of SRGs and DRGs so as to facilitate linking variation in expression profiles to variation in phenotype. Database URL: http://14.139.229.201.

OceanVideoLab: A Tool for Exploring Underwater Video

NASA Astrophysics Data System (ADS)

Ferrini, V. L.; Morton, J. J.; Wiener, C.

2016-02-01

Video imagery acquired with underwater vehicles is an essential tool for characterizing seafloor ecosystems and seafloor geology. It is a fundamental component of ocean exploration that facilitates real-time operations, augments multidisciplinary scientific research, and holds tremendous potential for public outreach and engagement. Acquiring, documenting, managing, preserving and providing access to large volumes of video acquired with underwater vehicles presents a variety of data stewardship challenges to the oceanographic community. As a result, only a fraction of underwater video content collected with research submersibles is documented, discoverable and/or viewable online. With more than 1 billion users, YouTube offers infrastructure that can be leveraged to help address some of the challenges associated with sharing underwater video with a broad global audience. Anyone can post content to YouTube, and some oceanographic organizations, such as the Schmidt Ocean Institute, have begun live-streaming video directly from underwater vehicles. OceanVideoLab (oceanvideolab.org) was developed to help improve access to underwater video through simple annotation, browse functionality, and integration with related environmental data. Any underwater video that is publicly accessible on YouTube can be registered with OceanVideoLab by simply providing a URL. It is strongly recommended that a navigational file also be supplied to enable geo-referencing of observations. Once a video is registered, it can be viewed and annotated using a simple user interface that integrates observations with vehicle navigation data if provided. This interface includes an interactive map and a list of previous annotations that allows users to jump to times of specific observations in the video. Future enhancements to OceanVideoLab will include the deployment of a search interface, the development of an application program interface (API) that will drive the search and enable querying of content by other systems/tools, the integration of related environmental data from complementary data systems (e.g. temperature, bathymetry), and the expansion of infrastructure to enable broad crowdsourcing of annotations.

VisBOL: Web-Based Tools for Synthetic Biology Design Visualization.

PubMed

McLaughlin, James Alastair; Pocock, Matthew; Mısırlı, Göksel; Madsen, Curtis; Wipat, Anil

2016-08-19

VisBOL is a Web-based application that allows the rendering of genetic circuit designs, enabling synthetic biologists to visually convey designs in SBOL visual format. VisBOL designs can be exported to formats including PNG and SVG images to be embedded in Web pages, presentations and publications. The VisBOL tool enables the automated generation of visualizations from designs specified using the Synthetic Biology Open Language (SBOL) version 2.0, as well as a range of well-known bioinformatics formats including GenBank and Pigeoncad notation. VisBOL is provided both as a user accessible Web site and as an open-source (BSD) JavaScript library that can be used to embed diagrams within other content and software.

Webpress: An Internet Outreach from NASA Dryden

NASA Technical Reports Server (NTRS)

Biezad, Daniel J.

1996-01-01

The Technology and Commercialization Office at NASA DRyden has developed many educational outreach programs for K-12 educators. This project concentrates on the internet portion of that effort, specifically focusing on the development of an internet tool for educators called Webpress. This tool will not only provide a user-friendly access to aeronautical topics and interesting individuals on the world wide web (web), but will also enable teachers to rapidly submit and display their own materials and links for use in the classroom.

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

PubMed

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

2018-04-04

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

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

Karp, Peter D.

Pathway Tools is a systems-biology software package written by SRI International (SRI) that produces Pathway/Genome Databases (PGDBs) for organisms with a sequenced genome. Pathway Tools also provides a wide range of capabilities for analyzing predicted metabolic networks and user-generated omics data. More than 5,000 academic, industrial, and government groups have licensed Pathway Tools. This user community includes researchers at all three DOE bioenergy centers, as well as academic and industrial metabolic engineering (ME) groups. An integral part of the Pathway Tools software is MetaCyc, a large, multiorganism database of metabolic pathways and enzymes that SRI and its academic collaborators manuallymore » curate. This project included two main goals: I. Enhance the MetaCyc content of bioenergy-related enzymes and pathways. II. Develop computational tools for engineering metabolic pathways that satisfy specified design goals, in particular for bioenergy-related pathways. In part I, SRI proposed to significantly expand the coverage of bioenergy-related metabolic information in MetaCyc, followed by the generation of organism-specific PGDBs for all energy-relevant organisms sequenced at the DOE Joint Genome Institute (JGI). Part I objectives included: 1: Expand the content of MetaCyc to include bioenergy-related enzymes and pathways. 2: Enhance the Pathway Tools software to enable display of complex polymer degradation processes. 3: Create new PGDBs for the energy-related organisms sequenced by JGI, update existing PGDBs with new MetaCyc content, and make these data available to JBEI via the BioCyc website. In part II, SRI proposed to develop an efficient computational tool for the engineering of metabolic pathways. Part II objectives included: 4: Develop computational tools for generating metabolic pathways that satisfy specified design goals, enabling users to specify parameters such as starting and ending compounds, and preferred or disallowed intermediate compounds. The pathways were to be generated using metabolic reactions from a reference database (DB). 5: Develop computational tools for ranking the pathways generated in objective (4) according to their optimality. The ranking criteria include stoichiometric yield, the number and cost of additional inputs and the cofactor compounds required by the pathway, pathway length, and pathway energetics. 6: Develop tools for visualizing generated pathways to facilitate the evaluation of a large space of generated pathways.« less

Web-based GIS: the vector-borne disease airline importation risk (VBD-AIR) tool

PubMed Central

2012-01-01

Background Over the past century, the size and complexity of the air travel network has increased dramatically. Nowadays, there are 29.6 million scheduled flights per year and around 2.7 billion passengers are transported annually. The rapid expansion of the network increasingly connects regions of endemic vector-borne disease with the rest of the world, resulting in challenges to health systems worldwide in terms of vector-borne pathogen importation and disease vector invasion events. Here we describe the development of a user-friendly Web-based GIS tool: the Vector-Borne Disease Airline Importation Risk Tool (VBD-AIR), to help better define the roles of airports and airlines in the transmission and spread of vector-borne diseases. Methods Spatial datasets on modeled global disease and vector distributions, as well as climatic and air network traffic data were assembled. These were combined to derive relative risk metrics via air travel for imported infections, imported vectors and onward transmission, and incorporated into a three-tier server architecture in a Model-View-Controller framework with distributed GIS components. A user-friendly web-portal was built that enables dynamic querying of the spatial databases to provide relevant information. Results The VBD-AIR tool constructed enables the user to explore the interrelationships among modeled global distributions of vector-borne infectious diseases (malaria. dengue, yellow fever and chikungunya) and international air service routes to quantify seasonally changing risks of vector and vector-borne disease importation and spread by air travel, forming an evidence base to help plan mitigation strategies. The VBD-AIR tool is available at http://www.vbd-air.com. Conclusions VBD-AIR supports a data flow that generates analytical results from disparate but complementary datasets into an organized cartographical presentation on a web map for the assessment of vector-borne disease movements on the air travel network. The framework built provides a flexible and robust informatics infrastructure by separating the modules of functionality through an ontological model for vector-borne disease. The VBD‒AIR tool is designed as an evidence base for visualizing the risks of vector-borne disease by air travel for a wide range of users, including planners and decisions makers based in state and local government, and in particular, those at international and domestic airports tasked with planning for health risks and allocating limited resources. PMID:22892045

Web-based GIS: the vector-borne disease airline importation risk (VBD-AIR) tool.

PubMed

Huang, Zhuojie; Das, Anirrudha; Qiu, Youliang; Tatem, Andrew J

2012-08-14

Over the past century, the size and complexity of the air travel network has increased dramatically. Nowadays, there are 29.6 million scheduled flights per year and around 2.7 billion passengers are transported annually. The rapid expansion of the network increasingly connects regions of endemic vector-borne disease with the rest of the world, resulting in challenges to health systems worldwide in terms of vector-borne pathogen importation and disease vector invasion events. Here we describe the development of a user-friendly Web-based GIS tool: the Vector-Borne Disease Airline Importation Risk Tool (VBD-AIR), to help better define the roles of airports and airlines in the transmission and spread of vector-borne diseases. Spatial datasets on modeled global disease and vector distributions, as well as climatic and air network traffic data were assembled. These were combined to derive relative risk metrics via air travel for imported infections, imported vectors and onward transmission, and incorporated into a three-tier server architecture in a Model-View-Controller framework with distributed GIS components. A user-friendly web-portal was built that enables dynamic querying of the spatial databases to provide relevant information. The VBD-AIR tool constructed enables the user to explore the interrelationships among modeled global distributions of vector-borne infectious diseases (malaria. dengue, yellow fever and chikungunya) and international air service routes to quantify seasonally changing risks of vector and vector-borne disease importation and spread by air travel, forming an evidence base to help plan mitigation strategies. The VBD-AIR tool is available at http://www.vbd-air.com. VBD-AIR supports a data flow that generates analytical results from disparate but complementary datasets into an organized cartographical presentation on a web map for the assessment of vector-borne disease movements on the air travel network. The framework built provides a flexible and robust informatics infrastructure by separating the modules of functionality through an ontological model for vector-borne disease. The VBD‒AIR tool is designed as an evidence base for visualizing the risks of vector-borne disease by air travel for a wide range of users, including planners and decisions makers based in state and local government, and in particular, those at international and domestic airports tasked with planning for health risks and allocating limited resources.

Inferring transposons activity chronology by TRANScendence - TEs database and de-novo mining tool.

PubMed

Startek, Michał Piotr; Nogły, Jakub; Gromadka, Agnieszka; Grzebelus, Dariusz; Gambin, Anna

2017-10-16

The constant progress in sequencing technology leads to ever increasing amounts of genomic data. In the light of current evidence transposable elements (TEs for short) are becoming useful tools for learning about the evolution of host genome. Therefore the software for genome-wide detection and analysis of TEs is of great interest. Here we describe the computational tool for mining, classifying and storing TEs from newly sequenced genomes. This is an online, web-based, user-friendly service, enabling users to upload their own genomic data, and perform de-novo searches for TEs. The detected TEs are automatically analyzed, compared to reference databases, annotated, clustered into families, and stored in TEs repository. Also, the genome-wide nesting structure of found elements are detected and analyzed by new method for inferring evolutionary history of TEs. We illustrate the functionality of our tool by performing a full-scale analyses of TE landscape in Medicago truncatula genome. TRANScendence is an effective tool for the de-novo annotation and classification of transposable elements in newly-acquired genomes. Its streamlined interface makes it well-suited for evolutionary studies.

Tools for Administration of a UNIX-Based Network

NASA Technical Reports Server (NTRS)

LeClaire, Stephen; Farrar, Edward

2004-01-01

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

Virtuality and efficiency - overcoming past antinomy in the remote collaboration experience

NASA Astrophysics Data System (ADS)

Fernandes, Joao; Bjorkli, Knut; Clavo, David Martin; Baron, Thomas

2010-04-01

Several recent initiatives have been put in place by the CERN IT Department to improve the user experience in remote dispersed meetings and remote collaboration at large in the LHC communities worldwide. We will present an analysis of the factors which were historically limiting the efficiency of remote dispersed meetings and describe the consequent actions which were undertaken at CERN to overcome these limitations. After giving a status update of the different equipment available at CERN to enable the virtual sessions and the various collaborative tools which are currently proposed to users, we will focus on the evolution of this market: how can the new technological trends (among others, HD videoconferencing, Telepresence, Unified Communications, etc.) impact positively the user experience and how to attain the best usage of them. Finally, by projecting ourselves in the future, we will give some hints as to how to answer the difficult question of selecting the next generation of collaborative tools: which set of tools among the various offers (systems like Vidyo H264 SVC, next generation EVO, Groupware offers, standard H323 systems, etc.) is best suited for our environment and how to unify this set for the common user. This will finally allow us to definitively overcome the past antinomy between virtuality and efficiency.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Enabling end-user network monitoring via the multicast consolidated proxy monitor

NASA Astrophysics Data System (ADS)

Kanwar, Anshuman; Almeroth, Kevin C.; Bhattacharyya, Supratik; Davy, Matthew

2001-07-01

The debugging of problems in IP multicast networks relies heavily on an eclectic set of stand-alone tools. These tools traditionally neither provide a consistent interface nor do they generate readily interpretable results. We propose the ``Multicast Consolidated Proxy Monitor''(MCPM), an integrated system for collecting, analyzing and presenting multicast monitoring results to both the end user and the network operator at the user's Internet Service Provider (ISP). The MCPM accesses network state information not normally visible to end users and acts as a proxy for disseminating this information. Functionally, through this architecture, we aim to a) provide a view of the multicast network at varying levels of granularity, b) provide end users with a limited ability to query the multicast infrastructure in real time, and c) protect the infrastructure from overwhelming amount of monitoring load through load control. Operationally, our scheme allows scaling to the ISPs dimensions, adaptability to new protocols (introduced as multicast evolves), threshold detection for crucial parameters and an access controlled, customizable interface design. Although the multicast scenario is used to illustrate the benefits of consolidated monitoring, the ultimate aim is to scale the scheme to unicast IP networks.

phylo-node: A molecular phylogenetic toolkit using Node.js.

PubMed

O'Halloran, Damien M

2017-01-01

Node.js is an open-source and cross-platform environment that provides a JavaScript codebase for back-end server-side applications. JavaScript has been used to develop very fast and user-friendly front-end tools for bioinformatic and phylogenetic analyses. However, no such toolkits are available using Node.js to conduct comprehensive molecular phylogenetic analysis. To address this problem, I have developed, phylo-node, which was developed using Node.js and provides a stable and scalable toolkit that allows the user to perform diverse molecular and phylogenetic tasks. phylo-node can execute the analysis and process the resulting outputs from a suite of software options that provides tools for read processing and genome alignment, sequence retrieval, multiple sequence alignment, primer design, evolutionary modeling, and phylogeny reconstruction. Furthermore, phylo-node enables the user to deploy server dependent applications, and also provides simple integration and interoperation with other Node modules and languages using Node inheritance patterns, and a customized piping module to support the production of diverse pipelines. phylo-node is open-source and freely available to all users without sign-up or login requirements. All source code and user guidelines are openly available at the GitHub repository: https://github.com/dohalloran/phylo-node.

OLTARIS: On-Line Tool for the Assessment of Radiation in Space

NASA Technical Reports Server (NTRS)

Singleterry, Robert C., Jr.; Blattnig, Steve R.; Clowdsley, Martha S.; Qualls, Garry D.; Sandridge, Christopher A.; Simonsen, Lisa C.; Norbury, John W.; Slaba, Tony C.; Walker, Steven A.; Badavi, Francis F.;

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters

PubMed Central

Ono, Keiichiro; Demchak, Barry; Ideker, Trey

2014-01-01

In this paper we present new data export modules for Cytoscape 3 that can generate network files for Cytoscape.js and D3.js. Cytoscape.js exporter is implemented as a core feature of Cytoscape 3, and D3.js exporter is available as a Cytoscape 3 app. These modules enable users to seamlessly export network and table data sets generated in Cytoscape to popular JavaScript library readable formats. In addition, we implemented template web applications for browser-based interactive network visualization that can be used as basis for complex data visualization applications for bioinformatics research. Example web applications created with these tools demonstrate how Cytoscape works in modern data visualization workflows built with traditional desktop tools and emerging web-based technologies. This interactivity enables researchers more flexibility than with static images, thereby greatly improving the quality of insights researchers can gain from them. PMID:25520778

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters.

PubMed

Ono, Keiichiro; Demchak, Barry; Ideker, Trey

2014-01-01

In this paper we present new data export modules for Cytoscape 3 that can generate network files for Cytoscape.js and D3.js. Cytoscape.js exporter is implemented as a core feature of Cytoscape 3, and D3.js exporter is available as a Cytoscape 3 app. These modules enable users to seamlessly export network and table data sets generated in Cytoscape to popular JavaScript library readable formats. In addition, we implemented template web applications for browser-based interactive network visualization that can be used as basis for complex data visualization applications for bioinformatics research. Example web applications created with these tools demonstrate how Cytoscape works in modern data visualization workflows built with traditional desktop tools and emerging web-based technologies. This interactivity enables researchers more flexibility than with static images, thereby greatly improving the quality of insights researchers can gain from them.

Use Cases for Combining Web Services with ArcPython Tools for Enabling Quality Control of Land Remote Sensing Data Products.

NASA Astrophysics Data System (ADS)

Krehbiel, C.; Maiersperger, T.; Friesz, A.; Harriman, L.; Quenzer, R.; Impecoven, K.

2016-12-01

Three major obstacles facing big Earth data users include data storage, management, and analysis. As the amount of satellite remote sensing data increases, so does the need for better data storage and management strategies to exploit the plethora of data now available. Standard GIS tools can help big Earth data users whom interact with and analyze increasingly large and diverse datasets. In this presentation we highlight how NASA's Land Processes Distributed Active Archive Center (LP DAAC) is tackling these big Earth data challenges. We provide a real life use case example to describe three tools and services provided by the LP DAAC to more efficiently exploit big Earth data in a GIS environment. First, we describe the Open-source Project for a Network Data Access Protocol (OPeNDAP), which calls to specific data, minimizing the amount of data that a user downloads and improves the efficiency of data downloading and processing. Next, we cover the LP DAAC's Application for Extracting and Exploring Analysis Ready Samples (AppEEARS), a web application interface for extracting and analyzing land remote sensing data. From there, we review an ArcPython toolbox that was developed to provide quality control services to land remote sensing data products. Locating and extracting specific subsets of larger big Earth datasets improves data storage and management efficiency for the end user, and quality control services provides a straightforward interpretation of big Earth data. These tools and services are beneficial to the GIS user community in terms of standardizing workflows and improving data storage, management, and analysis tactics.

A metadata reporting framework for standardization and synthesis of ecohydrological field observations

NASA Astrophysics Data System (ADS)

Christianson, D. S.; Varadharajan, C.; Detto, M.; Faybishenko, B.; Gimenez, B.; Jardine, K.; Negron Juarez, R. I.; Pastorello, G.; Powell, T.; Warren, J.; Wolfe, B.; McDowell, N. G.; Kueppers, L. M.; Chambers, J.; Agarwal, D.

2016-12-01

The U.S. Department of Energy's (DOE) Next Generation Ecosystem Experiment (NGEE) Tropics project aims to develop a process-rich tropical forest ecosystem model that is parameterized and benchmarked by field observations. Thus, data synthesis, quality assurance and quality control (QA/QC), and data product generation of a diverse and complex set of ecohydrological observations, including sapflux, leaf surface temperature, soil water content, and leaf gas exchange from sites across the Tropics, are required to support model simulations. We have developed a metadata reporting framework, implemented in conjunction with the NGEE Tropics Data Archive tool, to enable cross-site and cross-method comparison, data interpretability, and QA/QC. We employed a modified User-Centered Design approach, which involved short development cycles based on user-identified needs, and iterative testing with data providers and users. The metadata reporting framework currently has been implemented for sensor-based observations and leverages several existing metadata protocols. The framework consists of templates that define a multi-scale measurement position hierarchy, descriptions of measurement settings, and details about data collection and data file organization. The framework also enables data providers to define data-access permission settings, provenance, and referencing to enable appropriate data usage, citation, and attribution. In addition to describing the metadata reporting framework, we discuss tradeoffs and impressions from both data providers and users during the development process, focusing on the scalability, usability, and efficiency of the framework.

Applying a Data Stewardship Maturity Matrix to the NOAA Observing System Portfolio Integrated Assessment Process

NASA Astrophysics Data System (ADS)

Peng, G.; Austin, M.

2017-12-01

Identification and prioritization of targeted user community needs are not always considered until after data has been created and archived. Gaps in data curation and documentation in the data production and delivery phases limit data's broad utility specifically for decision makers. Expert understanding and knowledge of a particular dataset is often required as a part of the data and metadata curation process to establish the credibility of the data and support informed decision-making. To enhance curation practices, content from NOAA's Observing System Integrated Assessment (NOSIA) Value Tree, NOAA's Data Catalog/Digital Object Identifier (DOI) projects (collection-level metadata) have been integrated with Data/Stewardship Maturity Matrices (data and stewardship quality information) focused on assessment of user community needs. This results in user focused evidence based decision making tools created by NOAA's National Environmental Satellite, Data, and Information Service (NESDIS) through identification and assessment of data content gaps related to scientific knowledge and application to key areas of societal benefit. Through enabling user need feedback from the beginning of data creation through archive allows users to determine the quality and value of data that is fit for purpose. Data gap assessment and prioritization are presented in a user-friendly way using the data stewardship maturity matrices as measurement of data management quality. These decision maker tools encourages data producers and data providers/stewards to consider users' needs prior to data creation and dissemination resulting in user driven data requirements increasing return on investment. A use case focused on need for NOAA observations linked societal benefit will be used to demonstrate the value of these tools.

Online, Interactive Option Grid Patient Decision Aids and their Effect on User Preferences.

PubMed

Scalia, Peter; Durand, Marie-Anne; Kremer, Jan; Faber, Marjan; Elwyn, Glyn

2018-01-01

Randomized trials have shown that patient decision aids can modify users' preferred healthcare options, but research has yet to identify the attributes embedded in these tools that cause preferences to shift. The aim of this study was to investigate people's preferences as they used decision aids for 5 health decisions and, for each of the following: 1) determine if using the interactive Option Grid led to a pre-post shift in preferences; 2) determine which frequently asked questions (FAQs) led to preference shifts; 3) determine the FAQs that were rated as the most important as users compared options. Interactive Option Grid decision aids enable users to view attributes of available treatment or screening options, rate their importance, and specify their preferred options before and after decision aid use. The McNemar-Bowker paired test was used to compare stated pre-post preferences. Multinomial logistic regressions were conducted to investigate possible associations between covariates and preference shifts. Overall, 626 users completed the 5 most-used tools: 1) Amniocentesis test: yes or no? ( n = 73); 2) Angina: treatment options ( n = 88); 3) Breast cancer: surgical options ( n = 265); 4) Prostate Specific Antigen (PSA) test: yes or no? ( n = 82); 5) Statins for heart disease risk: yes or no? ( n = 118). The breast cancer, PSA, and statins Option Grid decision aids generated significant preference shifts. Generally, users shifted their preference when presented with the description of the available treatment options, and the risk associated with each option. The use of decision aids for some, but not all health decisions, was accompanied by a shift in user preferences. Users typically valued information associated with risks, and chose more risk averse options after completing the interactive tool.

Applications of the pipeline environment for visual informatics and genomics computations

PubMed Central

2011-01-01

Background Contemporary informatics and genomics research require efficient, flexible and robust management of large heterogeneous data, advanced computational tools, powerful visualization, reliable hardware infrastructure, interoperability of computational resources, and detailed data and analysis-protocol provenance. The Pipeline is a client-server distributed computational environment that facilitates the visual graphical construction, execution, monitoring, validation and dissemination of advanced data analysis protocols. Results This paper reports on the applications of the LONI Pipeline environment to address two informatics challenges - graphical management of diverse genomics tools, and the interoperability of informatics software. Specifically, this manuscript presents the concrete details of deploying general informatics suites and individual software tools to new hardware infrastructures, the design, validation and execution of new visual analysis protocols via the Pipeline graphical interface, and integration of diverse informatics tools via the Pipeline eXtensible Markup Language syntax. We demonstrate each of these processes using several established informatics packages (e.g., miBLAST, EMBOSS, mrFAST, GWASS, MAQ, SAMtools, Bowtie) for basic local sequence alignment and search, molecular biology data analysis, and genome-wide association studies. These examples demonstrate the power of the Pipeline graphical workflow environment to enable integration of bioinformatics resources which provide a well-defined syntax for dynamic specification of the input/output parameters and the run-time execution controls. Conclusions The LONI Pipeline environment http://pipeline.loni.ucla.edu provides a flexible graphical infrastructure for efficient biomedical computing and distributed informatics research. The interactive Pipeline resource manager enables the utilization and interoperability of diverse types of informatics resources. The Pipeline client-server model provides computational power to a broad spectrum of informatics investigators - experienced developers and novice users, user with or without access to advanced computational-resources (e.g., Grid, data), as well as basic and translational scientists. The open development, validation and dissemination of computational networks (pipeline workflows) facilitates the sharing of knowledge, tools, protocols and best practices, and enables the unbiased validation and replication of scientific findings by the entire community. PMID:21791102

Science opportunity analyzer - a multi-mission tool for planning

NASA Technical Reports Server (NTRS)

Streiffert, B. A.; Polanskey, C. A.; O'Reilly, T.; Colwell, J.

2002-01-01

For many years the diverse scientific community that supports JPL's wide variety ofinterplanetary space missions has needed a tool in order to plan and develop their experiments. The tool needs to be easily adapted to various mission types and portable to the user community. The Science Opportunity Analyzer, SOA, now in its third year of development, is intended to meet this need. SOA is a java-based application that is designed to enable scientists to identify and analyze opportunities for science observations from spacecraft. It differs from other planning tools in that it does not require an in-depth knowledge of the spacecraft command system or operation modes to begin high level planning. Users can, however, develop increasingly detailed levels of design. SOA consists of six major functions: Opportunity Search, Visualization, Observation Design, Constraint Checking, Data Output and Communications. Opportunity Search is a GUI driven interface to existing search engines that can be used to identify times when a spacecraft is in a specific geometrical relationship with other bodies in the solar system. This function can be used for advanced mission planning as well as for making last minute adjustments to mission sequences in response to trajectory modifications. Visualization is a key aspect of SOA. The user can view observation opportunities in either a 3D representation or as a 2D map projection. The user is given extensive flexibility to customize what is displayed in the view. Observation Design allows the user to orient the spacecraft and visualize the projection of the instrument field of view for that orientation using the same views as Opportunity Search. Constraint Checking is provided to validate various geometrical and physical aspects of an observation design. The user has the ability to easily create custom rules or to use official project-generated flight rules. This capability may also allow scientists to easily impact the cost to science if flight rule changes occur. Data Output generates information based on the spacecraft's trajectory, opportunity search results or based on a created observation. The data can be viewed either in tabular format or as a graph. Finally, SOA is unique in that it is designed to be able to communicate with a variety of existing planning and sequencing tools. From the very beginning SOA was designed with the user in mind. Extensive surveys of the potential user community were conducted in order to develop the software requirements. Throughout the development period, close ties have been maintained with the science community to insure that the tool maintains its user focus. Although development is still in its early stages, SOA is already developing a user community on the Cassini project, which is depending on this tool for their science planning. There are other tools at JPL that do various pieces of what SOA can do; however, there is no other tool which combines all these functions and presents them to the user in such a convenient, cohesive, and easy to use fashion.

Visualization and interaction tools for aerial photograph mosaics

NASA Astrophysics Data System (ADS)

Fernandes, João Pedro; Fonseca, Alexandra; Pereira, Luís; Faria, Adriano; Figueira, Helder; Henriques, Inês; Garção, Rita; Câmara, António

1997-05-01

This paper describes the development of a digital spatial library based on mosaics of digital orthophotos, called Interactive Portugal, that will enable users both to retrieve geospatial information existing in the Portuguese National System for Geographic Information World Wide Web server, and to develop local databases connected to the main system. A set of navigation, interaction, and visualization tools are proposed and discussed. They include sketching, dynamic sketching, and navigation capabilities over the digital orthophotos mosaics. Main applications of this digital spatial library are pointed out and discussed, namely for education, professional, and tourism markets. Future developments are considered. These developments are related to user reactions, technological advancements, and projects that also aim at delivering and exploring digital imagery on the World Wide Web. Future capabilities for site selection and change detection are also considered.

A New Architecture for Extending the Capabilities of the Copernicus Trajectory Optimization Program

NASA Technical Reports Server (NTRS)

Williams, Jacob

2015-01-01

This paper describes a new plugin architecture developed for the Copernicus spacecraft trajectory optimization program. Details of the software architecture design and development are described, as well as examples of how the capability can be used to extend the tool in order to expand the type of trajectory optimization problems that can be solved. The inclusion of plugins is a significant update to Copernicus, allowing user-created algorithms to be incorporated into the tool for the first time. The initial version of the new capability was released to the Copernicus user community with version 4.1 in March 2015, and additional refinements and improvements were included in the recent 4.2 release. It is proving quite useful, enabling Copernicus to solve problems that it was not able to solve before.

Felyx : A Free Open Software Solution for the Analysis of Large Earth Observation Datasets

NASA Astrophysics Data System (ADS)

Piolle, Jean-Francois; Shutler, Jamie; Poulter, David; Guidetti, Veronica; Donlon, Craig

2014-05-01

GHRSST project, by assembling large collections of earth observation data from various sources and agencies, has also raised the need for providing the user community with tools to inter-compare them, assess and monitor their quality. The ESA /Medspiration project, which implemented the first operating node of GHRSST system for Europe, also paved the way successfully towards such generic analytics tools by developing the High Resolution Diagnostic Dataset System (HR-DDS) and Satellite to In situ Multi-sensor Match-up Databases. Building on this heritage, ESA is now funding the development by IFREMER, PML and Pelamis of felyx, a web tool merging the two capabilities into a single software solution. It will consist in a free open software solution, written in python and javascript, whose aim is to provide Earth Observation data producers and users with an open-source, flexible and reusable tool to allow the quality and performance of data streams (satellite, in situ and model) to be easily monitored and studied. The primary concept of Felyx is to work as an extraction tool, subsetting source data over predefined target areas (which can be static or moving) : these data subsets, and associated metrics, can then be accessed by users or client applications either as raw files, automatic alerts and reports generated periodically, or through a flexible web interface enabling statistical analysis and visualization. Felyx presents itself as an open-source suite of tools, written in python and javascript, enabling : * subsetting large local or remote collections of Earth Observation data over predefined sites (geographical boxes) or moving targets (ship, buoy, hurricane), storing locally the extracted data (refered as miniProds). These miniProds constitute a much smaller representative subset of the original collection on which one can perform any kind of processing or assessment without having to cope with heavy volumes of data. * computing statistical metrics over these miniProds using for instance a set of usual statistical operators (mean, median, rms, ...), fully extensible and applicable to any variable of a dataset. These metrics are stored in a fast search engine, queryable by humans and automated applications. * reporting or alerting, based on user-defined inference rules, through various media (emails, twitter feeds,..) and devices (phones, tablets). * analysing miniProds and metrics through a web interface allowing to dig into this base of information and extracting useful knowledge through multidimensional interactive display functions (time series, scatterplots, histograms, maps). The services provided by felyx will be generic, deployable at users own premises and adaptable enough to integrate any kind of parameters. Users will be able to operate their own felyx instance at any location, on datasets and parameters of their own interest, and the various instances will be able to interact with each other, creating a web of felyx systems enabling aggregation and cross comparison of miniProds and metrics from multiple sources. Initially two instances will be operated simultaneously during a 6 months demonstration phase, at IFREMER - on sea surface temperature (for GHRSST community) and ocean waves datasets - and PML - on ocean colour. We will present results from the Felyx project, demonstrate how the GHRSST community can exploit Felyx and demonstrate how the wider community can make use of the GHRSST data within Felyx.

Sleuths Seek Secrets of High-Flying Schools

ERIC Educational Resources Information Center

Olson, Lynn

2005-01-01

This article reports on the increasing attempts to identify what have been dubbed high-flying schools and figure out what makes them tick to bring all students to higher levels of achievement. A free Web site, launched by the New York City-based Standard & Poor's, began providing a tool that enables users to identify schools that do better…

Equations with Technology: Different Tools, Different Views

ERIC Educational Resources Information Center

Drijvers, Paul; Barzel, Barbel

2012-01-01

Has technology revolutionised the mathematics classroom, or is it still a device waiting to be exploited for the benefit of the learner? There are applets that will enable the user to solve complex equations at the push of a button. So, does this jeopardise other methods, make other methods redundant, or even diminish other methods in the mind of…

Real English: A Translator to Enable Natural Language Man-Machine Conversation.

ERIC Educational Resources Information Center

Gautin, Harvey

This dissertation presents a pragmatic interpreter/translator called Real English to serve as a natural language man-machine communication interface in a multi-mode on-line information retrieval system. This multi-mode feature affords the user a library-like searching tool by giving him access to a dictionary, lexicon, thesaurus, synonym table,…

The Acquisition of Skill and Expertise in Massively Multiplayer Online Games

ERIC Educational Resources Information Center

Schrader, P. G.; McCreery, Michael

2008-01-01

Educational learning environments have changed dramatically in the last 20 years. Advances in technology have enabled the World Wide Web and a sundry of other tools. In response, many researchers have argued that one way to understand learning in a complex world is to examine user interactions within Massively Multiplayer Online Games (MMOGs) [Gee…

State-based verification of RTCP-nets with nuXmv

NASA Astrophysics Data System (ADS)

Biernacka, Agnieszka; Biernacki, Jerzy; Szpyrka, Marcin

2015-12-01

The paper deals with an algorithm of translation of RTCP-nets' (real-time coloured Petri nets) coverability graphs into nuXmv state machines. The approach enables users to verify RTCP-nets with model checking techniques provided by the nuXmv tool. Full details of the algorithm are presented and an illustrative example of the approach usefulness is provided.

NASA EOSDIS: Enabling Science by Improving User Knowledge

NASA Technical Reports Server (NTRS)

Lindsay, Francis; Brennan, Jennifer; Blumenfeld, Joshua

2016-01-01

Lessons learned and impacts of applying these newer methods are explained and include several examples from our current efforts such as the interactive, on-line webinars focusing on data discovery and access including tool usage, informal and informative data chats with data experts across our EOSDIS community, data user profile interviews with scientists actively using EOSDIS data in their research, and improved conference and meeting interactions via EOSDIS data interactively used during hyper-wall talks and Worldview application. The suite of internet-based, interactive capabilities and technologies has allowed our project to expand our user community by making the data and applications from numerous Earth science missions more engaging, approachable and meaningful.

Extensible Computational Chemistry Environment

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

2012-08-09

ECCE provides a sophisticated graphical user interface, scientific visualization tools, and the underlying data management framework enabling scientists to efficiently set up calculations and store, retrieve, and analyze the rapidly growing volumes of data produced by computational chemistry studies. ECCE was conceived as part of the Environmental Molecular Sciences Laboratory construction to solve the problem of researchers being able to effectively utilize complex computational chemistry codes and massively parallel high performance compute resources. Bringing the power of these codes and resources to the desktops of researcher and thus enabling world class research without users needing a detailed understanding of themore » inner workings of either the theoretical codes or the supercomputers needed to run them was a grand challenge problem in the original version of the EMSL. ECCE allows collaboration among researchers using a web-based data repository where the inputs and results for all calculations done within ECCE are organized. ECCE is a first of kind end-to-end problem solving environment for all phases of computational chemistry research: setting up calculations with sophisticated GUI and direct manipulation visualization tools, submitting and monitoring calculations on remote high performance supercomputers without having to be familiar with the details of using these compute resources, and performing results visualization and analysis including creating publication quality images. ECCE is a suite of tightly integrated applications that are employed as the user moves through the modeling process.« less

Improving Patient Experience and Primary Care Quality for Patients With Complex Chronic Disease Using the Electronic Patient-Reported Outcomes Tool: Adopting Qualitative Methods Into a User-Centered Design Approach

PubMed Central

Khan, Anum Irfan; Kuluski, Kerry; McKillop, Ian; Sharpe, Sarah; Bierman, Arlene S; Lyons, Renee F; Cott, Cheryl

2016-01-01

Background Many mHealth technologies do not meet the needs of patients with complex chronic disease and disabilities (CCDDs) who are among the highest users of health systems worldwide. Furthermore, many of the development methodologies used in the creation of mHealth and eHealth technologies lack the ability to embrace users with CCDD in the specification process. This paper describes how we adopted and modified development techniques to create the electronic Patient-Reported Outcomes (ePRO) tool, a patient-centered mHealth solution to help improve primary health care for patients experiencing CCDD. Objective This paper describes the design and development approach, specifically the process of incorporating qualitative research methods into user-centered design approaches to create the ePRO tool. Key lessons learned are offered as a guide for other eHealth and mHealth research and technology developers working with complex patient populations and their primary health care providers. Methods Guided by user-centered design principles, interpretive descriptive qualitative research methods were adopted to capture user experiences through interviews and working groups. Consistent with interpretive descriptive methods, an iterative analysis technique was used to generate findings, which were then organized in relation to the tool design and function to help systematically inform modifications to the tool. User feedback captured and analyzed through this method was used to challenge the design and inform the iterative development of the tool. Results Interviews with primary health care providers (n=7) and content experts (n=6), and four focus groups with patients and carers (n=14) along with a PICK analysis—Possible, Implementable, (to be) Challenged, (to be) Killed—guided development of the first prototype. The initial prototype was presented in three design working groups with patients/carers (n=5), providers (n=6), and experts (n=5). Working group findings were broken down into categories of what works and what does not work to inform modifications to the prototype. This latter phase led to a major shift in the purpose and design of the prototype, validating the importance of using iterative codesign processes. Conclusions Interpretive descriptive methods allow for an understanding of user experiences of patients with CCDD, their carers, and primary care providers. Qualitative methods help to capture and interpret user needs, and identify contextual barriers and enablers to tool adoption, informing a redesign to better suit the needs of this diverse user group. This study illustrates the value of adopting interpretive descriptive methods into user-centered mHealth tool design and can also serve to inform the design of other eHealth technologies. Our approach is particularly useful in requirements determination when developing for a complex user group and their health care providers. PMID:26892952

SWATShare- A Platform for Collaborative Hydrology Research and Education with Cyber-enabled Sharing, Running and Visualization of SWAT Models

NASA Astrophysics Data System (ADS)

Rajib, M. A.; Merwade, V.; Song, C.; Zhao, L.; Kim, I. L.; Zhe, S.

2014-12-01

Setting up of any hydrologic model requires a large amount of efforts including compilation of all the data, creation of input files, calibration and validation. Given the amount of efforts involved, it is possible that models for a watershed get created multiple times by multiple groups or organizations to accomplish different research, educational or policy goals. To reduce the duplication of efforts and enable collaboration among different groups or organizations around an already existing hydrology model, a platform is needed where anyone can search for existing models, perform simple scenario analysis and visualize model results. The creator and users of a model on such a platform can then collaborate to accomplish new research or educational objectives. From this perspective, a prototype cyber-infrastructure (CI), called SWATShare, is developed for sharing, running and visualizing Soil Water Assessment Tool (SWAT) models in an interactive GIS-enabled web environment. Users can utilize SWATShare to publish or upload their own models, search and download existing SWAT models developed by others, run simulations including calibration using high performance resources provided by XSEDE and Cloud. Besides running and sharing, SWATShare hosts a novel spatio-temporal visualization system for SWAT model outputs. In temporal scale, the system creates time-series plots for all the hydrology and water quality variables available along the reach as well as in watershed-level. In spatial scale, the system can dynamically generate sub-basin level thematic maps for any variable at any user-defined date or date range; and thereby, allowing users to run animations or download the data for subsequent analyses. In addition to research, SWATShare can also be used within a classroom setting as an educational tool for modeling and comparing the hydrologic processes under different geographic and climatic settings. SWATShare is publicly available at https://www.water-hub.org/swatshare.

π Scope: python based scientific workbench with visualization tool for MDSplus data

NASA Astrophysics Data System (ADS)

Shiraiwa, S.

2014-10-01

π Scope is a python based scientific data analysis and visualization tool constructed on wxPython and Matplotlib. Although it is designed to be a generic tool, the primary motivation for developing the new software is 1) to provide an updated tool to browse MDSplus data, with functionalities beyond dwscope and jScope, and 2) to provide a universal foundation to construct interface tools to perform computer simulation and modeling for Alcator C-Mod. It provides many features to visualize MDSplus data during tokamak experiments including overplotting different signals and discharges, various plot types (line, contour, image, etc.), in-panel data analysis using python scripts, and publication quality graphics generation. Additionally, the logic to produce multi-panel plots is designed to be backward compatible with dwscope, enabling smooth migration for dwscope users. πScope uses multi-threading to reduce data transfer latency, and its object-oriented design makes it easy to modify and expand while the open source nature allows portability. A built-in tree data browser allows a user to approach the data structure both from a GUI and a script, enabling relatively complex data analysis workflow to be built quickly. As an example, an IDL-based interface to perform GENRAY/CQL3D simulations was ported on πScope, thus allowing LHCD simulation to be run between-shot using C-Mod experimental profiles. This workflow is being used to generate a large database to develop a LHCD actuator model for the plasma control system. Supported by USDoE Award DE-FC02-99ER54512.

Innovating Data Discovery In NOAA OneStop By Integrating With Social Media

NASA Astrophysics Data System (ADS)

Jakositz, A.; McQuinn, E.; Delk, Z.; Shapiro, J.; Partee, R.; Richerson, E.

2017-12-01

Tasked with improving discovery of and access to NOAA data, the OneStop project has to consider a broad array of data types and end-users in the overall design. While work on the OneStop web interface and backend API is of utmost importance for enabling a variety of users to explore available NOAA data, the challenge of bringing those users to the OneStop portal in the first place remains. In this presentation, we highlight the benefits of using social media - namely YouTube - to attract users to both the data and tools existing in the NOAA realm. Furthermore, we discuss the ways in which varying data types can be discovered from the same portal, triggering different views (for instance, a streaming video), based on maintaining consistent metadata standards.

BioImageXD: an open, general-purpose and high-throughput image-processing platform.

PubMed

Kankaanpää, Pasi; Paavolainen, Lassi; Tiitta, Silja; Karjalainen, Mikko; Päivärinne, Joacim; Nieminen, Jonna; Marjomäki, Varpu; Heino, Jyrki; White, Daniel J

2012-06-28

BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes. We demonstrate its performance in a study of integrin clustering in response to selected inhibitors.

Documentation for MeshKit - Reactor Geometry (&mesh) Generator

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

Jain, Rajeev; Mahadevan, Vijay

2015-09-30

This report gives documentation for using MeshKit’s Reactor Geometry (and mesh) Generator (RGG) GUI and also briefly documents other algorithms and tools available in MeshKit. RGG is a program designed to aid in modeling and meshing of complex/large hexagonal and rectilinear reactor cores. RGG uses Argonne’s SIGMA interfaces, Qt and VTK to produce an intuitive user interface. By integrating a 3D view of the reactor with the meshing tools and combining them into one user interface, RGG streamlines the task of preparing a simulation mesh and enables real-time feedback that reduces accidental scripting mistakes that could waste hours of meshing.more » RGG interfaces with MeshKit tools to consolidate the meshing process, meaning that going from model to mesh is as easy as a button click. This report is designed to explain RGG v 2.0 interface and provide users with the knowledge and skills to pilot RGG successfully. Brief documentation of MeshKit source code, tools and other algorithms available are also presented for developers to extend and add new algorithms to MeshKit. RGG tools work in serial and parallel and have been used to model complex reactor core models consisting of conical pins, load pads, several thousands of axially varying material properties of instrumentation pins and other interstices meshes.« less

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

PubMed

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

2017-10-01

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

A voxel visualization and analysis system based on AutoCAD

NASA Astrophysics Data System (ADS)

Marschallinger, Robert

1996-05-01

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

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

NASA Astrophysics Data System (ADS)

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

2014-10-01

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

Design and development of an interactive medical teleconsultation system over the World Wide Web.

PubMed

Bai, J; Zhang, Y; Dai, B

1998-06-01

The objective of the medical teleconsultation system presented in this paper is to demonstrate the use of the World Wide Web (WWW) for telemedicine and interactive medical information exchange. The system, which is developed based on Java, could provide several basic Java tools to fulfill the requirements of medical applications, including a file manager, data tool, bulletin board, and digital audio tool. The digital audio tool uses point-to-point structure to enable two physicians to communicate directly through voice. The others use multipoint structure. The file manager manages the medical images stored in the WWW information server, which come from a hospital database. The data tool supports cooperative operations on the medical data between the participating physicians. The bulletin board enables the users to discuss special cases by writing text on the board, send their personal or group diagnostic reports on the cases, and reorganize the reports and store them in its report file for later use. The system provides a hardware-independent platform for physicians to interact with one another as well as to access medical information over the WWW.

Powered mobility intervention: understanding the position of tool use learning as part of implementing the ALP tool.

PubMed

Nilsson, Lisbeth; Durkin, Josephine

2017-10-01

To explore the knowledge necessary for adoption and implementation of the Assessment of Learning Powered mobility use (ALP) tool in different practice settings for both adults and children. To consult with a diverse population of professionals working with adults and children, in different countries and various settings; who were learning about or using the ALP tool, as part of exploring and implementing research findings. Classical grounded theory with a rigorous comparative analysis of data from informants together with reflections on our own rich experiences of powered mobility practice and comparisons with the literature. A core category learning tool use and a new theory of cognizing tool use, with its interdependent properties: motivation, confidence, permissiveness, attentiveness and co-construction has emerged which explains in greater depth what enables the application of the ALP tool. The scientific knowledge base on tool use learning and the new theory conveys the information necessary for practitioner's cognizing how to apply the learning approach of the ALP tool in order to enable tool use learning through powered mobility practice as a therapeutic intervention in its own right. This opens up the possibility for more children and adults to have access to learning through powered mobility practice. Implications for rehabilitation Tool use learning through powered mobility practice is a therapeutic intervention in its own right. Powered mobility practice can be used as a rehabilitation tool with individuals who may not need to become powered wheelchair users. Motivation, confidence, permissiveness, attentiveness and co-construction are key properties for enabling the application of the learning approach of the ALP tool. Labelling and the use of language, together with honing observational skills through viewing video footage, are key to developing successful learning partnerships.

Phytophthora database 2.0: update and future direction.

PubMed

Park, Bongsoo; Martin, Frank; Geiser, David M; Kim, Hye-Seon; Mansfield, Michele A; Nikolaeva, Ekaterina; Park, Sook-Young; Coffey, Michael D; Russo, Joseph; Kim, Seong H; Balci, Yilmaz; Abad, Gloria; Burgess, Treena; Grünwald, Niklaus J; Cheong, Kyeongchae; Choi, Jaeyoung; Lee, Yong-Hwan; Kang, Seogchan

2013-12-01

The online community resource Phytophthora database (PD) was developed to support accurate and rapid identification of Phytophthora and to help characterize and catalog the diversity and evolutionary relationships within the genus. Since its release in 2008, the sequence database has grown to cover 1 to 12 loci for ≈2,600 isolates (representing 138 described and provisional species). Sequences of multiple mitochondrial loci were added to complement nuclear loci-based phylogenetic analyses and diagnostic tool development. Key characteristics of most newly described and provisional species have been summarized. Other additions to improve the PD functionality include: (i) geographic information system tools that enable users to visualize the geographic origins of chosen isolates on a global-scale map, (ii) a tool for comparing genetic similarity between isolates via microsatellite markers to support population genetic studies, (iii) a comprehensive review of molecular diagnostics tools and relevant references, (iv) sequence alignments used to develop polymerase chain reaction-based diagnostics tools to support their utilization and new diagnostic tool development, and (v) an online community forum for sharing and preserving experience and knowledge accumulated in the global Phytophthora community. Here we present how these improvements can support users and discuss the PD's future direction.

Deploying the ODISEES Ontology-guided Search in the NASA Earth Exchange (NEX)

NASA Astrophysics Data System (ADS)

Huffer, E.; Gleason, J. L.; Cotnoir, M.; Spaulding, R.; Deardorff, G.

2016-12-01

Robust, semantically rich metadata can support data discovery and access, and facilitate machine-to-machine transactions with services such as data subsetting, regridding, and reformatting. Despite this, for users not already familiar with the data in a given archive, most metadata is insufficient to help them find appropriate data for their projects. With this in mind, the Ontology-driven Interactive Search Environment (ODISEES) Data Discovery Portal was developed to enable users to find and download data variables that satisfy precise, parameter-level criteria, even when they know little or nothing about the naming conventions employed by data providers, or where suitable data might be archived. ODISEES relies on an Earth science ontology and metadata repository that provide an ontological framework for describing NASA data holdings with enough detail and fidelity to enable researchers to find, compare and evaluate individual data variables. Users can search for data by indicating the specific parameters desired, and comparing the results in a table that lets them quickly determine which data is most suitable. ODISEES and OLYMPUS, a tool for generating the semantically enhanced metadata used by ODISEES, are being developed in collaboration with the NASA Earth Exchange (NEX) project at the NASA Ames Research Center to prototype a robust data discovery and access service that could be made available to NEX users. NEX is a collaborative platform that provides researchers with access to TB to PB-scale datasets and analysis tools to operate on those data. By integrating ODISEES into the NEX Web Portal we hope to enable NEX users to locate datasets relevant to their research and download them directly into the NAS environment, where they can run applications using those datasets on the NAS supercomputers. This poster will describe the prototype integration of ODISEES into the NEX portal development environment, the mechanism implemented to use NASA APIs to retrieve data, and the approach to transfer data into the NAS supercomputing environment. Finally, we will describe the end-to-end demonstration of the capabilities implemented. This work was funded by the Advanced Information Systems Technology Program of NASA's Research Opportunities in Space and Earth Science.

imDEV: a graphical user interface to R multivariate analysis tools in Microsoft Excel

PubMed Central

Grapov, Dmitry; Newman, John W.

2012-01-01

Summary: Interactive modules for Data Exploration and Visualization (imDEV) is a Microsoft Excel spreadsheet embedded application providing an integrated environment for the analysis of omics data through a user-friendly interface. Individual modules enables interactive and dynamic analyses of large data by interfacing R's multivariate statistics and highly customizable visualizations with the spreadsheet environment, aiding robust inferences and generating information-rich data visualizations. This tool provides access to multiple comparisons with false discovery correction, hierarchical clustering, principal and independent component analyses, partial least squares regression and discriminant analysis, through an intuitive interface for creating high-quality two- and a three-dimensional visualizations including scatter plot matrices, distribution plots, dendrograms, heat maps, biplots, trellis biplots and correlation networks. Availability and implementation: Freely available for download at http://sourceforge.net/projects/imdev/. Implemented in R and VBA and supported by Microsoft Excel (2003, 2007 and 2010). Contact: John.Newman@ars.usda.gov Supplementary Information: Installation instructions, tutorials and users manual are available at http://sourceforge.net/projects/imdev/. PMID:22815358

STITCHER 2.0: primer design for overlapping PCR applications

PubMed Central

O’Halloran, Damien M.; Uriagereka-Herburger, Isabel; Bode, Katrin

2017-01-01

Overlapping polymerase chain reaction (PCR) is a common technique used by researchers in very diverse fields that enables the user to ‘stitch’ individual pieces of DNA together. Previously, we have reported a web based tool called STITCHER that provides a platform for researchers to automate the design of primers for overlapping PCR applications. Here we present STITCHER 2.0, which represents a substantial update to STITCHER. STITCHER 2.0 is a newly designed web tool that automates the design of primers for overlapping PCR. Unlike STITCHER, STITCHER 2.0 considers diverse algorithmic parameters, and returns multiple result files that include a facility for the user to draw their own primers as well as comprehensive visual guides to the user’s input, output, and designed primers. These result files provide greater control and insight during experimental design and troubleshooting. STITCHER 2.0 is freely available to all users without signup or login requirements and can be accessed at the following webpage: www.ohalloranlab.net/STITCHER2.html. PMID:28358011

Updates to the Demographic and Spatial Allocation Models to ...

EPA Pesticide Factsheets

EPA announced the availability of the draft report, Updates to the Demographic and Spatial Allocation Models to Produce Integrated Climate and Land Use Scenarios (ICLUS) for a 30-day public comment period. The ICLUS version 2 (v2) modeling tool furthered land change modeling by providing nationwide housing development scenarios up to 2100. ICLUS V2 includes updated population and land use data sets and addressing limitations identified in ICLUS v1 in both the migration and spatial allocation models. The companion user guide describes the development of ICLUS v2 and the updates that were made to the original data sets and the demographic and spatial allocation models. [2017 UPDATE] Get the latest version of ICLUS and stay up-to-date by signing up to the ICLUS mailing list. The GIS tool enables users to run SERGoM with the population projections developed for the ICLUS project and allows users to modify the spatial allocation housing density across the landscape.

Using the Browser for Science: A Collaborative Toolkit for Astronomy

NASA Astrophysics Data System (ADS)

Connolly, A. J.; Smith, I.; Krughoff, K. S.; Gibson, R.

2011-07-01

Astronomical surveys have yielded hundreds of terabytes of catalogs and images that span many decades of the electromagnetic spectrum. Even when observatories provide user-friendly web interfaces, exploring these data resources remains a complex and daunting task. In contrast, gadgets and widgets have become popular in social networking (e.g. iGoogle, Facebook). They provide a simple way to make complex data easily accessible that can be customized based on the interest of the user. With ASCOT (an AStronomical COllaborative Toolkit) we expand on these concepts to provide a customizable and extensible gadget framework for use in science. Unlike iGoogle, where all of the gadgets are independent, the gadgets we develop communicate and share information, enabling users to visualize and interact with data through multiple, simultaneous views. With this approach, web-based applications for accessing and visualizing data can be generated easily and, by linking these tools together, integrated and powerful data analysis and discovery tools can be constructed.

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

PubMed Central

Palviainen, Marko; Kuusijärvi, Jarkko; Ovaska, Eila

2012-01-01

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

Data-Driven Software Framework for Web-Based ISS Telescience

NASA Technical Reports Server (NTRS)

Tso, Kam S.

2005-01-01

Software that enables authorized users to monitor and control scientific payloads aboard the International Space Station (ISS) from diverse terrestrial locations equipped with Internet connections is undergoing development. This software reflects a data-driven approach to distributed operations. A Web-based software framework leverages prior developments in Java and Extensible Markup Language (XML) to create portable code and portable data, to which one can gain access via Web-browser software on almost any common computer. Open-source software is used extensively to minimize cost; the framework also accommodates enterprise-class server software to satisfy needs for high performance and security. To accommodate the diversity of ISS experiments and users, the framework emphasizes openness and extensibility. Users can take advantage of available viewer software to create their own client programs according to their particular preferences, and can upload these programs for custom processing of data, generation of views, and planning of experiments. The same software system, possibly augmented with a subset of data and additional software tools, could be used for public outreach by enabling public users to replay telescience experiments, conduct their experiments with simulated payloads, and create their own client programs and other custom software.

Fact Sheets of CTAS and NASA Decision-Support Tools and Concepts

NASA Technical Reports Server (NTRS)

Lee, Katharine

2004-01-01

Distributed Air/Ground (DAG) Traffic Management (TM) is an integrated operational concept in which flight deck crews, air traffic service providers and aeronautical operational control personnel use distributed decision-making to enable user preferences and increase system capacity, while meeting air traffic management (ATM) requirements. It is a possible operational mode under the Free Flight concept outlined by the RTCA Task Force 3. The goal of DAG-TM is to enhance user flexibility/efficiency and increase system capacity, without adversely affecting system safety or restricting user accessibility to the National Airspace System (NAS). DAG-TM will be accomplished with a human-centered operational paradigm enabled by procedural and technological innovations. These innovations include automation aids, information sharing and Communication, Navigation, and Surveillance (CNS) / ATM technologies. The DAG-TM concept is intended to eliminate static restrictions to the maximum extent possible. In this paradigm, users may plan and operate according to their preferences - as the rule rather than the exception - with deviations occumng eyond the year 2015. Out of a total of 15 concept elements, 4 have been selected for initial sutidies (see Key Elements in sidebar). DAG-TM research is being performed at Ames, Glenn, and Langley Research Centers.

PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments.

PubMed

Usadel, Björn; Nagel, Axel; Steinhauser, Dirk; Gibon, Yves; Bläsing, Oliver E; Redestig, Henning; Sreenivasulu, Nese; Krall, Leonard; Hannah, Matthew A; Poree, Fabien; Fernie, Alisdair R; Stitt, Mark

2006-12-18

Microarray technology has become a widely accepted and standardized tool in biology. The first microarray data analysis programs were developed to support pair-wise comparison. However, as microarray experiments have become more routine, large scale experiments have become more common, which investigate multiple time points or sets of mutants or transgenics. To extract biological information from such high-throughput expression data, it is necessary to develop efficient analytical platforms, which combine manually curated gene ontologies with efficient visualization and navigation tools. Currently, most tools focus on a few limited biological aspects, rather than offering a holistic, integrated analysis. Here we introduce PageMan, a multiplatform, user-friendly, and stand-alone software tool that annotates, investigates, and condenses high-throughput microarray data in the context of functional ontologies. It includes a GUI tool to transform different ontologies into a suitable format, enabling the user to compare and choose between different ontologies. It is equipped with several statistical modules for data analysis, including over-representation analysis and Wilcoxon statistical testing. Results are exported in a graphical format for direct use, or for further editing in graphics programs.PageMan provides a fast overview of single treatments, allows genome-level responses to be compared across several microarray experiments covering, for example, stress responses at multiple time points. This aids in searching for trait-specific changes in pathways using mutants or transgenics, analyzing development time-courses, and comparison between species. In a case study, we analyze the results of publicly available microarrays of multiple cold stress experiments using PageMan, and compare the results to a previously published meta-analysis.PageMan offers a complete user's guide, a web-based over-representation analysis as well as a tutorial, and is freely available at http://mapman.mpimp-golm.mpg.de/pageman/. PageMan allows multiple microarray experiments to be efficiently condensed into a single page graphical display. The flexible interface allows data to be quickly and easily visualized, facilitating comparisons within experiments and to published experiments, thus enabling researchers to gain a rapid overview of the biological responses in the experiments.

Using NASA's Interactive Visualization and Image Extraction Tool AppEEARS to Assess Differences between MODIS and VIIRS

NASA Astrophysics Data System (ADS)

Neeley, S.

2017-12-01

The Visible Infrared Imaging Radiometer Suite (VIIRS) sensor aboard the Suomi-NPP satellite is designed to provide data continuity with the Moderate Resolution Imaging Spectroradiometer (MODIS) sensors aboard NASA's Terra and Aqua satellites. VIIRS data products are generated in a similar format as MODIS using modified algorithms and aim to extend the data lifecycle of MODIS products, which are widely used in a variety of scientific disciplines. However, there are differences in the characteristics of the instruments that could influence decision making when conducting a study involving a combination of products from both sensors. Inter-sensor comparison studies between VIIRS and MODIS have highlighted some of the inconsistencies between the sensors, including calibrated radiances, pixel sizes, swath widths, and spectral response functions of the bands. These differences should be well-understood among the science community as these inconsistencies could potentially effect the results of time-series analyses or land change studies that rely on using VIIRS and MODIS data products in combination. An efficient method to identify and better understand differences between data products will allow for the science community to make informed decisions when conducting analyses using a combination of VIIRS and MODIS data products. NASA's Application for Extracting and Exploring Analysis Ready Samples (AppEEARS) tool enables users to efficiently compare MODIS and VIIRS data products, including surface reflectance from 2012 to present. AppEEARS is a user-friendly image extraction tool used to order spatial and temporal data subsets, reproject data, and visualize output sample results before data download. AppEEARs allows users to compare MODIS and VIIRS data products by providing interactive visualizations and summary statistics of each dataset-either over a specific point or region of interest across a period of time. This tool enhances decision-making when using newly available VIIRS products combined with MODIS as it allows for data inconsistencies to be explored before the data is downloaded. Here, we demonstrate how AppEEARS enables users to perform comparisons across VIIRS and MODIS Surface Reflectance products and provide a detailed review of characteristic differences between the instruments.

From fragments to the whole: a comparison between cochlear implant users and normal-hearing listeners in music perception and enjoyment.

PubMed

Alexander, Ashlin J; Bartel, Lee; Friesen, Lendra; Shipp, David; Chen, Joseph

2011-02-01

Cochlear implants (CIs) allow many profoundly deaf individuals to regain speech understanding. However, the ability to understand speech does not necessarily guarantee music enjoyment. Enabling a CI user to recover the ability to perceive and enjoy the complexity of music remains a challenge determined by many factors. (1) To construct a novel, attention-based, diagnostic software tool (Music EAR) for the assessment of music enjoyment and perception and (2) to compare the results among three listener groups. Thirty-six subjects completed the Music EAR assessment tool: 12 normal-hearing musicians (NHMs), 12 normal-hearing nonmusicians (NHnMs), and 12 CI listeners. Subjects were required to (1) rate enjoyment of musical excerpts at three complexity levels; (2) differentiate five instrumental timbres; (3) recognize pitch pattern variation; and (4) identify target musical patterns embedded holistically in a melody. Enjoyment scores for CI users were comparable to those for NHMs and superior to those for NHnMs and revealed that implantees enjoyed classical music most. CI users performed significantly poorer in all categories of music perception compared to normal-hearing listeners. Overall CI user scores were lowest in those tasks requiring increased attention. Two high-performing subjects matched or outperformed NHnMs in pitch and timbre perception tasks. The Music EAR assessment tool provides a unique approach to the measurement of music perception and enjoyment in CI users. Together with auditory training evidence, the results provide considerable hope for further recovery of music appreciation through methodical rehabilitation.

Collaborative Aerial-Drawing System for Supporting Co-Creative Communication

NASA Astrophysics Data System (ADS)

Osaki, Akihiro; Taniguchi, Hiroyuki; Miwa, Yoshiyuki

This paper describes the collaborative augmented reality (AR) system with which multiple users can handwrite 3D lines in the air simultaneously and manipulate the lines directly in the real world. In addition, we propose a new technique for co-creative communication utilizing the 3D drawing activity. Up to now, the various 3D user interfaces have been proposed. Although most of them aim to solve the specific problems in the virtual environments, the possibility of the 3D drawing expression has not been explored yet. Accordingly, we paid special attention to the interaction with the real objects in daily life, and considered to manipulate real objects and 3D lines without any distinctions by the same action. The developed AR system consists of a stereoscopic head-mounted display, a drawing tool, 6DOF sensors measuring three-dimensional position and Euler angles, and the 3D user interface, which enables to push, grasp and pitch 3D lines directly by use of the drawing tool. Additionally users can pick up desired color from either a landscape or a virtual line through the direct interaction with this tool. For sharing 3D lines among multiple users at the same place, the distributed-type AR system has been developed that mutually sends and receives drawn data between systems. With the developed system, users can proceed to design jointly in the real space through arranging each 3D drawing by direct manipulation. Moreover, a new application to the entertainment has become possible to play sports like catch, fencing match, or the like.

Sequencing Data Discovery and Integration for Earth System Science with MetaSeek

NASA Astrophysics Data System (ADS)

Hoarfrost, A.; Brown, N.; Arnosti, C.

2017-12-01

Microbial communities play a central role in biogeochemical cycles. Sequencing data resources from environmental sources have grown exponentially in recent years, and represent a singular opportunity to investigate microbial interactions with Earth system processes. Carrying out such meta-analyses depends on our ability to discover and curate sequencing data into large-scale integrated datasets. However, such integration efforts are currently challenging and time-consuming, with sequencing data scattered across multiple repositories and metadata that is not easily or comprehensively searchable. MetaSeek is a sequencing data discovery tool that integrates sequencing metadata from all the major data repositories, allowing the user to search and filter on datasets in a lightweight application with an intuitive, easy-to-use web-based interface. Users can save and share curated datasets, while other users can browse these data integrations or use them as a jumping off point for their own curation. Missing and/or erroneous metadata are inferred automatically where possible, and where not possible, users are prompted to contribute to the improvement of the sequencing metadata pool by correcting and amending metadata errors. Once an integrated dataset has been curated, users can follow simple instructions to download their raw data and quickly begin their investigations. In addition to the online interface, the MetaSeek database is easily queryable via an open API, further enabling users and facilitating integrations of MetaSeek with other data curation tools. This tool lowers the barriers to curation and integration of environmental sequencing data, clearing the path forward to illuminating the ecosystem-scale interactions between biological and abiotic processes.

Human Connectome Project Informatics: quality control, database services, and data visualization

PubMed Central

Marcus, Daniel S.; Harms, Michael P.; Snyder, Abraham Z.; Jenkinson, Mark; Wilson, J Anthony; Glasser, Matthew F.; Barch, Deanna M.; Archie, Kevin A.; Burgess, Gregory C.; Ramaratnam, Mohana; Hodge, Michael; Horton, William; Herrick, Rick; Olsen, Timothy; McKay, Michael; House, Matthew; Hileman, Michael; Reid, Erin; Harwell, John; Coalson, Timothy; Schindler, Jon; Elam, Jennifer S.; Curtiss, Sandra W.; Van Essen, David C.

2013-01-01

The Human Connectome Project (HCP) has developed protocols, standard operating and quality control procedures, and a suite of informatics tools to enable high throughput data collection, data sharing, automated data processing and analysis, and data mining and visualization. Quality control procedures include methods to maintain data collection consistency over time, to measure head motion, and to establish quantitative modality-specific overall quality assessments. Database services developed as customizations of the XNAT imaging informatics platform support both internal daily operations and open access data sharing. The Connectome Workbench visualization environment enables user interaction with HCP data and is increasingly integrated with the HCP's database services. Here we describe the current state of these procedures and tools and their application in the ongoing HCP study. PMID:23707591

The Application of Remotely Sensed Data and Models to Benefit Conservation and Restoration Along the Northern Gulf of Mexico Coast

NASA Astrophysics Data System (ADS)

Quattrochi, D. A.; Estes, M. G., Jr.; Al-Hamdan, M. Z.; Thom, R.; Woodruff, D.; Judd, C.; Ellis, J. T.; Swann, R.; Johnson, H., III

2010-12-01

New data, tools, and capabilities for decision making are significant needs in the northern Gulf of Mexico and other coastal areas. The goal of this project is to support NASA’s Earth Science Mission Directorate and its Applied Science Program and the Gulf of Mexico Alliance by producing and providing NASA data and products that will benefit decision making by coastal resource managers and other end users in the Gulf region. Data and research products are being developed to assist coastal resource managers adapt and plan for changing conditions by evaluating how climate changes and urban expansion will impact land cover/land use (LCLU), hydrodynamics, water properties, and shallow water habitats; to identify priority areas for conservation and restoration; and to distribute datasets to end-users and facilitating user interaction with models. The proposed host sites for data products are NOAA’s National Coastal Data Development Center Regional Ecosystem Data Management, and Mississippi-Alabama Habitat Database. Tools will be available on the Gulf of Mexico Regional Collaborative website with links to data portals to enable end users to employ models and datasets to develop and evaluate LCLU and climate scenarios of particular interest. These data will benefit the Mobile Bay National Estuary Program in ongoing efforts to protect and restore the Fish River watershed and around Weeks Bay National Estuarine Research Reserve. The usefulness of data products and tools will be demonstrated at an end-user workshop.

The Application of Remotely Sensed Data and Models to Benefit Conservation and Restoration Along the Northern Gulf of Mexico Coast

NASA Technical Reports Server (NTRS)

Quattrochi, Dale; Estes, Maurice, Jr.; Al-Hamdan, Mohammad; Thom, Ron; Woodruff, Dana; Judd, Chaeli; Ellis, Jean; Swann, Roberta; Johnson, Hoyt, III

2010-01-01

New data, tools, and capabilities for decision making are significant needs in the northern Gulf of Mexico and other coastal areas. The goal of this project is to support NASA s Earth Science Mission Directorate and its Applied Science Program and the Gulf of Mexico Alliance by producing and providing NASA data and products that will benefit decision making by coastal resource managers and other end users in the Gulf region. Data and research products are being developed to assist coastal resource managers adapt and plan for changing conditions by evaluating how climate changes and urban expansion will impact land cover/land use (LCLU), hydrodynamics, water properties, and shallow water habitats; to identify priority areas for conservation and restoration; and to distribute datasets to end-users and facilitating user interaction with models. The proposed host sites for data products are NOAA s National Coastal Data Development Center Regional Ecosystem Data Management, and Mississippi-Alabama Habitat Database. Tools will be available on the Gulf of Mexico Regional Collaborative website with links to data portals to enable end users to employ models and datasets to develop and evaluate LCLU and climate scenarios of particular interest. These data will benefit the Mobile Bay National Estuary Program in ongoing efforts to protect and restore the Fish River watershed and around Weeks Bay National Estuarine Research Reserve. The usefulness of data products and tools will be demonstrated at an end-user workshop.

Web-based tool for visualization of electric field distribution in deep-seated body structures and planning of electroporation-based treatments.

PubMed

Marčan, Marija; Pavliha, Denis; Kos, Bor; Forjanič, Tadeja; Miklavčič, Damijan

2015-01-01

Treatments based on electroporation are a new and promising approach to treating tumors, especially non-resectable ones. The success of the treatment is, however, heavily dependent on coverage of the entire tumor volume with a sufficiently high electric field. Ensuring complete coverage in the case of deep-seated tumors is not trivial and can in best way be ensured by patient-specific treatment planning. The basis of the treatment planning process consists of two complex tasks: medical image segmentation, and numerical modeling and optimization. In addition to previously developed segmentation algorithms for several tissues (human liver, hepatic vessels, bone tissue and canine brain) and the algorithms for numerical modeling and optimization of treatment parameters, we developed a web-based tool to facilitate the translation of the algorithms and their application in the clinic. The developed web-based tool automatically builds a 3D model of the target tissue from the medical images uploaded by the user and then uses this 3D model to optimize treatment parameters. The tool enables the user to validate the results of the automatic segmentation and make corrections if necessary before delivering the final treatment plan. Evaluation of the tool was performed by five independent experts from four different institutions. During the evaluation, we gathered data concerning user experience and measured performance times for different components of the tool. Both user reports and performance times show significant reduction in treatment-planning complexity and time-consumption from 1-2 days to a few hours. The presented web-based tool is intended to facilitate the treatment planning process and reduce the time needed for it. It is crucial for facilitating expansion of electroporation-based treatments in the clinic and ensuring reliable treatment for the patients. The additional value of the tool is the possibility of easy upgrade and integration of modules with new functionalities as they are developed.

Web-based tool for visualization of electric field distribution in deep-seated body structures and planning of electroporation-based treatments

PubMed Central

2015-01-01

Background Treatments based on electroporation are a new and promising approach to treating tumors, especially non-resectable ones. The success of the treatment is, however, heavily dependent on coverage of the entire tumor volume with a sufficiently high electric field. Ensuring complete coverage in the case of deep-seated tumors is not trivial and can in best way be ensured by patient-specific treatment planning. The basis of the treatment planning process consists of two complex tasks: medical image segmentation, and numerical modeling and optimization. Methods In addition to previously developed segmentation algorithms for several tissues (human liver, hepatic vessels, bone tissue and canine brain) and the algorithms for numerical modeling and optimization of treatment parameters, we developed a web-based tool to facilitate the translation of the algorithms and their application in the clinic. The developed web-based tool automatically builds a 3D model of the target tissue from the medical images uploaded by the user and then uses this 3D model to optimize treatment parameters. The tool enables the user to validate the results of the automatic segmentation and make corrections if necessary before delivering the final treatment plan. Results Evaluation of the tool was performed by five independent experts from four different institutions. During the evaluation, we gathered data concerning user experience and measured performance times for different components of the tool. Both user reports and performance times show significant reduction in treatment-planning complexity and time-consumption from 1-2 days to a few hours. Conclusions The presented web-based tool is intended to facilitate the treatment planning process and reduce the time needed for it. It is crucial for facilitating expansion of electroporation-based treatments in the clinic and ensuring reliable treatment for the patients. The additional value of the tool is the possibility of easy upgrade and integration of modules with new functionalities as they are developed. PMID:26356007

In Interactive, Web-Based Approach to Metadata Authoring

NASA Technical Reports Server (NTRS)

Pollack, Janine; Wharton, Stephen W. (Technical Monitor)

2001-01-01

NASA's Global Change Master Directory (GCMD) serves a growing number of users by assisting the scientific community in the discovery of and linkage to Earth science data sets and related services. The GCMD holds over 8000 data set descriptions in Directory Interchange Format (DIF) and 200 data service descriptions in Service Entry Resource Format (SERF), encompassing the disciplines of geology, hydrology, oceanography, meteorology, and ecology. Data descriptions also contain geographic coverage information, thus allowing researchers to discover data pertaining to a particular geographic location, as well as subject of interest. The GCMD strives to be the preeminent data locator for world-wide directory level metadata. In this vein, scientists and data providers must have access to intuitive and efficient metadata authoring tools. Existing GCMD tools are not currently attracting. widespread usage. With usage being the prime indicator of utility, it has become apparent that current tools must be improved. As a result, the GCMD has released a new suite of web-based authoring tools that enable a user to create new data and service entries, as well as modify existing data entries. With these tools, a more interactive approach to metadata authoring is taken, as they feature a visual "checklist" of data/service fields that automatically update when a field is completed. In this way, the user can quickly gauge which of the required and optional fields have not been populated. With the release of these tools, the Earth science community will be further assisted in efficiently creating quality data and services metadata. Keywords: metadata, Earth science, metadata authoring tools

Web-Based Geographic Information System Tool for Accessing Hanford Site Environmental Data

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

Triplett, Mark B.; Seiple, Timothy E.; Watson, David J.

Data volume, complexity, and access issues pose severe challenges for analysts, regulators and stakeholders attempting to efficiently use legacy data to support decision making at the U.S. Department of Energy’s (DOE) Hanford Site. DOE has partnered with the Pacific Northwest National Laboratory (PNNL) on the PHOENIX (PNNL-Hanford Online Environmental Information System) project, which seeks to address data access, transparency, and integration challenges at Hanford to provide effective decision support. PHOENIX is a family of spatially-enabled web applications providing quick access to decades of valuable scientific data and insight through intuitive query, visualization, and analysis tools. PHOENIX realizes broad, public accessibilitymore » by relying only on ubiquitous web-browsers, eliminating the need for specialized software. It accommodates a wide range of users with intuitive user interfaces that require little or no training to quickly obtain and visualize data. Currently, PHOENIX is actively hosting three applications focused on groundwater monitoring, groundwater clean-up performance reporting, and in-tank monitoring. PHOENIX-based applications are being used to streamline investigative and analytical processes at Hanford, saving time and money. But more importantly, by integrating previously isolated datasets and developing relevant visualization and analysis tools, PHOENIX applications are enabling DOE to discover new correlations hidden in legacy data, allowing them to more effectively address complex issues at Hanford.« less

XCluSim: a visual analytics tool for interactively comparing multiple clustering results of bioinformatics data

PubMed Central

2015-01-01

Background Though cluster analysis has become a routine analytic task for bioinformatics research, it is still arduous for researchers to assess the quality of a clustering result. To select the best clustering method and its parameters for a dataset, researchers have to run multiple clustering algorithms and compare them. However, such a comparison task with multiple clustering results is cognitively demanding and laborious. Results In this paper, we present XCluSim, a visual analytics tool that enables users to interactively compare multiple clustering results based on the Visual Information Seeking Mantra. We build a taxonomy for categorizing existing techniques of clustering results visualization in terms of the Gestalt principles of grouping. Using the taxonomy, we choose the most appropriate interactive visualizations for presenting individual clustering results from different types of clustering algorithms. The efficacy of XCluSim is shown through case studies with a bioinformatician. Conclusions Compared to other relevant tools, XCluSim enables users to compare multiple clustering results in a more scalable manner. Moreover, XCluSim supports diverse clustering algorithms and dedicated visualizations and interactions for different types of clustering results, allowing more effective exploration of details on demand. Through case studies with a bioinformatics researcher, we received positive feedback on the functionalities of XCluSim, including its ability to help identify stably clustered items across multiple clustering results. PMID:26328893

Neuroimaging Study Designs, Computational Analyses and Data Provenance Using the LONI Pipeline

PubMed Central

Dinov, Ivo; Lozev, Kamen; Petrosyan, Petros; Liu, Zhizhong; Eggert, Paul; Pierce, Jonathan; Zamanyan, Alen; Chakrapani, Shruthi; Van Horn, John; Parker, D. Stott; Magsipoc, Rico; Leung, Kelvin; Gutman, Boris; Woods, Roger; Toga, Arthur

2010-01-01

Modern computational neuroscience employs diverse software tools and multidisciplinary expertise to analyze heterogeneous brain data. The classical problems of gathering meaningful data, fitting specific models, and discovering appropriate analysis and visualization tools give way to a new class of computational challenges—management of large and incongruous data, integration and interoperability of computational resources, and data provenance. We designed, implemented and validated a new paradigm for addressing these challenges in the neuroimaging field. Our solution is based on the LONI Pipeline environment [3], [4], a graphical workflow environment for constructing and executing complex data processing protocols. We developed study-design, database and visual language programming functionalities within the LONI Pipeline that enable the construction of complete, elaborate and robust graphical workflows for analyzing neuroimaging and other data. These workflows facilitate open sharing and communication of data and metadata, concrete processing protocols, result validation, and study replication among different investigators and research groups. The LONI Pipeline features include distributed grid-enabled infrastructure, virtualized execution environment, efficient integration, data provenance, validation and distribution of new computational tools, automated data format conversion, and an intuitive graphical user interface. We demonstrate the new LONI Pipeline features using large scale neuroimaging studies based on data from the International Consortium for Brain Mapping [5] and the Alzheimer's Disease Neuroimaging Initiative [6]. User guides, forums, instructions and downloads of the LONI Pipeline environment are available at http://pipeline.loni.ucla.edu. PMID:20927408

Vision-Based Haptic Feedback for Remote Micromanipulation in-SEM Environment

NASA Astrophysics Data System (ADS)

Bolopion, Aude; Dahmen, Christian; Stolle, Christian; Haliyo, Sinan; Régnier, Stéphane; Fatikow, Sergej

2012-07-01

This article presents an intuitive environment for remote micromanipulation composed of both haptic feedback and virtual reconstruction of the scene. To enable nonexpert users to perform complex teleoperated micromanipulation tasks, it is of utmost importance to provide them with information about the 3-D relative positions of the objects and the tools. Haptic feedback is an intuitive way to transmit such information. Since position sensors are not available at this scale, visual feedback is used to derive information about the scene. In this work, three different techniques are implemented, evaluated, and compared to derive the object positions from scanning electron microscope images. The modified correlation matching with generated template algorithm is accurate and provides reliable detection of objects. To track the tool, a marker-based approach is chosen since fast detection is required for stable haptic feedback. Information derived from these algorithms is used to propose an intuitive remote manipulation system that enables users situated in geographically distant sites to benefit from specific equipments, such as SEMs. Stability of the haptic feedback is ensured by the minimization of the delays, the computational efficiency of vision algorithms, and the proper tuning of the haptic coupling. Virtual guides are proposed to avoid any involuntary collisions between the tool and the objects. This approach is validated by a teleoperation involving melamine microspheres with a diameter of less than 2 μ m between Paris, France and Oldenburg, Germany.

Avionics System Architecture Tool

NASA Technical Reports Server (NTRS)

Chau, Savio; Hall, Ronald; Traylor, marcus; Whitfield, Adrian

2005-01-01

Avionics System Architecture Tool (ASAT) is a computer program intended for use during the avionics-system-architecture- design phase of the process of designing a spacecraft for a specific mission. ASAT enables simulation of the dynamics of the command-and-data-handling functions of the spacecraft avionics in the scenarios in which the spacecraft is expected to operate. ASAT is built upon I-Logix Statemate MAGNUM, providing a complement of dynamic system modeling tools, including a graphical user interface (GUI), modeling checking capabilities, and a simulation engine. ASAT augments this with a library of predefined avionics components and additional software to support building and analyzing avionics hardware architectures using these components.

Measurement Tools for the Immersive Visualization Environment: Steps Toward the Virtual Laboratory.

PubMed

Hagedorn, John G; Dunkers, Joy P; Satterfield, Steven G; Peskin, Adele P; Kelso, John T; Terrill, Judith E

2007-01-01

This paper describes a set of tools for performing measurements of objects in a virtual reality based immersive visualization environment. These tools enable the use of the immersive environment as an instrument for extracting quantitative information from data representations that hitherto had be used solely for qualitative examination. We provide, within the virtual environment, ways for the user to analyze and interact with the quantitative data generated. We describe results generated by these methods to obtain dimensional descriptors of tissue engineered medical products. We regard this toolbox as our first step in the implementation of a virtual measurement laboratory within an immersive visualization environment.

RE Data Explorer: Informing Variable Renewable Energy Grid Integration for Low Emission Development

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

Cox, Sarah L

The RE Data Explorer, developed by the National Renewable Energy Laboratory, is an innovative web-based analysis tool that utilizes geospatial and spatiotemporal renewable energy data to visualize, execute, and support analysis of renewable energy potential under various user-defined scenarios. This analysis can inform high-level prospecting, integrated planning, and policy making to enable low emission development.

An Assessment Tool to Detect Unique Characteristics of Cognitive Deficiency

DTIC Science & Technology

2017-06-01

psychological impairment and cognitive deficiency that results from either physical trauma, emotional distress or a combination of both factors, which we...27 To fully remove the DDM, we will integrate our cloud support into the...DANA codebase. We will integrate cloud authentication into DANA to enable users to store their data on the cloud and access the data from the DANA

An Integrated Management Support and Production Control System for Hardwood Forest Products

Treesearch

Guillermo A. Mendoza; Roger J. Meimban; William Sprouse; William G. Luppold; Philip A. Araman

1991-01-01

Spreadsheet and simulation models are tools which enable users to analyze a large number of variables affecting hardwood material utilization and profit in a systematic fashion. This paper describes two spreadsheet models; SEASaw and SEAIn, and a hardwood sawmill simulator. SEASaw is designed to estimate the amount of conversion from timber to lumber, while SEAIn is a...

A New Way of Using the Interactive Whiteboard in a High School Physics Classroom: A Case Study

ERIC Educational Resources Information Center

Gregorcic, Bor; Etkina, Eugenia; Planinsic, Gorazd

2018-01-01

In recent decades, the interactive whiteboard (IWB) has become a relatively common educational tool in Western schools. The IWB is essentially a large touch screen, that enables the user to interact with digital content in ways that are not possible with an ordinary computer-projector-canvas setup. However, the unique possibilities of IWBs are…

Using Enabling Technologies to Facilitate the Comparison of Satellite Observations with the Model Forecasts for Hurricane Study

NASA Astrophysics Data System (ADS)

Li, P.; Knosp, B.; Hristova-Veleva, S. M.; Niamsuwan, N.; Johnson, M. P.; Shen, T. P. J.; Tanelli, S.; Turk, J.; Vu, Q. A.

2014-12-01

Due to their complexity and volume, the satellite data are underutilized in today's hurricane research and operations. To better utilize these data, we developed the JPL Tropical Cyclone Information System (TCIS) - an Interactive Data Portal providing fusion between Near-Real-Time satellite observations and model forecasts to facilitate model evaluation and improvement. We have collected satellite observations and model forecasts in the Atlantic Basin and the East Pacific for the hurricane seasons since 2010 and supported the NASA Airborne Campaigns for Hurricane Study such as the Genesis and Rapid Intensification Processes (GRIP) in 2010 and the Hurricane and Severe Storm Sentinel (HS3) from 2012 to 2014. To enable the direct inter-comparisons of the satellite observations and the model forecasts, the TCIS was integrated with the NASA Earth Observing System Simulator Suite (NEOS3) to produce synthetic observations (e.g. simulated passive microwave brightness temperatures) from a number of operational hurricane forecast models (HWRF and GFS). An automated process was developed to trigger NEOS3 simulations via web services given the location and time of satellite observations, monitor the progress of the NEOS3 simulations, display the synthetic observation and ingest them into the TCIS database when they are done. In addition, three analysis tools, the joint PDF analysis of the brightness temperatures, ARCHER for finding the storm-center and the storm organization and the Wave Number Analysis tool for storm asymmetry and morphology analysis were integrated into TCIS to provide statistical and structural analysis on both observed and synthetic data. Interactive tools were built in the TCIS visualization system to allow the spatial and temporal selections of the datasets, the invocation of the tools with user specified parameters, and the display and the delivery of the results. In this presentation, we will describe the key enabling technologies behind the design of the TCIS interactive data portal and analysis tools, including the spatial database technology for the representation and query of the level 2 satellite data, the automatic process flow using web services, the interactive user interface using the Google Earth API, and a common and expandable Python wrapper to invoke the analysis tools.

GREAT: a web portal for Genome Regulatory Architecture Tools

PubMed Central

Bouyioukos, Costas; Bucchini, François; Elati, Mohamed; Képès, François

2016-01-01

GREAT (Genome REgulatory Architecture Tools) is a novel web portal for tools designed to generate user-friendly and biologically useful analysis of genome architecture and regulation. The online tools of GREAT are freely accessible and compatible with essentially any operating system which runs a modern browser. GREAT is based on the analysis of genome layout -defined as the respective positioning of co-functional genes- and its relation with chromosome architecture and gene expression. GREAT tools allow users to systematically detect regular patterns along co-functional genomic features in an automatic way consisting of three individual steps and respective interactive visualizations. In addition to the complete analysis of regularities, GREAT tools enable the use of periodicity and position information for improving the prediction of transcription factor binding sites using a multi-view machine learning approach. The outcome of this integrative approach features a multivariate analysis of the interplay between the location of a gene and its regulatory sequence. GREAT results are plotted in web interactive graphs and are available for download either as individual plots, self-contained interactive pages or as machine readable tables for downstream analysis. The GREAT portal can be reached at the following URL https://absynth.issb.genopole.fr/GREAT and each individual GREAT tool is available for downloading. PMID:27151196

A novel teaching system for industrial robots.

PubMed

Lin, Hsien-I; Lin, Yu-Hsiang

2014-03-27

The most important tool for controlling an industrial robotic arm is a teach pendant, which controls the robotic arm movement in work spaces and accomplishes teaching tasks. A good teaching tool should be easy to operate and can complete teaching tasks rapidly and effortlessly. In this study, a new teaching system is proposed for enabling users to operate robotic arms and accomplish teaching tasks easily. The proposed teaching system consists of the teach pen, optical markers on the pen, a motion capture system, and the pen tip estimation algorithm. With the marker positions captured by the motion capture system, the pose of the teach pen is accurately calculated by the pen tip algorithm and used to control the robot tool frame. In addition, Fitts' Law is adopted to verify the usefulness of this new system, and the results show that the system provides high accuracy, excellent operation performance, and a stable error rate. In addition, the system maintains superior performance, even when users work on platforms with different inclination angles.

A Novel Teaching System for Industrial Robots

PubMed Central

Lin, Hsien-I; Lin, Yu-Hsiang

2014-01-01

The most important tool for controlling an industrial robotic arm is a teach pendant, which controls the robotic arm movement in work spaces and accomplishes teaching tasks. A good teaching tool should be easy to operate and can complete teaching tasks rapidly and effortlessly. In this study, a new teaching system is proposed for enabling users to operate robotic arms and accomplish teaching tasks easily. The proposed teaching system consists of the teach pen, optical markers on the pen, a motion capture system, and the pen tip estimation algorithm. With the marker positions captured by the motion capture system, the pose of the teach pen is accurately calculated by the pen tip algorithm and used to control the robot tool frame. In addition, Fitts' Law is adopted to verify the usefulness of this new system, and the results show that the system provides high accuracy, excellent operation performance, and a stable error rate. In addition, the system maintains superior performance, even when users work on platforms with different inclination angles. PMID:24681669

Research-Based Monitoring, Prediction, and Analysis Tools of the Spacecraft Charging Environment for Spacecraft Users

NASA Technical Reports Server (NTRS)

Zheng, Yihua; Kuznetsova, Maria M.; Pulkkinen, Antti A.; Maddox, Marlo M.; Mays, Mona Leila

2015-01-01

The Space Weather Research Center (http://swrc. gsfc.nasa.gov) at NASA Goddard, part of the Community Coordinated Modeling Center (http://ccmc.gsfc.nasa.gov), is committed to providing research-based forecasts and notifications to address NASA's space weather needs, in addition to its critical role in space weather education. It provides a host of services including spacecraft anomaly resolution, historical impact analysis, real-time monitoring and forecasting, tailored space weather alerts and products, and weekly summaries and reports. In this paper, we focus on how (near) real-time data (both in space and on ground), in combination with modeling capabilities and an innovative dissemination system called the integrated Space Weather Analysis system (http://iswa.gsfc.nasa.gov), enable monitoring, analyzing, and predicting the spacecraft charging environment for spacecraft users. Relevant tools and resources are discussed.

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

PubMed

Oberortner, Ernst; Densmore, Douglas

2015-06-19

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

Mitochondrial Disease Sequence Data Resource (MSeqDR): a global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities.

PubMed

Falk, Marni J; Shen, Lishuang; Gonzalez, Michael; Leipzig, Jeremy; Lott, Marie T; Stassen, Alphons P M; Diroma, Maria Angela; Navarro-Gomez, Daniel; Yeske, Philip; Bai, Renkui; Boles, Richard G; Brilhante, Virginia; Ralph, David; DaRe, Jeana T; Shelton, Robert; Terry, Sharon F; Zhang, Zhe; Copeland, William C; van Oven, Mannis; Prokisch, Holger; Wallace, Douglas C; Attimonelli, Marcella; Krotoski, Danuta; Zuchner, Stephan; Gai, Xiaowu

2015-03-01

Success rates for genomic analyses of highly heterogeneous disorders can be greatly improved if a large cohort of patient data is assembled to enhance collective capabilities for accurate sequence variant annotation, analysis, and interpretation. Indeed, molecular diagnostics requires the establishment of robust data resources to enable data sharing that informs accurate understanding of genes, variants, and phenotypes. The "Mitochondrial Disease Sequence Data Resource (MSeqDR) Consortium" is a grass-roots effort facilitated by the United Mitochondrial Disease Foundation to identify and prioritize specific genomic data analysis needs of the global mitochondrial disease clinical and research community. A central Web portal (https://mseqdr.org) facilitates the coherent compilation, organization, annotation, and analysis of sequence data from both nuclear and mitochondrial genomes of individuals and families with suspected mitochondrial disease. This Web portal provides users with a flexible and expandable suite of resources to enable variant-, gene-, and exome-level sequence analysis in a secure, Web-based, and user-friendly fashion. Users can also elect to share data with other MSeqDR Consortium members, or even the general public, either by custom annotation tracks or through the use of a convenient distributed annotation system (DAS) mechanism. A range of data visualization and analysis tools are provided to facilitate user interrogation and understanding of genomic, and ultimately phenotypic, data of relevance to mitochondrial biology and disease. Currently available tools for nuclear and mitochondrial gene analyses include an MSeqDR GBrowse instance that hosts optimized mitochondrial disease and mitochondrial DNA (mtDNA) specific annotation tracks, as well as an MSeqDR locus-specific database (LSDB) that curates variant data on more than 1300 genes that have been implicated in mitochondrial disease and/or encode mitochondria-localized proteins. MSeqDR is integrated with a diverse array of mtDNA data analysis tools that are both freestanding and incorporated into an online exome-level dataset curation and analysis resource (GEM.app) that is being optimized to support needs of the MSeqDR community. In addition, MSeqDR supports mitochondrial disease phenotyping and ontology tools, and provides variant pathogenicity assessment features that enable community review, feedback, and integration with the public ClinVar variant annotation resource. A centralized Web-based informed consent process is being developed, with implementation of a Global Unique Identifier (GUID) system to integrate data deposited on a given individual from different sources. Community-based data deposition into MSeqDR has already begun. Future efforts will enhance capabilities to incorporate phenotypic data that enhance genomic data analyses. MSeqDR will fill the existing void in bioinformatics tools and centralized knowledge that are necessary to enable efficient nuclear and mtDNA genomic data interpretation by a range of shareholders across both clinical diagnostic and research settings. Ultimately, MSeqDR is focused on empowering the global mitochondrial disease community to better define and explore mitochondrial diseases. Copyright © 2014 Elsevier Inc. All rights reserved.

Mitochondrial Disease Sequence Data Resource (MSeqDR): A global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities

PubMed Central

Falk, Marni J.; Shen, Lishuang; Gonzalez, Michael; Leipzig, Jeremy; Lott, Marie T.; Stassen, Alphons P.M.; Diroma, Maria Angela; Navarro-Gomez, Daniel; Yeske, Philip; Bai, Renkui; Boles, Richard G.; Brilhante, Virginia; Ralph, David; DaRe, Jeana T.; Shelton, Robert; Terry, Sharon; Zhang, Zhe; Copeland, William C.; van Oven, Mannis; Prokisch, Holger; Wallace, Douglas C.; Attimonelli, Marcella; Krotoski, Danuta; Zuchner, Stephan; Gai, Xiaowu

2014-01-01

Success rates for genomic analyses of highly heterogeneous disorders can be greatly improved if a large cohort of patient data is assembled to enhance collective capabilities for accurate sequence variant annotation, analysis, and interpretation. Indeed, molecular diagnostics requires the establishment of robust data resources to enable data sharing that informs accurate understanding of genes, variants, and phenotypes. The “Mitochondrial Disease Sequence Data Resource (MSeqDR) Consortium” is a grass-roots effort facilitated by the United Mitochondrial Disease Foundation to identify and prioritize specific genomic data analysis needs of the global mitochondrial disease clinical and research community. A central Web portal (https://mseqdr.org) facilitates the coherent compilation, organization, annotation, and analysis of sequence data from both nuclear and mitochondrial genomes of individuals and families with suspected mitochondrial disease. This Web portal provides users with a flexible and expandable suite of resources to enable variant-, gene-, and exome-level sequence analysis in a secure, Web-based, and user-friendly fashion. Users can also elect to share data with other MSeqDR Consortium members, or even the general public, either by custom annotation tracks or through use of a convenient distributed annotation system (DAS) mechanism. A range of data visualization and analysis tools are provided to facilitate user interrogation and understanding of genomic, and ultimately phenotypic, data of relevance to mitochondrial biology and disease. Currently available tools for nuclear and mitochondrial gene analyses include an MSeqDR GBrowse instance that hosts optimized mitochondrial disease and mitochondrial DNA (mtDNA) specific annotation tracks, as well as an MSeqDR locus-specific database (LSDB) that curates variant data on more than 1,300 genes that have been implicated in mitochondrial disease and/or encode mitochondria-localized proteins. MSeqDR is integrated with a diverse array of mtDNA data analysis tools that are both freestanding and incorporated into an online exome-level dataset curation and analysis resource (GEM.app) that is being optimized to support needs of the MSeqDR community. In addition, MSeqDR supports mitochondrial disease phenotyping and ontology tools, and provides variant pathogenicity assessment features that enable community review, feedback, and integration with the public ClinVar variant annotation resource. A centralized Web-based informed consent process is being developed, with implementation of a Global Unique Identifier (GUID) system to integrate data deposited on a given individual from different sources. Community-based data deposition into MSeqDR has already begun. Future efforts will enhance capabilities to incorporate phenotypic data that enhance genomic data analyses. MSeqDR will fill the existing void in bioinformatics tools and centralized knowledge that are necessary to enable efficient nuclear and mtDNA genomic data interpretation by a range of shareholders across both clinical diagnostic and research settings. Ultimately, MSeqDR is focused on empowering the global mitochondrial disease community to better define and explore mitochondrial disease. PMID:25542617

Utility of Mobile phones to support In-situ data collection for Land Cover Mapping

NASA Astrophysics Data System (ADS)

Oduor, P.; Omondi, S.; Wahome, A.; Mugo, R. M.; Flores, A.

2017-12-01

With the compelling need to create better monitoring tools for our landscapes to enhance better decision making processes, it becomes imperative to do so in much more sophisticated yet simple ways. Making it possible to leverage untapped potential of our "lay men" at the same time enabling us to respond to the complexity of the information we have to get out. SERVIR Eastern and Southern Africa has developed a mobile app that can be utilized with very little prior knowledge or no knowledge at all to collect spatial information on land cover. This set of in-situ data can be collected by masses because the tools is very simple to use, and have this information fed in classification algorithms than can then be used to map out our ever changing landscape. The LULC Mapper is a subset of JiMap system and is able to pull the google earth imagery and open street maps to enable user familiarize with their location. It uses phone GPS, phone network information to map location coordinates and at the same time gives the user sample picture of what to categorize their landscape. The system is able to work offline and when user gets access to internet they can push the information into an amazon database as bulk data. The location details including geotagged photos allows the data to be used in development of a lot of spatial information including land cover data. The app is currently available in Google Play Store and will soon be uploaded on Appstore for utilization by a wider community. We foresee a lot of potential in this tool in terms of making data collection cheaper and affordable. Taking advantage of the advances made in phone technology. We envisage to do a data collection campaign where we can have the tool used for crowdsourcing.

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-01-01

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

From Streaming Data to Streaming Insights: The Impact of Data Velocities on Mental Models

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

Endert, Alexander; Pike, William A.; Cook, Kristin A.

The rise of Big Data has influenced the design and technical implementation of visual analytic tools required to handle the increased volumes, velocities, and varieties of data. This has required a set of data management and computational advancements to allow us to store and compute on such datasets. However, as the ultimate goal of visual analytic technology is to enable the discovery and creation of insights from the users, an under-explored area is understanding how these datasets impact their mental models. That is, how have the analytic processes and strategies of users changed? How have users changed their perception ofmore » how to leverage, and ask questions of, these datasets?« less

SU-F-T-94: Plan2pdf - a Software Tool for Automatic Plan Report for Philips Pinnacle TPS

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

Wu, C

Purpose: To implement an automatic electronic PDF plan reporting tool for Philips Pinnacle treatment planning system (TPS) Methods: An electronic treatment plan reporting software is developed by us to enable fully automatic PDF report from Pinnacle TPS to external EMR programs such as MOSAIQ. The tool is named “plan2pdf”. plan2pdf is implemented using Pinnacle scripts, Java and UNIX shell scripts, without any external program needed. plan2pdf supports full auto-mode and manual mode reporting. In full auto-mode, with a single mouse click, plan2pdf will generate a detailed Pinnacle plan report in PDF format, which includes customizable cover page, Pinnacle plan summary,more » orthogonal views through each plan POI and maximum dose point, DRR for each beam, serial transverse views captured throughout the dose grid at a user specified interval, DVH and scorecard windows. The final PDF report is also automatically bookmarked for each section above for convenient plan review. The final PDF report can either be saved on a user specified folder on Pinnacle, or it can be automatically exported to an EMR import folder via a user configured FTP service. In manual capture mode, plan2pdf allows users to capture any Pinnacle plan by full screen, individual window or rectangular ROI drawn on screen. Furthermore, to avoid possible patients’ plan mix-up during auto-mode reporting, a user conflict check feature is included in plan2pdf: it prompts user to wait if another patient is being exported by plan2pdf by another user. Results: plan2pdf is tested extensively and successfully at our institution consists of 5 centers, 15 dosimetrists and 10 physicists, running Pinnacle version 9.10 on Enterprise servers. Conclusion: plan2pdf provides a highly efficient, user friendly and clinical proven platform for all Philips Pinnacle users, to generate a detailed plan report in PDF format for external EMR systems.« less

Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment.

PubMed

Bohler, Anwesha; Eijssen, Lars M T; van Iersel, Martijn P; Leemans, Christ; Willighagen, Egon L; Kutmon, Martina; Jaillard, Magali; Evelo, Chris T

2015-08-23

Biological pathways are descriptive diagrams of biological processes widely used for functional analysis of differentially expressed genes or proteins. Primary data analysis, such as quality control, normalisation, and statistical analysis, is often performed in scripting languages like R, Perl, and Python. Subsequent pathway analysis is usually performed using dedicated external applications. Workflows involving manual use of multiple environments are time consuming and error prone. Therefore, tools are needed that enable pathway analysis directly within the same scripting languages used for primary data analyses. Existing tools have limited capability in terms of available pathway content, pathway editing and visualisation options, and export file formats. Consequently, making the full-fledged pathway analysis tool PathVisio available from various scripting languages will benefit researchers. We developed PathVisioRPC, an XMLRPC interface for the pathway analysis software PathVisio. PathVisioRPC enables creating and editing biological pathways, visualising data on pathways, performing pathway statistics, and exporting results in several image formats in multiple programming environments. We demonstrate PathVisioRPC functionalities using examples in Python. Subsequently, we analyse a publicly available NCBI GEO gene expression dataset studying tumour bearing mice treated with cyclophosphamide in R. The R scripts demonstrate how calls to existing R packages for data processing and calls to PathVisioRPC can directly work together. To further support R users, we have created RPathVisio simplifying the use of PathVisioRPC in this environment. We have also created a pathway module for the microarray data analysis portal ArrayAnalysis.org that calls the PathVisioRPC interface to perform pathway analysis. This module allows users to use PathVisio functionality online without having to download and install the software and exemplifies how the PathVisioRPC interface can be used by data analysis pipelines for functional analysis of processed genomics data. PathVisioRPC enables data visualisation and pathway analysis directly from within various analytical environments used for preliminary analyses. It supports the use of existing pathways from WikiPathways or pathways created using the RPC itself. It also enables automation of tasks performed using PathVisio, making it useful to PathVisio users performing repeated visualisation and analysis tasks. PathVisioRPC is freely available for academic and commercial use at http://projects.bigcat.unimaas.nl/pathvisiorpc.

Interactive entity resolution in relational data: a visual analytic tool and its evaluation.

PubMed

Kang, Hyunmo; Getoor, Lise; Shneiderman, Ben; Bilgic, Mustafa; Licamele, Louis

2008-01-01

Databases often contain uncertain and imprecise references to real-world entities. Entity resolution, the process of reconciling multiple references to underlying real-world entities, is an important data cleaning process required before accurate visualization or analysis of the data is possible. In many cases, in addition to noisy data describing entities, there is data describing the relationships among the entities. This relational data is important during the entity resolution process; it is useful both for the algorithms which determine likely database references to be resolved and for visual analytic tools which support the entity resolution process. In this paper, we introduce a novel user interface, D-Dupe, for interactive entity resolution in relational data. D-Dupe effectively combines relational entity resolution algorithms with a novel network visualization that enables users to make use of an entity's relational context for making resolution decisions. Since resolution decisions often are interdependent, D-Dupe facilitates understanding this complex process through animations which highlight combined inferences and a history mechanism which allows users to inspect chains of resolution decisions. An empirical study with 12 users confirmed the benefits of the relational context visualization on the performance of entity resolution tasks in relational data in terms of time as well as users' confidence and satisfaction.

Unifying Water Data Sources: How the CUAHSI Water Data Center is Enabling and Improving Access to a Growing Catalog of over 100 Data Providers

NASA Astrophysics Data System (ADS)

Pollak, J.; Berry, K.; Couch, A.; Arrigo, J.; Hooper, R. P.

2013-12-01

Scientific data about water are collected and distributed by numerous sources which can differ tremendously in scale. As competition for water resources increases, increasing access to and understanding of information about water will be critical. The mission of the new CUAHSI Water Data Center (WDC) is to provide those researchers who collect data a medium to publish their datasets and give those wanting to discover data the proper tools to efficiently find the data that they seek. These tools include standards-based data publication, data discovery tools based upon faceted and telescoping search, and a data analysis tool HydroDesktop that downloads and unifies data in standardized formats. The CUAHSI Hydrologic Information System (HIS) is a community developed and open source system for sharing water data. As a federated, web service oriented system it enables data publication for a diverse user population including scientific investigators (Research Coordination Networks, Critical Zone Observatories), government agencies (USGS, NASA, EPA), and citizen scientists (watershed associations). HydroDesktop is an end user application for data consumption in this system that the WDC supports. This application can be used for finding, downloading, and analyzing data from the HIS. It provides a GIS interface that allows users to incorporate spatial data that are not accessible via HIS, simple analysis tools to facilitate graphing and visualization, tools to export data to common file types, and provides an extensible architecture that developers can build upon. HydroDesktop, however, is just one example of a data access client for HIS. The web service oriented architecture enables data access by an unlimited number of clients provided they can consume the web services used in HIS. One such example developed at the WDC is the 'Faceted Search Client', which capitalizes upon exploratory search concepts to improve accuracy and precision during search. We highlight such features of the CUAHSI-HIS which make it particularly appropriate for providing unified access to several sources of water data. A growing community of researchers and educators are employing these tools for education; including sharing best practices around creating modules, supporting researchers and educators in accessing the services, and cataloging and sharing modules. The CUAHSI WDC is a community governed organization. Our agenda is driven by the community's voice through a Board of Directors and committees that decide strategic direction (new products), tactical decisions (product improvement), and evaluation of usability. By providing the aforementioned services within a community driven framework, we believe the WDC is providing critical services that include improving water data discoverability, accessibility and usability within a sustainable governance structure.

Framework for near-field-communication-based geo-localization and personalization for Android-based smartphones--application in hospital environments.

PubMed

Meng, Philipp; Fehre, Karsten; Rappelsberger, Andrea; Adlassnig, Klaus-Peter

2014-01-01

Various applications using near field communication (NFC) have been developed for the medical sector. As a method of short-range wireless contact-driven data transfer, NFC is a useful tool in medicine. It can be used to transfer data such as blood pressure, control adherence to medication, or transmit in vivo data. The first proposed general framework uses NFC as a mechanism for indoor geo-localization in hospitals. NFC geo-localization is economical compared to classical concepts using indoor GPS or WLAN triangulation, and the granularity of location retrieval can be defined at a tag level. Using this framework, we facilitate the development of medical applications that require exact indoor geo-localization. Multi-user Android systems are addressed in the second framework. Using private NFC tags, users are able to carry on their personal settings for enabled applications. This eliminates the need for multiple user accounts on common Android devices, improves usability, and eases technical administration. Based on the prototypes presented here, we show a novel concept of using NFC-enabled Android devices in hospital environments.

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

PubMed

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

2016-04-01

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

poRe: an R package for the visualization and analysis of nanopore sequencing data.

PubMed

Watson, Mick; Thomson, Marian; Risse, Judith; Talbot, Richard; Santoyo-Lopez, Javier; Gharbi, Karim; Blaxter, Mark

2015-01-01

The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the bioinformatics community will need to design and build a suite of tools specifically for MinION data. Here we present poRe, a package for R that enables users to manipulate, organize, summarize and visualize MinION nanopore sequencing data. As a package for R, poRe has been tested on Windows, Linux and MacOSX. Crucially, the Windows version allows users to analyse MinION data on the Windows laptop attached to the device. poRe is released as a package for R at http://sourceforge.net/projects/rpore/. A tutorial and further information are available at https://sourceforge.net/p/rpore/wiki/Home/. © The Author 2014. Published by Oxford University Press.

Micro-Analyzer: automatic preprocessing of Affymetrix microarray data.

PubMed

Guzzi, Pietro Hiram; Cannataro, Mario

2013-08-01

A current trend in genomics is the investigation of the cell mechanism using different technologies, in order to explain the relationship among genes, molecular processes and diseases. For instance, the combined use of gene-expression arrays and genomic arrays has been demonstrated as an effective instrument in clinical practice. Consequently, in a single experiment different kind of microarrays may be used, resulting in the production of different types of binary data (images and textual raw data). The analysis of microarray data requires an initial preprocessing phase, that makes raw data suitable for use on existing analysis platforms, such as the TIGR M4 (TM4) Suite. An additional challenge to be faced by emerging data analysis platforms is the ability to treat in a combined way those different microarray formats coupled with clinical data. In fact, resulting integrated data may include both numerical and symbolic data (e.g. gene expression and SNPs regarding molecular data), as well as temporal data (e.g. the response to a drug, time to progression and survival rate), regarding clinical data. Raw data preprocessing is a crucial step in analysis but is often performed in a manual and error prone way using different software tools. Thus novel, platform independent, and possibly open source tools enabling the semi-automatic preprocessing and annotation of different microarray data are needed. The paper presents Micro-Analyzer (Microarray Analyzer), a cross-platform tool for the automatic normalization, summarization and annotation of Affymetrix gene expression and SNP binary data. It represents the evolution of the μ-CS tool, extending the preprocessing to SNP arrays that were not allowed in μ-CS. The Micro-Analyzer is provided as a Java standalone tool and enables users to read, preprocess and analyse binary microarray data (gene expression and SNPs) by invoking TM4 platform. It avoids: (i) the manual invocation of external tools (e.g. the Affymetrix Power Tools), (ii) the manual loading of preprocessing libraries, and (iii) the management of intermediate files, such as results and metadata. Micro-Analyzer users can directly manage Affymetrix binary data without worrying about locating and invoking the proper preprocessing tools and chip-specific libraries. Moreover, users of the Micro-Analyzer tool can load the preprocessed data directly into the well-known TM4 platform, extending in such a way also the TM4 capabilities. Consequently, Micro Analyzer offers the following advantages: (i) it reduces possible errors in the preprocessing and further analysis phases, e.g. due to the incorrect choice of parameters or due to the use of old libraries, (ii) it enables the combined and centralized pre-processing of different arrays, (iii) it may enhance the quality of further analysis by storing the workflow, i.e. information about the preprocessing steps, and (iv) finally Micro-Analzyer is freely available as a standalone application at the project web site http://sourceforge.net/projects/microanalyzer/. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Towards Gesture-Based Multi-User Interactions in Collaborative Virtual Environments

NASA Astrophysics Data System (ADS)

Pretto, N.; Poiesi, F.

2017-11-01

We present a virtual reality (VR) setup that enables multiple users to participate in collaborative virtual environments and interact via gestures. A collaborative VR session is established through a network of users that is composed of a server and a set of clients. The server manages the communication amongst clients and is created by one of the users. Each user's VR setup consists of a Head Mounted Display (HMD) for immersive visualisation, a hand tracking system to interact with virtual objects and a single-hand joypad to move in the virtual environment. We use Google Cardboard as a HMD for the VR experience and a Leap Motion for hand tracking, thus making our solution low cost. We evaluate our VR setup though a forensics use case, where real-world objects pertaining to a simulated crime scene are included in a VR environment, acquired using a smartphone-based 3D reconstruction pipeline. Users can interact using virtual gesture-based tools such as pointers and rulers.

User applications driven by the community contribution framework MPContribs in the Materials Project

DOE PAGES

Huck, P.; Gunter, D.; Cholia, S.; ...

2015-10-12

This paper discusses how the MPContribs framework in the Materials Project (MP) allows user-contributed data to be shown and analyzed alongside the core MP database. The MP is a searchable database of electronic structure properties of over 65,000 bulk solid materials, which is accessible through a web-based science-gateway. We describe the motivation for enabling user contributions to the materials data and present the framework's features and challenges in the context of two real applications. These use cases illustrate how scientific collaborations can build applications with their own 'user-contributed' data using MPContribs. The Nanoporous Materials Explorer application provides a unique searchmore » interface to a novel dataset of hundreds of thousands of materials, each with tables of user-contributed values related to material adsorption and density at varying temperature and pressure. The Unified Theoretical and Experimental X-ray Spectroscopy application discusses a full workflow for the association, dissemination, and combined analyses of experimental data from the Advanced Light Source with MP's theoretical core data, using MPContribs tools for data formatting, management, and exploration. The capabilities being developed for these collaborations are serving as the model for how new materials data can be incorporated into the MP website with minimal staff overhead while giving powerful tools for data search and display to the user community.« less

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

PubMed

Yu, Kebing; Salomon, Arthur R

2009-12-01

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

Developing Web-based Tools for Collaborative Science and Public Outreach

NASA Astrophysics Data System (ADS)

Friedman, A.; Pizarro, O.; Williams, S. B.

2016-02-01

With the advances in high bandwidth communications and the proliferation of social media tools, education & outreach activities have become commonplace on ocean-bound research cruises. In parallel, advances in underwater robotics & other data collecting platforms, have made it possible to collect copious amounts of oceanographic data. This data then typically undergoes laborious, manual processing to transform it into quantitative information, which normally occurs post cruise resulting in significant lags between collecting data and using it for scientific discovery. This presentation discusses how appropriately designed software systems, can be used to fulfill multiple objectives and attempt to leverage public engagement in order to compliment science goals. We will present two software platforms: the first is a web browser based tool that was developed for real-time tracking of multiple underwater robots and ships. It was designed to allow anyone on board to view or control it on any device with a web browser. It opens up the possibility of remote teleoperation & engagement and was easily adapted to enable live streaming over the internet for public outreach. While the tracking system provided context and engaged people in real-time, it also directed interested participants to Squidle, another online system. Developed for scientists, Squidle supports data management, exploration & analysis and enables direct access to survey data reducing the lag in data processing. It provides a user-friendly streamlined interface that integrates advanced data management & online annotation tools. This system was adapted to provide a simplified user interface, tutorial instructions and a gamified ranking system to encourage "citizen science" participation. These examples show that through a flexible design approach, it is possible to leverage the development effort of creating science tools to facilitate outreach goals, opening up the possibility for acquiring large volumes of crowd-sourced data without compromising science objectives.

User-Centered Design of a Tablet Waiting Room Tool for Complex Patients to Prioritize Discussion Topics for Primary Care Visits.

PubMed

Lyles, Courtney R; Altschuler, Andrea; Chawla, Neetu; Kowalski, Christine; McQuillan, Deanna; Bayliss, Elizabeth; Heisler, Michele; Grant, Richard W

2016-09-14

Complex patients with multiple chronic conditions often face significant challenges communicating and coordinating with their primary care physicians. These challenges are exacerbated by the limited time allotted to primary care visits. Our aim was to employ a user-centered design process to create a tablet tool for use by patients for visit discussion prioritization. We employed user-centered design methods to create a tablet-based waiting room tool that enables complex patients to identify and set discussion topic priorities for their primary care visit. In an iterative design process, we completed one-on-one interviews with 40 patients and their 17 primary care providers, followed by three design sessions with a 12-patient group. We audiorecorded and transcribed all discussions and categorized major themes. In addition, we met with 15 key health communication, education, and technology leaders within our health system to further review the design and plan for broader implementation of the tool. In this paper, we present the significant changes made to the tablet tool at each phase of this design work. Patient feedback emphasized the need to make the tablet tool accessible for patients who lacked technical proficiency and to reduce the quantity and complexity of text presentation. Both patients and their providers identified specific content choices based on their personal experiences (eg, the ability to raise private or sensitive concerns) and recommended targeting new patients. Stakeholder groups provided essential input on the need to augment text with video and to create different versions of the videos to match sex and race/ethnicity of the actors with patients. User-centered design in collaboration with patients, providers, and key health stakeholders led to marked evolution in the initial content, layout, and target audience for a tablet waiting room tool intended to assist complex patients with setting visit discussion priorities.

Social Networking Adapted for Distributed Scientific Collaboration

NASA Technical Reports Server (NTRS)

Karimabadi, Homa

2012-01-01

Share is a social networking site with novel, specially designed feature sets to enable simultaneous remote collaboration and sharing of large data sets among scientists. The site will include not only the standard features found on popular consumer-oriented social networking sites such as Facebook and Myspace, but also a number of powerful tools to extend its functionality to a science collaboration site. A Virtual Observatory is a promising technology for making data accessible from various missions and instruments through a Web browser. Sci-Share augments services provided by Virtual Observatories by enabling distributed collaboration and sharing of downloaded and/or processed data among scientists. This will, in turn, increase science returns from NASA missions. Sci-Share also enables better utilization of NASA s high-performance computing resources by providing an easy and central mechanism to access and share large files on users space or those saved on mass storage. The most common means of remote scientific collaboration today remains the trio of e-mail for electronic communication, FTP for file sharing, and personalized Web sites for dissemination of papers and research results. Each of these tools has well-known limitations. Sci-Share transforms the social networking paradigm into a scientific collaboration environment by offering powerful tools for cooperative discourse and digital content sharing. Sci-Share differentiates itself by serving as an online repository for users digital content with the following unique features: a) Sharing of any file type, any size, from anywhere; b) Creation of projects and groups for controlled sharing; c) Module for sharing files on HPC (High Performance Computing) sites; d) Universal accessibility of staged files as embedded links on other sites (e.g. Facebook) and tools (e.g. e-mail); e) Drag-and-drop transfer of large files, replacing awkward e-mail attachments (and file size limitations); f) Enterprise-level data and messaging encryption; and g) Easy-to-use intuitive workflow.

Radio Astronomy Tools in Python: Spectral-cube, pvextractor, and more

NASA Astrophysics Data System (ADS)

Ginsburg, A.; Robitaille, T.; Beaumont, C.; Rosolowsky, E.; Leroy, A.; Brogan, C.; Hunter, T.; Teuben, P.; Brisbin, D.

2015-12-01

The radio-astro-tools organization has been established to facilitate development of radio and millimeter analysis tools by the scientific community. The first packages developed under its umbrella are: • The spectral-cube package, for reading, writing, and analyzing spectral data cubes • The pvextractor package for extracting position-velocity slices from position-position-velocity cubes along aribitrary paths • The radio-beam package to handle gaussian beams in the context of the astropy quantity and unit framework • casa-python to enable installation of these packages - and any other - into users' CASA environments without conflicting with the underlying CASA package. Community input in the form of code contributions, suggestions, questions and commments is welcome on all of these tools. They can all be found at http://radio-astro-tools.github.io.

SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees.

PubMed

Beccati, Alan; Gerken, Jan; Quast, Christian; Yilmaz, Pelin; Glöckner, Frank Oliver

2017-09-30

Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the interaction with the users to provide feedback for the further improvement of the taxonomic framework. The SILVA Tree Viewer is a web application designed for visualizing large phylogenetic trees without requiring the download of any software tool or data files. The SILVA Tree Viewer is based on Web Geographic Information Systems (Web-GIS) technology with a PostgreSQL backend. It enables zoom and pan functionalities similar to Google Maps. The SILVA Tree Viewer enables access to two phylogenetic (guide) trees provided by the SILVA database: the SSU Ref NR99 inferred from high-quality, full-length small subunit sequences, clustered at 99% sequence identity and the LSU Ref inferred from high-quality, full-length large subunit sequences. The Tree Viewer provides tree navigation, search and browse tools as well as an interactive feedback system to collect any kinds of requests ranging from taxonomy to data curation and improving the tool itself.

Real Time Metrics and Analysis of Integrated Arrival, Departure, and Surface Operations

NASA Technical Reports Server (NTRS)

Sharma, Shivanjli; Fergus, John

2017-01-01

To address the Integrated Arrival, Departure, and Surface (IADS) challenge, NASA is developing and demonstrating trajectory-based departure automation under a collaborative effort with the FAA and industry known Airspace Technology Demonstration 2 (ATD-2). ATD-2 builds upon and integrates previous NASA research capabilities that include the Spot and Runway Departure Advisor (SARDA), the Precision Departure Release Capability (PDRC), and the Terminal Sequencing and Spacing (TSAS) capability. As trajectory-based departure scheduling and collaborative decision making tools are introduced in order to reduce delays and uncertainties in taxi and climb operations across the National Airspace System, users of the tools across a number of roles benefit from a real time system that enables common situational awareness. A real time dashboard was developed to inform and present users notifications and integrated information regarding airport surface operations. The dashboard is a supplement to capabilities and tools that incorporate arrival, departure, and surface air-traffic operations concepts in a NextGen environment. In addition to shared situational awareness, the dashboard offers the ability to compute real time metrics and analysis to inform users about capacity, predictability, and efficiency of the system as a whole. This paper describes the architecture of the real time dashboard as well as an initial proposed set of metrics. The potential impact of the real time dashboard is studied at the site identified for initial deployment and demonstration in 2017: Charlotte-Douglas International Airport (CLT). The architecture of implementing such a tool as well as potential uses are presented for operations at CLT. Metrics computed in real time illustrate the opportunity to provide common situational awareness and inform users of system delay, throughput, taxi time, and airport capacity. In addition, common awareness of delays and the impact of takeoff and departure restrictions stemming from traffic flow management initiatives are explored. The potential of the real time tool to inform users of the predictability and efficiency of using a trajectory-based departure scheduling system is also discussed.

Analysis of Sea Level Rise in Action

NASA Astrophysics Data System (ADS)

Gill, K. M.; Huang, T.; Quach, N. T.; Boening, C.

2016-12-01

NASA's Sea Level Change Portal provides scientists and the general public with "one-stop" source for current sea level change information and data. Sea Level Rise research is a multidisciplinary research and in order to understand its causes, scientists must be able to access different measurements and to be able to compare them. The portal includes an interactive tool, called the Data Analysis Tool (DAT), for accessing, visualizing, and analyzing observations and models relevant to the study of Sea Level Rise. Using NEXUS, an open source, big data analytic technology developed at the Jet Propulsion Laboratory, the DAT is able provide user on-the-fly data analysis on all relevant parameters. DAT is composed of three major components: A dedicated instance of OnEarth (a WMTS service), NEXUS deep data analytic platform, and the JPL Common Mapping Client (CMC) for web browser based user interface (UI). Utilizing the global imagery, a user is capable of browsing the data in a visual manner and isolate areas of interest for further study. The interfaces "Analysis" tool provides tools for area or point selection, single and/or comparative dataset selection, and a range of options, algorithms, and plotting. This analysis component utilizes the Nexus cloud computing platform to provide on-demand processing of the data within the user-selected parameters and immediate display of the results. A RESTful web API is exposed for users comfortable with other interfaces and who may want to take advantage of the cloud computing capabilities. This talk discuss how DAT enables on-the-fly sea level research. The talk will introduce the DAT with an end-to-end tour of the tool with exploration and animating of available imagery, a demonstration of comparative analysis and plotting, and how to share and export data along with images for use in publications/presentations. The session will cover what kind of data is available, what kind of analysis is possible, and what are the outputs.

Custom controls

NASA Astrophysics Data System (ADS)

Butell, Bart

1996-02-01

Microsoft's Visual Basic (VB) and Borland's Delphi provide an extremely robust programming environment for delivering multimedia solutions for interactive kiosks, games and titles. Their object oriented use of standard and custom controls enable a user to build extremely powerful applications. A multipurpose, database enabled programming environment that can provide an event driven interface functions as a multimedia kernel. This kernel can provide a variety of authoring solutions (e.g. a timeline based model similar to Macromedia Director or a node authoring model similar to Icon Author). At the heart of the kernel is a set of low level multimedia components providing object oriented interfaces for graphics, audio, video and imaging. Data preparation tools (e.g., layout, palette and Sprite Editors) could be built to manage the media database. The flexible interface for VB allows the construction of an infinite number of user models. The proliferation of these models within a popular, easy to use environment will allow the vast developer segment of 'producer' types to bring their ideas to the market. This is the key to building exciting, content rich multimedia solutions. Microsoft's VB and Borland's Delphi environments combined with multimedia components enable these possibilities.

A web-tool to find spatially explicit climate-smart solutions for the sector agriculture

NASA Astrophysics Data System (ADS)

Verzandvoort, Simone; Kuikman, Peter; Walvoort, Dennis

2017-04-01

Europe faces the challenge to produce more food and more biomass for the bio-economy, to adapt its agricultural sector to negative consequences of climate change, and to reduce greenhouse gas emissions from agriculture. Climate-smart agriculture (CSA) solutions and technologies improve agriculture's productivity and provide economic growth and stability, increase resilience, and help to reduce GHG emissions from agricultural activities. The Climate Smart Agriculture Booster (CSAb) (http://csabooster.climate-kic.org/) is a Flagship Program under Climate-KIC, aiming to facilitate the adoption of CSA solutions and technologies in the European agro-food sector. This adoption requires spatially explicit, contextual information on farming activities and risks and opportunities related to climate change in regions across Europe. Other spatial information supporting adoption includes Information on where successful implementations were already done, on where CSA would profit from enabling policy conditions, and where markets or business opportunities for selling or purchasing technology and knowledge are located or emerging. The Spatial Solution Finder is a web-based spatial tool aiming to help agri-food companies (supply and processing), authorities or agricultural organisations find CSA solutions and technologies that fit local farmers and regions, and to demonstrate examples of successful implementations as well as expected impact at the farm and regional level. The tool is based on state of the art (geo)datasets of environmental and socio-economic conditions (partly open access, partly derived from previous research) and open source web-technology. The philosophy of the tool is that combining existing datasets with contextual information on the region of interest with personalized information entered by the user provides a suitable basis for offering a basket of options for CSA solutions and technologies. Solutions and technologies are recommended to the user based on similarity matrices assigning scores based on criteria relating to the technology (applicability, benefits, costs) and set by the user. The tool is being developed as part of the CSA Booster Flagship Programme in 2017. The design enables embedding the tool in the Open Innovation Platform of the CSAb and in other European platforms, communities and market places on the Internet related to natural capital and innovations. Continuous updating with new functionality and additional datasets during its lifetime is possible and secures that the tool remains up to date.

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

PubMed

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

2017-12-05

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

WebProtégé: A Collaborative Ontology Editor and Knowledge Acquisition Tool for the Web

PubMed Central

Tudorache, Tania; Nyulas, Csongor; Noy, Natalya F.; Musen, Mark A.

2012-01-01

In this paper, we present WebProtégé—a lightweight ontology editor and knowledge acquisition tool for the Web. With the wide adoption of Web 2.0 platforms and the gradual adoption of ontologies and Semantic Web technologies in the real world, we need ontology-development tools that are better suited for the novel ways of interacting, constructing and consuming knowledge. Users today take Web-based content creation and online collaboration for granted. WebProtégé integrates these features as part of the ontology development process itself. We tried to lower the entry barrier to ontology development by providing a tool that is accessible from any Web browser, has extensive support for collaboration, and a highly customizable and pluggable user interface that can be adapted to any level of user expertise. The declarative user interface enabled us to create custom knowledge-acquisition forms tailored for domain experts. We built WebProtégé using the existing Protégé infrastructure, which supports collaboration on the back end side, and the Google Web Toolkit for the front end. The generic and extensible infrastructure allowed us to easily deploy WebProtégé in production settings for several projects. We present the main features of WebProtégé and its architecture and describe briefly some of its uses for real-world projects. WebProtégé is free and open source. An online demo is available at http://webprotege.stanford.edu. PMID:23807872

RDFBuilder: a tool to automatically build RDF-based interfaces for MAGE-OM microarray data sources.

PubMed

Anguita, Alberto; Martin, Luis; Garcia-Remesal, Miguel; Maojo, Victor

2013-07-01

This paper presents RDFBuilder, a tool that enables RDF-based access to MAGE-ML-compliant microarray databases. We have developed a system that automatically transforms the MAGE-OM model and microarray data stored in the ArrayExpress database into RDF format. Additionally, the system automatically enables a SPARQL endpoint. This allows users to execute SPARQL queries for retrieving microarray data, either from specific experiments or from more than one experiment at a time. Our system optimizes response times by caching and reusing information from previous queries. In this paper, we describe our methods for achieving this transformation. We show that our approach is complementary to other existing initiatives, such as Bio2RDF, for accessing and retrieving data from the ArrayExpress database. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Collaborative Planetary GIS with JMARS

NASA Astrophysics Data System (ADS)

Dickenshied, S.; Christensen, P. R.; Edwards, C. S.; Prashad, L. C.; Anwar, S.; Engle, E.; Noss, D.; Jmars Development Team

2010-12-01

Traditional GIS tools have allowed users to work locally with their own datasets in their own computing environment. More recently, data providers have started offering online repositories of preprocessed data which helps minimize the learning curve required to access new datasets. The ideal collaborative GIS tool provides the functionality of a traditional GIS and easy access to preprocessed data repositories while also enabling users to contribute data, analysis, and ideas back into the very tools they're using. JMARS (Java Mission-planning and Analysis for Remote Sensing) is a suite of geospatial applications developed by the Mars Space Flight Facility at Arizona State University. This software is used for mission planning and scientific data analysis by several NASA missions, including Mars Odyssey, Mars Reconnaissance Orbiter, and the Lunar Reconnaissance Orbiter. It is used by scientists, researchers and students of all ages from more than 40 countries around the world. In addition to offering a rich set of global and regional maps and publicly released orbiter images, the JMARS software development team has been working on ways to encourage the creation of collaborative datasets. Bringing together users from diverse teams and backgrounds allows new features to be developed with an interest in making the application useful and accessible to as wide a potential audience as possible. Actively engaging the scientific community in development strategy and hands on tasks allows the creation of user driven data content that would not otherwise be possible. The first community generated dataset to result from this effort is a tool mapping peer-reviewed papers to the locations they relate to on Mars with links to ancillary data. This allows users of JMARS to browse to an area of interest and then quickly locate papers corresponding to that area. Alternately, users can search for published papers over a specified time interval and visually see what areas of Mars have received the most attention over the requested time span.

Building Energy Asset Score for Architects

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

Building Technologies Office

2015-01-01

The Building Energy Asset Score is a national standardized tool for evaluating the physical and structural energy efficiency of commercial and multifamily residential buildings. The Asset Score generates a simple energy efficiency rating that enables comparison among buildings, and identifies opportunities for users to invest in energy efficiency upgrades. It is web-based and free to use. This fact sheet discusses the value of the score for architects.

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

Building Technologies Office

The Building Energy Asset Score is a national standardized tool for evaluating the physical and structural energy efficiency of commercial and multifamily residential buildings. The Asset Score generates a simple energy efficiency rating that enables comparison among buildings, and identifies opportunities for users to invest in energy efficiency upgrades. It is web-based and free to use. This fact sheet discusses the value of the score for energy services companies, engineers and green building consultants.

Adoption of Social Networking in Education: A Study of the Use of Social Networks by Higher Education Students in Oman

ERIC Educational Resources Information Center

Al-Mukhaini, Elham M.; Al-Qayoudhi, Wafa S.; Al-Badi, Ali H.

2014-01-01

The use of social networks is a growing phenomenon, being increasingly important in both private and academic life. Social networks are used as tools to enable users to have social interaction. The use of social networks (SNs) complements and enhances the teaching in traditional classrooms. For example, YouTube, Facebook, wikis, and blogs provide…

The Power and Benefits of Concept Mapping: Measuring Use, Usefulness, Ease of Use, and Satisfaction. Research Report

ERIC Educational Resources Information Center

Freeman, Lee A.; Jessup, Leonard M.

2004-01-01

The power and benefits of concept mapping rest in four arenas: enabling shared understanding, the inclusion of affect, the balance of power, and client involvement. Concept mapping theory and research indicate concept maps (1) are appropriate tools to assist with communication, (2) are easy to use, and (3) are seen as beneficial by their users. An…

Sensor metadata blueprints and computer-aided editing for disciplined SensorML

NASA Astrophysics Data System (ADS)

Tagliolato, Paolo; Oggioni, Alessandro; Fugazza, Cristiano; Pepe, Monica; Carrara, Paola

2016-04-01

The need for continuous, accurate, and comprehensive environmental knowledge has led to an increase in sensor observation systems and networks. The Sensor Web Enablement (SWE) initiative has been promoted by the Open Geospatial Consortium (OGC) to foster interoperability among sensor systems. The provision of metadata according to the prescribed SensorML schema is a key component for achieving this and nevertheless availability of correct and exhaustive metadata cannot be taken for granted. On the one hand, it is awkward for users to provide sensor metadata because of the lack in user-oriented, dedicated tools. On the other, the specification of invariant information for a given sensor category or model (e.g., observed properties and units of measurement, manufacturer information, etc.), can be labor- and timeconsuming. Moreover, the provision of these details is error prone and subjective, i.e., may differ greatly across distinct descriptions for the same system. We provide a user-friendly, template-driven metadata authoring tool composed of a backend web service and an HTML5/javascript client. This results in a form-based user interface that conceals the high complexity of the underlying format. This tool also allows for plugging in external data sources providing authoritative definitions for the aforementioned invariant information. Leveraging these functionalities, we compiled a set of SensorML profiles, that is, sensor metadata blueprints allowing end users to focus only on the metadata items that are related to their specific deployment. The natural extension of this scenario is the involvement of end users and sensor manufacturers in the crowd-sourced evolution of this collection of prototypes. We describe the components and workflow of our framework for computer-aided management of sensor metadata.

Climate Model Diagnostic Analyzer Web Service System

NASA Astrophysics Data System (ADS)

Lee, S.; Pan, L.; Zhai, C.; Tang, B.; Jiang, J. H.

2014-12-01

We have developed a cloud-enabled web-service system that empowers physics-based, multi-variable model performance evaluations and diagnoses through the comprehensive and synergistic use of multiple observational data, reanalysis data, and model outputs. We have developed a methodology to transform an existing science application code into a web service using a Python wrapper interface and Python web service frameworks. The web-service system, called Climate Model Diagnostic Analyzer (CMDA), currently supports (1) all the observational datasets from Obs4MIPs and a few ocean datasets from NOAA and Argo, which can serve as observation-based reference data for model evaluation, (2) many of CMIP5 model outputs covering a broad range of atmosphere, ocean, and land variables from the CMIP5 specific historical runs and AMIP runs, and (3) ECMWF reanalysis outputs for several environmental variables in order to supplement observational datasets. Analysis capabilities currently supported by CMDA are (1) the calculation of annual and seasonal means of physical variables, (2) the calculation of time evolution of the means in any specified geographical region, (3) the calculation of correlation between two variables, (4) the calculation of difference between two variables, and (5) the conditional sampling of one physical variable with respect to another variable. A web user interface is chosen for CMDA because it not only lowers the learning curve and removes the adoption barrier of the tool but also enables instantaneous use, avoiding the hassle of local software installation and environment incompatibility. CMDA will be used as an educational tool for the summer school organized by JPL's Center for Climate Science in 2014. In order to support 30+ simultaneous users during the school, we have deployed CMDA to the Amazon cloud environment. The cloud-enabled CMDA will provide each student with a virtual machine while the user interaction with the system will remain the same through web-browser interfaces. The summer school will serve as a valuable testbed for the tool development, preparing CMDA to serve its target community: Earth-science modeling and model-analysis community.

Subsurface data visualization in Virtual Reality

NASA Astrophysics Data System (ADS)

Krijnen, Robbert; Smelik, Ruben; Appleton, Rick; van Maanen, Peter-Paul

2017-04-01

Due to their increasing complexity and size, visualization of geological data is becoming more and more important. It enables detailed examining and reviewing of large volumes of geological data and it is often used as a communication tool for reporting and education to demonstrate the importance of the geology to policy makers. In the Netherlands two types of nation-wide geological models are available: 1) Layer-based models in which the subsurface is represented by a series of tops and bases of geological or hydrogeological units, and 2) Voxel models in which the subsurface is subdivided in a regular grid of voxels that can contain different properties per voxel. The Geological Survey of the Netherlands (GSN) provides an interactive web portal that delivers maps and vertical cross-sections of such layer-based and voxel models. From this portal you can download a 3D subsurface viewer that can visualize the voxel model data of an area of 20 × 25 km with 100 × 100 × 5 meter voxel resolution on a desktop computer. Virtual Reality (VR) technology enables us to enhance the visualization of this volumetric data in a more natural way as compared to a standard desktop, keyboard mouse setup. The use of VR for data visualization is not new but recent developments has made expensive hardware and complex setups unnecessary. The availability of consumer of-the-shelf VR hardware enabled us to create an new intuitive and low visualization tool. A VR viewer has been implemented using the HTC Vive head set and allows visualization and analysis of the GSN voxel model data with geological or hydrogeological units. The user can navigate freely around the voxel data (20 × 25 km) which is presented in a virtual room at a scale of 2 × 2 or 3 × 3 meters. To enable analysis, e.g. hydraulic conductivity, the user can select filters to remove specific hydrogeological units. The user can also use slicing to cut-off specific sections of the voxel data to get a closer look. This slicing can be done in any direction using a 'virtual knife'. Future plans are to further improve performance from 30 up to 90 Hz update rate to reduce possible motion sickness, add more advanced filtering capabilities as well as a multi user setup, annotation capabilities and visualizing of historical data.

Correction tool for Active Shape Model based lumbar muscle segmentation.

PubMed

Valenzuela, Waldo; Ferguson, Stephen J; Ignasiak, Dominika; Diserens, Gaelle; Vermathen, Peter; Boesch, Chris; Reyes, Mauricio

2015-08-01

In the clinical environment, accuracy and speed of the image segmentation process plays a key role in the analysis of pathological regions. Despite advances in anatomic image segmentation, time-effective correction tools are commonly needed to improve segmentation results. Therefore, these tools must provide faster corrections with a low number of interactions, and a user-independent solution. In this work we present a new interactive correction method for correcting the image segmentation. Given an initial segmentation and the original image, our tool provides a 2D/3D environment, that enables 3D shape correction through simple 2D interactions. Our scheme is based on direct manipulation of free form deformation adapted to a 2D environment. This approach enables an intuitive and natural correction of 3D segmentation results. The developed method has been implemented into a software tool and has been evaluated for the task of lumbar muscle segmentation from Magnetic Resonance Images. Experimental results show that full segmentation correction could be performed within an average correction time of 6±4 minutes and an average of 68±37 number of interactions, while maintaining the quality of the final segmentation result within an average Dice coefficient of 0.92±0.03.

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

PubMed Central

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

2014-01-01

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

MGDS: Free, on-line, cutting-edge tools to enable the democratisation of geoscience data

NASA Astrophysics Data System (ADS)

Goodwillie, A. M.; Ryan, W. B.; O'Hara, S.; Ferrini, V.; Arko, R. A.; Coplan, J.; Chan, S.; Carbotte, S. M.; Nitsche, F. O.; Bonczkowski, J.; Morton, J. J.; Weissel, R.; Leung, A.

2010-12-01

The availability of user-friendly, effective cyber-information resources for accessing and manipulating geoscience data has grown rapidly in recent years. Based at Lamont-Doherty Earth Observatory the MGDS group has developed a number of free tools that have wide application across the geosciences for both educators and researchers. A simple web page (http://www.marine-geo.org/) allows users to search for and download many types of data by key word, geographical region, or published citation. The popular Create Maps and Grids function and the downloadable Google Earth-compatible KML files appeal to a wide user base. MGDS MediaBank galleries (http://media.marine-geo.org/) enable users to view and download compelling images that are purposefully selected for their educational value from NSF-funded field programs. GeoMapApp (http://www.geomapapp.org), a free map-based interactive tool that works on any machine, is increasingly being adopted across a broad suite of users from middle school students to university researchers. GeoMapApp allows users to plot, manipulate and present data in an intuitive geographical reference frame. GeoMapApp offers a convenient way to explore the wide range of built-in data sets, to quickly generate maps and images that aid visualisation and, when importing their own gridded and tabular data sets, to access the same rich built-in functionality. A user guide, short multi-media tutorials, and webinar are available on-line. The regularly-updated Global Multi-Resolution Topography (GMRT) Synthesis is used as the default GeoMapApp base map and is an increasingly popular means to rapidly create location maps. Additionally, the layer manager offers a fast way to overlay and compare multiple data sets and is augmented by the ability to alter layer transparency so that underlying layers become visible. Examples of GeoMapApp built-in data sets include high-resolution land topography and ocean floor bathymetry derived from satellite and multi-beam swath mapping systems - these can be profiled, shaded, and contoured; geo-registered geochemical sample analyses from the EarthChem database; plate boundary, earthquake and volcano catalogues; physical oceanography global and water column data; seafloor photos and Alvin dive video images; geological maps at various scales; and, high-quality coastline, lakes and rivers data. Customised data portals offer enhanced functionality for multi-channel seismic profiles, drill core logs, and earthquake animations. GeoMapApp is used in many MARGINS undergraduate-level off-the-shelf interactive learning activities called mini-lessons (http://serc.carleton.edu/margins/collection.html). Examples of educational applicability will be shown.

A Web Architecture to Geographically Interrogate CHIRPS Rainfall and eMODIS NDVI for Land Use Change

NASA Technical Reports Server (NTRS)

Burks, Jason E.; Limaye, Ashutosh

2014-01-01

Monitoring of rainfall and vegetation over the continent of Africa is important for assessing the status of crop health and agriculture, along with long-term changes in land use change. These issues can be addressed through examination of long-term precipitation (rainfall) data sets and remote sensing of land surface vegetation and land use types. Two products have been used previously to address these goals: the Climate Hazard Group Infrared Precipitation with Stations (CHIRPS) rainfall data, and multi-day composites of Normalized Difference Vegetation Index (NDVI) from the USGS eMODIS product. Combined, these are very large data sets that require unique tools and architecture to facilitate a variety of data analysis methods or data exploration by the end user community. To address these needs, a web-enabled system has been developed to allow end-users to interrogate CHIRPS rainfall and eMODIS NDVI data over the continent of Africa. The architecture allows end-users to use custom defined geometries, or the use of predefined political boundaries in their interrogation of the data. The massive amount of data interrogated by the system allows the end-users with only a web browser to extract vital information in order to investigate land use change and its causes. The system can be used to generate daily, monthly and yearly averages over a geographical area and range of dates of interest to the user. It also provides analysis of trends in precipitation or vegetation change for times of interest. The data provided back to the end-user is displayed in graphical form and can be exported for use in other, external tools. The development of this tool has significantly decreased the investment and requirements for end-users to use these two important datasets, while also allowing the flexibility to the end-user to limit the search to the area of interest.

A Review on the Bioinformatics Tools for Neuroimaging

PubMed Central

MAN, Mei Yen; ONG, Mei Sin; Mohamad, Mohd Saberi; DERIS, Safaai; SULONG, Ghazali; YUNUS, Jasmy; CHE HARUN, Fauzan Khairi

2015-01-01

Neuroimaging is a new technique used to create images of the structure and function of the nervous system in the human brain. Currently, it is crucial in scientific fields. Neuroimaging data are becoming of more interest among the circle of neuroimaging experts. Therefore, it is necessary to develop a large amount of neuroimaging tools. This paper gives an overview of the tools that have been used to image the structure and function of the nervous system. This information can help developers, experts, and users gain insight and a better understanding of the neuroimaging tools available, enabling better decision making in choosing tools of particular research interest. Sources, links, and descriptions of the application of each tool are provided in this paper as well. Lastly, this paper presents the language implemented, system requirements, strengths, and weaknesses of the tools that have been widely used to image the structure and function of the nervous system. PMID:27006633

National Fusion Collaboratory: Grid Computing for Simulations and Experiments

NASA Astrophysics Data System (ADS)

Greenwald, Martin

2004-05-01

The National Fusion Collaboratory Project is creating a computational grid designed to advance scientific understanding and innovation in magnetic fusion research by facilitating collaborations, enabling more effective integration of experiments, theory and modeling and allowing more efficient use of experimental facilities. The philosophy of FusionGrid is that data, codes, analysis routines, visualization tools, and communication tools should be thought of as network available services, easily used by the fusion scientist. In such an environment, access to services is stressed rather than portability. By building on a foundation of established computer science toolkits, deployment time can be minimized. These services all share the same basic infrastructure that allows for secure authentication and resource authorization which allows stakeholders to control their own resources such as computers, data and experiments. Code developers can control intellectual property, and fair use of shared resources can be demonstrated and controlled. A key goal is to shield scientific users from the implementation details such that transparency and ease-of-use are maximized. The first FusionGrid service deployed was the TRANSP code, a widely used tool for transport analysis. Tools for run preparation, submission, monitoring and management have been developed and shared among a wide user base. This approach saves user sites from the laborious effort of maintaining such a large and complex code while at the same time reducing the burden on the development team by avoiding the need to support a large number of heterogeneous installations. Shared visualization and A/V tools are being developed and deployed to enhance long-distance collaborations. These include desktop versions of the Access Grid, a highly capable multi-point remote conferencing tool and capabilities for sharing displays and analysis tools over local and wide-area networks.

Collaborative search in electronic health records.

PubMed

Zheng, Kai; Mei, Qiaozhu; Hanauer, David A

2011-05-01

A full-text search engine can be a useful tool for augmenting the reuse value of unstructured narrative data stored in electronic health records (EHR). A prominent barrier to the effective utilization of such tools originates from users' lack of search expertise and/or medical-domain knowledge. To mitigate the issue, the authors experimented with a 'collaborative search' feature through a homegrown EHR search engine that allows users to preserve their search knowledge and share it with others. This feature was inspired by the success of many social information-foraging techniques used on the web that leverage users' collective wisdom to improve the quality and efficiency of information retrieval. The authors conducted an empirical evaluation study over a 4-year period. The user sample consisted of 451 academic researchers, medical practitioners, and hospital administrators. The data were analyzed using a social-network analysis to delineate the structure of the user collaboration networks that mediated the diffusion of knowledge of search. The users embraced the concept with considerable enthusiasm. About half of the EHR searches processed by the system (0.44 million) were based on stored search knowledge; 0.16 million utilized shared knowledge made available by other users. The social-network analysis results also suggest that the user-collaboration networks engendered by the collaborative search feature played an instrumental role in enabling the transfer of search knowledge across people and domains. Applying collaborative search, a social information-foraging technique popularly used on the web, may provide the potential to improve the quality and efficiency of information retrieval in healthcare.

Collaborative search in electronic health records

PubMed Central

Mei, Qiaozhu; Hanauer, David A

2011-01-01

Objective A full-text search engine can be a useful tool for augmenting the reuse value of unstructured narrative data stored in electronic health records (EHR). A prominent barrier to the effective utilization of such tools originates from users' lack of search expertise and/or medical-domain knowledge. To mitigate the issue, the authors experimented with a ‘collaborative search’ feature through a homegrown EHR search engine that allows users to preserve their search knowledge and share it with others. This feature was inspired by the success of many social information-foraging techniques used on the web that leverage users' collective wisdom to improve the quality and efficiency of information retrieval. Design The authors conducted an empirical evaluation study over a 4-year period. The user sample consisted of 451 academic researchers, medical practitioners, and hospital administrators. The data were analyzed using a social-network analysis to delineate the structure of the user collaboration networks that mediated the diffusion of knowledge of search. Results The users embraced the concept with considerable enthusiasm. About half of the EHR searches processed by the system (0.44 million) were based on stored search knowledge; 0.16 million utilized shared knowledge made available by other users. The social-network analysis results also suggest that the user-collaboration networks engendered by the collaborative search feature played an instrumental role in enabling the transfer of search knowledge across people and domains. Conclusion Applying collaborative search, a social information-foraging technique popularly used on the web, may provide the potential to improve the quality and efficiency of information retrieval in healthcare. PMID:21486887

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

PubMed

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

2014-08-08

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

BioNSi: A Discrete Biological Network Simulator Tool.

PubMed

Rubinstein, Amir; Bracha, Noga; Rudner, Liat; Zucker, Noga; Sloin, Hadas E; Chor, Benny

2016-08-05

Modeling and simulation of biological networks is an effective and widely used research methodology. The Biological Network Simulator (BioNSi) is a tool for modeling biological networks and simulating their discrete-time dynamics, implemented as a Cytoscape App. BioNSi includes a visual representation of the network that enables researchers to construct, set the parameters, and observe network behavior under various conditions. To construct a network instance in BioNSi, only partial, qualitative biological data suffices. The tool is aimed for use by experimental biologists and requires no prior computational or mathematical expertise. BioNSi is freely available at http://bionsi.wix.com/bionsi , where a complete user guide and a step-by-step manual can also be found.

Orbit Design Based on the Global Maps of Telecom Metrics

NASA Technical Reports Server (NTRS)

Lee, Charles H.; Cheung, Kar-Ming; Edwards, Chad; Noreen, Gary K.; Vaisnys, Arvydas

2004-01-01

In this paper we describe an orbit design aide tool, called Telecom Orbit Analysis and Simulation Tool(TOAST). Although it can be used for studying and selecting orbits for any planet, we solely concentrate on its use for Mars. By specifying the six orbital elements for an orbit, a time frame of interest, a horizon mask angle, and some telecom parameters such as the transmitting power, frequency, antenna gains, antenna losses, link margin, received threshold powers for the rates, etc. this tool enables the user to view the animation of the orbit in two and three-dimensional different telecom metrics at any point on the Mars, namely the global planetary map.

imDEV: a graphical user interface to R multivariate analysis tools in Microsoft Excel.

PubMed

Grapov, Dmitry; Newman, John W

2012-09-01

Interactive modules for Data Exploration and Visualization (imDEV) is a Microsoft Excel spreadsheet embedded application providing an integrated environment for the analysis of omics data through a user-friendly interface. Individual modules enables interactive and dynamic analyses of large data by interfacing R's multivariate statistics and highly customizable visualizations with the spreadsheet environment, aiding robust inferences and generating information-rich data visualizations. This tool provides access to multiple comparisons with false discovery correction, hierarchical clustering, principal and independent component analyses, partial least squares regression and discriminant analysis, through an intuitive interface for creating high-quality two- and a three-dimensional visualizations including scatter plot matrices, distribution plots, dendrograms, heat maps, biplots, trellis biplots and correlation networks. Freely available for download at http://sourceforge.net/projects/imdev/. Implemented in R and VBA and supported by Microsoft Excel (2003, 2007 and 2010).

Software Verification of Orion Cockpit Displays

NASA Technical Reports Server (NTRS)

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

2017-01-01

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

User-oriented evaluation of mechanical single-channel axial pipettes.

PubMed

Sormunen, Erja; Nevala, Nina

2013-09-01

Hand tools should be designed so that they are comfortable to use, fit the hand and are user-oriented. Six different manual, single-channel axial pipettes were evaluated for such objective outcomes as muscular activity, wrist postures and efficiency, as well as for subjective outcomes concerning self-assessed features of pipette usability and musculoskeletal strain. Ten experienced laboratory employees volunteered for the study. The results showed that light and short pipettes with better tool comfort resulted in reduced muscular activity and perceived musculoskeletal strain when they were compared with a long and heavy pipette. There were no differences in the efficiency between the different pipettes. Combining both the objective and subjective measures enabled a broader evaluation of product usability. The results of this study can be used both in product development and as information on which to base the purchase of new pipettes for laboratory work. Copyright © 2012 Elsevier Ltd and The Ergonomics Society. All rights reserved.

Fuzzy Logic Engine

NASA Technical Reports Server (NTRS)

Howard, Ayanna

2005-01-01

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

Anatomical guidance for functional near-infrared spectroscopy: AtlasViewer tutorial

PubMed Central

Aasted, Christopher M.; Yücel, Meryem A.; Cooper, Robert J.; Dubb, Jay; Tsuzuki, Daisuke; Becerra, Lino; Petkov, Mike P.; Borsook, David; Dan, Ippeita; Boas, David A.

2015-01-01

Abstract. Functional near-infrared spectroscopy (fNIRS) is an optical imaging method that is used to noninvasively measure cerebral hemoglobin concentration changes induced by brain activation. Using structural guidance in fNIRS research enhances interpretation of results and facilitates making comparisons between studies. AtlasViewer is an open-source software package we have developed that incorporates multiple spatial registration tools to enable structural guidance in the interpretation of fNIRS studies. We introduce the reader to the layout of the AtlasViewer graphical user interface, the folder structure, and user files required in the creation of fNIRS probes containing sources and detectors registered to desired locations on the head, evaluating probe fabrication error and intersubject probe placement variability, and different procedures for estimating measurement sensitivity to different brain regions as well as image reconstruction performance. Further, we detail how AtlasViewer provides a generic head atlas for guiding interpretation of fNIRS results, but also permits users to provide subject-specific head anatomies to interpret their results. We anticipate that AtlasViewer will be a valuable tool in improving the anatomical interpretation of fNIRS studies. PMID:26157991

Software Tool Integrating Data Flow Diagrams and Petri Nets

NASA Technical Reports Server (NTRS)

Thronesbery, Carroll; Tavana, Madjid

2010-01-01

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

Integrated Instrument Simulator Suites for Earth Science

NASA Technical Reports Server (NTRS)

Tanelli, Simone; Tao, Wei-Kuo; Matsui, Toshihisa; Hostetler, Chris; Hair, Johnathan; Butler, Carolyn; Kuo, Kwo-Sen; Niamsuwan, Noppasin; Johnson, Michael P.; Jacob, Joseph C.;

IQARIS : a tool for the intelligent querying, analysis, and retrieval from information systems.

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

Hummel, J. R.; Silver, R. B.

Information glut is one of the primary characteristics of the electronic age. Managing such large volumes of information (e.g., keeping track of the types, where they are, their relationships, who controls them, etc.) can be done efficiently with an intelligent, user-oriented information management system. The purpose of this paper is to describe a concept for managing information resources based on an intelligent information technology system developed by the Argonne National Laboratory for managing digital libraries. The Argonne system, Intelligent Query (IQ), enables users to query digital libraries and view the holdings that match the query from different perspectives.

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

PubMed

Adolf-Bryfogle, Jared; Dunbrack, Roland L

2013-01-01

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

Collective Intelligence Generation from User Contributed Content

NASA Astrophysics Data System (ADS)

Solachidis, Vassilios; Mylonas, Phivos; Geyer-Schulz, Andreas; Hoser, Bettina; Chapman, Sam; Ciravegna, Fabio; Lanfranchi, Vita; Scherp, Ansgar; Staab, Steffen; Contopoulos, Costis; Gkika, Ioanna; Bakaimis, Byron; Smrz, Pavel; Kompatsiaris, Yiannis; Avrithis, Yannis

In this paper we provide a foundation for a new generation of services and tools. We define new ways of capturing, sharing and reusing information and intelligence provided by single users and communities, as well as organizations by enabling the extraction, generation, interpretation and management of Collective Intelligence from user generated digital multimedia content. Different layers of intelligence are generated, which together constitute the notion of Collective Intelligence. The automatic generation of Collective Intelligence constitutes a departure from traditional methods for information sharing, since information from both the multimedia content and social aspects will be merged, while at the same time the social dynamics will be taken into account. In the context of this work, we present two case studies: an Emergency Response and a Consumers Social Group case study.

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

Steed, Chad Allen

EDENx is a multivariate data visualization tool that allows interactive user driven analysis of large-scale data sets with high dimensionality. EDENx builds on our earlier system, called EDEN to enable analysis of more dimensions and larger scale data sets. EDENx provides an initial overview of summary statistics for each variable in the data set under investigation. EDENx allows the user to interact with graphical summary plots of the data to investigate subsets and their statistical associations. These plots include histograms, binned scatterplots, binned parallel coordinate plots, timeline plots, and graphical correlation indicators. From the EDENx interface, a user can selectmore » a subsample of interest and launch a more detailed data visualization via the EDEN system. EDENx is best suited for high-level, aggregate analysis tasks while EDEN is more appropriate for detail data investigations.« less

Updates to the Demographic and Spatial Allocation Models to ...

EPA Pesticide Factsheets

EPA's announced the availability of the final report, Updates to the Demographic and Spatial Allocation Models to Produce Integrated Climate and Land Use Scenarios (ICLUS) (Version 2). This update furthered land change modeling by providing nationwide housing development scenarios up to 2100. This newest version includes updated population and land use data sets and addresses limitations identified in ICLUS v1 in both the migration and spatial allocation models. The companion user guide (Final Report) describes the development of ICLUS v2 and the updates that were made to the original data sets and the demographic and spatial allocation models. The GIS tool enables users to run SERGoM with the population projections developed for the ICLUS project and allows users to modify the spatial allocation housing density across the landscape.

vvtools v. 1.0

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

Drake, Richard R.

Vvtools is a suite of testing tools, with a focus on reproducible verification and validation. They are written in pure Python, and contain a test harness and an automated process management tool. Users of vvtools can develop suites of verification and validation tests and run them on small to large high performance computing resources in an automated and reproducible way. The test harness enables complex processes to be performed in each test and even supports a one-level parent/child dependency between tests. It includes a built in capability to manage workloads requiring multiple processors and platforms that use batch queueing systems.

sRNAdb: A small non-coding RNA database for gram-positive bacteria

PubMed Central

2012-01-01

Background The class of small non-coding RNA molecules (sRNA) regulates gene expression by different mechanisms and enables bacteria to mount a physiological response due to adaptation to the environment or infection. Over the last decades the number of sRNAs has been increasing rapidly. Several databases like Rfam or fRNAdb were extended to include sRNAs as a class of its own. Furthermore new specialized databases like sRNAMap (gram-negative bacteria only) and sRNATarBase (target prediction) were established. To the best of the authors’ knowledge no database focusing on sRNAs from gram-positive bacteria is publicly available so far. Description In order to understand sRNA’s functional and phylogenetic relationships we have developed sRNAdb and provide tools for data analysis and visualization. The data compiled in our database is assembled from experiments as well as from bioinformatics analyses. The software enables comparison and visualization of gene loci surrounding the sRNAs of interest. To accomplish this, we use a client–server based approach. Offline versions of the database including analyses and visualization tools can easily be installed locally on the user’s computer. This feature facilitates customized local addition of unpublished sRNA candidates and related information such as promoters or terminators using tab-delimited files. Conclusion sRNAdb allows a user-friendly and comprehensive comparative analysis of sRNAs from available sequenced gram-positive prokaryotic replicons. Offline versions including analysis and visualization tools facilitate complex user specific bioinformatics analyses. PMID:22883983

EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management

PubMed Central

Barton, G; Abbott, J; Chiba, N; Huang, DW; Huang, Y; Krznaric, M; Mack-Smith, J; Saleem, A; Sherman, BT; Tiwari, B; Tomlinson, C; Aitman, T; Darlington, J; Game, L; Sternberg, MJE; Butcher, SA

2008-01-01

Background Microarray experimentation requires the application of complex analysis methods as well as the use of non-trivial computer technologies to manage the resultant large data sets. This, together with the proliferation of tools and techniques for microarray data analysis, makes it very challenging for a laboratory scientist to keep up-to-date with the latest developments in this field. Our aim was to develop a distributed e-support system for microarray data analysis and management. Results EMAAS (Extensible MicroArray Analysis System) is a multi-user rich internet application (RIA) providing simple, robust access to up-to-date resources for microarray data storage and analysis, combined with integrated tools to optimise real time user support and training. The system leverages the power of distributed computing to perform microarray analyses, and provides seamless access to resources located at various remote facilities. The EMAAS framework allows users to import microarray data from several sources to an underlying database, to pre-process, quality assess and analyse the data, to perform functional analyses, and to track data analysis steps, all through a single easy to use web portal. This interface offers distance support to users both in the form of video tutorials and via live screen feeds using the web conferencing tool EVO. A number of analysis packages, including R-Bioconductor and Affymetrix Power Tools have been integrated on the server side and are available programmatically through the Postgres-PLR library or on grid compute clusters. Integrated distributed resources include the functional annotation tool DAVID, GeneCards and the microarray data repositories GEO, CELSIUS and MiMiR. EMAAS currently supports analysis of Affymetrix 3' and Exon expression arrays, and the system is extensible to cater for other microarray and transcriptomic platforms. Conclusion EMAAS enables users to track and perform microarray data management and analysis tasks through a single easy-to-use web application. The system architecture is flexible and scalable to allow new array types, analysis algorithms and tools to be added with relative ease and to cope with large increases in data volume. PMID:19032776

Learning decision making through serious games.

PubMed

Kaczmarczyk, Joseph; Davidson, Richard; Bryden, Daniele; Haselden, Stephen; Vivekananda-Schmidt, Pirashanthie

2016-08-01

In Serious Games (SGs), educational content is integrated into a game so that learning is intrinsic to play, thereby motivating players and improving engagement. SGs enable learning by developing situated understanding in users and by enabling players to practise safe clinical decision making; however, the use of SGs in medical education is not well established. We aimed to design a game-based resource to teach clinical decision making to medical students, and to assess user perceptions of educational value, usability and the role for SGs in undergraduate training. An SG focusing on the acute management of tachyarrhythmias was developed. Third- and fourth-year medical students at the medical school were invited to use and evaluate the game using questionnaires and focus groups. We invited 479 students, and 281 accessed the game. Only 47 students completed the questionnaire and 31 students participated in the focus groups. The data suggest that SGs: (1) can allow students to rehearse taking responsibility for decision making; (2) are fun and motivational; (3) have a role in revising and consolidating knowledge; and (4) could be formative assessment tools. Serious Games enable learning by developing situated understanding in users SGs could be employed as adjuvant learning resources to develop students' skills and knowledge. Further empirical research is required to assess the added value of games in medical education. © 2015 John Wiley & Sons Ltd.

OpenTopography: Enabling Online Access to High-Resolution Lidar Topography Data and Processing Tools

NASA Astrophysics Data System (ADS)

Crosby, Christopher; Nandigam, Viswanath; Baru, Chaitan; Arrowsmith, J. Ramon

2013-04-01

High-resolution topography data acquired with lidar (light detection and ranging) technology are revolutionizing the way we study the Earth's surface and overlying vegetation. These data, collected from airborne, tripod, or mobile-mounted scanners have emerged as a fundamental tool for research on topics ranging from earthquake hazards to hillslope processes. Lidar data provide a digital representation of the earth's surface at a resolution sufficient to appropriately capture the processes that contribute to landscape evolution. The U.S. National Science Foundation-funded OpenTopography Facility (http://www.opentopography.org) is a web-based system designed to democratize access to earth science-oriented lidar topography data. OpenTopography provides free, online access to lidar data in a number of forms, including the raw point cloud and associated geospatial-processing tools for customized analysis. The point cloud data are co-located with on-demand processing tools to generate digital elevation models, and derived products and visualizations which allow users to quickly access data in a format appropriate for their scientific application. The OpenTopography system is built using a service-oriented architecture (SOA) that leverages cyberinfrastructure resources at the San Diego Supercomputer Center at the University of California San Diego to allow users, regardless of expertise level, to access these massive lidar datasets and derived products for use in research and teaching. OpenTopography hosts over 500 billion lidar returns covering 85,000 km2. These data are all in the public domain and are provided by a variety of partners under joint agreements and memoranda of understanding with OpenTopography. Partners include national facilities such as the NSF-funded National Center for Airborne Lidar Mapping (NCALM), as well as non-governmental organizations and local, state, and federal agencies. OpenTopography has become a hub for high-resolution topography resources. Datasets hosted by other organizations, as well as lidar-specific software, can be registered into the OpenTopography catalog, providing users a "one-stop shop" for such information. With several thousand active users, OpenTopography is an excellent example of a mature Spatial Data Infrastructure system that is enabling access to challenging data for research, education and outreach. Ongoing OpenTopography design and development work includes the archive and publication of datasets using digital object identifiers (DOIs); creation of a more flexible and scalable high-performance environment for processing of large datasets; expanded support for satellite and terrestrial lidar; and creation of a "pluggable" infrastructure for third-party programs and algorithms. OpenTopography has successfully created a facility for sharing lidar data. In the project's next phase, we are working to enable equally easy and successful sharing of services for processing and analysis of these data.

Improving e-book access via a library-developed full-text search tool.

PubMed

Foust, Jill E; Bergen, Phillip; Maxeiner, Gretchen L; Pawlowski, Peter N

2007-01-01

This paper reports on the development of a tool for searching the contents of licensed full-text electronic book (e-book) collections. The Health Sciences Library System (HSLS) provides services to the University of Pittsburgh's medical programs and large academic health system. The HSLS has developed an innovative tool for federated searching of its e-book collections. Built using the XML-based Vivísimo development environment, the tool enables a user to perform a full-text search of over 2,500 titles from the library's seven most highly used e-book collections. From a single "Google-style" query, results are returned as an integrated set of links pointing directly to relevant sections of the full text. Results are also grouped into categories that enable more precise retrieval without reformulation of the search. A heuristic evaluation demonstrated the usability of the tool and a web server log analysis indicated an acceptable level of usage. Based on its success, there are plans to increase the number of online book collections searched. This library's first foray into federated searching has produced an effective tool for searching across large collections of full-text e-books and has provided a good foundation for the development of other library-based federated searching products.

Improving e-book access via a library-developed full-text search tool*

PubMed Central

Foust, Jill E.; Bergen, Phillip; Maxeiner, Gretchen L.; Pawlowski, Peter N.

2007-01-01

Purpose: This paper reports on the development of a tool for searching the contents of licensed full-text electronic book (e-book) collections. Setting: The Health Sciences Library System (HSLS) provides services to the University of Pittsburgh's medical programs and large academic health system. Brief Description: The HSLS has developed an innovative tool for federated searching of its e-book collections. Built using the XML-based Vivísimo development environment, the tool enables a user to perform a full-text search of over 2,500 titles from the library's seven most highly used e-book collections. From a single “Google-style” query, results are returned as an integrated set of links pointing directly to relevant sections of the full text. Results are also grouped into categories that enable more precise retrieval without reformulation of the search. Results/Evaluation: A heuristic evaluation demonstrated the usability of the tool and a web server log analysis indicated an acceptable level of usage. Based on its success, there are plans to increase the number of online book collections searched. Conclusion: This library's first foray into federated searching has produced an effective tool for searching across large collections of full-text e-books and has provided a good foundation for the development of other library-based federated searching products. PMID:17252065

GREAT: a web portal for Genome Regulatory Architecture Tools.

PubMed

Bouyioukos, Costas; Bucchini, François; Elati, Mohamed; Képès, François

2016-07-08

GREAT (Genome REgulatory Architecture Tools) is a novel web portal for tools designed to generate user-friendly and biologically useful analysis of genome architecture and regulation. The online tools of GREAT are freely accessible and compatible with essentially any operating system which runs a modern browser. GREAT is based on the analysis of genome layout -defined as the respective positioning of co-functional genes- and its relation with chromosome architecture and gene expression. GREAT tools allow users to systematically detect regular patterns along co-functional genomic features in an automatic way consisting of three individual steps and respective interactive visualizations. In addition to the complete analysis of regularities, GREAT tools enable the use of periodicity and position information for improving the prediction of transcription factor binding sites using a multi-view machine learning approach. The outcome of this integrative approach features a multivariate analysis of the interplay between the location of a gene and its regulatory sequence. GREAT results are plotted in web interactive graphs and are available for download either as individual plots, self-contained interactive pages or as machine readable tables for downstream analysis. The GREAT portal can be reached at the following URL https://absynth.issb.genopole.fr/GREAT and each individual GREAT tool is available for downloading. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

JAva GUi for Applied Research (JAGUAR) v 3.0

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

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

Maser: one-stop platform for NGS big data from analysis to visualization

PubMed Central

Kinjo, Sonoko; Monma, Norikazu; Misu, Sadahiko; Kitamura, Norikazu; Imoto, Junichi; Yoshitake, Kazutoshi; Gojobori, Takashi; Ikeo, Kazuho

2018-01-01

Abstract A major challenge in analyzing the data from high-throughput next-generation sequencing (NGS) is how to handle the huge amounts of data and variety of NGS tools and visualize the resultant outputs. To address these issues, we developed a cloud-based data analysis platform, Maser (Management and Analysis System for Enormous Reads), and an original genome browser, Genome Explorer (GE). Maser enables users to manage up to 2 terabytes of data to conduct analyses with easy graphical user interface operations and offers analysis pipelines in which several individual tools are combined as a single pipeline for very common and standard analyses. GE automatically visualizes genome assembly and mapping results output from Maser pipelines, without requiring additional data upload. With this function, the Maser pipelines can graphically display the results output from all the embedded tools and mapping results in a web browser. Therefore Maser realized a more user-friendly analysis platform especially for beginners by improving graphical display and providing the selected standard pipelines that work with built-in genome browser. In addition, all the analyses executed on Maser are recorded in the analysis history, helping users to trace and repeat the analyses. The entire process of analysis and its histories can be shared with collaborators or opened to the public. In conclusion, our system is useful for managing, analyzing, and visualizing NGS data and achieves traceability, reproducibility, and transparency of NGS analysis. Database URL: http://cell-innovation.nig.ac.jp/maser/ PMID:29688385

Real Time Metrics and Analysis of Integrated Arrival, Departure, and Surface Operations

NASA Technical Reports Server (NTRS)

Sharma, Shivanjli; Fergus, John

2017-01-01

A real time dashboard was developed in order to inform and present users notifications and integrated information regarding airport surface operations. The dashboard is a supplement to capabilities and tools that incorporate arrival, departure, and surface air-traffic operations concepts in a NextGen environment. As trajectory-based departure scheduling and collaborative decision making tools are introduced in order to reduce delays and uncertainties in taxi and climb operations across the National Airspace System, users across a number of roles benefit from a real time system that enables common situational awareness. In addition to shared situational awareness the dashboard offers the ability to compute real time metrics and analysis to inform users about capacity, predictability, and efficiency of the system as a whole. This paper describes the architecture of the real time dashboard as well as an initial set of metrics computed on operational data. The potential impact of the real time dashboard is studied at the site identified for initial deployment and demonstration in 2017; Charlotte-Douglas International Airport. Analysis and metrics computed in real time illustrate the opportunity to provide common situational awareness and inform users of metrics across delay, throughput, taxi time, and airport capacity. In addition, common awareness of delays and the impact of takeoff and departure restrictions stemming from traffic flow management initiatives are explored. The potential of the real time tool to inform the predictability and efficiency of using a trajectory-based departure scheduling system is also discussed.

Check and Report Ebola (CARE) Hotline: The User Perspective of an Innovative Tool for Postarrival Monitoring of Ebola in the United States.

PubMed

McCarthy, Ilana Olin; Wojno, Abbey E; Joseph, Heather A; Teesdale, Scott

2017-11-14

The response to the 2014-2016 Ebola epidemic included an unprecedented effort from federal, state, and local public health authorities to monitor the health of travelers entering the United States from countries with Ebola outbreaks. The Check and Report Ebola (CARE) Hotline, a novel approach to monitoring, was designed to enable travelers to report their health status daily to an interactive voice recognition (IVR) system. The system was tested with 70 Centers for Disease Control and Prevention (CDC) federal employees returning from deployments in outbreak countries. The objective of this study was to describe the development of the CARE Hotline as a tool for postarrival monitoring and examine the usage characteristics and user experience of the tool during a public health emergency. Data were obtained from two sources. First, the CARE Hotline system produced a call log which summarized the usage characteristics of all 70 users' daily health reports. Second, we surveyed federal employees (n=70) who used the CARE Hotline to engage in monitoring. A total of 21 (21/70, 30%) respondents were included in the survey analytic sample. While the CARE Hotline was used for monitoring, 70 users completed a total of 1313 calls. We found that 94.06% (1235/1313) of calls were successful, and the average call time significantly decreased from the beginning of the monitoring period to the end by 32 seconds (Z score=-6.52, P<.001). CARE Hotline call log data were confirmed by user feedback; survey results indicated that users became more familiar with the system and found the system easier to use, from the beginning to the end of their monitoring period. The majority of the users were highly satisfied (90%, 19/21) with the system, indicating ease of use and convenience as primary reasons, and would recommend it for future monitoring efforts (90%, 19/21). The CARE Hotline garnered high user satisfaction, required minimal reporting time from users, and was an easily learned tool for monitoring. This phone-based technology can be modified for future public health emergencies. ©Ilana Olin McCarthy, Abbey E Wojno, Heather A Joseph, Scott Teesdale. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 14.11.2017.

Building Energy Asset Score for Building Owners

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

Building Technologies Office

2015-01-01

The Building Energy Asset Score is a national standardized tool for evaluating the physical and structural energy efficiency of commercial and multifamily residential buildings. The Asset Score generates a simple energy efficiency rating that enables comparison among buildings, and identifies opportunities for users to invest in energy efficiency upgrades. It is web-based and free to use. This fact sheet discusses the value of the score for building owners.

What Are the Usage Conditions of Web 2.0 Tools Faculty of Education Students?

ERIC Educational Resources Information Center

Agir, Ahmet

2014-01-01

As a result of advances in technology and then the emergence of using Internet in every step of life, web that provides access to the documents such as picture, audio, animation and text in Internet started to be used. At first, web consists of only visual and text pages that couldn't enable to make user's interaction. However, it is seen that not…

The Best of All Possible Worlds: Applying the Model Driven Architecture Approach to a JC3IEDM OWL Ontology Modeled in UML

DTIC Science & Technology

2014-06-01

from the ODM standard. Leveraging SPARX EA’s Java application programming interface (API), the team built a tool called OWL2EA that can ingest an OWL...server MySQL creates the physical schema that enables a user to store and retrieve data conforming to the vocabulary of the JC3IEDM. 6. GENERATING AN

Building Energy Asset Score for Real Estate Managers

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

Building Technologies Office

2015-01-01

The Building Energy Asset Score is a national standardized tool for evaluating the physical and structural energy efficiency of commercial and multifamily residential buildings. The Asset Score generates a simple energy efficiency rating that enables comparison among buildings, and identifies opportunities for users to invest in energy efficiency upgrades. It is web-based and free to use. This fact sheet discusses the value of the score for real estate managers.

Real Time Baseball Database

NASA Astrophysics Data System (ADS)

Fukue, Yasuhiro

The author describes the system outline, features and operations of "Nikkan Sports Realtime Basaball Database" which was developed and operated by Nikkan Sports Shimbun, K. K. The system enables to input numerical data of professional baseball games as they proceed simultaneously, and execute data updating at realtime, just-in-time. Other than serving as supporting tool for prepareing newspapers it is also available for broadcasting media, general users through NTT dial Q2 and others.

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

PubMed

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

2010-09-21

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

Large-scale gene function analysis with the PANTHER classification system.

PubMed

Mi, Huaiyu; Muruganujan, Anushya; Casagrande, John T; Thomas, Paul D

2013-08-01

The PANTHER (protein annotation through evolutionary relationship) classification system (http://www.pantherdb.org/) is a comprehensive system that combines gene function, ontology, pathways and statistical analysis tools that enable biologists to analyze large-scale, genome-wide data from sequencing, proteomics or gene expression experiments. The system is built with 82 complete genomes organized into gene families and subfamilies, and their evolutionary relationships are captured in phylogenetic trees, multiple sequence alignments and statistical models (hidden Markov models or HMMs). Genes are classified according to their function in several different ways: families and subfamilies are annotated with ontology terms (Gene Ontology (GO) and PANTHER protein class), and sequences are assigned to PANTHER pathways. The PANTHER website includes a suite of tools that enable users to browse and query gene functions, and to analyze large-scale experimental data with a number of statistical tests. It is widely used by bench scientists, bioinformaticians, computer scientists and systems biologists. In the 2013 release of PANTHER (v.8.0), in addition to an update of the data content, we redesigned the website interface to improve both user experience and the system's analytical capability. This protocol provides a detailed description of how to analyze genome-wide experimental data with the PANTHER classification system.

SimPhospho: a software tool enabling confident phosphosite assignment.

PubMed

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

2018-03-27

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

A novel methodology for estimating upper limits of major cost drivers for profitable conceptual launch system architectures

NASA Astrophysics Data System (ADS)

Rhodes, Russel E.; Byrd, Raymond J.

1998-01-01

This paper presents a ``back of the envelope'' technique for fast, timely, on-the-spot, assessment of affordability (profitability) of commercial space transportation architectural concepts. The tool presented here is not intended to replace conventional, detailed costing methodology. The process described enables ``quick look'' estimations and assumptions to effectively determine whether an initial concept (with its attendant cost estimating line items) provides focus for major leapfrog improvement. The Cost Charts Users Guide provides a generic sample tutorial, building an approximate understanding of the basic launch system cost factors and their representative magnitudes. This process will enable the user to develop a net ``cost (and price) per payload-mass unit to orbit'' incorporating a variety of significant cost drivers, supplemental to basic vehicle cost estimates. If acquisition cost and recurring cost factors (as a function of cost per payload-mass unit to orbit) do not meet the predetermined system-profitability goal, the concept in question will be clearly seen as non-competitive. Multiple analytical approaches, and applications of a variety of interrelated assumptions, can be examined in a quick, (on-the-spot) cost approximation analysis as this tool has inherent flexibility. The technique will allow determination of concept conformance to system objectives.

Unidata's Vision for Providing Comprehensive and End-to-end Data Services

NASA Astrophysics Data System (ADS)

Ramamurthy, M. K.

2009-05-01

This paper presents Unidata's vision for providing comprehensive, well-integrated, and end-to-end data services for the geosciences. These include an array of functions for collecting, finding, and accessing data; data management tools for generating, cataloging, and exchanging metadata; and submitting or publishing, sharing, analyzing, visualizing, and integrating data. When this vision is realized, users no matter where they are or how they are connected to the Internetwill be able to find and access a plethora of geosciences data and use Unidata-provided tools and services both productively and creatively in their research and education. What that vision means for the Unidata community is elucidated by drawing a simple analogy. Most of users are familiar with Amazon and eBay e-commerce sites and content sharing sites like YouTube and Flickr. On the eBay marketplace, people can sell practically anything at any time and buyers can share their experience of purchasing a product or the reputation of a seller. Likewise, at Amazon, thousands of merchants sell their goods and millions of customers not only buy those goods, but provide a review or opinion of the products they buy and share their experiences as purchasers. Similarly, YouTube and Flickr are sites tailored to video- and photo-sharing, respectively, where users can upload their own content and share it with millions of other users, including family and friends. What all these sites, together with social-networking applications like MySpace and Facebook, have enabled is a sense of a virtual community in which users can search and browse products or content, comment and rate those products from anywhere, at any time, and via any Internet- enabled device like an iPhone, laptop, or a desktop computer. In essence, these enterprises have fundamentally altered people's buying modes and behavior toward purchases. Unidata believes that similar approaches, appropriately tailored to meet the needs of the scientific community, can be adopted to provide and share geosciences data and actively collaborate in the future. For example, future case-study data access systems, in addition to providing datasets and tools, will provide services that allow users to provide commentaries on a weather event, say a hurricane, as well as provide feedback on the quality, usefulness, and interpretation of the datasets through integrated blogs, forums, and Wikis, along with uploading and sharing products they derive, ancillary materials that users might have gathered (such as photos and videos from the storm), and publications and curricular materials they develop, all through a single data portal. In essence, such case study collections will be "living" or dynamic, allowing users to be also contributors as they add value to and grow existing case study collections.

MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering

PubMed Central

Bonde, Mads T.; Klausen, Michael S.; Anderson, Mads V.; Wallin, Annika I.N.; Wang, Harris H.; Sommer, Morten O.A.

2014-01-01

Recombineering and multiplex automated genome engineering (MAGE) offer the possibility to rapidly modify multiple genomic or plasmid sites at high efficiencies. This enables efficient creation of genetic variants including both single mutants with specifically targeted modifications as well as combinatorial cell libraries. Manual design of oligonucleotides for these approaches can be tedious, time-consuming, and may not be practical for larger projects targeting many genomic sites. At present, the change from a desired phenotype (e.g. altered expression of a specific protein) to a designed MAGE oligo, which confers the corresponding genetic change, is performed manually. To address these challenges, we have developed the MAGE Oligo Design Tool (MODEST). This web-based tool allows designing of MAGE oligos for (i) tuning translation rates by modifying the ribosomal binding site, (ii) generating translational gene knockouts and (iii) introducing other coding or non-coding mutations, including amino acid substitutions, insertions, deletions and point mutations. The tool automatically designs oligos based on desired genotypic or phenotypic changes defined by the user, which can be used for high efficiency recombineering and MAGE. MODEST is available for free and is open to all users at http://modest.biosustain.dtu.dk. PMID:24838561

GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes.

PubMed

Hallin, Peter F; Stærfeldt, Hans-Henrik; Rotenberg, Eva; Binnewies, Tim T; Benham, Craig J; Ussery, David W

2009-09-25

We present an interactive web application for visualizing genomic data of prokaryotic chromosomes. The tool (GeneWiz browser) allows users to carry out various analyses such as mapping alignments of homologous genes to other genomes, mapping of short sequencing reads to a reference chromosome, and calculating DNA properties such as curvature or stacking energy along the chromosome. The GeneWiz browser produces an interactive graphic that enables zooming from a global scale down to single nucleotides, without changing the size of the plot. Its ability to disproportionally zoom provides optimal readability and increased functionality compared to other browsers. The tool allows the user to select the display of various genomic features, color setting and data ranges. Custom numerical data can be added to the plot allowing, for example, visualization of gene expression and regulation data. Further, standard atlases are pre-generated for all prokaryotic genomes available in GenBank, providing a fast overview of all available genomes, including recently deposited genome sequences. The tool is available online from http://www.cbs.dtu.dk/services/gwBrowser. Supplemental material including interactive atlases is available online at http://www.cbs.dtu.dk/services/gwBrowser/suppl/.

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

PubMed

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

2017-07-03

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

QuadBase2: web server for multiplexed guanine quadruplex mining and visualization

PubMed Central

Dhapola, Parashar; Chowdhury, Shantanu

2016-01-01

DNA guanine quadruplexes or G4s are non-canonical DNA secondary structures which affect genomic processes like replication, transcription and recombination. G4s are computationally identified by specific nucleotide motifs which are also called putative G4 (PG4) motifs. Despite the general relevance of these structures, there is currently no tool available that can allow batch queries and genome-wide analysis of these motifs in a user-friendly interface. QuadBase2 (quadbase.igib.res.in) presents a completely reinvented web server version of previously published QuadBase database. QuadBase2 enables users to mine PG4 motifs in up to 178 eukaryotes through the EuQuad module. This module interfaces with Ensembl Compara database, to allow users mine PG4 motifs in the orthologues of genes of interest across eukaryotes. PG4 motifs can be mined across genes and their promoter sequences in 1719 prokaryotes through ProQuad module. This module includes a feature that allows genome-wide mining of PG4 motifs and their visualization as circular histograms. TetraplexFinder, the module for mining PG4 motifs in user-provided sequences is now capable of handling up to 20 MB of data. QuadBase2 is a comprehensive PG4 motif mining tool that further expands the configurations and algorithms for mining PG4 motifs in a user-friendly way. PMID:27185890

Combining Archetypes, Ontologies and Formalization Enables Automated Computation of Quality Indicators.

PubMed

Legaz-García, María Del Carmen; Dentler, Kathrin; Fernández-Breis, Jesualdo Tomás; Cornet, Ronald

2017-01-01

ArchMS is a framework that represents clinical information and knowledge using ontologies in OWL, which facilitates semantic interoperability and thereby the exploitation and secondary use of clinical data. However, it does not yet support the automated assessment of quality of care. CLIF is a stepwise method to formalize quality indicators. The method has been implemented in the CLIF tool which supports its users in generating computable queries based on a patient data model which can be based on archetypes. To enable the automated computation of quality indicators using ontologies and archetypes, we tested whether ArchMS and the CLIF tool can be integrated. We successfully automated the process of generating SPARQL queries from quality indicators that have been formalized with CLIF and integrated them into ArchMS. Hence, ontologies and archetypes can be combined for the execution of formalized quality indicators.

GLobal Integrated Design Environment (GLIDE): A Concurrent Engineering Application

NASA Technical Reports Server (NTRS)

McGuire, Melissa L.; Kunkel, Matthew R.; Smith, David A.

2010-01-01

The GLobal Integrated Design Environment (GLIDE) is a client-server software application purpose-built to mitigate issues associated with real time data sharing in concurrent engineering environments and to facilitate discipline-to-discipline interaction between multiple engineers and researchers. GLIDE is implemented in multiple programming languages utilizing standardized web protocols to enable secure parameter data sharing between engineers and researchers across the Internet in closed and/or widely distributed working environments. A well defined, HyperText Transfer Protocol (HTTP) based Application Programming Interface (API) to the GLIDE client/server environment enables users to interact with GLIDE, and each other, within common and familiar tools. One such common tool, Microsoft Excel (Microsoft Corporation), paired with its add-in API for GLIDE, is discussed in this paper. The top-level examples given demonstrate how this interface improves the efficiency of the design process of a concurrent engineering study while reducing potential errors associated with manually sharing information between study participants.

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

PubMed

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

2012-01-01

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

Perceptions towards electronic cigarettes for smoking cessation among Stop Smoking Service users.

PubMed

Sherratt, Frances C; Newson, Lisa; Marcus, Michael W; Field, John K; Robinson, Jude

2016-05-01

Electronic cigarettes (e-cigarettes) are promoted as smoking cessation tools, yet they remain unavailable from Stop Smoking Services in England; the debate over their safety and efficacy is ongoing. This study was designed to explore perceptions and reasons for use or non-use of electronic cigarettes as smoking cessation tools, among individuals engaged in Stop Smoking Services. Semi-structured telephone interviews were undertaken with twenty participants engaged in Stop Smoking Services in the north-west of England. Participants comprised of both individuals who had tried e-cigarettes (n = 6) and those who had not (n = 14). Interviews were digitally recorded and transcribed verbatim. The transcripts were subject to thematic analysis, which explored participants' beliefs and experiences of e-cigarettes. A thematic analysis of transcripts suggested that the following three superordinate themes were prominent: (1) self-efficacy and beliefs in e-cigarettes; (2) e-cigarettes as a smoking cessation aid; and (3) cues for e-cigarette use. Participants, particularly never users, were especially concerned regarding e-cigarette efficacy and safety. Overall, participants largely expressed uncertainty regarding e-cigarette safety and efficacy, with some evidence of misunderstanding. Evidence of uncertainty and misunderstanding regarding information on e-cigarettes highlights the importance of providing smokers with concise, up-to-date information regarding e-cigarettes, enabling smokers to make informed treatment decisions. Furthermore, identification of potential predictors of e-cigarette use can be used to inform Stop Smoking Services provision and future research. What is already known on this subject? Research suggests that e-cigarettes may help smokers quit smoking, but further studies are needed. Electronic cigarette use in Stop Smoking Services has increased substantially in recent years, although e-cigarettes are currently not regulated. There is debate within the academic community regarding e-cigarette efficacy and safety. What does this study add? Service users interviewed in the current study felt uncertain regarding e-cigarette efficacy and safety. E-cigarette ever users viewed e-cigarettes as effective and safe, more often than never users. Accurate and up-to-date education will enable service users to make informed treatment decisions. © 2015 The British Psychological Society.

SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies

PubMed Central

Ryan, Michael C; Zeeberg, Barry R; Caplen, Natasha J; Cleland, James A; Kahn, Ari B; Liu, Hongfang; Weinstein, John N

2008-01-01

Background Over 60% of protein-coding genes in vertebrates express mRNAs that undergo alternative splicing. The resulting collection of transcript isoforms poses significant challenges for contemporary biological assays. For example, RT-PCR validation of gene expression microarray results may be unsuccessful if the two technologies target different splice variants. Effective use of sequence-based technologies requires knowledge of the specific splice variant(s) that are targeted. In addition, the critical roles of alternative splice forms in biological function and in disease suggest that assay results may be more informative if analyzed in the context of the targeted splice variant. Results A number of contemporary technologies are used for analyzing transcripts or proteins. To enable investigation of the impact of splice variation on the interpretation of data derived from those technologies, we have developed SpliceCenter. SpliceCenter is a suite of user-friendly, web-based applications that includes programs for analysis of RT-PCR primer/probe sets, effectors of RNAi, microarrays, and protein-targeting technologies. Both interactive and high-throughput implementations of the tools are provided. The interactive versions of SpliceCenter tools provide visualizations of a gene's alternative transcripts and probe target positions, enabling the user to identify which splice variants are or are not targeted. The high-throughput batch versions accept user query files and provide results in tabular form. When, for example, we used SpliceCenter's batch siRNA-Check to process the Cancer Genome Anatomy Project's large-scale shRNA library, we found that only 59% of the 50,766 shRNAs in the library target all known splice variants of the target gene, 32% target some but not all, and 9% do not target any currently annotated transcript. Conclusion SpliceCenter provides unique, user-friendly applications for assessing the impact of transcript variation on the design and interpretation of RT-PCR, RNAi, gene expression microarrays, antibody-based detection, and mass spectrometry proteomics. The tools are intended for use by bench biologists as well as bioinformaticists. PMID:18638396

New Human-Computer Interface Concepts for Mission Operations

NASA Technical Reports Server (NTRS)

Fox, Jeffrey A.; Hoxie, Mary Sue; Gillen, Dave; Parkinson, Christopher; Breed, Julie; Nickens, Stephanie; Baitinger, Mick

2000-01-01

The current climate of budget cuts has forced the space mission operations community to reconsider how it does business. Gone are the days of building one-of-kind control centers with teams of controllers working in shifts 24 hours per day, 7 days per week. Increasingly, automation is used to significantly reduce staffing needs. In some cases, missions are moving towards lights-out operations where the ground system is run semi-autonomously. On-call operators are brought in only to resolve anomalies. Some operations concepts also call for smaller operations teams to manage an entire family of spacecraft. In the not too distant future, a skeleton crew of full-time general knowledge operators will oversee the operations of large constellations of small spacecraft, while geographically distributed specialists will be assigned to emergency response teams based on their expertise. As the operations paradigms change, so too must the tools to support the mission operations team's tasks. Tools need to be built not only to automate routine tasks, but also to communicate varying types of information to the part-time, generalist, or on-call operators and specialists more effectively. Thus, the proper design of a system's user-system interface (USI) becomes even more importance than before. Also, because the users will be accessing these systems from various locations (e.g., control center, home, on the road) via different devices with varying display capabilities (e.g., workstations, home PCs, PDAS, pagers) over connections with various bandwidths (e.g., dial-up 56k, wireless 9.6k), the same software must have different USIs to support the different types of users, their equipment, and their environments. In other words, the software must now adapt to the needs of the users! This paper will focus on the needs and the challenges of designing USIs for mission operations. After providing a general discussion of these challenges, the paper will focus on the current efforts of creatin(y an effective USI for one specific suite of tools, SERS (The Spacecraft Emergency Response System), which has been built to enable lights-out operations. SERS is a Web-based collaborative environment that enables secure distributed fault management.

Logistics Process Analysis ToolProcess Analysis Tool

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

2008-03-31

LPAT is the resulting integrated system between ANL-developed Enhanced Logistics Intra Theater Support Tool (ELIST) sponsored by SDDC-TEA and the Fort Future Virtual Installation Tool (sponsored by CERL). The Fort Future Simulation Engine was an application written in the ANL Repast Simphony framework and used as the basis for the process Anlysis Tool (PAT) which evolved into a stand=-along tool for detailed process analysis at a location. Combined with ELIST, an inter-installation logistics component was added to enable users to define large logistical agent-based models without having to program. PAT is the evolution of an ANL-developed software system called Fortmore » Future Virtual Installation Tool (sponsored by CERL). The Fort Future Simulation Engine was an application written in the ANL Repast Simphony framework and used as the basis for the Process Analysis Tool(PAT) which evolved into a stand-alone tool for detailed process analysis at a location (sponsored by the SDDC-TEA).« less

OASIS 2: online application for survival analysis 2 with features for the analysis of maximal lifespan and healthspan in aging research.

PubMed

Han, Seong Kyu; Lee, Dongyeop; Lee, Heetak; Kim, Donghyo; Son, Heehwa G; Yang, Jae-Seong; Lee, Seung-Jae V; Kim, Sanguk

2016-08-30

Online application for survival analysis (OASIS) has served as a popular and convenient platform for the statistical analysis of various survival data, particularly in the field of aging research. With the recent advances in the fields of aging research that deal with complex survival data, we noticed a need for updates to the current version of OASIS. Here, we report OASIS 2 (http://sbi.postech.ac.kr/oasis2), which provides extended statistical tools for survival data and an enhanced user interface. In particular, OASIS 2 enables the statistical comparison of maximal lifespans, which is potentially useful for determining key factors that limit the lifespan of a population. Furthermore, OASIS 2 provides statistical and graphical tools that compare values in different conditions and times. That feature is useful for comparing age-associated changes in physiological activities, which can be used as indicators of "healthspan." We believe that OASIS 2 will serve as a standard platform for survival analysis with advanced and user-friendly statistical tools for experimental biologists in the field of aging research.

Enabling User Preferences Through Data Exchange

DOT National Transportation Integrated Search

1997-08-01

This paper describes a process, via user- air traffic management (ATM) data : exchange, for enabling user preferences in an ATM-based system. User : preferences may be defined in terms of a four-dimensional (4D) user-preferred : trajectory, or a seri...

A geodata warehouse: Using denormalisation techniques as a tool for delivering spatially enabled integrated geological information to geologists

NASA Astrophysics Data System (ADS)

Kingdon, Andrew; Nayembil, Martin L.; Richardson, Anne E.; Smith, A. Graham

2016-11-01

New requirements to understand geological properties in three dimensions have led to the development of PropBase, a data structure and delivery tools to deliver this. At the BGS, relational database management systems (RDBMS) has facilitated effective data management using normalised subject-based database designs with business rules in a centralised, vocabulary controlled, architecture. These have delivered effective data storage in a secure environment. However, isolated subject-oriented designs prevented efficient cross-domain querying of datasets. Additionally, the tools provided often did not enable effective data discovery as they struggled to resolve the complex underlying normalised structures providing poor data access speeds. Users developed bespoke access tools to structures they did not fully understand sometimes delivering them incorrect results. Therefore, BGS has developed PropBase, a generic denormalised data structure within an RDBMS to store property data, to facilitate rapid and standardised data discovery and access, incorporating 2D and 3D physical and chemical property data, with associated metadata. This includes scripts to populate and synchronise the layer with its data sources through structured input and transcription standards. A core component of the architecture includes, an optimised query object, to deliver geoscience information from a structure equivalent to a data warehouse. This enables optimised query performance to deliver data in multiple standardised formats using a web discovery tool. Semantic interoperability is enforced through vocabularies combined from all data sources facilitating searching of related terms. PropBase holds 28.1 million spatially enabled property data points from 10 source databases incorporating over 50 property data types with a vocabulary set that includes 557 property terms. By enabling property data searches across multiple databases PropBase has facilitated new scientific research, previously considered impractical. PropBase is easily extended to incorporate 4D data (time series) and is providing a baseline for new "big data" monitoring projects.

Free Web-based personal health records: an analysis of functionality.

PubMed

Fernández-Alemán, José Luis; Seva-Llor, Carlos Luis; Toval, Ambrosio; Ouhbi, Sofia; Fernández-Luque, Luis

2013-12-01

This paper analyzes and assesses the functionality of free Web-based PHRs as regards health information, user actions and connection with other tools. A systematic literature review in Medline, ACM Digital Library, IEEE Digital Library and ScienceDirect was used to select 19 free Web-based PHRs from the 47 PHRs identified. The results show that none of the PHRs selected met 100% of the 28 functions presented in this paper. Two free Web-based PHRs target a particular public. Around 90 % of the PHRs identified allow users throughout the world to create their own profiles without any geographical restrictions. Only half of the PHRs selected provide physicians with user actions. Few PHRs can connect with other tools. There was considerable variability in the types of data included in free Web-based PHRs. Functionality may have implications for PHR use and adoption, particularly as regards patients with chronic illnesses or disabilities. Support for standard medical document formats and protocols are required to enable data to be exchanged with other stakeholders in the health care domain. The results of our study may assist users in selecting the PHR that best fits their needs, since no significant connection exists between the number of functions of the PHRs identified and their popularity.

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

PubMed Central

Yu, Kebing; Salomon, Arthur R.

2010-01-01

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

a Standardized Approach to Topographic Data Processing and Workflow Management

NASA Astrophysics Data System (ADS)

Wheaton, J. M.; Bailey, P.; Glenn, N. F.; Hensleigh, J.; Hudak, A. T.; Shrestha, R.; Spaete, L.

2013-12-01

An ever-increasing list of options exist for collecting high resolution topographic data, including airborne LIDAR, terrestrial laser scanners, bathymetric SONAR and structure-from-motion. An equally rich, arguably overwhelming, variety of tools exists with which to organize, quality control, filter, analyze and summarize these data. However, scientists are often left to cobble together their analysis as a series of ad hoc steps, often using custom scripts and one-time processes that are poorly documented and rarely shared with the community. Even when literature-cited software tools are used, the input and output parameters differ from tool to tool. These parameters are rarely archived and the steps performed lost, making the analysis virtually impossible to replicate precisely. What is missing is a coherent, robust, framework for combining reliable, well-documented topographic data-processing steps into a workflow that can be repeated and even shared with others. We have taken several popular topographic data processing tools - including point cloud filtering and decimation as well as DEM differencing - and defined a common protocol for passing inputs and outputs between them. This presentation describes a free, public online portal that enables scientists to create custom workflows for processing topographic data using a number of popular topographic processing tools. Users provide the inputs required for each tool and in what sequence they want to combine them. This information is then stored for future reuse (and optionally sharing with others) before the user then downloads a single package that contains all the input and output specifications together with the software tools themselves. The user then launches the included batch file that executes the workflow on their local computer against their topographic data. This ZCloudTools architecture helps standardize, automate and archive topographic data processing. It also represents a forum for discovering and sharing effective topographic processing workflows.

The Python Spectral Analysis Tool (PySAT): A Powerful, Flexible, Preprocessing and Machine Learning Library and Interface

NASA Astrophysics Data System (ADS)

Anderson, R. B.; Finch, N.; Clegg, S. M.; Graff, T. G.; Morris, R. V.; Laura, J.; Gaddis, L. R.

2017-12-01

Machine learning is a powerful but underutilized approach that can enable planetary scientists to derive meaningful results from the rapidly-growing quantity of available spectral data. For example, regression methods such as Partial Least Squares (PLS) and Least Absolute Shrinkage and Selection Operator (LASSO), can be used to determine chemical concentrations from ChemCam and SuperCam Laser-Induced Breakdown Spectroscopy (LIBS) data [1]. Many scientists are interested in testing different spectral data processing and machine learning methods, but few have the time or expertise to write their own software to do so. We are therefore developing a free open-source library of software called the Python Spectral Analysis Tool (PySAT) along with a flexible, user-friendly graphical interface to enable scientists to process and analyze point spectral data without requiring significant programming or machine-learning expertise. A related but separately-funded effort is working to develop a graphical interface for orbital data [2]. The PySAT point-spectra tool includes common preprocessing steps (e.g. interpolation, normalization, masking, continuum removal, dimensionality reduction), plotting capabilities, and capabilities to prepare data for machine learning such as creating stratified folds for cross validation, defining training and test sets, and applying calibration transfer so that data collected on different instruments or under different conditions can be used together. The tool leverages the scikit-learn library [3] to enable users to train and compare the results from a variety of multivariate regression methods. It also includes the ability to combine multiple "sub-models" into an overall model, a method that has been shown to improve results and is currently used for ChemCam data [4]. Although development of the PySAT point-spectra tool has focused primarily on the analysis of LIBS spectra, the relevant steps and methods are applicable to any spectral data. The tool is available at https://github.com/USGS-Astrogeology/PySAT_Point_Spectra_GUI. [1] Clegg, S.M., et al. (2017) Spectrochim Acta B. 129, 64-85. [2] Gaddis, L. et al. (2017) 3rd Planetary Data Workshop, #1986. [3] http://scikit-learn.org/ [4] Anderson, R.B., et al. (2017) Spectrochim. Acta B. 129, 49-57.

gPKPDSim: a SimBiology®-based GUI application for PKPD modeling in drug development.

PubMed

Hosseini, Iraj; Gajjala, Anita; Bumbaca Yadav, Daniela; Sukumaran, Siddharth; Ramanujan, Saroja; Paxson, Ricardo; Gadkar, Kapil

2018-04-01

Modeling and simulation (M&S) is increasingly used in drug development to characterize pharmacokinetic-pharmacodynamic (PKPD) relationships and support various efforts such as target feasibility assessment, molecule selection, human PK projection, and preclinical and clinical dose and schedule determination. While model development typically require mathematical modeling expertise, model exploration and simulations could in many cases be performed by scientists in various disciplines to support the design, analysis and interpretation of experimental studies. To this end, we have developed a versatile graphical user interface (GUI) application to enable easy use of any model constructed in SimBiology ® to execute various common PKPD analyses. The MATLAB ® -based GUI application, called gPKPDSim, has a single screen interface and provides functionalities including simulation, data fitting (parameter estimation), population simulation (exploring the impact of parameter variability on the outputs of interest), and non-compartmental PK analysis. Further, gPKPDSim is a user-friendly tool with capabilities including interactive visualization, exporting of results and generation of presentation-ready figures. gPKPDSim was designed primarily for use in preclinical and translational drug development, although broader applications exist. gPKPDSim is a MATLAB ® -based open-source application and is publicly available to download from MATLAB ® Central™. We illustrate the use and features of gPKPDSim using multiple PKPD models to demonstrate the wide applications of this tool in pharmaceutical sciences. Overall, gPKPDSim provides an integrated, multi-purpose user-friendly GUI application to enable efficient use of PKPD models by scientists from various disciplines, regardless of their modeling expertise.

Machine learning for a Toolkit for Image Mining

NASA Technical Reports Server (NTRS)

Delanoy, Richard L.

1995-01-01

A prototype user environment is described that enables a user with very limited computer skills to collaborate with a computer algorithm to develop search tools (agents) that can be used for image analysis, creating metadata for tagging images, searching for images in an image database on the basis of image content, or as a component of computer vision algorithms. Agents are learned in an ongoing, two-way dialogue between the user and the algorithm. The user points to mistakes made in classification. The algorithm, in response, attempts to discover which image attributes are discriminating between objects of interest and clutter. It then builds a candidate agent and applies it to an input image, producing an 'interest' image highlighting features that are consistent with the set of objects and clutter indicated by the user. The dialogue repeats until the user is satisfied. The prototype environment, called the Toolkit for Image Mining (TIM) is currently capable of learning spectral and textural patterns. Learning exhibits rapid convergence to reasonable levels of performance and, when thoroughly trained, Fo appears to be competitive in discrimination accuracy with other classification techniques.

Visible Earthquakes: a web-based tool for visualizing and modeling InSAR earthquake data

NASA Astrophysics Data System (ADS)

Funning, G. J.; Cockett, R.

2012-12-01

InSAR (Interferometric Synthetic Aperture Radar) is a technique for measuring the deformation of the ground using satellite radar data. One of the principal applications of this method is in the study of earthquakes; in the past 20 years over 70 earthquakes have been studied in this way, and forthcoming satellite missions promise to enable the routine and timely study of events in the future. Despite the utility of the technique and its widespread adoption by the research community, InSAR does not feature in the teaching curricula of most university geoscience departments. This is, we believe, due to a lack of accessibility to software and data. Existing tools for the visualization and modeling of interferograms are often research-oriented, command line-based and/or prohibitively expensive. Here we present a new web-based interactive tool for comparing real InSAR data with simple elastic models. The overall design of this tool was focused on ease of access and use. This tool should allow interested nonspecialists to gain a feel for the use of such data and greatly facilitate integration of InSAR into upper division geoscience courses, giving students practice in comparing actual data to modeled results. The tool, provisionally named 'Visible Earthquakes', uses web-based technologies to instantly render the displacement field that would be observable using InSAR for a given fault location, geometry, orientation, and slip. The user can adjust these 'source parameters' using a simple, clickable interface, and see how these affect the resulting model interferogram. By visually matching the model interferogram to a real earthquake interferogram (processed separately and included in the web tool) a user can produce their own estimates of the earthquake's source parameters. Once satisfied with the fit of their models, users can submit their results and see how they compare with the distribution of all other contributed earthquake models, as well as the mean and median models. We envisage that the ensemble of contributed models will be useful both as a research resource and in the classroom. Locations of earthquakes derived from InSAR data have already been demonstrated to differ significantly from those obtained from global seismic networks (Weston et al., 2011), and the locations obtained by our users will enable us to identify systematic mislocations that are likely due to errors in Earth velocity models used to locate earthquakes. If the tool is incorporated into geophysics, tectonics and/or structural geology classes, in addition to familiarizing students with InSAR and elastic deformation modeling, the spread of different results for each individual earthquake will allow the teaching of concepts such as model uncertainty and non-uniqueness when modeling real scientific data. Additionally, the process students go through to optimize their estimates of fault parameters can easily be tied into teaching about the concepts of forward and inverse problems, which are common in geophysics.

Xray: N-dimensional, labeled arrays for analyzing physical datasets in Python

NASA Astrophysics Data System (ADS)

Hoyer, S.

2015-12-01

Efficient analysis of geophysical datasets requires tools that both preserve and utilize metadata, and that transparently scale to process large datas. Xray is such a tool, in the form of an open source Python library for analyzing the labeled, multi-dimensional array (tensor) datasets that are ubiquitous in the Earth sciences. Xray's approach pairs Python data structures based on the data model of the netCDF file format with the proven design and user interface of pandas, the popular Python data analysis library for labeled tabular data. On top of the NumPy array, xray adds labeled dimensions (e.g., "time") and coordinate values (e.g., "2015-04-10"), which it uses to enable a host of operations powered by these labels: selection, aggregation, alignment, broadcasting, split-apply-combine, interoperability with pandas and serialization to netCDF/HDF5. Many of these operations are enabled by xray's tight integration with pandas. Finally, to allow for easy parallelism and to enable its labeled data operations to scale to datasets that does not fit into memory, xray integrates with the parallel processing library dask.

Managing Sustainable Data Infrastructures: The Gestalt of EOSDIS

NASA Technical Reports Server (NTRS)

Behnke, Jeanne; Lowe, Dawn; Lindsay, Francis; Lynnes, Chris; Mitchell, Andrew

2016-01-01

EOSDIS epitomizes a System of Systems, whose many varied and distributed parts are integrated into a single, highly functional organized science data system. A distributed architecture was adopted to ensure discipline-specific support for the science data, while also leveraging standards and establishing policies and tools to enable interdisciplinary research, and analysis across multiple scientific instruments. The EOSDIS is composed of system elements such as geographically distributed archive centers used to manage the stewardship of data. The infrastructure consists of underlying capabilities connections that enable the primary system elements to function together. For example, one key infrastructure component is the common metadata repository, which enables discovery of all data within the EOSDIS system. EOSDIS employs processes and standards to ensure partners can work together effectively, and provide coherent services to users.

P2RP: a Web-based framework for the identification and analysis of regulatory proteins in prokaryotic genomes.

PubMed

Barakat, Mohamed; Ortet, Philippe; Whitworth, David E

2013-04-20

Regulatory proteins (RPs) such as transcription factors (TFs) and two-component system (TCS) proteins control how prokaryotic cells respond to changes in their external and/or internal state. Identification and annotation of TFs and TCSs is non-trivial, and between-genome comparisons are often confounded by different standards in annotation. There is a need for user-friendly, fast and convenient tools to allow researchers to overcome the inherent variability in annotation between genome sequences. We have developed the web-server P2RP (Predicted Prokaryotic Regulatory Proteins), which enables users to identify and annotate TFs and TCS proteins within their sequences of interest. Users can input amino acid or genomic DNA sequences, and predicted proteins therein are scanned for the possession of DNA-binding domains and/or TCS domains. RPs identified in this manner are categorised into families, unambiguously annotated, and a detailed description of their features generated, using an integrated software pipeline. P2RP results can then be outputted in user-specified formats. Biologists have an increasing need for fast and intuitively usable tools, which is why P2RP has been developed as an interactive system. As well as assisting experimental biologists to interrogate novel sequence data, it is hoped that P2RP will be built into genome annotation pipelines and re-annotation processes, to increase the consistency of RP annotation in public genomic sequences. P2RP is the first publicly available tool for predicting and analysing RP proteins in users' sequences. The server is freely available and can be accessed along with documentation at http://www.p2rp.org.

Beware of Geeks Bearing Gifts - Are we Meeting the Requirements of our User Communities?

NASA Astrophysics Data System (ADS)

Klump, J.

2007-12-01

The 20th century brought about an "information revolution" that has forever altered the way we work, communicate, and live. The way science has been conducted for the past 200 years has been challenged by new media of communication and for the dissemination of data. We now have the tools at hand, commonly called cyberinfrastructure, that enable new forms of global collaboration. But are we fully realising the potential of cyberinfrastructure? Has it become an integral part of our scientific culture? Tools developed in Earth and Space Science Informatics projects suffer the same effects like informatics developments in other fields. Many of the projects fail to meet user requirements, and they do so for a number of reasons. Besides a certain reluctance on the side of scientists to adopt new tools for conducting their research, many cyberinfrastructure projects suffer from "marketing myopia" (Levitt, 1960) in the way they try to "sell" their applications. According to Levitt, the difference between selling and marketing is that the former fulfils the needs of the seller and the latter the needs of the buyer. Cyberinfrastructure projects must stop trying to sell their achievements to the scientific community, and instead market them by considering the scientists" needs right at the beginning of their endeavours. Admittedly, the requirements of scientific user communities are "moving targets", because scientific workflows are often subject to ad-hoc changes, depending on the outcome of the preceding step. Another important risk factor, faced by many cyberinfrastructure projects, is that the designated user community is not aware of the availability of this new resource. This is where training and outreach are essential, especially to draw in early adopters of new technology and multipliers among researchers. Only cyberinfrastructure tools that truly serve their designated user community will eventually become part of the scientific infrastructure. This presentation looks at the factors and strategies that affect adoption of cyberinfrastructrures by the scientific community.

GeoViQua: quality-aware geospatial data discovery and evaluation

NASA Astrophysics Data System (ADS)

Bigagli, L.; Papeschi, F.; Mazzetti, P.; Nativi, S.

2012-04-01

GeoViQua (QUAlity aware VIsualization for the Global Earth Observation System of Systems) is a recently started FP7 project aiming at complementing the Global Earth Observation System of Systems (GEOSS) with rigorous data quality specifications and quality-aware capabilities, in order to improve reliability in scientific studies and policy decision-making. GeoViQua main scientific and technical objective is to enhance the GEOSS Common Infrastructure (GCI) providing the user community with innovative quality-aware search and evaluation tools, which will be integrated in the GEO-Portal, as well as made available to other end-user interfaces. To this end, GeoViQua will promote the extension of the current standard metadata for geographic information with accurate and expressive quality indicators, also contributing to the definition of a quality label (GEOLabel). GeoViQua proposed solutions will be assessed in several pilot case studies covering the whole Earth Observation chain, from remote sensing acquisition to data processing, to applications in the main GEOSS Societal Benefit Areas. This work presents the preliminary results of GeoViQua Work Package 4 "Enhanced geo-search tools" (WP4), started in January 2012. Its major anticipated technical innovations are search and evaluation tools that communicate and exploit data quality information from the GCI. In particular, GeoViQua will investigate a graphical search interface featuring a coherent and meaningful aggregation of statistics and metadata summaries (e.g. in the form of tables, charts), thus enabling end users to leverage quality constraints for data discovery and evaluation. Preparatory work on WP4 requirements indicated that users need the "best" data for their purpose, implying a high degree of subjectivity in judgment. This suggests that the GeoViQua system should exploit a combination of provider-generated metadata (objective indicators such as summary statistics), system-generated metadata (contextual/tracking information such as provenance of data and metadata), and user-generated metadata (informal user comments, usage information, rating, etc.). Moreover, metadata should include sufficiently complete access information, to allow rich data visualization and propagation. The following main enabling components are currently identified within WP4: - Quality-aware access services, e.g. a quality-aware extension of the OGC Sensor Observation Service (SOS-Q) specification, to support quality constraints for sensor data publishing and access; - Quality-aware discovery services, namely a quality-aware extension of the OGC Catalog Service for the Web (CSW-Q), to cope with quality constrained search; - Quality-augmentation broker (GeoViQua Broker), to support the linking and combination of the existing GCI metadata with GeoViQua- and user-generated metadata required to support the users in selecting the "best" data for their intended use. We are currently developing prototypes of the above quality-enabled geo-search components, that will be assessed in a sensor-based pilot case study in the next months. In particular, the GeoViQua Broker will be integrated with the EuroGEOSS Broker, to implement CSW-Q and federate (either via distribution or harvesting schemes) quality-aware data sources, GeoViQua will constitute a valuable test-bed for advancing the current best practices and standards in geospatial quality representation and exploitation. The research leading to these results has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013) under Grant Agreement n° 265178.

Mobile computing device as tools for college student education: a case on flashcards application

NASA Astrophysics Data System (ADS)

Kang, Congying

2012-04-01

Traditionally, college students always use flash cards as a tool to remember massive knowledge, such as nomenclature, structures, and reactions in chemistry. Educational and information technology have enabled flashcards viewed on computers, like Slides and PowerPoint, works as tunnels of drilling and feedback for the learners. The current generation of students is more capable of information technology and mobile computing devices. For example, they use their Mobile phones much more intensively everyday day. Trends of using Mobile phone as an educational tool is analyzed and a educational technology initiative is proposed, which use Mobile phone flash cards applications to help students learn biology and chemistry. Experiments show that users responded positively to these mobile flash cards.

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

PubMed

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

2004-11-01

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

MaGnET: Malaria Genome Exploration Tool.

PubMed

Sharman, Joanna L; Gerloff, Dietlind L

2013-09-15

The Malaria Genome Exploration Tool (MaGnET) is a software tool enabling intuitive 'exploration-style' visualization of functional genomics data relating to the malaria parasite, Plasmodium falciparum. MaGnET provides innovative integrated graphic displays for different datasets, including genomic location of genes, mRNA expression data, protein-protein interactions and more. Any selection of genes to explore made by the user is easily carried over between the different viewers for different datasets, and can be changed interactively at any point (without returning to a search). Free online use (Java Web Start) or download (Java application archive and MySQL database; requires local MySQL installation) at http://malariagenomeexplorer.org joanna.sharman@ed.ac.uk or dgerloff@ffame.org Supplementary data are available at Bioinformatics online.

IBES: a tool for creating instructions based on event segmentation

PubMed Central

Mura, Katharina; Petersen, Nils; Huff, Markus; Ghose, Tandra

2013-01-01

Receiving informative, well-structured, and well-designed instructions supports performance and memory in assembly tasks. We describe IBES, a tool with which users can quickly and easily create multimedia, step-by-step instructions by segmenting a video of a task into segments. In a validation study we demonstrate that the step-by-step structure of the visual instructions created by the tool corresponds to the natural event boundaries, which are assessed by event segmentation and are known to play an important role in memory processes. In one part of the study, 20 participants created instructions based on videos of two different scenarios by using the proposed tool. In the other part of the study, 10 and 12 participants respectively segmented videos of the same scenarios yielding event boundaries for coarse and fine events. We found that the visual steps chosen by the participants for creating the instruction manual had corresponding events in the event segmentation. The number of instructional steps was a compromise between the number of fine and coarse events. Our interpretation of results is that the tool picks up on natural human event perception processes of segmenting an ongoing activity into events and enables the convenient transfer into meaningful multimedia instructions for assembly tasks. We discuss the practical application of IBES, for example, creating manuals for differing expertise levels, and give suggestions for research on user-oriented instructional design based on this tool. PMID:24454296

IBES: a tool for creating instructions based on event segmentation.

PubMed

Mura, Katharina; Petersen, Nils; Huff, Markus; Ghose, Tandra

2013-12-26

Receiving informative, well-structured, and well-designed instructions supports performance and memory in assembly tasks. We describe IBES, a tool with which users can quickly and easily create multimedia, step-by-step instructions by segmenting a video of a task into segments. In a validation study we demonstrate that the step-by-step structure of the visual instructions created by the tool corresponds to the natural event boundaries, which are assessed by event segmentation and are known to play an important role in memory processes. In one part of the study, 20 participants created instructions based on videos of two different scenarios by using the proposed tool. In the other part of the study, 10 and 12 participants respectively segmented videos of the same scenarios yielding event boundaries for coarse and fine events. We found that the visual steps chosen by the participants for creating the instruction manual had corresponding events in the event segmentation. The number of instructional steps was a compromise between the number of fine and coarse events. Our interpretation of results is that the tool picks up on natural human event perception processes of segmenting an ongoing activity into events and enables the convenient transfer into meaningful multimedia instructions for assembly tasks. We discuss the practical application of IBES, for example, creating manuals for differing expertise levels, and give suggestions for research on user-oriented instructional design based on this tool.

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

PubMed Central

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

2016-01-01

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

Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics

PubMed Central

Giacomoni, Franck; Le Corguillé, Gildas; Monsoor, Misharl; Landi, Marion; Pericard, Pierre; Pétéra, Mélanie; Duperier, Christophe; Tremblay-Franco, Marie; Martin, Jean-François; Jacob, Daniel; Goulitquer, Sophie; Thévenot, Etienne A.; Caron, Christophe

2015-01-01

Summary: The complex, rapidly evolving field of computational metabolomics calls for collaborative infrastructures where the large volume of new algorithms for data pre-processing, statistical analysis and annotation can be readily integrated whatever the language, evaluated on reference datasets and chained to build ad hoc workflows for users. We have developed Workflow4Metabolomics (W4M), the first fully open-source and collaborative online platform for computational metabolomics. W4M is a virtual research environment built upon the Galaxy web-based platform technology. It enables ergonomic integration, exchange and running of individual modules and workflows. Alternatively, the whole W4M framework and computational tools can be downloaded as a virtual machine for local installation. Availability and implementation: http://workflow4metabolomics.org homepage enables users to open a private account and access the infrastructure. W4M is developed and maintained by the French Bioinformatics Institute (IFB) and the French Metabolomics and Fluxomics Infrastructure (MetaboHUB). Contact: contact@workflow4metabolomics.org PMID:25527831

Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics.

PubMed

Giacomoni, Franck; Le Corguillé, Gildas; Monsoor, Misharl; Landi, Marion; Pericard, Pierre; Pétéra, Mélanie; Duperier, Christophe; Tremblay-Franco, Marie; Martin, Jean-François; Jacob, Daniel; Goulitquer, Sophie; Thévenot, Etienne A; Caron, Christophe

2015-05-01

The complex, rapidly evolving field of computational metabolomics calls for collaborative infrastructures where the large volume of new algorithms for data pre-processing, statistical analysis and annotation can be readily integrated whatever the language, evaluated on reference datasets and chained to build ad hoc workflows for users. We have developed Workflow4Metabolomics (W4M), the first fully open-source and collaborative online platform for computational metabolomics. W4M is a virtual research environment built upon the Galaxy web-based platform technology. It enables ergonomic integration, exchange and running of individual modules and workflows. Alternatively, the whole W4M framework and computational tools can be downloaded as a virtual machine for local installation. http://workflow4metabolomics.org homepage enables users to open a private account and access the infrastructure. W4M is developed and maintained by the French Bioinformatics Institute (IFB) and the French Metabolomics and Fluxomics Infrastructure (MetaboHUB). contact@workflow4metabolomics.org. © The Author 2014. Published by Oxford University Press.

tranSMART: An Open Source and Community-Driven Informatics and Data Sharing Platform for Clinical and Translational Research.

PubMed

Athey, Brian D; Braxenthaler, Michael; Haas, Magali; Guo, Yike

2013-01-01

tranSMART is an emerging global open source public private partnership community developing a comprehensive informatics-based analysis and data-sharing cloud platform for clinical and translational research. The tranSMART consortium includes pharmaceutical and other companies, not-for-profits, academic entities, patient advocacy groups, and government stakeholders. The tranSMART value proposition relies on the concept that the global community of users, developers, and stakeholders are the best source of innovation for applications and for useful data. Continued development and use of the tranSMART platform will create a means to enable "pre-competitive" data sharing broadly, saving money and, potentially accelerating research translation to cures. Significant transformative effects of tranSMART includes 1) allowing for all its user community to benefit from experts globally, 2) capturing the best of innovation in analytic tools, 3) a growing 'big data' resource, 4) convergent standards, and 5) new informatics-enabled translational science in the pharma, academic, and not-for-profit sectors.

Institutional Transformation 2.5 Building Module Help Manual.

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

Villa, Daniel

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

Video-Game-Like Engine for Depicting Spacecraft Trajectories

NASA Technical Reports Server (NTRS)

Upchurch, Paul R.

2009-01-01

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

Processing Shotgun Proteomics Data on the Amazon Cloud with the Trans-Proteomic Pipeline*

PubMed Central

Slagel, Joseph; Mendoza, Luis; Shteynberg, David; Deutsch, Eric W.; Moritz, Robert L.

2015-01-01

Cloud computing, where scalable, on-demand compute cycles and storage are available as a service, has the potential to accelerate mass spectrometry-based proteomics research by providing simple, expandable, and affordable large-scale computing to all laboratories regardless of location or information technology expertise. We present new cloud computing functionality for the Trans-Proteomic Pipeline, a free and open-source suite of tools for the processing and analysis of tandem mass spectrometry datasets. Enabled with Amazon Web Services cloud computing, the Trans-Proteomic Pipeline now accesses large scale computing resources, limited only by the available Amazon Web Services infrastructure, for all users. The Trans-Proteomic Pipeline runs in an environment fully hosted on Amazon Web Services, where all software and data reside on cloud resources to tackle large search studies. In addition, it can also be run on a local computer with computationally intensive tasks launched onto the Amazon Elastic Compute Cloud service to greatly decrease analysis times. We describe the new Trans-Proteomic Pipeline cloud service components, compare the relative performance and costs of various Elastic Compute Cloud service instance types, and present on-line tutorials that enable users to learn how to deploy cloud computing technology rapidly with the Trans-Proteomic Pipeline. We provide tools for estimating the necessary computing resources and costs given the scale of a job and demonstrate the use of cloud enabled Trans-Proteomic Pipeline by performing over 1100 tandem mass spectrometry files through four proteomic search engines in 9 h and at a very low cost. PMID:25418363

Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline.

PubMed

Slagel, Joseph; Mendoza, Luis; Shteynberg, David; Deutsch, Eric W; Moritz, Robert L

2015-02-01

Cloud computing, where scalable, on-demand compute cycles and storage are available as a service, has the potential to accelerate mass spectrometry-based proteomics research by providing simple, expandable, and affordable large-scale computing to all laboratories regardless of location or information technology expertise. We present new cloud computing functionality for the Trans-Proteomic Pipeline, a free and open-source suite of tools for the processing and analysis of tandem mass spectrometry datasets. Enabled with Amazon Web Services cloud computing, the Trans-Proteomic Pipeline now accesses large scale computing resources, limited only by the available Amazon Web Services infrastructure, for all users. The Trans-Proteomic Pipeline runs in an environment fully hosted on Amazon Web Services, where all software and data reside on cloud resources to tackle large search studies. In addition, it can also be run on a local computer with computationally intensive tasks launched onto the Amazon Elastic Compute Cloud service to greatly decrease analysis times. We describe the new Trans-Proteomic Pipeline cloud service components, compare the relative performance and costs of various Elastic Compute Cloud service instance types, and present on-line tutorials that enable users to learn how to deploy cloud computing technology rapidly with the Trans-Proteomic Pipeline. We provide tools for estimating the necessary computing resources and costs given the scale of a job and demonstrate the use of cloud enabled Trans-Proteomic Pipeline by performing over 1100 tandem mass spectrometry files through four proteomic search engines in 9 h and at a very low cost. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Program For Generating Interactive Displays

NASA Technical Reports Server (NTRS)

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

Enabling Smart Workflows over Heterogeneous ID-Sensing Technologies

PubMed Central

Giner, Pau; Cetina, Carlos; Lacuesta, Raquel; Palacios, Guillermo

2012-01-01

Sensing technologies in mobile devices play a key role in reducing the gap between the physical and the digital world. The use of automatic identification capabilities can improve user participation in business processes where physical elements are involved (Smart Workflows). However, identifying all objects in the user surroundings does not automatically translate into meaningful services to the user. This work introduces Parkour, an architecture that allows the development of services that match the goals of each of the participants in a smart workflow. Parkour is based on a pluggable architecture that can be extended to provide support for new tasks and technologies. In order to facilitate the development of these plug-ins, tools that automate the development process are also provided. Several Parkour-based systems have been developed in order to validate the applicability of the proposal. PMID:23202193

A Java-based tool for creating KML files from GPS waypoints

NASA Astrophysics Data System (ADS)

Kinnicutt, P. G.; Rivard, C.; Rimer, S.

2008-12-01

Google Earth provides a free tool with powerful capabilities for visualizing geoscience images and data. Commercial software tools exist for doing sophisticated digitizing and spatial modeling , but for the purposes of presentation, visualization and overlaying aerial images with data Google Earth provides much of the functionality. Likewise, with current technologies in GPS (Global Positioning System) systems and with Google Earth Plus, it is possible to upload GPS waypoints, tracks and routes directly into Google Earth for visualization. However, older technology GPS units and even low-cost GPS units found today may lack the necessary communications interface to a computer (e.g. no Bluetooth, no WiFi, no USB, no Serial, etc.) or may have an incompatible interface, such as a Serial port but no USB adapter available. In such cases, any waypoints, tracks and routes saved in the GPS unit or recorded in a field notebook must be manually transferred to a computer for use in a GIS system or other program. This presentation describes a Java-based tool developed by the author which enables users to enter GPS coordinates in a user-friendly manner, then save these coordinates in a Keyhole MarkUp Language (KML) file format, for visualization in Google Earth. This tool either accepts user-interactive input or accepts input from a CSV (Comma Separated Value) file, which can be generated from any spreadsheet program. This tool accepts input in the form of lat/long or UTM (Universal Transverse Mercator) coordinates. This presentation describes this system's applicability through several small case studies. This free and lightweight tool simplifies the task of manually inputting GPS data into Google Earth for people working in the field without an automated mechanism for uploading the data; for instance, the user may not have internet connectivity or may not have the proper hardware or software. Since it is a Java application and not a web- based tool, it can be installed on one's field laptop and the GPS data can be manually entered without the need for internet connectivity. This tool provides a table view of the GPS data, but lacks a KML viewer to view the data overlain on top of an aerial view, as this viewer functionality is provided in Google Earth. The tool's primary contribution lies in its more convenient method for entering the GPS data manually when automated technologies are not available.

Building Energy Asset Score for State and Local Governments

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

Building Technologies Office

2015-01-01

The Building Energy Asset Score is a national standardized tool for evaluating the physical and structural energy efficiency of commercial and multifamily residential buildings. The Asset Score generates a simple energy efficiency rating that enables comparison among buildings, and identifies opportunities for users to invest in energy efficiency upgrades. It is web-based and free to use. This fact sheet discusses the value of the score for state and local governments.

SC3 - consensus clustering of single-cell RNA-Seq data

PubMed Central

Kiselev, Vladimir Yu.; Kirschner, Kristina; Schaub, Michael T.; Andrews, Tallulah; Yiu, Andrew; Chandra, Tamir; Natarajan, Kedar N; Reik, Wolf; Barahona, Mauricio; Green, Anthony R; Hemberg, Martin

2017-01-01

Single-cell RNA-seq (scRNA-seq) enables a quantitative cell-type characterisation based on global transcriptome profiles. We present Single-Cell Consensus Clustering (SC3), a user-friendly tool for unsupervised clustering which achieves high accuracy and robustness by combining multiple clustering solutions through a consensus approach. We demonstrate that SC3 is capable of identifying subclones based on the transcriptomes from neoplastic cells collected from patients. PMID:28346451

Expert Consensus Survey on Digital Health Tools for Patients With Serious Mental Illness: Optimizing for User Characteristics and User Support.

PubMed

Hatch, Ainslie; Hoffman, Julia E; Ross, Ruth; Docherty, John P

2018-06-12

Digital technology is increasingly being used to enhance health care in various areas of medicine. In the area of serious mental illness, it is important to understand the special characteristics of target users that may influence motivation and competence to use digital health tools, as well as the resources and training necessary for these patients to facilitate the use of this technology. The aim of this study was to conduct a quantitative expert consensus survey to identify key characteristics of target users (patients and health care professionals), barriers and facilitators for appropriate use, and resources needed to optimize the use of digital health tools in patients with serious mental illness. A panel of 40 experts in digital behavioral health who met the participation criteria completed a 19-question survey, rating predefined responses on a 9-point Likert scale. Consensus was determined using a chi-square test of score distributions across three ranges (1-3, 4-6, 7-9). Categorical ratings of first, second, or third line were designated based on the lowest category into which the CI of the mean ratings fell, with a boundary >6.5 for first line. Here, we report experts' responses to nine questions (265 options) that focused on (1) user characteristics that would promote or hinder the use of digital health tools, (2) potential benefits or motivators and barriers or unintended consequences of digital health tool use, and (3) support and training for patients and health care professionals. Among patient characteristics most likely to promote use of digital health tools, experts endorsed interest in using state-of-the-art technology, availability of necessary resources, good occupational functioning, and perception of the tool as beneficial. Certain disease-associated signs and symptoms (eg, more severe symptoms, substance abuse problems, and a chaotic living situation) were considered likely to make it difficult for patients to use digital health tools. Enthusiasm among health care professionals for digital health tools and availability of staff and equipment to support their use were identified as variables to enable health care professionals to successfully incorporate digital health tools into their practices. The experts identified a number of potential benefits of and barriers to use of digital health tools by patients and health care professionals. Experts agreed that both health care professionals and patients would need to be trained in the use of these new technologies. These results provide guidance to the mental health field on how to optimize the development and deployment of digital health tools for patients with serious mental illness. ©Ainslie Hatch, Julia E Hoffman, Ruth Ross, John P Docherty. Originally published in JMIR Mental Health (http://mental.jmir.org), 12.06.2018.

Extending the Lunar Mapping and Modeling Portal - New Capabilities and New Worlds

NASA Astrophysics Data System (ADS)

Day, B. H.; Law, E.; Arevalo, E.; Bui, B.; Chang, G.; Dodge, K.; Kim, R. M.; Malhotra, S.; Sadaqathullah, S.

2015-12-01

NASA's Lunar Mapping and Modeling Portal (LMMP) provides a web-based Portal and a suite of interactive visualization and analysis tools to enable mission planners, lunar scientists, and engineers to access mapped lunar data products from past and current lunar missions (http://lmmp.nasa.gov). During the past year, the capabilities and data served by LMMP have been significantly expanded. New interfaces are providing improved ways to access and visualize data. Many of the recent enhancements to LMMP have been specifically in response to the requirements of NASA's proposed Resource Prospector lunar rover, and as such, provide an excellent example of the application of LMMP to mission planning. At the request of NASA's Science Mission Directorate, LMMP's technology and capabilities are now being extended to additional planetary bodies. New portals for Vesta and Mars are the first of these new products to be released. On March 31, 2015, the LMMP team released Vesta Trek (http://vestatrek.jpl.nasa.gov), a web-based application applying LMMP technology to visualizations of the asteroid Vesta. Data gathered from multiple instruments aboard Dawn have been compiled into Vesta Trek's user-friendly set of tools, enabling users to study the asteroid's features. With an initial release on July 1, 2015, Mars Trek replicates the functionality of Vesta Trek for the surface of Mars. While the entire surface of Mars is covered, higher levels of resolution and greater numbers of data products are provided for special areas of interest. Early releases focus on past, current, and future robotic sites of operation. Future releases will add many new data products and analysis tools as Mars Trek has been selected for use in site selection for the Mars 2020 rover and in identifying potential human landing sites on Mars. Other destinations will follow soon. The user community is invited to provide suggestions and requests as the development team continues to expand the capabilities of LMMP, its related products, and the range of data and tools that they provide. This presentation will provide an overview of LMMP, Vesta Trek, and Mars Trek, demonstrate their uses and capabilities, highlight new features, and preview coming enhancements.

Oyster Fisheries App

NASA Technical Reports Server (NTRS)

Perez Guerrero, Geraldo A.; Armstrong, Duane; Underwood, Lauren

2015-01-01

This project is creating a cloud-enabled, HTML 5 web application to help oyster fishermen and state agencies apply Earth science to improve the management of this important natural and economic resource. The Oyster Fisheries app gathers and analyzes environmental and water quality information, and alerts fishermen and resources managers about problems in oyster fishing waters. An intuitive interface based on Google Maps displays the geospatial information and provides familiar interactive controls to the users. Alerts can be tailored to notify users when conditions in specific leases or public fishing areas require attention. The app is hosted on the Amazon Web Services cloud. It is being developed and tested using some of the latest web development tools such as web components and Polymer.

Development of expert systems for analyzing electronic documents

NASA Astrophysics Data System (ADS)

Abeer Yassin, Al-Azzawi; Shidlovskiy, S.; Jamal, A. A.

2018-05-01

The paper analyses a Database Management System (DBMS). Expert systems, Databases, and database technology have become an essential component of everyday life in the modern society. As databases are widely used in every organization with a computer system, data resource control and data management are very important [1]. DBMS is the most significant tool developed to serve multiple users in a database environment consisting of programs that enable users to create and maintain a database. This paper focuses on development of a database management system for General Directorate for education of Diyala in Iraq (GDED) using Clips, java Net-beans and Alfresco and system components, which were previously developed in Tomsk State University at the Faculty of Innovative Technology.

OLTARIS: On-Line Tool for the Assessment of Radiation in Space

NASA Technical Reports Server (NTRS)

Singleterry, Robert C., Jr.; Blattnig, Steve R.; Clowdsley, Martha S.; Qualls, Garry D.; Sandridge, Chris A.; Simonsen, Lisa C.; Norbury, John W.; Slaba, Tony C.; Walker, Steve A.; Badavi, Francis F.;

Recommendation Systems for Geoscience Data Portals Built by Analyzing Usage Patterns

NASA Astrophysics Data System (ADS)

Crosby, C.; Nandigam, V.; Baru, C.

2009-04-01

Since its launch five years ago, the National Science Foundation-funded GEON Project (www.geongrid.org) has been providing access to a variety of geoscience data sets such as geologic maps and other geographic information system (GIS)-oriented data, paleontologic databases, gravity and magnetics data and LiDAR topography via its online portal interface. In addition to data, the GEON Portal also provides web-based tools and other resources that enable users to process and interact with data. Examples of these tools include functions to dynamically map and integrate GIS data, compute synthetic seismograms, and to produce custom digital elevation models (DEMs) with user defined parameters such as resolution. The GEON portal built on the Gridsphere-portal framework allows us to capture user interaction with the system. In addition to the site access statistics captured by tools like Google Analystics which capture hits per unit time, search key words, operating systems, browsers, and referring sites, we also record additional statistics such as which data sets are being downloaded and in what formats, processing parameters, and navigation pathways through the portal. With over four years of data now available from the GEON Portal, this record of usage is a rich resource for exploring how earth scientists discover and utilize online data sets. Furthermore, we propose that this data could ultimately be harnessed to optimize the way users interact with the data portal, design intelligent processing and data management systems, and to make recommendations on algorithm settings and other available relevant data. The paradigm of integrating popular and commonly used patterns to make recommendations to a user is well established in the world of e-commerce where users receive suggestions on books, music and other products that they may find interesting based on their website browsing and purchasing history, as well as the patterns of fellow users who have made similar selections. However, this paradigm has not yet been explored for geoscience data portals. In this presentation we will present an initial analysis of user interaction and access statistics for the GEON OpenTopography LiDAR data distribution and processing system to illustrate what they reveal about user's spatial and temporal data access patterns, data processing parameter selections, and pathways through the data portal. We also demonstrate what these usage statistics can illustrate about aspects of the data sets that are of greatest interest. Finally, we explore how these usage statistics could be used to improve the user's experience in the data portal and to optimize how data access interfaces and tools are designed and implemented.

The AMMA information system

NASA Astrophysics Data System (ADS)

Fleury, Laurence; Brissebrat, Guillaume; Boichard, Jean-Luc; Cloché, Sophie; Eymard, Laurence; Mastrorillo, Laurence; Moulaye, Oumarou; Ramage, Karim; Favot, Florence; Roussot, Odile

2014-05-01

In the framework of the African Monsoon Multidisciplinary Analyses (AMMA) programme, several tools have been developed in order to facilitate and speed up data and information exchange between researchers from different disciplines. The AMMA information system includes (i) a multidisciplinary user-friendly data management and dissemination system, (ii) report and chart archives associated with display websites and (iii) a scientific paper exchange system. The AMMA information system is enriched by several previous (IMPETUS...) and following projects (FENNEC, ESCAPE, QweCI, DACCIWA…) and is becoming a reference information system about West Africa monsoon. (i) The AMMA project includes airborne, ground-based and ocean measurements, satellite data use, modelling studies and value-added product development. Therefore, the AMMA database user interface enables to access a great amount and a large variety of data: - 250 local observation datasets, that cover many geophysical components (atmosphere, ocean, soil, vegetation) and human activities (agronomy, health). They have been collected by operational networks from 1850 to present, long term monitoring research networks (CATCH, IDAF, PIRATA...) or scientific campaigns; - 1350 outputs of a socio-economics questionnaire; - 60 operational satellite products and several research products; - 10 output sets of meteorological and ocean operational models and 15 of research simulations. All the data are documented in compliance with metadata international standards, and delivered into standard formats. The data request user interface takes full advantage of the data and metadata base relational structure and enables users to elaborate easily multicriteria data requests (period, area, property, property value…). The AMMA data portal counts around 800 registered users and process about 50 data requests every month. The AMMA databases and data portal have been developed and are operated jointly by SEDOO and ESPRI in France: http://database.amma-international.org. The complete system is fully duplicated and operated by CRA in Niger: http://amma.agrhymet.ne/amma-data. (ii) A day-to-day chart and report display application has been designed and operated in order to monitor meteorological and environment information and to meet the observational team needs during the 2006 AMMA SOP (http://aoc.amma-international.org) and 2011 FENNEC campaigns (http://fenoc.sedoo.fr). At present the websites constitute a testimonial view on the campaigns and a preliminary investigation tool for researchers. Since 2011, the same application enables a group of French and Senegalese researchers and forecasters to share in near real time physical indices and diagnosis calculated from numerical weather operational forecasts, satellite products and in situ operational observations along the monsoon season, in order to better estimate, understand and anticipate the monsoon intraseasonal variability (http://misva.sedoo.fr). (iii) A collaborative WIKINDX tool has also been set online in order to gather together scientific publications, theses and communications of interest to AMMA: http://biblio.amma-international.org. Now the bibliographic database counts about 1200 references. It is the most exhaustive document collection about the West African monsoon available for all. Every scientist is invited to make use of the different AMMA online tools and data. Scientists or project leaders who have data management needs for existing or future datasets over West Africa are welcome to use the AMMA database framework and to contact ammaAdmin@sedoo.fr .

PIMMS tools for capturing metadata about simulations

NASA Astrophysics Data System (ADS)

Pascoe, Charlotte; Devine, Gerard; Tourte, Gregory; Pascoe, Stephen; Lawrence, Bryan; Barjat, Hannah

2013-04-01

PIMMS (Portable Infrastructure for the Metafor Metadata System) provides a method for consistent and comprehensive documentation of modelling activities that enables the sharing of simulation data and model configuration information. The aim of PIMMS is to package the metadata infrastructure developed by Metafor for CMIP5 so that it can be used by climate modelling groups in UK Universities. PIMMS tools capture information about simulations from the design of experiments to the implementation of experiments via simulations that run models. PIMMS uses the Metafor methodology which consists of a Common Information Model (CIM), Controlled Vocabularies (CV) and software tools. PIMMS software tools provide for the creation and consumption of CIM content via a web services infrastructure and portal developed by the ES-DOC community. PIMMS metadata integrates with the ESGF data infrastructure via the mapping of vocabularies onto ESGF facets. There are three paradigms of PIMMS metadata collection: Model Intercomparision Projects (MIPs) where a standard set of questions is asked of all models which perform standard sets of experiments. Disciplinary level metadata collection where a standard set of questions is asked of all models but experiments are specified by users. Bespoke metadata creation where the users define questions about both models and experiments. Examples will be shown of how PIMMS has been configured to suit each of these three paradigms. In each case PIMMS allows users to provide additional metadata beyond that which is asked for in an initial deployment. The primary target for PIMMS is the UK climate modelling community where it is common practice to reuse model configurations from other researchers. This culture of collaboration exists in part because climate models are very complex with many variables that can be modified. Therefore it has become common practice to begin a series of experiments by using another climate model configuration as a starting point. Usually this other configuration is provided by a researcher in the same research group or by a previous collaborator with whom there is an existing scientific relationship. Some efforts have been made at the university department level to create documentation but there is a wide diversity in the scope and purpose of this information. The consistent and comprehensive documentation enabled by PIMMS will enable the wider sharing of climate model data and configuration information. The PIMMS methodology assumes an initial effort to document standard model configurations. Once these descriptions have been created users need only describe the specific way in which their model configuration is different from the standard. Thus the documentation burden on the user is specific to the experiment they are performing and fits easily into the workflow of doing their science. PIMMS metadata is independent of data and as such is ideally suited for documenting model development. PIMMS provides a framework for sharing information about failed model configurations for which data are not kept, the negative results that don't appear in scientific literature. PIMMS is a UK project funded by JISC, The University of Reading, The University of Bristol and STFC.

Visualization for genomics: the Microbial Genome Viewer.

PubMed

Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

2004-07-22

A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

Natural language modeling

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

Sharp, J.K.

1997-11-01

This seminar describes a process and methodology that uses structured natural language to enable the construction of precise information requirements directly from users, experts, and managers. The main focus of this natural language approach is to create the precise information requirements and to do it in such a way that the business and technical experts are fully accountable for the results. These requirements can then be implemented using appropriate tools and technology. This requirement set is also a universal learning tool because it has all of the knowledge that is needed to understand a particular process (e.g., expense vouchers, projectmore » management, budget reviews, tax, laws, machine function).« less

Extending Iris: The VAO SED Analysis Tool

NASA Astrophysics Data System (ADS)

Laurino, O.; Busko, I.; Cresitello-Dittmar, M.; D'Abrusco, R.; Doe, S.; Evans, J.; Pevunova, O.

2013-10-01

Iris is a tool developed by the Virtual Astronomical Observatory (VAO) for building and analyzing Spectral Energy Distributions (SEDs). Iris was designed to be extensible, so that new components and models can be developed by third parties and then included at runtime. Iris can be extended in different ways: new file readers allow users to integrate data in custom formats into Iris SEDs; new models can be fitted to the data, in the form of template libraries for template fitting, data tables, and arbitrary Python functions. The interoperability-centered design of Iris and the Virtual Observatory standards and protocols can enable new science functionalities involving SED data.

Collections and user tools for utilization of persistent identifiers in cyberinfrastructures

NASA Astrophysics Data System (ADS)

Weigel, T.

2014-12-01

The main use of persistent identifiers (PIDs) for data objects has so far been for formal publication and citation purposes with a focus on long-term availability and trust. This core use case has now evolved and broadened to include basic data management tasks as identifiers are increasingly seen as a possible anchor element in the deluge of data for purposes of large-scale automation of tasks. The European Data Infrastructure (EUDAT) for instance uses PIDs in their back-end services and distinctly so for entities where the identifier may be more persistent than a resource with limited lifetime. Despite breaking with the traditional metaphor, this offers new opportunities for data management and end-user tools, but also requires a clear demonstrated benefit of value-added services because en masse identifier assignment does not come at zero costs. There are several obstacles to overcome when establishing identifiers at large scale. The administration of large numbers of identifiers can be cumbersome if they are treated in an isolated manner. Here, identifier collections can enable automated mass operations on groups of associated objects. Several use cases rely on base information that is rapidly available from the identifier systems without the need to retrieve objects, yet they will not work efficiently if the information is not consistently typed. Tools that span cyberinfrastructures and address scientific end-users unaware of the varying back-ends must overcome such obstacles. The Working Group on PID Information Types of the Research Data Alliance (RDA) has developed an interface specification and prototype to access and manipulate typed base information. Concrete prototypes for identifier collections exist as well. We will present some first data and provenance tracking tools that make extensive use of these recent developments and address different user needs that span from administrative tasks to individual end-user services with particular focus on data available from the Earth System Grid Federation (ESGF). We will compare the tools along their respective use cases with existing approaches and discuss benefits and limitations.

Enhanced STEM Learning with the GeoMapApp Data Exploration Tool

NASA Astrophysics Data System (ADS)

Goodwillie, A. M.

2014-12-01

GeoMapApp (http://www.geomapapp.org), is a free, map-based data discovery and visualisation tool developed with NSF funding at Lamont-Doherty Earth Observatory. GeoMapApp provides casual and specialist users alike with access to hundreds of built-in geoscience data sets covering geology, geophysics, geochemistry, oceanography, climatology, cryospherics, and the environment. Users can also import their own data tables, spreadsheets, shapefiles, grids and images. Simple manipulation and analysis tools combined with layering capabilities and engaging visualisations provide a powerful platform with which to explore and interrogate geoscience data in its proper geospatial context thus helping users to more easily gain insight into the meaning of the data. A global elevation base map covering the oceans as well as continents forms the backbone of GeoMapApp. The multi-resolution base map is updated regularly and includes data sources ranging from Space Shuttle elevation data for land areas to ultra-high-resolution surveys of coral reefs and seafloor hydrothermal vent fields. Examples of built-in data sets that can be layered over the elevation model include interactive earthquake and volcano data, plate tectonic velocities, hurricane tracks, land and ocean temperature, water column properties, age of the ocean floor, and deep submersible bottom photos. A versatile profiling tool provides instant access to data cross-sections. Contouring and 3-D views are also offered - the attached image shows a 3-D view of East Africa's Ngorongoro Crater as an example. Tabular data - both imported and built-in - can be displayed in a variety of ways and a lasso tool enables users to quickly select data points directly from the map. A range of STEM-based education material based upon GeoMapApp is already available, including a number of self-contained modules for school- and college-level students (http://www.geomapapp.org/education/contributed_material.html). More learning modules are planned, such as one on the effects of sea-level rise. GeoMapApp users include students, teachers, researchers, curriculum developers and outreach specialists.

A Security Architecture for Grid-enabling OGC Web Services

NASA Astrophysics Data System (ADS)

Angelini, Valerio; Petronzio, Luca

2010-05-01

In the proposed presentation we describe an architectural solution for enabling a secure access to Grids and possibly other large scale on-demand processing infrastructures through OGC (Open Geospatial Consortium) Web Services (OWS). This work has been carried out in the context of the security thread of the G-OWS Working Group. G-OWS (gLite enablement of OGC Web Services) is an international open initiative started in 2008 by the European CYCLOPS , GENESI-DR, and DORII Project Consortia in order to collect/coordinate experiences in the enablement of OWS's on top of the gLite Grid middleware. G-OWS investigates the problem of the development of Spatial Data and Information Infrastructures (SDI and SII) based on the Grid/Cloud capacity in order to enable Earth Science applications and tools. Concerning security issues, the integration of OWS compliant infrastructures and gLite Grids needs to address relevant challenges, due to their respective design principles. In fact OWS's are part of a Web based architecture that demands security aspects to other specifications, whereas the gLite middleware implements the Grid paradigm with a strong security model (the gLite Grid Security Infrastructure: GSI). In our work we propose a Security Architectural Framework allowing the seamless use of Grid-enabled OGC Web Services through the federation of existing security systems (mostly web based) with the gLite GSI. This is made possible mediating between different security realms, whose mutual trust is established in advance during the deployment of the system itself. Our architecture is composed of three different security tiers: the user's security system, a specific G-OWS security system, and the gLite Grid Security Infrastructure. Applying the separation-of-concerns principle, each of these tiers is responsible for controlling the access to a well-defined resource set, respectively: the user's organization resources, the geospatial resources and services, and the Grid resources. While the gLite middleware is tied to a consolidated security approach based on X.509 certificates, our system is able to support different kinds of user's security infrastructures. Our central component, the G-OWS Security Framework, is based on the OASIS WS-Trust specifications and on the OGC GeoRM architectural framework. This allows to satisfy advanced requirements such as the enforcement of specific geospatial policies and complex secure web service chained requests. The typical use case is represented by a scientist belonging to a given organization who issues a request to a G-OWS Grid-enabled Web Service. The system initially asks the user to authenticate to his/her organization's security system and, after verification of the user's security credentials, it translates the user's digital identity into a G-OWS identity. This identity is linked to a set of attributes describing the user's access rights to the G-OWS services and resources. Inside the G-OWS Security system, access restrictions are applied making use of the enhanced Geospatial capabilities specified by the OGC GeoXACML. If the required action needs to make use of the Grid environment the system checks if the user is entitled to access a Grid infrastructure. In that case his/her identity is translated to a temporary Grid security token using the Short Lived Credential Services (IGTF Standard). In our case, for the specific gLite Grid infrastructure, some information (VOMS Attributes) is plugged into the Grid Security Token to grant the access to the user's Virtual Organization Grid resources. The resulting token is used to submit the request to the Grid and also by the various gLite middleware elements to verify the user's grants. Basing on the presented framework, the G-OWS Security Working Group developed a prototype, enabling the execution of OGC Web Services on the EGEE Production Grid through the federation with a Shibboleth based security infrastructure. Future plans aim to integrate other Web authentication services such as OpenID, Kerberos and WS-Federation.

E-TALEN: a web tool to design TALENs for genome engineering.

PubMed

Heigwer, Florian; Kerr, Grainne; Walther, Nike; Glaeser, Kathrin; Pelz, Oliver; Breinig, Marco; Boutros, Michael

2013-11-01

Use of transcription activator-like effector nucleases (TALENs) is a promising new technique in the field of targeted genome engineering, editing and reverse genetics. Its applications span from introducing knockout mutations to endogenous tagging of proteins and targeted excision repair. Owing to this wide range of possible applications, there is a need for fast and user-friendly TALEN design tools. We developed E-TALEN (http://www.e-talen.org), a web-based tool to design TALENs for experiments of varying scale. E-TALEN enables the design of TALENs against a single target or a large number of target genes. We significantly extended previously published design concepts to consider genomic context and different applications. E-TALEN guides the user through an end-to-end design process of de novo TALEN pairs, which are specific to a certain sequence or genomic locus. Furthermore, E-TALEN offers a functionality to predict targeting and specificity for existing TALENs. Owing to the computational complexity of many of the steps in the design of TALENs, particular emphasis has been put on the implementation of fast yet accurate algorithms. We implemented a user-friendly interface, from the input parameters to the presentation of results. An additional feature of E-TALEN is the in-built sequence and annotation database available for many organisms, including human, mouse, zebrafish, Drosophila and Arabidopsis, which can be extended in the future.

Remote Sensing Time Series Product Tool

NASA Technical Reports Server (NTRS)

Predos, Don; Ryan, Robert E.; Ross, Kenton W.

2006-01-01

The TSPT (Time Series Product Tool) software was custom-designed for NASA to rapidly create and display single-band and band-combination time series, such as NDVI (Normalized Difference Vegetation Index) images, for wide-area crop surveillance and for other time-critical applications. The TSPT, developed in MATLAB, allows users to create and display various MODIS (Moderate Resolution Imaging Spectroradiometer) or simulated VIIRS (Visible/Infrared Imager Radiometer Suite) products as single images, as time series plots at a selected location, or as temporally processed image videos. Manually creating these types of products is extremely labor intensive; however, the TSPT development tool makes the process simplified and efficient. MODIS is ideal for monitoring large crop areas because of its wide swath (2330 km), its relatively small ground sample distance (250 m), and its high temporal revisit time (twice daily). Furthermore, because MODIS imagery is acquired daily, rapid changes in vegetative health can potentially be detected. The new TSPT technology provides users with the ability to temporally process high-revisit-rate satellite imagery, such as that acquired from MODIS and from its successor, the VIIRS. The TSPT features the important capability of fusing data from both MODIS instruments onboard the Terra and Aqua satellites, which drastically improves cloud statistics. With the TSPT, MODIS metadata is used to find and optionally remove bad and suspect data. Noise removal and temporal processing techniques allow users to create low-noise time series plots and image videos and to select settings and thresholds that tailor particular output products. The TSPT GUI (graphical user interface) provides an interactive environment for crafting what-if scenarios by enabling a user to repeat product generation using different settings and thresholds. The TSPT Application Programming Interface provides more fine-tuned control of product generation, allowing experienced programmers to bypass the GUI and to create more user-specific output products, such as comparison time plots or images. This type of time series analysis tool for remotely sensed imagery could be the basis of a large-area vegetation surveillance system. The TSPT has been used to generate NDVI time series over growing seasons in California and Argentina and for hurricane events, such as Hurricane Katrina.

Interaction Junk: User Interaction-Based Evaluation of Visual Analytic Systems

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

Endert, Alexander; North, Chris

2012-10-14

With the growing need for visualization to aid users in understanding large, complex datasets, the ability for users to interact and explore these datasets is critical. As visual analytic systems have advanced to leverage powerful computational models and data analytics capabilities, the modes by which users engage and interact with the information are limited. Often, users are taxed with directly manipulating parameters of these models through traditional GUIs (e.g., using sliders to directly manipulate the value of a parameter). However, the purpose of user interaction in visual analytic systems is to enable visual data exploration – where users can focusmore » on their task, as opposed to the tool or system. As a result, users can engage freely in data exploration and decision-making, for the purpose of gaining insight. In this position paper, we discuss how evaluating visual analytic systems can be approached through user interaction analysis, where the goal is to minimize the cognitive translation between the visual metaphor and the mode of interaction (i.e., reducing the “Interactionjunk”). We motivate this concept through a discussion of traditional GUIs used in visual analytics for direct manipulation of model parameters, and the importance of designing interactions the support visual data exploration.« less

BingEO: Enable Distributed Earth Observation Data for Environmental Research

NASA Astrophysics Data System (ADS)

Wu, H.; Yang, C.; Xu, Y.

2010-12-01

Our planet is facing great environmental challenges including global climate change, environmental vulnerability, extreme poverty, and a shortage of clean cheap energy. To address these problems, scientists are developing various models to analysis, forecast, simulate various geospatial phenomena to support critical decision making. These models not only challenge our computing technology, but also challenge us to feed huge demands of earth observation data. Through various policies and programs, open and free sharing of earth observation data are advocated in earth science. Currently, thousands of data sources are freely available online through open standards such as Web Map Service (WMS), Web Feature Service (WFS) and Web Coverage Service (WCS). Seamless sharing and access to these resources call for a spatial Cyberinfrastructure (CI) to enable the use of spatial data for the advancement of related applied sciences including environmental research. Based on Microsoft Bing Search Engine and Bing Map, a seamlessly integrated and visual tool is under development to bridge the gap between researchers/educators and earth observation data providers. With this tool, earth science researchers/educators can easily and visually find the best data sets for their research and education. The tool includes a registry and its related supporting module at server-side and an integrated portal as its client. The proposed portal, Bing Earth Observation (BingEO), is based on Bing Search and Bing Map to: 1) Use Bing Search to discover Web Map Services (WMS) resources available over the internet; 2) Develop and maintain a registry to manage all the available WMS resources and constantly monitor their service quality; 3) Allow users to manually register data services; 4) Provide a Bing Maps-based Web application to visualize the data on a high-quality and easy-to-manipulate map platform and enable users to select the best data layers online. Given the amount of observation data accumulated already and still growing, BingEO will allow these resources to be utilized more widely, intensively, efficiently and economically in earth science applications.

The OOI Ocean Education Portal: Enabling the Development of Online Data Investigations

NASA Astrophysics Data System (ADS)

Lichtenwalner, C. S.; McDonnell, J. D.; Crowley, M. F.; deCharon, A.; Companion, C. J.; Glenn, S. M.

2016-02-01

The Ocean Observatories Initiative (OOI) was designed to transform ocean science, by establishing a long-term, multi-instrument, multi-platform research infrastructure at 7 arrays around the word. This unprecedented investment in ocean observation, funded by the National Science Foundation, provides a rich opportunity to reshape ocean science education as well. As part of the initial construction effort, an online Ocean Education Portal was developed to support the creation and sharing of educational resources by undergraduate faculty at universities and community colleges. The portal includes a suite of tools that enable the development of online activities for use as group or individual projects, which can be used during lectures or as homework assignments. The site includes: 1) a suite of interactive educational data visualization tools that provide simple and targeted interfaces to interact with OOI datasets; 2) a concept map builder that can be used by both educators and students to build networked diagrams of their knowledge; and 3) a "data investigation" builder that allows faculty to assemble resources into coherent learning modules. The site also includes a "vocabulary navigator" that provides a visual way to discover and learn about the OOI's infrastructure and scientific design. The site allows users to browse an ever-growing database of resources created by the community, and likewise, users can share resources they create with others. As the OOI begins its 25-year operational phase, it is our hope that faculty will be able to use the tools and investigations on the Ocean Education Portal to bring real ocean science research to their undergraduate students.

EuPaGDT: a web tool tailored to design CRISPR guide RNAs for eukaryotic pathogens.

PubMed

Peng, Duo; Tarleton, Rick

2015-10-01

Recent development of CRISPR-Cas9 genome editing has enabled highly efficient and versatile manipulation of a variety of organisms and adaptation of the CRISPR-Cas9 system to eukaryotic pathogens has opened new avenues for studying these otherwise hard to manipulate organisms. Here we describe a webtool, Eukaryotic Pathogen gRNA Design Tool (EuPaGDT; available at http://grna.ctegd.uga.edu), which identifies guide RNA (gRNA) in input gene(s) to guide users in arriving at well-informed and appropriate gRNA design for many eukaryotic pathogens. Flexibility in gRNA design, accommodating unique eukaryotic pathogen (gene and genome) attributes and high-throughput gRNA design are the main features that distinguish EuPaGDT from other gRNA design tools. In addition to employing an array of known principles to score and rank gRNAs, EuPaGDT implements an effective on-target search algorithm to identify gRNA targeting multi-gene families, which are highly represented in these pathogens and play important roles in host-pathogen interactions. EuPaGDT also identifies and scores microhomology sequences flanking each gRNA targeted cut-site; these sites are often essential for the microhomology-mediated end joining process used for double-stranded break repair in these organisms. EuPaGDT also assists users in designing single-stranded oligonucleotides for homology directed repair. In batch processing mode, EuPaGDT is able to process genome-scale sequences, enabling preparation of gRNA libraries for large-scale screening projects.

ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface.

PubMed

Fähnrich, Anke; Krebbel, Moritz; Decker, Normann; Leucker, Martin; Lange, Felix D; Kalies, Kathrin; Möller, Steffen

2017-03-11

Next generation sequencing (NGS) technologies enable studies and analyses of the diversity of both T and B cell receptors (TCR and BCR) in human and animal systems to elucidate immune functions in health and disease. Over the last few years, several algorithms and tools have been developed to support respective analyses of raw sequencing data of the immune repertoire. These tools focus on distinct aspects of the data processing and require a strong bioinformatics background. To facilitate the analysis of T and B cell repertoires by less experienced users, software is needed that combines the most common tools for repertoire analysis. We introduce a graphical user interface (GUI) providing a complete analysis pipeline for processing raw NGS data for human and animal TCR and BCR clonotype determination and advanced differential repertoire studies. It provides two applications. ClonoCalc prepares the raw data for downstream analyses. It combines a demultiplexer for barcode splitting and employs MiXCR for paired-end read merging and the extraction of human and animal TCR/BCR sequences. ClonoPlot wraps the R package tcR and further contributes self-developed plots for the descriptive comparative investigation of immune repertoires. This workflow reduces the amount of programming required to perform the respective analyses and supports both communication and training between scientists and technicians, and across scientific disciplines. The Open Source development in Java and R is modular and invites advanced users to extend its functionality. Software and documentation are freely available at https://bitbucket.org/ClonoSuite/clonocalc-plot .

Automated Design Space Exploration with Aspen

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

Spafford, Kyle L.; Vetter, Jeffrey S.

Architects and applications scientists often use performance models to explore a multidimensional design space of architectural characteristics, algorithm designs, and application parameters. With traditional performance modeling tools, these explorations forced users to first develop a performance model and then repeatedly evaluate and analyze the model manually. These manual investigations proved laborious and error prone. More importantly, the complexity of this traditional process often forced users to simplify their investigations. To address this challenge of design space exploration, we extend our Aspen (Abstract Scalable Performance Engineering Notation) language with three new language constructs: user-defined resources, parameter ranges, and a collection ofmore » costs in the abstract machine model. Then, we use these constructs to enable automated design space exploration via a nonlinear optimization solver. We show how four interesting classes of design space exploration scenarios can be derived from Aspen models and formulated as pure nonlinear programs. The analysis tools are demonstrated using examples based on Aspen models for a three-dimensional Fast Fourier Transform, the CoMD molecular dynamics proxy application, and the DARPA Streaming Sensor Challenge Problem. Our results show that this approach can compose and solve arbitrary performance modeling questions quickly and rigorously when compared to the traditional manual approach.« less

Automated Design Space Exploration with Aspen

DOE PAGES

Spafford, Kyle L.; Vetter, Jeffrey S.

2015-01-01

Architects and applications scientists often use performance models to explore a multidimensional design space of architectural characteristics, algorithm designs, and application parameters. With traditional performance modeling tools, these explorations forced users to first develop a performance model and then repeatedly evaluate and analyze the model manually. These manual investigations proved laborious and error prone. More importantly, the complexity of this traditional process often forced users to simplify their investigations. To address this challenge of design space exploration, we extend our Aspen (Abstract Scalable Performance Engineering Notation) language with three new language constructs: user-defined resources, parameter ranges, and a collection ofmore » costs in the abstract machine model. Then, we use these constructs to enable automated design space exploration via a nonlinear optimization solver. We show how four interesting classes of design space exploration scenarios can be derived from Aspen models and formulated as pure nonlinear programs. The analysis tools are demonstrated using examples based on Aspen models for a three-dimensional Fast Fourier Transform, the CoMD molecular dynamics proxy application, and the DARPA Streaming Sensor Challenge Problem. Our results show that this approach can compose and solve arbitrary performance modeling questions quickly and rigorously when compared to the traditional manual approach.« less

Automation and hypermedia technology applications

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

Lotus Base: An integrated information portal for the model legume Lotus japonicus

PubMed Central

Mun, Terry; Bachmann, Asger; Gupta, Vikas; Stougaard, Jens; Andersen, Stig U.

2016-01-01

Lotus japonicus is a well-characterized model legume widely used in the study of plant-microbe interactions. However, datasets from various Lotus studies are poorly integrated and lack interoperability. We recognize the need for a comprehensive repository that allows comprehensive and dynamic exploration of Lotus genomic and transcriptomic data. Equally important are user-friendly in-browser tools designed for data visualization and interpretation. Here, we present Lotus Base, which opens to the research community a large, established LORE1 insertion mutant population containing an excess of 120,000 lines, and serves the end-user tightly integrated data from Lotus, such as the reference genome, annotated proteins, and expression profiling data. We report the integration of expression data from the L. japonicus gene expression atlas project, and the development of tools to cluster and export such data, allowing users to construct, visualize, and annotate co-expression gene networks. Lotus Base takes advantage of modern advances in browser technology to deliver powerful data interpretation for biologists. Its modular construction and publicly available application programming interface enable developers to tap into the wealth of integrated Lotus data. Lotus Base is freely accessible at: https://lotus.au.dk. PMID:28008948

Point Analysis in Java applied to histological images of the perforant pathway: a user's account.

PubMed

Scorcioni, Ruggero; Wright, Susan N; Patrick Card, J; Ascoli, Giorgio A; Barrionuevo, Germán

2008-01-01

The freeware Java tool Point Analysis in Java (PAJ), created to perform 3D point analysis, was tested in an independent laboratory setting. The input data consisted of images of the hippocampal perforant pathway from serial immunocytochemical localizations of the rat brain in multiple views at different resolutions. The low magnification set (x2 objective) comprised the entire perforant pathway, while the high magnification set (x100 objective) allowed the identification of individual fibers. A preliminary stereological study revealed a striking linear relationship between the fiber count at high magnification and the optical density at low magnification. PAJ enabled fast analysis for down-sampled data sets and a friendly interface with automated plot drawings. Noted strengths included the multi-platform support as well as the free availability of the source code, conducive to a broad user base and maximum flexibility for ad hoc requirements. PAJ has great potential to extend its usability by (a) improving its graphical user interface, (b) increasing its input size limit, (c) improving response time for large data sets, and (d) potentially being integrated with other Java graphical tools such as ImageJ.

Power Plant Model Validation Tool

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

The PPMV is used to validate generator model using disturbance recordings. The PPMV tool contains a collection of power plant models and model validation studies, as well as disturbance recordings from a number of historic grid events. The user can import data from a new disturbance into the database, which converts PMU and SCADA data into GE PSLF format, and then run the tool to validate (or invalidate) the model for a specific power plant against its actual performance. The PNNL PPMV tool enables the automation of the process of power plant model validation using disturbance recordings. The tool usesmore » PMU and SCADA measurements as input information. The tool automatically adjusts all required EPCL scripts and interacts with GE PSLF in the batch mode. The main tool features includes: The tool interacts with GE PSLF; The tool uses GE PSLF Play-In Function for generator model validation; Database of projects (model validation studies); Database of the historic events; Database of the power plant; The tool has advanced visualization capabilities; and The tool automatically generates reports« less

A repository based on a dynamically extensible data model supporting multidisciplinary research in neuroscience.

PubMed

Corradi, Luca; Porro, Ivan; Schenone, Andrea; Momeni, Parastoo; Ferrari, Raffaele; Nobili, Flavio; Ferrara, Michela; Arnulfo, Gabriele; Fato, Marco M

2012-10-08

Robust, extensible and distributed databases integrating clinical, imaging and molecular data represent a substantial challenge for modern neuroscience. It is even more difficult to provide extensible software environments able to effectively target the rapidly changing data requirements and structures of research experiments. There is an increasing request from the neuroscience community for software tools addressing technical challenges about: (i) supporting researchers in the medical field to carry out data analysis using integrated bioinformatics services and tools; (ii) handling multimodal/multiscale data and metadata, enabling the injection of several different data types according to structured schemas; (iii) providing high extensibility, in order to address different requirements deriving from a large variety of applications simply through a user runtime configuration. A dynamically extensible data structure supporting collaborative multidisciplinary research projects in neuroscience has been defined and implemented. We have considered extensibility issues from two different points of view. First, the improvement of data flexibility has been taken into account. This has been done through the development of a methodology for the dynamic creation and use of data types and related metadata, based on the definition of "meta" data model. This way, users are not constrainted to a set of predefined data and the model can be easily extensible and applicable to different contexts. Second, users have been enabled to easily customize and extend the experimental procedures in order to track each step of acquisition or analysis. This has been achieved through a process-event data structure, a multipurpose taxonomic schema composed by two generic main objects: events and processes. Then, a repository has been built based on such data model and structure, and deployed on distributed resources thanks to a Grid-based approach. Finally, data integration aspects have been addressed by providing the repository application with an efficient dynamic interface designed to enable the user to both easily query the data depending on defined datatypes and view all the data of every patient in an integrated and simple way. The results of our work have been twofold. First, a dynamically extensible data model has been implemented and tested based on a "meta" data-model enabling users to define their own data types independently from the application context. This data model has allowed users to dynamically include additional data types without the need of rebuilding the underlying database. Then a complex process-event data structure has been built, based on this data model, describing patient-centered diagnostic processes and merging information from data and metadata. Second, a repository implementing such a data structure has been deployed on a distributed Data Grid in order to provide scalability both in terms of data input and data storage and to exploit distributed data and computational approaches in order to share resources more efficiently. Moreover, data managing has been made possible through a friendly web interface. The driving principle of not being forced to preconfigured data types has been satisfied. It is up to users to dynamically configure the data model for the given experiment or data acquisition program, thus making it potentially suitable for customized applications. Based on such repository, data managing has been made possible through a friendly web interface. The driving principle of not being forced to preconfigured data types has been satisfied. It is up to users to dynamically configure the data model for the given experiment or data acquisition program, thus making it potentially suitable for customized applications.

A repository based on a dynamically extensible data model supporting multidisciplinary research in neuroscience

PubMed Central

2012-01-01

Background Robust, extensible and distributed databases integrating clinical, imaging and molecular data represent a substantial challenge for modern neuroscience. It is even more difficult to provide extensible software environments able to effectively target the rapidly changing data requirements and structures of research experiments. There is an increasing request from the neuroscience community for software tools addressing technical challenges about: (i) supporting researchers in the medical field to carry out data analysis using integrated bioinformatics services and tools; (ii) handling multimodal/multiscale data and metadata, enabling the injection of several different data types according to structured schemas; (iii) providing high extensibility, in order to address different requirements deriving from a large variety of applications simply through a user runtime configuration. Methods A dynamically extensible data structure supporting collaborative multidisciplinary research projects in neuroscience has been defined and implemented. We have considered extensibility issues from two different points of view. First, the improvement of data flexibility has been taken into account. This has been done through the development of a methodology for the dynamic creation and use of data types and related metadata, based on the definition of “meta” data model. This way, users are not constrainted to a set of predefined data and the model can be easily extensible and applicable to different contexts. Second, users have been enabled to easily customize and extend the experimental procedures in order to track each step of acquisition or analysis. This has been achieved through a process-event data structure, a multipurpose taxonomic schema composed by two generic main objects: events and processes. Then, a repository has been built based on such data model and structure, and deployed on distributed resources thanks to a Grid-based approach. Finally, data integration aspects have been addressed by providing the repository application with an efficient dynamic interface designed to enable the user to both easily query the data depending on defined datatypes and view all the data of every patient in an integrated and simple way. Results The results of our work have been twofold. First, a dynamically extensible data model has been implemented and tested based on a “meta” data-model enabling users to define their own data types independently from the application context. This data model has allowed users to dynamically include additional data types without the need of rebuilding the underlying database. Then a complex process-event data structure has been built, based on this data model, describing patient-centered diagnostic processes and merging information from data and metadata. Second, a repository implementing such a data structure has been deployed on a distributed Data Grid in order to provide scalability both in terms of data input and data storage and to exploit distributed data and computational approaches in order to share resources more efficiently. Moreover, data managing has been made possible through a friendly web interface. The driving principle of not being forced to preconfigured data types has been satisfied. It is up to users to dynamically configure the data model for the given experiment or data acquisition program, thus making it potentially suitable for customized applications. Conclusions Based on such repository, data managing has been made possible through a friendly web interface. The driving principle of not being forced to preconfigured data types has been satisfied. It is up to users to dynamically configure the data model for the given experiment or data acquisition program, thus making it potentially suitable for customized applications. PMID:23043673

A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal.

PubMed

Eijssen, Lars M T; Goelela, Varshna S; Kelder, Thomas; Adriaens, Michiel E; Evelo, Chris T; Radonjic, Marijana

2015-06-30

Illumina whole-genome expression bead arrays are a widely used platform for transcriptomics. Most of the tools available for the analysis of the resulting data are not easily applicable by less experienced users. ArrayAnalysis.org provides researchers with an easy-to-use and comprehensive interface to the functionality of R and Bioconductor packages for microarray data analysis. As a modular open source project, it allows developers to contribute modules that provide support for additional types of data or extend workflows. To enable data analysis of Illumina bead arrays for a broad user community, we have developed a module for ArrayAnalysis.org that provides a free and user-friendly web interface for quality control and pre-processing for these arrays. This module can be used together with existing modules for statistical and pathway analysis to provide a full workflow for Illumina gene expression data analysis. The module accepts data exported from Illumina's GenomeStudio, and provides the user with quality control plots and normalized data. The outputs are directly linked to the existing statistics module of ArrayAnalysis.org, but can also be downloaded for further downstream analysis in third-party tools. The Illumina bead arrays analysis module is available at http://www.arrayanalysis.org . A user guide, a tutorial demonstrating the analysis of an example dataset, and R scripts are available. The module can be used as a starting point for statistical evaluation and pathway analysis provided on the website or to generate processed input data for a broad range of applications in life sciences research.

cMapper: gene-centric connectivity mapper for EBI-RDF platform.

PubMed

Shoaib, Muhammad; Ansari, Adnan Ahmad; Ahn, Sung-Min

2017-01-15

In this era of biological big data, data integration has become a common task and a challenge for biologists. The Resource Description Framework (RDF) was developed to enable interoperability of heterogeneous datasets. The EBI-RDF platform enables an efficient data integration of six independent biological databases using RDF technologies and shared ontologies. However, to take advantage of this platform, biologists need to be familiar with RDF technologies and SPARQL query language. To overcome this practical limitation of the EBI-RDF platform, we developed cMapper, a web-based tool that enables biologists to search the EBI-RDF databases in a gene-centric manner without a thorough knowledge of RDF and SPARQL. cMapper allows biologists to search data entities in the EBI-RDF platform that are connected to genes or small molecules of interest in multiple biological contexts. The input to cMapper consists of a set of genes or small molecules, and the output are data entities in six independent EBI-RDF databases connected with the given genes or small molecules in the user's query. cMapper provides output to users in the form of a graph in which nodes represent data entities and the edges represent connections between data entities and inputted set of genes or small molecules. Furthermore, users can apply filters based on database, taxonomy, organ and pathways in order to focus on a core connectivity graph of their interest. Data entities from multiple databases are differentiated based on background colors. cMapper also enables users to investigate shared connections between genes or small molecules of interest. Users can view the output graph on a web browser or download it in either GraphML or JSON formats. cMapper is available as a web application with an integrated MySQL database. The web application was developed using Java and deployed on Tomcat server. We developed the user interface using HTML5, JQuery and the Cytoscape Graph API. cMapper can be accessed at http://cmapper.ewostech.net Readers can download the development manual from the website http://cmapper.ewostech.net/docs/cMapperDocumentation.pdf. Source Code is available at https://github.com/muhammadshoaib/cmapperContact:smahn@gachon.ac.krSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A lightweight and secure two factor anonymous authentication protocol for Global Mobility Networks.

PubMed

Baig, Ahmed Fraz; Hassan, Khwaja Mansoor Ul; Ghani, Anwar; Chaudhry, Shehzad Ashraf; Khan, Imran; Ashraf, Muhammad Usman

2018-01-01

Global Mobility Networks(GLOMONETs) in wireless communication permits the global roaming services that enable a user to leverage the mobile services in any foreign country. Technological growth in wireless communication is also accompanied by new security threats and challenges. A threat-proof authentication protocol in wireless communication may overcome the security flaws by allowing only legitimate users to access a particular service. Recently, Lee et al. found Mun et al. scheme vulnerable to different attacks and proposed an advanced secure scheme to overcome the security flaws. However, this article points out that Lee et al. scheme lacks user anonymity, inefficient user authentication, vulnerable to replay and DoS attacks and Lack of local password verification. Furthermore, this article presents a more robust anonymous authentication scheme to handle the threats and challenges found in Lee et al.'s protocol. The proposed protocol is formally verified with an automated tool(ProVerif). The proposed protocol has superior efficiency in comparison to the existing protocols.

Software-defined Quantum Networking Ecosystem

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

Humble, Travis S.; Sadlier, Ronald

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

A lightweight and secure two factor anonymous authentication protocol for Global Mobility Networks

PubMed Central

2018-01-01

Global Mobility Networks(GLOMONETs) in wireless communication permits the global roaming services that enable a user to leverage the mobile services in any foreign country. Technological growth in wireless communication is also accompanied by new security threats and challenges. A threat-proof authentication protocol in wireless communication may overcome the security flaws by allowing only legitimate users to access a particular service. Recently, Lee et al. found Mun et al. scheme vulnerable to different attacks and proposed an advanced secure scheme to overcome the security flaws. However, this article points out that Lee et al. scheme lacks user anonymity, inefficient user authentication, vulnerable to replay and DoS attacks and Lack of local password verification. Furthermore, this article presents a more robust anonymous authentication scheme to handle the threats and challenges found in Lee et al.’s protocol. The proposed protocol is formally verified with an automated tool(ProVerif). The proposed protocol has superior efficiency in comparison to the existing protocols. PMID:29702675

A web portal for hydrodynamical, cosmological simulations

NASA Astrophysics Data System (ADS)

Ragagnin, A.; Dolag, K.; Biffi, V.; Cadolle Bel, M.; Hammer, N. J.; Krukau, A.; Petkova, M.; Steinborn, D.

2017-07-01

This article describes a data centre hosting a web portal for accessing and sharing the output of large, cosmological, hydro-dynamical simulations with a broad scientific community. It also allows users to receive related scientific data products by directly processing the raw simulation data on a remote computing cluster. The data centre has a multi-layer structure: a web portal, a job control layer, a computing cluster and a HPC storage system. The outer layer enables users to choose an object from the simulations. Objects can be selected by visually inspecting 2D maps of the simulation data, by performing highly compounded and elaborated queries or graphically by plotting arbitrary combinations of properties. The user can run analysis tools on a chosen object. These services allow users to run analysis tools on the raw simulation data. The job control layer is responsible for handling and performing the analysis jobs, which are executed on a computing cluster. The innermost layer is formed by a HPC storage system which hosts the large, raw simulation data. The following services are available for the users: (I) CLUSTERINSPECT visualizes properties of member galaxies of a selected galaxy cluster; (II) SIMCUT returns the raw data of a sub-volume around a selected object from a simulation, containing all the original, hydro-dynamical quantities; (III) SMAC creates idealized 2D maps of various, physical quantities and observables of a selected object; (IV) PHOX generates virtual X-ray observations with specifications of various current and upcoming instruments.

NERIES: Seismic Data Gateways and User Composed Datasets Metadata Management

NASA Astrophysics Data System (ADS)

Spinuso, Alessandro; Trani, Luca; Kamb, Linus; Frobert, Laurent

2010-05-01

One of the NERIES EC project main objectives is to establish and improve the networking of seismic waveform data exchange and access among four main data centers in Europe: INGV, GFZ, ORFEUS and IPGP. Besides the implementation of the data backbone, several investigations and developments have been conducted in order to offer to the users the data available from this network, either programmatically or interactively. One of the challenges is to understand how to enable users` activities such as discovering, aggregating, describing and sharing datasets to obtain a decrease in the replication of similar data queries towards the network, exempting the data centers to guess and create useful pre-packed products. We`ve started to transfer this task more and more towards the users community, where the users` composed data products could be extensively re-used. The main link to the data is represented by a centralized webservice (SeismoLink) acting like a single access point to the whole data network. Users can download either waveform data or seismic station inventories directly from their own software routines by connecting to this webservice, which routes the request to the data centers. The provenance of the data is maintained and transferred to the users in the form of URIs, that identify the dataset and implicitly refer to the data provider. SeismoLink, combined with other webservices (eg EMSC-QuakeML earthquakes catalog service), is used from a community gateway such as the NERIES web portal (http://www.seismicportal.eu). Here the user interacts with a map based portlet which allows the dynamic composition of a data product, binding seismic event`s parameters with a set of seismic stations. The requested data is collected by the back-end processes of the portal, preserved and offered to the user in a personal data cart, where metadata can be generated interactively on-demand. The metadata, expressed in RDF, can also be remotely ingested. They offer rating, provenance and user annotation properties. Once generated they are included into a proprietary taxonomy, used by the overall architecture of the web portal. The metadata are made available through a SPARQL endpoint, thus allowing the datasets to be aggregated and shared among users in a meaningful way, enabling at the same time the development of third party visualization tools beyond the portal infrastructure. The SEE-GRID-SCI and the JISC-funded RapidSeis projects investigate the usage of this framework to enable the waveform data processing over the Grid.

The MetabolomeExpress Project: enabling web-based processing, analysis and transparent dissemination of GC/MS metabolomics datasets.

PubMed

Carroll, Adam J; Badger, Murray R; Harvey Millar, A

2010-07-14

Standardization of analytical approaches and reporting methods via community-wide collaboration can work synergistically with web-tool development to result in rapid community-driven expansion of online data repositories suitable for data mining and meta-analysis. In metabolomics, the inter-laboratory reproducibility of gas-chromatography/mass-spectrometry (GC/MS) makes it an obvious target for such development. While a number of web-tools offer access to datasets and/or tools for raw data processing and statistical analysis, none of these systems are currently set up to act as a public repository by easily accepting, processing and presenting publicly submitted GC/MS metabolomics datasets for public re-analysis. Here, we present MetabolomeExpress, a new File Transfer Protocol (FTP) server and web-tool for the online storage, processing, visualisation and statistical re-analysis of publicly submitted GC/MS metabolomics datasets. Users may search a quality-controlled database of metabolite response statistics from publicly submitted datasets by a number of parameters (eg. metabolite, species, organ/biofluid etc.). Users may also perform meta-analysis comparisons of multiple independent experiments or re-analyse public primary datasets via user-friendly tools for t-test, principal components analysis, hierarchical cluster analysis and correlation analysis. They may interact with chromatograms, mass spectra and peak detection results via an integrated raw data viewer. Researchers who register for a free account may upload (via FTP) their own data to the server for online processing via a novel raw data processing pipeline. MetabolomeExpress https://www.metabolome-express.org provides a new opportunity for the general metabolomics community to transparently present online the raw and processed GC/MS data underlying their metabolomics publications. Transparent sharing of these data will allow researchers to assess data quality and draw their own insights from published metabolomics datasets.

Closha: bioinformatics workflow system for the analysis of massive sequencing data.

PubMed

Ko, GunHwan; Kim, Pan-Gyu; Yoon, Jongcheol; Han, Gukhee; Park, Seong-Jin; Song, Wangho; Lee, Byungwook

2018-02-19

While next-generation sequencing (NGS) costs have fallen in recent years, the cost and complexity of computation remain substantial obstacles to the use of NGS in bio-medical care and genomic research. The rapidly increasing amounts of data available from the new high-throughput methods have made data processing infeasible without automated pipelines. The integration of data and analytic resources into workflow systems provides a solution to the problem by simplifying the task of data analysis. To address this challenge, we developed a cloud-based workflow management system, Closha, to provide fast and cost-effective analysis of massive genomic data. We implemented complex workflows making optimal use of high-performance computing clusters. Closha allows users to create multi-step analyses using drag and drop functionality and to modify the parameters of pipeline tools. Users can also import the Galaxy pipelines into Closha. Closha is a hybrid system that enables users to use both analysis programs providing traditional tools and MapReduce-based big data analysis programs simultaneously in a single pipeline. Thus, the execution of analytics algorithms can be parallelized, speeding up the whole process. We also developed a high-speed data transmission solution, KoDS, to transmit a large amount of data at a fast rate. KoDS has a file transfer speed of up to 10 times that of normal FTP and HTTP. The computer hardware for Closha is 660 CPU cores and 800 TB of disk storage, enabling 500 jobs to run at the same time. Closha is a scalable, cost-effective, and publicly available web service for large-scale genomic data analysis. Closha supports the reliable and highly scalable execution of sequencing analysis workflows in a fully automated manner. Closha provides a user-friendly interface to all genomic scientists to try to derive accurate results from NGS platform data. The Closha cloud server is freely available for use from http://closha.kobic.re.kr/ .

A new tool for supervised classification of satellite images available on web servers: Google Maps as a case study

NASA Astrophysics Data System (ADS)

García-Flores, Agustín.; Paz-Gallardo, Abel; Plaza, Antonio; Li, Jun

2016-10-01

This paper describes a new web platform dedicated to the classification of satellite images called Hypergim. The current implementation of this platform enables users to perform classification of satellite images from any part of the world thanks to the worldwide maps provided by Google Maps. To perform this classification, Hypergim uses unsupervised algorithms like Isodata and K-means. Here, we present an extension of the original platform in which we adapt Hypergim in order to use supervised algorithms to improve the classification results. This involves a significant modification of the user interface, providing the user with a way to obtain samples of classes present in the images to use in the training phase of the classification process. Another main goal of this development is to improve the runtime of the image classification process. To achieve this goal, we use a parallel implementation of the Random Forest classification algorithm. This implementation is a modification of the well-known CURFIL software package. The use of this type of algorithms to perform image classification is widespread today thanks to its precision and ease of training. The actual implementation of Random Forest was developed using CUDA platform, which enables us to exploit the potential of several models of NVIDIA graphics processing units using them to execute general purpose computing tasks as image classification algorithms. As well as CUDA, we use other parallel libraries as Intel Boost, taking advantage of the multithreading capabilities of modern CPUs. To ensure the best possible results, the platform is deployed in a cluster of commodity graphics processing units (GPUs), so that multiple users can use the tool in a concurrent way. The experimental results indicate that this new algorithm widely outperform the previous unsupervised algorithms implemented in Hypergim, both in runtime as well as precision of the actual classification of the images.

Web-based, GPU-accelerated, Monte Carlo simulation and visualization of indirect radiation imaging detector performance.

PubMed

Dong, Han; Sharma, Diksha; Badano, Aldo

2014-12-01

Monte Carlo simulations play a vital role in the understanding of the fundamental limitations, design, and optimization of existing and emerging medical imaging systems. Efforts in this area have resulted in the development of a wide variety of open-source software packages. One such package, hybridmantis, uses a novel hybrid concept to model indirect scintillator detectors by balancing the computational load using dual CPU and graphics processing unit (GPU) processors, obtaining computational efficiency with reasonable accuracy. In this work, the authors describe two open-source visualization interfaces, webmantis and visualmantis to facilitate the setup of computational experiments via hybridmantis. The visualization tools visualmantis and webmantis enable the user to control simulation properties through a user interface. In the case of webmantis, control via a web browser allows access through mobile devices such as smartphones or tablets. webmantis acts as a server back-end and communicates with an NVIDIA GPU computing cluster that can support multiuser environments where users can execute different experiments in parallel. The output consists of point response and pulse-height spectrum, and optical transport statistics generated by hybridmantis. The users can download the output images and statistics through a zip file for future reference. In addition, webmantis provides a visualization window that displays a few selected optical photon path as they get transported through the detector columns and allows the user to trace the history of the optical photons. The visualization tools visualmantis and webmantis provide features such as on the fly generation of pulse-height spectra and response functions for microcolumnar x-ray imagers while allowing users to save simulation parameters and results from prior experiments. The graphical interfaces simplify the simulation setup and allow the user to go directly from specifying input parameters to receiving visual feedback for the model predictions.

The Biomolecular Interaction Network Database and related tools 2005 update

PubMed Central

Alfarano, C.; Andrade, C. E.; Anthony, K.; Bahroos, N.; Bajec, M.; Bantoft, K.; Betel, D.; Bobechko, B.; Boutilier, K.; Burgess, E.; Buzadzija, K.; Cavero, R.; D'Abreo, C.; Donaldson, I.; Dorairajoo, D.; Dumontier, M. J.; Dumontier, M. R.; Earles, V.; Farrall, R.; Feldman, H.; Garderman, E.; Gong, Y.; Gonzaga, R.; Grytsan, V.; Gryz, E.; Gu, V.; Haldorsen, E.; Halupa, A.; Haw, R.; Hrvojic, A.; Hurrell, L.; Isserlin, R.; Jack, F.; Juma, F.; Khan, A.; Kon, T.; Konopinsky, S.; Le, V.; Lee, E.; Ling, S.; Magidin, M.; Moniakis, J.; Montojo, J.; Moore, S.; Muskat, B.; Ng, I.; Paraiso, J. P.; Parker, B.; Pintilie, G.; Pirone, R.; Salama, J. J.; Sgro, S.; Shan, T.; Shu, Y.; Siew, J.; Skinner, D.; Snyder, K.; Stasiuk, R.; Strumpf, D.; Tuekam, B.; Tao, S.; Wang, Z.; White, M.; Willis, R.; Wolting, C.; Wong, S.; Wrong, A.; Xin, C.; Yao, R.; Yates, B.; Zhang, S.; Zheng, K.; Pawson, T.; Ouellette, B. F. F.; Hogue, C. W. V.

2005-01-01

The Biomolecular Interaction Network Database (BIND) (http://bind.ca) archives biomolecular interaction, reaction, complex and pathway information. Our aim is to curate the details about molecular interactions that arise from published experimental research and to provide this information, as well as tools to enable data analysis, freely to researchers worldwide. BIND data are curated into a comprehensive machine-readable archive of computable information and provides users with methods to discover interactions and molecular mechanisms. BIND has worked to develop new methods for visualization that amplify the underlying annotation of genes and proteins to facilitate the study of molecular interaction networks. BIND has maintained an open database policy since its inception in 1999. Data growth has proceeded at a tremendous rate, approaching over 100 000 records. New services provided include a new BIND Query and Submission interface, a Standard Object Access Protocol service and the Small Molecule Interaction Database (http://smid.blueprint.org) that allows users to determine probable small molecule binding sites of new sequences and examine conserved binding residues. PMID:15608229

Interactome INSIDER: a structural interactome browser for genomic studies.

PubMed

Meyer, Michael J; Beltrán, Juan Felipe; Liang, Siqi; Fragoza, Robert; Rumack, Aaron; Liang, Jin; Wei, Xiaomu; Yu, Haiyuan

2018-01-01

We present Interactome INSIDER, a tool to link genomic variant information with structural protein-protein interactomes. Underlying this tool is the application of machine learning to predict protein interaction interfaces for 185,957 protein interactions with previously unresolved interfaces in human and seven model organisms, including the entire experimentally determined human binary interactome. Predicted interfaces exhibit functional properties similar to those of known interfaces, including enrichment for disease mutations and recurrent cancer mutations. Through 2,164 de novo mutagenesis experiments, we show that mutations of predicted and known interface residues disrupt interactions at a similar rate and much more frequently than mutations outside of predicted interfaces. To spur functional genomic studies, Interactome INSIDER (http://interactomeinsider.yulab.org) enables users to identify whether variants or disease mutations are enriched in known and predicted interaction interfaces at various resolutions. Users may explore known population variants, disease mutations, and somatic cancer mutations, or they may upload their own set of mutations for this purpose.

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

PubMed

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

2017-09-01

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

Exploration of SWRL Rule Bases through Visualization, Paraphrasing, and Categorization of Rules

NASA Astrophysics Data System (ADS)

Hassanpour, Saeed; O'Connor, Martin J.; Das, Amar K.

Rule bases are increasingly being used as repositories of knowledge content on the Semantic Web. As the size and complexity of these rule bases increases, developers and end users need methods of rule abstraction to facilitate rule management. In this paper, we describe a rule abstraction method for Semantic Web Rule Language (SWRL) rules that is based on lexical analysis and a set of heuristics. Our method results in a tree data structure that we exploit in creating techniques to visualize, paraphrase, and categorize SWRL rules. We evaluate our approach by applying it to several biomedical ontologies that contain SWRL rules, and show how the results reveal rule patterns within the rule base. We have implemented our method as a plug-in tool for Protégé-OWL, the most widely used ontology modeling software for the Semantic Web. Our tool can allow users to rapidly explore content and patterns in SWRL rule bases, enabling their acquisition and management.

Design and pilot evaluation of a system to develop computer-based site-specific practice guidelines from decision models.

PubMed

Sanders, G D; Nease, R F; Owens, D K

2000-01-01

Local tailoring of clinical practice guidelines (CPGs) requires experts in medicine and evidence synthesis unavailable in many practice settings. The authors' computer-based system enables developers and users to create, disseminate, and tailor CPGs, using normative decision models (DMs). ALCHEMIST, a web-based system, analyzes a DM, creates a CPG in the form of an annotated algorithm, and displays for the guideline user the optimal strategy. ALCHEMIST'S interface enables remote users to tailor the guideline by changing underlying input variables and observing the new annotated algorithm that is developed automatically. In a pilot evaluation of the system, a DM was used to evaluate strategies for staging non-small-cell lung cancer. Subjects (n = 15) compared the automatically created CPG with published guidelines for this staging and critiqued both using a previously developed instrument to rate the CPGs' usability, accountability, and accuracy on a scale of 0 (worst) to 2 (best), with higher scores reflecting higher quality. The mean overall score for the ALCHEMIST CPG was 1.502, compared with the published-CPG score of 0.987 (p = 0.002). The ALCHEMIST CPG scores for usability, accountability, and accuracy were 1.683, 1.393, and 1.430, respectively; the published CPG scores were 1.192, 0.941, and 0.830 (each comparison p < 0.05). On a scale of 1 (worst) to 5 (best), users' mean ratings of ALCHEMIST'S ease of use, usefulness of content, and presentation format were 4.76, 3.98, and 4.64, respectively. The results demonstrate the feasibility of a web-based system that automatically analyzes a DM and creates a CPG as an annotated algorithm, enabling remote users to develop site-specific CPGs. In the pilot evaluation, the ALCHEMIST guidelines met established criteria for quality and compared favorably with national CPGs. The high usability and usefulness ratings suggest that such systems can be a good tool for guideline development.

TopoDrive and ParticleFlow--Two Computer Models for Simulation and Visualization of Ground-Water Flow and Transport of Fluid Particles in Two Dimensions

USGS Publications Warehouse

Hsieh, Paul A.

2001-01-01

This report serves as a user?s guide for two computer models: TopoDrive and ParticleFlow. These two-dimensional models are designed to simulate two ground-water processes: topography-driven flow and advective transport of fluid particles. To simulate topography-driven flow, the user may specify the shape of the water table, which bounds the top of the vertical flow section. To simulate transport of fluid particles, the model domain is a rectangle with overall flow from left to right. In both cases, the flow is under steady state, and the distribution of hydraulic conductivity may be specified by the user. The models compute hydraulic head, ground-water flow paths, and the movement of fluid particles. An interactive visual interface enables the user to easily and quickly explore model behavior, and thereby better understand ground-water flow processes. In this regard, TopoDrive and ParticleFlow are not intended to be comprehensive modeling tools, but are designed for modeling at the exploratory or conceptual level, for visual demonstration, and for educational purposes.

Building Energy Asset Score for Utilities and Energy Efficiency Program Administrators

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

Building Technologies Office

2015-01-01

The Building Energy Asset Score is a national standardized tool for evaluating the physical and structural energy efficiency of commercial and multifamily residential buildings. The Asset Score generates a simple energy efficiency rating that enables comparison among buildings, and identifies opportunities for users to invest in energy efficiency upgrades. It is web-based and free to use. This fact sheet discusses the value of the score for utilities and energy efficiency program administrators.

Designing a Relational Database for the Basic School; Schools Command Web Enabled Officer and Enlisted Database (Sword)

DTIC Science & Technology

2002-06-01

Student memo for personnel MCLLS . . . . . . . . . . . . . . 75 i. Migrate data to SQL Server...The Web Server is on the same server as the SWORD database in the current version. 4: results set 5: dynamic HTML page 6: dynamic HTML page 3: SQL ...still be supported by Access. SQL Server would be a more viable tool for a fully developed application based on the number of potential users and

PLEXOS Input Data Generator

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

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

CyanoBase: the cyanobacteria genome database update 2010.

PubMed

Nakao, Mitsuteru; Okamoto, Shinobu; Kohara, Mitsuyo; Fujishiro, Tsunakazu; Fujisawa, Takatomo; Sato, Shusei; Tabata, Satoshi; Kaneko, Takakazu; Nakamura, Yasukazu

2010-01-01

CyanoBase (http://genome.kazusa.or.jp/cyanobase) is the genome database for cyanobacteria, which are model organisms for photosynthesis. The database houses cyanobacteria species information, complete genome sequences, genome-scale experiment data, gene information, gene annotations and mutant information. In this version, we updated these datasets and improved the navigation and the visual display of the data views. In addition, a web service API now enables users to retrieve the data in various formats with other tools, seamlessly.

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

PubMed

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

2011-04-01

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

Neurovascular Network Explorer 2.0: A Simple Tool for Exploring and Sharing a Database of Optogenetically-evoked Vasomotion in Mouse Cortex In Vivo.

PubMed

Uhlirova, Hana; Tian, Peifang; Kılıç, Kıvılcım; Thunemann, Martin; Sridhar, Vishnu B; Chmelik, Radim; Bartsch, Hauke; Dale, Anders M; Devor, Anna; Saisan, Payam A

2018-05-04

The importance of sharing experimental data in neuroscience grows with the amount and complexity of data acquired and various techniques used to obtain and process these data. However, the majority of experimental data, especially from individual studies of regular-sized laboratories never reach wider research community. A graphical user interface (GUI) engine called Neurovascular Network Explorer 2.0 (NNE 2.0) has been created as a tool for simple and low-cost sharing and exploring of vascular imaging data. NNE 2.0 interacts with a database containing optogenetically-evoked dilation/constriction time-courses of individual vessels measured in mice somatosensory cortex in vivo by 2-photon microscopy. NNE 2.0 enables selection and display of the time-courses based on different criteria (subject, branching order, cortical depth, vessel diameter, arteriolar tree) as well as simple mathematical manipulation (e.g. averaging, peak-normalization) and data export. It supports visualization of the vascular network in 3D and enables localization of the individual functional vessel diameter measurements within vascular trees. NNE 2.0, its source code, and the corresponding database are freely downloadable from UCSD Neurovascular Imaging Laboratory website 1 . The source code can be utilized by the users to explore the associated database or as a template for databasing and sharing their own experimental results provided the appropriate format.

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2017-08-01

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

Vision Forward for NASA's Astrophysics Education Program

NASA Astrophysics Data System (ADS)

Hasan, Hashima; Sheth, Kartik J.

2016-01-01

NASA has recently re-structured its Science Education program with the competitive selection of twenty-seven programs. Of these, ~60% are relevant to Astrophysics, and three have primarily Astrophysics content. A brief overview of the rationale for re-structuring will be presented. We have taken a strategic approach, building on our science-discipline based legacy and looking at new approaches given Stakeholder priorities. We plan to achieve our education goals with the selection of organizations that utilize NASA data, products, or processes to meet NASA's education objectives; and by enabling our scientists and engineers with education professionals, tools, and processes to better meet user needs. Highlights of the selected programs will be presented, and how they enable the vision going forward of achieving the goal of enabling NASA scientists and engineers to engage more effectively with learners of all ages.

PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways.

PubMed

Demir, E; Babur, O; Dogrusoz, U; Gursoy, A; Nisanci, G; Cetin-Atalay, R; Ozturk, M

2002-07-01

Availability of the sequences of entire genomes shifts the scientific curiosity towards the identification of function of the genomes in large scale as in genome studies. In the near future, data produced about cellular processes at molecular level will accumulate with an accelerating rate as a result of proteomics studies. In this regard, it is essential to develop tools for storing, integrating, accessing, and analyzing this data effectively. We define an ontology for a comprehensive representation of cellular events. The ontology presented here enables integration of fragmented or incomplete pathway information and supports manipulation and incorporation of the stored data, as well as multiple levels of abstraction. Based on this ontology, we present the architecture of an integrated environment named Patika (Pathway Analysis Tool for Integration and Knowledge Acquisition). Patika is composed of a server-side, scalable, object-oriented database and client-side editors to provide an integrated, multi-user environment for visualizing and manipulating network of cellular events. This tool features automated pathway layout, functional computation support, advanced querying and a user-friendly graphical interface. We expect that Patika will be a valuable tool for rapid knowledge acquisition, microarray generated large-scale data interpretation, disease gene identification, and drug development. A prototype of Patika is available upon request from the authors.

The HDF Product Designer - Interoperability in the First Mile

NASA Astrophysics Data System (ADS)

Lee, H.; Jelenak, A.; Habermann, T.

2014-12-01

Interoperable data have been a long-time goal in many scientific communities. The recent growth in analysis, visualization and mash-up applications that expect data stored in a standardized manner has brought the interoperability issue to the fore. On the other hand, producing interoperable data is often regarded as a sideline task in a typical research team for which resources are not readily available. The HDF Group is developing a software tool aimed at lessening the burden of creating data in standards-compliant, interoperable HDF5 files. The tool, named HDF Product Designer, lowers the threshold needed to design such files by providing a user interface that combines the rich HDF5 feature set with applicable metadata conventions. Users can quickly devise new HDF5 files while at the same time seamlessly incorporating the latest best practices and conventions from their community. That is what the term interoperability in the first mile means: enabling generation of interoperable data in HDF5 files from the onset of their production. The tool also incorporates collaborative features, allowing team approach in the file design, as well as easy transfer of best practices as they are being developed. The current state of the tool and the plans for future development will be presented. Constructive input from interested parties is always welcome.

Developing a Framework to Link Catchment Modelling tools to Decision Support Systems for Catchment Management and Planning

NASA Astrophysics Data System (ADS)

Adams, Russell; Owen, Gareth

2015-04-01

Over the past few years a series of catchment monitoring studies in the UK have developed a wide range of tools to enable managers and planners to make informed decisions to target several key outcomes. These outcomes include the mitigation of diffuse pollution and the reduction of flood risk. Good progress has been but additional steps are still required to link together more detailed models that represent catchment processes with the decision support systems (often termed matrices; i.e. DSMs) which form the basis of these planning and management tools. Examples include: (i) the FARM tools developed by the PROACTIVE team at Newcastle University to assess different catchment management options for mitigating against flooding events, (ii) TOPMANAGE, a suite of algorithms that link with high resolution DEMs to enable surface flow pathways, having the potential to be mitigated by Natural Flood Management (NFM) features (in order to target diffuse pollution due to nutrients and sediments) to be identified. To date, these DSMs have not been underpinned by models that can be run in real-time to quantify the benefits in terms of measurable reductions in flood or nutrient pollution risks. Their use has therefore been mostly as qualitative assessment tools. This study aims to adapt an existing spreadsheet-based model, the CRAFT, in order for it to become fully coupled to a DSM approach. Previous catchment scale applications of the CRAFT have focussed on meso-scale studies where any management interventions at a local scale are unlikely to be detectable at the monitoring point (the catchment outlet). The model has however been reasonably successful in identifying potential flow and transport pathways that link the headwater subcatchments to the outlet. Furthermore, recent enhancements to the model enable features such as sedimentation ponds and lagoons that can trap and remove nutrients and sediments to be added, once data become available from different types of NFM features to parameterise these. The model can be used to investigate runoff attenuation (in this case primarily through a lagged routing term applied to surface runoff) as a result of implementing mitigation measures. However to be fully integrated within a DSM framework requires the CRAFT to be linked to a user-friendly interface that will allow the user to modify key parameters, preferably using a web-based expert system, which will be explored further.

GeosciNET: Building a Global Geoinformatics Partnership

NASA Astrophysics Data System (ADS)

Snyder, W. S.; Lehnert, K. A.; Ito, E.; Harms, U.; Klump, J.

2008-12-01

GeosciNET is a collaboration of several existing geoinformatics efforts organized to provide a more effective data system for geoscience projects. Current members are: CoreWall (www.corewall.org), Geoinformatics for Geochemistry (GfG; www.geoinfogeochem.org), System for Earth Sample Registration (SESAR; www.geosamples.org ), GeoStrat SYS (www.geostratsys.org (formerly: PaleoStrat, www.paleostrat.org)), and the International Continental Drilling Program (ICDP; www.icdp-online.org). GeosciNET's basic goal is to advance coordination, complementarity, and interoperability, and minimize duplication of efforts among the involved partner systems in order to streamline the development and operation of geoinformatics efforts. We believe that by advancing the development and data holdings of its member groups, the overall value of each site will be significantly enhanced and better meet the needs of the users. With the existing membership, GeosciNET can offer a comprehensive, integrated system for data acquisition, dissemination, archiving, visualization, integration, and analysis. The system will enable a single researcher or a group of collaborators to keep track of, visualize, and digitally archive any type of sample- or stratigraphic-based data produced from drill holes, dredges, measured stratigraphic sections, the field, or the laboratory. The challenge is to build a linked system that provides users a library of research data as well as tools to input, discover, access, integrate, manipulate, analyze, and model interdisciplinary data - all without corrupting the original data and insuring that the data are attributed to the originator at all times. Science runs on data, but despite the importance of data (legacy or otherwise), there are currently few convenient mechanisms that enable users to easily input their data into databases. While some efforts such as GfG databases, PetDB and SedDB have worked hard to compile such data, only users' active participation can capture the major part of critical legacy data, and insure that new data enter the digital stream as they are generated. GeosciNET wants to lower the barriers so users can take advantage of geoinformatics resources and embrace its promise as the platform for doing the science of the future. Once these benefits are understood by the user community, the obstacles that currently exist in building a larger geoinformatics system will start to erode. User participation requires the proper tools such as translators that can recognize tags and parse the data accordingly, and incentives such as tools for visualization, synthesis and analysis, and digital collaboration space. A major focus for GeosciNET is to support individual researchers and projects that do not have their own dedicated data management and education and outreach programs. One of the greatest challenges for geoinformatics lies in being perceived as a friendly resource by its users where they can easily link their observations and analyses and integrate them with other data. GeosciNET will be experimenting with mechanisms to accomplish these goals.

Development of an interpretive simulation tool for the proton radiography technique

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

Levy, M. C., E-mail: levymc@stanford.edu; Lawrence Livermore National Laboratory, Livermore, California 94551; Ryutov, D. D.

2015-03-15

Proton radiography is a useful diagnostic of high energy density (HED) plasmas under active theoretical and experimental development. In this paper, we describe a new simulation tool that interacts realistic laser-driven point-like proton sources with three dimensional electromagnetic fields of arbitrary strength and structure and synthesizes the associated high resolution proton radiograph. The present tool’s numerical approach captures all relevant physics effects, including effects related to the formation of caustics. Electromagnetic fields can be imported from particle-in-cell or hydrodynamic codes in a streamlined fashion, and a library of electromagnetic field “primitives” is also provided. This latter capability allows users tomore » add a primitive, modify the field strength, rotate a primitive, and so on, while quickly generating a high resolution radiograph at each step. In this way, our tool enables the user to deconstruct features in a radiograph and interpret them in connection to specific underlying electromagnetic field elements. We show an example application of the tool in connection to experimental observations of the Weibel instability in counterstreaming plasmas, using ∼10{sup 8} particles generated from a realistic laser-driven point-like proton source, imaging fields which cover volumes of ∼10 mm{sup 3}. Insights derived from this application show that the tool can support understanding of HED plasmas.« less

Introduction to TAFI - A Matlab® toolbox for analysis of flexural isostasy

NASA Astrophysics Data System (ADS)

Jha, S.; Harry, D. L.; Schutt, D.

2016-12-01

The isostatic response of vertical tectonic loads emplaced on thin elastic plates overlying inviscid substrate and the corresponding gravity anomalies are commonly modeled using well established theories and methodologies of flexural analysis. However, such analysis requires some mathematical and coding expertise on part of users. With that in mind, we designed a new interactive Matlab® toolbox called Toolbox for Analysis of Flexural Isostasy (TAFI). TAFI allows users to create forward models (2-D and 3-D) of flexural deformation of the lithosphere and resulting gravity anomaly. TAFI computes Green's Functions for flexure of the elastic plate subjected to point or line loads, and analytical solution for harmonic loads. Flexure due to non-impulsive, distributed 2-D or 3-D loads are computed by convolving the appropriate Green's function with a user-supplied spatially discretized load function. The gravity anomaly associated with each density interface is calculated by using the Fourier Transform of flexural deflection of these interfaces and estimating the gravity in the wavenumber domain. All models created in TAFI are based on Matlab's intrinsic functions and do not require any specialized toolbox, function or library except those distributed with TAFI. Modeling functions within TAFI can be called from Matlab workspace, from within user written programs or from the TAFI's graphical user interface (GUI). The GUI enables the user to model the flexural deflection of lithosphere interactively, enabling real time comparison of model fit with observed data constraining the flexural deformation and gravity, facilitating rapid search for best fitting flexural model. TAFI is a very useful teaching and research tool and have been tested rigorously in graduate level teaching and basic research environment.

A Web-based graphical user interface for evidence-based decision making for health care allocations in rural areas

PubMed Central

Schuurman, Nadine; Leight, Margo; Berube, Myriam

2008-01-01

Background The creation of successful health policy and location of resources increasingly relies on evidence-based decision-making. The development of intuitive, accessible tools to analyse, display and disseminate spatial data potentially provides the basis for sound policy and resource allocation decisions. As health services are rationalized, the development of tools such graphical user interfaces (GUIs) is especially valuable at they assist decision makers in allocating resources such that the maximum number of people are served. GIS can used to develop GUIs that enable spatial decision making. Results We have created a Web-based GUI (wGUI) to assist health policy makers and administrators in the Canadian province of British Columbia make well-informed decisions about the location and allocation of time-sensitive service capacities in rural regions of the province. This tool integrates datasets for existing hospitals and services, regional populations and road networks to allow users to ascertain the percentage of population in any given service catchment who are served by a specific health service, or baskets of linked services. The wGUI allows policy makers to map trauma and obstetric services against rural populations within pre-specified travel distances, illustrating service capacity by region. Conclusion The wGUI can be used by health policy makers and administrators with little or no formal GIS training to visualize multiple health resource allocation scenarios. The GUI is poised to become a critical decision-making tool especially as evidence is increasingly required for distribution of health services. PMID:18793428

TREXMO: A Translation Tool to Support the Use of Regulatory Occupational Exposure Models.

PubMed

Savic, Nenad; Racordon, Dimitri; Buchs, Didier; Gasic, Bojan; Vernez, David

2016-10-01

Occupational exposure models vary significantly in their complexity, purpose, and the level of expertise required from the user. Different parameters in the same model may lead to different exposure estimates for the same exposure situation. This paper presents a tool developed to deal with this concern-TREXMO or TRanslation of EXposure MOdels. TREXMO integrates six commonly used occupational exposure models, namely, ART v.1.5, STOFFENMANAGER(®) v.5.1, ECETOC TRA v.3, MEASE v.1.02.01, EMKG-EXPO-TOOL, and EASE v.2.0. By enabling a semi-automatic translation between the parameters of these six models, TREXMO facilitates their simultaneous use. For a given exposure situation, defined by a set of parameters in one of the models, TREXMO provides the user with the most appropriate parameters to use in the other exposure models. Results showed that, once an exposure situation and parameters were set in ART, TREXMO reduced the number of possible outcomes in the other models by 1-4 orders of magnitude. The tool should manage to reduce the uncertain entry or selection of parameters in the six models, improve between-user reliability, and reduce the time required for running several models for a given exposure situation. In addition to these advantages, registrants of chemicals and authorities should benefit from more reliable exposure estimates for the risk characterization of dangerous chemicals under Regulation, Evaluation, Authorisation and restriction of CHemicals (REACH). © The Author 2016. Published by Oxford University Press on behalf of the British Occupational Hygiene Society.

Autonomous Multi-sensor Coordination: The Science Goal Monitor

NASA Technical Reports Server (NTRS)

Koratkar, Anuradha; Jung, John; Geiger, Jenny; Grosvenor, Sandy

2004-01-01

Next-generation science and exploration systems will employ new observation strategies that will use multiple sensors in a dynamic environment to provide high quality monitoring, self-consistent analyses and informed decision making. The Science Goal Monitor (SGM) is a prototype software tool being developed to explore the nature of automation necessary to enable dynamic observing of earth phenomenon. The tools being developed in SGM improve our ability to autonomously monitor multiple independent sensors and coordinate reactions to better observe the dynamic phenomena. The SGM system enables users to specify events of interest and how to react when an event is detected. The system monitors streams of data to identify occurrences of the key events previously specified by the scientist/user. When an event occurs, the system autonomously coordinates the execution of the users desired reactions between different sensors. The information can be used to rapidly respond to a variety of fast temporal events. Investigators will no longer have to rely on after-the-fact data analysis to determine what happened. Our paper describes a series of prototype demonstrations that we have developed using SGM and NASA's Earth Observing-1 (EO-1) satellite and Earth Observing Systems Aqua/Terra spacecrafts MODIS instrument. Our demonstrations show the promise of coordinating data from different sources, analyzing the data for a relevant event, autonomously updating and rapidly obtaining a follow-on relevant image. SGM is being used to investigate forest fires, floods and volcanic eruptions. We are now identifying new earth science scenarios that will have more complex SGM reasoning. By developing and testing a prototype in an operational environment, we are also establishing and gathering metrics to gauge the success of automating science campaigns.

I Want It, You've Got It - Effectively Connect Users to Geospatial Resources

NASA Astrophysics Data System (ADS)

White, C. E.

2012-12-01

How do users of scientific data find what they need? How do they know where to look, what to look for, how to evaluate, and - if they find the right resource - then how to get it? When the data is of a geospatial nature, other factors also come into play - is the data in a format/projection compatible with other data being used, does the user have access to tools that can analyze and display the data to adequately evaluate it, and does the user have knowledge on how to manage that access - especially if the data is being exposed by web services. Supporting users to connect them to geospatial data in a continually evolving technological climate is a challenge that reaches deeply into all levels of data management. In this talk, we will discuss specific challenges in how users discover and access resources, and how Esri has evolved solutions over time to more effectively connect users to what they need. Some of the challenges - and current solutions - that will be discussed are: balancing a straightforward user experience with rich functionality, providing simple descriptions while maintaining complete metadata, enabling data access to work with an organization's content while being compatible with other organizations' access mechanisms, and the ability to publish data once yet share it in many venues.

Computational techniques to enable visualizing shapes of objects of extra spatial dimensions

NASA Astrophysics Data System (ADS)

Black, Don Vaughn, II

Envisioning extra dimensions beyond the three of common experience is a daunting challenge for three dimensional observers. Intuition relies on experience gained in a three dimensional environment. Gaining experience with virtual four dimensional objects and virtual three manifolds in four-space on a personal computer may provide the basis for an intuitive grasp of four dimensions. In order to enable such a capability for ourselves, it is first necessary to devise and implement a computationally tractable method to visualize, explore, and manipulate objects of dimension beyond three on the personal computer. A technology is described in this dissertation to convert a representation of higher dimensional models into a format that may be displayed in realtime on graphics cards available on many off-the-shelf personal computers. As a result, an opportunity has been created to experience the shape of four dimensional objects on the desktop computer. The ultimate goal has been to provide the user a tangible and memorable experience with mathematical models of four dimensional objects such that the user can see the model from any user selected vantage point. By use of a 4D GUI, an arbitrary convex hull or 3D silhouette of the 4D model can be rotated, panned, scrolled, and zoomed until a suitable dimensionally reduced view or Aspect is obtained. The 4D GUI then allows the user to manipulate a 3-flat hyperplane cutting tool to slice the model at an arbitrary orientation and position to extract or "pluck" an embedded 3D slice or "aspect" from the embedding four-space. This plucked 3D aspect can be viewed from all angles via a conventional 3D viewer using three multiple POV viewports, and optionally exported to a third party CAD viewer for further manipulation. Plucking and Manipulating the Aspect provides a tangible experience for the end-user in the same manner as any 3D Computer Aided Design viewing and manipulation tool does for the engineer or a 3D video game provides for the nascent student.

IDEOM: an Excel interface for analysis of LC-MS-based metabolomics data.

PubMed

Creek, Darren J; Jankevics, Andris; Burgess, Karl E V; Breitling, Rainer; Barrett, Michael P

2012-04-01

The application of emerging metabolomics technologies to the comprehensive investigation of cellular biochemistry has been limited by bottlenecks in data processing, particularly noise filtering and metabolite identification. IDEOM provides a user-friendly data processing application that automates filtering and identification of metabolite peaks, paying particular attention to common sources of noise and false identifications generated by liquid chromatography-mass spectrometry (LC-MS) platforms. Building on advanced processing tools such as mzMatch and XCMS, it allows users to run a comprehensive pipeline for data analysis and visualization from a graphical user interface within Microsoft Excel, a familiar program for most biological scientists. IDEOM is provided free of charge at http://mzmatch.sourceforge.net/ideom.html, as a macro-enabled spreadsheet (.xlsb). Implementation requires Microsoft Excel (2007 or later). R is also required for full functionality. michael.barrett@glasgow.ac.uk Supplementary data are available at Bioinformatics online.

Conversion and Validation of Distribution System Model from a QSTS-Based Tool to a Real-Time Dynamic Phasor Simulator

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

Chamana, Manohar; Prabakar, Kumaraguru; Palmintier, Bryan

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

Conversion and Validation of Distribution System Model from a QSTS-Based Tool to a Real-Time Dynamic Phasor Simulator: Preprint

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

Chamana, Manohar; Prabakar, Kumaraguru; Palmintier, Bryan

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

The Water SWITCH-ON Spatial Information Platform (SIP)

NASA Astrophysics Data System (ADS)

Sala Calero, J., Sr.; Boot, G., Sr.; Dihé, P., Sr.; Arheimer, B.

2017-12-01

The amount of hydrological open data is continually growing and providing opportunities to the scientific community. Although the existing data portals (GEOSS Portal, INSPIRE community geoportal and others) enable access to open data, many users still find browsing through them difficult. Moreover, the time spent on gathering and preparing data usually is more significant than the time spent on the experiment itself. Thus, any improvement on searching, understanding, accessing or using open data is greatly beneficial. The Spatial Information Platform (SIP) has been developed to tackle these issues within the SWITCH-ON European Commission funded FP7 project. The SIP has been designed as a set of tools based on open standards that provide to the user all the necessary functionalities as described in the Publish-Find-Bind (PFB) pattern. In other words, this means that the SIP helps users to locate relevant and suitable data for their experiments analysis, to access and transform it (filtering, extraction, selection, conversion, aggregation). Moreover, the SIP can be used to provide descriptive information about the data and to publish it so others can find and use it. The SIP is based on existing open data protocols such as the OGC/CSW, OGC/WMS, OpenDAP and open-source components like PostgreSQL/PostGIS, GeoServer and pyCSW. The SIP is divided in three main user interfaces: the BYOD (Browse your open dataset) web interface, the Expert GUI tool and the Upload Data and Metadata web interface. The BYOD HTML5 client is the main entry point for users that want to browse through open data in the SIP. The BYOD has a map interface based on Leaflet JavaScript libraries so that the users can search more efficiently. The web-based Open Data Registration Tool is a user-friendly upload and metadata description interface (geographical extent, license, DOI generation). The Expert GUI is a desktop application that provides full metadata editing capabilities for the metadata moderators of the project. In conclusion, the Spatial Information Platform (SIP) provides to its community a set of tools for better understanding and ease of use of hydrological open-data. Moreover, the SIP has been based on well-known OGC standards that will allow the connection and data harvesting from popular open data portals such as the GEOSS system of systems.

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

PubMed

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

2017-02-01

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

Discovery and Analysis of Intersecting Datasets: JMARS as a Comparative Science Platform

NASA Astrophysics Data System (ADS)

Carter, S.; Christensen, P. R.; Dickenshied, S.; Anwar, S.; Noss, D.

2014-12-01

A great deal can be discovered from comparing and studying a chosen region or area on a planetary body. In this age, science has an enormous amount of instruments and data to study from; often the first obstacle can be finding the right information. Developed at Arizona State University, Java Mission-planning and Analysis for Remote Sensing (JMARS), enables users to easily find and study related datasets. JMARS supports a long list of planetary bodies in our solar system, including Earth, the Moon, Mars, and other planets, satellites, and asteroids. Within JMARS a user can start with a particular area and search for all datasets that have images/information intersecting that region of interest. Once a user has found data they are interested in comparing, they can view the image at once and see the numeric information at that location. This information can be analyzed in a few powerful ways. If the dataset of interest varies with time but the location stays constant, then the user may want to compare specific locations through time. This can be done the Investigate Tool in JMARS. Users can create a Data Spike and the information at that point will be plotted through time. If the region does not have a temporal dataset, then a different method would be suitable and involves a profile line. Also using the Investigate Tool, a user can create a Data Profile (a line which can contain as many vertices as necessary) and all numeric data underneath the line will be plotted on one graph for easy comparison. This can be used to compare differences between similar datasets - perhaps the same measurement but from different instruments - or to find correlations from one dataset to another. A third form of analysis is planned for future development. This method involves entire areas (polygons). Sampling of the different data sources beneath an area can reveal statistics like maximum, minimum, and average values, and standard deviation. These values can be compared to other data sources under the given area. JMARS has the ability to geographically locate and display a vast array of remote sensing data for a user. In addition to its powerful searching ability, it also enables users to compare datasets using the Data Spike and Data Profile techniques. Plots and tables from this data can be exported and used in presentations, papers, or external software for further study.

Description and evaluation of a serious game intervention to engage low secure service users with serious mental illness in the design and refurbishment of their environment.

PubMed

Fitzgerald, M M; Kirk, G D; Bristow, C A

2011-05-01

Service user involvement in all levels of healthcare provision is the expectation of UK government policy. Involvement should not only include participation in the planning and delivery of health care but also the exercise of choice and opinions about that care. In practice, however, service user engagement is most often tokenistic, involving post hoc consultation over plans already committed to by services. This paper explores an Occupational Therapy-led initiative to use the Serious Game format to engage low secure service users with serious mental illness in the design, layout and refurbishment of their unit. Among other things how medication was to be dispensed on the new unit was explored by this game and led to significant replanning in response to service user involvement. The game format was found to be a useful tool in facilitating communication between professionals and a traditionally marginalized and powerless client group. It enabled service users to have a voice, it provided a format for that voice to be heard and made possible service-led change in the planning process. © 2010 Blackwell Publishing.

Yet More Visualized JAMSTEC Cruise and Dive Information

NASA Astrophysics Data System (ADS)

Tomiyama, T.; Hase, H.; Fukuda, K.; Saito, H.; Kayo, M.; Matsuda, S.; Azuma, S.

2014-12-01

Every year, JAMSTEC performs about a hundred of research cruises and numerous dive surveys using its research vessels and submersibles. JAMSTEC provides data and samples obtained during these cruises and dives to international users through a series of data sites on the Internet. The "DARWIN (http://www.godac.jamstec.go.jp/darwin/e)" data site disseminates cruise and dive information. On DARWIN, users can search interested cruises and dives with a combination search form or an interactive tree menu, and find lists of observation data as well as links to surrounding databases. Document catalog, physical sample databases, and visual archive of dive surveys (e. g. in http://www.godac.jamstec.go.jp/jmedia/portal/e) are directly accessible from the lists. In 2014, DARWIN experienced an update, which was arranged mainly for enabling on-demand data visualization. Using　login users' functions, users can put listed data items into the virtual basket and then trim, plot and download the data. The visualization tools help users to quickly grasp the quality and characteristics of observation data. Meanwhile, JAMSTEC launched a new data site named "JDIVES (http://www.godac.jamstec.go.jp/jdives/e)"　to visualize data and sample information obtained by dive surveys. JDIVES shows tracks of dive surveys on the "Google Earth Plugin" and diagrams of deep-sea environmental data such as temperature, salinity, and depth. Submersible camera images and links to associated databases are placed along the dive tracks. The JDVIES interface enables users to perform so-called virtual dive surveys, which can help users to understand local geometries of dive spots and geological settings of associated data and samples. It is not easy for individual researchers to organize a huge amount of information recovered from each cruise and dive. The improved visibility and accessibility of JAMSTEC databases are advantageous not only for second-hand users, but also for on-board researchers themselves.

Using Linked Open Data and Semantic Integration to Search Across Geoscience Repositories

NASA Astrophysics Data System (ADS)

Mickle, A.; Raymond, L. M.; Shepherd, A.; Arko, R. A.; Carbotte, S. M.; Chandler, C. L.; Cheatham, M.; Fils, D.; Hitzler, P.; Janowicz, K.; Jones, M.; Krisnadhi, A.; Lehnert, K. A.; Narock, T.; Schildhauer, M.; Wiebe, P. H.

2014-12-01

The MBLWHOI Library is a partner in the OceanLink project, an NSF EarthCube Building Block, applying semantic technologies to enable knowledge discovery, sharing and integration. OceanLink is testing ontology design patterns that link together: two data repositories, Rolling Deck to Repository (R2R), Biological and Chemical Oceanography Data Management Office (BCO-DMO); the MBLWHOI Library Institutional Repository (IR) Woods Hole Open Access Server (WHOAS); National Science Foundation (NSF) funded awards; and American Geophysical Union (AGU) conference presentations. The Library is collaborating with scientific users, data managers, DSpace engineers, experts in ontology design patterns, and user interface developers to make WHOAS, a DSpace repository, linked open data enabled. The goal is to allow searching across repositories without any of the information providers having to change how they manage their collections. The tools developed for DSpace will be made available to the community of users. There are 257 registered DSpace repositories in the United Stated and over 1700 worldwide. Outcomes include: Integration of DSpace with OpenRDF Sesame triple store to provide SPARQL endpoint for the storage and query of RDF representation of DSpace resources, Mapping of DSpace resources to OceanLink ontology, and DSpace "data" add on to provide resolvable linked open data representation of DSpace resources.

Tigres Workflow Library: Supporting Scientific Pipelines on HPC Systems

DOE PAGES

Hendrix, Valerie; Fox, James; Ghoshal, Devarshi; ...

2016-07-21

The growth in scientific data volumes has resulted in the need for new tools that enable users to operate on and analyze data on large-scale resources. In the last decade, a number of scientific workflow tools have emerged. These tools often target distributed environments, and often need expert help to compose and execute the workflows. Data-intensive workflows are often ad-hoc, they involve an iterative development process that includes users composing and testing their workflows on desktops, and scaling up to larger systems. In this paper, we present the design and implementation of Tigres, a workflow library that supports the iterativemore » workflow development cycle of data-intensive workflows. Tigres provides an application programming interface to a set of programming templates i.e., sequence, parallel, split, merge, that can be used to compose and execute computational and data pipelines. We discuss the results of our evaluation of scientific and synthetic workflows showing Tigres performs with minimal template overheads (mean of 13 seconds over all experiments). We also discuss various factors (e.g., I/O performance, execution mechanisms) that affect the performance of scientific workflows on HPC systems.« less

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

USGS Publications Warehouse

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

2016-01-01

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

Tigres Workflow Library: Supporting Scientific Pipelines on HPC Systems

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

Hendrix, Valerie; Fox, James; Ghoshal, Devarshi

The growth in scientific data volumes has resulted in the need for new tools that enable users to operate on and analyze data on large-scale resources. In the last decade, a number of scientific workflow tools have emerged. These tools often target distributed environments, and often need expert help to compose and execute the workflows. Data-intensive workflows are often ad-hoc, they involve an iterative development process that includes users composing and testing their workflows on desktops, and scaling up to larger systems. In this paper, we present the design and implementation of Tigres, a workflow library that supports the iterativemore » workflow development cycle of data-intensive workflows. Tigres provides an application programming interface to a set of programming templates i.e., sequence, parallel, split, merge, that can be used to compose and execute computational and data pipelines. We discuss the results of our evaluation of scientific and synthetic workflows showing Tigres performs with minimal template overheads (mean of 13 seconds over all experiments). We also discuss various factors (e.g., I/O performance, execution mechanisms) that affect the performance of scientific workflows on HPC systems.« less

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

PubMed

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

2003-01-01

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

RISK REDUCTION WITH A FUZZY EXPERT EXPLORATION TOOL

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

Robert S. Balch; Ron Broadhead

2005-03-01

Incomplete or sparse data such as geologic or formation characteristics introduce a high level of risk for oil exploration and development projects. ''Expert'' systems developed and used in several disciplines and industries have demonstrated beneficial results when working with sparse data. State-of-the-art expert exploration tools, relying on a database, and computer maps generated by neural networks and user inputs, have been developed through the use of ''fuzzy'' logic, a mathematical treatment of imprecise or non-explicit parameters and values. Oil prospecting risk has been reduced with the use of these properly verified and validated ''Fuzzy Expert Exploration (FEE) Tools.'' Through themore » course of this project, FEE Tools and supporting software were developed for two producing formations in southeast New Mexico. Tools of this type can be beneficial in many regions of the U.S. by enabling risk reduction in oil and gas prospecting as well as decreased prospecting and development costs. In today's oil industry environment, many smaller exploration companies lack the resources of a pool of expert exploration personnel. Downsizing, volatile oil prices, and scarcity of domestic exploration funds have also affected larger companies, and will, with time, affect the end users of oil industry products in the U.S. as reserves are depleted. The FEE Tools benefit a diverse group in the U.S., allowing a more efficient use of scarce funds, and potentially reducing dependence on foreign oil and providing lower product prices for consumers.« less

The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs.

PubMed

Stocks, Matthew B; Mohorianu, Irina; Beckers, Matthew; Paicu, Claudia; Moxon, Simon; Thody, Joshua; Dalmay, Tamas; Moulton, Vincent

2018-05-02

RNA interference, a highly conserved regulatory mechanism, is mediated via small RNAs. Recent technical advances enabled the analysis of larger, complex datasets and the investigation of microRNAs and the less known small interfering RNAs. However, the size and intricacy of current data requires a comprehensive set of tools, able to discriminate the patterns from the low-level, noise-like, variation; numerous and varied suggestions from the community represent an invaluable source of ideas for future tools, the ability of the community to contribute to this software is essential. We present a new version of the UEA sRNA Workbench, reconfigured to allow an easy insertion of new tools/workflows. In its released form, it comprises of a suite of tools in a user-friendly environment, with enhanced capabilities for a comprehensive processing of sRNA-seq data e.g. tools for an accurate prediction of sRNA loci (CoLIde) and miRNA loci (miRCat2), as well as workflows to guide the users through common steps such as quality checking of the input data, normalization of abundances or detection of differential expression represent the first step in sRNA-seq analyses. The UEA sRNA Workbench is available at: http://srna-workbench.cmp.uea.ac.uk The source code is available at: https://github.com/sRNAworkbenchuea/UEA_sRNA_Workbench. v.moulton@uea.ac.uk.

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 potential to interact, so one can build a cluster of PCs, each equipped with a GPU, and use mpiDL to communicate between the nodes and GPULib to accelerate the computations on each node.

Giovanni - The Bridge Between Data and Science

NASA Technical Reports Server (NTRS)

Liu, Zhong; Acker, James

2017-01-01

This article describes new features in the Geospatial Interactive Online Visualization ANd aNalysis Infrastructure (Giovanni), a user-friendly online tool that enables visualization, analysis, and assessment of NASA Earth science data sets without downloading data and software. Since the satellite era began, data collected from Earth-observing satellites have been widely used in research and applications; however, using satellite-based data sets can still be a challenge to many. To facilitate data access and evaluation, as well as scientific exploration and discovery, the NASA Goddard Earth Sciences (GES) Data and Information Services Center (DISC) has developed Giovanni for a wide range of users around the world. This article describes the latest capabilities of Giovanni with examples, and discusses future plans for this innovative system.

A midas plugin to enable construction of reproducible web-based image processing pipelines

PubMed Central

Grauer, Michael; Reynolds, Patrick; Hoogstoel, Marion; Budin, Francois; Styner, Martin A.; Oguz, Ipek

2013-01-01

Image processing is an important quantitative technique for neuroscience researchers, but difficult for those who lack experience in the field. In this paper we present a web-based platform that allows an expert to create a brain image processing pipeline, enabling execution of that pipeline even by those biomedical researchers with limited image processing knowledge. These tools are implemented as a plugin for Midas, an open-source toolkit for creating web based scientific data storage and processing platforms. Using this plugin, an image processing expert can construct a pipeline, create a web-based User Interface, manage jobs, and visualize intermediate results. Pipelines are executed on a grid computing platform using BatchMake and HTCondor. This represents a new capability for biomedical researchers and offers an innovative platform for scientific collaboration. Current tools work well, but can be inaccessible for those lacking image processing expertise. Using this plugin, researchers in collaboration with image processing experts can create workflows with reasonable default settings and streamlined user interfaces, and data can be processed easily from a lab environment without the need for a powerful desktop computer. This platform allows simplified troubleshooting, centralized maintenance, and easy data sharing with collaborators. These capabilities enable reproducible science by sharing datasets and processing pipelines between collaborators. In this paper, we present a description of this innovative Midas plugin, along with results obtained from building and executing several ITK based image processing workflows for diffusion weighted MRI (DW MRI) of rodent brain images, as well as recommendations for building automated image processing pipelines. Although the particular image processing pipelines developed were focused on rodent brain MRI, the presented plugin can be used to support any executable or script-based pipeline. PMID:24416016

A midas plugin to enable construction of reproducible web-based image processing pipelines.

PubMed

Grauer, Michael; Reynolds, Patrick; Hoogstoel, Marion; Budin, Francois; Styner, Martin A; Oguz, Ipek

2013-01-01

Image processing is an important quantitative technique for neuroscience researchers, but difficult for those who lack experience in the field. In this paper we present a web-based platform that allows an expert to create a brain image processing pipeline, enabling execution of that pipeline even by those biomedical researchers with limited image processing knowledge. These tools are implemented as a plugin for Midas, an open-source toolkit for creating web based scientific data storage and processing platforms. Using this plugin, an image processing expert can construct a pipeline, create a web-based User Interface, manage jobs, and visualize intermediate results. Pipelines are executed on a grid computing platform using BatchMake and HTCondor. This represents a new capability for biomedical researchers and offers an innovative platform for scientific collaboration. Current tools work well, but can be inaccessible for those lacking image processing expertise. Using this plugin, researchers in collaboration with image processing experts can create workflows with reasonable default settings and streamlined user interfaces, and data can be processed easily from a lab environment without the need for a powerful desktop computer. This platform allows simplified troubleshooting, centralized maintenance, and easy data sharing with collaborators. These capabilities enable reproducible science by sharing datasets and processing pipelines between collaborators. In this paper, we present a description of this innovative Midas plugin, along with results obtained from building and executing several ITK based image processing workflows for diffusion weighted MRI (DW MRI) of rodent brain images, as well as recommendations for building automated image processing pipelines. Although the particular image processing pipelines developed were focused on rodent brain MRI, the presented plugin can be used to support any executable or script-based pipeline.

The Papillomavirus Episteme: a central resource for papillomavirus sequence data and analysis.

PubMed

Van Doorslaer, Koenraad; Tan, Qina; Xirasagar, Sandhya; Bandaru, Sandya; Gopalan, Vivek; Mohamoud, Yasmin; Huyen, Yentram; McBride, Alison A

2013-01-01

The goal of the Papillomavirus Episteme (PaVE) is to provide an integrated resource for the analysis of papillomavirus (PV) genome sequences and related information. The PaVE is a freely accessible, web-based tool (http://pave.niaid.nih.gov) created around a relational database, which enables storage, analysis and exchange of sequence information. From a design perspective, the PaVE adopts an Open Source software approach and stresses the integration and reuse of existing tools. Reference PV genome sequences have been extracted from publicly available databases and reannotated using a custom-created tool. To date, the PaVE contains 241 annotated PV genomes, 2245 genes and regions, 2004 protein sequences and 47 protein structures, which users can explore, analyze or download. The PaVE provides scientists with the data and tools needed to accelerate scientific progress for the study and treatment of diseases caused by PVs.

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

T.Rex is used to explore tabular data sets containing up to ten million records to help rapidly understand a previously unknown data set. Analysis can quickly identify patterns of interest and the records and fields that capture those patterns. T.Rex contains a growing set of deep analytical tools and supports robust export capabilities that selected data can be incorporated into to other specialized tools for further analysis. T.Rex is flexible in ingesting different types and formats of data, allowing the user to interactively experiment and perform trial and error guesses on the structure of the data; and also has amore » variety of linked visual analytic tools that enable exploration of the data to find relevant content, relationships among content, trends within the content, and capture knowledge about the content. Finally, T.Rex has a rich export capability, to extract relevant subsets of a larger data source, to further analyze their data in other analytic tools.« less

T.Rex

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

2016-06-08

T.Rex is used to explore tabular data sets containing up to ten million records to help rapidly understand a previously unknown data set. Analysis can quickly identify patterns of interest and the records and fields that capture those patterns. T.Rex contains a growing set of deep analytical tools and supports robust export capabilities that selected data can be incorporated into to other specialized tools for further analysis. T.Rex is flexible in ingesting different types and formats of data, allowing the user to interactively experiment and perform trial and error guesses on the structure of the data; and also has amore » variety of linked visual analytic tools that enable exploration of the data to find relevant content, relationships among content, trends within the content, and capture knowledge about the content. Finally, T.Rex has a rich export capability, to extract relevant subsets of a larger data source, to further analyze their data in other analytic tools.« less

The NASA Program Management Tool: A New Vision in Business Intelligence

NASA Technical Reports Server (NTRS)

Maluf, David A.; Swanson, Keith; Putz, Peter; Bell, David G.; Gawdiak, Yuri

2006-01-01

This paper describes a novel approach to business intelligence and program management for large technology enterprises like the U.S. National Aeronautics and Space Administration (NASA). Two key distinctions of the approach are that 1) standard business documents are the user interface, and 2) a "schema-less" XML database enables flexible integration of technology information for use by both humans and machines in a highly dynamic environment. The implementation utilizes patent-pending NASA software called the NASA Program Management Tool (PMT) and its underlying "schema-less" XML database called Netmark. Initial benefits of PMT include elimination of discrepancies between business documents that use the same information and "paperwork reduction" for program and project management in the form of reducing the effort required to understand standard reporting requirements and to comply with those reporting requirements. We project that the underlying approach to business intelligence will enable significant benefits in the timeliness, integrity and depth of business information available to decision makers on all organizational levels.

EMERALD: Coping with the Explosion of Seismic Data

NASA Astrophysics Data System (ADS)

West, J. D.; Fouch, M. J.; Arrowsmith, R.

2009-12-01

The geosciences are currently generating an unparalleled quantity of new public broadband seismic data with the establishment of large-scale seismic arrays such as the EarthScope USArray, which are enabling new and transformative scientific discoveries of the structure and dynamics of the Earth’s interior. Much of this explosion of data is a direct result of the formation of the IRIS consortium, which has enabled an unparalleled level of open exchange of seismic instrumentation, data, and methods. The production of these massive volumes of data has generated new and serious data management challenges for the seismological community. A significant challenge is the maintenance and updating of seismic metadata, which includes information such as station location, sensor orientation, instrument response, and clock timing data. This key information changes at unknown intervals, and the changes are not generally communicated to data users who have already downloaded and processed data. Another basic challenge is the ability to handle massive seismic datasets when waveform file volumes exceed the fundamental limitations of a computer’s operating system. A third, long-standing challenge is the difficulty of exchanging seismic processing codes between researchers; each scientist typically develops his or her own unique directory structure and file naming convention, requiring that codes developed by another researcher be rewritten before they can be used. To address these challenges, we are developing EMERALD (Explore, Manage, Edit, Reduce, & Analyze Large Datasets). The overarching goal of the EMERALD project is to enable more efficient and effective use of seismic datasets ranging from just a few hundred to millions of waveforms with a complete database-driven system, leading to higher quality seismic datasets for scientific analysis and enabling faster, more efficient scientific research. We will present a preliminary (beta) version of EMERALD, an integrated, extensible, standalone database server system based on the open-source PostgreSQL database engine. The system is designed for fast and easy processing of seismic datasets, and provides the necessary tools to manage very large datasets and all associated metadata. EMERALD provides methods for efficient preprocessing of seismic records; large record sets can be easily and quickly searched, reviewed, revised, reprocessed, and exported. EMERALD can retrieve and store station metadata and alert the user to metadata changes. The system provides many methods for visualizing data, analyzing dataset statistics, and tracking the processing history of individual datasets. EMERALD allows development and sharing of visualization and processing methods using any of 12 programming languages. EMERALD is designed to integrate existing software tools; the system provides wrapper functionality for existing widely-used programs such as GMT, SOD, and TauP. Users can interact with EMERALD via a web browser interface, or they can directly access their data from a variety of database-enabled external tools. Data can be imported and exported from the system in a variety of file formats, or can be directly requested and downloaded from the IRIS DMC from within EMERALD.

NASA SensorWeb and OGC Standards for Disaster Management

NASA Technical Reports Server (NTRS)

Mandl, Dan

2010-01-01

I. Goal: Enable user to cost-effectively find and create customized data products to help manage disasters; a) On-demand; b) Low cost and non-specialized tools such as Google Earth and browsers; c) Access via open network but with sufficient security. II. Use standards to interface various sensors and resultant data: a) Wrap sensors in Open Geospatial Consortium (OGC) standards; b) Wrap data processing algorithms and servers with OGC standards c) Use standardized workflows to orchestrate and script the creation of these data; products. III. Target Web 2.0 mass market: a) Make it simple and easy to use; b) Leverage new capabilities and tools that are emerging; c) Improve speed and responsiveness.

Algorithm Building and Learning Programming Languages Using a New Educational Paradigm

NASA Astrophysics Data System (ADS)

Jain, Anshul K.; Singhal, Manik; Gupta, Manu Sheel

2011-08-01

This research paper presents a new concept of using a single tool to associate syntax of various programming languages, algorithms and basic coding techniques. A simple framework has been programmed in Python that helps students learn skills to develop algorithms, and implement them in various programming languages. The tool provides an innovative and a unified graphical user interface for development of multimedia objects, educational games and applications. It also aids collaborative learning amongst students and teachers through an integrated mechanism based on Remote Procedure Calls. The paper also elucidates an innovative method for code generation to enable students to learn the basics of programming languages using drag-n-drop methods for image objects.

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

Chamana, Manohar; Prabakar, Kumaraguru; Palmintier, Bryan

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

MannDB: A microbial annotation database for protein characterization

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

Zhou, C; Lam, M; Smith, J

2006-05-19

MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-sourcemore » tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins) are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or when identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A web client browser enables viewing of computational results and downloaded annotations, and a query tool enables structured and free-text search capabilities. When available, links to external databases, including MvirDB, are provided. MannDB contains whole-proteome analyses for at least one representative organism from each category of biological threat organism listed by APHIS, CDC, HHS, NIAID, USDA, USFDA, and WHO. MannDB comprises a large number of genomes and comprehensive protein sequence analyses representing organisms listed as high-priority agents on the websites of several governmental organizations concerned with bio-terrorism. MannDB provides the user with a BLAST interface for comparison of native and non-native sequences and a query tool for conveniently selecting proteins of interest. In addition, the user has access to a web-based browser that compiles comprehensive and extensive reports.« less

J-Earth: An Essential Resource for Terrestrial Remote Sensing and Data Analysis

NASA Astrophysics Data System (ADS)

Dunn, S.; Rupp, J.; Cheeseman, S.; Christensen, P. R.; Prashad, L. C.; Dickenshied, S.; Anwar, S.; Noss, D.; Murray, K.

2011-12-01

There is a need for a software tool that has the ability to display and analyze various types of earth science and social data through a simple, user-friendly interface. The J-Earth software tool has been designed to be easily accessible for download and intuitive use, regardless of the technical background of the user base. This tool does not require courses or text books to learn to use, yet is powerful enough to allow a more general community of users to perform complex data analysis. Professions that will benefit from this tool range from geologists, geographers, and climatologists to sociologists, economists, and ecologists as well as policy makers. J-Earth was developed by the Arizona State University Mars Space Flight Facility as part of the JMARS (Java Mission-planning and Analysis for Remote Sensing) suite of open-source tools. The program is a Geographic Information Systems (GIS) application used for viewing and processing satellite and airborne remote sensing data. While the functionality of JMARS has historically focused on the research needs of the planetary science community, J-Earth has been designed for a much broader Earth-based user audience. NASA instrument products accessible within J-Earth include data from ASTER, GOES, Landsat, MODIS, and TIMS. While J-Earth contains exceptionally comprehensive and high resolution satellite-derived data and imagery, this tool also includes many socioeconomic data products from projects lead by international organizations and universities. Datasets used in J-Earth take the form of grids, rasters, remote sensor "stamps", maps, and shapefiles. Some highly demanded global datasets available within J-Earth include five levels of administrative/political boundaries, climate data for current conditions as well as models for future climates, population counts and densities, land cover/land use, and poverty indicators. While this application does share the same powerful functionality of JMARS, J-Earth's apperance is enhanced for much easier data analysis. J-Earth utilizes a layering system to view data from different sources which can then be exported, scaled, colored and superimposed for quick comparisons. Users may now perform spatial analysis over several diverse datasets with respect to a defined geographic area or the entire globe. In addition, several newly acquired global datasets contain a temporal dimension which when accessed through J-Earth, make this a unique and powerful tool for spatial analysis over time. The functionality and ease of use set J-Earth apart from all other terrestrial GIS software packages and enable endless social, political, and scientific possibilities

A real-time intercepting beam-profile monitor for a medical cyclotron

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

Hendriks, C.; Uittenbosch, T.; Cameron, D.

2013-11-15

There is a lack of real-time continuous beam-diagnostic tools for medical cyclotrons due to high power deposition during proton irradiation. To overcome this limitation, we have developed a profile monitor that is capable of providing continuous feedback about beam shape and current in real time while it is inserted in the beam path. This enables users to optimize the beam profile and observe fluctuations in the beam over time with periodic insertion of the monitor.

Managing Information On Technical Requirements

NASA Technical Reports Server (NTRS)

Mauldin, Lemuel E., III; Hammond, Dana P.

1993-01-01

Technical Requirements Analysis and Control Systems/Initial Operating Capability (TRACS/IOC) computer program provides supplemental software tools for analysis, control, and interchange of project requirements so qualified project members have access to pertinent project information, even if in different locations. Enables users to analyze and control requirements, serves as focal point for project requirements, and integrates system supporting efficient and consistent operations. TRACS/IOC is HyperCard stack for use on Macintosh computers running HyperCard 1.2 or later and Oracle 1.2 or later.

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

PubMed Central

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

2010-01-01

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

Engineering Analysis Using a Web-based Protocol

NASA Technical Reports Server (NTRS)

Schoeffler, James D.; Claus, Russell W.

2002-01-01

This paper reviews the development of a web-based framework for engineering analysis. A one-dimensional, high-speed analysis code called LAPIN was used in this study, but the approach can be generalized to any engineering analysis tool. The web-based framework enables users to store, retrieve, and execute an engineering analysis from a standard web-browser. We review the encapsulation of the engineering data into the eXtensible Markup Language (XML) and various design considerations in the storage and retrieval of application data.

Structured Analysis of the Logistics Support Analysis (LSA) Task, and Integrated Logistic Support (ILS) Element, ’Standardization and Interoperability (S and I)’.

DTIC Science & Technology

1988-11-01

system, using graphic techniques which enable users, analysts, and designers to get a clear and common picture of the system and how its parts fit...boxes into hierarchies suitable for computer implementation. ŗ. Structured Design uses tools, especially graphic ones, to render systems readily...LSA, PROCESSES, DATA FLOWS, DATA STORES, EX"RNAL ENTITIES, OVERALL SYSTEMS DESIGN PROCESS, over 19, ABSTRACT (Continue on reverse if necessary and