MITK-based segmentation of co-registered MRI for subject-related regional anesthesia simulation

NASA Astrophysics Data System (ADS)

Teich, Christian; Liao, Wei; Ullrich, Sebastian; Kuhlen, Torsten; Ntouba, Alexandre; Rossaint, Rolf; Ullisch, Marcus; Deserno, Thomas M.

2008-03-01

With a steadily increasing indication, regional anesthesia is still trained directly on the patient. To develop a virtual reality (VR)-based simulation, a patient model is needed containing several tissues, which have to be extracted from individual magnet resonance imaging (MRI) volume datasets. Due to the given modality and the different characteristics of the single tissues, an adequate segmentation can only be achieved by using a combination of segmentation algorithms. In this paper, we present a framework for creating an individual model from MRI scans of the patient. Our work splits in two parts. At first, an easy-to-use and extensible tool for handling the segmentation task on arbitrary datasets is provided. The key idea is to let the user create a segmentation for the given subject by running different processing steps in a purposive order and store them in a segmentation script for reuse on new datasets. For data handling and visualization, we utilize the Medical Imaging Interaction Toolkit (MITK), which is based on the Visualization Toolkit (VTK) and the Insight Segmentation and Registration Toolkit (ITK). The second part is to find suitable segmentation algorithms and respectively parameters for differentiating the tissues required by the RA simulation. For this purpose, a fuzzy c-means clustering algorithm combined with mathematical morphology operators and a geometric active contour-based approach is chosen. The segmentation process itself aims at operating with minimal user interaction, and the gained model fits the requirements of the simulation. First results are shown for both, male and female MRI of the pelvis.

Virtual hydrology observatory: an immersive visualization of hydrology modeling

NASA Astrophysics Data System (ADS)

Su, Simon; Cruz-Neira, Carolina; Habib, Emad; Gerndt, Andreas

2009-02-01

The Virtual Hydrology Observatory will provide students with the ability to observe the integrated hydrology simulation with an instructional interface by using a desktop based or immersive virtual reality setup. It is the goal of the virtual hydrology observatory application to facilitate the introduction of field experience and observational skills into hydrology courses through innovative virtual techniques that mimic activities during actual field visits. The simulation part of the application is developed from the integrated atmospheric forecast model: Weather Research and Forecasting (WRF), and the hydrology model: Gridded Surface/Subsurface Hydrologic Analysis (GSSHA). Both the output from WRF and GSSHA models are then used to generate the final visualization components of the Virtual Hydrology Observatory. The various visualization data processing techniques provided by VTK are 2D Delaunay triangulation and data optimization. Once all the visualization components are generated, they are integrated into the simulation data using VRFlowVis and VR Juggler software toolkit. VR Juggler is used primarily to provide the Virtual Hydrology Observatory application with fully immersive and real time 3D interaction experience; while VRFlowVis provides the integration framework for the hydrologic simulation data, graphical objects and user interaction. A six-sided CAVETM like system is used to run the Virtual Hydrology Observatory to provide the students with a fully immersive experience.

Milestone Completion Report WBS 1.3.5.05 ECP/VTK-m FY17Q4 [MS-17/03-06] Key Reduce / Spatial Division / Basic Advect / Normals STDA05-4.

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

Moreland, Kenneth D.

The FY17Q4 milestone of the ECP/VTK-m project includes the completion of a key-reduce scheduling mechanism, a spatial division algorithm, an algorithm for basic particle advection, and the computation of smoothed surface normals. With the completion of this milestone, we are able to, respectively, more easily group like elements (a common visualization algorithm operation), provide the fundamentals for geometric search structures, provide the fundamentals for many flow visualization algorithms, and provide more realistic rendering of surfaces approximated with facets.

The Resource, Spring 2002

DTIC Science & Technology

2002-01-01

wrappers to other widely used languages, namely TCL/TK, Java, and Python . VTK is very powerful and covers polygonal models and image processing classes and...follows: � Large Data Visualization and Rendering � Information Visualization for Beginners � Rendering and Visualization in Parallel Environments

Integration of information and volume visualization for analysis of cell lineage and gene expression during embryogenesis

NASA Astrophysics Data System (ADS)

Cedilnik, Andrej; Baumes, Jeffrey; Ibanez, Luis; Megason, Sean; Wylie, Brian

2008-01-01

Dramatic technological advances in the field of genomics have made it possible to sequence the complete genomes of many different organisms. With this overwhelming amount of data at hand, biologists are now confronted with the challenge of understanding the function of the many different elements of the genome. One of the best places to start gaining insight on the mechanisms by which the genome controls an organism is the study of embryogenesis. There are multiple and inter-related layers of information that must be established in order to understand how the genome controls the formation of an organism. One is cell lineage which describes how patterns of cell division give rise to different parts of an organism. Another is gene expression which describes when and where different genes are turned on. Both of these data types can now be acquired using fluorescent laser-scanning (confocal or 2-photon) microscopy of embryos tagged with fluorescent proteins to generate 3D movies of developing embryos. However, analyzing the wealth of resulting images requires tools capable of interactively visualizing several different types of information as well as being scalable to terabytes of data. This paper describes how the combination of existing large data volume visualization and the new Titan information visualization framework of the Visualization Toolkit (VTK) can be applied to the problem of studying the cell lineage of an organism. In particular, by linking the visualization of spatial and temporal gene expression data with novel ways of visualizing cell lineage data, users can study how the genome regulates different aspects of embryonic development.

Scientific Visualization of Radio Astronomy Data using Gesture Interaction

NASA Astrophysics Data System (ADS)

Mulumba, P.; Gain, J.; Marais, P.; Woudt, P.

2015-09-01

MeerKAT in South Africa (Meer = More Karoo Array Telescope) will require software to help visualize, interpret and interact with multidimensional data. While visualization of multi-dimensional data is a well explored topic, little work has been published on the design of intuitive interfaces to such systems. More specifically, the use of non-traditional interfaces (such as motion tracking and multi-touch) has not been widely investigated within the context of visualizing astronomy data. We hypothesize that a natural user interface would allow for easier data exploration which would in turn lead to certain kinds of visualizations (volumetric, multidimensional). To this end, we have developed a multi-platform scientific visualization system for FITS spectral data cubes using VTK (Visualization Toolkit) and a natural user interface to explore the interaction between a gesture input device and multidimensional data space. Our system supports visual transformations (translation, rotation and scaling) as well as sub-volume extraction and arbitrary slicing of 3D volumetric data. These tasks were implemented across three prototypes aimed at exploring different interaction strategies: standard (mouse/keyboard) interaction, volumetric gesture tracking (Leap Motion controller) and multi-touch interaction (multi-touch monitor). A Heuristic Evaluation revealed that the volumetric gesture tracking prototype shows great promise for interfacing with the depth component (z-axis) of 3D volumetric space across multiple transformations. However, this is limited by users needing to remember the required gestures. In comparison, the touch-based gesture navigation is typically more familiar to users as these gestures were engineered from standard multi-touch actions. Future work will address a complete usability test to evaluate and compare the different interaction modalities against the different visualization tasks.

Fast 3D Surface Extraction 2 pages (including abstract)

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

Sewell, Christopher Meyer; Patchett, John M.; Ahrens, James P.

Ocean scientists searching for isosurfaces and/or thresholds of interest in high resolution 3D datasets required a tedious and time-consuming interactive exploration experience. PISTON research and development activities are enabling ocean scientists to rapidly and interactively explore isosurfaces and thresholds in their large data sets using a simple slider with real time calculation and visualization of these features. Ocean Scientists can now visualize more features in less time, helping them gain a better understanding of the high resolution data sets they work with on a daily basis. Isosurface timings (512{sup 3} grid): VTK 7.7 s, Parallel VTK (48-core) 1.3 s, PISTONmore » OpenMP (48-core) 0.2 s, PISTON CUDA (Quadro 6000) 0.1 s.« less

Neuroanatomical affiliation visualization-interface system.

PubMed

Palombi, Olivier; Shin, Jae-Won; Watson, Charles; Paxinos, George

2006-01-01

A number of knowledge management systems have been developed to allow users to have access to large quantity of neuroanatomical data. The advent of three-dimensional (3D) visualization techniques allows users to interact with complex 3D object. In order to better understand the structural and functional organization of the brain, we present Neuroanatomical Affiliations Visualization-Interface System (NAVIS) as the original software to see brain structures and neuroanatomical affiliations in 3D. This version of NAVIS has made use of the fifth edition of "The Rat Brain in Stereotaxic coordinates" (Paxinos and Watson, 2005). The NAVIS development environment was based on the scripting language name Python, using visualization toolkit (VTK) as 3D-library and wxPython for the graphic user interface. The following manuscript is focused on the nucleus of the solitary tract (Sol) and the set of affiliated structures in the brain to illustrate the functionality of NAVIS. The nucleus of the Sol is the primary relay center of visceral and taste information, and consists of 14 distinct subnuclei that differ in cytoarchitecture, chemoarchitecture, connections, and function. In the present study, neuroanatomical projection data of the rat Sol were collected from selected literature in PubMed since 1975. Forty-nine identified projection data of Sol were inserted in NAVIS. The standard XML format used as an input for affiliation data allows NAVIS to update data online and/or allows users to manually change or update affiliation data. NAVIS can be extended to nuclei other than Sol.

Combined multispectral spatial frequency domain imaging and computed tomography system for intraoperative breast tumor margin assessment

NASA Astrophysics Data System (ADS)

McClatchy, D. M.; Rizzo, E. J.; Krishnaswamy, V.; Kanick, S. C.; Wells, W. A.; Paulsen, K. D.; Pogue, B. W.

2017-02-01

There is a dire clinical need for surgical margin guidance in breast conserving therapy (BCT). We present a multispectral spatial frequency domain imaging (SFDI) system, spanning the visible and near-infrared (NIR) wavelengths, combined with a shielded X-ray computed tomography (CT) system, designed for intraoperative breast tumor margin assessment. While the CT can provide a volumetric visualization of the tumor core and its spiculations, the co-registered SFDI can provide superficial and quantitative information about localized changes tissue morphology from light scattering parameters. These light scattering parameters include both model-based parameters of sub-diffusive light scattering related to the particle size scale distribution and also textural information of the high spatial frequency reflectance. Because the SFDI and CT components are rigidly fixed, a simple transformation can be used to simultaneously display the SFDI and CT data in the same coordinate system. This is achieved through the Visualization Toolkit (vtk) file format in the open-source Slicer medical imaging software package. In this manuscript, the instrumentation, data processing, and preliminary human specimen data will be presented. The ultimate goal of this work is to evaluate this technology in a prospective clinical trial, and the current limitations and engineering solutions to meet this goal will also be discussed.

Scientific Visualization for Atmospheric Data Analysis in Collaborative Virtual Environments

NASA Astrophysics Data System (ADS)

Engelke, Wito; Flatken, Markus; Garcia, Arturo S.; Bar, Christian; Gerndt, Andreas

2016-04-01

1 INTRODUCTION The three year European research project CROSS DRIVE (Collaborative Rover Operations and Planetary Science Analysis System based on Distributed Remote and Interactive Virtual Environments) started in January 2014. The research and development within this project is motivated by three use case studies: landing site characterization, atmospheric science and rover target selection [1]. Currently the implementation for the second use case is in its final phase [2]. Here, the requirements were generated based on the domain experts input and lead to development and integration of appropriate methods for visualization and analysis of atmospheric data. The methods range from volume rendering, interactive slicing, iso-surface techniques to interactive probing. All visualization methods are integrated in DLR's Terrain Rendering application. With this, the high resolution surface data visualization can be enriched with additional methods appropriate for atmospheric data sets. This results in an integrated virtual environment where the scientist has the possibility to interactively explore his data sets directly within the correct context. The data sets include volumetric data of the martian atmosphere, precomputed two dimensional maps and vertical profiles. In most cases the surface data as well as the atmospheric data has global coverage and is of time dependent nature. Furthermore, all interaction is synchronized between different connected application instances, allowing for collaborative sessions between distant experts. 2 VISUALIZATION TECHNIQUES Also the application is currently used for visualization of data sets related to Mars the techniques can be used for other data sets as well. Currently the prototype is capable of handling 2 and 2.5D surface data as well as 4D atmospheric data. Specifically, the surface data is presented using an LoD approach which is based on the HEALPix tessellation of a sphere [3, 4, 5] and can handle data sets in the order of terabytes. The combination of different data sources (e.g., MOLA, HRSC, HiRISE) and selection of presented data (e.g., infrared, spectral, imagery) is also supported. Furthermore, the data is presented unchanged and with the highest possible resolution for the target setup (e.g., power-wall, workstation, laptop) and view distance. The visualization techniques for the volumetric data sets can handle VTK [6] based data sets and also support different grid types as well as a time component. In detail, the integrated volume rendering uses a GPU based ray casting algorithm which was adapted to work in spherical coordinate systems. This approach results in interactive frame-rates without compromising visual fidelity. Besides direct visualization via volume rendering the prototype supports interactive slicing, extraction of iso-surfaces and probing. The latter can also be used for side-by-side comparison and on-the-fly diagram generation within the application. Similarily to the surface data a combination of different data sources is supported as well. For example, the extracted iso-surface of a scalar pressure field can be used for the visualization of the temperature. The software development is supported by the ViSTA VR-toolkit [7] and supports different target systems as well as a wide range of VR-devices. Furthermore, the prototype is scalable to run on laptops, workstations and cluster setups. REFERENCES [1] A. S. Garcia, D. J. Roberts, T. Fernando, C. Bar, R. Wolff, J. Dodiya, W. Engelke, and A. Gerndt, "A collaborative workspace architecture for strengthening collaboration among space scientists," in IEEE Aerospace Conference, (Big Sky, Montana, USA), 7-14 March 2015. [2] W. Engelke, "Mars Cartography VR System 2/3." German Aerospace Center (DLR), 2015. Project Deliverable D4.2. [3] E. Hivon, F. K. Hansen, and A. J. Banday, "The healpix primer," arXivpreprint astro-ph/9905275, 1999. [4] K. M. Gorski, E. Hivon, A. Banday, B. D. Wandelt, F. K. Hansen, M. Reinecke, and M. Bartelmann, "Healpix: a framework for high-resolution discretization and fast analysis of data distributed on the sphere," The Astrophysical Journal, vol. 622, no. 2, p. 759, 2005. [5] R. Westerteiger, A. Gerndt, and B. Hamann, "Spherical terrain render- ing using the hierarchical healpix grid," VLUDS, vol. 11, pp. 13-23, 2011. [6] W. Schroeder, K. Martin, and B. Lorensen, The Visualization Toolkit. Kitware, 4 ed., 2006. [7] T. van Reimersdahl, T. Kuhlen, A. Gerndt, J. Henrichs, and C. Bischof, "ViSTA: a multimodal, platform-independent VR-toolkit based on WTK, VTK, and MPI," in Proceedings of the 4th International Immersive Projection Technology Workshop (IPT), 2000.

To generate a finite element model of human thorax using the VCH dataset

NASA Astrophysics Data System (ADS)

Shi, Hui; Liu, Qian

2009-10-01

Purpose: To generate a three-dimensional (3D) finite element (FE) model of human thorax which may provide the basis of biomechanics simulation for the study of design effect and mechanism of safety belt when vehicle collision. Methods: Using manually or semi-manually segmented method, the interested area can be segmented from the VCH (Visible Chinese Human) dataset. The 3D surface model of thorax is visualized by using VTK (Visualization Toolkit) and further translated into (Stereo Lithography) STL format, which approximates the geometry of solid model by representing the boundaries with triangular facets. The data in STL format need to be normalized into NURBS surfaces and IGES format using software such as Geomagic Studio to provide archetype for reverse engineering. The 3D FE model was established using Ansys software. Results: The generated 3D FE model was an integrated thorax model which could reproduce human's complicated structure morphology including clavicle, ribs, spine and sternum. It was consisted of 1 044 179 elements in total. Conclusions: Compared with the previous thorax model, this FE model enhanced the authenticity and precision of results analysis obviously, which can provide a sound basis for analysis of human thorax biomechanical research. Furthermore, using the method above, we can also establish 3D FE models of some other organizes and tissues utilizing the VCH dataset.

Features extraction in anterior and posterior cruciate ligaments analysis.

PubMed

Zarychta, P

2015-12-01

The main aim of this research is finding the feature vectors of the anterior and posterior cruciate ligaments (ACL and PCL). These feature vectors have to clearly define the ligaments structure and make it easier to diagnose them. Extraction of feature vectors is obtained by analysis of both anterior and posterior cruciate ligaments. This procedure is performed after the extraction process of both ligaments. In the first stage in order to reduce the area of analysis a region of interest including cruciate ligaments (CL) is outlined in order to reduce the area of analysis. In this case, the fuzzy C-means algorithm with median modification helping to reduce blurred edges has been implemented. After finding the region of interest (ROI), the fuzzy connectedness procedure is performed. This procedure permits to extract the anterior and posterior cruciate ligament structures. In the last stage, on the basis of the extracted anterior and posterior cruciate ligament structures, 3-dimensional models of the anterior and posterior cruciate ligament are built and the feature vectors created. This methodology has been implemented in MATLAB and tested on clinical T1-weighted magnetic resonance imaging (MRI) slices of the knee joint. The 3D display is based on the Visualization Toolkit (VTK). Copyright © 2015 Elsevier Ltd. All rights reserved.

A Responsive Client for Distributed Visualization

NASA Astrophysics Data System (ADS)

Bollig, E. F.; Jensen, P. A.; Erlebacher, G.; Yuen, D. A.; Momsen, A. R.

2006-12-01

As grids, web services and distributed computing continue to gain popularity in the scientific community, demand for virtual laboratories likewise increases. Today organizations such as the Virtual Laboratory for Earth and Planetary Sciences (VLab) are dedicated to developing web-based portals to perform various simulations remotely while abstracting away details of the underlying computation. Two of the biggest challenges in portal- based computing are fast visualization and smooth interrogation without over taxing clients resources. In response to this challenge, we have expanded on our previous data storage strategy and thick client visualization scheme [1] to develop a client-centric distributed application that utilizes remote visualization of large datasets and makes use of the local graphics processor for improved interactivity. Rather than waste precious client resources for visualization, a combination of 3D graphics and 2D server bitmaps are used to simulate the look and feel of local rendering. Java Web Start and Java Bindings for OpenGL enable install-on- demand functionality as well as low level access to client graphics for all platforms. Powerful visualization services based on VTK and auto-generated by the WATT compiler [2] are accessible through a standard web API. Data is permanently stored on compute nodes while separate visualization nodes fetch data requested by clients, caching it locally to prevent unnecessary transfers. We will demonstrate application capabilities in the context of simulated charge density visualization within the VLab portal. In addition, we will address generalizations of our application to interact with a wider number of WATT services and performance bottlenecks. [1] Ananthuni, R., Karki, B.B., Bollig, E.F., da Silva, C.R.S., Erlebacher, G., "A Web-Based Visualization and Reposition Scheme for Scientific Data," In Press, Proceedings of the 2006 International Conference on Modeling Simulation and Visualization Methods (MSV'06) (2006). [2] Jensen, P.A., Yuen, D.A., Erlebacher, G., Bollig, E.F., Kigelman, D.G., Shukh, E.A., Automated Generation of Web Services for Visualization Toolkits, Eos Trans. AGU, 86(52), Fall Meet. Suppl., Abstract IN42A-06, 2005.

Dual-functioning peptides discovered by phage display increase the magnitude and specificity of BMSC attachment to mineralized biomaterials.

PubMed

Ramaraju, Harsha; Miller, Sharon J; Kohn, David H

2017-07-01

Design of biomaterials for cell-based therapies requires presentation of specific physical and chemical cues to cells, analogous to cues provided by native extracellular matrices (ECM). We previously identified a peptide sequence with high affinity towards apatite (VTKHLNQISQSY, VTK) using phage display. The aims of this study were to identify a human MSC-specific peptide sequence through phage display, combine it with the apatite-specific sequence, and verify the specificity of the combined dual-functioning peptide to both apatite and human bone marrow stromal cells. In this study, a combinatorial phage display identified the cell binding sequence (DPIYALSWSGMA, DPI) which was combined with the mineral binding sequence to generate the dual peptide DPI-VTK. DPI-VTK demonstrated significantly greater binding affinity (1/K D ) to apatite surfaces compared to VTK, phosphorylated VTK (VTK phos ), DPI-VTK phos , RGD-VTK, and peptide-free apatite surfaces (p < 0.01), while significantly increasing hBMSC adhesion strength (τ 50 , p < 0.01). MSCs demonstrated significantly greater adhesion strength to DPI-VTK compared to other cell types, while attachment of MC3T3 pre-osteoblasts and murine fibroblasts was limited (p < 0.01). MSCs on DPI-VTK coated surfaces also demonstrated increased spreading compared to pre-osteoblasts and fibroblasts. MSCs cultured on DPI-VTK coated apatite films exhibited significantly greater proliferation compared to controls (p < 0.001). Moreover, early and late stage osteogenic differentiation markers were elevated on DPI-VTK coated apatite films compared to controls. Taken together, phage display can identify non-obvious cell and material specific peptides to increase human MSC adhesion strength to specific biomaterial surfaces and subsequently increase cell proliferation and differentiation. These new peptides expand biomaterial design methodology for cell-based regeneration of bone defects. This strategy of combining cell and material binding phage display derived peptides is broadly applicable to a variety of systems requiring targeted adhesion of specific cell populations, and may be generalized to the engineering of any adhesion surface. Copyright © 2017 Elsevier Ltd. All rights reserved.

Mapping the spatial patterns of field traffic and traffic intensity to predict soil compaction risks at the field scale

NASA Astrophysics Data System (ADS)

Duttmann, Rainer; Kuhwald, Michael; Nolde, Michael

2015-04-01

Soil compaction is one of the main threats to cropland soils in present days. In contrast to easily visible phenomena of soil degradation, soil compaction, however, is obscured by other signals such as reduced crop yield, delayed crop growth, and the ponding of water, which makes it difficult to recognize and locate areas impacted by soil compaction directly. Although it is known that trafficking intensity is a key factor for soil compaction, until today only modest work has been concerned with the mapping of the spatially distributed patterns of field traffic and with the visual representation of the loads and pressures applied by farm traffic within single fields. A promising method for for spatial detection and mapping of soil compaction risks of individual fields is to process dGPS data, collected from vehicle-mounted GPS receivers and to compare the soil stress induced by farm machinery to the load bearing capacity derived from given soil map data. The application of position-based machinery data enables the mapping of vehicle movements over time as well as the assessment of trafficking intensity. It also facilitates the calculation of the trafficked area and the modeling of the loads and pressures applied to soil by individual vehicles. This paper focuses on the modeling and mapping of the spatial patterns of traffic intensity in silage maize fields during harvest, considering the spatio-temporal changes in wheel load and ground contact pressure along the loading sections. In addition to scenarios calculated for varying mechanical soil strengths, an example for visualizing the three-dimensional stress propagation inside the soil will be given, using the Visualization Toolkit (VTK) to construct 2D or 3D maps supporting to decision making due to sustainable field traffic management.

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

Moreland, Kenneth; Sewell, Christopher; Usher, William

Here, one of the most critical challenges for high-performance computing (HPC) scientific visualization is execution on massively threaded processors. Of the many fundamental changes we are seeing in HPC systems, one of the most profound is a reliance on new processor types optimized for execution bandwidth over latency hiding. Our current production scientific visualization software is not designed for these new types of architectures. To address this issue, the VTK-m framework serves as a container for algorithms, provides flexible data representation, and simplifies the design of visualization algorithms on new and future computer architecture.

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

Moreland, Kenneth; Sewell, Christopher; Usher, William

Execution on massively threaded processors is one of the most critical challenges for high-performance computing (HPC) scientific visualization. Of the many fundamental changes we are seeing in HPC systems, one of the most profound is a reliance on new processor types optimized for execution bandwidth over latency hiding. Moreover, our current production scientific visualization software is not designed for these new types of architectures. In order to address this issue, the VTK-m framework serves as a container for algorithms, provides flexible data representation, and simplifies the design of visualization algorithms on new and future computer architecture.

Automating Visualization Service Generation with the WATT Compiler

NASA Astrophysics Data System (ADS)

Bollig, E. F.; Lyness, M. D.; Erlebacher, G.; Yuen, D. A.

2007-12-01

As tasks and workflows become increasingly complex, software developers are devoting increasing attention to automation tools. Among many examples, the Automator tool from Apple collects components of a workflow into a single script, with very little effort on the part of the user. Tasks are most often described as a series of instructions. The granularity of the tasks dictates the tools to use. Compilers translate fine-grained instructions to assembler code, while scripting languages (ruby, perl) are used to describe a series of tasks at a higher level. Compilers can also be viewed as transformational tools: a cross-compiler can translate executable code written on one computer to assembler code understood on another, while transformational tools can translate from one high-level language to another. We are interested in creating visualization web services automatically, starting from stand-alone VTK (Visualization Toolkit) code written in Tcl. To this end, using the OCaml programming language, we have developed a compiler that translates Tcl into C++, including all the stubs, classes and methods to interface with gSOAP, a C++ implementation of the Soap 1.1/1.2 protocols. This compiler, referred to as the Web Automation and Translation Toolkit (WATT), is the first step towards automated creation of specialized visualization web services without input from the user. The WATT compiler seeks to automate all aspects of web service generation, including the transport layer, the division of labor and the details related to interface generation. The WATT compiler is part of ongoing efforts within the NSF funded VLab consortium [1] to facilitate and automate time-consuming tasks for the science related to understanding planetary materials. Through examples of services produced by WATT for the VLab portal, we will illustrate features, limitations and the improvements necessary to achieve the ultimate goal of complete and transparent automation in the generation of web services. In particular, we will detail the generation of a charge density visualization service applicable to output from the quantum calculations of the VLab computation workflows, plus another service for mantle convection visualization. We also discuss WATT-LIVE [2], a web-based interface that allows users to interact with WATT. With WATT-LIVE users submit Tcl code, retrieve its C++ translation with various files and scripts necessary to locally install the tailor-made web service, or launch the service for a limited session on our test server. This work is supported by NSF through the ITR grant NSF-0426867. [1] Virtual Laboratory for Earth and Planetary Materials, http://vlab.msi.umn.edu, September 2007. [2] WATT-LIVE website, http://vlab2.scs.fsu.edu/watt-live, September 2007.

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

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

Jiang, S; Dolly, S; Cai, B

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

ATDM Rover Milestone Report STDA02-1 (FY2017 Q4)

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

Larsen, Matt; Laney, Dan E.

We have successfully completed the MS-4/Y1 Milestone STDA02-1 for the Rover Project. This document describes the milestone and provides an overview of the technical details and artifacts of the milestone. This milestone is focused on building a GPU accelerated ray tracing package capable of doing multi-group radiography, both back-lit and with self-emission as well as serving as a volume rendering plot in VisIt and other VTK-based visualization tools. The long term goal is a package with in-situ capability, but for this first version integration into VisIt is the primary goal. Milestone Execution Plan: Create API for GPU Raytracer that supportsmore » multi-group transport (up to hundreds of groups); Implement components into one or more of: VTK-m, VisIt, and a new library/package implementation to be hosted on LLNL Bitbucket (initially), before releasing to the wider community.« less

Wavelet Transforms using VTK-m

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

Li, Shaomeng; Sewell, Christopher Meyer

2016-09-27

These are a set of slides that deal with the topics of wavelet transforms using VTK-m. First, wavelets are discussed and detailed, then VTK-m is discussed and detailed, then wavelets and VTK-m are looked at from a performance comparison, then from an accuracy comparison, and finally lessons learned, conclusion, and what is next. Lessons learned are the following: Launching worklets is expensive; Natural logic of performing 2D wavelet transform: Repeat the same 1D wavelet transform on every row, repeat the same 1D wavelet transform on every column, invoke the 1D wavelet worklet every time: num_rows x num_columns; VTK-m approach ofmore » performing 2D wavelet transform: Create a worklet for 2D that handles both rows and columns, invoke this new worklet only one time; Fast calculation, but cannot reuse 1D implementations.« less

Visualization Tools for Lattice QCD - Final Report

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

Massimo Di Pierro

2012-03-15

Our research project is about the development of visualization tools for Lattice QCD. We developed various tools by extending existing libraries, adding new algorithms, exposing new APIs, and creating web interfaces (including the new NERSC gauge connection web site). Our tools cover the full stack of operations from automating download of data, to generating VTK files (topological charge, plaquette, Polyakov lines, quark and meson propagators, currents), to turning the VTK files into images, movies, and web pages. Some of the tools have their own web interfaces. Some Lattice QCD visualization have been created in the past but, to our knowledge,more » our tools are the only ones of their kind since they are general purpose, customizable, and relatively easy to use. We believe they will be valuable to physicists working in the field. They can be used to better teach Lattice QCD concepts to new graduate students; they can be used to observe the changes in topological charge density and detect possible sources of bias in computations; they can be used to observe the convergence of the algorithms at a local level and determine possible problems; they can be used to probe heavy-light mesons with currents and determine their spatial distribution; they can be used to detect corrupted gauge configurations. There are some indirect results of this grant that will benefit a broader audience than Lattice QCD physicists.« less

New software for 3D fracture network analysis and visualization

NASA Astrophysics Data System (ADS)

Song, J.; Noh, Y.; Choi, Y.; Um, J.; Hwang, S.

2013-12-01

This study presents new software to perform analysis and visualization of the fracture network system in 3D. The developed software modules for the analysis and visualization, such as BOUNDARY, DISK3D, FNTWK3D, CSECT and BDM, have been developed using Microsoft Visual Basic.NET and Visualization TookKit (VTK) open-source library. Two case studies revealed that each module plays a role in construction of analysis domain, visualization of fracture geometry in 3D, calculation of equivalent pipes, production of cross-section map and management of borehole data, respectively. The developed software for analysis and visualization of the 3D fractured rock mass can be used to tackle the geomechanical problems related to strength, deformability and hydraulic behaviors of the fractured rock masses.

Milestone Completion Report WBS 1.3.5.05 ECP/VTK-m FY17Q3 [MS-17/02] Faceted Surface Normals STDA05-3.

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

Moreland, Kenneth D.

2017-07-01

The FY17Q3 milestone of the ECP/VTK-m project includes the completion of a VTK-m filter that computes normal vectors for surfaces. Normal vectors are those that point perpendicular to the surface and are an important direction when rendering the surface. The implementation includes the parallel algorithm itself, a filter module to simplify integrating it into other software, and documentation in the VTK-m Users’ Guide. With the completion of this milestone, we are able to necessary information to rendering systems to provide appropriate shading of surfaces. This milestone also feeds into subsequent milestones that progressively improve the approximation of surface direction.

ECP Milestone Report WBS 2.3.4.13 ECP/VTK-m FY18Q1 [MS-18/01-03] Multiblock / Gradients / Release STDA05-5.

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

Moreland, Kenneth D.; Pugmire, David; Geveci, Berk

The FY18Q1 milestone of the ECP/VTK-m project includes the implementation of a multiblock data set, the completion of a gradients filtering operation, and the release of version 1.1 of the VTK-m software. With the completion of this milestone, the new multiblock data set allows us to iteratively schedule algorithms on composite data structures such as assemblies or hierarchies like AMR. The new gradient algorithms approximate derivatives of fields in 3D structures with finite differences. Finally, the release of VTK-m version 1.1 tags a stable release of the software that can more easily be incorporated into external projects.

A Divergence Statistics Extension to VTK for Performance Analysis

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

Pebay, Philippe Pierre; Bennett, Janine Camille

This report follows the series of previous documents ([PT08, BPRT09b, PT09, BPT09, PT10, PB13], where we presented the parallel descriptive, correlative, multi-correlative, principal component analysis, contingency, k -means, order and auto-correlative statistics engines which we developed within the Visualization Tool Kit ( VTK ) as a scalable, parallel and versatile statistics package. We now report on a new engine which we developed for the calculation of divergence statistics, a concept which we hereafter explain and whose main goal is to quantify the discrepancy, in a stasticial manner akin to measuring a distance, between an observed empirical distribution and a theoretical,more » "ideal" one. The ease of use of the new diverence statistics engine is illustrated by the means of C++ code snippets. Although this new engine does not yet have a parallel implementation, it has already been applied to HPC performance analysis, of which we provide an example.« less

Conversion of NIMROD simulation results for graphical analysis using VisIt

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

Romero-Talamas, C A

Software routines developed to prepare NIMROD [C. R. Sovinec et al., J. Comp. Phys. 195, 355 (2004)] results for three-dimensional visualization from simulations of the Sustained Spheromak Physics Experiment (SSPX ) [E. B. Hooper et al., Nucl. Fusion 39, 863 (1999)] are presented here. The visualization is done by first converting the NIMROD output to a format known as legacy VTK and then loading it to VisIt, a graphical analysis tool that includes three-dimensional rendering and various mathematical operations for large data sets. Sample images obtained from the processing of NIMROD data with VisIt are included.

FROMS3D: New Software for 3-D Visualization of Fracture Network System in Fractured Rock Masses

NASA Astrophysics Data System (ADS)

Noh, Y. H.; Um, J. G.; Choi, Y.

2014-12-01

A new software (FROMS3D) is presented to visualize fracture network system in 3-D. The software consists of several modules that play roles in management of borehole and field fracture data, fracture network modelling, visualization of fracture geometry in 3-D and calculation and visualization of intersections and equivalent pipes between fractures. Intel Parallel Studio XE 2013, Visual Studio.NET 2010 and the open source VTK library were utilized as development tools to efficiently implement the modules and the graphical user interface of the software. The results have suggested that the developed software is effective in visualizing 3-D fracture network system, and can provide useful information to tackle the engineering geological problems related to strength, deformability and hydraulic behaviors of the fractured rock masses.

Osteoinductive recombinant silk fusion proteins for bone regeneration.

PubMed

Dinjaski, Nina; Plowright, Robyn; Zhou, Shun; Belton, David J; Perry, Carole C; Kaplan, David L

2017-02-01

Protein polymers provide a unique opportunity for tunable designs of material systems due to the genetic basis of sequence control. To address the challenge of biomineralization interfaces with protein based materials, we genetically engineered spider silks to design organic-inorganic hybrid systems. The spider silk inspired domain (SGRGGLGGQG AGAAAAAGGA GQGGYGGLGSQGT) 15 served as an organic scaffold to control material stability and to allow multiple modes of processing, whereas the hydroxyapatite binding domain VTKHLNQISQSY (VTK), provided control over osteogenesis. The VTK domain was fused either to the N-, C- or both terminals of the spider silk domain to understand the effect of position on material properties and mineralization. The addition of the VTK domain to silk did not affect the physical properties of the silk recombinant constructs, but it had a critical role in the induction of biomineralization. When the VTK domain was placed on both the C- and N-termini the formation of crystalline hydroxyapatite was significantly increased. In addition, all of the recombinant proteins in film format supported the growth and proliferation of human mesenchymal stem cells (hMSCs). Importantly, the presence of the VTK domain enhanced osteoinductive properties up to 3-fold compared to the control (silk alone without VTK). Therefore, silk-VTK fusion proteins have been shown suitable for mineralization and functionalization for specific biomedical applications. Organic-inorganic interfaces are integral to biomaterial functions in many areas of repair and regeneration. Several protein polymers have been investigated for this purpose. Despite their success the limited options to fine-tune their material properties, degradation patterns and functionalize them for each specific biomedical application limits their application. Various studies have shown that the biological performance of such proteins can be improved by genetic engineering. The present study provides data relating protein design parameters and functional outcome quantified by biomineralization and human mesenchymal stem cell differentiation. As such, it helps the design of osteoinductive recombinant biomaterials for bone regeneration. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

MAVEN Data Analysis and Visualization Toolkits

NASA Astrophysics Data System (ADS)

Harter, B., Jr.; DeWolfe, A. W.; Brain, D.; Chaffin, M.

2017-12-01

The Mars Atmospheric and Volatile Evolution (MAVEN) mission has been collecting data at Mars since September 2014. The MAVEN Science Data Center has developed software toolkits for analyzing and visualizing the science data. Our Data Intercomparison and Visualization Development Effort (DIVIDE) toolkit is written in IDL, and utilizes the widely used "tplot" IDL libraries. Recently, we have converted DIVIDE into Python in an effort to increase the accessibility of the MAVEN data. This conversion also necessitated the development of a Python version of the tplot libraries, which we have dubbed "PyTplot". PyTplot is generalized to work with missions beyond MAVEN, and our software is available on Github.

Implementation of an oblique-sectioning visualization tool for line-of-sight stereotactic neurosurgical navigation using the AVW toolkit

NASA Astrophysics Data System (ADS)

Bates, Lisa M.; Hanson, Dennis P.; Kall, Bruce A.; Meyer, Frederic B.; Robb, Richard A.

1998-06-01

An important clinical application of biomedical imaging and visualization techniques is provision of image guided neurosurgical planning and navigation techniques using interactive computer display systems in the operating room. Current systems provide interactive display of orthogonal images and 3D surface or volume renderings integrated with and guided by the location of a surgical probe. However, structures in the 'line-of-sight' path which lead to the surgical target cannot be directly visualized, presenting difficulty in obtaining full understanding of the 3D volumetric anatomic relationships necessary for effective neurosurgical navigation below the cortical surface. Complex vascular relationships and histologic boundaries like those found in artereovenous malformations (AVM's) also contribute to the difficulty in determining optimal approaches prior to actual surgical intervention. These difficulties demonstrate the need for interactive oblique imaging methods to provide 'line-of-sight' visualization. Capabilities for 'line-of- sight' interactive oblique sectioning are present in several current neurosurgical navigation systems. However, our implementation is novel, in that it utilizes a completely independent software toolkit, AVW (A Visualization Workshop) developed at the Mayo Biomedical Imaging Resource, integrated with a current neurosurgical navigation system, the COMPASS stereotactic system at Mayo Foundation. The toolkit is a comprehensive, C-callable imaging toolkit containing over 500 optimized imaging functions and structures. The powerful functionality and versatility of the AVW imaging toolkit provided facile integration and implementation of desired interactive oblique sectioning using a finite set of functions. The implementation of the AVW-based code resulted in higher-level functions for complete 'line-of-sight' visualization.

Python-based geometry preparation and simulation visualization toolkits for STEPS

PubMed Central

Chen, Weiliang; De Schutter, Erik

2014-01-01

STEPS is a stochastic reaction-diffusion simulation engine that implements a spatial extension of Gillespie's Stochastic Simulation Algorithm (SSA) in complex tetrahedral geometries. An extensive Python-based interface is provided to STEPS so that it can interact with the large number of scientific packages in Python. However, a gap existed between the interfaces of these packages and the STEPS user interface, where supporting toolkits could reduce the amount of scripting required for research projects. This paper introduces two new supporting toolkits that support geometry preparation and visualization for STEPS simulations. PMID:24782754

bioWidgets: data interaction components for genomics.

PubMed

Fischer, S; Crabtree, J; Brunk, B; Gibson, M; Overton, G C

1999-10-01

The presentation of genomics data in a perspicuous visual format is critical for its rapid interpretation and validation. Relatively few public database developers have the resources to implement sophisticated front-end user interfaces themselves. Accordingly, these developers would benefit from a reusable toolkit of user interface and data visualization components. We have designed the bioWidget toolkit as a set of JavaBean components. It includes a wide array of user interface components and defines an architecture for assembling applications. The toolkit is founded on established software engineering design patterns and principles, including componentry, Model-View-Controller, factored models and schema neutrality. As a proof of concept, we have used the bioWidget toolkit to create three extendible applications: AnnotView, BlastView and AlignView.

The connectome viewer toolkit: an open source framework to manage, analyze, and visualize connectomes.

PubMed

Gerhard, Stephan; Daducci, Alessandro; Lemkaddem, Alia; Meuli, Reto; Thiran, Jean-Philippe; Hagmann, Patric

2011-01-01

Advanced neuroinformatics tools are required for methods of connectome mapping, analysis, and visualization. The inherent multi-modality of connectome datasets poses new challenges for data organization, integration, and sharing. We have designed and implemented the Connectome Viewer Toolkit - a set of free and extensible open source neuroimaging tools written in Python. The key components of the toolkit are as follows: (1) The Connectome File Format is an XML-based container format to standardize multi-modal data integration and structured metadata annotation. (2) The Connectome File Format Library enables management and sharing of connectome files. (3) The Connectome Viewer is an integrated research and development environment for visualization and analysis of multi-modal connectome data. The Connectome Viewer's plugin architecture supports extensions with network analysis packages and an interactive scripting shell, to enable easy development and community contributions. Integration with tools from the scientific Python community allows the leveraging of numerous existing libraries for powerful connectome data mining, exploration, and comparison. We demonstrate the applicability of the Connectome Viewer Toolkit using Diffusion MRI datasets processed by the Connectome Mapper. The Connectome Viewer Toolkit is available from http://www.cmtk.org/

The Connectome Viewer Toolkit: An Open Source Framework to Manage, Analyze, and Visualize Connectomes

PubMed Central

Gerhard, Stephan; Daducci, Alessandro; Lemkaddem, Alia; Meuli, Reto; Thiran, Jean-Philippe; Hagmann, Patric

2011-01-01

Advanced neuroinformatics tools are required for methods of connectome mapping, analysis, and visualization. The inherent multi-modality of connectome datasets poses new challenges for data organization, integration, and sharing. We have designed and implemented the Connectome Viewer Toolkit – a set of free and extensible open source neuroimaging tools written in Python. The key components of the toolkit are as follows: (1) The Connectome File Format is an XML-based container format to standardize multi-modal data integration and structured metadata annotation. (2) The Connectome File Format Library enables management and sharing of connectome files. (3) The Connectome Viewer is an integrated research and development environment for visualization and analysis of multi-modal connectome data. The Connectome Viewer's plugin architecture supports extensions with network analysis packages and an interactive scripting shell, to enable easy development and community contributions. Integration with tools from the scientific Python community allows the leveraging of numerous existing libraries for powerful connectome data mining, exploration, and comparison. We demonstrate the applicability of the Connectome Viewer Toolkit using Diffusion MRI datasets processed by the Connectome Mapper. The Connectome Viewer Toolkit is available from http://www.cmtk.org/ PMID:21713110

The Application of the Montage Image Mosaic Engine To The Visualization Of Astronomical Images

NASA Astrophysics Data System (ADS)

Berriman, G. Bruce; Good, J. C.

2017-05-01

The Montage Image Mosaic Engine was designed as a scalable toolkit, written in C for performance and portability across *nix platforms, that assembles FITS images into mosaics. This code is freely available and has been widely used in the astronomy and IT communities for research, product generation, and for developing next-generation cyber-infrastructure. Recently, it has begun finding applicability in the field of visualization. This development has come about because the toolkit design allows easy integration into scalable systems that process data for subsequent visualization in a browser or client. The toolkit it includes a visualization tool suitable for automation and for integration into Python: mViewer creates, with a single command, complex multi-color images overlaid with coordinate displays, labels, and observation footprints, and includes an adaptive image histogram equalization method that preserves the structure of a stretched image over its dynamic range. The Montage toolkit contains functionality originally developed to support the creation and management of mosaics, but which also offers value to visualization: a background rectification algorithm that reveals the faint structure in an image; and tools for creating cutout and downsampled versions of large images. Version 5 of Montage offers support for visualizing data written in HEALPix sky-tessellation scheme, and functionality for processing and organizing images to comply with the TOAST sky-tessellation scheme required for consumption by the World Wide Telescope (WWT). Four online tutorials allow readers to reproduce and extend all the visualizations presented in this paper.

Toolkit of Available EPA Green Infrastructure Modeling ...

EPA Pesticide Factsheets

This webinar will present a toolkit consisting of five EPA green infrastructure models and tools, along with communication material. This toolkit can be used as a teaching and quick reference resource for use by planners and developers when making green infrastructure implementation decisions. It can also be used for low impact development design competitions. Models and tools included: Green Infrastructure Wizard (GIWiz), Watershed Management Optimization Support Tool (WMOST), Visualizing Ecosystem Land Management Assessments (VELMA) Model, Storm Water Management Model (SWMM), and the National Stormwater Calculator (SWC). This webinar will present a toolkit consisting of five EPA green infrastructure models and tools, along with communication material. This toolkit can be used as a teaching and quick reference resource for use by planners and developers when making green infrastructure implementation decisions. It can also be used for low impact development design competitions. Models and tools included: Green Infrastructure Wizard (GIWiz), Watershed Management Optimization Support Tool (WMOST), Visualizing Ecosystem Land Management Assessments (VELMA) Model, Storm Water Management Model (SWMM), and the National Stormwater Calculator (SWC).

ParaView visualization of Abaqus output on the mechanical deformation of complex microstructures

NASA Astrophysics Data System (ADS)

Liu, Qingbin; Li, Jiang; Liu, Jie

2017-02-01

Abaqus® is a popular software suite for finite element analysis. It delivers linear and nonlinear analyses of mechanical and fluid dynamics, includes multi-body system and multi-physics coupling. However, the visualization capability of Abaqus using its CAE module is limited. Models from microtomography have extremely complicated structures, and datasets of Abaqus output are huge, requiring a visualization tool more powerful than Abaqus/CAE. We convert Abaqus output into the XML-based VTK format by developing a Python script and then using ParaView to visualize the results. Such capabilities as volume rendering, tensor glyphs, superior animation and other filters allow ParaView to offer excellent visualizing manifestations. ParaView's parallel visualization makes it possible to visualize very big data. To support full parallel visualization, the Python script achieves data partitioning by reorganizing all nodes, elements and the corresponding results on those nodes and elements. The data partition scheme minimizes data redundancy and works efficiently. Given its good readability and extendibility, the script can be extended to the processing of more different problems in Abaqus. We share the script with Abaqus users on GitHub.

Phosphorylation-dependent mineral-type specificity for apatite-binding peptide sequences.

PubMed

Addison, William N; Miller, Sharon J; Ramaswamy, Janani; Mansouri, Ahmad; Kohn, David H; McKee, Marc D

2010-12-01

Apatite-binding peptides discovered by phage display provide an alternative design method for creating functional biomaterials for bone and tooth tissue repair. A limitation of this approach is the absence of display peptide phosphorylation--a post-translational modification important to mineral-binding proteins. To refine the material specificity of a recently identified apatite-binding peptide, and to determine critical design parameters (net charge, charge distribution, amino acid sequence and composition) controlling peptide affinity for mineral, we investigated the effects of phosphorylation and sequence scrambling on peptide adsorption to four different apatites (bone-like mineral, and three types of apatite containing initially 0, 5.6 and 10.5% carbonate). Phosphorylation of the VTKHLNQISQSY peptide (VTK peptide) led to a 10-fold increase in peptide adsorption (compared to nonphosphorylated peptide) to bone-like mineral, and a 2-fold increase in adsorption to the carbonated apatite, but there was no effect of phosphorylation on peptide affinity to pure hydroxyapatite (without carbonate). Sequence scrambling of the nonphosphorylated VTK peptide enhanced its specificity for the bone-like mineral, but scrambled phosphorylated VTK peptide (pVTK) did not significantly alter mineral-binding suggesting that despite the importance of sequence order and/or charge distribution to mineral-binding, the enhanced binding after phosphorylation exceeds any further enhancement by altered sequence order. Osteoblast culture mineralization was dose-dependently inhibited by pVTK and to a significantly lesser extent by scrambled pVTK, while the nonphosphorylated and scrambled forms had no effect, indicating that inhibition of osteoblast mineralization is dependent on both peptide sequence and charge. Computational modeling of peptide-mineral interactions indicated a favorable change in binding energy upon phosphorylation that was unaffected by scrambling. In conclusion, phosphorylation of serine residues increases peptide specificity for bone-like mineral, whose adsorption is determined primarily by sequence composition and net charge as opposed to sequence order. However, sequence order in addition to net charge modulates the mineralization of osteoblast cultures. The ability of such peptides to inhibit mineralization has potential utility in the management of pathologic calcification. Copyright © 2010 Elsevier Ltd. All rights reserved.

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

PubMed Central

Hardisty, Frank; Robinson, Anthony C.

2010-01-01

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

FY17Q4 Ristra project: Release Version 1.0 of a production toolkit

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

Hungerford, Aimee L.; Daniel, David John

2017-09-21

The Next Generation Code project will release Version 1.0 of a production toolkit for multi-physics application development on advanced architectures. Features of this toolkit will include remap and link utilities, control and state manager, setup, visualization and I/O, as well as support for a variety of mesh and particle data representations. Numerical physics packages that operate atop this foundational toolkit will be employed in a multi-physics demonstration problem and released to the community along with results from the demonstration.

Early Detection of Clinically Significant Prostate Cancer Using Ultrasonic Acoustic Radiation Force Impulse (ARFI) Imaging

DTIC Science & Technology

2017-10-01

Toolkit for rapid 3D visualization and image volume interpretation, followed by automated transducer positioning in a user-selected image plane for... Toolkit (IGSTK) to enable rapid 3D visualization and image volume interpretation followed by automated transducer positioning in the user-selected... careers in science, technology, and the humanities. What do you plan to do during the next reporting period to accomplish the goals? If this

Evaluation of the Vitek Card GPS105 and VTK-RO7.01 Software for Detection of Oxacillin Resistance in Clinically Relevant Coagulase-Negative Staphylococci

PubMed Central

Martinez, Fernando; Chandler, Laura J.; Reisner, Barbara S.; Woods, Gail L.

2001-01-01

The performance of Vitek cards GPS105 with software version VTK-R07.01 for detection of oxacillin resistance in coagulase-negative staphylococci (CoNS) was compared to disk diffusion and PCR detection for mecA. The sensitivity and specificity of the Vitek GPS105 method were 97.6 and 85.5%, respectively. PMID:11574604

SDAV Viz July Progress Update: LANL

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

Sewell, Christopher Meyer

2012-07-30

SDAV Viz July Progress Update: (1) VPIC (Vector Particle in Cell) Kinetic Plasma Simulation Code - (a) Implemented first version of an in-situ adapter based on Paraview CoProcessing Library, (b) Three pipelines: vtkDataSetMapper, vtkContourFilter, vtkPistonContour, (c) Next, resolve issue at boundaries of processor domains; add more advanced viz/analysis pipelines; (2) Halo finding/merger trees - (a) Summer student Wathsala W. from University of Utah is working on data-parallel halo finder algorithm using PISTON, (b) Timo Bremer (LLNL), Valerio Pascucci (Utah), George Zagaris (Kitware), and LANL people are interested in using merger trees for tracking the evolution of halos in cosmo simulations;more » discussed possible overlap with work by Salman Habib and Katrin Heitmann (Argonne) during their visit to LANL 7/11; (3) PISTON integration in ParaView - Now available from ParaView github.« less

The Computational Science Environment (CSE)

DTIC Science & Technology

2009-08-01

supported CSE platforms. Developers can also build against different versions of a particular package (e.g., Python-2.4 vs . Python-2.5) via a...8.2.1 TK Testing Error and Workaround It has been found that TK tends to produces more testing errors when using KDE , and in some instances, the test...suite freezes when reaching the TK select test. These issues have not been seen when using Gnome . 8.2.2 VTK Testing Error and Workaround VTK test

3D reconstruction and spatial auralization of the "Painted Dolmen" of Antelas

NASA Astrophysics Data System (ADS)

Dias, Paulo; Campos, Guilherme; Santos, Vítor; Casaleiro, Ricardo; Seco, Ricardo; Sousa Santos, Beatriz

2008-02-01

This paper presents preliminary results on the development of a 3D audiovisual model of the Anta Pintada (painted dolmen) of Antelas, a Neolithic chamber tomb located in Oliveira de Frades and listed as Portuguese national monument. The final aim of the project is to create a highly accurate Virtual Reality (VR) model of this unique archaeological site, capable of providing not only visual but also acoustic immersion based on its actual geometry and physical properties. The project started in May 2006 with in situ data acquisition. The 3D geometry of the chamber was captured using a Laser Range Finder. In order to combine the different scans into a complete 3D visual model, reconstruction software based on the Iterative Closest Point (ICP) algorithm was developed using the Visualization Toolkit (VTK). This software computes the boundaries of the room on a 3D uniform grid and populates its interior with "free-space nodes", through an iterative algorithm operating like a torchlight illuminating a dark room. The envelope of the resulting set of "free-space nodes" is used to generate a 3D iso-surface approximating the interior shape of the chamber. Each polygon of this surface is then assigned the acoustic absorption coefficient of the corresponding boundary material. A 3D audiovisual model operating in real-time was developed for a VR Environment comprising head-mounted display (HMD) I-glasses SVGAPro, an orientation sensor (tracker) InterTrax 2 with 3 Degrees Of Freedom (3DOF) and stereo headphones. The auralisation software is based on a geometric model. This constitutes a first approach, since geometric acoustics have well-known limitations in rooms with irregular surfaces. The immediate advantage lies in their inherent computational efficiency, which allows real-time operation. The program computes the early reflections forming the initial part of the chamber's impulse response (IR), which carry the most significant cues for source localisation. These early reflections are processed through Head Related Transfer Functions (HRTF) updated in real-time according to the orientation of the user's head, so that sound waves appear to come from the correct location in space, in agreement with the visual scene. The late-reverberation tail of the IR is generated by an algorithm designed to match the reverberation time of the chamber, calculated from the actual acoustic absorption coefficients of its surfaces. The sound output to the headphones is obtained by convolving the IR with anechoic recordings of the virtual audio source.

Milestone Completion Report WBS 1.3.5.05 ECP/VTK-m FY17Q2 [MS-17/01] Better Dynamic Types Design SDA05-1

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

Moreland, Kenneth D.

The FY17Q2 milestone of the ECP/VTK-m project, which is the first milestone, includes the completion of design documents for the introduction of virtual methods into the VTK-m framework. Specifically, the ability from within the code of a device (e.g. GPU or Xeon Phi) to jump to a virtual method specified at run time. This change will enable us to drastically reduce the compile time and the executable code size for the VTK-m library. Our first design introduced the idea of adding virtual functions to classes that are used during algorithm execution. (Virtual methods were previously banned from the so calledmore » execution environment.) The design was straightforward. VTK-m already has the generic concepts of an “array handle” that provides a uniform interface to memory of different structures and an “array portal” that provides generic access to said memory. These array handles and portals use C++ templating to adjust them to different memory structures. This composition provides a powerful ability to adapt to data sources, but requires knowing static types. The proposed design creates a template specialization of an array portal that decorates another array handle while hiding its type. In this way we can wrap any type of static array handle and then feed it to a single compiled instance of a function. The second design focused on the mechanics of implementing virtual methods on parallel devices with a focus on CUDA. Our initial experiments on CUDA showed a very large overhead for using virtual C++ classes with virtual methods, the standard approach. Instead, we are using an alternate method provided by C that uses function pointers. With the completion of this milestone, we are able to move to the implementation of objects with virtual (like) methods. The upshot will be much faster compile times and much smaller library/executable sizes.« less

Incorporating 3-dimensional models in online articles.

PubMed

Cevidanes, Lucia H S; Ruellas, Antonio C O; Jomier, Julien; Nguyen, Tung; Pieper, Steve; Budin, Francois; Styner, Martin; Paniagua, Beatriz

2015-05-01

The aims of this article are to introduce the capability to view and interact with 3-dimensional (3D) surface models in online publications, and to describe how to prepare surface models for such online 3D visualizations. Three-dimensional image analysis methods include image acquisition, construction of surface models, registration in a common coordinate system, visualization of overlays, and quantification of changes. Cone-beam computed tomography scans were acquired as volumetric images that can be visualized as 3D projected images or used to construct polygonal meshes or surfaces of specific anatomic structures of interest. The anatomic structures of interest in the scans can be labeled with color (3D volumetric label maps), and then the scans are registered in a common coordinate system using a target region as the reference. The registered 3D volumetric label maps can be saved in .obj, .ply, .stl, or .vtk file formats and used for overlays, quantification of differences in each of the 3 planes of space, or color-coded graphic displays of 3D surface distances. All registered 3D surface models in this study were saved in .vtk file format and loaded in the Elsevier 3D viewer. In this study, we describe possible ways to visualize the surface models constructed from cone-beam computed tomography images using 2D and 3D figures. The 3D surface models are available in the article's online version for viewing and downloading using the reader's software of choice. These 3D graphic displays are represented in the print version as 2D snapshots. Overlays and color-coded distance maps can be displayed using the reader's software of choice, allowing graphic assessment of the location and direction of changes or morphologic differences relative to the structure of reference. The interpretation of 3D overlays and quantitative color-coded maps requires basic knowledge of 3D image analysis. When submitting manuscripts, authors can now upload 3D models that will allow readers to interact with or download them. Such interaction with 3D models in online articles now will give readers and authors better understanding and visualization of the results. Copyright © 2015 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

User's manual for the two-dimensional transputer graphics toolkit

NASA Technical Reports Server (NTRS)

Ellis, Graham K.

1988-01-01

The user manual for the 2-D graphics toolkit for a transputer based parallel processor is presented. The toolkit consists of a package of 2-D display routines that can be used for the simulation visualizations. It supports multiple windows, double buffered screens for animations, and simple graphics transformations such as translation, rotation, and scaling. The display routines are written in occam to take advantage of the multiprocessing features available on transputers. The package is designed to run on a transputer separate from the graphics board.

canvasDesigner: A versatile interactive high-resolution scientific multi-panel visualization toolkit.

PubMed

Zhang, Baohong; Zhao, Shanrong; Neuhaus, Isaac

2018-05-03

We present a bioinformatics and systems biology visualization toolkit harmonizing real time interactive exploring and analyzing of big data, full-fledged customizing of look-n-feel, and producing multi-panel publication-ready figures in PDF format simultaneously. Source code and detailed user guides are available at http://canvasxpress.org, https://baohongz.github.io/canvasDesigner, and https://baohongz.github.io/canvasDesigner/demo_video.html. isaac.neuhaus@bms.com, baohong.zhang@pfizer.com, shanrong.zhao@pfizer.com. Supplementary materials are available at https://goo.gl/1uQygs.

An object oriented fully 3D tomography visual toolkit.

PubMed

Agostinelli, S; Paoli, G

2001-04-01

In this paper we present a modern object oriented component object model (COMM) C + + toolkit dedicated to fully 3D cone-beam tomography. The toolkit allows the display and visual manipulation of analytical phantoms, projection sets and volumetric data through a standard Windows graphical user interface. Data input/output is performed using proprietary file formats but import/export of industry standard file formats, including raw binary, Windows bitmap and AVI, ACR/NEMA DICOMM 3 and NCSA HDF is available. At the time of writing built-in implemented data manipulators include a basic phantom ray-tracer and a Matrox Genesis frame grabbing facility. A COMM plug-in interface is provided for user-defined custom backprojector algorithms: a simple Feldkamp ActiveX control, including source code, is provided as an example; our fast Feldkamp plug-in is also available.

Alexander Meets Michotte: A Simulation Tool Based on Pattern Programming and Phenomenology

ERIC Educational Resources Information Center

Basawapatna, Ashok

2016-01-01

Simulation and modeling activities, a key point of computational thinking, are currently not being integrated into the science classroom. This paper describes a new visual programming tool entitled the Simulation Creation Toolkit. The Simulation Creation Toolkit is a high level pattern-based phenomenological approach to bringing rapid simulation…

[Three-dimensional reconstruction of functional brain images].

PubMed

Inoue, M; Shoji, K; Kojima, H; Hirano, S; Naito, Y; Honjo, I

1999-08-01

We consider PET (positron emission tomography) measurement with SPM (Statistical Parametric Mapping) analysis to be one of the most useful methods to identify activated areas of the brain involved in language processing. SPM is an effective analytical method that detects markedly activated areas over the whole brain. However, with the conventional presentations of these functional brain images, such as horizontal slices, three directional projection, or brain surface coloring, makes understanding and interpreting the positional relationships among various brain areas difficult. Therefore, we developed three-dimensionally reconstructed images from these functional brain images to improve the interpretation. The subjects were 12 normal volunteers. The following three types of images were constructed: 1) routine images by SPM, 2) three-dimensional static images, and 3) three-dimensional dynamic images, after PET images were analyzed by SPM during daily dialog listening. The creation of images of both the three-dimensional static and dynamic types employed the volume rendering method by VTK (The Visualization Toolkit). Since the functional brain images did not include original brain images, we synthesized SPM and MRI brain images by self-made C++ programs. The three-dimensional dynamic images were made by sequencing static images with available software. Images of both the three-dimensional static and dynamic types were processed by a personal computer system. Our newly created images showed clearer positional relationships among activated brain areas compared to the conventional method. To date, functional brain images have been employed in fields such as neurology or neurosurgery, however, these images may be useful even in the field of otorhinolaryngology, to assess hearing and speech. Exact three-dimensional images based on functional brain images are important for exact and intuitive interpretation, and may lead to new developments in brain science. Currently, the surface model is the most common method of three-dimensional display. However, the volume rendering method may be more effective for imaging regions such as the brain.

SU-G-201-04: Can the Dynamic Library of Flap Applicators Replace Treatment Planning in Surface Brachytherapy?

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

Buzurovic, I; Devlin, P; Hansen, J

Purpose: Contemporary brachytherapy treatment planning systems-(TPS) include the applicator model libraries to improve digitization; however, the library of surface-flap-applicators-(SFA) is not incorporated into the commercial TPS. We propose the dynamic library-(DL) for SFA and investigate if such library can eliminate applicator reconstruction, source activation and dose normalization. Methods: DL was generated for the SFA using the C++class libraries of the Visualization Toolkit-(VTK) and Qt-application framework for complete abstraction of the graphical interface. DL was designed such that the user can initially choose the size of the applicator that corresponds to the one clinically placed to the patient. The virtual applicator-(VA)more » has an elastic property so that it can be registered to the clinical CT images with a real applicator-(RA) on it. The VA and RA matching is performed by adjusting the position and curvature of the VA. The VA does not elongate or change its size so each catheter could always be at a distance of 5mm from the skin and 10mm apart from the closest catheter maintaining the physical accuracy of the clinical setup. Upon the applicator placement, the dwell positions were automatically activated, and the dose is normalized to the prescription depth. The accuracy of source positioning was evaluated using various applicator sizes. Results: The accuracy of the applicator placement was in the sub-millimeter range. The time-study reveals that up to 50% of the planning time can be saved depending on the complexity of the clinical setup. Unlike in the classic approach, the planning time was not highly dependent on the applicator size. Conclusion: The practical benefits of the DL of the SFA were demonstrated. The time demanding planning processes can be partially automated. Consequently, the planner can dedicate effort to fine tuning, which can result in the improvement of the quality of treatment plans in surface brachytherapy.« less

Integrating segmentation methods from the Insight Toolkit into a visualization application.

PubMed

Martin, Ken; Ibáñez, Luis; Avila, Lisa; Barré, Sébastien; Kaspersen, Jon H

2005-12-01

The Insight Toolkit (ITK) initiative from the National Library of Medicine has provided a suite of state-of-the-art segmentation and registration algorithms ideally suited to volume visualization and analysis. A volume visualization application that effectively utilizes these algorithms provides many benefits: it allows access to ITK functionality for non-programmers, it creates a vehicle for sharing and comparing segmentation techniques, and it serves as a visual debugger for algorithm developers. This paper describes the integration of image processing functionalities provided by the ITK into VolView, a visualization application for high performance volume rendering. A free version of this visualization application is publicly available and is available in the online version of this paper. The process for developing ITK plugins for VolView according to the publicly available API is described in detail, and an application of ITK VolView plugins to the segmentation of Abdominal Aortic Aneurysms (AAAs) is presented. The source code of the ITK plugins is also publicly available and it is included in the online version.

Toward a Shared Vocabulary for Visual Analysis: An Analytic Toolkit for Deconstructing the Visual Design of Graphic Novels

ERIC Educational Resources Information Center

Connors, Sean P.

2012-01-01

Literacy educators might advocate using graphic novels to develop students' visual literacy skills, but teachers who lack a vocabulary for engaging in close analysis of visual texts may be reluctant to teach them. Recognizing this, teacher educators should equip preservice teachers with a vocabulary for analyzing visual texts. This article…

Tracker Toolkit

NASA Technical Reports Server (NTRS)

Lewis, Steven J.; Palacios, David M.

2013-01-01

This software can track multiple moving objects within a video stream simultaneously, use visual features to aid in the tracking, and initiate tracks based on object detection in a subregion. A simple programmatic interface allows plugging into larger image chain modeling suites. It extracts unique visual features for aid in tracking and later analysis, and includes sub-functionality for extracting visual features about an object identified within an image frame. Tracker Toolkit utilizes a feature extraction algorithm to tag each object with metadata features about its size, shape, color, and movement. Its functionality is independent of the scale of objects within a scene. The only assumption made on the tracked objects is that they move. There are no constraints on size within the scene, shape, or type of movement. The Tracker Toolkit is also capable of following an arbitrary number of objects in the same scene, identifying and propagating the track of each object from frame to frame. Target objects may be specified for tracking beforehand, or may be dynamically discovered within a tripwire region. Initialization of the Tracker Toolkit algorithm includes two steps: Initializing the data structures for tracked target objects, including targets preselected for tracking; and initializing the tripwire region. If no tripwire region is desired, this step is skipped. The tripwire region is an area within the frames that is always checked for new objects, and all new objects discovered within the region will be tracked until lost (by leaving the frame, stopping, or blending in to the background).

The Python ARM Radar Toolkit (Py-ART), a library for working with weather radar data in the Python programming language

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

Helmus, Jonathan J.; Collis, Scott M.

The Python ARM Radar Toolkit is a package for reading, visualizing, correcting and analysing data from weather radars. Development began to meet the needs of the Atmospheric Radiation Measurement Climate Research Facility and has since expanded to provide a general-purpose framework for working with data from weather radars in the Python programming language. The toolkit is built on top of libraries in the Scientific Python ecosystem including NumPy, SciPy, and matplotlib, and makes use of Cython for interfacing with existing radar libraries written in C and to speed up computationally demanding algorithms. As a result, the source code for themore » toolkit is available on GitHub and is distributed under a BSD license.« less

The Python ARM Radar Toolkit (Py-ART), a library for working with weather radar data in the Python programming language

DOE PAGES

Helmus, Jonathan J.; Collis, Scott M.

2016-07-18

The Python ARM Radar Toolkit is a package for reading, visualizing, correcting and analysing data from weather radars. Development began to meet the needs of the Atmospheric Radiation Measurement Climate Research Facility and has since expanded to provide a general-purpose framework for working with data from weather radars in the Python programming language. The toolkit is built on top of libraries in the Scientific Python ecosystem including NumPy, SciPy, and matplotlib, and makes use of Cython for interfacing with existing radar libraries written in C and to speed up computationally demanding algorithms. As a result, the source code for themore » toolkit is available on GitHub and is distributed under a BSD license.« less

Development of a new software for analyzing 3-D fracture network

NASA Astrophysics Data System (ADS)

Um, Jeong-Gi; Noh, Young-Hwan; Choi, Yosoon

2014-05-01

A new software is presented to analyze fracture network in 3-D. Recently, we completed the software package based on information given in EGU2013. The software consists of several modules that play roles in management of borehole data, stochastic modelling of fracture network, construction of analysis domain, visualization of fracture geometry in 3-D, calculation of equivalent pipes and production of cross-section diagrams. Intel Parallel Studio XE 2013, Visual Studio.NET 2010 and the open source VTK library were utilized as development tools to efficiently implement the modules and the graphical user interface of the software. A case study was performed to analyze 3-D fracture network system at the Upper Devonian Grosmont Formation in Alberta, Canada. The results have suggested that the developed software is effective in modelling and visualizing 3-D fracture network system, and can provide useful information to tackle the geomechanical problems related to strength, deformability and hydraulic behaviours of the fractured rock masses. This presentation describes the concept and details of the development and implementation of the software.

Unipro UGENE: a unified bioinformatics toolkit.

PubMed

Okonechnikov, Konstantin; Golosova, Olga; Fursov, Mikhail

2012-04-15

Unipro UGENE is a multiplatform open-source software with the main goal of assisting molecular biologists without much expertise in bioinformatics to manage, analyze and visualize their data. UGENE integrates widely used bioinformatics tools within a common user interface. The toolkit supports multiple biological data formats and allows the retrieval of data from remote data sources. It provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees and 3D structures. Most of the integrated algorithms are tuned for maximum performance by the usage of multithreading and special processor instructions. UGENE includes a visual environment for creating reusable workflows that can be launched on local resources or in a High Performance Computing (HPC) environment. UGENE is written in C++ using the Qt framework. The built-in plugin system and structured UGENE API make it possible to extend the toolkit with new functionality. UGENE binaries are freely available for MS Windows, Linux and Mac OS X at http://ugene.unipro.ru/download.html. UGENE code is licensed under the GPLv2; the information about the code licensing and copyright of integrated tools can be found in the LICENSE.3rd_party file provided with the source bundle.

Parallel auto-correlative statistics with VTK.

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

Pebay, Philippe Pierre; Bennett, Janine Camille

2013-08-01

This report summarizes existing statistical engines in VTK and presents both the serial and parallel auto-correlative statistics engines. It is a sequel to [PT08, BPRT09b, PT09, BPT09, PT10] which studied the parallel descriptive, correlative, multi-correlative, principal component analysis, contingency, k-means, and order statistics engines. The ease of use of the new parallel auto-correlative statistics engine is illustrated by the means of C++ code snippets and algorithm verification is provided. This report justifies the design of the statistics engines with parallel scalability in mind, and provides scalability and speed-up analysis results for the autocorrelative statistics engine.

WIRM: An Open Source Toolkit for Building Biomedical Web Applications

PubMed Central

Jakobovits, Rex M.; Rosse, Cornelius; Brinkley, James F.

2002-01-01

This article describes an innovative software toolkit that allows the creation of web applications that facilitate the acquisition, integration, and dissemination of multimedia biomedical data over the web, thereby reducing the cost of knowledge sharing. There is a lack of high-level web application development tools suitable for use by researchers, clinicians, and educators who are not skilled programmers. Our Web Interfacing Repository Manager (WIRM) is a software toolkit that reduces the complexity of building custom biomedical web applications. WIRM’s visual modeling tools enable domain experts to describe the structure of their knowledge, from which WIRM automatically generates full-featured, customizable content management systems. PMID:12386108

New Software Developments for Quality Mesh Generation and Optimization from Biomedical Imaging Data

PubMed Central

Yu, Zeyun; Wang, Jun; Gao, Zhanheng; Xu, Ming; Hoshijima, Masahiko

2013-01-01

In this paper we present a new software toolkit for generating and optimizing surface and volumetric meshes from three-dimensional (3D) biomedical imaging data, targeted at image-based finite element analysis of some biomedical activities in a single material domain. Our toolkit includes a series of geometric processing algorithms including surface re-meshing and quality-guaranteed tetrahedral mesh generation and optimization. All methods described have been encapsulated into a user-friendly graphical interface for easy manipulation and informative visualization of biomedical images and mesh models. Numerous examples are presented to demonstrate the effectiveness and efficiency of the described methods and toolkit. PMID:24252469

Sounds of silence: How to animate virtual worlds with sound

NASA Technical Reports Server (NTRS)

Astheimer, Peter

1993-01-01

Sounds are an integral and sometimes annoying part of our daily life. Virtual worlds which imitate natural environments gain a lot of authenticity from fast, high quality visualization combined with sound effects. Sounds help to increase the degree of immersion for human dwellers in imaginary worlds significantly. The virtual reality toolkit of IGD (Institute for Computer Graphics) features a broad range of standard visual and advanced real-time audio components which interpret an object-oriented definition of the scene. The virtual reality system 'Virtual Design' realized with the toolkit enables the designer of virtual worlds to create a true audiovisual environment. Several examples on video demonstrate the usage of the audio features in Virtual Design.

The Weather Radar Toolkit, National Oceanic and Atmospheric Administration (NOAA) National Climatic Data Center's support of interoperability and the Global Earth Observation System of Systems (GEOSS)

NASA Astrophysics Data System (ADS)

Ansari, S.; Del Greco, S.

2006-12-01

In February 2005, 61 countries around the World agreed on a 10 year plan to work towards building open systems for sharing geospatial data and services across different platforms worldwide. This system is known as the Global Earth Observation System of Systems (GEOSS). The objective of GEOSS focuses on easy access to environmental data and interoperability across different systems allowing participating countries to measure the "pulse" of the planet in an effort to advance society. In support of GEOSS goals, NOAA's National Climatic Data Center (NCDC) has developed radar visualization and data exporter tools in an open systems environment. The NCDC Weather Radar Toolkit (WRT) loads Weather Surveillance Radar 1988 Doppler (WSR-88D) volume scan (S-band) data, known as Level-II, and derived products, known as Level-III, into an Open Geospatial Consortium (OGC) compliant environment. The application is written entirely in Java and will run on any Java- supported platform including Windows, Macintosh and Linux/Unix. The application is launched via Java Web Start and runs on the client machine while accessing these data locally or remotely from the NCDC archive, NOAA FTP server or any URL or THREDDS Data Server. The WRT allows the data to be manipulated to create custom mosaics, composites and precipitation estimates. The WRT Viewer provides tools for custom data overlays, Web Map Service backgrounds, animations and basic filtering. The export of images and movies is provided in multiple formats. The WRT Data Exporter allows for data export in both vector polygon (Shapefile, Well-Known Text) and raster (GeoTIFF, ESRI Grid, VTK, NetCDF, GrADS) formats. By decoding the various Radar formats into the NetCDF Common Data Model, the exported NetCDF data becomes interoperable with existing software packages including THREDDS Data Server and the Integrated Data Viewer (IDV). The NCDC recently partnered with NOAA's National Severe Storms Lab (NSSL) to decode Sigmet C-band Doppler radar data providing the NCDC Viewer/Data Exporter the functionality to read C-Band. This also supports a bilateral agreement between the United States and Canada for data sharing and to support interoperability with the US WSR-88D and Environment Canada radar networks. In addition, the NCDC partnered with the University of Oklahoma to develop decoders to read a test bed of distributed X- band radars that are funded through the Collaborative Adaptive Sensing of the Atmosphere (CASA) project. The NCDC is also archiving the National Mosaic and Next Generation QPE (Q2) products from NSSL, which provide products such as three-dimensional reflectivity, composite reflectivity and precipitation estimates at a 1 km resolution. These three sources of Radar data are also supported in the WRT.

A Virtual World of Visualization

NASA Technical Reports Server (NTRS)

1998-01-01

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

PsyToolkit: a software package for programming psychological experiments using Linux.

PubMed

Stoet, Gijsbert

2010-11-01

PsyToolkit is a set of software tools for programming psychological experiments on Linux computers. Given that PsyToolkit is freely available under the Gnu Public License, open source, and designed such that it can easily be modified and extended for individual needs, it is suitable not only for technically oriented Linux users, but also for students, researchers on small budgets, and universities in developing countries. The software includes a high-level scripting language, a library for the programming language C, and a questionnaire presenter. The software easily integrates with other open source tools, such as the statistical software package R. PsyToolkit is designed to work with external hardware (including IoLab and Cedrus response keyboards and two common digital input/output boards) and to support millisecond timing precision. Four in-depth examples explain the basic functionality of PsyToolkit. Example 1 demonstrates a stimulus-response compatibility experiment. Example 2 demonstrates a novel mouse-controlled visual search experiment. Example 3 shows how to control light emitting diodes using PsyToolkit, and Example 4 shows how to build a light-detection sensor. The last two examples explain the electronic hardware setup such that they can even be used with other software packages.

Scientific Visualization Using the Flow Analysis Software Toolkit (FAST)

NASA Technical Reports Server (NTRS)

Bancroft, Gordon V.; Kelaita, Paul G.; Mccabe, R. Kevin; Merritt, Fergus J.; Plessel, Todd C.; Sandstrom, Timothy A.; West, John T.

1993-01-01

Over the past few years the Flow Analysis Software Toolkit (FAST) has matured into a useful tool for visualizing and analyzing scientific data on high-performance graphics workstations. Originally designed for visualizing the results of fluid dynamics research, FAST has demonstrated its flexibility by being used in several other areas of scientific research. These research areas include earth and space sciences, acid rain and ozone modelling, and automotive design, just to name a few. This paper describes the current status of FAST, including the basic concepts, architecture, existing functionality and features, and some of the known applications for which FAST is being used. A few of the applications, by both NASA and non-NASA agencies, are outlined in more detail. Described in the Outlines are the goals of each visualization project, the techniques or 'tricks' used lo produce the desired results, and custom modifications to FAST, if any, done to further enhance the analysis. Some of the future directions for FAST are also described.

New software developments for quality mesh generation and optimization from biomedical imaging data.

PubMed

Yu, Zeyun; Wang, Jun; Gao, Zhanheng; Xu, Ming; Hoshijima, Masahiko

2014-01-01

In this paper we present a new software toolkit for generating and optimizing surface and volumetric meshes from three-dimensional (3D) biomedical imaging data, targeted at image-based finite element analysis of some biomedical activities in a single material domain. Our toolkit includes a series of geometric processing algorithms including surface re-meshing and quality-guaranteed tetrahedral mesh generation and optimization. All methods described have been encapsulated into a user-friendly graphical interface for easy manipulation and informative visualization of biomedical images and mesh models. Numerous examples are presented to demonstrate the effectiveness and efficiency of the described methods and toolkit. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Vcs.js - Visualization Control System for the Web

NASA Astrophysics Data System (ADS)

Chaudhary, A.; Lipsa, D.; Doutriaux, C.; Beezley, J. D.; Williams, D. N.; Fries, S.; Harris, M. B.

2016-12-01

VCS is a general purpose visualization library, optimized for climate data, which is part of the UV-CDAT system. It provides a Python API for drawing 2D plots such as lineplots, scatter plots, Taylor diagrams, data colored by scalar values, vector glyphs, isocontours and map projections. VCS is based on the VTK library. Vcs.js is the corresponding JavaScript API, designed to be as close as possible to the original VCS Python API and to provide similar functionality for the Web. Vcs.js includes additional functionality when compared with VCS. This additional API is used to introspect data files available on the server and variables available in a data file. Vcs.js can display plots in the browser window. It always works with a server that reads a data file, extracts variables from the file and subsets the data. From this point, two alternate paths are possible. First the system can render the data on the server using VCS producing an image which is send to the browser to be displayed. This path works for for all plot types and produces a reference image identical with the images produced by VCS. This path uses the VTK-Web library. As an optimization, usable in certain conditions, a second path is possible. Data is packed, and sent to the browser which uses a JavaScript plotting library, such as plotly, to display the data. Plots that work well in the browser are line-plots, scatter-plots for any data and many other plot types for small data and supported grid types. As web technology matures, more plots could be supported for rendering in the browser. Rendering can be done either on the client or on the server and we expect that the best place to render will change depending on the available web technology, data transfer costs, server management costs and value provided to users. We intend to provide a flexible solution that allows for both client and server side rendering and a meaningful way to choose between the two. We provide a web-based user interface called vCdat which uses Vcs.js as its visualization library. Our paper will discuss the principles guiding our design choices for Vcs.js, present our design in detail and show a sample usage of the library.

A new open-source Python-based Space Weather data access, visualization, and analysis toolkit

NASA Astrophysics Data System (ADS)

de Larquier, S.; Ribeiro, A.; Frissell, N. A.; Spaleta, J.; Kunduri, B.; Thomas, E. G.; Ruohoniemi, J.; Baker, J. B.

2013-12-01

Space weather research relies heavily on combining and comparing data from multiple observational platforms. Current frameworks exist to aggregate some of the data sources, most based on file downloads via web or ftp interfaces. Empirical models are mostly fortran based and lack interfaces with more useful scripting languages. In an effort to improve data and model access, the SuperDARN community has been developing a Python-based Space Science Data Visualization Toolkit (DaViTpy). At the center of this development was a redesign of how our data (from 30 years of SuperDARN radars) was made available. Several access solutions are now wrapped into one convenient Python interface which probes local directories, a new remote NoSQL database, and an FTP server to retrieve the requested data based on availability. Motivated by the efficiency of this interface and the inherent need for data from multiple instruments, we implemented similar modules for other space science datasets (POES, OMNI, Kp, AE...), and also included fundamental empirical models with Python interfaces to enhance data analysis (IRI, HWM, MSIS...). All these modules and more are gathered in a single convenient toolkit, which is collaboratively developed and distributed using Github and continues to grow. While still in its early stages, we expect this toolkit will facilitate multi-instrument space weather research and improve scientific productivity.

Recent developments in Geant4

DOE PAGES

Allison, J.; Amako, K.; Apostolakis, J.; ...

2016-07-01

Geant4 is a software toolkit for the simulation of the passage of particles through matter. It is used by a large number of experiments and projects in a variety of application domains, including high energy physics, astrophysics and space science, medical physics and radiation protection. Over the past several years, major changes have been made to the toolkit in order to accommodate the needs of these user communities, and to efficiently exploit the growth of computing power made available by advances in technology. In conclusion, the adaptation of Geant4 to multithreading, advances in physics, detector modeling and visualization, extensions tomore » the toolkit, including biasing and reverse Monte Carlo, and tools for physics and release validation are discussed here.« less

Assessing the effectiveness of the Pesticides and Farmworker Health Toolkit: a curriculum for enhancing farmworkers' understanding of pesticide safety concepts.

PubMed

LePrevost, Catherine E; Storm, Julia F; Asuaje, Cesar R; Arellano, Consuelo; Cope, W Gregory

2014-01-01

Among agricultural workers, migrant and seasonal farmworkers have been recognized as a special risk population because these laborers encounter cultural challenges and linguistic barriers while attempting to maintain their safety and health within their working environments. The crop-specific Pesticides and Farmworker Health Toolkit (Toolkit) is a pesticide safety and health curriculum designed to communicate to farmworkers pesticide hazards commonly found in their working environments and to address Worker Protection Standard (WPS) pesticide training criteria for agricultural workers. The goal of this preliminary study was to test evaluation items for measuring knowledge increases among farmworkers and to assess the effectiveness of the Toolkit in improving farmworkers' knowledge of key WPS and risk communication concepts when the Toolkit lesson was delivered by trained trainers in the field. After receiving training on the curriculum, four participating trainers provided lessons using the Toolkit as part of their regular training responsibilities and orally administered a pre- and post-lesson evaluation instrument to 20 farmworker volunteers who were generally representative of the national farmworker population. Farmworker knowledge of pesticide safety messages significantly (P<.05) increased after participation in the lesson. Further, items with visual alternatives were found to be most useful in discriminating between more and less knowledgeable farmworkers. The pilot study suggests that the Pesticides and Farmworker Health Toolkit is an effective, research-based pesticide safety and health intervention for the at-risk farmworker population and identifies a testing format appropriate for evaluating the Toolkit and other similar interventions for farmworkers in the field.

SU-E-T-279: Realization of Three-Dimensional Conformal Dose Planning in Prostate Brachytherapy

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

Li, Z; Jiang, S; Yang, Z

2014-06-01

Purpose: Successful clinical treatment in prostate brachytherapy is largely dependent on the effectiveness of pre-surgery dose planning. Conventional dose planning method could hardly arrive at a satisfy result. In this abstract, a three-dimensional conformal localized dose planning method is put forward to ensure the accuracy and effectiveness of pre-implantation dose planning. Methods: Using Monte Carlo method, the pre-calculated 3-D dose map for single source is obtained. As for multiple seeds dose distribution, the maps are combined linearly to acquire the 3-D distribution. The 3-D dose distribution is exhibited in the form of isodose surface together with reconstructed 3-D organs groupmore » real-timely. Then it is possible to observe the dose exposure to target volume and normal tissues intuitively, thus achieving maximum dose irradiation to treatment target and minimum healthy tissues damage. In addition, the exfoliation display of different isodose surfaces can be realized applying multi-values contour extraction algorithm based on voxels. The needles could be displayed in the system by tracking the position of the implanted seeds in real time to conduct block research in optimizing insertion trajectory. Results: This study extends dose planning from two-dimensional to three-dimensional, realizing the three-dimensional conformal irradiation, which could eliminate the limitations of 2-D images and two-dimensional dose planning. A software platform is developed using VC++ and Visualization Toolkit (VTK) to perform dose planning. The 3-D model reconstruction time is within three seconds (on a Intel Core i5 PC). Block research could be conducted to avoid inaccurate insertion into sensitive organs or internal obstructions. Experiments on eight prostate cancer cases prove that this study could make the dose planning results more reasonable. Conclusion: The three-dimensional conformal dose planning method could improve the rationality of dose planning by safely reducing the large target margin and avoiding dose dead zones for prostate cancer treatment. 1) National Natural Science Foundation of People's Republic of China (No. 51175373); 2) New Century Educational Talents Plan of Chinese Education Ministry (NCET-10-0625); 3) Scientific and Technological Major Project, Tianjin (No. 12ZCDZSY10600)« less

SU-E-T-362: Automatic Catheter Reconstruction of Flap Applicators in HDR Surface Brachytherapy

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

Buzurovic, I; Devlin, P; Hansen, J

2014-06-01

Purpose: Catheter reconstruction is crucial for the accurate delivery of radiation dose in HDR brachytherapy. The process becomes complicated and time-consuming for large superficial clinical targets with a complex topology. A novel method for the automatic catheter reconstruction of flap applicators is proposed in this study. Methods: We have developed a program package capable of image manipulation, using C++class libraries of The-Visualization-Toolkit(VTK) software system. The workflow for automatic catheter reconstruction is: a)an anchor point is placed in 3D or in the axial view of the first slice at the tip of the first, last and middle points for the curvedmore » surface; b)similar points are placed on the last slice of the image set; c)the surface detection algorithm automatically registers the points to the images and applies the surface reconstruction filter; d)then a structured grid surface is generated through the center of the treatment catheters placed at a distance of 5mm from the patient's skin. As a result, a mesh-style plane is generated with the reconstructed catheters placed 10mm apart. To demonstrate automatic catheter reconstruction, we used CT images of patients diagnosed with cutaneous T-cell-lymphoma and imaged with Freiburg-Flap-Applicators (Nucletron™-Elekta, Netherlands). The coordinates for each catheter were generated and compared to the control points selected during the manual reconstruction for 16catheters and 368control point Results: The variation of the catheter tip positions between the automatically and manually reconstructed catheters was 0.17mm(SD=0.23mm). The position difference between the manually selected catheter control points and the corresponding points obtained automatically was 0.17mm in the x-direction (SD=0.23mm), 0.13mm in the y-direction (SD=0.22mm), and 0.14mm in the z-direction (SD=0.24mm). Conclusion: This study shows the feasibility of the automatic catheter reconstruction of flap applicators with a high level of positioning accuracy. Implementation of this technique has potential to decrease the planning time and may improve overall quality in superficial brachytherapy.« less

LibIsopach

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

Brunhart-Lupo, Nicholas

2016-12-06

LibIsopach is a toolkit for high performance distributed immersive visualization, leveraging modern OpenGL. It features a multi-process scenegraph, explicit instance rendering, mesh generation, and three-dimensional user interaction event processing.

3D Simulation of External Flooding Events for the RISMC Pathway

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

Prescott, Steven; Mandelli, Diego; Sampath, Ramprasad

2015-09-01

Incorporating 3D simulations as part of the Risk-Informed Safety Margins Characterization (RISMIC) Toolkit allows analysts to obtain a more complete picture of complex system behavior for events including external plant hazards. External events such as flooding have become more important recently – however these can be analyzed with existing and validated simulated physics toolkits. In this report, we describe these approaches specific to flooding-based analysis using an approach called Smoothed Particle Hydrodynamics. The theory, validation, and example applications of the 3D flooding simulation are described. Integrating these 3D simulation methods into computational risk analysis provides a spatial/visual aspect to themore » design, improves the realism of results, and can prove visual understanding to validate the analysis of flooding.« less

A Drosophila Toolkit for the Visualization and Quantification of Viral Replication Launched from Transgenic Genomes

PubMed Central

Wernet, Mathias F.; Klovstad, Martha; Clandinin, Thomas R.

2014-01-01

Arthropod RNA viruses pose a serious threat to human health, yet many aspects of their replication cycle remain incompletely understood. Here we describe a versatile Drosophila toolkit of transgenic, self-replicating genomes (‘replicons’) from Sindbis virus that allow rapid visualization and quantification of viral replication in vivo. We generated replicons expressing Luciferase for the quantification of viral replication, serving as useful new tools for large-scale genetic screens for identifying cellular pathways that influence viral replication. We also present a new binary system in which replication-deficient viral genomes can be activated ‘in trans’, through co-expression of an intact replicon contributing an RNA-dependent RNA polymerase. The utility of this toolkit for studying virus biology is demonstrated by the observation of stochastic exclusion between replicons expressing different fluorescent proteins, when co-expressed under control of the same cellular promoter. This process is analogous to ‘superinfection exclusion’ between virus particles in cell culture, a process that is incompletely understood. We show that viral polymerases strongly prefer to replicate the genome that encoded them, and that almost invariably only a single virus genome is stochastically chosen for replication in each cell. Our in vivo system now makes this process amenable to detailed genetic dissection. Thus, this toolkit allows the cell-type specific, quantitative study of viral replication in a genetic model organism, opening new avenues for molecular, genetic and pharmacological dissection of virus biology and tool development. PMID:25386852

Technical note: DIRART--A software suite for deformable image registration and adaptive radiotherapy research.

PubMed

Yang, Deshan; Brame, Scott; El Naqa, Issam; Aditya, Apte; Wu, Yu; Goddu, S Murty; Mutic, Sasa; Deasy, Joseph O; Low, Daniel A

2011-01-01

Recent years have witnessed tremendous progress in image guide radiotherapy technology and a growing interest in the possibilities for adapting treatment planning and delivery over the course of treatment. One obstacle faced by the research community has been the lack of a comprehensive open-source software toolkit dedicated for adaptive radiotherapy (ART). To address this need, the authors have developed a software suite called the Deformable Image Registration and Adaptive Radiotherapy Toolkit (DIRART). DIRART is an open-source toolkit developed in MATLAB. It is designed in an object-oriented style with focus on user-friendliness, features, and flexibility. It contains four classes of DIR algorithms, including the newer inverse consistency algorithms to provide consistent displacement vector field in both directions. It also contains common ART functions, an integrated graphical user interface, a variety of visualization and image-processing features, dose metric analysis functions, and interface routines. These interface routines make DIRART a powerful complement to the Computational Environment for Radiotherapy Research (CERR) and popular image-processing toolkits such as ITK. DIRART provides a set of image processing/registration algorithms and postprocessing functions to facilitate the development and testing of DIR algorithms. It also offers a good amount of options for DIR results visualization, evaluation, and validation. By exchanging data with treatment planning systems via DICOM-RT files and CERR, and by bringing image registration algorithms closer to radiotherapy applications, DIRART is potentially a convenient and flexible platform that may facilitate ART and DIR research. 0 2011 Ameri-

Data visualization and analysis tools for the MAVEN mission

NASA Astrophysics Data System (ADS)

Harter, B.; De Wolfe, A. W.; Putnam, B.; Brain, D.; Chaffin, M.

2016-12-01

The Mars Atmospheric and Volatile Evolution (MAVEN) mission has been collecting data at Mars since September 2014. We have developed new software tools for exploring and analyzing the science data. Our open-source Python toolkit for working with data from MAVEN and other missions is based on the widely-used "tplot" IDL toolkit. We have replicated all of the basic tplot functionality in Python, and use the bokeh and matplotlib libraries to generate interactive line plots and spectrograms, providing additional functionality beyond the capabilities of IDL graphics. These Python tools are generalized to work with missions beyond MAVEN, and our software is available on Github. We have also been exploring 3D graphics as a way to better visualize the MAVEN science data and models. We have constructed a 3D visualization of MAVEN's orbit using the CesiumJS library, which not only allows viewing of MAVEN's orientation and position, but also allows the display of selected science data sets and their variation over time.

Biomechanical ToolKit: Open-source framework to visualize and process biomechanical data.

PubMed

Barre, Arnaud; Armand, Stéphane

2014-04-01

C3D file format is widely used in the biomechanical field by companies and laboratories to store motion capture systems data. However, few software packages can visualize and modify the integrality of the data in the C3D file. Our objective was to develop an open-source and multi-platform framework to read, write, modify and visualize data from any motion analysis systems using standard (C3D) and proprietary file formats (used by many companies producing motion capture systems). The Biomechanical ToolKit (BTK) was developed to provide cost-effective and efficient tools for the biomechanical community to easily deal with motion analysis data. A large panel of operations is available to read, modify and process data through C++ API, bindings for high-level languages (Matlab, Octave, and Python), and standalone application (Mokka). All these tools are open-source and cross-platform and run on all major operating systems (Windows, Linux, MacOS X). Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

SlicerRT: radiation therapy research toolkit for 3D Slicer.

PubMed

Pinter, Csaba; Lasso, Andras; Wang, An; Jaffray, David; Fichtinger, Gabor

2012-10-01

Interest in adaptive radiation therapy research is constantly growing, but software tools available for researchers are mostly either expensive, closed proprietary applications, or free open-source packages with limited scope, extensibility, reliability, or user support. To address these limitations, we propose SlicerRT, a customizable, free, and open-source radiation therapy research toolkit. SlicerRT aspires to be an open-source toolkit for RT research, providing fast computations, convenient workflows for researchers, and a general image-guided therapy infrastructure to assist clinical translation of experimental therapeutic approaches. It is a medium into which RT researchers can integrate their methods and algorithms, and conduct comparative testing. SlicerRT was implemented as an extension for the widely used 3D Slicer medical image visualization and analysis application platform. SlicerRT provides functionality specifically designed for radiation therapy research, in addition to the powerful tools that 3D Slicer offers for visualization, registration, segmentation, and data management. The feature set of SlicerRT was defined through consensus discussions with a large pool of RT researchers, including both radiation oncologists and medical physicists. The development processes used were similar to those of 3D Slicer to ensure software quality. Standardized mechanisms of 3D Slicer were applied for documentation, distribution, and user support. The testing and validation environment was configured to automatically launch a regression test upon each software change and to perform comparison with ground truth results provided by other RT applications. Modules have been created for importing and loading DICOM-RT data, computing and displaying dose volume histograms, creating accumulated dose volumes, comparing dose volumes, and visualizing isodose lines and surfaces. The effectiveness of using 3D Slicer with the proposed SlicerRT extension for radiation therapy research was demonstrated on multiple use cases. A new open-source software toolkit has been developed for radiation therapy research. SlicerRT can import treatment plans from various sources into 3D Slicer for visualization, analysis, comparison, and processing. The provided algorithms are extensively tested and they are accessible through a convenient graphical user interface as well as a flexible application programming interface.

Octopus-toolkit: a workflow to automate mining of public epigenomic and transcriptomic next-generation sequencing data

PubMed Central

Kim, Taemook; Seo, Hogyu David; Hennighausen, Lothar; Lee, Daeyoup

2018-01-01

Abstract Octopus-toolkit is a stand-alone application for retrieving and processing large sets of next-generation sequencing (NGS) data with a single step. Octopus-toolkit is an automated set-up-and-analysis pipeline utilizing the Aspera, SRA Toolkit, FastQC, Trimmomatic, HISAT2, STAR, Samtools, and HOMER applications. All the applications are installed on the user's computer when the program starts. Upon the installation, it can automatically retrieve original files of various epigenomic and transcriptomic data sets, including ChIP-seq, ATAC-seq, DNase-seq, MeDIP-seq, MNase-seq and RNA-seq, from the gene expression omnibus data repository. The downloaded files can then be sequentially processed to generate BAM and BigWig files, which are used for advanced analyses and visualization. Currently, it can process NGS data from popular model genomes such as, human (Homo sapiens), mouse (Mus musculus), dog (Canis lupus familiaris), plant (Arabidopsis thaliana), zebrafish (Danio rerio), fruit fly (Drosophila melanogaster), worm (Caenorhabditis elegans), and budding yeast (Saccharomyces cerevisiae) genomes. With the processed files from Octopus-toolkit, the meta-analysis of various data sets, motif searches for DNA-binding proteins, and the identification of differentially expressed genes and/or protein-binding sites can be easily conducted with few commands by users. Overall, Octopus-toolkit facilitates the systematic and integrative analysis of available epigenomic and transcriptomic NGS big data. PMID:29420797

Analysis and visualization of intracardiac electrograms in diagnosis and research: Concept and application of KaPAVIE.

PubMed

Oesterlein, Tobias Georg; Schmid, Jochen; Bauer, Silvio; Jadidi, Amir; Schmitt, Claus; Dössel, Olaf; Luik, Armin

2016-04-01

Progress in biomedical engineering has improved the hardware available for diagnosis and treatment of cardiac arrhythmias. But although huge amounts of intracardiac electrograms (EGMs) can be acquired during electrophysiological examinations, there is still a lack of software aiding diagnosis. The development of novel algorithms for the automated analysis of EGMs has proven difficult, due to the highly interdisciplinary nature of this task and hampered data access in clinical systems. Thus we developed a software platform, which allows rapid implementation of new algorithms, verification of their functionality and suitable visualization for discussion in the clinical environment. A software for visualization was developed in Qt5 and C++ utilizing the class library of VTK. The algorithms for signal analysis were implemented in MATLAB. Clinical data for analysis was exported from electroanatomical mapping systems. The visualization software KaPAVIE (Karlsruhe Platform for Analysis and Visualization of Intracardiac Electrograms) was implemented and tested on several clinical datasets. Both common and novel algorithms were implemented which address important clinical questions in diagnosis of different arrhythmias. It proved useful in discussions with clinicians due to its interactive and user-friendly design. Time after export from the clinical mapping system to visualization is below 5min. KaPAVIE(2) is a powerful platform for the development of novel algorithms in the clinical environment. Simultaneous and interactive visualization of measured EGM data and the results of analysis will aid diagnosis and help understanding the underlying mechanisms of complex arrhythmias like atrial fibrillation. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

[Research on Three-dimensional Medical Image Reconstruction and Interaction Based on HTML5 and Visualization Toolkit].

PubMed

Gao, Peng; Liu, Peng; Su, Hongsen; Qiao, Liang

2015-04-01

Integrating visualization toolkit and the capability of interaction, bidirectional communication and graphics rendering which provided by HTML5, we explored and experimented on the feasibility of remote medical image reconstruction and interaction in pure Web. We prompted server-centric method which did not need to download the big medical data to local connections and avoided considering network transmission pressure and the three-dimensional (3D) rendering capability of client hardware. The method integrated remote medical image reconstruction and interaction into Web seamlessly, which was applicable to lower-end computers and mobile devices. Finally, we tested this method in the Internet and achieved real-time effects. This Web-based 3D reconstruction and interaction method, which crosses over internet terminals and performance limited devices, may be useful for remote medical assistant.

MITK-OpenIGTLink for combining open-source toolkits in real-time computer-assisted interventions.

PubMed

Klemm, Martin; Kirchner, Thomas; Gröhl, Janek; Cheray, Dominique; Nolden, Marco; Seitel, Alexander; Hoppe, Harald; Maier-Hein, Lena; Franz, Alfred M

2017-03-01

Due to rapid developments in the research areas of medical imaging, medical image processing and robotics, computer-assisted interventions (CAI) are becoming an integral part of modern patient care. From a software engineering point of view, these systems are highly complex and research can benefit greatly from reusing software components. This is supported by a number of open-source toolkits for medical imaging and CAI such as the medical imaging interaction toolkit (MITK), the public software library for ultrasound imaging research (PLUS) and 3D Slicer. An independent inter-toolkit communication such as the open image-guided therapy link (OpenIGTLink) can be used to combine the advantages of these toolkits and enable an easier realization of a clinical CAI workflow. MITK-OpenIGTLink is presented as a network interface within MITK that allows easy to use, asynchronous two-way messaging between MITK and clinical devices or other toolkits. Performance and interoperability tests with MITK-OpenIGTLink were carried out considering the whole CAI workflow from data acquisition over processing to visualization. We present how MITK-OpenIGTLink can be applied in different usage scenarios. In performance tests, tracking data were transmitted with a frame rate of up to 1000 Hz and a latency of 2.81 ms. Transmission of images with typical ultrasound (US) and greyscale high-definition (HD) resolutions of [Formula: see text] and [Formula: see text] is possible at up to 512 and 128 Hz, respectively. With the integration of OpenIGTLink into MITK, this protocol is now supported by all established open-source toolkits in the field. This eases interoperability between MITK and toolkits such as PLUS or 3D Slicer and facilitates cross-toolkit research collaborations. MITK and its submodule MITK-OpenIGTLink are provided open source under a BSD-style licence ( http://mitk.org ).

Monitoring Areal Snow Cover Using NASA Satellite Imagery

NASA Technical Reports Server (NTRS)

Harshburger, Brian J.; Blandford, Troy; Moore, Brandon

2011-01-01

The objective of this project is to develop products and tools to assist in the hydrologic modeling process, including tools to help prepare inputs for hydrologic models and improved methods for the visualization of streamflow forecasts. In addition, this project will facilitate the use of NASA satellite imagery (primarily snow cover imagery) by other federal and state agencies with operational streamflow forecasting responsibilities. A GIS software toolkit for monitoring areal snow cover extent and producing streamflow forecasts is being developed. This toolkit will be packaged as multiple extensions for ArcGIS 9.x and an opensource GIS software package. The toolkit will provide users with a means for ingesting NASA EOS satellite imagery (snow cover analysis), preparing hydrologic model inputs, and visualizing streamflow forecasts. Primary products include a software tool for predicting the presence of snow under clouds in satellite images; a software tool for producing gridded temperature and precipitation forecasts; and a suite of tools for visualizing hydrologic model forecasting results. The toolkit will be an expert system designed for operational users that need to generate accurate streamflow forecasts in a timely manner. The Remote Sensing of Snow Cover Toolbar will ingest snow cover imagery from multiple sources, including the MODIS Operational Snowcover Data and convert them to gridded datasets that can be readily used. Statistical techniques will then be applied to the gridded snow cover data to predict the presence of snow under cloud cover. The toolbar has the ability to ingest both binary and fractional snow cover data. Binary mapping techniques use a set of thresholds to determine whether a pixel contains snow or no snow. Fractional mapping techniques provide information regarding the percentage of each pixel that is covered with snow. After the imagery has been ingested, physiographic data is attached to each cell in the snow cover image. This data can be obtained from a digital elevation model (DEM) for the area of interest.

The Montage Image Mosaic Toolkit As A Visualization Engine.

NASA Astrophysics Data System (ADS)

Berriman, G. Bruce; Lerias, Angela; Good, John; Mandel, Eric; Pepper, Joshua

2018-01-01

The Montage toolkit has since 2003 been used to aggregate FITS images into mosaics for science analysis. It is now finding application as an engine for image visualization. One important reason is that the functionality developed for creating mosaics is also valuable in image visualization. An equally important (though perhaps less obvious) reason is that Montage is portable and is built on standard astrophysics toolkits, making it very easy to integrate into new environments. Montage models and rectifies the sky background to a common level and thus reveals faint, diffuse features; it offers an adaptive image stretching method that preserves the dynamic range of a FITS image when represented in PNG format; it provides utilities for creating cutouts of large images and downsampled versions of large images that can then be visualized on desktops or in browsers; it contains a fast reprojection algorithm intended for visualization; and it resamples and reprojects images to a common grid for subsequent multi-color visualization.This poster will highlight these visualization capabilities with the following examples:1. Creation of down-sampled multi-color images of a 16-wavelength Infrared Atlas of the Galactic Plane, sampled at 1 arcsec when created2. Integration into web-based image processing environment: JS9 is an interactive image display service for web browsers, desktops and mobile devices. It exploits the flux-preserving reprojection algorithms in Montage to transform diverse images to common image parameters for display. Select Montage programs have been compiled to Javascript/WebAssembly using the Emscripten compiler, which allows our reprojection algorithms to run in browsers at close to native speed.3. Creation of complex sky coverage maps: an multicolor all-sky map that shows the sky coverage of the Kepler and K2, KELT and TESS projects, overlaid on an all-sky 2MASS image.Montage is funded by the National Science Foundation under Grant Number ACI-1642453. JS9 is funded by the Chandra X-ray Center (NAS8-03060) and NASA's Universe of Learning (STScI-509913).

Generic Space Science Visualization in 2D/3D using SDDAS

NASA Astrophysics Data System (ADS)

Mukherjee, J.; Murphy, Z. B.; Gonzalez, C. A.; Muller, M.; Ybarra, S.

2017-12-01

The Southwest Data Display and Analysis System (SDDAS) is a flexible multi-mission / multi-instrument software system intended to support space physics data analysis, and has been in active development for over 20 years. For the Magnetospheric Multi-Scale (MMS), Juno, Cluster, and Mars Express missions, we have modified these generic tools for visualizing data in two and three dimensions. The SDDAS software is open source and makes use of various other open source packages, including VTK and Qwt. The software offers interactive plotting as well as a Python and Lua module to modify the data before plotting. In theory, by writing a Lua or Python module to read the data, any data could be used. Currently, the software can natively read data in IDFS, CEF, CDF, FITS, SEG-Y, ASCII, and XLS formats. We have integrated the software with other Python packages such as SPICE and SpacePy. Included with the visualization software is a database application and other utilities for managing data that can retrieve data from the Cluster Active Archive and Space Physics Data Facility at Goddard, as well as other local archives. Line plots, spectrograms, geographic, volume plots, strip charts, etc. are just some of the types of plots one can generate with SDDAS. Furthermore, due to the design, output is not limited to strictly visualization as SDDAS can also be used to generate stand-alone IDL or Python visualization code.. Lastly, SDDAS has been successfully used as a backend for several web based analysis systems as well.

Technical Note: DIRART – A software suite for deformable image registration and adaptive radiotherapy research

PubMed Central

Yang, Deshan; Brame, Scott; El Naqa, Issam; Aditya, Apte; Wu, Yu; Murty Goddu, S.; Mutic, Sasa; Deasy, Joseph O.; Low, Daniel A.

2011-01-01

Purpose: Recent years have witnessed tremendous progress in image guide radiotherapy technology and a growing interest in the possibilities for adapting treatment planning and delivery over the course of treatment. One obstacle faced by the research community has been the lack of a comprehensive open-source software toolkit dedicated for adaptive radiotherapy (ART). To address this need, the authors have developed a software suite called the Deformable Image Registration and Adaptive Radiotherapy Toolkit (DIRART). Methods:DIRART is an open-source toolkit developed in MATLAB. It is designed in an object-oriented style with focus on user-friendliness, features, and flexibility. It contains four classes of DIR algorithms, including the newer inverse consistency algorithms to provide consistent displacement vector field in both directions. It also contains common ART functions, an integrated graphical user interface, a variety of visualization and image-processing features, dose metric analysis functions, and interface routines. These interface routines make DIRART a powerful complement to the Computational Environment for Radiotherapy Research (CERR) and popular image-processing toolkits such as ITK. Results: DIRART provides a set of image processing∕registration algorithms and postprocessing functions to facilitate the development and testing of DIR algorithms. It also offers a good amount of options for DIR results visualization, evaluation, and validation. Conclusions: By exchanging data with treatment planning systems via DICOM-RT files and CERR, and by bringing image registration algorithms closer to radiotherapy applications, DIRART is potentially a convenient and flexible platform that may facilitate ART and DIR research. PMID:21361176

Genetic Engineering of Bee Gut Microbiome Bacteria with a Toolkit for Modular Assembly of Broad-Host-Range Plasmids.

PubMed

Leonard, Sean P; Perutka, Jiri; Powell, J Elijah; Geng, Peng; Richhart, Darby D; Byrom, Michelle; Kar, Shaunak; Davies, Bryan W; Ellington, Andrew D; Moran, Nancy A; Barrick, Jeffrey E

2018-05-18

Engineering the bacteria present in animal microbiomes promises to lead to breakthroughs in medicine and agriculture, but progress is hampered by a dearth of tools for genetically modifying the diverse species that comprise these communities. Here we present a toolkit of genetic parts for the modular construction of broad-host-range plasmids built around the RSF1010 replicon. Golden Gate assembly of parts in this toolkit can be used to rapidly test various antibiotic resistance markers, promoters, fluorescent reporters, and other coding sequences in newly isolated bacteria. We demonstrate the utility of this toolkit in multiple species of Proteobacteria that are native to the gut microbiomes of honey bees ( Apis mellifera) and bumble bees (B ombus sp.). Expressing fluorescent proteins in Snodgrassella alvi, Gilliamella apicola, Bartonella apis, and Serratia strains enables us to visualize how these bacteria colonize the bee gut. We also demonstrate CRISPRi repression in B. apis and use Cas9-facilitated knockout of an S. alvi adhesion gene to show that it is important for colonization of the gut. Beyond characterizing how the gut microbiome influences the health of these prominent pollinators, this bee microbiome toolkit (BTK) will be useful for engineering bacteria found in other natural microbial communities.

Multimodal Virtual Environments: MAGIC Toolkit and Visual-Haptic Interaction Paradigms

DTIC Science & Technology

1998-01-01

2.7.3 Load/Save Options ..... 2.7.4 Information Display .... 2.8 Library Files. 2.9 Evaluation .............. 3 Visual-Haptic Interactions 3.1...Northwestern University[ Colgate , 1994]. It is possible for a user to touch one side of a thin object and be propelled out the opposite side, because...when there is a high correlation in motion and force between the visual and haptic realms. * Chapter 7 concludes with an evaluation of the application

Creating CAD designs and performing their subsequent analysis using opensource solutions in Python

NASA Astrophysics Data System (ADS)

Iakushkin, Oleg O.; Sedova, Olga S.

2018-01-01

The paper discusses the concept of a system that encapsulates the transition from geometry building to strength tests. The solution we propose views the engineer as a programmer who is capable of coding the procedure for working with the modeli.e., to outline the necessary transformations and create cases for boundary conditions. We propose a prototype of such system. In our work, we used: Python programming language to create the program; Jupyter framework to create a single workspace visualization; pythonOCC library to implement CAD; FeniCS library to implement FEM; GMSH and VTK utilities. The prototype is launched on a platform which is a dynamically expandable multi-tenant cloud service providing users with all computing resources on demand. However, the system may be deployed locally for prototyping or work that does not involve resource-intensive computing. To make it possible, we used containerization, isolating the system in a Docker container.

2016 CSSE L3 Milestone: Deliver In Situ to XTD End Users

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

Patchett, John M.; Nouanesengsy, Boonthanome; Fasel, Patricia Kroll

This report summarizes the activities in FY16 toward satisfying the CSSE 2016 L3 milestone to deliver in situ to XTD end users of EAP codes. The Milestone was accomplished with ongoing work to ensure the capability is maintained and developed. Two XTD end users used the in situ capability in Rage. A production ParaView capability was created in the HPC and Desktop environment. Two new capabilities were added to ParaView in support of an EAP in situ workflow. We also worked with various support groups at the lab to deploy a production ParaView in the LANL environment for both desktopmore » and HPC systems. . In addition, for this milestone, we moved two VTK based filters from research objects into the production ParaView code to support a variety of standard visualization pipelines for our EAP codes.« less

Game engines and immersive displays

NASA Astrophysics Data System (ADS)

Chang, Benjamin; Destefano, Marc

2014-02-01

While virtual reality and digital games share many core technologies, the programming environments, toolkits, and workflows for developing games and VR environments are often distinct. VR toolkits designed for applications in visualization and simulation often have a different feature set or design philosophy than game engines, while popular game engines often lack support for VR hardware. Extending a game engine to support systems such as the CAVE gives developers a unified development environment and the ability to easily port projects, but involves challenges beyond just adding stereo 3D visuals. In this paper we outline the issues involved in adapting a game engine for use with an immersive display system including stereoscopy, tracking, and clustering, and present example implementation details using Unity3D. We discuss application development and workflow approaches including camera management, rendering synchronization, GUI design, and issues specific to Unity3D, and present examples of projects created for a multi-wall, clustered, stereoscopic display.

Image processing, geometric modeling and data management for development of a virtual bone surgery system.

PubMed

Niu, Qiang; Chi, Xiaoyi; Leu, Ming C; Ochoa, Jorge

2008-01-01

This paper describes image processing, geometric modeling and data management techniques for the development of a virtual bone surgery system. Image segmentation is used to divide CT scan data into different segments representing various regions of the bone. A region-growing algorithm is used to extract cortical bone and trabecular bone structures systematically and efficiently. Volume modeling is then used to represent the bone geometry based on the CT scan data. Material removal simulation is achieved by continuously performing Boolean subtraction of the surgical tool model from the bone model. A quadtree-based adaptive subdivision technique is developed to handle the large set of data in order to achieve the real-time simulation and visualization required for virtual bone surgery. A Marching Cubes algorithm is used to generate polygonal faces from the volumetric data. Rendering of the generated polygons is performed with the publicly available VTK (Visualization Tool Kit) software. Implementation of the developed techniques consists of developing a virtual bone-drilling software program, which allows the user to manipulate a virtual drill to make holes with the use of a PHANToM device on a bone model derived from real CT scan data.

First responder tracking and visualization for command and control toolkit

NASA Astrophysics Data System (ADS)

Woodley, Robert; Petrov, Plamen; Meisinger, Roger

2010-04-01

In order for First Responder Command and Control personnel to visualize incidents at urban building locations, DHS sponsored a small business research program to develop a tool to visualize 3D building interiors and movement of First Responders on site. 21st Century Systems, Inc. (21CSI), has developed a toolkit called Hierarchical Grid Referenced Normalized Display (HiGRND). HiGRND utilizes three components to provide a full spectrum of visualization tools to the First Responder. First, HiGRND visualizes the structure in 3D. Utilities in the 3D environment allow the user to switch between views (2D floor plans, 3D spatial, evacuation routes, etc.) and manually edit fast changing environments. HiGRND accepts CAD drawings and 3D digital objects and renders these in the 3D space. Second, HiGRND has a First Responder tracker that uses the transponder signals from First Responders to locate them in the virtual space. We use the movements of the First Responder to map the interior of structures. Finally, HiGRND can turn 2D blueprints into 3D objects. The 3D extruder extracts walls, symbols, and text from scanned blueprints to create the 3D mesh of the building. HiGRND increases the situational awareness of First Responders and allows them to make better, faster decisions in critical urban situations.

galstreams: Milky Way streams footprint library and toolkit

NASA Astrophysics Data System (ADS)

Mateu, Cecilia

2017-11-01

galstreams provides a compilation of spatial information for known stellar streams and overdensities in the Milky Way and includes Python tools for visualizing them. ASCII tables are also provided for quick viewing of the stream's footprints using TOPCAT (ascl:1101.010).

Assessing GPS Constellation Resiliency in an Urban Canyon Environment

DTIC Science & Technology

2015-03-26

Taipei, Taiwan as his area of interest. His GPS constellation is modeled in the Satellite Toolkit ( STK ) where augmentation satellites can be added and...interaction. SEAS also provides a visual display of the simulation which is useful for verification and debugging portions of the analysis. Furthermore...entire system. Interpreting the model is aided by the visual display of the agents moving in the region of inter- est. Furthermore, SEAS collects

FATES: a flexible analysis toolkit for the exploration of single-particle mass spectrometer data

NASA Astrophysics Data System (ADS)

Sultana, Camille M.; Cornwell, Gavin C.; Rodriguez, Paul; Prather, Kimberly A.

2017-04-01

Single-particle mass spectrometer (SPMS) analysis of aerosols has become increasingly popular since its invention in the 1990s. Today many iterations of commercial and lab-built SPMSs are in use worldwide. However, supporting analysis toolkits for these powerful instruments are outdated, have limited functionality, or are versions that are not available to the scientific community at large. In an effort to advance this field and allow better communication and collaboration between scientists, we have developed FATES (Flexible Analysis Toolkit for the Exploration of SPMS data), a MATLAB toolkit easily extensible to an array of SPMS designs and data formats. FATES was developed to minimize the computational demands of working with large data sets while still allowing easy maintenance, modification, and utilization by novice programmers. FATES permits scientists to explore, without constraint, complex SPMS data with simple scripts in a language popular for scientific numerical analysis. In addition FATES contains an array of data visualization graphic user interfaces (GUIs) which can aid both novice and expert users in calibration of raw data; exploration of the dependence of mass spectral characteristics on size, time, and peak intensity; and investigations of clustered data sets.

BIO::Phylo-phyloinformatic analysis using perl.

PubMed

Vos, Rutger A; Caravas, Jason; Hartmann, Klaas; Jensen, Mark A; Miller, Chase

2011-02-27

Phyloinformatic analyses involve large amounts of data and metadata of complex structure. Collecting, processing, analyzing, visualizing and summarizing these data and metadata should be done in steps that can be automated and reproduced. This requires flexible, modular toolkits that can represent, manipulate and persist phylogenetic data and metadata as objects with programmable interfaces. This paper presents Bio::Phylo, a Perl5 toolkit for phyloinformatic analysis. It implements classes and methods that are compatible with the well-known BioPerl toolkit, but is independent from it (making it easy to install) and features a richer API and a data model that is better able to manage the complex relationships between different fundamental data and metadata objects in phylogenetics. It supports commonly used file formats for phylogenetic data including the novel NeXML standard, which allows rich annotations of phylogenetic data to be stored and shared. Bio::Phylo can interact with BioPerl, thereby giving access to the file formats that BioPerl supports. Many methods for data simulation, transformation and manipulation, the analysis of tree shape, and tree visualization are provided. Bio::Phylo is composed of 59 richly documented Perl5 modules. It has been deployed successfully on a variety of computer architectures (including various Linux distributions, Mac OS X versions, Windows, Cygwin and UNIX-like systems). It is available as open source (GPL) software from http://search.cpan.org/dist/Bio-Phylo.

BIO::Phylo-phyloinformatic analysis using perl

PubMed Central

2011-01-01

Background Phyloinformatic analyses involve large amounts of data and metadata of complex structure. Collecting, processing, analyzing, visualizing and summarizing these data and metadata should be done in steps that can be automated and reproduced. This requires flexible, modular toolkits that can represent, manipulate and persist phylogenetic data and metadata as objects with programmable interfaces. Results This paper presents Bio::Phylo, a Perl5 toolkit for phyloinformatic analysis. It implements classes and methods that are compatible with the well-known BioPerl toolkit, but is independent from it (making it easy to install) and features a richer API and a data model that is better able to manage the complex relationships between different fundamental data and metadata objects in phylogenetics. It supports commonly used file formats for phylogenetic data including the novel NeXML standard, which allows rich annotations of phylogenetic data to be stored and shared. Bio::Phylo can interact with BioPerl, thereby giving access to the file formats that BioPerl supports. Many methods for data simulation, transformation and manipulation, the analysis of tree shape, and tree visualization are provided. Conclusions Bio::Phylo is composed of 59 richly documented Perl5 modules. It has been deployed successfully on a variety of computer architectures (including various Linux distributions, Mac OS X versions, Windows, Cygwin and UNIX-like systems). It is available as open source (GPL) software from http://search.cpan.org/dist/Bio-Phylo PMID:21352572

GIS Services, Visualization Products, and Interoperability at the National Oceanic and Atmospheric Administration (NOAA) National Climatic Data Center (NCDC)

NASA Astrophysics Data System (ADS)

Baldwin, R.; Ansari, S.; Reid, G.; Lott, N.; Del Greco, S.

2007-12-01

The main goal in developing and deploying Geographic Information System (GIS) services at NOAA's National Climatic Data Center (NCDC) is to provide users with simple access to data archives while integrating new and informative climate products. Several systems at NCDC provide a variety of climatic data in GIS formats and/or map viewers. The Online GIS Map Services provide users with data discovery options which flow into detailed product selection maps, which may be queried using standard "region finder" tools or gazetteer (geographical dictionary search) functions. Each tabbed selection offers steps to help users progress through the systems. A series of additional base map layers or data types have been added to provide companion information. New map services include: Severe Weather Data Inventory, Local Climatological Data, Divisional Data, Global Summary of the Day, and Normals/Extremes products. THREDDS Data Server technology is utilized to provide access to gridded multidimensional datasets such as Model, Satellite and Radar. This access allows users to download data as a gridded NetCDF file, which is readable by ArcGIS. In addition, users may subset the data for a specific geographic region, time period, height range or variable prior to download. The NCDC Weather Radar Toolkit (WRT) is a client tool which accesses Weather Surveillance Radar 1988 Doppler (WSR-88D) data locally or remotely from the NCDC archive, NOAA FTP server or any URL or THREDDS Data Server. The WRT Viewer provides tools for custom data overlays, Web Map Service backgrounds, animations and basic filtering. The export of images and movies is provided in multiple formats. The WRT Data Exporter allows for data export in both vector polygon (Shapefile, Well-Known Text) and raster (GeoTIFF, ESRI Grid, VTK, NetCDF, GrADS) formats. As more users become accustom to GIS, questions of better, cheaper, faster access soon follow. Expanding use and availability can best be accomplished through standards which promote interoperability. Our GIS related products provide Open Geospatial Consortium (OGC) compliant Web Map Services (WMS), Web Feature Services (WFS), Web Coverage Services (WCS) and Federal Geographic Data Committee (FGDC) metadata as a complement to the map viewers. KML/KMZ data files (soon to be compliant OGC specifications) also provide access.

Space-Based Telescopes for the Actionable Refinement of Ephemeris Systems and Test Engineering

DTIC Science & Technology

2011-12-01

Space Surveillance Network STARE Space-based Telescopes for the Actionable Refinement of Ephemeris STK Satellite Toolkit SV Space Vehicle TAMU...vacuum bake out and visual inspection. Additionally, it is prescribed that these tests be performed in accordance with GSFC-STD-7000, more commonly...environment that a FV will see in orbit. Tools such as Solid Works and NX-Ideas can be used to build CAD models to visually validate engineering

Visualization Software for VisIT Java Client

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

Billings, Jay Jay; Smith, Robert W

The VisIT Java Client (JVC) library is a lightweight thin client that is designed and written purely in the native language of Java (the Python & JavaScript versions of the library use the same concept) and communicates with any new unmodified standalone version of VisIT, a high performance computing parallel visualization toolkit, over traditional or web sockets and dynamically determines capabilities of the running VisIT instance whether local or remote.

Oak Ridge Bio-surveillance Toolkit (ORBiT): Integrating Big-Data Analytics with Visual Analysis for Public Health Dynamics

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

Ramanathan, Arvind; Pullum, Laura L; Steed, Chad A

In this position paper, we describe the design and implementation of the Oak Ridge Bio-surveillance Toolkit (ORBiT): a collection of novel statistical and machine learning tools implemented for (1) integrating heterogeneous traditional (e.g. emergency room visits, prescription sales data, etc.) and non-traditional (social media such as Twitter and Instagram) data sources, (2) analyzing large-scale datasets and (3) presenting the results from the analytics as a visual interface for the end-user to interact and provide feedback. We present examples of how ORBiT can be used to summarize ex- tremely large-scale datasets effectively and how user interactions can translate into the datamore » analytics process for bio-surveillance. We also present a strategy to estimate parameters relevant to dis- ease spread models from near real time data feeds and show how these estimates can be integrated with disease spread models for large-scale populations. We conclude with a perspective on how integrating data and visual analytics could lead to better forecasting and prediction of disease spread as well as improved awareness of disease susceptible regions.« less

Windows Memory Forensic Data Visualization

DTIC Science & Technology

2014-06-12

clustering characteristics (Bastian, et al, 2009). The software is written in Java and utilizes the OpenGL library for rendering graphical content...Toolkit 2 nd ed. Burlington MA: Syngress. D3noob. (2013, February 8). Using a MYSQL database as a source of data. Message posted to http

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.

The SpeX Prism Library Analysis Toolkit: Design Considerations and First Results

NASA Astrophysics Data System (ADS)

Burgasser, Adam J.; Aganze, Christian; Escala, Ivana; Lopez, Mike; Choban, Caleb; Jin, Yuhui; Iyer, Aishwarya; Tallis, Melisa; Suarez, Adrian; Sahi, Maitrayee

2016-01-01

Various observational and theoretical spectral libraries now exist for galaxies, stars, planets and other objects, which have proven useful for classification, interpretation, simulation and model development. Effective use of these libraries relies on analysis tools, which are often left to users to develop. In this poster, we describe a program to develop a combined spectral data repository and Python-based analysis toolkit for low-resolution spectra of very low mass dwarfs (late M, L and T dwarfs), which enables visualization, spectral index analysis, classification, atmosphere model comparison, and binary modeling for nearly 2000 library spectra and user-submitted data. The SpeX Prism Library Analysis Toolkit (SPLAT) is being constructed as a collaborative, student-centered, learning-through-research model with high school, undergraduate and graduate students and regional science teachers, who populate the database and build the analysis tools through quarterly challenge exercises and summer research projects. In this poster, I describe the design considerations of the toolkit, its current status and development plan, and report the first published results led by undergraduate students. The combined data and analysis tools are ideal for characterizing cool stellar and exoplanetary atmospheres (including direct exoplanetary spectra observations by Gemini/GPI, VLT/SPHERE, and JWST), and the toolkit design can be readily adapted for other spectral datasets as well.This material is based upon work supported by the National Aeronautics and Space Administration under Grant No. NNX15AI75G. SPLAT code can be found at https://github.com/aburgasser/splat.

Falling Less in Kansas: Development of a Fall Risk Reduction Toolkit

PubMed Central

Radebaugh, Teresa S.; Bahner, Candace A.; Ballard-Reisch, Deborah; Epp, Michael; Hale, LaDonna S.; Hanley, Rich; Kendrick, Karen; Rogers, Michael E.; Rogers, Nicole L.

2011-01-01

Falls are a serious health risk for older adults. But for those living in rural and frontier areas of the USA, the risks are higher because of limited access to health care providers and resources. This study employed a community-based participatory research approach to develop a fall prevention toolkit to be used by residents of rural and frontier areas without the assistance of health care providers. Qualitative data were gathered from both key informant interviews and focus groups with a broad range of participants. Data analysis revealed that to be effective and accepted, the toolkit should be not only evidence based but also practical, low-cost, self-explanatory, and usable without the assistance of a health care provider. Materials must be engaging, visually interesting, empowering, sensitive to reading level, and appropriate for low-vision users. These findings should be useful to other researchers developing education and awareness materials for older adults in rural areas. PMID:21941655

Visualization of the NASA ICON mission in 3d

NASA Astrophysics Data System (ADS)

Mendez, R. A., Jr.; Immel, T. J.; Miller, N.

2016-12-01

The ICON Explorer mission (http://icon.ssl.berkeley.edu) will provide several data products for the atmosphere and ionosphere after its launch in 2017. This project will support the mission by investigating the capability of these tools for visualization of current and predicted observatory characteristics and data acquisition. Visualization of this mission can be accomplished using tools like Google Earth or CesiumJS, as well assistance from Java or Python. Ideally we will bring this visualization into the homes of people without the need of additional software. The path of launching a standalone website, building this environment, and a full toolkit will be discussed. Eventually, the initial work could lead to the addition of a downloadable visualization packages for mission demonstration or science visualization.

WarpIV: In situ visualization and analysis of ion accelerator simulations

DOE PAGES

Rubel, Oliver; Loring, Burlen; Vay, Jean -Luc; ...

2016-05-09

The generation of short pulses of ion beams through the interaction of an intense laser with a plasma sheath offers the possibility of compact and cheaper ion sources for many applications--from fast ignition and radiography of dense targets to hadron therapy and injection into conventional accelerators. To enable the efficient analysis of large-scale, high-fidelity particle accelerator simulations using the Warp simulation suite, the authors introduce the Warp In situ Visualization Toolkit (WarpIV). WarpIV integrates state-of-the-art in situ visualization and analysis using VisIt with Warp, supports management and control of complex in situ visualization and analysis workflows, and implements integrated analyticsmore » to facilitate query- and feature-based data analytics and efficient large-scale data analysis. WarpIV enables for the first time distributed parallel, in situ visualization of the full simulation data using high-performance compute resources as the data is being generated by Warp. The authors describe the application of WarpIV to study and compare large 2D and 3D ion accelerator simulations, demonstrating significant differences in the acceleration process in 2D and 3D simulations. WarpIV is available to the public via https://bitbucket.org/berkeleylab/warpiv. The Warp In situ Visualization Toolkit (WarpIV) supports large-scale, parallel, in situ visualization and analysis and facilitates query- and feature-based analytics, enabling for the first time high-performance analysis of large-scale, high-fidelity particle accelerator simulations while the data is being generated by the Warp simulation suite. Furthermore, this supplemental material https://extras.computer.org/extra/mcg2016030022s1.pdf provides more details regarding the memory profiling and optimization and the Yee grid recentering optimization results discussed in the main article.« less

Astronomy Data Visualization with Blender

NASA Astrophysics Data System (ADS)

Kent, Brian R.

2015-08-01

We present innovative methods and techniques for using Blender, a 3D software package, in the visualization of astronomical data. N-body simulations, data cubes, galaxy and stellar catalogs, and planetary surface maps can be rendered in high quality videos for exploratory data analysis. Blender's API is Python based, making it advantageous for use in astronomy with flexible libraries like astroPy. Examples will be exhibited that showcase the features of the software in astronomical visualization paradigms. 2D and 3D voxel texture applications, animations, camera movement, and composite renders are introduced to the astronomer's toolkit and how they mesh with different forms of data.

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

Rubel, Oliver; Loring, Burlen; Vay, Jean -Luc

The generation of short pulses of ion beams through the interaction of an intense laser with a plasma sheath offers the possibility of compact and cheaper ion sources for many applications--from fast ignition and radiography of dense targets to hadron therapy and injection into conventional accelerators. To enable the efficient analysis of large-scale, high-fidelity particle accelerator simulations using the Warp simulation suite, the authors introduce the Warp In situ Visualization Toolkit (WarpIV). WarpIV integrates state-of-the-art in situ visualization and analysis using VisIt with Warp, supports management and control of complex in situ visualization and analysis workflows, and implements integrated analyticsmore » to facilitate query- and feature-based data analytics and efficient large-scale data analysis. WarpIV enables for the first time distributed parallel, in situ visualization of the full simulation data using high-performance compute resources as the data is being generated by Warp. The authors describe the application of WarpIV to study and compare large 2D and 3D ion accelerator simulations, demonstrating significant differences in the acceleration process in 2D and 3D simulations. WarpIV is available to the public via https://bitbucket.org/berkeleylab/warpiv. The Warp In situ Visualization Toolkit (WarpIV) supports large-scale, parallel, in situ visualization and analysis and facilitates query- and feature-based analytics, enabling for the first time high-performance analysis of large-scale, high-fidelity particle accelerator simulations while the data is being generated by the Warp simulation suite. Furthermore, this supplemental material https://extras.computer.org/extra/mcg2016030022s1.pdf provides more details regarding the memory profiling and optimization and the Yee grid recentering optimization results discussed in the main article.« less

Automated Verification of Design Patterns with LePUS3

NASA Technical Reports Server (NTRS)

Nicholson, Jonathan; Gasparis, Epameinondas; Eden, Ammon H.; Kazman, Rick

2009-01-01

Specification and [visual] modelling languages are expected to combine strong abstraction mechanisms with rigour, scalability, and parsimony. LePUS3 is a visual, object-oriented design description language axiomatized in a decidable subset of the first-order predicate logic. We demonstrate how LePUS3 is used to formally specify a structural design pattern and prove ( verify ) whether any JavaTM 1.4 program satisfies that specification. We also show how LePUS3 specifications (charts) are composed and how they are verified fully automatically in the Two-Tier Programming Toolkit.

Cancer-Related Analysis of Variants Toolkit (CRAVAT) | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

CRAVAT is an easy to use web-based tool for analysis of cancer variants (missense, nonsense, in-frame indel, frameshift indel, splice site). CRAVAT provides scores and a variety of annotations that assist in identification of important variants. Results are provided in an interactive, highly graphical webpage and include annotated 3D structure visualization. CRAVAT is also available for local or cloud-based installation as a Docker container. MuPIT provides 3D visualization of mutation clusters and functional annotation and is now integrated with CRAVAT.

VoroTop: Voronoi cell topology visualization and analysis toolkit

NASA Astrophysics Data System (ADS)

Lazar, Emanuel A.

2018-01-01

This paper introduces a new open-source software program called VoroTop, which uses Voronoi topology to analyze local structure in atomic systems. Strengths of this approach include its abilities to analyze high-temperature systems and to characterize complex structure such as grain boundaries. This approach enables the automated analysis of systems and mechanisms previously not possible.

An interactive visualization tool for mobile objects

NASA Astrophysics Data System (ADS)

Kobayashi, Tetsuo

Recent advancements in mobile devices---such as Global Positioning System (GPS), cellular phones, car navigation system, and radio-frequency identification (RFID)---have greatly influenced the nature and volume of data about individual-based movement in space and time. Due to the prevalence of mobile devices, vast amounts of mobile objects data are being produced and stored in databases, overwhelming the capacity of traditional spatial analytical methods. There is a growing need for discovering unexpected patterns, trends, and relationships that are hidden in the massive mobile objects data. Geographic visualization (GVis) and knowledge discovery in databases (KDD) are two major research fields that are associated with knowledge discovery and construction. Their major research challenges are the integration of GVis and KDD, enhancing the ability to handle large volume mobile objects data, and high interactivity between the computer and users of GVis and KDD tools. This dissertation proposes a visualization toolkit to enable highly interactive visual data exploration for mobile objects datasets. Vector algebraic representation and online analytical processing (OLAP) are utilized for managing and querying the mobile object data to accomplish high interactivity of the visualization tool. In addition, reconstructing trajectories at user-defined levels of temporal granularity with time aggregation methods allows exploration of the individual objects at different levels of movement generality. At a given level of generality, individual paths can be combined into synthetic summary paths based on three similarity measures, namely, locational similarity, directional similarity, and geometric similarity functions. A visualization toolkit based on the space-time cube concept exploits these functionalities to create a user-interactive environment for exploring mobile objects data. Furthermore, the characteristics of visualized trajectories are exported to be utilized for data mining, which leads to the integration of GVis and KDD. Case studies using three movement datasets (personal travel data survey in Lexington, Kentucky, wild chicken movement data in Thailand, and self-tracking data in Utah) demonstrate the potential of the system to extract meaningful patterns from the otherwise difficult to comprehend collections of space-time trajectories.

Analyzing microtomography data with Python and the scikit-image library.

PubMed

Gouillart, Emmanuelle; Nunez-Iglesias, Juan; van der Walt, Stéfan

2017-01-01

The exploration and processing of images is a vital aspect of the scientific workflows of many X-ray imaging modalities. Users require tools that combine interactivity, versatility, and performance. scikit-image is an open-source image processing toolkit for the Python language that supports a large variety of file formats and is compatible with 2D and 3D images. The toolkit exposes a simple programming interface, with thematic modules grouping functions according to their purpose, such as image restoration, segmentation, and measurements. scikit-image users benefit from a rich scientific Python ecosystem that contains many powerful libraries for tasks such as visualization or machine learning. scikit-image combines a gentle learning curve, versatile image processing capabilities, and the scalable performance required for the high-throughput analysis of X-ray imaging data.

MONTE: the next generation of mission design and navigation software

NASA Astrophysics Data System (ADS)

Evans, Scott; Taber, William; Drain, Theodore; Smith, Jonathon; Wu, Hsi-Cheng; Guevara, Michelle; Sunseri, Richard; Evans, James

2018-03-01

The Mission analysis, Operations and Navigation Toolkit Environment (MONTE) (Sunseri et al. in NASA Tech Briefs 36(9), 2012) is an astrodynamic toolkit produced by the Mission Design and Navigation Software Group at the Jet Propulsion Laboratory. It provides a single integrated environment for all phases of deep space and Earth orbiting missions. Capabilities include: trajectory optimization and analysis, operational orbit determination, flight path control, and 2D/3D visualization. MONTE is presented to the user as an importable Python language module. This allows a simple but powerful user interface via CLUI or script. In addition, the Python interface allows MONTE to be used seamlessly with other canonical scientific programming tools such as SciPy, NumPy, and Matplotlib. MONTE is the prime operational orbit determination software for all JPL navigated missions.

A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits.

PubMed

Czech, Lucas; Huerta-Cepas, Jaime; Stamatakis, Alexandros

2017-06-01

Phylogenetic trees are routinely visualized to present and interpret the evolutionary relationships of species. Most empirical evolutionary data studies contain a visualization of the inferred tree with branch support values. Ambiguous semantics in tree file formats can lead to erroneous tree visualizations and therefore to incorrect interpretations of phylogenetic analyses. Here, we discuss problems that arise when displaying branch values on trees after rerooting. Branch values are typically stored as node labels in the widely-used Newick tree format. However, such values are attributes of branches. Storing them as node labels can therefore yield errors when rerooting trees. This depends on the mostly implicit semantics that tools deploy to interpret node labels. We reviewed ten tree viewers and ten bioinformatics toolkits that can display and reroot trees. We found that 14 out of 20 of these tools do not permit users to select the semantics of node labels. Thus, unaware users might obtain incorrect results when rooting trees. We illustrate such incorrect mappings for several test cases and real examples taken from the literature. This review has already led to improvements in eight tools. We suggest tools should provide options that explicitly force users to define the semantics of node labels. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data

PubMed Central

Fernandez, Nicolas F.; Gundersen, Gregory W.; Rahman, Adeeb; Grimes, Mark L.; Rikova, Klarisa; Hornbeck, Peter; Ma’ayan, Avi

2017-01-01

Most tools developed to visualize hierarchically clustered heatmaps generate static images. Clustergrammer is a web-based visualization tool with interactive features such as: zooming, panning, filtering, reordering, sharing, performing enrichment analysis, and providing dynamic gene annotations. Clustergrammer can be used to generate shareable interactive visualizations by uploading a data table to a web-site, or by embedding Clustergrammer in Jupyter Notebooks. The Clustergrammer core libraries can also be used as a toolkit by developers to generate visualizations within their own applications. Clustergrammer is demonstrated using gene expression data from the cancer cell line encyclopedia (CCLE), original post-translational modification data collected from lung cancer cells lines by a mass spectrometry approach, and original cytometry by time of flight (CyTOF) single-cell proteomics data from blood. Clustergrammer enables producing interactive web based visualizations for the analysis of diverse biological data. PMID:28994825

Declarative language design for interactive visualization.

PubMed

Heer, Jeffrey; Bostock, Michael

2010-01-01

We investigate the design of declarative, domain-specific languages for constructing interactive visualizations. By separating specification from execution, declarative languages can simplify development, enable unobtrusive optimization, and support retargeting across platforms. We describe the design of the Protovis specification language and its implementation within an object-oriented, statically-typed programming language (Java). We demonstrate how to support rich visualizations without requiring a toolkit-specific data model and extend Protovis to enable declarative specification of animated transitions. To support cross-platform deployment, we introduce rendering and event-handling infrastructures decoupled from the runtime platform, letting designers retarget visualization specifications (e.g., from desktop to mobile phone) with reduced effort. We also explore optimizations such as runtime compilation of visualization specifications, parallelized execution, and hardware-accelerated rendering. We present benchmark studies measuring the performance gains provided by these optimizations and compare performance to existing Java-based visualization tools, demonstrating scalability improvements exceeding an order of magnitude.

The NetLogger Toolkit V2.0

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

Gunter, Dan; Lee, Jason; Stoufer, Martin

2003-03-28

The NetLogger Toolkit is designed to monitor, under actual operating conditions, the behavior of all the elements of the application-to-application communication path in order to determine exactly where time is spent within a complex system Using NetLogger, distnbuted application components are modified to produce timestamped logs of "interesting" events at all the critical points of the distributed system Events from each component are correlated, which allov^ one to characterize the performance of all aspects of the system and network in detail. The NetLogger Toolkit itself consists of four components an API and library of functions to simplify the generation ofmore » application-level event logs, a set of tools for collecting and sorting log files, an event archive system, and a tool for visualization and analysis of the log files In order to instrument an application to produce event logs, the application developer inserts calls to the NetLogger API at all the critical points in the code, then links the application with the NetLogger library All the tools in the NetLogger Toolkit share a common log format, and assume the existence of accurate and synchronized system clocks NetLogger messages can be logged using an easy-to-read text based format based on the lETF-proposed ULM format, or a binary format that can still be used through the same API but that is several times faster and smaller, with performance comparable or better than binary message formats such as MPI, XDR, SDDF-Binary, and PBIO. The NetLogger binary format is both highly efficient and self-describing, thus optimized for the dynamic message construction and parsing of application instrumentation. NetLogger includes an "activation" API that allows NetLogger logging to be turned on, off, or modified by changing an external file This IS useful for activating logging in daemons/services (e g GndFTP server). The NetLogger reliability API provides the ability to specify backup logging locations and penodically try to reconnect broken TCP pipe. A typical use for this is to store data on local disk while net is down. An event archiver can log one or more incoming NetLogger streams to a local disk file (netlogd) or to a mySQL database (netarchd). We have found exploratory, visual analysis of the log event data to be the most useful means of determining the causes of performance anomalies The NetLogger Visualization tool, niv, has been developed to provide a flexible and interactive graphical representation of system-level and application-level events.« less

Designing Tracking Software for Image-Guided Surgery Applications: IGSTK Experience

PubMed Central

Enquobahrie, Andinet; Gobbi, David; Turek, Matt; Cheng, Patrick; Yaniv, Ziv; Lindseth, Frank; Cleary, Kevin

2009-01-01

Objective Many image-guided surgery applications require tracking devices as part of their core functionality. The Image-Guided Surgery Toolkit (IGSTK) was designed and developed to interface tracking devices with software applications incorporating medical images. Methods IGSTK was designed as an open source C++ library that provides the basic components needed for fast prototyping and development of image-guided surgery applications. This library follows a component-based architecture with several components designed for specific sets of image-guided surgery functions. At the core of the toolkit is the tracker component that handles communication between a control computer and navigation device to gather pose measurements of surgical instruments present in the surgical scene. The representations of the tracked instruments are superimposed on anatomical images to provide visual feedback to the clinician during surgical procedures. Results The initial version of the IGSTK toolkit has been released in the public domain and several trackers are supported. The toolkit and related information are available at www.igstk.org. Conclusion With the increased popularity of minimally invasive procedures in health care, several tracking devices have been developed for medical applications. Designing and implementing high-quality and safe software to handle these different types of trackers in a common framework is a challenging task. It requires establishing key software design principles that emphasize abstraction, extensibility, reusability, fault-tolerance, and portability. IGSTK is an open source library that satisfies these needs for the image-guided surgery community. PMID:20037671

Integrating Space Systems Operations at the Marine Expeditionary Force Level

DTIC Science & Technology

2015-06-01

Electromagnetic Interference ENVI Environment for Visualizing Images EW Electronic Warfare xvi FA40 Space Operations Officer FEC Fires and Effects...Information Facility SFE Space Force Enhancement SIGINT Signals Intelligence SSA Space Situational Awareness SSE Space Support Element STK Systems...April 23, 2015. 65 • GPS Interference and Navigation Tool (GIANT) for providing GPS accuracy prediction reports • Systems Toolkit ( STK ) Analysis

An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework.

PubMed

Chen, Yi-An; Tripathi, Lokesh P; Mizuguchi, Kenji

2016-01-01

Data analysis is one of the most critical and challenging steps in drug discovery and disease biology. A user-friendly resource to visualize and analyse high-throughput data provides a powerful medium for both experimental and computational biologists to understand vastly different biological data types and obtain a concise, simplified and meaningful output for better knowledge discovery. We have previously developed TargetMine, an integrated data warehouse optimized for target prioritization. Here we describe how upgraded and newly modelled data types in TargetMine can now survey the wider biological and chemical data space, relevant to drug discovery and development. To enhance the scope of TargetMine from target prioritization to broad-based knowledge discovery, we have also developed a new auxiliary toolkit to assist with data analysis and visualization in TargetMine. This toolkit features interactive data analysis tools to query and analyse the biological data compiled within the TargetMine data warehouse. The enhanced system enables users to discover new hypotheses interactively by performing complicated searches with no programming and obtaining the results in an easy to comprehend output format. Database URL: http://targetmine.mizuguchilab.org. © The Author(s) 2016. Published by Oxford University Press.

An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework

PubMed Central

Chen, Yi-An; Tripathi, Lokesh P.; Mizuguchi, Kenji

2016-01-01

Data analysis is one of the most critical and challenging steps in drug discovery and disease biology. A user-friendly resource to visualize and analyse high-throughput data provides a powerful medium for both experimental and computational biologists to understand vastly different biological data types and obtain a concise, simplified and meaningful output for better knowledge discovery. We have previously developed TargetMine, an integrated data warehouse optimized for target prioritization. Here we describe how upgraded and newly modelled data types in TargetMine can now survey the wider biological and chemical data space, relevant to drug discovery and development. To enhance the scope of TargetMine from target prioritization to broad-based knowledge discovery, we have also developed a new auxiliary toolkit to assist with data analysis and visualization in TargetMine. This toolkit features interactive data analysis tools to query and analyse the biological data compiled within the TargetMine data warehouse. The enhanced system enables users to discover new hypotheses interactively by performing complicated searches with no programming and obtaining the results in an easy to comprehend output format. Database URL: http://targetmine.mizuguchilab.org PMID:26989145

Introducing GHOST: The Geospace/Heliosphere Observation & Simulation Tool-kit

NASA Astrophysics Data System (ADS)

Murphy, J. J.; Elkington, S. R.; Schmitt, P.; Wiltberger, M. J.; Baker, D. N.

2013-12-01

Simulation models of the heliospheric and geospace environments can provide key insights into the geoeffective potential of solar disturbances such as Coronal Mass Ejections and High Speed Solar Wind Streams. Advanced post processing of the results of these simulations greatly enhances the utility of these models for scientists and other researchers. Currently, no supported centralized tool exists for performing these processing tasks. With GHOST, we introduce a toolkit for the ParaView visualization environment that provides a centralized suite of tools suited for Space Physics post processing. Building on the work from the Center For Integrated Space Weather Modeling (CISM) Knowledge Transfer group, GHOST is an open-source tool suite for ParaView. The tool-kit plugin currently provides tools for reading LFM and Enlil data sets, and provides automated tools for data comparison with NASA's CDAweb database. As work progresses, many additional tools will be added and through open-source collaboration, we hope to add readers for additional model types, as well as any additional tools deemed necessary by the scientific public. The ultimate end goal of this work is to provide a complete Sun-to-Earth model analysis toolset.

Cal-Adapt: California's Climate Data Resource and Interactive Toolkit

NASA Astrophysics Data System (ADS)

Thomas, N.; Mukhtyar, S.; Wilhelm, S.; Galey, B.; Lehmer, E.

2016-12-01

Cal-Adapt is a web-based application that provides an interactive toolkit and information clearinghouse to help agencies, communities, local planners, resource managers, and the public understand climate change risks and impacts at the local level. The website offers interactive, visually compelling, and useful data visualization tools that show how climate change might affect California using downscaled continental climate data. Cal-Adapt is supporting California's Fourth Climate Change Assessment through providing access to the wealth of modeled and observed data and adaption-related information produced by California's scientific community. The site has been developed by UC Berkeley's Geospatial Innovation Facility (GIF) in collaboration with the California Energy Commission's (CEC) Research Program. The Cal-Adapt website allows decision makers, scientists and residents of California to turn research results and climate projections into effective adaptation decisions and policies. Since its release to the public in June 2011, Cal-Adapt has been visited by more than 94,000 unique visitors from over 180 countries, all 50 U.S. states, and 689 California localities. We will present several key visualizations that have been employed by Cal-Adapt's users to support their efforts to understand local impacts of climate change, indicate the breadth of data available, and delineate specific use cases. Recently, CEC and GIF have been developing and releasing Cal-Adapt 2.0, which includes updates and enhancements that are increasing its ease of use, information value, visualization tools, and data accessibility. We showcase how Cal-Adapt is evolving in response to feedback from a variety of sources to present finer-resolution downscaled data, and offer an open API that allows other organization to access Cal-Adapt climate data and build domain specific visualization and planning tools. Through a combination of locally relevant information, visualization tools, and access to primary data, Cal-Adapt allows users to investigate how the climate is projected to change in their areas of interest.

A Prototype Search Toolkit

NASA Astrophysics Data System (ADS)

Knepper, Margaret M.; Fox, Kevin L.; Frieder, Ophir

Information overload is now a reality. We no longer worry about obtaining a sufficient volume of data; we now are concerned with sifting and understanding the massive volumes of data available to us. To do so, we developed an integrated information processing toolkit that provides the user with a variety of ways to view their information. The views include keyword search results, a domain specific ranking system that allows for adaptively capturing topic vocabularies to customize and focus the search results, navigation pages for browsing, and a geospatial and temporal component to visualize results in time and space, and provide “what if” scenario playing. Integrating the information from different tools and sources gives the user additional information and another way to analyze the data. An example of the integration is illustrated on reports of the avian influenza (bird flu).

A Computational framework for telemedicine.

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

Foster, I.; von Laszewski, G.; Thiruvathukal, G. K.

1998-07-01

Emerging telemedicine applications require the ability to exploit diverse and geographically distributed resources. Highspeed networks are used to integrate advanced visualization devices, sophisticated instruments, large databases, archival storage devices, PCs, workstations, and supercomputers. This form of telemedical environment is similar to networked virtual supercomputers, also known as metacomputers. Metacomputers are already being used in many scientific application areas. In this article, we analyze requirements necessary for a telemedical computing infrastructure and compare them with requirements found in a typical metacomputing environment. We will show that metacomputing environments can be used to enable a more powerful and unified computational infrastructure formore » telemedicine. The Globus metacomputing toolkit can provide the necessary low level mechanisms to enable a large scale telemedical infrastructure. The Globus toolkit components are designed in a modular fashion and can be extended to support the specific requirements for telemedicine.« less

Remote Visualization and Remote Collaboration On Computational Fluid Dynamics

NASA Technical Reports Server (NTRS)

Watson, Val; Lasinski, T. A. (Technical Monitor)

1995-01-01

A new technology has been developed for remote visualization that provides remote, 3D, high resolution, dynamic, interactive viewing of scientific data (such as fluid dynamics simulations or measurements). Based on this technology, some World Wide Web sites on the Internet are providing fluid dynamics data for educational or testing purposes. This technology is also being used for remote collaboration in joint university, industry, and NASA projects in computational fluid dynamics and wind tunnel testing. Previously, remote visualization of dynamic data was done using video format (transmitting pixel information) such as video conferencing or MPEG movies on the Internet. The concept for this new technology is to send the raw data (e.g., grids, vectors, and scalars) along with viewing scripts over the Internet and have the pixels generated by a visualization tool running on the viewer's local workstation. The visualization tool that is currently used is FAST (Flow Analysis Software Toolkit).

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.

Tools for 3D scientific visualization in computational aerodynamics at NASA Ames Research Center

NASA Technical Reports Server (NTRS)

Bancroft, Gordon; Plessel, Todd; Merritt, Fergus; Watson, Val

1989-01-01

Hardware, software, and techniques used by the Fluid Dynamics Division (NASA) for performing visualization of computational aerodynamics, which can be applied to the visualization of flow fields from computer simulations of fluid dynamics about the Space Shuttle, are discussed. Three visualization techniques applied, post-processing, tracking, and steering, are described, as well as the post-processing software packages used, PLOT3D, SURF (Surface Modeller), GAS (Graphical Animation System), and FAST (Flow Analysis software Toolkit). Using post-processing methods a flow simulation was executed on a supercomputer and, after the simulation was complete, the results were processed for viewing. It is shown that the high-resolution, high-performance three-dimensional workstation combined with specially developed display and animation software provides a good tool for analyzing flow field solutions obtained from supercomputers.

Auditory presentation and synchronization in Adobe Flash and HTML5/JavaScript Web experiments.

PubMed

Reimers, Stian; Stewart, Neil

2016-09-01

Substantial recent research has examined the accuracy of presentation durations and response time measurements for visually presented stimuli in Web-based experiments, with a general conclusion that accuracy is acceptable for most kinds of experiments. However, many areas of behavioral research use auditory stimuli instead of, or in addition to, visual stimuli. Much less is known about auditory accuracy using standard Web-based testing procedures. We used a millisecond-accurate Black Box Toolkit to measure the actual durations of auditory stimuli and the synchronization of auditory and visual presentation onsets. We examined the distribution of timings for 100 presentations of auditory and visual stimuli across two computers with difference specs, three commonly used browsers, and code written in either Adobe Flash or JavaScript. We also examined different coding options for attempting to synchronize the auditory and visual onsets. Overall, we found that auditory durations were very consistent, but that the lags between visual and auditory onsets varied substantially across browsers and computer systems.

Business intelligence from social media: a study from the VAST Box Office Challenge.

PubMed

Lu, Yafeng; Wang, Feng; Maciejewski, Ross

2014-01-01

With over 16 million tweets per hour, 600 new blog posts per minute, and 400 million active users on Facebook, businesses have begun searching for ways to turn real-time consumer-based posts into actionable intelligence. The goal is to extract information from this noisy, unstructured data and use it for trend analysis and prediction. Current practices support the idea that visual analytics (VA) can help enable the effective analysis of such data. However, empirical evidence demonstrating the effectiveness of a VA solution is still lacking. A proposed VA toolkit extracts data from Bitly and Twitter to predict movie revenue and ratings. Results from the 2013 VAST Box Office Challenge demonstrate the benefit of an interactive environment for predictive analysis, compared to a purely statistical modeling approach. The VA approach used by the toolkit is generalizable to other domains involving social media data, such as sales forecasting and advertisement analysis.

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

PubMed Central

Wang, Yupeng; Tang, Haibao; DeBarry, Jeremy D.; Tan, Xu; Li, Jingping; Wang, Xiyin; Lee, Tae-ho; Jin, Huizhe; Marler, Barry; Guo, Hui; Kissinger, Jessica C.; Paterson, Andrew H.

2012-01-01

MCScan is an algorithm able to scan multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and align these regions using genes as anchors. The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by incorporating 14 utility programs for visualization of results and additional downstream analyses. Applications of MCScanX to several sequenced plant genomes and gene families are shown as examples. MCScanX can be used to effectively analyze chromosome structural changes, and reveal the history of gene family expansions that might contribute to the adaptation of lineages and taxa. An integrated view of various modes of gene duplication can supplement the traditional gene tree analysis in specific families. The source code and documentation of MCScanX are freely available at http://chibba.pgml.uga.edu/mcscan2/. PMID:22217600

ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data.

PubMed

Luo, Guan-Zheng; Yang, Wei; Ma, Ying-Ke; Wang, Xiu-Jie

2014-02-01

Integrative Short Reads NAvigator (ISRNA) is an online toolkit for analyzing high-throughput small RNA sequencing data. Besides the high-speed genome mapping function, ISRNA provides statistics for genomic location, length distribution and nucleotide composition bias analysis of sequence reads. Number of reads mapped to known microRNAs and other classes of short non-coding RNAs, coverage of short reads on genes, expression abundance of sequence reads as well as some other analysis functions are also supported. The versatile search functions enable users to select sequence reads according to their sub-sequences, expression abundance, genomic location, relationship to genes, etc. A specialized genome browser is integrated to visualize the genomic distribution of short reads. ISRNA also supports management and comparison among multiple datasets. ISRNA is implemented in Java/C++/Perl/MySQL and can be freely accessed at http://omicslab.genetics.ac.cn/ISRNA/.

ParCAT: A Parallel Climate Analysis Toolkit

NASA Astrophysics Data System (ADS)

Haugen, B.; Smith, B.; Steed, C.; Ricciuto, D. M.; Thornton, P. E.; Shipman, G.

2012-12-01

Climate science has employed increasingly complex models and simulations to analyze the past and predict the future of our climate. The size and dimensionality of climate simulation data has been growing with the complexity of the models. This growth in data is creating a widening gap between the data being produced and the tools necessary to analyze large, high dimensional data sets. With single run data sets increasing into 10's, 100's and even 1000's of gigabytes, parallel computing tools are becoming a necessity in order to analyze and compare climate simulation data. The Parallel Climate Analysis Toolkit (ParCAT) provides basic tools that efficiently use parallel computing techniques to narrow the gap between data set size and analysis tools. ParCAT was created as a collaborative effort between climate scientists and computer scientists in order to provide efficient parallel implementations of the computing tools that are of use to climate scientists. Some of the basic functionalities included in the toolkit are the ability to compute spatio-temporal means and variances, differences between two runs and histograms of the values in a data set. ParCAT is designed to facilitate the "heavy lifting" that is required for large, multidimensional data sets. The toolkit does not focus on performing the final visualizations and presentation of results but rather, reducing large data sets to smaller, more manageable summaries. The output from ParCAT is provided in commonly used file formats (NetCDF, CSV, ASCII) to allow for simple integration with other tools. The toolkit is currently implemented as a command line utility, but will likely also provide a C library for developers interested in tighter software integration. Elements of the toolkit are already being incorporated into projects such as UV-CDAT and CMDX. There is also an effort underway to implement portions of the CCSM Land Model Diagnostics package using ParCAT in conjunction with Python and gnuplot. ParCAT is implemented in C to provide efficient file IO. The file IO operations in the toolkit use the parallel-netcdf library; this enables the code to use the parallel IO capabilities of modern HPC systems. Analysis that currently requires an estimated 12+ hours with the traditional CCSM Land Model Diagnostics Package can now be performed in as little as 30 minutes on a single desktop workstation and a few minutes for relatively small jobs completed on modern HPC systems such as ORNL's Jaguar.

A topological framework for interactive queries on 3D models in the Web.

PubMed

Figueiredo, Mauro; Rodrigues, José I; Silvestre, Ivo; Veiga-Pires, Cristina

2014-01-01

Several technologies exist to create 3D content for the web. With X3D, WebGL, and X3DOM, it is possible to visualize and interact with 3D models in a web browser. Frequently, three-dimensional objects are stored using the X3D file format for the web. However, there is no explicit topological information, which makes it difficult to design fast algorithms for applications that require adjacency and incidence data. This paper presents a new open source toolkit TopTri (Topological model for Triangle meshes) for Web3D servers that builds the topological model for triangular meshes of manifold or nonmanifold models. Web3D client applications using this toolkit make queries to the web server to get adjacent and incidence information of vertices, edges, and faces. This paper shows the application of the topological information to get minimal local points and iso-lines in a 3D mesh in a web browser. As an application, we present also the interactive identification of stalactites in a cave chamber in a 3D web browser. Several tests show that even for large triangular meshes with millions of triangles, the adjacency and incidence information is returned in real time making the presented toolkit appropriate for interactive Web3D applications.

A Topological Framework for Interactive Queries on 3D Models in the Web

PubMed Central

Figueiredo, Mauro; Rodrigues, José I.; Silvestre, Ivo; Veiga-Pires, Cristina

2014-01-01

Several technologies exist to create 3D content for the web. With X3D, WebGL, and X3DOM, it is possible to visualize and interact with 3D models in a web browser. Frequently, three-dimensional objects are stored using the X3D file format for the web. However, there is no explicit topological information, which makes it difficult to design fast algorithms for applications that require adjacency and incidence data. This paper presents a new open source toolkit TopTri (Topological model for Triangle meshes) for Web3D servers that builds the topological model for triangular meshes of manifold or nonmanifold models. Web3D client applications using this toolkit make queries to the web server to get adjacent and incidence information of vertices, edges, and faces. This paper shows the application of the topological information to get minimal local points and iso-lines in a 3D mesh in a web browser. As an application, we present also the interactive identification of stalactites in a cave chamber in a 3D web browser. Several tests show that even for large triangular meshes with millions of triangles, the adjacency and incidence information is returned in real time making the presented toolkit appropriate for interactive Web3D applications. PMID:24977236

A signaling visualization toolkit to support rational design of combination therapies and biomarker discovery: SiViT.

PubMed

Bown, James L; Shovman, Mark; Robertson, Paul; Boiko, Andrei; Goltsov, Alexey; Mullen, Peter; Harrison, David J

2017-05-02

Targeted cancer therapy aims to disrupt aberrant cellular signalling pathways. Biomarkers are surrogates of pathway state, but there is limited success in translating candidate biomarkers to clinical practice due to the intrinsic complexity of pathway networks. Systems biology approaches afford better understanding of complex, dynamical interactions in signalling pathways targeted by anticancer drugs. However, adoption of dynamical modelling by clinicians and biologists is impeded by model inaccessibility. Drawing on computer games technology, we present a novel visualization toolkit, SiViT, that converts systems biology models of cancer cell signalling into interactive simulations that can be used without specialist computational expertise. SiViT allows clinicians and biologists to directly introduce for example loss of function mutations and specific inhibitors. SiViT animates the effects of these introductions on pathway dynamics, suggesting further experiments and assessing candidate biomarker effectiveness. In a systems biology model of Her2 signalling we experimentally validated predictions using SiViT, revealing the dynamics of biomarkers of drug resistance and highlighting the role of pathway crosstalk. No model is ever complete: the iteration of real data and simulation facilitates continued evolution of more accurate, useful models. SiViT will make accessible libraries of models to support preclinical research, combinatorial strategy design and biomarker discovery.

Enhancing knowledge discovery from cancer genomics data with Galaxy

PubMed Central

Albuquerque, Marco A.; Grande, Bruno M.; Ritch, Elie J.; Pararajalingam, Prasath; Jessa, Selin; Krzywinski, Martin; Grewal, Jasleen K.; Shah, Sohrab P.; Boutros, Paul C.

2017-01-01

Abstract The field of cancer genomics has demonstrated the power of massively parallel sequencing techniques to inform on the genes and specific alterations that drive tumor onset and progression. Although large comprehensive sequence data sets continue to be made increasingly available, data analysis remains an ongoing challenge, particularly for laboratories lacking dedicated resources and bioinformatics expertise. To address this, we have produced a collection of Galaxy tools that represent many popular algorithms for detecting somatic genetic alterations from cancer genome and exome data. We developed new methods for parallelization of these tools within Galaxy to accelerate runtime and have demonstrated their usability and summarized their runtimes on multiple cloud service providers. Some tools represent extensions or refinement of existing toolkits to yield visualizations suited to cohort-wide cancer genomic analysis. For example, we present Oncocircos and Oncoprintplus, which generate data-rich summaries of exome-derived somatic mutation. Workflows that integrate these to achieve data integration and visualizations are demonstrated on a cohort of 96 diffuse large B-cell lymphomas and enabled the discovery of multiple candidate lymphoma-related genes. Our toolkit is available from our GitHub repository as Galaxy tool and dependency definitions and has been deployed using virtualization on multiple platforms including Docker. PMID:28327945

Enhancing knowledge discovery from cancer genomics data with Galaxy.

PubMed

Albuquerque, Marco A; Grande, Bruno M; Ritch, Elie J; Pararajalingam, Prasath; Jessa, Selin; Krzywinski, Martin; Grewal, Jasleen K; Shah, Sohrab P; Boutros, Paul C; Morin, Ryan D

2017-05-01

The field of cancer genomics has demonstrated the power of massively parallel sequencing techniques to inform on the genes and specific alterations that drive tumor onset and progression. Although large comprehensive sequence data sets continue to be made increasingly available, data analysis remains an ongoing challenge, particularly for laboratories lacking dedicated resources and bioinformatics expertise. To address this, we have produced a collection of Galaxy tools that represent many popular algorithms for detecting somatic genetic alterations from cancer genome and exome data. We developed new methods for parallelization of these tools within Galaxy to accelerate runtime and have demonstrated their usability and summarized their runtimes on multiple cloud service providers. Some tools represent extensions or refinement of existing toolkits to yield visualizations suited to cohort-wide cancer genomic analysis. For example, we present Oncocircos and Oncoprintplus, which generate data-rich summaries of exome-derived somatic mutation. Workflows that integrate these to achieve data integration and visualizations are demonstrated on a cohort of 96 diffuse large B-cell lymphomas and enabled the discovery of multiple candidate lymphoma-related genes. Our toolkit is available from our GitHub repository as Galaxy tool and dependency definitions and has been deployed using virtualization on multiple platforms including Docker. © The Author 2017. Published by Oxford University Press.

FAST: A multi-processed environment for visualization of computational fluid dynamics

NASA Technical Reports Server (NTRS)

Bancroft, Gordon V.; Merritt, Fergus J.; Plessel, Todd C.; Kelaita, Paul G.; Mccabe, R. Kevin

1991-01-01

Three-dimensional, unsteady, multi-zoned fluid dynamics simulations over full scale aircraft are typical of the problems being investigated at NASA Ames' Numerical Aerodynamic Simulation (NAS) facility on CRAY2 and CRAY-YMP supercomputers. With multiple processor workstations available in the 10-30 Mflop range, we feel that these new developments in scientific computing warrant a new approach to the design and implementation of analysis tools. These larger, more complex problems create a need for new visualization techniques not possible with the existing software or systems available as of this writing. The visualization techniques will change as the supercomputing environment, and hence the scientific methods employed, evolves even further. The Flow Analysis Software Toolkit (FAST), an implementation of a software system for fluid mechanics analysis, is discussed.

Managing Spatial Selections With Contextual Snapshots

PubMed Central

Mindek, P; Gröller, M E; Bruckner, S

2014-01-01

Spatial selections are a ubiquitous concept in visualization. By localizing particular features, they can be analysed and compared in different views. However, the semantics of such selections often depend on specific parameter settings and it can be difficult to reconstruct them without additional information. In this paper, we present the concept of contextual snapshots as an effective means for managing spatial selections in visualized data. The selections are automatically associated with the context in which they have been created. Contextual snapshots can also be used as the basis for interactive integrated and linked views, which enable in-place investigation and comparison of multiple visual representations of data. Our approach is implemented as a flexible toolkit with well-defined interfaces for integration into existing systems. We demonstrate the power and generality of our techniques by applying them to several distinct scenarios such as the visualization of simulation data, the analysis of historical documents and the display of anatomical data. PMID:25821284

A software architecture for automating operations processes

NASA Technical Reports Server (NTRS)

Miller, Kevin J.

1994-01-01

The Operations Engineering Lab (OEL) at JPL has developed a software architecture based on an integrated toolkit approach for simplifying and automating mission operations tasks. The toolkit approach is based on building adaptable, reusable graphical tools that are integrated through a combination of libraries, scripts, and system-level user interface shells. The graphical interface shells are designed to integrate and visually guide a user through the complex steps in an operations process. They provide a user with an integrated system-level picture of an overall process, defining the required inputs and possible output through interactive on-screen graphics. The OEL has developed the software for building these process-oriented graphical user interface (GUI) shells. The OEL Shell development system (OEL Shell) is an extension of JPL's Widget Creation Library (WCL). The OEL Shell system can be used to easily build user interfaces for running complex processes, applications with extensive command-line interfaces, and tool-integration tasks. The interface shells display a logical process flow using arrows and box graphics. They also allow a user to select which output products are desired and which input sources are needed, eliminating the need to know which program and its associated command-line parameters must be executed in each case. The shells have also proved valuable for use as operations training tools because of the OEL Shell hypertext help environment. The OEL toolkit approach is guided by several principles, including the use of ASCII text file interfaces with a multimission format, Perl scripts for mission-specific adaptation code, and programs that include a simple command-line interface for batch mode processing. Projects can adapt the interface shells by simple changes to the resources configuration file. This approach has allowed the development of sophisticated, automated software systems that are easy, cheap, and fast to build. This paper will discuss our toolkit approach and the OEL Shell interface builder in the context of a real operations process example. The paper will discuss the design and implementation of a Ulysses toolkit for generating the mission sequence of events. The Sequence of Events Generation (SEG) system provides an adaptable multimission toolkit for producing a time-ordered listing and timeline display of spacecraft commands, state changes, and required ground activities.

Scalable descriptive and correlative statistics with Titan.

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

Thompson, David C.; Pebay, Philippe Pierre

This report summarizes the existing statistical engines in VTK/Titan and presents the parallel versions thereof which have already been implemented. The ease of use of these parallel engines is illustrated by the means of C++ code snippets. Furthermore, this report justifies the design of these engines with parallel scalability in mind; then, this theoretical property is verified with test runs that demonstrate optimal parallel speed-up with up to 200 processors.

A Grassroots Remote Sensing Toolkit Using Live Coding, Smartphones, Kites and Lightweight Drones.

PubMed

Anderson, K; Griffiths, D; DeBell, L; Hancock, S; Duffy, J P; Shutler, J D; Reinhardt, W J; Griffiths, A

2016-01-01

This manuscript describes the development of an android-based smartphone application for capturing aerial photographs and spatial metadata automatically, for use in grassroots mapping applications. The aim of the project was to exploit the plethora of on-board sensors within modern smartphones (accelerometer, GPS, compass, camera) to generate ready-to-use spatial data from lightweight aerial platforms such as drones or kites. A visual coding 'scheme blocks' framework was used to build the application ('app'), so that users could customise their own data capture tools in the field. The paper reports on the coding framework, then shows the results of test flights from kites and lightweight drones and finally shows how open-source geospatial toolkits were used to generate geographical information system (GIS)-ready GeoTIFF images from the metadata stored by the app. Two Android smartphones were used in testing-a high specification OnePlus One handset and a lower cost Acer Liquid Z3 handset, to test the operational limits of the app on phones with different sensor sets. We demonstrate that best results were obtained when the phone was attached to a stable single line kite or to a gliding drone. Results show that engine or motor vibrations from powered aircraft required dampening to ensure capture of high quality images. We demonstrate how the products generated from the open-source processing workflow are easily used in GIS. The app can be downloaded freely from the Google store by searching for 'UAV toolkit' (UAV toolkit 2016), and used wherever an Android smartphone and aerial platform are available to deliver rapid spatial data (e.g. in supporting decision-making in humanitarian disaster-relief zones, in teaching or for grassroots remote sensing and democratic mapping).

IBiSA_Tools: A Computational Toolkit for Ion-Binding State Analysis in Molecular Dynamics Trajectories of Ion Channels.

PubMed

Kasahara, Kota; Kinoshita, Kengo

2016-01-01

Ion conduction mechanisms of ion channels are a long-standing conundrum. Although the molecular dynamics (MD) method has been extensively used to simulate ion conduction dynamics at the atomic level, analysis and interpretation of MD results are not straightforward due to complexity of the dynamics. In our previous reports, we proposed an analytical method called ion-binding state analysis to scrutinize and summarize ion conduction mechanisms by taking advantage of a variety of analytical protocols, e.g., the complex network analysis, sequence alignment, and hierarchical clustering. This approach effectively revealed the ion conduction mechanisms and their dependence on the conditions, i.e., ion concentration and membrane voltage. Here, we present an easy-to-use computational toolkit for ion-binding state analysis, called IBiSA_tools. This toolkit consists of a C++ program and a series of Python and R scripts. From the trajectory file of MD simulations and a structure file, users can generate several images and statistics of ion conduction processes. A complex network named ion-binding state graph is generated in a standard graph format (graph modeling language; GML), which can be visualized by standard network analyzers such as Cytoscape. As a tutorial, a trajectory of a 50 ns MD simulation of the Kv1.2 channel is also distributed with the toolkit. Users can trace the entire process of ion-binding state analysis step by step. The novel method for analysis of ion conduction mechanisms of ion channels can be easily used by means of IBiSA_tools. This software is distributed under an open source license at the following URL: http://www.ritsumei.ac.jp/~ktkshr/ibisa_tools/.

ETE: a python Environment for Tree Exploration.

PubMed

Huerta-Cepas, Jaime; Dopazo, Joaquín; Gabaldón, Toni

2010-01-13

Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them. However, such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale. Here we present the Environment for Tree Exploration (ETE), a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis of tree partitions, has support for the extended newick format, provides an integrated node annotation system and permits to link trees to external data such as multiple sequence alignments or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including phylogeny-based orthology prediction and cluster validation techniques. Finally, ETE's programmable tree drawing engine can be used to automate the graphical rendering of trees with customized node-specific visualizations. ETE provides a complete set of methods to manipulate tree data structures that extends current functionality in other bioinformatic toolkits of a more general purpose. ETE is free software and can be downloaded from http://ete.cgenomics.org.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

ETE: a python Environment for Tree Exploration

PubMed Central

2010-01-01

Background Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them. However, such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale. Results Here we present the Environment for Tree Exploration (ETE), a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis of tree partitions, has support for the extended newick format, provides an integrated node annotation system and permits to link trees to external data such as multiple sequence alignments or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including phylogeny-based orthology prediction and cluster validation techniques. Finally, ETE's programmable tree drawing engine can be used to automate the graphical rendering of trees with customized node-specific visualizations. Conclusions ETE provides a complete set of methods to manipulate tree data structures that extends current functionality in other bioinformatic toolkits of a more general purpose. ETE is free software and can be downloaded from http://ete.cgenomics.org. PMID:20070885

Visualizing relativity: The OpenRelativity project

NASA Astrophysics Data System (ADS)

Sherin, Zachary W.; Cheu, Ryan; Tan, Philip; Kortemeyer, Gerd

2016-05-01

We present OpenRelativity, an open-source toolkit to simulate effects of special relativity within the popular Unity game engine. Intended for game developers, educators, and anyone interested in physics, OpenRelativity can help people create, test, and share experiments to explore the effects of special relativity. We describe the underlying physics and some of the implementation details of this toolset with the hope that engaging games and interactive relativistic "laboratory" experiments might be implemented.

The use of ambient audio to increase safety and immersion in location-based games

NASA Astrophysics Data System (ADS)

Kurczak, John Jason

The purpose of this thesis is to propose an alternative type of interface for mobile software being used while walking or running. Our work addresses the problem of visual user interfaces for mobile software be- ing potentially unsafe for pedestrians, and not being very immersive when used for location-based games. In addition, location-based games and applications can be dif- ficult to develop when directly interfacing with the sensors used to track the user's location. These problems need to be addressed because portable computing devices are be- coming a popular tool for navigation, playing games, and accessing the internet while walking. This poses a safety problem for mobile users, who may be paying too much attention to their device to notice and react to hazards in their environment. The difficulty of developing location-based games and other location-aware applications may significantly hinder the prevalence of applications that explore new interaction techniques for ubiquitous computing. We created the TREC toolkit to address the issues with tracking sensors while developing location-based games and applications. We have developed functional location-based applications with TREC to demonstrate the amount of work that can be saved by using this toolkit. In order to have a safer and more immersive alternative to visual interfaces, we have developed ambient audio interfaces for use with mobile applications. Ambient audio uses continuous streams of sound over headphones to present information to mobile users without distracting them from walking safely. In order to test the effectiveness of ambient audio, we ran a study to compare ambient audio with handheld visual interfaces in a location-based game. We compared players' ability to safely navigate the environment, their sense of immersion in the game, and their performance at the in-game tasks. We found that ambient audio was able to significantly increase players' safety and sense of immersion compared to a visual interface, while players performed signifi- cantly better at the game tasks when using the visual interface. This makes ambient audio a legitimate alternative to visual interfaces for mobile users when safety and immersion are a priority.

Large-scale automated image analysis for computational profiling of brain tissue surrounding implanted neuroprosthetic devices using Python.

PubMed

Rey-Villamizar, Nicolas; Somasundar, Vinay; Megjhani, Murad; Xu, Yan; Lu, Yanbin; Padmanabhan, Raghav; Trett, Kristen; Shain, William; Roysam, Badri

2014-01-01

In this article, we describe the use of Python for large-scale automated server-based bio-image analysis in FARSIGHT, a free and open-source toolkit of image analysis methods for quantitative studies of complex and dynamic tissue microenvironments imaged by modern optical microscopes, including confocal, multi-spectral, multi-photon, and time-lapse systems. The core FARSIGHT modules for image segmentation, feature extraction, tracking, and machine learning are written in C++, leveraging widely used libraries including ITK, VTK, Boost, and Qt. For solving complex image analysis tasks, these modules must be combined into scripts using Python. As a concrete example, we consider the problem of analyzing 3-D multi-spectral images of brain tissue surrounding implanted neuroprosthetic devices, acquired using high-throughput multi-spectral spinning disk step-and-repeat confocal microscopy. The resulting images typically contain 5 fluorescent channels. Each channel consists of 6000 × 10,000 × 500 voxels with 16 bits/voxel, implying image sizes exceeding 250 GB. These images must be mosaicked, pre-processed to overcome imaging artifacts, and segmented to enable cellular-scale feature extraction. The features are used to identify cell types, and perform large-scale analysis for identifying spatial distributions of specific cell types relative to the device. Python was used to build a server-based script (Dell 910 PowerEdge servers with 4 sockets/server with 10 cores each, 2 threads per core and 1TB of RAM running on Red Hat Enterprise Linux linked to a RAID 5 SAN) capable of routinely handling image datasets at this scale and performing all these processing steps in a collaborative multi-user multi-platform environment. Our Python script enables efficient data storage and movement between computers and storage servers, logs all the processing steps, and performs full multi-threaded execution of all codes, including open and closed-source third party libraries.

Open cyberGIS software for geospatial research and education in the big data era

NASA Astrophysics Data System (ADS)

Wang, Shaowen; Liu, Yan; Padmanabhan, Anand

CyberGIS represents an interdisciplinary field combining advanced cyberinfrastructure, geographic information science and systems (GIS), spatial analysis and modeling, and a number of geospatial domains to improve research productivity and enable scientific breakthroughs. It has emerged as new-generation GIS that enable unprecedented advances in data-driven knowledge discovery, visualization and visual analytics, and collaborative problem solving and decision-making. This paper describes three open software strategies-open access, source, and integration-to serve various research and education purposes of diverse geospatial communities. These strategies have been implemented in a leading-edge cyberGIS software environment through three corresponding software modalities: CyberGIS Gateway, Toolkit, and Middleware, and achieved broad and significant impacts.

A qualitative study of clinic and community member perspectives on intervention toolkits: "Unless the toolkit is used it won't help solve the problem".

PubMed

Davis, Melinda M; Howk, Sonya; Spurlock, Margaret; McGinnis, Paul B; Cohen, Deborah J; Fagnan, Lyle J

2017-07-18

Intervention toolkits are common products of grant-funded research in public health and primary care settings. Toolkits are designed to address the knowledge translation gap by speeding implementation and dissemination of research into practice. However, few studies describe characteristics of effective intervention toolkits and their implementation. Therefore, we conducted this study to explore what clinic and community-based users want in intervention toolkits and to identify the factors that support application in practice. In this qualitative descriptive study we conducted focus groups and interviews with a purposive sample of community health coalition members, public health experts, and primary care professionals between November 2010 and January 2012. The transdisciplinary research team used thematic analysis to identify themes and a cross-case comparative analysis to explore variation by participant role and toolkit experience. Ninety six participants representing primary care (n = 54, 56%) and community settings (n = 42, 44%) participated in 18 sessions (13 focus groups, five key informant interviews). Participants ranged from those naïve through expert in toolkit development; many reported limited application of toolkits in actual practice. Participants wanted toolkits targeted at the right audience and demonstrated to be effective. Well organized toolkits, often with a quick start guide, with tools that were easy to tailor and apply were desired. Irrespective of perceived quality, participants experienced with practice change emphasized that leadership, staff buy-in, and facilitative support was essential for intervention toolkits to be translated into changes in clinic or public -health practice. Given the emphasis on toolkits in supporting implementation and dissemination of research and clinical guidelines, studies are warranted to determine when and how toolkits are used. Funders, policy makers, researchers, and leaders in primary care and public health are encouraged to allocate resources to foster both toolkit development and implementation. Support, through practice facilitation and organizational leadership, are critical for translating knowledge from intervention toolkits into practice.

FlowGo: An Educational Kit for Fluid Dynamics and Heat Transfer

NASA Astrophysics Data System (ADS)

Guri, Dominic; Portsmore, Merredith; Kemmerling, Erica

2015-11-01

The authors have designed and prototyped an educational toolkit that will help middle-school-aged students learn fundamental fluid mechanics and heat transfer concepts in a hands-on play environment. The kit allows kids to build arbitrary flow rigs to solve fluid mechanics and heat transfer challenge problems. Similar kits for other engineering fields, such as structural and electrical engineering, have resulted in pedagogical improvements, particularly in early engineering education, where visual demonstrations have a significant impact. Using the FlowGo kit, students will be able to conduct experiments and develop new design ideas to solve challenge problems such as building plant watering systems or modeling water and sewage reticulation. The toolkit consists of components such as tubes, junctions, and reservoirs that easily snap together via a modular, universal connector. Designed with the Massachusetts K-12 science standards in mind, this kit is intended to be affordable and suitable for classroom use. Results and user feedback from students conducting preliminary tests of the kit will be presented.

DynaMIT: the dynamic motif integration toolkit

PubMed Central

Dassi, Erik; Quattrone, Alessandro

2016-01-01

De-novo motif search is a frequently applied bioinformatics procedure to identify and prioritize recurrent elements in sequences sets for biological investigation, such as the ones derived from high-throughput differential expression experiments. Several algorithms have been developed to perform motif search, employing widely different approaches and often giving divergent results. In order to maximize the power of these investigations and ultimately be able to draft solid biological hypotheses, there is the need for applying multiple tools on the same sequences and merge the obtained results. However, motif reporting formats and statistical evaluation methods currently make such an integration task difficult to perform and mostly restricted to specific scenarios. We thus introduce here the Dynamic Motif Integration Toolkit (DynaMIT), an extremely flexible platform allowing to identify motifs employing multiple algorithms, integrate them by means of a user-selected strategy and visualize results in several ways; furthermore, the platform is user-extendible in all its aspects. DynaMIT is freely available at http://cibioltg.bitbucket.org. PMID:26253738

Fast and Exact Fiber Surfaces for Tetrahedral Meshes.

PubMed

Klacansky, Pavol; Tierny, Julien; Carr, Hamish; Zhao Geng

2017-07-01

Isosurfaces are fundamental geometrical objects for the analysis and visualization of volumetric scalar fields. Recent work has generalized them to bivariate volumetric fields with fiber surfaces, the pre-image of polygons in range space. However, the existing algorithm for their computation is approximate, and is limited to closed polygons. Moreover, its runtime performance does not allow instantaneous updates of the fiber surfaces upon user edits of the polygons. Overall, these limitations prevent a reliable and interactive exploration of the space of fiber surfaces. This paper introduces the first algorithm for the exact computation of fiber surfaces in tetrahedral meshes. It assumes no restriction on the topology of the input polygon, handles degenerate cases and better captures sharp features induced by polygon bends. The algorithm also allows visualization of individual fibers on the output surface, better illustrating their relationship with data features in range space. To enable truly interactive exploration sessions, we further improve the runtime performance of this algorithm. In particular, we show that it is trivially parallelizable and that it scales nearly linearly with the number of cores. Further, we study acceleration data-structures both in geometrical domain and range space and we show how to generalize interval trees used in isosurface extraction to fiber surface extraction. Experiments demonstrate the superiority of our algorithm over previous work, both in terms of accuracy and running time, with up to two orders of magnitude speedups. This improvement enables interactive edits of range polygons with instantaneous updates of the fiber surface for exploration purpose. A VTK-based reference implementation is provided as additional material to reproduce our results.

Stroke

MedlinePlus

... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ...

HTC Vive MeVisLab integration via OpenVR for medical applications

PubMed Central

Egger, Jan; Gall, Markus; Wallner, Jürgen; Boechat, Pedro; Hann, Alexander; Li, Xing; Chen, Xiaojun; Schmalstieg, Dieter

2017-01-01

Virtual Reality, an immersive technology that replicates an environment via computer-simulated reality, gets a lot of attention in the entertainment industry. However, VR has also great potential in other areas, like the medical domain, Examples are intervention planning, training and simulation. This is especially of use in medical operations, where an aesthetic outcome is important, like for facial surgeries. Alas, importing medical data into Virtual Reality devices is not necessarily trivial, in particular, when a direct connection to a proprietary application is desired. Moreover, most researcher do not build their medical applications from scratch, but rather leverage platforms like MeVisLab, MITK, OsiriX or 3D Slicer. These platforms have in common that they use libraries like ITK and VTK, and provide a convenient graphical interface. However, ITK and VTK do not support Virtual Reality directly. In this study, the usage of a Virtual Reality device for medical data under the MeVisLab platform is presented. The OpenVR library is integrated into the MeVisLab platform, allowing a direct and uncomplicated usage of the head mounted display HTC Vive inside the MeVisLab platform. Medical data coming from other MeVisLab modules can directly be connected per drag-and-drop to the Virtual Reality module, rendering the data inside the HTC Vive for immersive virtual reality inspection. PMID:28323840

HTC Vive MeVisLab integration via OpenVR for medical applications.

PubMed

Egger, Jan; Gall, Markus; Wallner, Jürgen; Boechat, Pedro; Hann, Alexander; Li, Xing; Chen, Xiaojun; Schmalstieg, Dieter

2017-01-01

Virtual Reality, an immersive technology that replicates an environment via computer-simulated reality, gets a lot of attention in the entertainment industry. However, VR has also great potential in other areas, like the medical domain, Examples are intervention planning, training and simulation. This is especially of use in medical operations, where an aesthetic outcome is important, like for facial surgeries. Alas, importing medical data into Virtual Reality devices is not necessarily trivial, in particular, when a direct connection to a proprietary application is desired. Moreover, most researcher do not build their medical applications from scratch, but rather leverage platforms like MeVisLab, MITK, OsiriX or 3D Slicer. These platforms have in common that they use libraries like ITK and VTK, and provide a convenient graphical interface. However, ITK and VTK do not support Virtual Reality directly. In this study, the usage of a Virtual Reality device for medical data under the MeVisLab platform is presented. The OpenVR library is integrated into the MeVisLab platform, allowing a direct and uncomplicated usage of the head mounted display HTC Vive inside the MeVisLab platform. Medical data coming from other MeVisLab modules can directly be connected per drag-and-drop to the Virtual Reality module, rendering the data inside the HTC Vive for immersive virtual reality inspection.

Varicose Veins

MedlinePlus

... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ...

Tribal Green Building Toolkit

EPA Pesticide Factsheets

This Tribal Green Building Toolkit (Toolkit) is designed to help tribal officials, community members, planners, developers, and architects develop and adopt building codes to support green building practices. Anyone can use this toolkit!

Find an Interventional Radiologist

MedlinePlus

... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ...

Society of Interventional Radiology

MedlinePlus

... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ...

Hereditary Hemorrhagic Telangiectasia - HHT

MedlinePlus

... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ...

Child Abuse - Multiple Languages

MedlinePlus

... Section Healthy Living Toolkit: Violence In the Home - English PDF Healthy Living Toolkit: Violence In the Home - ... Section Healthy Living Toolkit: Violence In the Home - English PDF Healthy Living Toolkit: Violence In the Home - ...

Wind Integration National Dataset Toolkit | Grid Modernization | NREL

Science.gov Websites

information, share tips The WIND Toolkit includes meteorological conditions and turbine power for more than Integration National Dataset Toolkit Wind Integration National Dataset Toolkit The Wind Integration National Dataset (WIND) Toolkit is an update and expansion of the Eastern Wind Integration Data Set and

A Software Agent Toolkit for Effective Information Processing in the Battle Command Domain

DTIC Science & Technology

2006-11-01

the ADE will be based on a popular Integrated Development Environment (IDE) such as NetBeans or Eclipse. We further specified that the IDE is to be...JBuilder, NetBeans , and Eclipse. We quickly eliminated Visual Studio and JBuilder because they did not meet our basic requirements of being Java...based and freely obtainable. This left us with NetBeans and Eclipse. Each is a solid IDE with features that permit extensions well suited to our

Web based tools for visualizing imaging data and development of XNATView, a zero footprint image viewer

PubMed Central

Gutman, David A.; Dunn, William D.; Cobb, Jake; Stoner, Richard M.; Kalpathy-Cramer, Jayashree; Erickson, Bradley

2014-01-01

Advances in web technologies now allow direct visualization of imaging data sets without necessitating the download of large file sets or the installation of software. This allows centralization of file storage and facilitates image review and analysis. XNATView is a light framework recently developed in our lab to visualize DICOM images stored in The Extensible Neuroimaging Archive Toolkit (XNAT). It consists of a PyXNAT-based framework to wrap around the REST application programming interface (API) and query the data in XNAT. XNATView was developed to simplify quality assurance, help organize imaging data, and facilitate data sharing for intra- and inter-laboratory collaborations. Its zero-footprint design allows the user to connect to XNAT from a web browser, navigate through projects, experiments, and subjects, and view DICOM images with accompanying metadata all within a single viewing instance. PMID:24904399

Chronic pelvic pain (pelvic congestion syndrome)

MedlinePlus

... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ...

VAAPA: a web platform for visualization and analysis of alternative polyadenylation.

PubMed

Guan, Jinting; Fu, Jingyi; Wu, Mingcheng; Chen, Longteng; Ji, Guoli; Quinn Li, Qingshun; Wu, Xiaohui

2015-02-01

Polyadenylation [poly(A)] is an essential process during the maturation of most mRNAs in eukaryotes. Alternative polyadenylation (APA) as an important layer of gene expression regulation has been increasingly recognized in various species. Here, a web platform for visualization and analysis of alternative polyadenylation (VAAPA) was developed. This platform can visualize the distribution of poly(A) sites and poly(A) clusters of a gene or a section of a chromosome. It can also highlight genes with switched APA sites among different conditions. VAAPA is an easy-to-use web-based tool that provides functions of poly(A) site query, data uploading, downloading, and APA sites visualization. It was designed in a multi-tier architecture and developed based on Smart GWT (Google Web Toolkit) using Java as the development language. VAAPA will be a valuable addition to the community for the comprehensive study of APA, not only by making the high quality poly(A) site data more accessible, but also by providing users with numerous valuable functions for poly(A) site analysis and visualization. Copyright © 2014 Elsevier Ltd. All rights reserved.

Towards a Web-Enabled Geovisualization and Analytics Platform for the Energy and Water Nexus

NASA Astrophysics Data System (ADS)

Sanyal, J.; Chandola, V.; Sorokine, A.; Allen, M.; Berres, A.; Pang, H.; Karthik, R.; Nugent, P.; McManamay, R.; Stewart, R.; Bhaduri, B. L.

2017-12-01

Interactive data analytics are playing an increasingly vital role in the generation of new, critical insights regarding the complex dynamics of the energy/water nexus (EWN) and its interactions with climate variability and change. Integration of impacts, adaptation, and vulnerability (IAV) science with emerging, and increasingly critical, data science capabilities offers a promising potential to meet the needs of the EWN community. To enable the exploration of pertinent research questions, a web-based geospatial visualization platform is being built that integrates a data analysis toolbox with advanced data fusion and data visualization capabilities to create a knowledge discovery framework for the EWN. The system, when fully built out, will offer several geospatial visualization capabilities including statistical visual analytics, clustering, principal-component analysis, dynamic time warping, support uncertainty visualization and the exploration of data provenance, as well as support machine learning discoveries to render diverse types of geospatial data and facilitate interactive analysis. Key components in the system architecture includes NASA's WebWorldWind, the Globus toolkit, postgresql, as well as other custom built software modules.

A Qualitative Evaluation of Web-Based Cancer Care Quality Improvement Toolkit Use in the Veterans Health Administration.

PubMed

Bowman, Candice; Luck, Jeff; Gale, Randall C; Smith, Nina; York, Laura S; Asch, Steven

2015-01-01

Disease severity, complexity, and patient burden highlight cancer care as a target for quality improvement (QI) interventions. The Veterans Health Administration (VHA) implemented a series of disease-specific online cancer care QI toolkits. To describe characteristics of the toolkits, target users, and VHA cancer care facilities that influenced toolkit access and use and assess whether such resources were beneficial for users. Deductive content analysis of detailed notes from 94 telephone interviews with individuals from 48 VHA facilities. We evaluated toolkit access and use across cancer types, participation in learning collaboratives, and affiliation with VHA cancer care facilities. The presence of champions was identified as a strong facilitator of toolkit use, and learning collaboratives were important for spreading information about toolkit availability. Identified barriers included lack of personnel and financial resources and complicated approval processes to support tool use. Online cancer care toolkits are well received across cancer specialties and provider types. Clinicians, administrators, and QI staff may benefit from the availability of toolkits as they become more reliant on rapid access to strategies that support comprehensive delivery of evidence-based care. Toolkits should be considered as a complement to other QI approaches.

Data Visualization Challenges and Opportunities in User-Oriented Application Development

NASA Astrophysics Data System (ADS)

Pilone, D.; Quinn, P.; Mitchell, A. E.; Baynes, K.; Shum, D.

2015-12-01

This talk introduces the audience to some of the very real challenges associated with visualizing data from disparate data sources as encountered during the development of real world applications. In addition to the fundamental challenges of dealing with the data and imagery, this talk discusses usability problems encountered while trying to provide interactive and user-friendly visualization tools. At the end of this talk the audience will be aware of some of the pitfalls of data visualization along with tools and techniques to help mitigate them. There are many sources of variable resolution visualizations of science data available to application developers including NASA's Global Imagery Browse Services (GIBS), however integrating and leveraging visualizations in modern applications faces a number of challenges, including: - Varying visualized Earth "tile sizes" resulting in challenges merging disparate sources - Multiple visualization frameworks and toolkits with varying strengths and weaknesses - Global composite imagery vs. imagery matching EOSDIS granule distribution - Challenges visualizing geographically overlapping data with different temporal bounds - User interaction with overlapping or collocated data - Complex data boundaries and shapes combined with multi-orbit data and polar projections - Discovering the availability of visualizations and the specific parameters, color palettes, and configurations used to produce them In addition to discussing the challenges and approaches involved in visualizing disparate data, we will discuss solutions and components we'll be making available as open source to encourage reuse and accelerate application development.

Software Aids Visualization of Computed Unsteady Flow

NASA Technical Reports Server (NTRS)

Kao, David; Kenwright, David

2003-01-01

Unsteady Flow Analysis Toolkit (UFAT) is a computer program that synthesizes motions of time-dependent flows represented by very large sets of data generated in computational fluid dynamics simulations. Prior to the development of UFAT, it was necessary to rely on static, single-snapshot depictions of time-dependent flows generated by flow-visualization software designed for steady flows. Whereas it typically takes weeks to analyze the results of a largescale unsteady-flow simulation by use of steady-flow visualization software, the analysis time is reduced to hours when UFAT is used. UFAT can be used to generate graphical objects of flow visualization results using multi-block curvilinear grids in the format of a previously developed NASA data-visualization program, PLOT3D. These graphical objects can be rendered using FAST, another popular flow visualization software developed at NASA. Flow-visualization techniques that can be exploited by use of UFAT include time-dependent tracking of particles, detection of vortex cores, extractions of stream ribbons and surfaces, and tetrahedral decomposition for optimal particle tracking. Unique computational features of UFAT include capabilities for automatic (batch) processing, restart, memory mapping, and parallel processing. These capabilities significantly reduce analysis time and storage requirements, relative to those of prior flow-visualization software. UFAT can be executed on a variety of supercomputers.

EHDViz: clinical dashboard development using open-source technologies

PubMed Central

Badgeley, Marcus A; Shameer, Khader; Glicksberg, Benjamin S; Tomlinson, Max S; Levin, Matthew A; McCormick, Patrick J; Kasarskis, Andrew; Reich, David L; Dudley, Joel T

2016-01-01

Objective To design, develop and prototype clinical dashboards to integrate high-frequency health and wellness data streams using interactive and real-time data visualisation and analytics modalities. Materials and methods We developed a clinical dashboard development framework called electronic healthcare data visualization (EHDViz) toolkit for generating web-based, real-time clinical dashboards for visualising heterogeneous biomedical, healthcare and wellness data. The EHDViz is an extensible toolkit that uses R packages for data management, normalisation and producing high-quality visualisations over the web using R/Shiny web server architecture. We have developed use cases to illustrate utility of EHDViz in different scenarios of clinical and wellness setting as a visualisation aid for improving healthcare delivery. Results Using EHDViz, we prototyped clinical dashboards to demonstrate the contextual versatility of EHDViz toolkit. An outpatient cohort was used to visualise population health management tasks (n=14 221), and an inpatient cohort was used to visualise real-time acuity risk in a clinical unit (n=445), and a quantified-self example using wellness data from a fitness activity monitor worn by a single individual was also discussed (n-of-1). The back-end system retrieves relevant data from data source, populates the main panel of the application and integrates user-defined data features in real-time and renders output using modern web browsers. The visualisation elements can be customised using health features, disease names, procedure names or medical codes to populate the visualisations. The source code of EHDViz and various prototypes developed using EHDViz are available in the public domain at http://ehdviz.dudleylab.org. Conclusions Collaborative data visualisations, wellness trend predictions, risk estimation, proactive acuity status monitoring and knowledge of complex disease indicators are essential components of implementing data-driven precision medicine. As an open-source visualisation framework capable of integrating health assessment, EHDViz aims to be a valuable toolkit for rapid design, development and implementation of scalable clinical data visualisation dashboards. PMID:27013597

The Seismic Tool-Kit (STK): an open source software for seismology and signal processing.

NASA Astrophysics Data System (ADS)

Reymond, Dominique

2016-04-01

We present an open source software project (GNU public license), named STK: Seismic ToolKit, that is dedicated mainly for seismology and signal processing. The STK project that started in 2007, is hosted by SourceForge.net, and count more than 19 500 downloads at the date of writing. The STK project is composed of two main branches: First, a graphical interface dedicated to signal processing (in the SAC format (SAC_ASCII and SAC_BIN): where the signal can be plotted, zoomed, filtered, integrated, derivated, ... etc. (a large variety of IFR and FIR filter is proposed). The estimation of spectral density of the signal are performed via the Fourier transform, with visualization of the Power Spectral Density (PSD) in linear or log scale, and also the evolutive time-frequency representation (or sonagram). The 3-components signals can be also processed for estimating their polarization properties, either for a given window, or either for evolutive windows along the time. This polarization analysis is useful for extracting the polarized noises, differentiating P waves, Rayleigh waves, Love waves, ... etc. Secondly, a panel of Utilities-Program are proposed for working in a terminal mode, with basic programs for computing azimuth and distance in spherical geometry, inter/auto-correlation, spectral density, time-frequency for an entire directory of signals, focal planes, and main components axis, radiation pattern of P waves, Polarization analysis of different waves (including noize), under/over-sampling the signals, cubic-spline smoothing, and linear/non linear regression analysis of data set. A MINimum library of Linear AlGebra (MIN-LINAG) is also provided for computing the main matrix process like: QR/QL decomposition, Cholesky solve of linear system, finding eigen value/eigen vectors, QR-solve/Eigen-solve of linear equations systems ... etc. STK is developed in C/C++, mainly under Linux OS, and it has been also partially implemented under MS-Windows. Usefull links: http://sourceforge.net/projects/seismic-toolkit/ http://sourceforge.net/p/seismic-toolkit/wiki/browse_pages/

Integration of the HTC Vive into the medical platform MeVisLab

NASA Astrophysics Data System (ADS)

Egger, Jan; Gall, Markus; Wallner, Jürgen; de Almeida Germano Boechat, Pedro; Hann, Alexander; Li, Xing; Chen, Xiaojun; Schmalstieg, Dieter

2017-03-01

Virtual Reality (VR) is an immersive technology that replicates an environment via computer-simulated reality. VR gets a lot of attention in computer games but has also great potential in other areas, like the medical domain. Examples are planning, simulations and training of medical interventions, like for facial surgeries where an aesthetic outcome is important. However, importing medical data into VR devices is not trivial, especially when a direct connection and visualization from your own application is needed. Furthermore, most researcher don't build their medical applications from scratch, rather they use platforms, like MeVisLab, Slicer or MITK. The platforms have in common that they integrate and build upon on libraries like ITK and VTK, further providing a more convenient graphical interface to them for the user. In this contribution, we demonstrate the usage of a VR device for medical data under MeVisLab. Therefore, we integrated the OpenVR library into MeVisLab as an own module. This enables the direct and uncomplicated usage of head mounted displays, like the HTC Vive under MeVisLab. Summarized, medical data from other MeVisLab modules can directly be connected per drag-and-drop to our VR module and will be rendered inside the HTC Vive for an immersive inspection.

Every Place Counts Leadership Academy : transportation toolkit quick guide

DOT National Transportation Integrated Search

2016-12-01

This is a quick guide to the Transportation Toolkit. The Transportation Toolkit is meant to explain the transportation process to members of the public with no prior knowledge of transportation. The Toolkit is meant to demystify transportation and he...

Object Toolkit Version 4.3 User’s Manual

DTIC Science & Technology

2016-12-31

unlimited. (OPS-17-12855 dtd 19 Jan 2017) 13. SUPPLEMENTARY NOTES 14. ABSTRACT Object Toolkit is a finite - element model builder specifically designed for...INTRODUCTION 1 What Is Object Toolkit? Object Toolkit is a finite - element model builder specifically designed for creating representations of spacecraft...Nascap-2k and EPIC, the user is not required to purchase or learn expensive finite element generators to create system models. Second, Object Toolkit

Overview of EVE - the event visualization environment of ROOT

NASA Astrophysics Data System (ADS)

Tadel, Matevž

2010-04-01

EVE is a high-level visualization library using ROOT's data-processing, GUI and OpenGL interfaces. It is designed as a framework for object management offering hierarchical data organization, object interaction and visualization via GUI and OpenGL representations. Automatic creation of 2D projected views is also supported. On the other hand, it can serve as an event visualization toolkit satisfying most HEP requirements: visualization of geometry, simulated and reconstructed data such as hits, clusters, tracks and calorimeter information. Special classes are available for visualization of raw-data. Object-interaction layer allows for easy selection and highlighting of objects and their derived representations (projections) across several views (3D, Rho-Z, R-Phi). Object-specific tooltips are provided in both GUI and GL views. The visual-configuration layer of EVE is built around a data-base of template objects that can be applied to specific instances of visualization objects to ensure consistent object presentation. The data-base can be retrieved from a file, edited during the framework operation and stored to file. EVE prototype was developed within the ALICE collaboration and has been included into ROOT in December 2007. Since then all EVE components have reached maturity. EVE is used as the base of AliEve visualization framework in ALICE, Firework physics-oriented event-display in CMS, and as the visualization engine of FairRoot in FAIR.

Near Real Time Integration of Satellite and Radar Data for Probabilistic Nearcasting of Severe Weather

NASA Astrophysics Data System (ADS)

Pilone, D.; Quinn, P.; Mitchell, A. E.; Baynes, K.; Shum, D.

2014-12-01

This talk introduces the audience to some of the very real challenges associated with visualizing data from disparate data sources as encountered during the development of real world applications. In addition to the fundamental challenges of dealing with the data and imagery, this talk discusses usability problems encountered while trying to provide interactive and user-friendly visualization tools. At the end of this talk the audience will be aware of some of the pitfalls of data visualization along with tools and techniques to help mitigate them. There are many sources of variable resolution visualizations of science data available to application developers including NASA's Global Imagery Browse Services (GIBS), however integrating and leveraging visualizations in modern applications faces a number of challenges, including: - Varying visualized Earth "tile sizes" resulting in challenges merging disparate sources - Multiple visualization frameworks and toolkits with varying strengths and weaknesses - Global composite imagery vs. imagery matching EOSDIS granule distribution - Challenges visualizing geographically overlapping data with different temporal bounds - User interaction with overlapping or collocated data - Complex data boundaries and shapes combined with multi-orbit data and polar projections - Discovering the availability of visualizations and the specific parameters, color palettes, and configurations used to produce them In addition to discussing the challenges and approaches involved in visualizing disparate data, we will discuss solutions and components we'll be making available as open source to encourage reuse and accelerate application development.

Exploring High-D Spaces with Multiform Matrices and Small Multiples

PubMed Central

MacEachren, Alan; Dai, Xiping; Hardisty, Frank; Guo, Diansheng; Lengerich, Gene

2011-01-01

We introduce an approach to visual analysis of multivariate data that integrates several methods from information visualization, exploratory data analysis (EDA), and geovisualization. The approach leverages the component-based architecture implemented in GeoVISTA Studio to construct a flexible, multiview, tightly (but generically) coordinated, EDA toolkit. This toolkit builds upon traditional ideas behind both small multiples and scatterplot matrices in three fundamental ways. First, we develop a general, MultiForm, Bivariate Matrix and a complementary MultiForm, Bivariate Small Multiple plot in which different bivariate representation forms can be used in combination. We demonstrate the flexibility of this approach with matrices and small multiples that depict multivariate data through combinations of: scatterplots, bivariate maps, and space-filling displays. Second, we apply a measure of conditional entropy to (a) identify variables from a high-dimensional data set that are likely to display interesting relationships and (b) generate a default order of these variables in the matrix or small multiple display. Third, we add conditioning, a kind of dynamic query/filtering in which supplementary (undisplayed) variables are used to constrain the view onto variables that are displayed. Conditioning allows the effects of one or more well understood variables to be removed from the analysis, making relationships among remaining variables easier to explore. We illustrate the individual and combined functionality enabled by this approach through application to analysis of cancer diagnosis and mortality data and their associated covariates and risk factors. PMID:21947129

"Handy Manny" and the Emergent Literacy Technology Toolkit

ERIC Educational Resources Information Center

Hourcade, Jack J.; Parette, Howard P., Jr.; Boeckmann, Nichole; Blum, Craig

2010-01-01

This paper outlines the use of a technology toolkit to support emergent literacy curriculum and instruction in early childhood education settings. Components of the toolkit include hardware and software that can facilitate key emergent literacy skills. Implementation of the comprehensive technology toolkit enhances the development of these…

Risk of Resource Failure and Toolkit Variation in Small-Scale Farmers and Herders

PubMed Central

Collard, Mark; Ruttle, April; Buchanan, Briggs; O’Brien, Michael J.

2012-01-01

Recent work suggests that global variation in toolkit structure among hunter-gatherers is driven by risk of resource failure such that as risk of resource failure increases, toolkits become more diverse and complex. Here we report a study in which we investigated whether the toolkits of small-scale farmers and herders are influenced by risk of resource failure in the same way. In the study, we applied simple linear and multiple regression analysis to data from 45 small-scale food-producing groups to test the risk hypothesis. Our results were not consistent with the hypothesis; none of the risk variables we examined had a significant impact on toolkit diversity or on toolkit complexity. It appears, therefore, that the drivers of toolkit structure differ between hunter-gatherers and small-scale food-producers. PMID:22844421

The effectiveness of toolkits as knowledge translation strategies for integrating evidence into clinical care: a systematic review

PubMed Central

Yamada, Janet; Shorkey, Allyson; Barwick, Melanie; Widger, Kimberley; Stevens, Bonnie J

2015-01-01

Objectives The aim of this systematic review was to evaluate the effectiveness of toolkits as a knowledge translation (KT) strategy for facilitating the implementation of evidence into clinical care. Toolkits include multiple resources for educating and/or facilitating behaviour change. Design Systematic review of the literature on toolkits. Methods A search was conducted on MEDLINE, EMBASE, PsycINFO and CINAHL. Studies were included if they evaluated the effectiveness of a toolkit to support the integration of evidence into clinical care, and if the KT goal(s) of the study were to inform, share knowledge, build awareness, change practice, change behaviour, and/or clinical outcomes in healthcare settings, inform policy, or to commercialise an innovation. Screening of studies, assessment of methodological quality and data extraction for the included studies were conducted by at least two reviewers. Results 39 relevant studies were included for full review; 8 were rated as moderate to strong methodologically with clinical outcomes that could be somewhat attributed to the toolkit. Three of the eight studies evaluated the toolkit as a single KT intervention, while five embedded the toolkit into a multistrategy intervention. Six of the eight toolkits were partially or mostly effective in changing clinical outcomes and six studies reported on implementation outcomes. The types of resources embedded within toolkits varied but included predominantly educational materials. Conclusions Future toolkits should be informed by high-quality evidence and theory, and should be evaluated using rigorous study designs to explain the factors underlying their effectiveness and successful implementation. PMID:25869686

BCM: toolkit for Bayesian analysis of Computational Models using samplers.

PubMed

Thijssen, Bram; Dijkstra, Tjeerd M H; Heskes, Tom; Wessels, Lodewyk F A

2016-10-21

Computational models in biology are characterized by a large degree of uncertainty. This uncertainty can be analyzed with Bayesian statistics, however, the sampling algorithms that are frequently used for calculating Bayesian statistical estimates are computationally demanding, and each algorithm has unique advantages and disadvantages. It is typically unclear, before starting an analysis, which algorithm will perform well on a given computational model. We present BCM, a toolkit for the Bayesian analysis of Computational Models using samplers. It provides efficient, multithreaded implementations of eleven algorithms for sampling from posterior probability distributions and for calculating marginal likelihoods. BCM includes tools to simplify the process of model specification and scripts for visualizing the results. The flexible architecture allows it to be used on diverse types of biological computational models. In an example inference task using a model of the cell cycle based on ordinary differential equations, BCM is significantly more efficient than existing software packages, allowing more challenging inference problems to be solved. BCM represents an efficient one-stop-shop for computational modelers wishing to use sampler-based Bayesian statistics.

PRISM: An open source framework for the interactive design of GPU volume rendering shaders.

PubMed

Drouin, Simon; Collins, D Louis

2018-01-01

Direct volume rendering has become an essential tool to explore and analyse 3D medical images. Despite several advances in the field, it remains a challenge to produce an image that highlights the anatomy of interest, avoids occlusion of important structures, provides an intuitive perception of shape and depth while retaining sufficient contextual information. Although the computer graphics community has proposed several solutions to address specific visualization problems, the medical imaging community still lacks a general volume rendering implementation that can address a wide variety of visualization use cases while avoiding complexity. In this paper, we propose a new open source framework called the Programmable Ray Integration Shading Model, or PRISM, that implements a complete GPU ray-casting solution where critical parts of the ray integration algorithm can be replaced to produce new volume rendering effects. A graphical user interface allows clinical users to easily experiment with pre-existing rendering effect building blocks drawn from an open database. For programmers, the interface enables real-time editing of the code inside the blocks. We show that in its default mode, the PRISM framework produces images very similar to those produced by a widely-adopted direct volume rendering implementation in VTK at comparable frame rates. More importantly, we demonstrate the flexibility of the framework by showing how several volume rendering techniques can be implemented in PRISM with no more than a few lines of code. Finally, we demonstrate the simplicity of our system in a usability study with 5 medical imaging expert subjects who have none or little experience with volume rendering. The PRISM framework has the potential to greatly accelerate development of volume rendering for medical applications by promoting sharing and enabling faster development iterations and easier collaboration between engineers and clinical personnel.

PRISM: An open source framework for the interactive design of GPU volume rendering shaders

PubMed Central

Collins, D. Louis

2018-01-01

Direct volume rendering has become an essential tool to explore and analyse 3D medical images. Despite several advances in the field, it remains a challenge to produce an image that highlights the anatomy of interest, avoids occlusion of important structures, provides an intuitive perception of shape and depth while retaining sufficient contextual information. Although the computer graphics community has proposed several solutions to address specific visualization problems, the medical imaging community still lacks a general volume rendering implementation that can address a wide variety of visualization use cases while avoiding complexity. In this paper, we propose a new open source framework called the Programmable Ray Integration Shading Model, or PRISM, that implements a complete GPU ray-casting solution where critical parts of the ray integration algorithm can be replaced to produce new volume rendering effects. A graphical user interface allows clinical users to easily experiment with pre-existing rendering effect building blocks drawn from an open database. For programmers, the interface enables real-time editing of the code inside the blocks. We show that in its default mode, the PRISM framework produces images very similar to those produced by a widely-adopted direct volume rendering implementation in VTK at comparable frame rates. More importantly, we demonstrate the flexibility of the framework by showing how several volume rendering techniques can be implemented in PRISM with no more than a few lines of code. Finally, we demonstrate the simplicity of our system in a usability study with 5 medical imaging expert subjects who have none or little experience with volume rendering. The PRISM framework has the potential to greatly accelerate development of volume rendering for medical applications by promoting sharing and enabling faster development iterations and easier collaboration between engineers and clinical personnel. PMID:29534069

Multimethod evaluation of the VA's peer-to-peer Toolkit for patient-centered medical home implementation.

PubMed

Luck, Jeff; Bowman, Candice; York, Laura; Midboe, Amanda; Taylor, Thomas; Gale, Randall; Asch, Steven

2014-07-01

Effective implementation of the patient-centered medical home (PCMH) in primary care practices requires training and other resources, such as online toolkits, to share strategies and materials. The Veterans Health Administration (VA) developed an online Toolkit of user-sourced tools to support teams implementing its Patient Aligned Care Team (PACT) medical home model. To present findings from an evaluation of the PACT Toolkit, including use, variation across facilities, effect of social marketing, and factors influencing use. The Toolkit is an online repository of ready-to-use tools created by VA clinic staff that physicians, nurses, and other team members may share, download, and adopt in order to more effectively implement PCMH principles and improve local performance on VA metrics. Multimethod evaluation using: (1) website usage analytics, (2) an online survey of the PACT community of practice's use of the Toolkit, and (3) key informant interviews. Survey respondents were PACT team members and coaches (n = 544) at 136 VA facilities. Interview respondents were Toolkit users and non-users (n = 32). For survey data, multivariable logistic models were used to predict Toolkit awareness and use. Interviews and open-text survey comments were coded using a "common themes" framework. The Consolidated Framework for Implementation Research (CFIR) guided data collection and analyses. The Toolkit was used by 6,745 staff in the first 19 months of availability. Among members of the target audience, 80 % had heard of the Toolkit, and of those, 70 % had visited the website. Tools had been implemented at 65 % of facilities. Qualitative findings revealed a range of user perspectives from enthusiastic support to lack of sufficient time to browse the Toolkit. An online Toolkit to support PCMH implementation was used at VA facilities nationwide. Other complex health care organizations may benefit from adopting similar online peer-to-peer resource libraries.

Evaluation of an Extension-Delivered Resource for Accelerating Progress in Childhood Obesity Prevention: The BEPA-Toolkit

ERIC Educational Resources Information Center

Gunter, Katherine B.; Abi Nader, Patrick; Armington, Amanda; Hicks, John C.; John, Deborah

2017-01-01

The Balanced Energy Physical Activity Toolkit, or the BEPA-Toolkit, supports physical activity (PA) programming via Extension in elementary schools. In a pilot study, we evaluated the effectiveness of the BEPA-Toolkit as used by teachers through Supplemental Nutrition Assistance Program Education partnerships. We surveyed teachers (n = 57)…

A Software Tool for Estimation of Burden of Infectious Diseases in Europe Using Incidence-Based Disability Adjusted Life Years

PubMed Central

Lewandowski, Daniel; Mangen, Marie-Josee J.; Plass, Dietrich; McDonald, Scott A.; van Lier, Alies; Haagsma, Juanita A.; Maringhini, Guido; Pini, Alessandro; Kramarz, Piotr; Kretzschmar, Mirjam E.

2017-01-01

The burden of disease framework facilitates the assessment of the health impact of diseases through the use of summary measures of population health such as Disability-Adjusted Life Years (DALYs). However, calculating, interpreting and communicating the results of studies using this methodology poses a challenge. The aim of the Burden of Communicable Disease in Europe (BCoDE) project is to summarize the impact of communicable disease in the European Union and European Economic Area Member States (EU/EEA MS). To meet this goal, a user-friendly software tool (BCoDE toolkit), was developed. This stand-alone application, written in C++, is open-access and freely available for download from the website of the European Centre for Disease Prevention and Control (ECDC). With the BCoDE toolkit, one can calculate DALYs by simply entering the age group- and sex-specific number of cases for one or more of selected sets of 32 communicable diseases (CDs) and 6 healthcare associated infections (HAIs). Disease progression models (i.e., outcome trees) for these communicable diseases were created following a thorough literature review of their disease progression pathway. The BCoDE toolkit runs Monte Carlo simulations of the input parameters and provides disease-specific results, including 95% uncertainty intervals, and permits comparisons between the different disease models entered. Results can be displayed as mean and median overall DALYs, DALYs per 100,000 population, and DALYs related to mortality vs. disability. Visualization options summarize complex epidemiological data, with the goal of improving communication and knowledge transfer for decision-making. PMID:28107447

ASERA: A spectrum eye recognition assistant for quasar spectra

NASA Astrophysics Data System (ADS)

Yuan, Hailong; Zhang, Haotong; Zhang, Yanxia; Lei, Yajuan; Dong, Yiqiao; Zhao, Yongheng

2013-11-01

Spectral type recognition is an important and fundamental step of large sky survey projects in the data reduction for further scientific research, like parameter measurement and statistic work. It tends out to be a huge job to manually inspect the low quality spectra produced from the massive spectroscopic survey, where the automatic pipeline may not provide confident type classification results. In order to improve the efficiency and effectiveness of spectral classification, we develop a semi-automated toolkit named ASERA, ASpectrum Eye Recognition Assistant. The main purpose of ASERA is to help the user in quasar spectral recognition and redshift measurement. Furthermore it can also be used to recognize various types of spectra of stars, galaxies and AGNs (Active Galactic Nucleus). It is an interactive software allowing the user to visualize observed spectra, superimpose template spectra from the Sloan Digital Sky Survey (SDSS), and interactively access related spectral line information. It is an efficient and user-friendly toolkit for the accurate classification of spectra observed by LAMOST (the Large Sky Area Multi-object Fiber Spectroscopic Telescope). The toolkit is available in two modes: a Java standalone application and a Java applet. ASERA has a few functions, such as wavelength and flux scale setting, zoom in and out, redshift estimation, spectral line identification, which helps user to improve the spectral classification accuracy especially for low quality spectra and reduce the labor of eyeball check. The function and performance of this tool is displayed through the recognition of several quasar spectra and a late type stellar spectrum from the LAMOST Pilot survey. Its future expansion capabilities are discussed.

A Software Tool for Estimation of Burden of Infectious Diseases in Europe Using Incidence-Based Disability Adjusted Life Years.

PubMed

Colzani, Edoardo; Cassini, Alessandro; Lewandowski, Daniel; Mangen, Marie-Josee J; Plass, Dietrich; McDonald, Scott A; van Lier, Alies; Haagsma, Juanita A; Maringhini, Guido; Pini, Alessandro; Kramarz, Piotr; Kretzschmar, Mirjam E

2017-01-01

The burden of disease framework facilitates the assessment of the health impact of diseases through the use of summary measures of population health such as Disability-Adjusted Life Years (DALYs). However, calculating, interpreting and communicating the results of studies using this methodology poses a challenge. The aim of the Burden of Communicable Disease in Europe (BCoDE) project is to summarize the impact of communicable disease in the European Union and European Economic Area Member States (EU/EEA MS). To meet this goal, a user-friendly software tool (BCoDE toolkit), was developed. This stand-alone application, written in C++, is open-access and freely available for download from the website of the European Centre for Disease Prevention and Control (ECDC). With the BCoDE toolkit, one can calculate DALYs by simply entering the age group- and sex-specific number of cases for one or more of selected sets of 32 communicable diseases (CDs) and 6 healthcare associated infections (HAIs). Disease progression models (i.e., outcome trees) for these communicable diseases were created following a thorough literature review of their disease progression pathway. The BCoDE toolkit runs Monte Carlo simulations of the input parameters and provides disease-specific results, including 95% uncertainty intervals, and permits comparisons between the different disease models entered. Results can be displayed as mean and median overall DALYs, DALYs per 100,000 population, and DALYs related to mortality vs. disability. Visualization options summarize complex epidemiological data, with the goal of improving communication and knowledge transfer for decision-making.

An Integrated Multivariable Visualization Tool for Marine Sanctuary Climate Assessments

NASA Astrophysics Data System (ADS)

Shein, K. A.; Johnston, S.; Stachniewicz, J.; Duncan, B.; Cecil, D.; Ansari, S.; Urzen, M.

2012-12-01

The comprehensive development and use of ecological climate impact assessments by ecosystem managers can be limited by data access and visualization methods that require a priori knowledge about the various large and complex climate data products necessary to those impact assessments. In addition, it can be difficult to geographically and temporally integrate climate and ecological data to fully characterize climate-driven ecological impacts. To address these considerations, we have enhanced and extended the functionality of the NOAA National Climatic Data Center's Weather and Climate Toolkit (WCT). The WCT is a freely available Java-based tool designed to access and display NCDC's georeferenced climate data products (e.g., satellite, radar, and reanalysis gridded data). However, the WCT requires users already know how to obtain the data products, which products are preferred for a given variable, and which products are most relevant to their needs. Developed in cooperation with research and management customers at the Gulf of the Farallones National Marine Sanctuary, the Integrated Marine Protected Area Climate Tools (IMPACT) modification to the WCT simplifies or eliminates these requirements, while simultaneously adding core analytical functionality to the tool. Designed for use by marine ecosystem managers, WCT-IMPACT accesses a suite of data products that have been identified as relevant to marine ecosystem climate impact assessments, such as NOAA's Climate Data Records. WCT-IMPACT regularly crops these products to the geographic boundaries of each included marine protected area (MPA), and those clipped regions are processed to produce MPA-specific analytics. The tool retrieves the most appropriate data files based on the user selection of MPA, environmental variable(s), and time frame. Once the data are loaded, they may be visualized, explored, analyzed, and exported to other formats (e.g., Google KML). Multiple variables may be simultaneously visualized using a 4-panel display and compared via a variety of statistics such as difference, probability, or correlation maps.; NCDC's Weather and Climate Toolkit image of NARR-A non-convective cloud cover (%) over the Pacific Coast on June 17, 2012 at 09:00 GMT.

MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data

PubMed Central

Moore, Eider B; Poliakov, Andrew V; Lincoln, Peter; Brinkley, James F

2007-01-01

Background Three-dimensional (3-D) visualization of multimodality neuroimaging data provides a powerful technique for viewing the relationship between structure and function. A number of applications are available that include some aspect of 3-D visualization, including both free and commercial products. These applications range from highly specific programs for a single modality, to general purpose toolkits that include many image processing functions in addition to visualization. However, few if any of these combine both stand-alone and remote multi-modality visualization in an open source, portable and extensible tool that is easy to install and use, yet can be included as a component of a larger information system. Results We have developed a new open source multimodality 3-D visualization application, called MindSeer, that has these features: integrated and interactive 3-D volume and surface visualization, Java and Java3D for true cross-platform portability, one-click installation and startup, integrated data management to help organize large studies, extensibility through plugins, transparent remote visualization, and the ability to be integrated into larger information management systems. We describe the design and implementation of the system, as well as several case studies that demonstrate its utility. These case studies are available as tutorials or demos on the associated website: . Conclusion MindSeer provides a powerful visualization tool for multimodality neuroimaging data. Its architecture and unique features also allow it to be extended into other visualization domains within biomedicine. PMID:17937818

MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data.

PubMed

Moore, Eider B; Poliakov, Andrew V; Lincoln, Peter; Brinkley, James F

2007-10-15

Three-dimensional (3-D) visualization of multimodality neuroimaging data provides a powerful technique for viewing the relationship between structure and function. A number of applications are available that include some aspect of 3-D visualization, including both free and commercial products. These applications range from highly specific programs for a single modality, to general purpose toolkits that include many image processing functions in addition to visualization. However, few if any of these combine both stand-alone and remote multi-modality visualization in an open source, portable and extensible tool that is easy to install and use, yet can be included as a component of a larger information system. We have developed a new open source multimodality 3-D visualization application, called MindSeer, that has these features: integrated and interactive 3-D volume and surface visualization, Java and Java3D for true cross-platform portability, one-click installation and startup, integrated data management to help organize large studies, extensibility through plugins, transparent remote visualization, and the ability to be integrated into larger information management systems. We describe the design and implementation of the system, as well as several case studies that demonstrate its utility. These case studies are available as tutorials or demos on the associated website: http://sig.biostr.washington.edu/projects/MindSeer. MindSeer provides a powerful visualization tool for multimodality neuroimaging data. Its architecture and unique features also allow it to be extended into other visualization domains within biomedicine.

JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals.

PubMed

Rosen, Jebediah; Handy, Kyle; Gillan, André; Smith, Rob

2017-11-06

Despite the ubiquity of mass spectrometry (MS), data processing tools can be surprisingly limited. To date, there is no stand-alone, cross-platform 3-D visualizer for MS data. Available visualization toolkits require large libraries with multiple dependencies and are not well suited for custom MS data processing modules, such as MS storage systems or data processing algorithms. We present JS-MS, a 3-D, modular JavaScript client application for viewing MS data. JS-MS provides several advantages over existing MS viewers, such as a dependency-free, browser-based, one click, cross-platform install and better navigation interfaces. The client includes a modular Java backend with a novel streaming.mzML parser to demonstrate the API-based serving of MS data to the viewer. JS-MS enables custom MS data processing and evaluation by providing fast, 3-D visualization using improved navigation without dependencies. JS-MS is publicly available with a GPLv2 license at github.com/optimusmoose/jsms.

Implementing a user-driven online quality improvement toolkit for cancer care.

PubMed

Luck, Jeff; York, Laura S; Bowman, Candice; Gale, Randall C; Smith, Nina; Asch, Steven M

2015-05-01

Peer-to-peer collaboration within integrated health systems requires a mechanism for sharing quality improvement lessons. The Veterans Health Administration (VA) developed online compendia of tools linked to specific cancer quality indicators. We evaluated awareness and use of the toolkits, variation across facilities, impact of social marketing, and factors influencing toolkit use. A diffusion of innovations conceptual framework guided the collection of user activity data from the Toolkit Series SharePoint site and an online survey of potential Lung Cancer Care Toolkit users. The VA Toolkit Series site had 5,088 unique visitors in its first 22 months; 5% of users accounted for 40% of page views. Social marketing communications were correlated with site usage. Of survey respondents (n = 355), 54% had visited the site, of whom 24% downloaded at least one tool. Respondents' awareness of the lung cancer quality performance of their facility, and facility participation in quality improvement collaboratives, were positively associated with Toolkit Series site use. Facility-level lung cancer tool implementation varied widely across tool types. The VA Toolkit Series achieved widespread use and a high degree of user engagement, although use varied widely across facilities. The most active users were aware of and active in cancer care quality improvement. Toolkit use seemed to be reinforced by other quality improvement activities. A combination of user-driven tool creation and centralized toolkit development seemed to be effective for leveraging health information technology to spread disease-specific quality improvement tools within an integrated health care system. Copyright © 2015 by American Society of Clinical Oncology.

Network Science Research Laboratory (NSRL) Discrete Event Toolkit

DTIC Science & Technology

2016-01-01

ARL-TR-7579 ● JAN 2016 US Army Research Laboratory Network Science Research Laboratory (NSRL) Discrete Event Toolkit by...Laboratory (NSRL) Discrete Event Toolkit by Theron Trout and Andrew J Toth Computational and Information Sciences Directorate, ARL...Research Laboratory (NSRL) Discrete Event Toolkit 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Theron Trout

T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life.

PubMed

Carbone, Ignazio; White, James B; Miadlikowska, Jolanta; Arnold, A Elizabeth; Miller, Mark A; Kauff, Frank; U'Ren, Jana M; May, Georgiana; Lutzoni, François

2017-04-15

High-quality phylogenetic placement of sequence data has the potential to greatly accelerate studies of the diversity, systematics, ecology and functional biology of diverse groups. We developed the Tree-Based Alignment Selector (T-BAS) toolkit to allow evolutionary placement and visualization of diverse DNA sequences representing unknown taxa within a robust phylogenetic context, and to permit the downloading of highly curated, single- and multi-locus alignments for specific clades. In its initial form, T-BAS v1.0 uses a core phylogeny of 979 taxa (including 23 outgroup taxa, as well as 61 orders, 175 families and 496 genera) representing all 13 classes of largest subphylum of Fungi-Pezizomycotina (Ascomycota)-based on sequence alignments for six loci (nr5.8S, nrLSU, nrSSU, mtSSU, RPB1, RPB2 ). T-BAS v1.0 has three main uses: (i) Users may download alignments and voucher tables for members of the Pezizomycotina directly from the reference tree, facilitating systematics studies of focal clades. (ii) Users may upload sequence files with reads representing unknown taxa and place these on the phylogeny using either BLAST or phylogeny-based approaches, and then use the displayed tree to select reference taxa to include when downloading alignments. The placement of unknowns can be performed for large numbers of Sanger sequences obtained from fungal cultures and for alignable, short reads of environmental amplicons. (iii) User-customizable metadata can be visualized on the tree. T-BAS Version 1.0 is available online at http://tbas.hpc.ncsu.edu . Registration is required to access the CIPRES Science Gateway and NSF XSEDE's large computational resources. icarbon@ncsu.edu. 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

SIGKit: a New Data-based Software for Learning Introductory Geophysics

NASA Astrophysics Data System (ADS)

Zhang, Y.; Kruse, S.; George, O.; Esmaeili, S.; Papadimitrios, K. S.; Bank, C. G.; Cadmus, A.; Kenneally, N.; Patton, K.; Brusher, J.

2016-12-01

Students of diverse academic backgrounds take introductory geophysics courses to learn the theory of a variety of measurement and analysis methods with the expectation to be able to apply their basic knowledge to real data. Ideally, such data is collected in field courses and also used in lecture-based courses because they provide a critical context for better learning and understanding of geophysical methods. Each method requires a separate software package for the data processing steps, and the complexity and variety of professional software makes the path through data processing to data interpretation a strenuous learning process for students and a challenging teaching task for instructors. SIGKit (Student Investigation of Geophysics Toolkit) being developed as a collaboration between the University of South Florida, the University of Toronto, and MathWorks intends to address these shortcomings by showing the most essential processing steps and allowing students to visualize the underlying physics of the various methods. It is based on MATLAB software and offered as an easy-to-use graphical user interface and packaged so it can run as an executable in the classroom and the field even on computers without MATLAB licenses. An evaluation of the software based on student feedback from focus-group interviews and think-aloud observations helps drive its development and refinement. The toolkit provides a logical gateway into the more sophisticated and costly software students will encounter later in their training and careers by combining essential visualization, modeling, processing, and analysis steps for seismic, GPR, magnetics, gravity, resistivity, and electromagnetic data.

Full 3D visualization tool-kit for Monte Carlo and deterministic transport codes

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

Frambati, S.; Frignani, M.

2012-07-01

We propose a package of tools capable of translating the geometric inputs and outputs of many Monte Carlo and deterministic radiation transport codes into open source file formats. These tools are aimed at bridging the gap between trusted, widely-used radiation analysis codes and very powerful, more recent and commonly used visualization software, thus supporting the design process and helping with shielding optimization. Three main lines of development were followed: mesh-based analysis of Monte Carlo codes, mesh-based analysis of deterministic codes and Monte Carlo surface meshing. The developed kit is considered a powerful and cost-effective tool in the computer-aided design formore » radiation transport code users of the nuclear world, and in particular in the fields of core design and radiation analysis. (authors)« less

TOOLKIT, Version 2. 0

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

Schroeder, E.; Bagot, B.; McNeill, R.L.

1990-05-09

The purpose of this User's Guide is to show by example many of the features of Toolkit II. Some examples will be copies of screens as they appear while running the Toolkit. Other examples will show what the user should enter in various situations; in these instances, what the computer asserts will be in boldface and what the user responds will be in regular type. The User's Guide is divided into four sections. The first section, FOCUS Databases'', will give a broad overview of the Focus administrative databases that are available on the VAX; easy-to-use reports are available for mostmore » of them in the Toolkit. The second section, Getting Started'', will cover the steps necessary to log onto the Computer Center VAX cluster and how to start Focus and the Toolkit. The third section, Using the Toolkit'', will discuss some of the features in the Toolkit -- the available reports and how to access them, as well as some utilities. The fourth section, Helpful Hints'', will cover some useful facts about the VAX and Focus as well as some of the more common problems that can occur. The Toolkit is not set in concrete but is continually being revised and improved. If you have any opinions as to changes that you would like to see made to the Toolkit or new features that you would like included, please let us know. Since we do try to respond to the needs of the user and make periodic improvement to the Toolkit, this User's Guide may not correspond exactly to what is available in the computer. In general, changes are made to provide new options or features; rarely is an existing feature deleted.« less

Local Foods, Local Places Toolkit

EPA Pesticide Factsheets

Toolkit to help communities that want to use local foods to spur revitalization. The toolkit gives step-by-step instructions to help communities plan and host a workshop and create an action plan to implement.

Provider perceptions of an integrated primary care quality improvement strategy: The PPAQ toolkit.

PubMed

Beehler, Gregory P; Lilienthal, Kaitlin R

2017-02-01

The Primary Care Behavioral Health (PCBH) model of integrated primary care is challenging to implement with high fidelity. The Primary Care Behavioral Health Provider Adherence Questionnaire (PPAQ) was designed to assess provider adherence to essential model components and has recently been adapted into a quality improvement toolkit. The aim of this pilot project was to gather preliminary feedback on providers' perceptions of the acceptability and utility of the PPAQ toolkit for making beneficial practice changes. Twelve mental health providers working in Department of Veterans Affairs integrated primary care clinics participated in semistructured interviews to gather quantitative and qualitative data. Descriptive statistics and qualitative content analysis were used to analyze data. Providers identified several positive features of the PPAQ toolkit organization and structure that resulted in high ratings of acceptability, while also identifying several toolkit components in need of modification to improve usability. Toolkit content was considered highly representative of the (PCBH) model and therefore could be used as a diagnostic self-assessment of model adherence. The toolkit was considered to be high in applicability to providers regardless of their degree of prior professional preparation or current clinical setting. Additionally, providers identified several system-level contextual factors that could impact the usefulness of the toolkit. These findings suggest that frontline mental health providers working in (PCBH) settings may be receptive to using an adherence-focused toolkit for ongoing quality improvement. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Green Infrastructure Modeling Toolkit

EPA Pesticide Factsheets

EPA's Green Infrastructure Modeling Toolkit is a toolkit of 5 EPA green infrastructure models and tools, along with communication materials, that can be used as a teaching tool and a quick reference resource when making GI implementation decisions.

EHDViz: clinical dashboard development using open-source technologies.

PubMed

Badgeley, Marcus A; Shameer, Khader; Glicksberg, Benjamin S; Tomlinson, Max S; Levin, Matthew A; McCormick, Patrick J; Kasarskis, Andrew; Reich, David L; Dudley, Joel T

2016-03-24

To design, develop and prototype clinical dashboards to integrate high-frequency health and wellness data streams using interactive and real-time data visualisation and analytics modalities. We developed a clinical dashboard development framework called electronic healthcare data visualization (EHDViz) toolkit for generating web-based, real-time clinical dashboards for visualising heterogeneous biomedical, healthcare and wellness data. The EHDViz is an extensible toolkit that uses R packages for data management, normalisation and producing high-quality visualisations over the web using R/Shiny web server architecture. We have developed use cases to illustrate utility of EHDViz in different scenarios of clinical and wellness setting as a visualisation aid for improving healthcare delivery. Using EHDViz, we prototyped clinical dashboards to demonstrate the contextual versatility of EHDViz toolkit. An outpatient cohort was used to visualise population health management tasks (n=14,221), and an inpatient cohort was used to visualise real-time acuity risk in a clinical unit (n=445), and a quantified-self example using wellness data from a fitness activity monitor worn by a single individual was also discussed (n-of-1). The back-end system retrieves relevant data from data source, populates the main panel of the application and integrates user-defined data features in real-time and renders output using modern web browsers. The visualisation elements can be customised using health features, disease names, procedure names or medical codes to populate the visualisations. The source code of EHDViz and various prototypes developed using EHDViz are available in the public domain at http://ehdviz.dudleylab.org. Collaborative data visualisations, wellness trend predictions, risk estimation, proactive acuity status monitoring and knowledge of complex disease indicators are essential components of implementing data-driven precision medicine. As an open-source visualisation framework capable of integrating health assessment, EHDViz aims to be a valuable toolkit for rapid design, development and implementation of scalable clinical data visualisation dashboards. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

The Seismic Tool-Kit (STK): An Open Source Software For Learning the Basis of Signal Processing and Seismology.

NASA Astrophysics Data System (ADS)

Reymond, D.

2016-12-01

We present an open source software project (GNU public license), named STK: Seismic Tool-Kit, that is dedicated mainly for learning signal processing and seismology. The STK project that started in 2007, is hosted by SourceForge.net, and count more than 20000 downloads at the date of writing.The STK project is composed of two main branches:First, a graphical interface dedicated to signal processing (in the SAC format (SAC_ASCII and SAC_BIN): where the signal can be plotted, zoomed, filtered, integrated, derivated, ... etc. (a large variety of IFR and FIR filter is proposed). The passage in the frequency domain via the Fourier transform is used to introduce the estimation of spectral density of the signal , with visualization of the Power Spectral Density (PSD) in linear or log scale, and also the evolutive time-frequency representation (or sonagram). The 3-components signals can be also processed for estimating their polarization properties, either for a given window, or either for evolutive windows along the time. This polarization analysis is useful for extracting the polarized noises, differentiating P waves, Rayleigh waves, Love waves, ... etc. Secondly, a panel of Utilities-Program are proposed for working in a terminal mode, with basic programs for computing azimuth and distance in spherical geometry, inter/auto-correlation, spectral density, time-frequency for an entire directory of signals, focal planes, and main components axis, radiation pattern of P waves, Polarization analysis of different waves (including noise), under/over-sampling the signals, cubic-spline smoothing, and linear/non linear regression analysis of data set. STK is developed in C/C++, mainly under Linux OS, and it has been also partially implemented under MS-Windows. STK has been used in some schools for viewing and plotting seismic records provided by IRIS, and it has been used as a practical support for teaching the basis of signal processing. Useful links:http://sourceforge.net/projects/seismic-toolkit/http://sourceforge.net/p/seismic-toolkit/wiki/browse_pages/

College Women's Health

MedlinePlus

... the College Women's Social Media Kit! College Women's Social Media Toolkit Use the Social Media Toolkit to share health tips with your campus ... toolkit includes resources for young women including sample social media messages, flyers and blogs posts. NEW Social Media ...

Every Place Counts Leadership Academy transportation toolkit

DOT National Transportation Integrated Search

2016-12-01

The Transportation Toolkit is meant to explain the transportation process to members of the public with no prior knowledge of transportation. The Toolkit is meant to demystify transportation and help people engage in local transportation decision-mak...

Matlab based Toolkits used to Interface with Optical Design Software for NASA's James Webb Space Telescope

NASA Technical Reports Server (NTRS)

Howard, Joseph

2007-01-01

The viewgraph presentation provides an introduction to the James Webb Space Telescope (JWST). The first part provides a brief overview of Matlab toolkits including CodeV, OSLO, and Zemax Toolkits. The toolkit overview examines purpose, layout, how Matlab gets data from CodeV, function layout, and using cvHELP. The second part provides examples of use with JWST, including wavefront sensitivities and alignment simulations.

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit

PubMed Central

O'Boyle, Noel M; Morley, Chris; Hutchison, Geoffrey R

2008-01-01

Background Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We describe Pybel, a Python module that provides access to the OpenBabel toolkit. Results Pybel wraps the direct toolkit bindings to simplify common tasks such as reading and writing molecular files and calculating fingerprints. Extensive use is made of Python iterators to simplify loops such as that over all the molecules in a file. A Pybel Molecule can be easily interconverted to an OpenBabel OBMol to access those methods or attributes not wrapped by Pybel. Conclusion Pybel allows cheminformaticians to rapidly develop Python scripts that manipulate chemical information. It is open source, available cross-platform, and offers the power of the OpenBabel toolkit to Python programmers. PMID:18328109

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit.

PubMed

O'Boyle, Noel M; Morley, Chris; Hutchison, Geoffrey R

2008-03-09

Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We describe Pybel, a Python module that provides access to the OpenBabel toolkit. Pybel wraps the direct toolkit bindings to simplify common tasks such as reading and writing molecular files and calculating fingerprints. Extensive use is made of Python iterators to simplify loops such as that over all the molecules in a file. A Pybel Molecule can be easily interconverted to an OpenBabel OBMol to access those methods or attributes not wrapped by Pybel. Pybel allows cheminformaticians to rapidly develop Python scripts that manipulate chemical information. It is open source, available cross-platform, and offers the power of the OpenBabel toolkit to Python programmers.

Capturing Petascale Application Characteristics with the Sequoia Toolkit

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

Vetter, Jeffrey S; Bhatia, Nikhil; Grobelny, Eric M

2005-01-01

Characterization of the computation, communication, memory, and I/O demands of current scientific applications is crucial for identifying which technologies will enable petascale scientific computing. In this paper, we present the Sequoia Toolkit for characterizing HPC applications. The Sequoia Toolkit consists of the Sequoia trace capture library and the Sequoia Event Analysis Library, or SEAL, that facilitates the development of tools for analyzing Sequoia event traces. Using the Sequoia Toolkit, we have characterized the behavior of application runs with up to 2048 application processes. To illustrate the use of the Sequoia Toolkit, we present a preliminary characterization of LAMMPS, a molecularmore » dynamics application of great interest to the computational biology community.« less

A Grassroots Remote Sensing Toolkit Using Live Coding, Smartphones, Kites and Lightweight Drones

PubMed Central

Anderson, K.; Griffiths, D.; DeBell, L.; Hancock, S.; Duffy, J. P.; Shutler, J. D.; Reinhardt, W. J.; Griffiths, A.

2016-01-01

This manuscript describes the development of an android-based smartphone application for capturing aerial photographs and spatial metadata automatically, for use in grassroots mapping applications. The aim of the project was to exploit the plethora of on-board sensors within modern smartphones (accelerometer, GPS, compass, camera) to generate ready-to-use spatial data from lightweight aerial platforms such as drones or kites. A visual coding ‘scheme blocks’ framework was used to build the application (‘app’), so that users could customise their own data capture tools in the field. The paper reports on the coding framework, then shows the results of test flights from kites and lightweight drones and finally shows how open-source geospatial toolkits were used to generate geographical information system (GIS)-ready GeoTIFF images from the metadata stored by the app. Two Android smartphones were used in testing–a high specification OnePlus One handset and a lower cost Acer Liquid Z3 handset, to test the operational limits of the app on phones with different sensor sets. We demonstrate that best results were obtained when the phone was attached to a stable single line kite or to a gliding drone. Results show that engine or motor vibrations from powered aircraft required dampening to ensure capture of high quality images. We demonstrate how the products generated from the open-source processing workflow are easily used in GIS. The app can be downloaded freely from the Google store by searching for ‘UAV toolkit’ (UAV toolkit 2016), and used wherever an Android smartphone and aerial platform are available to deliver rapid spatial data (e.g. in supporting decision-making in humanitarian disaster-relief zones, in teaching or for grassroots remote sensing and democratic mapping). PMID:27144310

A graphical user interface (GUI) toolkit for the calculation of three-dimensional (3D) multi-phase biological effective dose (BED) distributions including statistical analyses.

PubMed

Kauweloa, Kevin I; Gutierrez, Alonso N; Stathakis, Sotirios; Papanikolaou, Niko; Mavroidis, Panayiotis

2016-07-01

A toolkit has been developed for calculating the 3-dimensional biological effective dose (BED) distributions in multi-phase, external beam radiotherapy treatments such as those applied in liver stereotactic body radiation therapy (SBRT) and in multi-prescription treatments. This toolkit also provides a wide range of statistical results related to dose and BED distributions. MATLAB 2010a, version 7.10 was used to create this GUI toolkit. The input data consist of the dose distribution matrices, organ contour coordinates, and treatment planning parameters from the treatment planning system (TPS). The toolkit has the capability of calculating the multi-phase BED distributions using different formulas (denoted as true and approximate). Following the calculations of the BED distributions, the dose and BED distributions can be viewed in different projections (e.g. coronal, sagittal and transverse). The different elements of this toolkit are presented and the important steps for the execution of its calculations are illustrated. The toolkit is applied on brain, head & neck and prostate cancer patients, who received primary and boost phases in order to demonstrate its capability in calculating BED distributions, as well as measuring the inaccuracy and imprecision of the approximate BED distributions. Finally, the clinical situations in which the use of the present toolkit would have a significant clinical impact are indicated. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

The Comprehension Toolkit

ERIC Educational Resources Information Center

Harvey, Stephanie; Goudvis, Anne

2005-01-01

"The Comprehension Toolkit" focuses on reading, writing, talking, listening, and investigating, to deepen understanding of nonfiction texts. With a focus on strategic thinking, this toolkit's lessons provide a foundation for developing independent readers and learners. It also provides an alternative to the traditional assign and correct…

JAVA Stereo Display Toolkit

NASA Technical Reports Server (NTRS)

Edmonds, Karina

2008-01-01

This toolkit provides a common interface for displaying graphical user interface (GUI) components in stereo using either specialized stereo display hardware (e.g., liquid crystal shutter or polarized glasses) or anaglyph display (red/blue glasses) on standard workstation displays. An application using this toolkit will work without modification in either environment, allowing stereo software to reach a wider audience without sacrificing high-quality display on dedicated hardware. The toolkit is written in Java for use with the Swing GUI Toolkit and has cross-platform compatibility. It hooks into the graphics system, allowing any standard Swing component to be displayed in stereo. It uses the OpenGL graphics library to control the stereo hardware and to perform the rendering. It also supports anaglyph and special stereo hardware using the same API (application-program interface), and has the ability to simulate color stereo in anaglyph mode by combining the red band of the left image with the green/blue bands of the right image. This is a low-level toolkit that accomplishes simply the display of components (including the JadeDisplay image display component). It does not include higher-level functions such as disparity adjustment, 3D cursor, or overlays all of which can be built using this toolkit.

Code Parallelization with CAPO: A User Manual

NASA Technical Reports Server (NTRS)

Jin, Hao-Qiang; Frumkin, Michael; Yan, Jerry; Biegel, Bryan (Technical Monitor)

2001-01-01

A software tool has been developed to assist the parallelization of scientific codes. This tool, CAPO, extends an existing parallelization toolkit, CAPTools developed at the University of Greenwich, to generate OpenMP parallel codes for shared memory architectures. This is an interactive toolkit to transform a serial Fortran application code to an equivalent parallel version of the software - in a small fraction of the time normally required for a manual parallelization. We first discuss the way in which loop types are categorized and how efficient OpenMP directives can be defined and inserted into the existing code using the in-depth interprocedural analysis. The use of the toolkit on a number of application codes ranging from benchmark to real-world application codes is presented. This will demonstrate the great potential of using the toolkit to quickly parallelize serial programs as well as the good performance achievable on a large number of toolkit to quickly parallelize serial programs as well as the good performance achievable on a large number of processors. The second part of the document gives references to the parameters and the graphic user interface implemented in the toolkit. Finally a set of tutorials is included for hands-on experiences with this toolkit.

Hydropower Regulatory and Permitting Information Desktop (RAPID) Toolkit

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

Levine, Aaron L

Hydropower Regulatory and Permitting Information Desktop (RAPID) Toolkit presentation from the WPTO FY14-FY16 Peer Review. The toolkit is aimed at regulatory agencies, consultants, project developers, the public, and any other party interested in learning more about the hydropower regulatory process.

Student Success Center Toolkit

ERIC Educational Resources Information Center

Jobs For the Future, 2014

2014-01-01

"Student Success Center Toolkit" is a compilation of materials organized to assist Student Success Center directors as they staff, launch, operate, and sustain Centers. The toolkit features materials created and used by existing Centers, such as staffing and budgeting templates, launch materials, sample meeting agendas, and fundraising…

Veterinary Immunology Committee Toolkit Workshop 2010: Progress and plans

USDA-ARS?s Scientific Manuscript database

The Third Veterinary Immunology Committee (VIC) Toolkit Workshop took place at the Ninth International Veterinary Immunology Symposium (IVIS) in Tokyo, Japan on August 18, 2020. The Workshop built on previous Toolkit Workshops and covered various aspects of reagent development, commercialisation an...

77 FR 73023 - U.S. Environmental Solutions Toolkit

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-07

... foreign end-users of environmental technologies that will outline U.S. approaches to a series of environmental problems and highlight participating U.S. vendors of relevant U.S. technologies. The Toolkit will... DEPARTMENT OF COMMERCE International Trade Administration U.S. Environmental Solutions Toolkit...

Development of an educational 'toolkit' for health professionals and their patients with prediabetes: the WAKEUP study (Ways of Addressing Knowledge Education and Understanding in Pre-diabetes).

PubMed

Evans, P H; Greaves, C; Winder, R; Fearn-Smith, J; Campbell, J L

2007-07-01

To identify key messages about pre-diabetes and to design, develop and pilot an educational toolkit to address the information needs of patients and health professionals. Mixed qualitative methodology within an action research framework. Focus group interviews with patients and health professionals and discussion with an expert reference group aimed to identify the important messages and produce a draft toolkit. Two action research cycles were then conducted in two general practices, during which the draft toolkit was used and video-taped consultations and follow-up patient interviews provided further data. Framework analysis techniques were used to examine the data and to elicit action points for improving the toolkit. The key messages about pre-diabetes concerned the seriousness of the condition, the preventability of progression to diabetes, and the need for lifestyle change. As well as feedback on the acceptability and use of the toolkit, four main themes were identified in the data: knowledge and education needs (of both patients and health professionals); communicating knowledge and motivating change; redesign of practice systems to support pre-diabetes management and the role of the health professional. The toolkit we developed was found to be an acceptable and useful resource for both patients and health practitioners. Three key messages about pre-diabetes were identified. A toolkit of information materials for patients with pre-diabetes and the health professionals and ideas for improving practice systems for managing pre-diabetes were developed and successfully piloted. Further work is needed to establish the best mode of delivery of the WAKEUP toolkit.

DEEP MOTIF DASHBOARD: VISUALIZING AND UNDERSTANDING GENOMIC SEQUENCES USING DEEP NEURAL NETWORKS.

PubMed

Lanchantin, Jack; Singh, Ritambhara; Wang, Beilun; Qi, Yanjun

2017-01-01

Deep neural network (DNN) models have recently obtained state-of-the-art prediction accuracy for the transcription factor binding (TFBS) site classification task. However, it remains unclear how these approaches identify meaningful DNA sequence signals and give insights as to why TFs bind to certain locations. In this paper, we propose a toolkit called the Deep Motif Dashboard (DeMo Dashboard) which provides a suite of visualization strategies to extract motifs, or sequence patterns from deep neural network models for TFBS classification. We demonstrate how to visualize and understand three important DNN models: convolutional, recurrent, and convolutional-recurrent networks. Our first visualization method is finding a test sequence's saliency map which uses first-order derivatives to describe the importance of each nucleotide in making the final prediction. Second, considering recurrent models make predictions in a temporal manner (from one end of a TFBS sequence to the other), we introduce temporal output scores, indicating the prediction score of a model over time for a sequential input. Lastly, a class-specific visualization strategy finds the optimal input sequence for a given TFBS positive class via stochastic gradient optimization. Our experimental results indicate that a convolutional-recurrent architecture performs the best among the three architectures. The visualization techniques indicate that CNN-RNN makes predictions by modeling both motifs as well as dependencies among them.

Deep Motif Dashboard: Visualizing and Understanding Genomic Sequences Using Deep Neural Networks

PubMed Central

Lanchantin, Jack; Singh, Ritambhara; Wang, Beilun; Qi, Yanjun

2018-01-01

Deep neural network (DNN) models have recently obtained state-of-the-art prediction accuracy for the transcription factor binding (TFBS) site classification task. However, it remains unclear how these approaches identify meaningful DNA sequence signals and give insights as to why TFs bind to certain locations. In this paper, we propose a toolkit called the Deep Motif Dashboard (DeMo Dashboard) which provides a suite of visualization strategies to extract motifs, or sequence patterns from deep neural network models for TFBS classification. We demonstrate how to visualize and understand three important DNN models: convolutional, recurrent, and convolutional-recurrent networks. Our first visualization method is finding a test sequence’s saliency map which uses first-order derivatives to describe the importance of each nucleotide in making the final prediction. Second, considering recurrent models make predictions in a temporal manner (from one end of a TFBS sequence to the other), we introduce temporal output scores, indicating the prediction score of a model over time for a sequential input. Lastly, a class-specific visualization strategy finds the optimal input sequence for a given TFBS positive class via stochastic gradient optimization. Our experimental results indicate that a convolutional-recurrent architecture performs the best among the three architectures. The visualization techniques indicate that CNN-RNN makes predictions by modeling both motifs as well as dependencies among them. PMID:27896980

Evaluating the decision accuracy and speed of clinical data visualizations.

PubMed

Pieczkiewicz, David S; Finkelstein, Stanley M

2010-01-01

Clinicians face an increasing volume of biomedical data. Assessing the efficacy of systems that enable accurate and timely clinical decision making merits corresponding attention. This paper discusses the multiple-reader multiple-case (MRMC) experimental design and linear mixed models as means of assessing and comparing decision accuracy and latency (time) for decision tasks in which clinician readers must interpret visual displays of data. These tools can assess and compare decision accuracy and latency (time). These experimental and statistical techniques, used extensively in radiology imaging studies, offer a number of practical and analytic advantages over more traditional quantitative methods such as percent-correct measurements and ANOVAs, and are recommended for their statistical efficiency and generalizability. An example analysis using readily available, free, and commercial statistical software is provided as an appendix. While these techniques are not appropriate for all evaluation questions, they can provide a valuable addition to the evaluative toolkit of medical informatics research.

Toolkit for visualization of the cellular structure and organelles in Aspergillus niger.

PubMed

Buren, Emiel B J Ten; Karrenbelt, Michiel A P; Lingemann, Marit; Chordia, Shreyans; Deng, Ying; Hu, JingJing; Verest, Johanna M; Wu, Vincen; Gonzalez, Teresita J Bello; Heck, Ruben G A van; Odoni, Dorett I; Schonewille, Tom; Straat, Laura van der; Graaff, Leo H de; Passel, Mark W J van

2014-12-19

Aspergillus niger is a filamentous fungus that is extensively used in industrial fermentations for protein expression and the production of organic acids. Inherent biosynthetic capabilities, such as the capacity to secrete these biomolecules in high amounts, make A. niger an attractive production host. Although A. niger is renowned for this ability, the knowledge of the molecular components that underlie its production capacity, intercellular trafficking processes and secretion mechanisms is far from complete. Here, we introduce a standardized set of tools, consisting of an N-terminal GFP-actin fusion and codon optimized eforRed chromoprotein. Expression of the GFP-actin construct facilitates visualization of the actin filaments of the cytoskeleton, whereas expression of the chromoprotein construct results in a clearly distinguishable red phenotype. These experimentally validated constructs constitute the first set of standardized A. niger biomarkers, which can be used to study morphology, intercellular trafficking, and secretion phenomena.

Nanowire arrays restore vision in blind mice.

PubMed

Tang, Jing; Qin, Nan; Chong, Yan; Diao, Yupu; Yiliguma; Wang, Zhexuan; Xue, Tian; Jiang, Min; Zhang, Jiayi; Zheng, Gengfeng

2018-03-06

The restoration of light response with complex spatiotemporal features in retinal degenerative diseases towards retinal prosthesis has proven to be a considerable challenge over the past decades. Herein, inspired by the structure and function of photoreceptors in retinas, we develop artificial photoreceptors based on gold nanoparticle-decorated titania nanowire arrays, for restoration of visual responses in the blind mice with degenerated photoreceptors. Green, blue and near UV light responses in the retinal ganglion cells (RGCs) are restored with a spatial resolution better than 100 µm. ON responses in RGCs are blocked by glutamatergic antagonists, suggesting functional preservation of the remaining retinal circuits. Moreover, neurons in the primary visual cortex respond to light after subretinal implant of nanowire arrays. Improvement in pupillary light reflex suggests the behavioral recovery of light sensitivity. Our study will shed light on the development of a new generation of optoelectronic toolkits for subretinal prosthetic devices.

Interactive Visualization of Computational Fluid Dynamics using Mosaic

NASA Technical Reports Server (NTRS)

Clucas, Jean; Watson, Velvin; Chancellor, Marisa K. (Technical Monitor)

1994-01-01

The Web provides new Methods for accessing Information world-wide, but the current text-and-pictures approach neither utilizes all the Web's possibilities not provides for its limitations. While the inclusion of pictures and animations in a paper communicates more effectively than text alone, It Is essentially an extension of the concept of "publication." Also, as use of the Web increases putting images and animations online will quickly load even the "Information Superhighway." We need to find forms of communication that take advantage of the special nature of the Web. This paper presents one approach: the use of the Internet and the Mosaic interface for data sharing and collaborative analysis. We will describe (and In the presentation, demonstrate) our approach: using FAST (Flow Analysis Software Toolkit), a scientific visualization package, as a data viewer and interactive tool called from MOSAIC. Our intent is to stimulate the development of other tools that utilize the unique nature of electronic communication.

Toolkit of Available EPA Green Infrastructure Modeling Software. National Stormwater Calculator

EPA Science Inventory

This webinar will present a toolkit consisting of five EPA green infrastructure models and tools, along with communication material. This toolkit can be used as a teaching and quick reference resource for use by planners and developers when making green infrastructure implementat...

Teacher Quality Toolkit

ERIC Educational Resources Information Center

Lauer, Patricia A.; Dean, Ceri B.

2004-01-01

This Teacher Quality Toolkit aims to support the continuum of teacher learning by providing tools that institutions of higher education, districts, and schools can use to improve both preservice and inservice teacher education. The toolkit incorporates McREL?s accumulated knowledge and experience related to teacher quality and standards-based…

77 FR 73022 - U.S. Environmental Solutions Toolkit

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-07

... Commerce continues to develop the web- based U.S. Environmental Solutions Toolkit to be used by foreign environmental officials and foreign end-users of environmental technologies that will outline U.S. approaches to... DEPARTMENT OF COMMERCE International Trade Administration U.S. Environmental Solutions Toolkit...

Cinfony – combining Open Source cheminformatics toolkits behind a common interface

PubMed Central

O'Boyle, Noel M; Hutchison, Geoffrey R

2008-01-01

Background Open Source cheminformatics toolkits such as OpenBabel, the CDK and the RDKit share the same core functionality but support different sets of file formats and forcefields, and calculate different fingerprints and descriptors. Despite their complementary features, using these toolkits in the same program is difficult as they are implemented in different languages (C++ versus Java), have different underlying chemical models and have different application programming interfaces (APIs). Results We describe Cinfony, a Python module that presents a common interface to all three of these toolkits, allowing the user to easily combine methods and results from any of the toolkits. In general, the run time of the Cinfony modules is almost as fast as accessing the underlying toolkits directly from C++ or Java, but Cinfony makes it much easier to carry out common tasks in cheminformatics such as reading file formats and calculating descriptors. Conclusion By providing a simplified interface and improving interoperability, Cinfony makes it easy to combine complementary features of OpenBabel, the CDK and the RDKit. PMID:19055766

Using Galaxy to Perform Large-Scale Interactive Data Analyses

PubMed Central

Hillman-Jackson, Jennifer; Clements, Dave; Blankenberg, Daniel; Taylor, James; Nekrutenko, Anton

2012-01-01

Innovations in biomedical research technologies continue to provide experimental biologists with novel and increasingly large genomic and high-throughput data resources to be analyzed. As creating and obtaining data has become easier, the key decision faced by many researchers is a practical one: where and how should an analysis be performed? Datasets are large and analysis tool set-up and use is riddled with complexities outside of the scope of core research activities. The authors believe that Galaxy (galaxyproject.org) provides a powerful solution that simplifies data acquisition and analysis in an intuitive web-application, granting all researchers access to key informatics tools previously only available to computational specialists working in Unix-based environments. We will demonstrate through a series of biomedically relevant protocols how Galaxy specifically brings together 1) data retrieval from public and private sources, for example, UCSC’s Eukaryote and Microbial Genome Browsers (genome.ucsc.edu), 2) custom tools (wrapped Unix functions, format standardization/conversions, interval operations) and 3rd party analysis tools, for example, Bowtie/Tuxedo Suite (bowtie-bio.sourceforge.net), Lastz (www.bx.psu.edu/~rsharris/lastz/), SAMTools (samtools.sourceforge.net), FASTX-toolkit (hannonlab.cshl.edu/fastx_toolkit), and MACS (liulab.dfci.harvard.edu/MACS), and creates results formatted for visualization in tools such as the Galaxy Track Browser (GTB, galaxyproject.org/wiki/Learn/Visualization), UCSC Genome Browser (genome.ucsc.edu), Ensembl (www.ensembl.org), and GeneTrack (genetrack.bx.psu.edu). Galaxy rapidly has become the most popular choice for integrated next generation sequencing (NGS) analytics and collaboration, where users can perform, document, and share complex analysis within a single interface in an unprecedented number of ways. PMID:18428782

Free DICOM de-identification tools in clinical research: functioning and safety of patient privacy.

PubMed

Aryanto, K Y E; Oudkerk, M; van Ooijen, P M A

2015-12-01

To compare non-commercial DICOM toolkits for their de-identification ability in removing a patient's personal health information (PHI) from a DICOM header. Ten DICOM toolkits were selected for de-identification tests. Tests were performed by using the system's default de-identification profile and, subsequently, the tools' best adjusted settings. We aimed to eliminate fifty elements considered to contain identifying patient information. The tools were also examined for their respective methods of customization. Only one tool was able to de-identify all required elements with the default setting. Not all of the toolkits provide a customizable de-identification profile. Six tools allowed changes by selecting the provided profiles, giving input through a graphical user interface (GUI) or configuration text file, or providing the appropriate command-line arguments. Using adjusted settings, four of those six toolkits were able to perform full de-identification. Only five tools could properly de-identify the defined DICOM elements, and in four cases, only after careful customization. Therefore, free DICOM toolkits should be used with extreme care to prevent the risk of disclosing PHI, especially when using the default configuration. In case optimal security is required, one of the five toolkits is proposed. • Free DICOM toolkits should be carefully used to prevent patient identity disclosure. • Each DICOM tool produces its own specific outcomes from the de-identification process. • In case optimal security is required, using one DICOM toolkit is proposed.

WATERSHED HEALTH ASSESSMENT TOOLS-INVESTIGATING FISHERIES (WHAT-IF): A MODELING TOOLKIT FOR WATERSHED AND FISHERIES MANAGEMENT

EPA Science Inventory

The Watershed Health Assessment Tools-Investigating Fisheries (WHAT-IF) is a decision-analysis modeling toolkit for personal computers that supports watershed and fisheries management. The WHAT-IF toolkit includes a relational database, help-system functions and documentation, a...

Designing and Delivering Intensive Interventions: A Teacher's Toolkit

ERIC Educational Resources Information Center

Murray, Christy S.; Coleman, Meghan A.; Vaughn, Sharon; Wanzek, Jeanne; Roberts, Greg

2012-01-01

This toolkit provides activities and resources to assist practitioners in designing and delivering intensive interventions in reading and mathematics for K-12 students with significant learning difficulties and disabilities. Grounded in research, this toolkit is based on the Center on Instruction's "Intensive Interventions for Students Struggling…

The National Informal STEM Education Network

Science.gov Websites

Evaluation and Research Kits Explore Science: Earth & Space toolkit Building with Biology Kit Explore 2018 toolkits now available for download. Download the 2018 Digital Toolkit! Building with Biology ACTIVITY KIT Building with Biology Conversations and activities about synthetic biology; this emerging

78 FR 14773 - U.S. Environmental Solutions Toolkit-Landfill Standards

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-07

... and foreign end-users of environmental technologies that will outline U.S. approaches to a series of environmental problems and highlight participating U.S. vendors of relevant U.S. technologies. The Toolkit will... DEPARTMENT OF COMMERCE International Trade Administration U.S. Environmental Solutions Toolkit...

The joy of interactive modeling

NASA Astrophysics Data System (ADS)

Donchyts, Gennadii; Baart, Fedor; van Dam, Arthur; Jagers, Bert

2013-04-01

The conventional way of working with hydrodynamical models usually consists of the following steps: 1) define a schematization (e.g., in a graphical user interface, or by editing input files) 2) run model from start to end 3) visualize results 4) repeat any of the previous steps. This cycle commonly takes up from hours to several days. What if we can make this happen instantly? As most of the research done using numerical models is in fact qualitative and exploratory (Oreskes et al., 1994), why not use these models as such? How can we adapt models so that we can edit model input, run and visualize results at the same time? More and more, interactive models become available as online apps, mainly for demonstration and educational purposes. These models often simplify the physics behind flows and run on simplified model geometries, particularly when compared with state-of-the-art scientific simulation packages. Here we show how the aforementioned conventional standalone models ("static, run once") can be transformed into interactive models. The basic concepts behind turning existing (conventional) model engines into interactive engines are the following. The engine does not run the model from start to end, but is always available in memory, and can be fed by new boundary conditions, or state changes at any time. The model can be run continuously, per step, or up to a specified time. The Hollywood principle dictates how the model engine is instructed from 'outside', instead of the model engine taking all necessary actions on its own initiative. The underlying techniques that facilitate these concepts are introspection of the computation engine, which exposes its state variables, and control functions, e.g. for time stepping, via a standardized interface, such as BMI (Peckam et. al., 2012). In this work we have used a shallow water flow model engine D-Flow Flexible Mesh. The model was converted from executable to a library, and coupled to the graphical modelling environment Delta Shell. Both the engine and the environment are open source tools under active development at Deltares. The combination provides direct interactive control over the time loop and model state, and offers live 3D visualization of the running model using VTK library.

78 FR 58520 - U.S. Environmental Solutions Toolkit

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-24

... notice sets forth a request for input from U.S. businesses capable of exporting their goods or services... and foreign end-users of environmental technologies The Toolkit outline U.S. approaches to a series of environmental problems and highlight participating U.S. vendors of relevant U.S. technologies. The Toolkit will...

Practitioner Data Use in Schools: Workshop Toolkit. REL 2015-043

ERIC Educational Resources Information Center

Bocala, Candice; Henry, Susan F.; Mundry, Susan; Morgan, Claire

2014-01-01

The "Practitioner Data Use in Schools: Workshop Toolkit" is designed to help practitioners systematically and accurately use data to inform their teaching practice. The toolkit includes an agenda, slide deck, participant workbook, and facilitator's guide and covers the following topics: developing data literacy, engaging in a cycle of…

Language Access Toolkit: An Organizing and Advocacy Resource for Community-Based Youth Programs

ERIC Educational Resources Information Center

Beyersdorf, Mark Ro

2013-01-01

Asian American Legal Defense and Education Fund (AALDEF) developed this language access toolkit to share the expertise and experiences of National Asian American Education Advocates Network (NAAEA) member organizations with other community organizations interested in developing language access campaigns. This toolkit includes an overview of…

Diagnosing turbulence for research aircraft safety using open source toolkits

NASA Astrophysics Data System (ADS)

Lang, T. J.; Guy, N.

Open source software toolkits have been developed and applied to diagnose in-cloud turbulence in the vicinity of Earth science research aircraft, via analysis of ground-based Doppler radar data. Based on multiple retrospective analyses, these toolkits show promise for detecting significant turbulence well prior to cloud penetrations by research aircraft. A pilot study demonstrated the ability to provide mission scientists turbulence estimates in near real time during an actual field campaign, and thus these toolkits are recommended for usage in future cloud-penetrating aircraft field campaigns.

Software reuse in spacecraft planning and scheduling systems

NASA Technical Reports Server (NTRS)

Mclean, David; Tuchman, Alan; Broseghini, Todd; Yen, Wen; Page, Brenda; Johnson, Jay; Bogovich, Lynn; Burkhardt, Chris; Mcintyre, James; Klein, Scott

1993-01-01

The use of a software toolkit and development methodology that supports software reuse is described. The toolkit includes source-code-level library modules and stand-alone tools which support such tasks as data reformatting and report generation, simple relational database applications, user interfaces, tactical planning, strategic planning and documentation. The current toolkit is written in C and supports applications that run on IBM-PC's under DOS and UNlX-based workstations under OpenLook and Motif. The toolkit is fully integrated for building scheduling systems that reuse AI knowledge base technology. A typical scheduling scenario and three examples of applications that utilize the reuse toolkit will be briefly described. In addition to the tools themselves, a description of the software evolution and reuse methodology that was used is presented.

Development of an evidence-informed leisure time physical activity resource for adults with spinal cord injury: the SCI Get Fit Toolkit.

PubMed

Arbour-Nicitopoulos, K P; Martin Ginis, K A; Latimer-Cheung, A E; Bourne, C; Campbell, D; Cappe, S; Ginis, S; Hicks, A L; Pomerleau, P; Smith, K

2013-06-01

To systematically develop an evidence-informed leisure time physical activity (LTPA) resource for adults with spinal cord injury (SCI). Canada. The Appraisal of Guidelines, Research and Evaluation (AGREE) II protocol was used to develop a toolkit to teach and encourage adults with SCI how to make smart and informed choices about being physically active. A multidisciplinary expert panel appraised the evidence and generated specific recommendations for the content of the toolkit. Pilot testing was conducted to refine the toolkit's presentation. Recommendations emanating from the consultation process were that the toolkit be a brief, evidence-based resource that contains images of adults with tetraplegia and paraplegia, and links to more detailed online information. The content of the toolkit should include the physical activity guidelines (PAGs) for adults with SCI, activities tailored to manual and power chair users, the benefits of LTPA, and strategies to overcome common LTPA barriers for adults with SCI. The inclusion of action plans and safety tips was also recommended. These recommendations have resulted in the development of an evidence-informed LTPA resource to assist adults with SCI in meeting the PAGs. This toolkit will have important implications for consumers, health care professionals and policy makers for encouraging LTPA in the SCI community.

A framework for measurement and harmonization of pediatric multiple sclerosis etiologic research studies: The Pediatric MS Tool-Kit.

PubMed

Magalhaes, Sandra; Banwell, Brenda; Bar-Or, Amit; Fortier, Isabel; Hanwell, Heather E; Lim, Ming; Matt, Georg E; Neuteboom, Rinze F; O'Riordan, David L; Schneider, Paul K; Pugliatti, Maura; Shatenstein, Bryna; Tansey, Catherine M; Wassmer, Evangeline; Wolfson, Christina

2018-06-01

While studying the etiology of multiple sclerosis (MS) in children has several methodological advantages over studying etiology in adults, studies are limited by small sample sizes. Using a rigorous methodological process, we developed the Pediatric MS Tool-Kit, a measurement framework that includes a minimal set of core variables to assess etiological risk factors. We solicited input from the International Pediatric MS Study Group to select three risk factors: environmental tobacco smoke (ETS) exposure, sun exposure, and vitamin D intake. To develop the Tool-Kit, we used a Delphi study involving a working group of epidemiologists, neurologists, and content experts from North America and Europe. The Tool-Kit includes six core variables to measure ETS, six to measure sun exposure, and six to measure vitamin D intake. The Tool-Kit can be accessed online ( www.maelstrom-research.org/mica/network/tool-kit ). The goals of the Tool-Kit are to enhance exposure measurement in newly designed pediatric MS studies and comparability of results across studies, and in the longer term to facilitate harmonization of studies, a methodological approach that can be used to circumvent issues of small sample sizes. We believe the Tool-Kit will prove to be a valuable resource to guide pediatric MS researchers in developing study-specific questionnaire.

Implementation of the Good School Toolkit in Uganda: a quantitative process evaluation of a successful violence prevention program.

PubMed

Knight, Louise; Allen, Elizabeth; Mirembe, Angel; Nakuti, Janet; Namy, Sophie; Child, Jennifer C; Sturgess, Joanna; Kyegombe, Nambusi; Walakira, Eddy J; Elbourne, Diana; Naker, Dipak; Devries, Karen M

2018-05-09

The Good School Toolkit, a complex behavioural intervention designed by Raising Voices a Ugandan NGO, reduced past week physical violence from school staff to primary students by an average of 42% in a recent randomised controlled trial. This process evaluation quantitatively examines what was implemented across the twenty-one intervention schools, variations in school prevalence of violence after the intervention, factors that influence exposure to the intervention and factors associated with students' experience of physical violence from staff at study endline. Implementation measures were captured prospectively in the twenty-one intervention schools over four school terms from 2012 to 2014 and Toolkit exposure captured in the student (n = 1921) and staff (n = 286) endline cross-sectional surveys in 2014. Implementation measures and the prevalence of violence are summarised across schools and are assessed for correlation using Spearman's Rank Correlation Coefficient. Regression models are used to explore individual factors associated with Toolkit exposure and with physical violence at endline. School prevalence of past week physical violence from staff against students ranged from 7% to 65% across schools at endline. Schools with higher mean levels of teacher Toolkit exposure had larger decreases in violence during the study. Students in schools categorised as implementing a 'low' number of program school-led activities reported less exposure to the Toolkit. Higher student Toolkit exposure was associated with decreased odds of experiencing physical violence from staff (OR: 0.76, 95%CI: 0.67-0.86, p-value< 0.001). Girls, students reporting poorer mental health and students in a lower grade were less exposed to the toolkit. After the intervention, and when adjusting for individual Toolkit exposure, some students remained at increased risk of experiencing violence from staff, including, girls, students reporting poorer mental health, students who experienced other violence and those reporting difficulty with self-care. Our results suggest that increasing students and teachers exposure to the Good School Toolkit within schools has the potential to bring about further reductions in violence. Effectiveness of the Toolkit may be increased by further targeting and supporting teachers' engagement with girls and students with mental health difficulties. The trial is registered at clinicaltrials.gov , NCT01678846, August 24th 2012.

ESA Atmospheric Toolbox

NASA Astrophysics Data System (ADS)

Niemeijer, Sander

2017-04-01

The ESA Atmospheric Toolbox (BEAT) is one of the ESA Sentinel Toolboxes. It consists of a set of software components to read, analyze, and visualize a wide range of atmospheric data products. In addition to the upcoming Sentinel-5P mission it supports a wide range of other atmospheric data products, including those of previous ESA missions, ESA Third Party missions, Copernicus Atmosphere Monitoring Service (CAMS), ground based data, etc. The toolbox consists of three main components that are called CODA, HARP and VISAN. CODA provides interfaces for direct reading of data from earth observation data files. These interfaces consist of command line applications, libraries, direct interfaces to scientific applications (IDL and MATLAB), and direct interfaces to programming languages (C, Fortran, Python, and Java). CODA provides a single interface to access data in a wide variety of data formats, including ASCII, binary, XML, netCDF, HDF4, HDF5, CDF, GRIB, RINEX, and SP3. HARP is a toolkit for reading, processing and inter-comparing satellite remote sensing data, model data, in-situ data, and ground based remote sensing data. The main goal of HARP is to assist in the inter-comparison of datasets. By appropriately chaining calls to HARP command line tools one can pre-process datasets such that two datasets that need to be compared end up having the same temporal/spatial grid, same data format/structure, and same physical unit. The toolkit comes with its own data format conventions, the HARP format, which is based on netcdf/HDF. Ingestion routines (based on CODA) allow conversion from a wide variety of atmospheric data products to this common format. In addition, the toolbox provides a wide range of operations to perform conversions on the data such as unit conversions, quantity conversions (e.g. number density to volume mixing ratios), regridding, vertical smoothing using averaging kernels, collocation of two datasets, etc. VISAN is a cross-platform visualization and analysis application for atmospheric data and can be used to visualize and analyze the data that you retrieve using the CODA and HARP interfaces. The application uses the Python language as the means through which you provide commands to the application. The Python interfaces for CODA and HARP are included so you can directly ingest product data from within VISAN. Powerful visualization functionality for 2D plots and geographical plots in VISAN will allow you to directly visualize the ingested data. All components from the ESA Atmospheric Toolbox are Open Source and freely available. Software packages can be downloaded from the BEAT website: http://stcorp.nl/beat/

Educator Toolkits on Second Victim Syndrome, Mindfulness and Meditation, and Positive Psychology: The 2017 Resident Wellness Consensus Summit

PubMed Central

Smart, Jon; Zdradzinski, Michael; Roth, Sarah; Gende, Alecia; Conroy, Kylie; Battaglioli, Nicole

2018-01-01

Introduction Burnout, depression, and suicidality among residents of all specialties have become a critical focus of attention for the medical education community. Methods As part of the 2017 Resident Wellness Consensus Summit in Las Vegas, Nevada, resident participants from 31 programs collaborated in the Educator Toolkit workgroup. Over a seven-month period leading up to the summit, this workgroup convened virtually in the Wellness Think Tank, an online resident community, to perform a literature review and draft curricular plans on three core wellness topics. These topics were second victim syndrome, mindfulness and meditation, and positive psychology. At the live summit event, the workgroup expanded to include residents outside the Wellness Think Tank to obtain a broader consensus of the evidence-based toolkits for these three topics. Results Three educator toolkits were developed. The second victim syndrome toolkit has four modules, each with a pre-reading material and a leader (educator) guide. In the mindfulness and meditation toolkit, there are three modules with a leader guide in addition to a longitudinal, guided meditation plan. The positive psychology toolkit has two modules, each with a leader guide and a PowerPoint slide set. These toolkits provide educators the necessary resources, reading materials, and lesson plans to implement didactic sessions in their residency curriculum. Conclusion Residents from across the world collaborated and convened to reach a consensus on high-yield—and potentially high-impact—lesson plans that programs can use to promote and improve resident wellness. These lesson plans may stand alone or be incorporated into a larger wellness curriculum. PMID:29560061

Educator Toolkits on Second Victim Syndrome, Mindfulness and Meditation, and Positive Psychology: The 2017 Resident Wellness Consensus Summit.

PubMed

Chung, Arlene S; Smart, Jon; Zdradzinski, Michael; Roth, Sarah; Gende, Alecia; Conroy, Kylie; Battaglioli, Nicole

2018-03-01

Burnout, depression, and suicidality among residents of all specialties have become a critical focus of attention for the medical education community. As part of the 2017 Resident Wellness Consensus Summit in Las Vegas, Nevada, resident participants from 31 programs collaborated in the Educator Toolkit workgroup. Over a seven-month period leading up to the summit, this workgroup convened virtually in the Wellness Think Tank, an online resident community, to perform a literature review and draft curricular plans on three core wellness topics. These topics were second victim syndrome, mindfulness and meditation, and positive psychology. At the live summit event, the workgroup expanded to include residents outside the Wellness Think Tank to obtain a broader consensus of the evidence-based toolkits for these three topics. Three educator toolkits were developed. The second victim syndrome toolkit has four modules, each with a pre-reading material and a leader (educator) guide. In the mindfulness and meditation toolkit, there are three modules with a leader guide in addition to a longitudinal, guided meditation plan. The positive psychology toolkit has two modules, each with a leader guide and a PowerPoint slide set. These toolkits provide educators the necessary resources, reading materials, and lesson plans to implement didactic sessions in their residency curriculum. Residents from across the world collaborated and convened to reach a consensus on high-yield-and potentially high-impact-lesson plans that programs can use to promote and improve resident wellness. These lesson plans may stand alone or be incorporated into a larger wellness curriculum.

The RAPID Toolkit: Facilitating Utility-Scale Renewable Energy Development

Science.gov Websites

energy and bulk transmission projects. The RAPID Toolkit, developed by the National Renewable Energy Renewable Energy Development The RAPID Toolkit: Facilitating Utility-Scale Renewable Energy Development information about federal, state, and local permitting and regulations for utility-scale renewable energy and

Quality Assurance Toolkit for Distance Higher Education Institutions and Programmes

ERIC Educational Resources Information Center

Rama, Kondapalli, Ed.; Hope, Andrea, Ed.

2009-01-01

The Commonwealth of Learning is proud to partner with the Sri Lankan Ministry of Higher Education and UNESCO to produce this "Quality Assurance Toolkit for Distance Higher Education Institutions and Programmes". The Toolkit has been prepared with three features. First, it is a generic document on quality assurance, complete with a…

75 FR 35038 - Agency Information Collection Activities; Proposed Collection; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-21

... components of the RED, as well as the needs of culturally and linguistically diverse patients; (2) To pre-test the revised RED Toolkit in ten varied hospital settings, evaluating how the RED Toolkit is... intensity of technical assistance (TA). (3) To modify the revised RED Toolkit based on pre-testing and to...

Transition Toolkit 3.0: Meeting the Educational Needs of Youth Exposed to the Juvenile Justice System. Third Edition

ERIC Educational Resources Information Center

Clark, Heather Griller; Mathur, Sarup; Brock, Leslie; O'Cummings, Mindee; Milligan, DeAngela

2016-01-01

The third edition of the National Technical Assistance Center for the Education of Neglected or Delinquent Children and Youth's (NDTAC's) "Transition Toolkit" provides updated information on existing policies, practices, strategies, and resources for transition that build on field experience and research. The "Toolkit" offers…

Problem posing and cultural tailoring: developing an HIV/AIDS health literacy toolkit with the African American community.

PubMed

Rikard, R V; Thompson, Maxine S; Head, Rachel; McNeil, Carlotta; White, Caressa

2012-09-01

The rate of HIV infection among African Americans is disproportionately higher than for other racial groups in the United States. Previous research suggests that low level of health literacy (HL) is an underlying factor to explain racial disparities in the prevalence and incidence of HIV/AIDS. The present research describes a community and university project to develop a culturally tailored HIV/AIDS HL toolkit in the African American community. Paulo Freire's pedagogical philosophy and problem-posing methodology served as the guiding framework throughout the development process. Developing the HIV/AIDS HL toolkit occurred in a two-stage process. In Stage 1, a nonprofit organization and research team established a collaborative partnership to develop a culturally tailored HIV/AIDS HL toolkit. In Stage 2, African American community members participated in focus groups conducted as Freirian cultural circles to further refine the HIV/AIDS HL toolkit. In both stages, problem posing engaged participants' knowledge, experiences, and concerns to evaluate a working draft toolkit. The discussion and implications highlight how Freire's pedagogical philosophy and methodology enhances the development of culturally tailored health information.

Care Models of eHealth Services: A Case Study on the Design of a Business Model for an Online Precare Service.

PubMed

van Meeuwen, Dorine Pd; van Walt Meijer, Quirine J; Simonse, Lianne Wl

2015-03-24

With a growing population of health care clients in the future, the organization of high-quality and cost-effective service providing becomes an increasing challenge. New online eHealth services are proposed as innovative options for the future. Yet, a major barrier to these services appears to be the lack of new business model designs. Although design efforts generally result in visual models, no such artifacts have been found in the literature on business model design. This paper investigates business model design in eHealth service practices from a design perspective. It adopts a research by design approach and seeks to unravel what characteristics of business models determine an online service and what are important value exchanges between health professionals and clients. The objective of the study was to analyze the construction of care models in-depth, framing the essential elements of a business model, and design a new care model that structures these elements for the particular context of an online pre-care service in practice. This research employs a qualitative method of an in-depth case study in which different perspectives on constructing a care model are investigated. Data are collected by using the visual business modeling toolkit, designed to cocreate and visualize the business model. The cocreated models are transcribed and analyzed per actor perspective, transactions, and value attributes. We revealed eight new actors in the business model for providing the service. Essential actors are: the intermediary network coordinator connecting companies, the service dedicated information technology specialists, and the service dedicated health specialist. In the transactions for every service providing we found a certain type of contract, such as a license contract and service contracts for precare services and software products. In addition to the efficiency, quality, and convenience, important value attributes appeared to be: timelines, privacy and credibility, availability, pleasantness, and social interaction. Based on the in-depth insights from the actor perspectives, the business model for online precare services is modeled with a visual design. A new care model of the online precare service is designed and compiled of building blocks for the business model. For the construction of a care model, actors, transactions, and value attributes are essential elements. The design of a care model structures these elements in a visual way. Guided by the business modeling toolkit, the care model design artifact is visualized in the context of an online precare service. Important building blocks include: provision of an online flow of information with regular interactions to the client stimulates self-management of personal health and service-dedicated health expert ensure an increase of the perceived quality of the eHealth service.

Care Models of eHealth Services: A Case Study on the Design of a Business Model for an Online Precare Service

PubMed Central

2015-01-01

Background With a growing population of health care clients in the future, the organization of high-quality and cost-effective service providing becomes an increasing challenge. New online eHealth services are proposed as innovative options for the future. Yet, a major barrier to these services appears to be the lack of new business model designs. Although design efforts generally result in visual models, no such artifacts have been found in the literature on business model design. This paper investigates business model design in eHealth service practices from a design perspective. It adopts a research by design approach and seeks to unravel what characteristics of business models determine an online service and what are important value exchanges between health professionals and clients. Objective The objective of the study was to analyze the construction of care models in-depth, framing the essential elements of a business model, and design a new care model that structures these elements for the particular context of an online pre-care service in practice. Methods This research employs a qualitative method of an in-depth case study in which different perspectives on constructing a care model are investigated. Data are collected by using the visual business modeling toolkit, designed to cocreate and visualize the business model. The cocreated models are transcribed and analyzed per actor perspective, transactions, and value attributes. Results We revealed eight new actors in the business model for providing the service. Essential actors are: the intermediary network coordinator connecting companies, the service dedicated information technology specialists, and the service dedicated health specialist. In the transactions for every service providing we found a certain type of contract, such as a license contract and service contracts for precare services and software products. In addition to the efficiency, quality, and convenience, important value attributes appeared to be: timelines, privacy and credibility, availability, pleasantness, and social interaction. Based on the in-depth insights from the actor perspectives, the business model for online precare services is modeled with a visual design. A new care model of the online precare service is designed and compiled of building blocks for the business model. Conclusions For the construction of a care model, actors, transactions, and value attributes are essential elements. The design of a care model structures these elements in a visual way. Guided by the business modeling toolkit, the care model design artifact is visualized in the context of an online precare service. Important building blocks include: provision of an online flow of information with regular interactions to the client stimulates self-management of personal health and service-dedicated health expert ensure an increase of the perceived quality of the eHealth service. PMID:25831094

Web-Altairis: An Internet-Enabled Ground System

NASA Technical Reports Server (NTRS)

Miller, Phil; Coleman, Jason; Gemoets, Darren; Hughes, Kevin

2000-01-01

This paper describes Web-Altairis, an Internet-enabled ground system software package funded by the Advanced Automation and Architectures Branch (Code 588) of NASA's Goddard Space Flight Center. Web-Altairis supports the trend towards "lights out" ground systems, where the control center is unattended and problems are resolved by remote operators. This client/server software runs on most popular platforms and provides for remote data visualization using the rich functionality of the VisAGE toolkit. Web-Altairis also supports satellite commanding over the Internet. This paper describes the structure of Web-Altairis and VisAGE, the underlying technologies, the provisions for security, and our experiences in developing and testing the software.

Alarm rationalization: practical experience rationalizing alarm configuration for an accelerator subsystem

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

Kasemir, Kay; Hartman, Steven M

2009-01-01

A new alarm system toolkit has been implemented at SNS. The toolkit handles the Central Control Room (CCR) 'annunciator', or audio alarms. For the new alarm system to be effective, the alarms must be meaningful and properly configured. Along with the implementation of the new alarm toolkit, a thorough documentation and rationalization of the alarm configuration is taking place. Requirements and maintenance of a robust alarm configuration have been gathered from system and operations experts. In this paper we present our practical experience with the vacuum system alarm handling configuration of the alarm toolkit.

Demonstration of the Health Literacy Universal Precautions Toolkit

PubMed Central

Mabachi, Natabhona M.; Cifuentes, Maribel; Barnard, Juliana; Brega, Angela G.; Albright, Karen; Weiss, Barry D.; Brach, Cindy; West, David

2016-01-01

The Agency for Healthcare Research and Quality Health Literacy Universal Precautions Toolkit was developed to help primary care practices assess and make changes to improve communication with and support for patients. Twelve diverse primary care practices implemented assigned tools over a 6-month period. Qualitative results revealed challenges practices experienced during implementation, including competing demands, bureaucratic hurdles, technological challenges, limited quality improvement experience, and limited leadership support. Practices used the Toolkit flexibly and recognized the efficiencies of implementing tools in tandem and in coordination with other quality improvement initiatives. Practices recommended reducing Toolkit density and making specific refinements. PMID:27232681

Demonstration of the Health Literacy Universal Precautions Toolkit: Lessons for Quality Improvement.

PubMed

Mabachi, Natabhona M; Cifuentes, Maribel; Barnard, Juliana; Brega, Angela G; Albright, Karen; Weiss, Barry D; Brach, Cindy; West, David

2016-01-01

The Agency for Healthcare Research and Quality Health Literacy Universal Precautions Toolkit was developed to help primary care practices assess and make changes to improve communication with and support for patients. Twelve diverse primary care practices implemented assigned tools over a 6-month period. Qualitative results revealed challenges practices experienced during implementation, including competing demands, bureaucratic hurdles, technological challenges, limited quality improvement experience, and limited leadership support. Practices used the Toolkit flexibly and recognized the efficiencies of implementing tools in tandem and in coordination with other quality improvement initiatives. Practices recommended reducing Toolkit density and making specific refinements.

The nursing human resource planning best practice toolkit: creating a best practice resource for nursing managers.

PubMed

Vincent, Leslie; Beduz, Mary Agnes

2010-05-01

Evidence of acute nursing shortages in urban hospitals has been surfacing since 2000. Further, new graduate nurses account for more than 50% of total nurse turnover in some hospitals and between 35% and 60% of new graduates change workplace during the first year. Critical to organizational success, first line nurse managers must have the knowledge and skills to ensure the accurate projection of nursing resource requirements and to develop proactive recruitment and retention programs that are effective, promote positive nursing socialization, and provide early exposure to the clinical setting. The Nursing Human Resource Planning Best Practice Toolkit project supported the creation of a network of teaching and community hospitals to develop a best practice toolkit in nursing human resource planning targeted at first line nursing managers. The toolkit includes the development of a framework including the conceptual building blocks of planning tools, manager interventions, retention and recruitment and professional practice models. The development of the toolkit involved conducting a review of the literature for best practices in nursing human resource planning, using a mixed method approach to data collection including a survey and extensive interviews of managers and completing a comprehensive scan of human resource practices in the participating organizations. This paper will provide an overview of the process used to develop the toolkit, a description of the toolkit contents and a reflection on the outcomes of the project.

A proposal for a spiritual care assessment toolkit for religious volunteers and volunteer service users.

PubMed

Liu, Yi-Jung

2014-10-01

Based on the idea that volunteer services in healthcare settings should focus on the service users' best interests and providing holistic care for the body, mind, and spirit, the aim of this study was to propose an assessment toolkit for assessing the effectiveness of religious volunteers and improving their service. By analyzing and categorizing the results of previous studies, we incorporated effective care goals and methods in the proposed religious and spiritual care assessment toolkit. Two versions of the toolkit were created. The service users' version comprises 10 questions grouped into the following five dimensions: "physical care," "psychological and emotional support," "social relationships," "religious and spiritual care," and "hope restoration." Each question could either be answered with "yes" or "no". The volunteers' version contains 14 specific care goals and 31 care methods, in addition to the 10 care dimensions in the residents' version. A small sample of 25 experts was asked to judge the usefulness of each of the toolkit items for evaluating volunteers' effectiveness. Although some experts questioned the volunteer's capacity, however, to improve the spiritual care capacity and effectiveness provided by volunteers is the main purpose of developing this assessment toolkit. The toolkit developed in this study may not be applicable to other countries, and only addressed patients' general spiritual needs. Volunteers should receive special training in caring for people with special needs.

Toolkit for Evaluating Alignment of Instructional and Assessment Materials to the Common Core State Standards

ERIC Educational Resources Information Center

Achieve, Inc., 2014

2014-01-01

In joint partnership, Achieve, The Council of Chief State School Officers, and Student Achievement Partners have developed a Toolkit for Evaluating the Alignment of Instructional and Assessment Materials to the Common Core State Standards. The Toolkit is a set of interrelated, freely available instruments for evaluating alignment to the CCSS; each…

A Data Audit and Analysis Toolkit To Support Assessment of the First College Year.

ERIC Educational Resources Information Center

Paulson, Karen

This "toolkit" provides a process by which institutions can identify and use information resources to enhance the experiences and outcomes of first-year students. The toolkit contains a "Technical Manual" designed for use by the technical personnel who will be conducting the data audit and associated analyses. Administrators who want more…

Citizen Observatories: A Standards Based Architecture

NASA Astrophysics Data System (ADS)

Simonis, Ingo

2015-04-01

A number of large-scale research projects are currently under way exploring the various components of citizen observatories, e.g. CITI-SENSE (http://www.citi-sense.eu), Citclops (http://citclops.eu), COBWEB (http://cobwebproject.eu), OMNISCIENTIS (http://www.omniscientis.eu), and WeSenseIt (http://www.wesenseit.eu). Common to all projects is the motivation to develop a platform enabling effective participation by citizens in environmental projects, while considering important aspects such as security, privacy, long-term storage and availability, accessibility of raw and processed data and its proper integration into catalogues and international exchange and collaboration systems such as GEOSS or INSPIRE. This paper describes the software architecture implemented for setting up crowdsourcing campaigns using standardized components, interfaces, security features, and distribution capabilities. It illustrates the Citizen Observatory Toolkit, a software suite that allows defining crowdsourcing campaigns, to invite registered and unregistered participants to participate in crowdsourcing campaigns, and to analyze, process, and visualize raw and quality enhanced crowd sourcing data and derived products. The Citizen Observatory Toolkit is not a single software product. Instead, it is a framework of components that are built using internationally adopted standards wherever possible (e.g. OGC standards from Sensor Web Enablement, GeoPackage, and Web Mapping and Processing Services, as well as security and metadata/cataloguing standards), defines profiles of those standards where necessary (e.g. SWE O&M profile, SensorML profile), and implements design decisions based on the motivation to maximize interoperability and reusability of all components. The toolkit contains tools to set up, manage and maintain crowdsourcing campaigns, allows building on-demand apps optimized for the specific sampling focus, supports offline and online sampling modes using modern cell phones with built-in sensing technologies, automates the upload of the raw data, and handles conflation services to match quality requirements and analysis challenges. The strict implementation of all components using internationally adopted standards ensures maximal interoperability and reusability of all components. The Citizen Observatory Toolkit is currently developed as part of the COBWEB research project. COBWEB is partially funded by the European Programme FP7/2007-2013 under grant agreement n° 308513; part of the topic ENV.2012.6.5-1 "Developing community based environmental monitoring and information systems using innovative and novel earth observation applications.

A Matlab toolkit for three-dimensional electrical impedance tomography: a contribution to the Electrical Impedance and Diffuse Optical Reconstruction Software project

NASA Astrophysics Data System (ADS)

Polydorides, Nick; Lionheart, William R. B.

2002-12-01

The objective of the Electrical Impedance and Diffuse Optical Reconstruction Software project is to develop freely available software that can be used to reconstruct electrical or optical material properties from boundary measurements. Nonlinear and ill posed problems such as electrical impedance and optical tomography are typically approached using a finite element model for the forward calculations and a regularized nonlinear solver for obtaining a unique and stable inverse solution. Most of the commercially available finite element programs are unsuitable for solving these problems because of their conventional inefficient way of calculating the Jacobian, and their lack of accurate electrode modelling. A complete package for the two-dimensional EIT problem was officially released by Vauhkonen et al at the second half of 2000. However most industrial and medical electrical imaging problems are fundamentally three-dimensional. To assist the development we have developed and released a free toolkit of Matlab routines which can be employed to solve the forward and inverse EIT problems in three dimensions based on the complete electrode model along with some basic visualization utilities, in the hope that it will stimulate further development. We also include a derivation of the formula for the Jacobian (or sensitivity) matrix based on the complete electrode model.

Development and evaluation of the environment and communication assessment toolkit with speech-language pathologists.

PubMed

Bruce, Carrie; Brush, Jennifer A; Sanford, Jon A; Calkins, Margaret P

2013-04-01

Communication dysfunction that results from dementia can be exacerbated by environmental barriers such as inadequate lighting, noisy conditions, poor or absent environmental cues, and visual clutter. Speech-language pathologists (SLPs) should address these environmental barriers as part of a comprehensive treatment plan for clients with dementia. The Environment and Communication Assessment Toolkit for Dementia Care (ECAT) was evaluated by SLPs to determine: (1) changes in awareness of environmental factors prior to and after training; (2) impact of the ECAT on practice as measured by changes in the number of environmental modifications recommended and made prior to and after training; (3) utility of the information as measured by the helpfulness, amount of new information, and usefulness of the ECAT; and (4) usability of the ECAT materials based on ease of use. The SLPs used the ECAT with clients with dementia who had functional limitations and required substantial assistance with daily activities. Results indicate that the ECAT is an effective tool for SLPs, providing information about the impact of the environment on communication and supplying sufficient resources to make recommendations and implement effective interventions. The ECAT successfully increased awareness of environmental modifications, influenced the practice of recommending environmental modifications, and had utility in diverse aspects of clinical practice. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Development of an Integrated Human Factors Toolkit

NASA Technical Reports Server (NTRS)

Resnick, Marc L.

2003-01-01

An effective integration of human abilities and limitations is crucial to the success of all NASA missions. The Integrated Human Factors Toolkit facilitates this integration by assisting system designers and analysts to select the human factors tools that are most appropriate for the needs of each project. The HF Toolkit contains information about a broad variety of human factors tools addressing human requirements in the physical, information processing and human reliability domains. Analysis of each tool includes consideration of the most appropriate design stage, the amount of expertise in human factors that is required, the amount of experience with the tool and the target job tasks that are needed, and other factors that are critical for successful use of the tool. The benefits of the Toolkit include improved safety, reliability and effectiveness of NASA systems throughout the agency. This report outlines the initial stages of development for the Integrated Human Factors Toolkit.

Field tests of a participatory ergonomics toolkit for Total Worker Health

PubMed Central

Kernan, Laura; Plaku-Alakbarova, Bora; Robertson, Michelle; Warren, Nicholas; Henning, Robert

2018-01-01

Growing interest in Total Worker Health® (TWH) programs to advance worker safety, health and well-being motivated development of a toolkit to guide their implementation. Iterative design of a program toolkit occurred in which participatory ergonomics (PE) served as the primary basis to plan integrated TWH interventions in four diverse organizations. The toolkit provided start-up guides for committee formation and training, and a structured PE process for generating integrated TWH interventions. Process data from program facilitators and participants throughout program implementation were used for iterative toolkit design. Program success depended on organizational commitment to regular design team meetings with a trained facilitator, the availability of subject matter experts on ergonomics and health to support the design process, and retraining whenever committee turnover occurred. A two committee structure (employee Design Team, management Steering Committee) provided advantages over a single, multilevel committee structure, and enhanced the planning, communication, and team-work skills of participants. PMID:28166897

Fall TIPS: strategies to promote adoption and use of a fall prevention toolkit.

PubMed

Dykes, Patricia C; Carroll, Diane L; Hurley, Ann; Gersh-Zaremski, Ronna; Kennedy, Ann; Kurowski, Jan; Tierney, Kim; Benoit, Angela; Chang, Frank; Lipsitz, Stuart; Pang, Justine; Tsurkova, Ruslana; Zuyov, Lyubov; Middleton, Blackford

2009-11-14

Patient falls are serious problems in hospitals. Risk factors for falls are well understood and nurses routinely assess for fall risk on all hospitalized patients. However, the link from nursing assessment of fall risk, to identification and communication of tailored interventions to prevent falls is yet to be established. The Fall TIPS (Tailoring Interventions for Patient Safety) Toolkit was developed to leverage existing practices and workflows and to employ information technology to improve fall prevention practices. The purpose of this paper is to describe the Fall TIPS Toolkit and to report on strategies used to drive adoption of the Toolkit in four acute care hospitals. Using the IHI "Framework for Spread" as a conceptual model, the research team describes the "spread" of the Fall TIPS Toolkit as means to integrate effective fall prevention practices into the workflow of interdisciplinary caregivers, patients and family members.

Netgram: Visualizing Communities in Evolving Networks

PubMed Central

Mall, Raghvendra; Langone, Rocco; Suykens, Johan A. K.

2015-01-01

Real-world complex networks are dynamic in nature and change over time. The change is usually observed in the interactions within the network over time. Complex networks exhibit community like structures. A key feature of the dynamics of complex networks is the evolution of communities over time. Several methods have been proposed to detect and track the evolution of these groups over time. However, there is no generic tool which visualizes all the aspects of group evolution in dynamic networks including birth, death, splitting, merging, expansion, shrinkage and continuation of groups. In this paper, we propose Netgram: a tool for visualizing evolution of communities in time-evolving graphs. Netgram maintains evolution of communities over 2 consecutive time-stamps in tables which are used to create a query database using the sql outer-join operation. It uses a line-based visualization technique which adheres to certain design principles and aesthetic guidelines. Netgram uses a greedy solution to order the initial community information provided by the evolutionary clustering technique such that we have fewer line cross-overs in the visualization. This makes it easier to track the progress of individual communities in time evolving graphs. Netgram is a generic toolkit which can be used with any evolutionary community detection algorithm as illustrated in our experiments. We use Netgram for visualization of topic evolution in the NIPS conference over a period of 11 years and observe the emergence and merging of several disciplines in the field of information processing systems. PMID:26356538

HFEM3D

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

Weiss, Chester J

Software solves the three-dimensional Poisson equation div(k(grad(u)) = f, by the finite element method for the case when material properties, k, are distributed over hierarchy of edges, facets and tetrahedra in the finite element mesh. Method is described in Weiss, CJ, Finite element analysis for model parameters distributed on a hierarchy of geometric simplices, Geophysics, v82, E155-167, doi:10.1190/GEO2017-0058.1 (2017). A standard finite element method for solving Poisson’s equation is augmented by including in the 3D stiffness matrix additional 2D and 1D stiffness matrices representing the contributions from material properties associated with mesh faces and edges, respectively. The resulting linear systemmore » is solved iteratively using the conjugate gradient method with Jacobi preconditioning. To minimize computer storage for program execution, the linear solver computes matrix-vector contractions element-by-element over the mesh, without explicit storage of the global stiffness matrix. Program output vtk compliant for visualization and rendering by 3rd party software. Program uses dynamic memory allocation and as such there are no hard limits on problem size outside of those imposed by the operating system and configuration on which the software is run. Dimension, N, of the finite element solution vector is constrained by the the addressable space in 32-vs-64 bit operating systems. Total storage requirements for the problem. Total working space required for the program is approximately 13*N double precision words.« less

CAVE2: a hybrid reality environment for immersive simulation and information analysis

NASA Astrophysics Data System (ADS)

Febretti, Alessandro; Nishimoto, Arthur; Thigpen, Terrance; Talandis, Jonas; Long, Lance; Pirtle, J. D.; Peterka, Tom; Verlo, Alan; Brown, Maxine; Plepys, Dana; Sandin, Dan; Renambot, Luc; Johnson, Andrew; Leigh, Jason

2013-03-01

Hybrid Reality Environments represent a new kind of visualization spaces that blur the line between virtual environments and high resolution tiled display walls. This paper outlines the design and implementation of the CAVE2TM Hybrid Reality Environment. CAVE2 is the world's first near-seamless flat-panel-based, surround-screen immersive system. Unique to CAVE2 is that it will enable users to simultaneously view both 2D and 3D information, providing more flexibility for mixed media applications. CAVE2 is a cylindrical system of 24 feet in diameter and 8 feet tall, and consists of 72 near-seamless, off-axisoptimized passive stereo LCD panels, creating an approximately 320 degree panoramic environment for displaying information at 37 Megapixels (in stereoscopic 3D) or 74 Megapixels in 2D and at a horizontal visual acuity of 20/20. Custom LCD panels with shifted polarizers were built so the images in the top and bottom rows of LCDs are optimized for vertical off-center viewing- allowing viewers to come closer to the displays while minimizing ghosting. CAVE2 is designed to support multiple operating modes. In the Fully Immersive mode, the entire room can be dedicated to one virtual simulation. In 2D model, the room can operate like a traditional tiled display wall enabling users to work with large numbers of documents at the same time. In the Hybrid mode, a mixture of both 2D and 3D applications can be simultaneously supported. The ability to treat immersive work spaces in this Hybrid way has never been achieved before, and leverages the special abilities of CAVE2 to enable researchers to seamlessly interact with large collections of 2D and 3D data. To realize this hybrid ability, we merged the Scalable Adaptive Graphics Environment (SAGE) - a system for supporting 2D tiled displays, with Omegalib - a virtual reality middleware supporting OpenGL, OpenSceneGraph and Vtk applications.

Building an Open-source Simulation Platform of Acoustic Radiation Force-based Breast Elastography

PubMed Central

Wang, Yu; Peng, Bo; Jiang, Jingfeng

2017-01-01

Ultrasound-based elastography including strain elastography (SE), acoustic radiation force Impulse (ARFI) imaging, point shear wave elastography (pSWE) and supersonic shear imaging (SSI) have been used to differentiate breast tumors among other clinical applications. The objective of this study is to extend a previously published virtual simulation platform built for ultrasound quasi-static breast elastography toward acoustic radiation force-based breast elastography. Consequently, the extended virtual breast elastography simulation platform can be used to validate image pixels with known underlying soft tissue properties (i.e. “ground truth”) in complex, heterogeneous media, enhancing confidence in elastographic image interpretations. The proposed virtual breast elastography system inherited four key components from the previously published virtual simulation platform: an ultrasound simulator (Field II), a mesh generator (Tetgen), a finite element solver (FEBio) and a visualization and data processing package (VTK). Using a simple message passing mechanism, functionalities have now been extended to acoustic radiation force-based elastography simulations. Examples involving three different numerical breast models with increasing complexity – one uniform model, one simple inclusion model and one virtual complex breast model derived from magnetic resonance imaging data, were used to demonstrate capabilities of this extended virtual platform. Overall, simulation results were compared with the published results. In the uniform model, the estimated shear wave speed (SWS) values were within 4% compared to the predetermined SWS values. In the simple inclusion and the complex breast models, SWS values of all hard inclusions in soft backgrounds were slightly underestimated, similar to what has been reported. The elastic contrast values and visual observation show that ARFI images have higher spatial resolution, while SSI images can provide higher inclusion-to-background contrast. In summary, our initial results were consistent with our expectations and what have been reported in the literature. The proposed (open-source) simulation platform can serve as a single gateway to perform many elastographic simulations in a transparent manner, thereby promoting collaborative developments. PMID:28075330

Building an open-source simulation platform of acoustic radiation force-based breast elastography

NASA Astrophysics Data System (ADS)

Wang, Yu; Peng, Bo; Jiang, Jingfeng

2017-03-01

Ultrasound-based elastography including strain elastography, acoustic radiation force impulse (ARFI) imaging, point shear wave elastography and supersonic shear imaging (SSI) have been used to differentiate breast tumors among other clinical applications. The objective of this study is to extend a previously published virtual simulation platform built for ultrasound quasi-static breast elastography toward acoustic radiation force-based breast elastography. Consequently, the extended virtual breast elastography simulation platform can be used to validate image pixels with known underlying soft tissue properties (i.e. ‘ground truth’) in complex, heterogeneous media, enhancing confidence in elastographic image interpretations. The proposed virtual breast elastography system inherited four key components from the previously published virtual simulation platform: an ultrasound simulator (Field II), a mesh generator (Tetgen), a finite element solver (FEBio) and a visualization and data processing package (VTK). Using a simple message passing mechanism, functionalities have now been extended to acoustic radiation force-based elastography simulations. Examples involving three different numerical breast models with increasing complexity—one uniform model, one simple inclusion model and one virtual complex breast model derived from magnetic resonance imaging data, were used to demonstrate capabilities of this extended virtual platform. Overall, simulation results were compared with the published results. In the uniform model, the estimated shear wave speed (SWS) values were within 4% compared to the predetermined SWS values. In the simple inclusion and the complex breast models, SWS values of all hard inclusions in soft backgrounds were slightly underestimated, similar to what has been reported. The elastic contrast values and visual observation show that ARFI images have higher spatial resolution, while SSI images can provide higher inclusion-to-background contrast. In summary, our initial results were consistent with our expectations and what have been reported in the literature. The proposed (open-source) simulation platform can serve as a single gateway to perform many elastographic simulations in a transparent manner, thereby promoting collaborative developments.

Building Emergency Contraception Awareness among Adolescents. A Toolkit for Schools and Community-Based Organizations.

ERIC Educational Resources Information Center

Simkin, Linda; Radosh, Alice; Nelsesteun, Kari; Silverstein, Stacy

This toolkit presents emergency contraception (EC) as a method to help adolescent women avoid pregnancy and abortion after unprotected sexual intercourse. The sections of this toolkit are designed to help increase your knowledge of EC and stay up to date. They provide suggestions for increasing EC awareness in the workplace, whether it is a school…

The Customer Flow Toolkit: A Framework for Designing High Quality Customer Services.

ERIC Educational Resources Information Center

New York Association of Training and Employment Professionals, Albany.

This document presents a toolkit to assist staff involved in the design and development of New York's one-stop system. Section 1 describes the preplanning issues to be addressed and the intended outcomes that serve as the framework for creation of the customer flow toolkit. Section 2 outlines the following strategies to assist in designing local…

HIV Prevention in Schools: A Tool Kit for Education Leaders.

ERIC Educational Resources Information Center

Office of the Surgeon General (DHHS/PHS), Washington, DC.

This packet of materials is Phase 1 of a toolkit designed to enlighten education leaders about the need for HIV prevention for youth, especially in communities of color. One element of the toolkit is a VHS videotape that features a brief message from former Surgeon General, Dr. David Satcher. The toolkit also includes a copy of a letter sent to…

Toolkit of Resources for Engaging Parents and Community as Partners in Education. Part I: Building an Understanding of Family and Community Engagement

ERIC Educational Resources Information Center

Regional Educational Laboratory Pacific, 2014

2014-01-01

This toolkit is designed to guide school staff in strengthening partnerships with families and community members to support student learning. This toolkit offers an integrated approach to family and community engagement, bringing together research, promising practices, and a wide range of useful tools and resources with explanations and directions…

Toolkit for a Workshop on Building a Culture of Data Use. REL 2015-063

ERIC Educational Resources Information Center

Gerzon, Nancy; Guckenburg, Sarah

2015-01-01

The Culture of Data Use Workshop Toolkit helps school and district teams apply research to practice as they establish and support a culture of data use in their educational setting. The field-tested workshop toolkit guides teams through a set of structured activities to develop an understanding of data-use research in schools and to analyze…

Implementing Project Based Survey Research Skills to Grade Six ELP Students with "The Survey Toolkit" and "TinkerPlots"[R

ERIC Educational Resources Information Center

Walsh, Thomas, Jr.

2011-01-01

"Survey Toolkit Collecting Information, Analyzing Data and Writing Reports" (Walsh, 2009a) is discussed as a survey research curriculum used by the author's sixth grade students. The report describes the implementation of "The Survey Toolkit" curriculum and "TinkerPlots"[R] software to provide instruction to students learning a project based…

Overview and Meteorological Validation of the Wind Integration National Dataset toolkit

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

Draxl, C.; Hodge, B. M.; Clifton, A.

2015-04-13

The Wind Integration National Dataset (WIND) Toolkit described in this report fulfills these requirements, and constitutes a state-of-the-art national wind resource data set covering the contiguous United States from 2007 to 2013 for use in a variety of next-generation wind integration analyses and wind power planning. The toolkit is a wind resource data set, wind forecast data set, and wind power production and forecast data set derived from the Weather Research and Forecasting (WRF) numerical weather prediction model. WIND Toolkit data are available online for over 116,000 land-based and 10,000 offshore sites representing existing and potential wind facilities.

An open source toolkit for medical imaging de-identification.

PubMed

González, David Rodríguez; Carpenter, Trevor; van Hemert, Jano I; Wardlaw, Joanna

2010-08-01

Medical imaging acquired for clinical purposes can have several legitimate secondary uses in research projects and teaching libraries. No commonly accepted solution for anonymising these images exists because the amount of personal data that should be preserved varies case by case. Our objective is to provide a flexible mechanism for anonymising Digital Imaging and Communications in Medicine (DICOM) data that meets the requirements for deployment in multicentre trials. We reviewed our current de-identification practices and defined the relevant use cases to extract the requirements for the de-identification process. We then used these requirements in the design and implementation of the toolkit. Finally, we tested the toolkit taking as a reference those requirements, including a multicentre deployment. The toolkit successfully anonymised DICOM data from various sources. Furthermore, it was shown that it could forward anonymous data to remote destinations, remove burned-in annotations, and add tracking information to the header. The toolkit also implements the DICOM standard confidentiality mechanism. A DICOM de-identification toolkit that facilitates the enforcement of privacy policies was developed. It is highly extensible, provides the necessary flexibility to account for different de-identification requirements and has a low adoption barrier for new users.

The Reconstruction Toolkit (RTK), an open-source cone-beam CT reconstruction toolkit based on the Insight Toolkit (ITK)

NASA Astrophysics Data System (ADS)

Rit, S.; Vila Oliva, M.; Brousmiche, S.; Labarbe, R.; Sarrut, D.; Sharp, G. C.

2014-03-01

We propose the Reconstruction Toolkit (RTK, http://www.openrtk.org), an open-source toolkit for fast cone-beam CT reconstruction, based on the Insight Toolkit (ITK) and using GPU code extracted from Plastimatch. RTK is developed by an open consortium (see affiliations) under the non-contaminating Apache 2.0 license. The quality of the platform is daily checked with regression tests in partnership with Kitware, the company supporting ITK. Several features are already available: Elekta, Varian and IBA inputs, multi-threaded Feldkamp-David-Kress reconstruction on CPU and GPU, Parker short scan weighting, multi-threaded CPU and GPU forward projectors, etc. Each feature is either accessible through command line tools or C++ classes that can be included in independent software. A MIDAS community has been opened to share CatPhan datasets of several vendors (Elekta, Varian and IBA). RTK will be used in the upcoming cone-beam CT scanner developed by IBA for proton therapy rooms. Many features are under development: new input format support, iterative reconstruction, hybrid Monte Carlo / deterministic CBCT simulation, etc. RTK has been built to freely share tomographic reconstruction developments between researchers and is open for new contributions.

Development of an Online Toolkit for Measuring Performance in Health Emergency Response Exercises.

PubMed

Agboola, Foluso; Bernard, Dorothy; Savoia, Elena; Biddinger, Paul D

2015-10-01

Exercises that simulate emergency scenarios are accepted widely as an essential component of a robust Emergency Preparedness program. Unfortunately, the variability in the quality of the exercises conducted, and the lack of standardized processes to measure performance, has limited the value of exercises in measuring preparedness. In order to help health organizations improve the quality and standardization of the performance data they collect during simulated emergencies, a model online exercise evaluation toolkit was developed using performance measures tested in over 60 Emergency Preparedness exercises. The exercise evaluation toolkit contains three major components: (1) a database of measures that can be used to assess performance during an emergency response exercise; (2) a standardized data collection tool (form); and (3) a program that populates the data collection tool with the measures that have been selected by the user from the database. The evaluation toolkit was pilot tested from January through September 2014 in collaboration with 14 partnering organizations representing 10 public health agencies and four health care agencies from eight states across the US. Exercise planners from the partnering organizations were asked to use the toolkit for their exercise evaluation process and were interviewed to provide feedback on the use of the toolkit, the generated evaluation tool, and the usefulness of the data being gathered for the development of the exercise after-action report. Ninety-three percent (93%) of exercise planners reported that they found the online database of performance measures appropriate for the creation of exercise evaluation forms, and they stated that they would use it again for future exercises. Seventy-two percent (72%) liked the exercise evaluation form that was generated from the toolkit, and 93% reported that the data collected by the use of the evaluation form were useful in gauging their organization's performance during the exercise. Seventy-nine percent (79%) of exercise planners preferred the evaluation form generated by the toolkit to other forms of evaluations. Results of this project show that users found the newly developed toolkit to be user friendly and more relevant to measurement of specific public health and health care capabilities than other tools currently available. The developed toolkit may contribute to the further advancement of developing a valid approach to exercise performance measurement.

Facilitated family presence at resuscitation: effectiveness of a nursing student toolkit.

PubMed

Kantrowitz-Gordon, Ira; Bennett, Deborah; Wise Stauffer, Debra; Champ-Gibson, Erla; Fitzgerald, Cynthia; Corbett, Cynthia

2013-10-01

Facilitated family presence at resuscitation is endorsed by multiple nursing and specialty practice organizations. Implementation of this practice is not universal so there is a need to increase familiarity and competence with facilitated family presence at resuscitation during this significant life event. One strategy to promote this practice is to use a nursing student toolkit for pre-licensure and graduate nursing students. The toolkit includes short video simulations of facilitated family presence at resuscitation, a PowerPoint presentation of evidence-based practice, and questions to facilitate guided discussion. This study tested the effectiveness of this toolkit in increasing nursing students' knowledge, perceptions, and confidence in facilitated family presence at resuscitation. Nursing students from five universities in the United States completed the Family Presence Risk-Benefit Scale, Family Presence Self-Confidence Scale, and a knowledge test before and after the intervention. Implementing the facilitated family presence at resuscitation toolkit significantly increased nursing students' knowledge, perceptions, and confidence related to facilitated family presence at resuscitation (p<.001). The effect size was large for knowledge (d=.90) and perceptions (d=1.04) and moderate for confidence (d=.51). The facilitated family presence at resuscitation toolkit used in this study had a positive impact on students' knowledge, perception of benefits and risks, and self-confidence in facilitated family presence at resuscitation. The toolkit provides students a structured opportunity to consider the presence of family members at resuscitation prior to encountering this situation in clinical practice. Copyright © 2012 Elsevier Ltd. All rights reserved.

Behavioral Genetic Toolkits: Toward the Evolutionary Origins of Complex Phenotypes.

PubMed

Rittschof, C C; Robinson, G E

2016-01-01

The discovery of toolkit genes, which are highly conserved genes that consistently regulate the development of similar morphological phenotypes across diverse species, is one of the most well-known observations in the field of evolutionary developmental biology. Surprisingly, this phenomenon is also relevant for a wide array of behavioral phenotypes, despite the fact that these phenotypes are highly complex and regulated by many genes operating in diverse tissues. In this chapter, we review the use of the toolkit concept in the context of behavior, noting the challenges of comparing behaviors and genes across diverse species, but emphasizing the successes in identifying genetic toolkits for behavior; these successes are largely attributable to the creative research approaches fueled by advances in behavioral genomics. We have two general goals: (1) to acknowledge the groundbreaking progress in this field, which offers new approaches to the difficult but exciting challenge of understanding the evolutionary genetic basis of behaviors, some of the most complex phenotypes known, and (2) to provide a theoretical framework that encompasses the scope of behavioral genetic toolkit studies in order to clearly articulate the research questions relevant to the toolkit concept. We emphasize areas for growth and highlight the emerging approaches that are being used to drive the field forward. Behavioral genetic toolkit research has elevated the use of integrative and comparative approaches in the study of behavior, with potentially broad implications for evolutionary biologists and behavioral ecologists alike. © 2016 Elsevier Inc. All rights reserved.

Wind Integration National Dataset (WIND) Toolkit; NREL (National Renewable Energy Laboratory)

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

Draxl, Caroline; Hodge, Bri-Mathias

A webinar about the Wind Integration National Dataset (WIND) Toolkit was presented by Bri-Mathias Hodge and Caroline Draxl on July 14, 2015. It was hosted by the Southern Alliance for Clean Energy. The toolkit is a grid integration data set that contains meteorological and power data at a 5-minute resolution across the continental United States for 7 years and hourly power forecasts.

Toolkit of Resources for Engaging Families and the Community as Partners in Education: Part 2: Building a Cultural Bridge. REL 2016-151

ERIC Educational Resources Information Center

Garcia, Maria Elena; Frunzi, Kay; Dean, Ceri B.; Flores, Nieves; Miller, Kirsten B.

2016-01-01

The Toolkit of Resources for Engaging Families and the Community as Partners in Education is a four-part resource that brings together research, promising practices, and useful tools and resources to guide educators in strengthening partnerships with families and community members to support student learning. The toolkit defines family and…

Semantic Web Technologies for Mobile Context-Aware Services

DTIC Science & Technology

2006-03-01

for Context-Aware Service Provisioning 6 Communication toolkit (http, e-mail, IM, etc.) User interaction manager Platform manager White & yellow ...NAICS] North American Industry Classification System , http://www.census.gov/epcd/www/naics.html [OS00] Opermann, R., and Specht , M., A Context...toolkit (http, e-mail, IM, etc.) User interaction manager Platform manager White & yellow pages MAS administration toolkit N ET W O R K knowledge

Toolkit of Resources for Engaging Parents and Community as Partners in Education. Part 3: Building Trusting Relationships with Families & Community through Effective Communication

ERIC Educational Resources Information Center

Regional Educational Laboratory Pacific, 2015

2015-01-01

This toolkit is designed to guide school staff in strengthening partnerships with families and community members to support student learning. This toolkit offers an integrated approach to family and community engagement, bringing together research, promising practices, and a wide range of useful tools and resources with explanations and directions…

Designing and evaluating an interprofessional shared decision-making and goal-setting decision aid for patients with diabetes in clinical care--systematic decision aid development and study protocol.

PubMed

Yu, Catherine H; Stacey, Dawn; Sale, Joanna; Hall, Susan; Kaplan, David M; Ivers, Noah; Rezmovitz, Jeremy; Leung, Fok-Han; Shah, Baiju R; Straus, Sharon E

2014-01-22

Care of patients with diabetes often occurs in the context of other chronic illness. Competing disease priorities and competing patient-physician priorities present challenges in the provision of care for the complex patient. Guideline implementation interventions to date do not acknowledge these intricacies of clinical practice. As a result, patients and providers are left overwhelmed and paralyzed by the sheer volume of recommendations and tasks. An individualized approach to the patient with diabetes and multiple comorbid conditions using shared decision-making (SDM) and goal setting has been advocated as a patient-centred approach that may facilitate prioritization of treatment options. Furthermore, incorporating interprofessional integration into practice may overcome barriers to implementation. However, these strategies have not been taken up extensively in clinical practice. To systematically develop and test an interprofessional SDM and goal-setting toolkit for patients with diabetes and other chronic diseases, following the Knowledge to Action framework. 1. Feasibility study: Individual interviews with primary care physicians, nurses, dietitians, pharmacists, and patients with diabetes will be conducted, exploring their experiences with shared decision-making and priority-setting, including facilitators and barriers, the relevance of a decision aid and toolkit for priority-setting, and how best to integrate it into practice.2. Toolkit development: Based on this data, an evidence-based multi-component SDM toolkit will be developed. The toolkit will be reviewed by content experts (primary care, endocrinology, geriatricians, nurses, dietitians, pharmacists, patients) for accuracy and comprehensiveness.3. Heuristic evaluation: A human factors engineer will review the toolkit and identify, list and categorize usability issues by severity.4. Usability testing: This will be done using cognitive task analysis.5. Iterative refinement: Throughout the development process, the toolkit will be refined through several iterative cycles of feedback and redesign. Interprofessional shared decision-making regarding priority-setting with the use of a decision aid toolkit may help prioritize care of individuals with multiple comorbid conditions. Adhering to principles of user-centered design, we will develop and refine a toolkit to assess the feasibility of this approach.

Designing and evaluating an interprofessional shared decision-making and goal-setting decision aid for patients with diabetes in clinical care - systematic decision aid development and study protocol

PubMed Central

2014-01-01

Background Care of patients with diabetes often occurs in the context of other chronic illness. Competing disease priorities and competing patient-physician priorities present challenges in the provision of care for the complex patient. Guideline implementation interventions to date do not acknowledge these intricacies of clinical practice. As a result, patients and providers are left overwhelmed and paralyzed by the sheer volume of recommendations and tasks. An individualized approach to the patient with diabetes and multiple comorbid conditions using shared decision-making (SDM) and goal setting has been advocated as a patient-centred approach that may facilitate prioritization of treatment options. Furthermore, incorporating interprofessional integration into practice may overcome barriers to implementation. However, these strategies have not been taken up extensively in clinical practice. Objectives To systematically develop and test an interprofessional SDM and goal-setting toolkit for patients with diabetes and other chronic diseases, following the Knowledge to Action framework. Methods 1. Feasibility study: Individual interviews with primary care physicians, nurses, dietitians, pharmacists, and patients with diabetes will be conducted, exploring their experiences with shared decision-making and priority-setting, including facilitators and barriers, the relevance of a decision aid and toolkit for priority-setting, and how best to integrate it into practice. 2. Toolkit development: Based on this data, an evidence-based multi-component SDM toolkit will be developed. The toolkit will be reviewed by content experts (primary care, endocrinology, geriatricians, nurses, dietitians, pharmacists, patients) for accuracy and comprehensiveness. 3. Heuristic evaluation: A human factors engineer will review the toolkit and identify, list and categorize usability issues by severity. 4. Usability testing: This will be done using cognitive task analysis. 5. Iterative refinement: Throughout the development process, the toolkit will be refined through several iterative cycles of feedback and redesign. Discussion Interprofessional shared decision-making regarding priority-setting with the use of a decision aid toolkit may help prioritize care of individuals with multiple comorbid conditions. Adhering to principles of user-centered design, we will develop and refine a toolkit to assess the feasibility of this approach. PMID:24450385

Designing a ticket to ride with the Cognitive Work Analysis Design Toolkit.

PubMed

Read, Gemma J M; Salmon, Paul M; Lenné, Michael G; Jenkins, Daniel P

2015-01-01

Cognitive work analysis has been applied in the design of numerous sociotechnical systems. The process used to translate analysis outputs into design concepts, however, is not always clear. Moreover, structured processes for translating the outputs of ergonomics methods into concrete designs are lacking. This paper introduces the Cognitive Work Analysis Design Toolkit (CWA-DT), a design approach which has been developed specifically to provide a structured means of incorporating cognitive work analysis outputs in design using design principles and values derived from sociotechnical systems theory. This paper outlines the CWA-DT and describes its application in a public transport ticketing design case study. Qualitative and quantitative evaluations of the process provide promising early evidence that the toolkit fulfils the evaluation criteria identified for its success, with opportunities for improvement also highlighted. The Cognitive Work Analysis Design Toolkit has been developed to provide ergonomics practitioners with a structured approach for translating the outputs of cognitive work analysis into design solutions. This paper demonstrates an application of the toolkit and provides evaluation findings.

Field tests of a participatory ergonomics toolkit for Total Worker Health.

PubMed

Nobrega, Suzanne; Kernan, Laura; Plaku-Alakbarova, Bora; Robertson, Michelle; Warren, Nicholas; Henning, Robert

2017-04-01

Growing interest in Total Worker Health ® (TWH) programs to advance worker safety, health and well-being motivated development of a toolkit to guide their implementation. Iterative design of a program toolkit occurred in which participatory ergonomics (PE) served as the primary basis to plan integrated TWH interventions in four diverse organizations. The toolkit provided start-up guides for committee formation and training, and a structured PE process for generating integrated TWH interventions. Process data from program facilitators and participants throughout program implementation were used for iterative toolkit design. Program success depended on organizational commitment to regular design team meetings with a trained facilitator, the availability of subject matter experts on ergonomics and health to support the design process, and retraining whenever committee turnover occurred. A two committee structure (employee Design Team, management Steering Committee) provided advantages over a single, multilevel committee structure, and enhanced the planning, communication, and teamwork skills of participants. Copyright © 2016 Elsevier Ltd. All rights reserved.

Measures of Success for Earth System Science Education: The DLESE Evaluation Services and the Evaluation Toolkit Collection

NASA Astrophysics Data System (ADS)

McCaffrey, M. S.; Buhr, S. M.; Lynds, S.

2005-12-01

Increased agency emphasis upon the integration of research and education coupled with the ability to provide students with access to digital background materials, learning activities and primary data sources has begun to revolutionize Earth science education in formal and informal settings. The DLESE Evaluation Services team and the related Evaluation Toolkit collection (http://www.dlese.org/cms/evalservices/ ) provides services and tools for education project leads and educators. Through the Evaluation Toolkit, educators may access high-quality digital materials to assess students' cognitive gains, examples of alternative assessments, and case studies and exemplars of authentic research. The DLESE Evaluation Services team provides support for those who are developing evaluation plans on an as-requested basis. In addition, the Toolkit provides authoritative peer reviewed articlesabout evaluation research techniques and strategies of particular importance to geoscience education. This paper will provide an overview of the DLESE Evaluation Toolkit and discuss challenges and best practices for assessing student learning and evaluating Earth system sciences education in a digital world.

Respiratory Protection Toolkit: Providing Guidance Without Changing Requirements-Can We Make an Impact?

PubMed

Bien, Elizabeth Ann; Gillespie, Gordon Lee; Betcher, Cynthia Ann; Thrasher, Terri L; Mingerink, Donna R

2016-12-01

International travel and infectious respiratory illnesses worldwide place health care workers (HCWs) at increasing risk of respiratory exposures. To ensure the highest quality safety initiatives, one health care system used a quality improvement model of Plan-Do-Study-Act and guidance from Occupational Safety and Health Administration's (OSHA) May 2015 Hospital Respiratory Protection Program (RPP) Toolkit to assess a current program. The toolkit aided in identification of opportunities for improvement within their well-designed RPP. One opportunity was requiring respirator use during aerosol-generating procedures for specific infectious illnesses. Observation data demonstrated opportunities to mitigate controllable risks including strap placement, user seal check, and reuse of disposable N95 filtering facepiece respirators. Subsequent interdisciplinary collaboration resulted in other ideas to decrease risks and increase protection from potentially infectious respiratory illnesses. The toolkit's comprehensive document to evaluate the program showed that while the OSHA standards have not changed, the addition of the toolkit can better protect HCWs. © 2016 The Author(s).

Can a workbook work? Examining whether a practitioner evaluation toolkit can promote instrumental use.

PubMed

Campbell, Rebecca; Townsend, Stephanie M; Shaw, Jessica; Karim, Nidal; Markowitz, Jenifer

2015-10-01

In large-scale, multi-site contexts, developing and disseminating practitioner-oriented evaluation toolkits are an increasingly common strategy for building evaluation capacity. Toolkits explain the evaluation process, present evaluation design choices, and offer step-by-step guidance to practitioners. To date, there has been limited research on whether such resources truly foster the successful design, implementation, and use of evaluation findings. In this paper, we describe a multi-site project in which we developed a practitioner evaluation toolkit and then studied the extent to which the toolkit and accompanying technical assistance was effective in promoting successful completion of local-level evaluations and fostering instrumental use of the findings (i.e., whether programs directly used their findings to improve practice, see Patton, 2008). Forensic nurse practitioners from six geographically dispersed service programs completed methodologically rigorous evaluations; furthermore, all six programs used the findings to create programmatic and community-level changes to improve local practice. Implications for evaluation capacity building are discussed. Copyright © 2015 Elsevier Ltd. All rights reserved.

A novel medical image data-based multi-physics simulation platform for computational life sciences.

PubMed

Neufeld, Esra; Szczerba, Dominik; Chavannes, Nicolas; Kuster, Niels

2013-04-06

Simulating and modelling complex biological systems in computational life sciences requires specialized software tools that can perform medical image data-based modelling, jointly visualize the data and computational results, and handle large, complex, realistic and often noisy anatomical models. The required novel solvers must provide the power to model the physics, biology and physiology of living tissue within the full complexity of the human anatomy (e.g. neuronal activity, perfusion and ultrasound propagation). A multi-physics simulation platform satisfying these requirements has been developed for applications including device development and optimization, safety assessment, basic research, and treatment planning. This simulation platform consists of detailed, parametrized anatomical models, a segmentation and meshing tool, a wide range of solvers and optimizers, a framework for the rapid development of specialized and parallelized finite element method solvers, a visualization toolkit-based visualization engine, a Python scripting interface for customized applications, a coupling framework, and more. Core components are cross-platform compatible and use open formats. Several examples of applications are presented: hyperthermia cancer treatment planning, tumour growth modelling, evaluating the magneto-haemodynamic effect as a biomarker and physics-based morphing of anatomical models.

A scalable architecture for extracting, aligning, linking, and visualizing multi-Int data

NASA Astrophysics Data System (ADS)

Knoblock, Craig A.; Szekely, Pedro

2015-05-01

An analyst today has a tremendous amount of data available, but each of the various data sources typically exists in their own silos, so an analyst has limited ability to see an integrated view of the data and has little or no access to contextual information that could help in understanding the data. We have developed the Domain-Insight Graph (DIG) system, an innovative architecture for extracting, aligning, linking, and visualizing massive amounts of domain-specific content from unstructured sources. Under the DARPA Memex program we have already successfully applied this architecture to multiple application domains, including the enormous international problem of human trafficking, where we extracted, aligned and linked data from 50 million online Web pages. DIG builds on our Karma data integration toolkit, which makes it easy to rapidly integrate structured data from a variety of sources, including databases, spreadsheets, XML, JSON, and Web services. The ability to integrate Web services allows Karma to pull in live data from the various social media sites, such as Twitter, Instagram, and OpenStreetMaps. DIG then indexes the integrated data and provides an easy to use interface for query, visualization, and analysis.

Equalizer: a scalable parallel rendering framework.

PubMed

Eilemann, Stefan; Makhinya, Maxim; Pajarola, Renato

2009-01-01

Continuing improvements in CPU and GPU performances as well as increasing multi-core processor and cluster-based parallelism demand for flexible and scalable parallel rendering solutions that can exploit multipipe hardware accelerated graphics. In fact, to achieve interactive visualization, scalable rendering systems are essential to cope with the rapid growth of data sets. However, parallel rendering systems are non-trivial to develop and often only application specific implementations have been proposed. The task of developing a scalable parallel rendering framework is even more difficult if it should be generic to support various types of data and visualization applications, and at the same time work efficiently on a cluster with distributed graphics cards. In this paper we introduce a novel system called Equalizer, a toolkit for scalable parallel rendering based on OpenGL which provides an application programming interface (API) to develop scalable graphics applications for a wide range of systems ranging from large distributed visualization clusters and multi-processor multipipe graphics systems to single-processor single-pipe desktop machines. We describe the system architecture, the basic API, discuss its advantages over previous approaches, present example configurations and usage scenarios as well as scalability results.

Automated Neuropsychological Assessment Metrics, Version 4 (ANAM4): Examination of Select Psychometric Properties and Administration Procedures

DTIC Science & Technology

2016-12-01

2017 was approved in August 2016. The supplemental project has 2 primary objectives: • Recommend cognitive assessment tools/approaches ( toolkit ) from...strategies for use in future military-relevant environments The supplemental project has two primary deliverables: • Proposed Toolkit of cognitive...6 Vet Final Report and Cognitive performance recommendations through Steering Committee Task 7 Provide Toolkit Report 16 Months 8-12 Task 8

Toolkit of Resources for Engaging Families and the Community as Partners in Education. Part 1: Building an Understanding of Family and Community Engagement. REL 2016-148

ERIC Educational Resources Information Center

Garcia, Maria Elena; Frunzi, Kay; Dean, Ceri B.; Flores, Nieves; Miller, Kirsten B.

2016-01-01

The Toolkit of Resources for Engaging Families and the Community as Partners in Education is a four-part resource that brings together research, promising practices, and useful tools and resources to guide educators in strengthening partnerships with families and community members to support student learning. The toolkit defines family and…

Toolkit of Resources for Engaging Families and the Community as Partners in Education: Part 3: Building Trusting Relationships with Families and the Community through Effective Communication. REL 2016-152

ERIC Educational Resources Information Center

Garcia, Maria Elena; Frunzi, Kay; Dean, Ceri B.; Flores, Nieves; Miller, Kirsten B.

2016-01-01

The Toolkit of Resources for Engaging Families and the Community as Partners in Education is a four-part resource that brings together research, promising practices, and useful tools and resources to guide educators in strengthening partnerships with families and community members to support student learning. The toolkit defines family and…

BRDF profile of Tyvek and its implementation in the Geant4 simulation toolkit.

PubMed

Nozka, Libor; Pech, Miroslav; Hiklova, Helena; Mandat, Dusan; Hrabovsky, Miroslav; Schovanek, Petr; Palatka, Miroslav

2011-02-28

Diffuse and specular characteristics of the Tyvek 1025-BL material are reported with respect to their implementation in the Geant4 Monte Carlo simulation toolkit. This toolkit incorporates the UNIFIED model. Coefficients defined by the UNIFIED model were calculated from the bidirectional reflectance distribution function (BRDF) profiles measured with a scatterometer for several angles of incidence. Results were amended with profile measurements made by a profilometer.

SIGKit: Software for Introductory Geophysics Toolkit

NASA Astrophysics Data System (ADS)

Kruse, S.; Bank, C. G.; Esmaeili, S.; Jazayeri, S.; Liu, S.; Stoikopoulos, N.

2017-12-01

The Software for Introductory Geophysics Toolkit (SIGKit) affords students the opportunity to create model data and perform simple processing of field data for various geophysical methods. SIGkit provides a graphical user interface built with the MATLAB programming language, but can run even without a MATLAB installation. At this time SIGkit allows students to pick first arrivals and match a two-layer model to seismic refraction data; grid total-field magnetic data, extract a profile, and compare this to a synthetic profile; and perform simple processing steps (subtraction of a mean trace, hyperbola fit) to ground-penetrating radar data. We also have preliminary tools for gravity, resistivity, and EM data representation and analysis. SIGkit is being built by students for students, and the intent of the toolkit is to provide an intuitive interface for simple data analysis and understanding of the methods, and act as an entrance to more sophisticated software. The toolkit has been used in introductory courses as well as field courses. First reactions from students are positive. Think-aloud observations of students using the toolkit have helped identify problems and helped shape it. We are planning to compare the learning outcomes of students who have used the toolkit in a field course to students in a previous course to test its effectiveness.

The development of an artificial organic networks toolkit for LabVIEW.

PubMed

Ponce, Hiram; Ponce, Pedro; Molina, Arturo

2015-03-15

Two of the most challenging problems that scientists and researchers face when they want to experiment with new cutting-edge algorithms are the time-consuming for encoding and the difficulties for linking them with other technologies and devices. In that sense, this article introduces the artificial organic networks toolkit for LabVIEW™ (AON-TL) from the implementation point of view. The toolkit is based on the framework provided by the artificial organic networks technique, giving it the potential to add new algorithms in the future based on this technique. Moreover, the toolkit inherits both the rapid prototyping and the easy-to-use characteristics of the LabVIEW™ software (e.g., graphical programming, transparent usage of other softwares and devices, built-in programming event-driven for user interfaces), to make it simple for the end-user. In fact, the article describes the global architecture of the toolkit, with particular emphasis in the software implementation of the so-called artificial hydrocarbon networks algorithm. Lastly, the article includes two case studies for engineering purposes (i.e., sensor characterization) and chemistry applications (i.e., blood-brain barrier partitioning data model) to show the usage of the toolkit and the potential scalability of the artificial organic networks technique. © 2015 Wiley Periodicals, Inc.

ASERA: A Spectrum Eye Recognition Assistant

NASA Astrophysics Data System (ADS)

Yuan, Hailong; Zhang, Haotong; Zhang, Yanxia; Lei, Yajuan; Dong, Yiqiao; Zhao, Yongheng

2018-04-01

ASERA, ASpectrum Eye Recognition Assistant, aids in quasar spectral recognition and redshift measurement and can also be used to recognize various types of spectra of stars, galaxies and AGNs (Active Galactic Nucleus). This interactive software allows users to visualize observed spectra, superimpose template spectra from the Sloan Digital Sky Survey (SDSS), and interactively access related spectral line information. ASERA is an efficient and user-friendly semi-automated toolkit for the accurate classification of spectra observed by LAMOST (the Large Sky Area Multi-object Fiber Spectroscopic Telescope) and is available as a standalone Java application and as a Java applet. The software offers several functions, including wavelength and flux scale settings, zoom in and out, redshift estimation, and spectral line identification.

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

Christon, Mark A.; Bakosi, Jozsef; Lowrie, Robert B.

Hydra-TH is a hybrid finite-element/finite-volume code built using the Hydra toolkit specifically to attack a broad class of incompressible, viscous fluid dynamics problems prevalent in the thermalhydraulics community. The purpose for this manual is provide sufficient information for an experience analyst to use Hydra-TH in an effective way. The Hydra-TH User's Manual present a brief overview of capabilities and visualization interfaces. The execution and restart models are described before turning to the detailed description of keyword input. Finally, a series of example problems are presented with sufficient data to permit the user to verify the local installation of Hydra-TH, andmore » to permit a convenient starting point for more detailed and complex analyses.« less

Monte-Carlo Geant4 numerical simulation of experiments at 247-MeV proton microscope

NASA Astrophysics Data System (ADS)

Kantsyrev, A. V.; Skoblyakov, A. V.; Bogdanov, A. V.; Golubev, A. A.; Shilkin, N. S.; Yuriev, D. S.; Mintsev, V. B.

2018-01-01

A radiographic facility for an investigation of fast dynamic processes with areal density of targets up to 5 g/cm2 is under development on the basis of high-current proton linear accelerator at the Institute for Nuclear Research (Troitsk, Russia). A virtual model of the proton microscope developed in a software toolkit Geant4 is presented in the article. Fullscale Monte-Carlo numerical simulation of static radiographic experiments at energy of a proton beam 247 MeV was performed. The results of simulation of proton radiography experiments with static model of shock-compressed xenon are presented. The results of visualization of copper and polymethyl methacrylate step wedges static targets also described.

AutoMicromanager: A microscopy scripting toolkit for LABVIEW and other programming environments

NASA Astrophysics Data System (ADS)

Ashcroft, Brian Alan; Oosterkamp, Tjerk

2010-11-01

We present a scripting toolkit for the acquisition and analysis of a wide variety of imaging data by integrating the ease of use of various programming environments such as LABVIEW, IGOR PRO, MATLAB, SCILAB, and others. This toolkit is designed to allow the user to quickly program a variety of standard microscopy components for custom microscopy applications allowing much more flexibility than other packages. Included are both programming tools as well as graphical user interface classes allowing a standard, consistent, and easy to maintain scripting environment. This programming toolkit allows easy access to most commonly used cameras, stages, and shutters through the Micromanager project so the scripter can focus on their custom application instead of boilerplate code generation.

AutoMicromanager: a microscopy scripting toolkit for LABVIEW and other programming environments.

PubMed

Ashcroft, Brian Alan; Oosterkamp, Tjerk

2010-11-01

We present a scripting toolkit for the acquisition and analysis of a wide variety of imaging data by integrating the ease of use of various programming environments such as LABVIEW, IGOR PRO, MATLAB, SCILAB, and others. This toolkit is designed to allow the user to quickly program a variety of standard microscopy components for custom microscopy applications allowing much more flexibility than other packages. Included are both programming tools as well as graphical user interface classes allowing a standard, consistent, and easy to maintain scripting environment. This programming toolkit allows easy access to most commonly used cameras, stages, and shutters through the Micromanager project so the scripter can focus on their custom application instead of boilerplate code generation.

Kekule.js: An Open Source JavaScript Chemoinformatics Toolkit.

PubMed

Jiang, Chen; Jin, Xi; Dong, Ying; Chen, Ming

2016-06-27

Kekule.js is an open-source, object-oriented JavaScript toolkit for chemoinformatics. It provides methods for many common tasks in molecular informatics, including chemical data input/output (I/O), two- and three-dimensional (2D/3D) rendering of chemical structure, stereo identification, ring perception, structure comparison, and substructure search. Encapsulated widgets to display and edit chemical structures directly in web context are also supplied. Developed with web standards, the toolkit is ideal for building chemoinformatics applications over the Internet. Moreover, it is highly platform-independent and can also be used in desktop or mobile environments. Some initial applications, such as plugins for inputting chemical structures on the web and uses in chemistry education, have been developed based on the toolkit.

Desensitized Optimal Filtering and Sensor Fusion Toolkit

NASA Technical Reports Server (NTRS)

Karlgaard, Christopher D.

2015-01-01

Analytical Mechanics Associates, Inc., has developed a software toolkit that filters and processes navigational data from multiple sensor sources. A key component of the toolkit is a trajectory optimization technique that reduces the sensitivity of Kalman filters with respect to model parameter uncertainties. The sensor fusion toolkit also integrates recent advances in adaptive Kalman and sigma-point filters for non-Gaussian problems with error statistics. This Phase II effort provides new filtering and sensor fusion techniques in a convenient package that can be used as a stand-alone application for ground support and/or onboard use. Its modular architecture enables ready integration with existing tools. A suite of sensor models and noise distribution as well as Monte Carlo analysis capability are included to enable statistical performance evaluations.

SimITK: rapid ITK prototyping using the Simulink visual programming environment

NASA Astrophysics Data System (ADS)

Dickinson, A. W. L.; Mousavi, P.; Gobbi, D. G.; Abolmaesumi, P.

2011-03-01

The Insight Segmentation and Registration Toolkit (ITK) is a long-established, software package used for image analysis, visualization, and image-guided surgery applications. This package is a collection of C++ libraries, that can pose usability problems for users without C++ programming experience. To bridge the gap between the programming complexities and the required learning curve of ITK, we present a higher-level visual programming environment that represents ITK methods and classes by wrapping them into "blocks" within MATLAB's visual programming environment, Simulink. These blocks can be connected to form workflows: visual schematics that closely represent the structure of a C++ program. Due to the heavily C++ templated nature of ITK, direct interaction between Simulink and ITK requires an intermediary to convert their respective datatypes and allow intercommunication. We have developed a "Virtual Block" that serves as an intermediate wrapper around the ITK class and is responsible for resolving the templated datatypes used by ITK to native types used by Simulink. Presently, the wrapping procedure for SimITK is semi-automatic in that it requires XML descriptions of the ITK classes as a starting point, as this data is used to create all other necessary integration files. The generation of all source code and object code from the XML is done automatically by a CMake build script that yields Simulink blocks as the final result. An example 3D segmentation workflow using cranial-CT data as well as a 3D MR-to-CT registration workflow are presented as a proof-of-concept.

SimITK: visual programming of the ITK image-processing library within Simulink.

PubMed

Dickinson, Andrew W L; Abolmaesumi, Purang; Gobbi, David G; Mousavi, Parvin

2014-04-01

The Insight Segmentation and Registration Toolkit (ITK) is a software library used for image analysis, visualization, and image-guided surgery applications. ITK is a collection of C++ classes that poses the challenge of a steep learning curve should the user not have appropriate C++ programming experience. To remove the programming complexities and facilitate rapid prototyping, an implementation of ITK within a higher-level visual programming environment is presented: SimITK. ITK functionalities are automatically wrapped into "blocks" within Simulink, the visual programming environment of MATLAB, where these blocks can be connected to form workflows: visual schematics that closely represent the structure of a C++ program. The heavily templated C++ nature of ITK does not facilitate direct interaction between Simulink and ITK; an intermediary is required to convert respective data types and allow intercommunication. As such, a SimITK "Virtual Block" has been developed that serves as a wrapper around an ITK class which is capable of resolving the ITK data types to native Simulink data types. Part of the challenge surrounding this implementation involves automatically capturing and storing the pertinent class information that need to be refined from an initial state prior to being reflected within the final block representation. The primary result from the SimITK wrapping procedure is multiple Simulink block libraries. From these libraries, blocks are selected and interconnected to demonstrate two examples: a 3D segmentation workflow and a 3D multimodal registration workflow. Compared to their pure-code equivalents, the workflows highlight ITK usability through an alternative visual interpretation of the code that abstracts away potentially confusing technicalities.

NeuroPigPen: A Scalable Toolkit for Processing Electrophysiological Signal Data in Neuroscience Applications Using Apache Pig

PubMed Central

Sahoo, Satya S.; Wei, Annan; Valdez, Joshua; Wang, Li; Zonjy, Bilal; Tatsuoka, Curtis; Loparo, Kenneth A.; Lhatoo, Samden D.

2016-01-01

The recent advances in neurological imaging and sensing technologies have led to rapid increase in the volume, rate of data generation, and variety of neuroscience data. This “neuroscience Big data” represents a significant opportunity for the biomedical research community to design experiments using data with greater timescale, large number of attributes, and statistically significant data size. The results from these new data-driven research techniques can advance our understanding of complex neurological disorders, help model long-term effects of brain injuries, and provide new insights into dynamics of brain networks. However, many existing neuroinformatics data processing and analysis tools were not built to manage large volume of data, which makes it difficult for researchers to effectively leverage this available data to advance their research. We introduce a new toolkit called NeuroPigPen that was developed using Apache Hadoop and Pig data flow language to address the challenges posed by large-scale electrophysiological signal data. NeuroPigPen is a modular toolkit that can process large volumes of electrophysiological signal data, such as Electroencephalogram (EEG), Electrocardiogram (ECG), and blood oxygen levels (SpO2), using a new distributed storage model called Cloudwave Signal Format (CSF) that supports easy partitioning and storage of signal data on commodity hardware. NeuroPigPen was developed with three design principles: (a) Scalability—the ability to efficiently process increasing volumes of data; (b) Adaptability—the toolkit can be deployed across different computing configurations; and (c) Ease of programming—the toolkit can be easily used to compose multi-step data processing pipelines using high-level programming constructs. The NeuroPigPen toolkit was evaluated using 750 GB of electrophysiological signal data over a variety of Hadoop cluster configurations ranging from 3 to 30 Data nodes. The evaluation results demonstrate that the toolkit is highly scalable and adaptable, which makes it suitable for use in neuroscience applications as a scalable data processing toolkit. As part of the ongoing extension of NeuroPigPen, we are developing new modules to support statistical functions to analyze signal data for brain connectivity research. In addition, the toolkit is being extended to allow integration with scientific workflow systems. NeuroPigPen is released under BSD license at: https://sites.google.com/a/case.edu/neuropigpen/. PMID:27375472

NeuroPigPen: A Scalable Toolkit for Processing Electrophysiological Signal Data in Neuroscience Applications Using Apache Pig.

PubMed

Sahoo, Satya S; Wei, Annan; Valdez, Joshua; Wang, Li; Zonjy, Bilal; Tatsuoka, Curtis; Loparo, Kenneth A; Lhatoo, Samden D

2016-01-01

The recent advances in neurological imaging and sensing technologies have led to rapid increase in the volume, rate of data generation, and variety of neuroscience data. This "neuroscience Big data" represents a significant opportunity for the biomedical research community to design experiments using data with greater timescale, large number of attributes, and statistically significant data size. The results from these new data-driven research techniques can advance our understanding of complex neurological disorders, help model long-term effects of brain injuries, and provide new insights into dynamics of brain networks. However, many existing neuroinformatics data processing and analysis tools were not built to manage large volume of data, which makes it difficult for researchers to effectively leverage this available data to advance their research. We introduce a new toolkit called NeuroPigPen that was developed using Apache Hadoop and Pig data flow language to address the challenges posed by large-scale electrophysiological signal data. NeuroPigPen is a modular toolkit that can process large volumes of electrophysiological signal data, such as Electroencephalogram (EEG), Electrocardiogram (ECG), and blood oxygen levels (SpO2), using a new distributed storage model called Cloudwave Signal Format (CSF) that supports easy partitioning and storage of signal data on commodity hardware. NeuroPigPen was developed with three design principles: (a) Scalability-the ability to efficiently process increasing volumes of data; (b) Adaptability-the toolkit can be deployed across different computing configurations; and (c) Ease of programming-the toolkit can be easily used to compose multi-step data processing pipelines using high-level programming constructs. The NeuroPigPen toolkit was evaluated using 750 GB of electrophysiological signal data over a variety of Hadoop cluster configurations ranging from 3 to 30 Data nodes. The evaluation results demonstrate that the toolkit is highly scalable and adaptable, which makes it suitable for use in neuroscience applications as a scalable data processing toolkit. As part of the ongoing extension of NeuroPigPen, we are developing new modules to support statistical functions to analyze signal data for brain connectivity research. In addition, the toolkit is being extended to allow integration with scientific workflow systems. NeuroPigPen is released under BSD license at: https://sites.google.com/a/case.edu/neuropigpen/.

Facilitating interprofessional evidence-based practice in paediatric rehabilitation: development, implementation and evaluation of an online toolkit for health professionals.

PubMed

Glegg, Stephanie M N; Livingstone, Roslyn; Montgomery, Ivonne

2016-01-01

Lack of time, competencies, resources and supports are documented as barriers to evidence-based practice (EBP). This paper introduces a recently developed web-based toolkit designed to assist interprofessional clinicians in implementing EBP within a paediatric rehabilitation setting. EBP theory, models, frameworks and tools were applied or adapted in the development of the online resources, which formed the basis of a larger support strategy incorporating interactive workshops, knowledge broker facilitation and mentoring. The highly accessed toolkit contains flowcharts with embedded information sheets, resources and templates to streamline, quantify and document outcomes throughout the EBP process. Case examples relevance to occupational therapy and physical therapy highlight the utility and application of the toolkit in a clinical paediatric setting. Workshops were highly rated by learners for clinical relevance, presentation level and effectiveness. Eight evidence syntheses have been created and 79 interventions have been evaluated since the strategy's inception in January 2011. The toolkit resources streamlined and supported EBP processes, promoting consistency in quality and presentation of outputs. The online toolkit can be a useful tool to facilitate clinicians' use of EBP in order to meet the needs of the clients and families whom they support. Implications for Rehabilitation A comprehensive online EBP toolkit for interprofessional clinicians is available to streamline the EBP process and to support learning needs regardless of competency level. Multi-method facilitation support, including interactive education, e-learning, clinical librarian services and knowledge brokering, is a valued but cost-restrictive supplement to the implementation of online EBP resources. EBP resources are not one-size-fits-all; targeted appraisal tools, models and frameworks may be integrated to improve their utility for specific sectors, which may limit them for others.

Application development environment for advanced digital workstations

NASA Astrophysics Data System (ADS)

Valentino, Daniel J.; Harreld, Michael R.; Liu, Brent J.; Brown, Matthew S.; Huang, Lu J.

1998-06-01

One remaining barrier to the clinical acceptance of electronic imaging and information systems is the difficulty in providing intuitive access to the information needed for a specific clinical task (such as reaching a diagnosis or tracking clinical progress). The purpose of this research was to create a development environment that enables the design and implementation of advanced digital imaging workstations. We used formal data and process modeling to identify the diagnostic and quantitative data that radiologists use and the tasks that they typically perform to make clinical decisions. We studied a diverse range of radiology applications, including diagnostic neuroradiology in an academic medical center, pediatric radiology in a children's hospital, screening mammography in a breast cancer center, and thoracic radiology consultation for an oncology clinic. We used object- oriented analysis to develop software toolkits that enable a programmer to rapidly implement applications that closely match clinical tasks. The toolkits support browsing patient information, integrating patient images and reports, manipulating images, and making quantitative measurements on images. Collectively, we refer to these toolkits as the UCLA Digital ViewBox toolkit (ViewBox/Tk). We used the ViewBox/Tk to rapidly prototype and develop a number of diverse medical imaging applications. Our task-based toolkit approach enabled rapid and iterative prototyping of workstations that matched clinical tasks. The toolkit functionality and performance provided a 'hands-on' feeling for manipulating images, and for accessing textual information and reports. The toolkits directly support a new concept for protocol based-reading of diagnostic studies. The design supports the implementation of network-based application services (e.g., prefetching, workflow management, and post-processing) that will facilitate the development of future clinical applications.

Using stakeholder perspectives to develop an ePrescribing toolkit for NHS Hospitals: a questionnaire study.

PubMed

Lee, Lisa; Cresswell, Kathrin; Slee, Ann; Slight, Sarah P; Coleman, Jamie; Sheikh, Aziz

2014-10-01

To evaluate how an online toolkit may support ePrescribing deployments in National Health Service hospitals, by assessing the type of knowledge-based resources currently sought by key stakeholders. Questionnaire-based survey of attendees at a national ePrescribing symposium. 2013 National ePrescribing Symposium in London, UK. Eighty-four delegates were eligible for inclusion in the survey, of whom 70 completed and returned the questionnaire. Estimate of the usefulness and type of content to be included in an ePrescribing toolkit. Interest in a toolkit designed to support the implementation and use of ePrescribing systems was high (n = 64; 91.4%). As could be expected given the current dearth of such a resource, few respondents (n = 2; 2.9%) had access or used an ePrescribing toolkit at the time of the survey. Anticipated users for the toolkit included implementation (n = 62; 88.6%) and information technology (n = 61; 87.1%) teams, pharmacists (n = 61; 87.1%), doctors (n = 58; 82.9%) and nurses (n = 56; 80.0%). Summary guidance for every stage of the implementation (n = 48; 68.6%), planning and monitoring tools (n = 47; 67.1%) and case studies of hospitals' experiences (n = 45; 64.3%) were considered the most useful types of content. There is a clear need for reliable and up-to-date knowledge to support ePrescribing system deployments and longer term use. The findings highlight how a toolkit may become a useful instrument for the management of knowledge in the field, not least by allowing the exchange of ideas and shared learning.

The PRIDE (Partnership to Improve Diabetes Education) Toolkit: Development and Evaluation of Novel Literacy and Culturally Sensitive Diabetes Education Materials.

PubMed

Wolff, Kathleen; Chambers, Laura; Bumol, Stefan; White, Richard O; Gregory, Becky Pratt; Davis, Dianne; Rothman, Russell L

2016-02-01

Patients with low literacy, low numeracy, and/or linguistic needs can experience challenges understanding diabetes information and applying concepts to their self-management. The authors designed a toolkit of education materials that are sensitive to patients' literacy and numeracy levels, language preferences, and cultural norms and that encourage shared goal setting to improve diabetes self-management and health outcomes. The Partnership to Improve Diabetes Education (PRIDE) toolkit was developed to facilitate diabetes self-management education and support. The PRIDE toolkit includes a comprehensive set of 30 interactive education modules in English and Spanish to support diabetes self-management activities. The toolkit builds upon the authors' previously validated Diabetes Literacy and Numeracy Education Toolkit (DLNET) by adding a focus on shared goal setting, addressing the needs of Spanish-speaking patients, and including a broader range of diabetes management topics. Each PRIDE module was evaluated using the Suitability Assessment of Materials (SAM) instrument to determine the material's cultural appropriateness and its sensitivity to the needs of patients with low literacy and low numeracy. Reading grade level was also assessed using the Automated Readability Index (ARI), Coleman-Liau, Flesch-Kincaid, Fry, and SMOG formulas. The average reading grade level of the materials was 5.3 (SD 1.0), with a mean SAM of 91.2 (SD 5.4). All of the 30 modules received a "superior" score (SAM >70%) when evaluated by 2 independent raters. The PRIDE toolkit modules can be used by all members of a multidisciplinary team to assist patients with low literacy and low numeracy in managing their diabetes. © 2015 The Author(s).

Does the Good Schools Toolkit Reduce Physical, Sexual and Emotional Violence, and Injuries, in Girls and Boys equally? A Cluster-Randomised Controlled Trial.

PubMed

Devries, Karen M; Knight, Louise; Allen, Elizabeth; Parkes, Jenny; Kyegombe, Nambusi; Naker, Dipak

2017-10-01

We aimed to investigate whether the Good School Toolkit reduced emotional violence, severe physical violence, sexual violence and injuries from school staff to students, as well as emotional, physical and sexual violence between peers, in Ugandan primary schools. We performed a two-arm cluster randomised controlled trial with parallel assignment. Forty-two schools in one district were allocated to intervention (n = 21) or wait-list control (n = 21) arms in 2012. We did cross-sectional baseline and endline surveys in 2012 and 2014, and the Good School Toolkit intervention was implemented for 18 months between surveys. Analyses were by intention to treat and are adjusted for clustering within schools and for baseline school-level proportions of outcomes. The Toolkit was associated with an overall reduction in any form of violence from staff and/or peers in the past week towards both male (aOR = 0.34, 95%CI 0.22-0.53) and female students (aOR = 0.55, 95%CI 0.36-0.84). Injuries as a result of violence from school staff were also lower in male (aOR = 0.36, 95%CI 0.20-0.65) and female students (aOR = 0.51, 95%CI 0.29-0.90). Although the Toolkit seems to be effective at reducing violence in both sexes, there is some suggestion that the Toolkit may have stronger effects in boys than girls. The Toolkit is a promising intervention to reduce a wide range of different forms of violence from school staff and between peers in schools, and should be urgently considered for scale-up. Further research is needed to investigate how the intervention could engage more successfully with girls.

Improving the Effectiveness of Medication Review: Guidance from the Health Literacy Universal Precautions Toolkit.

PubMed

Weiss, Barry D; Brega, Angela G; LeBlanc, William G; Mabachi, Natabhona M; Barnard, Juliana; Albright, Karen; Cifuentes, Maribel; Brach, Cindy; West, David R

2016-01-01

Although routine medication reviews in primary care practice are recommended to identify drug therapy problems, it is often difficult to get patients to bring all their medications to office visits. The objective of this study was to determine whether the medication review tool in the Agency for Healthcare Research and Quality Health Literacy Universal Precautions Toolkit can help to improve medication reviews in primary care practices. The toolkit's "Brown Bag Medication Review" was implemented in a rural private practice in Missouri and an urban teaching practice in California. Practices recorded outcomes of medication reviews with 45 patients before toolkit implementation and then changed their medication review processes based on guidance in the toolkit. Six months later we conducted interviews with practice staff to identify changes made as a result of implementing the tool, and practices recorded outcomes of medication reviews with 41 additional patients. Data analyses compared differences in whether all medications were brought to visits, the number of medications reviewed, drug therapy problems identified, and changes in medication regimens before and after implementation. Interviews revealed that practices made the changes recommended in the toolkit to encourage patients to bring medications to office visits. Evaluation before and after implementation revealed a 3-fold increase in the percentage of patients who brought all their prescription medications and a 6-fold increase in the number of prescription medications brought to office visits. The percentage of reviews in which drug therapy problems were identified doubled, as did the percentage of medication regimens revised. Use of the Health Literacy Universal Precautions Toolkit can help to identify drug therapy problems. © Copyright 2016 by the American Board of Family Medicine.

Using stakeholder perspectives to develop an ePrescribing toolkit for NHS Hospitals: a questionnaire study

PubMed Central

Cresswell, Kathrin; Slee, Ann; Slight, Sarah P; Coleman, Jamie; Sheikh, Aziz

2014-01-01

Summary Objective To evaluate how an online toolkit may support ePrescribing deployments in National Health Service hospitals, by assessing the type of knowledge-based resources currently sought by key stakeholders. Design Questionnaire-based survey of attendees at a national ePrescribing symposium. Setting 2013 National ePrescribing Symposium in London, UK. Participants Eighty-four delegates were eligible for inclusion in the survey, of whom 70 completed and returned the questionnaire. Main outcome measures Estimate of the usefulness and type of content to be included in an ePrescribing toolkit. Results Interest in a toolkit designed to support the implementation and use of ePrescribing systems was high (n = 64; 91.4%). As could be expected given the current dearth of such a resource, few respondents (n = 2; 2.9%) had access or used an ePrescribing toolkit at the time of the survey. Anticipated users for the toolkit included implementation (n = 62; 88.6%) and information technology (n = 61; 87.1%) teams, pharmacists (n = 61; 87.1%), doctors (n = 58; 82.9%) and nurses (n = 56; 80.0%). Summary guidance for every stage of the implementation (n = 48; 68.6%), planning and monitoring tools (n = 47; 67.1%) and case studies of hospitals’ experiences (n = 45; 64.3%) were considered the most useful types of content. Conclusions There is a clear need for reliable and up-to-date knowledge to support ePrescribing system deployments and longer term use. The findings highlight how a toolkit may become a useful instrument for the management of knowledge in the field, not least by allowing the exchange of ideas and shared learning. PMID:25383199

Automated Instrumentation, Monitoring and Visualization of PVM Programs Using AIMS

NASA Technical Reports Server (NTRS)

Mehra, Pankaj; VanVoorst, Brian; Yan, Jerry; Lum, Henry, Jr. (Technical Monitor)

1994-01-01

We present views and analysis of the execution of several PVM (Parallel Virtual Machine) codes for Computational Fluid Dynamics on a networks of Sparcstations, including: (1) NAS Parallel Benchmarks CG and MG; (2) a multi-partitioning algorithm for NAS Parallel Benchmark SP; and (3) an overset grid flowsolver. These views and analysis were obtained using our Automated Instrumentation and Monitoring System (AIMS) version 3.0, a toolkit for debugging the performance of PVM programs. We will describe the architecture, operation and application of AIMS. The AIMS toolkit contains: (1) Xinstrument, which can automatically instrument various computational and communication constructs in message-passing parallel programs; (2) Monitor, a library of runtime trace-collection routines; (3) VK (Visual Kernel), an execution-animation tool with source-code clickback; and (4) Tally, a tool for statistical analysis of execution profiles. Currently, Xinstrument can handle C and Fortran 77 programs using PVM 3.2.x; Monitor has been implemented and tested on Sun 4 systems running SunOS 4.1.2; and VK uses XIIR5 and Motif 1.2. Data and views obtained using AIMS clearly illustrate several characteristic features of executing parallel programs on networked workstations: (1) the impact of long message latencies; (2) the impact of multiprogramming overheads and associated load imbalance; (3) cache and virtual-memory effects; and (4) significant skews between workstation clocks. Interestingly, AIMS can compensate for constant skew (zero drift) by calibrating the skew between a parent and its spawned children. In addition, AIMS' skew-compensation algorithm can adjust timestamps in a way that eliminates physically impossible communications (e.g., messages going backwards in time). Our current efforts are directed toward creating new views to explain the observed performance of PVM programs. Some of the features planned for the near future include: (1) ConfigView, showing the physical topology of the virtual machine, inferred using specially formatted IP (Internet Protocol) packets: and (2) LoadView, synchronous animation of PVM-program execution and resource-utilization patterns.

Online and classroom tools for Climate Change Education

NASA Astrophysics Data System (ADS)

Samenow, J. P.; Scott, K.

2004-12-01

EPA's Office of Atmospheric Programs has developed unique tools for educating students about the science of global warming and on actions that help address the issue. These tools have been highly successful and used in hundreds of classrooms across the country. EPA's Global Warming Kids' Site features interactive web-based animations for educating children, grades 4-8, about climate change. The animations illustrate how human activities likely influence the climate system through processes such as the greenhouse effect and carbon and water cycles. The pages also contain interactive quizzes. See: http://www.epa.gov/globalwarming/kids/animations.html For advanced high school and college students, EPA is nearing completion on the development of interactive visualizations of the emissions and climate scenarios featured in the Intergovernmental Panel on Climate Change's Third Assessment Report. These visualizations allow students to choose a scenario and see how emissions, the climate and the earth's surface change over time. The Global Warming Wheelcard Classroom Activity Kit is designed to help teachers of middle school students introduce the concept of human induced global warming in the context of how rates of energy usage can influence the increase or eventual slowing of climate change. The Climate Change, Wildlife, and Wildlands Toolkit for Teachers and Interpreters was produced in a partnership among three agencies - EPA, US Fish and Wildlife Service and the National Park Service (NPS). Both classroom teachers and outdoor interpreters find it useful in conveying information about climate change science and impacts to their students and visitors. The development of the toolkit led to a larger program between EPA and NPS that assists parks in inventorying their emissions, creating action plans, and talking to the public about what they are doing - a "lead by example" type program that the two agencies hope to replicate in other venues in the coming year.

Visual management of large scale data mining projects.

PubMed

Shah, I; Hunter, L

2000-01-01

This paper describes a unified framework for visualizing the preparations for, and results of, hundreds of machine learning experiments. These experiments were designed to improve the accuracy of enzyme functional predictions from sequence, and in many cases were successful. Our system provides graphical user interfaces for defining and exploring training datasets and various representational alternatives, for inspecting the hypotheses induced by various types of learning algorithms, for visualizing the global results, and for inspecting in detail results for specific training sets (functions) and examples (proteins). The visualization tools serve as a navigational aid through a large amount of sequence data and induced knowledge. They provided significant help in understanding both the significance and the underlying biological explanations of our successes and failures. Using these visualizations it was possible to efficiently identify weaknesses of the modular sequence representations and induction algorithms which suggest better learning strategies. The context in which our data mining visualization toolkit was developed was the problem of accurately predicting enzyme function from protein sequence data. Previous work demonstrated that approximately 6% of enzyme protein sequences are likely to be assigned incorrect functions on the basis of sequence similarity alone. In order to test the hypothesis that more detailed sequence analysis using machine learning techniques and modular domain representations could address many of these failures, we designed a series of more than 250 experiments using information-theoretic decision tree induction and naive Bayesian learning on local sequence domain representations of problematic enzyme function classes. In more than half of these cases, our methods were able to perfectly discriminate among various possible functions of similar sequences. We developed and tested our visualization techniques on this application.

Wired Widgets: Agile Visualization for Space Situational Awareness

NASA Astrophysics Data System (ADS)

Gerschefske, K.; Witmer, J.

2012-09-01

Continued advancement in sensors and analysis techniques have resulted in a wealth of Space Situational Awareness (SSA) data, made available via tools and Service Oriented Architectures (SOA) such as those in the Joint Space Operations Center Mission Systems (JMS) environment. Current visualization software cannot quickly adapt to rapidly changing missions and data, preventing operators and analysts from performing their jobs effectively. The value of this wealth of SSA data is not fully realized, as the operators' existing software is not built with the flexibility to consume new or changing sources of data or to rapidly customize their visualization as the mission evolves. While tools like the JMS user-defined operational picture (UDOP) have begun to fill this gap, this paper presents a further evolution, leveraging Web 2.0 technologies for maximum agility. We demonstrate a flexible Web widget framework with inter-widget data sharing, publish-subscribe eventing, and an API providing the basis for consumption of new data sources and adaptable visualization. Wired Widgets offers cross-portal widgets along with a widget communication framework and development toolkit for rapid new widget development, giving operators the ability to answer relevant questions as the mission evolves. Wired Widgets has been applied in a number of dynamic mission domains including disaster response, combat operations, and noncombatant evacuation scenarios. The variety of applications demonstrate that Wired Widgets provides a flexible, data driven solution for visualization in changing environments. In this paper, we show how, deployed in the Ozone Widget Framework portal environment, Wired Widgets can provide an agile, web-based visualization to support the SSA mission. Furthermore, we discuss how the tenets of agile visualization can generally be applied to the SSA problem space to provide operators flexibility, potentially informing future acquisition and system development.

Pcetk: A pDynamo-based Toolkit for Protonation State Calculations in Proteins.

PubMed

Feliks, Mikolaj; Field, Martin J

2015-10-26

Pcetk (a pDynamo-based continuum electrostatic toolkit) is an open-source, object-oriented toolkit for the calculation of proton binding energetics in proteins. The toolkit is a module of the pDynamo software library, combining the versatility of the Python scripting language and the efficiency of the compiled languages, C and Cython. In the toolkit, we have connected pDynamo to the external Poisson-Boltzmann solver, extended-MEAD. Our goal was to provide a modern and extensible environment for the calculation of protonation states, electrostatic energies, titration curves, and other electrostatic-dependent properties of proteins. Pcetk is freely available under the CeCILL license, which is compatible with the GNU General Public License. The toolkit can be found on the Web at the address http://github.com/mfx9/pcetk. The calculation of protonation states in proteins requires a knowledge of pKa values of protonatable groups in aqueous solution. However, for some groups, such as protonatable ligands bound to protein, the pKa aq values are often difficult to obtain from experiment. As a complement to Pcetk, we revisit an earlier computational method for the estimation of pKa aq values that has an accuracy of ± 0.5 pKa-units or better. Finally, we verify the Pcetk module and the method for estimating pKa aq values with different model cases.

A Toolkit to assess health needs for congenital disorders in low- and middle-income countries: an instrument for public health action.

PubMed

Nacul, L C; Stewart, A; Alberg, C; Chowdhury, S; Darlison, M W; Grollman, C; Hall, A; Modell, B; Moorthie, S; Sagoo, G S; Burton, H

2014-06-01

In 2010 the World Health Assembly called for action to improve the care and prevention of congenital disorders, noting that technical guidance would be required for this task, especially in low- and middle-income countries. Responding to this call, we have developed a freely available web-accessible Toolkit for assessing health needs for congenital disorders. Materials for the Toolkit website (http://toolkit.phgfoundation.org) were prepared by an iterative process of writing, discussion and modification by the project team, with advice from external experts. A customized database was developed using epidemiological, demographic, socio-economic and health-services data from a range of validated sources. Document-processing and data integration software combines data from the database with a template to generate topic- and country-specific Calculator documents for quantitative analysis. The Toolkit guides users through selection of topics (including both clinical conditions and relevant health services), assembly and evaluation of qualitative and quantitative information, assessment of the potential effects of selected interventions, and planning and prioritization of actions to reduce the risk or prevalence of congenital disorders. The Toolkit enables users without epidemiological or public health expertise to undertake health needs assessment as a prerequisite for strategic planning in relation to congenital disorders in their country or region. © The Author 2013. Published by Oxford University Press on behalf of Faculty of Public Health.

New Careers in Nursing Scholar Alumni Toolkit: Development of an Innovative Resource for Transition to Practice.

PubMed

Mauro, Ann Marie P; Escallier, Lori A; Rosario-Sim, Maria G

2016-01-01

The transition from student to professional nurse is challenging and may be more difficult for underrepresented minority nurses. The Robert Wood Johnson Foundation New Careers in Nursing (NCIN) program supported development of a toolkit that would serve as a transition-to-practice resource to promote retention of NCIN alumni and other new nurses. Thirteen recent NCIN alumni (54% male, 23% Hispanic/Latino, 23% African Americans) from 3 schools gave preliminary content feedback. An e-mail survey was sent to a convenience sample of 29 recent NCIN alumni who evaluated the draft toolkit using a Likert scale (poor = 1; excellent = 5). Twenty NCIN alumni draft toolkit reviewers (response rate 69%) were primarily female (80%) and Hispanic/Latino (40%). Individual chapters' mean overall rating of 4.67 demonstrated strong validation. Mean scores for overall toolkit content (4.57), usability (4.5), relevance (4.79), and quality (4.71) were also excellent. Qualitative comments were analyzed using thematic content analysis and supported the toolkit's relevance and utility. A multilevel peer review process was also conducted. Peer reviewer feedback resulted in a 6-chapter document that offers resources for successful transition to practice and lays the groundwork for continued professional growth. Future research is needed to determine the ideal time to introduce this resource. Copyright © 2016 Elsevier Inc. All rights reserved.

Third Party TMDL Development Toolkit

EPA Pesticide Factsheets

Water Environment Federation's toolkit provides basic steps in which an organization or group other than the lead water quality agency takes responsibility for developing the TMDL document and supporting analysis.

UTOPIA-User-Friendly Tools for Operating Informatics Applications.

PubMed

Pettifer, S R; Sinnott, J R; Attwood, T K

2004-01-01

Bioinformaticians routinely analyse vast amounts of information held both in large remote databases and in flat data files hosted on local machines. The contemporary toolkit available for this purpose consists of an ad hoc collection of data manipulation tools, scripting languages and visualization systems; these must often be combined in complex and bespoke ways, the result frequently being an unwieldy artefact capable of one specific task, which cannot easily be exploited or extended by other practitioners. Owing to the sizes of current databases and the scale of the analyses necessary, routine bioinformatics tasks are often automated, but many still require the unique experience and intuition of human researchers: this requires tools that support real-time interaction with complex datasets. Many existing tools have poor user interfaces and limited real-time performance when applied to realistically large datasets; much of the user's cognitive capacity is therefore focused on controlling the tool rather than on performing the research. The UTOPIA project is addressing some of these issues by building reusable software components that can be combined to make useful applications in the field of bioinformatics. Expertise in the fields of human computer interaction, high-performance rendering, and distributed systems is being guided by bioinformaticians and end-user biologists to create a toolkit that is both architecturally sound from a computing point of view, and directly addresses end-user and application-developer requirements.

Limestone percussion tools from the late Early Pleistocene sites of Barranco León and Fuente Nueva 3 (Orce, Spain).

PubMed

Barsky, Deborah; Vergès, Josep-María; Sala, Robert; Menéndez, Leticia; Toro-Moyano, Isidro

2015-11-19

In recent years, there is growing interest in the study of percussion scars and breakage patterns on hammerstones, cores and tools from Oldowan African and Eurasian lithic assemblages. Oldowan stone toolkits generally contain abundant small-sized flakes and their corresponding cores, and are characterized by their structural dichotomy of heavy- and light-duty tools. This paper explores the significance of the lesser known heavy-duty tool component, providing data from the late Lower Pleistocene sites of Barranco León and Fuente Nueva 3 (Orce, Spain), dated 1.4-1.2 Myr. Using quantitative and qualitative data from the large-sized limestone industries from these two major sites, we present a new methodology highlighting their morpho-technological features. In the light of the results, we discuss the shortfalls of extant classificatory methods for interpreting the role of percussive technology in early toolkits. This work is rooted in an experimental program designed to reproduce the wide range of percussion marks observed on the limestone artefacts from these two sites. A visual and descriptive reference is provided as an interpretative aid for future comparative research. Further experiments using a variety of materials and gestures are still needed before the elusive traces yield the secrets of the kinds of percussive activities carried out by hominins at these, and other, Oldowan sites. © 2015 The Author(s).

Limestone percussion tools from the late Early Pleistocene sites of Barranco León and Fuente Nueva 3 (Orce, Spain)

PubMed Central

Barsky, Deborah; Vergès, Josep-María; Sala, Robert; Menéndez, Leticia; Toro-Moyano, Isidro

2015-01-01

In recent years, there is growing interest in the study of percussion scars and breakage patterns on hammerstones, cores and tools from Oldowan African and Eurasian lithic assemblages. Oldowan stone toolkits generally contain abundant small-sized flakes and their corresponding cores, and are characterized by their structural dichotomy of heavy- and light-duty tools. This paper explores the significance of the lesser known heavy-duty tool component, providing data from the late Lower Pleistocene sites of Barranco León and Fuente Nueva 3 (Orce, Spain), dated 1.4–1.2 Myr. Using quantitative and qualitative data from the large-sized limestone industries from these two major sites, we present a new methodology highlighting their morpho-technological features. In the light of the results, we discuss the shortfalls of extant classificatory methods for interpreting the role of percussive technology in early toolkits. This work is rooted in an experimental program designed to reproduce the wide range of percussion marks observed on the limestone artefacts from these two sites. A visual and descriptive reference is provided as an interpretative aid for future comparative research. Further experiments using a variety of materials and gestures are still needed before the elusive traces yield the secrets of the kinds of percussive activities carried out by hominins at these, and other, Oldowan sites. PMID:26483530

Field Ground Truthing Data Collector - a Mobile Toolkit for Image Analysis and Processing

NASA Astrophysics Data System (ADS)

Meng, X.

2012-07-01

Field Ground Truthing Data Collector is one of the four key components of the NASA funded ICCaRS project, being developed in Southeast Michigan. The ICCaRS ground truthing toolkit entertains comprehensive functions: 1) Field functions, including determining locations through GPS, gathering and geo-referencing visual data, laying out ground control points for AEROKAT flights, measuring the flight distance and height, and entering observations of land cover (and use) and health conditions of ecosystems and environments in the vicinity of the flight field; 2) Server synchronization functions, such as, downloading study-area maps, aerial photos and satellite images, uploading and synchronizing field-collected data with the distributed databases, calling the geospatial web services on the server side to conduct spatial querying, image analysis and processing, and receiving the processed results in field for near-real-time validation; and 3) Social network communication functions for direct technical assistance and pedagogical support, e.g., having video-conference calls in field with the supporting educators, scientists, and technologists, participating in Webinars, or engaging discussions with other-learning portals. This customized software package is being built on Apple iPhone/iPad and Google Maps/Earth. The technical infrastructures, data models, coupling methods between distributed geospatial data processing and field data collector tools, remote communication interfaces, coding schema, and functional flow charts will be illustrated and explained at the presentation. A pilot case study will be also demonstrated.

An approach to improve the care of mid-life women through the implementation of a Women’s Health Assessment Tool/Clinical Decision Support toolkit

PubMed Central

Silvestrin, Terry M; Steenrod, Anna W; Coyne, Karin S; Gross, David E; Esinduy, Canan B; Kodsi, Angela B; Slifka, Gayle J; Abraham, Lucy; Araiza, Anna L; Bushmakin, Andrew G; Luo, Xuemei

2016-01-01

The objectives of this study are to describe the implementation process of the Women’s Health Assessment Tool/Clinical Decision Support toolkit and summarize patients’ and clinicians’ perceptions of the toolkit. The Women’s Health Assessment Tool/Clinical Decision Support toolkit was piloted at three clinical sites over a 4-month period in Washington State to evaluate health outcomes among mid-life women. The implementation involved a multistep process and engagement of multiple stakeholders over 18 months. Two-thirds of patients (n = 76/110) and clinicians (n = 8/12) participating in pilot completed feedback surveys; five clinicians participated in qualitative interviews. Most patients felt more prepared for their annual visit (69.7%) and that quality of care improved (68.4%) while clinicians reported streamlined patient visits and improved communication with patients. The Women’s Health Assessment Tool/Clinical Decision Support toolkit offers a unique approach to introduce and address some of the key health issues that affect mid-life women. PMID:27558508

GESearch: An Interactive GUI Tool for Identifying Gene Expression Signature.

PubMed

Ye, Ning; Yin, Hengfu; Liu, Jingjing; Dai, Xiaogang; Yin, Tongming

2015-01-01

The huge amount of gene expression data generated by microarray and next-generation sequencing technologies present challenges to exploit their biological meanings. When searching for the coexpression genes, the data mining process is largely affected by selection of algorithms. Thus, it is highly desirable to provide multiple options of algorithms in the user-friendly analytical toolkit to explore the gene expression signatures. For this purpose, we developed GESearch, an interactive graphical user interface (GUI) toolkit, which is written in MATLAB and supports a variety of gene expression data files. This analytical toolkit provides four models, including the mean, the regression, the delegate, and the ensemble models, to identify the coexpression genes, and enables the users to filter data and to select gene expression patterns by browsing the display window or by importing knowledge-based genes. Subsequently, the utility of this analytical toolkit is demonstrated by analyzing two sets of real-life microarray datasets from cell-cycle experiments. Overall, we have developed an interactive GUI toolkit that allows for choosing multiple algorithms for analyzing the gene expression signatures.

Enhancing the sustainability and climate resiliency of health care facilities: a comparison of initiatives and toolkits.

PubMed

Balbus, John; Berry, Peter; Brettle, Meagan; Jagnarine-Azan, Shalini; Soares, Agnes; Ugarte, Ciro; Varangu, Linda; Prats, Elena Villalobos

2016-09-01

Extreme weather events have revealed the vulnerability of health care facilities and the extent of devastation to the community when they fail. With climate change anticipated to increase extreme weather and its impacts worldwide-severe droughts, floods, heat waves, and related vector-borne diseases-health care officials need to understand and address the vulnerabilities of their health care systems and take action to improve resiliency in ways that also meet sustainability goals. Generally, the health sector is among a country's largest consumers of energy and a significant source of greenhouse gas emissions. Now it has the opportunity lead climate mitigation, while reducing energy, water, and other costs. This Special Report summarizes several initiatives and compares three toolkits for implementing sustainability and resiliency measures for health care facilities: the Canadian Health Care Facility Climate Change Resiliency Toolkit, the U.S. Sustainable and Climate Resilient Health Care Facilities Toolkit, and the PAHO SMART Hospitals Toolkit of the World Health Organization/Pan American Health Organization. These tools and the lessons learned can provide a critical starting point for any health system in the Americas.

A Software Toolkit to Study Systematic Uncertainties of the Physics Models of the Geant4 Simulation Package

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

Genser, Krzysztof; Hatcher, Robert; Kelsey, Michael

The Geant4 simulation toolkit is used to model interactions between particles and matter. Geant4 employs a set of validated physics models that span a wide range of interaction energies. These models rely on measured cross-sections and phenomenological models with the physically motivated parameters that are tuned to cover many application domains. To study what uncertainties are associated with the Geant4 physics models we have designed and implemented a comprehensive, modular, user-friendly software toolkit that allows the variation of one or more parameters of one or more Geant4 physics models involved in simulation studies. It also enables analysis of multiple variantsmore » of the resulting physics observables of interest in order to estimate the uncertainties associated with the simulation model choices. Based on modern event-processing infrastructure software, the toolkit offers a variety of attractive features, e.g. exible run-time con gurable work ow, comprehensive bookkeeping, easy to expand collection of analytical components. Design, implementation technology, and key functionalities of the toolkit are presented in this paper and illustrated with selected results.« less

CRISPR-Cas9 Toolkit for Actinomycete Genome Editing.

PubMed

Tong, Yaojun; Robertsen, Helene Lunde; Blin, Kai; Weber, Tilmann; Lee, Sang Yup

2018-01-01

Bacteria of the order Actinomycetales are one of the most important sources of bioactive natural products, which are the source of many drugs. However, many of them still lack efficient genome editing methods, some strains even cannot be manipulated at all. This restricts systematic metabolic engineering approaches for boosting known and discovering novel natural products. In order to facilitate the genome editing for actinomycetes, we developed a CRISPR-Cas9 toolkit with high efficiency for actinomyces genome editing. This basic toolkit includes a software for spacer (sgRNA) identification, a system for in-frame gene/gene cluster knockout, a system for gene loss-of-function study, a system for generating a random size deletion library, and a system for gene knockdown. For the latter, a uracil-specific excision reagent (USER) cloning technology was adapted to simplify the CRISPR vector construction process. The application of this toolkit was successfully demonstrated by perturbation of genomes of Streptomyces coelicolor A3(2) and Streptomyces collinus Tü 365. The CRISPR-Cas9 toolkit and related protocol described here can be widely used for metabolic engineering of actinomycetes.

Transportation librarian's toolkit

DOT National Transportation Integrated Search

2007-12-01

The Transportation Librarians Toolkit is a product of the Transportation Library Connectivity pooled fund study, TPF- 5(105), a collaborative, grass-roots effort by transportation libraries to enhance information accessibility and professional expert...

Integrated Systems Health Management (ISHM) Toolkit

NASA Technical Reports Server (NTRS)

Venkatesh, Meera; Kapadia, Ravi; Walker, Mark; Wilkins, Kim

2013-01-01

A framework of software components has been implemented to facilitate the development of ISHM systems according to a methodology based on Reliability Centered Maintenance (RCM). This framework is collectively referred to as the Toolkit and was developed using General Atomics' Health MAP (TM) technology. The toolkit is intended to provide assistance to software developers of mission-critical system health monitoring applications in the specification, implementation, configuration, and deployment of such applications. In addition to software tools designed to facilitate these objectives, the toolkit also provides direction to software developers in accordance with an ISHM specification and development methodology. The development tools are based on an RCM approach for the development of ISHM systems. This approach focuses on defining, detecting, and predicting the likelihood of system functional failures and their undesirable consequences.

The Lean and Environment Toolkit

EPA Pesticide Factsheets

This Lean and Environment Toolkit assembles practical experience collected by the U.S. Environmental Protection Agency (EPA) and partner companies and organizations that have experience with coordinating Lean implementation and environmental management.

A Machine Learning and Optimization Toolkit for the Swarm

DTIC Science & Technology

2014-11-17

Machine   Learning  and  Op0miza0on   Toolkit  for  the  Swarm   Ilge  Akkaya,  Shuhei  Emoto...3. DATES COVERED 00-00-2014 to 00-00-2014 4. TITLE AND SUBTITLE A Machine Learning and Optimization Toolkit for the Swarm 5a. CONTRACT NUMBER... machine   learning   methodologies  by  providing  the  right  interfaces  between   machine   learning  tools  and

A clinical research analytics toolkit for cohort study.

PubMed

Yu, Yiqin; Zhu, Yu; Sun, Xingzhi; Tao, Ying; Zhang, Shuo; Xu, Linhao; Pan, Yue

2012-01-01

This paper presents a clinical informatics toolkit that can assist physicians to conduct cohort studies effectively and efficiently. The toolkit has three key features: 1) support of procedures defined in epidemiology, 2) recommendation of statistical methods in data analysis, and 3) automatic generation of research reports. On one hand, our system can help physicians control research quality by leveraging the integrated knowledge of epidemiology and medical statistics; on the other hand, it can improve productivity by reducing the complexities for physicians during their cohort studies.

UQTk Version 3.0.3 User Manual

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

Sargsyan, Khachik; Safta, Cosmin; Chowdhary, Kamaljit Singh

2017-05-01

The UQ Toolkit (UQTk) is a collection of libraries and tools for the quantification of uncertainty in numerical model predictions. Version 3.0.3 offers intrusive and non-intrusive methods for propagating input uncertainties through computational models, tools for sen- sitivity analysis, methods for sparse surrogate construction, and Bayesian inference tools for inferring parameters from experimental data. This manual discusses the download and installation process for UQTk, provides pointers to the UQ methods used in the toolkit, and describes some of the examples provided with the toolkit.

DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in head and neck cancer research.

PubMed

Fedorov, Andriy; Clunie, David; Ulrich, Ethan; Bauer, Christian; Wahle, Andreas; Brown, Bartley; Onken, Michael; Riesmeier, Jörg; Pieper, Steve; Kikinis, Ron; Buatti, John; Beichel, Reinhard R

2016-01-01

Background. Imaging biomarkers hold tremendous promise for precision medicine clinical applications. Development of such biomarkers relies heavily on image post-processing tools for automated image quantitation. Their deployment in the context of clinical research necessitates interoperability with the clinical systems. Comparison with the established outcomes and evaluation tasks motivate integration of the clinical and imaging data, and the use of standardized approaches to support annotation and sharing of the analysis results and semantics. We developed the methodology and tools to support these tasks in Positron Emission Tomography and Computed Tomography (PET/CT) quantitative imaging (QI) biomarker development applied to head and neck cancer (HNC) treatment response assessment, using the Digital Imaging and Communications in Medicine (DICOM(®)) international standard and free open-source software. Methods. Quantitative analysis of PET/CT imaging data collected on patients undergoing treatment for HNC was conducted. Processing steps included Standardized Uptake Value (SUV) normalization of the images, segmentation of the tumor using manual and semi-automatic approaches, automatic segmentation of the reference regions, and extraction of the volumetric segmentation-based measurements. Suitable components of the DICOM standard were identified to model the various types of data produced by the analysis. A developer toolkit of conversion routines and an Application Programming Interface (API) were contributed and applied to create a standards-based representation of the data. Results. DICOM Real World Value Mapping, Segmentation and Structured Reporting objects were utilized for standards-compliant representation of the PET/CT QI analysis results and relevant clinical data. A number of correction proposals to the standard were developed. The open-source DICOM toolkit (DCMTK) was improved to simplify the task of DICOM encoding by introducing new API abstractions. Conversion and visualization tools utilizing this toolkit were developed. The encoded objects were validated for consistency and interoperability. The resulting dataset was deposited in the QIN-HEADNECK collection of The Cancer Imaging Archive (TCIA). Supporting tools for data analysis and DICOM conversion were made available as free open-source software. Discussion. We presented a detailed investigation of the development and application of the DICOM model, as well as the supporting open-source tools and toolkits, to accommodate representation of the research data in QI biomarker development. We demonstrated that the DICOM standard can be used to represent the types of data relevant in HNC QI biomarker development, and encode their complex relationships. The resulting annotated objects are amenable to data mining applications, and are interoperable with a variety of systems that support the DICOM standard.

Food: Too Good to Waste Implementation Guide and Toolkit

EPA Pesticide Factsheets

The Food: Too Good to Waste (FTGTW) Implementation Guide and Toolkit is designed for community organizations, local governments, households and others interested in reducing wasteful household food management practices.

Development of a toolkit and glossary to aid in the adaptation of health technology assessment (HTA) reports for use in different contexts.

PubMed

Chase, D; Rosten, C; Turner, S; Hicks, N; Milne, R

2009-11-01

To develop a health technology assessment (HTA) adaptation toolkit and glossary of adaptation terms for use by HTA agencies within EU member states to support them in adapting HTA reports written for other contexts. The toolkit and glossary were developed by a partnership of 28 HTA agencies and networks across Europe (EUnetHTA work package 5), led by the UK National Coordinating Centre for Health Technology Assessment (NCCHTA). Methods employed for the two resources were literature searching, a survey of adaptation experience, two rounds of a Delphi survey, meetings of the partnership and drawing on the expertise and experience of the partnership, two rounds of review, and two rounds of quality assurance testing. All partners were requested to provide input into each stage of development. The resulting toolkit is a collection of resources, in the form of checklists of questions on relevance, reliability and transferability of data and information, and links to useful websites, that help the user assess whether data and information in existing HTA reports can be adapted for a different setting. The toolkit is designed for the adaptation of evidence synthesis rather than primary research. The accompanying glossary provides descriptions of meanings for HTA adaptation terms from HTA agencies across Europe. It seeks to highlight differences in the use and understanding of each word by HTA agencies. The toolkit and glossary are available for use by all HTA agencies and can be accessed via www.eunethta.net/. These resources have been developed to help HTA agencies make better use of HTA reports produced elsewhere. They can be used by policy-makers and clinicians to aid in understanding HTA reports written for other contexts. The main implication of this work is that there is the potential for the adaptation of HTA reports and, if utilised, this should release resources to enable the development of further HTA reports. Recommendations for the further development of the toolkit include the potential to develop an interactive web-based version and to extend the toolkit to facilitate the adaptation of HTA reports on diagnostic testing and screening.

The Development and Evaluation of an Online Healthcare Toolkit for Autistic Adults and their Primary Care Providers.

PubMed

Nicolaidis, Christina; Raymaker, Dora; McDonald, Katherine; Kapp, Steven; Weiner, Michael; Ashkenazy, Elesia; Gerrity, Martha; Kripke, Clarissa; Platt, Laura; Baggs, Amelia

2016-10-01

The healthcare system is ill-equipped to meet the needs of adults on the autism spectrum. Our goal was to use a community-based participatory research (CBPR) approach to develop and evaluate tools to facilitate the primary healthcare of autistic adults. Toolkit development included cognitive interviewing and test-retest reliability studies. Evaluation consisted of a mixed-methods, single-arm pre/post-intervention comparison. A total of 259 autistic adults and 51 primary care providers (PCPs) residing in the United States. The AASPIRE Healthcare toolkit includes the Autism Healthcare Accommodations Tool (AHAT)-a tool that allows patients to create a personalized accommodations report for their PCP-and general healthcare- and autism-related information, worksheets, checklists, and resources for patients and healthcare providers. Satisfaction with patient-provider communication, healthcare self-efficacy, barriers to healthcare, and satisfaction with the toolkit's usability and utility; responses to open-ended questions. Preliminary testing of the AHAT demonstrated strong content validity and adequate test-retest stability. Almost all patient participants (>94 %) felt that the AHAT and the toolkit were easy to use, important, and useful. In pre/post-intervention comparisons, the mean number of barriers decreased (from 4.07 to 2.82, p < 0.0001), healthcare self-efficacy increased (from 37.9 to 39.4, p = 0.02), and satisfaction with PCP communication improved (from 30.9 to 32.6, p = 0.03). Patients stated that the toolkit helped clarify their needs, enabled them to self-advocate and prepare for visits more effectively, and positively influenced provider behavior. Most of the PCPs surveyed read the AHAT (97 %), rated it as moderately or very useful (82 %), and would recommend it to other patients (87 %). The CBPR process resulted in a reliable healthcare accommodation tool and a highly accessible healthcare toolkit. Patients and providers indicated that the tools positively impacted healthcare interactions. The toolkit has the potential to reduce barriers to healthcare and improve healthcare self-efficacy and patient-provider communication.

A patient and public involvement (PPI) toolkit for meaningful and flexible involvement in clinical trials - a work in progress.

PubMed

Bagley, Heather J; Short, Hannah; Harman, Nicola L; Hickey, Helen R; Gamble, Carrol L; Woolfall, Kerry; Young, Bridget; Williamson, Paula R

2016-01-01

Funders of research are increasingly requiring researchers to involve patients and the public in their research. Patient and public involvement (PPI) in research can potentially help researchers make sure that the design of their research is relevant, that it is participant friendly and ethically sound. Using and sharing PPI resources can benefit those involved in undertaking PPI, but existing PPI resources are not used consistently and this can lead to duplication of effort. This paper describes how we are developing a toolkit to support clinical trials teams in a clinical trials unit. The toolkit will provide a key 'off the shelf' resource to support trial teams with limited resources, in undertaking PPI. Key activities in further developing and maintaining the toolkit are to: ● listen to the views and experience of both research teams and patient and public contributors who use the tools; ● modify the tools based on our experience of using them; ● identify the need for future tools; ● update the toolkit based on any newly identified resources that come to light; ● raise awareness of the toolkit and ● work in collaboration with others to either develop or test out PPI resources in order to reduce duplication of work in PPI. Background Patient and public involvement (PPI) in research is increasingly a funder requirement due to the potential benefits in the design of relevant, participant friendly, ethically sound research. The use and sharing of resources can benefit PPI, but available resources are not consistently used leading to duplication of effort. This paper describes a developing toolkit to support clinical trials teams to undertake effective and meaningful PPI. Methods The first phase in developing the toolkit was to describe which PPI activities should be considered in the pathway of a clinical trial and at what stage these activities should take place. This pathway was informed through review of the type and timing of PPI activities within trials coordinated by the Clinical Trials Research Centre and previously described areas of potential PPI impact in trials. In the second phase, key websites around PPI and identification of resources opportunistically, e.g. in conversation with other trialists or social media, were used to identify resources. Tools were developed where gaps existed. Results A flowchart was developed describing PPI activities that should be considered in the clinical trial pathway and the point at which these activities should happen. Three toolkit domains were identified: planning PPI; supporting PPI; recording and evaluating PPI. Four main activities and corresponding tools were identified under the planning for PPI: developing a plan; identifying patient and public contributors; allocating appropriate costs; and managing expectations. In supporting PPI, tools were developed to review participant information sheets. These tools, which require a summary of potential trial participant characteristics and circumstances help to clarify requirements and expectations of PPI review. For recording and evaluating PPI, the planned PPI interventions should be monitored in terms of impact, and a tool to monitor public contributor experience is in development. Conclusions This toolkit provides a developing 'off the shelf' resource to support trial teams with limited resources in undertaking PPI. Key activities in further developing and maintaining the toolkit are to: listen to the views and experience of both research teams and public contributors using the tools, to identify the need for future tools, to modify tools based on experience of their use; to update the toolkit based on any newly identified resources that come to light; to raise awareness of the toolkit and to work in collaboration with others to both develop and test out PPI resources in order to reduce duplication of work in PPI.

THE SMALL BODY GEOPHYSICAL ANALYSIS TOOL

NASA Astrophysics Data System (ADS)

Bercovici, Benjamin; McMahon, Jay

2017-10-01

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

Lean and Information Technology Toolkit

EPA Pesticide Factsheets

The Lean and Information Technology Toolkit is a how-to guide which provides resources to environmental agencies to help them use Lean Startup, Lean process improvement, and Agile tools to streamline and automate processes.

Health Information in Kirundi (Rundi)

MedlinePlus

... Abuse Healthy Living Toolkit: Violence In the Home - English PDF Healthy Living Toolkit: Violence In the Home - ... Parents on Talking to Children About the Flu - English PDF Advice for Parents on Talking to Children ...

78 FR 14774 - U.S. Environmental Solutions Toolkit-Universal Waste

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-07

... following list: (a) Mercury Recycling Technology (b) E-Waste Recycling Technology (c) CRT Recycling Technology (d) Lamp Crushing Systems For purposes of participation in the Toolkit, ``United States exporter...

Virtual Solar Energy Center: A Case Study of the Use of Advanced Visualization Techniques for the Comprehension of Complex Engineering Products and Processes

NASA Astrophysics Data System (ADS)

Ritter, Kenneth August, III

Industry has a continuing need to train its workforce on recent engineering developments, but many engineering products and processes are hard to explain because of limitations of size, visibility, time scale, cost, and safety. The product or process might be difficult to see because it is either very large or very small, because it is enclosed within an opaque container, or because it happens very fast or very slowly. Some engineering products and processes are also costly or unsafe to use for training purposes, and sometimes the domain expert is not physically available at the training location. All these limitations can potentially be addressed using advanced visualization techniques such as virtual reality. This dissertation describes the development of an immersive virtual reality application using the Six Sigma DMADV process to explain the main equipment and processes used in a concentrating solar power plant. The virtual solar energy center (VEC) application was initially developed and tested in a Cave Automatic Virtual Environment (CAVE) during 2013 and 2014. The software programs used for development were SolidWorks, 3ds Max Design, and Unity 3D. Current hardware and software technologies that could complement this research were analyzed. The NVIDA GRID Visual Computing Appliance (VCA) was chosen as the rendering solution for animating complex CAD models in this application. The MiddleVR software toolkit was selected as the toolkit for VR interactions and CAVE display. A non-immersive 3D version of the VEC application was tested and shown to be an effective training tool in late 2015. An immersive networked version of the VEC allows the user to receive live instruction from a trainer being projected via depth camera imagery from a remote location. Four comparative analysis studies were performed. These studies used the average normalized gain from pre-test scores to determine the effectiveness of the various training methods. With the DMADV approach, solutions were identified and verified during each iteration of the development, which saved valuable time and resulted in better results being achieved in each revision of the application, with the final version having 88% positive responses and same effectiveness as other methods assessed.

Water Quality Trading Toolkit for Permit Writers

EPA Pesticide Factsheets

The Water Quality Trading Toolkit for Permit Writers is EPA’s first “how-to” manual on designing and implementing water quality trading programs. It helps NPDES permitting authorities incorporate trading provisions into permits.

Heart Health for Women

MedlinePlus

... more about how you can participate. Heart Health Social Media Toolkit The FDA Office of Women's Health offers ... informed about heart health. Use the Heart Health Social Media Toolkit to encourage women in your network to ...

An evaluation capacity building toolkit for principal investigators of undergraduate research experiences: A demonstration of transforming theory into practice.

PubMed

Rorrer, Audrey S

2016-04-01

This paper describes the approach and process undertaken to develop evaluation capacity among the leaders of a federally funded undergraduate research program. An evaluation toolkit was developed for Computer and Information Sciences and Engineering(1) Research Experiences for Undergraduates(2) (CISE REU) programs to address the ongoing need for evaluation capacity among principal investigators who manage program evaluation. The toolkit was the result of collaboration within the CISE REU community with the purpose being to provide targeted instructional resources and tools for quality program evaluation. Challenges were to balance the desire for standardized assessment with the responsibility to account for individual program contexts. Toolkit contents included instructional materials about evaluation practice, a standardized applicant management tool, and a modulated outcomes measure. Resulting benefits from toolkit deployment were having cost effective, sustainable evaluation tools, a community evaluation forum, and aggregate measurement of key program outcomes for the national program. Lessons learned included the imperative of understanding the evaluation context, engaging stakeholders, and building stakeholder trust. Results from project measures are presented along with a discussion of guidelines for facilitating evaluation capacity building that will serve a variety of contexts. Copyright © 2016. Published by Elsevier Ltd.

Health Care Facilities Resilient to Climate Change Impacts

PubMed Central

Paterson, Jaclyn; Berry, Peter; Ebi, Kristie; Varangu, Linda

2014-01-01

Climate change will increase the frequency and magnitude of extreme weather events and create risks that will impact health care facilities. Health care facilities will need to assess climate change risks and adopt adaptive management strategies to be resilient, but guidance tools are lacking. In this study, a toolkit was developed for health care facility officials to assess the resiliency of their facility to climate change impacts. A mixed methods approach was used to develop climate change resiliency indicators to inform the development of the toolkit. The toolkit consists of a checklist for officials who work in areas of emergency management, facilities management and health care services and supply chain management, a facilitator’s guide for administering the checklist, and a resource guidebook to inform adaptation. Six health care facilities representing three provinces in Canada piloted the checklist. Senior level officials with expertise in the aforementioned areas were invited to review the checklist, provide feedback during qualitative interviews and review the final toolkit at a stakeholder workshop. The toolkit helps health care facility officials identify gaps in climate change preparedness, direct allocation of adaptation resources and inform strategic planning to increase resiliency to climate change. PMID:25522050

Current Status of VO Compliant Data Service in Japanese Virtual Observatory

NASA Astrophysics Data System (ADS)

Shirasaki, Y.; Komiya, Y.; Ohishi, M.; Mizumoto, Y.; Ishihara, Y.; Tsutsumi, J.; Hiyama, T.; Nakamoto, H.; Sakamoto, M.

2012-09-01

In these years, standards to build a Virtual Observatory (VO) data service have been established with the efforts in the International Virtual Observatory Alliance (IVOA). We applied these newly established standards (SSAP, TAP) to our VO service toolkit which was developed to implement earlier VO standards SIAP and (deprecated) SkyNode. The toolkit can be easily installed and provides a GUI interface to construct and manage VO service. In this paper, we describes the architecture of our toolkit and how it is used to start hosting VO service.

Loss of Coolant Accident (LOCA) / Emergency Core Coolant System (ECCS Evaluation of Risk-Informed Margins Management Strategies for a Representative Pressurized Water Reactor (PWR)

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

Szilard, Ronaldo Henriques

A Risk Informed Safety Margin Characterization (RISMC) toolkit and methodology are proposed for investigating nuclear power plant core, fuels design and safety analysis, including postulated Loss-of-Coolant Accident (LOCA) analysis. This toolkit, under an integrated evaluation model framework, is name LOCA toolkit for the US (LOTUS). This demonstration includes coupled analysis of core design, fuel design, thermal hydraulics and systems analysis, using advanced risk analysis tools and methods to investigate a wide range of results.

WIND Toolkit Power Data Site Index

DOE Data Explorer

Draxl, Caroline; Mathias-Hodge, Bri

2016-10-19

This spreadsheet contains per-site metadata for the WIND Toolkit sites and serves as an index for the raw data hosted on Globus connect (nrel#globus:/globusro/met_data). Aside from the metadata, per site average power and capacity factor are given. This data was prepared by 3TIER under contract by NREL and is public domain. Authoritative documentation on the creation of the underlying dataset is at: Final Report on the Creation of the Wind Integration National Dataset (WIND) Toolkit and API: http://www.nrel.gov/docs/fy16osti/66189.pdf

LEGO Mindstorms NXT for elderly and visually impaired people in need: A platform.

PubMed

Al-Halhouli, Ala'aldeen; Qitouqa, Hala; Malkosh, Nancy; Shubbak, Alaa; Al-Gharabli, Samer; Hamad, Eyad

2016-07-27

This paper presents the employment of LEGO Mindstorms NXT robotics as core component of low cost multidisciplinary platform for assisting elderly and visually impaired people. LEGO Mindstorms system offers a plug-and-play programmable robotics toolkit, incorporating construction guides, microcontrollers and sensors, all connected via a comprehensive programming language. It facilitates, without special training and at low cost, the use of such device for interpersonal communication and for handling multiple tasks required for elderly and visually impaired people in-need. The research project provides a model for larger-scale implementation, tackling the issues of creating additional functions in order to assist people in-need. The new functions were built and programmed using MATLAB through a user friendly Graphical User Interface (GUI). Power consumption problem, besides the integration of WiFi connection has been resolved, incorporating GPS application on smart phones enhanced the guiding and tracking functions. We believe that developing and expanding the system to encompass a range of applications beyond the initial design schematics to ease conducting a limited number of pre-described protocols. However, the beneficiaries for the proposed research would be limited to elderly people who require assistance within their household as assistive-robot to facilitate a low-cost solution for a highly demanding health circumstance.

WebViz:A Web-based Collaborative Interactive Visualization System for large-Scale Data Sets

NASA Astrophysics Data System (ADS)

Yuen, D. A.; McArthur, E.; Weiss, R. M.; Zhou, J.; Yao, B.

2010-12-01

WebViz is a web-based application designed to conduct collaborative, interactive visualizations of large data sets for multiple users, allowing researchers situated all over the world to utilize the visualization services offered by the University of Minnesota’s Laboratory for Computational Sciences and Engineering (LCSE). This ongoing project has been built upon over the last 3 1/2 years .The motivation behind WebViz lies primarily with the need to parse through an increasing amount of data produced by the scientific community as a result of larger and faster multicore and massively parallel computers coming to the market, including the use of general purpose GPU computing. WebViz allows these large data sets to be visualized online by anyone with an account. The application allows users to save time and resources by visualizing data ‘on the fly’, wherever he or she may be located. By leveraging AJAX via the Google Web Toolkit (http://code.google.com/webtoolkit/), we are able to provide users with a remote, web portal to LCSE's (http://www.lcse.umn.edu) large-scale interactive visualization system already in place at the University of Minnesota. LCSE’s custom hierarchical volume rendering software provides high resolution visualizations on the order of 15 million pixels and has been employed for visualizing data primarily from simulations in astrophysics to geophysical fluid dynamics . In the current version of WebViz, we have implemented a highly extensible back-end framework built around HTTP "server push" technology. The web application is accessible via a variety of devices including netbooks, iPhones, and other web and javascript-enabled cell phones. Features in the current version include the ability for users to (1) securely login (2) launch multiple visualizations (3) conduct collaborative visualization sessions (4) delegate control aspects of a visualization to others and (5) engage in collaborative chats with other users within the user interface of the web application. These features are all in addition to a full range of essential visualization functions including 3-D camera and object orientation, position manipulation, time-stepping control, and custom color/alpha mapping.

The 2016 ACCP Pharmacotherapy Didactic Curriculum Toolkit.

PubMed

Schwinghammer, Terry L; Crannage, Andrew J; Boyce, Eric G; Bradley, Bridget; Christensen, Alyssa; Dunnenberger, Henry M; Fravel, Michelle; Gurgle, Holly; Hammond, Drayton A; Kwon, Jennifer; Slain, Douglas; Wargo, Kurt A

2016-11-01

The 2016 American College of Clinical Pharmacy (ACCP) Educational Affairs Committee was charged with updating and contemporizing ACCP's 2009 Pharmacotherapy Didactic Curriculum Toolkit. The toolkit has been designed to guide schools and colleges of pharmacy in developing, maintaining, and modifying their curricula. The 2016 committee reviewed the recent medical literature and other documents to identify disease states that are responsive to drug therapy. Diseases and content topics were organized by organ system, when feasible, and grouped into tiers as defined by practice competency. Tier 1 topics should be taught in a manner that prepares all students to provide collaborative, patient-centered care upon graduation and licensure. Tier 2 topics are generally taught in the professional curriculum, but students may require additional knowledge or skills after graduation (e.g., residency training) to achieve competency in providing direct patient care. Tier 3 topics may not be taught in the professional curriculum; thus, graduates will be required to obtain the necessary knowledge and skills on their own to provide direct patient care, if required in their practice. The 2016 toolkit contains 276 diseases and content topics, of which 87 (32%) are categorized as tier 1, 133 (48%) as tier 2, and 56 (20%) as tier 3. The large number of tier 1 topics will require schools and colleges to use creative pedagogical strategies to achieve the necessary practice competencies. Almost half of the topics (48%) are tier 2, highlighting the importance of postgraduate residency training or equivalent practice experience to competently care for patients with these disorders. The Pharmacotherapy Didactic Curriculum Toolkit will continue to be updated to provide guidance to faculty at schools and colleges of pharmacy as these academic pharmacy institutions regularly evaluate and modify their curricula to keep abreast of scientific advances and associated practice changes. Access the current Pharmacotherapy Didactic Curriculum Toolkit at http://www.accp.com/docs/positions/misc/Toolkit_final.pdf. © 2016 Pharmacotherapy Publications, Inc.

Patient-Centered Personal Health Record and Portal Implementation Toolkit for Ambulatory Clinics: A Feasibility Study.

PubMed

Nahm, Eun-Shim; Diblasi, Catherine; Gonzales, Eva; Silver, Kristi; Zhu, Shijun; Sagherian, Knar; Kongs, Katherine

2017-04-01

Personal health records and patient portals have been shown to be effective in managing chronic illnesses. Despite recent nationwide implementation efforts, the personal health record and patient portal adoption rates among patients are low, and the lack of support for patients using the programs remains a critical gap in most implementation processes. In this study, we implemented the Patient-Centered Personal Health Record and Patient Portal Implementation Toolkit in a large diabetes/endocrinology center and assessed its preliminary impact on personal health record and patient portal knowledge, self-efficacy, patient-provider communication, and adherence to treatment plans. Patient-Centered Personal Health Record and Patient Portal Implementation Toolkit is composed of Patient-Centered Personal Health Record and Patient Portal Implementation Toolkit-General, clinic-level resources for clinicians, staff, and patients, and Patient-Centered Personal Health Record and Patient Portal Implementation Toolkit Plus, an optional 4-week online resource program for patients ("MyHealthPortal"). First, Patient-Centered Personal Health Record and Patient Portal Implementation Toolkit-General was implemented, and all clinicians and staff were educated about the center's personal health record and patient portal. Then general patient education was initiated, while a randomized controlled trial was conducted to test the preliminary effects of "MyHealthPortal" using a small sample (n = 74) with three observations (baseline and 4 and 12 weeks). The intervention group showed significantly greater improvement than the control group in patient-provider communication at 4 weeks (t56 = 3.00, P = .004). For other variables, the intervention group tended to show greater improvement; however, the differences were not significant. In this preliminary study, Patient-Centered Personal Health Record and Patient Portal Implementation Toolkit showed potential for filling the gap in the current personal health record and patient portal implementation process. Further studies are needed using larger samples in other settings to ascertain if these results are generalizable to other populations.

The Ames MER microscopic imager toolkit

USGS Publications Warehouse

Sargent, R.; Deans, Matthew; Kunz, C.; Sims, M.; Herkenhoff, K.

2005-01-01

12The Mars Exploration Rovers, Spirit and Opportunity, have spent several successful months on Mars, returning gigabytes of images and spectral data to scientists on Earth. One of the instruments on the MER rovers, the Athena Microscopic Imager (MI), is a fixed focus, megapixel camera providing a ??3mm depth of field and a 31??31mm field of view at a working distance of 63 mm from the lens to the object being imaged. In order to maximize the science return from this instrument, we developed the Ames MI Toolkit and supported its use during the primary mission. The MI Toolkit is a set of programs that operate on collections of MI images, with the goal of making the data more understandable to the scientists on the ground. Because of the limited depth of field of the camera, and the often highly variable topography of the terrain being imaged, MI images of a given rock are often taken as a stack, with the Instrument Deployment Device (IDD) moving along a computed normal vector, pausing every few millimeters for the MI to acquire an image. The MI Toolkit provides image registration and focal section merging, which combine these images to form a single, maximally in-focus image, while compensating for changes in lighting as well as parallax due to the motion of the camera. The MI Toolkit also provides a 3-D reconstruction of the surface being imaged using stereo and can embed 2-D MI images as texture maps into 3-D meshes produced by other imagers on board the rover to provide context. The 2-D images and 3-D meshes output from the Toolkit are easily viewed by scientists using other mission tools, such as Viz or the MI Browser.This paper describes the MI Toolkit in detail, as well as our experience using it with scientists at JPL during the primary MER mission. ?? 2005 IEEE.

The Ames MER Microscopic Imager Toolkit

NASA Technical Reports Server (NTRS)

Sargent, Randy; Deans, Matthew; Kunz, Clayton; Sims, Michael; Herkenhoff, Ken

2005-01-01

The Mars Exploration Rovers, Spirit and Opportunity, have spent several successful months on Mars, returning gigabytes of images and spectral data to scientists on Earth. One of the instruments on the MER rovers, the Athena Microscopic Imager (MI), is a fixed focus, megapixel camera providing a plus or minus mm depth of field and a 3lx31mm field of view at a working distance of 63 mm from the lens to the object being imaged. In order to maximize the science return from this instrument, we developed the Ames MI Toolkit and supported its use during the primary mission. The MI Toolkit is a set of programs that operate on collections of MI images, with the goal of making the data more understandable to the scientists on the ground. Because of the limited depth of field of the camera, and the often highly variable topography of the terrain being imaged, MI images of a given rock are often taken as a stack, with the Instrument Deployment Device (IDD) moving along a computed normal vector, pausing every few millimeters for the MI to acquire an image. The MI Toolkit provides image registration and focal section merging, which combine these images to form a single, maximally in-focus image, while compensating for changes in lighting as well as parallax due to the motion of the camera. The MI Toolkit also provides a 3-D reconstruction of the surface being imaged using stereo and can embed 2-D MI images as texture maps into 3-D meshes produced by other imagers on board the rover to provide context. The 2-D images and 3-D meshes output from the Toolkit are easily viewed by scientists using other mission tools, such as Viz or the MI Browser. This paper describes the MI Toolkit in detail, as well as our experience using it with scientists at JPL during the primary MER mission.

Investigating the feasibility of Visualising Complex Space Weather Data in a CAVE

NASA Astrophysics Data System (ADS)

Loughlin, S.; Habash Krause, L.

2013-12-01

The purpose of this study was to investigate the feasibility of visualising complex space weather data in a Cave Automatic Virtual Environment (CAVE). Space weather is increasingly causing disruptions on Earth, such as power outages and disrupting communication to satellites. We wanted to display this space weather data within the CAVE since the data from instruments, models and simulations are typically too complex to understand on their own, especially when they are of 7 dimensions. To accomplish this, I created a VTK to NetCDF converter. NetCDF is a science data format, which stores array oriented scientific data. The format is maintained by the University Corporation for Atmospheric Research, and is used extensively by the atmospheric and space communities.

Ridesharing options analysis and practitioners' toolkit

DOT National Transportation Integrated Search

2010-12-01

The purpose of this toolkit is to elaborate upon the recent changes in ridesharing, introduce the wide variety that exists in ridesharing programs today, and the developments in technology and funding availability that create greater incentives for p...

Energy Savings Performance Contract Energy Sales Agreement Toolkit

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

None

FEMP developed the Energy Savings Performance Contracting Energy Sales Agreement (ESPC ESA) Toolkit to provide federal agency contracting officers and other acquisition team members with information that will facilitate the timely execution of ESPC ESA projects.

Engineering and algorithm design for an image processing Api: a technical report on ITK--the Insight Toolkit.

PubMed

Yoo, Terry S; Ackerman, Michael J; Lorensen, William E; Schroeder, Will; Chalana, Vikram; Aylward, Stephen; Metaxas, Dimitris; Whitaker, Ross

2002-01-01

We present the detailed planning and execution of the Insight Toolkit (ITK), an application programmers interface (API) for the segmentation and registration of medical image data. This public resource has been developed through the NLM Visible Human Project, and is in beta test as an open-source software offering under cost-free licensing. The toolkit concentrates on 3D medical data segmentation and registration algorithms, multimodal and multiresolution capabilities, and portable platform independent support for Windows, Linux/Unix systems. This toolkit was built using current practices in software engineering. Specifically, we embraced the concept of generic programming during the development of these tools, working extensively with C++ templates and the freedom and flexibility they allow. Software development tools for distributed consortium-based code development have been created and are also publicly available. We discuss our assumptions, design decisions, and some lessons learned.

The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation.

PubMed

Kocher, Jean-Pierre A; Quest, Daniel J; Duffy, Patrick; Meiners, Michael A; Moore, Raymond M; Rider, David; Hossain, Asif; Hart, Steven N; Dinu, Valentin

2014-07-01

The Biological Reference Repository (BioR) is a toolkit for annotating variants. BioR stores public and user-specific annotation sources in indexed JSON-encoded flat files (catalogs). The BioR toolkit provides the functionality to combine and retrieve annotation from these catalogs via the command-line interface. Several catalogs from commonly used annotation sources and instructions for creating user-specific catalogs are provided. Commands from the toolkit can be combined with other UNIX commands for advanced annotation processing. We also provide instructions for the development of custom annotation pipelines. The package is implemented in Java and makes use of external tools written in Java and Perl. The toolkit can be executed on Mac OS X 10.5 and above or any Linux distribution. The BioR application, quickstart, and user guide documents and many biological examples are available at http://bioinformaticstools.mayo.edu. © The Author 2014. Published by Oxford University Press.

Security Hardened Cyber Components for Nuclear Power Plants: Phase I SBIR Final Technical Report

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

Franusich, Michael D.

SpiralGen, Inc. built a proof-of-concept toolkit for enhancing the cyber security of nuclear power plants and other critical infrastructure with high-assurance instrumentation and control code. The toolkit is based on technology from the DARPA High-Assurance Cyber Military Systems (HACMS) program, which has focused on applying the science of formal methods to the formidable set of problems involved in securing cyber physical systems. The primary challenges beyond HACMS in developing this toolkit were to make the new technology usable by control system engineers and compatible with the regulatory and commercial constraints of the nuclear power industry. The toolkit, packaged as amore » Simulink add-on, allows a system designer to assemble a high-assurance component from formally specified and proven blocks and generate provably correct control and monitor code for that subsystem.« less

A Collaborative Decision Environment for UAV Operations

NASA Technical Reports Server (NTRS)

D'Ortenzio, Matthew V.; Enomoto, Francis Y.; Johan, Sandra L.

2005-01-01

NASA is developing Intelligent Mission Management (IMM) technology for science missions employing long endurance unmanned aerial vehicles (UAV's). The IMM groundbased component is the Collaborative Decision Environment (CDE), a ground system that provides the Mission/Science team with situational awareness, collaboration, and decisionmaking tools. The CDE is used for pre-flight planning, mission monitoring, and visualization of acquired data. It integrates external data products used for planning and executing a mission, such as weather, satellite data products, and topographic maps by leveraging established and emerging Open Geospatial Consortium (OGC) standards to acquire external data products via the Internet, and an industry standard geographic information system (GIs) toolkit for visualization As a Science/Mission team may be geographically dispersed, the CDE is capable of providing access to remote users across wide area networks using Web Services technology. A prototype CDE is being developed for an instrument checkout flight on a manned aircraft in the fall of 2005, in preparation for a full deployment in support of the US Forest Service and NASA Ames Western States Fire Mission in 2006.

Margins of safety provided by COSHH Essentials and the ILO Chemical Control Toolkit.

PubMed

Jones, Rachael M; Nicas, Mark

2006-03-01

COSHH Essentials, developed by the UK Health and Safety Executive, and the Chemical Control Toolkit (Toolkit) proposed by the International Labor Organization, are 'control banding' approaches to workplace risk management intended for use by proprietors of small and medium-sized businesses. Both systems group chemical substances into hazard bands based on toxicological endpoint and potency. COSSH Essentials uses the European Union's Risk-phrases (R-phrases), whereas the Toolkit uses R-phrases and the Globally Harmonized System (GHS) of Classification and Labeling of Chemicals. Each hazard band is associated with a range of airborne concentrations, termed exposure bands, which are to be attained by the implementation of recommended control technologies. Here we analyze the margin of safety afforded by the systems and, for each hazard band, define the minimal margin as the ratio of the minimum airborne concentration that produced the toxicological endpoint of interest in experimental animals to the maximum concentration in workplace air permitted by the exposure band. We found that the minimal margins were always <100, with some ranging to <1, and inversely related to molecular weight. The Toolkit-GHS system generally produced margins equal to or larger than COSHH Essentials, suggesting that the Toolkit-GHS system is more protective of worker health. Although, these systems predict exposures comparable with current occupational exposure limits, we argue that the minimal margins are better indicators of health protection. Further, given the small margins observed, we feel it is important that revisions of these systems provide the exposure bands to users, so as to permit evaluation of control technology capture efficiency.

Effects of a Short Video-Based Resident-as-Teacher Training Toolkit on Resident Teaching.

PubMed

Ricciotti, Hope A; Freret, Taylor S; Aluko, Ashley; McKeon, Bri Anne; Haviland, Miriam J; Newman, Lori R

2017-10-01

To pilot a short video-based resident-as-teacher training toolkit and assess its effect on resident teaching skills in clinical settings. A video-based resident-as-teacher training toolkit was previously developed by educational experts at Beth Israel Deaconess Medical Center, Harvard Medical School. Residents were recruited from two academic hospitals, watched two videos from the toolkit ("Clinical Teaching Skills" and "Effective Clinical Supervision"), and completed an accompanying self-study guide. A novel assessment instrument for evaluating the effect of the toolkit on teaching was created through a modified Delphi process. Before and after the intervention, residents were observed leading a clinical teaching encounter and scored using the 15-item assessment instrument. The primary outcome of interest was the change in number of skills exhibited, which was assessed using the Wilcoxon signed-rank test. Twenty-eight residents from two academic hospitals were enrolled, and 20 (71%) completed all phases of the study. More than one third of residents who volunteered to participate reported no prior formal teacher training. After completing two training modules, residents demonstrated a significant increase in the median number of teaching skills exhibited in a clinical teaching encounter, from 7.5 (interquartile range 6.5-9.5) to 10.0 (interquartile range 9.0-11.5; P<.001). Of the 15 teaching skills assessed, there were significant improvements in asking for the learner's perspective (P=.01), providing feedback (P=.005), and encouraging questions (P=.046). Using a resident-as-teacher video-based toolkit was associated with improvements in teaching skills in residents from multiple specialties.

Innovations and Challenges of Implementing a Glucose Gel Toolkit for Neonatal Hypoglycemia.

PubMed

Hammer, Denise; Pohl, Carla; Jacobs, Peggy J; Kaufman, Susan; Drury, Brenda

2018-05-24

Transient neonatal hypoglycemia occurs most commonly in newborns who are small for gestational age, large for gestational age, infants of diabetic mothers, and late preterm infants. An exact blood glucose value has not been determined for neonatal hypoglycemia, and it is important to note that poor neurologic outcomes can occur if hypoglycemia is left untreated. Interventions that separate mothers and newborns, as well as use of formula to treat hypoglycemia, have the potential to disrupt exclusive breastfeeding. To determine whether implementation of a toolkit designed to support staff in the adaptation of the practice change for management of newborns at risk for hypoglycemia, that includes 40% glucose gel in an obstetric unit with a level 2 nursery will decrease admissions to the Intermediate Care Nursery, and increase exclusive breastfeeding. This descriptive study used a retrospective chart review for pre/postimplementation of the Management of Newborns at Risk for Hypoglycemia Toolkit (Toolkit) using a convenience sample of at-risk newborns in the first 2 days of life to evaluate the proposed outcomes. Following implementation of the Toolkit, at-risk newborns had a clinically but not statistically significant 6.5% increase in exclusive breastfeeding and a clinically but not statistically significant 5% decrease in admissions to the Intermediate Care Nursery. The Toolkit was designed for ease of staff use and to improve outcomes for the at-risk newborn. Future research includes replication at other level 2 and level 1 obstetric centers and investigation into the number of 40% glucose gel doses that can safely be administered.

Improved quality of care for patients infected or colonised with ESBL-producing Enterobacteriaceae in a French teaching hospital: impact of an interventional prospective study and development of specific tools.

PubMed

Mondain, Véronique; Lieutier, Florence; Pulcini, Céline; Degand, Nicolas; Landraud, Luce; Ruimy, Raymond; Fosse, Thierry; Roger, Pierre Marie

2018-05-01

The increasing incidence of ESBL-producing Enterobacteriaceae (ESBL-E) in France prompted the publication of national recommendations in 2010. Based on these, we developed a toolkit and a warning system to optimise management of ESBL-E infected or colonised patients in both community and hospital settings. The impact of this initiative on quality of care was assessed in a teaching hospital. The ESBL toolkit was developed in 2011 during multidisciplinary meetings involving a regional network of hospital, private clinic and laboratory staff in Southeastern France. It includes antibiotic treatment protocols, a check list, mail templates and a patient information sheet focusing on infection control. Upon identification of ESBL-E, the warning system involves alerting the attending physician and the infectious disease (ID) advisor, with immediate, advice-based implementation of the toolkit. The procedure and toolkit were tested in our teaching hospital. Patient management was compared before and after implementation of the toolkit over two 3-month periods (July-October 2010 and 2012). Implementation of the ESBL-E warning system and ESBL-E toolkit was tested for 87 patients in 2010 and 92 patients in 2012, resulting in improved patient management: expert advice sought and followed (16 vs 97%), information provided to the patient's general practitioner (18 vs 63%) and coding of the condition in the patient's medical file (17 vs 59%), respectively. Our multidisciplinary strategy improved quality of care for in-patients infected or colonised with ESBL-E, increasing compliance with national recommendations.

RISMC Toolkit and Methodology Research and Development Plan for External Hazards Analysis

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

Coleman, Justin Leigh

This report includes the description and development plan for a Risk Informed Safety Margins Characterization (RISMC) toolkit and methodology that will evaluate multihazard risk in an integrated manner to support the operating nuclear fleet.

Resource Toolkit for Working with Education Service Providers

ERIC Educational Resources Information Center

National Association of Charter School Authorizers (NJ1), 2005

2005-01-01

This resource toolkit for working education service providers contains four sections. Section 1, "Roles Responsibilities, and Relationships," contains: (1) "Purchasing Services from an Educational Management Organization," excerpted from "The Charter School Administrative and Governance Guide" (Massachusetts Dept. of…

Reusable Client-Side JavaScript Modules for Immersive Web-Based Real-Time Collaborative Neuroimage Visualization.

PubMed

Bernal-Rusiel, Jorge L; Rannou, Nicolas; Gollub, Randy L; Pieper, Steve; Murphy, Shawn; Robertson, Richard; Grant, Patricia E; Pienaar, Rudolph

2017-01-01

In this paper we present a web-based software solution to the problem of implementing real-time collaborative neuroimage visualization. In both clinical and research settings, simple and powerful access to imaging technologies across multiple devices is becoming increasingly useful. Prior technical solutions have used a server-side rendering and push-to-client model wherein only the server has the full image dataset. We propose a rich client solution in which each client has all the data and uses the Google Drive Realtime API for state synchronization. We have developed a small set of reusable client-side object-oriented JavaScript modules that make use of the XTK toolkit, a popular open-source JavaScript library also developed by our team, for the in-browser rendering and visualization of brain image volumes. Efficient realtime communication among the remote instances is achieved by using just a small JSON object, comprising a representation of the XTK image renderers' state, as the Google Drive Realtime collaborative data model. The developed open-source JavaScript modules have already been instantiated in a web-app called MedView , a distributed collaborative neuroimage visualization application that is delivered to the users over the web without requiring the installation of any extra software or browser plugin. This responsive application allows multiple physically distant physicians or researchers to cooperate in real time to reach a diagnosis or scientific conclusion. It also serves as a proof of concept for the capabilities of the presented technological solution.

KinImmerse: Macromolecular VR for NMR ensembles

PubMed Central

Block, Jeremy N; Zielinski, David J; Chen, Vincent B; Davis, Ian W; Vinson, E Claire; Brady, Rachael; Richardson, Jane S; Richardson, David C

2009-01-01

Background In molecular applications, virtual reality (VR) and immersive virtual environments have generally been used and valued for the visual and interactive experience – to enhance intuition and communicate excitement – rather than as part of the actual research process. In contrast, this work develops a software infrastructure for research use and illustrates such use on a specific case. Methods The Syzygy open-source toolkit for VR software was used to write the KinImmerse program, which translates the molecular capabilities of the kinemage graphics format into software for display and manipulation in the DiVE (Duke immersive Virtual Environment) or other VR system. KinImmerse is supported by the flexible display construction and editing features in the KiNG kinemage viewer and it implements new forms of user interaction in the DiVE. Results In addition to molecular visualizations and navigation, KinImmerse provides a set of research tools for manipulation, identification, co-centering of multiple models, free-form 3D annotation, and output of results. The molecular research test case analyzes the local neighborhood around an individual atom within an ensemble of nuclear magnetic resonance (NMR) models, enabling immersive visual comparison of the local conformation with the local NMR experimental data, including target curves for residual dipolar couplings (RDCs). Conclusion The promise of KinImmerse for production-level molecular research in the DiVE is shown by the locally co-centered RDC visualization developed there, which gave new insights now being pursued in wider data analysis. PMID:19222844

Improving safety on rural local and tribal roads safety toolkit.

DOT National Transportation Integrated Search

2014-08-01

Rural roadway safety is an important issue for communities throughout the country and presents a challenge for state, local, and Tribal agencies. The Improving Safety on Rural Local and Tribal Roads Safety Toolkit was created to help rural local ...

A methodological toolkit for field assessments of artisanally mined alluvial diamond deposits

USGS Publications Warehouse

Chirico, Peter G.; Malpeli, Katherine C.

2014-01-01

This toolkit provides a standardized checklist of critical issues relevant to artisanal mining-related field research. An integrated sociophysical geographic approach to collecting data at artisanal mine sites is outlined. The implementation and results of a multistakeholder approach to data collection, carried out in the assessment of Guinea’s artisanally mined diamond deposits, also are summarized. This toolkit, based on recent and successful field campaigns in West Africa, has been developed as a reference document to assist other government agencies or organizations in collecting the data necessary for artisanal diamond mining or similar natural resource assessments.

TRSkit: A Simple Digital Library Toolkit

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Esler, Sandra L.

1997-01-01

This paper introduces TRSkit, a simple and effective toolkit for building digital libraries on the World Wide Web. The toolkit was developed for the creation of the Langley Technical Report Server and the NASA Technical Report Server, but is applicable to most simple distribution paradigms. TRSkit contains a handful of freely available software components designed to be run under the UNIX operating system and served via the World Wide Web. The intended customer is the person that must continuously and synchronously distribute anywhere from 100 - 100,000's of information units and does not have extensive resources to devote to the problem.

Toolkit for testing scientific CCD cameras

NASA Astrophysics Data System (ADS)

Uzycki, Janusz; Mankiewicz, Lech; Molak, Marcin; Wrochna, Grzegorz

2006-03-01

The CCD Toolkit (1) is a software tool for testing CCD cameras which allows to measure important characteristics of a camera like readout noise, total gain, dark current, 'hot' pixels, useful area, etc. The application makes a statistical analysis of images saved in files with FITS format, commonly used in astronomy. A graphical interface is based on the ROOT package, which offers high functionality and flexibility. The program was developed in a way to ensure future compatibility with different operating systems: Windows and Linux. The CCD Toolkit was created for the "Pie of the Sky" project collaboration (2).

RAVE—a Detector-independent vertex reconstruction toolkit

NASA Astrophysics Data System (ADS)

Waltenberger, Wolfgang; Mitaroff, Winfried; Moser, Fabian

2007-10-01

A detector-independent toolkit for vertex reconstruction (RAVE ) is being developed, along with a standalone framework (VERTIGO ) for testing, analyzing and debugging. The core algorithms represent state of the art for geometric vertex finding and fitting by both linear (Kalman filter) and robust estimation methods. Main design goals are ease of use, flexibility for embedding into existing software frameworks, extensibility, and openness. The implementation is based on modern object-oriented techniques, is coded in C++ with interfaces for Java and Python, and follows an open-source approach. A beta release is available. VERTIGO = "vertex reconstruction toolkit and interface to generic objects".

Methodology for the development of a taxonomy and toolkit to evaluate health-related habits and lifestyle (eVITAL)

PubMed Central

2010-01-01

Background Chronic diseases cause an ever-increasing percentage of morbidity and mortality, but many have modifiable risk factors. Many behaviors that predispose or protect an individual to chronic disease are interrelated, and therefore are best approached using an integrated model of health and the longevity paradigm, using years lived without disability as the endpoint. Findings This study used a 4-phase mixed qualitative design to create a taxonomy and related online toolkit for the evaluation of health-related habits. Core members of a working group conducted a literature review and created a framing document that defined relevant constructs. This document was revised, first by a working group and then by a series of multidisciplinary expert groups. The working group and expert panels also designed a systematic evaluation of health behaviors and risks, which was computerized and evaluated for feasibility. A demonstration study of the toolkit was performed in 11 healthy volunteers. Discussion In this protocol, we used forms of the community intelligence approach, including frame analysis, feasibility, and demonstration, to develop a clinical taxonomy and an online toolkit with standardized procedures for screening and evaluation of multiple domains of health, with a focus on longevity and the goal of integrating the toolkit into routine clinical practice. Trial Registration IMSERSO registry 200700012672 PMID:20334642

Implementing a Breastfeeding Toolkit for Nursing Education.

PubMed

Folker-Maglaya, Catherine; Pylman, Maureen E; Couch, Kimberly A; Spatz, Diane L; Marzalik, Penny R

All health professional organizations recommend exclusive breastfeeding for at least 6 months, with continued breastfeeding for 1 year or more after birth. Women cite lack of support from health professionals as a barrier to breastfeeding. Meanwhile, breastfeeding education is not considered essential to basic nursing education and students are not adequately prepared to support breastfeeding women. Therefore, a toolkit of comprehensive evidence-based breastfeeding educational materials was developed to provide essential breastfeeding knowledge. A study was performed to determine the effectiveness of the breastfeeding toolkit education in an associate degree nursing program. A pretest/posttest survey design with intervention and comparison groups was used. One hundred fourteen students completed pre- and posttests. Student knowledge was measured using a 12-item survey derived with minor modifications from Marzalik's 2004 instrument measuring breastfeeding knowledge. When pre- and posttests scores were compared within groups, both groups' knowledge scores increased. A change score was calculated with a significantly higher mean score for the intervention group. When regression analysis was used to control for the pretest score, belonging to the intervention group increased student scores but not significantly. The toolkit was developed to provide a curriculum that demonstrates enhanced learning to prepare nursing students for practice. The toolkit could be used in other settings, such as to educate staff nurses working with childbearing families.

The Automatic Parallelisation of Scientific Application Codes Using a Computer Aided Parallelisation Toolkit

NASA Technical Reports Server (NTRS)

Ierotheou, C.; Johnson, S.; Leggett, P.; Cross, M.; Evans, E.; Jin, Hao-Qiang; Frumkin, M.; Yan, J.; Biegel, Bryan (Technical Monitor)

2001-01-01

The shared-memory programming model is a very effective way to achieve parallelism on shared memory parallel computers. Historically, the lack of a programming standard for using directives and the rather limited performance due to scalability have affected the take-up of this programming model approach. Significant progress has been made in hardware and software technologies, as a result the performance of parallel programs with compiler directives has also made improvements. The introduction of an industrial standard for shared-memory programming with directives, OpenMP, has also addressed the issue of portability. In this study, we have extended the computer aided parallelization toolkit (developed at the University of Greenwich), to automatically generate OpenMP based parallel programs with nominal user assistance. We outline the way in which loop types are categorized and how efficient OpenMP directives can be defined and placed using the in-depth interprocedural analysis that is carried out by the toolkit. We also discuss the application of the toolkit on the NAS Parallel Benchmarks and a number of real-world application codes. This work not only demonstrates the great potential of using the toolkit to quickly parallelize serial programs but also the good performance achievable on up to 300 processors for hybrid message passing and directive-based parallelizations.

Tailored prevention of inpatient falls: development and usability testing of the fall TIPS toolkit.

PubMed

Zuyev, Lyubov; Benoit, Angela N; Chang, Frank Y; Dykes, Patricia C

2011-02-01

Patient falls and fall-related injuries are serious problems in hospitals. The Fall TIPS application aims to prevent patient falls by translating routine nursing fall risk assessment into a decision support intervention that communicates fall risk status and creates a tailored evidence-based plan of care that is accessible to the care team, patients, and family members. In our design and implementation of the Fall TIPS toolkit, we used the Spiral Software Development Life Cycle model. Three output tools available to be generated from the toolkit are bed poster, plan of care, and patient education handout. A preliminary design of the application was based on initial requirements defined by project leaders and informed by focus groups with end users. Preliminary design partially simulated the paper version of the Morse Fall Scale currently used in hospitals involved in the research study. Strengths and weaknesses of the first prototype were identified by heuristic evaluation. Usability testing was performed at sites where research study is implemented. Suggestions mentioned by end users participating in usability studies were either directly incorporated into the toolkit and output tools, were slightly modified, or will be addressed during training. The next step is implementation of the fall prevention toolkit on the pilot testing units.

Testing Video and Social Media for Engaging Users of the U.S. Climate Resilience Toolkit

NASA Astrophysics Data System (ADS)

Green, C. J.; Gardiner, N.; Niepold, F., III; Esposito, C.

2015-12-01

We developed a custom video production stye and a method for analyzing social media behavior so that we may deliberately build and track audience growth for decision-support tools and case studies within the U.S. Climate Resilience Toolkit. The new style of video focuses quickly on decision processes; its 30s format is well-suited for deployment through social media. We measured both traffic and engagement with video using Google Analytics. Each video included an embedded tag, allowing us to measure viewers' behavior: whether or not they entered the toolkit website; the duration of their session on the website; and the number pages they visited in that session. Results showed that video promotion was more effective on Facebook than Twitter. Facebook links generated twice the number of visits to the toolkit. Videos also increased Facebook interaction overall. Because most Facebook users are return visitors, this campaign did not substantially draw new site visitors. We continue to research and apply these methods in a targeted engagement and outreach campaign that utilizes the theory of social diffusion and social influence strategies to grow our audience of "influential" decision-makers and people within their social networks. Our goal is to increase access and use of the U.S. Climate Resilience Toolkit.

Spice Tools Supporting Planetary Remote Sensing

NASA Astrophysics Data System (ADS)

Acton, C.; Bachman, N.; Semenov, B.; Wright, E.

2016-06-01

NASA's "SPICE"* ancillary information system has gradually become the de facto international standard for providing scientists the fundamental observation geometry needed to perform photogrammetry, map making and other kinds of planetary science data analysis. SPICE provides position and orientation ephemerides of both the robotic spacecraft and the target body; target body size and shape data; instrument mounting alignment and field-of-view geometry; reference frame specifications; and underlying time system conversions. SPICE comprises not only data, but also a large suite of software, known as the SPICE Toolkit, used to access those data and subsequently compute derived quantities-items such as instrument viewing latitude/longitude, lighting angles, altitude, etc. In existence since the days of the Magellan mission to Venus, the SPICE system has continuously grown to better meet the needs of scientists and engineers. For example, originally the SPICE Toolkit was offered only in Fortran 77, but is now available in C, IDL, MATLAB, and Java Native Interface. SPICE calculations were originally available only using APIs (subroutines), but can now be executed using a client-server interface to a geometry engine. Originally SPICE "products" were only available in numeric form, but now SPICE data visualization is also available. The SPICE components are free of cost, license and export restrictions. Substantial tutorials and programming lessons help new users learn to employ SPICE calculations in their own programs. The SPICE system is implemented and maintained by the Navigation and Ancillary Information Facility (NAIF)-a component of NASA's Planetary Data System (PDS). * Spacecraft, Planet, Instrument, Camera-matrix, Events

Precise positioning of an intraoral distractor using augmented reality in patients with hemifacial microsomia.

PubMed

Qu, Miao; Hou, Yikang; Xu, Yourong; Shen, Congcong; Zhu, Ming; Xie, Le; Wang, Hao; Zhang, Yan; Chai, Gang

2015-01-01

Through three-dimensional real time imaging, augmented reality (AR) can provide an overlay of the anatomical structure, or visual cues for specific landmarks. In this study, an AR Toolkit was used for distraction osteogenesis with hemifacial microsomia to define the mandibular osteotomy line and assist with intraoral distractor placement. 20 patients with hemifacial microsomia were studied and were randomly assigned to experimental and control groups. Pre-operative computed tomography was used in both groups, whereas AR was used in the experimental group. Afterwards, pre- and post-operative computed tomographic scans of both groups were superimposed, and several measurements were made and analysed. Both the conventional method and AR technique achieved proper positioning of the osteotomy planes, although the AR was more accurate. The difference in average vertical distance from the coronoid and condyle process to the pre- and post-operative cutting planes was significant (p < 0.01) between the two groups, whereas no significant difference (p > 0.05) was observed in the average angle between the two planes. The difference in deviations between the intersection points of the overlaid mandible across two cutting planes was also significant (p < 0.01). This study reports on an efficient approach for guiding intraoperative distraction osteogenesis. Augmented reality tools such as the AR Toolkit may be helpful for precise positioning of intraoral distractors in patients with hemifacial microsomia in craniofacial surgery. Copyright © 2014 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

SatelliteDL: a Toolkit for Analysis of Heterogeneous Satellite Datasets

NASA Astrophysics Data System (ADS)

Galloy, M. D.; Fillmore, D.

2014-12-01

SatelliteDL is an IDL toolkit for the analysis of satellite Earth observations from a diverse set of platforms and sensors. The core function of the toolkit is the spatial and temporal alignment of satellite swath and geostationary data. The design features an abstraction layer that allows for easy inclusion of new datasets in a modular way. Our overarching objective is to create utilities that automate the mundane aspects of satellite data analysis, are extensible and maintainable, and do not place limitations on the analysis itself. IDL has a powerful suite of statistical and visualization tools that can be used in conjunction with SatelliteDL. Toward this end we have constructed SatelliteDL to include (1) HTML and LaTeX API document generation,(2) a unit test framework,(3) automatic message and error logs,(4) HTML and LaTeX plot and table generation, and(5) several real world examples with bundled datasets available for download. For ease of use, datasets, variables and optional workflows may be specified in a flexible format configuration file. Configuration statements may specify, for example, a region and date range, and the creation of images, plots and statistical summary tables for a long list of variables. SatelliteDL enforces data provenance; all data should be traceable and reproducible. The output NetCDF file metadata holds a complete history of the original datasets and their transformations, and a method exists to reconstruct a configuration file from this information. Release 0.1.0 distributes with ingest methods for GOES, MODIS, VIIRS and CERES radiance data (L1) as well as select 2D atmosphere products (L2) such as aerosol and cloud (MODIS and VIIRS) and radiant flux (CERES). Future releases will provide ingest methods for ocean and land surface products, gridded and time averaged datasets (L3 Daily, Monthly and Yearly), and support for 3D products such as temperature and water vapor profiles. Emphasis will be on NPP Sensor, Environmental and Climate Data Records as they become available. To obtain SatelliteDL, please visit the project website at http://www.txcorp.com/SatelliteDL

Marine Debris and Plastic Source Reduction Toolkit

EPA Pesticide Factsheets

Many plastic food service ware items originate on college and university campuses—in cafeterias, snack rooms, cafés, and eateries with take-out dining options. This Campus Toolkit is a detailed “how to” guide for reducing plastic waste on college campuses.

77 FR 73023 - U.S. Environmental Solutions Toolkit

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-07

... officials and foreign end-users of environmental technologies that will outline U.S. [[Page 73024.... approaches to solving environmental problems and to U.S. companies that can export related technologies. The... DEPARTMENT OF COMMERCE International Trade Administration U.S. Environmental Solutions Toolkit...

THE EPANET PROGRAMMER'S TOOLKIT FOR ANALYSIS OF WATER DISTRIBUTION SYSTEMS

EPA Science Inventory

The EPANET Programmer's Toolkit is a collection of functions that helps simplify computer programming of water distribution network analyses. the functions can be used to read in a pipe network description file, modify selected component properties, run multiple hydraulic and wa...

Accuracy of Assessment of Eligibility for Early Medical Abortion by Community Health Workers in Ethiopia, India and South Africa.

PubMed

Johnston, Heidi Bart; Ganatra, Bela; Nguyen, My Huong; Habib, Ndema; Afework, Mesganaw Fantahun; Harries, Jane; Iyengar, Kirti; Moodley, Jennifer; Lema, Hailu Yeneneh; Constant, Deborah; Sen, Swapnaleen

2016-01-01

To assess the accuracy of assessment of eligibility for early medical abortion by community health workers using a simple checklist toolkit. Diagnostic accuracy study. Ethiopia, India and South Africa. Two hundred seventeen women in Ethiopia, 258 in India and 236 in South Africa were enrolled into the study. A checklist toolkit to determine eligibility for early medical abortion was validated by comparing results of clinician and community health worker assessment of eligibility using the checklist toolkit with the reference standard exam. Accuracy was over 90% and the negative likelihood ratio <0.1 at all three sites when used by clinician assessors. Positive likelihood ratios were 4.3 in Ethiopia, 5.8 in India and 6.3 in South Africa. When used by community health workers the overall accuracy of the toolkit was 92% in Ethiopia, 80% in India and 77% in South Africa negative likelihood ratios were 0.08 in Ethiopia, 0.25 in India and 0.22 in South Africa and positive likelihood ratios were 5.9 in Ethiopia and 2.0 in India and South Africa. The checklist toolkit, as used by clinicians, was excellent at ruling out participants who were not eligible, and moderately effective at ruling in participants who were eligible for medical abortion. Results were promising when used by community health workers particularly in Ethiopia where they had more prior experience with use of diagnostic aids and longer professional training. The checklist toolkit assessments resulted in some participants being wrongly assessed as eligible for medical abortion which is an area of concern. Further research is needed to streamline the components of the tool, explore optimal duration and content of training for community health workers, and test feasibility and acceptability.

An evaluation of a toolkit for the early detection, management, and control of carbapenemase-producing Enterobacteriaceae: a survey of acute hospital trusts in England.

PubMed

Coope, C M; Verlander, N Q; Schneider, A; Hopkins, S; Welfare, W; Johnson, A P; Patel, B; Oliver, I

2018-03-09

Following hospital outbreaks of carbapenemase-producing Enterobacteriaceae (CPE), Public Health England published a toolkit in December 2013 to promote the early detection, management, and control of CPE colonization and infection in acute hospital settings. To examine awareness, uptake, implementation and usefulness of the CPE toolkit and identify potential barriers and facilitators to its adoption in order to inform future guidance. A cross-sectional survey of National Health Service (NHS) acute trusts was conducted in May 2016. Descriptive analysis and multivariable regression models were conducted, and narrative responses were analysed thematically and informed using behaviour change theory. Most (92%) acute trusts had a written CPE plan. Fewer (75%) reported consistent compliance with screening and isolation of CPE risk patients. Lower prioritization and weaker senior management support for CPE prevention were associated with poorer compliance. Awareness of the CPE toolkit was high and all trusts with patients infected or colonized with CPE had used the toolkit either as provided (32%), or to inform (65%) their own local CPE plan. Despite this, many respondents (80%) did not believe that the CPE toolkit guidance offered an effective means to prevent CPE or was practical to follow. CPE prevention and control requires robust IPC measures. Successful implementation can be hindered by a complex set of factors related to their practical execution, insufficient resources and a lack of confidence in the effectiveness of the guidance. Future CPE guidance would benefit from substantive user involvement, processes for ongoing feedback, and regular guidance updates. Copyright © 2018 The Healthcare Infection Society. All rights reserved.

A randomized controlled trial to test the efficacy of the SCI Get Fit Toolkit on leisure-time physical activity behaviour and social-cognitive processes in adults with spinal cord injury.

PubMed

Arbour-Nicitopoulos, Kelly P; Sweet, Shane N; Lamontagne, Marie-Eve; Ginis, Kathleen A Martin; Jeske, Samantha; Routhier, François; Latimer-Cheung, Amy E

2017-01-01

Single blind, two-group randomized controlled trial. To evaluate the efficacy of the SCI Get Fit Toolkit delivered online on theoretical constructs and moderate-to-vigorous physical activity (MVPA) among adults with SCI. Ontario and Quebec, Canada. Inactive, English- and French-speaking Canadian adults with traumatic SCI with Internet access, and no self-reported cognitive or memory impairments. Participants ( N =90 M age =48.12±11.29 years; 79% male) were randomized to view the SCI Get Fit Toolkit or the Physical Activity Guidelines for adults with SCI (PAG-SCI) online. Primary (intentions) and secondary (outcome expectancies, self-efficacy, planning and MVPA behaviour) outcomes were assessed over a 1-month period. Of the 90 participants randomized, 77 were included in the analyses. Participants viewed the experimental stimuli only briefly, reading the 4-page toolkit for approximately 2.5 min longer than the 1-page guideline document. No condition effects were found for intentions, outcome expectancies, self-efficacy, and planning (ΔR 2 ⩽0.03). Individuals in the toolkit condition were more likely to participate in at least one bout of 20 min of MVPA behaviour at 1-week post-intervention compared to individuals in the guidelines condition (OR=3.54, 95% CI=0.95, 13.17). However, no differences were found when examining change in weekly minutes of MVPA or comparing whether participants met the PAG-SCI. No firm conclusions can be made regarding the impact of the SCI Get Fit Toolkit in comparison to the PAG-SCI on social cognitions and MVPA behaviour. The limited online access to this resource may partially explain these null findings.

Development and formative evaluation of the e-Health Implementation Toolkit (e-HIT).

PubMed

Murray, Elizabeth; May, Carl; Mair, Frances

2010-10-18

The use of Information and Communication Technology (ICT) or e-Health is seen as essential for a modern, cost-effective health service. However, there are well documented problems with implementation of e-Health initiatives, despite the existence of a great deal of research into how best to implement e-Health (an example of the gap between research and practice). This paper reports on the development and formative evaluation of an e-Health Implementation Toolkit (e-HIT) which aims to summarise and synthesise new and existing research on implementation of e-Health initiatives, and present it to senior managers in a user-friendly format. The content of the e-HIT was derived by combining data from a systematic review of reviews of barriers and facilitators to implementation of e-Health initiatives with qualitative data derived from interviews of "implementers", that is people who had been charged with implementing an e-Health initiative. These data were summarised, synthesised and combined with the constructs from the Normalisation Process Model. The software for the toolkit was developed by a commercial company (RocketScience). Formative evaluation was undertaken by obtaining user feedback. There are three components to the toolkit--a section on background and instructions for use aimed at novice users; the toolkit itself; and the report generated by completing the toolkit. It is available to download from http://www.ucl.ac.uk/pcph/research/ehealth/documents/e-HIT.xls. The e-HIT shows potential as a tool for enhancing future e-Health implementations. Further work is needed to make it fully web-enabled, and to determine its predictive potential for future implementations.

Development and formative evaluation of the e-Health Implementation Toolkit (e-HIT)

PubMed Central

2010-01-01

Background The use of Information and Communication Technology (ICT) or e-Health is seen as essential for a modern, cost-effective health service. However, there are well documented problems with implementation of e-Health initiatives, despite the existence of a great deal of research into how best to implement e-Health (an example of the gap between research and practice). This paper reports on the development and formative evaluation of an e-Health Implementation Toolkit (e-HIT) which aims to summarise and synthesise new and existing research on implementation of e-Health initiatives, and present it to senior managers in a user-friendly format. Results The content of the e-HIT was derived by combining data from a systematic review of reviews of barriers and facilitators to implementation of e-Health initiatives with qualitative data derived from interviews of "implementers", that is people who had been charged with implementing an e-Health initiative. These data were summarised, synthesised and combined with the constructs from the Normalisation Process Model. The software for the toolkit was developed by a commercial company (RocketScience). Formative evaluation was undertaken by obtaining user feedback. There are three components to the toolkit - a section on background and instructions for use aimed at novice users; the toolkit itself; and the report generated by completing the toolkit. It is available to download from http://www.ucl.ac.uk/pcph/research/ehealth/documents/e-HIT.xls Conclusions The e-HIT shows potential as a tool for enhancing future e-Health implementations. Further work is needed to make it fully web-enabled, and to determine its predictive potential for future implementations. PMID:20955594

PAGANI Toolkit: Parallel graph-theoretical analysis package for brain network big data.

PubMed

Du, Haixiao; Xia, Mingrui; Zhao, Kang; Liao, Xuhong; Yang, Huazhong; Wang, Yu; He, Yong

2018-05-01

The recent collection of unprecedented quantities of neuroimaging data with high spatial resolution has led to brain network big data. However, a toolkit for fast and scalable computational solutions is still lacking. Here, we developed the PArallel Graph-theoretical ANalysIs (PAGANI) Toolkit based on a hybrid central processing unit-graphics processing unit (CPU-GPU) framework with a graphical user interface to facilitate the mapping and characterization of high-resolution brain networks. Specifically, the toolkit provides flexible parameters for users to customize computations of graph metrics in brain network analyses. As an empirical example, the PAGANI Toolkit was applied to individual voxel-based brain networks with ∼200,000 nodes that were derived from a resting-state fMRI dataset of 624 healthy young adults from the Human Connectome Project. Using a personal computer, this toolbox completed all computations in ∼27 h for one subject, which is markedly less than the 118 h required with a single-thread implementation. The voxel-based functional brain networks exhibited prominent small-world characteristics and densely connected hubs, which were mainly located in the medial and lateral fronto-parietal cortices. Moreover, the female group had significantly higher modularity and nodal betweenness centrality mainly in the medial/lateral fronto-parietal and occipital cortices than the male group. Significant correlations between the intelligence quotient and nodal metrics were also observed in several frontal regions. Collectively, the PAGANI Toolkit shows high computational performance and good scalability for analyzing connectome big data and provides a friendly interface without the complicated configuration of computing environments, thereby facilitating high-resolution connectomics research in health and disease. © 2018 Wiley Periodicals, Inc.

Keep It Sacred | National Native Network

Science.gov Websites

Detection Health Care Coverage Get Involved Resources NNN Webinar Archive Newsletter Archive Podcasts Cancer Guide Tribal Public Health Data Toolkits Smoke-Free Policy Toolkit Success Stories Resource Library Colorectal Cancer Diabetes Fact Sheets & Contact General Health Problems & Cancers General State

Literacy Toolkit

ERIC Educational Resources Information Center

Center for Best Practices in Early Childhood Education, 2005

2005-01-01

The toolkit contains print and electronic resources, including (1) "eMERGing Literacy and Technology: Working Together", A 492 page curriculum guide; (2) "LitTECH Interactive Presents: The Beginning of Literacy", a DVD that provides and overview linking technology to the concepts of emerging literacy; (3) "Your Preschool Classroom Computer Center:…

A Software Toolkit to Study Systematic Uncertainties of the Physics Models of the Geant4 Simulation Package

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

Genser, Krzysztof; Hatcher, Robert; Perdue, Gabriel

2016-11-10

The Geant4 toolkit is used to model interactions between particles and matter. Geant4 employs a set of validated physics models that span a wide range of interaction energies. These models are tuned to cover a large variety of possible applications. This raises the critical question of what uncertainties are associated with the Geant4 physics model, or group of models, involved in a simulation project. To address the challenge, we have designed and implemented a comprehen- sive, modular, user-friendly software toolkit that allows the variation of one or more parameters of one or more Geant4 physics models involved in simulation studies.more » It also enables analysis of multiple variants of the resulting physics observables of interest in order to estimate the uncertain- ties associated with the simulation model choices. Key functionalities of the toolkit are presented in this paper and are illustrated with selected results.« less

Toolkit for US colleges/schools of pharmacy to prepare learners for careers in academia.

PubMed

Haines, Seena L; Summa, Maria A; Peeters, Michael J; Dy-Boarman, Eliza A; Boyle, Jaclyn A; Clifford, Kalin M; Willson, Megan N

2017-09-01

The objective of this article is to provide an academic toolkit for use by colleges/schools of pharmacy to prepare student pharmacists/residents for academic careers. Through the American Association of Colleges of Pharmac (AACP) Section of Pharmacy Practice, the Student Resident Engagement Task Force (SRETF) collated teaching materials used by colleges/schools of pharmacy from a previously reported national survey. The SRETF developed a toolkit for student pharmacists/residents interested in academic pharmacy. Eighteen institutions provided materials; five provided materials describing didactic coursework; over fifteen provided materials for an academia-focused Advanced Pharmacy Practice Experiences (APPE), while one provided materials for an APPE teaching-research elective. SRETF members created a syllabus template and sample lesson plan by integrating submitted resources. Submissions still needed to complete the toolkit include examples of curricular tracks and certificate programs. Pharmacy faculty vacancies still exist in pharmacy education. Engaging student pharmacists/residents about academia pillars of teaching, scholarship and service is critical for the future success of the academy. Published by Elsevier Inc.

Hydrogen quantitative risk assessment workshop proceedings.

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

Groth, Katrina M.; Harris, Aaron P.

2013-09-01

The Quantitative Risk Assessment (QRA) Toolkit Introduction Workshop was held at Energetics on June 11-12. The workshop was co-hosted by Sandia National Laboratories (Sandia) and HySafe, the International Association for Hydrogen Safety. The objective of the workshop was twofold: (1) Present a hydrogen-specific methodology and toolkit (currently under development) for conducting QRA to support the development of codes and standards and safety assessments of hydrogen-fueled vehicles and fueling stations, and (2) Obtain feedback on the needs of early-stage users (hydrogen as well as potential leveraging for Compressed Natural Gas [CNG], and Liquefied Natural Gas [LNG]) and set priorities for %E2%80%9CVersionmore » 1%E2%80%9D of the toolkit in the context of the commercial evolution of hydrogen fuel cell electric vehicles (FCEV). The workshop consisted of an introduction and three technical sessions: Risk Informed Development and Approach; CNG/LNG Applications; and Introduction of a Hydrogen Specific QRA Toolkit.« less

Assessing Coverage of Population-Based and Targeted Fortification Programs with the Use of the Fortification Assessment Coverage Toolkit (FACT): Background, Toolkit Development, and Supplement Overview.

PubMed

Friesen, Valerie M; Aaron, Grant J; Myatt, Mark; Neufeld, Lynnette M

2017-05-01

Food fortification is a widely used approach to increase micronutrient intake in the diet. High coverage is essential for achieving impact. Data on coverage is limited in many countries, and tools to assess coverage of fortification programs have not been standardized. In 2013, the Global Alliance for Improved Nutrition developed the Fortification Assessment Coverage Toolkit (FACT) to carry out coverage assessments in both population-based (i.e., staple foods and/or condiments) and targeted (e.g., infant and young child) fortification programs. The toolkit was designed to generate evidence on program coverage and the use of fortified foods to provide timely and programmatically relevant information for decision making. This supplement presents results from FACT surveys that assessed the coverage of population-based and targeted food fortification programs across 14 countries. It then discusses the policy and program implications of the findings for the potential for impact and program improvement.

DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in head and neck cancer research

PubMed Central

Clunie, David; Ulrich, Ethan; Bauer, Christian; Wahle, Andreas; Brown, Bartley; Onken, Michael; Riesmeier, Jörg; Pieper, Steve; Kikinis, Ron; Buatti, John; Beichel, Reinhard R.

2016-01-01

Background. Imaging biomarkers hold tremendous promise for precision medicine clinical applications. Development of such biomarkers relies heavily on image post-processing tools for automated image quantitation. Their deployment in the context of clinical research necessitates interoperability with the clinical systems. Comparison with the established outcomes and evaluation tasks motivate integration of the clinical and imaging data, and the use of standardized approaches to support annotation and sharing of the analysis results and semantics. We developed the methodology and tools to support these tasks in Positron Emission Tomography and Computed Tomography (PET/CT) quantitative imaging (QI) biomarker development applied to head and neck cancer (HNC) treatment response assessment, using the Digital Imaging and Communications in Medicine (DICOM®) international standard and free open-source software. Methods. Quantitative analysis of PET/CT imaging data collected on patients undergoing treatment for HNC was conducted. Processing steps included Standardized Uptake Value (SUV) normalization of the images, segmentation of the tumor using manual and semi-automatic approaches, automatic segmentation of the reference regions, and extraction of the volumetric segmentation-based measurements. Suitable components of the DICOM standard were identified to model the various types of data produced by the analysis. A developer toolkit of conversion routines and an Application Programming Interface (API) were contributed and applied to create a standards-based representation of the data. Results. DICOM Real World Value Mapping, Segmentation and Structured Reporting objects were utilized for standards-compliant representation of the PET/CT QI analysis results and relevant clinical data. A number of correction proposals to the standard were developed. The open-source DICOM toolkit (DCMTK) was improved to simplify the task of DICOM encoding by introducing new API abstractions. Conversion and visualization tools utilizing this toolkit were developed. The encoded objects were validated for consistency and interoperability. The resulting dataset was deposited in the QIN-HEADNECK collection of The Cancer Imaging Archive (TCIA). Supporting tools for data analysis and DICOM conversion were made available as free open-source software. Discussion. We presented a detailed investigation of the development and application of the DICOM model, as well as the supporting open-source tools and toolkits, to accommodate representation of the research data in QI biomarker development. We demonstrated that the DICOM standard can be used to represent the types of data relevant in HNC QI biomarker development, and encode their complex relationships. The resulting annotated objects are amenable to data mining applications, and are interoperable with a variety of systems that support the DICOM standard. PMID:27257542

Perspectives of healthcare providers and HIV-affected individuals and couples during the development of a Safer Conception Counseling Toolkit in Kenya: stigma, fears, and recommendations for the delivery of services.

PubMed

Mmeje, Okeoma; Njoroge, Betty; Akama, Eliud; Leddy, Anna; Breitnauer, Brooke; Darbes, Lynae; Brown, Joelle

2016-01-01

Reproduction is important to many HIV-affected individuals and couples and healthcare providers (HCPs) are responsible for providing resources to help them safely conceive while minimizing the risk of sexual and perinatal HIV transmission. In order to fulfill their reproductive goals, HIV-affected individuals and their partners need access to information regarding safer methods of conception. The objective of this qualitative study was to develop a Safer Conception Counseling Toolkit that can be used to train HCPs and counsel HIV-affected individuals and couples in HIV care and treatment clinics in Kenya. We conducted a two-phased qualitative study among HCPs and HIV-affected individuals and couples from eight HIV care and treatment sites in Kisumu, Kenya. We conducted in-depth interviews (IDIs) and focus group discussions (FGDs) to assess the perspectives of HCPs and HIV-affected individuals and couples in order to develop and refine the content of the Toolkit. Subsequently, IDIs were conducted among HCPs who were trained using the Toolkit and FGDs among HIV-affected individuals and couples who were counseled with the Toolkit. HIV-related stigma, fears, and recommendations for delivery of safer conception counseling were assessed during the discussions. One hundred and six individuals participated in FGDs and IDIs; 29 HCPs, 49 HIV-affected women and men, and 14 HIV-serodiscordant couples. Participants indicated that a safer conception counseling and training program for HCPs is needed and that routine provision of safer conception counseling may promote maternal and child health by enhancing reproductive autonomy among HIV-affected couples. They also reported that the Toolkit may help dispel the stigma and fears associated with reproduction in HIV-affected couples, while supporting them in achieving their reproductive goals. Additional research is needed to evaluate the Safer Conception Toolkit in order to support its implementation and use in HIV care and treatment programs in Kenya and other HIV endemic regions of sub-Saharan Africa.

WIND Toolkit Offshore Summary Dataset

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

Draxl, Caroline; Musial, Walt; Scott, George

This dataset contains summary statistics for offshore wind resources for the continental United States derived from the Wind Integration National Datatset (WIND) Toolkit. These data are available in two formats: GDB - Compressed geodatabases containing statistical summaries aligned with lease blocks (aliquots) stored in a GIS format. These data are partitioned into Pacific, Atlantic, and Gulf resource regions. HDF5 - Statistical summaries of all points in the offshore Pacific, Atlantic, and Gulf offshore regions. These data are located on the original WIND Toolkit grid and have not been reassigned or downsampled to lease blocks. These data were developed under contractmore » by NREL for the Bureau of Oceanic Energy Management (BOEM).« less

Land surface Verification Toolkit (LVT)

NASA Technical Reports Server (NTRS)

Kumar, Sujay V.

2017-01-01

LVT is a framework developed to provide an automated, consolidated environment for systematic land surface model evaluation Includes support for a range of in-situ, remote-sensing and other model and reanalysis products. Supports the analysis of outputs from various LIS subsystems, including LIS-DA, LIS-OPT, LIS-UE. Note: The Land Information System Verification Toolkit (LVT) is a NASA software tool designed to enable the evaluation, analysis and comparison of outputs generated by the Land Information System (LIS). The LVT software is released under the terms and conditions of the NASA Open Source Agreement (NOSA) Version 1.1 or later. Land Information System Verification Toolkit (LVT) NOSA.

An Industrial Physics Toolkit

NASA Astrophysics Data System (ADS)

Cummings, Bill

2004-03-01

Physicists possess many skills highly valued in industrial companies. However, with the exception of a decreasing number of positions in long range research at large companies, job openings in industry rarely say "Physicist Required." One key to a successful industrial career is to know what subset of your physics skills is most highly valued by a given industry and to continue to build these skills while working. This combination of skills from both academic and industrial experience becomes your "Industrial Physics Toolkit" and is a transferable resource when you change positions or companies. This presentation will describe how one builds and sells your own "Industrial Physics Toolkit" using concrete examples from the speaker's industrial experience.

RAPID Toolkit Creates Smooth Flow Toward New Projects

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

Levine, Aaron; Young, Katherine

2016-07-01

Uncertainty about the duration and outcome of the permitting process has historically been seen as a deterrent to investment in renewable energy projects, including new hydropower projects. What if the process were clearer, smoother, faster? That's the purpose of the Regulatory and Permitting Information Desktop (RAPID) Toolkit, developed by the National Renewable Energy Laboratory (NREL) with funding from the U.S. Department of Energy (DOE) Office of Energy Efficiency and Renewable Energy and the Western Governors' Association. Now, the RAPID Toolkit is being expanded to include information about developing and permitting hydropower projects, with initial outreach and information gathering occurring duringmore » 2015.« less

Open source tools and toolkits for bioinformatics: significance, and where are we?

PubMed

Stajich, Jason E; Lapp, Hilmar

2006-09-01

This review summarizes important work in open-source bioinformatics software that has occurred over the past couple of years. The survey is intended to illustrate how programs and toolkits whose source code has been developed or released under an Open Source license have changed informatics-heavy areas of life science research. Rather than creating a comprehensive list of all tools developed over the last 2-3 years, we use a few selected projects encompassing toolkit libraries, analysis tools, data analysis environments and interoperability standards to show how freely available and modifiable open-source software can serve as the foundation for building important applications, analysis workflows and resources.

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.

A Toolkit to Implement Graduate Attributes in Geography Curricula

ERIC Educational Resources Information Center

Spronken-Smith, Rachel; McLean, Angela; Smith, Nell; Bond, Carol; Jenkins, Martin; Marshall, Stephen; Frielick, Stanley

2016-01-01

This article uses findings from a project on engagement with graduate outcomes across higher education institutions in New Zealand to produce a toolkit for implementing graduate attributes in geography curricula. Key facets include strong leadership; academic developers to facilitate conversations about graduate attributes and teaching towards…

Developments in Geometric Metadata and Tools at the PDS Ring-Moon Systems Node

NASA Astrophysics Data System (ADS)

Showalter, M. R.; Ballard, L.; French, R. S.; Gordon, M. K.; Tiscareno, M. S.

2018-04-01

Object-Oriented Python/SPICE (OOPS) is an overlay on the SPICE toolkit that vastly simplifies and speeds up geometry calculations for planetary data products. This toolkit is the basis for much of the development at the PDS Ring-Moon Systems Node.

Teacher Quality Toolkit. 2nd Edition

ERIC Educational Resources Information Center

Lauer, Patricia A.; Dean, Ceri B.; Martin-Glenn, Mya L.; Asensio, Margaret L.

2005-01-01

The Teacher Quality Toolkit addresses the continuum of teacher learning by providing tools that can be used to improve both preservice, and inservice teacher education. Each chapter provides self assessment tools that can guide progress toward improved teacher quality and describes resources for designing exemplary programs and practices. Chapters…

WHU at TREC KBA Vital Filtering Track 2014

DTIC Science & Technology

2014-11-01

view the problem as a classification problem and use Stanford NLP Toolkit to extract necessary information. Various kinds of features are leveraged to...profile of an entity. Our approach is to view the problem as a classification problem and use Stanford NLP Toolkit to extract necessary information

Basic Internet Software Toolkit.

ERIC Educational Resources Information Center

Buchanan, Larry

1998-01-01

Once schools are connected to the Internet, the next step is getting network workstations configured for Internet access. This article describes a basic toolkit comprising software currently available on the Internet for free or modest cost. Lists URLs for Web browser, Telnet, FTP, file decompression, portable document format (PDF) reader,…

Field trials of a novel toolkit for evaluating 'intangible' values-related dimensions of projects.

PubMed

Burford, Gemma; Velasco, Ismael; Janoušková, Svatava; Zahradnik, Martin; Hak, Tomas; Podger, Dimity; Piggot, Georgia; Harder, Marie K

2013-02-01

A novel toolkit has been developed, using an original approach to develop its components, for the purpose of evaluating 'soft' outcomes and processes that have previously been generally considered 'intangible': those which are specifically values based. This represents a step-wise, significant, change in provision for the assessment of values-based achievements that are of absolutely key importance to most civil society organisations (CSOs) and values-based businesses, and fills a known gap in evaluation practice. In this paper, we demonstrate the significance and rigour of the toolkit by presenting an evaluation of it in three diverse scenarios where different CSOs use it to co-evaluate locally relevant outcomes and processes to obtain results which are both meaningful to them and potentially comparable across organisations. A key strength of the toolkit is its original use of a prior generated, peer-elicited 'menu' of values-based indicators which provides a framework for user CSOs to localise. Principles of participatory, process-based and utilisation-focused evaluation are embedded in this toolkit and shown to be critical to its success, achieving high face-validity and wide applicability. The emerging contribution of this next-generation evaluation tool to other fields, such as environmental values, development and environmental sustainable development, shared values, business, education and organisational change is outlined. Copyright © 2012 Elsevier Ltd. All rights reserved.

Practical computational toolkits for dendrimers and dendrons structure design.

PubMed

Martinho, Nuno; Silva, Liana C; Florindo, Helena F; Brocchini, Steve; Barata, Teresa; Zloh, Mire

2017-09-01

Dendrimers and dendrons offer an excellent platform for developing novel drug delivery systems and medicines. The rational design and further development of these repetitively branched systems are restricted by difficulties in scalable synthesis and structural determination, which can be overcome by judicious use of molecular modelling and molecular simulations. A major difficulty to utilise in silico studies to design dendrimers lies in the laborious generation of their structures. Current modelling tools utilise automated assembly of simpler dendrimers or the inefficient manual assembly of monomer precursors to generate more complicated dendrimer structures. Herein we describe two novel graphical user interface toolkits written in Python that provide an improved degree of automation for rapid assembly of dendrimers and generation of their 2D and 3D structures. Our first toolkit uses the RDkit library, SMILES nomenclature of monomers and SMARTS reaction nomenclature to generate SMILES and mol files of dendrimers without 3D coordinates. These files are used for simple graphical representations and storing their structures in databases. The second toolkit assembles complex topology dendrimers from monomers to construct 3D dendrimer structures to be used as starting points for simulation using existing and widely available software and force fields. Both tools were validated for ease-of-use to prototype dendrimer structure and the second toolkit was especially relevant for dendrimers of high complexity and size.

Practical computational toolkits for dendrimers and dendrons structure design

NASA Astrophysics Data System (ADS)

Martinho, Nuno; Silva, Liana C.; Florindo, Helena F.; Brocchini, Steve; Barata, Teresa; Zloh, Mire

2017-09-01

Dendrimers and dendrons offer an excellent platform for developing novel drug delivery systems and medicines. The rational design and further development of these repetitively branched systems are restricted by difficulties in scalable synthesis and structural determination, which can be overcome by judicious use of molecular modelling and molecular simulations. A major difficulty to utilise in silico studies to design dendrimers lies in the laborious generation of their structures. Current modelling tools utilise automated assembly of simpler dendrimers or the inefficient manual assembly of monomer precursors to generate more complicated dendrimer structures. Herein we describe two novel graphical user interface toolkits written in Python that provide an improved degree of automation for rapid assembly of dendrimers and generation of their 2D and 3D structures. Our first toolkit uses the RDkit library, SMILES nomenclature of monomers and SMARTS reaction nomenclature to generate SMILES and mol files of dendrimers without 3D coordinates. These files are used for simple graphical representations and storing their structures in databases. The second toolkit assembles complex topology dendrimers from monomers to construct 3D dendrimer structures to be used as starting points for simulation using existing and widely available software and force fields. Both tools were validated for ease-of-use to prototype dendrimer structure and the second toolkit was especially relevant for dendrimers of high complexity and size.

The ProteoRed MIAPE web toolkit: A User-friendly Framework to Connect and Share Proteomics Standards*

PubMed Central

Medina-Aunon, J. Alberto; Martínez-Bartolomé, Salvador; López-García, Miguel A.; Salazar, Emilio; Navajas, Rosana; Jones, Andrew R.; Paradela, Alberto; Albar, Juan P.

2011-01-01

The development of the HUPO-PSI's (Proteomics Standards Initiative) standard data formats and MIAPE (Minimum Information About a Proteomics Experiment) guidelines should improve proteomics data sharing within the scientific community. Proteomics journals have encouraged the use of these standards and guidelines to improve the quality of experimental reporting and ease the evaluation and publication of manuscripts. However, there is an evident lack of bioinformatics tools specifically designed to create and edit standard file formats and reports, or embed them within proteomics workflows. In this article, we describe a new web-based software suite (The ProteoRed MIAPE web toolkit) that performs several complementary roles related to proteomic data standards. First, it can verify that the reports fulfill the minimum information requirements of the corresponding MIAPE modules, highlighting inconsistencies or missing information. Second, the toolkit can convert several XML-based data standards directly into human readable MIAPE reports stored within the ProteoRed MIAPE repository. Finally, it can also perform the reverse operation, allowing users to export from MIAPE reports into XML files for computational processing, data sharing, or public database submission. The toolkit is thus the first application capable of automatically linking the PSI's MIAPE modules with the corresponding XML data exchange standards, enabling bidirectional conversions. This toolkit is freely available at http://www.proteored.org/MIAPE/. PMID:21983993

The Liquid Argon Software Toolkit (LArSoft): Goals, Status and Plan

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

Pordes, Rush; Snider, Erica

LArSoft is a toolkit that provides a software infrastructure and algorithms for the simulation, reconstruction and analysis of events in Liquid Argon Time Projection Chambers (LArTPCs). It is used by the ArgoNeuT, LArIAT, MicroBooNE, DUNE (including 35ton prototype and ProtoDUNE) and SBND experiments. The LArSoft collaboration provides an environment for the development, use, and sharing of code across experiments. The ultimate goal is to develop fully automatic processes for reconstruction and analysis of LArTPC events. The toolkit is based on the art framework and has a well-defined architecture to interface to other packages, including to GEANT4 and GENIE simulation softwaremore » and the Pandora software development kit for pattern recognition. It is designed to facilitate and support the evolution of algorithms including their transition to new computing platforms. The development of the toolkit is driven by the scientific stakeholders involved. The core infrastructure includes standard definitions of types and constants, means to input experiment geometries as well as meta and event- data in several formats, and relevant general utilities. Examples of algorithms experiments have contributed to date are: photon-propagation; particle identification; hit finding, track finding and fitting; electromagnetic shower identification and reconstruction. We report on the status of the toolkit and plans for future work.« less

Organizational Context Matters: A Research Toolkit for Conducting Standardized Case Studies of Integrated Care Initiatives

PubMed Central

Grudniewicz, Agnes; Gray, Carolyn Steele; Wodchis, Walter P.; Carswell, Peter; Baker, G. Ross

2017-01-01

Introduction: The variable success of integrated care initiatives has led experts to recommend tailoring design and implementation to the organizational context. Yet, organizational contexts are rarely described, understood, or measured with sufficient depth and breadth in empirical studies or in practice. We thus lack knowledge of when and specifically how organizational contexts matter. To facilitate the accumulation of evidence, we developed a research toolkit for conducting case studies using standardized measures of the (inter-)organizational context for integrating care. Theory and Methods: We used a multi-method approach to develop the research toolkit: (1) development and validation of the Context and Capabilities for Integrating Care (CCIC) Framework, (2) identification, assessment, and selection of survey instruments, (3) development of document review methods, (4) development of interview guide resources, and (5) pilot testing of the document review guidelines, consolidated survey, and interview guide. Results: The toolkit provides a framework and measurement tools that examine 18 organizational and inter-organizational factors that affect the implementation and success of integrated care initiatives. Discussion and Conclusion: The toolkit can be used to characterize and compare organizational contexts across cases and enable comparison of results across studies. This information can enhance our understanding of the influence of organizational contexts, support the transfer of best practices, and help explain why some integrated care initiatives succeed and some fail. PMID:28970750

TiConverter: A training image converting tool for multiple-point geostatistics

NASA Astrophysics Data System (ADS)

Fadlelmula F., Mohamed M.; Killough, John; Fraim, Michael

2016-11-01

TiConverter is a tool developed to ease the application of multiple-point geostatistics whether by the open source Stanford Geostatistical Modeling Software (SGeMS) or other available commercial software. TiConverter has a user-friendly interface and it allows the conversion of 2D training images into numerical representations in four different file formats without the need for additional code writing. These are the ASCII (.txt), the geostatistical software library (GSLIB) (.txt), the Isatis (.dat), and the VTK formats. It performs the conversion based on the RGB color system. In addition, TiConverter offers several useful tools including image resizing, smoothing, and segmenting tools. The purpose of this study is to introduce the TiConverter, and to demonstrate its application and advantages with several examples from the literature.

ActiveSeismoPick3D - automatic first arrival determination for large active seismic arrays

NASA Astrophysics Data System (ADS)

Paffrath, Marcel; Küperkoch, Ludger; Wehling-Benatelli, Sebastian; Friederich, Wolfgang

2016-04-01

We developed a tool for automatic determination of first arrivals in active seismic data based on an approach, that utilises higher order statistics (HOS) and the Akaike information criterion (AIC), commonly used in seismology, but not in active seismics. Automatic picking is highly desirable in active seismics as the number of data provided by large seismic arrays rapidly exceeds of what an analyst can evaluate in a reasonable amount of time. To bring the functionality of automatic phase picking into the context of active data, the software package ActiveSeismoPick3D was developed in Python. It uses a modified algorithm for the determination of first arrivals which searches for the HOS maximum in unfiltered data. Additionally, it offers tools for manual quality control and postprocessing, e.g. various visualisation and repicking functionalities. For flexibility, the tool also includes methods for the preparation of geometry information of large seismic arrays and improved interfaces to the Fast Marching Tomography Package (FMTOMO), which can be used for the prediction of travel times and inversion for subsurface properties. Output files are generated in the VTK format, allowing the 3D visualization of e.g. the inversion results. As a test case, a data set consisting of 9216 traces from 64 shots was gathered, recorded at 144 receivers deployed in a regular 2D array of a size of 100 x 100 m. ActiveSeismoPick3D automatically checks the determined first arrivals by a dynamic signal to noise ratio threshold. From the data a 3D model of the subsurface was generated using the export functionality of the package and FMTOMO.

Automated Instrumentation, Monitoring and Visualization of PVM Programs Using AIMS

NASA Technical Reports Server (NTRS)

Mehra, Pankaj; VanVoorst, Brian; Yan, Jerry; Tucker, Deanne (Technical Monitor)

1994-01-01

We present views and analysis of the execution of several PVM codes for Computational Fluid Dynamics on a network of Sparcstations, including (a) NAS Parallel benchmarks CG and MG (White, Alund and Sunderam 1993); (b) a multi-partitioning algorithm for NAS Parallel Benchmark SP (Wijngaart 1993); and (c) an overset grid flowsolver (Smith 1993). These views and analysis were obtained using our Automated Instrumentation and Monitoring System (AIMS) version 3.0, a toolkit for debugging the performance of PVM programs. We will describe the architecture, operation and application of AIMS. The AIMS toolkit contains (a) Xinstrument, which can automatically instrument various computational and communication constructs in message-passing parallel programs; (b) Monitor, a library of run-time trace-collection routines; (c) VK (Visual Kernel), an execution-animation tool with source-code clickback; and (d) Tally, a tool for statistical analysis of execution profiles. Currently, Xinstrument can handle C and Fortran77 programs using PVM 3.2.x; Monitor has been implemented and tested on Sun 4 systems running SunOS 4.1.2; and VK uses X11R5 and Motif 1.2. Data and views obtained using AIMS clearly illustrate several characteristic features of executing parallel programs on networked workstations: (a) the impact of long message latencies; (b) the impact of multiprogramming overheads and associated load imbalance; (c) cache and virtual-memory effects; and (4significant skews between workstation clocks. Interestingly, AIMS can compensate for constant skew (zero drift) by calibrating the skew between a parent and its spawned children. In addition, AIMS' skew-compensation algorithm can adjust timestamps in a way that eliminates physically impossible communications (e.g., messages going backwards in time). Our current efforts are directed toward creating new views to explain the observed performance of PVM programs. Some of the features planned for the near future include: (a) ConfigView, showing the physical topology of the virtual machine, inferred using specially formatted IP (Internet Protocol) packets; and (b) LoadView, synchronous animation of PVM-program execution and resource-utilization patterns.

Understanding Disabilities in American Indian and Alaska Native Communities. Toolkit Guide.

ERIC Educational Resources Information Center

National Council on Disability, Washington, DC.

This "toolkit" document is intended to provide a culturally appropriate set of resources to address the unique political and legal concerns of people with disabilities in American Indian/Alaska Native (AI/AN) communities. It provides information on education, health, vocational rehabilitation (VR), independent living, model approaches, and…

Object Toolkit Version 4.2 Users Manual

DTIC Science & Technology

2014-10-31

48 Figure 39. Geocentric Orbit Dialog Box...Z Side at (0.44, -0.44, 1.46). ............................................ 114 Figure 133. Geocentric Orbit Dialog Box...building an object for MEM, Object Toolkit has an Orbit menu that allows the user to specify and edit a heliocentric or geocentric orbit. The dialog

Educating Globally Competent Citizens: A Toolkit. Second Edition

ERIC Educational Resources Information Center

Elliott-Gower, Steven; Falk, Dennis R.; Shapiro, Martin

2012-01-01

Educating Globally Competent Citizens, a product of AASCU's American Democracy Project and its Global Engagement Initiative, introduces readers to a set of global challenges facing society based on the Center for Strategic and International Studies' 7 Revolutions. The toolkit is designed to aid faculty in incorporating global challenges into new…

75 FR 53969 - Office of Community Services: Notice To Award an Expansion Supplement

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-02

... related to job creation and new initiatives that target careers in energy efficiency and other...; and (3) collects, develops, and disseminates resources related to job creation and careers related to... through professional consultations and peer assistance sessions; and online toolkit(s). The T/TA CAP will...

The Student Writing Toolkit: Enhancing Undergraduate Teaching of Scientific Writing in the Biological Sciences

ERIC Educational Resources Information Center

Dirrigl, Frank J., Jr.; Noe, Mark

2014-01-01

Teaching scientific writing in biology classes is challenging for both students and instructors. This article offers and reviews several useful "toolkit" items that improve student writing. These include sentence and paper-length templates, funnelling and compartmentalisation, and preparing compendiums of corrections. In addition,…

The Archivists' Toolkit: Another Step toward Streamlined Archival Processing

ERIC Educational Resources Information Center

Westbrook, Bradley D.; Mandell, Lee; Shepherd, Kelcy; Stevens, Brian; Varghese, Jason

2006-01-01

The Archivists' Toolkit is a software application currently in development and designed to support the creation and management of archival information. This article summarizes the development of the application, including some of the problems the application is designed to resolve. Primary emphasis is placed on describing the application's…

Healthy People 2010: Oral Health Toolkit

ERIC Educational Resources Information Center

Isman, Beverly

2007-01-01

The purpose of this Toolkit is to provide guidance, technical tools, and resources to help states, territories, tribes and communities develop and implement successful oral health components of Healthy People 2010 plans as well as other oral health plans. These plans are useful for: (1) promoting, implementing and tracking oral health objectives;…

Using Toolkits to Achieve STEM Enterprise Learning Outcomes

ERIC Educational Resources Information Center

Watts, Carys A.; Wray, Katie

2012-01-01

Purpose: The purpose of this paper is to evaluate the effectiveness of using several commercial tools in science, technology, engineering and maths (STEM) subjects for enterprise education at Newcastle University, UK. Design/methodology/approach: The paper provides an overview of existing toolkit use in higher education, before reviewing where and…

BAT - The Bayesian analysis toolkit

NASA Astrophysics Data System (ADS)

Caldwell, Allen; Kollár, Daniel; Kröninger, Kevin

2009-11-01

We describe the development of a new toolkit for data analysis. The analysis package is based on Bayes' Theorem, and is realized with the use of Markov Chain Monte Carlo. This gives access to the full posterior probability distribution. Parameter estimation, limit setting and uncertainty propagation are implemented in a straightforward manner.

A Toolkit for Teacher Engagement

ERIC Educational Resources Information Center

Grantmakers for Education, 2014

2014-01-01

Teachers are critical to the success of education grantmaking strategies, yet in talking with them we discovered that the world of philanthropy is often a mystery. GFE's Toolkit for Teacher Engagement aims to assist funders in authentically and effectively involving teachers in the education reform and innovation process. Built directly from the…

The Mentoring Toolkit 2.0: Resources for Developing Programs for Incarcerated Youth. Guide

ERIC Educational Resources Information Center

Zaugg, Nathan; Jarjoura, Roger

2017-01-01

"The Mentoring Toolkit 2.0: Resources for Developing Programs for Incarcerated Youth" provides information, program descriptions, and links to important resources that can assist juvenile correctional facilities and other organizations to design effective mentoring programs for neglected and delinquent youth, particularly those who are…

Making Schools the Model for Healthier Environments Toolkit: What It Is

ERIC Educational Resources Information Center

Robert Wood Johnson Foundation, 2012

2012-01-01

Healthy students perform better. Poor nutrition and inadequate physical activity can affect not only academic achievement, but also other factors such as absenteeism, classroom behavior, ability to concentrate, self-esteem, cognitive performance, and test scores. This toolkit provides information to help make schools the model for healthier…

Policy to Performance Toolkit: Transitioning Adults to Opportunity

ERIC Educational Resources Information Center

Alamprese, Judith A.; Limardo, Chrys

2012-01-01

The "Policy to Performance Toolkit" is designed to provide state adult education staff and key stakeholders with guidance and tools to use in developing, implementing, and monitoring state policies and their associated practices that support an effective state adult basic education (ABE) to postsecondary education and training transition…

Excellence in Teaching End-of-Life Care. A New Multimedia Toolkit for Nurse Educators.

ERIC Educational Resources Information Center

Wilkie, Diana J.; Judge, Kay M.; Wells, Marjorie J.; Berkley, Ila Meredith

2001-01-01

Describes a multimedia toolkit for teaching palliative care in nursing, which contains modules on end-of-life topics: comfort, connections, ethics, grief, impact, and well-being. Other contents include myths, definitions, pre- and postassessments, teaching materials, case studies, learning activities, and resources. (SK)

A Toolkit for Forward/Inverse Problems in Electrocardiography within the SCIRun Problem Solving Environment

PubMed Central

Burton, Brett M; Tate, Jess D; Erem, Burak; Swenson, Darrell J; Wang, Dafang F; Steffen, Michael; Brooks, Dana H; van Dam, Peter M; Macleod, Rob S

2012-01-01

Computational modeling in electrocardiography often requires the examination of cardiac forward and inverse problems in order to non-invasively analyze physiological events that are otherwise inaccessible or unethical to explore. The study of these models can be performed in the open-source SCIRun problem solving environment developed at the Center for Integrative Biomedical Computing (CIBC). A new toolkit within SCIRun provides researchers with essential frameworks for constructing and manipulating electrocardiographic forward and inverse models in a highly efficient and interactive way. The toolkit contains sample networks, tutorials and documentation which direct users through SCIRun-specific approaches in the assembly and execution of these specific problems. PMID:22254301

Knowledge information management toolkit and method

DOEpatents

Hempstead, Antoinette R.; Brown, Kenneth L.

2006-08-15

A system is provided for managing user entry and/or modification of knowledge information into a knowledge base file having an integrator support component and a data source access support component. The system includes processing circuitry, memory, a user interface, and a knowledge base toolkit. The memory communicates with the processing circuitry and is configured to store at least one knowledge base. The user interface communicates with the processing circuitry and is configured for user entry and/or modification of knowledge pieces within a knowledge base. The knowledge base toolkit is configured for converting knowledge in at least one knowledge base from a first knowledge base form into a second knowledge base form. A method is also provided.

Reusable Client-Side JavaScript Modules for Immersive Web-Based Real-Time Collaborative Neuroimage Visualization

PubMed Central

Bernal-Rusiel, Jorge L.; Rannou, Nicolas; Gollub, Randy L.; Pieper, Steve; Murphy, Shawn; Robertson, Richard; Grant, Patricia E.; Pienaar, Rudolph

2017-01-01

In this paper we present a web-based software solution to the problem of implementing real-time collaborative neuroimage visualization. In both clinical and research settings, simple and powerful access to imaging technologies across multiple devices is becoming increasingly useful. Prior technical solutions have used a server-side rendering and push-to-client model wherein only the server has the full image dataset. We propose a rich client solution in which each client has all the data and uses the Google Drive Realtime API for state synchronization. We have developed a small set of reusable client-side object-oriented JavaScript modules that make use of the XTK toolkit, a popular open-source JavaScript library also developed by our team, for the in-browser rendering and visualization of brain image volumes. Efficient realtime communication among the remote instances is achieved by using just a small JSON object, comprising a representation of the XTK image renderers' state, as the Google Drive Realtime collaborative data model. The developed open-source JavaScript modules have already been instantiated in a web-app called MedView, a distributed collaborative neuroimage visualization application that is delivered to the users over the web without requiring the installation of any extra software or browser plugin. This responsive application allows multiple physically distant physicians or researchers to cooperate in real time to reach a diagnosis or scientific conclusion. It also serves as a proof of concept for the capabilities of the presented technological solution. PMID:28507515

Using an Assistive Technology Toolkit to Promote Inclusion

ERIC Educational Resources Information Center

Judge, Sharon; Floyd, Kim; Jeffs, Tara

2008-01-01

Although the use of assistive technology for young children is increasing, the lack of awareness and the lack of training continue to act as major barriers to providers using assistive technology. This article describes an assistive technology toolkit designed for use with young children with disabilities that can be easily assembled and…

Roles of the Volunteer in Development: Toolkits for Building Capacity.

ERIC Educational Resources Information Center

Slater, Marsha; Allsman, Ava; Savage, Ron; Havens, Lani; Blohm, Judee; Raftery, Kate

This document, which was developed to assist Peace Corps volunteers and those responsible for training them, presents an introductory booklet and six toolkits for use in the training provided to and by volunteers involved in community development. All the materials emphasize long-term participatory approaches to sustainable development and a…

Building Management Information Systems to Coordinate Citywide Afterschool Programs: A Toolkit for Cities. Executive Summary

ERIC Educational Resources Information Center

Kingsley, Chris

2012-01-01

This executive summary describes highlights from the report, "Building Management Information Systems to Coordinate Citywide Afterschool Programs: A Toolkit for Cities." City-led efforts to build coordinated systems of afterschool programming are an important strategy for improving the health, safety and academic preparedness of children…

Build an Assistive Technology Toolkit

ERIC Educational Resources Information Center

Ahrens, Kelly

2011-01-01

Assistive technology (AT) by its very nature consists of a variety of personal and customized tools for multiple learning styles and physical challenges. The author not only encourages students, parents, and educators to advocate for AT services, she also wants them to go a step further and build their own AT toolkits that can instill independence…

College Access and Success for Students Experiencing Homelessness: A Toolkit for Educators and Service Providers

ERIC Educational Resources Information Center

Dukes, Christina

2013-01-01

This toolkit serves as a comprehensive resource on the issue of higher education access and success for homeless students, including information on understanding homeless students, assisting homeless students in choosing a school, helping homeless students pay for application-related expenses, assisting homeless students in finding financial aid…

Evaluating Teaching Development Activities in Higher Education: A Toolkit

ERIC Educational Resources Information Center

Kneale, Pauline; Winter, Jennie; Turner, Rebecca; Spowart, Lucy; Hughes, Jane; McKenna, Colleen; Muneer, Reema

2016-01-01

This toolkit is developed as a resource for providers of teaching-related continuing professional development (CPD) in higher education (HE). It focuses on capturing the longer-term value and impact of CPD for teachers and learners, and moving away from immediate satisfaction measures. It is informed by the literature on evaluating higher…

Building a "Motivation Toolkit" for Teaching Information Literacy.

ERIC Educational Resources Information Center

Moyer, Susan L.; Small, Ruth V.

2001-01-01

Discusses the need to motivate students to make information literacy programs successful and demonstrates how a middle school library media specialist used Small and Arnone's Motivation Overlay for Information Skills Instruction to build a set of customized toolkits to improve student research that includes the Big6[TM] approach to library and…

Toolkit Approach to Integrating Library Resources into the Learning Management System

ERIC Educational Resources Information Center

Black, Elizabeth L.

2008-01-01

As use of learning management systems (LMS) increases, it is essential that librarians are there. Ohio State University Libraries took a toolkit approach to integrate library content in the LMS to facilitate creative and flexible interactions between librarians, students and faculty in Ohio State University's large and decentralized academic…

Task Oriented Tools for Information Retrieval

ERIC Educational Resources Information Center

Yang, Peilin

2017-01-01

Information Retrieval (IR) is one of the most evolving research fields and has drawn extensive attention in recent years. Because of its empirical nature, the advance of the IR field is closely related to the development of various toolkits. While the traditional IR toolkit mainly provides a platform to evaluate the effectiveness of retrieval…

After-School Toolkit: Tips, Techniques and Templates for Improving Program Quality

ERIC Educational Resources Information Center

Gutierrez, Nora; Bradshaw, Molly; Furano, Kathryn

2008-01-01

This toolkit offers program managers a hands-on guide for implementing quality programming in the after-school hours. The kit includes tools and techniques that increased the quality of literacy programming and helped improve student reading gains in the Communities Organizing Resources to Advance Learning (CORAL) initiative of The James Irvine…

JGOMAS: New Approach to AI Teaching

ERIC Educational Resources Information Center

Barella, A.; Valero, S.; Carrascosa, C.

2009-01-01

This paper presents a new environment for teaching practical work in AI subjects. The main purpose of this environment is to make AI techniques more appealing to students and to facilitate the use of the toolkits which are currently widely used in research and development. This new environment has a toolkit for developing and executing agents,…

EMERGO: A Methodology and Toolkit for Developing Serious Games in Higher Education

ERIC Educational Resources Information Center

Nadolski, Rob J.; Hummel, Hans G. K.; van den Brink, Henk J.; Hoefakker, Ruud E.; Slootmaker, Aad; Kurvers, Hub J.; Storm, Jeroen

2008-01-01

Societal changes demand educators to apply new pedagogical approaches. Many educational stakeholders feel that serious games could play a key role in fulfilling this demand, and they lick their chops when looking at the booming industry of leisure games. However, current toolkits for developing leisure games show severe shortcomings when applied…

Starting from Scratch: Greening Your Game Day--The Collegiate Football Sustainable Materials Management Toolkit. Version 1.0

ERIC Educational Resources Information Center

Association for the Advancement of Sustainability in Higher Education, 2011

2011-01-01

The "Collegiate Football Sustainable Materials Management Toolkit" was researched by student interns in the Virginia Tech Office of Energy & Sustainability, developed in collaboration with the US EPA (US Environmental Protection Agency) and a national panel of technical experts from universities across the nation, and driven forward…

A Toolkit for Designing and Implementing Effective Title I Schoolwide Programs

ERIC Educational Resources Information Center

New, Wendy Jo; Rhines, Chris; Walter, Fran; Klekotka, Peggie

2005-01-01

This toolkit is designed to provide educational leaders with information, tools, resources, and practical examples to help schools to effectively implement Title I schoolwide programs. It is intended to serve as a useful resource for states, districts, and schools to use, along with other resources and technical support, to create or refine…

Ready, Set, Respect! GLSEN's Elementary School Toolkit

ERIC Educational Resources Information Center

Gay, Lesbian and Straight Education Network (GLSEN), 2012

2012-01-01

"Ready, Set, Respect!" provides a set of tools to help elementary school educators ensure that all students feel safe and respected and develop respectful attitudes and behaviors. It is not a program to be followed but instead is designed to help educators prepare themselves for teaching about and modeling respect. The toolkit responds to…

pypet: A Python Toolkit for Data Management of Parameter Explorations

PubMed Central

Meyer, Robert; Obermayer, Klaus

2016-01-01

pypet (Python parameter exploration toolkit) is a new multi-platform Python toolkit for managing numerical simulations. Sampling the space of model parameters is a key aspect of simulations and numerical experiments. pypet is designed to allow easy and arbitrary sampling of trajectories through a parameter space beyond simple grid searches. pypet collects and stores both simulation parameters and results in a single HDF5 file. This collective storage allows fast and convenient loading of data for further analyses. pypet provides various additional features such as multiprocessing and parallelization of simulations, dynamic loading of data, integration of git version control, and supervision of experiments via the electronic lab notebook Sumatra. pypet supports a rich set of data formats, including native Python types, Numpy and Scipy data, Pandas DataFrames, and BRIAN(2) quantities. Besides these formats, users can easily extend the toolkit to allow customized data types. pypet is a flexible tool suited for both short Python scripts and large scale projects. pypet's various features, especially the tight link between parameters and results, promote reproducible research in computational neuroscience and simulation-based disciplines. PMID:27610080

pypet: A Python Toolkit for Data Management of Parameter Explorations.

PubMed

Meyer, Robert; Obermayer, Klaus

2016-01-01

pypet (Python parameter exploration toolkit) is a new multi-platform Python toolkit for managing numerical simulations. Sampling the space of model parameters is a key aspect of simulations and numerical experiments. pypet is designed to allow easy and arbitrary sampling of trajectories through a parameter space beyond simple grid searches. pypet collects and stores both simulation parameters and results in a single HDF5 file. This collective storage allows fast and convenient loading of data for further analyses. pypet provides various additional features such as multiprocessing and parallelization of simulations, dynamic loading of data, integration of git version control, and supervision of experiments via the electronic lab notebook Sumatra. pypet supports a rich set of data formats, including native Python types, Numpy and Scipy data, Pandas DataFrames, and BRIAN(2) quantities. Besides these formats, users can easily extend the toolkit to allow customized data types. pypet is a flexible tool suited for both short Python scripts and large scale projects. pypet's various features, especially the tight link between parameters and results, promote reproducible research in computational neuroscience and simulation-based disciplines.