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.

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.

The design of an intelligent human-computer interface for the test, control and monitor system

NASA Technical Reports Server (NTRS)

Shoaff, William D.

1988-01-01

The graphical intelligence and assistance capabilities of a human-computer interface for the Test, Control, and Monitor System at Kennedy Space Center are explored. The report focuses on how a particular commercial off-the-shelf graphical software package, Data Views, can be used to produce tools that build widgets such as menus, text panels, graphs, icons, windows, and ultimately complete interfaces for monitoring data from an application; controlling an application by providing input data to it; and testing an application by both monitoring and controlling it. A complete set of tools for building interfaces is described in a manual for the TCMS toolkit. Simple tools create primitive widgets such as lines, rectangles and text strings. Intermediate level tools create pictographs from primitive widgets, and connect processes to either text strings or pictographs. Other tools create input objects; Data Views supports output objects directly, thus output objects are not considered. Finally, a set of utilities for executing, monitoring use, editing, and displaying the content of interfaces is included in the toolkit.

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...

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.

LogiKit - assisting complex logic specification and implementation for embedded control systems

NASA Astrophysics Data System (ADS)

Diglio, A.; Nicolodi, B.

2002-07-01

LogiKit provides an overall lifecycle solution. LogiKit is a powerful software engineering case toolkit for requirements specification, simulation and documentation. LogiKit also provides an automatic ADA software design, code and unit test generator.

A flooding induced station blackout analysis for a pressurized water reactor using the RISMC toolkit

DOE PAGES

Mandelli, Diego; Prescott, Steven; Smith, Curtis; ...

2015-05-17

In this paper we evaluate the impact of a power uprate on a pressurized water reactor (PWR) for a tsunami-induced flooding test case. This analysis is performed using the RISMC toolkit: the RELAP-7 and RAVEN codes. RELAP-7 is the new generation of system analysis codes that is responsible for simulating the thermal-hydraulic dynamics of PWR and boiling water reactor systems. RAVEN has two capabilities: to act as a controller of the RELAP-7 simulation (e.g., component/system activation) and to perform statistical analyses. In our case, the simulation of the flooding is performed by using an advanced smooth particle hydrodynamics code calledmore » NEUTRINO. The obtained results allow the user to investigate and quantify the impact of timing and sequencing of events on system safety. The impact of power uprate is determined in terms of both core damage probability and safety margins.« less

Multi Infrastructure Control and Optimization Toolkit, Resilient Design Module (MICOT-RDT), version 2.X

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

Bent, Russell; Nagarajan, Harsha; Yamangil, Emre

2016-06-24

MICOT is a tool for optimizing and controlling infrastructure systems. In includes modules for optimizing the operations of an infrastructure structure (for example optimal dispatch), designing infrastructure systems, restoring infrastructures systems, resiliency, preparing for natural disasters, interdicting networks, state estimation, sensor placement, and simulation of infrastructure systems. It implements algorithms developed at LANL that have been published in the academic community. This is a release of the of resilient design module of the MICOT.

THYME: Toolkit for Hybrid Modeling of Electric Power Systems

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

Nutaro Kalyan Perumalla, James Joseph

2011-01-01

THYME is an object oriented library for building models of wide area control and communications in electric power systems. This software is designed as a module to be used with existing open source simulators for discrete event systems in general and communication systems in particular. THYME consists of a typical model for simulating electro-mechanical transients (e.g., as are used in dynamic stability studies), data handling objects to work with CDF and PTI formatted power flow data, and sample models of discrete sensors and controllers.

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.

The Medical Imaging Interaction Toolkit: challenges and advances : 10 years of open-source development.

PubMed

Nolden, Marco; Zelzer, Sascha; Seitel, Alexander; Wald, Diana; Müller, Michael; Franz, Alfred M; Maleike, Daniel; Fangerau, Markus; Baumhauer, Matthias; Maier-Hein, Lena; Maier-Hein, Klaus H; Meinzer, Hans-Peter; Wolf, Ivo

2013-07-01

The Medical Imaging Interaction Toolkit (MITK) has been available as open-source software for almost 10 years now. In this period the requirements of software systems in the medical image processing domain have become increasingly complex. The aim of this paper is to show how MITK evolved into a software system that is able to cover all steps of a clinical workflow including data retrieval, image analysis, diagnosis, treatment planning, intervention support, and treatment control. MITK provides modularization and extensibility on different levels. In addition to the original toolkit, a module system, micro services for small, system-wide features, a service-oriented architecture based on the Open Services Gateway initiative (OSGi) standard, and an extensible and configurable application framework allow MITK to be used, extended and deployed as needed. A refined software process was implemented to deliver high-quality software, ease the fulfillment of regulatory requirements, and enable teamwork in mixed-competence teams. MITK has been applied by a worldwide community and integrated into a variety of solutions, either at the toolkit level or as an application framework with custom extensions. The MITK Workbench has been released as a highly extensible and customizable end-user application. Optional support for tool tracking, image-guided therapy, diffusion imaging as well as various external packages (e.g. CTK, DCMTK, OpenCV, SOFA, Python) is available. MITK has also been used in several FDA/CE-certified applications, which demonstrates the high-quality software and rigorous development process. MITK provides a versatile platform with a high degree of modularization and interoperability and is well suited to meet the challenging tasks of today's and tomorrow's clinically motivated research.

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.

Software Testbed for Developing and Evaluating Integrated Autonomous Systems

DTIC Science & Technology

2015-03-01

EUROPA planning system for plan generation. The adaptive controller executes the new plan, using augmented, hierarchical finite state machines to...using the Internet Communications Engine ( ICE ), an object-oriented toolkit for building distributed applications. TABLE OF CONTENTS 1...ANML model is translated into the New Domain Definition Language (NDDL) and sent to NASA???s EUROPA planning system for plan generation. The adaptive

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…

Scalable Deployment of Advanced Building Energy Management Systems

DTIC Science & Technology

2013-06-01

Building Automation and Control Network BDAS Building Data Acquisition System BEM building energy model BIM building information modeling BMS...A prototype toolkit to seamlessly and automatically transfer a Building Information Model ( BIM ) to a Building Energy Model (BEM) has been...circumvent the need to manually construct and maintain a detailed building energy simulation model . This detailed

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

Banding the world together; the global growth of control banding and qualitative occupational risk management.

PubMed

Zalk, David M; Heussen, Ga Henri

2011-12-01

Control Banding (CB) strategies to prevent work-related illness and injury for 2.5 billion workers without access to health and safety professionals has grown exponentially this last decade. CB originates from the pharmaceutical industry to control active pharmaceutical ingredients without a complete toxicological basis and therefore no occupational exposure limits. CB applications have broadened into chemicals in general - including new emerging risks like nanomaterials and recently into ergonomics and injury prevention. CB is an action-oriented qualitative risk assessment strategy offering solutions and control measures to users through "toolkits". Chemical CB toolkits are user-friendly approaches used to achieve workplace controls in the absence of firm toxicological and quantitative exposure information. The model (technical) validation of these toolkits is well described, however firm operational analyses (implementation aspects) are lacking. Consequentially, it is often not known if toolkit use leads to successful interventions at individual workplaces. This might lead to virtual safe workplaces without knowing if workers are truly protected. Upcoming international strategies from the World Health Organization Collaborating Centers request assistance in developing and evaluating action-oriented procedures for workplace risk assessment and control. It is expected that to fulfill this strategy's goals, CB approaches will continue its important growth in protecting workers.

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.

Using the Model Coupling Toolkit to couple earth system models

USGS Publications Warehouse

Warner, J.C.; Perlin, N.; Skyllingstad, E.D.

2008-01-01

Continued advances in computational resources are providing the opportunity to operate more sophisticated numerical models. Additionally, there is an increasing demand for multidisciplinary studies that include interactions between different physical processes. Therefore there is a strong desire to develop coupled modeling systems that utilize existing models and allow efficient data exchange and model control. The basic system would entail model "1" running on "M" processors and model "2" running on "N" processors, with efficient exchange of model fields at predetermined synchronization intervals. Here we demonstrate two coupled systems: the coupling of the ocean circulation model Regional Ocean Modeling System (ROMS) to the surface wave model Simulating WAves Nearshore (SWAN), and the coupling of ROMS to the atmospheric model Coupled Ocean Atmosphere Prediction System (COAMPS). Both coupled systems use the Model Coupling Toolkit (MCT) as a mechanism for operation control and inter-model distributed memory transfer of model variables. In this paper we describe requirements and other options for model coupling, explain the MCT library, ROMS, SWAN and COAMPS models, methods for grid decomposition and sparse matrix interpolation, and provide an example from each coupled system. Methods presented in this paper are clearly applicable for coupling of other types of models. ?? 2008 Elsevier Ltd. All rights reserved.

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…

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.

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.

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…

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.

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.

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.

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

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.

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...

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.

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.

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…

Distribution of a Generic Mission Planning and Scheduling Toolkit for Astronomical Spacecraft

NASA Technical Reports Server (NTRS)

Kleiner, Steven C.

1996-01-01

Work is progressing as outlined in the proposal for this contract. A working planning and scheduling system has been documented and packaged and made available to the WIRE Small Explorer group at JPL, the FUSE group at JHU, the NASA/GSFC Laboratory for Astronomy and Solar Physics and the Advanced Planning and Scheduling Branch at STScI. The package is running successfully on the WIRE computer system. It is expected that the WIRE will reuse significant portions of the SWAS code in its system. This scheduling system itself was tested successfully against the spacecraft hardware in December 1995. A fully automatic scheduling module has been developed and is being added to the toolkit. In order to maximize reuse, the code is being reorganized during the current build into object-oriented class libraries. A paper describing the toolkit has been written and is included in the software distribution. We have experienced interference between the export and production versions of the toolkit. We will be requesting permission to reprogram funds in order to purchase a standalone PC onto which to offload the export version.

A Generic Expert Scheduling System Architecture and Toolkit: GUESS (Generically Used Expert Scheduling System)

NASA Technical Reports Server (NTRS)

Liebowitz, Jay; Krishnamurthy, Vijaya; Rodens, Ira; Houston, Chapman; Liebowitz, Alisa; Baek, Seung; Radko, Joe; Zeide, Janet

1996-01-01

Scheduling has become an increasingly important element in today's society and workplace. Within the NASA environment, scheduling is one of the most frequently performed and challenging functions. Towards meeting NASA's scheduling needs, a research version of a generic expert scheduling system architecture and toolkit has been developed. This final report describes the development and testing of GUESS (Generically Used Expert Scheduling System).

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).

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.

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.

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.

Software Tools for Formal Specification and Verification of Distributed Real-Time Systems

DTIC Science & Technology

1994-07-29

time systems and to evaluate the design. The evaluation of the design includes investigation of both the capability and potential usefulness of the toolkit environment and the feasibility of its implementation....The goals of Phase 1 are to design in detail a toolkit environment based on formal methods for the specification and verification of distributed real

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...

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.

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

Modeling of a Flooding Induced Station Blackout for a Pressurized Water Reactor Using the RISMC Toolkit

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

Mandelli, Diego; Prescott, Steven R; Smith, Curtis L

2011-07-01

In the Risk Informed Safety Margin Characterization (RISMC) approach we want to understand not just the frequency of an event like core damage, but how close we are (or are not) to key safety-related events and how might we increase our safety margins. The RISMC Pathway uses the probabilistic margin approach to quantify impacts to reliability and safety by coupling both probabilistic (via stochastic simulation) and mechanistic (via physics models) approaches. This coupling takes place through the interchange of physical parameters and operational or accident scenarios. In this paper we apply the RISMC approach to evaluate the impact of amore » power uprate on a pressurized water reactor (PWR) for a tsunami-induced flooding test case. This analysis is performed using the RISMC toolkit: RELAP-7 and RAVEN codes. RELAP-7 is the new generation of system analysis codes that is responsible for simulating the thermal-hydraulic dynamics of PWR and boiling water reactor systems. RAVEN has two capabilities: to act as a controller of the RELAP-7 simulation (e.g., system activation) and to perform statistical analyses (e.g., run multiple RELAP-7 simulations where sequencing/timing of events have been changed according to a set of stochastic distributions). By using the RISMC toolkit, we can evaluate how power uprate affects the system recovery measures needed to avoid core damage after the PWR lost all available AC power by a tsunami induced flooding. The simulation of the actual flooding is performed by using a smooth particle hydrodynamics code: NEUTRINO.« less

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.

MAKER-P: a tool-kit for the creation, management, and quality control of plant genome annotations

USDA-ARS?s Scientific Manuscript database

We have optimized and extended the widely used annotation-engine MAKER for use on plant genomes. We have benchmarked the resulting software, MAKER-P, using the A. thaliana genome and the TAIR10 gene models. Here we demonstrate the ability of the MAKER-P toolkit to generate de novo repeat databases, ...

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.

Mission Simulation Toolkit

NASA Technical Reports Server (NTRS)

Pisaich, Gregory; Flueckiger, Lorenzo; Neukom, Christian; Wagner, Mike; Buchanan, Eric; Plice, Laura

2007-01-01

The Mission Simulation Toolkit (MST) is a flexible software system for autonomy research. It was developed as part of the Mission Simulation Facility (MSF) project that was started in 2001 to facilitate the development of autonomous planetary robotic missions. Autonomy is a key enabling factor for robotic exploration. There has been a large gap between autonomy software (at the research level), and software that is ready for insertion into near-term space missions. The MST bridges this gap by providing a simulation framework and a suite of tools for supporting research and maturation of autonomy. MST uses a distributed framework based on the High Level Architecture (HLA) standard. A key feature of the MST framework is the ability to plug in new models to replace existing ones with the same services. This enables significant simulation flexibility, particularly the mixing and control of fidelity level. In addition, the MST provides automatic code generation from robot interfaces defined with the Unified Modeling Language (UML), methods for maintaining synchronization across distributed simulation systems, XML-based robot description, and an environment server. Finally, the MSF supports a number of third-party products including dynamic models and terrain databases. Although the communication objects and some of the simulation components that are provided with this toolkit are specifically designed for terrestrial surface rovers, the MST can be applied to any other domain, such as aerial, aquatic, or space.

The Microsoft Biology Foundation Applications for High-Throughput Sequencing

PubMed Central

Mercer, S.

2010-01-01

w9-2 The need for reusable libraries of bioinformatics functions has been recognized for many years and a number of language-specific toolkits have been constructed. Such toolkits have served as valuable nucleation points for the community, promoting the sharing of code and establishing standards. The majority of DNA sequencing machines and many other standard pieces of lab equipment are controlled by PCs using Windows, and a Microsoft genomics toolkit would enable initial processing and quality control to happen closer to the instrumentation and provide opportunities for added-value services within core facilities. The Microsoft Biology Foundation (MBF) is an open source software library, freely available for both commercial and academic use, available as an early-stage betafrom mbf.codeplex.com. This presentation will describe the structure and goals of MBF and demonstrate some of its uses.

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.

The Visualization Toolkit (VTK): Rewriting the rendering code for modern graphics cards

NASA Astrophysics Data System (ADS)

Hanwell, Marcus D.; Martin, Kenneth M.; Chaudhary, Aashish; Avila, Lisa S.

2015-09-01

The Visualization Toolkit (VTK) is an open source, permissively licensed, cross-platform toolkit for scientific data processing, visualization, and data analysis. It is over two decades old, originally developed for a very different graphics card architecture. Modern graphics cards feature fully programmable, highly parallelized architectures with large core counts. VTK's rendering code was rewritten to take advantage of modern graphics cards, maintaining most of the toolkit's programming interfaces. This offers the opportunity to compare the performance of old and new rendering code on the same systems/cards. Significant improvements in rendering speeds and memory footprints mean that scientific data can be visualized in greater detail than ever before. The widespread use of VTK means that these improvements will reap significant benefits.

Evaluation of the Tobii EyeX Eye tracking controller and Matlab toolkit for research.

PubMed

Gibaldi, Agostino; Vanegas, Mauricio; Bex, Peter J; Maiello, Guido

2017-06-01

The Tobii Eyex Controller is a new low-cost binocular eye tracker marketed for integration in gaming and consumer applications. The manufacturers claim that the system was conceived for natural eye gaze interaction, does not require continuous recalibration, and allows moderate head movements. The Controller is provided with a SDK to foster the development of new eye tracking applications. We review the characteristics of the device for its possible use in scientific research. We develop and evaluate an open source Matlab Toolkit that can be employed to interface with the EyeX device for gaze recording in behavioral experiments. The Toolkit provides calibration procedures tailored to both binocular and monocular experiments, as well as procedures to evaluate other eye tracking devices. The observed performance of the EyeX (i.e. accuracy < 0.6°, precision < 0.25°, latency < 50 ms and sampling frequency ≈55 Hz), is sufficient for some classes of research application. The device can be successfully employed to measure fixation parameters, saccadic, smooth pursuit and vergence eye movements. However, the relatively low sampling rate and moderate precision limit the suitability of the EyeX for monitoring micro-saccadic eye movements or for real-time gaze-contingent stimulus control. For these applications, research grade, high-cost eye tracking technology may still be necessary. Therefore, despite its limitations with respect to high-end devices, the EyeX has the potential to further the dissemination of eye tracking technology to a broad audience, and could be a valuable asset in consumer and gaming applications as well as a subset of basic and clinical research settings.

New Tools for a New Terrain Air Force Support to Special Operations in the Cyber Environment

DTIC Science & Technology

2016-08-01

54 3 PREFACE As a career targeteer for the US...capabilities of a toolkit of cyber options, from hardware on the front lines to “digital reachback” relationships with USCYBERCOM, is to leave...of career fields, including, but not limited to, cyberspace operations, intelligence, aircrew operations, command and control systems operations, and

Mission Operations and Navigation Toolkit Environment

NASA Technical Reports Server (NTRS)

Sunseri, Richard F.; Wu, Hsi-Cheng; Hanna, Robert A.; Mossey, Michael P.; Duncan, Courtney B.; Evans, Scott E.; Evans, James R.; Drain, Theodore R.; Guevara, Michelle M.; Martin Mur, Tomas J.;

Model Analyst’s Toolkit User Guide, Version 7.1.0

DTIC Science & Technology

2015-08-01

Help > About)  Environment details ( operating system )  metronome.log file, located in your MAT 7.1.0 installation folder  Any log file that...requirements to run the Model Analyst’s Toolkit:  Windows XP operating system (or higher) with Service Pack 2 and all critical Windows updates installed...application icon on your desktop  Create a Quick Launch icon – Creates a MAT application icon on the taskbar for operating systems released

Preparing for the Flu (Including 2009 H1N1 Flu): A Communication Toolkit for Schools (Grades K-12)

ERIC Educational Resources Information Center

Centers for Disease Control and Prevention, 2010

2010-01-01

The purpose of "Preparing for the Flu: A Communication Toolkit for Schools" is to provide basic information and communication resources to help school administrators implement recommendations from CDC's (Centers for Disease Control and Prevention) Guidance for State and Local Public Health Officials and School Administrators for School (K-12)…

Use of the MATRIXx Integrated Toolkit on the Microwave Anisotropy Probe Attitude Control System

NASA Technical Reports Server (NTRS)

Ward, David K.; Andrews, Stephen F.; McComas, David C.; ODonnell, James R., Jr.

1999-01-01

Recent advances in analytical software tools allow the analysis, simulation, flight code, and documentation of an algorithm to be generated from a single source, all within one integrated analytical design package. NASA's Microwave Anisotropy Probe project has used one such package, Integrated Systems' MATRIXx suite, in the design of the spacecraft's Attitude Control System. The project's experience with the linear analysis, simulation, code generation, and documentation tools will be presented and compared with more traditional development tools. In particular, the quality of the flight software generated will be examined in detail. Finally, lessons learned on each of the tools will be shared.

Intelligent Tutoring Systems for Procedural Task Training of Remote Payload Operations at NASA

NASA Technical Reports Server (NTRS)

Ong, James; Noneman, Steven

2000-01-01

Intelligent Tutoring Systems (ITSs) encode and apply the subject matter and teaching expertise of experienced instructors to provide students with individualized instruction automatically. ITSs complement training simulators by providing automated instruction when it is not economical or feasible to dedicate an instructor to each student during training simulations. Despite their proven training effectiveness and favorable operating cost, however, relatively few ITSs are in use. This is largely because it is usually costly and difficult to encode the task knowledge used by the ITS to evaluate the student's actions and assess the student's performance. Procedural tasks are tasks for which there exist procedures, guidelines, and strategies that determine the correct set of steps to be taken within each situation. To lower the cost and difficulty of creating tutoring systems for procedural task training, Stottler Henke Associates, Inc. (SHAI) worked closely with the Operations Training Group at NASA's Marshall Space Flight Center to develop the Task Tutor Toolkit (T (exp 3)), a generic tutoring system shell and scenario authoring tool. The Task Tutor Toolkit employs a case-based reasoning approach where the instructor creates a procedure template that specifies the range of student actions that are "correct" within each scenario. Because each procedure template is specific to a single scenario, the system can employ relatively simple reasoning methods to represent a correct set of actions and assess student performance. This simplicity enables a non-programmer to specify task knowledge quickly and easily by via graphical user interface, using a "demonstrate, generalize, and annotate" paradigm, that recognizes the range of possible valid actions and infers principles understood (or misunderstood) by the student when those actions are carried out. The Task Tutor Toolkit was also designed to be modular and general, so that it can be interfaced with a wide range of training simulators and support a variety of training domains. SHAI and NASA applied the Task Tutor Toolkit to create the Remote Payload Operations Tutor (RPOT). RPOT is a specific tutoring system application which lets scientists who are new to space mission operations learn to monitor and control their experiments aboard the International Space Station according to NASA payload regulations, guidelines, and procedures. The RPOT simulator lets students practice these skills by monitoring the telemetry variable values of a simple, hypothetical experiment, sending commands to the experiment, coordinating with NASA personnel via voice communication loops, and submitting and retrieving information via documents and forms. At the end of each scenario, RPOT displays the principles correctly or incorrectly demonstrated by the student, along with explanations and background information. The effectiveness of RPOT and the Task Tutor Toolkit are currently under evaluation at NASA.

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.

Wavefront Control Toolbox for James Webb Space Telescope Testbed

NASA Technical Reports Server (NTRS)

Shiri, Ron; Aronstein, David L.; Smith, Jeffery Scott; Dean, Bruce H.; Sabatke, Erin

2007-01-01

We have developed a Matlab toolbox for wavefront control of optical systems. We have applied this toolbox to the optical models of James Webb Space Telescope (JWST) in general and to the JWST Testbed Telescope (TBT) in particular, implementing both unconstrained and constrained wavefront optimization to correct for possible misalignments present on the segmented primary mirror or the monolithic secondary mirror. The optical models implemented in Zemax optical design program and information is exchanged between Matlab and Zemax via the Dynamic Data Exchange (DDE) interface. The model configuration is managed using the XML protocol. The optimization algorithm uses influence functions for each adjustable degree of freedom of the optical mode. The iterative and non-iterative algorithms have been developed to converge to a local minimum of the root-mean-square (rms) of wavefront error using singular value decomposition technique of the control matrix of influence functions. The toolkit is highly modular and allows the user to choose control strategies for the degrees of freedom to be adjusted on a given iteration and wavefront convergence criterion. As the influence functions are nonlinear over the control parameter space, the toolkit also allows for trade-offs between frequency of updating the local influence functions and execution speed. The functionality of the toolbox and the validity of the underlying algorithms have been verified through extensive simulations.

The UK Earth System Models Marine Biogeochemical Evaluation Toolkit, BGC-val

NASA Astrophysics Data System (ADS)

de Mora, Lee

2017-04-01

The Biogeochemical Validation toolkit, BGC-val, is a model and grid independent python-based marine model evaluation framework that automates much of the validation of the marine component of an Earth System Model. BGC-val was initially developed to be a flexible and extensible system to evaluate the spin up of the marine UK Earth System Model (UKESM). However, the grid-independence and flexibility means that it is straightforward to adapt the BGC-val framework to evaluate other marine models. In addition to the marine component of the UKESM, this toolkit has been adapted to compare multiple models, including models from the CMIP5 and iMarNet inter-comparison projects. The BGC-val toolkit produces multiple levels of analysis which are presented in a simple to use interactive html5 document. Level 1 contains time series analyses, showing the development over time of many important biogeochemical and physical ocean metrics, such as the Global primary production or the Drake passage current. The second level of BGC-val is an in-depth spatial analyses of a single point in time. This is a series of point to point comparison of model and data in various regions, such as a comparison of Surface Nitrate in the model vs data from the world ocean atlas. The third level analyses are specialised ad-hoc packages to go in-depth on a specific question, such as the development of Oxygen minimum zones in the Equatorial Pacific. In additional to the three levels, the html5 document opens with a Level 0 table showing a summary of the status of the model run. The beta version of this toolkit is available via the Plymouth Marine Laboratory Gitlab server and uses the BSD 3 clause license.

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).

Real-time control using open source RTOS

NASA Astrophysics Data System (ADS)

Irwin, Philip C.; Johnson, Richard L., Jr.

2002-12-01

Complex telescope systems such as interferometers tend to rely heavily on hard real-time operating systems (RTOS). It has been standard practice at NASA's Jet Propulsion Laboratory (JPL) and many other institutions to use costly commercial RTOSs and hardware. After developing a real-time toolkit for VxWorks on the PowerPC platform (dubbed RTC), the interferometry group at JPL is porting this code to the real-time Application Interface (RTAI), an open source RTOS that is essentially an extension to the Linux kernel. This port has the potential to reduce software and hardware costs for future projects, while increasing the level of performance. The goals of this paper are to briefly describe the RTC toolkit, highlight the successes and pitfalls of porting the toolkit from VxWorks to Linux-RTAI, and to discuss future enhancements that will be implemented as a direct result of this port. The first port of any body of code is always the most difficult since it uncovers the OS-specific calls and forces "red flags" into those portions of the code. For this reason, It has also been a huge benefit that the project chose a generic, platform independent OS extension, ACE, and its CORBA counterpart, TAO. This port of RTC will pave the way for conversions to other environments, the most interesting of which is a non-real-time simulation environment, currently being considered by the Space Interferometry Mission (SIM) and the Terrestrial Planet Finder (TPF) Projects.

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.

Evaluation of a commercial system for CAMAC-based control of the Chalk River Laboratories tandem-accelerator-superconducting-cyclotron complexcomplex

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

Greiner, B.F.; Caswell, D.J.; Slater, W.R.

1992-04-01

This paper discusses the control system of the Tandem Accelerator Superconducting Cyclotron (TASCC) of AECL Research at its Chalk River Laboratories which is presently based on a PDP-11 computer and the IAS operating system. The estimated expense of a custom conversion of the system to a current, equivalent operating system is prohibitive. The authors have evaluated a commercial control package from VISTA Control Systems based on VAX microcomputers and the VMS operating system. Vsystem offers a modern, graphical operator interface, an extensive software toolkit for configuration of the system and a multi-feature data-logging capability, all of which far surpass themore » functionality of the present control system. However, the implementation of some familiar, practical features that TASCC operators find to be essential has proven to be challenging. The assessment of Vsystem, which is described in terms of presently perceived strengths and weaknesses, is, on balance, very positive.« less

77 FR 45337 - U.S. Environmental Solutions Toolkit

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-31

... services relevant to (a) groundwater remediation; (b) mercury emissions control from power plants; (c...) Groundwater remediation (b) Mercury emissions control from power plants (c) Emissions control from large...

CDC's Health Equity Resource Toolkit: disseminating guidance for state practitioners to address obesity disparities.

PubMed

Payne, Gayle Holmes; James, Stephen D; Hawley, Lisa; Corrigan, Bethany; Kramer, Rachel E; Overton, Samantha N; Farris, Rosanne P; Wasilewski, Yvonne

2015-01-01

Obesity has been on the rise in the United States over the past three decades, and is high. In addition to population-wide trends, it is clear that obesity affects some groups more than others and can be associated with age, income, education, gender, race and ethnicity, and geographic region. To reverse the obesity epidemic, the Centers for Disease Control and Prevention) promotes evidence-based and practice-informed strategies to address nutrition and physical activity environments and behaviors. These public health strategies require translation into actionable approaches that can be implemented by state and local entities to address disparities. The Centers for Disease Control and Prevention used findings from an expert panel meeting to guide the development and dissemination of the Health Equity Resource Toolkit for State Practitioners Addressing Obesity Disparities (available at http://www.cdc.gov/obesity/health_equity/toolkit.html). The Toolkit helps public health practitioners take a systematic approach to program planning using a health equity lens. The Toolkit provides a six-step process for planning, implementing, and evaluating strategies to address obesity disparities. Each section contains (a) a basic description of the steps of the process and suggested evidence-informed actions to help address obesity disparities, (b) practical tools for carrying out activities to help reduce obesity disparities, and (c) a "real-world" case study of a successful state-level effort to address obesity with a focus on health equity that is particularly relevant to the content in that section. Hyperlinks to additional resources are included throughout. © 2014 Society for Public Health Education.

CDC’s Health Equity Resource Toolkit: Disseminating Guidance for State Practitioners to Address Obesity Disparities

PubMed Central

Payne, Gayle Holmes; James, Stephen D.; Hawley, Lisa; Corrigan, Bethany; Kramer, Rachel E.; Overton, Samantha N.; Farris, Rosanne P.; Wasilewski, Yvonne

2015-01-01

Obesity has been on the rise in the United States over the past three decades, and is high. In addition to population-wide trends, it is clear that obesity affects some groups more than others and can be associated with age, income, education, gender, race and ethnicity, and geographic region. To reverse the obesity epidemic, the Centers for Disease Control and Prevention) promotes evidence-based and practice-informed strategies to address nutrition and physical activity environments and behaviors. These public health strategies require translation into actionable approaches that can be implemented by state and local entities to address disparities. The Centers for Disease Control and Prevention used findings from an expert panel meeting to guide the development and dissemination of the Health Equity Resource Toolkit for State Practitioners Addressing Obesity Disparities (available at http://www.cdc.gov/obesity/health_equity/toolkit.html). The Toolkit helps public health practitioners take a systematic approach to program planning using a health equity lens. The Toolkit provides a six-step process for planning, implementing, and evaluating strategies to address obesity disparities. Each section contains (a) a basic description of the steps of the process and suggested evidence-informed actions to help address obesity disparities, (b) practical tools for carrying out activities to help reduce obesity disparities, and (c) a “real-world” case study of a successful state-level effort to address obesity with a focus on health equity that is particularly relevant to the content in that section. Hyperlinks to additional resources are included throughout. PMID:24962967

Effect of the good school toolkit on school staff mental health, sense of job satisfaction and perceptions of school climate: Secondary analysis of a cluster randomised trial.

PubMed

Kayiwa, Joshua; Clarke, Kelly; Knight, Louise; Allen, Elizabeth; Walakira, Eddy; Namy, Sophie; Merrill, Katherine G; Naker, Dipak; Devries, Karen

2017-08-01

The Good School Toolkit, a complex behavioural intervention delivered in Ugandan primary schools, has been shown to reduce school staff-perpetrated physical violence against students. We aimed to assess the effect of this intervention on staff members' mental health, sense of job satisfaction and perception of school climate. We analysed data from a cluster-randomised trial administered in 42 primary schools in Luwero district, Uganda. The trial was comprised of cross-sectional baseline (June/July 2012) and endline (June/July 2014) surveys among staff and students. Twenty-one schools were randomly selected to receive the Toolkit, whilst 21 schools constituted a wait-listed control group. We generated composite measures to assess staff members' perceptions of the school climate and job satisfaction. The trial is registered at clinicaltrials.gov (NCT01678846). No schools dropped out of the study and all 591 staff members who completed the endline survey were included in the analysis. Staff in schools receiving the Toolkit had more positive perspectives of their school climate compared to staff in control schools (difference in mean scores 2.19, 95% Confidence Interval 0.92, 3.39). We did not find any significant differences for job satisfaction and mental health. In conclusion, interventions like the Good School Toolkit that reduce physical violence by school staff against students can improve staff perceptions of the school climate, and could help to build more positive working and learning environments in Ugandan schools. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

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 ).

Process analytical technology in the pharmaceutical industry: a toolkit for continuous improvement.

PubMed

Scott, Bradley; Wilcock, Anne

2006-01-01

Process analytical technology (PAT) refers to a series of tools used to ensure that quality is built into products while at the same time improving the understanding of processes, increasing efficiency, and decreasing costs. It has not been widely adopted by the pharmaceutical industry. As the setting for this paper, the current pharmaceutical manufacturing paradigm and PAT guidance to date are discussed prior to the review of PAT principles and tools, benefits, and challenges. The PAT toolkit contains process analyzers, multivariate analysis tools, process control tools, and continuous improvement/knowledge management/information technology systems. The integration and implementation of these tools is complex, and has resulted in uncertainty with respect to both regulation and validation. The paucity of staff knowledgeable in this area may complicate adoption. Studies to quantitate the benefits resulting from the adoption of PAT within the pharmaceutical industry would be a valuable addition to the qualitative studies that are currently available.

An open-source framework for testing tracking devices using Lego Mindstorms

NASA Astrophysics Data System (ADS)

Jomier, Julien; Ibanez, Luis; Enquobahrie, Andinet; Pace, Danielle; Cleary, Kevin

2009-02-01

In this paper, we present an open-source framework for testing tracking devices in surgical navigation applications. At the core of image-guided intervention systems is the tracking interface that handles communication with the tracking device and gathers tracking information. Given that the correctness of tracking information is critical for protecting patient safety and for ensuring the successful execution of an intervention, the tracking software component needs to be thoroughly tested on a regular basis. Furthermore, with widespread use of extreme programming methodology that emphasizes continuous and incremental testing of application components, testing design becomes critical. While it is easy to automate most of the testing process, it is often more difficult to test components that require manual intervention such as tracking device. Our framework consists of a robotic arm built from a set of Lego Mindstorms and an open-source toolkit written in C++ to control the robot movements and assess the accuracy of the tracking devices. The application program interface (API) is cross-platform and runs on Windows, Linux and MacOS. We applied this framework for the continuous testing of the Image-Guided Surgery Toolkit (IGSTK), an open-source toolkit for image-guided surgery and shown that regression testing on tracking devices can be performed at low cost and improve significantly the quality of the software.

Targeted Cancer Therapy Systems: An In Silico Study of Radiohalogenated Ligands in the Estrogen Receptor and the Synthesis of a Molecular Toolkit for the Fabrication of Customizable Nanoparticles

NASA Astrophysics Data System (ADS)

Barnsley, Kelton K.

Chemotherapy is often limited by off-target toxicity and the development of multi-drug resistance in response to treatment. Strategies which reduce off-target toxicity by passively or actively targeting cancer cells may improve the efficacy of chemotherapy. Herein, two projects relating to targeted therapy are described. In the first project, the binding modes of 1,1-bis(4-hydroxyphenyl)-2-phenylethylenes (THPEs), a class of synthetic estrogens previously developed by our group, in the human estrogen receptor alpha-ligand binding domain were studied using molecular modeling programs YASARA AutoDock and Schrodinger Glide. The results were internally consistent and supported the observation that a bromine or iodine atom at the 2-position of the THPEs contributes positively to their binding in the estrogen receptor. In the second project, a "molecular toolkit" approach to the synthesis of multifunctional nanoparticles was envisioned. Our hypothesis was that the physical and chemical properties of the final product could be defined by controlling the types and relative amounts of prefunctionalized polymer units (PPUs) as well as the emulsification conditions. The design and syntheses of heterobifunctional linkers and other components for a preliminary molecular toolkit are reported, and the literature on select heterobifunctional aliphatic linkers is examined.

Teaching the Physician-Manager Role to Psychiatric Residents: Development and Implementation of a Pilot Curriculum

ERIC Educational Resources Information Center

Stergiopoulos, Vicky; Maggi, Julie; Sockalingam, Sanjeev

2009-01-01

Objective: The authors describe a pilot physician-manager curriculum designed to address the learning needs of psychiatric residents in administrative psychiatry and health systems. Methods: The pilot curriculum includes a junior and a senior toolkit of four workshops each. The junior toolkit introduces postgraduate-year two (PGY-2) residents to…

EduSpeak[R]: A Speech Recognition and Pronunciation Scoring Toolkit for Computer-Aided Language Learning Applications

ERIC Educational Resources Information Center

Franco, Horacio; Bratt, Harry; Rossier, Romain; Rao Gadde, Venkata; Shriberg, Elizabeth; Abrash, Victor; Precoda, Kristin

2010-01-01

SRI International's EduSpeak[R] system is a software development toolkit that enables developers of interactive language education software to use state-of-the-art speech recognition and pronunciation scoring technology. Automatic pronunciation scoring allows the computer to provide feedback on the overall quality of pronunciation and to point to…

Lessons learned on the Ground Test Accelerator control system

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

Kozubal, A.J.; Weiss, R.E.

1994-09-01

When we initiated the control system design for the Ground Test Accelerator (GTA), we envisioned a system that would be flexible enough to handle the changing requirements of an experimental project. This control system would use a developers` toolkit to reduce the cost and time to develop applications for GTA, and through the use of open standards, the system would accommodate unforeseen requirements as they arose. Furthermore, we would attempt to demonstrate on GTA a level of automation far beyond that achieved by existing accelerator control systems. How well did we achieve these goals? What were the stumbling blocks tomore » deploying the control system, and what assumptions did we make about requirements that turned out to be incorrect? In this paper we look at the process of developing a control system that evolved into what is now the ``Experimental Physics and Industrial Control System`` (EPICS). Also, we assess the impact of this system on the GTA project, as well as the impact of GTA on EPICS. The lessons learned on GTA will be valuable for future projects.« less

Cyber Security Audit and Attack Detection Toolkit

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

Peterson, Dale

2012-05-31

This goal of this project was to develop cyber security audit and attack detection tools for industrial control systems (ICS). Digital Bond developed and released a tool named Bandolier that audits ICS components commonly used in the energy sector against an optimal security configuration. The Portaledge Project developed a capability for the PI Historian, the most widely used Historian in the energy sector, to aggregate security events and detect cyber attacks.

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.

Geological hazards: from early warning systems to public health toolkits.

PubMed

Samarasundera, Edgar; Hansell, Anna; Leibovici, Didier; Horwell, Claire J; Anand, Suchith; Oppenheimer, Clive

2014-11-01

Extreme geological events, such as earthquakes, are a significant global concern and sometimes their consequences can be devastating. Geographic information plays a critical role in health protection regarding hazards, and there are a range of initiatives using geographic information to communicate risk as well as to support early warning systems operated by geologists. Nevertheless we consider there to remain shortfalls in translating information on extreme geological events into health protection tools, and suggest that social scientists have an important role to play in aiding the development of a new generation of toolkits aimed at public health practitioners. This viewpoint piece reviews the state of the art in this domain and proposes potential contributions different stakeholder groups, including social scientists, could bring to the development of new toolkits. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

The control system of the polarized internal target of ANKE at COSY

NASA Astrophysics Data System (ADS)

Kleines, H.; Sarkadi, J.; Zwoll, K.; Engels, R.; Grigoryev, K.; Mikirtychyants, M.; Nekipelov, M.; Rathmann, F.; Seyfarth, H.; Kravtsov, P.; Vasilyev, A.

2006-05-01

The polarized internal target for the ANKE experiment at the Cooler Synchrotron COSY of the Forschungszentrum Jülich utilizes a polarized atomic beam source to feed a storage cell with polarized hydrogen or deuterium atoms. The nuclear polarization is measured with a Lamb-shift polarimeter. For common control of the two systems, industrial equipment was selected providing reliable, long-term support and remote control of the target as well as measurement and optimization of its operating parameters. The interlock system has been implemented on the basis of SIEMENS SIMATIC S7-300 family of programmable logic controllers. In order to unify the interfacing to the control computer, all front-end equipment is connected via the PROFIBUS DP fieldbus. The process control software was implemented using the Windows-based WinCC toolkit from SIEMENS. The variety of components, to be controlled, and the logical structure of the control and interlock system are described. Finally, a number of applications derived from the present development to other, new installations are briefly mentioned.

The HARNESS Workbench: Unified and Adaptive Access to Diverse HPC Platforms

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

Sunderam, Vaidy S.

2012-03-20

The primary goal of the Harness WorkBench (HWB) project is to investigate innovative software environments that will help enhance the overall productivity of applications science on diverse HPC platforms. Two complementary frameworks were designed: one, a virtualized command toolkit for application building, deployment, and execution, that provides a common view across diverse HPC systems, in particular the DOE leadership computing platforms (Cray, IBM, SGI, and clusters); and two, a unified runtime environment that consolidates access to runtime services via an adaptive framework for execution-time and post processing activities. A prototype of the first was developed based on the concept ofmore » a 'system-call virtual machine' (SCVM), to enhance portability of the HPC application deployment process across heterogeneous high-end machines. The SCVM approach to portable builds is based on the insertion of toolkit-interpretable directives into original application build scripts. Modifications resulting from these directives preserve the semantics of the original build instruction flow. The execution of the build script is controlled by our toolkit that intercepts build script commands in a manner transparent to the end-user. We have applied this approach to a scientific production code (Gamess-US) on the Cray-XT5 machine. The second facet, termed Unibus, aims to facilitate provisioning and aggregation of multifaceted resources from resource providers and end-users perspectives. To achieve that, Unibus proposes a Capability Model and mediators (resource drivers) to virtualize access to diverse resources, and soft and successive conditioning to enable automatic and user-transparent resource provisioning. A proof of concept implementation has demonstrated the viability of this approach on high end machines, grid systems and computing clouds.« less

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.

Cluster Randomized Trial of a Toolkit and Early Vaccine Delivery to Improve Childhood Influenza Vaccination Rates in Primary Care

PubMed Central

Zimmerman, Richard K.; Nowalk, Mary Patricia; Lin, Chyongchiou Jeng; Hannibal, Kristin; Moehling, Krissy K.; Huang, Hsin-Hui; Matambanadzo, Annamore; Troy, Judith; Allred, Norma J.; Gallik, Greg; Reis, Evelyn C.

2014-01-01

Purpose To increase childhood influenza vaccination rates using a toolkit and early vaccine delivery in a randomized cluster trial. Methods Twenty primary care practices treating children (range for n=536-8,183) were randomly assigned to Intervention and Control arms to test the effectiveness of an evidence-based practice improvement toolkit (4 Pillars Toolkit) and early vaccine supplies for use among disadvantaged children on influenza vaccination rates among children 6 months-18 years. Follow-up staff meetings and surveys were used to assess use and acceptability of the intervention strategies in the Intervention arm. Rates for the 2010-2011 and 2011-2012 influenza seasons were compared. Two-level generalized linear mixed modeling was used to evaluate outcomes. Results Overall increases in influenza vaccination rates were significantly greater in the Intervention arm (7.9 percentage points) compared with the Control arm (4.4 percentage points; P<0.034). These rate changes represent 4522 additional doses in the Intervention arm vs. 1,390 additional doses in the Control arm. This effect of the intervention was observed despite the fact that rates increased significantly in both arms - 8/10 Intervention (P<0.001) and 7/10 Control sites (P-values 0.04 to <0.001). Rates in two Intervention sites with pre-intervention vaccination rates >58% did not significantly increase. In regression analyses, a child's likelihood of being vaccinated was significantly higher with: younger age, white race (Odds ratio [OR]=1.29; 95% confidence interval [CI]=1.23-1.34), having commercial insurance (OR=1.30; 95%CI=1.25-1.35), higher pre-intervention practice vaccination rate (OR=1.25; 95%CI=1.16-1.34), and being in the Intervention arm (OR=1.23; 95%CI=1.01-1.50). Early delivery of influenza vaccine was rated by Intervention practices as an effective strategy for raising rates. Conclusions Implementation of a multi-strategy toolkit and early vaccine supplies can significantly improve influenza vaccination rates among children in primary care practices but the effect may be less pronounced in practices with moderate to high existing vaccination rates. PMID:24793941

Effect of an educational toolkit on quality of care: a pragmatic cluster randomized trial.

PubMed

Shah, Baiju R; Bhattacharyya, Onil; Yu, Catherine H Y; Mamdani, Muhammad M; Parsons, Janet A; Straus, Sharon E; Zwarenstein, Merrick

2014-02-01

Printed educational materials for clinician education are one of the most commonly used approaches for quality improvement. The objective of this pragmatic cluster randomized trial was to evaluate the effectiveness of an educational toolkit focusing on cardiovascular disease screening and risk reduction in people with diabetes. All 933,789 people aged ≥40 years with diagnosed diabetes in Ontario, Canada were studied using population-level administrative databases, with additional clinical outcome data collected from a random sample of 1,592 high risk patients. Family practices were randomly assigned to receive the educational toolkit in June 2009 (intervention group) or May 2010 (control group). The primary outcome in the administrative data study, death or non-fatal myocardial infarction, occurred in 11,736 (2.5%) patients in the intervention group and 11,536 (2.5%) in the control group (p = 0.77). The primary outcome in the clinical data study, use of a statin, occurred in 700 (88.1%) patients in the intervention group and 725 (90.1%) in the control group (p = 0.26). Pre-specified secondary outcomes, including other clinical events, processes of care, and measures of risk factor control, were also not improved by the intervention. A limitation is the high baseline rate of statin prescribing in this population. The educational toolkit did not improve quality of care or cardiovascular outcomes in a population with diabetes. Despite being relatively easy and inexpensive to implement, printed educational materials were not effective. The study highlights the need for a rigorous and scientifically based approach to the development, dissemination, and evaluation of quality improvement interventions. http://www.ClinicalTrials.gov NCT01411865 and NCT01026688.

Ground Operations Autonomous Control and Integrated Health Management

NASA Technical Reports Server (NTRS)

Figueroa, Fernando; Walker, Mark; Wilkins, Kim; Johnson, Robert; Sass, Jared; Youney, Justin

2014-01-01

An intelligent autonomous control capability has been developed and is currently being validated in ground cryogenic fluid management operations. The capability embodies a physical architecture consistent with typical launch infrastructure and control systems, augmented by a higher level autonomous control (AC) system enabled to make knowledge-based decisions. The AC system is supported by an integrated system health management (ISHM) capability that detects anomalies, diagnoses causes, determines effects, and could predict future anomalies. AC is implemented using the concept of programmed sequences that could be considered to be building blocks of more generic mission plans. A sequence is a series of steps, and each executes actions once conditions for the step are met (e.g. desired temperatures or fluid state are achieved). For autonomous capability, conditions must consider also health management outcomes, as they will determine whether or not an action is executed, or how an action may be executed, or if an alternative action is executed instead. Aside from health, higher level objectives can also drive how a mission is carried out. The capability was developed using the G2 software environment (www.gensym.com) augmented by a NASA Toolkit that significantly shortens time to deployment. G2 is a commercial product to develop intelligent applications. It is fully object oriented. The core of the capability is a Domain Model of the system where all elements of the system are represented as objects (sensors, instruments, components, pipes, etc.). Reasoning and decision making can be done with all elements in the domain model. The toolkit also enables implementation of failure modes and effects analysis (FMEA), which are represented as root cause trees. FMEA's are programmed graphically, they are reusable, as they address generic FMEA referring to classes of subsystems or objects and their functional relationships. User interfaces for integrated awareness by operators have been created.

SIGMA Release v1.2 - Capabilities, Enhancements and Fixes

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

Mahadevan, Vijay; Grindeanu, Iulian R.; Ray, Navamita

In this report, we present details on SIGMA toolkit along with its component structure, capabilities, and feature additions in FY15, release cycles, and continuous integration process. These software processes along with updated documentation are imperative to successfully integrate and utilize in several applications including the SHARP coupled analysis toolkit for reactor core systems funded under the NEAMS DOE-NE program.

A cost effective and high fidelity fluoroscopy simulator using the Image-Guided Surgery Toolkit (IGSTK)

NASA Astrophysics Data System (ADS)

Gong, Ren Hui; Jenkins, Brad; Sze, Raymond W.; Yaniv, Ziv

2014-03-01

The skills required for obtaining informative x-ray fluoroscopy images are currently acquired while trainees provide clinical care. As a consequence, trainees and patients are exposed to higher doses of radiation. Use of simulation has the potential to reduce this radiation exposure by enabling trainees to improve their skills in a safe environment prior to treating patients. We describe a low cost, high fidelity, fluoroscopy simulation system. Our system enables operators to practice their skills using the clinical device and simulated x-rays of a virtual patient. The patient is represented using a set of temporal Computed Tomography (CT) images, corresponding to the underlying dynamic processes. Simulated x-ray images, digitally reconstructed radiographs (DRRs), are generated from the CTs using ray-casting with customizable machine specific imaging parameters. To establish the spatial relationship between the CT and the fluoroscopy device, the CT is virtually attached to a patient phantom and a web camera is used to track the phantom's pose. The camera is mounted on the fluoroscope's intensifier and the relationship between it and the x-ray source is obtained via calibration. To control image acquisition the operator moves the fluoroscope as in normal operation mode. Control of zoom, collimation and image save is done using a keypad mounted alongside the device's control panel. Implementation is based on the Image-Guided Surgery Toolkit (IGSTK), and the use of the graphics processing unit (GPU) for accelerated image generation. Our system was evaluated by 11 clinicians and was found to be sufficiently realistic for training purposes.

What Veterans Bring to Civilian Workplaces: A Prototype Toolkit for Helping Veterans Communicate to Private-Sector Employers About the Nontechnical Skills Taught in the Military

DTIC Science & Technology

2014-01-01

healthier and more prosperous. RAND is nonprofit, nonpartisan, and committed to the public interest. RAND’s publications do not necessarily reflect ...Toolkit 5 Continuous learning (related terms: adaptive learning, willingness to learn, active learning, metacognition ): Takes the necessary...when not under direct supervision; displays self -discipline and self -control; diligently checks work to ensure that all essential details have been

What Veterans Bring to Civilian Workplaces: A Prototype Toolkit for Helping Veterans Communicate to Private-Sector Employers About the Nontechnical Skills Taught in the Military

DTIC Science & Technology

2015-01-01

reflect the opinions of its research clients and sponsors. Support RAND Make a tax-deductible charitable contribution at www.rand.org/giving...This Toolkit 5 Continuous learning (related terms: adaptive learning, willingness to learn, active learning, metacognition ): Takes the necessary...even when not under direct supervision; displays self -discipline and self -control; diligently checks work to ensure that all essential details have

Integrating existing software toolkits into VO system

NASA Astrophysics Data System (ADS)

Cui, Chenzhou; Zhao, Yong-Heng; Wang, Xiaoqian; Sang, Jian; Luo, Ze

2004-09-01

Virtual Observatory (VO) is a collection of interoperating data archives and software tools. Taking advantages of the latest information technologies, it aims to provide a data-intensively online research environment for astronomers all around the world. A large number of high-qualified astronomical software packages and libraries are powerful and easy of use, and have been widely used by astronomers for many years. Integrating those toolkits into the VO system is a necessary and important task for the VO developers. VO architecture greatly depends on Grid and Web services, consequently the general VO integration route is "Java Ready - Grid Ready - VO Ready". In the paper, we discuss the importance of VO integration for existing toolkits and discuss the possible solutions. We introduce two efforts in the field from China-VO project, "gImageMagick" and "Galactic abundance gradients statistical research under grid environment". We also discuss what additional work should be done to convert Grid service to VO service.

An automatic speech recognition system with speaker-independent identification support

NASA Astrophysics Data System (ADS)

Caranica, Alexandru; Burileanu, Corneliu

2015-02-01

The novelty of this work relies on the application of an open source research software toolkit (CMU Sphinx) to train, build and evaluate a speech recognition system, with speaker-independent support, for voice-controlled hardware applications. Moreover, we propose to use the trained acoustic model to successfully decode offline voice commands on embedded hardware, such as an ARMv6 low-cost SoC, Raspberry PI. This type of single-board computer, mainly used for educational and research activities, can serve as a proof-of-concept software and hardware stack for low cost voice automation systems.

Integrating security in a group oriented distributed system

NASA Technical Reports Server (NTRS)

Reiter, Michael; Birman, Kenneth; Gong, LI

1992-01-01

A distributed security architecture is proposed for incorporation into group oriented distributed systems, and in particular, into the Isis distributed programming toolkit. The primary goal of the architecture is to make common group oriented abstractions robust in hostile settings, in order to facilitate the construction of high performance distributed applications that can tolerate both component failures and malicious attacks. These abstractions include process groups and causal group multicast. Moreover, a delegation and access control scheme is proposed for use in group oriented systems. The focus is the security architecture; particular cryptosystems and key exchange protocols are not emphasized.

Enabling Microscopic Simulators to Perform System Level Tasks: A System-Identification Based, Closure-on-Demand Toolkit for Multiscale Simulation Stability/Bifurcation Analysis, Optimization and Control

DTIC Science & Technology

2006-10-01

The objective was to construct a bridge between existing and future microscopic simulation codes ( kMC , MD, MC, BD, LB etc.) and traditional, continuum...kinetic Monte Carlo, kMC , equilibrium MC, Lattice-Boltzmann, LB, Brownian Dynamics, BD, or general agent-based, AB) simulators. It also, fortuitously...cond-mat/0310460 at arXiv.org. 27. Coarse Projective kMC Integration: Forward/Reverse Initial and Boundary Value Problems", R. Rico-Martinez, C. W

DDS as middleware of the Southern African Large Telescope control system

NASA Astrophysics Data System (ADS)

Maartens, Deneys S.; Brink, Janus D.

2016-07-01

The Southern African Large Telescope (SALT) software control system1 is realised as a distributed control system, implemented predominantly in National Instruments' LabVIEW. The telescope control subsystems communicate using cyclic, state-based messages. Currently, transmitting a message is accomplished by performing an HTTP PUT request to a WebDAV directory on a centralised Apache web server, while receiving is based on polling the web server for new messages. While the method works, it presents a number of drawbacks; a scalable distributed communication solution with minimal overhead is a better fit for control systems. This paper describes our exploration of the Data Distribution Service (DDS). DDS is a formal standard specification, defined by the Object Management Group (OMG), that presents a data-centric publish-subscribe model for distributed application communication and integration. It provides an infrastructure for platform- independent many-to-many communication. A number of vendors provide implementations of the DDS standard; RTI, in particular, provides a DDS toolkit for LabVIEW. This toolkit has been evaluated against the needs of SALT, and a few deficiencies have been identified. We have developed our own implementation that interfaces LabVIEW to DDS in order to address our specific needs. Our LabVIEW DDS interface implementation is built against the RTI DDS Core component, provided by RTI under their Open Community Source licence. Our needs dictate that the interface implementation be platform independent. Since we have access to the RTI DDS Core source code, we are able to build the RTI DDS libraries for any of the platforms on which we require support. The communications functionality is based on UDP multicasting. Multicasting is an efficient communications mechanism with low overheads which avoids duplicated point-to-point transmission of data on a network where there are multiple recipients of the data. In the paper we present a performance evaluation of DDS against the current HTTP-based implementation as well as the historical DataSocket implementation. We conclude with a summary and describe future work.

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.

Protocol: a multi-level intervention program to reduce stress in 9-1-1 telecommunicators.

PubMed

Meischke, Hendrika; Lilly, Michelle; Beaton, Randal; Calhoun, Rebecca; Tu, Ann; Stangenes, Scott; Painter, Ian; Revere, Debra; Baseman, Janet

2018-05-02

Nationwide, emergency response systems depend on 9-1-1 telecommunicators to prioritize, triage, and dispatch assistance to those in distress. 9-1-1 call center telecommunicators (TCs) are challenged by acute and chronic workplace stressors: tense interactions with citizen callers in crisis; overtime; shift-work; ever-changing technologies; and negative work culture, including co-worker conflict. This workforce is also subject to routine exposures to secondary traumatization while handling calls involving emergency situations and while making time urgent, high stake decisions over the phone. Our study aims to test the effectiveness of a multi-part intervention to reduce stress in 9-1-1 TCs through an online mindfulness training and a toolkit containing workplace stressor reduction resources. The study employs a randomized controlled trial design with three data collection points. The multi-part intervention includes an individual-level online mindfulness training and a call center-level organizational stress reduction toolkit. 160 TCs will be recruited from 9-1-1 call centers, complete a baseline survey at enrollment, and are randomly assigned to an intervention or a control group. Intervention group participants will start a 7-week online mindfulness training developed in-house and tailored to 9-1-1 TCs and their call center environment; control participants will be "waitlisted" and start the training after the study period ends. Following the intervention group's completion of the mindfulness training, all participants complete a second survey. Next, the online toolkit with call-center wide stress reduction resources is made available to managers of all participating call centers. After 3 months, a third survey will be completed by all participants. The primary outcome is 9-1-1 TCs' self-reported symptoms of stress at three time points as measured by the C-SOSI (Calgary Symptoms of Stress Inventory). Secondary outcomes will include: perceptions of social work environment (measured by metrics of social support and network conflict); mindfulness; and perceptions of social work environment and mindfulness as mediators of stress reduction. This study will evaluate the effectiveness of an online mindfulness training and call center-wide stress reduction toolkit in reducing self-reported stress in 9-1-1 TCs. The results of this study will add to the growing body of research on worksite stress reduction programs. ClinicalTrials.gov Registration Number: NCT02961621 Registered on November 7, 2016 (retrospectively registered).

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.

An economic toolkit for identifying the cost of emergency medical services (EMS) systems: detailed methodology of the EMS Cost Analysis Project (EMSCAP).

PubMed

Lerner, E Brooke; Garrison, Herbert G; Nichol, Graham; Maio, Ronald F; Lookman, Hunaid A; Sheahan, William D; Franz, Timothy R; Austad, James D; Ginster, Aaron M; Spaite, Daniel W

2012-02-01

Calculating the cost of an emergency medical services (EMS) system using a standardized method is important for determining the value of EMS. This article describes the development of a methodology for calculating the cost of an EMS system to its community. This includes a tool for calculating the cost of EMS (the "cost workbook") and detailed directions for determining cost (the "cost guide"). The 12-step process that was developed is consistent with current theories of health economics, applicable to prehospital care, flexible enough to be used in varying sizes and types of EMS systems, and comprehensive enough to provide meaningful conclusions. It was developed by an expert panel (the EMS Cost Analysis Project [EMSCAP] investigator team) in an iterative process that included pilot testing the process in three diverse communities. The iterative process allowed ongoing modification of the toolkit during the development phase, based upon direct, practical, ongoing interaction with the EMS systems that were using the toolkit. The resulting methodology estimates EMS system costs within a user-defined community, allowing either the number of patients treated or the estimated number of lives saved by EMS to be assessed in light of the cost of those efforts. Much controversy exists about the cost of EMS and whether the resources spent for this purpose are justified. However, the existence of a validated toolkit that provides a standardized process will allow meaningful assessments and comparisons to be made and will supply objective information to inform EMS and community officials who are tasked with determining the utilization of scarce societal resources. © 2012 by the Society for Academic Emergency Medicine.

Rapid ISS Power Availability Simulator

NASA Technical Reports Server (NTRS)

Downing, Nicholas

2011-01-01

The ISS (International Space Station) Power Resource Officers (PROs) needed a tool to automate the calculation of thousands of ISS power availability simulations used to generate power constraint matrices. Each matrix contains 864 cells, and each cell represents a single power simulation that must be run. The tools available to the flight controllers were very operator intensive and not conducive to rapidly running the thousands of simulations necessary to generate the power constraint data. SOLAR is a Java-based tool that leverages commercial-off-the-shelf software (Satellite Toolkit) and an existing in-house ISS EPS model (SPEED) to rapidly perform thousands of power availability simulations. SOLAR has a very modular architecture and consists of a series of plug-ins that are loosely coupled. The modular architecture of the software allows for the easy replacement of the ISS power system model simulator, re-use of the Satellite Toolkit integration code, and separation of the user interface from the core logic. Satellite Toolkit (STK) is used to generate ISS eclipse and insulation times, solar beta angle, position of the solar arrays over time, and the amount of shadowing on the solar arrays, which is then provided to SPEED to calculate power generation forecasts. The power planning turn-around time is reduced from three months to two weeks (83-percent decrease) using SOLAR, and the amount of PRO power planning support effort is reduced by an estimated 30 percent.

Knowledge Translation to Optimize Adult Inpatient Glycemic Management with Basal Bolus Insulin Therapy and Improve Patient Outcomes.

PubMed

Helmle, Karmon E; Chacko, Sunita; Chan, Trevor; Drake, Alison; Edwards, Alun L; Moore, Glenda E; Philp, Leta C; Popeski, Naomi; Roedler, Rhonda L; Rogers, Edwin J R; Zimmermann, Gabrielle L; McKeen, Julie

2017-12-27

To develop and evaluate a Basal Bolus Insulin Therapy (BBIT) Knowledge Translation toolkit to address barriers to adoption of established best practice with BBIT in the care of adult inpatients. This study was conducted in 2 phases and focused on the hospitalist provider group across 4 acute care facilities in Calgary. Phase 1 involved a qualitative evaluation of provider and site specific barriers and facilitators, which were mapped to validated interventions using behaviour change theory. This informed the co-development and optimization of the BBIT Knowledge Translation toolkit, with each tool targeting a specific barrier to improved diabetes care practice, including BBIT ordering. In Phase 2, the BBIT Knowledge Translation toolkit was implemented and evaluated, focusing on BBIT ordering frequency, as well as secondary outcomes of hyperglycemia (patient-days with BG >14.0 mmol/L), hypoglycemia (patient-days with BG <4.0 mmol/L), and acute length of stay. Implementation of the BBIT Knowledge Translation toolkit resulted in a significant 13% absolute increase in BBIT ordering. Hyperglycemic patient-days were significantly reduced, with no increase in hypoglycemia. There was a significant, absolute 14% reduction in length of stay. The implementation of an evidence-informed, multifaceted BBIT Knowledge Translation toolkit effectively reduced a deeply entrenched in-patient diabetes care gap. The resulting sustained practice change improved patient clinical and system resource utilization outcomes. This systemic approach to implementation will guide further scale and spread of glycemic optimization initiatives. Copyright © 2018 Diabetes Canada. Published by Elsevier Inc. All rights reserved.

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.

[Research and implementation of the TLS network transport security technology based on DICOM standard].

PubMed

Lu, Xiaoqi; Wang, Lei; Zhao, Jianfeng

2012-02-01

With the development of medical information, Picture Archiving and Communications System (PACS), Hospital Information System/Radiology Information System(HIS/RIS) and other medical information management system become popular and developed, and interoperability between these systems becomes more frequent. So, these enclosed systems will be open and regionalized by means of network, and this is inevitable. If the trend becomes true, the security of information transmission may be the first problem to be solved. Based on the need for network security, we investigated the Digital Imaging and Communications in Medicine (DICOM) Standard and Transport Layer Security (TLS) Protocol, and implemented the TLS transmission of the DICOM medical information with OpenSSL toolkit and DCMTK toolkit.

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.

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 ...

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

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/.

Everware toolkit. Supporting reproducible science and challenge-driven education.

NASA Astrophysics Data System (ADS)

Ustyuzhanin, A.; Head, T.; Babuschkin, I.; Tiunov, A.

2017-10-01

Modern science clearly demands for a higher level of reproducibility and collaboration. To make research fully reproducible one has to take care of several aspects: research protocol description, data access, environment preservation, workflow pipeline, and analysis script preservation. Version control systems like git help with the workflow and analysis scripts part. Virtualization techniques like Docker or Vagrant can help deal with environments. Jupyter notebooks are a powerful platform for conducting research in a collaborative manner. We present project Everware that seamlessly integrates git repository management systems such as Github or Gitlab, Docker and Jupyter helping with a) sharing results of real research and b) boosts education activities. With the help of Everware one can not only share the final artifacts of research but all the depth of the research process. This been shown to be extremely helpful during organization of several data analysis hackathons and machine learning schools. Using Everware participants could start from an existing solution instead of starting from scratch. They could start contributing immediately. Everware allows its users to make use of their own computational resources to run the workflows they are interested in, which leads to higher scalability of the toolkit.

Development and application of a generic CFD toolkit covering the heat flows in combined solid-liquid systems with emphasis on the thermal design of HiLumi superconducting magnets

NASA Astrophysics Data System (ADS)

Bozza, Gennaro; Malecha, Ziemowit M.; Van Weelderen, Rob

2016-12-01

The main objective of this work is to develop a robust multi-region numerical toolkit for the modeling of heat flows in combined solid-liquid systems. Specifically heat transfer in complex cryogenic system geometries involving super-fluid helium. The incentive originates from the need to support the design of superconductive magnets in the framework of the HiLumi-LHC project (Brüning and Rossi, 2015) [1]. The intent is, instead of solving heat flows in restricted domains, to be able to model a full magnet section in one go including all relevant construction details as accurately as possible. The toolkit was applied to the so-called MQXF quadrupole magnet design. Parametrisation studies were used to find a compromise in thermal design and electro-mechanical construction constraints. The cooling performance is evaluated in terms of temperature margin of the magnets under full steady state heat load conditions and in terms of maximal sustainable load. We also present transient response to pulse heat loads of varying duration and power and the system response to time-varying cold source temperatures.

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 ...

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.

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.

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.

Real-Time Payload Control and Monitoring on the World Wide Web

NASA Technical Reports Server (NTRS)

Sun, Charles; Windrem, May; Givens, John J. (Technical Monitor)

1998-01-01

World Wide Web (W3) technologies such as the Hypertext Transfer Protocol (HTTP) and the Java object-oriented programming environment offer a powerful, yet relatively inexpensive, framework for distributed application software development. This paper describes the design of a real-time payload control and monitoring system that was developed with W3 technologies at NASA Ames Research Center. Based on Java Development Toolkit (JDK) 1.1, the system uses an event-driven "publish and subscribe" approach to inter-process communication and graphical user-interface construction. A C Language Integrated Production System (CLIPS) compatible inference engine provides the back-end intelligent data processing capability, while Oracle Relational Database Management System (RDBMS) provides the data management function. Preliminary evaluation shows acceptable performance for some classes of payloads, with Java's portability and multimedia support identified as the most significant benefit.

Digital Field Mapping with the British Geological Survey

NASA Astrophysics Data System (ADS)

Leslie, Graham; Smith, Nichola; Jordan, Colm

2014-05-01

The BGS•SIGMA project was initiated in 2001 in response to a major stakeholder review of onshore mapping within the British Geological Survey (BGS). That review proposed a significant change for BGS with the recommendation that digital methods should be implemented for field mapping and data compilation. The BGS•SIGMA project (System for Integrated Geoscience MApping) is an integrated workflow for geoscientific surveying and visualisation using digital methods for geological data visualisation, recording and interpretation, in both 2D and 3D. The project has defined and documented an underpinning framework of best practice for survey and information management, best practice that has then informed the design brief and specification for a toolkit to support this new methodology. The project has now delivered BGS•SIGMA2012. BGS•SIGMA2012 is a integrated toolkit which enables assembly and interrogation/visualisation of existing geological information; capture of, and integration with, new data and geological interpretations; and delivery of 3D digital products and services. From its early days as a system which used PocketGIS run on Husky Fex21 hardware, to the present day system which runs on ruggedized tablet PCs with integrated GPS units, the system has evolved into a complete digital mapping and compilation system. BGS•SIGMA2012 uses a highly customised version of ESRI's ArcGIS 10 and 10.1 with a fully relational Access 2007/2010 geodatabase. BGS•SIGMA2012 is the third external release of our award-winning digital field mapping toolkit. The first free external release of the award-winning digital field mapping toolkit was in 2009, with the third version (BGS-SIGMAmobile2012 v1.01) released on our website (http://www.bgs.ac.uk/research/sigma/home.html) in 2013. The BGS•SIGMAmobile toolkit formed the major part of the first two releases but this new version integrates the BGS•SIGMAdesktop functionality that BGS routinely uses to transform our field data into corporate standard geological models and derivative map outputs. BGS•SIGMA2012 is the default toolkit within BGS for bedrock and superficial geological mapping and other data acquisition projects across the UK, both onshore and offshore. It is used in mapping projects in Africa, the Middle East and the USA, and has been taken to Japan as part of the Tohoku tsunami damage assessment project. It is also successfully being used worldwide by other geological surveys e.g. Norway and Tanzania; by universities including Leicester, Keele and Kyoto, and by organisations such as Vale Mining in Brazil and the Montana Bureau of Mines and Geology. It is used globally, with over 2000 licenses downloaded worldwide to date and in use on all seven continents. Development of the system is still ongoing as a result of both user feedback and the changing face of technology. Investigations into the development of a BGS•SIGMA smartphone app are currently taking place alongside system developments such as a new and more streamlined data entry system.

The semantic measures library and toolkit: fast computation of semantic similarity and relatedness using biomedical ontologies.

PubMed

Harispe, Sébastien; Ranwez, Sylvie; Janaqi, Stefan; Montmain, Jacky

2014-03-01

The semantic measures library and toolkit are robust open-source and easy to use software solutions dedicated to semantic measures. They can be used for large-scale computations and analyses of semantic similarities between terms/concepts defined in terminologies and ontologies. The comparison of entities (e.g. genes) annotated by concepts is also supported. A large collection of measures is available. Not limited to a specific application context, the library and the toolkit can be used with various controlled vocabularies and ontology specifications (e.g. Open Biomedical Ontology, Resource Description Framework). The project targets both designers and practitioners of semantic measures providing a JAVA library, as well as a command-line tool that can be used on personal computers or computer clusters. Downloads, documentation, tutorials, evaluation and support are available at http://www.semantic-measures-library.org.

Improving linear transport infrastructure efficiency by automated learning and optimised predictive maintenance techniques (INFRALERT)

NASA Astrophysics Data System (ADS)

Jiménez-Redondo, Noemi; Calle-Cordón, Alvaro; Kandler, Ute; Simroth, Axel; Morales, Francisco J.; Reyes, Antonio; Odelius, Johan; Thaduri, Aditya; Morgado, Joao; Duarte, Emmanuele

2017-09-01

The on-going H2020 project INFRALERT aims to increase rail and road infrastructure capacity in the current framework of increased transportation demand by developing and deploying solutions to optimise maintenance interventions planning. It includes two real pilots for road and railways infrastructure. INFRALERT develops an ICT platform (the expert-based Infrastructure Management System, eIMS) which follows a modular approach including several expert-based toolkits. This paper presents the methodologies and preliminary results of the toolkits for i) nowcasting and forecasting of asset condition, ii) alert generation, iii) RAMS & LCC analysis and iv) decision support. The results of these toolkits in a meshed road network in Portugal under the jurisdiction of Infraestruturas de Portugal (IP) are presented showing the capabilities of the approaches.

The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis

PubMed Central

Rampp, Markus; Soddemann, Thomas; Lederer, Hermann

2006-01-01

We describe a versatile and extensible integrated bioinformatics toolkit for the analysis of biological sequences over the Internet. The web portal offers convenient interactive access to a growing pool of chainable bioinformatics software tools and databases that are centrally installed and maintained by the RZG. Currently, supported tasks comprise sequence similarity searches in public or user-supplied databases, computation and validation of multiple sequence alignments, phylogenetic analysis and protein–structure prediction. Individual tools can be seamlessly chained into pipelines allowing the user to conveniently process complex workflows without the necessity to take care of any format conversions or tedious parsing of intermediate results. The toolkit is part of the Max-Planck Integrated Gene Analysis System (MIGenAS) of the Max Planck Society available at (click ‘Start Toolkit’). PMID:16844980

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.

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...

A prototype forensic toolkit for industrial-control-systems incident response

NASA Astrophysics Data System (ADS)

Carr, Nickolas B.; Rowe, Neil C.

2015-05-01

Industrial control systems (ICSs) are an important part of critical infrastructure in cyberspace. They are especially vulnerable to cyber-attacks because of their legacy hardware and software and the difficulty of changing it. We first survey the history of intrusions into ICSs, the more serious of which involved a continuing adversary presence on an ICS network. We discuss some common vulnerabilities and the categories of possible attacks, noting the frequent use of software written a long time ago. We propose a framework for designing ICS incident response under the constraints that no new software must be required and that interventions cannot impede the continuous processing that is the norm for such systems. We then discuss a prototype toolkit we built using the Windows Management Instrumentation Command-Line tool for host-based analysis and the Bro intrusion-detection software for network-based analysis. Particularly useful techniques we used were learning the historical range of parameters of numeric quantities so as to recognize anomalies, learning the usual addresses of connections to a node, observing Internet addresses (usually rare), observing anomalous network protocols such as unencrypted data transfers, observing unusual scheduled tasks, and comparing key files through registry entries and hash values to find malicious modifications. We tested our methods on actual data from ICSs including publicly-available data, voluntarily-submitted data, and researcher-provided "advanced persistent threat" data. We found instances of interesting behavior in our experiments. Intrusions were generally easy to see because of the repetitive nature of most processing on ICSs, but operators need to be motivated to look.

Influences on the adoption of patient safety innovation in primary care: a qualitative exploration of staff perspectives.

PubMed

Litchfield, Ian; Gill, Paramjit; Avery, Tony; Campbell, Stephen; Perryman, Katherine; Marsden, Kate; Greenfield, Sheila

2018-05-22

Primary care is changing rapidly to meet the needs of an ageing and chronically ill population. New ways of working are called for yet the introduction of innovative service interventions is complicated by organisational challenges arising from its scale and diversity and the growing complexity of patients and their care. One such intervention is the multi-strand, single platform, Patient Safety Toolkit developed to help practices provide safer care in this dynamic and pressured environment where the likelihood of adverse incidents is increasing. Here we describe the attitudes of staff toward these tools and how their implementation was shaped by a number of contextual factors specific to each practice. The Patient Safety Toolkit comprised six tools; a system of rapid note review, an online staff survey, a patient safety questionnaire, prescribing safety indicators, a medicines reconciliation tool, and a safe systems checklist. We implemented these tools at practices across the Midlands, the North West, and the South Coast of England and conducted semi-structured interviews to determine staff perspectives on their effectiveness and applicability. The Toolkit was used in 46 practices and a total of 39 follow-up interviews were conducted. Three key influences emerged on the implementation of the Toolkit these related to their ease of use and the novelty of the information they provide; whether their implementation required additional staff training or practice resource; and finally factors specific to the practice's local environment such as overlapping initiatives orchestrated by their CCG. The concept of a balanced toolkit to address a range of safety issues proved popular. A number of barriers and facilitators emerged in particular those tools that provided relevant information with a minimum impact on practice resource were favoured. Individual practice circumstances also played a role. Practices with IT aware staff were at an advantage and those previously utilising patient safety initiatives were less likely to adopt additional tools with overlapping outputs. By acknowledging these influences we can better interpret reaction to and adoption of individual elements of the toolkit and optimise future implementation.

KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies.

PubMed

Mapleson, Daniel; Garcia Accinelli, Gonzalo; Kettleborough, George; Wright, Jonathan; Clavijo, Bernardo J

2017-02-15

De novo assembly of whole genome shotgun (WGS) next-generation sequencing (NGS) data benefits from high-quality input with high coverage. However, in practice, determining the quality and quantity of useful reads quickly and in a reference-free manner is not trivial. Gaining a better understanding of the WGS data, and how that data is utilized by assemblers, provides useful insights that can inform the assembly process and result in better assemblies. We present the K-mer Analysis Toolkit (KAT): a multi-purpose software toolkit for reference-free quality control (QC) of WGS reads and de novo genome assemblies, primarily via their k-mer frequencies and GC composition. KAT enables users to assess levels of errors, bias and contamination at various stages of the assembly process. In this paper we highlight KAT's ability to provide valuable insights into assembly composition and quality of genome assemblies through pairwise comparison of k-mers present in both input reads and the assemblies. KAT is available under the GPLv3 license at: https://github.com/TGAC/KAT . bernardo.clavijo@earlham.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Evaluation of effective dose with chest digital tomosynthesis system using Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Kim, Dohyeon; Jo, Byungdu; Lee, Youngjin; Park, Su-Jin; Lee, Dong-Hoon; Kim, Hee-Joung

2015-03-01

Chest digital tomosynthesis (CDT) system has recently been introduced and studied. This system offers the potential to be a substantial improvement over conventional chest radiography for the lung nodule detection and reduces the radiation dose with limited angles. PC-based Monte Carlo program (PCXMC) simulation toolkit (STUK, Helsinki, Finland) is widely used to evaluate radiation dose in CDT system. However, this toolkit has two significant limits. Although PCXMC is not possible to describe a model for every individual patient and does not describe the accurate X-ray beam spectrum, Geant4 Application for Tomographic Emission (GATE) simulation describes the various size of phantom for individual patient and proper X-ray spectrum. However, few studies have been conducted to evaluate effective dose in CDT system with the Monte Carlo simulation toolkit using GATE. The purpose of this study was to evaluate effective dose in virtual infant chest phantom of posterior-anterior (PA) view in CDT system using GATE simulation. We obtained the effective dose at different tube angles by applying dose actor function in GATE simulation which was commonly used to obtain the medical radiation dosimetry. The results indicated that GATE simulation was useful to estimate distribution of absorbed dose. Consequently, we obtained the acceptable distribution of effective dose at each projection. These results indicated that GATE simulation can be alternative method of calculating effective dose in CDT applications.

Atlas Toolkit: Fast registration of 3D morphological datasets in the absence of landmarks

PubMed Central

Grocott, Timothy; Thomas, Paul; Münsterberg, Andrea E.

2016-01-01

Image registration is a gateway technology for Developmental Systems Biology, enabling computational analysis of related datasets within a shared coordinate system. Many registration tools rely on landmarks to ensure that datasets are correctly aligned; yet suitable landmarks are not present in many datasets. Atlas Toolkit is a Fiji/ImageJ plugin collection offering elastic group-wise registration of 3D morphological datasets, guided by segmentation of the interesting morphology. We demonstrate the method by combinatorial mapping of cell signalling events in the developing eyes of chick embryos, and use the integrated datasets to predictively enumerate Gene Regulatory Network states. PMID:26864723

Atlas Toolkit: Fast registration of 3D morphological datasets in the absence of landmarks.

PubMed

Grocott, Timothy; Thomas, Paul; Münsterberg, Andrea E

2016-02-11

Image registration is a gateway technology for Developmental Systems Biology, enabling computational analysis of related datasets within a shared coordinate system. Many registration tools rely on landmarks to ensure that datasets are correctly aligned; yet suitable landmarks are not present in many datasets. Atlas Toolkit is a Fiji/ImageJ plugin collection offering elastic group-wise registration of 3D morphological datasets, guided by segmentation of the interesting morphology. We demonstrate the method by combinatorial mapping of cell signalling events in the developing eyes of chick embryos, and use the integrated datasets to predictively enumerate Gene Regulatory Network states.

"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…

FHIR Healthcare Directories: Adopting Shared Interfaces to Achieve Interoperable Medical Device Data Integration.

PubMed

Tyndall, Timothy; Tyndall, Ayami

2018-01-01

Healthcare directories are vital for interoperability among healthcare providers, researchers and patients. Past efforts at directory services have not provided the tools to allow integration of the diverse data sources. Many are overly strict, incompatible with legacy databases, and do not provide Data Provenance. A more architecture-independent system is needed to enable secure, GDPR-compatible (8) service discovery across organizational boundaries. We review our development of a portable Data Provenance Toolkit supporting provenance within Health Information Exchange (HIE) systems. The Toolkit has been integrated with client software and successfully leveraged in clinical data integration. The Toolkit validates provenance stored in a Blockchain or Directory record and creates provenance signatures, providing standardized provenance that moves with the data. This healthcare directory suite implements discovery of healthcare data by HIE and EHR systems via FHIR. Shortcomings of past directory efforts include the ability to map complex datasets and enabling interoperability via exchange endpoint discovery. By delivering data without dictating how it is stored we improve exchange and facilitate discovery on a multi-national level through open source, fully interoperable tools. With the development of Data Provenance resources we enhance exchange and improve security and usability throughout the health data continuum.

Integration Toolkit and Methods (ITKM) Corporate Data Integration Tools (CDIT). Review of the State-of-the-Art with Respect to Integration Toolkits and Methods (ITKM)

DTIC Science & Technology

1992-06-01

system capabilities \\Jch as memory management and network communications are provided by a virtual machine-type operating environment. Various human ...thinking. The elements of this substrate include representational formality, genericity, a method of formal analysis, and augmentation of human analytical...the form of identifying: the data entity itself; its aliases (including how the data is presented th programs or human users in the form of copy

A population-based randomized controlled trial of the effect of combining a pedometer with an intervention toolkit on physical activity among individuals with low levels of physical activity or fitness.

PubMed

Petersen, Christina Bjørk; Severin, Maria; Hansen, Andreas Wolff; Curtis, Tine; Grønbæk, Morten; Tolstrup, Janne Schurmann

2012-02-01

To examine if receiving a pedometer along with an intervention toolkit is associated with increased physical activity, aerobic fitness and better self-rated health among individuals with low levels of physical activity or fitness. The intervention was nested in the Danish Health Examination Survey (DANHES) and carried out in 2008. Participants were randomly assigned to either a pedometer group (n=326) or a control group (n=329). Physical activity, aerobic fitness, and self-rated health were measured at baseline and at 3-month follow-up, and differences were tested by Wilcoxons signed rank tests and Chi-squared tests. At follow-up, no significant differences in physical activity, aerobic fitness and self-rated health were found between the groups. However, the oldest participants in the pedometer group reported significantly more walking time compared to the controls (controls=368 min/week, pedometer group=680 min/week, P=0.05). Among participants who completed the intervention, a significant effect on total walking time was observed (median difference=225 min/week, P=0.04). The results suggest that receiving a pedometer and along with an intervention toolkit can increase walking time in older individuals, but not in younger individuals. Thus, this type of intervention offers great potential for promoting physical activity in older individuals. NCT01071811. Copyright © 2011 Elsevier Inc. All rights reserved.

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

Backtracking behaviour in lost ants: an additional strategy in their navigational toolkit

PubMed Central

Wystrach, Antoine; Schwarz, Sebastian; Baniel, Alice; Cheng, Ken

2013-01-01

Ants use multiple sources of information to navigate, but do not integrate all this information into a unified representation of the world. Rather, the available information appears to serve three distinct main navigational systems: path integration, systematic search and the use of learnt information—mainly via vision. Here, we report on an additional behaviour that suggests a supplemental system in the ant's navigational toolkit: ‘backtracking’. Homing ants, having almost reached their nest but, suddenly displaced to unfamiliar areas, did not show the characteristic undirected headings of systematic searches. Instead, these ants backtracked in the compass direction opposite to the path that they had just travelled. The ecological function of this behaviour is clear as we show it increases the chances of returning to familiar terrain. Importantly, the mechanistic implications of this behaviour stress an extra level of cognitive complexity in ant navigation. Our results imply: (i) the presence of a type of ‘memory of the current trip’ allowing lost ants to take into account the familiar view recently experienced, and (ii) direct sharing of information across different navigational systems. We propose a revised architecture of the ant's navigational toolkit illustrating how the different systems may interact to produce adaptive behaviours. PMID:23966644

Evolution of the Calcium-Based Intracellular Signaling System

PubMed Central

Marchadier, Elodie; Oates, Matt E.; Fang, Hai; Donoghue, Philip C.J.; Hetherington, Alistair M.; Gough, Julian

2016-01-01

To progress our understanding of molecular evolution from a collection of well-studied genes toward the level of the cell, we must consider whole systems. Here, we reveal the evolution of an important intracellular signaling system. The calcium-signaling toolkit is made up of different multidomain proteins that have undergone duplication, recombination, sequence divergence, and selection. The picture of evolution, considering the repertoire of proteins in the toolkit of both extant organisms and ancestors, is radically different from that of other systems. In eukaryotes, the repertoire increased in both abundance and diversity at a far greater rate than general genomic expansion. We describe how calcium-based intracellular signaling evolution differs not only in rate but in nature, and how this correlates with the disparity of plants and animals. PMID:27358427

Monte Carlo treatment planning with modulated electron radiotherapy: framework development and application

NASA Astrophysics Data System (ADS)

Alexander, Andrew William

Within the field of medical physics, Monte Carlo radiation transport simulations are considered to be the most accurate method for the determination of dose distributions in patients. The McGill Monte Carlo treatment planning system (MMCTP), provides a flexible software environment to integrate Monte Carlo simulations with current and new treatment modalities. A developing treatment modality called energy and intensity modulated electron radiotherapy (MERT) is a promising modality, which has the fundamental capabilities to enhance the dosimetry of superficial targets. An objective of this work is to advance the research and development of MERT with the end goal of clinical use. To this end, we present the MMCTP system with an integrated toolkit for MERT planning and delivery of MERT fields. Delivery is achieved using an automated "few leaf electron collimator" (FLEC) and a controller. Aside from the MERT planning toolkit, the MMCTP system required numerous add-ons to perform the complex task of large-scale autonomous Monte Carlo simulations. The first was a DICOM import filter, followed by the implementation of DOSXYZnrc as a dose calculation engine and by logic methods for submitting and updating the status of Monte Carlo simulations. Within this work we validated the MMCTP system with a head and neck Monte Carlo recalculation study performed by a medical dosimetrist. The impact of MMCTP lies in the fact that it allows for systematic and platform independent large-scale Monte Carlo dose calculations for different treatment sites and treatment modalities. In addition to the MERT planning tools, various optimization algorithms were created external to MMCTP. The algorithms produced MERT treatment plans based on dose volume constraints that employ Monte Carlo pre-generated patient-specific kernels. The Monte Carlo kernels are generated from patient-specific Monte Carlo dose distributions within MMCTP. The structure of the MERT planning toolkit software and optimization algorithms are demonstrated. We investigated the clinical significance of MERT on spinal irradiation, breast boost irradiation, and a head and neck sarcoma cancer site using several parameters to analyze the treatment plans. Finally, we investigated the idea of mixed beam photon and electron treatment planning. Photon optimization treatment planning tools were included within the MERT planning toolkit for the purpose of mixed beam optimization. In conclusion, this thesis work has resulted in the development of an advanced framework for photon and electron Monte Carlo treatment planning studies and the development of an inverse planning system for photon, electron or mixed beam radiotherapy (MBRT). The justification and validation of this work is found within the results of the planning studies, which have demonstrated dosimetric advantages to using MERT or MBRT in comparison to clinical treatment alternatives.

Fiia: A Model-Based Approach to Engineering Collaborative Augmented Reality

NASA Astrophysics Data System (ADS)

Wolfe, Christopher; Smith, J. David; Phillips, W. Greg; Graham, T. C. Nicholas

Augmented reality systems often involve collaboration among groups of people. While there are numerous toolkits that aid the development of such augmented reality groupware systems (e.g., ARToolkit and Groupkit), there remains an enormous gap between the specification of an AR groupware application and its implementation. In this chapter, we present Fiia, a toolkit which simplifies the development of collaborative AR applications. Developers specify the structure of their applications using the Fiia modeling language, which abstracts details of networking and provides high-level support for specifying adapters between the physical and virtual world. The Fiia.Net runtime system then maps this conceptual model to a runtime implementation. We illustrate Fiia via Raptor, an augmented reality application used to help small groups collaboratively prototype video games.

Economic evaluation of the Good School Toolkit: an intervention for reducing violence in primary schools in Uganda.

PubMed

Greco, Giulia; Knight, Louise; Ssekadde, Willington; Namy, Sophie; Naker, Dipak; Devries, Karen

2018-01-01

This paper presents the cost and cost-effectiveness of the Good School Toolkit (GST), a programme aimed at reducing physical violence perpetrated by school staff to students in Uganda. The effectiveness of the Toolkit was tested with a cluster randomised controlled trial in 42 primary schools in Luwero District, Uganda. A full economic costing evaluation and cost-effectiveness analysis were conducted alongside the trial. Both financial and economic costs were collected retrospectively from the provider's perspective to estimate total and unit costs. The total cost of setting up and running the Toolkit over the 18-month trial period is estimated at US$397 233, excluding process monitor (M&E) activities. The cost to run the intervention is US$7429 per school annually, or US$15 per primary school pupil annually, in the trial intervention schools. It is estimated that the intervention has averted 1620 cases of past-week physical violence during the 18-month implementation period. The total cost per case of violence averted is US$244, and the annual implementation cost is US$96 per case averted during the trial. The GST is a cost-effective intervention for reducing violence against pupils in primary schools in Uganda. It compares favourably against other violence reduction interventions in the region.

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 Powerful Toolkit for Synthetic Biology: Over 3.8 Billion Years of Evolution

NASA Technical Reports Server (NTRS)

Rothschild, Lynn J.

2010-01-01

The combination of evolutionary with engineering principles will enhance synthetic biology. Conversely, synthetic biology has the potential to enrich evolutionary biology by explaining why some adaptive space is empty, on Earth or elsewhere. Synthetic biology, the design and construction of artificial biological systems, substitutes bio-engineering for evolution, which is seen as an obstacle. But because evolution has produced the complexity and diversity of life, it provides a proven toolkit of genetic materials and principles available to synthetic biology. Evolution operates on the population level, with the populations composed of unique individuals that are historical entities. The source of genetic novelty includes mutation, gene regulation, sex, symbiosis, and interspecies gene transfer. At a phenotypic level, variation derives from regulatory control, replication and diversification of components, compartmentalization, sexual selection and speciation, among others. Variation is limited by physical constraints such as diffusion, and chemical constraints such as reaction rates and membrane fluidity. While some of these tools of evolution are currently in use in synthetic biology, all ought to be examined for utility. A hybrid approach of synthetic biology coupled with fine-tuning through evolution is suggested

A powerful toolkit for synthetic biology: Over 3.8 billion years of evolution.

PubMed

Rothschild, Lynn J

2010-04-01

The combination of evolutionary with engineering principles will enhance synthetic biology. Conversely, synthetic biology has the potential to enrich evolutionary biology by explaining why some adaptive space is empty, on Earth or elsewhere. Synthetic biology, the design and construction of artificial biological systems, substitutes bio-engineering for evolution, which is seen as an obstacle. But because evolution has produced the complexity and diversity of life, it provides a proven toolkit of genetic materials and principles available to synthetic biology. Evolution operates on the population level, with the populations composed of unique individuals that are historical entities. The source of genetic novelty includes mutation, gene regulation, sex, symbiosis, and interspecies gene transfer. At a phenotypic level, variation derives from regulatory control, replication and diversification of components, compartmentalization, sexual selection and speciation, among others. Variation is limited by physical constraints such as diffusion, and chemical constraints such as reaction rates and membrane fluidity. While some of these tools of evolution are currently in use in synthetic biology, all ought to be examined for utility. A hybrid approach of synthetic biology coupled with fine-tuning through evolution is suggested.

NAIF Toolkit - Extended

NASA Technical Reports Server (NTRS)

Acton, Charles H., Jr.; Bachman, Nathaniel J.; Semenov, Boris V.; Wright, Edward D.

2010-01-01

The Navigation Ancillary Infor ma tion Facility (NAIF) at JPL, acting under the direction of NASA s Office of Space Science, has built a data system named SPICE (Spacecraft Planet Instrument Cmatrix Events) to assist scientists in planning and interpreting scientific observations (see figure). SPICE provides geometric and some other ancillary information needed to recover the full value of science instrument data, including correlation of individual instrument data sets with data from other instruments on the same or other spacecraft. This data system is used to produce space mission observation geometry data sets known as SPICE kernels. It is also used to read SPICE kernels and to compute derived quantities such as positions, orientations, lighting angles, etc. The SPICE toolkit consists of a subroutine/ function library, executable programs (both large applications and simple utilities that focus on kernel management), and simple examples of using SPICE toolkit subroutines. This software is very accurate, thoroughly tested, and portable to all computers. It is extremely stable and reusable on all missions. Since the previous version, three significant capabilities have been added: Interactive Data Language (IDL) interface, MATLAB interface, and a geometric event finder subsystem.

Rural Aging

MedlinePlus

... Toolkits Economic Impact Analysis Tool Community Health Gateway Sustainability Planning Tools Testing New Approaches Rural Health IT ... to the Centers for Disease Control and Prevention report, The State of Aging and Health in America ...

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.

NiftySim: A GPU-based nonlinear finite element package for simulation of soft tissue biomechanics.

PubMed

Johnsen, Stian F; Taylor, Zeike A; Clarkson, Matthew J; Hipwell, John; Modat, Marc; Eiben, Bjoern; Han, Lianghao; Hu, Yipeng; Mertzanidou, Thomy; Hawkes, David J; Ourselin, Sebastien

2015-07-01

NiftySim, an open-source finite element toolkit, has been designed to allow incorporation of high-performance soft tissue simulation capabilities into biomedical applications. The toolkit provides the option of execution on fast graphics processing unit (GPU) hardware, numerous constitutive models and solid-element options, membrane and shell elements, and contact modelling facilities, in a simple to use library. The toolkit is founded on the total Lagrangian explicit dynamics (TLEDs) algorithm, which has been shown to be efficient and accurate for simulation of soft tissues. The base code is written in C[Formula: see text], and GPU execution is achieved using the nVidia CUDA framework. In most cases, interaction with the underlying solvers can be achieved through a single Simulator class, which may be embedded directly in third-party applications such as, surgical guidance systems. Advanced capabilities such as contact modelling and nonlinear constitutive models are also provided, as are more experimental technologies like reduced order modelling. A consistent description of the underlying solution algorithm, its implementation with a focus on GPU execution, and examples of the toolkit's usage in biomedical applications are provided. Efficient mapping of the TLED algorithm to parallel hardware results in very high computational performance, far exceeding that available in commercial packages. The NiftySim toolkit provides high-performance soft tissue simulation capabilities using GPU technology for biomechanical simulation research applications in medical image computing, surgical simulation, and surgical guidance applications.

A Cas9-based toolkit to program gene expression in Saccharomyces cerevisiae

DOE PAGES

Reider Apel, Amanda; d'Espaux, Leo; Wehrs, Maren; ...

2016-11-28

Despite the extensive use of Saccharomyces cerevisiae as a platform for synthetic biology, strain engineering remains slow and laborious. Here, we employ CRISPR/Cas9 technology to build a cloning-free toolkit that addresses commonly encountered obstacles in metabolic engineering, including chromosomal integration locus and promoter selection, as well as protein localization and solubility. The toolkit includes 23 Cas9-sgRNA plasmids, 37 promoters of various strengths and temporal expression profiles, and 10 protein-localization, degradation and solubility tags. We facilitated the use of these parts via a web-based tool, that automates the generation of DNA fragments for integration. Our system builds upon existing gene editingmore » methods in the thoroughness with which the parts are standardized and characterized, the types and number of parts available and the ease with which our methodology can be used to perform genetic edits in yeast. We demonstrated the applicability of this toolkit by optimizing the expression of a challenging but industrially important enzyme, taxadiene synthase (TXS). This approach enabled us to diagnose an issue with TXS solubility, the resolution of which yielded a 25-fold improvement in taxadiene production.« less

A Cas9-based toolkit to program gene expression in Saccharomyces cerevisiae

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

Reider Apel, Amanda; d'Espaux, Leo; Wehrs, Maren

Despite the extensive use of Saccharomyces cerevisiae as a platform for synthetic biology, strain engineering remains slow and laborious. Here, we employ CRISPR/Cas9 technology to build a cloning-free toolkit that addresses commonly encountered obstacles in metabolic engineering, including chromosomal integration locus and promoter selection, as well as protein localization and solubility. The toolkit includes 23 Cas9-sgRNA plasmids, 37 promoters of various strengths and temporal expression profiles, and 10 protein-localization, degradation and solubility tags. We facilitated the use of these parts via a web-based tool, that automates the generation of DNA fragments for integration. Our system builds upon existing gene editingmore » methods in the thoroughness with which the parts are standardized and characterized, the types and number of parts available and the ease with which our methodology can be used to perform genetic edits in yeast. We demonstrated the applicability of this toolkit by optimizing the expression of a challenging but industrially important enzyme, taxadiene synthase (TXS). This approach enabled us to diagnose an issue with TXS solubility, the resolution of which yielded a 25-fold improvement in taxadiene production.« less

Telescience Resource Kit (TReK)

NASA Technical Reports Server (NTRS)

Lippincott, Jeff

2015-01-01

Telescience Resource Kit (TReK) is one of the Huntsville Operations Support Center (HOSC) remote operations solutions. It can be used to monitor and control International Space Station (ISS) payloads from anywhere in the world. It is comprised of a suite of software applications and libraries that provide generic data system capabilities and access to HOSC services. The TReK Software has been operational since 2000. A new cross-platform version of TReK is under development. The new software is being released in phases during the 2014-2016 timeframe. The TReK Release 3.x series of software is the original TReK software that has been operational since 2000. This software runs on Windows. It contains capabilities to support traditional telemetry and commanding using CCSDS (Consultative Committee for Space Data Systems) packets. The TReK Release 4.x series of software is the new cross platform software. It runs on Windows and Linux. The new TReK software will support communication using standard IP protocols and traditional telemetry and commanding. All the software listed above is compatible and can be installed and run together on Windows. The new TReK software contains a suite of software that can be used by payload developers on the ground and onboard (TReK Toolkit). TReK Toolkit is a suite of lightweight libraries and utility applications for use onboard and on the ground. TReK Desktop is the full suite of TReK software -most useful on the ground. When TReK Desktop is released, the TReK installation program will provide the option to choose just the TReK Toolkit portion of the software or the full TReK Desktop suite. The ISS program is providing the TReK Toolkit software as a generic flight software capability offered as a standard service to payloads. TReK Software Verification was conducted during the April/May 2015 timeframe. Payload teams using the TReK software onboard can reference the TReK software verification. TReK will be demonstrated on-orbit running on an ISS provided T61p laptop. Target Timeframe: September 2015 -2016. The on-orbit demonstration will collect benchmark metrics, and will be used in the future to provide live demonstrations during ISS Payload Conferences. Benchmark metrics and demonstrations will address the protocols described in SSP 52050-0047 Ku Forward section 3.3.7. (Associated term: CCSDS File Delivery Protocol (CFDP)).

Formal Verification Toolkit for Requirements and Early Design Stages

NASA Technical Reports Server (NTRS)

Badger, Julia M.; Miller, Sheena Judson

2011-01-01

Efficient flight software development from natural language requirements needs an effective way to test designs earlier in the software design cycle. A method to automatically derive logical safety constraints and the design state space from natural language requirements is described. The constraints can then be checked using a logical consistency checker and also be used in a symbolic model checker to verify the early design of the system. This method was used to verify a hybrid control design for the suit ports on NASA Johnson Space Center's Space Exploration Vehicle against safety requirements.

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 Java-Enabled Interactive Graphical Gas Turbine Propulsion System Simulator

NASA Technical Reports Server (NTRS)

Reed, John A.; Afjeh, Abdollah A.

1997-01-01

This paper describes a gas turbine simulation system which utilizes the newly developed Java language environment software system. The system provides an interactive graphical environment which allows the quick and efficient construction and analysis of arbitrary gas turbine propulsion systems. The simulation system couples a graphical user interface, developed using the Java Abstract Window Toolkit, and a transient, space- averaged, aero-thermodynamic gas turbine analysis method, both entirely coded in the Java language. The combined package provides analytical, graphical and data management tools which allow the user to construct and control engine simulations by manipulating graphical objects on the computer display screen. Distributed simulations, including parallel processing and distributed database access across the Internet and World-Wide Web (WWW), are made possible through services provided by the Java environment.

An open-source LabVIEW application toolkit for phasic heart rate analysis in psychophysiological research.

PubMed

Duley, Aaron R; Janelle, Christopher M; Coombes, Stephen A

2004-11-01

The cardiovascular system has been extensively measured in a variety of research and clinical domains. Despite technological and methodological advances in cardiovascular science, the analysis and evaluation of phasic changes in heart rate persists as a way to assess numerous psychological concomitants. Some researchers, however, have pointed to constraints on data analysis when evaluating cardiac activity indexed by heart rate or heart period. Thus, an off-line application toolkit for heart rate analysis is presented. The program, written with National Instruments' LabVIEW, incorporates a variety of tools for off-line extraction and analysis of heart rate data. Current methods and issues concerning heart rate analysis are highlighted, and how the toolkit provides a flexible environment to ameliorate common problems that typically lead to trial rejection is discussed. Source code for this program may be downloaded from the Psychonomic Society Web archive at www.psychonomic.org/archive/.

The interactive learning toolkit: technology and the classroom

NASA Astrophysics Data System (ADS)

Lukoff, Brian; Tucker, Laura

2011-04-01

Peer Instruction (PI) and Just-in-Time-Teaching (JiTT) have been shown to increase both students' conceptual understanding and problem-solving skills. However, the time investment for the instructor to prepare appropriate conceptual questions and manage student JiTT responses is one of the main implementation hurdles. To overcome this we have developed the Interactive Learning Toolkit (ILT), a course management system specifically designed to support PI and JiTT. We are working to integrate the ILT with a fully interactive classroom system where students can use their laptops and smartphones to respond to ConcepTests in class. The goal is to use technology to engage students in conceptual thinking both in and out of the classroom.

Study on Web-Based Tool for Regional Agriculture Industry Structure Optimization Using Ajax

NASA Astrophysics Data System (ADS)

Huang, Xiaodong; Zhu, Yeping

According to the research status of regional agriculture industry structure adjustment information system and the current development of information technology, this paper takes web-based regional agriculture industry structure optimization tool as research target. This paper introduces Ajax technology and related application frameworks to build an auxiliary toolkit of decision support system for agricultural policy maker and economy researcher. The toolkit includes a “one page” style component of regional agriculture industry structure optimization which provides agile arguments setting method that enables applying sensitivity analysis and usage of data and comparative advantage analysis result, and a component that can solve the linear programming model and its dual problem by simplex method.

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

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.

The Wind Integration National Dataset (WIND) toolkit (Presentation)

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

Caroline Draxl: NREL

2014-01-01

Regional wind integration studies require detailed wind power output data at many locations to perform simulations of how the power system will operate under high penetration scenarios. The wind datasets that serve as inputs into the study must realistically reflect the ramping characteristics, spatial and temporal correlations, and capacity factors of the simulated wind plants, as well as being time synchronized with available load profiles.As described in this presentation, the WIND Toolkit fulfills these requirements by providing a state-of-the-art national (US) wind resource, power production and forecast dataset.

Testability, Test Automation and Test Driven Development for the Trick Simulation Toolkit

NASA Technical Reports Server (NTRS)

Penn, John

2014-01-01

This paper describes the adoption of a Test Driven Development approach and a Continuous Integration System in the development of the Trick Simulation Toolkit, a generic simulation development environment for creating high fidelity training and engineering simulations at the NASA Johnson Space Center and many other NASA facilities. It describes the approach, and the significant benefits seen, such as fast, thorough and clear test feedback every time code is checked into the code repository. It also describes an approach that encourages development of code that is testable and adaptable.

PDDL4J: a planning domain description library for java

NASA Astrophysics Data System (ADS)

Pellier, D.; Fiorino, H.

2018-01-01

PDDL4J (Planning Domain Description Library for Java) is an open source toolkit for Java cross-platform developers meant (1) to provide state-of-the-art planners based on the Pddl language, and (2) to facilitate research works on new planners. In this article, we present an overview of the Automated Planning concepts and languages. We present some planning systems and their most significant applications. Then, we detail the Pddl4j toolkit with an emphasis on the available informative structures, heuristics and search algorithms.

Content Analysis in Systems Engineering Acquisition Activities

DTIC Science & Technology

2016-04-30

Acquisition Activities Karen Holness, Assistant Professor, NPS Update on the Department of the Navy Systems Engineering Career Competency Model Clifford...systems engineering toolkit . Having a common analysis tool that is easy to use would support the feedback of observed system performance trends from the

Integrating surgical robots into the next medical toolkit.

PubMed

Lai, Fuji; Entin, Eileen

2006-01-01

Surgical robots hold much promise for revolutionizing the field of surgery and improving surgical care. However, despite the potential advantages they offer, there are multiple barriers to adoption and integration into practice that may prevent these systems from realizing their full potential benefit. This study elucidated some of the most salient considerations that need to be addressed for integration of new technologies such as robotic systems into the operating room of the future as it evolves into a complex system of systems. We conducted in-depth interviews with operating room team members and other stakeholders to identify potential barriers in areas of workflow, teamwork, training, clinical acceptance, and human-system interaction. The findings of this study will inform an approach for the design and integration of robotics and related computer-assisted technologies into the next medical toolkit for "computer-enhanced surgery" to improve patient safety and healthcare quality.

The Good Schools Toolkit to prevent violence against children in Ugandan primary schools: study protocol for a cluster randomised controlled trial.

PubMed

Devries, Karen M; Allen, Elizabeth; Child, Jennifer C; Walakira, Eddy; Parkes, Jenny; Elbourne, Diana; Watts, Charlotte; Naker, Dipak

2013-07-24

We aim to evaluate the effectiveness of the Good School Toolkit, developed by Raising Voices, in preventing violence against children attending school and in improving child mental health and educational outcomes. We are conducting a two-arm cluster randomised controlled trial with parallel assignment in Luwero District, Uganda. We will also conduct a qualitative study, a process evaluation and an economic evaluation. A total of 42 schools, representative of Luwero District, Uganda, were allocated to receive the Toolkit plus implementation support, or were allocated to a wait-list control condition. Our main analysis will involve a cross-sectional comparison of the prevalence of past-week violence from school staff as reported by children in intervention and control primary schools at follow-up.At least 60 children per school and all school staff members will be interviewed at follow-up. Data collection involves a combination of mobile phone-based, interviewer-completed questionnaires and paper-and-pen educational tests. Survey instruments include the ISPCAN Child Abuse Screening Tools to assess experiences of violence; the Strengths and Difficulties Questionnaire to measure symptoms of common childhood mental disorders; and word recognition, reading comprehension, spelling, arithmetic and sustained attention tests adapted from an intervention trial in Kenya. To our knowledge, this is the first study to rigorously investigate the effects of any intervention to prevent violence from school staff to children in primary school in a low-income setting. We hope the results will be informative across the African region and in other settings. clinicaltrials.gov NCT01678846.

When paradigms collide at the road rail interface: evaluation of a sociotechnical systems theory design toolkit for cognitive work analysis.

PubMed

Read, Gemma J M; Salmon, Paul M; Lenné, Michael G

2016-09-01

The Cognitive Work Analysis Design Toolkit (CWA-DT) is a recently developed approach that provides guidance and tools to assist in applying the outputs of CWA to design processes to incorporate the values and principles of sociotechnical systems theory. In this paper, the CWA-DT is evaluated based on an application to improve safety at rail level crossings. The evaluation considered the extent to which the CWA-DT met pre-defined methodological criteria and aligned with sociotechnical values and principles. Both process and outcome measures were taken based on the ratings of workshop participants and human factors experts. Overall, workshop participants were positive about the process and indicated that it met the methodological criteria and sociotechnical values. However, expert ratings suggested that the CWA-DT achieved only limited success in producing RLX designs that fully aligned with the sociotechnical approach. Discussion about the appropriateness of the sociotechnical approach in a public safety context is provided. Practitioner Summary: Human factors and ergonomics practitioners need evidence of the effectiveness of methods. A design toolkit for cognitive work analysis, incorporating values and principles from sociotechnical systems theory, was applied to create innovative designs for rail level crossings. Evaluation results based on the application are provided and discussed.

FAST: framework for heterogeneous medical image computing and visualization.

PubMed

Smistad, Erik; Bozorgi, Mohammadmehdi; Lindseth, Frank

2015-11-01

Computer systems are becoming increasingly heterogeneous in the sense that they consist of different processors, such as multi-core CPUs and graphic processing units. As the amount of medical image data increases, it is crucial to exploit the computational power of these processors. However, this is currently difficult due to several factors, such as driver errors, processor differences, and the need for low-level memory handling. This paper presents a novel FrAmework for heterogeneouS medical image compuTing and visualization (FAST). The framework aims to make it easier to simultaneously process and visualize medical images efficiently on heterogeneous systems. FAST uses common image processing programming paradigms and hides the details of memory handling from the user, while enabling the use of all processors and cores on a system. The framework is open-source, cross-platform and available online. Code examples and performance measurements are presented to show the simplicity and efficiency of FAST. The results are compared to the insight toolkit (ITK) and the visualization toolkit (VTK) and show that the presented framework is faster with up to 20 times speedup on several common medical imaging algorithms. FAST enables efficient medical image computing and visualization on heterogeneous systems. Code examples and performance evaluations have demonstrated that the toolkit is both easy to use and performs better than existing frameworks, such as ITK and VTK.

QALMA: A computational toolkit for the analysis of quality protocols for medical linear accelerators in radiation therapy

NASA Astrophysics Data System (ADS)

Rahman, Md Mushfiqur; Lei, Yu; Kalantzis, Georgios

2018-01-01

Quality Assurance (QA) for medical linear accelerator (linac) is one of the primary concerns in external beam radiation Therapy. Continued advancements in clinical accelerators and computer control technology make the QA procedures more complex and time consuming which often, adequate software accompanied with specific phantoms is required. To ameliorate that matter, we introduce QALMA (Quality Assurance for Linac with MATLAB), a MALAB toolkit which aims to simplify the quantitative analysis of QA for linac which includes Star-Shot analysis, Picket Fence test, Winston-Lutz test, Multileaf Collimator (MLC) log file analysis and verification of light & radiation field coincidence test.

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.

TOPAS Tool for Particle Simulation

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

Perl, Joseph

2013-05-30

TOPAS lets users simulate the passage of subatomic particles moving through any kind of radiation therapy treatment system, can import a patient geometry, can record dose and other quantities, has advanced graphics, and is fully four-dimensional (3D plus time) to handle the most challenging time-dependent aspects of modern cancer treatments.TOPAS unlocks the power of the most accurate particle transport simulation technique, the Monte Carlo (MC) method, while removing the painstaking coding work such methods used to require. Research physicists can use TOPAS to improve delivery systems towards safer and more effective radiation therapy treatments, easily setting up and running complexmore » simulations that previously used to take months of preparation. Clinical physicists can use TOPAS to increase accuracy while reducing side effects, simulating patient-specific treatment plans at the touch of a button. TOPAS is designed as a “user code” layered on top of the Geant4 Simulation Toolkit. TOPAS includes the standard Geant4 toolkit, plus additional code to make Geant4 easier to control and to extend Geant4 functionality. TOPAS aims to make proton simulation both “reliable” and “repeatable.” “Reliable” means both accurate physics and a high likelihood to simulate precisely what the user intended to simulate, reducing issues of wrong units, wrong materials, wrong scoring locations, etc. “Repeatable” means not just getting the same result from one simulation to another, but being able to easily restore a previously used setup and reducing sources of error when a setup is passed from one user to another. TOPAS control system incorporates key lessons from safety management, proactively removing possible sources of user error such as line-ordering mistakes In control files. TOPAS has been used to model proton therapy treatment examples including the UCSF eye treatment head, the MGH stereotactic alignment in radiosurgery treatment head and the MGH gantry treatment heads in passive scattering and scanning modes, and has demonstrated dose calculation based on patient-specific CT data.« less

Economic evaluation of the Good School Toolkit: an intervention for reducing violence in primary schools in Uganda

PubMed Central

Knight, Louise; Ssekadde, Willington; Namy, Sophie; Naker, Dipak; Devries, Karen

2018-01-01

Introduction This paper presents the cost and cost-effectiveness of the Good School Toolkit (GST), a programme aimed at reducing physical violence perpetrated by school staff to students in Uganda. Methods The effectiveness of the Toolkit was tested with a cluster randomised controlled trial in 42 primary schools in Luwero District, Uganda. A full economic costing evaluation and cost-effectiveness analysis were conducted alongside the trial. Both financial and economic costs were collected retrospectively from the provider’s perspective to estimate total and unit costs. Results The total cost of setting up and running the Toolkit over the 18-month trial period is estimated at US$397 233, excluding process monitor (M&E) activities. The cost to run the intervention is US$7429 per school annually, or US$15 per primary school pupil annually, in the trial intervention schools. It is estimated that the intervention has averted 1620 cases of past-week physical violence during the 18-month implementation period. The total cost per case of violence averted is US$244, and the annual implementation cost is US$96 per case averted during the trial. Conclusions The GST is a cost-effective intervention for reducing violence against pupils in primary schools in Uganda. It compares favourably against other violence reduction interventions in the region. PMID:29707243

The Ohio Gestational Diabetes Postpartum Care Learning Collaborative: Development of a Quality Improvement Initiative to Improve Systems of Care for Women.

PubMed

Shellhaas, Cynthia; Conrey, Elizabeth; Crane, Dushka; Lorenz, Allison; Wapner, Andrew; Oza-Frank, Reena; Bouchard, Jo

2016-11-01

Objectives To improve clinical practice and increase postpartum visit Type 2 diabetes mellitus (T2DM) screening rates in women with a history of gestational diabetes mellitus (GDM). Methods We recruited clinical sites with at least half of pregnant patients enrolled in Medicaid to participate in an 18-month quality improvement (QI) project. To support clinical practice changes, we developed provider and patient toolkits with educational and clinical practice resources. Clinical subject-matter experts facilitated a learning network to train sites and promote discussion and learning among sites. Sites submitted data from patient chart reviews monthly for key measures that we used to provide rapid-cycle feedback. Providers were surveyed at completion regarding toolkit usefulness and satisfaction. Results Of fifteen practices recruited, twelve remained actively engaged. We disseminated more than 70 provider and 2345 patient toolkits. Documented delivery of patient education improved for timely GDM prenatal screening, reduction of future T2DM risk, smoking cessation, and family planning. Sites reported toolkits were useful and easy to use. Of women for whom postpartum data were available, 67 % had a documented postpartum visit and 33 % had a postpartum T2DM screen. Lack of information sharing between prenatal and postpartum care providers was are barriers to provision and documentation of care. Conclusions for Practice QI and toolkit resources may improve the quality of prenatal education. However, postpartum care did not reach optimal levels. Future work should focus on strategies to support coordination of care between obstetrical and primary care providers.

Applying change management metaphors to a national e-Health strategy.

PubMed

Saunders, Chad; Scott, Richard E

2014-01-01

Recent attempts at a collective understanding of how to develop an e-Health strategy have addressed the individual organisation, collection of organisations, and national levels. At the national level the World Health Organisation's National eHealth Strategy Toolkit serves as an exemplar that consolidates knowledge in this area, guides practical implementations, and identifies areas for future research. A key implication of this toolkit is the considerable number of organisational changes required to successfully apply their ideas in practice. This study looks critically at the confluence of change management and e-Health strategy using metaphors that underpin established models of change management. Several of Morgan's organisational metaphors are presented (highlighting varied beliefs and assumptions regarding how change is enacted, who is responsible for the change, and guiding principles for that change), and used to provide a framework. Attention is then directed to several prominent models of change management that exemplify one or more of these metaphors, and these theoretical insights are applied to evaluate the World Health Organisation's National eHealth Strategy Toolkit. The paper presents areas for consideration when using the WHO/ITU toolkit, and suggestions on how to improve its use in practice. The goal is to seek insight regarding the optimal sequence of steps needed to ensure successful implementation and integration of e-health into health systems using change management models. No single model, toolkit, or guideline will offer all the needed answers, but clarity around the underlying metaphors informing the change management models being used provides valuable insight so potentially challenging areas can be avoided or mitigated.

A New Simulation Framework for Autonomy in Robotic Missions

NASA Technical Reports Server (NTRS)

Flueckiger, Lorenzo; Neukom, Christian

2003-01-01

Autonomy is a key factor in remote robotic exploration and there is significant activity addressing the application of autonomy to remote robots. It has become increasingly important to have simulation tools available to test the autonomy algorithms. While indus1;rial robotics benefits from a variety of high quality simulation tools, researchers developing autonomous software are still dependent primarily on block-world simulations. The Mission Simulation Facility I(MSF) project addresses this shortcoming with a simulation toolkit that will enable developers of autonomous control systems to test their system s performance against a set of integrated, standardized simulations of NASA mission scenarios. MSF provides a distributed architecture that connects the autonomous system to a set of simulated components replacing the robot hardware and its environment.

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.

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.

The Revolution Continues: Newly Discovered Systems Expand the CRISPR-Cas Toolkit.

PubMed

Murugan, Karthik; Babu, Kesavan; Sundaresan, Ramya; Rajan, Rakhi; Sashital, Dipali G

2017-10-05

CRISPR-Cas systems defend prokaryotes against bacteriophages and mobile genetic elements and serve as the basis for revolutionary tools for genetic engineering. Class 2 CRISPR-Cas systems use single Cas endonucleases paired with guide RNAs to cleave complementary nucleic acid targets, enabling programmable sequence-specific targeting with minimal machinery. Recent discoveries of previously unidentified CRISPR-Cas systems have uncovered a deep reservoir of potential biotechnological tools beyond the well-characterized Type II Cas9 systems. Here we review the current mechanistic understanding of newly discovered single-protein Cas endonucleases. Comparison of these Cas effectors reveals substantial mechanistic diversity, underscoring the phylogenetic divergence of related CRISPR-Cas systems. This diversity has enabled further expansion of CRISPR-Cas biotechnological toolkits, with wide-ranging applications from genome editing to diagnostic tools based on various Cas endonuclease activities. These advances highlight the exciting prospects for future tools based on the continually expanding set of CRISPR-Cas systems. Copyright © 2017 Elsevier Inc. All rights reserved.

Software Reviews.

ERIC Educational Resources Information Center

Science and Children, 1988

1988-01-01

Reviews five software packages for use with school age children. Includes "Science Toolkit Module 2: Earthquake Lab"; "Adaptations and Identification"; "Geoworld"; "Body Systems II Series: The Blood System: A Liquid of Life," all for Apple II, and "Science Courseware: Life Science/Biology" for…

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.

Electro-optical co-simulation for integrated CMOS photonic circuits with VerilogA.

PubMed

Sorace-Agaskar, Cheryl; Leu, Jonathan; Watts, Michael R; Stojanovic, Vladimir

2015-10-19

We present a Cadence toolkit library written in VerilogA for simulation of electro-optical systems. We have identified and described a set of fundamental photonic components at the physical level such that characteristics of composite devices (e.g. ring modulators) are created organically - by simple instantiation of fundamental primitives. Both the amplitude and phase of optical signals as well as optical-electrical interactions are simulated. We show that the results match other simulations and analytic solutions that have previously been compared to theory for both simple devices, such as ring resonators, and more complicated devices and systems such as single-sideband modulators, WDM links and Pound Drever Hall Locking loops. We also illustrate the capability of such toolkit for co-simulation with electronic circuits, which is a key enabler of the electro-optic system development and verification.

Engineering control of bacterial cellulose production using a genetic toolkit and a new cellulose-producing strain

PubMed Central

Florea, Michael; Hagemann, Henrik; Santosa, Gabriella; Micklem, Chris N.; Spencer-Milnes, Xenia; de Arroyo Garcia, Laura; Paschou, Despoina; Lazenbatt, Christopher; Kong, Deze; Chughtai, Haroon; Jensen, Kirsten; Freemont, Paul S.; Kitney, Richard; Reeve, Benjamin; Ellis, Tom

2016-01-01

Bacterial cellulose is a strong and ultrapure form of cellulose produced naturally by several species of the Acetobacteraceae. Its high strength, purity, and biocompatibility make it of great interest to materials science; however, precise control of its biosynthesis has remained a challenge for biotechnology. Here we isolate a strain of Komagataeibacter rhaeticus (K. rhaeticus iGEM) that can produce cellulose at high yields, grow in low-nitrogen conditions, and is highly resistant to toxic chemicals. We achieved external control over its bacterial cellulose production through development of a modular genetic toolkit that enables rational reprogramming of the cell. To further its use as an organism for biotechnology, we sequenced its genome and demonstrate genetic circuits that enable functionalization and patterning of heterologous gene expression within the cellulose matrix. This work lays the foundations for using genetic engineering to produce cellulose-based materials, with numerous applications in basic science, materials engineering, and biotechnology. PMID:27247386

Engineering control of bacterial cellulose production using a genetic toolkit and a new cellulose-producing strain.

PubMed

Florea, Michael; Hagemann, Henrik; Santosa, Gabriella; Abbott, James; Micklem, Chris N; Spencer-Milnes, Xenia; de Arroyo Garcia, Laura; Paschou, Despoina; Lazenbatt, Christopher; Kong, Deze; Chughtai, Haroon; Jensen, Kirsten; Freemont, Paul S; Kitney, Richard; Reeve, Benjamin; Ellis, Tom

2016-06-14

Bacterial cellulose is a strong and ultrapure form of cellulose produced naturally by several species of the Acetobacteraceae Its high strength, purity, and biocompatibility make it of great interest to materials science; however, precise control of its biosynthesis has remained a challenge for biotechnology. Here we isolate a strain of Komagataeibacter rhaeticus (K. rhaeticus iGEM) that can produce cellulose at high yields, grow in low-nitrogen conditions, and is highly resistant to toxic chemicals. We achieved external control over its bacterial cellulose production through development of a modular genetic toolkit that enables rational reprogramming of the cell. To further its use as an organism for biotechnology, we sequenced its genome and demonstrate genetic circuits that enable functionalization and patterning of heterologous gene expression within the cellulose matrix. This work lays the foundations for using genetic engineering to produce cellulose-based materials, with numerous applications in basic science, materials engineering, and biotechnology.

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

SPICE-Based Python Packages for ESA Solar System Exploration Mission's Geometry Exploitation

NASA Astrophysics Data System (ADS)

Costa, M.; Grass, M.

2018-04-01

This contribution outlines three Python packages to provide an enhanced and extended usage of SPICE Toolkit APIS providing higher-level functions and data quick-look capabilities focused on European Space Agency solar system exploration missions.

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…

The case for randomized controlled trials to assess the impact of clinical information systems.

PubMed

Liu, Joseph L Y; Wyatt, Jeremy C

2011-01-01

There is a persistent view of a significant minority in the medical informatics community that the randomized controlled trial (RCT) has a limited role to play in evaluating clinical information systems. A common reason voiced by skeptics is that these systems are fundamentally different from drug interventions, so the RCT is irrelevant. There is an urgent need to promote the use of RCTs, given the shift to evidence-based policy and the need to demonstrate cost-effectiveness of these systems. The authors suggest returning to first principles and argue that what is required is clarity about how to match methods to evaluation questions. The authors address common concerns about RCTs, and the extent to which they are fallacious, and also discuss the challenges of conducting RCTs in informatics and alternative study designs when randomized trials are infeasible. While neither a perfect nor universal evaluation method, RCTs form an important part of an evaluator's toolkit.

The case for randomized controlled trials to assess the impact of clinical information systems

PubMed Central

Wyatt, Jeremy C

2011-01-01

There is a persistent view of a significant minority in the medical informatics community that the randomized controlled trial (RCT) has a limited role to play in evaluating clinical information systems. A common reason voiced by skeptics is that these systems are fundamentally different from drug interventions, so the RCT is irrelevant. There is an urgent need to promote the use of RCTs, given the shift to evidence-based policy and the need to demonstrate cost-effectiveness of these systems. The authors suggest returning to first principles and argue that what is required is clarity about how to match methods to evaluation questions. The authors address common concerns about RCTs, and the extent to which they are fallacious, and also discuss the challenges of conducting RCTs in informatics and alternative study designs when randomized trials are infeasible. While neither a perfect nor universal evaluation method, RCTs form an important part of an evaluator's toolkit. PMID:21270132

The Good Schools Toolkit to prevent violence against children in Ugandan primary schools: study protocol for a cluster randomised controlled trial

PubMed Central

2013-01-01

Background We aim to evaluate the effectiveness of the Good School Toolkit, developed by Raising Voices, in preventing violence against children attending school and in improving child mental health and educational outcomes. Methods/design We are conducting a two-arm cluster randomised controlled trial with parallel assignment in Luwero District, Uganda. We will also conduct a qualitative study, a process evaluation and an economic evaluation. A total of 42 schools, representative of Luwero District, Uganda, were allocated to receive the Toolkit plus implementation support, or were allocated to a wait-list control condition. Our main analysis will involve a cross-sectional comparison of the prevalence of past-week violence from school staff as reported by children in intervention and control primary schools at follow-up. At least 60 children per school and all school staff members will be interviewed at follow-up. Data collection involves a combination of mobile phone-based, interviewer-completed questionnaires and paper-and-pen educational tests. Survey instruments include the ISPCAN Child Abuse Screening Tools to assess experiences of violence; the Strengths and Difficulties Questionnaire to measure symptoms of common childhood mental disorders; and word recognition, reading comprehension, spelling, arithmetic and sustained attention tests adapted from an intervention trial in Kenya. Discussion To our knowledge, this is the first study to rigorously investigate the effects of any intervention to prevent violence from school staff to children in primary school in a low-income setting. We hope the results will be informative across the African region and in other settings. Trial registration clinicaltrials.gov NCT01678846 PMID:23883138

Reducing Physical Violence Toward Primary School Students With Disabilities.

PubMed

Devries, Karen; Kuper, Hannah; Knight, Louise; Allen, Elizabeth; Kyegombe, Nambusi; Banks, Lena Morgon; Kelly, Susan; Naker, Dipak

2018-03-01

We tested whether the Good School Toolkit reduces physical violence from peers and school staff toward students with and without disabilities in Ugandan primary schools. We conducted a cluster randomized controlled trial, with data collected via cross-sectional surveys in 2012 and 2014. Forty-two primary schools in Luwero District, Uganda, were randomly assigned to receive the Good School Toolkit for 18 months, or to a waitlisted control group. The primary outcome was past week physical violence from school staff, measured by primary 5, 6, and 7 students' (aged 11-14 years) self-reports using the International Society for the Prevention of Child Abuse and Neglect Child Abuse Screening Tool-Child Institutional. Disability was assessed through the six Short Set Washington Group questions on functioning. Analyses were by intention to treat. At endline, 53% of control group students with no functional difficulties reported violence from peers or school staff, versus 84% of students with a disability. Prevalence of past week physical violence from school staff was lower in intervention schools than in the control schools after the intervention, in students with no functional difficulties (adjusted odds ratio [aOR] = .41, 95% confidence interval [CI .26-.65]), students with some functional difficulties (aOR = .36, 95% CI .21-.63), and students with disabilities (aOR = .29, 95% CI .14-.59). The intervention also reduced violence from peers in young adolescents, with no evidence of a difference in effect by disability status. The Good School Toolkit is an effective intervention to reduce violence perpetrated by peers and school staff against young adolescents with disabilities in Ugandan primary schools. Copyright © 2017 The Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

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.

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...

Multiphysics Application Coupling Toolkit

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

Campbell, Michael T.

2013-12-02

This particular consortium implementation of the software integration infrastructure will, in large part, refactor portions of the Rocstar multiphysics infrastructure. Development of this infrastructure originated at the University of Illinois DOE ASCI Center for Simulation of Advanced Rockets (CSAR) to support the center's massively parallel multiphysics simulation application, Rocstar, and has continued at IllinoisRocstar, a small company formed near the end of the University-based program. IllinoisRocstar is now licensing these new developments as free, open source, in hopes to help improve their own and others' access to infrastructure which can be readily utilized in developing coupled or composite software systems;more » with particular attention to more rapid production and utilization of multiphysics applications in the HPC environment. There are two major pieces to the consortium implementation, the Application Component Toolkit (ACT), and the Multiphysics Application Coupling Toolkit (MPACT). The current development focus is the ACT, which is (will be) the substrate for MPACT. The ACT itself is built up from the components described in the technical approach. In particular, the ACT has the following major components: 1.The Component Object Manager (COM): The COM package provides encapsulation of user applications, and their data. COM also provides the inter-component function call mechanism. 2.The System Integration Manager (SIM): The SIM package provides constructs and mechanisms for orchestrating composite systems of multiply integrated pieces.« less

Solar Integration National Dataset Toolkit | Grid Modernization | NREL

Science.gov Websites

system with them. As system topology, operation practices, and electrics power markets evolve, system data sets (for solar, wind, and load, among others) that accurately represent system conditions. For injection into the power system at each location. Related Publications NREL Develops Sub-Hour Solar Power

Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression

PubMed Central

Luo, Michelle L.; Mullis, Adam S.; Leenay, Ryan T.; Beisel, Chase L.

2015-01-01

CRISPR-Cas systems have shown tremendous promise as heterologous tools for genome editing and transcriptional regulation. Because these RNA-directed immune systems are found in most prokaryotes, an opportunity exists to harness the endogenous systems as convenient tools in these organisms. Here, we report that the Type I-E CRISPR-Cas system in Escherichia coli can be co-opted for programmable transcriptional repression. We found that deletion of the signature cas3 gene converted this immune system into a programmable gene regulator capable of reversible gene silencing of heterologous and endogenous genes. Targeting promoter regions yielded the strongest repression, whereas targeting coding regions showed consistent strand bias. Furthermore, multi-targeting CRISPR arrays could generate complex phenotypes. This strategy offers a simple approach to convert many endogenous Type I systems into transcriptional regulators, thereby expanding the available toolkit for CRISPR-mediated genetic control while creating new opportunities for genome-wide screens and pathway engineering. PMID:25326321

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

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.

PubMed

Swertz, Morris A; Dijkstra, Martijn; Adamusiak, Tomasz; van der Velde, Joeri K; Kanterakis, Alexandros; Roos, Erik T; Lops, Joris; Thorisson, Gudmundur A; Arends, Danny; Byelas, George; Muilu, Juha; Brookes, Anthony J; de Brock, Engbert O; Jansen, Ritsert C; Parkinson, Helen

2010-12-21

There is a huge demand on bioinformaticians to provide their biologists with user friendly and scalable software infrastructures to capture, exchange, and exploit the unprecedented amounts of new *omics data. We here present MOLGENIS, a generic, open source, software toolkit to quickly produce the bespoke MOLecular GENetics Information Systems needed. The MOLGENIS toolkit provides bioinformaticians with a simple language to model biological data structures and user interfaces. At the push of a button, MOLGENIS' generator suite automatically translates these models into a feature-rich, ready-to-use web application including database, user interfaces, exchange formats, and scriptable interfaces. Each generator is a template of SQL, JAVA, R, or HTML code that would require much effort to write by hand. This 'model-driven' method ensures reuse of best practices and improves quality because the modeling language and generators are shared between all MOLGENIS applications, so that errors are found quickly and improvements are shared easily by a re-generation. A plug-in mechanism ensures that both the generator suite and generated product can be customized just as much as hand-written software. In recent years we have successfully evaluated the MOLGENIS toolkit for the rapid prototyping of many types of biomedical applications, including next-generation sequencing, GWAS, QTL, proteomics and biobanking. Writing 500 lines of model XML typically replaces 15,000 lines of hand-written programming code, which allows for quick adaptation if the information system is not yet to the biologist's satisfaction. Each application generated with MOLGENIS comes with an optimized database back-end, user interfaces for biologists to manage and exploit their data, programming interfaces for bioinformaticians to script analysis tools in R, Java, SOAP, REST/JSON and RDF, a tab-delimited file format to ease upload and exchange of data, and detailed technical documentation. Existing databases can be quickly enhanced with MOLGENIS generated interfaces using the 'ExtractModel' procedure. The MOLGENIS toolkit provides bioinformaticians with a simple model to quickly generate flexible web platforms for all possible genomic, molecular and phenotypic experiments with a richness of interfaces not provided by other tools. All the software and manuals are available free as LGPLv3 open source at http://www.molgenis.org.

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

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...

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.

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.

Tank Information System (tis): a Case Study in Migrating Web Mapping Application from Flex to Dojo for Arcgis Server and then to Open Source

NASA Astrophysics Data System (ADS)

Pulsani, B. R.

2017-11-01

Tank Information System is a web application which provides comprehensive information about minor irrigation tanks of Telangana State. As part of the program, a web mapping application using Flex and ArcGIS server was developed to make the data available to the public. In course of time as Flex be-came outdated, a migration of the client interface to the latest JavaScript based technologies was carried out. Initially, the Flex based application was migrated to ArcGIS JavaScript API using Dojo Toolkit. Both the client applications used published services from ArcGIS server. To check the migration pattern from proprietary to open source, the JavaScript based ArcGIS application was later migrated to OpenLayers and Dojo Toolkit which used published service from GeoServer. The migration pattern noticed in the study especially emphasizes upon the use of Dojo Toolkit and PostgreSQL database for ArcGIS server so that migration to open source could be performed effortlessly. The current ap-plication provides a case in study which could assist organizations in migrating their proprietary based ArcGIS web applications to open source. Furthermore, the study reveals cost benefits of adopting open source against commercial software's.

Comparison of GEANT4 very low energy cross section models with experimental data in water.

PubMed

Incerti, S; Ivanchenko, A; Karamitros, M; Mantero, A; Moretto, P; Tran, H N; Mascialino, B; Champion, C; Ivanchenko, V N; Bernal, M A; Francis, Z; Villagrasa, C; Baldacchin, G; Guèye, P; Capra, R; Nieminen, P; Zacharatou, C

2010-09-01

The GEANT4 general-purpose Monte Carlo simulation toolkit is able to simulate physical interaction processes of electrons, hydrogen and helium atoms with charge states (H0, H+) and (He0, He+, He2+), respectively, in liquid water, the main component of biological systems, down to the electron volt regime and the submicrometer scale, providing GEANT4 users with the so-called "GEANT4-DNA" physics models suitable for microdosimetry simulation applications. The corresponding software has been recently re-engineered in order to provide GEANT4 users with a coherent and unique approach to the simulation of electromagnetic interactions within the GEANT4 toolkit framework (since GEANT4 version 9.3 beta). This work presents a quantitative comparison of these physics models with a collection of experimental data in water collected from the literature. An evaluation of the closeness between the total and differential cross section models available in the GEANT4 toolkit for microdosimetry and experimental reference data is performed using a dedicated statistical toolkit that includes the Kolmogorov-Smirnov statistical test. The authors used experimental data acquired in water vapor as direct measurements in the liquid phase are not yet available in the literature. Comparisons with several recommendations are also presented. The authors have assessed the compatibility of experimental data with GEANT4 microdosimetry models by means of quantitative methods. The results show that microdosimetric measurements in liquid water are necessary to assess quantitatively the validity of the software implementation for the liquid water phase. Nevertheless, a comparison with existing experimental data in water vapor provides a qualitative appreciation of the plausibility of the simulation models. The existing reference data themselves should undergo a critical interpretation and selection, as some of the series exhibit significant deviations from each other. The GEANT4-DNA physics models available in the GEANT4 toolkit have been compared in this article to available experimental data in the water vapor phase as well as to several published recommendations on the mass stopping power. These models represent a first step in the extension of the GEANT4 Monte Carlo toolkit to the simulation of biological effects of ionizing radiation.

Optochemical Control of Protein Localization and Activity within Cell-like Compartments.

PubMed

Caldwell, Reese M; Bermudez, Jessica G; Thai, David; Aonbangkhen, Chanat; Schuster, Benjamin S; Courtney, Taylor; Deiters, Alexander; Hammer, Daniel A; Chenoweth, David M; Good, Matthew C

2018-05-08

We report inducible dimerization strategies for controlling protein positioning, enzymatic activity, and organelle assembly inside synthetic cell-like compartments upon photostimulation. Using a photocaged TMP-Haloligand compound, we demonstrate small molecule and light-induced dimerization of DHFR and Haloenzyme to localize proteins to a compartment boundary and reconstitute tripartite sfGFP assembly. Using photocaged rapamycin and fragments of split TEV protease fused to FRB and FKBP, we establish optical triggering of protease activity inside cell-size compartments. We apply light-inducible protease activation to initiate assembly of membraneless organelles, demonstrating the applicability of these tools for characterizing cell biological processes in vitro. This modular toolkit, which affords spatial and temporal control of protein function in a minimal cell-like system, represents a critical step toward the reconstitution of a tunable synthetic cell, built from the bottom up.

Livermore Big Artificial Neural Network Toolkit

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

Essen, Brian Van; Jacobs, Sam; Kim, Hyojin

2016-07-01

LBANN is a toolkit that is designed to train artificial neural networks efficiently on high performance computing architectures. It is optimized to take advantages of key High Performance Computing features to accelerate neural network training. Specifically it is optimized for low-latency, high bandwidth interconnects, node-local NVRAM, node-local GPU accelerators, and high bandwidth parallel file systems. It is built on top of the open source Elemental distributed-memory dense and spars-direct linear algebra and optimization library that is released under the BSD license. The algorithms contained within LBANN are drawn from the academic literature and implemented to work within a distributed-memory framework.

Ten years of maintaining and expanding a microbial genome and metagenome analysis system.

PubMed

Markowitz, Victor M; Chen, I-Min A; Chu, Ken; Pati, Amrita; Ivanova, Natalia N; Kyrpides, Nikos C

2015-11-01

Launched in March 2005, the Integrated Microbial Genomes (IMG) system is a comprehensive data management system that supports multidimensional comparative analysis of genomic data. At the core of the IMG system is a data warehouse that contains genome and metagenome datasets sequenced at the Joint Genome Institute or provided by scientific users, as well as public genome datasets available at the National Center for Biotechnology Information Genbank sequence data archive. Genomes and metagenome datasets are processed using IMG's microbial genome and metagenome sequence data processing pipelines and are integrated into the data warehouse using IMG's data integration toolkits. Microbial genome and metagenome application specific data marts and user interfaces provide access to different subsets of IMG's data and analysis toolkits. This review article revisits IMG's original aims, highlights key milestones reached by the system during the past 10 years, and discusses the main challenges faced by a rapidly expanding system, in particular the complexity of maintaining such a system in an academic setting with limited budgets and computing and data management infrastructure. Copyright © 2015 Elsevier Ltd. All rights reserved.

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.

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.

Developing Signal-Pattern-Recognition Programs

NASA Technical Reports Server (NTRS)

Shelton, Robert O.; Hammen, David

2006-01-01

Pattern Interpretation and Recognition Application Toolkit Environment (PIRATE) is a block-oriented software system that aids the development of application programs that analyze signals in real time in order to recognize signal patterns that are indicative of conditions or events of interest. PIRATE was originally intended for use in writing application programs to recognize patterns in space-shuttle telemetry signals received at Johnson Space Center's Mission Control Center: application programs were sought to (1) monitor electric currents on shuttle ac power busses to recognize activations of specific power-consuming devices, (2) monitor various pressures and infer the states of affected systems by applying a Kalman filter to the pressure signals, (3) determine fuel-leak rates from sensor data, (4) detect faults in gyroscopes through analysis of system measurements in the frequency domain, and (5) determine drift rates in inertial measurement units by regressing measurements against time. PIRATE can also be used to develop signal-pattern-recognition software for different purposes -- for example, to monitor and control manufacturing processes.

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...

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.

Industry Application ECCS / LOCA Integrated Cladding/Emergency Core Cooling System Performance: Demonstration of LOTUS-Baseline Coupled Analysis of the South Texas Plant Model

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

Zhang, Hongbin; Szilard, Ronaldo; Epiney, Aaron

Under the auspices of the DOE LWRS Program RISMC Industry Application ECCS/LOCA, INL has engaged staff from both South Texas Project (STP) and the Texas A&M University (TAMU) to produce a generic pressurized water reactor (PWR) model including reactor core, clad/fuel design and systems thermal hydraulics based on the South Texas Project (STP) nuclear power plant, a 4-Loop Westinghouse PWR. A RISMC toolkit, named LOCA Toolkit for the U.S. (LOTUS), has been developed for use in this generic PWR plant model to assess safety margins for the proposed NRC 10 CFR 50.46c rule, Emergency Core Cooling System (ECCS) performance duringmore » LOCA. This demonstration includes coupled analysis of core design, fuel design, thermalhydraulics and systems analysis, using advanced risk analysis tools and methods to investigate a wide range of results. Within this context, a multi-physics best estimate plus uncertainty (MPBEPU) methodology framework is proposed.« less

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.

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.

A YEAR-LONG MM5 EVALUATION USING A MODEL EVALUATION TOOLKIT

EPA Science Inventory

Air quality modeling has expanded in both sophistication and application over the past decade. Meteorological and air quality modeling tools are being used for research, forecasting, and regulatory related emission control strategies. Results from air quality simulations have far...

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.

The Mathlet Toolkit: Creating Dynamic Applets for Differential Equations and Dynamical Systems

ERIC Educational Resources Information Center

Decker, Robert

2011-01-01

Dynamic/interactive graphing applets can be used to supplement standard computer algebra systems such as Maple, Mathematica, Derive, or TI calculators, in courses such as Calculus, Differential Equations, and Dynamical Systems. The addition of this type of software can lead to discovery learning, with students developing their own conjectures, and…

Critical Appraisal Toolkit (CAT) for assessing multiple types of evidence

PubMed Central

Moralejo, D; Ogunremi, T; Dunn, K

2017-01-01

Healthcare professionals are often expected to critically appraise research evidence in order to make recommendations for practice and policy development. Here we describe the Critical Appraisal Toolkit (CAT) currently used by the Public Health Agency of Canada. The CAT consists of: algorithms to identify the type of study design, three separate tools (for appraisal of analytic studies, descriptive studies and literature reviews), additional tools to support the appraisal process, and guidance for summarizing evidence and drawing conclusions about a body of evidence. Although the toolkit was created to assist in the development of national guidelines related to infection prevention and control, clinicians, policy makers and students can use it to guide appraisal of any health-related quantitative research. Participants in a pilot test completed a total of 101 critical appraisals and found that the CAT was user-friendly and helpful in the process of critical appraisal. Feedback from participants of the pilot test of the CAT informed further revisions prior to its release. The CAT adds to the arsenal of available tools and can be especially useful when the best available evidence comes from non-clinical trials and/or studies with weak designs, where other tools may not be easily applied. PMID:29770086

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…

ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour.

PubMed

Evans, Stephanie; Alden, Kieran; Cucurull-Sanchez, Lourdes; Larminie, Christopher; Coles, Mark C; Kullberg, Marika C; Timmis, Jon

2017-02-01

A calibrated computational model reflects behaviours that are expected or observed in a complex system, providing a baseline upon which sensitivity analysis techniques can be used to analyse pathways that may impact model responses. However, calibration of a model where a behaviour depends on an intervention introduced after a defined time point is difficult, as model responses may be dependent on the conditions at the time the intervention is applied. We present ASPASIA (Automated Simulation Parameter Alteration and SensItivity Analysis), a cross-platform, open-source Java toolkit that addresses a key deficiency in software tools for understanding the impact an intervention has on system behaviour for models specified in Systems Biology Markup Language (SBML). ASPASIA can generate and modify models using SBML solver output as an initial parameter set, allowing interventions to be applied once a steady state has been reached. Additionally, multiple SBML models can be generated where a subset of parameter values are perturbed using local and global sensitivity analysis techniques, revealing the model's sensitivity to the intervention. To illustrate the capabilities of ASPASIA, we demonstrate how this tool has generated novel hypotheses regarding the mechanisms by which Th17-cell plasticity may be controlled in vivo. By using ASPASIA in conjunction with an SBML model of Th17-cell polarisation, we predict that promotion of the Th1-associated transcription factor T-bet, rather than inhibition of the Th17-associated transcription factor RORγt, is sufficient to drive switching of Th17 cells towards an IFN-γ-producing phenotype. Our approach can be applied to all SBML-encoded models to predict the effect that intervention strategies have on system behaviour. ASPASIA, released under the Artistic License (2.0), can be downloaded from http://www.york.ac.uk/ycil/software.

Modeling the tagged-neutron UXO identification technique using the Geant4 toolkit

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

Zhou Y.; Mitra S.; Zhu X.

2011-10-16

It is proposed to use 14 MeV neutrons tagged by the associated particle neutron time-of-flight technique (APnTOF) to identify the fillers of unexploded ordnances (UXO) by characterizing their carbon, nitrogen and oxygen contents. To facilitate the design and construction of a prototype system, a preliminary simulation model was developed, using the Geant4 toolkit. This work established the toolkit environment for (a) generating tagged neutrons, (b) their transport and interactions within a sample to induce emission and detection of characteristic gamma-rays, and (c) 2D and 3D-image reconstruction of the interrogated object using the neutron and gamma-ray time-of-flight information. Using the modeling,more » this article demonstrates the novelty of the tagged-neutron approach for extracting useful signals with high signal-to-background discrimination of an object-of-interest from that of its environment. Simulations indicated that an UXO filled with the RDX explosive, hexogen (C{sub 3}H{sub 6}O{sub 6}N{sub 6}), can be identified to a depth of 20 cm when buried in soil.« less

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.

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.

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-

Improving the fundamentals of care for older people in the acute hospital setting: facilitating practice improvement using a Knowledge Translation Toolkit.

PubMed

Wiechula, Rick; Kitson, Alison; Marcoionni, Danni; Page, Tammy; Zeitz, Kathryn; Silverston, Heidi

2009-12-01

This paper reports on a structured facilitation program where seven interdisciplinary teams conducted projects aimed at improving the care of the older person in the acute sector. Aims  To develop and implement a structured intervention known as the Knowledge Translation (KT) Toolkit to improve the fundamentals of care for the older person in the acute care sector. Three hypotheses were tested: (i) frontline staff can be facilitated to use existing quality improvement tools and techniques and other resources (the KT Toolkit) in order to improve care of older people in the acute hospital setting; (ii) fundamental aspects of care for older people in the acute hospital setting can be improved through the introduction and use of specific evidence-based guidelines by frontline staff; and (iii) innovations can be introduced and improvements made to care within a 12-month cycle/timeframe with appropriate facilitation. Methods  Using realistic evaluation methodology the impact of a structured facilitation program (the KT Toolkit) was assessed with the aim of providing a deeper understanding of how a range of tools, techniques and strategies may be used by clinicians to improve care. The intervention comprised three elements: the facilitation team recruited for specific knowledge, skills and expertise in KT, evidence-based practice and quality and safety; the facilitation, including a structured program of education, ongoing support and communication; and finally the components of the toolkit including elements already used within the study organisation. Results  Small improvements in care were shown. The results for the individual projects varied from clarifying issues of concern and planning ongoing activities, to changing existing practices, to improving actual patient outcomes such as reducing functional decline. More importantly the study described how teams of clinicians can be facilitated using a structured program to conduct practice improvement activities with sufficient flexibility to meet the individual needs of the teams. Conclusions  The range of tools in the KT Toolkit were found to be helpful, but not all tools needed to be used to achieve successful results. Facilitation of the teams was a central feature of the KT Toolkit and allowed clinicians to retain control of their projects; however, finding the balance between structuring the process and enabling teams to maintain ownership and control was an ongoing challenge. Clinicians may not have the requisite skills and experience in basic standard setting, audit and evaluation and it was therefore important to address this throughout the project. In time this builds capacity throughout the organisation. Identifying evidence to support practice is a challenge to clinicians. Evidence-based guidelines often lack specificity and were found to be difficult to assimilate easily into everyday practice. Evidence to inform practice needs to be provided in a variety of forms and formats that allow clinicians to easily identify the source of the evidence and then develop local standards specific to their needs. The work that began with this project will continue - all teams felt that the work was only starting rather than concluding. This created momentum, motivation and greater ownership of improvements at local level. © 2009 The Authors. Journal Compilation © Blackwell Publishing Asia Pty Ltd.

Hospital Disaster Preparedness in Italy: a preliminary study utilizing the World Health Organization Hospital Emergency Response Evaluation Toolkit.

PubMed

Ingrassia, Pier L; Mangini, Marco; Azzaretto, Massimo; Ciaramitaro, Ilenia; Costa, Laura; Burkle, Frederick M; Della Corte, Francesco; Djalali, Ahmadreza

2016-12-01

Natural and human-initiated disasters are occurring with greater devastating consequences and increased frequency. During these events, hospitals have the burden to care for acutely ill and injured patients. The aim of this study was to evaluate the level of disaster preparedness of Italian hospitals. Site visits were conducted from January, 2014 to December, 2014. The hospital emergency response checklist, developed by the WHO, was used as an evaluation toolkit. It consists of 92 items classified as 9 key components, such as command and control, triage, and critical services. The status of each component was determined by consensus of 3 independent evaluators. The study selected 15 hospitals from different areas in Italy. Out of the 15 hospitals, 12 were considered to be at insufficients level of preparedness, only 3 were considered to have an effective level of preparedness. The average preparedness of all components were lower than the optimal level suggested by the WHO checklist. The study revealed that a large majority of Italian hospitals evaluated are not well prepared to manage potential disasters. Also, all important elements of hospital preparedness, such as the command system, surge capacity, and safety, were insufficiently implemented. Nationwide standards, guidelines and procedures are required to improve hospital disaster preparedness in Italy.

CSPICE - A C Version of JPL's SPICELIB Toolkit

NASA Technical Reports Server (NTRS)

Wright, E.

1999-01-01

The Navigation Ancillary Information Facility (NAIF), under the direction of NASA's Office of Space Science, built the SPICE data system to assist scientists with planning and interpretation of scientific observations from space borne-instruments.

Practice Doesn't Always Make Perfect: A Qualitative Study Explaining Why a Trial of an Educational Toolkit Did Not Improve Quality of Care.

PubMed

Parsons, Janet A; Yu, Catherine H Y; Baker, Natalie A; Mamdani, Muhammad M; Bhattacharyya, Onil; Zwarenstein, Merrick; Shah, Baiju R

2016-01-01

Diabetes is a chronic disease commonly managed by family physicians, with the most prevalent complication being cardiovascular disease (CVD). Clinical practice guidelines have been developed to support clinicians in the care of diabetic patients. We conducted a pragmatic cluster randomized controlled trial (RCT) of a printed educational toolkit aimed at improving CVD management in diabetes in primary care, and found no effect, and indeed, the possibility of some harm. We conducted a qualitative evaluation to study the strategy for guideline implementation employed in this trial, and to understand its effects. This paper focuses solely on the qualitative findings, as the RCT's quantitative results have already been reported elsewhere. All family practices in the province of Ontario had been randomized to receive the educational toolkit by mail, in either the summer of 2009 (intervention arm) or the spring of 2010 (control arm).A subset of 80 family physicians (representing approximately 10% of the practices randomized and approached, with records on 1,592 randomly selected patients with diabetes at high risk for CVD) then took part in a chart audit and reflective feedback exercise related to their own practice in comparison to the guideline recommendations. They were asked to complete two forms (one pre- and one post-audit) in order to understand their awareness of the guidelines pre-trial, their expectations regarding their individual performance pre-audit, and their reflections on their audit results. In addition, individual interviews with thirteen other family physicians were conducted. Textual data from interview transcripts and written commentary from the pre- and post-audit forms underwent qualitative descriptive analysis to identify common themes and patterns. Analysis revealed four main themes: impressions of the toolkit, awareness was not the issue, 'it's not me it's my patients', and chart audit as a more effective intervention than the toolkit. Participants saw neither the toolkit content nor its dissemination strategy to be effective, indicating they perceived themselves to be aware of the guidelines pre-trial. However, their accounts also indicated that they may be struggling to prioritize CVD management in the midst of competing demands for their attention. Upon receiving their chart audit results, many participants expressed surprise that they had not performed better. They reported that the audit results would be an important motivator for behaviour change. The qualitative findings outlined in this paper offer important insights into why the intervention was not effective. They also demonstrate that physicians have unperceived needs relative to CVD management and that the chart audit served to identify shortcomings in their practice of which they had been hitherto unaware. The findings also indicate that new methods of intervention development and implementation should be explored. This is important given the high prevalence of diabetes worldwide; appropriate CVD management is critical to addressing the morbidity and mortality associated with the disease.

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…

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.

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.

Methodology for the preliminary design of high performance schools in hot and humid climates

NASA Astrophysics Data System (ADS)

Im, Piljae

A methodology to develop an easy-to-use toolkit for the preliminary design of high performance schools in hot and humid climates was presented. The toolkit proposed in this research will allow decision makers without simulation knowledge easily to evaluate accurately energy efficient measures for K-5 schools, which would contribute to the accelerated dissemination of energy efficient design. For the development of the toolkit, first, a survey was performed to identify high performance measures available today being implemented in new K-5 school buildings. Then an existing case-study school building in a hot and humid climate was selected and analyzed to understand the energy use pattern in a school building and to be used in developing a calibrated simulation. Based on the information from the previous step, an as-built and calibrated simulation was then developed. To accomplish this, five calibration steps were performed to match the simulation results with the measured energy use. The five steps include: (1) Using an actual 2006 weather file with measured solar radiation, (2) Modifying lighting & equipment schedule using ASHRAE's RP-1093 methods, (3) Using actual equipment performance curves (i.e., scroll chiller), (4) Using the Winkelmann's method for the underground floor heat transfer, and (5) Modifying the HVAC and room setpoint temperature based on the measured field data. Next, the calibrated simulation of the case-study K-5 school was compared to an ASHRAE Standard 90.1-1999 code-compliant school. In the next step, the energy savings potentials from the application of several high performance measures to an equivalent ASHRAE Standard 90.1-1999 code-compliant school. The high performance measures applied included the recommendations from the ASHRAE Advanced Energy Design Guides (AEDG) for K-12 and other high performance measures from the literature review as well as a daylighting strategy and solar PV and thermal systems. The results show that the net energy consumption of the final high performance school with the solar thermal and a solar PV system would be 1,162.1 MMBtu, which corresponds to the 14.9 kBtu/sqft-yr of EUI. The calculated final energy and cost savings over the code compliant school are 68.2% and 69.9%, respectively. As a final step of the research, specifications for a simplified easy-to-use toolkit were then developed, and a prototype screenshot of the toolkit was developed. The toolkit is expected to be used by non-technical decision-maker to select and evaluate high performance measures for a new school building in terms of energy and cost savings in a quick and easy way.

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.

Robust Requirements Tracing via Internet Search Technology: Improving an IV and V Technique. Phase 2

NASA Technical Reports Server (NTRS)

Hayes, Jane; Dekhtyar, Alex

2004-01-01

There are three major objectives to this phase of the work. (1) Improvement of Information Retrieval (IR) methods for Independent Verification and Validation (IV&V) requirements tracing. Information Retrieval methods are typically developed for very large (order of millions - tens of millions and more documents) document collections and therefore, most successfully used methods somewhat sacrifice precision and recall in order to achieve efficiency. At the same time typical IR systems treat all user queries as independent of each other and assume that relevance of documents to queries is subjective for each user. The IV&V requirements tracing problem has a much smaller data set to operate on, even for large software development projects; the set of queries is predetermined by the high-level specification document and individual requirements considered as query input to IR methods are not necessarily independent from each other. Namely, knowledge about the links for one requirement may be helpful in determining the links of another requirement. Finally, while the final decision on the exact form of the traceability matrix still belongs to the IV&V analyst, his/her decisions are much less arbitrary than those of an Internet search engine user. All this suggests that the information available to us in the framework of the IV&V tracing problem can be successfully leveraged to enhance standard IR techniques, which in turn would lead to increased recall and precision. We developed several new methods during Phase II; (2) IV&V requirements tracing IR toolkit. Based on the methods developed in Phase I and their improvements developed in Phase II, we built a toolkit of IR methods for IV&V requirements tracing. The toolkit has been integrated, at the data level, with SAIC's SuperTracePlus (STP) tool; (3) Toolkit testing. We tested the methods included in the IV&V requirements tracing IR toolkit on a number of projects.

chemf: A purely functional chemistry toolkit.

PubMed

Höck, Stefan; Riedl, Rainer

2012-12-20

Although programming in a type-safe and referentially transparent style offers several advantages over working with mutable data structures and side effects, this style of programming has not seen much use in chemistry-related software. Since functional programming languages were designed with referential transparency in mind, these languages offer a lot of support when writing immutable data structures and side-effects free code. We therefore started implementing our own toolkit based on the above programming paradigms in a modern, versatile programming language. We present our initial results with functional programming in chemistry by first describing an immutable data structure for molecular graphs together with a couple of simple algorithms to calculate basic molecular properties before writing a complete SMILES parser in accordance with the OpenSMILES specification. Along the way we show how to deal with input validation, error handling, bulk operations, and parallelization in a purely functional way. At the end we also analyze and improve our algorithms and data structures in terms of performance and compare it to existing toolkits both object-oriented and purely functional. All code was written in Scala, a modern multi-paradigm programming language with a strong support for functional programming and a highly sophisticated type system. We have successfully made the first important steps towards a purely functional chemistry toolkit. The data structures and algorithms presented in this article perform well while at the same time they can be safely used in parallelized applications, such as computer aided drug design experiments, without further adjustments. This stands in contrast to existing object-oriented toolkits where thread safety of data structures and algorithms is a deliberate design decision that can be hard to implement. Finally, the level of type-safety achieved by Scala highly increased the reliability of our code as well as the productivity of the programmers involved in this project.

chemf: A purely functional chemistry toolkit

PubMed Central

2012-01-01

Background Although programming in a type-safe and referentially transparent style offers several advantages over working with mutable data structures and side effects, this style of programming has not seen much use in chemistry-related software. Since functional programming languages were designed with referential transparency in mind, these languages offer a lot of support when writing immutable data structures and side-effects free code. We therefore started implementing our own toolkit based on the above programming paradigms in a modern, versatile programming language. Results We present our initial results with functional programming in chemistry by first describing an immutable data structure for molecular graphs together with a couple of simple algorithms to calculate basic molecular properties before writing a complete SMILES parser in accordance with the OpenSMILES specification. Along the way we show how to deal with input validation, error handling, bulk operations, and parallelization in a purely functional way. At the end we also analyze and improve our algorithms and data structures in terms of performance and compare it to existing toolkits both object-oriented and purely functional. All code was written in Scala, a modern multi-paradigm programming language with a strong support for functional programming and a highly sophisticated type system. Conclusions We have successfully made the first important steps towards a purely functional chemistry toolkit. The data structures and algorithms presented in this article perform well while at the same time they can be safely used in parallelized applications, such as computer aided drug design experiments, without further adjustments. This stands in contrast to existing object-oriented toolkits where thread safety of data structures and algorithms is a deliberate design decision that can be hard to implement. Finally, the level of type-safety achieved by Scala highly increased the reliability of our code as well as the productivity of the programmers involved in this project. PMID:23253942

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button

PubMed Central

2010-01-01

Background There is a huge demand on bioinformaticians to provide their biologists with user friendly and scalable software infrastructures to capture, exchange, and exploit the unprecedented amounts of new *omics data. We here present MOLGENIS, a generic, open source, software toolkit to quickly produce the bespoke MOLecular GENetics Information Systems needed. Methods The MOLGENIS toolkit provides bioinformaticians with a simple language to model biological data structures and user interfaces. At the push of a button, MOLGENIS’ generator suite automatically translates these models into a feature-rich, ready-to-use web application including database, user interfaces, exchange formats, and scriptable interfaces. Each generator is a template of SQL, JAVA, R, or HTML code that would require much effort to write by hand. This ‘model-driven’ method ensures reuse of best practices and improves quality because the modeling language and generators are shared between all MOLGENIS applications, so that errors are found quickly and improvements are shared easily by a re-generation. A plug-in mechanism ensures that both the generator suite and generated product can be customized just as much as hand-written software. Results In recent years we have successfully evaluated the MOLGENIS toolkit for the rapid prototyping of many types of biomedical applications, including next-generation sequencing, GWAS, QTL, proteomics and biobanking. Writing 500 lines of model XML typically replaces 15,000 lines of hand-written programming code, which allows for quick adaptation if the information system is not yet to the biologist’s satisfaction. Each application generated with MOLGENIS comes with an optimized database back-end, user interfaces for biologists to manage and exploit their data, programming interfaces for bioinformaticians to script analysis tools in R, Java, SOAP, REST/JSON and RDF, a tab-delimited file format to ease upload and exchange of data, and detailed technical documentation. Existing databases can be quickly enhanced with MOLGENIS generated interfaces using the ‘ExtractModel’ procedure. Conclusions The MOLGENIS toolkit provides bioinformaticians with a simple model to quickly generate flexible web platforms for all possible genomic, molecular and phenotypic experiments with a richness of interfaces not provided by other tools. All the software and manuals are available free as LGPLv3 open source at http://www.molgenis.org. PMID:21210979

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.

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.

Design and Control of Modular Spine-Like Tensegrity Structures

NASA Technical Reports Server (NTRS)

Mirletz, Brian T.; Park, In-Won; Flemons, Thomas E.; Agogino, Adrian K.; Quinn, Roger D.; SunSpiral, Vytas

2014-01-01

We present a methodology enabled by the NASA Tensegrity Robotics Toolkit (NTRT) for the rapid structural design of tensegrity robots in simulation and an approach for developing control systems using central pattern generators, local impedance controllers, and parameter optimization techniques to determine effective locomotion strategies for the robot. Biomimetic tensegrity structures provide advantageous properties to robotic locomotion and manipulation tasks, such as their adaptability and force distribution properties, flexibility, energy efficiency, and access to extreme terrains. While strides have been made in designing insightful static biotensegrity structures, gaining a clear understanding of how a particular structure can efficiently move has been an open problem. The tools in the NTRT enable the rapid exploration of the dynamics of a given morphology, and the links between structure, controllability, and resulting gait efficiency. To highlight the effectiveness of the NTRT at this exploration of morphology and control, we will provide examples from the designs and locomotion of four different modular spine-like tensegrity robots.

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…

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

The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences

PubMed Central

Portales-Casamar, Elodie; Arenillas, David; Lim, Jonathan; Swanson, Magdalena I.; Jiang, Steven; McCallum, Anthony; Kirov, Stefan; Wasserman, Wyeth W.

2009-01-01

The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein–DNA binding to cellular reporter gene assays. Data collections can be made available to the public, or restricted to specific system users. The data ‘boutiques’ within the shopping-mall-inspired system facilitate the analysis of genomics data and the creation of predictive models of gene regulation. Since its initial release, PAZAR has grown in terms of data, features and through the addition of an associated package of software tools called the ORCA toolkit (ORCAtk). ORCAtk allows users to rapidly develop analyses based on the information stored in the PAZAR system. PAZAR is available at http://www.pazar.info. ORCAtk can be accessed through convenient buttons located in the PAZAR pages or via our website at http://www.cisreg.ca/ORCAtk. PMID:18971253

THE AUTOMATED GEOSPATIAL WATERSHED ASSESSMENT TOOL

EPA Science Inventory

A toolkit for distributed hydrologic modeling at multiple scales using a geographic information system is presented. This open-source, freely available software was developed through a collaborative endeavor involving two Universities and two government agencies. Called the Auto...

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.

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/

Planetary Space Weather Services for the Europlanet 2020 Research Infrastructure

NASA Astrophysics Data System (ADS)

André, Nicolas; Grande, Manuel

2016-04-01

Under Horizon 2020, the Europlanet 2020 Research Infrastructure (EPN2020-RI) will include an entirely new Virtual Access Service, WP5 VA1 "Planetary Space Weather Services" (PSWS) that will extend the concepts of space weather and space situational awareness to other planets in our Solar System and in particular to spacecraft that voyage through it. VA1 will make five entirely new 'toolkits' accessible to the research community and to industrial partners planning for space missions: a general planetary space weather toolkit, as well as three toolkits dedicated to the following key planetary environments: Mars (in support ExoMars), comets (building on the expected success of the ESA Rosetta mission), and outer planets (in preparation for the ESA JUICE mission to be launched in 2022). This will give the European planetary science community new methods, interfaces, functionalities and/or plugins dedicated to planetary space weather in the tools and models available within the partner institutes. It will also create a novel event-diary toolkit aiming at predicting and detecting planetary events like meteor showers and impacts. A variety of tools (in the form of web applications, standalone software, or numerical models in various degrees of implementation) are available for tracing propagation of planetary and/or solar events through the Solar System and modelling the response of the planetary environment (surfaces, atmospheres, ionospheres, and magnetospheres) to those events. But these tools were not originally designed for planetary event prediction and space weather applications. So WP10 JRA4 "Planetary Space Weather Services" (PSWS) will provide the additional research and tailoring required to apply them for these purposes. The overall objectives of this Joint Research Aactivities will be to review, test, improve and adapt methods and tools available within the partner institutes in order to make prototype planetary event and space weather services operational in Europe at the end of the programme. Europlanet 2020 RI has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 654208.

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).

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.

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.

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.

Integrating the visualization concept of the medical imaging interaction toolkit (MITK) into the XIP-Builder visual programming environment

NASA Astrophysics Data System (ADS)

Wolf, Ivo; Nolden, Marco; Schwarz, Tobias; Meinzer, Hans-Peter

2010-02-01

The Medical Imaging Interaction Toolkit (MITK) and the eXtensible Imaging Platform (XIP) both aim at facilitating the development of medical imaging applications, but provide support on different levels. MITK offers support from the toolkit level, whereas XIP comes with a visual programming environment. XIP is strongly based on Open Inventor. Open Inventor with its scene graph-based rendering paradigm was not specifically designed for medical imaging, but focuses on creating dedicated visualizations. MITK has a visualization concept with a model-view-controller like design that assists in implementing multiple, consistent views on the same data, which is typically required in medical imaging. In addition, MITK defines a unified means of describing position, orientation, bounds, and (if required) local deformation of data and views, supporting e.g. images acquired with gantry tilt and curved reformations. The actual rendering is largely delegated to the Visualization Toolkit (VTK). This paper presents an approach of how to integrate the visualization concept of MITK with XIP, especially into the XIP-Builder. This is a first step of combining the advantages of both platforms. It enables experimenting with algorithms in the XIP visual programming environment without requiring a detailed understanding of Open Inventor. Using MITK-based add-ons to XIP, any number of data objects (images, surfaces, etc.) produced by algorithms can simply be added to an MITK DataStorage object and rendered into any number of slice-based (2D) or 3D views. Both MITK and XIP are open-source C++ platforms. The extensions presented in this paper will be available from www.mitk.org.

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

National Intelligent Transportation Systems Program Plan: Five-Year Horizon

DOT National Transportation Integrated Search

2013-06-01

This white paper is a follow-up to the Volpe Center report for FHWA, Ridesharing Options Analysis and Practitioners Toolkit. The white paper provides an update to current ridesharing options and further explores technology and policy develop...

Solar Sail Spaceflight Simulation

NASA Technical Reports Server (NTRS)

Lisano, Michael; Evans, James; Ellis, Jordan; Schimmels, John; Roberts, Timothy; Rios-Reyes, Leonel; Scheeres, Daniel; Bladt, Jeff; Lawrence, Dale; Piggott, Scott

2007-01-01

The Solar Sail Spaceflight Simulation Software (S5) toolkit provides solar-sail designers with an integrated environment for designing optimal solar-sail trajectories, and then studying the attitude dynamics/control, navigation, and trajectory control/correction of sails during realistic mission simulations. Unique features include a high-fidelity solar radiation pressure model suitable for arbitrarily-shaped solar sails, a solar-sail trajectory optimizer, capability to develop solar-sail navigation filter simulations, solar-sail attitude control models, and solar-sail high-fidelity force models.

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

Fitting methods to paradigms: are ergonomics methods fit for systems thinking?

PubMed

Salmon, Paul M; Walker, Guy H; M Read, Gemma J; Goode, Natassia; Stanton, Neville A

2017-02-01

The issues being tackled within ergonomics problem spaces are shifting. Although existing paradigms appear relevant for modern day systems, it is worth questioning whether our methods are. This paper asks whether the complexities of systems thinking, a currently ubiquitous ergonomics paradigm, are outpacing the capabilities of our methodological toolkit. This is achieved through examining the contemporary ergonomics problem space and the extent to which ergonomics methods can meet the challenges posed. Specifically, five key areas within the ergonomics paradigm of systems thinking are focused on: normal performance as a cause of accidents, accident prediction, system migration, systems concepts and ergonomics in design. The methods available for pursuing each line of inquiry are discussed, along with their ability to respond to key requirements. In doing so, a series of new methodological requirements and capabilities are identified. It is argued that further methodological development is required to provide researchers and practitioners with appropriate tools to explore both contemporary and future problems. Practitioner Summary: Ergonomics methods are the cornerstone of our discipline. This paper examines whether our current methodological toolkit is fit for purpose given the changing nature of ergonomics problems. The findings provide key research and practice requirements for methodological development.

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

Doing accelerator physics using SDDS, UNIX, and EPICS

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

Borland, M.; Emery, L.; Sereno, N.

1995-12-31

The use of the SDDS (Self-Describing Data Sets) file protocol, together with the UNIX operating system and EPICS (Experimental Physics and Industrial Controls System), has proved powerful during the commissioning of the APS (Advanced Photon Source) accelerator complex. The SDDS file protocol has permitted a tool-oriented approach to developing applications, wherein generic programs axe written that function as part of multiple applications. While EPICS-specific tools were written for data collection, automated experiment execution, closed-loop control, and so forth, data processing and display axe done with the SDDS Toolkit. Experiments and data reduction axe implemented as UNIX shell scripts that coordinatemore » the execution of EPICS specific tools and SDDS tools. Because of the power and generic nature of the individual tools and of the UNIX shell environment, automated experiments can be prepared and executed rapidly in response to unanticipated needs or new ideas. Examples are given of application of this methodology to beam motion characterization, beam-position-monitor offset measurements, and klystron characterization.« less

[Medical professionals on the subject of their core values: the importance of practice-based stories and intrinsic motivation].

PubMed

Witman, Yolande; van den Kerkhof, Peter C M; Braat, Didi D M

2013-01-01

In the current system for guaranteeing quality of care, emphasis is placed firmly on external control of professionals. We looked for a way to appeal to the intrinsic motivation of medical professionals and to discover what they mean by 'good work'. This was achieved with the aid of reflective sessions using the toolkit 'Good Work': in four sessions three different groups of medical professionals (medical department chairs, residents and interns) from a Dutch university hospital reflected on the topics 'excellence', 'moral responsibility' and 'personal engagement'. The participants exchanged practice-based stories during the sessions. The most important theme was moral responsibility, with its accompanying dilemmas. The sessions gave rise to feelings of mutual acknowledgement, recognition, inspiration and motivation. Sharing meaningful practice-based stories can be considered as a 'moment of learning', strengthening professional identity and stimulating intrinsic motivation. More space for this form of reflection might restore the balance with external control systems.

Toolkit for the Automated Characterization of Optical Trapping Forces on Microscopic Particles

NASA Astrophysics Data System (ADS)

Glaser, Joseph; Hoeprich, David; Resnick, Andrew

2014-03-01

Optical traps have been in use in microbiological studies for the past 40 years to obtain noninvasive control of microscopic particles. However, the magnitude of the applied forces is often unknown. Therefore, we have developed an automated data acquisition and processing system which characterizes trap properties for known particle geometries. Extensive experiments and measurements utilizing well-characterized objects were performed and compared to literature to confirm the system's performance. This system will enable the future analysis of a trapped primary cilium, a slender rod-shaped organelle with aspect ratio L/R >30, where `L' is the cilium length and `R' the cilium diameter. The trapping of cilia is of primary importance, as it will lead to the precise measurements of mechanical properties of the organelle and its significance to the epithelial cell. Support from the National Institutes of Health, 1R15DK092716 is gratefully acknowledged.

Parameter Sweep and Optimization of Loosely Coupled Simulations Using the DAKOTA Toolkit

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

Elwasif, Wael R; Bernholdt, David E; Pannala, Sreekanth

2012-01-01

The increasing availability of large scale computing capabilities has accelerated the development of high-fidelity coupled simulations. Such simulations typically involve the integration of models that implement various aspects of the complex phenomena under investigation. Coupled simulations are playing an integral role in fields such as climate modeling, earth systems modeling, rocket simulations, computational chemistry, fusion research, and many other computational fields. Model coupling provides scientists with systematic ways to virtually explore the physical, mathematical, and computational aspects of the problem. Such exploration is rarely done using a single execution of a simulation, but rather by aggregating the results from manymore » simulation runs that, together, serve to bring to light novel knowledge about the system under investigation. Furthermore, it is often the case (particularly in engineering disciplines) that the study of the underlying system takes the form of an optimization regime, where the control parameter space is explored to optimize an objective functions that captures system realizability, cost, performance, or a combination thereof. Novel and flexible frameworks that facilitate the integration of the disparate models into a holistic simulation are used to perform this research, while making efficient use of the available computational resources. In this paper, we describe the integration of the DAKOTA optimization and parameter sweep toolkit with the Integrated Plasma Simulator (IPS), a component-based framework for loosely coupled simulations. The integration allows DAKOTA to exploit the internal task and resource management of the IPS to dynamically instantiate simulation instances within a single IPS instance, allowing for greater control over the trade-off between efficiency of resource utilization and time to completion. We present a case study showing the use of the combined DAKOTA-IPS system to aid in the design of a lithium ion battery (LIB) cell, by studying a coupled system involving the electrochemistry and ion transport at the lower length scales and thermal energy transport at the device scales. The DAKOTA-IPS system provides a flexible tool for use in optimization and parameter sweep studies involving loosely coupled simulations that is suitable for use in situations where changes to the constituent components in the coupled simulation are impractical due to intellectual property or code heritage issues.« less

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.

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.

Developing a middleware to support HDF data access in ArcGIS

NASA Astrophysics Data System (ADS)

Sun, M.; Jiang, Y.; Yang, C. P.

2014-12-01

Hierarchical Data Format (HDF) is the standard data format for the NASA Earth Observing System (EOS) data products, like the MODIS level-3 data. These data have been widely used in long-term study of the land surface, biosphere, atmosphere, and oceans of the Earth. Several toolkits have been developed to access HDF data, such as the HDF viewer and Geospatial Data Abstraction Library (GDAL), etc. ArcGIS integrated the GDAL providing data user a Graphical User Interface (GUI) to read HDF data. However, there are still some problems when using the toolkits:for example, 1) the projection information is not recognized correctly, 2) the image is dispalyed inverted, and 3) the tool lacks of capability to read the third dimension information stored in the data subsets, etc. Accordingly, in this study we attempt to improve the current HDF toolkits to address the aformentioned issues. Considering the wide-usage of ArcGIS, we develop a middleware for ArcGIS based on GDAL to solve the particular data access problems happening in ArcGIS, so that data users can access HDF data successfully and perform further data analysis with the ArcGIS geoprocessing tools.

Evaluating the parent-adolescent communication toolkit: Usability and preliminary content effectiveness of an online intervention.

PubMed

Toombs, Elaine; Unruh, Anita; McGrath, Patrick

2018-01-01

This study aimed to assess the Parent-Adolescent Communication Toolkit, an online intervention designed to help improve parent communication with their adolescents. Participant preferences for two module delivery systems (sequential and unrestricted module access) were identified. Usability assessment of the PACT intervention was completed using pre-test and posttest comparisons. Usability data, including participant completion and satisfaction ratings were examined. Parents ( N  =   18) of adolescents were randomized to a sequential or unrestricted chapter access group. Parent participants completed pre-test measures, the PACT intervention and posttest measures. Participants provided feedback for the intervention to improve modules and provided usability ratings. Adolescent pre- and posttest ratings were evaluated. Usability ratings were high and parent feedback was positive. The sequential module access groups rated the intervention content higher and completed more content than the unrestricted chapter access group, indicating support for the sequential access design. Parent mean posttest communication scores were significantly higher ( p  <   .05) than pre-test scores. No significant differences were detected for adolescent participants. Findings suggest that the Parent-Adolescent Communication Toolkit has potential to improve parent-adolescent communication but further effectiveness assessment is required.

Iterative user centered design for development of a patient-centered fall prevention toolkit.

PubMed

Katsulis, Zachary; Ergai, Awatef; Leung, Wai Yin; Schenkel, Laura; Rai, Amisha; Adelman, Jason; Benneyan, James; Bates, David W; Dykes, Patricia C

2016-09-01

Due to the large number of falls that occur in hospital settings, inpatient fall prevention is a topic of great interest to patients and health care providers. The use of electronic decision support that tailors fall prevention strategy to patient-specific risk factors, known as Fall T.I.P.S (Tailoring Interventions for Patient Safety), has proven to be an effective approach for decreasing hospital falls. A paper version of the Fall T.I.P.S toolkit was developed primarily for hospitals that do not have the resources to implement the electronic solution; however, more work is needed to optimize the effectiveness of the paper version of this tool. We examined the use of human factors techniques in the redesign of the existing paper fall prevention tool with the goal of increasing ease of use and decreasing inpatient falls. The inclusion of patients and clinical staff in the redesign of the existing tool was done to increase adoption of the tool and fall prevention best practices. The redesigned paper Fall T.I.P.S toolkit showcased a built in clinical decision support system and increased ease of use over the existing version. Copyright © 2016 Elsevier Ltd. All rights reserved.

The WHO-ITU national eHealth strategy toolkit as an effective approach to national strategy development and implementation.

PubMed

Hamilton, Clayton

2013-01-01

With few exceptions, national eHealth strategies are the pivotal tools upon which the launch or refocusing of national eHealth programmes is hinged. The process of their development obviates cross-sector ministerial commitment led by the Ministry of Health. Yet countries often grapple with the task of strategy development and best efforts frequently fail to address strategic components of eHealth key to ensure successful implementation and stakeholder engagement. This can result in strategies that are narrowly focused, with an overemphasis placed on achieving technical outcomes. Without a clear link to a broader vision of health system development and a firm commitment from partners, the ability of a strategy to shape development of a national eHealth framework will be undermined and crucial momentum for implementation will be lost. WHO and ITU have sought to address this issue through the development of the National eHealth Strategy Toolkit that provides a basis for the components and processes to be considered in a strategy development or refocusing exercise. We look at this toolkit and highlight those areas which the countries should consider in formulating their national eHealth strategy.

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

von Laszewski, G.; Gawor, J.; Lane, P.

In this paper we report on the features of the Java Commodity Grid Kit (Java CoG Kit). The Java CoG Kit provides middleware for accessing Grid functionality from the Java framework. Java CoG Kit middleware is general enough to design a variety of advanced Grid applications with quite different user requirements. Access to the Grid is established via Globus Toolkit protocols, allowing the Java CoG Kit to also communicate with the services distributed as part of the C Globus Toolkit reference implementation. Thus, the Java CoG Kit provides Grid developers with the ability to utilize the Grid, as well asmore » numerous additional libraries and frameworks developed by the Java community to enable network, Internet, enterprise and peer-to-peer computing. A variety of projects have successfully used the client libraries of the Java CoG Kit to access Grids driven by the C Globus Toolkit software. In this paper we also report on the efforts to develop serverside Java CoG Kit components. As part of this research we have implemented a prototype pure Java resource management system that enables one to run Grid jobs on platforms on which a Java virtual machine is supported, including Windows NT machines.« less

STOCK: Structure mapper and online coarse-graining kit for molecular simulations

DOE PAGES

Bevc, Staš; Junghans, Christoph; Praprotnik, Matej

2015-03-15

We present a web toolkit STructure mapper and Online Coarse-graining Kit for setting up coarse-grained molecular simulations. The kit consists of two tools: structure mapping and Boltzmann inversion tools. The aim of the first tool is to define a molecular mapping from high, e.g. all-atom, to low, i.e. coarse-grained, resolution. Using a graphical user interface it generates input files, which are compatible with standard coarse-graining packages, e.g. VOTCA and DL_CGMAP. Our second tool generates effective potentials for coarse-grained simulations preserving the structural properties, e.g. radial distribution functions, of the underlying higher resolution model. The required distribution functions can be providedmore » by any simulation package. Simulations are performed on a local machine and only the distributions are uploaded to the server. The applicability of the toolkit is validated by mapping atomistic pentane and polyalanine molecules to a coarse-grained representation. Effective potentials are derived for systems of TIP3P (transferable intermolecular potential 3 point) water molecules and salt solution. The presented coarse-graining web toolkit is available at http://stock.cmm.ki.si.« less

XPAT: a toolkit to conduct cross-platform association studies with heterogeneous sequencing datasets.

PubMed

Yu, Yao; Hu, Hao; Bohlender, Ryan J; Hu, Fulan; Chen, Jiun-Sheng; Holt, Carson; Fowler, Jerry; Guthery, Stephen L; Scheet, Paul; Hildebrandt, Michelle A T; Yandell, Mark; Huff, Chad D

2018-04-06

High-throughput sequencing data are increasingly being made available to the research community for secondary analyses, providing new opportunities for large-scale association studies. However, heterogeneity in target capture and sequencing technologies often introduce strong technological stratification biases that overwhelm subtle signals of association in studies of complex traits. Here, we introduce the Cross-Platform Association Toolkit, XPAT, which provides a suite of tools designed to support and conduct large-scale association studies with heterogeneous sequencing datasets. XPAT includes tools to support cross-platform aware variant calling, quality control filtering, gene-based association testing and rare variant effect size estimation. To evaluate the performance of XPAT, we conducted case-control association studies for three diseases, including 783 breast cancer cases, 272 ovarian cancer cases, 205 Crohn disease cases and 3507 shared controls (including 1722 females) using sequencing data from multiple sources. XPAT greatly reduced Type I error inflation in the case-control analyses, while replicating many previously identified disease-gene associations. We also show that association tests conducted with XPAT using cross-platform data have comparable performance to tests using matched platform data. XPAT enables new association studies that combine existing sequencing datasets to identify genetic loci associated with common diseases and other complex traits.

Agricultural biodiversity in the post-genomics era

USDA-ARS?s Scientific Manuscript database

The toolkit available for assessing and utilizing biological diversity within agricultural systems is rapidly expanding. In particular, genome and transcriptome re-sequencing as well as genome complexity reduction techniques are gaining popularity as the cost of generating short read sequence data d...

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.

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).

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.

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.

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

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.

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.

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

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Formulation and Realisation of Evaluation Policy: Inconcistencies and Problematic Issues

ERIC Educational Resources Information Center

Skedsmo, Guri

2011-01-01

The introduction of the national evaluation system in the Norwegian education system can be described as a shift in the Norwegian educational policy from the use of input oriented policy instruments towards a more output oriented policy. The new tool-kit consists of different evaluation tools, such as standardised tests, diagonistic tests etc.…

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...

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

The Model Analyst’s Toolkit: Scientific Model Development, Analysis, and Validation

DTIC Science & Technology

2014-08-20

many different synthetic series can be generated at once. If the series already exists in the dataset, it is updated to reflect the new values. The...Testing for causality: a personal viewpoint. Journal of Economic Dynamics and Control, 2, 329-352. Manning, C., Raghavan, R., and Schutze , H. (2008

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.

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.

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

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.

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.

State Fall Prevention Coalitions as Systems Change Agents: An Emphasis on Policy.

PubMed

Schneider, Ellen C; Smith, Matthew Lee; Ory, Marcia G; Altpeter, Mary; Beattie, Bonita Lynn; Scheirer, Mary Ann; Shubert, Tiffany E

2016-03-01

Falls among older adults are an escalating public health issue, which requires a multidisciplinary and multilevel approach to affect systems change to effectively address this problem. The National Council on Aging established the Falls Free® Initiative, enfolding and facilitating statewide Fall Prevention Coalitions. Fall Free® activities included developing the State Policy Toolkit for Advancing Falls Prevention to promote sustainable change by supporting the dissemination and adoption of evidence-based strategies. To (1) determine if the policies being implemented were recommended and supported by the Toolkit, (2) identify the perceived barriers and facilitators to implementing policies, and (3) identify Coalitions' current and future fall prevention policy activities. A 63-item online survey was distributed to State Coalition Leads. Descriptive statistics (frequencies and counts) were used to describe Coalition characteristics and activities. Coalitions had several similarities, and varied greatly in their number of member organizations and members as well as meeting frequencies. Key activities included building partnerships, disseminating programs, and pursuing at least one of the eight National Council on Aging-recommended policy goals. The most commonly reported facilitator was active support from the Coalition Leads, whereas the lack of funding was the most cited barrier. This study serves as the first national census of empirical evidence regarding Falls Coalitions' composition, goals, and activities. Results indicate that Coalitions are actively pursuing evidence-based policies but could benefit from additional technical assistance and resources. Findings support the value of Toolkit recommendations by documenting what is feasible and being implemented. Knowledge about facilitators and barriers will inform future efforts to foster sustainable systems change in states with active Coalitions and encourage Coalitions in other states. © 2015 Society for Public Health Education.

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.

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.

SimPackJ/S: a web-oriented toolkit for discrete event simulation

NASA Astrophysics Data System (ADS)

Park, Minho; Fishwick, Paul A.

2002-07-01

SimPackJ/S is the JavaScript and Java version of SimPack, which means SimPackJ/S is a collection of JavaScript and Java libraries and executable programs for computer simulations. The main purpose of creating SimPackJ/S is that we allow existing SimPack users to expand simulation areas and provide future users with a freeware simulation toolkit to simulate and model a system in web environments. One of the goals for this paper is to introduce SimPackJ/S. The other goal is to propose translation rules for converting C to JavaScript and Java. Most parts demonstrate the translation rules with examples. In addition, we discuss a 3D dynamic system model and overview an approach to 3D dynamic systems using SimPackJ/S. We explain an interface between SimPackJ/S and the 3D language--Virtual Reality Modeling Language (VRML). This paper documents how to translate C to JavaScript and Java and how to utilize SimPackJ/S within a 3D web environment.

Molecular diagnostic toolkit for Rhizophagus irregularis isolate DAOM-197198 using quantitative PCR assay targeting the mitochondrial genome.

PubMed

Badri, Amine; Stefani, Franck O P; Lachance, Geneviève; Roy-Arcand, Line; Beaudet, Denis; Vialle, Agathe; Hijri, Mohamed

2016-10-01

Rhizophagus irregularis (previously named Glomus irregulare) is one of the most widespread and common arbuscular mycorrhizal fungal (AMF) species. It has been recovered worldwide in agricultural and natural soils, and the isolate DAOM-197198 has been utilized as a commercial inoculant for two decades. Despite the ecological and economical importance of this taxon, specific markers for quantification of propagules by quantitative real-time PCR (qPCR) are extremely limited and none have been rigorously validated for quality control of manufactured products such as biofertilizers. From the sequencing of 14 complete AMF mitochondrial (mt) genomes, a qPCR assay using a hydrolysis probe designed in the single copy cox3-rnl intergenic region was tested and validated to specifically and accurately quantify the spores of R. irregularis isolate DAOM-197198. Specificity tests were performed using standard PCR and qPCR, and results clearly showed that the primers specifically amplified the isolate DAOM-197198, yielding a PCR product of 106 bp. According to the qPCR analyses on spores produced in vitro, the average copy number of mt genomes per spore was 3172 ± 304 SE (n = 6). Quantification assays were successfully undertaken on known and unknown samples in liquid suspensions and commercial dry formulations to show the accuracy, precision, robustness, and reproducibility of the qPCR assay. This study provides a powerful molecular toolkit specifically designed to quantify spores of the model AMF isolate DAOM-197198. The approach of molecular toolkit used in our study could be applied to other AMF taxa and will be useful to research institutions and governmental and industrial laboratories running routine quality control of AMF-based products.

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 ...

The Good School Toolkit for reducing physical violence from school staff to primary school students: a cluster-randomised controlled trial in Uganda.

PubMed

Devries, Karen M; Knight, Louise; Child, Jennifer C; Mirembe, Angel; Nakuti, Janet; Jones, Rebecca; Sturgess, Joanna; Allen, Elizabeth; Kyegombe, Nambusi; Parkes, Jenny; Walakira, Eddy; Elbourne, Diana; Watts, Charlotte; Naker, Dipak

2015-07-01

Violence against children from school staff is widespread in various settings, but few interventions address this. We tested whether the Good School Toolkit-a complex behavioural intervention designed by Ugandan not-for-profit organisation Raising Voices-could reduce physical violence from school staff to Ugandan primary school children. We randomly selected 42 primary schools (clusters) from 151 schools in Luwero District, Uganda, with more than 40 primary 5 students and no existing governance interventions. All schools agreed to be enrolled. All students in primary 5, 6, and 7 (approximate ages 11-14 years) and all staff members who spoke either English or Luganda and could provide informed consent were eligible for participation in cross-sectional baseline and endline surveys in June-July 2012 and 2014, respectively. We randomly assigned 21 schools to receive the Good School Toolkit and 21 to a waitlisted control group in September, 2012. The intervention was implemented from September, 2012, to April, 2014. Owing to the nature of the intervention, it was not possible to mask assignment. The primary outcome, assessed in 2014, was past week physical violence from school staff, measured by students' self-reports using the International Society for the Prevention of Child Abuse and Neglect Child Abuse Screening Tool-Child Institutional. Analyses were by intention to treat, and are adjusted for clustering within schools and for baseline school-level means of continuous outcomes. The trial is registered at clinicaltrials.gov, NCT01678846. No schools left the study. At 18-month follow-up, 3820 (92·4%) of 4138 randomly sampled students participated in a cross-sectional survey. Prevalence of past week physical violence was lower in the intervention schools (595/1921, 31·0%) than in the control schools (924/1899, 48·7%; odds ratio 0·40, 95% CI 0·26-0·64, p<0·0001). No adverse events related to the intervention were detected, but 434 children were referred to child protective services because of what they disclosed in the follow-up survey. The Good School Toolkit is an effective intervention to reduce violence against children from school staff in Ugandan primary schools. MRC, DfID, Wellcome Trust, Hewlett Foundation. Copyright © 2015 Devries et al. Open access article published under the terms of CC BY. Published by Elsevier Ltd.. All rights reserved.

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

Simulation of Radiation Damage to Neural Cells with the Geant4-DNA Toolkit

NASA Astrophysics Data System (ADS)

Bayarchimeg, Lkhagvaa; Batmunkh, Munkhbaatar; Belov, Oleg; Lkhagva, Oidov

2018-02-01

To help in understanding the physical and biological mechanisms underlying effects of cosmic and therapeutic types of radiation on the central nervous system (CNS), we have developed an original neuron application based on the Geant4 Monte Carlo simulation toolkit, in particular on its biophysical extension Geant4-DNA. The applied simulation technique provides a tool for the simulation of physical, physico-chemical and chemical processes (e.g. production of water radiolysis species in the vicinity of neurons) in realistic geometrical model of neural cells exposed to ionizing radiation. The present study evaluates the microscopic energy depositions and water radiolysis species yields within a detailed structure of a selected neuron taking into account its soma, dendrites, axon and spines following irradiation with carbon and iron ions.

A personal health information toolkit for health intervention research.

PubMed

Kizakevich, Paul N; Eckhoff, Randall; Weger, Stacey; Weeks, Adam; Brown, Janice; Bryant, Stephanie; Bakalov, Vesselina; Zhang, Yuying; Lyden, Jennifer; Spira, James

2014-01-01

With the emergence of mobile health (mHealth) apps, there is a growing demand for better tools for developing and evaluating mobile health interventions. Recently we developed the Personal Health Intervention Toolkit (PHIT), a software framework which eases app implementation and facilitates scientific evaluation. PHIT integrates self-report and physiological sensor instruments, evidence-based advisor logic, and self-help interventions such as meditation, health education, and cognitive behavior change. PHIT can be used to facilitate research, interventions for chronic diseases, risky behaviors, sleep, medication adherence, environmental monitoring, momentary data collection health screening, and clinical decision support. In a series of usability evaluations, participants reported an overall usability score of 4.5 on a 1-5 Likert scale and an 85 score on the System Usability Scale, indicating a high percentile rank of 95%.

Atrioventricular junction (AVJ) motion tracking: a software tool with ITK/VTK/Qt.

PubMed

Pengdong Xiao; Shuang Leng; Xiaodan Zhao; Hua Zou; Ru San Tan; Wong, Philip; Liang Zhong

2016-08-01

The quantitative measurement of the Atrioventricular Junction (AVJ) motion is an important index for ventricular functions of one cardiac cycle including systole and diastole. In this paper, a software tool that can conduct AVJ motion tracking from cardiovascular magnetic resonance (CMR) images is presented by using Insight Segmentation and Registration Toolkit (ITK), The Visualization Toolkit (VTK) and Qt. The software tool is written in C++ by using Visual Studio Community 2013 integrated development environment (IDE) containing both an editor and a Microsoft complier. The software package has been successfully implemented. From the software engineering practice, it is concluded that ITK, VTK, and Qt are very handy software systems to implement automatic image analysis functions for CMR images such as quantitative measure of motion by visual tracking.

Developing Climate Resilience Toolkit Decision Support Training Sectio

NASA Astrophysics Data System (ADS)

Livezey, M. M.; Herring, D.; Keck, J.; Meyers, J. C.

2014-12-01

The Climate Resilience Toolkit (CRT) is a Federal government effort to address the U.S. President's Climate Action Plan and Executive Order for Climate Preparedness. The toolkit will provide access to tools and products useful for climate-sensitive decision making. To optimize the user experience, the toolkit will also provide access to training materials. The National Oceanic and Atmospheric Administration (NOAA) has been building a climate training capability for 15 years. The target audience for the training has historically been mainly NOAA staff with some modified training programs for external users and stakeholders. NOAA is now using this climate training capacity for the CRT. To organize the CRT training section, we collaborated with the Association of Climate Change Officers to determine the best strategy and identified four additional complimentary skills needed for successful decision making: climate literacy, environmental literacy, risk assessment and management, and strategic execution and monitoring. Developing the climate literacy skills requires knowledge of climate variability and change, as well as an introduction to the suite of available products and services. For the development of an environmental literacy category, specific topics needed include knowledge of climate impacts on specific environmental systems. Climate risk assessment and management introduces a process for decision making and provides knowledge on communication of climate information and integration of climate information in planning processes. The strategic execution and monitoring category provides information on use of NOAA climate products, services, and partnership opportunities for decision making. In order to use the existing training modules, it was necessary to assess their level of complexity, catalog them, and develop guidance for users on a curriculum to take advantage of the training resources to enhance their learning experience. With the development of this CRT training section, NOAA has made significant progress in sharing resources with the external community.

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).

Dynamical patterning modules: physico-genetic determinants of morphological development and evolution

NASA Astrophysics Data System (ADS)

Newman, Stuart A.; Bhat, Ramray

2008-03-01

The shapes and forms of multicellular organisms arise by the generation of new cell states and types and changes in the numbers and rearrangements of the various kinds of cells. While morphogenesis and pattern formation in all animal species are widely recognized to be mediated by the gene products of an evolutionarily conserved 'developmental-genetic toolkit', the link between these molecular players and the physics underlying these processes has been generally ignored. This paper introduces the concept of 'dynamical patterning modules' (DPMs), units consisting of one or more products of the 'toolkit' genes that mobilize physical processes characteristic of chemically and mechanically excitable meso- to macroscopic systems such as cell aggregates: cohesion, viscoelasticity, diffusion, spatiotemporal heterogeneity based on lateral inhibition and multistable and oscillatory dynamics. We suggest that ancient toolkit gene products, most predating the emergence of multicellularity, assumed novel morphogenetic functions due to change in the scale and context inherent to multicellularity. We show that DPMs, acting individually and in concert with each other, constitute a 'pattern language' capable of generating all metazoan body plans and organ forms. The physical dimension of developmental causation implies that multicellular forms during the explosive radiation of animal body plans in the middle Cambrian, approximately 530 million years ago, could have explored an extensive morphospace without concomitant genotypic change or selection for adaptation. The morphologically plastic body plans and organ forms generated by DPMs, and their ontogenetic trajectories, would subsequently have been stabilized and consolidated by natural selection and genetic drift. This perspective also solves the apparent 'molecular homology-analogy paradox', whereby widely divergent modern animal types utilize the same molecular toolkit during development by proposing, in contrast to the Neo-Darwinian principle, that phenotypic disparity early in evolution occurred in advance of, rather than closely tracked, genotypic change.

The genome of Romanomermis culicivorax: revealing fundamental changes in the core developmental genetic toolkit in Nematoda

PubMed Central

2013-01-01

Background The genetics of development in the nematode Caenorhabditis elegans has been described in exquisite detail. The phylum Nematoda has two classes: Chromadorea (which includes C. elegans) and the Enoplea. While the development of many chromadorean species resembles closely that of C. elegans, enoplean nematodes show markedly different patterns of early cell division and cell fate assignment. Embryogenesis of the enoplean Romanomermis culicivorax has been studied in detail, but the genetic circuitry underpinning development in this species has not been explored. Results We generated a draft genome for R. culicivorax and compared its gene content with that of C. elegans, a second enoplean, the vertebrate parasite Trichinella spiralis, and a representative arthropod, Tribolium castaneum. This comparison revealed that R. culicivorax has retained components of the conserved ecdysozoan developmental gene toolkit lost in C. elegans. T. spiralis has independently lost even more of this toolkit than has C. elegans. However, the C. elegans toolkit is not simply depauperate, as many novel genes essential for embryogenesis in C. elegans are not found in, or have only extremely divergent homologues in R. culicivorax and T. spiralis. Our data imply fundamental differences in the genetic programmes not only for early cell specification but also others such as vulva formation and sex determination. Conclusions Despite the apparent morphological conservatism, major differences in the molecular logic of development have evolved within the phylum Nematoda. R. culicivorax serves as a tractable system to contrast C. elegans and understand how divergent genomic and thus regulatory backgrounds nevertheless generate a conserved phenotype. The R. culicivorax draft genome will promote use of this species as a research model. PMID:24373391

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 ...

15 CFR Supplement No. 5 to Part 742 - Encryption Registration

Code of Federal Regulations, 2013 CFR

2013-01-01

... registration, i.e., the information as described in this Supplement, submitted as a support documentation... (h) Smartcards or other identity management (i) Computer or network forensics (j) Software (i) Operating systems (ii) Applications (k) Toolkits/ASICs/components (l) Information security including secure...

15 CFR Supplement No. 5 to Part 742 - Encryption Registration

Code of Federal Regulations, 2011 CFR

2011-01-01

... registration, i.e., the information as described in this Supplement, submitted as a support documentation... (h) Smartcards or other identity management (i) Computer or network forensics (j) Software (i) Operating systems (ii) Applications (k) Toolkits/ASICs/components (l) Information security including secure...

15 CFR Supplement No. 5 to Part 742 - Encryption Registration

Code of Federal Regulations, 2014 CFR

2014-01-01

... registration, i.e., the information as described in this Supplement, submitted as a support documentation... (h) Smartcards or other identity management (i) Computer or network forensics (j) Software (i) Operating systems (ii) Applications (k) Toolkits/ASICs/components (l) Information security including secure...

15 CFR Supplement No. 5 to Part 742 - Encryption Registration

Code of Federal Regulations, 2012 CFR

2012-01-01

... registration, i.e., the information as described in this Supplement, submitted as a support documentation... (h) Smartcards or other identity management (i) Computer or network forensics (j) Software (i) Operating systems (ii) Applications (k) Toolkits/ASICs/components (l) Information security including secure...

Prescription and over-the-counter medications tool kit (April, 2011 version)

DOT National Transportation Integrated Search

2011-04-01

This Toolkit is a compilation of policies, procedures, forms, and training resources that represent the best practices being used throughout the U.S. by a variety of transit systems. It does not represent all of the effective means that transit syste...

Computerized Self-Administered Measures of Mood and Appetite for Older Adults: The Novel Assessment of Nutrition and Ageing Toolkit.

PubMed

Brown, Laura J E; Adlam, Tim; Hwang, Faustina; Khadra, Hassan; Maclean, Linda M; Rudd, Bridey; Smith, Tom; Timon, Claire; Williams, Elizabeth A; Astell, Arlene J

2018-02-01

The "Novel Assessment of Nutrition and Ageing" (NANA) toolkit is a computerized system for collecting longitudinal information about older adults' health and behavior. Here, we describe the validation of six items for measuring older adults' self-reported mood and appetite as part of the NANA system. In Study 1, 48 community-living older adults (aged 65-89 years) completed NANA measures of their current mood and appetite alongside standard paper measures, on three occasions, in a laboratory setting. In Study 2, 40 community-living older adults (aged 64-88 years) completed daily NANA measures of momentary mood and appetite in their own homes, unsupervised, alongside additional measures of health and behavior, over three 7-day periods. The NANA measures were significantly correlated with standard measures of mood and appetite, and showed stability over time. They show utility for tracking mood and appetite longitudinally, and for better understanding links with other aspects of health and behavior.

BioPig: a Hadoop-based analytic toolkit for large-scale sequence data.

PubMed

Nordberg, Henrik; Bhatia, Karan; Wang, Kai; Wang, Zhong

2013-12-01

The recent revolution in sequencing technologies has led to an exponential growth of sequence data. As a result, most of the current bioinformatics tools become obsolete as they fail to scale with data. To tackle this 'data deluge', here we introduce the BioPig sequence analysis toolkit as one of the solutions that scale to data and computation. We built BioPig on the Apache's Hadoop MapReduce system and the Pig data flow language. Compared with traditional serial and MPI-based algorithms, BioPig has three major advantages: first, BioPig's programmability greatly reduces development time for parallel bioinformatics applications; second, testing BioPig with up to 500 Gb sequences demonstrates that it scales automatically with size of data; and finally, BioPig can be ported without modification on many Hadoop infrastructures, as tested with Magellan system at National Energy Research Scientific Computing Center and the Amazon Elastic Compute Cloud. In summary, BioPig represents a novel program framework with the potential to greatly accelerate data-intensive bioinformatics analysis.

EHR implementation in South Africa: how do we get it right?

PubMed

Yogeswaran, Parimalaranie; Wright, Graham

2010-01-01

In an environment of expanding demand on the health care system to provide equitable, accessible and safe health care, usage of information communication technology is one of the strategies identified to fulfil such expectations. Electronic Health Record (EHR) is an important tool towards achieving better health care using such technology, although, across the world EHR implementation has experienced a high failure rate. Nevertheless South Africa has made a strategic decision to implement EHR system in the public health sector. An evaluation toolkit was developed, to measure the state of readiness of health institutions in South Africa in implementing EHR based on Kaplan and Norton's work on Balanced Score Card (BSC), and the subsequent variant model developed by Protti. A Critical Success Factor (CSF) scorecard to assess the state of readiness and a Balanced Score Card matrix to be used as a strategic framework was developed. These tools were validated using critiques by a panel of experts. The toolkit developed has the potential to assist the organization towards a better EHR implementation path.

X-Windows Socket Widget Class

NASA Technical Reports Server (NTRS)

Barry, Matthew R.

2006-01-01

The X-Windows Socket Widget Class ("Class" is used here in the object-oriented-programming sense of the word) was devised to simplify the task of implementing network connections for graphical-user-interface (GUI) computer programs. UNIX Transmission Control Protocol/Internet Protocol (TCP/IP) socket programming libraries require many method calls to configure, operate, and destroy sockets. Most X Windows GUI programs use widget sets or toolkits to facilitate management of complex objects. The widget standards facilitate construction of toolkits and application programs. The X-Windows Socket Widget Class encapsulates UNIX TCP/IP socket-management tasks within the framework of an X Windows widget. Using the widget framework, X Windows GUI programs can treat one or more network socket instances in the same manner as that of other graphical widgets, making it easier to program sockets. Wrapping ISP socket programming libraries inside a widget framework enables a programmer to treat a network interface as though it were a GUI.

Microscopic Simulations of Charge Transport in Disordered Organic Semiconductors

PubMed Central

2011-01-01

Charge carrier dynamics in an organic semiconductor can often be described in terms of charge hopping between localized states. The hopping rates depend on electronic coupling elements, reorganization energies, and driving forces, which vary as a function of position and orientation of the molecules. The exact evaluation of these contributions in a molecular assembly is computationally prohibitive. Various, often semiempirical, approximations are employed instead. In this work, we review some of these approaches and introduce a software toolkit which implements them. The purpose of the toolkit is to simplify the workflow for charge transport simulations, provide a uniform error control for the methods and a flexible platform for their development, and eventually allow in silico prescreening of organic semiconductors for specific applications. All implemented methods are illustrated by studying charge transport in amorphous films of tris-(8-hydroxyquinoline)aluminum, a common organic semiconductor. PMID:22076120

ISIS and META projects

NASA Technical Reports Server (NTRS)

Birman, Kenneth; Cooper, Robert; Marzullo, Keith

1990-01-01

ISIS and META are two distributed systems projects at Cornell University. The ISIS project, has developed a new methodology, virtual synchrony, for writing robust distributed software. This approach is directly supported by the ISIS Toolkit, a programming system that is distributed to over 300 academic and industrial sites. Several interesting applications that exploit the strengths of ISIS, including an NFS-compatible replicated file system, are being developed. The META project, is about distributed control in a soft real time environment incorporating feedback. This domain encompasses examples as diverse as monitoring inventory and consumption on a factory floor and performing load-balancing on a distributed computing system. One of the first uses of META is for distributed application management: the tasks of configuring a distributed program, dynamically adapting to failures, and monitoring its performance. Recent progress and current plans are presented. This approach to distributed computing, a philosophy that is believed to significantly distinguish the work from that of others in the field, is explained.

Programming your way out of the past: ISIS and the META Project

NASA Technical Reports Server (NTRS)

Birman, Kenneth P.; Marzullo, Keith

1989-01-01

The ISIS distributed programming system and the META Project are described. The ISIS programming toolkit is an aid to low-level programming that makes it easy to build fault-tolerant distributed applications that exploit replication and concurrent execution. The META Project is reexamining high-level mechanisms such as the filesystem, shell language, and administration tools in distributed systems.

An Integrated Systems Genetics and Omics Toolkit to Probe Gene Function.

PubMed

Li, Hao; Wang, Xu; Rukina, Daria; Huang, Qingyao; Lin, Tao; Sorrentino, Vincenzo; Zhang, Hongbo; Bou Sleiman, Maroun; Arends, Danny; McDaid, Aaron; Luan, Peiling; Ziari, Naveed; Velázquez-Villegas, Laura A; Gariani, Karim; Kutalik, Zoltan; Schoonjans, Kristina; Radcliffe, Richard A; Prins, Pjotr; Morgenthaler, Stephan; Williams, Robert W; Auwerx, Johan

2018-01-24

Identifying genetic and environmental factors that impact complex traits and common diseases is a high biomedical priority. Here, we developed, validated, and implemented a series of multi-layered systems approaches, including (expression-based) phenome-wide association, transcriptome-/proteome-wide association, and (reverse-) mediation analysis, in an open-access web server (systems-genetics.org) to expedite the systems dissection of gene function. We applied these approaches to multi-omics datasets from the BXD mouse genetic reference population, and identified and validated associations between genes and clinical and molecular phenotypes, including previously unreported links between Rpl26 and body weight, and Cpt1a and lipid metabolism. Furthermore, through mediation and reverse-mediation analysis we established regulatory relations between genes, such as the co-regulation of BCKDHA and BCKDHB protein levels, and identified targets of transcription factors E2F6, ZFP277, and ZKSCAN1. Our multifaceted toolkit enabled the identification of gene-gene and gene-phenotype links that are robust and that translate well across populations and species, and can be universally applied to any populations with multi-omics datasets. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

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

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.

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

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

A fast - Monte Carlo toolkit on GPU for treatment plan dose recalculation in proton therapy

NASA Astrophysics Data System (ADS)

Senzacqua, M.; Schiavi, A.; Patera, V.; Pioli, S.; Battistoni, G.; Ciocca, M.; Mairani, A.; Magro, G.; Molinelli, S.

2017-10-01

In the context of the particle therapy a crucial role is played by Treatment Planning Systems (TPSs), tools aimed to compute and optimize the tratment plan. Nowadays one of the major issues related to the TPS in particle therapy is the large CPU time needed. We developed a software toolkit (FRED) for reducing dose recalculation time by exploiting Graphics Processing Units (GPU) hardware. Thanks to their high parallelization capability, GPUs significantly reduce the computation time, up to factor 100 respect to a standard CPU running software. The transport of proton beams in the patient is accurately described through Monte Carlo methods. Physical processes reproduced are: Multiple Coulomb Scattering, energy straggling and nuclear interactions of protons with the main nuclei composing the biological tissues. FRED toolkit does not rely on the water equivalent translation of tissues, but exploits the Computed Tomography anatomical information by reconstructing and simulating the atomic composition of each crossed tissue. FRED can be used as an efficient tool for dose recalculation, on the day of the treatment. In fact it can provide in about one minute on standard hardware the dose map obtained combining the treatment plan, earlier computed by the TPS, and the current patient anatomic arrangement.

New Additions to the Toolkit for Forward/Inverse Problems in Electrocardiography within the SCIRun Problem Solving Environment.

PubMed

Coll-Font, Jaume; Burton, Brett M; Tate, Jess D; Erem, Burak; Swenson, Darrel J; Wang, Dafang; Brooks, Dana H; van Dam, Peter; Macleod, Rob S

2014-09-01

Cardiac electrical imaging often requires the examination of different forward and inverse problem formulations based on mathematical and numerical approximations of the underlying source and the intervening volume conductor that can generate the associated voltages on the surface of the body. If the goal is to recover the source on the heart from body surface potentials, the solution strategy must include numerical techniques that can incorporate appropriate constraints and recover useful solutions, even though the problem is badly posed. Creating complete software solutions to such problems is a daunting undertaking. In order to make such tools more accessible to a broad array of researchers, the Center for Integrative Biomedical Computing (CIBC) has made an ECG forward/inverse toolkit available within the open source SCIRun system. Here we report on three new methods added to the inverse suite of the toolkit. These new algorithms, namely a Total Variation method, a non-decreasing TMP inverse and a spline-based inverse, consist of two inverse methods that take advantage of the temporal structure of the heart potentials and one that leverages the spatial characteristics of the transmembrane potentials. These three methods further expand the possibilities of researchers in cardiology to explore and compare solutions to their particular imaging problem.

Teaching the physician-manager role to psychiatric residents: development and implementation of a pilot curriculum.

PubMed

Stergiopoulos, Vicky; Maggi, Julie; Sockalingam, Sanjeev

2009-01-01

The authors describe a pilot physician-manager curriculum designed to address the learning needs of psychiatric residents in administrative psychiatry and health systems. The pilot curriculum includes a junior and a senior toolkit of four workshops each. The junior toolkit introduces postgraduate-year two (PGY-2) residents to the principles of teamwork, conflict resolution, quality improvement, and program planning and evaluation. The senior toolkit exposes PGY-4 residents to leadership and change management, organizational structures, mental health and addictions reform, and self and career development. Following curriculum implementation at the University of Toronto, residents rated the importance and clinical relevance of curriculum objectives and commented on the strengths and weaknesses of the workshops and areas needing improvement. The pilot curriculum was successfully introduced at the University of Toronto in 2006. Residents rated the curriculum very highly and commented that interactive learning and contextually relevant topics are essential in meeting their needs. It is possible to successfully introduce a physician-manager curriculum early during psychiatric residency training, to match the specific needs of clinical rotations. Interactive techniques and clinical illustrations may be crucial in facilitating teaching and learning the physician-manager role. The authors discuss barriers, facilitators, and critical success factors in implementing such a curriculum.

Genome and epigenome engineering CRISPR toolkit for in vivo modulation of cis-regulatory interactions and gene expression in the chicken embryo.

PubMed

Williams, Ruth M; Senanayake, Upeka; Artibani, Mara; Taylor, Gunes; Wells, Daniel; Ahmed, Ahmed Ashour; Sauka-Spengler, Tatjana

2018-02-23

CRISPR/Cas9 genome engineering has revolutionised all aspects of biological research, with epigenome engineering transforming gene regulation studies. Here, we present an optimised, adaptable toolkit enabling genome and epigenome engineering in the chicken embryo, and demonstrate its utility by probing gene regulatory interactions mediated by neural crest enhancers. First, we optimise novel efficient guide-RNA mini expression vectors utilising chick U6 promoters, provide a strategy for rapid somatic gene knockout and establish a protocol for evaluation of mutational penetrance by targeted next-generation sequencing. We show that CRISPR/Cas9-mediated disruption of transcription factors causes a reduction in their cognate enhancer-driven reporter activity. Next, we assess endogenous enhancer function using both enhancer deletion and nuclease-deficient Cas9 (dCas9) effector fusions to modulate enhancer chromatin landscape, thus providing the first report of epigenome engineering in a developing embryo. Finally, we use the synergistic activation mediator (SAM) system to activate an endogenous target promoter. The novel genome and epigenome engineering toolkit developed here enables manipulation of endogenous gene expression and enhancer activity in chicken embryos, facilitating high-resolution analysis of gene regulatory interactions in vivo . © 2018. Published by The Company of Biologists Ltd.

Planetary Space Weather Service: Part of the the Europlanet 2020 Research Infrastructure

NASA Astrophysics Data System (ADS)

Grande, Manuel; Andre, Nicolas

2016-07-01

Over the next four years the Europlanet 2020 Research Infrastructure will set up an entirely new European Planetary Space Weather service (PSWS). Europlanet RI is a part of of Horizon 2020 (EPN2020-RI, http://www.europlanet-2020-ri.eu). The Virtual Access Service, WP5 VA1 "Planetary Space Weather Services" will extend the concepts of space weather and space situational awareness to other planets in our Solar System and in particular to spacecraft that voyage through it. VA1 will make five entirely new 'toolkits' accessible to the research community and to industrial partners planning for space missions: a general planetary space weather toolkit, as well as three toolkits dedicated to the following key planetary environments: Mars (in support ExoMars), comets (building on the expected success of the ESA Rosetta mission), and outer planets (in preparation for the ESA JUICE mission to be launched in 2022). This will give the European planetary science community new methods, interfaces, functionalities and/or plugins dedicated to planetary space weather in the tools and models available within the partner institutes. It will also create a novel event-diary toolkit aiming at predicting and detecting planetary events like meteor showers and impacts. A variety of tools (in the form of web applications, standalone software, or numerical models in various degrees of implementation) are available for tracing propagation of planetary and/or solar events through the Solar System and modelling the response of the planetary environment (surfaces, atmospheres, ionospheres, and magnetospheres) to those events. But these tools were not originally designed for planetary event prediction and space weather applications. So WP10 JRA4 "Planetary Space Weather Services" (PSWS) will provide the additional research and tailoring required to apply them for these purposes. The overall objectives of this Joint Research Aactivities will be to review, test, improve and adapt methods and tools available within the partner institutes in order to make prototype planetary event and space weather services operational in Europe at the end of the programme. Europlanet 2020 RI has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 654208.

A knowledge-based flight status monitor for real-time application in digital avionics systems

NASA Technical Reports Server (NTRS)

Duke, E. L.; Disbrow, J. D.; Butler, G. F.

1989-01-01

The Dryden Flight Research Facility of the National Aeronautics and Space Administration (NASA) Ames Research Center (Ames-Dryden) is the principal NASA facility for the flight testing and evaluation of new and complex avionics systems. To aid in the interpretation of system health and status data, a knowledge-based flight status monitor was designed. The monitor was designed to use fault indicators from the onboard system which are telemetered to the ground and processed by a rule-based model of the aircraft failure management system to give timely advice and recommendations in the mission control room. One of the important constraints on the flight status monitor is the need to operate in real time, and to pursue this aspect, a joint research activity between NASA Ames-Dryden and the Royal Aerospace Establishment (RAE) on real-time knowledge-based systems was established. Under this agreement, the original LISP knowledge base for the flight status monitor was reimplemented using the intelligent knowledge-based system toolkit, MUSE, which was developed under RAE sponsorship. Details of the flight status monitor and the MUSE implementation are presented.

QUANTUM NETWORKS WITH SINGLE ATOMS, PHOTONS AND PHONONS

DTIC Science & Technology

2016-10-04

methodology, the NSSEFF research required an interdisciplinary ’toolkit’ from atomic physics, quantum optics, and nano-photonics for the control ...achieve a very small non -guided decay rate, i.e. Γ′ ’ 0.5Γ0. Moreover, one can engineer flatter bands, which leads to an increase of the group index...without the need to investigate over a wide range of PCW designs with different photonic band structures. To fully control spin-exchange coefficients

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.

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.

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

Impact of an interprofessional shared decision-making and goal-setting decision aid for patients with diabetes on decisional conflict--study protocol for a randomized controlled trial.

PubMed

Yu, Catherine H; Ivers, Noah M; Stacey, Dawn; Rezmovitz, Jeremy; Telner, Deanna; Thorpe, Kevin; Hall, Susan; Settino, Marc; Kaplan, David M; Coons, Michael; Sodhi, Sumeet; Sale, Joanna; Straus, Sharon E

2015-06-27

Competing health concerns present real obstacles to people living with diabetes and other chronic diseases as well as to their primary care providers. Guideline implementation interventions rarely acknowledge this, leaving both patients and providers feeling overwhelmed by the volume of recommended actions. Interprofessional (IP) shared decision-making (SDM) with the use of decision aids may help to set treatment priorities. We developed an evidence-based SDM intervention for patients with diabetes and other conditions that was framed by the IP-SDM model and followed a user-centered approach. Our objective in the present study is to pilot an IP-SDM and goal-setting toolkit following the Knowledge-to-Action Framework to assess (1) intervention fidelity and the feasibility of conducting a larger trial and (2) impact on decisional conflict, diabetes distress, health-related quality of life and patient assessment of chronic illness care. A two-step, parallel-group, clustered randomized controlled trial (RCT) will be conducted, with the primary goal being to assess intervention fidelity and the feasibility of conducting a larger RCT. The first step is a provider-directed implementation only; the second (after a 6-month delay) involves both provider- and patient-directed implementation. Half of the clusters will be assigned to receive the IP-SDM toolkit, and the other will be assigned to be mailed a diabetes guidelines summary. Individual interviews with patients, their family members and health care providers will be conducted upon trial completion to explore toolkit use. A secondary purpose of this trial is to gather estimates of the toolkit's impact on decisional conflict. Secondary outcomes include diabetes distress, quality of life and chronic illness care, which will be assessed on the basis of patient-completed questionnaires of validated scales at baseline and at 6 and 12 months. Multilevel hierarchical regression models will be used to account for the clustered nature of the data. An individualized approach to patients with multiple chronic conditions using SDM and goal setting is a desirable strategy for achieving guideline-concordant treatment in a patient-centered fashion. Our pilot trial will provide insights regarding strategies for the routine implementation of such interventions in clinical practice, and it will offer an assessment of the impact of this approach. Clinicaltrials.gov Identifier: NCT02379078. Date of Registration: 11 February 2015.

From transistor to trapped-ion computers for quantum chemistry.

PubMed

Yung, M-H; Casanova, J; Mezzacapo, A; McClean, J; Lamata, L; Aspuru-Guzik, A; Solano, E

2014-01-07

Over the last few decades, quantum chemistry has progressed through the development of computational methods based on modern digital computers. However, these methods can hardly fulfill the exponentially-growing resource requirements when applied to large quantum systems. As pointed out by Feynman, this restriction is intrinsic to all computational models based on classical physics. Recently, the rapid advancement of trapped-ion technologies has opened new possibilities for quantum control and quantum simulations. Here, we present an efficient toolkit that exploits both the internal and motional degrees of freedom of trapped ions for solving problems in quantum chemistry, including molecular electronic structure, molecular dynamics, and vibronic coupling. We focus on applications that go beyond the capacity of classical computers, but may be realizable on state-of-the-art trapped-ion systems. These results allow us to envision a new paradigm of quantum chemistry that shifts from the current transistor to a near-future trapped-ion-based technology.

Work Experience Report

NASA Technical Reports Server (NTRS)

Guo, Daniel

2017-01-01

The NASA Platform for Autonomous Systems (NPAS) toolkit is currently being used at the NASA John C. Stennis Space Center (SSC) to develop the INSIGHT program, which will autonomously monitor and control the Nitrogen System of the High Pressure Gas Facility (HPGF) on site. The INSIGHT program is in need of generic timing capabilities in order to perform timing based actions such as pump usage timing and sequence step timing. The purpose of this project was to develop a timing module that could fulfill these requirements and be adaptable for expanded use in the future. The code was written in Gensym G2 software platform, the same as INSIGHT, and was written generically to ensure compatibility with any G2 program. Currently, the module has two timing capabilities, a stopwatch function and a countdown function. Although the module has gone through some functionality testing, actual integration of the module into NPAS and the INSIGHT program is contingent on the module passing later checks.

From transistor to trapped-ion computers for quantum chemistry

PubMed Central

Yung, M.-H.; Casanova, J.; Mezzacapo, A.; McClean, J.; Lamata, L.; Aspuru-Guzik, A.; Solano, E.

2014-01-01

Over the last few decades, quantum chemistry has progressed through the development of computational methods based on modern digital computers. However, these methods can hardly fulfill the exponentially-growing resource requirements when applied to large quantum systems. As pointed out by Feynman, this restriction is intrinsic to all computational models based on classical physics. Recently, the rapid advancement of trapped-ion technologies has opened new possibilities for quantum control and quantum simulations. Here, we present an efficient toolkit that exploits both the internal and motional degrees of freedom of trapped ions for solving problems in quantum chemistry, including molecular electronic structure, molecular dynamics, and vibronic coupling. We focus on applications that go beyond the capacity of classical computers, but may be realizable on state-of-the-art trapped-ion systems. These results allow us to envision a new paradigm of quantum chemistry that shifts from the current transistor to a near-future trapped-ion-based technology. PMID:24395054

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.

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…

Peripheral infrastructure vectors and an extended set of plant parts for the Modular Cloning system

PubMed Central

Kretschmer, Carola; Gruetzner, Ramona; Löfke, Christian; Dagdas, Yasin; Bürstenbinder, Katharina; Marillonnet, Sylvestre

2018-01-01

Standardized DNA assembly strategies facilitate the generation of multigene constructs from collections of building blocks in plant synthetic biology. A common syntax for hierarchical DNA assembly following the Golden Gate principle employing Type IIs restriction endonucleases was recently developed, and underlies the Modular Cloning and GoldenBraid systems. In these systems, transcriptional units and/or multigene constructs are assembled from libraries of standardized building blocks, also referred to as phytobricks, in several hierarchical levels and by iterative Golden Gate reactions. Here, a toolkit containing further modules for the novel DNA assembly standards was developed. Intended for use with Modular Cloning, most modules are also compatible with GoldenBraid. Firstly, a collection of approximately 80 additional phytobricks is provided, comprising e.g. modules for inducible expression systems, promoters or epitope tags. Furthermore, DNA modules were developed for connecting Modular Cloning and Gateway cloning, either for toggling between systems or for standardized Gateway destination vector assembly. Finally, first instances of a “peripheral infrastructure” around Modular Cloning are presented: While available toolkits are designed for the assembly of plant transformation constructs, vectors were created to also use coding sequence-containing phytobricks directly in yeast two hybrid interaction or bacterial infection assays. The presented material will further enhance versatility of hierarchical DNA assembly strategies. PMID:29847550

Flexible Environments for Grand-Challenge Simulation in Climate Science

NASA Astrophysics Data System (ADS)

Pierrehumbert, R.; Tobis, M.; Lin, J.; Dieterich, C.; Caballero, R.

2004-12-01

Current climate models are monolithic codes, generally in Fortran, aimed at high-performance simulation of the modern climate. Though they adequately serve their designated purpose, they present major barriers to application in other problems. Tailoring them to paleoclimate of planetary simulations, for instance, takes months of work. Theoretical studies, where one may want to remove selected processes or break feedback loops, are similarly hindered. Further, current climate models are of little value in education, since the implementation of textbook concepts and equations in the code is obscured by technical detail. The Climate Systems Center at the University of Chicago seeks to overcome these limitations by bringing modern object-oriented design into the business of climate modeling. Our ultimate goal is to produce an end-to-end modeling environment capable of configuring anything from a simple single-column radiative-convective model to a full 3-D coupled climate model using a uniform, flexible interface. Technically, the modeling environment is implemented as a Python-based software component toolkit: key number-crunching procedures are implemented as discrete, compiled-language components 'glued' together and co-ordinated by Python, combining the high performance of compiled languages and the flexibility and extensibility of Python. We are incrementally working towards this final objective following a series of distinct, complementary lines. We will present an overview of these activities, including PyOM, a Python-based finite-difference ocean model allowing run-time selection of different Arakawa grids and physical parameterizations; CliMT, an atmospheric modeling toolkit providing a library of 'legacy' radiative, convective and dynamical modules which can be knitted into dynamical models, and PyCCSM, a version of NCAR's Community Climate System Model in which the coupler and run-control architecture are re-implemented in Python, augmenting its flexibility and adaptability.

Keeping Kids Moving: How Equitable Transportation Policy Can Prevent Childhood Obesity Toolkit--Resource List

ERIC Educational Resources Information Center

Robert Wood Johnson Foundation, 2012

2012-01-01

This list of resources offers promising strategies that communities and policymakers can use to make sustainable advances in achieving equitable transportation systems. Resources are organized into seven categories: transportation equity, Safe Routes to School, school siting, complete streets, non-motorized transportation, community design, and…

The ISIS Project: Real Experience with a Fault Tolerant Programming System

NASA Technical Reports Server (NTRS)

Birman, Kenneth; Cooper, Robert

1990-01-01

The ISIS project has developed a distributed programming toolkit and a collection of higher level applications based on these tools. ISIS is now in use at more than 300 locations world-wise. The lessons (and surprises) gained from this experience with the real world are discussed.

Advancements in Wind Integration Study Data Modeling: The Wind Integration National Dataset (WIND) Toolkit; Preprint

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

Draxl, C.; Hodge, B. M.; Orwig, K.

2013-10-01

Regional wind integration studies in the United States require detailed wind power output data at many locations to perform simulations of how the power system will operate under high-penetration scenarios. The wind data sets that serve as inputs into the study must realistically reflect the ramping characteristics, spatial and temporal correlations, and capacity factors of the simulated wind plants, as well as be time synchronized with available load profiles. The Wind Integration National Dataset (WIND) Toolkit described in this paper fulfills these requirements. A wind resource dataset, wind power production time series, and simulated forecasts from a numerical weather predictionmore » model run on a nationwide 2-km grid at 5-min resolution will be made publicly available for more than 110,000 onshore and offshore wind power production sites.« less

Brainlab: A Python Toolkit to Aid in the Design, Simulation, and Analysis of Spiking Neural Networks with the NeoCortical Simulator.

PubMed

Drewes, Rich; Zou, Quan; Goodman, Philip H

2009-01-01

Neuroscience modeling experiments often involve multiple complex neural network and cell model variants, complex input stimuli and input protocols, followed by complex data analysis. Coordinating all this complexity becomes a central difficulty for the experimenter. The Python programming language, along with its extensive library packages, has emerged as a leading "glue" tool for managing all sorts of complex programmatic tasks. This paper describes a toolkit called Brainlab, written in Python, that leverages Python's strengths for the task of managing the general complexity of neuroscience modeling experiments. Brainlab was also designed to overcome the major difficulties of working with the NCS (NeoCortical Simulator) environment in particular. Brainlab is an integrated model-building, experimentation, and data analysis environment for the powerful parallel spiking neural network simulator system NCS.

Brainlab: A Python Toolkit to Aid in the Design, Simulation, and Analysis of Spiking Neural Networks with the NeoCortical Simulator

PubMed Central

Drewes, Rich; Zou, Quan; Goodman, Philip H.

2008-01-01

Neuroscience modeling experiments often involve multiple complex neural network and cell model variants, complex input stimuli and input protocols, followed by complex data analysis. Coordinating all this complexity becomes a central difficulty for the experimenter. The Python programming language, along with its extensive library packages, has emerged as a leading “glue” tool for managing all sorts of complex programmatic tasks. This paper describes a toolkit called Brainlab, written in Python, that leverages Python's strengths for the task of managing the general complexity of neuroscience modeling experiments. Brainlab was also designed to overcome the major difficulties of working with the NCS (NeoCortical Simulator) environment in particular. Brainlab is an integrated model-building, experimentation, and data analysis environment for the powerful parallel spiking neural network simulator system NCS. PMID:19506707

The Exoplanet Characterization ToolKit (ExoCTK)

NASA Astrophysics Data System (ADS)

Stevenson, Kevin; Fowler, Julia; Lewis, Nikole K.; Fraine, Jonathan; Pueyo, Laurent; Valenti, Jeff; Bruno, Giovanni; Filippazzo, Joseph; Hill, Matthew; Batalha, Natasha E.; Bushra, Rafia

2018-01-01

The success of exoplanet characterization depends critically on a patchwork of analysis tools and spectroscopic libraries that currently require extensive development and lack a centralized support system. Due to the complexity of spectroscopic analyses and initial time commitment required to become productive, there are currently a limited number of teams that are actively advancing the field. New teams with significant expertise, but without the proper tools, face prohibitively steep hills to climb before they can contribute. As a solution, we are developing an open-source, modular data analysis package in Python and a publicly facing web interface focused primarily on atmospheric characterization of exoplanets and exoplanet transit observation planning with JWST. The foundation of these software tools and libraries exist within pockets of the exoplanet community. Our project will gather these seedling tools and grow a robust, uniform, and well maintained exoplanet characterization toolkit.

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).

Toward autonomous driving: The CMU Navlab. II - Architecture and systems

NASA Technical Reports Server (NTRS)

Thorpe, Charles; Hebert, Martial; Kanade, Takeo; Shafer, Steven

1991-01-01

A description is given of EDDIE, the architecture for the Navlab mobile robot which provides a toolkit for building specific systems quickly and easily. Included in the discussion are the annotated maps used by EDDIE and the Navlab's road-following system, called the Autonomous Mail Vehicle, which was built using EDDIE and its annotated maps as a basis. The contributions of the Navlab project and the lessons learned from it are examined.

Medical document anonymization with a semantic lexicon.

PubMed Central

Ruch, P.; Baud, R. H.; Rassinoux, A. M.; Bouillon, P.; Robert, G.

2000-01-01

We present an original system for locating and removing personally-identifying information in patient records. In this experiment, anonymization is seen as a particular case of knowledge extraction. We use natural language processing tools provided by the MEDTAG framework: a semantic lexicon specialized in medicine, and a toolkit for word-sense and morpho-syntactic tagging. The system finds 98-99% of all personally-identifying information. PMID:11079980

Toward an automated signature recognition toolkit for mission operations

NASA Technical Reports Server (NTRS)

Cleghorn, T.; Laird, P; Perrine, L.; Culbert, C.; Macha, M.; Saul, R.; Hammen, D.; Moebes, T.; Shelton, R.

1994-01-01

Signature recognition is the problem of identifying an event or events from its time series. The generic problem has numerous applications to science and engineering. At NASA's Johnson Space Center, for example, mission control personnel, using electronic displays and strip chart recorders, monitor telemetry data from three-phase electrical buses on the Space Shuttle and maintain records of device activation and deactivation. Since few electrical devices have sensors to indicate their actual status, changes of state are inferred from characteristic current and voltage fluctuations. Controllers recognize these events both by examining the waveform signatures and by listening to audio channels between ground and crew. Recently the authors have developed a prototype system that identifies major electrical events from the telemetry and displays them on a workstation. Eventually the system will be able to identify accurately the signatures of over fifty distinct events in real time, while contending with noise, intermittent loss of signal, overlapping events, and other complications. This system is just one of many possible signature recognition applications in Mission Control. While much of the technology underlying these applications is the same, each application has unique data characteristics, and every control position has its own interface and performance requirements. There is a need, therefore, for CASE tools that can reduce the time to implement a running signature recognition application from months to weeks or days. This paper describes our work to date and our future plans.

Toward an automated signature recognition toolkit for mission operations

NASA Astrophysics Data System (ADS)

Cleghorn, T.; Laird, P.; Perrine, L.; Culbert, C.; Macha, M.; Saul, R.; Hammen, D.; Moebes, T.; Shelton, R.

1994-10-01

Signature recognition is the problem of identifying an event or events from its time series. The generic problem has numerous applications to science and engineering. At NASA's Johnson Space Center, for example, mission control personnel, using electronic displays and strip chart recorders, monitor telemetry data from three-phase electrical buses on the Space Shuttle and maintain records of device activation and deactivation. Since few electrical devices have sensors to indicate their actual status, changes of state are inferred from characteristic current and voltage fluctuations. Controllers recognize these events both by examining the waveform signatures and by listening to audio channels between ground and crew. Recently the authors have developed a prototype system that identifies major electrical events from the telemetry and displays them on a workstation. Eventually the system will be able to identify accurately the signatures of over fifty distinct events in real time, while contending with noise, intermittent loss of signal, overlapping events, and other complications. This system is just one of many possible signature recognition applications in Mission Control. While much of the technology underlying these applications is the same, each application has unique data characteristics, and every control position has its own interface and performance requirements. There is a need, therefore, for CASE tools that can reduce the time to implement a running signature recognition application from months to weeks or days. This paper describes our work to date and our future plans.

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.

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

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.

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.

The integrated contaminant elution and tracer test toolkit, ICET3, for improved characterization of mass transfer, attenuation, and mass removal

NASA Astrophysics Data System (ADS)

Brusseau, Mark L.; Guo, Zhilin

2018-01-01

It is evident based on historical data that groundwater contaminant plumes persist at many sites, requiring costly long-term management. High-resolution site-characterization methods are needed to support accurate risk assessments and to select, design, and operate effective remediation operations. Most subsurface characterization methods are generally limited in their ability to provide unambiguous, real-time delineation of specific processes affecting mass-transfer, transformation, and mass removal, and accurate estimation of associated rates. An integrated contaminant elution and tracer test toolkit, comprising a set of local-scale groundwater extraction-and injection tests, was developed to ameliorate the primary limitations associated with standard characterization methods. The test employs extended groundwater extraction to stress the system and induce hydraulic and concentration gradients. Clean water can be injected, which removes the resident aqueous contaminant mass present in the higher-permeability zones and isolates the test zone from the surrounding plume. This ensures that the concentrations and fluxes measured within the isolated area are directly and predominantly influenced by the local mass-transfer and transformation processes controlling mass removal. A suite of standard and novel tracers can be used to delineate specific mass-transfer and attenuation processes that are active at a given site, and to quantify the associated mass-transfer and transformation rates. The conceptual basis for the test is first presented, followed by an illustrative application based on simulations produced with a 3-D mathematical model and a brief case study application.

NASA Tech Briefs, February 2014

NASA Technical Reports Server (NTRS)

2014-01-01

Topics include: JWST Integrated Simulation and Test (JIST) Core; Software for Non-Contact Measurement of an Individual's Heart Rate Using a Common Camera; Rapid Infrared Pixel Grating Response Testbed; Temperature Measurement and Stabilization in a Birefringent Whispering Gallery Resonator; JWST IV and V Simulation and Test (JIST) Solid State Recorder (SSR) Simulator; Development of a Precision Thermal Doubler for Deep Space; Improving Friction Stir Welds Using Laser Peening; Methodology of Evaluating Margins of Safety in Critical Brazed Joints; Interactive Inventory Monitoring; Sensor for Spatial Detection of Single-Event Effects in Semiconductor-Based Electronics; Reworked CCGA-624 Interconnect Package Reliability for Extreme Thermal Environments; Current-Controlled Output Driver for Directly Coupled Loads; Bulk Metallic Glasses and Matrix Composites as Spacecraft Shielding; Touch Temperature Coating for Electrical Equipment on Spacecraft; Li-Ion Electrolytes Containing Flame-Retardant Additives; Autonomous Robotic Manipulation (ARM); CARVE Log; Platform Perspective Toolkit; Convex Hull-Based Plume and Anomaly Detection; Pre-Filtration of GOSAT Data Using Only Level 1 Data and an Intelligent Filter to Remove Low Clouds; Affordability Comparison Tool - ACT; "Ascent - Commemorating Shuttle" for iPad; Cassini Mission App; Light-Weight Workflow Engine: A Server for Executing Generic Workflows; Model for System Engineering of the CheMin Instrument; Timeline Central Concepts; Parallel Particle Filter Toolkit; Particle Filter Simulation and Analysis Enabling Non-Traditional Navigation; Quasi-Terminator Orbits for Mapping Small Primitive Bodies; The Subgrid-Scale Scalar Variance Under Supercritical Pressure Conditions; Sliding Gait for ATHLETE Mobility; and Automated Generation of Adaptive Filter Using a Genetic Algorithm and Cyclic Rule Reduction.

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...

CLAMP - a toolkit for efficiently building customized clinical natural language processing pipelines.

PubMed

Soysal, Ergin; Wang, Jingqi; Jiang, Min; Wu, Yonghui; Pakhomov, Serguei; Liu, Hongfang; Xu, Hua

2017-11-24

Existing general clinical natural language processing (NLP) systems such as MetaMap and Clinical Text Analysis and Knowledge Extraction System have been successfully applied to information extraction from clinical text. However, end users often have to customize existing systems for their individual tasks, which can require substantial NLP skills. Here we present CLAMP (Clinical Language Annotation, Modeling, and Processing), a newly developed clinical NLP toolkit that provides not only state-of-the-art NLP components, but also a user-friendly graphic user interface that can help users quickly build customized NLP pipelines for their individual applications. Our evaluation shows that the CLAMP default pipeline achieved good performance on named entity recognition and concept encoding. We also demonstrate the efficiency of the CLAMP graphic user interface in building customized, high-performance NLP pipelines with 2 use cases, extracting smoking status and lab test values. CLAMP is publicly available for research use, and we believe it is a unique asset for the clinical NLP community. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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.

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.

The ISIS project: Fault-tolerance in large distributed systems

NASA Technical Reports Server (NTRS)

Birman, Kenneth P.; Marzullo, Keith

1990-01-01

The semi-annual status report covers activities of the ISIS project during the second half of 1989. The project had several independent objectives: (1) At the level of the ISIS Toolkit, ISIS release V2.0 was completed, containing bypass communication protocols. Performance of the system is greatly enhanced by this change, but the initial software release is limited in some respects. (2) The Meta project focused on the definition of the Lomita programming language for specifying rules that monitor sensors for conditions of interest and triggering appropriate reactions. This design was completed, and implementation of Lomita is underway on the Meta 2.0 platform. (3) The Deceit file system effort completed a prototype. It is planned to make Deceit available for use in two hospital information systems. (4) A long-haul communication subsystem project was completed and can be used as part of ISIS. This effort resulted in tools for linking ISIS systems on different LANs together over long-haul communications lines. (5) Magic Lantern, a graphical tool for building application monitoring and control interfaces, is included as part of the general ISIS releases.

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.

A review of midwifery in Mongolia utilising the 'Strengthening Midwifery Toolkit'.

PubMed

Kildea, Sue; Larsson, Margareta; Govind, Salik

2012-12-01

The World Health Organization (WHO) developed the 'Strengthening Midwifery Toolkit' in response to an international emphasis on increasing midwifery's role in providing maternal newborn health services. It was used to assist a review of midwifery in Mongolia. A rapid situational assessment included site visits to eight health facilities and four educational institutions resulting in 30 key informant interviews and six focus group discussions (67 midwives and students). A desk review of pertinent documents (n=19) was undertaken. Data collected included assessments of: midwife competency (n=96), scope of practice (n=2), health facilities (n=8), educational institutions (n=4), legislation and regulation (n=1), and midwifery (n=4) Feldsher-Nurse (n=4) and Bachelor-Nurse (n=1) curricula. Stakeholders in Mongolia are committed to strengthening midwifery across the country to better align with international standards. This requires: a long-term investment in reorientating the health workforce and educational institutions, regulatory changes, educational investment, job description changes which will impact on other maternal newborn health service providers. Additional support and incentives for providers in rural and remote areas is needed and investment in health facilities to enable appropriate infection control; and adequate provision of essential equipment and drugs, are important strategies needed to protect staff. Maternity emergency training is required across the country. The Midwifery Toolkit was adapted to suit the local context and provided an excellent framework for this review. Copyright © 2011 Australian College of Midwives. Published by Elsevier Ltd. All rights reserved.

B-HIT - A Tool for Harvesting and Indexing Biodiversity Data

PubMed Central

Barker, Katharine; Braak, Kyle; Cawsey, E. Margaret; Coddington, Jonathan; Robertson, Tim; Whitacre, Jamie

2015-01-01

With the rapidly growing number of data publishers, the process of harvesting and indexing information to offer advanced search and discovery becomes a critical bottleneck in globally distributed primary biodiversity data infrastructures. The Global Biodiversity Information Facility (GBIF) implemented a Harvesting and Indexing Toolkit (HIT), which largely automates data harvesting activities for hundreds of collection and observational data providers. The team of the Botanic Garden and Botanical Museum Berlin-Dahlem has extended this well-established system with a range of additional functions, including improved processing of multiple taxon identifications, the ability to represent associations between specimen and observation units, new data quality control and new reporting capabilities. The open source software B-HIT can be freely installed and used for setting up thematic networks serving the demands of particular user groups. PMID:26544980

B-HIT - A Tool for Harvesting and Indexing Biodiversity Data.

PubMed

Kelbert, Patricia; Droege, Gabriele; Barker, Katharine; Braak, Kyle; Cawsey, E Margaret; Coddington, Jonathan; Robertson, Tim; Whitacre, Jamie; Güntsch, Anton

2015-01-01

With the rapidly growing number of data publishers, the process of harvesting and indexing information to offer advanced search and discovery becomes a critical bottleneck in globally distributed primary biodiversity data infrastructures. The Global Biodiversity Information Facility (GBIF) implemented a Harvesting and Indexing Toolkit (HIT), which largely automates data harvesting activities for hundreds of collection and observational data providers. The team of the Botanic Garden and Botanical Museum Berlin-Dahlem has extended this well-established system with a range of additional functions, including improved processing of multiple taxon identifications, the ability to represent associations between specimen and observation units, new data quality control and new reporting capabilities. The open source software B-HIT can be freely installed and used for setting up thematic networks serving the demands of particular user groups.

An expanding toolkit for preclinical pre-erythrocytic malaria vaccine development: bridging traditional mouse malaria models and human trials

PubMed Central

Steel, Ryan WJ; Kappe, Stefan HI; Sack, Brandon K

2016-01-01

Malaria remains a significant public health burden with 214 million new infections and over 400,000 deaths in 2015. Elucidating relevant Plasmodium parasite biology can lead to the identification of novel ways to control and ultimately eliminate the parasite within geographic areas. Particularly, the development of an effective vaccine that targets the clinically silent pre-erythrocytic stages of infection would significantly augment existing malaria elimination tools by preventing both the onset of blood-stage infection/disease as well as spread of the parasite through mosquito transmission. In this Perspective, we discuss the role of small animal models in pre-erythrocytic stage vaccine development, highlighting how human liver-chimeric and human immune system mice are emerging as valuable components of these efforts. PMID:27855488

An expanding toolkit for preclinical pre-erythrocytic malaria vaccine development: bridging traditional mouse malaria models and human trials.

PubMed

Steel, Ryan Wj; Kappe, Stefan Hi; Sack, Brandon K

2016-12-01

Malaria remains a significant public health burden with 214 million new infections and over 400,000 deaths in 2015. Elucidating relevant Plasmodium parasite biology can lead to the identification of novel ways to control and ultimately eliminate the parasite within geographic areas. Particularly, the development of an effective vaccine that targets the clinically silent pre-erythrocytic stages of infection would significantly augment existing malaria elimination tools by preventing both the onset of blood-stage infection/disease as well as spread of the parasite through mosquito transmission. In this Perspective, we discuss the role of small animal models in pre-erythrocytic stage vaccine development, highlighting how human liver-chimeric and human immune system mice are emerging as valuable components of these efforts.

The Common Ground Preparedness Framework: A Comprehensive Description of Public Health Emergency Preparedness

PubMed Central

Theadore, Fred; Jellison, James B.

2012-01-01

Currently, public health emergency preparedness (PHEP) is not well defined. Discussions about public health preparedness often make little progress, for lack of a shared understanding of the topic. We present a concise yet comprehensive framework describing PHEP activities. The framework, which was refined for 3 years by state and local health departments, uses terms easily recognized by the public health workforce within an information flow consistent with the National Incident Management System. To assess the framework's completeness, strengths, and weaknesses, we compare it to 4 other frameworks: the RAND Corporation's PREPARE Pandemic Influenza Quality Improvement Toolkit, the National Response Framework's Public Health and Medical Services Functional Areas, the National Health Security Strategy Capabilities List, and the Centers for Disease Control and Prevention's PHEP Capabilities. PMID:22397343

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.

Tested Tools You Can Use: Evaluating Earth System Science Courses

NASA Astrophysics Data System (ADS)

Lee, S. P.; Prakash, A.; Reider, D.; Baker, D.

2006-12-01

Earth System Science Education for the 21st Century (ESSE 21) has created a public access on-line evaluation resource available at http://esse21.usra.edu/evaltoolkit in collaboration with the ESSE 21 institutions, PIs, and evaluators. The purpose of the ESSE toolkit is to offer examples of how evaluation and assessment are/have been used in Earth System Science courses and programs. Our goal is to help instructors recognize different types of assessment and evaluation tools and uses that have proved useful in these courses and provide models for designing assessments in new courses. We have included actual examples of evaluations used by ESSE institution faculty in their own courses. This is not a comprehensive toolkit on educational evaluation and assessment, but it does provide several examples of evaluations that have been used successfully in Earth System Science courses and links to many good web resources on course evaluation. We have provided examples of assessments that are designed to collect information from students before, during and after courses. Some, presented in different formats, are designed to assess what students learn, others are designed to provide course instructors with information they can use to revise their courses. These assessments range from content tests to portfolios, from feedback forms to interviews, and from concept maps to attitude surveys.

Building Management Information Systems to Coordinate Citywide Afterschool Programs: A Toolkit for Cities

ERIC Educational Resources Information Center

Kingsley, Chris

2012-01-01

The National League of Cities (NLC), through its Institute for Youth, Education and Families, produced this report to help city leaders, senior municipal staff and their local partners answer those questions as they work to strengthen and coordinate services for youth and families, particularly for those cities building comprehensive afterschool…

Tumor Immunotherapy by Gene-circuit Recruited Immunomodulatory Systems (TIGRIS) for Prostate Cancer

DTIC Science & Technology

2017-09-01

Fu, X., Huang, W., and Cai, Z. (2014). Syn- thesizing AND gate genetic circuits based on CRISPR -Cas9 for identification of bladder cancer cells. Nat...and Lu, T.K. (2014). Multi- plexed and programmable regulation of gene networks with an integrated RNA and CRISPR /Cas toolkit in human cells. Mol

Building the Technology Toolkit of Marketing Students: The Emerging Technologies in Marketing Initiative

ERIC Educational Resources Information Center

Miller, Fred L.; Mangold, W. Glynn; Roach, Joy; Holmes, Terry

2013-01-01

New information technologies are transforming marketing practice, leading to calls for marketing academics to focus their research and teaching more tightly on areas relevant to practitioners. Developments in e-commerce, business geographic information systems (GIS), and social media offer powerful marketing tools to nontechnical users. This paper…

Visualising biological data: a semantic approach to tool and database integration

PubMed Central

Pettifer, Steve; Thorne, David; McDermott, Philip; Marsh, James; Villéger, Alice; Kell, Douglas B; Attwood, Teresa K

2009-01-01

Motivation In the biological sciences, the need to analyse vast amounts of information has become commonplace. Such large-scale analyses often involve drawing together data from a variety of different databases, held remotely on the internet or locally on in-house servers. Supporting these tasks are ad hoc collections of data-manipulation tools, scripting languages and visualisation software, which are often combined in arcane ways to create cumbersome systems that have been customised for a particular purpose, and are consequently not readily adaptable to other uses. For many day-to-day bioinformatics tasks, the sizes of current databases, and the scale of the analyses necessary, now demand increasing levels of automation; nevertheless, the unique experience and intuition of human researchers is still required to interpret the end results in any meaningful biological way. Putting humans in the loop requires tools to support real-time interaction with these vast and complex data-sets. Numerous tools do exist for this purpose, but many do not have optimal interfaces, most are effectively isolated from other tools and databases owing to incompatible data formats, and many have limited real-time performance when applied to realistically large data-sets: much of the user's cognitive capacity is therefore focused on controlling the software and manipulating esoteric file formats rather than on performing the research. Methods To confront these issues, harnessing expertise in human-computer interaction (HCI), high-performance rendering and distributed systems, and guided by bioinformaticians and end-user biologists, we are building reusable software components that, together, create a toolkit that is both architecturally sound from a computing point of view, and addresses both user and developer requirements. Key to the system's usability is its direct exploitation of semantics, which, crucially, gives individual components knowledge of their own functionality and allows them to interoperate seamlessly, removing many of the existing barriers and bottlenecks from standard bioinformatics tasks. Results The toolkit, named Utopia, is freely available from . PMID:19534744

Visualising biological data: a semantic approach to tool and database integration.

PubMed

Pettifer, Steve; Thorne, David; McDermott, Philip; Marsh, James; Villéger, Alice; Kell, Douglas B; Attwood, Teresa K

2009-06-16

In the biological sciences, the need to analyse vast amounts of information has become commonplace. Such large-scale analyses often involve drawing together data from a variety of different databases, held remotely on the internet or locally on in-house servers. Supporting these tasks are ad hoc collections of data-manipulation tools, scripting languages and visualisation software, which are often combined in arcane ways to create cumbersome systems that have been customized for a particular purpose, and are consequently not readily adaptable to other uses. For many day-to-day bioinformatics tasks, the sizes of current databases, and the scale of the analyses necessary, now demand increasing levels of automation; nevertheless, the unique experience and intuition of human researchers is still required to interpret the end results in any meaningful biological way. Putting humans in the loop requires tools to support real-time interaction with these vast and complex data-sets. Numerous tools do exist for this purpose, but many do not have optimal interfaces, most are effectively isolated from other tools and databases owing to incompatible data formats, and many have limited real-time performance when applied to realistically large data-sets: much of the user's cognitive capacity is therefore focused on controlling the software and manipulating esoteric file formats rather than on performing the research. To confront these issues, harnessing expertise in human-computer interaction (HCI), high-performance rendering and distributed systems, and guided by bioinformaticians and end-user biologists, we are building reusable software components that, together, create a toolkit that is both architecturally sound from a computing point of view, and addresses both user and developer requirements. Key to the system's usability is its direct exploitation of semantics, which, crucially, gives individual components knowledge of their own functionality and allows them to interoperate seamlessly, removing many of the existing barriers and bottlenecks from standard bioinformatics tasks. The toolkit, named Utopia, is freely available from http://utopia.cs.man.ac.uk/.

Using Discrete Event Simulation for Programming Model Exploration at Extreme-Scale: Macroscale Components for the Structural Simulation Toolkit (SST).

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

Wilke, Jeremiah J; Kenny, Joseph P.

2015-02-01

Discrete event simulation provides a powerful mechanism for designing and testing new extreme- scale programming models for high-performance computing. Rather than debug, run, and wait for results on an actual system, design can first iterate through a simulator. This is particularly useful when test beds cannot be used, i.e. to explore hardware or scales that do not yet exist or are inaccessible. Here we detail the macroscale components of the structural simulation toolkit (SST). Instead of depending on trace replay or state machines, the simulator is architected to execute real code on real software stacks. Our particular user-space threading frameworkmore » allows massive scales to be simulated even on small clusters. The link between the discrete event core and the threading framework allows interesting performance metrics like call graphs to be collected from a simulated run. Performance analysis via simulation can thus become an important phase in extreme-scale programming model and runtime system design via the SST macroscale components.« less

DAKOTA Design Analysis Kit for Optimization and Terascale

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

Adams, Brian M.; Dalbey, Keith R.; Eldred, Michael S.

2010-02-24

The DAKOTA (Design Analysis Kit for Optimization and Terascale Applications) toolkit provides a flexible and extensible interface between simulation codes (computational models) and iterative analysis methods. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the DAKOTA toolkit provides a flexible and extensible problem-solving environment for design and analysis of computational models on high performance computers.A user provides a set of DAKOTA commands in an input file and launches DAKOTA. DAKOTA invokes instances of the computational models, collects their results, and performs systems analyses. DAKOTA contains algorithms for optimization with gradient and nongradient-basedmore » methods; uncertainty quantification with sampling, reliability, polynomial chaos, stochastic collocation, and epistemic methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as hybrid optimization, surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. Services for parallel computing, simulation interfacing, approximation modeling, fault tolerance, restart, and graphics are also included.« less

Security Assessment Simulation Toolkit (SAST) Final Report

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

Meitzler, Wayne D.; Ouderkirk, Steven J.; Hughes, Chad O.

2009-11-15

The Department of Defense Technical Support Working Group (DoD TSWG) investment in the Pacific Northwest National Laboratory (PNNL) Security Assessment Simulation Toolkit (SAST) research planted a technology seed that germinated into a suite of follow-on Research and Development (R&D) projects culminating in software that is used by multiple DoD organizations. The DoD TSWG technology transfer goal for SAST is already in progress. The Defense Information Systems Agency (DISA), the Defense-wide Information Assurance Program (DIAP), the Marine Corps, Office Of Naval Research (ONR) National Center For Advanced Secure Systems Research (NCASSR) and Office Of Secretary Of Defense International Exercise Program (OSDmore » NII) are currently investing to take SAST to the next level. PNNL currently distributes the software to over 6 government organizations and 30 DoD users. For the past five DoD wide Bulwark Defender exercises, the adoption of this new technology created an expanding role for SAST. In 2009, SAST was also used in the OSD NII International Exercise and is currently scheduled for use in 2010.« less

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.

Stakeholder Application of NOAA/NWS River Forecasts: Oil and Water?

NASA Astrophysics Data System (ADS)

Werner, K.; Averyt, K.; Bardlsey, T.; Owen, G.

2011-12-01

The literature strongly suggests that water management seldom uses forecasts for decision making despite the proven skill of the prediction system and the obvious application of these forecasts to mitigate risk. The literature also suggests that forecast usage is motivated most strongly by risk of failure of the water management objectives. In the semi-arid western United States where water demand has grown such that it roughly equals the long term supply, risk of failure has become pervasive. In the Colorado Basin, the US National Weather Service's Colorado Basin River Forecast Center (CBRFC) has partnered with the Western Water Assessment (WWA) and the Climate Assessment for the Southwest (CLIMAS) to develop a toolkit for stakeholder engagement and application of seasonal streamflow predictions. This toolkit has been used to facilitate several meetings both in the Colorado Basin and elsewhere to assess the factors that motivate, deter, and improve the application of forecasts in this region. The toolkit includes idealized (1) scenario exercises where participants are asked to apply forecasts to real world water management problems, (2) web based exercises where participants gain experience with forecasts and other online forecast tools, and (3) surveys that assess respondents' experience with and perceptions of forecasts and climate science. This talk will present preliminary results from this effort as well as how the CBRFC has adopted the results into its stakeholder engagement strategies.

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

Development of a web-based toolkit to support improvement of care coordination in primary care.

PubMed

Ganz, David A; Barnard, Jenny M; Smith, Nina Z Y; Miake-Lye, Isomi M; Delevan, Deborah M; Simon, Alissa; Rose, Danielle E; Stockdale, Susan E; Chang, Evelyn T; Noël, Polly H; Finley, Erin P; Lee, Martin L; Zulman, Donna M; Cordasco, Kristina M; Rubenstein, Lisa V

2018-05-23

Promising practices for the coordination of chronic care exist, but how to select and share these practices to support quality improvement within a healthcare system is uncertain. This study describes an approach for selecting high-quality tools for an online care coordination toolkit to be used in Veterans Health Administration (VA) primary care practices. We evaluated tools in three steps: (1) an initial screening to identify tools relevant to care coordination in VA primary care, (2) a two-clinician expert review process assessing tool characteristics (e.g. frequency of problem addressed, linkage to patients' experience of care, effect on practice workflow, and sustainability with existing resources) and assigning each tool a summary rating, and (3) semi-structured interviews with VA patients and frontline clinicians and staff. Of 300 potentially relevant tools identified by searching online resources, 65, 38, and 18 remained after steps one, two and three, respectively. The 18 tools cover five topics: managing referrals to specialty care, medication management, patient after-visit summary, patient activation materials, agenda setting, patient pre-visit packet, and provider contact information for patients. The final toolkit provides access to the 18 tools, as well as detailed information about tools' expected benefits, and resources required for tool implementation. Future care coordination efforts can benefit from systematically reviewing available tools to identify those that are high quality and relevant.

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

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.

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

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

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.

An Automated Method for Identifying Inconsistencies within Diagrammatic Software Requirements Specifications

NASA Technical Reports Server (NTRS)

Zhang, Zhong

1997-01-01

The development of large-scale, composite software in a geographically distributed environment is an evolutionary process. Often, in such evolving systems, striving for consistency is complicated by many factors, because development participants have various locations, skills, responsibilities, roles, opinions, languages, terminology and different degrees of abstraction they employ. This naturally leads to many partial specifications or viewpoints. These multiple views on the system being developed usually overlap. From another aspect, these multiple views give rise to the potential for inconsistency. Existing CASE tools do not efficiently manage inconsistencies in distributed development environment for a large-scale project. Based on the ViewPoints framework the WHERE (Web-Based Hypertext Environment for requirements Evolution) toolkit aims to tackle inconsistency management issues within geographically distributed software development projects. Consequently, WHERE project helps make more robust software and support software assurance process. The long term goal of WHERE tools aims to the inconsistency analysis and management in requirements specifications. A framework based on Graph Grammar theory and TCMJAVA toolkit is proposed to detect inconsistencies among viewpoints. This systematic approach uses three basic operations (UNION, DIFFERENCE, INTERSECTION) to study the static behaviors of graphic and tabular notations. From these operations, subgraphs Query, Selection, Merge, Replacement operations can be derived. This approach uses graph PRODUCTIONS (rewriting rules) to study the dynamic transformations of graphs. We discuss the feasibility of implementation these operations. Also, We present the process of porting original TCM (Toolkit for Conceptual Modeling) project from C++ to Java programming language in this thesis. A scenario based on NASA International Space Station Specification is discussed to show the applicability of our approach. Finally, conclusion and future work about inconsistency management issues in WHERE project will be summarized.

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer.

PubMed

Wong, Wing Chung; Kim, Dewey; Carter, Hannah; Diekhans, Mark; Ryan, Michael C; Karchin, Rachel

2011-08-01

Thousands of cancer exomes are currently being sequenced, yielding millions of non-synonymous single nucleotide variants (SNVs) of possible relevance to disease etiology. Here, we provide a software toolkit to prioritize SNVs based on their predicted contribution to tumorigenesis. It includes a database of precomputed, predictive features covering all positions in the annotated human exome and can be used either stand-alone or as part of a larger variant discovery pipeline. MySQL database, source code and binaries freely available for academic/government use at http://wiki.chasmsoftware.org, Source in Python and C++. Requires 32 or 64-bit Linux system (tested on Fedora Core 8,10,11 and Ubuntu 10), 2.5*≤ Python <3.0*, MySQL server >5.0, 60 GB available hard disk space (50 MB for software and data files, 40 GB for MySQL database dump when uncompressed), 2 GB of RAM.

Integrating the protein and metabolic engineering toolkits for next-generation chemical biosynthesis.

PubMed

Pirie, Christopher M; De Mey, Marjan; Jones Prather, Kristala L; Ajikumar, Parayil Kumaran

2013-04-19

Through microbial engineering, biosynthesis has the potential to produce thousands of chemicals used in everyday life. Metabolic engineering and synthetic biology are fields driven by the manipulation of genes, genetic regulatory systems, and enzymatic pathways for developing highly productive microbial strains. Fundamentally, it is the biochemical characteristics of the enzymes themselves that dictate flux through a biosynthetic pathway toward the product of interest. As metabolic engineers target sophisticated secondary metabolites, there has been little recognition of the reduced catalytic activity and increased substrate/product promiscuity of the corresponding enzymes compared to those of central metabolism. Thus, fine-tuning these enzymatic characteristics through protein engineering is paramount for developing high-productivity microbial strains for secondary metabolites. Here, we describe the importance of protein engineering for advancing metabolic engineering of secondary metabolism pathways. This pathway integrated enzyme optimization can enhance the collective toolkit of microbial engineering to shape the future of chemical manufacturing.

Data Exploration Toolkit for serial diffraction experiments

DOE PAGES

Zeldin, Oliver B.; Brewster, Aaron S.; Hattne, Johan; ...

2015-01-23

Ultrafast diffraction at X-ray free-electron lasers (XFELs) has the potential to yield new insights into important biological systems that produce radiation-sensitive crystals. An unavoidable feature of the 'diffraction before destruction' nature of these experiments is that images are obtained from many distinct crystals and/or different regions of the same crystal. Combined with other sources of XFEL shot-to-shot variation, this introduces significant heterogeneity into the diffraction data, complicating processing and interpretation. To enable researchers to get the most from their collected data, a toolkit is presented that provides insights into the quality of, and the variation present in, serial crystallography datamore » sets. These tools operate on the unmerged, partial intensity integration results from many individual crystals, and can be used on two levels: firstly to guide the experimental strategy during data collection, and secondly to help users make informed choices during data processing.« less

The Trick Simulation Toolkit: A NASA/Opensource Framework for Running Time Based Physics Models

NASA Technical Reports Server (NTRS)

Penn, John M.

2016-01-01

The Trick Simulation Toolkit is a simulation development environment used to create high fidelity training and engineering simulations at the NASA Johnson Space Center and many other NASA facilities. Its purpose is to generate a simulation executable from a collection of user-supplied models and a simulation definition file. For each Trick-based simulation, Trick automatically provides job scheduling, numerical integration, the ability to write and restore human readable checkpoints, data recording, interactive variable manipulation, a run-time interpreter, and many other commonly needed capabilities. This allows simulation developers to concentrate on their domain expertise and the algorithms and equations of their models. Also included in Trick are tools for plotting recorded data and various other supporting utilities and libraries. Trick is written in C/C++ and Java and supports both Linux and MacOSX computer operating systems. This paper describes Trick's design and use at NASA Johnson Space Center.

Water Security Toolkit User Manual: Version 1.3 | Science ...

EPA Pesticide Factsheets

User manual: Data Product/Software The Water Security Toolkit (WST) is a suite of tools that help provide the information necessary to make good decisions resulting in the minimization of further human exposure to contaminants, and the maximization of the effectiveness of intervention strategies. WST assists in the evaluation of multiple response actions in order to select the most beneficial consequence management strategy. It includes hydraulic and water quality modeling software and optimization methodologies to identify: (1) sensor locations to detect contamination, (2) locations in the network in which the contamination was introduced, (3) hydrants to remove contaminated water from the distribution system, (4) locations in the network to inject decontamination agents to inactivate, remove or destroy contaminants, (5) locations in the network to take grab sample to confirm contamination or cleanup and (6) valves to close in order to isolate contaminated areas of the network.

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…

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.

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