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Sample records for informatics evaluation toolkit

  1. The DLESE Evaluation Toolkit Project

    NASA Astrophysics Data System (ADS)

    Buhr, S. M.; Barker, L. J.; Marlino, M.

    2002-12-01

    The Evaluation Toolkit and Community project is a new Digital Library for Earth System Education (DLESE) collection designed to raise awareness of project evaluation within the geoscience education community, and to enable principal investigators, teachers, and evaluators to implement project evaluation more readily. This new resource is grounded in the needs of geoscience educators, and will provide a virtual home for a geoscience education evaluation community. The goals of the project are to 1) provide a robust collection of evaluation resources useful for Earth systems educators, 2) establish a forum and community for evaluation dialogue within DLESE, and 3) disseminate the resources through the DLESE infrastructure and through professional society workshops and proceedings. Collaboration and expertise in education, geoscience and evaluation are necessary if we are to conduct the best possible geoscience education. The Toolkit allows users to engage in evaluation at whichever level best suits their needs, get more evaluation professional development if desired, and access the expertise of other segments of the community. To date, a test web site has been built and populated, initial community feedback from the DLESE and broader community is being garnered, and we have begun to heighten awareness of geoscience education evaluation within our community. The web site contains features that allow users to access professional development about evaluation, search and find evaluation resources, submit resources, find or offer evaluation services, sign up for upcoming workshops, take the user survey, and submit calendar items. The evaluation resource matrix currently contains resources that have met our initial review. The resources are currently organized by type; they will become searchable on multiple dimensions of project type, audience, objectives and evaluation resource type as efforts to develop a collection-specific search engine mature. The peer review

  2. ChemDoodle Web Components: HTML5 toolkit for chemical graphics, interfaces, and informatics.

    PubMed

    Burger, Melanie C

    2015-01-01

    ChemDoodle Web Components (abbreviated CWC, iChemLabs, LLC) is a light-weight (~340 KB) JavaScript/HTML5 toolkit for chemical graphics, structure editing, interfaces, and informatics based on the proprietary ChemDoodle desktop software. The library uses and WebGL technologies and other HTML5 features to provide solutions for creating chemistry-related applications for the web on desktop and mobile platforms. CWC can serve a broad range of scientific disciplines including crystallography, materials science, organic and inorganic chemistry, biochemistry and chemical biology. CWC is freely available for in-house use and is open source (GPL v3) for all other uses.Graphical abstractAdd interactive 2D and 3D chemical sketchers, graphics, and spectra to websites and apps with ChemDoodle Web Components.

  3. Methods for Evaluating Text Extraction Toolkits: An Exploratory Investigation

    DTIC Science & Technology

    2015-01-22

    M T R 1 4 0 4 4 3 R 2 M I T R E T E C H N I C A L R E P O R T Methods for Evaluating Text Extraction Toolkits: An...JAN 2015 2. REPORT TYPE 3. DATES COVERED 00-00-2015 to 00-00-2015 4. TITLE AND SUBTITLE Methods for Evaluating Text Extraction Toolkits: An...DISTRIBUTION/AVAILABILITY STATEMENT Approved for public release; distribution unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT Text extraction

  4. The Extensible Neuroimaging Archive Toolkit: an informatics platform for managing, exploring, and sharing neuroimaging data.

    PubMed

    Marcus, Daniel S; Olsen, Timothy R; Ramaratnam, Mohana; Buckner, Randy L

    2007-01-01

    The Extensible Neuroimaging Archive Toolkit (XNAT) is a software platform designed to facilitate common management and productivity tasks for neuroimaging and associated data. In particular, XNAT enables qualitycontrol procedures and provides secure access to and storage of data. XNAT follows a threetiered architecture that includes a data archive, user interface, and middleware engine. Data can be entered into the archive as XML or through data entry forms. Newly added data are stored in a virtual quarantine until an authorized user has validated it. XNAT subsequently maintains a history profile to track all changes made to the managed data. User access to the archive is provided by a secure web application. The web application provides a number of quality control and productivity features, including data entry forms, data-type-specific searches, searches that combine across data types, detailed reports, and listings of experimental data, upload/download tools, access to standard laboratory workflows, and administration and security tools. XNAT also includes an online image viewer that supports a number of common neuroimaging formats, including DICOM and Analyze. The viewer can be extended to support additional formats and to generate custom displays. By managing data with XNAT, laboratories are prepared to better maintain the long-term integrity of their data, to explore emergent relations across data types, and to share their data with the broader neuroimaging community.

  5. Improving the Evaluation Model for the Lithuanian Informatics Olympiads

    ERIC Educational Resources Information Center

    Skupiene, Jurate

    2010-01-01

    The Lithuanian Informatics Olympiads (LitIO) is a problem solving programming contest for students in secondary education. The work of the student to be evaluated is an algorithm designed by the student and implemented as a working program. The current evaluation process involves both automated (for correctness and performance of programs with the…

  6. Summative evaluation of a baccalaureate nursing informatics curriculum.

    PubMed Central

    Travis, L. L.; Hudak, C. A.; Brennan, P. F.

    1995-01-01

    This paper describes the fifth stage in the process of designing, implementing and evaluating the nursing informatics courses incorporated into a baccalaureate nursing program. The challenge is to construct an evolving nursing informatics curriculum so as to provide nursing professionals with the foundations for affecting health care delivery. The basic components of the curriculum framework are information, technology, and clinical care process. Information on the two groups of graduates who have completed the four course sequence and the one group of graduates who have been in practice will be discussed. PMID:8563330

  7. 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…

  8. 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 (CCSS). The Toolkit is a set of interrelated, freely available instruments for evaluating alignment to the…

  9. Evaluation of biomedical informatics innovations and their impact on public health.

    PubMed

    Sarkar, I N

    2012-01-01

    This issue of Methods of Information in Medicine contains four feature articles that are focused on the theme of evaluation. Evaluation approaches are increasingly essential in the assessment of determining the potential impact of contemporary informatics innovations. The featured articles offer practical perspectives to determining the impact of advancements. Internationally, there are significant advances being made across biomedical informatics and its related sub-disciplines. As with any scientific discipline, it is important for practitioners to be able to relate the potential importance of findings. To this end, it is especially important for biomedical informaticians to convey, in a quantifiable and comparable form, the significance of the informatics findings -not only to peers but also to those across the biomedical research spectrum. As such, the feature articles in this issue describe the evaluation of core infrastructure and fundamental informatics innovations as well as evaluation of informatics-based resources that are a core aspect of public health initiatives.

  10. A viewpoint on evidence-based health informatics, based on a pilot survey on evaluation studies in health care informatics.

    PubMed

    Ammenwerth, Elske; de Keizer, Nicolette

    2007-01-01

    Concerned about evidence-based health informatics, the authors conducted a limited pilot survey attempting to determine how many IT evaluation studies in health care are never published, and why. A survey distributed to 722 academics had a low response rate, with 136 respondents giving instructive comments on 217 evaluation studies. Of those studies, half were published in international journals, and more than one-third were never published. Reasons for not publishing (with multiple reasons per study possible) included: "results not of interest for others" (1/3 of all studies), "publication in preparation" (1/3), "no time for publication" (1/5), "limited scientific quality of study" (1/6), "political or legal reasons" (1/7), and "study only conducted for internal use" (1/8). Those reasons for non-publication in health informatics resembled those reported in other fields. Publication bias (preference for positive studies) did not appear to be a major issue. The authors believe that widespread application of guidelines in conducting health informatics evaluation studies and utilization of a registry for evaluation study results could improve the evidence base of the field.

  11. Development and evaluation of a toolkit to assess partnership readiness for community-based participatory research.

    PubMed

    Andrews, Jeannette O; Cox, Melissa J; Newman, Susan D; Meadows, Otha

    2011-01-01

    An earlier investigation by academic and community co-investigators led to the development of the Partnership Readiness for Community-Based Participatory Research (CBPR) Model, which defined major dimensions and key indicators of partnership readiness. As a next step in this process, we used qualitative methods, cognitive pretesting, and expert reviews to develop a working guide, or toolkit, based on the model for academic and community partners to assess and leverage their readiness for CBPR. The 75-page toolkit is designed as a qualitative assessment promoting equal voice and transparent, bi-directional discussions among all the partners. The toolkit is formatted to direct individual partner assessments, followed by team assessments, discussions, and action plans to optimize their goodness of fit, capacity, and operations to conduct CBPR. The toolkit has been piloted with two cohorts in the Medical University of South Carolina's (MUSC) Community Engaged Scholars (CES) Program with promising results from process and outcome evaluation data.

  12. Pathology Informatics Essentials for Residents: A flexible informatics curriculum linked to Accreditation Council for Graduate Medical Education milestones

    PubMed Central

    Henricks, Walter H; Karcher, Donald S; Harrison, James H; Sinard, John H; Riben, Michael W; Boyer, Philip J; Plath, Sue; Thompson, Arlene; Pantanowitz, Liron

    2016-01-01

    Context: Recognition of the importance of informatics to the practice of pathology has surged. Training residents in pathology informatics have been a daunting task for most residency programs in the United States because faculty often lacks experience and training resources. Nevertheless, developing resident competence in informatics is essential for the future of pathology as a specialty. Objective: The objective of the study is to develop and deliver a pathology informatics curriculum and instructional framework that guides pathology residency programs in training residents in critical pathology informatics knowledge and skills and meets Accreditation Council for Graduate Medical Education Informatics Milestones. Design: The College of American Pathologists, Association of Pathology Chairs, and Association for Pathology Informatics formed a partnership and expert work group to identify critical pathology informatics training outcomes and to create a highly adaptable curriculum and instructional approach, supported by a multiyear change management strategy. Results: Pathology Informatics Essentials for Residents (PIER) is a rigorous approach for educating all pathology residents in important pathology informatics knowledge and skills. PIER includes an instructional resource guide and toolkit for incorporating informatics training into residency programs that vary in needs, size, settings, and resources. PIER is available at http://www.apcprods.org/PIER (accessed April 6, 2016). Conclusions: PIER is an important contribution to informatics training in pathology residency programs. PIER introduces pathology trainees to broadly useful informatics concepts and tools that are relevant to practice. PIER provides residency program directors with a means to implement a standardized informatics training curriculum, to adapt the approach to local program needs, and to evaluate resident performance and progress over time. PMID:27563486

  13. Methodological framework for evaluating clinical processes: A cognitive informatics perspective.

    PubMed

    Kannampallil, Thomas G; Abraham, Joanna; Patel, Vimla L

    2016-12-01

    We propose a methodological framework for evaluating clinical cognitive activities in complex real-world environments that provides a guiding framework for characterizing the patterns of activities. This approach, which we refer to as a process-based approach, is particularly relevant to cognitive informatics (CI) research-an interdisciplinary domain utilizing cognitive approaches in the study of computing systems and applications-as it provides new ways for understanding human information processing, interactions, and behaviors. Using this approach involves the identification of a process of interest (e.g., a clinical workflow), and the contributing sequences of activities in that process (e.g., medication ordering). A variety of analytical approaches can then be used to characterize the inherent dependencies and relations within the contributing activities within the considered process. Using examples drawn from our own research and the extant research literature, we describe the theoretical foundations of the process-based approach, relevant practical and pragmatic considerations for using such an approach, and a generic framework for applying this approach for evaluation studies in clinical settings. We also discuss the potential for this approach in future evaluations of interactive clinical systems, given the need for new approaches for evaluation, and significant opportunities for automated, unobtrusive data collection.

  14. 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.

  15. Development and Pilot Test of the RAND Suicide Prevention Program Evaluation Toolkit

    DTIC Science & Technology

    2013-01-01

    Prevention Program Evaluation Toolkit Joie D . Acosta, Rajeev Ramchand, Amariah Becker, Alexandria Felton Prepared for the Office of the Secretary of...testing of the toolkit: Thomas Burke, Christopher Dorr, Colonel John Forbes, Robert Gardiner, Jackie Garrick , Malcolm Hawkins, Joan Hunter, Jan Kemp...2004 2005 2006 2007 2008 2009 2010 A ci tv e d u ty s u ic id e ra te p er 1 00 ,0 00 0 5 10 15 20 25 30 DoD Army Air Force Marine Corps Navy 2

  16. Logic Models for Program Design, Implementation, and Evaluation: Workshop Toolkit. REL 2015-057

    ERIC Educational Resources Information Center

    Shakman, Karen; Rodriguez, Sheila M.

    2015-01-01

    The Logic Model Workshop Toolkit is designed to help practitioners learn the purpose of logic models, the different elements of a logic model, and the appropriate steps for developing and using a logic model for program evaluation. Topics covered in the sessions include an overview of logic models, the elements of a logic model, an introduction to…

  17. Development and Evaluation of an Integrated Pest Management Toolkit for Child Care Providers

    ERIC Educational Resources Information Center

    Alkon, Abbey; Kalmar, Evie; Leonard, Victoria; Flint, Mary Louise; Kuo, Devina; Davidson, Nita; Bradman, Asa

    2012-01-01

    Young children and early care and education (ECE) staff are exposed to pesticides used to manage pests in ECE facilities in the United States and elsewhere. The objective of this pilot study was to encourage child care programs to reduce pesticide use and child exposures by developing and evaluating an Integrated Pest Management (IPM) Toolkit for…

  18. STARE-HI – Statement on Reporting of Evaluation Studies in Health Informatics

    PubMed Central

    Brender, J.; Talmon, J.; de Keizer, N.; Nykänen, P.; Rigby, M.; Ammenwerth, E.

    2013-01-01

    Summary Background Improving the quality of reporting of evaluation studies in health informatics is an important requirement towards the vision of evidence-based health informatics. The STARE-HI – Statement on Reporting of Evaluation Studies in health informatics, published in 2009, provides guidelines on the elements to be contained in an evaluation study report. Objectives To elaborate on and provide a rationale for the principles of STARE-HI and to guide authors and readers of evaluation studies in health informatics by providing explanatory examples of reporting. Methods A group of methodologists, researchers and editors prepared the present elaboration of the STARE-HI statement and selected examples from the literature. Results The 35 STARE-HI items to be addressed in evaluation papers describing health informatics interventions are discussed one by one and each is extended with examples and elaborations. Conclusion The STARE-HI statement and this elaboration document should be helpful resources to improve reporting of both quantitative and qualitative evaluation studies. Evaluation manuscripts adhering to the principles will enable readers of such papers to better place the studies in a proper context and judge their validity and generalizability, and thus in turn optimize the exploitation of the evidence contained therein. Limitations This paper is based on experiences of a group of editors, reviewers, authors of systematic reviews and readers of the scientific literature. The applicability of the details of these principles has to evolve as a function of their use in practice. PMID:24155788

  19. Leveraging change to integrate library and informatics competencies into a new CTSC curriculum: a program evaluation.

    PubMed

    Kroth, Philip J; Phillips, Holly E; Eldredge, Jonathan D

    2009-07-01

    This program evaluation reports on the curricular development and integration of library, biomedical informatics, and scholarly communications (LBS) skills into a required informatics course for a new graduate degree program in the University of New Mexico's Clinical and Translational Sciences Center (CTSC). The course built on the opportunity presented by the new degree program to integrate LBS competencies rarely included in most traditional clinical research training programs. This report tracks the experiences and evaluations of two cohorts of graduate students who have completed the course. This article presents lessons learned on curricular integration and offers thoughts for future work.

  20. Assessing Community Informatics: A Review of Methodological Approaches for Evaluating Community Networks and Community Technology Centers.

    ERIC Educational Resources Information Center

    O'Neil, Dara

    2002-01-01

    Analyzes the emerging community informatics evaluation literature to develop an understanding of the indicators used to gauge project impacts in community networks and community technology centers. The study finds that community networks and community technology center assessments fall into five key areas: strong democracy; social capital;…

  1. Omics Informatics: From Scattered Individual Software Tools to Integrated Workflow Management Systems.

    PubMed

    Ma, Tianle; Zhang, Aidong

    2016-02-26

    Omic data analyses pose great informatics challenges. As an emerging subfield of bioinformatics, omics informatics focuses on analyzing multi-omic data efficiently and effectively, and is gaining momentum. There are two underlying trends in the expansion of omics informatics landscape: the explosion of scattered individual omics informatics tools with each of which focuses on a specific task in both single- and multi- omic settings, and the fast-evolving integrated software platforms such as workflow management systems that can assemble multiple tools into pipelines and streamline integrative analysis for complicated tasks. In this survey, we give a holistic view of omics informatics, from scattered individual informatics tools to integrated workflow management systems. We not only outline the landscape and challenges of omics informatics, but also sample a number of widely used and cutting-edge algorithms in omics data analysis to give readers a fine-grained view. We survey various workflow management systems (WMSs), classify them into three levels of WMSs from simple software toolkits to integrated multi-omic analytical platforms, and point out the emerging needs for developing intelligent workflow management systems. We also discuss the challenges, strategies and some existing work in systematic evaluation of omics informatics tools. We conclude by providing future perspectives of emerging fields and new frontiers in omics informatics.

  2. A case study of evaluating informatics impact on diffusion of scientific knowledge.

    PubMed

    Katz, Susan B

    2008-11-06

    This case study poster uses a newly developed framework to evaluate an informatics effort in its public health context. The electronic clearance system being evaluated provides the potential for increasing the speed and quality of scientific diffusion of knowledge, and thus translation of research into practice. A graphical logic model and tabular results of the evaluation are presented. Public health history suggests potential benefits of more timely and coordinated diffusion of scientific information.

  3. The informatics nurse specialist role in electronic health record usability evaluation.

    PubMed

    Rojas, Crystal L; Seckman, Charlotte A

    2014-05-01

    Health information technology is revolutionizing the way we interact with health-related data. One example of this can be seen in the rising adoption rates of electronic health records by healthcare providers. Nursing plays a vital role in electronic health record adoption, not only because of their numbers but also their intimate understanding of workflow. The success of an electronic health record also relies on how usable the software is for clinicians, and a thorough usability evaluation is needed before implementing a system within an organization. Not all nurses have the knowledge and skills to perform extensive usability testing; therefore, the informatics nurse specialist plays a critical role in the process. This article will discuss core usability principles, provide a framework for applying these concepts, and explore the role of the informatics nurse specialist in electronic health record evaluation. Health information technology is fundamentally changing the clinical practice environment, and many nurses are seeking leadership positions in the field of informatics. As technology and software become more sophisticated, usability principles must be used under theguidance of the informatics nurse specialist to provide a relevant, robust, and well-designed electronic health record to address the needs of the busy clinician.

  4. 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.

  5. 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

  6. Toolkit for evaluating genes required for proliferation and survival using tetracycline-regulated RNAi.

    PubMed

    Zuber, Johannes; McJunkin, Katherine; Fellmann, Christof; Dow, Lukas E; Taylor, Meredith J; Hannon, Gregory J; Lowe, Scott W

    2011-01-01

    Short hairpin RNAs (shRNAs) are versatile tools for analyzing loss-of-function phenotypes in vitro and in vivo. However, their use for studying genes involved in proliferation and survival, which are potential therapeutic targets in cancer and other diseases, is confounded by the strong selective advantage of cells in which shRNA expression is inefficient. We therefore developed a toolkit that combines Tet-regulated miR30-shRNA technology, robust transactivator expression and two fluorescent reporters to track and isolate cells with potent target knockdown. We demonstrated that this system improves the study of essential genes and was sufficiently robust to eradicate aggressive cancer in mice by suppressing a single gene. Further, we applied this system for in vivo negative-selection screening with pooled shRNAs and propose a streamlined, inexpensive workflow that will facilitate the use of RNA interference (RNAi) for the identification and evaluation of essential therapeutic targets.

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

    PubMed

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

    2016-07-11

    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.

  8. Land Surface Verification Toolkit (LVT) - A Generalized Framework for Land Surface Model Evaluation

    NASA Technical Reports Server (NTRS)

    Kumar, Sujay V.; Peters-Lidard, Christa D.; Santanello, Joseph; Harrison, Ken; Liu, Yuqiong; Shaw, Michael

    2011-01-01

    Model evaluation and verification are key in improving the usage and applicability of simulation models for real-world applications. In this article, the development and capabilities of a formal system for land surface model evaluation called the Land surface Verification Toolkit (LVT) is described. LVT is designed to provide an integrated environment for systematic land model evaluation and facilitates a range of verification approaches and analysis capabilities. LVT operates across multiple temporal and spatial scales and employs a large suite of in-situ, remotely sensed and other model and reanalysis datasets in their native formats. In addition to the traditional accuracy-based measures, LVT also includes uncertainty and ensemble diagnostics, information theory measures, spatial similarity metrics and scale decomposition techniques that provide novel ways for performing diagnostic model evaluations. Though LVT was originally designed to support the land surface modeling and data assimilation framework known as the Land Information System (LIS), it also supports hydrological data products from other, non-LIS environments. In addition, the analysis of diagnostics from various computational subsystems of LIS including data assimilation, optimization and uncertainty estimation are supported within LVT. Together, LIS and LVT provide a robust end-to-end environment for enabling the concepts of model data fusion for hydrological applications. The evolving capabilities of LVT framework are expected to facilitate rapid model evaluation efforts and aid the definition and refinement of formal evaluation procedures for the land surface modeling community.

  9. MISR Toolkit

    Atmospheric Science Data Center

    2014-05-07

    ...   The MISR Toolkit (MTK) is a simplified programming interface to access MISR Level 1B2, Level 2, and ancillary data ... of MISR Toolkit was tested on Linux32 Fedora Core 19, Linux 64 Fedora Core 19, Mac OS X 10.6.8 (Intel), Windows XP (x86), and Windows ...

  10. Developing and Evaluating Criteria to Help Reviewers of Biomedical Informatics Manuscripts

    PubMed Central

    Ammenwerth, Elske; Wolff, Astrid C.; Knaup, Petra; Ulmer, Hanno; Skonetzki, Stefan; van Bemmel, Jan H.; McCray, Alexa T.; Haux, Reinhold; Kulikowski, Casimir

    2003-01-01

    Peer-reviewed publication of scientific research results represents the most important means of their communication. The authors have annually reviewed a large heterogeneous set of papers to produce the International Medical Informatics Association (IMIA) Yearbook of Medical Informatics. To support an objective and high-quality review process, the authors attempted to provide reviewers with a set of refined quality criteria, comprised of 80 general criteria and an additional 60 criteria for specific types of manuscripts. Authors conducted a randomized controlled trial, with 18 reviewers, to evaluate application of the refined criteria on review outcomes. Whereas the trial found that reviewers applying the criteria graded papers more strictly (lower overall scores), and that junior reviewers appreciated the availability of the criteria, there was no overall change in the interrater variability in reviewing the manuscripts. The authors describe their experience as a “case report” and provide a reference to the refined quality review criteria without claiming that the criteria represent a validated instrument for quantitative quality measurement. PMID:12807814

  11. A NOVEL SAFER CONCEPTION COUNSELING TOOLKIT FOR THE PREVENTION OF HIV: A MIXED-METHODS EVALUATION IN KISUMU, KENYA

    PubMed Central

    Brown, Joelle; Njoroge, Betty; Akama, Eliud; Breitnauer, Brooke; Leddy, Anna; Darbes, Lynae; Omondi, Richard; Mmeje, Okeoma

    2017-01-01

    Safer conception strategies can prevent HIV transmission between HIV-discordant partners while allowing them to conceive. However, HIV care providers in sub-Saharan Africa report they are not trained in safer conception, and patients are not routinely offered safer conception services. This mixed-methods pilot study evaluated the impact, acceptability, and feasibility of a novel Safer Conception Counseling Toolkit among providers and patients in Kenya. We enrolled 20 HIV-positive women, 10 HIV-discordant couples, and 10 providers from HIV care and treatment clinics. Providers completed questionnaires before/after training, and then counseled HIV-affected patients. Change in patient knowledge was assessed before/after counseling. Qualitative interviews were conducted among providers and patients. The Toolkit was associated with large, significant increases in patient knowledge, and provider confidence, knowledge, and favorable attitudes toward safer conception counseling; 20% felt confident before versus 100% after training (p < 0.01). PMID:27925487

  12. Management and Evaluation of a Pan-Canadian Graduate Training Program in Health Informatics

    ERIC Educational Resources Information Center

    Hebert, Marilynne; Lau, Francis

    2010-01-01

    Eight Canadian universities partnered to establish a Collaborative Health Informatics PhD/Postdoc Strategic Training Program (CHPSTP). The 6-year goal was to increase research capacity in health informatics in Canada. Three cohorts of 20 trainees participated in the training, which included online Research Learning Experiences, annual face-to-face…

  13. Biomedical informatics and translational medicine.

    PubMed

    Sarkar, Indra Neil

    2010-02-26

    Biomedical informatics involves a core set of methodologies that can provide a foundation for crossing the "translational barriers" associated with translational medicine. To this end, the fundamental aspects of biomedical informatics (e.g., bioinformatics, imaging informatics, clinical informatics, and public health informatics) may be essential in helping improve the ability to bring basic research findings to the bedside, evaluate the efficacy of interventions across communities, and enable the assessment of the eventual impact of translational medicine innovations on health policies. Here, a brief description is provided for a selection of key biomedical informatics topics (Decision Support, Natural Language Processing, Standards, Information Retrieval, and Electronic Health Records) and their relevance to translational medicine. Based on contributions and advancements in each of these topic areas, the article proposes that biomedical informatics practitioners ("biomedical informaticians") can be essential members of translational medicine teams.

  14. Evaluating the AMIA-OHSU 10x10 Program to Train Healthcare Professionals in Medical Informatics

    PubMed Central

    Feldman, Sue S.; Hersh, William

    2008-01-01

    The promise of health information technology (HIT) has led to calls for a larger and better trained work-force in medical informatics. University programs in applied health and biomedical informatics have been evolving in an effort to address the need for health-care professionals to be trained in informatics. One such evolution is the American Medical Informatics Association’s (AMIA) 10x10 program. To assess current delivery and content models, participant satisfaction, and how graduates have benefited from the program in career or education advancement, all students who completed the Oregon Health & Science University (OHSU) offering of the AMIA 10x10 course through the end of 2006 were surveyed. We found that the 10x10 program is approaching AMIA’s goals, and that there are potential areas for content and delivery modifications. Further research in defining the optimal competencies of the medical informatics workforce and its optimal education is needed. PMID:18999199

  15. [Biomedical informatics].

    PubMed

    Capurro, Daniel; Soto, Mauricio; Vivent, Macarena; Lopetegui, Marcelo; Herskovic, Jorge R

    2011-12-01

    Biomedical Informatics is a new discipline that arose from the need to incorporate information technologies to the generation, storage, distribution and analysis of information in the domain of biomedical sciences. This discipline comprises basic biomedical informatics, and public health informatics. The development of the discipline in Chile has been modest and most projects have originated from the interest of individual people or institutions, without a systematic and coordinated national development. Considering the unique features of health care system of our country, research in the area of biomedical informatics is becoming an imperative.

  16. Redesigning Schools to Reach Every Student with Excellent Teachers: Teacher & Staff Selection, Development, & Evaluation Toolkit

    ERIC Educational Resources Information Center

    Public Impact, 2012

    2012-01-01

    This toolkit is a companion to the school models provided on OpportunityCulture.org. The school models use job redesign and technology to extend the reach of excellent teachers to more students, for more pay, within budget. Most of these school models create new roles and collaborative teams, enabling all teachers and staff to develop and…

  17. Informatics Moments

    ERIC Educational Resources Information Center

    Williams, Kate

    2012-01-01

    The informatics moment is the moment when a person seeks help in using some digital technology that is new to him or her. This article examines the informatics moment in people's everyday lives as they sought help at a branch public library. Four types of literacy were involved: basic literacy (reading and writing), computer literacy (use of a…

  18. Evaluation of the Cow Rumen Metagenome; Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies(Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    SciTech Connect

    Sczyrba, Alex

    2011-10-13

    DOE JGI's Alex Sczyrba on "Evaluation of the Cow Rumen Metagenome" and "Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  19. Evaluation of the Cow Rumen Metagenome; Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies(Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema

    Sczyrba, Alex [DOE JGI

    2016-07-12

    DOE JGI's Alex Sczyrba on "Evaluation of the Cow Rumen Metagenome" and "Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  20. Now We Know: Assessing Sexual Assault Criminal Justice Case Processing in an Urban Community Using the Sexual Assault Nurse Practitioner Evaluation Toolkit.

    PubMed

    Valentine, Julie L; Shaw, Jessica; Lark, Alyssa; Campbell, Rebecca

    2016-01-01

    Campbell and colleagues developed an evaluation Toolkit for use by sexual assault nurse examiners (SANEs) to assess criminal case outcomes in adult sexual assault cases seen by SANE programs (Campbell, Townsend, Shaw, Karim, & Markowitz, 2014; Campbell, Bybee, et al., 2014). The Toolkit provides step-by-step directions and an easy-to-use statistical program. This study describes implementation of the Toolkit in Salt Lake County, the first site outside the pilot sites to utilize the program. The Toolkit revealed that, in Salt Lake County from 2003 to 2011, only 6% of adult sexual assault cases were successfully prosecuted. These findings prompted multiple community discussions, media attention, and a call to action to improve the investigation and prosecution of adult sexual assault cases. The primary purpose of this case report is to encourage other SANE teams and communities to use the Toolkit by sharing the successful experience of Salt Lake County in implementing the Toolkit.Video Abstract available for additional insights from Dr. Valentine (see Supplemental Digital Content 1, http://links.lww.com/JFN/A19).

  1. Quantitative and Qualitative Evaluation of The Structural Designing of Medical Informatics Dynamic Encyclopedia

    PubMed Central

    Safdari, Reza; Shahmoradi, Leila; Hosseini-beheshti, Molouk-sadat; Nejad, Ahmadreza Farzaneh; Hosseiniravandi, Mohammad

    2015-01-01

    Introduction: Encyclopedias and their compilation have become so prevalent as a valid cultural medium in the world. The daily development of computer industry and the expansion of various sciences have made indispensable the compilation of electronic, specialized encyclopedias, especially the web-based ones. Materials and Methods: This is an applied-developmental study conducted in 2014. First, the main terms in the field of medical informatics were gathered using MeSH Online 2014 and the supplementary terms of each were determined, and then the tree diagram of the terms was drawn based on their relationship in MeSH. Based on the studies done by the researchers, the tree diagram of the encyclopedia was drawn with respect to the existing areas in this field, and the terms gathered were put in related domains. Findings: In MeSH, 75 preferred terms together with 249 supplementary ones were indexed. One of the informatics’ sub-branches is biomedical informatics and health which itself consists of three sub-divisions of bioinformatics, clinical informatics, and health informatics. Medical informatics which is a subdivision of clinical informatics has developed from the three fields of medical sciences, management and social sciences, and computational sciences and mathematics. Results and Discussion: Medical Informatics is created of confluence and fusion and applications of the three major scientific branches include health and biological sciences, social sciences and management sciences, computing and mathematical sciences, and according to that the structure of MeSH is weak for future development of Encyclopedia of Medical Informatics. PMID:26635440

  2. Informatic nephrology.

    PubMed

    Musso, Carlos; Aguilera, Jerónimo; Otero, Carlos; Vilas, Manuel; Luna, Daniel; de Quirós, Fernán González Bernaldo

    2013-08-01

    Biomedical informatics in Health (BIH) is the discipline in charge of capturing, handling and using information in health and biomedicine in order to improve the processes involved with assistance and management. Informatic nephrology has appeared as a product of the combination between conventional nephrology with BIH and its development has been considerable in the assistance as well as in the academic field. Regarding the former, there is increasing evidence that informatics technology can make nephrological assistance be better in quality (effective, accessible, safe and satisfying), improve patient's adherence, optimize patient's and practitioner's time, improve physical space and achieve health cost reduction. Among its main elements, we find electronic medical and personal health records, clinical decision support system, tele-nephrology, and recording and monitoring devices. Additionally, regarding the academic field, informatics and Internet contribute to education and research in the nephrological field. In conclusion, informatics nephrology represents a new field which will influence the future of nephrology.

  3. 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:…

  4. Commercial off-the-shelf consumer health informatics interventions: recommendations for their design, evaluation and redesign

    PubMed Central

    Zayas-Cabán, Teresa

    2011-01-01

    Objective The goal of this paper is to describe the successful application of a use case-based evaluation approach to guide the effective design, evaluation and redesign of inexpensive, commercial, off-the-shelf consumer health informatics (CHI) interventions. Design Researchers developed four CHI intervention use cases representing two distinct patient populations (patients with diabetes with high blood pressure, post-bariatric surgery patients), two commercial off-the-shelf CHI applications (Microsoft HealthVault, Google Health), and related devices (blood pressure monitor, pedometer, weight scale). Three patient proxies tested each intervention for 10 days. Measurements The patient proxies recorded their challenges while completing use case tasks, rating the severity of each challenge based on how much it hindered their use of the intervention. Two independent evaluators categorized the challenges by human factors domain (physical, cognitive, macroergonomic). Results The use case-based approach resulted in the identification of 122 challenges, with 12% physical, 50% cognitive and 38% macroergonomic. Thirty-nine challenges (32%) were at least moderately severe. Nine of 22 use case tasks (41%) accounted for 72% of the challenges. Limitations The study used two patient proxies and addressed two specific patient populations and low-cost, off-the-shelf CHI interventions, which may not perfectly generalize to a larger number of proxies, actual patient populations, or other CHI interventions. Conclusion CHI designers can employ the use case-based evaluation approach to assess the fit of a CHI intervention with patients' health work, in the context of their daily activities and environment, which would be difficult or impossible to evaluate by laboratory-based studies. PMID:21727206

  5. 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.

  6. Graph algorithms in the titan toolkit.

    SciTech Connect

    McLendon, William Clarence, III; Wylie, Brian Neil

    2009-10-01

    Graph algorithms are a key component in a wide variety of intelligence analysis activities. The Graph-Based Informatics for Non-Proliferation and Counter-Terrorism project addresses the critical need of making these graph algorithms accessible to Sandia analysts in a manner that is both intuitive and effective. Specifically we describe the design and implementation of an open source toolkit for doing graph analysis, informatics, and visualization that provides Sandia with novel analysis capability for non-proliferation and counter-terrorism.

  7. Museum Informatics.

    ERIC Educational Resources Information Center

    Marty, Paul F.; Rayward, W. Boyd; Twidale, Michael B.

    2003-01-01

    Discusses museum informatics that studies how information science and technology affect the museum environment. Examines digital technology; information organization and access; digitization, personal computers, and the Internet; data sharing; standards; social impacts of new technologies; collaboration; consortia; multimedia exhibits; virtual…

  8. Tracker Toolkit

    NASA Technical Reports Server (NTRS)

    Lewis, Steven J.; Palacios, David M.

    2013-01-01

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

  9. 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!

  10. Toolkit for Monitoring and Evaluation of Indoor Residual Spraying for Visceral Leishmaniasis Control in the Indian Subcontinent: Application and Results

    PubMed Central

    Huda, M. Mamun; Mondal, Dinesh; Kumar, Vijay; Das, Pradeep; Sharma, S. N.; Das, Murari Lal; Roy, Lolita; Gurung, Chitra Kumar; Banjara, Megha Raj; Akhter, Shireen; Maheswary, Narayan Prosad; Kroeger, Axel; Chowdhury, Rajib

    2011-01-01

    Background. We field tested and validated a newly developed monitoring and evaluation (M&E) toolkit for indoor residual spraying to be used by the supervisors at different levels of the national kala-azar elimination programs in Bangladesh, India and Nepal. Methods. Methods included document analysis, in-depth interviews, direct observation of spraying squads, and entomological-chemical assessments (bioassay, susceptibility test, chemical analysis of insecticide residues on sprayed surfaces, vector density measurements at baseline, and three follow-up surveys). Results. We found that the documentation at district offices was fairly complete; important shortcomings included insufficient training of spraying squads and supervisors, deficient spray equipment, poor spraying performance, lack of protective clothing, limited coverage of houses resulting in low bioavailability of the insecticide on sprayed surfaces, and reduced vector susceptibility to DDT in India, which limited the impact on vector densities. Conclusion. The M&E toolkit is a useful instrument for detecting constraints in IRS operations and to trigger timely response. PMID:21811510

  11. Educating translational researchers in research informatics principles and methods: an evaluation of a model online course and plans for its dissemination.

    PubMed

    Friedman, Robert; Kudesia, Valmeek; Sebastiani, Paola; Monti, Stefano; Misquitta, Donald; Peterson, Kirsten; Whinfield, James; Stoeckle, Rebecca

    2013-01-01

    Translational research generates and/or uses very large amounts of diverse data. Informatics principles and methods address datasets that are large and complex, whereas few translational researchers know these principles and methods and many cannot design, carry out, or analyze the results of these studies optimally. With few exceptions, informatics education has not been directed to researchers, especially established researchers. To fill this gap, we carried out a formal needs assessment of research informatics education of translational researchers, focusing on established researchers. Using the results, we developed a model curriculum for educating researchers in research informatics and a first generation model online course in research informatics for researchers. We are completing a formal evaluation of this online course with a diverse group of translational researchers. From the results of this evaluation, we will create a second version of the online course, a dissemination plan to make it available to researchers nationally, and a plan to enhance the course over time. We will discuss the implications for the future of translational research and research informatics.

  12. A unified toolkit for information and scientific visualization

    NASA Astrophysics Data System (ADS)

    Wylie, Brian; Baumes, Jeffrey

    2009-01-01

    We present an expansion of the popular open source Visualization Toolkit (VTK) to support the ingestion, processing, and display of informatics data. The result is a flexible, component-based pipeline framework for the integration and deployment of algorithms in the scientific and informatics fields. This project, code named "Titan", is one of the first efforts to address the unification of information and scientific visualization in a systematic fashion. The result includes a wide range of informatics-oriented functionality: database access, graph algorithms, graph layouts, views, charts, UI components and more. Further, the data distribution, parallel processing and client/server capabilities of VTK provide an excellent platform for scalable analysis.

  13. BIT: Biosignal Igniter Toolkit.

    PubMed

    da Silva, Hugo Plácido; Lourenço, André; Fred, Ana; Martins, Raúl

    2014-06-01

    The study of biosignals has had a transforming role in multiple aspects of our society, which go well beyond the health sciences domains to which they were traditionally associated with. While biomedical engineering is a classical discipline where the topic is amply covered, today biosignals are a matter of interest for students, researchers and hobbyists in areas including computer science, informatics, electrical engineering, among others. Regardless of the context, the use of biosignals in experimental activities and practical projects is heavily bounded by the cost, and limited access to adequate support materials. In this paper we present an accessible, albeit versatile toolkit, composed of low-cost hardware and software, which was created to reinforce the engagement of different people in the field of biosignals. The hardware consists of a modular wireless biosignal acquisition system that can be used to support classroom activities, interface with other devices, or perform rapid prototyping of end-user applications. The software comprehends a set of programming APIs, a biosignal processing toolbox, and a framework for real time data acquisition and postprocessing.

  14. Health Informatics.

    ERIC Educational Resources Information Center

    Russell, Marie; Brittain, J. Michael

    2002-01-01

    Identifies current trends and issues in health informatics with examples of applications, particularly in English-speaking countries. Topics include health systems, professionals, and patients; consumer health information; electronic medical records; nursing; privacy and confidentiality; finding and using information; the Internet; e-mail;…

  15. The Design and Evaluation of "CAPTools"--A Computer Aided Parallelization Toolkit

    NASA Technical Reports Server (NTRS)

    Yan, Jerry; Frumkin, Michael; Hribar, Michelle; Jin, Haoqiang; Waheed, Abdul; Johnson, Steve; Cross, Jark; Evans, Emyr; Ierotheou, Constantinos; Leggett, Pete; Saini, Subhash (Technical Monitor)

    1998-01-01

    Writing applications for high performance computers is a challenging task. Although writing code by hand still offers the best performance, it is extremely costly and often not very portable. The Computer Aided Parallelization Tools (CAPTools) are a toolkit designed to help automate the mapping of sequential FORTRAN scientific applications onto multiprocessors. CAPTools consists of the following major components: an inter-procedural dependence analysis module that incorporates user knowledge; a 'self-propagating' data partitioning module driven via user guidance; an execution control mask generation and optimization module for the user to fine tune parallel processing of individual partitions; a program transformation/restructuring facility for source code clean up and optimization; a set of browsers through which the user interacts with CAPTools at each stage of the parallelization process; and a code generator supporting multiple programming paradigms on various multiprocessors. Besides describing the rationale behind the architecture of CAPTools, the parallelization process is illustrated via case studies involving structured and unstructured meshes. The programming process and the performance of the generated parallel programs are compared against other programming alternatives based on the NAS Parallel Benchmarks, ARC3D and other scientific applications. Based on these results, a discussion on the feasibility of constructing architectural independent parallel applications is presented.

  16. An Approach for All in Pharmacy Informatics Education.

    PubMed

    Fox, Brent I; Flynn, Allen; Clauson, Kevin A; Seaton, Terry L; Breeden, Elizabeth

    2017-03-25

    Computerization is transforming health care. All clinicians are users of health information technology (HIT). Understanding fundamental principles of informatics, the field focused on information needs and uses, is essential if HIT is going to support improved patient outcomes. Informatics education for clinicians is a national priority. Additionally, some informatics experts are needed to bring about innovations in HIT. A common approach to pharmacy informatics education has been slow to develop. Meanwhile, accreditation standards for informatics in pharmacy education continue to evolve. A gap remains in the implementation of informatics education for all pharmacy students and it is unclear what expert informatics training should cover. In this article, we propose the first of two complementary approaches to informatics education in pharmacy: to incorporate fundamental informatics education into pharmacy curricula for all students. The second approach, to train those students interested in becoming informatics experts to design, develop, implement, and evaluate HIT, will be presented in a subsequent issue of the Journal.

  17. An Approach for All in Pharmacy Informatics Education

    PubMed Central

    Flynn, Allen; Clauson, Kevin A.; Seaton, Terry L.; Breeden, Elizabeth

    2017-01-01

    Computerization is transforming health care. All clinicians are users of health information technology (HIT). Understanding fundamental principles of informatics, the field focused on information needs and uses, is essential if HIT is going to support improved patient outcomes. Informatics education for clinicians is a national priority. Additionally, some informatics experts are needed to bring about innovations in HIT. A common approach to pharmacy informatics education has been slow to develop. Meanwhile, accreditation standards for informatics in pharmacy education continue to evolve. A gap remains in the implementation of informatics education for all pharmacy students and it is unclear what expert informatics training should cover. In this article, we propose the first of two complementary approaches to informatics education in pharmacy: to incorporate fundamental informatics education into pharmacy curricula for all students. The second approach, to train those students interested in becoming informatics experts to design, develop, implement, and evaluate HIT, will be presented in a subsequent issue of the Journal. PMID:28381898

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

    PubMed Central

    Coles, Mark C.; Kullberg, Marika C.; Timmis, Jon

    2017-01-01

    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. PMID:28158307

  19. Climate Informatics

    NASA Technical Reports Server (NTRS)

    Monteleoni, Claire; Schmidt, Gavin A.; Alexander, Francis J.; Niculescu-Mizil, Alexandru; Steinhaeuser, Karsten; Tippett, Michael; Banerjee, Arindam; Blumenthal, M. Benno; Ganguly, Auroop R.; Smerdon, Jason E.; Tedesco, Marco

    2013-01-01

    The impacts of present and potential future climate change will be one of the most important scientific and societal challenges in the 21st century. Given observed changes in temperature, sea ice, and sea level, improving our understanding of the climate system is an international priority. This system is characterized by complex phenomena that are imperfectly observed and even more imperfectly simulated. But with an ever-growing supply of climate data from satellites and environmental sensors, the magnitude of data and climate model output is beginning to overwhelm the relatively simple tools currently used to analyze them. A computational approach will therefore be indispensable for these analysis challenges. This chapter introduces the fledgling research discipline climate informatics: collaborations between climate scientists and machine learning researchers in order to bridge this gap between data and understanding. We hope that the study of climate informatics will accelerate discovery in answering pressing questions in climate science.

  20. 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.

  1. A usability evaluation toolkit for In-Vehicle Information Systems (IVISs).

    PubMed

    Harvey, Catherine; Stanton, Neville A; Pickering, Carl A; McDonald, Mike; Zheng, Pengjun

    2011-05-01

    Usability must be defined specifically for the context of use of the particular system under investigation. This specific context of use should also be used to guide the definition of specific usability criteria and the selection of appropriate evaluation methods. There are four principles which can guide the selection of evaluation methods, relating to the information required in the evaluation, the stage at which to apply methods, the resources required and the people involved in the evaluation. This paper presents a framework for the evaluation of usability in the context of In-Vehicle Information Systems (IVISs). This framework guides designers through defining usability criteria for an evaluation, selecting appropriate evaluation methods and applying those methods. These stages form an iterative process of design-evaluation-redesign with the overall aim of improving the usability of IVISs and enhancing the driving experience, without compromising the safety of the driver.

  2. The emerging role of educational informatics.

    PubMed

    Weiner, Elizabeth E; Trangenstein, Patricia A

    2009-01-01

    Initial growth in the field of nursing informatics has centered primarily on the clinical setting. Much has been written about the systems developed and evaluated and possible new roles that one can play in the clinical environment. The educational arena has not fared as well. Early attention has been focused on the integration of educational technology or on competency-based skills in informatics according to program levels of students. This paper will focus on the emerging role of educational informatics. Examples will provide nurses with a better understanding of the roles played by the educational informaticist in crafting the science of nursing informatics to produce better nursing education outcomes.

  3. Planning and Selecting Evaluation Designs for Leadership Training: A Toolkit for Nurse Managers and Educators.

    PubMed

    Dunne, Simon; Lunn, Cora; Kirwan, Marcia; Matthews, Anne; Condell, Sarah

    2015-01-01

    Leadership development training and education for nurses is a priority in modern health care systems. Consequently, effective evaluation of nurse leadership development programs is essential for managers and educators in health care organizations to determine the impact of such programs on staff behaviors and patient outcomes. Our team has identified a framework for the evaluation of the design and implementation of such programs. Following this, we provide practical tools for the selection of evaluation methodologies for leadership development programs for use by health care educators and program commissioners.

  4. A clinical research analytics toolkit for cohort study.

    PubMed

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

    2012-01-01

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

  5. Evaluation of an automatic multiple sclerosis lesion quantification tool in an informatics-based MS e-folder system

    NASA Astrophysics Data System (ADS)

    Ma, Kevin; Fernandez, James; Amezcua, Lilyana; Lerner, Alex; Liu, Brent

    2011-03-01

    Multiple sclerosis (MS) is a demyelinating disease of the central nervous system. The chronic nature of MS necessitates multiple MRI studies to track disease progression. We have presented an imaging informatics decision-support system, called MS eFolder, designed to integrate patient clinical data with MR images and a computer-aided detection (CAD) component for automatic white matter lesion quantification. The purpose of the MS eFolder is to comprehensively present MS patient data for clinicians and radiologists, while providing a lesion quantification tool that can be objective and consistent for MS tracking in longitudinal studies. The MS CAD algorithm is based on the K-nearest neighbor (KNN) principles and has been integrated within the eFolder system. Currently, the system has been completed and the CAD algorithm for quantifying MS lesions has undergone the expert evaluation in order to validate system performance and accuracy. The evaluation methodology has been developed and the data has been collected, including over 100 MS MRI cases with various age and ethnic backgrounds. The preliminary results of the evaluation are expected to include sensitivity and specificity of lesion and non-lesion voxels in the white matter, the effectiveness of different probability thresholds for each voxel, and comparison between CAD quantification results and radiologists' manual readings. The results aim to show the effectiveness of a MS lesion CAD system to be used in a clinical setting, as well as a step closer to full clinical implementation of the eFolder system.

  6. Working with Evaluation Stakeholders: A Rationale, Step-Wise Approach and Toolkit

    ERIC Educational Resources Information Center

    Bryson, John M.; Patton, Michael Quinn; Bowman, Ruth A.

    2011-01-01

    In the broad field of evaluation, the importance of stakeholders is often acknowledged and different categories of stakeholders are identified. Far less frequent is careful attention to analysis of stakeholders' interests, needs, concerns, power, priorities, and perspectives and subsequent application of that knowledge to the design of…

  7. Design and evaluation of an imaging informatics system for analytics-based decision support in radiation therapy

    NASA Astrophysics Data System (ADS)

    Deshpande, Ruchi; DeMarco, John; Liu, Brent J.

    2015-03-01

    We have developed a comprehensive DICOM RT specific database of retrospective treatment planning data for radiation therapy of head and neck cancer. Further, we have designed and built an imaging informatics module that utilizes this database to perform data mining. The end-goal of this data mining system is to provide radiation therapy decision support for incoming head and neck cancer patients, by identifying best practices from previous patients who had the most similar tumor geometries. Since the performance of such systems often depends on the size and quality of the retrospective database, we have also placed an emphasis on developing infrastructure and strategies to encourage data sharing and participation from multiple institutions. The infrastructure and decision support algorithm have both been tested and evaluated with 51 sets of retrospective treatment planning data of head and neck cancer patients. We will present the overall design and architecture of our system, an overview of our decision support mechanism as well as the results of our evaluation.

  8. Monte Carlo simulation of Ray-Scan 64 PET system and performance evaluation using GATE toolkit

    NASA Astrophysics Data System (ADS)

    Li, Suying; Zhang, Qiushi; Vuletic, Ivan; Xie, Zhaoheng; Yang, Kun; Ren, Qiushi

    2017-02-01

    In this study, we aimed to develop a GATE model for the simulation of Ray-Scan 64 PET scanner and model its performance characteristics. A detailed implementation of system geometry and physical process were included in the simulation model. Then we modeled the performance characteristics of Ray-Scan 64 PET system for the first time, based on National Electrical Manufacturers Association (NEMA) NU-2 2007 protocols and validated the model against experimental measurement, including spatial resolution, sensitivity, counting rates and noise equivalent count rate (NECR). Moreover, an accurate dead time module was investigated to simulate the counting rate performance. Overall results showed reasonable agreement between simulation and experimental data. The validation results showed the reliability and feasibility of the GATE model to evaluate major performance of Ray-Scan 64 PET system. It provided a useful tool for a wide range of research applications.

  9. Evaluation of a toolkit to improve cardiovascular disease screening and treatment for people with type 2 diabetes: protocol for a cluster-randomized pragmatic trial

    PubMed Central

    2010-01-01

    Background The gap between the level of care recommended by evidence-based clinical practice guidelines and the actual care delivered to patients in practice has been well established. The Canadian Diabetes Association (CDA) created an implementation strategy to improve the implementation of its 2008 guidelines. This study will evaluate the impact of the strategy to improve cardiovascular disease (CVD) screening, prevention and treatment for people with diabetes. Design A pragmatic cluster-randomized trial will be conducted to evaluate the CDA's CVD Toolkit. All family physicians in Ontario, Canada were randomly allocated to receive the Toolkit, which includes several printed educational materials targeting CVD screening, prevention and treatment, either in spring 2009 (intervention arm) or in spring 2010 (control arm). Randomization occurred at the level of the practice. Forty family physicians from each arm will be recruited to participate, and the medical records for 20 of their diabetic patients at high risk for CVD will be retrospectively reviewed. Outcome measures will be assessed for each patient between July 2009 and March 2010. The primary outcome will be that the patient is receiving a statin. Secondary outcomes will include 1) the receipt of an angiotensin converting enzyme inhibitor or angiotensin receptor blocker, 2) various intermediate measures (A1c, blood pressure, LDL-cholesterol, total-/HDL-cholesterol ratio, body mass index and waist circumference), and 3) clinical inertia (the failure to change therapy in response to an abnormal A1c, blood pressure or cholesterol reading). The analysis will be carried out using multilevel hierarchical logistic regression models to account for the clustered nature of the data. The group assignment will be a physician-level variable. In addition, a process evaluation study with six focus groups of family physicians will assess the acceptability of the CDA's Toolkit and will explore factors contributing to any

  10. 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…

  11. Guiding the design of evaluations of innovations in health informatics: a framework and a case study of the SMArt SHARP evaluation.

    PubMed

    Ramly, Edmond; Brennan, Patricia Flatley

    2012-01-01

    Development of health information systems innovations is necessary to create a better future for health and health care, but evaluating them is challenging. This paper examines the problem of evaluating health IT projects in which innovation is agile, adaptive, and emergent, and in which innovation diffusion and production are interlinked. We introduce a typology of mindsets for evaluation design that are typically used in health informatics: optimality, contingency, and usefulness, and make the case for a modularity mindset. We propose a model that shifts the unit of analysis from an evaluation as a whole, to specific modules of an evaluation, such as purpose, target, and methods. We then use retrospective participant observation to illustrate the approach using a case study: the ONC SHARP Harvard project developing the SMArt platform (smartplaforms.org). We find that the proposed modular approach to evaluation design provides a balanced alternative to standard archetypical designs on the one hand, and fully custom-made designs, on the other hand.

  12. TOOLKIT, Version 2. 0

    SciTech Connect

    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 most 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.

  13. Design and Evaluation of a Health-Focused Personal Informatics Application with Support for Generalized Goal Management

    ERIC Educational Resources Information Center

    Medynskiy, Yevgeniy

    2012-01-01

    The practice of health self-management offers behavioral and problem-solving strategies that can effectively promote responsibility for one's own wellbeing, improve one's health outcomes, and decrease the cost of health services. Personal informatics applications support health self-management by allowing their users to easily track…

  14. Emergency care toolkits.

    PubMed

    Black, Steven

    2004-06-01

    Emergency care services are the focus of a series of toolkits developed by the NHS National electronic Library for Health to provide resources for emergency care leads and others involved in modernising emergency care, writes Steven Black.

  15. Hydropower RAPID Toolkit

    SciTech Connect

    2016-12-01

    This fact sheet provides a brief overview of the U.S. Department of Energy (DOE) Hydropower Regulatory and Permitting Information Desktop (RAPID) Toolkit including its capabilities, features, and benefits.

  16. A National Agenda for Public Health Informatics

    PubMed Central

    Yasnoff, William A.; Overhage, J. Marc; Humphreys, Betsy L.; LaVenture, Martin

    2001-01-01

    The AMIA 2001 Spring Congress brought together members of the the public health and informatics communities to develop a national agenda for public health informatics. Discussions of funding and governance; architecture and infrastructure; standards and vocabulary; research, evaluation, and best practices; privacy, confidentiality, and security; and training and workforce resulted in 74 recommendations with two key themes—that all stakeholders need to be engaged in coordinated activities related to public health information architecture, standards, confidentiality, best practices, and research; and that informatics training is needed throughout the public health workforce. Implementation of this consensus agenda will help promote progress in the application of information technology to improve public health. PMID:11687561

  17. Usability testing in medical informatics: cognitive approaches to evaluation of information systems and user interfaces.

    PubMed Central

    Kushniruk, A. W.; Patel, V. L.; Cimino, J. J.

    1997-01-01

    This paper describes an approach to the evaluation of health care information technologies based on usability engineering and a methodological framework from the study of medical cognition. The approach involves collection of a rich set of data including video recording of health care workers as they interact with systems, such as computerized patient records and decision support tools. The methodology can be applied in the laboratory setting, typically involving subjects "thinking aloud" as they interact with a system. A similar approach to data collection and analysis can also be extended to study of computer systems in the "live" environment of hospital clinics. Our approach is also influenced from work in the area of cognitive task analysis, which aims to characterize the decision making and reasoning of subjects of varied levels of expertise as they interact with information technology in carrying out representative tasks. The stages involved in conducting cognitively-based usability analyses are detailed and the application of such analysis in the iterative process of system and interface development is discussed. PMID:9357620

  18. JAVA Stereo Display Toolkit

    NASA Technical Reports Server (NTRS)

    Edmonds, Karina

    2008-01-01

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

  19. The Einstein Toolkit

    NASA Astrophysics Data System (ADS)

    Löffler, Frank

    2012-03-01

    The Einstein Toolkit Consortium is developing and supporting open software for relativistic astrophysics. Its aim is to provide the core computational tools that can enable new science, broaden our community, facilitate interdisciplinary research and take advantage of petascale computers and advanced cyberinfrastructure. The Einstein Toolkit currently consists of an open set of over 100 modules for the Cactus framework, primarily for computational relativity along with associated tools for simulation management and visualization. The toolkit includes solvers for vacuum spacetimes as well as relativistic magneto-hydrodynamics, along with modules for initial data, analysis and computational infrastructure. These modules have been developed and improved over many years by many different researchers. The Einstein Toolkit is supported by a distributed model, combining core support of software, tools, and documentation in its own repositories and through partnerships with other developers who contribute open software and coordinate together on development. As of January 2012 it has 68 registered members from 30 research groups world-wide. This talk will present the current capabilities of the Einstein Toolkit and will point to information how to leverage it for future research.

  20. Accelerating the deployment of a health information technology and informatics workforce through education, training, research, and evaluation.

    PubMed

    Lorenzi, Nancy; Bloomrosen, Meryl

    2011-01-01

    Supported by stronger and more coordinated US federal funding and policies, driven by goals to deliver care more efficiently, and motivated to provide high quality care for an aging and more diverse population, public-private-sector organisations are redoubling efforts to implement information systems. Thus, there is a critical need to increase and broaden the pool of workers who can help organizations maximise the effectiveness of their investments in technology. There are in the US various current health informatics education and training initiatives and ongoing efforts to accelerate Health IT workforce development.

  1. 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.

  2. Curricula Challenges and Informatics Competencies for Nurse Educators.

    PubMed

    Kinnunen, Ulla-Mari; Rajalahti, Elina; Cummings, Elizabeth; Borycki, Elizabeth M

    2017-01-01

    Nursing informatics competencies are fundamental to nursing practice in all areas of nursing work, including direct patient care, administration and education. The recent activity relating to the development of nursing informatics competencies for beginning level nurses has exposed a paucity of understanding of the requirements for nursing informatics competencies for nurse educators. So, whilst the challenge of educating faculty to teach informatics has been limited, research into such competencies is required to meet this challenge. This paper describes the challenges and issues associated with nursing informatics competency development for faculty, outlines the capabilities of faculty, and presents a vision for the future of informatics education for faculty. The final requirement of the introduction of new competencies is to determine appropriate evaluation measures that reflect the requirements of all stakeholders.

  3. 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,…

  4. Origins of Medical Informatics

    PubMed Central

    Collen, Morris F.

    1986-01-01

    Medical informatics is a new knowledge domain of computer and information science, engineering and technology in all fields of health and medicine, including research, education and practice. Medical informatics has evolved over the past 30 years as medicine learned to exploit the extraordinary capabilities of the electronic digital computer to better meet its complex information needs. The first articles on this subject appeared in the 1950s, the number of publications rapidly increased in the 1960s and medical informatics was identified as a new specialty in the 1970s. PMID:3544507

  5. NBII-SAIN Data Management Toolkit

    USGS Publications Warehouse

    Burley, Thomas E.; Peine, John D.

    2009-01-01

    The Strategic Plan for the U.S. Geological Survey Biological Informatics Program (2005-2009) recognizes the need for effective data management: Though the Federal government invests more than $600 million per year in biological data collection, it is difficult to address these issues because of limited accessibility and lack of standards for data and information...variable quality, sources, methods, and formats (for example observations in the field, museum specimens, and satellite images) present additional challenges. This is further complicated by the fast-moving target of emerging and changing technologies such as GPS and GIS. Even though these technologies offer new solutions, they also create new informatics challenges (Ruggiero and others, 2005). The USGS National Biological Information Infrastructure program, hereafter referred to as NBII, is charged with the mission to improve the way data and information are gathered, documented, stored, and accessed. The central objective of this project is a direct reflection of the purpose of NBII as described by John Mosesso, Program Manager of the U.S. Geological Survey-Biological Informatics Program-GAP Analysis: At the outset, the reason for bringing about NBII was that there were significant amounts of data and information scattered all over the U.S., not accessible, in incompatible formats, and that NBII was tasked with addressing this problem...NBII's focus is to pull data together that truly matters to someone or communities. Essentially, the core questions are: 1) what are the issues, 2) where is the data, and 3) how can we make it usable and accessible (John Mosesso, U.S. Geological Survey, oral commun., 2006). Redundancy in data collection can be a major issue when multiple stakeholders are involved with a common effort. In 2001 the U.S. General Accounting Office (USGAO) estimated that about 50 percent of the Federal government's geospatial data at the time was redundant. In addition, approximately 80

  6. 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

  7. Solving a methodological challenge in work stress evaluation with the Stress Assessment and Research Toolkit (StART): a study protocol

    PubMed Central

    2013-01-01

    Background Stress evaluation is a field of strong interest and challenging due to several methodological aspects in the evaluation process. The aim of this study is to propose a study protocol to test a new method (i.e., the Stress Assessment and Research Toolkit) to assess psychosocial risk factors at work. Design This method addresses several methodological issues (e.g., subjective vs. objective, qualitative vs quantitative data) by assessing work-related stressors using different kinds of data: i) organisational archival data (organisational indicators sheet); ii) qualitative data (focus group); iii) worker perception (questionnaire); and iv) observational data (observational checklist) using mixed methods research. In addition, it allows positive and negative aspects of work to be considered conjointly, using an approach that considers at the same time job demands and job resources. Discussion The integration of these sources of data can reduce the theoretical and methodological bias related to stress research in the work setting, allows researchers and professionals to obtain a reliable description of workers’ stress, providing a more articulate vision of psychosocial risks, and allows a large amount of data to be collected. Finally, the implementation of the method ensures in the long term a primary prevention for psychosocial risk management in that it aims to reduce or modify the intensity, frequency or duration of organisational demands. PMID:23799950

  8. Informatics in Turkey

    NASA Technical Reports Server (NTRS)

    Cakir, Serhat

    1994-01-01

    In the last twenty years the rapid change in the informatics sector has had economic and social impact on private and government activities. The Supreme Council for Science and Technology of Turkey assigned highest priority to the informatics in its meeting in February 1993. With this advice TUBITAK (The Scientific and Technical Research Council of Turkey) intends to give a strong impulse to development of a research policy in this field.

  9. 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.

  10. An imaging informatics-based ePR (electronic patient record) system for providing decision support in evaluating dose optimization in stroke rehabilitation

    NASA Astrophysics Data System (ADS)

    Liu, Brent J.; Winstein, Carolee; Wang, Ximing; Konersman, Matt; Martinez, Clarisa; Schweighofer, Nicolas

    2012-02-01

    Stroke is one of the major causes of death and disability in America. After stroke, about 65% of survivors still suffer from severe paresis, while rehabilitation treatment strategy after stroke plays an essential role in recovery. Currently, there is a clinical trial (NIH award #HD065438) to determine the optimal dose of rehabilitation for persistent recovery of arm and hand paresis. For DOSE (Dose Optimization Stroke Evaluation), laboratory-based measurements, such as the Wolf Motor Function test, behavioral questionnaires (e.g. Motor Activity Log-MAL), and MR, DTI, and Transcranial Magnetic Stimulation (TMS) imaging studies are planned. Current data collection processes are tedious and reside in various standalone systems including hardcopy forms. In order to improve the efficiency of this clinical trial and facilitate decision support, a web-based imaging informatics system has been implemented together with utilizing mobile devices (eg, iPAD, tablet PC's, laptops) for collecting input data and integrating all multi-media data into a single system. The system aims to provide clinical imaging informatics management and a platform to develop tools to predict the treatment effect based on the imaging studies and the treatment dosage with mathematical models. Since there is a large amount of information to be recorded within the DOSE project, the system provides clinical data entry through mobile device applications thus allowing users to collect data at the point of patient interaction without typing into a desktop computer, which is inconvenient. Imaging analysis tools will also be developed for structural MRI, DTI, and TMS imaging studies that will be integrated within the system and correlated with the clinical and behavioral data. This system provides a research platform for future development of mathematical models to evaluate the differences between prediction and reality and thus improve and refine the models rapidly and efficiently.

  11. Clinical microbiology informatics.

    PubMed

    Rhoads, Daniel D; Sintchenko, Vitali; Rauch, Carol A; Pantanowitz, Liron

    2014-10-01

    The clinical microbiology laboratory has responsibilities ranging from characterizing the causative agent in a patient's infection to helping detect global disease outbreaks. All of these processes are increasingly becoming partnered more intimately with informatics. Effective application of informatics tools can increase the accuracy, timeliness, and completeness of microbiology testing while decreasing the laboratory workload, which can lead to optimized laboratory workflow and decreased costs. Informatics is poised to be increasingly relevant in clinical microbiology, with the advent of total laboratory automation, complex instrument interfaces, electronic health records, clinical decision support tools, and the clinical implementation of microbial genome sequencing. This review discusses the diverse informatics aspects that are relevant to the clinical microbiology laboratory, including the following: the microbiology laboratory information system, decision support tools, expert systems, instrument interfaces, total laboratory automation, telemicrobiology, automated image analysis, nucleic acid sequence databases, electronic reporting of infectious agents to public health agencies, and disease outbreak surveillance. The breadth and utility of informatics tools used in clinical microbiology have made them indispensable to contemporary clinical and laboratory practice. Continued advances in technology and development of these informatics tools will further improve patient and public health care in the future.

  12. What is biomedical informatics?

    PubMed

    Bernstam, Elmer V; Smith, Jack W; Johnson, Todd R

    2010-02-01

    Biomedical informatics lacks a clear and theoretically-grounded definition. Many proposed definitions focus on data, information, and knowledge, but do not provide an adequate definition of these terms. Leveraging insights from the philosophy of information, we define informatics as the science of information, where information is data plus meaning. Biomedical informatics is the science of information as applied to or studied in the context of biomedicine. Defining the object of study of informatics as data plus meaning clearly distinguishes the field from related fields, such as computer science, statistics and biomedicine, which have different objects of study. The emphasis on data plus meaning also suggests that biomedical informatics problems tend to be difficult when they deal with concepts that are hard to capture using formal, computational definitions. In other words, problems where meaning must be considered are more difficult than problems where manipulating data without regard for meaning is sufficient. Furthermore, the definition implies that informatics research, teaching, and service should focus on biomedical information as data plus meaning rather than only computer applications in biomedicine.

  13. Clinical Microbiology Informatics

    PubMed Central

    Sintchenko, Vitali; Rauch, Carol A.; Pantanowitz, Liron

    2014-01-01

    SUMMARY The clinical microbiology laboratory has responsibilities ranging from characterizing the causative agent in a patient's infection to helping detect global disease outbreaks. All of these processes are increasingly becoming partnered more intimately with informatics. Effective application of informatics tools can increase the accuracy, timeliness, and completeness of microbiology testing while decreasing the laboratory workload, which can lead to optimized laboratory workflow and decreased costs. Informatics is poised to be increasingly relevant in clinical microbiology, with the advent of total laboratory automation, complex instrument interfaces, electronic health records, clinical decision support tools, and the clinical implementation of microbial genome sequencing. This review discusses the diverse informatics aspects that are relevant to the clinical microbiology laboratory, including the following: the microbiology laboratory information system, decision support tools, expert systems, instrument interfaces, total laboratory automation, telemicrobiology, automated image analysis, nucleic acid sequence databases, electronic reporting of infectious agents to public health agencies, and disease outbreak surveillance. The breadth and utility of informatics tools used in clinical microbiology have made them indispensable to contemporary clinical and laboratory practice. Continued advances in technology and development of these informatics tools will further improve patient and public health care in the future. PMID:25278581

  14. An Informatics Approach to Evaluating Combined Chemical Exposures from Consumer Products: A Case Study of Asthma-Associated Chemicals and Potential Endocrine Disruptors

    PubMed Central

    Gabb, Henry A.; Blake, Catherine

    2016-01-01

    Background: Simultaneous or sequential exposure to multiple environmental stressors can affect chemical toxicity. Cumulative risk assessments consider multiple stressors but it is impractical to test every chemical combination to which people are exposed. New methods are needed to prioritize chemical combinations based on their prevalence and possible health impacts. Objectives: We introduce an informatics approach that uses publicly available data to identify chemicals that co-occur in consumer products, which account for a significant proportion of overall chemical load. Methods: Fifty-five asthma-associated and endocrine disrupting chemicals (target chemicals) were selected. A database of 38,975 distinct consumer products and 32,231 distinct ingredient names was created from online sources, and PubChem and the Unified Medical Language System were used to resolve synonymous ingredient names. Synonymous ingredient names are different names for the same chemical (e.g., vitamin E and tocopherol). Results: Nearly one-third of the products (11,688 products, 30%) contained ≥ 1 target chemical and 5,229 products (13%) contained > 1. Of the 55 target chemicals, 31 (56%) appear in ≥ 1 product and 19 (35%) appear under more than one name. The most frequent three-way chemical combination (2-phenoxyethanol, methyl paraben, and ethyl paraben) appears in 1,059 products. Further work is needed to assess combined chemical exposures related to the use of multiple products. Conclusions: The informatics approach increased the number of products considered in a traditional analysis by two orders of magnitude, but missing/incomplete product labels can limit the effectiveness of this approach. Such an approach must resolve synonymy to ensure that chemicals of interest are not missed. Commonly occurring chemical combinations can be used to prioritize cumulative toxicology risk assessments. Citation: Gabb HA, Blake C. 2016. An informatics approach to evaluating combined chemical

  15. What Is Primary Care Informatics?

    PubMed Central

    de Lusignan, Simon

    2003-01-01

    Primary care informatics is an emerging academic discipline that remains undefined. The unique nature of primary care necessitates the development of its own informatics discipline. A definition of primary care informatics is proposed, which encompasses the distinctive nature of primary care. The core concepts and theory that should underpin it are described. Primary care informatics is defined as a science and as a subset of health informatics. The proposed definition is intended to focus the development of a generalizable core theory for this informatics subspecialty. PMID:12668690

  16. Alma Data Mining Toolkit

    NASA Astrophysics Data System (ADS)

    Friedel, Douglas; Looney, Leslie; Teuben, Peter J.; Pound, Marc W.; Rauch, Kevin P.; Mundy, Lee; Harris, Robert J.; Xu, Lisa

    2016-06-01

    ADMIT (ALMA Data Mining Toolkit) is a Python based pipeline toolkit for the creation and analysis of new science products from ALMA data. ADMIT quickly provides users with a detailed overview of their science products, for example: line identifications, line 'cutout' cubes, moment maps, and emission type analysis (e.g., feature detection). Users can download the small ADMIT pipeline product (< 20MB), analyze the results, then fine-tune and re-run the ADMIT pipeline (or any part thereof) on their own machines and interactively inspect the results. ADMIT has both a web browser and command line interface available for this purpose. By analyzing multiple data cubes simultaneously, data mining between many astronomical sources and line transitions are possible. Users are also able to enhance the capabilities of ADMIT by creating customized ADMIT tasks satisfying any special processing needs. We will present some of the salient features of ADMIT and example use cases.

  17. Earth Science Informatics - Overview

    NASA Technical Reports Server (NTRS)

    Ramapriyan, H. K.

    2015-01-01

    Over the last 10-15 years, significant advances have been made in information management, there are an increasing number of individuals entering the field of information management as it applies to Geoscience and Remote Sensing data, and the field of informatics has come to its own. Informatics is the science and technology of applying computers and computational methods to the systematic analysis, management, interchange, and representation of science data, information, and knowledge. Informatics also includes the use of computers and computational methods to support decision making and applications. Earth Science Informatics (ESI, a.k.a. geoinformatics) is the application of informatics in the Earth science domain. ESI is a rapidly developing discipline integrating computer science, information science, and Earth science. Major national and international research and infrastructure projects in ESI have been carried out or are on-going. Notable among these are: the Global Earth Observation System of Systems (GEOSS), the European Commissions INSPIRE, the U.S. NSDI and Geospatial One-Stop, the NASA EOSDIS, and the NSF DataONE, EarthCube and Cyberinfrastructure for Geoinformatics. More than 18 departments and agencies in the U.S. federal government have been active in Earth science informatics. All major space agencies in the world, have been involved in ESI research and application activities. In the United States, the Federation of Earth Science Information Partners (ESIP), whose membership includes nearly 150 organizations (government, academic and commercial) dedicated to managing, delivering and applying Earth science data, has been working on many ESI topics since 1998. The Committee on Earth Observation Satellites (CEOS)s Working Group on Information Systems and Services (WGISS) has been actively coordinating the ESI activities among the space agencies. Remote Sensing; Earth Science Informatics, Data Systems; Data Services; Metadata

  18. A Collaborative Informatics Infrastructure for Multi-scale Science

    SciTech Connect

    Myers, J D; Allison, T C; Bittner, S; Didier, B; Frenklach, M; Green, Jr., W H; Ho, Y; Hewson, J; Koegler, W; Lansing, C; Leahy, D; Lee, M; McCoy, R; Minkoff, M; Nijsure, S; von Laszewski, G; Montoya, D; Pancerella, C; Pinzon, R; Pitz, W J; Rahn, L A; Ruscis, B; Schuchardt, K; Stephan, E; Wagner, A; Windus, T; Yang, C

    2005-05-11

    The Collaboratory for Multi-scale Chemical Science (CMCS) is developing a powerful informatics-based approach to synthesizing multi-scale information to support a systems-based research approach and is applying it in support of combustion research. An open source multi-scale informatics toolkit is being developed that addresses a number of issues core to the emerging concept of knowledge grids including provenance tracking and lightweight federation of data and application resources into cross-scale information flows. The CMCS portal is currently in use by a number of high-profile pilot groups and is playing a significant role in enabling their efforts to improve and extend community maintained chemical reference information.

  19. A Collaborative Informatics Infrastructure for Multi-scale Science

    SciTech Connect

    Myers, James D.; Allison, Thomas C.; Bittner, Sandra; Didier, Brett T.; Frenklach, Michael; Green, William H.; Ho, Yen-Ling; Hewson, John; Koegler, Wendy S.; Lansing, Carina S.; Leahy, David; Lee, Michael; McCoy, Renata; Minkoff, Michael; Nijsure, Sandeep; von Laszewski, Gregor; Montoya, David W.; Pancerella, Carmen M.; Pinzon, Reinhardt; Pitz, William; Rahn, Larry; Ruscic, Branko; Schuchardt, Karen L.; Stephan, Eric G.; Wagner, Albert F.; Windus, Theresa L.; Yang, Christine

    2004-03-28

    The Collaboratory for Multi-scale Chemical Science (CMCS) is developing a powerful informatics-based approach to synthesizing multi-scale information to support a systems-based research approach and is applying it in support of combustion research. An open source multi-scale informatics toolkit is being developed that addresses a number of issues core to the emerging concept of knowledge grids including provenance tracking and lightweight federation of data and application resources into cross-scale information flows. The CMCS portal is currently in use by a number of high-profile pilot groups and is playing a significant role in enabling their efforts to improve and extend community maintained chemical reference information.

  20. A Collaborative Informatics Infrastructure for Multi-scale Science

    SciTech Connect

    Myers, James D.; Allison, Thomas C.; Bittner, Sandra J.; Didier, Brett T.; Frenklach, Michael; Green, William H.; Ho, Yen-Ling; Hewson, John; Koegler, Wendy S.; Lansing, Carina S.; Leahy, David; Lee, Michael; McCoy, Renata; Minkoff, Michael; Nijsure, Sandeep; von Laszewski, Gregor; Montoya, David; Oluwole, Luwi; Pancerella, Carmen M.; Pinzon, Reinhardt; Pitz, William; Rahn, Larry A.; Ruscic, Branko; Schuchardt, Karen L.; Stephan, Eric G.; Wagner, Al; Windus, Theresa L.; Yang, Christine

    2005-10-01

    The Collaboratory for Multi-scale Chemical Science (CMCS) is developing a powerful informatics-based approach to synthesizing multi-scale information to support a systems-based research approach and is applying it in support of combustion research. An open source multi-scale informatics toolkit is being developed that addresses a number of issues core to the emerging concept of knowledge grids including provenance tracking and lightweight federation of data and application resources into cross-scale information flows. The CMCS portal is currently in use by a number of high-profile pilot groups and is playing a significant role in enabling their efforts to improve and extend community maintained chemical reference information.

  1. Bridging the divide: the need for translational informatics.

    PubMed

    Gaughan, Andy

    2006-01-01

    Translational science promises to deliver real benefit to the pharmaceutical industry, reducing attrition and affording high quality, efficacious medicines. The development and use of biomarkers aims to reduce drug development risks and generate a better understanding of disease. Informatics is an essential component of the translational science toolkit; researchers must be able to work effectively with biomarker data, and the capture and reuse of knowledge is vital for long-term success. An analysis of current data and knowledge management practices in the translational science area is presented.

  2. Multi-Sensory Informatics Education

    ERIC Educational Resources Information Center

    Katai, Zoltan; Toth, Laszlo; Adorjani, Alpar Karoly

    2014-01-01

    A recent report by the joint Informatics Europe & ACM Europe Working Group on Informatics Education emphasizes that: (1) computational thinking is an important ability that all people should possess; (2) informatics-based concepts, abilities and skills are teachable, and must be included in the primary and particularly in the secondary school…

  3. Quantum Approach to Informatics

    NASA Astrophysics Data System (ADS)

    Stenholm, Stig; Suominen, Kalle-Antti

    2005-08-01

    An essential overview of quantum information Information, whether inscribed as a mark on a stone tablet or encoded as a magnetic domain on a hard drive, must be stored in a physical object and thus made subject to the laws of physics. Traditionally, information processing such as computation occurred in a framework governed by laws of classical physics. However, information can also be stored and processed using the states of matter described by non-classical quantum theory. Understanding this quantum information, a fundamentally different type of information, has been a major project of physicists and information theorists in recent years, and recent experimental research has started to yield promising results. Quantum Approach to Informatics fills the need for a concise introduction to this burgeoning new field, offering an intuitive approach for readers in both the physics and information science communities, as well as in related fields. Only a basic background in quantum theory is required, and the text keeps the focus on bringing this theory to bear on contemporary informatics. Instead of proofs and other highly formal structures, detailed examples present the material, making this a uniquely accessible introduction to quantum informatics. Topics covered include: * An introduction to quantum information and the qubit * Concepts and methods of quantum theory important for informatics * The application of information concepts to quantum physics * Quantum information processing and computing * Quantum gates * Error correction using quantum-based methods * Physical realizations of quantum computing circuits A helpful and economical resource for understanding this exciting new application of quantum theory to informatics, Quantum Approach to Informatics provides students and researchers in physics and information science, as well as other interested readers with some scientific background, with an essential overview of the field.

  4. 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.

  5. My-Peer Toolkit [1.0]: Developing an Online Resource for Planning and Evaluating Peer-Based Youth Programs

    ERIC Educational Resources Information Center

    Hildebrand, Janina; Lobo, Roanna; Hallett, Jonathan; Brown, Graham; Maycock, Bruce

    2012-01-01

    Peer-based youth services provided by small non-profit community organisations have grown in number over the past two decades in response to an increasing need for informal, youth-friendly, accessible and confidential early intervention services. However, gaps in the evidence base and a general lack of evaluation capacity of service providers…

  6. Multiphysics Application Coupling Toolkit

    SciTech Connect

    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; 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.

  7. 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.

  8. 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.

  9. RAS - Target Identification - Informatics

    Cancer.gov

    The RAS Informatics lab group develops tools to track and analyze “big data” from the RAS Initiative, as well as analyzes data from external projects. By integrating internal and external data, this group helps improve understanding of RAS-driven cancers.

  10. Informatics: A Brief Survey.

    ERIC Educational Resources Information Center

    He, Shaoyi

    2003-01-01

    Provides a brief survey of informatics, defined as the application of information technology to various fields, with respect to its historical background, disciplinary identity, fundamental aspects, applications, and challenges. Highlights include biological, clinical, dental, environmental, geomatics, health, legal, management, medical, museum,…

  11. ECCE Toolkit: Prototyping Sensor-Based Interaction.

    PubMed

    Bellucci, Andrea; Aedo, Ignacio; Díaz, Paloma

    2017-02-23

    Building and exploring physical user interfaces requires high technical skills and hours of specialized work. The behavior of multiple devices with heterogeneous input/output channels and connectivity has to be programmed in a context where not only the software interface matters, but also the hardware components are critical (e.g., sensors and actuators). Prototyping physical interaction is hindered by the challenges of: (1) programming interactions among physical sensors/actuators and digital interfaces; (2) implementing functionality for different platforms in different programming languages; and (3) building custom electronic-incorporated objects. We present ECCE (Entities, Components, Couplings and Ecosystems), a toolkit for non-programmers that copes with these issues by abstracting from low-level implementations, thus lowering the complexity of prototyping small-scale, sensor-based physical interfaces to support the design process. A user evaluation provides insights and use cases of the kind of applications that can be developed with the toolkit.

  12. ECCE Toolkit: Prototyping Sensor-Based Interaction

    PubMed Central

    Bellucci, Andrea; Aedo, Ignacio; Díaz, Paloma

    2017-01-01

    Building and exploring physical user interfaces requires high technical skills and hours of specialized work. The behavior of multiple devices with heterogeneous input/output channels and connectivity has to be programmed in a context where not only the software interface matters, but also the hardware components are critical (e.g., sensors and actuators). Prototyping physical interaction is hindered by the challenges of: (1) programming interactions among physical sensors/actuators and digital interfaces; (2) implementing functionality for different platforms in different programming languages; and (3) building custom electronic-incorporated objects. We present ECCE (Entities, Components, Couplings and Ecosystems), a toolkit for non-programmers that copes with these issues by abstracting from low-level implementations, thus lowering the complexity of prototyping small-scale, sensor-based physical interfaces to support the design process. A user evaluation provides insights and use cases of the kind of applications that can be developed with the toolkit. PMID:28241502

  13. Einstein Toolkit for Relativistic Astrophysics

    NASA Astrophysics Data System (ADS)

    Collaborative Effort

    2011-02-01

    The Einstein Toolkit is a collection of software components and tools for simulating and analyzing general relativistic astrophysical systems. Such systems include gravitational wave space-times, collisions of compact objects such as black holes or neutron stars, accretion onto compact objects, core collapse supernovae and Gamma-Ray Bursts. The Einstein Toolkit builds on numerous software efforts in the numerical relativity community including CactusEinstein, Whisky, and Carpet. The Einstein Toolkit currently uses the Cactus Framework as the underlying computational infrastructure that provides large-scale parallelization, general computational components, and a model for collaborative, portable code development.

  14. 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).

  15. 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.

  16. 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.

  17. 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.

  18. Informatics competencies for nurse practitioners.

    PubMed

    Curran, Christine R

    2003-08-01

    Informatics knowledge and skills are essential if clinicians are to master the large volume of information generated in healthcare today. Thus, it is vital that informatics competencies be defined for nursing and incorporated into both curricula and practice. Staggers, Gassert, and Curran have defined informatics competencies for four general levels of nursing practice. However, informatics competencies by role (eg, those specific for advanced practice nursing) have not been defined and validated. This article presents an initial proposed list of informatics competencies essential for nurse practitioner education and practice. To this list, derived from the work of Staggers et al., 1 has been added informatics competencies related to evidence-based practice. Two nurse informaticists and six nurse practitioners, who are program directors, were involved in the development of the proposed competencies. The next step will be to validate these competencies via research.

  19. Informatics Metrics and Measures for a Smart Public Health Systems Approach: Information Science Perspective.

    PubMed

    Carney, Timothy Jay; Shea, Christopher Michael

    2017-01-01

    Public health informatics is an evolving domain in which practices constantly change to meet the demands of a highly complex public health and healthcare delivery system. Given the emergence of various concepts, such as learning health systems, smart health systems, and adaptive complex health systems, health informatics professionals would benefit from a common set of measures and capabilities to inform our modeling, measuring, and managing of health system "smartness." Here, we introduce the concepts of organizational complexity, problem/issue complexity, and situational awareness as three codependent drivers of smart public health systems characteristics. We also propose seven smart public health systems measures and capabilities that are important in a public health informatics professional's toolkit.

  20. Informatics Metrics and Measures for a Smart Public Health Systems Approach: Information Science Perspective

    PubMed Central

    Shea, Christopher Michael

    2017-01-01

    Public health informatics is an evolving domain in which practices constantly change to meet the demands of a highly complex public health and healthcare delivery system. Given the emergence of various concepts, such as learning health systems, smart health systems, and adaptive complex health systems, health informatics professionals would benefit from a common set of measures and capabilities to inform our modeling, measuring, and managing of health system “smartness.” Here, we introduce the concepts of organizational complexity, problem/issue complexity, and situational awareness as three codependent drivers of smart public health systems characteristics. We also propose seven smart public health systems measures and capabilities that are important in a public health informatics professional's toolkit. PMID:28167999

  1. 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

  2. The 2005 Australian Informatics Competition

    ERIC Educational Resources Information Center

    Clark, David

    2006-01-01

    This article describes the Australian Informatics Competition (AIC), a non-programming competition aimed at identifying students with potential in programming and algorithmic design. It is the first step in identifying students to represent Australia at the International Olympiad in Informatics. The main aim of the AIC is to increase awareness of…

  3. Informatics applied to cytology.

    PubMed

    Pantanowitz, Liron; Hornish, Maryanne; Goulart, Robert A

    2008-12-29

    Automation and emerging information technologies are being adopted by cytology laboratories to augment Pap test screening and improve diagnostic accuracy. As a result, informatics, the application of computers and information systems to information management, has become essential for the successful operation of the cytopathology laboratory. This review describes how laboratory information management systems can be used to achieve an automated and seamless workflow process. The utilization of software, electronic databases and spreadsheets to perform necessary quality control measures are discussed, as well as a Lean production system and Six Sigma approach, to reduce errors in the cytopathology laboratory.

  4. Informatics applied to cytology

    PubMed Central

    Hornish, Maryanne; Goulart, Robert A.

    2008-01-01

    Automation and emerging information technologies are being adopted by cytology laboratories to augment Pap test screening and improve diagnostic accuracy. As a result, informatics, the application of computers and information systems to information management, has become essential for the successful operation of the cytopathology laboratory. This review describes how laboratory information management systems can be used to achieve an automated and seamless workflow process. The utilization of software, electronic databases and spreadsheets to perform necessary quality control measures are discussed, as well as a Lean production system and Six Sigma approach, to reduce errors in the cytopathology laboratory. PMID:19495402

  5. Nursing informatics competencies: bibliometric analysis.

    PubMed

    Kokol, Peter; Blažun, Helena; Vošner, Janez; Saranto, Kaija

    2014-01-01

    Information and communication technology is developing rapidly and it is incorporated in many health care processes, but in spite of that fact we can still notice that nursing informatics competencies had received limited attention in basic nursing education curricula in Europe and especially in Eastern European countries. The purpose of the present paper is to present the results of a bibliometric analysis of the nursing informatics competencies scientific literature production. We applied the bibliometrics analysis to the corpus of 332 papers found in SCOPUS, related to nursing informatics competencies. The results showed that there is a positive trend in the number of published papers per year, indicating the increased research interest in nursing informatics competencies. Despite the fact that the first paper was published in Denmark, the most prolific country regarding the research in nursing informatics competencies is United States as are their institutions and authors.

  6. A Scalable Analysis Toolkit

    NASA Technical Reports Server (NTRS)

    Aiken, Alexander

    2001-01-01

    The Scalable Analysis Toolkit (SAT) project aimed to demonstrate that it is feasible and useful to statically detect software bugs in very large systems. The technical focus of the project was on a relatively new class of constraint-based techniques for analysis software, where the desired facts about programs (e.g., the presence of a particular bug) are phrased as constraint problems to be solved. At the beginning of this project, the most successful forms of formal software analysis were limited forms of automatic theorem proving (as exemplified by the analyses used in language type systems and optimizing compilers), semi-automatic theorem proving for full verification, and model checking. With a few notable exceptions these approaches had not been demonstrated to scale to software systems of even 50,000 lines of code. Realistic approaches to large-scale software analysis cannot hope to make every conceivable formal method scale. Thus, the SAT approach is to mix different methods in one application by using coarse and fast but still adequate methods at the largest scales, and reserving the use of more precise but also more expensive methods at smaller scales for critical aspects (that is, aspects critical to the analysis problem under consideration) of a software system. The principled method proposed for combining a heterogeneous collection of formal systems with different scalability characteristics is mixed constraints. This idea had been used previously in small-scale applications with encouraging results: using mostly coarse methods and narrowly targeted precise methods, useful information (meaning the discovery of bugs in real programs) was obtained with excellent scalability.

  7. toolkit computational mesh conceptual model.

    SciTech Connect

    Baur, David G.; Edwards, Harold Carter; Cochran, William K.; Williams, Alan B.; Sjaardema, Gregory D.

    2010-03-01

    The Sierra Toolkit computational mesh is a software library intended to support massively parallel multi-physics computations on dynamically changing unstructured meshes. This domain of intended use is inherently complex due to distributed memory parallelism, parallel scalability, heterogeneity of physics, heterogeneous discretization of an unstructured mesh, and runtime adaptation of the mesh. Management of this inherent complexity begins with a conceptual analysis and modeling of this domain of intended use; i.e., development of a domain model. The Sierra Toolkit computational mesh software library is designed and implemented based upon this domain model. Software developers using, maintaining, or extending the Sierra Toolkit computational mesh library must be familiar with the concepts/domain model presented in this report.

  8. Comparative Informatics Analysis to Evaluate Site-Specific Protein Oxidation in Multidimensional LC-MS/MS Data

    SciTech Connect

    McClintock, Carlee; Parks, Jerry M; Bern, Marshall; Ghattyvenkatakrishna, Pavan K; Hettich, Robert {Bob} L

    2013-01-01

    Redox proteomics has yielded molecular insight into diseases of protein dysfunction attributable to oxidative stress, underscoring the need for robust detection of protein oxidation products. Additionally, oxidative protein surface mapping techniques utilize hydroxyl radicals to gain structural insight about solvent exposure. Interpretation of tandem mass spectral data is a critical challenge for such investigations, because reactive oxygen species target a wide breadth of amino acids. Additionally, oxidized peptides may be generated in a wide range of abundances since the reactivity of hydroxyl radicals with different amino acids spans three orders of magnitude. Taken together, these attributes of oxidative footprinting pose both experimental and computational challenges to detecting oxidized peptides that are naturally less abundant than their unoxidized counterparts. In this study, three model proteins were oxidized electrochemically and analyzed at both the intact protein and peptide levels. A multidimensional chromatographic strategy was utilized to expand the dynamic range of oxidized peptides measurements. Peptide mass spectral data were searched by the hybrid software packages Inspect and Byonic, which incorporate de novo elements of spectral interpretation into a database search. This dynamic search capacity accommodates the challenge of searching for more than forty oxidative mass shifts that can occur in a staggering variety of possible combinatorial occurrences. A prevailing set of oxidized residues was identified with this comparative approach, and evaluation of these sites was informed by solvent accessible surface area gleaned through molecular dynamics simulations. Along with increased levels of oxidation around highly reactive hotspot sites as expected, the enhanced sensitivity of these measurements uncovered a surprising level of oxidation on less reactive residues.

  9. Comparative Informatics Analysis to Evaluate Site-Specific Protein Oxidation in Multidimensional LC-MS/MS Data

    PubMed Central

    McClintock, Carlee S.; Parks, Jerry M.; Bern, Marshall; GhattyVenkataKrishna, Pavan K.; Hettich, Robert L.

    2013-01-01

    Redox proteomics has yielded molecular insight into diseases of protein dysfunction attributable to oxidative stress, underscoring the need for robust detection of protein oxidation products. Additionally, oxidative protein surface mapping techniques utilize hydroxyl radicals to gain structural insight about solvent exposure. Interpretation of tandem mass spectral data is a critical challenge for such investigations, because reactive oxygen species target a wide breadth of amino acids. Additionally, oxidized peptides may be generated in a wide range of abundances since the reactivity of hydroxyl radicals with different amino acids spans three orders of magnitude. Taken together, these attributes of oxidative footprinting pose both experimental and computational challenges to detecting oxidized peptides that are naturally less abundant than their unoxidized counterparts. In this study, three model proteins were oxidized electrochemically and analyzed at both the intact protein and peptide levels. A multidimensional chromatographic strategy was utilized to expand the dynamic range of oxidized peptide measurements. Peptide mass spectral data were searched by the “hybrid” software packages Inspect and Byonic, which incorporate de novo elements of spectral interpretation into a database search. This dynamic search capacity accommodates the challenge of searching for more than forty oxidative mass shifts that can occur in a staggering variety of possible combinatorial occurrences. A prevailing set of oxidized residues was identified with this comparative approach, and evaluation of these sites was informed by solvent accessible surface area gleaned through molecular dynamics simulations. Along with increased levels of oxidation around highly reactive “hotspot” sites as expected, the enhanced sensitivity of these measurements uncovered a surprising level of oxidation on less reactive residues. PMID:23827042

  10. Informatics in radiology: evaluation of an e-learning platform for teaching medical students competency in ordering radiologic examinations.

    PubMed

    Marshall, Nina L; Spooner, Muirne; Galvin, P Leo; Ti, Joanna P; McElvaney, N Gerald; Lee, Michael J

    2011-01-01

    A preliminary audit of orders for computed tomography was performed to evaluate the typical performance of interns ordering radiologic examinations. According to the audit, the interns showed only minimal improvement after 8 months of work experience. The online radiology ordering module (ROM) program included baseline assessment of student performance (part I), online learning with the ROM (part II), and follow-up assessment of performance with simulated ordering with the ROM (part III). A curriculum blueprint determined the content of the ROM program, with an emphasis on practical issues, including provision of logistic information, clinical details, and safety-related information. Appropriate standards were developed by a committee of experts, and detailed scoring systems were devised for assessment. The ROM program was successful in addressing practical issues in a simulated setting. In the part I assessment, the mean score for noting contraindications for contrast media was 24%; this score increased to 59% in the part III assessment (P = .004). Similarly, notification of methicillin-resistant Staphylococcus aureus status and pregnancy status and provision of referring physician contact information improved significantly. The quality of the clinical notes was stable, with good initial scores. Part III testing showed overall improvement, with the mean score increasing from 61% to 76% (P < .0001). In general, medical students lack the core knowledge that is needed for good-quality ordering of radiology services, and the experience typically afforded to interns does not address this lack of knowledge. The ROM program was a successful intervention that resulted in statistically significant improvements in the quality of radiologic examination orders, particularly with regard to logistic and radiation safety issues.

  11. Trends in publication of nursing informatics research.

    PubMed

    Kim, Hyeoneui; Ohno-Machado, Lucila; Oh, Janet; Jiang, Xiaoqian

    2014-01-01

    We analyzed 741 journal articles on nursing informatics published in 7 biomedical/nursing informatics journals and 6 nursing journals from 2005 to 2013 to begin to understand publication trends in nursing informatics research and identify gaps. We assigned a research theme to each article using AMIA 2014 theme categories and normalized the citation counts using time from publication. Overall, nursing informatics research covered a broad spectrum of research topics in biomedical informatics and publication topics seem to be well aligned with the high priority research agenda identified by the nursing informatics community. The research themes with highest volume of publication were Clinical Workflow and Human Factors, Consumer Informatics and Personal Health Records, and Clinical Informatics, for which an increasing trend in publication was noted. Articles on Informatics Education and Workforce Development; Data Mining, NLP, Information Extraction; and Clinical Informatics showed steady and high volume of citations.

  12. Trends in Publication of Nursing Informatics Research

    PubMed Central

    Kim, Hyeoneui; Ohno-Machado, Lucila; Oh, Janet; Jiang, Xiaoqian

    2014-01-01

    We analyzed 741 journal articles on nursing informatics published in 7 biomedical/nursing informatics journals and 6 nursing journals from 2005 to 2013 to begin to understand publication trends in nursing informatics research and identify gaps. We assigned a research theme to each article using AMIA 2014 theme categories and normalized the citation counts using time from publication. Overall, nursing informatics research covered a broad spectrum of research topics in biomedical informatics and publication topics seem to be well aligned with the high priority research agenda identified by the nursing informatics community. The research themes with highest volume of publication were Clinical Workflow and Human Factors, Consumer Informatics and Personal Health Records, and Clinical Informatics, for which an increasing trend in publication was noted. Articles on Informatics Education and Workforce Development; Data Mining, NLP, Information Extraction; and Clinical Informatics showed steady and high volume of citations. PMID:25954387

  13. Distributed medical informatics education using internet2.

    PubMed

    Tidmarsh, Patrica J; Cummings, Joseph; Hersh, William R; Freidman, Charles P

    2002-01-01

    The curricula of most medical informatics training programs are incomplete. We used Internet2-based videoconferencing to expand the educational opportunities of medical informatics students at Oregon Health & Science University and the University of Pittsburgh. Students and faculty in both programs shared extra-curricular research conferences and journal club meetings. A course in Information Retrieval was made available to students in both programs. The conferences, meetings and class were well accepted by participants. A few problems were experienced with the technology, some of which were resolved, and some non-technical challenges to distributing academic conferences, meetings and coursework were also uncovered. We plan to continue our efforts with expanded course and extra-curricular offerings and a more comprehensive evaluation strategy.

  14. Distributed medical informatics education using internet2.

    PubMed Central

    Tidmarsh, Patrica J.; Cummings, Joseph; Hersh, William R.; Freidman, Charles P.

    2002-01-01

    The curricula of most medical informatics training programs are incomplete. We used Internet2-based videoconferencing to expand the educational opportunities of medical informatics students at Oregon Health & Science University and the University of Pittsburgh. Students and faculty in both programs shared extra-curricular research conferences and journal club meetings. A course in Information Retrieval was made available to students in both programs. The conferences, meetings and class were well accepted by participants. A few problems were experienced with the technology, some of which were resolved, and some non-technical challenges to distributing academic conferences, meetings and coursework were also uncovered. We plan to continue our efforts with expanded course and extra-curricular offerings and a more comprehensive evaluation strategy. PMID:12463932

  15. It’s Just (Academic) Business: A Use Case in Improving Informatics Operations with Business Intelligence

    PubMed Central

    McIntosh, Leslie D.; Zabarovskaya, Connie; Uhlmansiek, Mary

    2015-01-01

    Academic biomedical informatics cores are beholden to funding agencies, institutional administration, collaborating researchers, and external agencies for ongoing funding and support. Services provided and translational research outcomes are increasingly important to monitor, report and analyze, to demonstrate value provided to the organization and the greater scientific community. Thus, informatics operations are also business operations. As such, adopting business intelligence practices offers an opportunity to improve the efficiency of evaluation efforts while fulfilling reporting requirements. Organizing informatics development documentation, service requests, and work performed with adaptable tools have greatly facilitated these and related business activities within our informatics center. Through the identification and measurement of key performance indicators, informatics objectives and results are now quickly and nimbly assessed using dashboards. Acceptance of the informatics operation as a business venture and the adoption of business intelligence strategies has allowed for data-driven decision making, faster corrective action, and greater transparency for interested stakeholders. PMID:26306252

  16. It's Just (Academic) Business: A Use Case in Improving Informatics Operations with Business Intelligence.

    PubMed

    McIntosh, Leslie D; Zabarovskaya, Connie; Uhlmansiek, Mary

    2015-01-01

    Academic biomedical informatics cores are beholden to funding agencies, institutional administration, collaborating researchers, and external agencies for ongoing funding and support. Services provided and translational research outcomes are increasingly important to monitor, report and analyze, to demonstrate value provided to the organization and the greater scientific community. Thus, informatics operations are also business operations. As such, adopting business intelligence practices offers an opportunity to improve the efficiency of evaluation efforts while fulfilling reporting requirements. Organizing informatics development documentation, service requests, and work performed with adaptable tools have greatly facilitated these and related business activities within our informatics center. Through the identification and measurement of key performance indicators, informatics objectives and results are now quickly and nimbly assessed using dashboards. Acceptance of the informatics operation as a business venture and the adoption of business intelligence strategies has allowed for data-driven decision making, faster corrective action, and greater transparency for interested stakeholders.

  17. Comparison of open-source visual analytics toolkits

    NASA Astrophysics Data System (ADS)

    Harger, John R.; Crossno, Patricia J.

    2012-01-01

    We present the results of the first stage of a two-stage evaluation of open source visual analytics packages. This stage is a broad feature comparison over a range of open source toolkits. Although we had originally intended to restrict ourselves to comparing visual analytics toolkits, we quickly found that very few were available. So we expanded our study to include information visualization, graph analysis, and statistical packages. We examine three aspects of each toolkit: visualization functions, analysis capabilities, and development environments. With respect to development environments, we look at platforms, language bindings, multi-threading/parallelism, user interface frameworks, ease of installation, documentation, and whether the package is still being actively developed.

  18. Bioimage Informatics for Big Data.

    PubMed

    Peng, Hanchuan; Zhou, Jie; Zhou, Zhi; Bria, Alessandro; Li, Yujie; Kleissas, Dean Mark; Drenkow, Nathan G; Long, Brian; Liu, Xiaoxiao; Chen, Hanbo

    2016-01-01

    Bioimage informatics is a field wherein high-throughput image informatics methods are used to solve challenging scientific problems related to biology and medicine. When the image datasets become larger and more complicated, many conventional image analysis approaches are no longer applicable. Here, we discuss two critical challenges of large-scale bioimage informatics applications, namely, data accessibility and adaptive data analysis. We highlight case studies to show that these challenges can be tackled based on distributed image computing as well as machine learning of image examples in a multidimensional environment.

  19. The PRIDE (Partnership to Improve Diabetes Education) Toolkit

    PubMed Central

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

    2016-01-01

    Purpose 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. Methods 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. Conclusions 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. PMID:26647414

  20. The pathology informatics curriculum wiki: Harnessing the power of user-generated content

    PubMed Central

    Kim, Ji Yeon; Gudewicz, Thomas M.; Dighe, Anand S.; Gilbertson, John R.

    2010-01-01

    Background: The need for informatics training as part of pathology training has never been so critical, but pathology informatics is a wide and complex field and very few programs currently have the resources to provide comprehensive educational pathology informatics experiences to their residents. In this article, we present the “pathology informatics curriculum wiki”, an open, on-line wiki that indexes the pathology informatics content in a larger public wiki, Wikipedia, (and other online content) and organizes it into educational modules based on the 2003 standard curriculum approved by the Association for Pathology Informatics (API). Methods and Results: In addition to implementing the curriculum wiki at http://pathinformatics.wikispaces.com, we have evaluated pathology informatics content in Wikipedia. Of the 199 non-duplicate terms in the API curriculum, 90% have at least one associated Wikipedia article. Furthermore, evaluation of articles on a five-point Likert scale showed high scores for comprehensiveness (4.05), quality (4.08), currency (4.18), and utility for the beginner (3.85) and advanced (3.93) learners. These results are compelling and support the thesis that Wikipedia articles can be used as the foundation for a basic curriculum in pathology informatics. Conclusions: The pathology informatics community now has the infrastructure needed to collaboratively and openly create, maintain and distribute the pathology informatics content worldwide (Wikipedia) and also the environment (the curriculum wiki) to draw upon its own resources to index and organize this content as a sustainable basic pathology informatics educational resource. The remaining challenges are numerous, but largest by far will be to convince the pathologists to take the time and effort required to build pathology informatics content in Wikipedia and to index and organize this content for education in the curriculum wiki. PMID:20805963

  1. A case control study to improve accuracy of an electronic fall prevention toolkit.

    PubMed

    Dykes, Patricia C; I-Ching, Evita Hou; Soukup, Jane R; Chang, Frank; Lipsitz, Stuart

    2012-01-01

    Patient falls are a serious and commonly report adverse event in hospitals. In 2009, our team conducted the first randomized control trial of a health information technology-based intervention that significantly reduced falls in acute care hospitals. However, some patients on intervention units with access to the electronic toolkit fell. The purpose of this case control study was to use data mining and modeling techniques to identify the factors associated with falls in hospitalized patients when the toolkit was in place. Our ultimate aim was to apply our findings to improve the toolkit logic and to generate practice recommendations. The results of our evaluation suggest that the fall prevention toolkit logic is accurate but strategies are needed to improve adherence with the fall prevention intervention recommendations generated by the electronic toolkit.

  2. The origins of informatics.

    PubMed Central

    Collen, M F

    1994-01-01

    This article summarizes the origins of informatics, which is based on the science, engineering, and technology of computer hardware, software, and communications. In just four decades, from the 1950s to the 1990s, computer technology has progressed from slow, first-generation vacuum tubes, through the invention of the transistor and its incorporation into microprocessor chips, and ultimately, to fast, fourth-generation very-large-scale-integrated silicon chips. Programming has undergone a parallel transformation, from cumbersome, first-generation, machine languages to efficient, fourth-generation application-oriented languages. Communication has evolved from simple copper wires to complex fiberoptic cables in computer-linked networks. The digital computer has profound implications for the development and practice of clinical medicine. PMID:7719803

  3. A Toolkit for Teacher Engagement

    ERIC Educational Resources Information Center

    Grantmakers for Education, 2014

    2014-01-01

    Teachers are critical to the success of education grantmaking strategies, yet in talking with them we discovered that the world of philanthropy is often a mystery. GFE's Toolkit for Teacher Engagement aims to assist funders in authentically and effectively involving teachers in the education reform and innovation process. Built directly from the…

  4. Applying natural language processing toolkits to electronic health records - an experience report.

    PubMed

    Barrett, Neil; Weber-Jahnke, Jens H

    2009-01-01

    A natural language challenge devised by Informatics for Integrating Biology and the Bedside (i2b2) was to analyze free-text health data to construct a multi-class, multi-label classification system focused on obesity and its co-morbidities. This report presents a case study in which a natural language processing (NLP) toolkit, called NLTK, was used in the challenge. This report provides a brief review of NLP in the context of EHR applications, briefly surveys and contrasts some existing NLP toolkits, and reports on our experiences with the i2b2 case study. Our efforts uncovered issues including the lack of human annotated physician notes for use as NLP training data, differences between conventional free-text and medical notes, and potential hardware and software limitations affecting future projects.

  5. Using Toolkits to Achieve STEM Enterprise Learning Outcomes

    ERIC Educational Resources Information Center

    Watts, Carys A.; Wray, Katie

    2012-01-01

    Purpose: The purpose of this paper is to evaluate the effectiveness of using several commercial tools in science, technology, engineering and maths (STEM) subjects for enterprise education at Newcastle University, UK. Design/methodology/approach: The paper provides an overview of existing toolkit use in higher education, before reviewing where and…

  6. Informatics — EDRN Public Portal

    Cancer.gov

    The EDRN provides a comprehensive informatics activity which includes a number of tools and an integrated knowledge environment for capturing, managing, integrating, and sharing results from across EDRN's cancer biomarker research network.

  7. Score Calculation in Informatics Contests Using Multiple Criteria Decision Methods

    ERIC Educational Resources Information Center

    Skupiene, Jurate

    2011-01-01

    The Lithuanian Informatics Olympiad is a problem solving contest for high school students. The work of each contestant is evaluated in terms of several criteria, where each criterion is measured according to its own scale (but the same scale for each contestant). Several jury members are involved in the evaluation. This paper analyses the problem…

  8. Bioimage Informatics in the context of Drosophila research.

    PubMed

    Jug, Florian; Pietzsch, Tobias; Preibisch, Stephan; Tomancak, Pavel

    2014-06-15

    Modern biological research relies heavily on microscopic imaging. The advanced genetic toolkit of Drosophila makes it possible to label molecular and cellular components with unprecedented level of specificity necessitating the application of the most sophisticated imaging technologies. Imaging in Drosophila spans all scales from single molecules to the entire populations of adult organisms, from electron microscopy to live imaging of developmental processes. As the imaging approaches become more complex and ambitious, there is an increasing need for quantitative, computer-mediated image processing and analysis to make sense of the imagery. Bioimage Informatics is an emerging research field that covers all aspects of biological image analysis from data handling, through processing, to quantitative measurements, analysis and data presentation. Some of the most advanced, large scale projects, combining cutting edge imaging with complex bioimage informatics pipelines, are realized in the Drosophila research community. In this review, we discuss the current research in biological image analysis specifically relevant to the type of systems level image datasets that are uniquely available for the Drosophila model system. We focus on how state-of-the-art computer vision algorithms are impacting the ability of Drosophila researchers to analyze biological systems in space and time. We pay particular attention to how these algorithmic advances from computer science are made usable to practicing biologists through open source platforms and how biologists can themselves participate in their further development.

  9. Emerging Vaccine Informatics

    PubMed Central

    He, Yongqun; Rappuoli, Rino; De Groot, Anne S.; Chen, Robert T.

    2010-01-01

    Vaccine informatics is an emerging research area that focuses on development and applications of bioinformatics methods that can be used to facilitate every aspect of the preclinical, clinical, and postlicensure vaccine enterprises. Many immunoinformatics algorithms and resources have been developed to predict T- and B-cell immune epitopes for epitope vaccine development and protective immunity analysis. Vaccine protein candidates are predictable in silico from genome sequences using reverse vaccinology. Systematic transcriptomics and proteomics gene expression analyses facilitate rational vaccine design and identification of gene responses that are correlates of protection in vivo. Mathematical simulations have been used to model host-pathogen interactions and improve vaccine production and vaccination protocols. Computational methods have also been used for development of immunization registries or immunization information systems, assessment of vaccine safety and efficacy, and immunization modeling. Computational literature mining and databases effectively process, mine, and store large amounts of vaccine literature and data. Vaccine Ontology (VO) has been initiated to integrate various vaccine data and support automated reasoning. PMID:21772787

  10. Parallel Power Grid Simulation Toolkit

    SciTech Connect

    Smith, Steve; Kelley, Brian; Banks, Lawrence; Top, Philip; Woodward, Carol

    2015-09-14

    ParGrid is a 'wrapper' that integrates a coupled Power Grid Simulation toolkit consisting of a library to manage the synchronization and communication of independent simulations. The included library code in ParGid, named FSKIT, is intended to support the coupling multiple continuous and discrete even parallel simulations. The code is designed using modern object oriented C++ methods utilizing C++11 and current Boost libraries to ensure compatibility with multiple operating systems and environments.

  11. Using Informatics to Improve the Care of Patients Susceptible to Malignant Hyperthermia.

    PubMed

    Denholm, Bonnie G

    2016-04-01

    Perioperative nurses and nurse leaders should understand how to apply a nursing informatics framework and informatics concepts to strengthen data interpretation, transitions in care, and engagement with patients susceptible to malignant hyperthermia (MH) and their family members. Patient outcomes can be improved when informatics solutions facilitate identifying risks, clinical decision making in a crisis situation, retrieving priority information during transitions of care, and involving patients in planning care. Incorporating informatics solutions into existing quality improvement processes can help evaluate knowledge and preparedness related to managing care for a patient in an MH crisis. Informatics solutions can also help enhance interoperability by evaluating workflow related to transitions in care. Perioperative nurses and nurse leaders should advocate for diligence in submitting reports of MH-suspected events to databases. Improved data collection and data sharing enhance aggregated standardized data sets, which can advance research and increase the quality of evidence available with which to guide practice.

  12. Mapping the Materials Genome through Combinatorial Informatics

    NASA Astrophysics Data System (ADS)

    Rajan, Krishna

    2012-02-01

    The recently announced White House Materials Genome Initiative provides an exciting challenge to the materials science community. To meet that challenge one needs to address a critical question, namely what is the materials genome? Some guide on how to the answer this question can be gained by recognizing that a ``gene'' is a carrier of information. In the biological sciences, discovering how to manipulate these genes has generated exciting discoveries in fundamental molecular biology as well as significant advances in biotechnology. Scaling that up to molecular, cellular length scales and beyond, has spawned from genomics, fields such as proteomics, metabolomics and essentially systems biology. The ``omics'' approach requires that one needs to discover and track these ``carriers of information'' and then correlate that information to predict behavior. A similar challenge lies in materials science, where there is a diverse array of modalities of materials ``discovery'' ranging from new materials chemistries and molecular arrangements with novel properties, to the development and design of new micro- and mesoscale structures. Hence to meaningfully adapt the spirit of ``genomics'' style research in materials science, we need to first identify and map the ``genes'' across different materials science applications On the experimental side, combinatorial experiments have opened a new approach to generate data in a high throughput manner, but without a clear way to link that to models, the full value of that data is not realized. Hence along with experimental and computational materials science, we need to add a ``third leg'' to our toolkit to make the ``Materials Genome'' a reality, the science of Materials Informatics. In this presentation we provide an overview of how information science coupled to materials science can in fact achieve the goal of mapping the ``Materials Genome''.

  13. Stormwater BMP Effectiveness Toolkit

    EPA Science Inventory

    US EPA has identified the effectiveness of Stormwater Best Management Practices (BMPs) as a priority research need. Effective protection of biotic integrity requires that processes maintaining the diversity of physical habitats be protected. Methods are needed to evaluate the e...

  14. Instructional Improvement Cycle: A Teacher's Toolkit for Collecting and Analyzing Data on Instructional Strategies. REL 2015-080

    ERIC Educational Resources Information Center

    Cherasaro, Trudy L.; Reale, Marianne L.; Haystead, Mark; Marzano, Robert J.

    2015-01-01

    This toolkit, developed by Regional Educational Laboratory (REL) Central in collaboration with York Public Schools in Nebraska, provides a process and tools to help teachers use data from their classroom assessments to evaluate promising practices. The toolkit provides teachers with guidance on how to deliberately apply and study one classroom…

  15. Consumer health informatics: a consensus description and commentary from American Medical Informatics Association members.

    PubMed Central

    Houston, T. K.; Chang, B. L.; Brown, S.; Kukafka, R.

    2001-01-01

    BACKGROUND: Although interest in Consumer Health Informatics (CHI) has increased, a consensus definition of CHI does not yet exist. PURPOSE: To conduct a hypothesis-generating survey of AMIA members regarding definition and research agenda for CHI. METHODS: We solicited participation among AMIA members in an Internet-based survey focusing on issues related to a definition of CHI. RESULTS: One hundred thirty-five AMIA members responded. Participants indicated a broad spectrum of topics important to CHI including "self-help for disease management" and "patient access to their own medical records." CHI research was felt to rely heavily on public health methods such as epidemiology and outcomes research, a paradigm shift from traditional medical informatics. Responses indicated a perceived lack of funding and need for further research in CHI. CONCLUSIONS: A working definition should emphasize the multidisciplinary nature of CHI, include consumer input into CHI design, and focus on public health approaches to evaluation. PMID:11825193

  16. Bioimage informatics for experimental biology.

    PubMed

    Swedlow, Jason R; Goldberg, Ilya G; Eliceiri, Kevin W

    2009-01-01

    Over the past twenty years there have been great advances in light microscopy with the result that multidimensional imaging has driven a revolution in modern biology. The development of new approaches of data acquisition is reported frequently, and yet the significant data management and analysis challenges presented by these new complex datasets remain largely unsolved. As in the well-developed field of genome bioinformatics, central repositories are and will be key resources, but there is a critical need for informatics tools in individual laboratories to help manage, share, visualize, and analyze image data. In this article we present the recent efforts by the bioimage informatics community to tackle these challenges, and discuss our own vision for future development of bioimage informatics solutions.

  17. Translational Bioinformatics and Clinical Research (Biomedical) Informatics.

    PubMed

    Sirintrapun, S Joseph; Zehir, Ahmet; Syed, Aijazuddin; Gao, JianJiong; Schultz, Nikolaus; Cheng, Donavan T

    2016-03-01

    Translational bioinformatics and clinical research (biomedical) informatics are the primary domains related to informatics activities that support translational research. Translational bioinformatics focuses on computational techniques in genetics, molecular biology, and systems biology. Clinical research (biomedical) informatics involves the use of informatics in discovery and management of new knowledge relating to health and disease. This article details 3 projects that are hybrid applications of translational bioinformatics and clinical research (biomedical) informatics: The Cancer Genome Atlas, the cBioPortal for Cancer Genomics, and the Memorial Sloan Kettering Cancer Center clinical variants and results database, all designed to facilitate insights into cancer biology and clinical/therapeutic correlations.

  18. Translational Bioinformatics and Clinical Research (Biomedical) Informatics.

    PubMed

    Sirintrapun, S Joseph; Zehir, Ahmet; Syed, Aijazuddin; Gao, JianJiong; Schultz, Nikolaus; Cheng, Donavan T

    2015-06-01

    Translational bioinformatics and clinical research (biomedical) informatics are the primary domains related to informatics activities that support translational research. Translational bioinformatics focuses on computational techniques in genetics, molecular biology, and systems biology. Clinical research (biomedical) informatics involves the use of informatics in discovery and management of new knowledge relating to health and disease. This article details 3 projects that are hybrid applications of translational bioinformatics and clinical research (biomedical) informatics: The Cancer Genome Atlas, the cBioPortal for Cancer Genomics, and the Memorial Sloan Kettering Cancer Center clinical variants and results database, all designed to facilitate insights into cancer biology and clinical/therapeutic correlations.

  19. The REACH Youth Program Learning Toolkit

    ERIC Educational Resources Information Center

    Sierra Health Foundation, 2011

    2011-01-01

    Believing in the value of using video documentaries and data as learning tools, members of the REACH technical assistance team collaborated to develop this toolkit. The learning toolkit was designed using and/or incorporating components of the "Engaging Youth in Community Change: Outcomes and Lessons Learned from Sierra Health Foundation's…

  20. Design Optimization Toolkit: Users' Manual

    SciTech Connect

    Aguilo Valentin, Miguel Alejandro

    2014-07-01

    The Design Optimization Toolkit (DOTk) is a stand-alone C++ software package intended to solve complex design optimization problems. DOTk software package provides a range of solution methods that are suited for gradient/nongradient-based optimization, large scale constrained optimization, and topology optimization. DOTk was design to have a flexible user interface to allow easy access to DOTk solution methods from external engineering software packages. This inherent flexibility makes DOTk barely intrusive to other engineering software packages. As part of this inherent flexibility, DOTk software package provides an easy-to-use MATLAB interface that enables users to call DOTk solution methods directly from the MATLAB command window.

  1. Python-ARM Radar Toolkit

    SciTech Connect

    Jonathan Helmus, Scott Collis

    2013-03-17

    The Python-ARM Radar Toolkit (Py-ART) is a collection of radar quality control and retrieval codes which all work on two unifying Python objects: the PyRadar and PyGrid objects. By building ingests to several popular radar formats and then abstracting the interface Py-ART greatly simplifies data processing over several other available utilities. In addition Py-ART makes use of Numpy arrays as its primary storage mechanism enabling use of existing and extensive community software tools.

  2. Improving Bridging from Informatics Theory to Practice

    PubMed Central

    Haux, R.

    2015-01-01

    Background In 1962, Methods of Information in Medicine (MIM) began to publish papers on the methodology and scientific fundamentals of managing data, information, and knowledge in biomedicine and health care. Meeting an increasing demand for research about practical implementation of health information systems, the journal Applied Clinical Informatics (ACI) was launched in 2009. Both journals are official journals of the International Medical Informatics Association (IMIA). Objectives Based on prior analyses, we aimed to describe major topics published in MIM during 2014 and to explore whether theory of MIM influenced practice of ACI. Our objectives were further to describe lessons learned and to discuss possible editorial policies to improve bridging from theory to practice. Methods We conducted a retrospective, observational study reviewing MIM articles published during 2014 (N=61) and analyzing reference lists of ACI articles from 2014 (N=70). Lessons learned and opinions about MIM editorial policies were developed in consensus by the two authors. These have been influenced by discussions with the journal’s associate editors and editorial board members. Results The publication topics of MIM in 2014 were broad, covering biomedical and health informatics, medical biometry and epidemiology. Important topics discussed were biosignal interpretation, boosting methodologies, citation analysis, health-enabling and ambient assistive technologies, health record banking, safety, and standards. Nine ACI practice articles from 2014 cited eighteen MIM theory papers from any year. These nine ACI articles covered mainly the areas of clinical documentation and medication-related decision support. The methodological basis they cited from was almost exclusively related to evaluation. We could show some direct links where theory impacted practice. These links are however few in relation to the total amount of papers published. Conclusions Editorial policies such as publishing

  3. Developing an Open-Source Bibliometric Ranking Website Using Google Scholar Citation Profiles for Researchers in the Field of Biomedical Informatics.

    PubMed

    Sittig, Dean F; McCoy, Allison B; Wright, Adam; Lin, Jimmy

    2015-01-01

    We developed the Biomedical Informatics Researchers ranking website (rank.informatics-review.com) to overcome many of the limitations of previous scientific productivity ranking strategies. The website is composed of four key components that work together to create an automatically updating ranking website: (1) list of biomedical informatics researchers, (2) Google Scholar scraper, (3) display page, and (4) updater. The site has been useful to other groups in evaluating researchers, such as tenure and promotions committees in interpreting the various citation statistics reported by candidates. Creation of the Biomedical Informatics Researchers ranking website highlights the vast differences in scholarly productivity among members of the biomedical informatics research community.

  4. An Introduction to the Einstein Toolkit

    NASA Astrophysics Data System (ADS)

    Zilhão, Miguel; Löffler, Frank

    2013-09-01

    We give an introduction to the Einstein Toolkit, a mature, open-source computational infrastructure for numerical relativity based on the Cactus Framework, for the target group of new users. This toolkit is composed of several different modules, is developed by researchers from different institutions throughout the world and is in active continuous development. Documentation for the toolkit and its several modules is often scattered across different locations, a difficulty new users may at times have to struggle with. Scientific papers exist describing the toolkit and its methods in detail, but they might be overwhelming at first. With these lecture notes we hope to provide an initial overview for new users. We cover how to obtain, compile and run the toolkit, and give an overview of some of the tools and modules provided with it.

  5. Policy Implications of Education Informatics

    ERIC Educational Resources Information Center

    Carr, Jo Ann; O'Brien, Nancy P.

    2010-01-01

    Background/Context: This concluding article identifies the policy implications of education informatics and explores impacts of current copyright laws, legislative structures, publishing practices, and education organizations. Synthesizing the discussions in the preceding articles, this article highlights the importance of designing information…

  6. Deep Learning for Health Informatics.

    PubMed

    Ravi, Daniele; Wong, Charence; Deligianni, Fani; Berthelot, Melissa; Andreu-Perez, Javier; Lo, Benny; Yang, Guang-Zhong

    2017-01-01

    With a massive influx of multimodality data, the role of data analytics in health informatics has grown rapidly in the last decade. This has also prompted increasing interests in the generation of analytical, data driven models based on machine learning in health informatics. Deep learning, a technique with its foundation in artificial neural networks, is emerging in recent years as a powerful tool for machine learning, promising to reshape the future of artificial intelligence. Rapid improvements in computational power, fast data storage, and parallelization have also contributed to the rapid uptake of the technology in addition to its predictive power and ability to generate automatically optimized high-level features and semantic interpretation from the input data. This article presents a comprehensive up-to-date review of research employing deep learning in health informatics, providing a critical analysis of the relative merit, and potential pitfalls of the technique as well as its future outlook. The paper mainly focuses on key applications of deep learning in the fields of translational bioinformatics, medical imaging, pervasive sensing, medical informatics, and public health.

  7. Admit: Alma Data Mining Toolkit

    NASA Astrophysics Data System (ADS)

    Friedel, Douglas; Looney, Leslie; Xu, Lisa; Pound, Marc W.; Teuben, Peter J.; Rauch, Kevin P.; Mundy, Lee; Kern, Jeffrey S.

    2015-06-01

    ADMIT (ALMA Data Mining Toolkit) is a toolkit for the creation and analysis of new science products from ALMA data. ADMIT is an ALMA Development Project written purely in Python. While specifically targeted for ALMA science and production use after the ALMA pipeline, it is designed to be generally applicable to radio-astronomical data. ADMIT quickly provides users with a detailed overview of their science products: line identifications, line 'cutout' cubes, moment maps, emission type analysis (e.g., feature detection), etc. Users can download the small ADMIT pipeline product (<20MB), analyze the results, then fine-tune and re-run the ADMIT pipeline (or any part thereof) on their own machines and interactively inspect the results. ADMIT will have both a GUI and command line interface available for this purpose. By analyzing multiple data cubes simultaneously, data mining between many astronomical sources and line transitions will be possible. Users will also be able to enhance the capabilities of ADMIT by creating customized ADMIT tasks satisfying any special processing needs. Future implementations of ADMIT may include EVLA and other instruments.

  8. The SCRAM tool-kit

    NASA Technical Reports Server (NTRS)

    Tamir, David; Flanigan, Lee A.; Weeks, Jack L.; Siewert, Thomas A.; Kimbrough, Andrew G.; Mcclure, Sidney R.

    1994-01-01

    This paper proposes a new series of on-orbit capabilities to support the near-term Hubble Space Telescope, Extended Duration Orbiter, Long Duration Orbiter, Space Station Freedom, other orbital platforms, and even the future manned Lunar/Mars missions. These proposed capabilities form a toolkit termed Space Construction, Repair, and Maintenance (SCRAM). SCRAM addresses both intra-Vehicular Activity (IVA) and Extra-Vehicular Activity (EVA) needs. SCRAM provides a variety of tools which enable welding, brazing, cutting, coating, heating, and cleaning, as well as corresponding nondestructive examination. Near-term IVA-SCRAM applications include repair and modification to fluid lines, structure, and laboratory equipment inside a shirt-sleeve environment (i.e. inside Spacelab or Space Station). Near-term EVA-SCRAM applications include construction of fluid lines and structural members, repair of punctures by orbital debris, refurbishment of surfaces eroded by contaminants. The SCRAM tool-kit also promises future EVA applications involving mass production tasks automated by robotics and artificial intelligence, for construction of large truss, aerobrake, and nuclear reactor shadow shields structures. The leading candidate tool processes for SCRAM, currently undergoing research and development, include Electron Beam, Gas Tungsten Arc, Plasma Arc, and Laser Beam. A series of strategic space flight experiments would make SCRAM available to help conquer the space frontier.

  9. Incorporating Informatics for Integrating Biology and the Bedside (i2b2) into Predoctoral Trainee Curriculum to Evaluate Student-Generated Hypotheses.

    PubMed

    Schieffer, Kathleen M; Peters, Douglas G; Richter, Chesney K; Loc, Welley S; Pawelczyk, James A

    2015-12-01

    As part of the Clinical and Translational Science Institute predoctoral TL1 training program at the Pennsylvania State University, a multidisciplinary team of predoctoral trainees representing the Chemistry, Neurosurgery, Nutritional Sciences, and Public Health Sciences departments were introduced to the NIH-sponsored Informatics for Integrating Biology and the Bedside (i2b2) database to test the following student-generated hypothesis: children with iron deficiency anemia (IDA) are at increased risk of attention deficit-hyperactivity disorder (ADHD). Children aged 4-12 and 4-17 years were categorized into IDA and control groups. De-identified medical records from the Penn State Milton S. Hershey Medical Center (HMC) and the Virginia Commonwealth University Medical Center (VCUMC) were used for the analysis. Overall, ADHD prevalence at each institution was lower than 2011 state estimates. There was a significant association between IDA and ADHD in the 4-17-year-old age group for all children (OR: 1.902 [95% CI: 1.363-2.656]), Caucasian children (OR: 1.802 [95% CI: 1.133-2.864]), and African American children (OR: 1.865 [95% CI: 1.152-3.021]). Clinical and Translational Science Award (CTSA) infrastructure is particularly useful for trainees to answer de novo scientific questions with minimal additional training and technical expertise. Moreover, projects can be expanded by collaborating within the CTSA network.

  10. Agent Toolkit Satisfaction and Use in Higher Education.

    ERIC Educational Resources Information Center

    Serenko, Alexander; Detlor, Brian

    2003-01-01

    Examined instructors' satisfaction with and use of intelligent agent toolkits in the classroom. Found that no single uniform toolkit satisfied the needs of instructors. Moreover, satisfaction levels were influenced primarily by user interactions with the toolkit, followed to a lesser extent by toolkit performance and functionality. (EV)

  11. [A biomedical signal processing toolkit programmed by Java].

    PubMed

    Xie, Haiyuan

    2012-09-01

    According to the biomedical signal characteristics, a new biomedical signal processing toolkit is developed. The toolkit is programmed by Java. It is used in basic digital signal processing, random signal processing and etc. All the methods in toolkit has been tested, the program is robust. The feature of the toolkit is detailed explained, easy use and good practicability.

  12. The Biodiversity Informatics Potential Index

    PubMed Central

    2011-01-01

    Background Biodiversity informatics is a relatively new discipline extending computer science in the context of biodiversity data, and its development to date has not been uniform throughout the world. Digitizing effort and capacity building are costly, and ways should be found to prioritize them rationally. The proposed 'Biodiversity Informatics Potential (BIP) Index' seeks to fulfill such a prioritization role. We propose that the potential for biodiversity informatics be assessed through three concepts: (a) the intrinsic biodiversity potential (the biological richness or ecological diversity) of a country; (b) the capacity of the country to generate biodiversity data records; and (c) the availability of technical infrastructure in a country for managing and publishing such records. Methods Broadly, the techniques used to construct the BIP Index were rank correlation, multiple regression analysis, principal components analysis and optimization by linear programming. We built the BIP Index by finding a parsimonious set of country-level human, economic and environmental variables that best predicted the availability of primary biodiversity data accessible through the Global Biodiversity Information Facility (GBIF) network, and constructing an optimized model with these variables. The model was then applied to all countries for which sufficient data existed, to obtain a score for each country. Countries were ranked according to that score. Results Many of the current GBIF participants ranked highly in the BIP Index, although some of them seemed not to have realized their biodiversity informatics potential. The BIP Index attributed low ranking to most non-participant countries; however, a few of them scored highly, suggesting that these would be high-return new participants if encouraged to contribute towards the GBIF mission of free and open access to biodiversity data. Conclusions The BIP Index could potentially help in (a) identifying countries most likely to

  13. An introduction to the Lagan alignment toolkit.

    PubMed

    Brudno, Michael

    2007-01-01

    The Lagan Toolkit is a software package for comparison of genomic sequences. It includes the CHAOS local alignment program, LAGAN global alignment program for two, or more sequences and Shuffle-LAGAN, a "glocal" alignment method that handles genomic rearrangements in a global alignment framework. The alignment programs included in the Lagan Toolkit have been widely used to compare genomes of many organisms, from bacteria to large mammalian genomes. This chapter provides an overview of the algorithms used by the LAGAN programs to construct genomic alignments, explains how to build alignments using either the standalone program or the web server, and discusses some of the common pitfalls users encounter when using the toolkit.

  14. On combining computational differentiation and toolkits for parallel scientific computing.

    SciTech Connect

    Bischof, C. H.; Buecker, H. M.; Hovland, P. D.

    2000-06-08

    Automatic differentiation is a powerful technique for evaluating derivatives of functions given in the form of a high-level programming language such as Fortran, C, or C++. The program is treated as a potentially very long sequence of elementary statements to which the chain rule of differential calculus is applied over and over again. Combining automatic differentiation and the organizational structure of toolkits for parallel scientific computing provides a mechanism for evaluating derivatives by exploiting mathematical insight on a higher level. In these toolkits, algorithmic structures such as BLAS-like operations, linear and nonlinear solvers, or integrators for ordinary differential equations can be identified by their standardized interfaces and recognized as high-level mathematical objects rather than as a sequence of elementary statements. In this note, the differentiation of a linear solver with respect to some parameter vector is taken as an example. Mathematical insight is used to reformulate this problem into the solution of multiple linear systems that share the same coefficient matrix but differ in their right-hand sides. The experiments reported here use ADIC, a tool for the automatic differentiation of C programs, and PETSC, an object-oriented toolkit for the parallel solution of scientific problems modeled by partial differential equations.

  15. Designing a Composable Geometric Toolkit for Versatility in Applications to Simulation Development

    NASA Technical Reports Server (NTRS)

    Reed, Gregory S.; Campbell, Thomas

    2008-01-01

    Conceived and implemented through the development of probabilistic risk assessment simulations for Project Constellation, the Geometric Toolkit allows users to create, analyze, and visualize relationships between geometric shapes in three-space using the MATLAB computing environment. The key output of the toolkit is an analysis of how emanations from one "source" geometry (e.g., a leak in a pipe) will affect another "target" geometry (e.g., another heat-sensitive component). It can import computer-aided design (CAD) depictions of a system to be analyzed, allowing the user to reliably and easily represent components within the design and determine the relationships between them, ultimately supporting more technical or physics-based simulations that use the toolkit. We opted to develop a variety of modular, interconnecting software tools to extend the scope of the toolkit, providing the capability to support a range of applications. This concept of simulation composability allows specially-developed tools to be reused by assembling them in various combinations. As a result, the concepts described here and implemented in this toolkit have a wide range of applications outside the domain of risk assessment. To that end, the Geometric Toolkit has been evaluated for use in other unrelated applications due to the advantages provided by its underlying design.

  16. Translational informatics: an industry perspective.

    PubMed

    Cantor, Michael N

    2012-01-01

    Translational informatics (TI) is extremely important for the pharmaceutical industry, especially as the bar for regulatory approval of new medications is set higher and higher. This paper will explore three specific areas in the drug development lifecycle, from tools developed by precompetitive consortia to standardized clinical data collection to the effective delivery of medications using clinical decision support, in which TI has a major role to play. Advancing TI will require investment in new tools and algorithms, as well as ensuring that translational issues are addressed early in the design process of informatics projects, and also given higher weight in funding or publication decisions. Ultimately, the source of translational tools and differences between academia and industry are secondary, as long as they move towards the shared goal of improving health.

  17. Translational informatics: an industry perspective

    PubMed Central

    2012-01-01

    Translational informatics (TI) is extremely important for the pharmaceutical industry, especially as the bar for regulatory approval of new medications is set higher and higher. This paper will explore three specific areas in the drug development lifecycle, from tools developed by precompetitive consortia to standardized clinical data collection to the effective delivery of medications using clinical decision support, in which TI has a major role to play. Advancing TI will require investment in new tools and algorithms, as well as ensuring that translational issues are addressed early in the design process of informatics projects, and also given higher weight in funding or publication decisions. Ultimately, the source of translational tools and differences between academia and industry are secondary, as long as they move towards the shared goal of improving health. PMID:22237867

  18. The scope and direction of health informatics

    NASA Technical Reports Server (NTRS)

    McGinnis, Patrick J.

    2002-01-01

    Health Informatics (HI) is a dynamic discipline based on the medical sciences, information sciences, and cognitive sciences. Its domain can broadly be defined as medical information management. The purpose of this paper is to provide an overview of this domain, discuss the current "state of the art," and indicate the likely growth areas for health informatics. The sources of information used in this paper are selected publications from the literature of Health Informatics, HI 5300: Introduction to Health Informatics, which is a course from the Department of Health Informatics at the University of Texas Houston Health Sciences Center, and the author's personal experience in practicing telemedicine and implementing an electronic medical record at the NASA-Johnson Space Center. The conclusion is that the direction of Health Informatics is in the direction of data management, transfer, and representation via electronic medical records and the Internet.

  19. The Scope and Direction of Health Informatics

    NASA Technical Reports Server (NTRS)

    McGinnis, Patrick J.

    2001-01-01

    Health Informatics (HI) is a dynamic discipline based upon the medical sciences, information sciences, and cognitive sciences. Its domain is can broadly be defined as medical information management. The purpose of this paper is to provide an overview of this domain, discuss the current "state of the art" , and indicate the likely growth areas for health informatics. The sources of information utilized in this paper are selected publications from the literature of Health Informatics, HI 5300: Introduction to Health Informatics, which is a course from the Department of Health Informatics at the University of Texas Houston Health Sciences Center, and the author's personal experience in practicing telemedicine and implementing an electronic medical record at the NASA Johnson Space Center. The conclusion is that the direction of Health Informatics is in the direction of data management, transfer, and representation via electronic medical records and the Internet.

  20. Informatics competencies for healthcare professionals: the Technology Informatics Guiding Education Reform (TIGER) Initiative model.

    PubMed

    Hebda, Toni L; Calderone, Terri L

    2012-01-01

    A growing awareness exists that informatics competencies are essential skills for healthcare professionals today, yet the development of these competencies lags behind the need. The Technology Informatics Guiding Education Reform (TIGER) Initiative represents a comprehensive, interdisciplinary effort that is well suited to the integration of informatics into education, practice, administration, and research environments. This article briefly discusses the background and significance of the TIGER Initiative and why it may be used as a model to instill informatics among the healthcare professionals globally.

  1. The WellingTONNE Challenge Toolkit: Using the RE-AIM Framework to Evaluate a Community Resource Promoting Healthy Lifestyle Behaviours

    ERIC Educational Resources Information Center

    Caperchione, Cristina; Coulson, Fiona

    2010-01-01

    Objective: The RE-AIM framework has been recognized as a tool to evaluate the adoption, delivery, and sustainability of an intervention, and estimate its potential public health impact. In this study four dimensions of the RE-AIM framework (adoption, implementation, effectiveness, and maintenance) were used to evaluate the WellingTONNE Challenge…

  2. Flightspeed Integral Image Analysis Toolkit

    NASA Technical Reports Server (NTRS)

    Thompson, David R.

    2009-01-01

    The Flightspeed Integral Image Analysis Toolkit (FIIAT) is a C library that provides image analysis functions in a single, portable package. It provides basic low-level filtering, texture analysis, and subwindow descriptor for applications dealing with image interpretation and object recognition. Designed with spaceflight in mind, it addresses: Ease of integration (minimal external dependencies) Fast, real-time operation using integer arithmetic where possible (useful for platforms lacking a dedicated floatingpoint processor) Written entirely in C (easily modified) Mostly static memory allocation 8-bit image data The basic goal of the FIIAT library is to compute meaningful numerical descriptors for images or rectangular image regions. These n-vectors can then be used directly for novelty detection or pattern recognition, or as a feature space for higher-level pattern recognition tasks. The library provides routines for leveraging training data to derive descriptors that are most useful for a specific data set. Its runtime algorithms exploit a structure known as the "integral image." This is a caching method that permits fast summation of values within rectangular regions of an image. This integral frame facilitates a wide range of fast image-processing functions. This toolkit has applicability to a wide range of autonomous image analysis tasks in the space-flight domain, including novelty detection, object and scene classification, target detection for autonomous instrument placement, and science analysis of geomorphology. It makes real-time texture and pattern recognition possible for platforms with severe computational restraints. The software provides an order of magnitude speed increase over alternative software libraries currently in use by the research community. FIIAT can commercially support intelligent video cameras used in intelligent surveillance. It is also useful for object recognition by robots or other autonomous vehicles

  3. 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.

  4. Cognitive hacking and intelligence and security informatics

    NASA Astrophysics Data System (ADS)

    Thompson, Paul

    2004-08-01

    This paper describes research on cognitive and semantic attacks on computer systems and their users. Several countermeasures against such attacks are described, including a description of a prototype News Verifier system. It is argued that because misinformation and deception play a much more significant role in intelligence and security informatics than in other informatics disciplines such as science, medicine, and the law, a new science of intelligence and security informatics must concern itself with semantic attacks and countermeasures.

  5. Two years of German summer school of nursing informatics: Did we reach the goals?

    PubMed

    Bürkle, T; Schrader, U

    2000-09-01

    This paper describes a continuous effort to improve the knowledge of nursing informatics among German nurses. The authors have co-operated in the nursing informatics working group of the German Medical Informatics Association GMDS. Besides, one of the authors has been active in the European summer school of nursing informatics (Essoni) for several years. The authors have now established a national counterpart to the Essoni program, the German summer school of nursing informatics. This event in German language is centred around nursing informatics topics. Students may opt for one of the several study tracks to gain insight in topics such as nursing classifications and nursing terminologies, clinical information systems and their implementation or teaching requirements in nursing informatics. They go through a 5-day curriculum consisting of plenary sessions, lectures and opportunities for self learning and self teaching. At the end they demonstrate to the fellow students from the other tracks what they have achieved in their own field of study. The German Summer School is open to interested nurses, nurse executives and nurse teachers. In this paper, we will describe the curriculum, talk about the participants and show results of the questionnaire-based evaluation for the first two events in 1998 and 1999.

  6. 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.

  7. 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.

  8. Network Visualization Design Using Prefuse Visualization Toolkit

    DTIC Science & Technology

    2008-03-01

    Lipinski. “ JULIUS - An Extendable Software Framework for Surgi- cal Planning”. Caesar , Berlin, Germany, 2001. URL http://www.caesar.de/ fileadmin/user upload... Julius framework and Ball modelar . . . . . 13 2.9 PNode class hierarchy showing monolithic Piccolo toolkit design [3... JULIUS [24] (used for medical imaging). However, all frameworks studied, except one, selected OpenGL as 12 their graphical visualization toolkit. This

  9. Performance of the ISIS Distributed Computing Toolkit

    DTIC Science & Technology

    1994-06-22

    Best Available Copy .. A a ~ d ~ . 1) - . Fs’A aiaer rnrgC"opyr~IL tI.ru~ Performance of the ISIS Distributed Computing Toolkit* Kenneth P. Birman...isis.com. Please cite as Technical Report TR-94-1432, Dept. of Computer Science, Cornell University. Performance of the Isis Distributed Computing Toolkit... Distributed computing , performance, process groups, atomic broadcast, causal and total message ordering, cbcast, abcast, multiple process groups

  10. Integrating Health Information Technology Safety into Nursing Informatics Competencies.

    PubMed

    Borycki, Elizabeth M; Cummings, Elizabeth; Kushniruk, Andre W; Saranto, Kaija

    2017-01-01

    Nursing informatics competencies are constantly changing in response to advances in the health information technology (HIT) industry and research emerging from the fields of nursing and health informatics. In this paper we build off the work of Staggers and colleagues in defining nursing informatics competencies at five levels: the beginning nurse, the experienced nurse, the nursing informatics specialist, the nursing informatics innovator and the nursing informatics researcher in the area of HIT safety. The work represents a significant contribution to the literature in the area of nursing informatics competency development as it extends nursing informatics competencies to include those focused on the area of technology-induced errors and HIT safety.

  11. The Chief Clinical Informatics Officer (CCIO)

    PubMed Central

    Sengstack, Patricia; Thyvalikakath, Thankam Paul; Poikonen, John; Middleton, Blackford; Payne, Thomas; Lehmann, Christoph U

    2016-01-01

    Summary Introduction The emerging operational role of the “Chief Clinical Informatics Officer” (CCIO) remains heterogeneous with individuals deriving from a variety of clinical settings and backgrounds. The CCIO is defined in title, responsibility, and scope of practice by local organizations. The term encompasses the more commonly used Chief Medical Informatics Officer (CMIO) and Chief Nursing Informatics Officer (CNIO) as well as the rarely used Chief Pharmacy Informatics Officer (CPIO) and Chief Dental Informatics Officer (CDIO). Background The American Medical Informatics Association (AMIA) identified a need to better delineate the knowledge, education, skillsets, and operational scope of the CCIO in an attempt to address the challenges surrounding the professional development and the hiring processes of CCIOs. Discussion An AMIA task force developed knowledge, education, and operational skillset recommendations for CCIOs focusing on the common core aspect and describing individual differences based on Clinical Informatics focus. The task force concluded that while the role of the CCIO currently is diverse, a growing body of Clinical Informatics and increasing certification efforts are resulting in increased homogeneity. The task force advised that 1.) To achieve a predictable and desirable skillset, the CCIO must complete clearly defined and specified Clinical Informatics education and training. 2.) Future education and training must reflect the changing body of knowledge and must be guided by changing day-to-day informatics challenges. Conclusion A better defined and specified education and skillset for all CCIO positions will motivate the CCIO workforce and empower them to perform the job of a 21st century CCIO. Formally educated and trained CCIOs will provide a competitive advantage to their respective enterprise by fully utilizing the power of Informatics science. PMID:27081413

  12. Measuring nursing informatics competencies of practicing nurses in Korea: Nursing Informatics Competencies Questionnaire.

    PubMed

    Chung, Seon Yoon; Staggers, Nancy

    2014-12-01

    Informatics competencies are a necessity for contemporary nurses. However, few researchers have investigated informatics competencies for practicing nurses. A full set of Informatics competencies, an instrument to measure these competencies, and potential influencing factors have yet to be identified for practicing nurses. The Nursing Informatics Competencies Questionnaire was designed, tested for psychometrics, and used to measure beginning and experienced levels of practice. A pilot study using 54 nurses ensured item comprehension and clarity. Internal consistency and face and content validity were established. A cross-sectional survey was then conducted on 230 nurses in Seoul, Korea, to determine construct validity, describe a complete set of informatics competencies, and explore possible influencing factors on existing informatics competencies. Principal components analysis, descriptive statistics, and multiple regression were used for data analysis. Principal components analysis gives support for the Nursing Informatics Competencies Questionnaire construct validity. Survey results indicate that involvement in a managerial position and self-directed informatics-related education may be more influential for improving informatics competencies, whereas general clinical experience and workplace settings are not. This study provides a foundation for understanding how informatics competencies might be integrated throughout nurses' work lives and how to develop appropriate strategies to support nurses in their informatics practice in clinical settings.

  13. Informatics Education in Italian Secondary Schools

    ERIC Educational Resources Information Center

    Bellettini, Carlo; Lonati, Violetta; Malchiodi, Dario; Monga, Mattia; Morpurgo, Anna; Torelli, Mauro; Zecca, Luisa

    2014-01-01

    This article describes the state of informatics education in the Italian secondary schools, highlighting how the learning objectives set up by the Ministry of Education are difficult to meet, due to the fact that the subject is often taught by teachers not holding an informatics degree, the lack of suitable teaching material and the expectations…

  14. Medical Informatics: Market for IS/IT.

    ERIC Educational Resources Information Center

    Morris, Theodore Allan

    2002-01-01

    Uses co-occurrence analysis of INSPEC classification codes and thesaurus terms assigned to medical informatics (biomedical information) journal articles and proceedings papers to reveal a more complete perspective of how information science and information technology (IS/IT) authors view medical informatics. Discusses results of cluster analysis…

  15. Teaching Some Informatics Concepts Using Formal System

    ERIC Educational Resources Information Center

    Yang, Sojung; Park, Seongbin

    2014-01-01

    There are many important issues in informatics and many agree that algorithms and programming are most important issues that need to be included in informatics education (Dagiene and Jevsikova, 2012). In this paper, we propose how some of these issues can be easily taught using the notion of a formal system which consists of axioms and inference…

  16. The Teaching of Informatics for Business Students

    ERIC Educational Resources Information Center

    Sora, Sebastian A.

    2008-01-01

    Informatics is a branch of computer science that concerns itself, in actuality, with the use of information systems. The objective of this paper is to focus on the business curriculum for graduate students and their gaining proficiency in informatics so that they can understand the concept of information, the access of information, the use of…

  17. Medical Informatics in Academic Health Science Centers.

    ERIC Educational Resources Information Center

    Frisse, Mark E.

    1992-01-01

    An analysis of the state of medical informatics, the application of computer and information technology to biomedicine, looks at trends and concerns, including integration of traditionally distinct enterprises (clinical information systems, financial information, scholarly support activities, infrastructures); informatics career choice and…

  18. The Weather and Climate Toolkit

    NASA Astrophysics Data System (ADS)

    Ansari, S.; Del Greco, S.; Hankins, B.

    2010-12-01

    The Weather and Climate Toolkit (WCT) is free, platform independent software distributed from NOAA’s National Climatic Data Center (NCDC). The WCT allows the visualization and data export of weather and climate data, including Radar, Satellite and Model data. By leveraging the NetCDF for Java library and Common Data Model, the WCT is extremely scalable and capable of supporting many new datasets in the future. Gridded NetCDF files (regular and irregularly spaced, using Climate-Forecast (CF) conventions) are supported, along with many other formats including GRIB. The WCT provides tools for custom data overlays, Web Map Service (WMS) background maps, animations and basic filtering. The export of images and movies is provided in multiple formats. The WCT Data Export Wizard allows for data export in both vector polygon/point (Shapefile, Well-Known Text) and raster (GeoTIFF, ESRI Grid, VTK, Gridded NetCDF) formats. These data export features promote the interoperability of weather and climate information with various scientific communities and common software packages such as ArcGIS, Google Earth, MatLAB, GrADS and R. The WCT also supports an embedded, integrated Google Earth instance. The Google Earth Browser Plugin allows seamless visualization of data on a native 3-D Google Earth instance linked to the standard 2-D map. Level-II NEXRAD data for Hurricane Katrina GPCP (Global Precipitation Product), visualized in 2-D and internal Google Earth view.

  19. Clinical informatics in critical care.

    PubMed

    Martich, G Daniel; Waldmann, Carl S; Imhoff, Michael

    2004-01-01

    Health care information systems have the potential to enable better care of patients in much the same manner as the widespread use of the automobile and telephone did in the early 20th century. The car and phone were rapidly accepted and embraced throughout the world when these breakthroughs occurred. However, the automation of health care with use of computerized information systems has not been as widely accepted and implemented as computer technology use in all other sectors of the global economy. In this article, the authors examine the need, risks, and rewards of clinical informatics in health care as well as its specific relationship to critical care medicine.

  20. Five Periods in Development of Medical Informatics

    PubMed Central

    Masic, Izet

    2014-01-01

    Medical informatics, as scientific discipline, has to do with all aspects of understanding and promoting the effective organization, analysis, management, and use of information in health care. While the field of Medical informatics shares the general scope of these interests with some other health care specialities and disciplines, Medical (Health) informatics has developed its own areas of emphasis and approaches that have set it apart from other disciplines and specialities. For the last fifties of 20th century and some more years of 21st century, Medical informatics had the five time periods of characteristic development. In this paper author shortly described main scientific innovations and inventors who created development of Medical informatics. PMID:24648619

  1. Medical informatics between technology, philosophy and science.

    PubMed

    Masic, Izet

    2004-01-01

    Medical (health) informatics occupies the central place in all the segments of modern medicine in the past thirty years--in practical work, education and scientific research. In all that, computers have taken over the most important role and are used intensively for the development of the health information systems. Following activities develop within the area of health informatics: health-documentation, health-statistics, health-informatics and biomedical scientific and professional information. The medical informatics as the separate medical discipline very quickly gets developed, both in Bosnia and Herzegovina. In our country, the medical informatics is a separate subject for the last ten years, regarding to the Medical curriculum at the biomedical faculties in Bosnia and Herzegovina is in accordance with the project of the education related to Bologna declaration and the project EURO MEDICINA.

  2. AMIA members’ “vital signs”: what the HIT implementation listserv says about goals for AMIA and for medical informatics

    PubMed Central

    Ravvaz, Kourosh; Kuziemsky, Craig; Koppel, Ross; Kaplan, Bonnie; Adams, Samantha A.; Adams, Martha B.

    2015-01-01

    The health information technology (HIT) implementation listserv was conceived as a way to combine a substantial portion of American Medical Informatics Association (AMIA) members who belonged to four working groups (WGs): CIS, Evaluation, ELSI, and POI. Other AMIA members joined in significant numbers. It immediately became a major forum for discussing medical informatics, informatics policies, and discussion of the purpose of AMIA itself. The listserv membership approximates 25% of AMIA’s members and has generated over 6,000 posts. We report on a survey of the listserv’s members: what members think about the listserv; what participants want for medical informatics; how they think those goals should be achieved, and what AMIA’s role should be in this process. The listserv provides vital signs about AMIA and hopes for informatics. We combine qualitative analysis of members’ comments and responses about the listserv using ATLAS.ti qualitative text analysis tool and a word cloud generator. PMID:26958245

  3. How can we improve Science, Technology, Engineering, and Math education to encourage careers in Biomedical and Pathology Informatics?

    PubMed Central

    Uppal, Rahul; Mandava, Gunasheil; Romagnoli, Katrina M.; King, Andrew J.; Draper, Amie J.; Handen, Adam L.; Fisher, Arielle M.; Becich, Michael J.; Dutta-Moscato, Joyeeta

    2016-01-01

    The Computer Science, Biology, and Biomedical Informatics (CoSBBI) program was initiated in 2011 to expose the critical role of informatics in biomedicine to talented high school students.[1] By involving them in Science, Technology, Engineering, and Math (STEM) training at the high school level and providing mentorship and research opportunities throughout the formative years of their education, CoSBBI creates a research infrastructure designed to develop young informaticians. Our central premise is that the trajectory necessary to be an expert in the emerging fields of biomedical informatics and pathology informatics requires accelerated learning at an early age.In our 4th year of CoSBBI as a part of the University of Pittsburgh Cancer Institute (UPCI) Academy (http://www.upci.upmc.edu/summeracademy/), and our 2nd year of CoSBBI as an independent informatics-based academy, we enhanced our classroom curriculum, added hands-on computer science instruction, and expanded research projects to include clinical informatics. We also conducted a qualitative evaluation of the program to identify areas that need improvement in order to achieve our goal of creating a pipeline of exceptionally well-trained applicants for both the disciplines of pathology informatics and biomedical informatics in the era of big data and personalized medicine. PMID:26955500

  4. How can we improve Science, Technology, Engineering, and Math education to encourage careers in Biomedical and Pathology Informatics?

    PubMed

    Uppal, Rahul; Mandava, Gunasheil; Romagnoli, Katrina M; King, Andrew J; Draper, Amie J; Handen, Adam L; Fisher, Arielle M; Becich, Michael J; Dutta-Moscato, Joyeeta

    2016-01-01

    The Computer Science, Biology, and Biomedical Informatics (CoSBBI) program was initiated in 2011 to expose the critical role of informatics in biomedicine to talented high school students.[1] By involving them in Science, Technology, Engineering, and Math (STEM) training at the high school level and providing mentorship and research opportunities throughout the formative years of their education, CoSBBI creates a research infrastructure designed to develop young informaticians. Our central premise is that the trajectory necessary to be an expert in the emerging fields of biomedical informatics and pathology informatics requires accelerated learning at an early age.In our 4(th) year of CoSBBI as a part of the University of Pittsburgh Cancer Institute (UPCI) Academy (http://www.upci.upmc.edu/summeracademy/), and our 2nd year of CoSBBI as an independent informatics-based academy, we enhanced our classroom curriculum, added hands-on computer science instruction, and expanded research projects to include clinical informatics. We also conducted a qualitative evaluation of the program to identify areas that need improvement in order to achieve our goal of creating a pipeline of exceptionally well-trained applicants for both the disciplines of pathology informatics and biomedical informatics in the era of big data and personalized medicine.

  5. The MITK image guided therapy toolkit and its application for augmented reality in laparoscopic prostate surgery

    NASA Astrophysics Data System (ADS)

    Baumhauer, Matthias; Neuhaus, Jochen; Fritzsche, Klaus; Meinzer, Hans-Peter

    2010-02-01

    Image Guided Therapy (IGT) faces researchers with high demands and efforts in system design, prototype implementation, and evaluation. The lack of standardized software tools, like algorithm implementations, tracking device and tool setups, and data processing methods escalate the labor for system development and sustainable system evaluation. In this paper, a new toolkit component of the Medical Imaging and Interaction Toolkit (MITK), the MITK-IGT, and its exemplary application for computer-assisted prostate surgery are presented. MITK-IGT aims at integrating software tools, algorithms and tracking device interfaces into the MITK toolkit to provide a comprehensive software framework for computer aided diagnosis support, therapy planning, treatment support, and radiological follow-up. An exemplary application of the MITK-IGT framework is introduced with a surgical navigation system for laparos-copic prostate surgery. It illustrates the broad range of application possibilities provided by the framework, as well as its simple extensibility with custom algorithms and other software modules.

  6. Publication trends in the medical informatics literature: 20 years of "Medical Informatics" in MeSH

    PubMed Central

    2009-01-01

    Background The purpose of this study is to identify publication output, and research areas, as well as descriptively and quantitatively characterize the field of medical informatics through publication trend analysis over a twenty year period (1987–2006). Methods A bibliometric analysis of medical informatics citations indexed in Medline was performed using publication trends, journal frequency, impact factors, MeSH term frequencies and characteristics of citations. Results There were 77,023 medical informatics articles published during this 20 year period in 4,644 unique journals. The average annual article publication growth rate was 12%. The 50 identified medical informatics MeSH terms are rarely assigned together to the same document and are almost exclusively paired with a non-medical informatics MeSH term, suggesting a strong interdisciplinary trend. Trends in citations, journals, and MeSH categories of medical informatics output for the 20-year period are summarized. Average impact factor scores and weighted average impact factor scores increased over the 20-year period with two notable growth periods. Conclusion There is a steadily growing presence and increasing visibility of medical informatics literature over the years. Patterns in research output that seem to characterize the historic trends and current components of the field of medical informatics suggest it may be a maturing discipline, and highlight specific journals in which the medical informatics literature appears most frequently, including general medical journals as well as informatics-specific journals. PMID:19159472

  7. Start/Pat; A parallel-programming toolkit

    SciTech Connect

    Appelbe, B.; Smith, K. ); McDowell, C. )

    1989-07-01

    How can you make Fortran code parallel without isolating the programmer from learning to understand and exploit parallelism effectively. With an interactive toolkit that automates parallelization as it educates. This paper discusses the Start/Pat toolkit.

  8. Integrated Systems Health Management (ISHM) Toolkit

    NASA Technical Reports Server (NTRS)

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

    2013-01-01

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

  9. 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.

  10. The Future of Public Health Informatics: Alternative Scenarios and Recommended Strategies

    PubMed Central

    Edmunds, Margo; Thorpe, Lorna; Sepulveda, Martin; Bezold, Clem; Ross, David A.

    2014-01-01

    Background: In October 2013, the Public Health Informatics Institute (PHII) and Institute for Alternative Futures (IAF) convened a multidisciplinary group of experts to evaluate forces shaping public health informatics (PHI) in the United States, with the aim of identifying upcoming challenges and opportunities. The PHI workshop was funded by the Robert Wood Johnson Foundation as part of its larger strategic planning process for public health and primary care. Workshop Context: During the two-day workshop, nine experts from the public and private sectors analyzed and discussed the implications of four scenarios regarding the United States economy, health care system, information technology (IT) sector, and their potential impacts on public health in the next 10 years, by 2023. Workshop participants considered the potential role of the public health sector in addressing population health challenges in each scenario, and then identified specific informatics goals and strategies needed for the sector to succeed in this role. Recommendations and Conclusion: Participants developed recommendations for the public health informatics field and for public health overall in the coming decade. These included the need to rely more heavily on intersectoral collaborations across public and private sectors, to improve data infrastructure and workforce capacity at all levels of the public health enterprise, to expand the evidence base regarding effectiveness of informatics-based public health initiatives, and to communicate strategically with elected officials and other key stakeholders regarding the potential for informatics-based solutions to have an impact on population health. PMID:25848630

  11. A nursing informatics research agenda for 2008-18: contextual influences and key components.

    PubMed

    Bakken, Suzanne; Stone, Patricia W; Larson, Elaine L

    2008-01-01

    The context for nursing informatics research has changed significantly since the National Institute of Nursing Research-funded Nursing Informatics Research Agenda was published in 1993 and the Delphi study of nursing informatics research priorities reported a decade ago. The authors focus on 3 specific aspects of context--genomic health care, shifting research paradigms, and social (Web 2.0) technologies--that must be considered in formulating a nursing informatics research agenda. These influences are illustrated using the significant issue of healthcare associated infections (HAI). A nursing informatics research agenda for 2008-18 must expand users of interest to include interdisciplinary researchers; build upon the knowledge gained in nursing concept representation to address genomic and environmental data; guide the reengineering of nursing practice; harness new technologies to empower patients and their caregivers for collaborative knowledge development; develop user-configurable software approaches that support complex data visualization, analysis, and predictive modeling; facilitate the development of middle-range nursing informatics theories; and encourage innovative evaluation methodologies that attend to human-computer interface factors and organizational context.

  12. "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…

  13. 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.

  14. 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.

  15. Advancing Climate Change and Impacts Science Through Climate Informatics

    NASA Astrophysics Data System (ADS)

    Lenhardt, W.; Pouchard, L. C.; King, A. W.; Branstetter, M. L.; Kao, S.; Wang, D.

    2010-12-01

    This poster will outline the work to date on developing a climate informatics capability at Oak Ridge National Laboratory (ORNL). The central proposition of this effort is that the application of informatics and information science to the domain of climate change science is an essential means to bridge the realm of high performance computing (HPC) and domain science. The goal is to facilitate knowledge capture and the creation of new scientific insights. For example, a climate informatics capability will help with the understanding and use of model results in domain sciences that were not originally in the scope. From there, HPC can also benefit from feedback as the new approaches may lead to better parameterization in the models. In this poster we will summarize the challenges associated with climate change science that can benefit from the systematic application of informatics and we will highlight our work to date in creating the climate informatics capability to address these types of challenges. We have identified three areas that are particularly challenging in the context of climate change science: 1) integrating model and observational data across different spatial and temporal scales, 2) model linkages, i.e. climate models linked to other models such as hydrologic models, and 3) model diagnostics. Each of these has a methodological component and an informatics component. Our project under way at ORNL seeks to develop new approaches and tools in the context of linking climate change and water issues. We are basing our work on the following four use cases: 1) Evaluation/test of CCSM4 biases in hydrology (precipitation, soil water, runoff, river discharge) over the Rio Grande Basin. User: climate modeler. 2) Investigation of projected changes in hydrology of Rio Grande Basin using the VIC (Variable Infiltration Capacity Macroscale) Hydrologic Model. User: watershed hydrologist/modeler. 3) Impact of climate change on agricultural productivity of the Rio Grande

  16. Milestones: Critical Elements in Clinical Informatics Fellowship Programs

    PubMed Central

    Lehmann, Christoph U.; Munger, Benson

    2016-01-01

    Summary Background Milestones refer to points along a continuum of a competency from novice to expert. Resident and fellow assessment and program evaluation processes adopted by the ACGME include the mandate that programs report the educational progress of residents and fellows twice annually utilizing Milestones developed by a specialty specific ACGME working group of experts. Milestones in clinical training programs are largely unmapped to specific assessment tools. Residents and fellows are mainly assessed using locally derived assessment instruments. These assessments are then reviewed by the Clinical Competency Committee which assigns and reports trainee ratings using the specialty specific reporting Milestones. Methods and Results The challenge and opportunity facing the nascent specialty of Clinical Informatics is how to optimally utilize this framework across a growing number of accredited fellowships. The authors review how a mapped milestone framework, in which each required sub-competency is mapped to a single milestone assessment grid, can enable the use of milestones for multiple uses including individualized learning plans, fellow assessments, and program evaluation. Furthermore, such a mapped strategy will foster the ability to compare fellow progress within and between Clinical Informatics Fellowships in a structured and reliable fashion. Clinical Informatics currently has far less variability across programs and thus could easily utilize a more tightly defined set of milestones with a clear mapping to sub-competencies. This approach would enable greater standardization of assessment instruments and processes across programs while allowing for variability in how those sub-competencies are taught. Conclusions A mapped strategy for Milestones offers significant advantages for Clinical Informatics programs. PMID:27081414

  17. 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

  18. 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.

  19. Autism Speaks Toolkits: Resources for Busy Physicians.

    PubMed

    Bellando, Jayne; Fussell, Jill J; Lopez, Maya

    2016-02-01

    Given the increased prevalence of autism spectrum disorders (ASD), it is likely that busy primary care providers (PCP) are providing care to individuals with ASD in their practice. Autism Speaks provides a wealth of educational, medical, and treatment/intervention information resources for PCPs and families, including at least 32 toolkits. This article serves to familiarize PCPs and families on the different toolkits that are available on the Autism Speaks website. This article is intended to increase physicians' knowledge on the issues that families with children with ASD frequently encounter, to increase their ability to share evidence-based information to guide treatment and care for affected families in their practice.

  20. Anchor Toolkit - a secure mobile agent system

    SciTech Connect

    Mudumbai, Srilekha S.; Johnston, William; Essiari, Abdelilah

    1999-05-19

    Mobile agent technology facilitates intelligent operation insoftware systems with less human interaction. Major challenge todeployment of mobile agents include secure transmission of agents andpreventing unauthorized access to resources between interacting systems,as either hosts, or agents, or both can act maliciously. The Anchortoolkit, designed by LBNL, handles the transmission and secure managementof mobile agents in a heterogeneous distributed computing environment. Itprovides users with the option of incorporating their security managers.This paper concentrates on the architecture, features, access control anddeployment of Anchor toolkit. Application of this toolkit in a securedistributed CVS environment is discussed as a case study.

  1. Career development initiatives in biomedical health informatics.

    PubMed

    Wagholikar, Amol

    2012-01-01

    The disciplines of biomedical engineering and health informatics complement each other. These two scientific fields sometimes strive independently to deliver better health care services. The rapid evolution in data-intensive methods has made practitioners to think about reviewing the educational needs of the biomedical health informatics workforces. This paper discusses the changing skills requirements in biomedical health informatics discipline. The author reports on the challenges faced by IEEE Engineering in Medicine and Biology (EMBS) in the context of continuous career development of the EMBS members. This paper discusses Queensland chapter's initiative towards an integrated career development to address challenges faced by IEEE EMBS.

  2. Case-based medical informatics

    PubMed Central

    Pantazi, Stefan V; Arocha, José F; Moehr, Jochen R

    2004-01-01

    Background The "applied" nature distinguishes applied sciences from theoretical sciences. To emphasize this distinction, we begin with a general, meta-level overview of the scientific endeavor. We introduce the knowledge spectrum and four interconnected modalities of knowledge. In addition to the traditional differentiation between implicit and explicit knowledge we outline the concepts of general and individual knowledge. We connect general knowledge with the "frame problem," a fundamental issue of artificial intelligence, and individual knowledge with another important paradigm of artificial intelligence, case-based reasoning, a method of individual knowledge processing that aims at solving new problems based on the solutions to similar past problems. We outline the fundamental differences between Medical Informatics and theoretical sciences and propose that Medical Informatics research should advance individual knowledge processing (case-based reasoning) and that natural language processing research is an important step towards this goal that may have ethical implications for patient-centered health medicine. Discussion We focus on fundamental aspects of decision-making, which connect human expertise with individual knowledge processing. We continue with a knowledge spectrum perspective on biomedical knowledge and conclude that case-based reasoning is the paradigm that can advance towards personalized healthcare and that can enable the education of patients and providers. We center the discussion on formal methods of knowledge representation around the frame problem. We propose a context-dependent view on the notion of "meaning" and advocate the need for case-based reasoning research and natural language processing. In the context of memory based knowledge processing, pattern recognition, comparison and analogy-making, we conclude that while humans seem to naturally support the case-based reasoning paradigm (memory of past experiences of problem-solving and

  3. Informatics and the Clinical Laboratory

    PubMed Central

    Jones, Richard G; Johnson, Owen A; Batstone, Gifford

    2014-01-01

    The nature of pathology services is changing under the combined pressures of increasing workloads, cost constraints and technological advancement. In the face of this, laboratory systems need to meet new demands for data exchange with clinical electronic record systems for test requesting and results reporting. As these needs develop, new challenges are emerging especially with respect to the format and content of the datasets which are being exchanged. If the potential for the inclusion of intelligent systems in both these areas is to be realised, the continued dialogue between clinicians and laboratory information specialists is of paramount importance. Requirements of information technology (IT) in pathology, now extend well beyond the provision of purely analytical data. With the aim of achieving seamless integration of laboratory data into the total clinical pathway, ‘Informatics’ – the art and science of turning data into useful information – is becoming increasingly important in laboratory medicine. Informatics is a powerful tool in pathology – whether in implementing processes for pathology modernisation, introducing new diagnostic modalities (e.g. proteomics, genomics), providing timely and evidence-based disease management, or enabling best use of limited and often costly resources. Providing appropriate information to empowered and interested patients – which requires critical assessment of the ever-increasing volume of information available – can also benefit greatly from appropriate use of informatics in enhancing self-management of long term conditions. The increasing demands placed on pathology information systems in the context of wider developmental change in healthcare delivery are explored in this review. General trends in medical informatics are reflected in current priorities for laboratory medicine, including the need for unified electronic records, computerised order entry, data security and recovery, and audit. We conclude that

  4. CaGrid Workflow Toolkit: A taverna based workflow tool for cancer grid

    PubMed Central

    2010-01-01

    Background In biological and medical domain, the use of web services made the data and computation functionality accessible in a unified manner, which helped automate the data pipeline that was previously performed manually. Workflow technology is widely used in the orchestration of multiple services to facilitate in-silico research. Cancer Biomedical Informatics Grid (caBIG) is an information network enabling the sharing of cancer research related resources and caGrid is its underlying service-based computation infrastructure. CaBIG requires that services are composed and orchestrated in a given sequence to realize data pipelines, which are often called scientific workflows. Results CaGrid selected Taverna as its workflow execution system of choice due to its integration with web service technology and support for a wide range of web services, plug-in architecture to cater for easy integration of third party extensions, etc. The caGrid Workflow Toolkit (or the toolkit for short), an extension to the Taverna workflow system, is designed and implemented to ease building and running caGrid workflows. It provides users with support for various phases in using workflows: service discovery, composition and orchestration, data access, and secure service invocation, which have been identified by the caGrid community as challenging in a multi-institutional and cross-discipline domain. Conclusions By extending the Taverna Workbench, caGrid Workflow Toolkit provided a comprehensive solution to compose and coordinate services in caGrid, which would otherwise remain isolated and disconnected from each other. Using it users can access more than 140 services and are offered with a rich set of features including discovery of data and analytical services, query and transfer of data, security protections for service invocations, state management in service interactions, and sharing of workflows, experiences and best practices. The proposed solution is general enough to be

  5. Nursing informatics, outcomes, and quality improvement.

    PubMed

    Charters, Kathleen G

    2003-08-01

    Nursing informatics actively supports nursing by providing standard language systems, databases, decision support, readily accessible research results, and technology assessments. Through normalized datasets spanning an entire enterprise or other large demographic, nursing informatics tools support improvement of healthcare by answering questions about patient outcomes and quality improvement on an enterprise scale, and by providing documentation for business process definition, business process engineering, and strategic planning. Nursing informatics tools provide a way for advanced practice nurses to examine their practice and the effect of their actions on patient outcomes. Analysis of patient outcomes may lead to initiatives for quality improvement. Supported by nursing informatics tools, successful advance practice nurses leverage their quality improvement initiatives against the enterprise strategic plan to gain leadership support and resources.

  6. Biomedical informatics in Switzerland: need for action.

    PubMed

    Lovis, Christian; Blaser, Jürg

    2015-01-01

    Biomedical informatics (BMI) is an umbrella scientific field that covers many domains, as defined several years ago by the International Medical Informatics Association and the American Medical Informatics Association, two leading players in the field. For example, one of the domains of BMI is clinical informatics, which has been formally recognised as a medical subspecialty by the American Board of Medical Specialty since 2011. Most OECD (Organisation for Economic Co-operation and Development) countries offer very strong curricula in the field of BMI, strong research and development funding with clear tracks and, for most of them, inclusion of BMI in the curricula of health professionals, but BMI remains only marginally recognised in Switzerland. Recent major changes, however, such as the future federal law on electronic patient records, the personalised health initiative or the growing empowerment of citizens towards their health data, are adding much weight to the need for BMI capacity-building in Switzerland.

  7. Big Data: Are Biomedical and Health Informatics Training Programs Ready?

    PubMed Central

    Hersh, W.; Ganesh, A. U. Jai

    2014-01-01

    Summary Objectives The growing volume and diversity of health and biomedical data indicate that the era of Big Data has arrived for healthcare. This has many implications for informatics, not only in terms of implementing and evaluating information systems, but also for the work and training of informatics researchers and professionals. This article addresses the question: What do biomedical and health informaticians working in analytics and Big Data need to know? Methods We hypothesize a set of skills that we hope will be discussed among academic and other informaticians. Results The set of skills includes: Programming - especially with data-oriented tools, such as SQL and statistical programming languages; Statistics - working knowledge to apply tools and techniques; Domain knowledge - depending on one’s area of work, bioscience or health care; and Communication - being able to understand needs of people and organizations, and articulate results back to them. Conclusions Biomedical and health informatics educational programs must introduce concepts of analytics, Big Data, and the underlying skills to use and apply them into their curricula. The development of new coursework should focus on those who will become experts, with training aiming to provide skills in “deep analytical talent” as well as those who need knowledge to support such individuals. PMID:25123740

  8. 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).

  9. A Toolkit for Stimulating Productive Thinking

    ERIC Educational Resources Information Center

    Janssen, Fred; de Hullu, Els

    2008-01-01

    Students need tools, thinking skills, to help them think actively and in depth about biological phenomena. They need to know what kind of questions to ask and how to find answers to those questions. In this article we present a toolkit with 12 "thinking tools" for asking and answering questions about biological phenomena from different…

  10. Plus 50: Business Community Outreach Toolkit

    ERIC Educational Resources Information Center

    American Association of Community Colleges (NJ1), 2009

    2009-01-01

    This toolkit is designed to support you in building partnerships with the business community. It includes a series of fact sheets you can distribute to employers that discuss the value in hiring plus 50 workers. Individual sections contain footnotes. (Contains 5 web resources.)

  11. Ready, Set, Respect! GLSEN's Elementary School Toolkit

    ERIC Educational Resources Information Center

    Gay, Lesbian and Straight Education Network (GLSEN), 2012

    2012-01-01

    "Ready, Set, Respect!" provides a set of tools to help elementary school educators ensure that all students feel safe and respected and develop respectful attitudes and behaviors. It is not a program to be followed but instead is designed to help educators prepare themselves for teaching about and modeling respect. The toolkit responds to…

  12. Sandia multispectral analyst remote sensing toolkit (SMART).

    SciTech Connect

    Post, Brian Nelson; Smith, Jody Lynn; Geib, Peter L.; Nandy, Prabal; Wang, Nancy Nairong

    2003-03-01

    This remote sensing science and exploitation work focused on exploitation algorithms and methods targeted at the analyst. SMART is a 'plug-in' to commercial remote sensing software that provides algorithms to enhance the utility of the Multispectral Thermal Imager (MTI) and other multispectral satellite data. This toolkit has been licensed to 22 government organizations.

  13. Media Toolkit for Anti-Drug Action.

    ERIC Educational Resources Information Center

    Office of National Drug Control Policy, Washington, DC.

    This toolkit provides proven methods, models, and templates for tying anti-drug efforts to the National Youth Anti-Drug Media Campaign. It helps organizations deliver the Campaign's messages to the media and to other groups and individuals who care about keeping the nation's youth drug free. Eight sections focus on: (1) "Campaign…

  14. The Two-Way Immersion Toolkit

    ERIC Educational Resources Information Center

    Howard, Elizabeth; Sugarman, Julie; Perdomo, Marleny; Adger, Carolyn Temple

    2005-01-01

    This Toolkit is meant to be a resource for teachers, parents, and administrators involved with two-way immersion (TWI) programs, particularly those at the elementary level. Two-way immersion is a form of dual language instruction that brings together students from two native language groups for language, literacy, and academic content instruction…

  15. Virginia Adult Education Health Literacy Toolkit.

    ERIC Educational Resources Information Center

    Singleton, Kate, Comp.

    This toolkit is a resource to help adult education instructors and administrators better understand the problem of health literacy as it affects their learners. It is designed to support creative approaches to helping learners increase their health literacy as they engage in sound, productive adult literacy instruction. Information resources are…

  16. Healthy People 2010: Oral Health Toolkit

    ERIC Educational Resources Information Center

    Isman, Beverly

    2007-01-01

    The purpose of this Toolkit is to provide guidance, technical tools, and resources to help states, territories, tribes and communities develop and implement successful oral health components of Healthy People 2010 plans as well as other oral health plans. These plans are useful for: (1) promoting, implementing and tracking oral health objectives;…

  17. 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.

  18. A Toolkit for the Effective Teaching Assistant

    ERIC Educational Resources Information Center

    Tyrer, Richard; Gunn, Stuart; Lee, Chris; Parker, Maureen; Pittman, Mary; Townsend, Mark

    2004-01-01

    This book offers the notion of a "toolkit" to allow Teaching Assistants (TAs) and colleagues to review and revise their thinking and practice about real issues and challenges in managing individuals, groups, colleagues and themselves in school. In a rapidly changing educational environment the book focuses on combining the underpinning knowledge…

  19. Advanced Extravehicular Mobility Unit Informatics Software Design

    NASA Technical Reports Server (NTRS)

    Wright, Theodore

    2014-01-01

    This is a description of the software design for the 2013 edition of the Advanced Extravehicular Mobility Unit (AEMU) Informatics computer assembly. The Informatics system is an optional part of the space suit assembly. It adds a graphical interface for displaying suit status, timelines, procedures, and caution and warning information. In the future it will display maps with GPS position data, and video and still images captured by the astronaut.

  20. Evolution of Trends in European Medical Informatics

    PubMed Central

    I. Mihalas, George

    2014-01-01

    This presentation attempts to analyze the trends in Medical Informatics along half a century, in the European socio-political and technological development context. Based on the major characteristics which seem dominant in some periods, a staging is proposed, with a description of each period – the context, major ideas, views and events. A summary of major features of each period is also added. This paper has an original presentation of the evolution of major trends in medical informatics. PMID:24648618

  1. Development of an Online Toolkit for Measuring Commercial Building Energy Efficiency Performance -- Scoping Study

    SciTech Connect

    Wang, Na

    2013-03-13

    This study analyzes the market needs for building performance evaluation tools. It identifies the existing gaps and provides a roadmap for the U.S. Department of Energy (DOE) to develop a toolkit with which to optimize energy performance of a commercial building over its life cycle.

  2. Courseware Review: Broderbund Software: Science Toolkit Master Module and Module 1 - Speed and Motion.

    ERIC Educational Resources Information Center

    Cline, Robert A.; Risley, John S.

    1988-01-01

    Reviews the computer software, "Science Toolkit," made by Broderbund Software. The software covers experiments on light, temperature, timing, motion, speed, and frequency by using interfacing equipment. Provides an evaluation and four typical monitor displays. Concludes that it is an excellent software package. (YP)

  3. Global Arrays Parallel Programming Toolkit

    SciTech Connect

    Nieplocha, Jaroslaw; Krishnan, Manoj Kumar; Palmer, Bruce J.; Tipparaju, Vinod; Harrison, Robert J.; Chavarría-Miranda, Daniel

    2011-01-01

    The two predominant classes of programming models for parallel computing are distributed memory and shared memory. Both shared memory and distributed memory models have advantages and shortcomings. Shared memory model is much easier to use but it ignores data locality/placement. Given the hierarchical nature of the memory subsystems in modern computers this characteristic can have a negative impact on performance and scalability. Careful code restructuring to increase data reuse and replacing fine grain load/stores with block access to shared data can address the problem and yield performance for shared memory that is competitive with message-passing. However, this performance comes at the cost of compromising the ease of use that the shared memory model advertises. Distributed memory models, such as message-passing or one-sided communication, offer performance and scalability but they are difficult to program. The Global Arrays toolkit attempts to offer the best features of both models. It implements a shared-memory programming model in which data locality is managed by the programmer. This management is achieved by calls to functions that transfer data between a global address space (a distributed array) and local storage. In this respect, the GA model has similarities to the distributed shared-memory models that provide an explicit acquire/release protocol. However, the GA model acknowledges that remote data is slower to access than local data and allows data locality to be specified by the programmer and hence managed. GA is related to the global address space languages such as UPC, Titanium, and, to a lesser extent, Co-Array Fortran. In addition, by providing a set of data-parallel operations, GA is also related to data-parallel languages such as HPF, ZPL, and Data Parallel C. However, the Global Array programming model is implemented as a library that works with most languages used for technical computing and does not rely on compiler technology for achieving

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

    PubMed Central

    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

    Background 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. Methods 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. Results 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. Conclusions Use of the Health Literacy Universal Precautions Toolkit can help to identify drug therapy problems. PMID:26769873

  5. Incorporating Health Information Technology and Pharmacy Informatics in a Pharmacy Professional Didactic Curriculum -with a Team-based Learning Approach.

    PubMed

    Hincapie, Ana L; Cutler, Timothy W; Fingado, Amanda R

    2016-08-25

    Objective. To incorporate a pharmacy informatics program in the didactic curriculum of a team-based learning institution and to assess students' knowledge of and confidence with health informatics during the course. Design. A previously developed online pharmacy informatics course was adapted and implemented into a team-based learning (TBL) 3-credit-hour drug information course for doctor of pharmacy (PharmD) students in their second didactic year. During a period of five weeks (15 contact hours), students used the online pharmacy informatics modules as part of their readiness assurance process. Additional material was developed to comply with the TBL principles. Online pre/postsurveys were administered to evaluate knowledge gained and students' perceptions of the informatics program. Assessment. Eighty-three second-year students (84% response rate) completed the surveys. Participants' knowledge of electronic health records, computerized physician order entry, pharmacy information systems, and clinical decision support was significantly improved. Additionally, their confidence significantly improved in terms of describing health informatics terminology, describing the benefits and barriers of using health information technology, and understanding reasons for systematically processing health information. Conclusion. Students responded favorably to the incorporation of pharmacy informatics content into a drug information course using a TBL approach. Students met the learning objectives of seven thematic areas and had positive attitudes toward the course after its completion.

  6. Incorporating Health Information Technology and Pharmacy Informatics in a Pharmacy Professional Didactic Curriculum -with a Team-based Learning Approach

    PubMed Central

    Cutler, Timothy W.; Fingado, Amanda R.

    2016-01-01

    Objective. To incorporate a pharmacy informatics program in the didactic curriculum of a team-based learning institution and to assess students’ knowledge of and confidence with health informatics during the course. Design. A previously developed online pharmacy informatics course was adapted and implemented into a team-based learning (TBL) 3-credit-hour drug information course for doctor of pharmacy (PharmD) students in their second didactic year. During a period of five weeks (15 contact hours), students used the online pharmacy informatics modules as part of their readiness assurance process. Additional material was developed to comply with the TBL principles. Online pre/postsurveys were administered to evaluate knowledge gained and students’ perceptions of the informatics program. Assessment. Eighty-three second-year students (84% response rate) completed the surveys. Participants’ knowledge of electronic health records, computerized physician order entry, pharmacy information systems, and clinical decision support was significantly improved. Additionally, their confidence significantly improved in terms of describing health informatics terminology, describing the benefits and barriers of using health information technology, and understanding reasons for systematically processing health information. Conclusion. Students responded favorably to the incorporation of pharmacy informatics content into a drug information course using a TBL approach. Students met the learning objectives of seven thematic areas and had positive attitudes toward the course after its completion. PMID:27667844

  7. Informatics and Media Education--Designing a Curriculum for Media Education in Teacher Training with Regard to Basic Areas of Informatics.

    ERIC Educational Resources Information Center

    Magenheim, Johannes; Schulte, Carsten; Scheel, Olaf

    The Didactics of Informatics research group at the University of Paderborn (Germany) is involved in efforts to design, implement and evaluate a curriculum for Media education for prospective teachers at the secondary school level. One major issue is the question of whether it is necessary for future teachers to learn the basic concepts of…

  8. Digital Libraries and Recent Medical Informatics Research. Findings from the IMIA Yearbook of Medical Informatics 2001.

    PubMed

    Ammenwerth, E; Knaup, P; Maier, C; Mludek, V; Singer, R; Skonetzki, S; Wolff, A C; Haux, R; Kulikowski, C

    2001-05-01

    The Yearbook of Medical Informatics is published annually by the International Medical Informatics Association (IMIA) and contains a selection of recent excellent papers on medical informatics research (http://www.med.uni-heidelberg.de/mi/yearbook/index.htm). The special topic of the just published Yearbook 2001 is "Digital Libraries and Medicine". Digital libraries have changed dramatically and will continue to change the way we work with medical knowledge. The selected papers present recent research and new results on digital libraries. As usual, the Yearbook 2001 also contains a variety of papers on other subjects relevant to medical informatics, such as Electronic Patient Records, Health Information Systems, Health and Clinical Management, Decision Support Systems, Education, as well as Image and Signal Processing. This paper will briefly introduce the contributions covering digital libraries and will show how medical informatics research contributes to this important topic.

  9. An informatics agenda for public health: summarized recommendations from the 2011 AMIA PHI Conference.

    PubMed

    Massoudi, Barbara L; Goodman, Kenneth W; Gotham, Ivan J; Holmes, John H; Lang, Lisa; Miner, Kathleen; Potenziani, David D; Richards, Janise; Turner, Anne M; Fu, Paul C

    2012-01-01

    The AMIA Public Health Informatics 2011 Conference brought together members of the public health and health informatics communities to revisit the national agenda developed at the AMIA Spring Congress in 2001, assess the progress that has been made in the past decade, and develop recommendations to further guide the field. Participants met in five discussion tracks: technical framework; research and evaluation; ethics; education, professional training, and workforce development; and sustainability. Participants identified 62 recommendations, which clustered into three key themes related to the need to (1) enhance communication and information sharing within the public health informatics community, (2) improve the consistency of public health informatics through common public health terminologies, rigorous evaluation methodologies, and competency-based training, and (3) promote effective coordination and leadership that will champion and drive the field forward. The agenda and recommendations from the meeting will be disseminated and discussed throughout the public health and informatics communities. Both communities stand to gain much by working together to use these recommendations to further advance the application of information technology to improve health.

  10. X-Informatics: Practical Semantic Science

    NASA Astrophysics Data System (ADS)

    Borne, K. D.

    2009-12-01

    The discipline of data science is merging with multiple science disciplines to form new X-informatics research disciplines. They are almost too numerous to name, but they include geoinformatics, bioinformatics, cheminformatics, biodiversity informatics, ecoinformatics, materials informatics, and the emerging discipline of astroinformatics. Within any X-informatics discipline, the information granules are unique to that discipline -- e.g., gene sequences in bio, the sky object in astro, and the spatial object in geo (such as points, lines, and polygons in the vector model, and pixels in the raster model). Nevertheless the goals are similar: transparent data re-use across subdisciplines and within education settings, information and data integration and fusion, personalization of user interactions with the data collection, semantic search and retrieval, and knowledge discovery. The implementation of an X-informatics framework enables these semantic e-science research goals. We describe the concepts, challenges, and new developments associated with the new discipline of astroinformatics, and how geoinformatics provides valuable lessons learned and a model for practical semantic science within a traditional science discipline through the accretion of data science methodologies (such as formal metadata creation, data models, data mining, information retrieval, knowledge engineering, provenance, taxonomies, and ontologies). The emerging concept of data-as-a-service (DaaS) builds upon the concept of smart data (or data DNA) for intelligent data management, automated workflows, and intelligent processing. Smart data, defined through X-informatics, enables several practical semantic science use cases, including self-discovery, data intelligence, automatic recommendations, relevance analysis, dimension reduction, feature selection, constraint-based mining, interdisciplinary data re-use, knowledge-sharing, data use in education, and more. We describe these concepts within the

  11. Design, implementation and operation of a multimodality research imaging informatics repository

    PubMed Central

    2015-01-01

    Background Biomedical imaging research increasingly involves acquiring, managing and processing large amounts of distributed imaging data. Integrated systems that combine data, meta-data and workflows are crucial for realising the opportunities presented by advances in imaging facilities. Methods This paper describes the design, implementation and operation of a multi-modality research imaging data management system that manages imaging data obtained from biomedical imaging scanners operated at Monash Biomedical Imaging (MBI), Monash University in Melbourne, Australia. In addition to Digital Imaging and Communications in Medicine (DICOM) images, raw data and non-DICOM biomedical data can be archived and distributed by the system. Imaging data are annotated with meta-data according to a study-centric data model and, therefore, scientific users can find, download and process data easily. Results The research imaging data management system ensures long-term usability, integrity inter-operability and integration of large imaging data. Research users can securely browse and download stored images and data, and upload processed data via subject-oriented informatics frameworks including the Distributed and Reflective Informatics System (DaRIS), and the Extensible Neuroimaging Archive Toolkit (XNAT). PMID:25870760

  12. svmPRAT: SVM-based Protein Residue Annotation Toolkit

    PubMed Central

    2009-01-01

    Background Over the last decade several prediction methods have been developed for determining the structural and functional properties of individual protein residues using sequence and sequence-derived information. Most of these methods are based on support vector machines as they provide accurate and generalizable prediction models. Results We present a general purpose protein residue annotation toolkit (svmPRAT) to allow biologists to formulate residue-wise prediction problems. svmPRAT formulates the annotation problem as a classification or regression problem using support vector machines. One of the key features of svmPRAT is its ease of use in incorporating any user-provided information in the form of feature matrices. For every residue svmPRAT captures local information around the reside to create fixed length feature vectors. svmPRAT implements accurate and fast kernel functions, and also introduces a flexible window-based encoding scheme that accurately captures signals and pattern for training effective predictive models. Conclusions In this work we evaluate svmPRAT on several classification and regression problems including disorder prediction, residue-wise contact order estimation, DNA-binding site prediction, and local structure alphabet prediction. svmPRAT has also been used for the development of state-of-the-art transmembrane helix prediction method called TOPTMH, and secondary structure prediction method called YASSPP. This toolkit developed provides practitioners an efficient and easy-to-use tool for a wide variety of annotation problems. Availability: http://www.cs.gmu.edu/~mlbio/svmprat PMID:20028521

  13. 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.

  14. Biomedical informatics training at Stanford in the 21st century.

    PubMed

    Altman, Russ B; Klein, Teri E

    2007-02-01

    The Stanford Biomedical Informatics training program began with a focus on clinical informatics, and has now evolved into a general program of biomedical informatics training, including clinical informatics, bioinformatics and imaging informatics. The program offers PhD, MS, distance MS, certificate programs, and is now affiliated with an undergraduate major in biomedical computation. Current dynamics include (1) increased activity in informatics within other training programs in biology and the information sciences (2) increased desire among informatics students to gain laboratory experience, (3) increased demand for computational collaboration among biomedical researchers, and (4) interaction with the newly formed Department of Bioengineering at Stanford University. The core focus on research training-the development and application of novel informatics methods for biomedical research-keeps the program centered in the midst of this period of growth and diversification.

  15. A toolkit for detecting technical surprise.

    SciTech Connect

    Trahan, Michael Wayne; Foehse, Mark C.

    2010-10-01

    The detection of a scientific or technological surprise within a secretive country or institute is very difficult. The ability to detect such surprises would allow analysts to identify the capabilities that could be a military or economic threat to national security. Sandia's current approach utilizing ThreatView has been successful in revealing potential technological surprises. However, as data sets become larger, it becomes critical to use algorithms as filters along with the visualization environments. Our two-year LDRD had two primary goals. First, we developed a tool, a Self-Organizing Map (SOM), to extend ThreatView and improve our understanding of the issues involved in working with textual data sets. Second, we developed a toolkit for detecting indicators of technical surprise in textual data sets. Our toolkit has been successfully used to perform technology assessments for the Science & Technology Intelligence (S&TI) program.

  16. The Interactive Learning Toolkit: supporting interactive classrooms

    NASA Astrophysics Data System (ADS)

    Dutta, S.; McCauley, V.; Mazur, E.

    2004-05-01

    Research-based interactive learning techniques have dramatically improved student understanding. We have created the 'Interactive Learning Toolkit' (ILT), a web-based learning management system, to help implement two such pedagogies: Just in Time Teaching and Peer Instruction. Our main goal in developing this toolkit is to save the instructor time and effort and to use technology to facilitate the interaction between the students and the instructor (and between students themselves). After a brief review of both pedagogies, we will demonstrate the many exciting new features of the ILT. We will show how technology can not only implement, but also supplement and improve these pedagogies. We would like acknowdge grants from NSF and DEAS, Harvard University

  17. 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.

  18. [Medical informatics--today and tomorrow].

    PubMed

    Dezelić, Gjuro

    2007-09-01

    The status of medical informatics, a comparatively new biomedical discipline beginning to develop in the second half of the 20th century, is described at the transition into the 21st century. The appearance of new information and communication technologies, among which Internet nas special importance, was a major impulse to the development of medical informatics in its different fields. Health information systems are integrating, while at the same time, by distribution of their parts, they become available to the individual healthcare user. These processes put the problems of interoperability and standardization into the focus of contemporary medical informatics. The electronic health record is recognized as a key instrument of modern healthcare systems, and its development and implementation are being planned at many places. Whereas the research and application of medical decision support systems are stagnating, new disciplines have emerged such as telemedicine, cybermedicine and bioinformatics. The perspectives of the future development of medical informatics are described. In the appendix, a chronology of the development of medical informatics from its beginning to the present time is given.

  19. Medical Informatics Education & Research in Greece

    PubMed Central

    Chouvarda, I.

    2015-01-01

    Summary Objectives This paper aims to present an overview of the medical informatics landscape in Greece, to describe the Greek ehealth background and to highlight the main education and research axes in medical informatics, along with activities, achievements and pitfalls. Methods With respect to research and education, formal and informal sources were investigated and information was collected and presented in a qualitative manner, including also quantitative indicators when possible. Results Greece has adopted and applied medical informatics education in various ways, including undergraduate courses in health sciences schools as well as multidisciplinary postgraduate courses. There is a continuous research effort, and large participation in EU-wide initiatives, in all the spectrum of medical informatics research, with notable scientific contributions, although technology maturation is not without barriers. Wide-scale deployment of eHealth is anticipated in the healthcare system in the near future. While ePrescription deployment has been an important step, ICT for integrated care and telehealth have a lot of room for further deployment. Conclusions Greece is a valuable contributor in the European medical informatics arena, and has the potential to offer more as long as the barriers of research and innovation fragmentation are addressed and alleviated. PMID:26123910

  20. Chapter 17: bioimage informatics for systems pharmacology.

    PubMed

    Li, Fuhai; Yin, Zheng; Jin, Guangxu; Zhao, Hong; Wong, Stephen T C

    2013-04-01

    Recent advances in automated high-resolution fluorescence microscopy and robotic handling have made the systematic and cost effective study of diverse morphological changes within a large population of cells possible under a variety of perturbations, e.g., drugs, compounds, metal catalysts, RNA interference (RNAi). Cell population-based studies deviate from conventional microscopy studies on a few cells, and could provide stronger statistical power for drawing experimental observations and conclusions. However, it is challenging to manually extract and quantify phenotypic changes from the large amounts of complex image data generated. Thus, bioimage informatics approaches are needed to rapidly and objectively quantify and analyze the image data. This paper provides an overview of the bioimage informatics challenges and approaches in image-based studies for drug and target discovery. The concepts and capabilities of image-based screening are first illustrated by a few practical examples investigating different kinds of phenotypic changes caEditorsused by drugs, compounds, or RNAi. The bioimage analysis approaches, including object detection, segmentation, and tracking, are then described. Subsequently, the quantitative features, phenotype identification, and multidimensional profile analysis for profiling the effects of drugs and targets are summarized. Moreover, a number of publicly available software packages for bioimage informatics are listed for further reference. It is expected that this review will help readers, including those without bioimage informatics expertise, understand the capabilities, approaches, and tools of bioimage informatics and apply them to advance their own studies.

  1. HVAC Fault Detection and Diagnosis Toolkit

    SciTech Connect

    Haves, Philip; Xu, Peng; Kim, Moosung

    2004-12-31

    This toolkit supports component-level model-based fault detection methods in commercial building HVAC systems. The toolbox consists of five basic modules: a parameter estimator for model calibration, a preprocessor, an AHU model simulator, a steady-state detector, and a comparator. Each of these modules and the fuzzy logic rules for fault diagnosis are described in detail. The toolbox is written in C++ and also invokes the SPARK simulation program.

  2. The Bio* toolkits--a brief overview.

    PubMed

    Mangalam, Harry

    2002-09-01

    Bioinformatics research is often difficult to do with commercial software. The Open Source BioPerl, BioPython and Biojava projects provide toolkits with multiple functionality that make it easier to create customised pipelines or analysis. This review briefly compares the quirks of the underlying languages and the functionality, documentation, utility and relative advantages of the Bio counterparts, particularly from the point of view of the beginning biologist programmer.

  3. SIERRA Toolkit v. 2.0

    SciTech Connect

    Coffey, Todd; Williams, Alan; Bhardwaj, Manoj; Galze, David; Okusanya, Tolulope; Roehrig, Nathaniel; Wilson, Christopher; Crane, Nathan; Xavier, Patrick

    2016-09-14

    The SIERRA Toolkit is a collection of libraries to facilitate the development of parallel engineering analysis applications. These libraries supply basic core services that an engineering application may need such as a parallel distributed and dynamic mesh database (for unstructured meshes), mechanics algorithm support (parallel infrastructure only), interfaces to parallel solvers, parallel mesh and data I/O, and various utilities (timers, diagnostic tools, etc.)

  4. 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.; Attiyah, Ahlam A.

    2009-01-01

    MONTE (Mission Operations and Navigation Toolkit Environment) Release 7.3 is an extensible software system designed to support trajectory and navigation analysis/design for space missions. MONTE is intended to replace the current navigation and trajectory analysis software systems, which, at the time of this reporting, are used by JPL's Navigation and Mission Design section. The software provides an integrated, simplified, and flexible system that can be easily maintained to serve the needs of future missions in need of navigation services.

  5. Application experiences with the Globus toolkit.

    SciTech Connect

    Brunett, S.

    1998-06-09

    The Globus grid toolkit is a collection of software components designed to support the development of applications for high-performance distributed computing environments, or ''computational grids'' [14]. The Globus toolkit is an implementation of a ''bag of services'' architecture, which provides application and tool developers not with a monolithic system but rather with a set of stand-alone services. Each Globus component provides a basic service, such as authentication, resource allocation, information, communication, fault detection, and remote data access. Different applications and tools can combine these services in different ways to construct ''grid-enabled'' systems. The Globus toolkit has been used to construct the Globus Ubiquitous Supercomputing Testbed, or GUSTO: a large-scale testbed spanning 20 sites and included over 4000 compute nodes for a total compute power of over 2 TFLOPS. Over the past six months, we and others have used this testbed to conduct a variety of application experiments, including multi-user collaborative environments (tele-immersion), computational steering, distributed supercomputing, and high throughput computing. The goal of this paper is to review what has been learned from these experiments regarding the effectiveness of the toolkit approach. To this end, we describe two of the application experiments in detail, noting what worked well and what worked less well. The two applications are a distributed supercomputing application, SF-Express, in which multiple supercomputers are harnessed to perform large distributed interactive simulations; and a tele-immersion application, CAVERNsoft, in which the focus is on connecting multiple people to a distributed simulated world.

  6. Tactical Level Commander and Staff Toolkit

    DTIC Science & Technology

    2010-01-01

    communications may require such a determination to be made on the spot , by the chaplain, based on the information available at the time. 4. The support...injuries, other medical symptoms may include: • Fever • Difficulty breathing • Persistent cough • Confusion DSCA Handbook Tactical Level...with a fever and shaking chills should seek immediate medical attention. DSCA Handbook Tactical Level Commander and Staff Toolkit 5-60

  7. Health Informatics and E-health Curriculum for Clinical Health Profession Degrees.

    PubMed

    Gray, Kathleen; Choo, Dawn; Butler-Henderson, Kerryn; Whetton, Sue; Maeder, Anthony

    2015-01-01

    The project reported in this paper models a new approach to making health informatics and e-health education widely available to students in a range of Australian clinical health profession degrees. The development of a Masters level subject uses design-based research to apply educational quality assurance practices which are consistent with university qualification frameworks, and with clinical health profession education standards; at the same time it gives recognition to health informatics as a specialised profession in its own right. The paper presents details of (a) design with reference to the Australian Qualifications Framework and CHIA competencies, (b) peer review within a three-university teaching team, (c) external review by experts from the professions, (d) cross-institutional interprofessional online learning, (e) methods for evaluating student learning experiences and outcomes, and (f) mechanisms for making the curriculum openly available to interested parties. The project has sought and found demand among clinical health professionals for formal health informatics and e-health education that is designed for them. It has helped the educators and organisations involved to understand the need for nuanced and complementary health informatics educational offerings in Australian universities. These insights may aid in further efforts to address substantive and systemic challenges that clinical informatics faces in Australia.

  8. A Racial Equity Toolkit for Midwifery Organizations.

    PubMed

    Gordon, Wendy M

    2016-11-01

    Midwifery associations are increasing awareness and commitment to racial equity in the profession and in the communities we serve. Moving these commitments from words into action may be facilitated by a racial equity toolkit to help guide midwifery organizations to consider all policies, initiatives, and actions with a racial equity lens. Racial equity impact analyses have been used in recent years by various governmental agencies in the United States and abroad with positive results, and emerging literature indicates that nonprofit organizations are having similarly positive results. This article proposes a framework for midwifery organizations to incorporate a racial equity toolkit, starting with explicit intentions of the organization with regard to racial equity in the profession. Indicators of success are elucidated as the next step, followed by the use of a racial equity impact analysis worksheet. This worksheet is applied by teams or committees when considering new policies or initiatives to examine those actions through a racial equity lens. An organizational change team and equity advisory groups are essential in assisting organizational leadership to forecast potential negative and positive impacts. Examples of the components of a midwifery-specific racial equity toolkit are included.

  9. An analytical toolkit for polyploid willow discrimination

    PubMed Central

    Guo, Wei; Hou, Jing; Yin, Tongming; Chen, Yingnan

    2016-01-01

    Polyploid breeding is an important means for creating elite willow cultivars, and therefore provokes an active demand for discriminating the ploidy levels of natural willow stands. In this study, we established an analytical toolkit for polyploid willow identification by combining molecular markers and flow cytometry (FCM). A total of 10 single-copy fully informative SSRs were chosen for marker-aided selection based on a segregation test with a full-sib willow pedigree and a mutability test with a collection of natural willow stands. Aided by these molecular markers, we performed polyploid selection in two tree species and two shrub species of the genus Salix. The ploidy levels of the investigated samples were further examined using a flow cytometer. It was previously shown that results from marker-aided selection were consistent with those from FCM measurements. Based on ploidy level assessment in different willow species, it was found that tree willows were dominantly tetraploid, whereas shrub willows were most frequently diploid. With this analytical toolkit, polyploids can be rapidly screened from a large number of natural stands; thereafter, the exact ploidy levels of the polyploid candidates can be efficiently confirmed by FCM. This analytical toolkit will greatly enhance polyploid breeding programs for willows. PMID:27934953

  10. Stormwater BMP Effectiveness Assessment Toolkit

    EPA Science Inventory

    US EPA has identified stormwater BMP effectiveness as a priority research need. Effective protection of biotic integrity requires that processes maintaining the diversity of physical habitats be protected. Methods are needed to evaluate the effectiveness of existing Stormwater ...

  11. IPHIE: an International Partnership in Health Informatics Education.

    PubMed

    Jaspers, M W; Gardner, R M; Gatewood, L C; Haux, R; Leven, F J; Limburg, M; Ravesloot, J H; Schmidt, D; Wetter, T

    2000-01-01

    Medical informatics contributes significantly to high quality and efficient health care and medical research. The need for well educated professionals in the field of medical informatics therefore is now worldwide recognized. Students of medicine, computer science/informatics are educated in the field of medical informatics and dedicated curricula on medical informatics have emerged. To advance and further develop the beneficial role of medical informatics in the medical field, an international orientation of health and medical informatics students seems an indispensable part of their training. An international orientation and education of medical informatics students may help to accelerate the dissemination of acquired knowledge and skills in the field and the promotion of medical informatics research results on a more global level. Some years ago, the departments of medical informatics of the university of Heidelberg/university of applied sciences Heilbronn and the university of Amsterdam decided to co-operate in the field of medical informatics. Now, this co-operation has grown out to an International Partnership of Health Informatics Education (IPHIE) of 5 universities, i.e. the university of Heidelberg, the university of Heilbronn, the university of Minnesota, the university of Utah and the university of Amsterdam. This paper presents the rationale behind this international partnership, the state of the art of the co-operation and our future plans for expanding this international co-operation.

  12. Core content for the subspecialty of clinical informatics.

    PubMed

    Gardner, Reed M; Overhage, J Marc; Steen, Elaine B; Munger, Benson S; Holmes, John H; Williamson, Jeffrey J; Detmer, Don E

    2009-01-01

    The Core Content for Clinical Informatics defines the boundaries of the discipline and informs the Program Requirements for Fellowship Education in Clinical Informatics. The Core Content includes four major categories: fundamentals, clinical decision making and care process improvement, health information systems, and leadership and management of change. The AMIA Board of Directors approved the Core Content for Clinical Informatics in November 2008.

  13. Health informatics: moving from a discipline to a science.

    PubMed

    Turley, James P

    2009-01-01

    This paper examines the historical definitions of Health (Biomedical) Informatics. It is clear that a majority of the definitions refer to Health Informatics as a discipline. Rather it can be argued that the maturation of Health Informatics is beginning to culminate in a distinct science. This progress need to be reflected in academic programs as well as our conferences and publications.

  14. Image informatics in systems biology applications

    NASA Astrophysics Data System (ADS)

    Wong, Stephen T. C.

    2005-02-01

    Digital optical microscopy, coupled with parallel processing and a large arsenal of labeling techniques, offers tremendous values to localize, identify, and characterize cells and molecules. This generates many image informatics challenges in requiring new algorithms and tools to extract, classify, correlate, and model image features and content from massive amounts of cellular and molecular images acquired. Image informatics aims to fill this gap. Coupling automated microscopy and image analysis with biostatistical and data mining techniques to provide a system biologic approach in studying the cells, the basic unit of life, potentially leads to many exciting applications in life and health sciences. In this presentation, we describe certain new system biology applications enabled by image informatics technology.

  15. NASA Biomedical Informatics Capabilities and Needs

    NASA Technical Reports Server (NTRS)

    Johnson-Throop, Kathy A.

    2009-01-01

    To improve on-orbit clinical capabilities by developing and providing operational support for intelligent, robust, reliable, and secure, enterprise-wide and comprehensive health care and biomedical informatics systems with increasing levels of autonomy, for use on Earth, low Earth orbit & exploration class missions. Biomedical Informatics is an emerging discipline that has been defined as the study, invention, and implementation of structures and algorithms to improve communication, understanding and management of medical information. The end objective of biomedical informatics is the coalescing of data, knowledge, and the tools necessary to apply that data and knowledge in the decision-making process, at the time and place that a decision needs to be made.

  16. Earth Science Informatics Comes of Age

    NASA Technical Reports Server (NTRS)

    Jodha, Siri; Khalsa, S.; Ramachandran, Rahul

    2014-01-01

    The volume and complexity of Earth science data have steadily increased, placing ever-greater demands on researchers, software developers and data managers tasked with handling such data. Additional demands arise from requirements being levied by funding agencies and governments to better manage, preserve and provide open access to data. Fortunately, over the past 10-15 years significant advances in information technology, such as increased processing power, advanced programming languages, more sophisticated and practical standards, and near-ubiquitous internet access have made the jobs of those acquiring, processing, distributing and archiving data easier. These advances have also led to an increasing number of individuals entering the field of informatics as it applies to Geoscience and Remote Sensing. Informatics is the science and technology of applying computers and computational methods to the systematic analysis, management, interchange, and representation of data, information, and knowledge. Informatics also encompasses the use of computers and computational methods to support decisionmaking and other applications for societal benefits.

  17. Capturing Petascale Application Characteristics with the Sequoia Toolkit

    SciTech Connect

    Vetter, Jeffrey S; Bhatia, Nikhil; Grobelny, Eric M; Roth, Philip C

    2005-09-01

    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 molecular dynamics application of great interest to the computational biology community.

  18. Nursing Informatics Research Priorities for the Future: Recommendations from an International Survey.

    PubMed

    Peltonen, Laura-Maria; Topaz, Maxim; Ronquillo, Charlene; Pruinelli, Lisiane; Sarmiento, Raymond Francis; Badger, Martha K; Ali, Samira; Lewis, Adrienne; Georgsson, Mattias; Jeon, Eunjoo; Tayaben, Jude L; Kuo, Chiu-Hsiang; Islam, Tasneem; Sommer, Janine; Jung, Hyunggu; Eler, Gabrielle Jacklin; Alhuwail, Dari

    2016-01-01

    We present one part of the results of an international survey exploring current and future nursing informatics (NI) research trends. The study was conducted by the International Medical Informatics Association Nursing Informatics Special Interest Group (IMIA-NISIG) Student Working Group. Based on findings from this cross-sectional study, we identified future NI research priorities. We used snowball sampling technique to reach respondents from academia and practice. Data were collected between August and September 2015. Altogether, 373 responses from 44 countries were analyzed. The identified top ten NI trends were big data science, standardized terminologies (clinical evaluation/implementation), education and competencies, clinical decision support, mobile health, usability, patient safety, data exchange and interoperability, patient engagement, and clinical quality measures. Acknowledging these research priorities can enhance successful future development of NI to better support clinicians and promote health internationally.

  19. Design of a Community-Engaged Health Informatics Platform with an Architecture of Participation.

    PubMed

    Millery, Mari; Ramos, Wilson; Lien, Chueh; Aguirre, Alejandra N; Kukafka, Rita

    2015-01-01

    Community-engaged health informatics (CEHI) applies information technology and participatory approaches to improve the health of communities. Our objective was to translate the concept of CEHI into a usable and replicable informatics platform that will facilitate community-engaged practice and research. The setting is a diverse urban neighborhood in New York City. The methods included community asset mapping, stakeholder interviews, logic modeling, analysis of affordances in open-source tools, elicitation of use cases and requirements, and a survey of early adopters. Based on synthesis of data collected, GetHealthyHeigths.org (GHH) was developed using open-source LAMP stack and Drupal content management software. Drupal's organic groups module was used for novel participatory functionality, along with detailed user roles and permissions. Future work includes evaluation of GHH and its impact on agency and service networks. We plan to expand GHH with additional functionality to further support CEHI by combining informatics solutions with community engagement to improve health.

  20. Use of bio-informatics assessment schema (BIAS) to improve diagnosis and prognosis of myocardial perfusion data: results from the NHLBI-sponsored women’s ischemia syndrome evaluation (WISE)

    PubMed Central

    Pohost, Gerald M.; Bairey Merz, C. Noel; Shaw, Leslee J.; Sopko, George; Rogers, William J.; Sharaf, Barry L.; Pepine, Carl J.; Thompson, Diane V.; Rayarao, Geetha; Tauxe, Lindsey; Kelsey, Sheryl F.; Biederman, Robert W. W.

    2016-01-01

    Background We introduce an algorithmic approach to optimize diagnostic and prognostic value of gated cardiac single photon emission computed tomography (SPECT) and magnetic resonance (MR) myocardial perfusion imaging (MPI) modalities in women with suspected myocardial ischemia. The novel approach: bio-informatics assessment schema (BIAS) forms a mathematical model utilizing MPI data and cardiac metrics generated by one modality to predict the MPI status of another modality. The model identifies cardiac features that either enhance or mask the image-based evidence of ischemia. For each patient, the BIAS model value is used to set an appropriate threshold for the detection of ischemia. Methods Women (n=130), with symptoms and signs of suspected myocardial ischemia, underwent MPI assessment for regional perfusion defects using two different modalities: gated SPECT and MR. To determine perfusion status, MR data were evaluated qualitatively (MRIQL) and semi-quantitatively (MRISQ) while SPECT data were evaluated using conventional clinical criteria. Evaluators were masked to results of the alternate modality. These MPI status readings were designated “original”. Two regression models designated “BIAS” models were generated to model MPI status obtained with one modality (e.g., MRI) compared with a second modality (e.g., SPECT), but importantly, the BIAS models did not include the primary Original MPI reading of the predicting modality. Instead, the BIAS models included auxiliary measurements like left ventricular chamber volumes and myocardial wall thickness. For each modality, the BIAS model was used to set a progressive threshold for interpretation of MPI status. Women were then followed for 38±14 months for the development of a first major adverse cardiovascular event [MACE: CV death, nonfatal myocardial infarction (MI) or hospitalization for heart failure]. Original and BIAS-augmented perfusion status were compared in their ability to detect coronary artery

  1. Informatics approaches to understanding TGFβ pathway regulation

    PubMed Central

    Kahlem, Pascal; Newfeld, Stuart J.

    2009-01-01

    Summary In recent years, informatics studies have predicted several new ways in which the transforming growth factor β (TGFβ) signaling pathway can be post-translationally regulated. Subsequently, many of these predictions were experimentally validated. These approaches include phylogenetic predictions for the phosphorylation, sumoylation and ubiquitylation of pathway components, as well as kinetic models of endocytosis, phosphorylation and nucleo-cytoplasmic shuttling. We review these studies and provide a brief `how to' guide for phylogenetics. Our hope is to stimulate experimental tests of informatics-based predictions for TGFβ signaling, as well as for other signaling pathways, and to expand the number of developmental pathways that are being analyzed computationally. PMID:19855015

  2. The Informatics Opportunities at the Intersection of Patient Safety and Clinical Informatics

    PubMed Central

    Kilbridge, Peter M.; Classen, David C.

    2008-01-01

    Health care providers have a basic responsibility to protect patients from accidental harm. At the institutional level, creating safe health care organizations necessitates a systematic approach. Effective use of informatics to enhance safety requires the establishment and use of standards for concept definitions and for data exchange, development of acceptable models for knowledge representation, incentives for adoption of electronic health records, support for adverse event detection and reporting, and greater investment in research at the intersection of informatics and patient safety. Leading organizations have demonstrated that health care informatics approaches can improve safety. Nevertheless, significant obstacles today limit optimal application of health informatics to safety within most provider environments. The authors offer a series of recommendations for addressing these challenges. PMID:18436896

  3. Parametrization of macrolide antibiotics using the force field toolkit.

    PubMed

    Pavlova, Anna; Gumbart, James C

    2015-10-15

    Macrolides are an important class of antibiotics that target the bacterial ribosome. Computer simulations of macrolides are limited as specific force field parameters have not been previously developed for them. Here, we determine CHARMM-compatible force field parameters for erythromycin, azithromycin, and telithromycin, using the force field toolkit (ffTK) plugin in VMD. Because of their large size, novel approaches for parametrizing them had to be developed. Two methods for determining partial atomic charges, from interactions with TIP3P water and from the electrostatic potential, as well as several approaches for fitting the dihedral parameters were tested. The performance of the different parameter sets was evaluated by molecular dynamics simulations of the macrolides in ribosome, with a distinct improvement in maintenance of key interactions observed after refinement of the initial parameters. Based on the results of the macrolide tests, recommended procedures for parametrizing very large molecules using ffTK are given.

  4. Upgrading the safety toolkit: Initiatives of the accident analysis subgroup

    SciTech Connect

    O'Kula, K.R.; Chung, D.Y.

    1999-07-01

    Since its inception, the Accident Analysis Subgroup (AAS) of the Energy Facility Contractors Group (EFCOG) has been a leading organization promoting development and application of appropriate methodologies for safety analysis of US Department of Energy (DOE) installations. The AAS, one of seven chartered by the EFCOG Safety Analysis Working Group, has performed an oversight function and provided direction to several technical groups. These efforts have been instrumental toward formal evaluation of computer models, improving the pedigree on high-use computer models, and development of the user-friendly Accident Analysis Guidebook (AAG). All of these improvements have improved the analytical toolkit for best complying with DOE orders and standards shaping safety analysis reports (SARs) and related documentation. Major support for these objectives has been through DOE/DP-45.

  5. A toolkit for MSDs prevention--WHO and IEA context.

    PubMed

    Caple, David C

    2012-01-01

    Many simple MSD risk management tools have been developed by ergonomists for use by workers and employers with little or no training to undertake injury prevention programs in their workplace. However, currently there is no "toolkit" which places such tools within an holistic, participative ergonomics framework and provides guidance on how best to use individual tools. It is proposed that such an holistic approach should entail initial analysis and evaluation of underlying systems of work and related health and performance indicators, prior to focusing in assessment of MSD risks stemming from particular hazards. Depending on the context, more narrowly focused tools might then be selected to assess risk associated with jobs or tasks identified as problematic. This approach ensures that biomechanical risk factors are considered within a broad context of organizational and psychosocial risk factors. This is consistent with current research evidence on work- related causes of MSDs.

  6. Margins of safety provided by COSHH Essentials and the ILO Chemical Control Toolkit.

    PubMed

    Jones, Rachael M; Nicas, Mark

    2006-03-01

    COSHH Essentials, developed by the UK Health and Safety Executive, and the Chemical Control Toolkit (Toolkit) proposed by the International Labor Organization, are 'control banding' approaches to workplace risk management intended for use by proprietors of small and medium-sized businesses. Both systems group chemical substances into hazard bands based on toxicological endpoint and potency. COSSH Essentials uses the European Union's Risk-phrases (R-phrases), whereas the Toolkit uses R-phrases and the Globally Harmonized System (GHS) of Classification and Labeling of Chemicals. Each hazard band is associated with a range of airborne concentrations, termed exposure bands, which are to be attained by the implementation of recommended control technologies. Here we analyze the margin of safety afforded by the systems and, for each hazard band, define the minimal margin as the ratio of the minimum airborne concentration that produced the toxicological endpoint of interest in experimental animals to the maximum concentration in workplace air permitted by the exposure band. We found that the minimal margins were always <100, with some ranging to <1, and inversely related to molecular weight. The Toolkit-GHS system generally produced margins equal to or larger than COSHH Essentials, suggesting that the Toolkit-GHS system is more protective of worker health. Although, these systems predict exposures comparable with current occupational exposure limits, we argue that the minimal margins are better indicators of health protection. Further, given the small margins observed, we feel it is important that revisions of these systems provide the exposure bands to users, so as to permit evaluation of control technology capture efficiency.

  7. Cognitive informatics in biomedicine and healthcare.

    PubMed

    Patel, Vimla L; Kannampallil, Thomas G

    2015-02-01

    Cognitive Informatics (CI) is a burgeoning interdisciplinary domain comprising of the cognitive and information sciences that focuses on human information processing, mechanisms and processes within the context of computing and computer applications. Based on a review of articles published in the Journal of Biomedical Informatics (JBI) between January 2001 and March 2014, we identified 57 articles that focused on topics related to cognitive informatics. We found that while the acceptance of CI into the mainstream informatics research literature is relatively recent, its impact has been significant - from characterizing the limits of clinician problem-solving and reasoning behavior, to describing coordination and communication patterns of distributed clinical teams, to developing sustainable and cognitively-plausible interventions for supporting clinician activities. Additionally, we found that most research contributions fell under the topics of decision-making, usability and distributed team activities with a focus on studying behavioral and cognitive aspects of clinical personnel, as they performed their activities or interacted with health information systems. We summarize our findings within the context of the current areas of CI research, future research directions and current and future challenges for CI researchers.

  8. Medical informatics and bioinformatics: a bibliometric study

    PubMed Central

    Bansard, Jean-Yves; Rebholz-Schuhman, Dietrich; Cameron, Graham; Clark, Dominic; van Mulligen, Erik; Beltrame, Francesco; Del Hoyo Barbolla, Eva; Martin-Sanchez, Fernando; Milanesi, Luciano; Tollis, Ioannis; Van der Lei, Johan; Coatrieux, Jean-Louis

    2007-01-01

    This paper reports on an analysis of the bioinformatics and medical informatics literature with the objective to identify upcoming trends that are shared among both research fields to derive benefits from potential collaborative initiatives for their future. Our results present the main characteristics of the two fields and show that these domains are still relatively separated. PMID:17521073

  9. Geo-Engineering through Internet Informatics (GEMINI)

    SciTech Connect

    Doveton, John H.; Watney, W. Lynn

    2003-03-06

    The program, for development and methodologies, was a 3-year interdisciplinary effort to develop an interactive, integrated Internet Website named GEMINI (Geo-Engineering Modeling through Internet Informatics) that would build real-time geo-engineering reservoir models for the Internet using the latest technology in Web applications.

  10. Informatics and Standards for Nanomedicine Technology

    PubMed Central

    Thomas, Dennis G.; Klaessig, Fred; Harper, Stacey L.; Fritts, Martin; Hoover, Mark D.; Gaheen, Sharon; Stokes, Todd H.; Reznik-Zellen, Rebecca; Freund, Elaine T.; Klemm, Juli D.; Paik, David S.; Baker, Nathan A.

    2011-01-01

    There are several issues to be addressed concerning the management and effective use of information (or data), generated from nanotechnology studies in biomedical research and medicine. These data are large in volume, diverse in content, and are beset with gaps and ambiguities in the description and characterization of nanomaterials. In this work, we have reviewed three areas of nanomedicine informatics: information resources; taxonomies, controlled vocabularies, and ontologies; and information standards. Informatics methods and standards in each of these areas are critical for enabling collaboration, data sharing, unambiguous representation and interpretation of data, semantic (meaningful) search and integration of data; and for ensuring data quality, reliability, and reproducibility. In particular, we have considered four types of information standards in this review, which are standard characterization protocols, common terminology standards, minimum information standards, and standard data communication (exchange) formats. Currently, due to gaps and ambiguities in the data, it is also difficult to apply computational methods and machine learning techniques to analyze, interpret and recognize patterns in data that are high dimensional in nature, and also to relate variations in nanomaterial properties to variations in their chemical composition, synthesis, characterization protocols, etc. Progress towards resolving the issues of information management in nanomedicine using informatics methods and standards discussed in this review will be essential to the rapidly growing field of nanomedicine informatics. PMID:21721140

  11. Pharmacy informatics in controlled substances research.

    PubMed

    Lin, Jia-Ling; Vahabzadeh, Massoud; Mezghanni, Mustapha; Na, Paul J; Leff, Michelle; Contoreggi, Carlo

    2008-11-06

    Pharmacies have become essential components in support of clinical research. Their operations become highly complex when preponderance of prescriptions is composed of controlled substances. Application of informatics will result in more efficient operations. We present the Pharmacy Information Management System (PIMS) that includes a set of decision support systems to address the pharmacy challenges and is integrated into our electronic health record system.

  12. Optimizing Clinical Research Participant Selection with Informatics.

    PubMed

    Weng, Chunhua

    2015-11-01

    Clinical research participants are often not reflective of real-world patients due to overly restrictive eligibility criteria. Meanwhile, unselected participants introduce confounding factors and reduce research efficiency. Biomedical informatics, especially Big Data increasingly made available from electronic health records, offers promising aids to optimize research participant selection through data-driven transparency.

  13. Medical informatics and telemedicine: A vision

    NASA Technical Reports Server (NTRS)

    Clemmer, Terry P.

    1991-01-01

    The goal of medical informatics is to improve care. This requires the commitment and harmonious collaboration between the computer scientists and clinicians and an integrated database. The vision described is how medical information systems are going to impact the way medical care is delivered in the future.

  14. Disease model curation improvements at Mouse Genome Informatics

    PubMed Central

    Bello, Susan M.; Richardson, Joel E.; Davis, Allan P.; Wiegers, Thomas C.; Mattingly, Carolyn J.; Dolan, Mary E.; Smith, Cynthia L.; Blake, Judith A.; Eppig, Janan T.

    2012-01-01

    Optimal curation of human diseases requires an ontology or structured vocabulary that contains terms familiar to end users, is robust enough to support multiple levels of annotation granularity, is limited to disease terms and is stable enough to avoid extensive reannotation following updates. At Mouse Genome Informatics (MGI), we currently use disease terms from Online Mendelian Inheritance in Man (OMIM) to curate mouse models of human disease. While OMIM provides highly detailed disease records that are familiar to many in the medical community, it lacks structure to support multilevel annotation. To improve disease annotation at MGI, we evaluated the merged Medical Subject Headings (MeSH) and OMIM disease vocabulary created by the Comparative Toxicogenomics Database (CTD) project. Overlaying MeSH onto OMIM provides hierarchical access to broad disease terms, a feature missing from the OMIM. We created an extended version of the vocabulary to meet the genetic disease-specific curation needs at MGI. Here we describe our evaluation of the CTD application, the extensions made by MGI and discuss the strengths and weaknesses of this approach. Database URL: http://www.informatics.jax.org/ PMID:22434831

  15. Current Status of Nursing Informatics Education in Korea

    PubMed Central

    Jeon, Eunjoo; Kim, Jeongeun; Lee, Ji-Hyun; Kim, Jungha; Jin, Meiling; Ahn, Shinae; Jun, Jooyeon; Song, Healim; On, Jeongah; Jung, Hyesil; Hong, Yeong Joo; Yim, Suran

    2016-01-01

    Objectives This study presents the current status of nursing informatics education, the content covered in nursing informatics courses, the faculty efficacy, and the barriers to and additional supports for teaching nursing informatics in Korea. Methods A set of questionnaires consisting of an 18-item questionnaire for nursing informatics education, a 6-item questionnaire for faculty efficacy, and 2 open-ended questions for barriers and additional supports were sent to 204 nursing schools via email and the postal service. Nursing schools offering nursing informatics were further asked to send their syllabuses. The subjects taught were analyzed using nursing informatics competency categories and other responses were tailed using descriptive statistics. Results A total of 72 schools (35.3%) responded to the survey, of which 38 reported that they offered nursing informatics courses in their undergraduate nursing programs. Nursing informatics courses at 11 schools were taught by a professor with a degree majoring in nursing informatics. Computer technology was the most frequently taught subject (27 schools), followed by information systems used for practice (25 schools). The faculty efficacy was 3.76 ± 0.86 (out of 5). The most frequently reported barrier to teaching nursing informatics (n = 9) was lack of awareness of the importance of nursing informatics. Training and educational opportunities was the most requested additional support. Conclusions Nursing informatics education has increased during the last decade in Korea. However, the proportions of faculty with degrees in nursing informatics and number of schools offering nursing informatics courses have not increased much. Thus, a greater focus is needed on training faculty and developing the courses. PMID:27200224

  16. Veterinary Immunology Committee Toolkit Workshop 2010: Progress and plans

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  17. 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…

  18. 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…

  19. Livermore Big Artificial Neural Network Toolkit

    SciTech Connect

    Essen, Brian Van; Jacobs, Sam; Kim, Hyojin; Dryden, Nikoli; Moon, Tim

    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.

  20. A flexible genetic toolkit for arthropod neurogenesis

    PubMed Central

    Stollewerk, Angelika

    2016-01-01

    Arthropods show considerable variations in early neurogenesis. This includes the pattern of specification, division and movement of neural precursors and progenitors. In all metazoans with nervous systems, including arthropods, conserved genes regulate neurogenesis, which raises the question of how the various morphological mechanisms have emerged and how the same genetic toolkit might generate different morphological outcomes. Here I address this question by comparing neurogenesis across arthropods and show how variations in the regulation and function of the neural genes might explain this phenomenon and how they might have facilitated the evolution of the diverse morphological mechanisms of neurogenesis. PMID:26598727

  1. An Incident Management Preparedness and Coordination Toolkit

    SciTech Connect

    Koch, Daniel B; Payne, Patricia W

    2012-01-01

    Although the use of Geographic Information Systems (GIS) by centrally-located operations staff is well established in the area of emergency response, utilization by first responders in the field is uneven. Cost, complexity, and connectivity are often the deciding factors preventing wider adoption. For the past several years, Oak Ridge National Laboratory (ORNL) has been developing a mobile GIS solution using free and open-source software targeting the needs of front-line personnel. Termed IMPACT, for Incident Management Preparedness and Coordination Toolkit, this ORNL application can complement existing GIS infrastructure and extend its power and capabilities to responders first on the scene of a natural or man-made disaster.

  2. 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.

  3. ADMIT: The ALMA Data Mining Toolkit

    NASA Astrophysics Data System (ADS)

    Teuben, P.; Pound, M.; Mundy, L.; Rauch, K.; Friedel, D.; Looney, L.; Xu, L.; Kern, J.

    2015-09-01

    ADMIT (ALMA Data Mining ToolkiT), a toolkit for the creation of new science products from ALMA data, is being developed as an ALMA Development Project. It is written in Python and, while specifically targeted for a uniform analysis of the ALMA science products that come out of the ALMA pipeline, it is designed to be generally applicable to (radio) astronomical data. It first provides users with a detailed view of their science products created by ADMIT inside the ALMA pipeline: line identifications, line ‘cutout' cubes, moment maps, emission type analysis (e.g., feature detection). Using descriptor vectors the ALMA data archive is enriched with useful information to make archive data mining possible. Users can also opt to download the (small) ADMIT pipeline product, then fine-tune and re-run the pipeline and inspect their hopefully improved data. By running many projects in a parallel fashion, data mining between many astronomical sources and line transitions will also be possible. Future implementations of ADMIT may include EVLA and other instruments.

  4. The Virtual Physiological Human ToolKit.

    PubMed

    Cooper, Jonathan; Cervenansky, Frederic; De Fabritiis, Gianni; Fenner, John; Friboulet, Denis; Giorgino, Toni; Manos, Steven; Martelli, Yves; Villà-Freixa, Jordi; Zasada, Stefan; Lloyd, Sharon; McCormack, Keith; Coveney, Peter V

    2010-08-28

    The Virtual Physiological Human (VPH) is a major European e-Science initiative intended to support the development of patient-specific computer models and their application in personalized and predictive healthcare. The VPH Network of Excellence (VPH-NoE) project is tasked with facilitating interaction between the various VPH projects and addressing issues of common concern. A key deliverable is the 'VPH ToolKit'--a collection of tools, methodologies and services to support and enable VPH research, integrating and extending existing work across Europe towards greater interoperability and sustainability. Owing to the diverse nature of the field, a single monolithic 'toolkit' is incapable of addressing the needs of the VPH. Rather, the VPH ToolKit should be considered more as a 'toolbox' of relevant technologies, interacting around a common set of standards. The latter apply to the information used by tools, including any data and the VPH models themselves, and also to the naming and categorizing of entities and concepts involved. Furthermore, the technologies and methodologies available need to be widely disseminated, and relevant tools and services easily found by researchers. The VPH-NoE has thus created an online resource for the VPH community to meet this need. It consists of a database of tools, methods and services for VPH research, with a Web front-end. This has facilities for searching the database, for adding or updating entries, and for providing user feedback on entries. Anyone is welcome to contribute.

  5. The Best Ever Alarm System Toolkit

    SciTech Connect

    Kasemir, Kay; Chen, Xihui; Danilova, Katia

    2009-01-01

    Learning from our experience with the standard Experimental Physics and Industrial Control System (EPICS) alarm handler (ALH) as well as a similar intermediate approach based on script-generated operator screens, we developed the Best Ever Alarm System Toolkit (BEAST). It is based on Java and Eclipse on the Control System Studio (CSS) platform, using a relational database (RDB) to store the configuration and log actions. It employs a Java Message Service (JMS) for communication between the modular pieces of the toolkit, which include an Alarm Server to maintain the current alarm state, an arbitrary number of Alarm Client user interfaces (GUI), and tools to annunciate alarms or log alarm related actions. Web reports allow us to monitor the alarm system performance and spot deficiencies in the alarm configuration. The Alarm Client GUI not only gives the end users various ways to view alarms in tree and table, but also makes it easy to access the guidance information, the related operator displays and other CSS tools. It also allows online configuration to be simply modified from the GUI. Coupled with a good "alarm philosophy" on how to provide useful alarms, we can finally improve the configuration to achieve an effective alarm system.

  6. MI-Lab - A Laboratory Environment for Medical Informatics Students.

    PubMed

    Brandt, Karsten; Löbe, Matthias; Schaaf, Michael; Jahn, Franziska; Winter, Alfred; Stäubert, Sebastian

    2016-01-01

    Medical research and health care highly depend on the use of information technology. There is a wide range of application systems (patient administration system, laboratory information system, communication server etc.) and heterogeneous data types (administrative data, clinical data, laboratory data, image data, genomic data etc.). Students and researchers do not often have the possibility to use productive application systems of e.g. hospitals or medical practices to gain practical experiences or examine new components and technologies. Therefore, the aim of this project is to develop a dedicated laboratory environment for patient health care and clinical research. Essential application systems were identified and a suitable architecture was designed for this purpose. It is accompanied by a teaching plan that considers learning modules for bachelor and master degrees in medical informatics. We implemented the laboratory environment called MI-Lab with multiple free and open source software components. All components are installed on virtual machines and/or Docker containers. This modular architecture creates a flexible system which can be deployed in various scenarios. The preliminary evaluation results suggests that laboratory environments like MI-Lab work well in teaching practical aspects of medical informatics and are widely accepted by students.

  7. Partnerships for College Access and Success: Using Partnerships as a Strategy. A Technical Assistance, Toolkit, and Resource Guide

    ERIC Educational Resources Information Center

    Academy for Educational Development, 2008

    2008-01-01

    "Partnerships for College Access and Success: A Technical Assistance Guide, Toolkit and Resource Guide" reflects lessons learned from four years of planning, implementation and evaluation work through the Partnerships for College Access and Success (PCAS) initiative. It is the result of the collaboration between AED (Academy for Educational…

  8. Informatics and public health at CDC.

    PubMed

    McNabb, Scott J N; Koo, D; Seligman, J

    2006-12-22

    Since CDC acquired its first mainframe computer in 1964, the use of information technology in public health practice has grown steadily and, during the past 2 decades, dramatically. Public health informatics (PHI) arrived on the scene during the 1990s after medical informatics (intersecting information technology, medicine, and health care) and bioinformatics (intersecting mathematics, statistics, computer science, and molecular biology). Similarly, PHI merged the disciplines of information science and computer science to public health practice, research, and learning. Using strategies and standards, practitioners employ PHI tools and training to maximize health impacts at local, state, and national levels. They develop and deploy information technology solutions that provide accurate, timely, and secure information to guide public health action.

  9. Open source bioimage informatics for cell biology.

    PubMed

    Swedlow, Jason R; Eliceiri, Kevin W

    2009-11-01

    Significant technical advances in imaging, molecular biology and genomics have fueled a revolution in cell biology, in that the molecular and structural processes of the cell are now visualized and measured routinely. Driving much of this recent development has been the advent of computational tools for the acquisition, visualization, analysis and dissemination of these datasets. These tools collectively make up a new subfield of computational biology called bioimage informatics, which is facilitated by open source approaches. We discuss why open source tools for image informatics in cell biology are needed, some of the key general attributes of what make an open source imaging application successful, and point to opportunities for further operability that should greatly accelerate future cell biology discovery.

  10. Distributed Medical Informatics Education Using Internet2

    PubMed Central

    Cummings, Joseph; Tidmarsh, Patricia; Hersh, William; Friedman, Charles

    2001-01-01

    The subject expertise of most medical informatics training programs funded by the National Library of Medicine (NLM) is incomplete. This not only limits the topical content students from individual sites are taught, but also restricts the project work they can undertake. This goal of this pilot project is to enable students in the informatics programs at two different sites - Oregon Health Sciences University (OHSU) and University of Pittsburgh (UP) - to have access to a broader range of faculty, their subject expertise, and other students with whom to collaborate using high-speed networking and distance learning modalities. Students at OHSU and UP participate in real time training program activities via IP-based/Internet2 videoconferences.

  11. The young person's guide to biomedical informatics.

    PubMed

    van Bemmel, Jan H

    2006-01-01

    In a retrospective review, a parallel is drawn between the challenges by which a research department in biomedical informatics is confronted and those of a symphony orchestra. In both areas, different disciplines and different groups of instruments can be discerned. The importance of mastering one's instrument and the harmony between the team members is stressed. The conductor has to stimulate the individual players so that they can all have a successful career. Competition between orchestras and performance assessments determine survival and success. A record of refereed publications is crucial for continued existence. Conclusions are that biomedical informatics is typically multidisciplinary, that hypotheses underlying research should be carefully formulated, that the time from research to application may easily take 20 years or more, that mutual trust and knowing each other's competences is essential for success, that a good leader gives enough room to all team members to develop their careers, and that the outcomes of assessment studies are related to the quality of publications.

  12. Informatics, machine learning and computational medicinal chemistry.

    PubMed

    Mitchell, John B O

    2011-03-01

    This article reviews the use of informatics and computational chemistry methods in medicinal chemistry, with special consideration of how computational techniques can be adapted and extended to obtain more and higher-quality information. Special consideration is given to the computation of protein-ligand binding affinities, to the prediction of off-target bioactivities, bioactivity spectra and computational toxicology, and also to calculating absorption-, distribution-, metabolism- and excretion-relevant properties, such as solubility.

  13. Research Strategies for Biomedical and Health Informatics

    PubMed Central

    Kulikowski, Casimir A.; Bakken, Suzanne; de Lusignan, Simon; Kimura, Michio; Koch, Sabine; Mantas, John; Maojo, Victor; Marschollek, Michael; Martin-Sanchez, Fernando; Moen, Anne; Park, Hyeoun-Ae; Sarkar, Indra Neil; Leong, Tze Yun; McCray, Alexa T.

    2017-01-01

    Summary Background Medical informatics, or biomedical and health informatics (BMHI), has become an established scientific discipline. In all such disciplines there is a certain inertia to persist in focusing on well-established research areas and to hold on to well-known research methodologies rather than adopting new ones, which may be more appropriate. Objectives To search for answers to the following questions: What are research fields in informatics, which are not being currently adequately addressed, and which methodological approaches might be insufficiently used? Do we know about reasons? What could be consequences of change for research and for education? Methods Outstanding informatics scientists were invited to three panel sessions on this topic in leading international conferences (MIE 2015, Medinfo 2015, HEC 2016) in order to get their answers to these questions. Results A variety of themes emerged in the set of answers provided by the panellists. Some panellists took the theoretical foundations of the field for granted, while several questioned whether the field was actually grounded in a strong theoretical foundation. Panellists proposed a range of suggestions for new or improved approaches, methodologies, and techniques to enhance the BMHI research agenda. Conclusions The field of BMHI is on the one hand maturing as an academic community and intellectual endeavour. On the other hand vendor-supplied solutions may be too readily and uncritically accepted in health care practice. There is a high chance that BMHI will continue to flourish as an important discipline; its innovative interventions might then reach the original objectives of advancing science and improving health care outcomes.

  14. Interrogating the druggable genome with structural informatics.

    PubMed

    Hambly, Kevin; Danzer, Joseph; Muskal, Steven; Debe, Derek A

    2006-08-01

    Structural genomics projects are producing protein structure data at an unprecedented rate. In this paper, we present the Target Informatics Platform (TIP), a novel structural informatics approach for amplifying the rapidly expanding body of experimental protein structure information to enhance the discovery and optimization of small molecule protein modulators on a genomic scale. In TIP, existing experimental structure information is augmented using a homology modeling approach, and binding sites across multiple target families are compared using a clique detection algorithm. We report here a detailed analysis of the structural coverage for the set of druggable human targets, highlighting drug target families where the level of structural knowledge is currently quite high, as well as those areas where structural knowledge is sparse. Furthermore, we demonstrate the utility of TIP's intra- and inter-family binding site similarity analysis using a series of retrospective case studies. Our analysis underscores the utility of a structural informatics infrastructure for extracting drug discovery-relevant information from structural data, aiding researchers in the identification of lead discovery and optimization opportunities as well as potential "off-target" liabilities.

  15. Materials Informatics: Statistical Modeling in Material Science.

    PubMed

    Yosipof, Abraham; Shimanovich, Klimentiy; Senderowitz, Hanoch

    2016-12-01

    Material informatics is engaged with the application of informatic principles to materials science in order to assist in the discovery and development of new materials. Central to the field is the application of data mining techniques and in particular machine learning approaches, often referred to as Quantitative Structure Activity Relationship (QSAR) modeling, to derive predictive models for a variety of materials-related "activities". Such models can accelerate the development of new materials with favorable properties and provide insight into the factors governing these properties. Here we provide a comparison between medicinal chemistry/drug design and materials-related QSAR modeling and highlight the importance of developing new, materials-specific descriptors. We survey some of the most recent QSAR models developed in materials science with focus on energetic materials and on solar cells. Finally we present new examples of material-informatic analyses of solar cells libraries produced from metal oxides using combinatorial material synthesis. Different analyses lead to interesting physical insights as well as to the design of new cells with potentially improved photovoltaic parameters.

  16. 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

  17. A Longitudinal Social Network Analysis of the Editorial Boards of Medical Informatics and Bioinformatics Journals

    PubMed Central

    Malin, Bradley; Carley, Kathleen

    2007-01-01

    Objective The goal of this research is to learn how the editorial staffs of bioinformatics and medical informatics journals provide support for cross-community exposure. Models such as co-citation and co-author analysis measure the relationships between researchers; but they do not capture how environments that support knowledge transfer across communities are organized. Methods In this paper, we propose a social network analysis model to study how editorial boards integrate researchers from disparate communities. We evaluate our model by building relational networks based on the editorial boards of approximately 40 journals that serve as research outlets in medical informatics and bioinformatics. We track the evolution of editorial relationships through a longitudinal investigation over the years 2000 through 2005. Results Our findings suggest that there are research journals that support the collocation of editorial board members from the bioinformatics and medical informatics communities. Network centrality metrics indicate that editorial board members are located in the intersection of the communities and that the number of individuals in the intersection is growing with time. Conclusions Social network analysis methods provide insight into the relationships between the medical informatics and bioinformatics communities. The number of editorial board members facilitating the publication intersection of the communities has grown, but the intersection remains dependent on a small group of individuals and fragile. PMID:17329730

  18. Informatics Systems and Tools to Facilitate Patient-centered Care Coordination

    PubMed Central

    Kneale, L.

    2015-01-01

    Summary Introduction There is a growing international focus on patient-centered care. A model designed to facilitate this type of care in the primary care setting is the patient-centered medical home. This model of care strives to be patient-focused, comprehensive, team-based, coordinated, accessible, and focused on quality and safety of care. Objective The objective of this paper is to identify the current status and future trends of patient-centered care and the role of informatics systems and tools in facilitating this model of care. Methods In this paper we review recent scientific literature of the past four years to identify trends and state of current evidence when it comes to patient-centered care overall, and more specifically medical homes. Results There are several studies that indicate growth and development in seven informatics areas within patient-centered care, namely clinical decision support, registries, team care, care transitions, personal health records, telehealth, and measurement. In some cases we are still lacking large randomized clinical trials and the evidence base is not always solid, but findings strongly indicate the potential of informatics to support patient-centered care. Conclusion Current evidence indicates that advancements have been made in implementing and evaluating patient-centered care models. Technical, legal, and practical challenges still remain. Further examination of the impact of patient-centered informatics tools and systems on clinical outcomes is needed. PMID:26293847

  19. 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

  20. 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

  1. Public Health and Epidemiology Informatics: Recent Research and Trends in the United States

    PubMed Central

    Dixon, B. E.; Kharrazi, H.

    2015-01-01

    Summary Objectives To survey advances in public health and epidemiology informatics over the past three years. Methods We conducted a review of English-language research works conducted in the domain of public health informatics (PHI), and published in MEDLINE between January 2012 and December 2014, where information and communication technology (ICT) was a primary subject, or a main component of the study methodology. Selected articles were synthesized using a thematic analysis using the Essential Services of Public Health as a typology. Results Based on themes that emerged, we organized the advances into a model where applications that support the Essential Services are, in turn, supported by a socio-technical infrastructure that relies on government policies and ethical principles. That infrastructure, in turn, depends upon education and training of the public health workforce, development that creates novel or adapts existing infrastructure, and research that evaluates the success of the infrastructure. Finally, the persistence and growth of infrastructure depends on financial sustainability. Conclusions Public health informatics is a field that is growing in breadth, depth, and complexity. Several Essential Services have benefited from informatics, notably, “Monitor Health,” “Diagnose & Investigate,” and “Evaluate.” Yet many Essential Services still have not yet benefited from advances such as maturing electronic health record systems, interoperability amongst health information systems, analytics for population health management, use of social media among consumers, and educational certification in clinical informatics. There is much work to be done to further advance the science of PHI as well as its impact on public health practice. PMID:26293869

  2. Knowledge, Skills, and Resources for Pharmacy Informatics Education

    PubMed Central

    Fox, Brent I.; Flynn, Allen J.; Fortier, Christopher R.; Clauson, Kevin A.

    2011-01-01

    Pharmacy has an established history of technology use to support business processes. Pharmacy informatics education within doctor of pharmacy programs, however, is inconsistent, despite its inclusion as a requirement in the 2007 Accreditation Council for Pharmacy Education Standards and Guidelines. This manuscript describes pharmacy informatics knowledge and skills that all graduating pharmacy students should possess, conceptualized within the framework of the medication use process. Additionally, we suggest core source materials and specific learning activities to support pharmacy informatics education. We conclude with a brief discussion of emerging changes in the practice model. These changes are facilitated by pharmacy informatics and will inevitably become commonplace in our graduates’ practice environment. PMID:21829267

  3. The future of biomedical informatics: a perspective from academia.

    PubMed

    Shortliffe, Edward H

    2012-01-01

    Academic biomedical informatics has achieved great successes through research contributions over several decades, now reflected in a thriving commercial marketplace for electronic health records and other informatics tools. That very success, coupled with changes in the ability of governments to support research at past levels, is forcing a reconsideration of the directions and emphases for faculty members in informatics academic units. This paper discusses those forces and proposes areas of emphasis that will strengthen the academic discipline as it evolves in the years ahead. The focus is on the role of academic informaticians as practitioners of informatics, as researchers, and as educators.

  4. Crossing the chasm: information technology to biomedical informatics.

    PubMed

    Fahy, Brenda G; Balke, C William; Umberger, Gloria H; Talbert, Jeffery; Canales, Denise Niles; Steltenkamp, Carol L; Conigliaro, Joseph

    2011-06-01

    Accelerating the translation of new scientific discoveries to improve human health and disease management is the overall goal of a series of initiatives integrated in the National Institutes of Health (NIH) "Roadmap for Medical Research." The Clinical and Translational Science Award (CTSA) program is, arguably, the most visible component of the NIH Roadmap providing resources to institutions to transform their clinical and translational research enterprises along the goals of the Roadmap. The CTSA program emphasizes biomedical informatics as a critical component for the accomplishment of the NIH's translational objectives. To be optimally effective, emerging biomedical informatics programs must link with the information technology platforms of the enterprise clinical operations within academic health centers.This report details one academic health center's transdisciplinary initiative to create an integrated academic discipline of biomedical informatics through the development of its infrastructure for clinical and translational science infrastructure and response to the CTSA mechanism. This approach required a detailed informatics strategy to accomplish these goals. This transdisciplinary initiative was the impetus for creation of a specialized biomedical informatics core, the Center for Biomedical Informatics (CBI). Development of the CBI codified the need to incorporate medical informatics including quality and safety informatics and enterprise clinical information systems within the CBI. This article describes the steps taken to develop the biomedical informatics infrastructure, its integration with clinical systems at one academic health center, successes achieved, and barriers encountered during these efforts.

  5. Crossing the Chasm: Information Technology to Biomedical Informatics

    PubMed Central

    Fahy, Brenda G.; Balke, C. William; Umberger, Gloria H.; Talbert, Jeffery; Canales, Denise Niles; Steltenkamp, Carol L.; Conigliaro, Joseph

    2011-01-01

    Accelerating the translation of new scientific discoveries to improve human health and disease management is the overall goal of a series of initiatives integrated in the National Institutes of Health (NIH) “Roadmap for Medical Research.” The Clinical and Translational Research Award (CTSA) program is, arguably, the most visible component of the NIH Roadmap providing resources to institutions to transform their clinical and translational research enterprises along the goals of the Roadmap. The CTSA program emphasizes biomedical informatics as a critical component for the accomplishment of the NIH’s translational objectives. To be optimally effective, emerging biomedical informatics programs must link with the information technology (IT) platforms of the enterprise clinical operations within academic health centers. This report details one academic health center’s transdisciplinary initiative to create an integrated academic discipline of biomedical informatics through the development of its infrastructure for clinical and translational science infrastructure and response to the CTSA mechanism. This approach required a detailed informatics strategy to accomplish these goals. This transdisciplinary initiative was the impetus for creation of a specialized biomedical informatics core, the Center for Biomedical Informatics (CBI). Development of the CBI codified the need to incorporate medical informatics including quality and safety informatics and enterprise clinical information systems within the CBI. This paper describes the steps taken to develop the biomedical informatics infrastructure, its integration with clinical systems at one academic health center, successes achieved, and barriers encountered during these efforts. PMID:21383632

  6. WIST: toolkit for rapid, customized LIMS development

    PubMed Central

    Huang, Y. Wayne; Arkin, Adam P.; Chandonia, John-Marc

    2011-01-01

    Summary: Workflow Information Storage Toolkit (WIST) is a set of application programming interfaces and web applications that allow for the rapid development of customized laboratory information management systems (LIMS). WIST provides common LIMS input components, and allows them to be arranged and configured using a flexible language that specifies each component's visual and semantic characteristics. WIST includes a complete set of web applications for adding, editing and viewing data, as well as a powerful setup tool that can build new LIMS modules by analyzing existing database schema. Availability and implementation: WIST is implemented in Perl and may be obtained from http://vimss.sf.net under the BSD license. Contact: jmchandonia@lbl.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21258060

  7. Monitoring Extreme-scale Lustre Toolkit

    SciTech Connect

    Brim, Michael J; Lothian, Josh

    2015-01-01

    We discuss the design and ongoing development of the Monitoring Extreme-scale Lustre Toolkit (MELT), a unified Lustre performance monitoring and analysis infrastructure that provides continuous, low-overhead summary information on the health and performance of Lustre, as well as on-demand, in-depth problem diagnosis and root-cause analysis. The MELT infrastructure leverages a distributed overlay network to enable monitoring of center-wide Lustre filesystems where clients are located across many network domains. We preview interactive command-line utilities that help administrators and users to observe Lustre performance at various levels of resolution, from individual servers or clients to whole filesystems, including job-level reporting. Finally, we discuss our future plans for automating the root-cause analysis of common Lustre performance problems.

  8. Introduction to the Geant4 Simulation toolkit

    SciTech Connect

    Guatelli, S.; Cutajar, D.; Rosenfeld, A. B.; Oborn, B.

    2011-05-05

    Geant4 is a Monte Carlo simulation Toolkit, describing the interactions of particles with matter. Geant4 is widely used in radiation physics research, from High Energy Physics, to medical physics and space science, thanks to its sophisticated physics component, coupled with advanced functionality in geometry description. Geant4 is widely used at the Centre for Medical Radiation Physics (CMRP), at the University of Wollongong, to characterise and optimise novel detector concepts, radiotherapy treatments, and imaging solutions. This lecture consists of an introduction to Monte Carlo method, and to Geant4. Particular attention will be devoted to the Geant4 physics component, and to the physics models describing electromagnetic and hadronic physics interactions. The second part of the lecture will be focused on the methodology to adopt to develop a Geant4 simulation application.

  9. 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

  10. TEVA-SPOT Toolkit 1.2

    SciTech Connect

    Berry, Jonathan; Riesen, Lee Ann; Hart, William

    2007-07-26

    The TEVA-SPOT Toolkit (SPOT) supports the design of contaminant warning systems (CWSs) that use real-time sensors to detect contaminants in municipal water distribution networks. Specifically, SPOT provides the capability to select the locations for installing sensors in order to maximize the utility and effectiveness of the CWS. SPOT models the sensor placement process as an optimization problem, and the user can specify a wide range of performance objectives for contaminant warning system design, including population health effects, time to detection, extent of contamination, volume consumed and number of failed detections. For example, a SPOT user can integrate expert knowledge during the design process by specigying required sensor placements or designating network locations as forbidden. Further, cost considerations can be integrated by limiting the design with user-specified installation costs at each location.

  11. Introducing the Ginga FITS Viewer and Toolkit

    NASA Astrophysics Data System (ADS)

    Jeschke, E.; Inagaki, T.; Kackley, R.

    2013-10-01

    We introduce Ginga, a new open-source FITS viewer and toolkit based on Python astronomical packages such as pyfits, numpy, scipy, matplotlib, and pywcs. For developers, we present a set of Python classes for viewing FITS files under the modern Gtk and Qt widget sets and a more full-featured viewer that has a plugin architecture. We further describe how plugins can be written to extend the viewer with many different capabilities. The software may be of interest to software developers who are looking for a solution for integrating FITS visualization into their Python programs and end users interested in a new and different FITS viewer that is not based on Tcl/Tk widget technology. The software has been released under a BSD license.

  12. The Insight ToolKit image registration framework

    PubMed Central

    Avants, Brian B.; Tustison, Nicholas J.; Stauffer, Michael; Song, Gang; Wu, Baohua; Gee, James C.

    2014-01-01

    Publicly available scientific resources help establish evaluation standards, provide a platform for teaching and improve reproducibility. Version 4 of the Insight ToolKit (ITK4) seeks to establish new standards in publicly available image registration methodology. ITK4 makes several advances in comparison to previous versions of ITK. ITK4 supports both multivariate images and objective functions; it also unifies high-dimensional (deformation field) and low-dimensional (affine) transformations with metrics that are reusable across transform types and with composite transforms that allow arbitrary series of geometric mappings to be chained together seamlessly. Metrics and optimizers take advantage of multi-core resources, when available. Furthermore, ITK4 reduces the parameter optimization burden via principled heuristics that automatically set scaling across disparate parameter types (rotations vs. translations). A related approach also constrains steps sizes for gradient-based optimizers. The result is that tuning for different metrics and/or image pairs is rarely necessary allowing the researcher to more easily focus on design/comparison of registration strategies. In total, the ITK4 contribution is intended as a structure to support reproducible research practices, will provide a more extensive foundation against which to evaluate new work in image registration and also enable application level programmers a broad suite of tools on which to build. Finally, we contextualize this work with a reference registration evaluation study with application to pediatric brain labeling.1 PMID:24817849

  13. 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…

  14. Charon Message-Passing Toolkit for Scientific Computations

    NASA Technical Reports Server (NTRS)

    VanderWijngarrt, Rob F.; Saini, Subhash (Technical Monitor)

    1998-01-01

    The Charon toolkit for piecemeal development of high-efficiency parallel programs for scientific computing is described. The portable toolkit, callable from C and Fortran, provides flexible domain decompositions and high-level distributed constructs for easy translation of serial legacy code or design to distributed environments. Gradual tuning can subsequently be applied to obtain high performance, possibly by using explicit message passing. Charon also features general structured communications that support stencil-based computations with complex recurrences. Through the separation of partitioning and distribution, the toolkit can also be used for blocking of uni-processor code, and for debugging of parallel algorithms on serial machines. An elaborate review of recent parallelization aids is presented to highlight the need for a toolkit like Charon. Some performance results of parallelizing the NAS Parallel Benchmark SP program using Charon are given, showing good scalability. Some performance results of parallelizing the NAS Parallel Benchmark SP program using Charon are given, showing good scalability.

  15. Charon Message-Passing Toolkit for Scientific Computations

    NASA Technical Reports Server (NTRS)

    VanderWijngaart, Rob F.; Saini, Subhash (Technical Monitor)

    1998-01-01

    The Charon toolkit for piecemeal development of high-efficiency parallel programs for scientific computing is described. The portable toolkit, callable from C and Fortran, provides flexible domain decompositions and high-level distributed constructs for easy translation of serial legacy code or design to distributed environments. Gradual tuning can subsequently be applied to obtain high performance, possibly by using explicit message passing. Charon also features general structured communications that support stencil-based computations with complex recurrences. Through the separation of partitioning and distribution, the toolkit can also be used for blocking of uni-processor code, and for debugging of parallel algorithms on serial machines. An elaborate review of recent parallelization aids is presented to highlight the need for a toolkit like Charon. Some performance results of parallelizing the NAS Parallel Benchmark SP program using Charon are given, showing good scalability.

  16. The Radar Software Toolkit: Anaylsis software for the ITM community

    NASA Astrophysics Data System (ADS)

    Barnes, R. J.; Greenwald, R.

    2005-05-01

    The Radar Software Toolkit is a collection of data analysis, modelling and visualization tools originally developed for the SuperDARN project. It has evolved over the years into a robust, multi-platform software toolkit for working with a variety of ITM data sets including data from the Polar, TIMED and ACE spacecraft, ground based magnetometers, Incoherrent Scatter Radars, and SuperDARN. The toolkit includes implementations of the Altitude Adjusted Coordinate System (AACGM), the International Geomagnetic Reference Field (IGRF), SGP4 and a set of coordinate transform functions. It also includes a sophisticated XML based data visualization system. The toolkit is written using a combination of ANSI C, Java and the Interactive Data Language (IDL) and has been tested on a variety of platforms.

  17. General relativistic magneto-hydrodynamics with the Einstein Toolkit

    NASA Astrophysics Data System (ADS)

    Moesta, Philipp; Mundim, Bruno; Faber, Joshua; Noble, Scott; Bode, Tanja; Haas, Roland; Loeffler, Frank; Ott, Christian; Reisswig, Christian; Schnetter, Erik

    2013-04-01

    The Einstein Toolkit Consortium is developing and supporting open software for relativistic astrophysics. Its aim is to provide the core computational tools that can enable new science, broaden our community, facilitate interdisciplinary research and take advantage of petascale computers and advanced cyberinfrastructure. The Einstein Toolkit currently consists of an open set of over 100 modules for the Cactus framework, primarily for computational relativity along with associated tools for simulation management and visualization. The toolkit includes solvers for vacuum spacetimes as well as relativistic magneto-hydrodynamics. This talk will present the current capabilities of the Einstein Toolkit with a particular focus on recent improvements made to the general relativistic magneto-hydrodynamics modeling and will point to information how to leverage it for future research.

  18. 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.

  19. Case study: factors in defining the nurse informatics specialist role.

    PubMed

    Hassett, Margaret

    2006-01-01

    Healthcare organizations, consultant groups, vendor companies, and academic institutions feel the challenge to enhance user experiences with information systems. To meet this challenge, organizations and companies are looking to better understand and utilize a variety of informatics roles to further marketing, business, or healthcare goals. Nursing is one practice area that can support the successful integration of information systems development, implementation, support, and user experience. However, the definition and development of such a role or position has met with mixed success. This article explores some of the issues and influences related to the role's development. The issues, impacts, and influences have been identified based on healthcare business assessment, job description analysis, employment and project evaluations, and professional standards set by the American Nurses Association.

  20. 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

  1. 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.

  2. An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics

    NASA Astrophysics Data System (ADS)

    Wu, Chaochao; Monroe, Matthew E.; Xu, Zhe; Slysz, Gordon W.; Payne, Samuel H.; Rodland, Karin D.; Liu, Tao; Smith, Richard D.

    2015-12-01

    The comprehensive MS analysis of the peptidome, the intracellular and intercellular products of protein degradation, has the potential to provide novel insights on endogenous proteolytic processing and its utility in disease diagnosis and prognosis. Along with the advances in MS instrumentation and related platforms, a plethora of proteomics data analysis tools have been applied for direct use in peptidomics; however, an evaluation of the currently available informatics pipelines for peptidomics data analysis has yet to be reported. In this study, we began by evaluating the results of several popular MS/MS database search engines, including MS-GF+, SEQUEST, and MS-Align+, for peptidomics data analysis, followed by identification and label-free quantification using the well-established accurate mass and time (AMT) tag and newly developed informed quantification (IQ) approaches, both based on direct LC-MS analysis. Our results demonstrated that MS-GF+ outperformed both SEQUEST and MS-Align+ in identifying peptidome peptides. Using a database established from MS-GF+ peptide identifications, both the AMT tag and IQ approaches provided significantly deeper peptidome coverage and less missing data for each individual data set than the MS/MS methods, while achieving robust label-free quantification. Besides having an excellent correlation with the AMT tag quantification results, IQ also provided slightly higher peptidome coverage. Taken together, we propose an optimized informatics pipeline combining MS-GF+ for initial database searching with IQ (or AMT tag) approaches for identification and label-free quantification for high-throughput, comprehensive, and quantitative peptidomics analysis.

  3. An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics

    SciTech Connect

    Wu, Chaochao; Monroe, Matthew E.; Xu, Zhe; Slysz, Gordon W.; Payne, Samuel H.; Rodland, Karin D.; Liu, Tao; Smith, Richard D.

    2015-12-26

    Comprehensive MS analysis of peptidome, the intracellular and intercellular products of protein degradation, has the potential to provide novel insights on endogenous proteolytic processing and their utility in disease diagnosis and prognosis. Along with the advances in MS instrumentation, a plethora of proteomics data analysis tools have been applied for direct use in peptidomics; however an evaluation of the currently available informatics pipelines for peptidomics data analysis has yet to be reported. In this study, we set off by evaluating the results of several popular MS/MS database search engines including MS-GF+, SEQUEST and MS-Align+ for peptidomics data analysis, followed by identification and label-free quantification using the well-established accurate mass and time (AMT) tag and newly developed informed quantification (IQ) approaches, both based on direct LC-MS analysis. Our result demonstrated that MS-GF+ outperformed both SEQUEST and MS-Align+ in identifying peptidome peptides. Using a database established from the MS-GF+ peptide identifications, both the AMT tag and IQ approaches provided significantly deeper peptidome coverage and less missing value for each individual data set than the MS/MS methods, while achieving robust label-free quantification. Besides having an excellent correlation with the AMT tag quantification results, IQ also provided slightly higher peptidome coverage than AMT. Taken together, we propose an optimal informatics pipeline combining MS-GF+ for initial database searching with IQ (or AMT) for identification and label-free quantification for high-throughput, comprehensive and quantitative peptidomics analysis.

  4. 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.

  5. Creating a pipeline of talent for informatics: STEM initiative for high school students in computer science, biology, and biomedical informatics

    PubMed Central

    Dutta-Moscato, Joyeeta; Gopalakrishnan, Vanathi; Lotze, Michael T.; Becich, Michael J.

    2014-01-01

    This editorial provides insights into how informatics can attract highly trained students by involving them in science, technology, engineering, and math (STEM) training at the high school level and continuing to provide mentorship and research opportunities through the formative years of their education. Our central premise is that the trajectory necessary to be expert in the emergent fields in front of them requires acceleration at an early time point. Both pathology (and biomedical) informatics are new disciplines which would benefit from involvement by students at an early stage of their education. In 2009, Michael T Lotze MD, Kirsten Livesey (then a medical student, now a medical resident at University of Pittsburgh Medical Center (UPMC)), Richard Hersheberger, PhD (Currently, Dean at Roswell Park), and Megan Seippel, MS (the administrator) launched the University of Pittsburgh Cancer Institute (UPCI) Summer Academy to bring high school students for an 8 week summer academy focused on Cancer Biology. Initially, pathology and biomedical informatics were involved only in the classroom component of the UPCI Summer Academy. In 2011, due to popular interest, an informatics track called Computer Science, Biology and Biomedical Informatics (CoSBBI) was launched. CoSBBI currently acts as a feeder program for the undergraduate degree program in bioinformatics at the University of Pittsburgh, which is a joint degree offered by the Departments of Biology and Computer Science. We believe training in bioinformatics is the best foundation for students interested in future careers in pathology informatics or biomedical informatics. We describe our approach to the recruitment, training and research mentoring of high school students to create a pipeline of exceptionally well-trained applicants for both the disciplines of pathology informatics and biomedical informatics. We emphasize here how mentoring of high school students in pathology informatics and biomedical informatics

  6. Creating a pipeline of talent for informatics: STEM initiative for high school students in computer science, biology, and biomedical informatics.

    PubMed

    Dutta-Moscato, Joyeeta; Gopalakrishnan, Vanathi; Lotze, Michael T; Becich, Michael J

    2014-01-01

    This editorial provides insights into how informatics can attract highly trained students by involving them in science, technology, engineering, and math (STEM) training at the high school level and continuing to provide mentorship and research opportunities through the formative years of their education. Our central premise is that the trajectory necessary to be expert in the emergent fields in front of them requires acceleration at an early time point. Both pathology (and biomedical) informatics are new disciplines which would benefit from involvement by students at an early stage of their education. In 2009, Michael T Lotze MD, Kirsten Livesey (then a medical student, now a medical resident at University of Pittsburgh Medical Center (UPMC)), Richard Hersheberger, PhD (Currently, Dean at Roswell Park), and Megan Seippel, MS (the administrator) launched the University of Pittsburgh Cancer Institute (UPCI) Summer Academy to bring high school students for an 8 week summer academy focused on Cancer Biology. Initially, pathology and biomedical informatics were involved only in the classroom component of the UPCI Summer Academy. In 2011, due to popular interest, an informatics track called Computer Science, Biology and Biomedical Informatics (CoSBBI) was launched. CoSBBI currently acts as a feeder program for the undergraduate degree program in bioinformatics at the University of Pittsburgh, which is a joint degree offered by the Departments of Biology and Computer Science. We believe training in bioinformatics is the best foundation for students interested in future careers in pathology informatics or biomedical informatics. We describe our approach to the recruitment, training and research mentoring of high school students to create a pipeline of exceptionally well-trained applicants for both the disciplines of pathology informatics and biomedical informatics. We emphasize here how mentoring of high school students in pathology informatics and biomedical informatics

  7. Office of Biological Informatics and Outreach geospatial technology activities

    USGS Publications Warehouse

    ,

    1998-01-01

    The U.S. Geological Survey (USGS) Office of Biological Informatics and Outreach (OBIO) in Reston, Virginia, and its Center for Biological Informatics (CBI) in Denver, Colorado, provide leadership in the development and use of geospatial technologies to advance the Nation's biological science activities.

  8. The Recurrence Relations in Teaching Students of Informatics

    ERIC Educational Resources Information Center

    Bakoev, Valentin P.

    2010-01-01

    The topic "Recurrence relations" and its place in teaching students of Informatics is discussed in this paper. We represent many arguments about the importance, the necessity and the benefit of studying this subject by Informatics students. They are based on investigation of some fundamental books and textbooks on Discrete Mathematics,…

  9. Massive Open Online Course for Health Informatics Education

    PubMed Central

    2014-01-01

    Objectives This paper outlines a new method of teaching health informatics to large numbers of students from around the world through a Massive Open Online Course (MOOC). Methods The Health Informatics Forum is one of examples of MOOCs through a social networking site for educating health informatics students and professionals. It is running a MOOC for students from around the world that uses creative commons licenced content funded by the US government and developed by five US universities. The content is delivered through narrated lectures with slides that can be viewed online with discussion threads on the forum for class interactions. Students can maintain a professional profile, upload photos and files, write their own blog posts and post discussion threads on the forum. Results The Health Informatics Forum MOOC has been accessed by 11,316 unique users from 127 countries from August 2, 2012 to January 24, 2014. Most users accessed the MOOC via a desktop computer, followed by tablets and mobile devices and 55% of users were female. Over 400,000 unique users have now accessed the wider Health Informatics Forum since it was established in 2008. Conclusions Advances in health informatics and educational technology have both created a demand for online learning material in health informatics and a solution for providing it. By using a MOOC delivered through a social networking platform it is hoped that high quality health informatics education will be able to be delivered to a large global audience of future health informaticians without cost. PMID:24872906

  10. Characteristics of Information Systems and Business Informatics Study Programs

    ERIC Educational Resources Information Center

    Helfert, Markus

    2011-01-01

    Over the last decade there is an intensive discussion within the Information Systems (IS) and Informatics community about the characteristics and identity of the discipline. Simultaneously with the discussion, there is an ongoing debate on essential skills and capabilities of IS and Business Informatics graduates as well as the profile of IS…

  11. Publication trends and impact factors in the Medical Informatics literature.

    PubMed

    Lavallie, Donna L; Wolf, Fredric M

    2005-01-01

    We survey the "evolution" of the field of Medical Informatics by describing trends in volume(quantity) of Medical Informatics-indexed publications, identifying major journals of publication and their focus areas and presenting trends in impact factor scores during the 1994-2003 period. Changes in total impact-scores suggest an increasing trend of publication in journals of higher impact.

  12. The Impact of Imaging Informatics Fellowships.

    PubMed

    Liao, Geraldine J; Nagy, Paul G; Cook, Tessa S

    2016-08-01

    Imaging informatics (II) is an area within clinical informatics that is particularly important in the field of radiology. Provider groups have begun employing dedicated radiologist-informaticists to bridge medical, information technology and administrative functions, and academic institutions are meeting this demand through formal II fellowships. However, little is known about how these programs influence graduates' careers and perceptions about professional development. We electronically surveyed 26 graduates from US II fellowships and consensus leaders in the II community-many of whom were subspecialty diagnostic radiologists (68%) employed within academic institutions (48%)-about the perceived impact of II fellowships on career development and advancement. All graduates felt that II fellowship made them more valuable to employers, with the majority of reporting ongoing II roles (78%) and continued used of competencies (61%) and skills (56%) gained during fellowship in their current jobs. Other key benefits included access to mentors, protected time for academic work, networking opportunities, and positive impacts of annual compensation. Of respondents without II fellowship training, all would recommend fellowships to current trainees given the ability to gain a "still rare" but "essential skill set" that is "critical for future leaders in radiology" and "better job opportunities." While some respondents felt that II fellowships needed further formalization and standardization, most (85%) disagreed with requiring a 2-year II fellowship in order to qualify for board certification in clinical informatics. Instead, most believed that fellowships should be integrated with clinical residency or fellowship training while preserving formal didactics and unstructured project time. More work is needed to understand existing variations in II fellowship training structure and identify the optimal format for programs targeted at radiologists.

  13. [Standards in Medical Informatics: Fundamentals and Applications].

    PubMed

    Suárez-Obando, Fernando; Camacho Sánchez, Jhon

    2013-09-01

    The use of computers in medical practice has enabled novel forms of communication to be developed in health care. The optimization of communication processes is achieved through the use of standards to harmonize the exchange of information and provide a common language for all those involved. This article describes the concept of a standard applied to medical informatics and its importance in the development of various applications, such as computational representation of medical knowledge, disease classification and coding systems, medical literature searches and integration of biological and clinical sciences.

  14. Integrating problem-based learning in a nursing informatics curriculum.

    PubMed

    Demiris, George; Zierler, Brenda

    2010-02-01

    In recent years employers in health care organizations have been recognizing the need for nurses to enter the workforce with a set of informatics competencies. Numerous nursing informatics programs have been established worldwide. The challenge becomes to explore innovative tools that will equip nurses with the appropriate skills to utilize information technology to improve health care quality and patient safety and redesign health care services. This paper presents the introduction of problem-based learning (PBL) modules into an existing nursing informatics curriculum, the Clinical Informatics and Patient Centered Technologies Master program at the School of Nursing, University of Washington. Additionally, we discuss recommendations and challenges associated with the integration of PBL in nursing informatics graduate education including the need for facilitators, flexible technology platforms, promotion and documentation of group work, faculty training and supervision by a program committee.

  15. Exploring the biomedical and health informatics educational programs in europe.

    PubMed

    Manifava, Eirini; Kolokathi, Aikaterini; Mantas, John

    2014-01-01

    The Health Information Technology can improve public health, quality of health care etc. Thus, it is important for professionals to be well educated by training programs. The aim of this paper is to record all the educational programs with specializations in Health Informatics, Medical Informatics, Bioinformatics, Biomedical Informatics and Biomedical Engineering in European Universities and Institutions. An on-line research was conducted on Scopus, PubMed, Scholar Google, and Google. More than 150 universities and colleges in Europe conduct educational programs for these domains. The majority them, expertise in Biomedical Engineering (31%), 22% of the educational programs correspond to Bioinformatics, while Health Informatics studies have 18%. On the last few years, a growth of Health informatics professionals has been observed in Europe.

  16. An information technology emphasis in biomedical informatics education.

    PubMed

    Kane, Michael D; Brewer, Jeffrey L

    2007-02-01

    Unprecedented growth in the interdisciplinary domain of biomedical informatics reflects the recent advancements in genomic sequence availability, high-content biotechnology screening systems, as well as the expectations of computational biology to command a leading role in drug discovery and disease characterization. These forces have moved much of life sciences research almost completely into the computational domain. Importantly, educational training in biomedical informatics has been limited to students enrolled in the life sciences curricula, yet much of the skills needed to succeed in biomedical informatics involve or augment training in information technology curricula. This manuscript describes the methods and rationale for training students enrolled in information technology curricula in the field of biomedical informatics, which augments the existing information technology curriculum and provides training on specific subjects in Biomedical Informatics not emphasized in bioinformatics courses offered in life science programs, and does not require prerequisite courses in the life sciences.

  17. [Medical informatics education at the Medical School in Tuzla].

    PubMed

    Sabanović, Zekerijah; Mujcinagić, Alija

    2004-01-01

    Medical informatics is a specific and interdisciplinary science which involves many participants of the health system like: patients, physicians, nurses, managers, administrators, computer experts, students, with the different level of education and understanding, different approaches and expectations. Education of medical informatics requests organization solutions of high quality and necessary equipment for its realization. Educational programs are also limited by student's basic knowledge of informatics from secondary schools. For assessment of this knowledge we have conducted special designed questionnaire at the first year of undergraduate study which results confirm our thesis that great number of students entered the faculty with the lack of basic knowledge from informatics area. In this paper was presented level of organization and education of medical informatics at the Medical faculty and University Clinical Center of Tuzla, with its characteristics through which this system has been passed since 1990.

  18. E-ELT modeling and simulation toolkits: philosophy and progress status

    NASA Astrophysics Data System (ADS)

    Sedghi, B.; Muller, M.; Bonnet, H.; Esselborn, M.; Le Louarn, M.; Clare, R.; Koch, F.

    2011-09-01

    To predict the performance of the E-ELT three sets of toolkits are developed at ESO: i) The main structure and associated optical unit dynamical and feedback control toolkit, ii) Active optics and phasing toolkit, and iii) adaptive optics simulation toolkit. There was a deliberate policy not to integrate all of the systems into a massive model and tool. The dynamical and control time scale differences are used to separate the simulation environments and tools. Therefore, each toolkit contains an appropriate detail of the problem and holds sufficient overlap with the others to ensure the consistency of the results. In this paper, these toolkits together with some examples are presented.

  19. Geographically distributed complementary content-based image retrieval systems for biomedical image informatics.

    PubMed

    Antani, Sameer K; Deserno, Thomas M; Long, L Rodney; Thoma, George R

    2007-01-01

    There is a significant increase in the use of medical images in clinical medicine, disease research, and education. While the literature lists several successful systems for content-based image retrieval and image management methods, they have been unable to make significant inroads in routine medical informatics. This can be attributed to the following: (i) the challenging nature of medical images, (ii) need for specialized methods specific to each image type and detail, (iii) lack of advances in image indexing methods, and (iv) lack of a uniform data and resource exchange framework between complementary systems. Most systems tend to focus on varying degrees of the first two items, making them very versatile in a small sampling of the variety of medical images but unable to share their strengths. This paper proposes to overcome these shortcomings by defining a data and resource exchange framework using open standards and software to develop geographically distributed toolkits. As proof-of-concept, we describe the coupling of two complementary geographically separated systems: the IRMA system at Aachen University of Technology in Germany, and the SPIRS system at the U. S. National Library of Medicine in the United States of America.

  20. The microRNA toolkit of insects

    PubMed Central

    Ylla, Guillem; Fromm, Bastian; Piulachs, Maria-Dolors; Belles, Xavier

    2016-01-01

    Is there a correlation between miRNA diversity and levels of organismic complexity? Exhibiting extraordinary levels of morphological and developmental complexity, insects are the most diverse animal class on earth. Their evolutionary success was in particular shaped by the innovation of holometabolan metamorphosis in endopterygotes. Previously, miRNA evolution had been linked to morphological complexity, but astonishing variation in the currently available miRNA complements of insects made this link unclear. To address this issue, we sequenced the miRNA complement of the hemimetabolan Blattella germanica and reannotated that of two other hemimetabolan species, Locusta migratoria and Acyrthosiphon pisum, and of four holometabolan species, Apis mellifera, Tribolium castaneum, Bombyx mori and Drosophila melanogaster. Our analyses show that the variation of insect miRNAs is an artefact mainly resulting from poor sampling and inaccurate miRNA annotation, and that insects share a conserved microRNA toolkit of 65 families exhibiting very low variation. For example, the evolutionary shift toward a complete metamorphosis was accompanied only by the acquisition of three and the loss of one miRNA families. PMID:27883064

  1. UQ Toolkit v 2.0

    SciTech Connect

    2013-10-03

    The Uncertainty Quantification (UQ) Toolkit is a software library for the characterizaton and propagation of uncertainties in computational models. For the characterization of uncertainties, Bayesian inference tools are provided to infer uncertain model parameters, as well as Bayesian compressive sensing methods for discovering sparse representations of high-dimensional input-output response surfaces, and also Karhunen-Loève expansions for representing stochastic processes. Uncertain parameters are treated as random variables and represented with Polynomial Chaos expansions (PCEs). The library implements several spectral basis function types (e.g. Hermite basis functions in terms of Gaussian random variables or Legendre basis functions in terms of uniform random variables) that can be used to represent random variables with PCEs. For propagation of uncertainty, tools are provided to propagate PCEs that describe the input uncertainty through the computational model using either intrusive methods (Galerkin projection of equations onto basis functions) or non-intrusive methods (perform deterministic operation at sampled values of the random values and project the obtained results onto basis functions).

  2. Modelling toolkit for simulation of maglev devices

    NASA Astrophysics Data System (ADS)

    Peña-Roche, J.; Badía-Majós, A.

    2017-01-01

    A stand-alone App1 has been developed, focused on obtaining information about relevant engineering properties of magnetic levitation systems. Our modelling toolkit provides real time simulations of 2D magneto-mechanical quantities for superconductor (SC)/permanent magnet structures. The source code is open and may be customised for a variety of configurations. Ultimately, it relies on the variational statement of the critical state model for the superconducting component and has been verified against experimental data for YBaCuO/NdFeB assemblies. On a quantitative basis, the values of the arising forces, induced superconducting currents, as well as a plot of the magnetic field lines are displayed upon selection of an arbitrary trajectory of the magnet in the vicinity of the SC. The stability issues related to the cooling process, as well as the maximum attainable forces for a given material and geometry are immediately observed. Due to the complexity of the problem, a strategy based on cluster computing, database compression, and real-time post-processing on the device has been implemented.

  3. UQ Toolkit v. 3.0

    SciTech Connect

    Sargsyan, Khachik; Safta, Cosmin; Chowdhary, Kenny; de Bord, Sarah; Debusschere, Bert

    2016-09-14

    The Uncertainty Quantification (UQ) Toolkit is a software library for the characterization and propagation of uncertainties in computational models. This library provides Bayesian inference tools to infer uncertain model parameters, Bayesian compressive sensing methods for discovering sparse representations of high-dimensional input-output response surfaces, methods for constructing Karhunen-Loève representations of stochastic processes, and global sensitivity analysis tools used to compute Sobol indices in order to characterize the importance of uncertain inputs or the interactions between them. The basis for many of these methods relies on representing random variables with Polynomial Chaos expansions (PCEs). This library implements several spectral basis function types (e.g. Hermite basis functions in terms of Gaussian random variables or Legendre basis functions in terms of uniform random variables) that can be used to represent random variables with PCEs. For the propagation of uncertainty, tools are provided to propagate PCEs that describe the input uncertainty through the computational model using either intrusive methods (Galerkin projection of equations onto basis functions) or non-intrusive methods (perform deterministic operation at sampled values of the random values and project the obtained results onto basis functions).

  4. The NOAA Weather and Climate Toolkit

    NASA Astrophysics Data System (ADS)

    Ansari, S.; Hutchins, C.; Del Greco, S.

    2008-12-01

    The NOAA Weather and Climate Toolkit (WCT) is an application that provides simple visualization and data export of weather and climate data archived at the National Climatic Data Center (NCDC) and other organizations. The WCT is built on the Unidata Common Data Model and supports defined feature types such as Grid, Radial, Point, Time Series and Trajectory. Current NCDC datasets supported include NEXRAD Radar data, GOES Satellite imagery, NOMADS Model Data, Integrated Surface Data and the U.S. Drought Monitor (part of the National Integrated Drought Information System (NIDIS)). The WCT Viewer provides tools for displaying custom data overlays, Web Map Services (WMS), animations and basic filters. The export of images and movies is provided in multiple formats. The WCT Data Exporter allows for data export in both vector polygon (Shapefile, Well-Known Text) and raster (GeoTIFF, Arc/Info ASCII Grid, VTK, NetCDF) formats. By decoding and exporting data into multiple common formats, a diverse user community can perform analysis using familiar tools such as ArcGIS, MatLAB and IDL. This brings new users to a vast array of weather and climate data at NCDC.

  5. Security Assessment Simulation Toolkit (SAST) Final Report

    SciTech Connect

    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 (OSD 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.

  6. Asteroids Outreach Toolkit Development: Using Iterative Feedback In Informal Education

    NASA Astrophysics Data System (ADS)

    White, Vivian; Berendsen, M.; Gurton, S.; Dusenbery, P. B.

    2011-01-01

    The Night Sky Network is a collaboration of close to 350 astronomy clubs across the US that actively engage in public outreach within their communities. Since 2004, the Astronomical Society of the Pacific has been creating outreach ToolKits filled with carefully crafted sets of physical materials designed to help these volunteer clubs explain the wonders of the night sky to the public. The effectiveness of the ToolKit activities and demonstrations is the direct result of a thorough testing and vetting process. Find out how this iterative assessment process can help other programs create useful tools for both formal and informal educators. The current Space Rocks Outreach ToolKit focuses on explaining asteroids, comets, and meteorites to the general public using quick, big-picture activities that get audiences involved. Eight previous ToolKits cover a wide range of topics from the Moon to black holes. In each case, amateur astronomers and the public helped direct the development the activities along the way through surveys, focus groups, and active field-testing. The resulting activities have been embraced by the larger informal learning community and are enthusiastically being delivered to millions of people across the US and around the world. Each ToolKit is delivered free of charge to active Night Sky Network astronomy clubs. All activity write-ups are available free to download at the website listed here. Amateur astronomers receive frequent questions from the public about Earth impacts, meteors, and comets so this set of activities will help them explain the dynamics of these phenomena to the public. The Space Rocks ToolKit resources complement the Great Balls of Fire museum exhibit produced by Space Science Institute's National Center for Interactive Learning and scheduled for release in 2011. NSF has funded this national traveling exhibition and outreach ToolKit under Grant DRL-0813528.

  7. Health informatics model for helminthiasis in Thailand.

    PubMed

    Nithikathkul, C; Trevanich, A; Wongsaroj, T; Wongsawad, C; Reungsang, P

    2016-09-26

    At the beginning of the new millennium, helminth infections continue to be prevalent, particularly among impoverished populations. This study attempts to create the first health informatics model of helminthiasis in Thailand. The authors investigate how a health informatics model could be used to predict the control and eradication in a national control campaign. Fish-borne helminthiasis caused by Opisthorchis viverrini remains a major public health problem in many parts of South-East Asia, including Thailand, Lao PDR, Vietnam and Cambodia. The epicentre of this disease is located in north-east Thailand, where high prevalence coexists with a high incidence of cholangiocarcinoma (CHCA). The current report was conducted to determine a mathematical model of surveillance for helminthiasis while also using a geographic information system. The fish-borne helminthiasis model or the predicted equation was Y1 = 3.028 + 0.020 (elevation) - 2.098 (clay). For soil-transmitted helminthiasis, the mathematical model or the predicted equation was Y2 = -1.559 + 0.005 (rainfall) + 0.004 (elevation) - 2.198 (clay). The Ministry of Public Health has concluded that mass treatment for helminthiasis in the Thai population, targeting high-risk individuals, may be a cost-effective way to allocate limited funds. This type of approach, as well as further study on the correlation of clinical symptoms with environmental and geographic information, may offer a novel strategy to the helminth crisis.

  8. Contemporary issues in transfusion medicine informatics

    PubMed Central

    Sharma, Gaurav; Parwani, Anil V.; Raval, Jay S.; Triulzi, Darrell J.; Benjamin, Richard J.; Pantanowitz, Liron

    2011-01-01

    The Transfusion Medicine Service (TMS) covers diverse clinical and laboratory-based services that must be delivered with accuracy, efficiency and reliability. TMS oversight is shared by multiple regulatory agencies that cover product manufacturing and validation standards geared toward patient safety. These demands present significant informatics challenges. Over the past few decades, TMS information systems have improved to better handle blood product manufacturing, inventory, delivery, tracking and documentation. Audit trails and access to electronic databases have greatly facilitated product traceability and biovigilance efforts. Modern blood bank computing has enabled novel applications such as the electronic crossmatch, kiosk-based blood product delivery systems, and self-administered computerized blood donor interview and eligibility determination. With increasing use of barcoding technology, there has been a marked improvement in patient and specimen identification. Moreover, the emergence of national and international labeling standards such as ISBT 128 have facilitated the availability, movement and tracking of blood products across national and international boundaries. TMS has only recently begun to leverage the electronic medical record to address quality issues in transfusion practice and promote standardized documentation within institutions. With improved technology, future growth is expected in blood bank automation and product labeling with applications such as radio frequency identification devices. This article reviews several of these key informatics issues relevant to the contemporary practice of TMS. PMID:21383927

  9. Fractal Image Informatics: from SEM to DEM

    NASA Astrophysics Data System (ADS)

    Oleschko, K.; Parrot, J.-F.; Korvin, G.; Esteves, M.; Vauclin, M.; Torres-Argüelles, V.; Salado, C. Gaona; Cherkasov, S.

    2008-05-01

    In this paper, we introduce a new branch of Fractal Geometry: Fractal Image Informatics, devoted to the systematic and standardized fractal analysis of images of natural systems. The methods of this discipline are based on the properties of multiscale images of selfaffine fractal surfaces. As proved in the paper, the image inherits the scaling and lacunarity of the surface and of its reflectance distribution [Korvin, 2005]. We claim that the fractal analysis of these images must be done without any smoothing, thresholding or binarization. Two new tools of Fractal Image Informatics, firmagram analysis (FA) and generalized lacunarity (GL), are presented and discussed in details. These techniques are applicable to any kind of image or to any observed positive-valued physical field, and can be used to correlate between images. It will be shown, by a modified Grassberger-Hentschel-Procaccia approach [Phys. Lett. 97A, 227 (1983); Physica 8D, 435 (1983)] that GL obeys the same scaling law as the Allain-Cloitre lacunarity [Phys. Rev. A 44, 3552 (1991)] but is free of the problems associated with gliding boxes. Several applications are shown from Soil Physics, Surface Science, and other fields.

  10. Translational Research from an Informatics Perspective

    NASA Technical Reports Server (NTRS)

    Bernstam, Elmer; Meric-Bernstam, Funda; Johnson-Throop, Kathy A.; Turley, James P.; Smith, Jack W.

    2007-01-01

    Clinical and translational research (CTR) is an essential part of a sustainable global health system. Informatics is now recognized as an important en-abler of CTR and informaticians are increasingly called upon to help CTR efforts. The US National Institutes of Health mandated biomedical informatics activity as part of its new national CTR grant initiative, the Clinical and Translational Science Award (CTSA). Traditionally, translational re-search was defined as the translation of laboratory discoveries to patient care (bench to bedside). We argue, however, that there are many other kinds of translational research. Indeed, translational re-search requires the translation of knowledge dis-covered in one domain to another domain and is therefore an information-based activity. In this panel, we will expand upon this view of translational research and present three different examples of translation to illustrate the point: 1) bench to bedside, 2) Earth to space and 3) academia to community. We will conclude with a discussion of our local translational research efforts that draw on each of the three examples.

  11. Bayesian Analysis of the Pattern Informatics Technique

    NASA Astrophysics Data System (ADS)

    Cho, N.; Tiampo, K.; Klein, W.; Rundle, J.

    2007-12-01

    The pattern informatics (PI) [Rundle et al., 2000; Tiampo et al., 2002; Holliday et al., 2005] is a technique that uses phase dynamics in order to quantify temporal variations in seismicity patterns. This technique has shown interesting results for forecasting earthquakes with magnitude greater than or equal to 5 in southern California from 2000 to 2010 [Rundle et al., 2002]. In this work, a Bayesian approach is used to obtain a modified updated version of the PI called Bayesian pattern informatics (BPI). This alternative method uses the PI result as a prior probability and models such as ETAS [Ogata, 1988, 2004; Helmstetter and Sornette, 2002] or BASS [Turcotte et al., 2007] in order to obtain the likelihood. Its result is similar to the one obtained by the PI: the determination of regions, known as hotspots, that are most susceptible to the occurrence of events with M=5 and larger during the forecast period. As an initial test, retrospective forecasts for the southern California region from 1990 to 2000 were made with both the BPI and the PI techniques, and the results are discussed in this work.

  12. Medical Informatics and the Science of Cognition

    PubMed Central

    Patel, Vimla L.; Kaufman, David R.

    1998-01-01

    Recent developments in medical informatics research have afforded possibilities for great advances in health care delivery. These exciting opportunities also present formidable challenges to the implementation and integration of technologies in the workplace. As in most domains, there is a gulf between technologic artifacts and end users. Since medical practice is a human endeavor, there is a need for bridging disciplines to enable clinicians to benefit from rapid technologic advances. This in turn necessitates a broadening of disciplinary boundaries to consider cognitive and social factors pertaining to the design and use of technology. The authors argue for a place of prominence for cognitive science. Cognitive science provides a framework for the analysis and modeling of complex human performance and has considerable applicability to a range of issues in informatics. Its methods have been employed to illuminate different facets of design and implementation. This approach has also yielded insights into the mechanisms and processes involved in collaborative design. Cognitive scientific methods and theories are illustrated in the context of two examples that examine human-computer interaction in medical contexts and computer-mediated collaborative processes. The framework outlined in this paper can be used to refine the process of iterative design, end-user training, and productive practice. PMID:9824797

  13. The Configuration Space Toolkit (C-Space Toolkit or CSTK) Ver. 2.5 beta

    SciTech Connect

    Chen, Pang-Chieh; Hwang, Yong; Xavier, Patrick; Lewis, Christopher; Lafarge, Robert; & Watterberg, Peter

    2010-02-24

    The C-Space Toolkit provides a software library that makes it easier to program motion planning, simulation, robotics, and virtual reality codes using the Configuration Space abstraction. Key functionality (1) enables the user to special create representations of movable and stationary rigid geometric objects, and (2) perform fast distance, interference (clash) detection, collision detection, closest-feature pairs, and contact queries in terms of object configuration. Not only can queries be computed at any given point in configuration space, but they can be done exactly over linear-translational path segments and approximately for rotational path segments. Interference detection and distance computations can be done with respect to the Minkowski sum of the original geometry and a piece of convex geometry. The Toolkit takes as raw model input (1) collections of convex polygons that form the boundaries of models and (2) convex polyhedra, cones, cylinders, and discs that are models and model components. Configurations are given in terms of homogeneous transforms. A simple OpenGL-based system for displaying and animating the geometric objects is included in the implementation. This version, 2.5 Beta, incorporates feature additions and enhancements, improvements in algorithms, improved robustness, bug fixes and cleaned-up source code, better compliance with standards and recent programming convention, changes to the build process for the software, support for more recent hardware and software platforms, and improvements to documentation and source-code comments.

  14. Empowered Consumers and the Health Care Team: A Dynamic Model of Health Informatics.

    PubMed

    Mancuso, Peggy J; Myneni, Sahiti

    2016-01-01

    This article presents a dynamic new model of health informatics. Within the model, the focus of health informatics changes from the provider to the consumer and incorporates the dynamic relationship of technological change to health care. Bioinformatics is the scientific discipline that is translated into care through the practice of health informatics. The loci of health informatics practices are the consumer (consumer informatics), the patient (clinical informatics), and the community (public health informatics). The continuum from individual to community interacts with and contributes to health care technology, which is represented as a constantly changing progressive wave.

  15. The Einstein Toolkit: a community computational infrastructure for relativistic astrophysics

    NASA Astrophysics Data System (ADS)

    Löffler, Frank; Faber, Joshua; Bentivegna, Eloisa; Bode, Tanja; Diener, Peter; Haas, Roland; Hinder, Ian; Mundim, Bruno C.; Ott, Christian D.; Schnetter, Erik; Allen, Gabrielle; Campanelli, Manuela; Laguna, Pablo

    2012-06-01

    We describe the Einstein Toolkit, a community-driven, freely accessible computational infrastructure intended for use in numerical relativity, relativistic astrophysics, and other applications. The toolkit, developed by a collaboration involving researchers from multiple institutions around the world, combines a core set of components needed to simulate astrophysical objects such as black holes, compact objects, and collapsing stars, as well as a full suite of analysis tools. The Einstein Toolkit is currently based on the Cactus framework for high-performance computing and the Carpet adaptive mesh refinement driver. It implements spacetime evolution via the BSSN evolution system and general relativistic hydrodynamics in a finite-volume discretization. The toolkit is under continuous development and contains many new code components that have been publicly released for the first time and are described in this paper. We discuss the motivation behind the release of the toolkit, the philosophy underlying its development, and the goals of the project. A summary of the implemented numerical techniques is included, as are results of numerical test covering a variety of sample astrophysical problems.

  16. The MPI Bioinformatics Toolkit for protein sequence analysis.

    PubMed

    Biegert, Andreas; Mayer, Christian; Remmert, Michael; Söding, Johannes; Lupas, Andrei N

    2006-07-01

    The MPI Bioinformatics Toolkit is an interactive web service which offers access to a great variety of public and in-house bioinformatics tools. They are grouped into different sections that support sequence searches, multiple alignment, secondary and tertiary structure prediction and classification. Several public tools are offered in customized versions that extend their functionality. For example, PSI-BLAST can be run against regularly updated standard databases, customized user databases or selectable sets of genomes. Another tool, Quick2D, integrates the results of various secondary structure, transmembrane and disorder prediction programs into one view. The Toolkit provides a friendly and intuitive user interface with an online help facility. As a key feature, various tools are interconnected so that the results of one tool can be forwarded to other tools. One could run PSI-BLAST, parse out a multiple alignment of selected hits and send the results to a cluster analysis tool. The Toolkit framework and the tools developed in-house will be packaged and freely available under the GNU Lesser General Public Licence (LGPL). The Toolkit can be accessed at http://toolkit.tuebingen.mpg.de.

  17. The history of pathology informatics: A global perspective

    PubMed Central

    Park, Seung; Parwani, Anil V.; Aller, Raymond D.; Banach, Lech; Becich, Michael J.; Borkenfeld, Stephan; Carter, Alexis B.; Friedman, Bruce A.; Rojo, Marcial Garcia; Georgiou, Andrew; Kayser, Gian; Kayser, Klaus; Legg, Michael; Naugler, Christopher; Sawai, Takashi; Weiner, Hal; Winsten, Dennis; Pantanowitz, Liron

    2013-01-01

    Pathology informatics has evolved to varying levels around the world. The history of pathology informatics in different countries is a tale with many dimensions. At first glance, it is the familiar story of individuals solving problems that arise in their clinical practice to enhance efficiency, better manage (e.g., digitize) laboratory information, as well as exploit emerging information technologies. Under the surface, however, lie powerful resource, regulatory, and societal forces that helped shape our discipline into what it is today. In this monograph, for the first time in the history of our discipline, we collectively perform a global review of the field of pathology informatics. In doing so, we illustrate how general far-reaching trends such as the advent of computers, the Internet and digital imaging have affected pathology informatics in the world at large. Major drivers in the field included the need for pathologists to comply with national standards for health information technology and telepathology applications to meet the scarcity of pathology services and trained people in certain countries. Following trials by a multitude of investigators, not all of them successful, it is apparent that innovation alone did not assure the success of many informatics tools and solutions. Common, ongoing barriers to the widespread adoption of informatics devices include poor information technology infrastructure in undeveloped areas, the cost of technology, and regulatory issues. This review offers a deeper understanding of how pathology informatics historically developed and provides insights into what the promising future might hold. PMID:23869286

  18. Use of statistical analysis in the biomedical informatics literature.

    PubMed

    Scotch, Matthew; Duggal, Mona; Brandt, Cynthia; Lin, Zhenqui; Shiffman, Richard

    2010-01-01

    Statistics is an essential aspect of biomedical informatics. To examine the use of statistics in informatics research, a literature review of recent articles in two high-impact factor biomedical informatics journals, the Journal of American Medical Informatics Association (JAMIA) and the International Journal of Medical Informatics was conducted. The use of statistical methods in each paper was examined. Articles of original investigations from 2000 to 2007 were reviewed. For each journal, the results by statistical methods were analyzed as: descriptive, elementary, multivariable, other regression, machine learning, and other statistics. For both journals, descriptive statistics were most often used. Elementary statistics such as t tests, chi(2), and Wilcoxon tests were much more frequent in JAMIA, while machine learning approaches such as decision trees and support vector machines were similar in occurrence across the journals. Also, the use of diagnostic statistics such as sensitivity, specificity, precision, and recall, was more frequent in JAMIA. These results highlight the use of statistics in informatics and the need for biomedical informatics scientists to have, as a minimum, proficiency in descriptive and elementary statistics.

  19. A modular informatics platform for effective support of collaborative and multicenter studies in cardiology.

    PubMed

    Marinelli, Martina; Positano, Vincenzo; Lorenzoni, Valentina; Caselli, Chiara; Mangione, Maurizio; Marcheschi, Paolo; Puzzuoli, Stefano; Esposito, Natalia; L'Abbate, Giuseppe Andrea; Neglia, Danilo

    2016-12-01

    Collaborative and multicenter studies permit a large number of patients to be enrolled within a reasonable time and providing the opportunity to collect different data. Informatics platforms play an important role in management, storage, and exchange of data between the participants involved in the study. In this article, we describe a modular informatics platform designed and developed to support collaborative and multicenter studies in cardiology. In each developed module, data management is implemented following local defined protocols. The modular characteristic of the developed platform allows independent transfer of different kinds of data, such as biological samples, imaging raw data, and patients' digital information. Moreover, it offers safe central storage of the data collected during the study. The developed platform was successfully tested during a European collaborative and multicenter study, focused on evaluating multimodal non-invasive imaging to diagnose and characterize ischemic heart disease.

  20. Chemical Descriptors Library (CDL): a generic, open source software library for chemical informatics.

    PubMed

    Sykora, Vladimir J; Leahy, David E

    2008-10-01

    In this article the Chemical Descriptors Library (CDL), a generic, open source software library for chemical informatics is introduced. The library is written using standard-compliant C++ programming language. The CDL provides a generic interface for traversing the structure of a molecular graph and accessing its properties. As a result, the software offers flexibility, reusability, and maintainability. This interface has been used to develop several chemical informatics algorithms, including molecular text format parsers and writers; substructure, pharmacophore, and atom type fingerprints; and both common substructure search and SMARTS search. The algorithms are described and evaluated on 3 data sets comprising 1000, 50000, and 100000 small molecules, respectively. The properties of the algorithms in terms of complexity analysis and processing times are presented and discussed.

  1. Coalescing medical systems: a challenge for health informatics in a global world.

    PubMed

    Stranieri, Andrew; Vaughan, Stephen

    2010-01-01

    As globalisation advances, patients in many nations increasingly access diverse medical systems including Western medicine, Traditional Chinese Medicine, Homeopathy and Ayervedic medicine. The trend toward co-existence of medical systems presents challenges for health informatics including the need to develop standards that can encompass the diversity required, the need to develop software applications that effectively inter-operate across diverse systems and the need to support patients when evaluating competing systems. This article advances the notion that the challenges can most effectively be met with the development of informatics approaches that do not assume the superiority of one medical system over another. Argument visualization to support patient decision making in selecting an appropriate medical system is presented as an application that exemplifies this stance.

  2. Teaching and learning "on the run": ready-to-use toolkits in busy clinical settings.

    PubMed

    Cleary, Michelle; Walter, Garry

    2010-06-01

    Clinicians should strongly consider using toolkits in their workplaces with students on clinical placement. These toolkits could include brief quizzes, crossword puzzles, vignettes, role-playing, storytelling, or reflective activities to engage students in context-specific, collaborative learning.

  3. Nursing Informatics Beyond 2020; An Interactive Workshop Exploring Our Futures.

    PubMed

    Murray, Peter J

    2016-01-01

    This interactive workshop will reflect on and update participants' views on possible future scenarios for the development of health and nursing informatics. The NI2006 Post Congress Conference discussed the future nature and scope of nursing informatics, nursing and healthcare, as viewed from likely developments between 2006 and 2020 [1]. Brief synposes from the NI2006 conference will be presented, with summaries of speakers' views on changes and progress since. Workshop participants will discuss major themes and changes, with a view to updating views on possible futures for nursing, healthcare and informatics.

  4. Gap analysis of biomedical informatics graduate education competencies.

    PubMed

    Ritko, Anna L; Odlum, Michelle

    2013-01-01

    Graduate training in biomedical informatics (BMI) is evolving rapidly. BMI graduate programs differ in informatics domain, delivery method, degrees granted, as well as breadth and depth of curricular competencies. Using the current American Medical Informatics Association (AMIA) definition of BMI core competencies as a framework, we identified and labeled course offerings within graduate programs. From our qualitative analysis, gaps between defined competencies and curricula emerged. Topics missing from existing graduate curricula include community health, translational and clinical research, knowledge representation, data mining, communication and evidence-based practice.

  5. The Medical Informatics Program at the National University of Singapore.

    PubMed

    Lun, K C; Leong, T Y; Ong, K; Raghavan, R; Pung, H K

    1998-01-01

    The Medical Informatics Program at the National University of Singapore was established in September 1996 with a $4 million joint funding from the National Science and Technology Board and the Ministry of Education. The primary aims of the research program are to undertake upstream basic research in medical informatics and to build a critical mass of medical informatics expertise to meet long-term research goals and to effect technology transfer to the health sector of Singapore. Research projects fall into five groups: Clinical Decision Systems, Health Information Systems, Biomedical Datamining Systems, Medical Education Systems and Medical Networking, Applications Development and Integration Systems.

  6. Gap Analysis of Biomedical Informatics Graduate Education Competencies

    PubMed Central

    Ritko, Anna L.; Odlum, Michelle

    2013-01-01

    Graduate training in biomedical informatics (BMI) is evolving rapidly. BMI graduate programs differ in informatics domain, delivery method, degrees granted, as well as breadth and depth of curricular competencies. Using the current American Medical Informatics Association (AMIA) definition of BMI core competencies as a framework, we identified and labeled course offerings within graduate programs. From our qualitative analysis, gaps between defined competencies and curricula emerged. Topics missing from existing graduate curricula include community health, translational and clinical research, knowledge representation, data mining, communication and evidence-based practice. PMID:24551403

  7. An epigenetic toolkit allows for diverse genome architectures in eukaryotes

    PubMed Central

    Maurer-Alcalá, Xyrus X.; Katz, Laura A.

    2015-01-01

    Genome architecture varies considerably among eukaryotes in terms of both size and structure (e.g. distribution of sequences within the genome, elimination of DNA during formation of somatic nuclei). The diversity in eukaryotic genome architectures and the dynamic processes that they undergo are only possible due to the well-developed nature of an epigenetic toolkit, which likely existed in the Last Eukaryotic Common Ancestor (LECA). This toolkit may have arisen as a means of navigating the genomic conflict that arose from the expansion of transposable elements within the ancestral eukaryotic genome. This toolkit has been coopted to support the dynamic nature of genomes in lineages across the eukaryotic tree of life. Here we highlight how the changes in genome architecture in diverse eukaryotes are regulated by epigenetic processes by focusing on DNA elimination, genome rearrangements, and adaptive changes to genome architecture. The ability to epigenetically modify and regulate genomes has contributed greatly to the diversity of eukaryotes observed today. PMID:26649755

  8. Measure Up Pressure Down: Provider Toolkit to Improve Hypertension Control.

    PubMed

    Torres, Jennifer

    2016-05-01

    Hypertension is one of the most important risk factors for heart disease, stroke, kidney failure, and diabetes complications. Nearly one in three Americans adults has high blood pressure, and the cost associated with treating this condition is staggering. The Measure Up Pressure Down: Provider Toolkit to Improve Hypertension Control is a resource developed by the American Medical Group Foundation in partnership with the American Medical Group Association. The goal of this toolkit is to mobilize health care practitioners to work together through team-based approaches to achieve an 80% control rate of high blood pressure among their patient population. The toolkit can be used by health educators, clinic administrators, physicians, students, and other clinic staff as a step-by-step resource for developing the infrastructure needed to better identify and treat individuals with high blood pressure or other chronic conditions.

  9. Validation of Power Output for the WIND Toolkit

    SciTech Connect

    King, J.; Clifton, A.; Hodge, B. M.

    2014-09-01

    Renewable energy integration studies require wind data sets of high quality with realistic representations of the variability, ramping characteristics, and forecast performance for current wind power plants. The Wind Integration National Data Set (WIND) Toolkit is meant to be an update for and expansion of the original data sets created for the weather years from 2004 through 2006 during the Western Wind and Solar Integration Study and the Eastern Wind Integration Study. The WIND Toolkit expands these data sets to include the entire continental United States, increasing the total number of sites represented, and it includes the weather years from 2007 through 2012. In addition, the WIND Toolkit has a finer resolution for both the temporal and geographic dimensions. Three separate data sets will be created: a meteorological data set, a wind power data set, and a forecast data set. This report describes the validation of the wind power data set.

  10. An epigenetic toolkit allows for diverse genome architectures in eukaryotes.

    PubMed

    Maurer-Alcalá, Xyrus X; Katz, Laura A

    2015-12-01

    Genome architecture varies considerably among eukaryotes in terms of both size and structure (e.g. distribution of sequences within the genome, elimination of DNA during formation of somatic nuclei). The diversity in eukaryotic genome architectures and the dynamic processes are only possible due to the well-developed epigenetic toolkit, which probably existed in the Last Eukaryotic Common Ancestor (LECA). This toolkit may have arisen as a means of navigating the genomic conflict that arose from the expansion of transposable elements within the ancestral eukaryotic genome. This toolkit has been coopted to support the dynamic nature of genomes in lineages across the eukaryotic tree of life. Here we highlight how the changes in genome architecture in diverse eukaryotes are regulated by epigenetic processes, such as DNA elimination, genome rearrangements, and adaptive changes to genome architecture. The ability to epigenetically modify and regulate genomes has contributed greatly to the diversity of eukaryotes observed today.

  11. Performance analysis of the Globus Toolkit Monitoring and Discovery Service, MDS2.

    SciTech Connect

    Zhang, X.; Schopf, J. M.; Mathematics and Computer Science; Univ. of Chicago

    2004-01-01

    Monitoring and information services form a key component of a distributed system, or grid. A quantitative study of such services can aid in understanding the performance limitations, advise in the deployment of the monitoring system, and help evaluate future development work. To this end, we examined the performance of the Globus Toolkit/spl reg/ Monitoring and Discovery Service (MDS2) by instrumenting its main services using NetLogger. Our study shows a strong advantage to caching or prefetching the data, as well as the need to have primary components at well-connected sites.

  12. Introduction to Metagenomics at DOE JGI: Program Overview and Program Informatics (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema

    Tringe, Susannah [DOE JGI

    2016-07-12

    Susannah Tringe of the DOE Joint Genome Institute talks about the Program Overview and Program Informatics at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011

  13. eVITAL: A Preliminary Taxonomy and Electronic Toolkit of Health-Related Habits and Lifestyle

    PubMed Central

    Salvador-Carulla, Luis; Olson Walsh, Carolyn; Alonso, Federico; Gómez, Rafael; de Teresa, Carlos; Cabo-Soler, José Ricardo; Cano, Antonio; Ruiz, Mencía

    2012-01-01

    Objectives. To create a preliminary taxonomy and related toolkit of health-related habits (HrH) following a person-centered approach with a focus on primary care. Methods. From 2003–2009, a working group (n = 6 physicians) defined the knowledge base, created a framing document, and selected evaluation tools using an iterative process. Multidisciplinary focus groups (n = 29 health professionals) revised the document and evaluation protocol and participated in a feasibility study and review of the model based on a demonstration study with 11 adult volunteers in Antequera, Spain. Results. The preliminary taxonomy contains 6 domains of HrH and 1 domain of additional health descriptors, 3 subdomains, 43 dimensions, and 141 subdimensions. The evaluation tool was completed by the 11 volunteers. The eVITAL toolkit contains history and examination items for 4 levels of engagement: self-assessment, basic primary care, extended primary care, and specialty care. There was positive feedback from the volunteers and experts, but concern about the length of the evaluation. Conclusions. We present the first taxonomy of HrH, which may aid the development of the new models of care such as the personal contextual factors of the International Classification of Functioning (ICF) and the positive and negative components of the multilevel person-centered integrative diagnosis model. PMID:22545016

  14. Medical imaging, PACS, and imaging informatics: retrospective.

    PubMed

    Huang, H K

    2014-01-01

    Historical reviews of PACS (picture archiving and communication system) and imaging informatics development from different points of view have been published in the past (Huang in Euro J Radiol 78:163-176, 2011; Lemke in Euro J Radiol 78:177-183, 2011; Inamura and Jong in Euro J Radiol 78:184-189, 2011). This retrospective attempts to look at the topic from a different angle by identifying certain basic medical imaging inventions in the 1960s and 1970s which had conceptually defined basic components of PACS guiding its course of development in the 1980s and 1990s, as well as subsequent imaging informatics research in the 2000s. In medical imaging, the emphasis was on the innovations at Georgetown University in Washington, DC, in the 1960s and 1970s. During the 1980s and 1990s, research and training support from US government agencies and public and private medical imaging manufacturers became available for training of young talents in biomedical physics and for developing the key components required for PACS development. In the 2000s, computer hardware and software as well as communication networks advanced by leaps and bounds, opening the door for medical imaging informatics to flourish. Because many key components required for the PACS operation were developed by the UCLA PACS Team and its collaborative partners in the 1980s, this presentation is centered on that aspect. During this period, substantial collaborative research efforts by many individual teams in the US and in Japan were highlighted. Credits are due particularly to the Pattern Recognition Laboratory at Georgetown University, and the computed radiography (CR) development at the Fuji Electric Corp. in collaboration with Stanford University in the 1970s; the Image Processing Laboratory at UCLA in the 1980s-1990s; as well as the early PACS development at the Hokkaido University, Sapporo, Japan, in the late 1970s, and film scanner and digital radiography developed by Konishiroku Photo Ind. Co. Ltd

  15. A primer on precision medicine informatics.

    PubMed

    Sboner, Andrea; Elemento, Olivier

    2016-01-01

    In this review, we describe key components of a computational infrastructure for a precision medicine program that is based on clinical-grade genomic sequencing. Specific aspects covered in this review include software components and hardware infrastructure, reporting, integration into Electronic Health Records for routine clinical use and regulatory aspects. We emphasize informatics components related to reproducibility and reliability in genomic testing, regulatory compliance, traceability and documentation of processes, integration into clinical workflows, privacy requirements, prioritization and interpretation of results to report based on clinical needs, rapidly evolving knowledge base of genomic alterations and clinical treatments and return of results in a timely and predictable fashion. We also seek to differentiate between the use of precision medicine in germline and cancer.

  16. Nursing informatics competences still challenging nurse educators.

    PubMed

    Rajalahti, Elina; Saranto, Kaija

    2012-01-01

    In recent years nursing documentation has been one of the most important development areas of nursing informatics (NI) in Finland. The purpose of this study is to describe the development of the nurse educators' competences in nursing documentation during a project called eNNI. The eNNI project (2008-2010) was a cooperative project by nurse educators and working life experts. The goal of the project was to implement the national documentation model and thereby improve operational processes at workplaces. The study includes pre- and post-test questioning of NI applications with a web-based questionnaire (n=136). The data were analyzed with distribution, cross-tabulations and average tests and descriptive statistic multivariate method. According to the results, the ICT skills of the nurse educators were good at the end of the project, and they had good information literacy competence. On the other hand, their advanced NI skills left room for improvement.

  17. Informatics Enabled Behavioral Medicine in Oncology

    PubMed Central

    Hesse, Bradford W.; Suls, Jerry M.

    2011-01-01

    For the practicing physician, the behavioral implications of preventing, diagnosing, and treating cancer are many and varied. Fortunately, an enhanced capacity in informatics may help create a redesigned ecosystem in which applying evidence-based principles from behavioral medicine will become a routine part of care. Innovation to support this evolution will be spurred by the “meaningful use” criteria stipulated by the Health Information Technology for Economic and Clinical Health (HITECH) Act of 2009, and by focused research and development efforts within the broader health information ecosystem. The implications for how to better integrate evidence-based principles in behavioral medicine into oncology care through both spheres of development are discussed within the framework of the cancer control continuum. The promise of using the data collected through these tools to accelerate discovery in psycho-oncology is also discussed. If nurtured appropriately, these developments should help accelerate successes against cancer by altering the behavioral milieu. PMID:21799329

  18. [Looking for evidence-based medical informatics].

    PubMed

    Coiera, Enrico

    2016-03-01

    e-Health is experiencing a difficult time. On the one side, the forecast is for a bright digital health future created by precision medicine and smart devices. On the other hand, most large scale e-health projects struggle to make a difference and are often controversial. Both futures fail because they are not evidence-based. Medical informatics should follow the example of evidence-based medicine, i.e. conduct rigorous research that gives us evidence to solve real world problems, synthesise that evidence and then apply it strictly. We already have the tools for creating a different universe. What we need is evidence, will, a culture of learning, and hard work.

  19. The cancer translational research informatics platform

    PubMed Central

    McConnell, Patrick; Dash, Rajesh C; Chilukuri, Ram; Pietrobon, Ricardo; Johnson, Kimberly; Annechiarico, Robert; Cuticchia, A Jamie

    2008-01-01

    Background Despite the pressing need for the creation of applications that facilitate the aggregation of clinical and molecular data, most current applications are proprietary and lack the necessary compliance with standards that would allow for cross-institutional data exchange. In line with its mission of accelerating research discoveries and improving patient outcomes by linking networks of researchers, physicians, and patients focused on cancer research, caBIG (cancer Biomedical Informatics Grid™) has sponsored the creation of the caTRIP (Cancer Translational Research Informatics Platform) tool, with the purpose of aggregating clinical and molecular data in a repository that is user-friendly, easily accessible, as well as compliant with regulatory requirements of privacy and security. Results caTRIP has been developed as an N-tier architecture, with three primary tiers: domain services, the distributed query engine, and the graphical user interface, primarily making use of the caGrid infrastructure to ensure compatibility with other tools currently developed by caBIG. The application interface was designed so that users can construct queries using either the Simple Interface via drop-down menus or the Advanced Interface for more sophisticated searching strategies to using drag-and-drop. Furthermore, the application addresses the security concerns of authentication, authorization, and delegation, as well as an automated honest broker service for deidentifying data. Conclusion Currently being deployed at Duke University and a few other centers, we expect that caTRIP will make a significant contribution to further the development of translational research through the facilitation of its data exchange and storage processes. PMID:19108734

  20. Eco-informatics and natural resource management

    USGS Publications Warehouse

    Cushing, J.B.; Wilson, T.; Borning, A.; Delcambre, L.; Bowker, G.; Frame, M.; Schnase, J.; Sonntag, W.; Fulop, J.; Hert, C.; Hovy, E.; Jones, J.; Landis, E.; Schweik, C.; Brandt, L.; Gregg, V.; Spengler, S.

    2006-01-01

    This project highlight reports on the 2004 workshop [1], as well as follow-up activities in 2005 and 2006, regarding how informatics tools can help manage natural resources and decide policy. The workshop was sponsored jointly by sponsored by the NSF, NBII, NASA, and EPA, and attended by practitioners from government and non-government agencies, and university researchers from the computer, social, and ecological sciences. The workshop presented the significant information technology (IT) problems that resource managers face when integrating ecological or environmental information to make decisions. These IT problems fall into five categories: data presentation, data gaps, tools, indicators, and policy making and implementation. To alleviate such problems, we recommend informatics research in four IT areas, as defined in this abstract and our final report: modeling and simulation, data quality, information integration and ontologies, and social and human aspects. Additionally, we recommend that funding agencies provide infrastructure and some changes in funding habits to assure cycles of innovation in the domain were addressed. Follow-on activities to the workshop subsequent to dg.o 2005 included: an invited talk presenting workshop results at DILS 2005, publication of the workshop final report by the NBII [1], and a poster at the NBII All Hands Meeting (Oct. 2005). We also expect a special issue of the JIIS to appear in 2006 that addresses some of these questions. As we go to press, no solicitation by funding agencies has as yet been published, but various NASA and NBII, and NSF cyber-infrastructure and DG research efforts now underway address the above issues.

  1. Deconstructing the toolkit: creativity and risk in the NHS workforce.

    PubMed

    Allen, Von; Brodzinski, Emma

    2009-12-01

    Deconstructing the Toolkit explores the current desire for toolkits that promise failsafe structures to facilitate creative success. The paper examines this cultural phenomenon within the context of the risk-averse workplace-with particular focus on the NHS. The writers draw on Derrida and deconstructionism to reflect upon the principles of creativity and the possibilities for being creative within the workplace. Through reference to The Extra Mile project facilitated by Open Art, the paper examines the importance of engaging with an aesthetic of creativity and embracing a more holistic approach to the problems and potential of the creative process.

  2. PyCogent: a toolkit for making sense from sequence

    PubMed Central

    Knight, Rob; Maxwell, Peter; Birmingham, Amanda; Carnes, Jason; Caporaso, J Gregory; Easton, Brett C; Eaton, Michael; Hamady, Micah; Lindsay, Helen; Liu, Zongzhi; Lozupone, Catherine; McDonald, Daniel; Robeson, Michael; Sammut, Raymond; Smit, Sandra; Wakefield, Matthew J; Widmann, Jeremy; Wikman, Shandy; Wilson, Stephanie; Ying, Hua; Huttley, Gavin A

    2007-01-01

    We have implemented in Python the COmparative GENomic Toolkit, a fully integrated and thoroughly tested framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics. PyCogent includes connectors to remote databases, built-in generalized probabilistic techniques for working with biological sequences, and controllers for third-party applications. The toolkit takes advantage of parallel architectures and runs on a range of hardware and operating systems, and is available under the general public license from . PMID:17708774

  3. RAPID Toolkit Creates Smooth Flow Toward New Projects

    SciTech Connect

    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 during 2015.

  4. 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".

  5. Network algorithms for information analysis using the Titan Toolkit.

    SciTech Connect

    McLendon, William Clarence, III; Baumes, Jeffrey; Wilson, Andrew T.; Wylie, Brian Neil; Shead, Timothy M.

    2010-07-01

    The analysis of networked activities is dramatically more challenging than many traditional kinds of analysis. A network is defined by a set of entities (people, organizations, banks, computers, etc.) linked by various types of relationships. These entities and relationships are often uninteresting alone, and only become significant in aggregate. The analysis and visualization of these networks is one of the driving factors behind the creation of the Titan Toolkit. Given the broad set of problem domains and the wide ranging databases in use by the information analysis community, the Titan Toolkit's flexible, component based pipeline provides an excellent platform for constructing specific combinations of network algorithms and visualizations.

  6. 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/.

  7. A Short History of Medical Informatics in Bosnia and Herzegovina

    PubMed Central

    Masic, Izet

    2014-01-01

    The health informatics profession in Bosnia and Herzegovina has relatively long history. Thirty five years from the introduction of the first automatic manipulation of data, thirty years from the establishment of Society for Medical Informatics BiH, twenty years from the establishment of the Scientific journal “Acta Informatica Medica (Acta Inform Med”, indexed in PubMed, PubMed Central Scopus, Embase, etc.), twenty years on from the establishment of the first Cathedra for Medical Informatics on Biomedical Faculties in Bosnia and Herzegovina, ten years on from the introduction of the method of “Distance learning” in medical curriculum. The author of this article is eager to mark the importance of the above mentioned Anniversaries in the development of Health informatics in Bosnia and Herzegovina and have attempted, very briefly, to present the most significant events and persons with essential roles throughout this period. PMID:24648621

  8. Visualizing simulated learning experiences through the use of informatics tools.

    PubMed

    Thompson, Teri L; Warren, Judith J

    2009-01-01

    High-fidelity simulation technology is a growing educational technology. Designing effective simulations requires the use of informatics tools such as UML modeling. This poster demonstrates the steps in modeling a simulation exercise.

  9. SWOT Analysis on Medical Informatics and Development Strategies

    ERIC Educational Resources Information Center

    Ma, Xiaoyan; Han, Zhongdong; Ma, Hua

    2015-01-01

    This article aims at clarifying the strategic significance of developing medical informatics, conducting SWOT analysis on this discipline and hence establishing the strategic objectives and focal points for its development.

  10. [HYGIENIC ASSESSMENT OF INFORMATIZATION OF EDUCATION AND UP-BRINGING].

    PubMed

    Kuchma, V R; Tkachuk, E A

    2015-01-01

    During the last decade the quality of children's health declined, the level of children's aggression and aggressiveness increased. The consistent trend to increasing the quantity of children with the signs of motor disinhibition in different forms and manifestations was noted. In a study on the example of educational institutions of Irkutsk there was made an assessment of the impact of the intensification and informatization of education and up-bringing with the use of the index of the level of informatization. In preschool children over the information period mental performance was found to be characterized by an increase in the speed and decline in the quality of information processing, there are dominated increased aggressive background and unmotivated fears "out home", there are reduced values of endurance ratio of the cardiovascular system, higher levels of morbidity rate were noted. There was proposed a hygienic assessment of informatization of education and up-bringing with the use of the index of the level of informatization.

  11. Antecedents of the People and Organizational Aspects of Medical Informatics

    PubMed Central

    Lorenzi, Nancy M.; Riley, Robert T.; Blyth, Andrew J. C.; Southon, Gray; Dixon, Bradley J.

    1997-01-01

    Abstract People and organizational issues are critical in both implementing medical informatics systems and in dealing with the altered organizations that new systems often create. The people and organizational issues area—like medical informatics itself—is a blend of many disciplines. The academic disciplines of psychology, sociology, social psychology, social anthropology, organizational behavior and organizational development, management, and cognitive sciences are rich with research with significant potential to ease the introduction and on-going use of information technology in today's complex health systems. These academic areas contribute research data and core information for better understanding of such issues as the importance of and processes for creating future direction; managing a complex change process; effective strategies for involving individuals and groups in the informatics effort; and effectively managing the altered organization. This article reviews the behavioral and business referent disciplines that can potentially contribute to improved implementations and on-going management of change in the medical informatics arena. PMID:9067874

  12. Developing a Capstone Course within a Health Informatics Program

    PubMed Central

    Hackbarth, Gary; Cata, Teuta; Cole, Laura

    2012-01-01

    This article discusses the ongoing development of a health informatics capstone program in a Midwest university from the hiring of a program coordinator to the development of a capstone course, through initial student results. University health informatics programs require a strong academic program to be successful but also require a spirited program coordinator to manage resources and organize an effective capstone course. This is particularly true of health informatics master's programs that support health industry career fields, whereby employers can locate and work with a pool of qualified applicants. The analysis of students’ logs confirms that students’ areas of focus and concern are consistent with course objectives and company work requirements during the work-study portion of the student capstone project. The article further discusses lessons learned and future improvements to be made in the health informatics capstone course. PMID:22783150

  13. A short history of medical informatics in bosnia and herzegovina.

    PubMed

    Masic, Izet

    2014-02-01

    The health informatics profession in Bosnia and Herzegovina has relatively long history. Thirty five years from the introduction of the first automatic manipulation of data, thirty years from the establishment of Society for Medical Informatics BiH, twenty years from the establishment of the Scientific journal "Acta Informatica Medica (Acta Inform Med", indexed in PubMed, PubMed Central Scopus, Embase, etc.), twenty years on from the establishment of the first Cathedra for Medical Informatics on Biomedical Faculties in Bosnia and Herzegovina, ten years on from the introduction of the method of "Distance learning" in medical curriculum. The author of this article is eager to mark the importance of the above mentioned Anniversaries in the development of Health informatics in Bosnia and Herzegovina and have attempted, very briefly, to present the most significant events and persons with essential roles throughout this period.

  14. Climate Informatics: Accelerating Discovering in Climate Science with Machine Learning

    NASA Technical Reports Server (NTRS)

    Monteleoni, Claire; Schmidt, Gavin A.; McQuade, Scott

    2014-01-01

    The goal of climate informatics, an emerging discipline, is to inspire collaboration between climate scientists and data scientists, in order to develop tools to analyze complex and ever-growing amounts of observed and simulated climate data, and thereby bridge the gap between data and understanding. Here, recent climate informatics work is presented, along with details of some of the field's remaining challenges. Given the impact of climate change, understanding the climate system is an international priority. The goal of climate informatics is to inspire collaboration between climate scientists and data scientists, in order to develop tools to analyze complex and ever-growing amounts of observed and simulated climate data, and thereby bridge the gap between data and understanding. Here, recent climate informatics work is presented, along with details of some of the remaining challenges.

  15. New study program: Interdisciplinary Postgraduate Specialist Study in Medical Informatics.

    PubMed

    Hercigonja-Szekeres, Mira; Simić, Diana; Božikov, Jadranka; Vondra, Petra

    2014-01-01

    Paper presents an overview of the EU funded Project of Curriculum Development for Interdisciplinary Postgraduate Specialist Study in Medical Informatics named MEDINFO to be introduced in Croatia. The target group for the program is formed by professionals in any of the areas of medicine, IT professionals working on applications of IT for health and researchers and teachers in medical informatics. In addition to Croatian students, the program will also provide opportunity for enrolling students from a wider region of Southeast Europe. Project partners are two faculties of the University of Zagreb - Faculty of Organization and Informatics from Varaždin and School of Medicine, Andrija Štampar School of Public Health from Zagreb with the Croatian Society for Medical Informatics, Croatian Chamber of Economy, and Ericsson Nikola Tesla Company as associates.

  16. Excellence in Computational Biology and Informatics — EDRN Public Portal

    Cancer.gov

    9th Early Detection Research Network (EDRN) Scientific Workshop. Excellence in Computational Biology and Informatics: Sponsored by the EDRN Data Sharing Subcommittee Moderator: Daniel Crichton, M.S., NASA Jet Propulsion Laboratory

  17. High school coaches' assessments, intentions to use, and use of a concussion prevention toolkit: Centers for Disease Control and Prevention's heads up: concussion in high school sports.

    PubMed

    Sawyer, Richard J; Hamdallah, Myriam; White, Debbie; Pruzan, Marcia; Mitchko, Jane; Huitric, Michele

    2010-01-01

    This study evaluated school coaches' perceptions, assessments, and use of a toolkit to prevent and manage concussions among school athletes. A computer-assisted telephone survey was conducted with a stratified, random sample of high school coaches (n = 497; response rate = 39.3%; cooperation rate = 81.5%) from five states. Most reported that they had used or planned to use kit materials. Most (81%) in schools with a written plan for preventing and managing concussions indicated that the toolkit could be used to improve it and 96% of coaches in schools without a plan indicated that the kit could be used to develop one. Most assessed the kit as visually appealing, easy to use, and containing appropriate content. There were no significant differences among coaches with differing professional experience or for sports with different injury rates. Among those with other concussion-prevention materials, most indicated greater satisfaction with the toolkit.

  18. Design of a Community-Engaged Health Informatics Platform with an Architecture of Participation

    PubMed Central

    Millery, Mari; Ramos, Wilson; Lien, Chueh; Aguirre, Alejandra N.; Kukafka, Rita

    2015-01-01

    Community-engaged health informatics (CEHI) applies information technology and participatory approaches to improve the health of communities. Our objective was to translate the concept of CEHI into a usable and replicable informatics platform that will facilitate community-engaged practice and research. The setting is a diverse urban neighborhood in New York City. The methods included community asset mapping, stakeholder interviews, logic modeling, analysis of affordances in open-source tools, elicitation of use cases and requirements, and a survey of early adopters. Based on synthesis of data collected, GetHealthyHeigths.org (GHH) was developed using open-source LAMP stack and Drupal content management software. Drupal’s organic groups module was used for novel participatory functionality, along with detailed user roles and permissions. Future work includes evaluation of GHH and its impact on agency and service networks. We plan to expand GHH with additional functionality to further support CEHI by combining informatics solutions with community engagement to improve health. PMID:26958227

  19. Baseline assessment of public health informatics competencies in two Hudson Valley health departments.

    PubMed

    Cunningham, Diana J; Ascher, Marie T; Viola, Deborah; Visintainer, Paul F

    2007-01-01

    Information technology has the capability to improve the way public health is practiced. Realization of this potential is possible only with a workforce ready to utilize these technologies. This project team assessed informatics competencies of employees in two county departments of health. The goal was to determine the status quo in terms of informatics competencies by surveying current levels of proficiency and relevance, and identify areas of needed training. A survey was adapted from the recommendations of a Working Group document by the Centers for Disease Control and Prevention and administered to all employees in the two health departments. Respondents evaluated proficiency and relevance for each of 26 recommended competencies. A gap score was generated between these two measures; results were compared to the recommendations of the Working Group. The following data for each job level are presented: mean gap scores by competency class; the percentage of respondents demonstrating a gap in the competencies reported to be most relevant; and the percentage of respondents meeting the target recommendations of the Working Group. The percentage of respondents who reached the targets was low in higher-level staff. And overall, employees reported low levels of relevance for most of the competencies. The average public health employee does not feel that prescribed informatics competencies are relevant to their work. Before the public health system can take advantage of information technology, relevant employee skills should be identified or developed. There needs to be a shift in thinking that will recognize the promise of information technology in everyday work.

  20. Incident Management Preparedness and Coordination Toolkit

    SciTech Connect

    Koch, Daniel B.

    2013-04-01

    As with many professions, safety planners and first responders tend to be specialists in certain areas. To be truly useful, tools should be tailored to meet their specific needs. Thus, general software suites aimed at the professional geographic information system (GIS) community might not be the best solution for a first responder with little training in GIS terminology and techniques. On the other hand, commonly used web-based map viewers may not have the capability to be customized for the planning, response, and recovery (PR&R) mission. Data formats should be open and foster easy information flow among local, state, and federal partners. Tools should be free or low-cost to address real-world budget constraints at the local level. They also need to work both with and without a network connection to be robust. The Incident Management Preparedness and Coordination Toolkit (IMPACT) can satisfy many of these needs while working in harmony with established systems at the local, state, and federal levels. The IMPACT software framework, termed the Geospatial Integrated Problem Solving Environment (GIPSE), organizes tasks, tools, and resources for the end user. It uses the concept of software wizards to both customize and extend its functionality. On the Tasks panel are a number of buttons used to initiate various operations. Similar to macros, these task buttons launch scripts that utilize the full functionality of the underlying foundational components such as the SQL spatial database and ORNL-developed map editor. The user is presented with a series of instruction pages which are implemented with HTML for interactivity. On each page are links which initiate specific actions such as creating a map showing various features. Additional tasks may be quickly programmed and added to the panel. The end user can customize the graphical interface to faciltate its use during an emergency. One of the major components of IMPACT is the ORNL Geospatial Viewer (OGV). It is used to

  1. TU-F-BRD-01: Biomedical Informatics for Medical Physicists

    SciTech Connect

    Phillips, M; Kalet, I; McNutt, T; Smith, W

    2014-06-15

    Biomedical informatics encompasses a very large domain of knowledge and applications. This broad and loosely defined field can make it difficult to navigate. Physicists often are called upon to provide informatics services and/or to take part in projects involving principles of the field. The purpose of the presentations in this symposium is to help medical physicists gain some knowledge about the breadth of the field and how, in the current clinical and research environment, they can participate and contribute. Three talks have been designed to give an overview from the perspective of physicists and to provide a more in-depth discussion in two areas. One of the primary purposes, and the main subject of the first talk, is to help physicists achieve a perspective about the range of the topics and concepts that fall under the heading of 'informatics'. The approach is to de-mystify topics and jargon and to help physicists find resources in the field should they need them. The other talks explore two areas of biomedical informatics in more depth. The goal is to highlight two domains of intense current interest--databases and models--in enough depth into current approaches so that an adequate background for independent inquiry is achieved. These two areas will serve as good examples of how physicists, using informatics principles, can contribute to oncology practice and research. Learning Objectives: To understand how the principles of biomedical informatics are used by medical physicists. To put the relevant informatics concepts in perspective with regard to biomedicine in general. To use clinical database design as an example of biomedical informatics. To provide a solid background into the problems and issues of the design and use of data and databases in radiation oncology. To use modeling in the service of decision support systems as an example of modeling methods and data use. To provide a background into how uncertainty in our data and knowledge can be

  2. The golden era of biomedical informatics has begun.

    PubMed

    Moore, Jason H; Holmes, John H

    2016-01-01

    Biomedical informatics has become a central focus for many academic medical centers and universities as biomedical research because increasingly reliant on the processing, analysis, and interpretation of large volumes of data, information, and knowledge. We posit here that this is the beginning of the golden era of biomedical informatics with opportunity for this maturing discipline to have a substantial impact on the biggest questions and challenges facing efforts to improve human health and the healthcare system.

  3. Next generation informatics for big data in precision medicine era.

    PubMed

    Zhang, Yuji; Zhu, Qian; Liu, Hongfang

    2015-01-01

    The rise of data-intensive biology, advances in informatics technology, and changes in the way health care is delivered has created an compelling opportunity to allow us investigate biomedical questions in the context of "big data" and develop knowledge systems to support precision medicine. To promote such data mining and informatics technology development in precision medicine, we hosted two international informatics workshops in 2014: 1) the first workshop on Data Mining in Biomedical informatics and Healthcare, in conjunction with the 18th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD 2014), and 2) the first workshop on Translational biomedical and clinical informatics, in conjunction with the 8th International Conference on Systems Biology and the 4th Translational Bioinformatics Conference (ISB/TBC 2014). This thematic issue of BioData Mining presents a series of selected papers from these two international workshops, aiming to address the data mining needs in the informatics field due to the deluge of "big data" generated by next generation biotechnologies such as next generation sequencing, metabolomics, and proteomics, as well as the structured and unstructured biomedical and healthcare data from electronic health records. We are grateful for the BioData Mining's willingness to produce this forward-looking thematic issue.

  4. Geospatial Toolkits and Resource Maps for Selected Countries from the National Renewable Energy Laboratory (NREL)

    DOE Data Explorer

    NREL developed the Geospatial Toolkit (GsT), a map-based software application that integrates resource data and geographic information systems (GIS) for integrated resource assessment. A variety of agencies within countries, along with global datasets, provided country-specific data. Originally developed in 2005, the Geospatial Toolkit was completely redesigned and re-released in November 2010 to provide a more modern, easier-to-use interface with considerably faster analytical querying capabilities. Toolkits are available for 21 countries and each one can be downloaded separately. The source code for the toolkit is also available. [Taken and edited from http://www.nrel.gov/international/geospatial_toolkits.html

  5. Educating Globally Competent Citizens: A Toolkit. Second Edition

    ERIC Educational Resources Information Center

    Elliott-Gower, Steven; Falk, Dennis R.; Shapiro, Martin

    2012-01-01

    Educating Globally Competent Citizens, a product of AASCU's American Democracy Project and its Global Engagement Initiative, introduces readers to a set of global challenges facing society based on the Center for Strategic and International Studies' 7 Revolutions. The toolkit is designed to aid faculty in incorporating global challenges into new…

  6. Using AASL's "Health and Wellness" and "Crisis Toolkits"

    ERIC Educational Resources Information Center

    Logan, Debra Kay

    2009-01-01

    Whether a school library program is the picture of good health in a state that mandates a professionally staffed library media center in every building or is suffering in a low-wealth district that is facing drastic cuts, the recently launched toolkits by the American Association of School Librarians (AASL) are stocked with useful strategies and…

  7. 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…

  8. Roles of the Volunteer in Development: Toolkits for Building Capacity.

    ERIC Educational Resources Information Center

    Slater, Marsha; Allsman, Ava; Savage, Ron; Havens, Lani; Blohm, Judee; Raftery, Kate

    This document, which was developed to assist Peace Corps volunteers and those responsible for training them, presents an introductory booklet and six toolkits for use in the training provided to and by volunteers involved in community development. All the materials emphasize long-term participatory approaches to sustainable development and a…

  9. The Archivists' Toolkit: Another Step toward Streamlined Archival Processing

    ERIC Educational Resources Information Center

    Westbrook, Bradley D.; Mandell, Lee; Shepherd, Kelcy; Stevens, Brian; Varghese, Jason

    2006-01-01

    The Archivists' Toolkit is a software application currently in development and designed to support the creation and management of archival information. This article summarizes the development of the application, including some of the problems the application is designed to resolve. Primary emphasis is placed on describing the application's…

  10. Cubit Mesh Generation Toolkit V11.1

    SciTech Connect

    HANKS, BYRON; KERR, ROBERT; KNUPP, PATRICK; MAEZ, JONATHAN; WHITE, DAVID; MITCHELL, SCOTT; OWEN, STEVEN; SHEPHERD, JASON; TAUTGES, TIMOTHY; MELANDER, DARRYL; BLACKER, TEDDY; BORDEN, MICHAEL; BREWER, MICHAEL; CLARK, BRETT; FORTIER, LESLIE; KALLAHER, JENNA; PEBAY, PHILIPPE; STATEN, MATTHEW; VINEYARD, CRAIG; GROVER, BENJAMIN; BENZLEY, STEVEN; SIMPSON, CLINTON; NIELSON, ERIC; KOPP, JOEL; STORM, STEVE; NUGENT, MARK; WALTON, KIRK; BORDEN, MIKE; ERNST, CORY; FOWLER, JOHN; KRAFTCHECL, JASON; STEPHNSON, MIKE; YEOU, RAMMAGAY; MERKLEY, KARL; METERS, RAY; DEWET, MARK; RICHARDS, SARA; PENDLEY, KEVIN; MORRIS, RANDY; RICHARDSON, MARK; VYAS, VED; SHOWMAN, SAM; HAYS, ALEX; TIDWELL, BOYD; MILLAR, ALEX

    2009-03-25

    CUBIT prepares models to be used in computer-based simulation of real-world events. CUBIT is a full-featured software toolkit for robust generation of two- and three-dimensional finite element meshes (grids) and geometry preparation. Its main goal is to reduce the time to generate meshes, particularly large hex meshes of complicated, interlocking assemblies.

  11. The Data Toolkit: Ten Tools for Supporting School Improvement

    ERIC Educational Resources Information Center

    Hess, Robert T.; Robbins, Pam

    2012-01-01

    Using data for school improvement is a key goal of Race to the Top, and now is the time to make data-driven school improvement a priority. However, many educators are drowning in data. Boost your professional learning community's ability to translate data into action with this new book from Pam Robbins and Robert T. Hess. "The Data Toolkit"…

  12. The MPI Bioinformatics Toolkit for protein sequence analysis

    PubMed Central

    Biegert, Andreas; Mayer, Christian; Remmert, Michael; Söding, Johannes; Lupas, Andrei N.

    2006-01-01

    The MPI Bioinformatics Toolkit is an interactive web service which offers access to a great variety of public and in-house bioinformatics tools. They are grouped into different sections that support sequence searches, multiple alignment, secondary and tertiary structure prediction and classification. Several public tools are offered in customized versions that extend their functionality. For example, PSI-BLAST can be run against regularly updated standard databases, customized user databases or selectable sets of genomes. Another tool, Quick2D, integrates the results of various secondary structure, transmembrane and disorder prediction programs into one view. The Toolkit provides a friendly and intuitive user interface with an online help facility. As a key feature, various tools are interconnected so that the results of one tool can be forwarded to other tools. One could run PSI-BLAST, parse out a multiple alignment of selected hits and send the results to a cluster analysis tool. The Toolkit framework and the tools developed in-house will be packaged and freely available under the GNU Lesser General Public Licence (LGPL). The Toolkit can be accessed at . PMID:16845021

  13. ELCAT: An E-Learning Content Adaptation Toolkit

    ERIC Educational Resources Information Center

    Clements, Iain; Xu, Zhijie

    2005-01-01

    Purpose: The purpose of this paper is to present an e-learning content adaptation toolkit--ELCAT--that helps to achieve the objectives of the KTP project No. 3509. Design/methodology/approach: The chosen methodology is absolutely practical. The tool was put into motion and results were observed as university and the collaborating company members…

  14. A Beginning Rural Principal's Toolkit: A Guide for Success

    ERIC Educational Resources Information Center

    Ashton, Brian; Duncan, Heather E.

    2012-01-01

    The purpose of this article is to explore both the challenges and skills needed to effectively assume a leadership position and thus to create an entry plan or "toolkit" for a new rural school leader. The entry plan acts as a guide beginning principals may use to navigate the unavoidable confusion that comes with leadership. It also assists…

  15. 77 FR 73023 - U.S. Environmental Solutions Toolkit

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-07

    ... supplying relevant goods and services to foreign buyers. United States exporters interested in being listed... the Toolkit, ``United States exporter'' has the meaning found in 15 U.S.C. 4721(j), which provides: ``United States exporter means (A) a United States citizen; (B) a corporation, partnership, or...

  16. 77 FR 73022 - U.S. Environmental Solutions Toolkit

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-07

    ... identification of U.S. vendors capable of supplying relevant goods and services to foreign buyers. United States... tanks. For purposes of participation in the Toolkit, ``United States exporter'' has the meaning found in 15 U.S.C. 4721(j), which provides: ``United States exporter means (A) a United States citizen; (B)...

  17. 77 FR 73023 - U.S. Environmental Solutions Toolkit

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-07

    .... vendors capable of supplying relevant goods and services to foreign buyers. United States exporters... purposes of participation in the Toolkit, ``United States exporter'' has the meaning found in 15 U.S.C. 4721(j), which provides: ``United States exporter means (A) a United States citizen; (B) a...

  18. Simulation toolkit with CMOS detector in the framework of hadrontherapy

    NASA Astrophysics Data System (ADS)

    Rescigno, R.; Finck, Ch.; Juliani, D.; Baudot, J.; Dauvergne, D.; Dedes, G.; Krimmer, J.; Ray, C.; Reithinger, V.; Rousseau, M.; Testa, E.; Winter, M.

    2014-03-01

    Proton imaging can be seen as a powerful technique for on-line monitoring of ion range during carbon ion therapy irradiation. The protons detection technique uses, as three-dimensional tracking system, a set of CMOS sensor planes. A simulation toolkit based on GEANT4 and ROOT is presented including detector response and reconstruction algorithm.

  19. Using an Assistive Technology Toolkit to Promote Inclusion

    ERIC Educational Resources Information Center

    Judge, Sharon; Floyd, Kim; Jeffs, Tara

    2008-01-01

    Although the use of assistive technology for young children is increasing, the lack of awareness and the lack of training continue to act as major barriers to providers using assistive technology. This article describes an assistive technology toolkit designed for use with young children with disabilities that can be easily assembled and…

  20. 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...

  1. Capturing and Using Knowledge about the Use of Visualization Toolkits

    SciTech Connect

    Del Rio, Nicholas R.; Pinheiro da Silva, Paulo

    2012-11-02

    When constructing visualization pipelines using toolkits such as Visualization Toolkit (VTK) and Generic Mapping Tools (GMT), developers must understand (1) what toolkit operators will transform their data from its raw state to some required view state and (2) what viewers are available to present the generated view. Traditionally, developers learn about how to construct visualization pipelines by reading documentation and inspecting code examples, which can be costly in terms of the time and effort expended. Once an initial pipeline is constructed, developers may still have to undergo a trial and error process before a satisfactory visualization is generated. This paper presents the Visualization Knowledge Project (VisKo) that is built on a knowledge base of visualization toolkit operators and how they can be piped together to form visualization pipelines. Developers may now rely on VisKo to guide them when constructing visualization pipelines and in some cases, when VisKo has complete knowledge about some set of operators (i.e., sequencing and parameter settings), automatically generate a fully functional visualization pipeline.

  2. The Complete Guide to RTI: An Implementation Toolkit

    ERIC Educational Resources Information Center

    Burton, Dolores; Kappenberg, John

    2012-01-01

    This comprehensive toolkit will bring you up to speed on why RTI is one of the most important educational initiatives in recent history and sets the stage for its future role in teacher education and practice. The authors demonstrate innovative ways to use RTI to inform instruction and guide curriculum development in inclusive classroom settings.…

  3. Policy to Performance Toolkit: Transitioning Adults to Opportunity

    ERIC Educational Resources Information Center

    Alamprese, Judith A.; Limardo, Chrys

    2012-01-01

    The "Policy to Performance Toolkit" is designed to provide state adult education staff and key stakeholders with guidance and tools to use in developing, implementing, and monitoring state policies and their associated practices that support an effective state adult basic education (ABE) to postsecondary education and training transition…

  4. Evolving the US Climate Resilience Toolkit to Support a Climate-Smart Nation

    NASA Astrophysics Data System (ADS)

    Tilmes, C.; Niepold, F., III; Fox, J. F.; Herring, D.; Dahlman, L. E.; Hall, N.; Gardiner, N.

    2015-12-01

    Communities, businesses, resource managers, and decision-makers at all levels of government need information to understand and ameliorate climate-related risks. Likewise, climate information can expose latent opportunities. Moving from climate science to social and economic decisions raises complex questions about how to communicate the causes and impacts of climate variability and change; how to characterize and quantify vulnerabilities, risks, and opportunities faced by communities and businesses; and how to make and implement "win-win" adaptation plans at local, regional, and national scales. A broad coalition of federal agencies launched the U.S. Climate Resilience Toolkit (toolkit.climate.gov) in November 2014 to help our nation build resilience to climate-related extreme events. The site's primary audience is planners and decision makers in business, resource management, and government (at all levels) who seek science-based climate information and tools to help them in their near- and long-term planning. The Executive Office of the President assembled a task force of dozens of subject experts from across the 13 agencies of the U.S. Global Change Research Program to guide the site's development. The site's ongoing evolution is driven by feedback from the target audience. For example, based on feedback, climate projections will soon play a more prominent role in the site's "Climate Explorer" tool and case studies. The site's five-step adaptation planning process is being improved to better facilitate people getting started and to provide clear benchmarks for evaluating progress along the way. In this session, we will share lessons learned from a series of user engagements around the nation and evidence that the Toolkit couples climate information with actionable decision-making processes in ways that are helping Americans build resilience to climate-related stressors.

  5. Mission and Sustainability of Informatics for Integrating Biology and the Bedside (i2b2)

    PubMed Central

    Murphy, Shawn; Wilcox, Adam

    2014-01-01

    Introduction: A visible example of a successfully disseminated research project in the healthcare space is Informatics for Integrating Biology and the Bedside, or i2b2. The project serves to provide the software that can allow a researcher to do direct, self-serve queries against the electronic healthcare data form a hospital. The goals of these queries are to find cohorts of patients that fit specific profiles, while providing for patient privacy and discretion. Sustaining this resource and keeping its direction has always been a challenge, but ever more so as the ten year National Centers for Biomedical Computing (NCBCs) sunset their funding. Findings: Building on the i2b2 structures has helped the dissemination plans for grants leveraging it because it is a disseminated national resource. While this has not directly increased the support of i2b2 internally, it has increased the ability of institutions to leverage the resource and generally leads to increased institutional support. Discussion: The successful development, use, and dissemination i2b2 has been significant in clinical research and informatics. Its evolution has been from a local research data infrastructure to one disseminated more broadly than any other product of the National Centers for Biomedical Computing, and an infrastructure spawning larger investments than were originally used to create it. Throughout this, there were two main lessons about the benefits of dissemination: that people have great creativity in utilizing a resource in different ways and that broader system use can make the system more robust. One option for long-term sustainability of the central authority would be to translate the function to an industry partner. Another option currently being pursued is to create a foundation that would be a central authority for the project. Conclusion: Over the past 10 years, i2b2 has risen to be an important staple in the toolkit of health care researchers. There are now over 110 hospitals

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

    SciTech Connect

    Mandelli, Diego; Prescott, Steven R; Smith, Curtis L; Alfonsi, Andrea; Rabiti, Cristian; Cogliati, Joshua J; Kinoshita, Robert A

    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 a 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.

  7. WE-E-12A-01: Medical Physics 1.0 to 2.0: MRI, Displays, Informatics

    SciTech Connect

    Pickens, D; Flynn, M; Peck, D

    2014-06-15

    Medical Physics 2.0 is a bold vision for an existential transition of clinical imaging physics in face of the new realities of value-based and evidence-based medicine, comparative effectiveness, and meaningful use. It speaks to how clinical imaging physics can expand beyond traditional insular models of inspection and acceptance testing, oriented toward compliance, towards team-based models of operational engagement, prospective definition and assurance of effective use, and retrospective evaluation of clinical performance. Organized into four sessions of the AAPM, this particular session focuses on three specific modalities as outlined below. MRI 2.0: This presentation will look into the future of clinical MR imaging and what the clinical medical physicist will need to be doing as the technology of MR imaging evolves. Many of the measurement techniques used today will need to be expanded to address the advent of higher field imaging systems and dedicated imagers for specialty applications. Included will be the need to address quality assurance and testing metrics for multi-channel MR imagers and hybrid devices such as MR/PET systems. New pulse sequences and acquisition methods, increasing use of MR spectroscopy, and real-time guidance procedures will place the burden on the medical physicist to define and use new tools to properly evaluate these systems, but the clinical applications must be understood so that these tools are use correctly. Finally, new rules, clinical requirements, and regulations will mean that the medical physicist must actively work to keep her/his sites compliant and must work closely with physicians to ensure best performance of these systems. Informatics Display 1.0 to 2.0: Medical displays are an integral part of medical imaging operation. The DICOM and AAPM (TG18) efforts have led to clear definitions of performance requirements of monochrome medical displays that can be followed by medical physicists to ensure proper performance. However

  8. The Methods Behind 2015 Informatics Capacity and Needs Assessment Study

    PubMed Central

    2016-01-01

    The 2015 Informatics Needs and Capacity of Local Health Departments (LHDs) survey is the most recent comprehensive source of quantitative data on LHD informatics. Conducted by the National Association of County & City Health Officials (NACCHO), this is the third nationally representative quantitative study of LHD informatics since 2009. The previous 2 comprehensive quantitative assessments were conducted by NACCHO in 2009-2010 and 2011. Given that public health informatics is rapidly evolving, the 2015 Informatics survey is a much-needed country-wide assessment of the current informatics needs and capacities of LHDs. This article outlines detailed methodology used in the 2015 Informatics survey, including instrument development, pretesting, sampling design and sample size, survey administration, and sampling weights. A 9-member advisory committee representing federal, state, and local health agency representatives guided the design and implementation of this study. The survey instrument was organized into 6 topic areas: demographics, physical infrastructure, skills and capacity available, public health workforce development needs, electronic health records, and health information exchange. The instrument was pretested with a sample of 20 LHDs and subsequently pilot-tested with 30 LHDs. The survey was administered via the Qualtrics survey software to the sample of 650 LHDs, selected using stratified random sampling. The survey was fielded for approximately 8 weeks and 324 usable responses were received, constituting a response rate of 50%. Statistical weights were developed to account for 3 factors: (a) disproportionate response rate by population size (using 7 population strata), (b) oversampling of LHDs with larger population sizes, and (c) sampling rather than a census approach. PMID:27684627

  9. A Delphi study to determine baseline informatics competencies for nurse managers.

    PubMed

    Hart, Michael D

    2010-01-01

    The objective of this research study was to produce a job-specific list of informatics competencies for generic nurse manager positions. In 2002, Staggers et al (Nurs Res. 2002;51(6):383-390) identified a list of core nursing informatics competencies at four levels of nursing practice but concluded that job-specific competencies still needed to be developed. An expert panel utilized the Master List of Nursing Informatics Competencies produced in the 2002 study by Staggers et al to define the job-specific informatics competencies appropriate for generic nurse manager positions. A three-round Delphi study was utilized to establish the core competencies appropriate for this job-specific position. Participants were expert informatics nurses in the US Veterans' Healthcare System. Based on the Four Levels of Practice defined in the 2002 study by Staggers et al, the panel identified the level 2 experienced nurse as most appropriate for generic nurse manager positions. For the purposes of review, each practice level was considered to include the competencies of the levels below it. Therefore, having selected level 2 experienced nurse, this necessitated the review of levels 1 and 2, which totaled 69 competencies. From the available 69 competencies, the panel selected a total of 49 core competencies appropriate for generic nurse manager positions. This Delphi research study chose to focus on a single job-specific position to take one small step toward the recommendation of Staggers et al to identify job-specific competencies. The generic nurse manager position was selected as it is a vital position in providing leadership and support within all institutions. While the study raises several questions about how the panel elected some competencies over others, it also begins to define which levels of competencies and categories are most appropriate. With this information at hand, the next logical step would be to establish associated tools for competency development and

  10. Nursing informatics: state of the science.

    PubMed

    Henry, S B

    1995-12-01

    The phenomena of interest in nursing informatics are nursing data, nursing information and nursing knowledge. The current state of knowledge related to these phenomena suggests four implications for the development of systems to support nursing. First, research has provided evidence that knowledge and experience is related to the quality of nursing assessment, diagnosis or clinical inference, and planning of nursing care, and also that knowledge is task-specific. Information technology can provide access to a variety of information resources, such as knowledge bases and decision support systems, to increase the level of knowledge of the nurse decision-maker. Second, structured patient assessment forms with linkages to knowledge bases of diagnoses have the potential to improve the quality of the patient assessment and the accuracy of the diagnosis or clinical inference. Third, studies on planning care have demonstrated the complexity of the task when a number of options are potentially appropriate. Model-based decision support applications such as decision analysis and multi-attribute utility theory can assist the clinicians and patients to analyse and compare the treatment alternatives in a systematic manner. Fourth, there is modest support for demonstrating the relationship between the process and outcomes of clinical decision making. Large databases built upon nursing data are needed to further examine this relationship.

  11. Lost and found in behavioral informatics.

    PubMed

    Haendel, Melissa A; Chesler, Elissa J

    2012-01-01

    From early anatomical lesion studies to the molecular and cellular methods of today, a wealth of technologies have provided increasingly sophisticated strategies for identifying and characterizing the biological basis of behaviors. Bioinformatics is a growing discipline that has emerged from the practical needs of modern biology, and the history of systematics and ontology in data integration and scientific knowledge construction. This revolution in biology has resulted in a capability to couple the rich molecular, anatomical, and psychological assays with advances in data dissemination and integration. However, behavioral science poses unique challenges for biology and medicine, and many unique resources have been developed to take advantage of the strategies and technologies of an informatics approach. The collective developments of this diverse and interdisciplinary field span the fundamentals of database development and data integration, ontology development, text mining, genetics, genomics, high-throughput analytics, image analysis and archiving, and numerous others. For the behavioral sciences, this provides a fundamental shift in our ability to associate and dissociate behavioral processes and relate biological and behavioral entities, thereby pinpointing the biological basis of behavior.

  12. 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. Par

  13. Simplifying operations with an uplink/downlink integration toolkit

    NASA Technical Reports Server (NTRS)

    Murphy, Susan C.; Miller, Kevin J.; Guerrero, Ana Maria; Joe, Chester; Louie, John J.; Aguilera, Christine

    1994-01-01

    The Operations Engineering Lab (OEL) at JPL has developed a simple, generic toolkit to integrate the uplink/downlink processes, (often called closing the loop), in JPL's Multimission Ground Data System. This toolkit provides capabilities for integrating telemetry verification points with predicted spacecraft commands and ground events in the Mission Sequence Of Events (SOE) document. In the JPL ground data system, the uplink processing functions and the downlink processing functions are separate subsystems that are not well integrated because of the nature of planetary missions with large one-way light times for spacecraft-to-ground communication. Our new closed-loop monitoring tool allows an analyst or mission controller to view and save uplink commands and ground events with their corresponding downlinked telemetry values regardless of the delay in downlink telemetry and without requiring real-time intervention by the user. An SOE document is a time-ordered list of all the planned ground and spacecraft events, including all commands, sequence loads, ground events, significant mission activities, spacecraft status, and resource allocations. The SOE document is generated by expansion and integration of spacecraft sequence files, ground station allocations, navigation files, and other ground event files. This SOE generation process has been automated within the OEL and includes a graphical, object-oriented SOE editor and real-time viewing tool running under X/Motif. The SOE toolkit was used as the framework for the integrated implementation. The SOE is used by flight engineers to coordinate their operations tasks, serving as a predict data set in ground operations and mission control. The closed-loop SOE toolkit allows simple, automated integration of predicted uplink events with correlated telemetry points in a single SOE document for on-screen viewing and archiving. It automatically interfaces with existing real-time or non real-time sources of information, to

  14. Investigating Informatics Activity, Control, and Training Needs in Large, Medium, and Small Health Departments

    PubMed Central

    Arnold, Ryan; Yang, Biru

    2016-01-01

    Introduction: A recent National Association of City & County Health Officials survey shed light on informatics workforce development needs. Local health departments (LHDs) of various jurisdictional sizes and control over informatics may differ on training needs and activity. Understanding the precise nature of this variation will allow stakeholders to appropriately develop workforce development tools to advance the field. Objective: To understand the informatics training needs for LHDs of different jurisdictional sizes. Methods: Survey responses were analyzed by comparing training needs and LHD population size. Results: Larger health departments consistently reported having greater informatics-related capacity and informatics-related training needs. Quantitative data analysis was identified as a primary need for large LHDs. In addition, LHDs that report higher control of informatics/information technology were able to engage in more informatics activities. Conclusion: Smaller LHDs need additional resources to improve informatics-related capacity and engagement with the field. PMID:27684621

  15. Innovation in transformative nursing leadership: nursing informatics competencies and roles.

    PubMed

    Remus, Sally; Kennedy, Margaret Ann

    2012-12-01

    In a recent brief to the Canadian Nurses Association's National Expert Commission on the Health of Our Nation, the Academy of Canadian Executive Nurses (ACEN) discussed leadership needs in the Canadian healthcare system, and promoted the pivotal role of nursing executives in transforming Canada's healthcare system into an integrated patient-centric system. Included among several recommendations was the need to develop innovative leadership competencies that enable nurse leaders to lead and advance transformative health system change. This paper focuses on an emerging "avant-garde executive leadership competency" recommended for today's health leaders to guide health system transformation. Specifically, this competency is articulated as "state of the art communication and technology savvy," and it implies linkages between nursing informatics competencies and transformational leadership roles for nurse executive. The authors of this paper propose that distinct nursing informatics competencies are required to augment traditional executive skills to support transformational outcomes of safe, integrated, high-quality care delivery through knowledge-driven care. International trends involving nursing informatics competencies and the evolution of new corporate informatics roles, such as chief nursing informatics officers (CNIOs), are demonstrating value and advanced transformational leadership as nursing executive roles that are informed by clinical data.

  16. Building Confidence in the Community Ice Sheet Model (CISM) with LIVVkit, the Land Ice Validation and Verification Toolkit

    NASA Astrophysics Data System (ADS)

    Kennedy, J. H.; Bennett, A. R.; Evans, K. J.; Worley, P.; Price, S. F.; Hoffman, M. J.

    2015-12-01

    Using an ice flow model to make inferences of real world systems requires a high level of confidence in the model. Verification and validation (V&V) is a set of techniques that are used to quantify confidence and build credibility. We are developing LIVVkit (Land Ice Verification and Validation toolkit), a comprehensive V&V toolkit for ice sheet models, to help scientists make robust inferences of real world systems with their models. LIVVkit is written in python, due to its wide usage throughout the scientific community and should be easily accessible to a large number of users. The toolkit provides resources for data assimilation, verification testing, validation testing, and performance evaluations. A website is created automatically which presents the testing results in a comprehensive and user-friendly way. LIVVkit allows scientists and developers to implement reusable validation tests of model applications and build confidence in their ice flow model. Currently, we are working with scientific users and developers of the Community Ice Sheet Model (CISM) for the development of LIVVkit, but LIVVkit is designed to be extensible to other ice flow models.

  17. Developing Mixed Reality Educational Applications: The Virtual Touch Toolkit.

    PubMed

    Mateu, Juan; Lasala, María José; Alamán, Xavier

    2015-08-31

    In this paper, we present Virtual Touch, a toolkit that allows the development of educational activities through a mixed reality environment such that, using various tangible elements, the interconnection of a virtual world with the real world is enabled. The main goal of Virtual Touch is to facilitate the installation, configuration and programming of different types of technologies, abstracting the creator of educational applications from the technical details involving the use of tangible interfaces and virtual worlds. Therefore, it is specially designed to enable teachers to themselves create educational activities for their students in a simple way, taking into account that teachers generally lack advanced knowledge in computer programming and electronics. The toolkit has been used to develop various educational applications that have been tested in two secondary education high schools in Spain.

  18. 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.

  19. ProtoMD: A prototyping toolkit for multiscale molecular dynamics

    NASA Astrophysics Data System (ADS)

    Somogyi, Endre; Mansour, Andrew Abi; Ortoleva, Peter J.

    2016-05-01

    ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales, such as the atomic to the mesoscopic scale, via coevolving microscopic and coarse-grained (CG) variables. ProtoMD can be also be used to calibrate parameters needed in traditional CG-MD methods. The toolkit integrates 'GROMACS wrapper' to initiate MD simulations, and 'MDAnalysis' to analyze and manipulate trajectory files. It facilitates experimentation with a spectrum of coarse-grained variables, prototyping rare events (such as chemical reactions), or simulating nanocharacterization experiments such as terahertz spectroscopy, AFM, nanopore, and time-of-flight mass spectroscopy. ProtoMD is written in python and is freely available under the GNU General Public License from github.com/CTCNano/proto_md.

  20. Developing Mixed Reality Educational Applications: The Virtual Touch Toolkit

    PubMed Central

    Mateu, Juan; Lasala, María José; Alamán, Xavier

    2015-01-01

    In this paper, we present Virtual Touch, a toolkit that allows the development of educational activities through a mixed reality environment such that, using various tangible elements, the interconnection of a virtual world with the real world is enabled. The main goal of Virtual Touch is to facilitate the installation, configuration and programming of different types of technologies, abstracting the creator of educational applications from the technical details involving the use of tangible interfaces and virtual worlds. Therefore, it is specially designed to enable teachers to themselves create educational activities for their students in a simple way, taking into account that teachers generally lack advanced knowledge in computer programming and electronics. The toolkit has been used to develop various educational applications that have been tested in two secondary education high schools in Spain. PMID:26334275

  1. CRAVAT: cancer-related analysis of variants toolkit

    PubMed Central

    Douville, Christopher; Carter, Hannah; Kim, Rick; Niknafs, Noushin; Diekhans, Mark; Stenson, Peter D.; Cooper, David N.; Ryan, Michael; Karchin, Rachel

    2013-01-01

    Summary: Advances in sequencing technology have greatly reduced the costs incurred in collecting raw sequencing data. Academic laboratories and researchers therefore now have access to very large datasets of genomic alterations but limited time and computational resources to analyse their potential biological importance. Here, we provide a web-based application, Cancer-Related Analysis of Variants Toolkit, designed with an easy-to-use interface to facilitate the high-throughput assessment and prioritization of genes and missense alterations important for cancer tumorigenesis. Cancer-Related Analysis of Variants Toolkit provides predictive scores for germline variants, somatic mutations and relative gene importance, as well as annotations from published literature and databases. Results are emailed to users as MS Excel spreadsheets and/or tab-separated text files. Availability: http://www.cravat.us/ Contact: karchin@jhu.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23325621

  2. G EANT4—a simulation toolkit

    NASA Astrophysics Data System (ADS)

    Agostinelli, S.; Allison, J.; Amako, K.; Apostolakis, J.; Araujo, H.; Arce, P.; Asai, M.; Axen, D.; Banerjee, S.; Barrand, G.; Behner, F.; Bellagamba, L.; Boudreau, J.; Broglia, L.; Brunengo, A.; Burkhardt, H.; Chauvie, S.; Chuma, J.; Chytracek, R.; Cooperman, G.; Cosmo, G.; Degtyarenko, P.; Dell'Acqua, A.; Depaola, G.; Dietrich, D.; Enami, R.; Feliciello, A.; Ferguson, C.; Fesefeldt, H.; Folger, G.; Foppiano, F.; Forti, A.; Garelli, S.; Giani, S.; Giannitrapani, R.; Gibin, D.; Gómez Cadenas, J. J.; González, I.; Gracia Abril, G.; Greeniaus, G.; Greiner, W.; Grichine, V.; Grossheim, A.; Guatelli, S.; Gumplinger, P.; Hamatsu, R.; Hashimoto, K.; Hasui, H.; Heikkinen, A.; Howard, A.; Ivanchenko, V.; Johnson, A.; Jones, F. W.; Kallenbach, J.; Kanaya, N.; Kawabata, M.; Kawabata, Y.; Kawaguti, M.; Kelner, S.; Kent, P.; Kimura, A.; Kodama, T.; Kokoulin, R.; Kossov, M.; Kurashige, H.; Lamanna, E.; Lampén, T.; Lara, V.; Lefebure, V.; Lei, F.; Liendl, M.; Lockman, W.; Longo, F.; Magni, S.; Maire, M.; Medernach, E.; Minamimoto, K.; Mora de Freitas, P.; Morita, Y.; Murakami, K.; Nagamatu, M.; Nartallo, R.; Nieminen, P.; Nishimura, T.; Ohtsubo, K.; Okamura, M.; O'Neale, S.; Oohata, Y.; Paech, K.; Perl, J.; Pfeiffer, A.; Pia, M. G.; Ranjard, F.; Rybin, A.; Sadilov, S.; Di Salvo, E.; Santin, G.; Sasaki, T.; Savvas, N.; Sawada, Y.; Scherer, S.; Sei, S.; Sirotenko, V.; Smith, D.; Starkov, N.; Stoecker, H.; Sulkimo, J.; Takahata, M.; Tanaka, S.; Tcherniaev, E.; Safai Tehrani, E.; Tropeano, M.; Truscott, P.; Uno, H.; Urban, L.; Urban, P.; Verderi, M.; Walkden, A.; Wander, W.; Weber, H.; Wellisch, J. P.; Wenaus, T.; Williams, D. C.; Wright, D.; Yamada, T.; Yoshida, H.; Zschiesche, D.; G EANT4 Collaboration

    2003-07-01

    G EANT4 is a toolkit for simulating the passage of particles through matter. It includes a complete range of functionality including tracking, geometry, physics models and hits. The physics processes offered cover a comprehensive range, including electromagnetic, hadronic and optical processes, a large set of long-lived particles, materials and elements, over a wide energy range starting, in some cases, from 250 eV and extending in others to the TeV energy range. It has been designed and constructed to expose the physics models utilised, to handle complex geometries, and to enable its easy adaptation for optimal use in different sets of applications. The toolkit is the result of a worldwide collaboration of physicists and software engineers. It has been created exploiting software engineering and object-oriented technology and implemented in the C++ programming language. It has been used in applications in particle physics, nuclear physics, accelerator design, space engineering and medical physics.

  3. A toolkit for epithermal neutron beam characterisation in BNCT.

    PubMed

    Auterinen, Iiro; Serén, Tom; Uusi-Simola, Jouni; Kosunen, Antti; Savolainen, Sauli

    2004-01-01

    Methods for dosimetry of epithermal neutron beams used in boron neutron capture therapy (BNCT) have been developed and utilised within the Finnish BNCT project as well as within a European project for a code of practise for the dosimetry of BNCT. One outcome has been a travelling toolkit for BNCT dosimetry. It consists of activation detectors and ionisation chambers. The free-beam neutron spectrum is measured with a set of activation foils of different isotopes irradiated both in a Cd-capsule and without it. Neutron flux (thermal and epithermal) distribution in phantoms is measured using activation of Mn and Au foils, and Cu wire. Ionisation chamber (IC) measurements are performed both in-free-beam and in-phantom for determination of the neutron and gamma dose components. This toolkit has also been used at other BNCT facilities in Europe, the USA, Argentina and Japan.

  4. Programmatic Role of Education Libraries in Informatics to Support Preservice Teacher Preparation Programs

    ERIC Educational Resources Information Center

    Farmer, Lesley S. J.

    2010-01-01

    Background/Context: The management, processing, and transformation of information constitute central tasks in education. Education informatics intersects the theories and practices of both informatics and education. In particular, informatics aids in the systematic incorporation of technology as educational stakeholders represent, process, and…

  5. Enhancing "Mathematics for Informatics" and its Correlation with Student Pass Rates

    ERIC Educational Resources Information Center

    Divjak, B.; Erjavec, Z.

    2008-01-01

    In this article, changes in "Mathematics for Informatics" at the Faculty of Organisation and Informatics in the University of Zagreb are described, and correlated with students pass rates. Students at the Faculty work in an interdisciplinary field, studying Informatics within a business context. The main reason for introducing the…

  6. Interpreting concept learning in cognitive informatics and granular computing.

    PubMed

    Yao, Yiyu

    2009-08-01

    Cognitive informatics and granular computing are two emerging fields of study concerning information and knowledge processing. A central notion to this processing is information and knowledge granularity. Concepts, as the basic units of thought underlying human intelligence and communication, may play a fundamental role when integrating the results from the two fields in terms of information and knowledge coding, representation, communication, and processing. While cognitive informatics focuses on information processing in the abstract, in machines, and in the brain, granular computing models such processing at multiple levels of granularity. In this paper, we examine a conceptual framework for concept learning from the viewpoints of cognitive informatics and granular computing. Within the framework, we interpret concept learning based on a layered model of knowledge discovery.

  7. Dental Informatics in India: Time to Embrace the Change.

    PubMed

    Chhabra, Kumar Gaurav; Mulla, Salma H; Deolia, Shravani Govind; Chhabra, Chaya; Singh, Jagjeet; Marwaha, Baldeep Singh

    2016-03-01

    Dental informatics is comparatively a juvenile and new field that has noteworthy potential for supporting clinical care, research, education and management. This field utilizes computer science, information sciences and the application of same to espouse dentistry. However, in the under-developed and developing countries almost most of the dentists are unacquainted about dental informatics, its goals, what it is capable of achieving and by what means they can get involved into it. Despite of emerging advances, certain conflicts also go along with it such as, professional under representation, security issues of the stored information due to universal access to computers high speed internet connections. Endnote software was used as resource material to collect literature which was carefully arranged in a synchronized way. Hence, the purpose of this review was to give an overall scenario of dental informatics, its applications, challenges and recommendations for further enhancement in this area.

  8. Dental Informatics in India: Time to Embrace the Change

    PubMed Central

    Mulla, Salma H.; Deolia, Shravani Govind; Chhabra, Chaya; Singh, Jagjeet; Marwaha, Baldeep Singh

    2016-01-01

    Dental informatics is comparatively a juvenile and new field that has noteworthy potential for supporting clinical care, research, education and management. This field utilizes computer science, information sciences and the application of same to espouse dentistry. However, in the under-developed and developing countries almost most of the dentists are unacquainted about dental informatics, its goals, what it is capable of achieving and by what means they can get involved into it. Despite of emerging advances, certain conflicts also go along with it such as, professional under representation, security issues of the stored information due to universal access to computers high speed internet connections. Endnote software was used as resource material to collect literature which was carefully arranged in a synchronized way. Hence, the purpose of this review was to give an overall scenario of dental informatics, its applications, challenges and recommendations for further enhancement in this area. PMID:27135022

  9. The Question Concerning Narration of Self in Health Informatics.

    PubMed

    Botin, Lars

    2015-01-01

    Narration is central, even crucial, when it comes to embracing the whole individual, continuity of care, and responsible (ethical) handling of the technological construction of the self that takes place in health informatics. This paper will deal with the role of narratives in the construction of health informatics platforms and how different voices should have space for speech on these platforms. Theoretically the paper takes an outset in the actant model for narratives by the French-Lithuanian theorist of linguistics and literature A.-J. Greimas and post-phenomenological readings of human-technology interactions. The main assumption is that certain interactions and voices are absent from the construction of health informatics platforms, because regarded as outside the text of computational and medical practice and expertise. This has implications for what concerns meaning and understanding regarding both the actual users (physicians and medical staff) and excluded users (patients and citizens).

  10. The Evaluation Toolkit: A Work-in-Progress.

    ERIC Educational Resources Information Center

    Benton Foundation, Washington, DC.

    "The E-Rate in America" (February 2000) was one of the earliest efforts to assess the impact of the then-new federal program. In this second phase of the study, the Benton Foundation and the Center for Children and Technology continue to investigate the E-Rate while developing new tools to assist teachers, administrators, and…

  11. Object Toolkit Version 4.2 Users Manual

    DTIC Science & Technology

    2014-10-31

    Figure 2. Nascap-2k Model of the MESSENGER Spacecraft , Showing Biased Solar Array Surfaces...The Panel Is 4.4 m in Width and 7 m in Length. It Is Seven Elements Wide and Fifteen Elements Long. The Front Side Is Material Solar Cells and the...While all of these figures show spacecraft , the object generated is not limited to spacecraft . A single instrument can be an Object Toolkit object as

  12. Integrated Architectural Level Power-Performance Modeling Toolkit

    DTIC Science & Technology

    2004-08-20

    laptop) systems. We utilize the MET/ Turandot toolkit originally developed at IBM TJ Watson Research Center as the underlying PowerPC...microarchitecture performance simulator [3]. Turandot is flexible enough to model a broad range of microarchitectures and has undergone extensive validation [3...In addition, Turandot has been augmented with power models to explore power-performance tradeoffs in an internal IBM tool called PowerTimer [4

  13. Business plans--tips from the toolkit 6.

    PubMed

    Steer, Neville

    2010-07-01

    General practice is a business. Most practices can stay afloat by having appointments, billing patients, managing the administration processes and working long hours. What distinguishes the high performance organisation from the average organisation is a business plan. This article examines how to create a simple business plan that can be applied to the general practice setting and is drawn from material contained in The Royal Australian College of General Practitioners' 'General practice management toolkit'.

  14. Risk of resource failure and toolkit variation in small-scale farmers and herders.

    PubMed

    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.

  15. Guide to Using the WIND Toolkit Validation Code

    SciTech Connect

    Lieberman-Cribbin, W.; Draxl, C.; Clifton, A.

    2014-12-01

    In response to the U.S. Department of Energy's goal of using 20% wind energy by 2030, the Wind Integration National Dataset (WIND) Toolkit was created to provide information on wind speed, wind direction, temperature, surface air pressure, and air density on more than 126,000 locations across the United States from 2007 to 2013. The numerical weather prediction model output, gridded at 2-km and at a 5-minute resolution, was further converted to detail the wind power production time series of existing and potential wind facility sites. For users of the dataset it is important that the information presented in the WIND Toolkit is accurate and that errors are known, as then corrective steps can be taken. Therefore, we provide validation code written in R that will be made public to provide users with tools to validate data of their own locations. Validation is based on statistical analyses of wind speed, using error metrics such as bias, root-mean-square error, centered root-mean-square error, mean absolute error, and percent error. Plots of diurnal cycles, annual cycles, wind roses, histograms of wind speed, and quantile-quantile plots are created to visualize how well observational data compares to model data. Ideally, validation will confirm beneficial locations to utilize wind energy and encourage regional wind integration studies using the WIND Toolkit.

  16. 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

  17. The WMTSA Wavelet Toolkit for Data Analysis in the Geosciences

    NASA Astrophysics Data System (ADS)

    Cornish, C. R.; Percival, D. B.; Bretherton, C. S.

    2003-12-01

    Whereas Fourier analysis and similar spectral techniques are widely used for data analysis in the geosciences, their application is based on the assumption that the analyzed signal is stationary and well-sampled. However, many phenomena of interest in the natural environment are transitory and non-stationary. Furthermore, limited sampling of observations results in datasets that are incomplete and vary in sampling rates and durations. Wavelet decomposition techniques do not require the assumption of signal stationary. Additionally wavelet analysis methods can accommodate data series of any length, be used for signal filtering and reconstruction, and allow the localization of spectral signatures in time. We present an overview of the WMTSA toolkit, which is an implementation of the wavelet methods for time series analysis presented by Percival and Walden (2000). The WMTSA toolkit is being developed for multiple programming platforms (including Matlab, R, C) and being made available to the greater scientific community to use in their data analysis applications. We will demonstrate an application and results of using the WMTSA toolkit to the study of turbulence in the atmospheric boundary layer. Reference: D. B. Percival and A. T. Walden (2000), Wavelet Methods for Time Series Analysis. Cambridge, England: Cambridge University Press.

  18. 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.

  19. Lesion registration for longitudinal disease tracking in an imaging informatics-based multiple sclerosis eFolder

    NASA Astrophysics Data System (ADS)

    Ma, Kevin; Liu, Joseph; Zhang, Xuejun; Lerner, Alex; Shiroishi, Mark; Amezcua, Lilyana; Liu, Brent

    2016-03-01

    We have designed and developed a multiple sclerosis eFolder system for patient data storage, image viewing, and automatic lesion quantification results stored in DICOM-SR format. The web-based system aims to be integrated in DICOM-compliant clinical and research environments to aid clinicians in patient treatments and data analysis. The system needs to quantify lesion volumes, identify and register lesion locations to track shifts in volume and quantity of lesions in a longitudinal study. In order to perform lesion registration, we have developed a brain warping and normalizing methodology using Statistical Parametric Mapping (SPM) MATLAB toolkit for brain MRI. Patients' brain MR images are processed via SPM's normalization processes, and the brain images are analyzed and warped according to the tissue probability map. Lesion identification and contouring are completed by neuroradiologists, and lesion volume quantification is completed by the eFolder's CAD program. Lesion comparison results in longitudinal studies show key growth and active regions. The results display successful lesion registration and tracking over a longitudinal study. Lesion change results are graphically represented in the web-based user interface, and users are able to correlate patient progress and changes in the MRI images. The completed lesion and disease tracking tool would enable the eFolder to provide complete patient profiles, improve the efficiency of patient care, and perform comprehensive data analysis through an integrated imaging informatics system.

  20. Passage Retrieval and Evaluation

    DTIC Science & Technology

    2005-02-01

    queries, is IDF(t) = log „ # docs. in corpus + 1 0.5 + # docs. t appears in « . (6) This rather ad hoc scoring formula is implemented in the Lemur ...problems with passage R-precision as an evaluation metric. Fernando was instrumental in extending the Lemur toolkit to make all of these experiments...and C. Zhai. The lemur toolkit for language modeling and information retrieval. http://www.cs.cmu.edu/∼ lemur /, 2003. [6] C. Buckley and E. M

  1. Imaging informatics: essential tools for the delivery of imaging services.

    PubMed

    Mendelson, David S; Rubin, Daniel L

    2013-10-01

    There are rapid changes occurring in the health care environment. Radiologists face new challenges but also new opportunities. The purpose of this report is to review how new informatics tools and developments can help the radiologist respond to the drive for safety, quality, and efficiency. These tools will be of assistance in conducting research and education. They not only provide greater efficiency in traditional operations but also open new pathways for the delivery of new services and imaging technologies. Our future as a specialty is dependent on integrating these informatics solutions into our daily practice.

  2. Role of Informatics in Patient Safety and Quality Assurance.

    PubMed

    Nakhleh, Raouf E

    2015-06-01

    Quality assurance encompasses monitoring daily processes for accurate, timely, and complete reports in surgical pathology. Quality assurance also includes implementation of policies and procedures that prevent or detect errors in a timely manner. This article presents uses of informatics in quality assurance. Three main foci are critical to the general improvement of diagnostic surgical pathology. First is the application of informatics to specimen identification with lean methods for real-time statistical control of specimen receipt and processing. Second is the development of case reviews before sign-out. Third is the development of information technology in communication of results to assure treatment in a timely manner.

  3. Observations on sustainable and ubiquitous healthcare informatics from Florence Nightingale.

    PubMed

    Betts, Helen J; Wright, Graham

    2009-01-01

    As nurses around the world prepare to celebrate the centenary of the death of Florence Nightingale in 2010 this paper reviews her work on using information, especially statistics, to analyze and manage patient care and links that to current developments in informatics. It then examines assistive technologies and how they may impact on nursing practice in the future and links these developments to the writings of Florence Nightingale. The paper concludes by suggesting that in progressing towards sustainable and ubiquitous healthcare informatics we need to study history in order to learn from the lessons of Florence Nightingale and other healthcare pioneers.

  4. A Primer on Aspects of Cognition for Medical Informatics

    PubMed Central

    Patel, Vimla L.; Arocha, José F.; Kaufman, David R.

    2001-01-01

    As a multidisciplinary field, medical informatics draws on a range of disciplines, such as computer science, information science, and the social and cognitive sciences. The cognitive sciences can provide important insights into the nature of the processes involved in human– computer interaction and help improve the design of medical information systems by providing insight into the roles that knowledge, memory, and strategies play in a variety of cognitive activities. In this paper, the authors survey literature on aspects of medical cognition and provide a set of claims that they consider to be important in medical informatics. PMID:11418539

  5. 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.

  6. GEO-ENGINEERING MODELING THROUGH INTERNET INFORMATICS (GEMINI)

    SciTech Connect

    W. Lynn Watney; John H. Doveton

    2004-05-13

    GEMINI (Geo-Engineering Modeling through Internet Informatics) is a public-domain web application focused on analysis and modeling of petroleum reservoirs and plays (http://www.kgs.ukans.edu/Gemini/index.html). GEMINI creates a virtual project by ''on-the-fly'' assembly and analysis of on-line data either from the Kansas Geological Survey or uploaded from the user. GEMINI's suite of geological and engineering web applications for reservoir analysis include: (1) petrofacies-based core and log modeling using an interactive relational rock catalog and log analysis modules; (2) a well profile module; (3) interactive cross sections to display ''marked'' wireline logs; (4) deterministic gridding and mapping of petrophysical data; (5) calculation and mapping of layer volumetrics; (6) material balance calculations; (7) PVT calculator; (8) DST analyst, (9) automated hydrocarbon association navigator (KHAN) for database mining, and (10) tutorial and help functions. The Kansas Hydrocarbon Association Navigator (KHAN) utilizes petrophysical databases to estimate hydrocarbon pay or other constituent at a play- or field-scale. Databases analyzed and displayed include digital logs, core analysis and photos, DST, and production data. GEMINI accommodates distant collaborations using secure password protection and authorized access. Assembled data, analyses, charts, and maps can readily be moved to other applications. GEMINI's target audience includes small independents and consultants seeking to find, quantitatively characterize, and develop subtle and bypassed pays by leveraging the growing base of digital data resources. Participating companies involved in the testing and evaluation of GEMINI included Anadarko, BP, Conoco-Phillips, Lario, Mull, Murfin, and Pioneer Resources.

  7. The Supercomputer Toolkit and Its Applications

    DTIC Science & Technology

    1990-07-01

    demonstrate that the long-term motion of the planet Pluto , and by implication the dynamics of the Solar System, is chaotic [3]. This required integrating the...that the motion of Pluto is chaotic," Science, Volume 241, 22 July 1988. [4] A. Berlin, "Partial evaluation applied to numerical computation", in

  8. Metropolis revisited: the evolving role of librarians in informatics education for the health professions

    PubMed Central

    King, Samuel B.; Lapidus, Mariana

    2015-01-01

    Objective: The authors' goal was to assess changes in the role of librarians in informatics education from 2004 to 2013. This is a follow-up to “Metropolis Redux: The Unique Importance of Library Skills in Informatics,” a 2004 survey of informatics programs. Methods: An electronic survey was conducted in January 2013 and sent to librarians via the MEDLIB-L email discussion list, the library section of the American Association of Colleges of Pharmacy, the Medical Informatics Section of the Medical Library Association, the Information Technology Interest Group of the Association of College and Research Libraries/New England Region, and various library directors across the country. Results: Librarians from fifty-five institutions responded to the survey. Of these respondents, thirty-four included librarians in nonlibrary aspects of informatics training. Fifteen institutions have librarians participating in leadership positions in their informatics programs. Compared to the earlier survey, the role of librarians has evolved. Conclusions: Librarians possess skills that enable them to participate in informatics programs beyond a narrow library focus. Librarians currently perform significant leadership roles in informatics education. There are opportunities for librarian interdisciplinary collaboration in informatics programs. Implications: Informatics is much more than the study of technology. The information skills that librarians bring to the table enrich and broaden the study of informatics in addition to adding value to the library profession itself. PMID:25552939

  9. Technological Ecosystems in Health Informatics: A Brief Review Article

    PubMed Central

    WU, Zhongmei; ZHANG, Xiuxiu; CHEN, Ying; ZHANG, Yan

    2016-01-01

    Background: The existing models of information technology in health sciences have full scope of betterment and extension. The high demand pressures, public expectations, advanced platforms all collectively contribute towards hospital environment, which has to be kept in kind while designing of advanced technological ecosystem for information technology. Moreover, for the smooth conduct and operation of information system advanced management avenues are also essential in hospitals. It is the top priority of every hospital to deal with the essential needs of care for patients within the available resources of human and financial outputs. In these situations of high demand, the technological ecosystems in health informatics come in to play and prove its importance and role. The present review article would enlighten all these aspects of these ecosystems in hospital management and health care informatics. Methods: We searched the electronic database of MEDLINE, EMBASE, and PubMed for clinical controlled trials, pre-clinical studies reporting utilizaiono of ecosysyem advances in health information technology. Results: The primary outcome of eligible studies included confirmation of importance and role of advances ecosystems in health informatics. It was observed that technological ecosystems are the backbone of health informatics. Conclusion: Advancements in technological ecosystems are essential for proper functioning of health information system in clinical setting. PMID:27957459

  10. A solo hospital librarian's experience in clinical informatics.

    PubMed

    Miles, Alisha

    2015-01-01

    This column reviews some of a solo librarian's experiences that led to involvement with the hospital Clinical Informatics Team. This included work on the electronic health record (EHR), computerized physician order entry (CPOE) system, development of order sets, and participation in the Physician Technology Committee.

  11. A stimulus to define informatics and health information technology

    PubMed Central

    2009-01-01

    Background Despite the growing interest by leaders, policy makers, and others, the terminology of health information technology as well as biomedical and health informatics is poorly understood and not even agreed upon by academics and professionals in the field. Discussion The paper, presented as a Debate to encourage further discussion and disagreement, provides definitions of the major terminology used in biomedical and health informatics and health information technology. For informatics, it focuses on the words that modify the term as well as individuals who practice the discipline. Other categories of related terms are covered as well, from the associated disciplines of computer science, information technolog and health information management to the major application categories of applications used. The discussion closes with a classification of individuals who work in the largest segment of the field, namely clinical informatics. Summary The goal of presenting in Debate format is to provide a starting point for discussion to reach a documented consensus on the definition and use of these terms. PMID:19445665

  12. An Informatics Approach to Establishing a Sustainable Public Health Community

    ERIC Educational Resources Information Center

    Kriseman, Jeffrey Michael

    2012-01-01

    This work involved the analysis of a public health system, and the design, development and deployment of enterprise informatics architecture, and sustainable community methods to address problems with the current public health system. Specifically, assessment of the Nationally Notifiable Disease Surveillance System (NNDSS) was instrumental in…

  13. A current perspective on medical informatics and health sciences librarianship

    PubMed Central

    Perry, Gerald J.; Roderer, Nancy K.; Assar, Soraya

    2005-01-01

    Objective: The article offers a current perspective on medical informatics and health sciences librarianship. Narrative: The authors: (1) discuss how definitions of medical informatics have changed in relation to health sciences librarianship and the broader domain of information science; (2) compare the missions of health sciences librarianship and health sciences informatics, reviewing the characteristics of both disciplines; (3) propose a new definition of health sciences informatics; (4) consider the research agendas of both disciplines and the possibility that they have merged; and (5) conclude with some comments about actions and roles for health sciences librarians to flourish in the biomedical information environment of today and tomorrow. Summary: Boundaries are disappearing between the sources and types of and uses for health information managed by informaticians and librarians. Definitions of the professional domains of each have been impacted by these changes in information. Evolving definitions reflect the increasingly overlapping research agendas of both disciplines. Professionals in these disciplines are increasingly functioning collaboratively as “boundary spanners,” incorporating human factors that unite technology with health care delivery. PMID:15858622

  14. The Integration of Nursing Informatics in Delaware Nursing Education Programs

    ERIC Educational Resources Information Center

    Wheeler, Bernadette

    2016-01-01

    Over the past decade, there has been a conversion to electronic health records (EHRs) in an effort to improve patient care, access, and efficiency. The goal, which has been supported by federal initiatives, is to meaningfully use informatics to improve the safety and quality of patient care as a major force in improving healthcare. How nurses…

  15. BING: biomedical informatics pipeline for Next Generation Sequencing.

    PubMed

    Kriseman, Jeffrey; Busick, Christopher; Szelinger, Szabolcs; Dinu, Valentin

    2010-06-01

    High throughput parallel genomic sequencing (Next Generation Sequencing, NGS) shifts the bottleneck in sequencing processes from experimental data production to computationally intensive informatics-based data analysis. This manuscript introduces a biomedical informatics pipeline (BING) for the analysis of NGS data that offers several novel computational approaches to 1. image alignment, 2. signal correlation, compensation, separation, and pixel-based cluster registration, 3. signal measurement and base calling, 4. quality control and accuracy measurement. These approaches address many of the informatics challenges, including image processing, computational performance, and accuracy. These new algorithms are benchmarked against the Illumina Genome Analysis Pipeline. BING is the one of the first software tools to perform pixel-based analysis of NGS data. When compared to the Illumina informatics tool, BING's pixel-based approach produces a significant increase in the number of sequence reads, while reducing the computational time per experiment and error rate (<2%). This approach has the potential of increasing the density and throughput of NGS technologies.

  16. An Abridged History of Medical Informatics Education in Europe

    PubMed Central

    Hasman, Arie; Mantas, John; Zarubina, Tatyana

    2014-01-01

    This contribution presents the development of medical informatics education in Europe. It does not discuss all developments that took place. Rather it discerns several themes that indicate the progress in the field, starting from the initiation phase to the final quality control phase. PMID:24648617

  17. School Subject Informatics (Computer Science) in Russia: Educational Relevant Areas

    ERIC Educational Resources Information Center

    Khenner, Evgeniy; Semakin, Igor

    2014-01-01

    This article deals with some aspects of studying Informatics in Russian schools. Those aspects are part of the "third dimension" of the Darmstadt model (they are also projected on the other two dimensions of this model) and include evolution of the subject, regulatory norms conforming to the Federal Educational Standards, the learning…

  18. Pre-School Teachers' Informatics and Information Literacy

    ERIC Educational Resources Information Center

    Tatkovic, Nevenka; Ruzic, Maja; Pecaric, Dilda

    2006-01-01

    The life and activities of every man in the period of transition from the second into the third millennium have been marked by epochal changes which appear as the consequence of scientific and technological revolution dominated by highly developed information and communication technology. Informatics and information education based on information…

  19. Informatics Teaching from the Students' Point of View

    ERIC Educational Resources Information Center

    Zahorec, Jan; Haskova, Alena

    2013-01-01

    Branches of science and technical/engineering study have for a long time been the less favoured disciplines and students have not been interested in studying them. Informatics/computer education, based on its character, belongs to these disciplines, but on the contrary it belongs rather to the group of popular school subjects. The paper presents…

  20. Informatics--Preparation for the Realities of the Future.

    ERIC Educational Resources Information Center

    Kotze, Paula

    The paper describes the informatics curriculum (the study of computer hardware and software as a tool in problem solving) in a special school for gifted children in South Africa. The program's aims (including development of a structured approach to general problem solving and stimulation of pupil interest in technology) are listed and discussed. A…