Computer Language Settings and Canadian Spellings

Science.gov (United States)

Shuttleworth, Roger

2011-01-01

The language settings used on personal computers interact with the spell-checker in Microsoft Word, which directly affects the flagging of spellings that are deemed incorrect. This study examined the language settings of personal computers owned by a group of Canadian university students. Of 21 computers examined, only eight had their Windows…

A Novel Computational Tool for Mining Real-Life Data: Application in the Metastatic Colorectal Cancer Care Setting.

Directory of Open Access Journals (Sweden)

Nava Siegelmann-Danieli

Full Text Available Randomized clinical trials constitute the gold-standard for evaluating new anti-cancer therapies; however, real-life data are key in complementing clinically useful information. We developed a computational tool for real-life data analysis and applied it to the metastatic colorectal cancer (mCRC setting. This tool addressed the impact of oncology/non-oncology parameters on treatment patterns and clinical outcomes.The developed tool enables extraction of any computerized information including comorbidities and use of drugs (oncological/non-oncological per individual HMO member. The study in which we evaluated this tool was a retrospective cohort study that included Maccabi Healthcare Services members with mCRC receiving bevacizumab with fluoropyrimidines (FP, FP plus oxaliplatin (FP-O, or FP plus irinotecan (FP-I in the first-line between 9/2006 and 12/2013.The analysis included 753 patients of whom 15.4% underwent subsequent metastasectomy (the Surgery group. For the entire cohort, median overall survival (OS was 20.5 months; in the Surgery group, median duration of bevacizumab-containing therapy (DOT pre-surgery was 6.1 months; median OS was not reached. In the Non-surgery group, median OS and DOT were 18.7 and 11.4 months, respectively; no significant OS differences were noted between FP-O and FP-I, whereas FP use was associated with shorter OS (12.3 month; p <0.002; notably, these patients were older. Patients who received both FP-O- and FP-I-based regimens achieved numerically longer OS vs. those who received only one of these regimens (22.1 [19.9-24.0] vs. 18.9 [15.5-21.9] months. Among patients assessed for wild-type KRAS and treated with subsequent anti-EGFR agent, OS was 25.4 months and 18.7 months for 124 treated vs. 37 non-treated patients (non-significant. Cox analysis (controlling for age and gender identified several non-oncology parameters associated with poorer clinical outcomes including concurrent use of diuretics and proton

A Real-Time Plagiarism Detection Tool for Computer-Based Assessments

Science.gov (United States)

Jeske, Heimo J.; Lall, Manoj; Kogeda, Okuthe P.

2018-01-01

Aim/Purpose: The aim of this article is to develop a tool to detect plagiarism in real time amongst students being evaluated for learning in a computer-based assessment setting. Background: Cheating or copying all or part of source code of a program is a serious concern to academic institutions. Many academic institutions apply a combination of…

Data Sets, Ensemble Cloud Computing, and the University Library (Invited)

Science.gov (United States)

Plale, B. A.

2013-12-01

The environmental researcher at the public university has new resources at their disposal to aid in research and publishing. Cloud computing provides compute cycles on demand for analysis and modeling scenarios. Cloud computing is attractive for e-Science because of the ease with which cores can be accessed on demand, and because the virtual machine implementation that underlies cloud computing reduces the cost of porting a numeric or analysis code to a new platform. At the university, many libraries at larger universities are developing the e-Science skills to serve as repositories of record for publishable data sets. But these are confusing times for the publication of data sets from environmental research. The large publishers of scientific literature are advocating a process whereby data sets are tightly tied to a publication. In other words, a paper published in the scientific literature that gives results based on data, must have an associated data set accessible that backs up the results. This approach supports reproducibility of results in that publishers maintain a repository for the papers they publish, and the data sets that the papers used. Does such a solution that maps one data set (or subset) to one paper fit the needs of the environmental researcher who among other things uses complex models, mines longitudinal data bases, and generates observational results? The second school of thought has emerged out of NSF, NOAA, and NASA funded efforts over time: data sets exist coherent at a location, such as occurs at National Snow and Ice Data Center (NSIDC). But when a collection is coherent, reproducibility of individual results is more challenging. We argue for a third complementary option: the university repository as a location for data sets produced as a result of university-based research. This location for a repository relies on the expertise developing in the university libraries across the country, and leverages tools, such as are being developed

VISTA - computational tools for comparative genomics

Energy Technology Data Exchange (ETDEWEB)

Frazer, Kelly A.; Pachter, Lior; Poliakov, Alexander; Rubin,Edward M.; Dubchak, Inna

2004-01-01

Comparison of DNA sequences from different species is a fundamental method for identifying functional elements in genomes. Here we describe the VISTA family of tools created to assist biologists in carrying out this task. Our first VISTA server at http://www-gsd.lbl.gov/VISTA/ was launched in the summer of 2000 and was designed to align long genomic sequences and visualize these alignments with associated functional annotations. Currently the VISTA site includes multiple comparative genomics tools and provides users with rich capabilities to browse pre-computed whole-genome alignments of large vertebrate genomes and other groups of organisms with VISTA Browser, submit their own sequences of interest to several VISTA servers for various types of comparative analysis, and obtain detailed comparative analysis results for a set of cardiovascular genes. We illustrate capabilities of the VISTA site by the analysis of a 180 kilobase (kb) interval on human chromosome 5 that encodes for the kinesin family member3A (KIF3A) protein.

Computer-aided translation tools

DEFF Research Database (Denmark)

Christensen, Tina Paulsen; Schjoldager, Anne

2016-01-01

in Denmark is rather high in general, but limited in the case of machine translation (MT) tools: While most TSPs use translation-memory (TM) software, often in combination with a terminology management system (TMS), only very few have implemented MT, which is criticised for its low quality output, especially......The paper reports on a questionnaire survey from 2013 of the uptake and use of computer-aided translation (CAT) tools by Danish translation service providers (TSPs) and discusses how these tools appear to have impacted on the Danish translation industry. According to our results, the uptake...

Computer-Based Tools for Evaluating Graphical User Interfaces

Science.gov (United States)

Moore, Loretta A.

1997-01-01

The user interface is the component of a software system that connects two very complex system: humans and computers. Each of these two systems impose certain requirements on the final product. The user is the judge of the usability and utility of the system; the computer software and hardware are the tools with which the interface is constructed. Mistakes are sometimes made in designing and developing user interfaces because the designers and developers have limited knowledge about human performance (e.g., problem solving, decision making, planning, and reasoning). Even those trained in user interface design make mistakes because they are unable to address all of the known requirements and constraints on design. Evaluation of the user inter-face is therefore a critical phase of the user interface development process. Evaluation should not be considered the final phase of design; but it should be part of an iterative design cycle with the output of evaluation being feed back into design. The goal of this research was to develop a set of computer-based tools for objectively evaluating graphical user interfaces. The research was organized into three phases. The first phase resulted in the development of an embedded evaluation tool which evaluates the usability of a graphical user interface based on a user's performance. An expert system to assist in the design and evaluation of user interfaces based upon rules and guidelines was developed during the second phase. During the final phase of the research an automatic layout tool to be used in the initial design of graphical inter- faces was developed. The research was coordinated with NASA Marshall Space Flight Center's Mission Operations Laboratory's efforts in developing onboard payload display specifications for the Space Station.

Evaluating a computational support tool for set-based configuration of production systems : Results from an industrial case

NARCIS (Netherlands)

Unglert, Johannes; Hoekstra, Sipke; Jauregui Becker, Juan Manuel

2017-01-01

This paper describes research conducted in the context of an industrial case dealing with the design of re configurable cellular manufacturing systems. Reconfiguring such systems represents a complex task due to the interdependences between the constituent subsystems. A novel computational tool was

Integrating Computational Science Tools into a Thermodynamics Course

Science.gov (United States)

Vieira, Camilo; Magana, Alejandra J.; García, R. Edwin; Jana, Aniruddha; Krafcik, Matthew

2018-01-01

Computational tools and methods have permeated multiple science and engineering disciplines, because they enable scientists and engineers to process large amounts of data, represent abstract phenomena, and to model and simulate complex concepts. In order to prepare future engineers with the ability to use computational tools in the context of their disciplines, some universities have started to integrate these tools within core courses. This paper evaluates the effect of introducing three computational modules within a thermodynamics course on student disciplinary learning and self-beliefs about computation. The results suggest that using worked examples paired to computer simulations to implement these modules have a positive effect on (1) student disciplinary learning, (2) student perceived ability to do scientific computing, and (3) student perceived ability to do computer programming. These effects were identified regardless of the students' prior experiences with computer programming.

Tools for Embedded Computing Systems Software

Science.gov (United States)

1978-01-01

A workshop was held to assess the state of tools for embedded systems software and to determine directions for tool development. A synopsis of the talk and the key figures of each workshop presentation, together with chairmen summaries, are presented. The presentations covered four major areas: (1) tools and the software environment (development and testing); (2) tools and software requirements, design, and specification; (3) tools and language processors; and (4) tools and verification and validation (analysis and testing). The utility and contribution of existing tools and research results for the development and testing of embedded computing systems software are described and assessed.

Data Center IT Equipment Energy Assessment Tools: Current State of Commercial Tools, Proposal for a Future Set of Assessment Tools

Energy Technology Data Exchange (ETDEWEB)

Radhakrishnan, Ben D. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); National Univ., San Diego, CA (United States). School of Engineering

2012-06-30

This research project, which was conducted during the Summer and Fall of 2011, investigated some commercially available assessment tools with a focus on IT equipment to see if such tools could round out the DC Pro tool suite. In this research, the assessment capabilities of the various tools were compiled to help make “non-biased” information available to the public. This research should not be considered to be exhaustive on all existing vendor tools although a number of vendors were contacted. Large IT equipment OEM’s like IBM and Dell provide their proprietary internal automated software which does not work on any other IT equipment. However, found two companies with products that showed promise in performing automated assessments for IT equipment from different OEM vendors. This report documents the research and provides a list of software products reviewed, contacts and websites, product details, discussions with specific companies, a set of recommendations, and next steps. As a result of this research, a simple 3-level approach to an IT assessment tool is proposed along with an example of an assessment using a simple IT equipment data collection tool (Level 1, spreadsheet). The tool has been reviewed with the Green Grid and LBNL staff. The initial feedback has been positive although further refinement to the tool will be necessary. Proposed next steps include a field trial of at least two vendors’ software in two different data centers with an objective to prove the concept, ascertain the extent of energy and computational assessment, ease of installation and opportunities for continuous improvement. Based on the discussions, field trials (or case studies) are proposed with two vendors – JouleX (expected to be completed in 2012) and Sentilla.

The GLEaMviz computational tool, a publicly available software to explore realistic epidemic spreading scenarios at the global scale

Directory of Open Access Journals (Sweden)

Quaggiotto Marco

2011-02-01

Full Text Available Abstract Background Computational models play an increasingly important role in the assessment and control of public health crises, as demonstrated during the 2009 H1N1 influenza pandemic. Much research has been done in recent years in the development of sophisticated data-driven models for realistic computer-based simulations of infectious disease spreading. However, only a few computational tools are presently available for assessing scenarios, predicting epidemic evolutions, and managing health emergencies that can benefit a broad audience of users including policy makers and health institutions. Results We present "GLEaMviz", a publicly available software system that simulates the spread of emerging human-to-human infectious diseases across the world. The GLEaMviz tool comprises three components: the client application, the proxy middleware, and the simulation engine. The latter two components constitute the GLEaMviz server. The simulation engine leverages on the Global Epidemic and Mobility (GLEaM framework, a stochastic computational scheme that integrates worldwide high-resolution demographic and mobility data to simulate disease spread on the global scale. The GLEaMviz design aims at maximizing flexibility in defining the disease compartmental model and configuring the simulation scenario; it allows the user to set a variety of parameters including: compartment-specific features, transition values, and environmental effects. The output is a dynamic map and a corresponding set of charts that quantitatively describe the geo-temporal evolution of the disease. The software is designed as a client-server system. The multi-platform client, which can be installed on the user's local machine, is used to set up simulations that will be executed on the server, thus avoiding specific requirements for large computational capabilities on the user side. Conclusions The user-friendly graphical interface of the GLEaMviz tool, along with its high level

Elementary mathematical and computational tools for electrical and computer engineers using Matlab

CERN Document Server

Manassah, Jamal T

2013-01-01

Ideal for use as a short-course textbook and for self-study Elementary Mathematical and Computational Tools for Electrical and Computer Engineers Using MATLAB fills that gap. Accessible after just one semester of calculus, it introduces the many practical analytical and numerical tools that are essential to success both in future studies and in professional life. Sharply focused on the needs of the electrical and computer engineering communities, the text provides a wealth of relevant exercises and design problems. Changes in MATLAB's version 6.0 are included in a special addendum.

Computer-Aided Modelling Methods and Tools

DEFF Research Database (Denmark)

Cameron, Ian; Gani, Rafiqul

2011-01-01

The development of models for a range of applications requires methods and tools. In many cases a reference model is required that allows the generation of application specific models that are fit for purpose. There are a range of computer aided modelling tools available that help to define the m...

Workshop on Software Development Tools for Petascale Computing

Energy Technology Data Exchange (ETDEWEB)

Vetter, Jeffrey [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Georgia Inst. of Technology, Atlanta, GA (United States)

2007-08-01

Petascale computing systems will soon be available to the DOE science community. Recent studies in the productivity of HPC platforms point to better software environments as a key enabler to science on these systems. To prepare for the deployment and productive use of these petascale platforms, the DOE science and general HPC community must have the software development tools, such as performance analyzers and debuggers that meet application requirements for scalability, functionality, reliability, and ease of use. In this report, we identify and prioritize the research opportunities in the area of software development tools for high performance computing. To facilitate this effort, DOE hosted a group of 55 leading international experts in this area at the Software Development Tools for PetaScale Computing (SDTPC) Workshop, which was held in Washington, D.C. on August 1 and 2, 2007. Software development tools serve as an important interface between the application teams and the target HPC architectures. Broadly speaking, these roles can be decomposed into three categories: performance tools, correctness tools, and development environments. Accordingly, this SDTPC report has four technical thrusts: performance tools, correctness tools, development environment infrastructures, and scalable tool infrastructures. The last thrust primarily targets tool developers per se, rather than end users. Finally, this report identifies non-technical strategic challenges that impact most tool development. The organizing committee emphasizes that many critical areas are outside the scope of this charter; these important areas include system software, compilers, and I/O.

Benchmarking therapeutic drug monitoring software: a review of available computer tools.

Science.gov (United States)

Fuchs, Aline; Csajka, Chantal; Thoma, Yann; Buclin, Thierry; Widmer, Nicolas

2013-01-01

settings. Each software tool must therefore be regarded with respect to the individual needs of hospitals or clinicians. Programs should be easy and fast for routine activities, including for non-experienced users. Computer-assisted TDM is gaining growing interest and should further improve, especially in terms of information system interfacing, user friendliness, data storage capability and report generation.

Applications of computational tools in biosciences and medical engineering

CERN Document Server

Altenbach, Holm

2015-01-01

 This book presents the latest developments and applications of computational tools related to the biosciences and medical engineering. It also reports the findings of different multi-disciplinary research projects, for example, from the areas of scaffolds and synthetic bones, implants and medical devices, and medical materials. It is also shown that the application of computational tools often requires mathematical and experimental methods. Computational tools such as the finite element methods, computer-aided design and optimization as well as visualization techniques such as computed axial tomography open up completely new research fields that combine the fields of engineering and bio/medical. Nevertheless, there are still hurdles since both directions are based on quite different ways of education. Often even the “language” can vary from discipline to discipline.

Defining Effectiveness Using Finite Sets A Study on Computability

DEFF Research Database (Denmark)

Macedo, Hugo Daniel dos Santos; Haeusler, Edward H.; Garcia, Alex

2016-01-01

finite sets and uses category theory as its mathematical foundations. The model relies on the fact that every function between finite sets is computable, and that the finite composition of such functions is also computable. Our approach is an alternative to the traditional model-theoretical based works...... which rely on (ZFC) set theory as a mathematical foundation, and our approach is also novel when compared to the already existing works using category theory to approach computability results. Moreover, we show how to encode Turing machine computations in the model, thus concluding the model expresses...

GPU-FS-kNN: a software tool for fast and scalable kNN computation using GPUs.

Directory of Open Access Journals (Sweden)

Ahmed Shamsul Arefin

Full Text Available BACKGROUND: The analysis of biological networks has become a major challenge due to the recent development of high-throughput techniques that are rapidly producing very large data sets. The exploding volumes of biological data are craving for extreme computational power and special computing facilities (i.e. super-computers. An inexpensive solution, such as General Purpose computation based on Graphics Processing Units (GPGPU, can be adapted to tackle this challenge, but the limitation of the device internal memory can pose a new problem of scalability. An efficient data and computational parallelism with partitioning is required to provide a fast and scalable solution to this problem. RESULTS: We propose an efficient parallel formulation of the k-Nearest Neighbour (kNN search problem, which is a popular method for classifying objects in several fields of research, such as pattern recognition, machine learning and bioinformatics. Being very simple and straightforward, the performance of the kNN search degrades dramatically for large data sets, since the task is computationally intensive. The proposed approach is not only fast but also scalable to large-scale instances. Based on our approach, we implemented a software tool GPU-FS-kNN (GPU-based Fast and Scalable k-Nearest Neighbour for CUDA enabled GPUs. The basic approach is simple and adaptable to other available GPU architectures. We observed speed-ups of 50-60 times compared with CPU implementation on a well-known breast microarray study and its associated data sets. CONCLUSION: Our GPU-based Fast and Scalable k-Nearest Neighbour search technique (GPU-FS-kNN provides a significant performance improvement for nearest neighbour computation in large-scale networks. Source code and the software tool is available under GNU Public License (GPL at https://sourceforge.net/p/gpufsknn/.

Primary care physicians’ perspectives on computer-based health risk assessment tools for chronic diseases: a mixed methods study

Directory of Open Access Journals (Sweden)

Teja Voruganti

2015-09-01

Full Text Available Background Health risk assessment tools compute an individual’s risk of developing a disease. Routine use of such tools by primary care physicians (PCPs is potentially useful in chronic disease prevention. We sought physicians’ awareness and perceptions of the usefulness, usability and feasibility of performing assessments with computer-based risk assessment tools in primary care settings.Methods Focus groups and usability testing with a computer-based risk assessment tool were conducted with PCPs from both university-affiliated and community-based practices. Analysis was derived from grounded theory methodology.Results PCPs (n = 30 were aware of several risk assessment tools although only select tools were used routinely. The decision to use a tool depended on how use impacted practice workflow and whether the tool had credibility. Participants felt that embedding tools in the electronic medical records (EMRs system might allow for health information from the medical record to auto-populate into the tool. User comprehension of risk could also be improved with computer-based interfaces that present risk in different formats.Conclusions In this study, PCPs chose to use certain tools more regularly because of usability and credibility. Despite there being differences in the particular tools a clinical practice used, there was general appreciation for the usefulness of tools for different clinical situations. Participants characterised particular features of an ideal tool, feeling strongly that embedding risk assessment tools in the EMR would maximise accessibility and use of the tool for chronic disease management. However, appropriate practice workflow integration and features that facilitate patient understanding at point-of-care are also essential. 

Computer Assisted Advising Tool (CAAT).

Science.gov (United States)

Matsen, Marie E.

Lane Community College's Computer Assisted Advising Tool (CAAT) is used by counselors to assist students in developing a plan for the completion of a degree or certificate. CAAT was designed to facilitate student advisement from matriculation to graduation by comparing degree requirements with the courses completed by students. Three major sources…

HPCToolkit: performance tools for scientific computing

Energy Technology Data Exchange (ETDEWEB)

Tallent, N; Mellor-Crummey, J; Adhianto, L; Fagan, M; Krentel, M [Department of Computer Science, Rice University, Houston, TX 77005 (United States)

2008-07-15

As part of the U.S. Department of Energy's Scientific Discovery through Advanced Computing (SciDAC) program, science teams are tackling problems that require simulation and modeling on petascale computers. As part of activities associated with the SciDAC Center for Scalable Application Development Software (CScADS) and the Performance Engineering Research Institute (PERI), Rice University is building software tools for performance analysis of scientific applications on the leadership-class platforms. In this poster abstract, we briefly describe the HPCToolkit performance tools and how they can be used to pinpoint bottlenecks in SPMD and multi-threaded parallel codes. We demonstrate HPCToolkit's utility by applying it to two SciDAC applications: the S3D code for simulation of turbulent combustion and the MFDn code for ab initio calculations of microscopic structure of nuclei.

HPCToolkit: performance tools for scientific computing

International Nuclear Information System (INIS)

Tallent, N; Mellor-Crummey, J; Adhianto, L; Fagan, M; Krentel, M

2008-01-01

As part of the U.S. Department of Energy's Scientific Discovery through Advanced Computing (SciDAC) program, science teams are tackling problems that require simulation and modeling on petascale computers. As part of activities associated with the SciDAC Center for Scalable Application Development Software (CScADS) and the Performance Engineering Research Institute (PERI), Rice University is building software tools for performance analysis of scientific applications on the leadership-class platforms. In this poster abstract, we briefly describe the HPCToolkit performance tools and how they can be used to pinpoint bottlenecks in SPMD and multi-threaded parallel codes. We demonstrate HPCToolkit's utility by applying it to two SciDAC applications: the S3D code for simulation of turbulent combustion and the MFDn code for ab initio calculations of microscopic structure of nuclei

iTools: a framework for classification, categorization and integration of computational biology resources.

Directory of Open Access Journals (Sweden)

Ivo D Dinov

2008-05-01

Full Text Available The advancement of the computational biology field hinges on progress in three fundamental directions--the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources--data, software tools and web-services. The iTools design, implementation and resource meta-data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long

Network computing infrastructure to share tools and data in global nuclear energy partnership

International Nuclear Information System (INIS)

Kim, Guehee; Suzuki, Yoshio; Teshima, Naoya

2010-01-01

CCSE/JAEA (Center for Computational Science and e-Systems/Japan Atomic Energy Agency) integrated a prototype system of a network computing infrastructure for sharing tools and data to support the U.S. and Japan collaboration in GNEP (Global Nuclear Energy Partnership). We focused on three technical issues to apply our information process infrastructure, which are accessibility, security, and usability. In designing the prototype system, we integrated and improved both network and Web technologies. For the accessibility issue, we adopted SSL-VPN (Security Socket Layer - Virtual Private Network) technology for the access beyond firewalls. For the security issue, we developed an authentication gateway based on the PKI (Public Key Infrastructure) authentication mechanism to strengthen the security. Also, we set fine access control policy to shared tools and data and used shared key based encryption method to protect tools and data against leakage to third parties. For the usability issue, we chose Web browsers as user interface and developed Web application to provide functions to support sharing tools and data. By using WebDAV (Web-based Distributed Authoring and Versioning) function, users can manipulate shared tools and data through the Windows-like folder environment. We implemented the prototype system in Grid infrastructure for atomic energy research: AEGIS (Atomic Energy Grid Infrastructure) developed by CCSE/JAEA. The prototype system was applied for the trial use in the first period of GNEP. (author)

Development of a Computational Tool for Measuring Organizational Competitiveness in the Photovoltaic Power Plants

Directory of Open Access Journals (Sweden)

Carmen B. Rosa

2018-04-01

Full Text Available Photovoltaic (PV power generation is embedded in a globally competitive environment. This characteristic forces PV power plants to perform most processes relevant for their competitiveness with maximum efficiency. From managers’ point of view, the evaluation of solar energy performance from installed plants is justified to indicate their level of organizational competitiveness, which supports the decision-making process. This manuscript purposes a computational tool that graphically presents the level of competitiveness of PV power plants units based on performance indicators. This tool was developed by using the Key Performance Indicators (KPIs concept, which represents a set of measures focusing on the most critical aspects for the success of the organizations. The KPIs encompass four Fundamental Viewpoints (FV: Strategic Alliances, Solar Energy Monitoring, Management and Strategic Processes, and Power Generation Innovations. These four FVs were deployed on 26 Critical Success Factors (CSFs and 39 KPIs. Sequentially, the tool was applied in four solar generation plants, where three presented an organizational competitiveness global level “potentially competitive”. The proposed computational tool allows managers to assess the degree of organization competitiveness as well as aid in prospecting of future scenarios and decision-making.

New tools to aid in scientific computing and visualization

International Nuclear Information System (INIS)

Wallace, M.G.; Christian-Frear, T.L.

1992-01-01

In this paper, two computer programs are described which aid in the pre- and post-processing of computer generated data. CoMeT (Computational Mechanics Toolkit) is a customizable, interactive, graphical, menu-driven program that provides the analyst with a consistent user-friendly interface to analysis codes. Trans Vol (Transparent Volume Visualization) is a specialized tool for the scientific three-dimensional visualization of complex solids by the technique of volume rendering. Both tools are described in basic detail along with an application example concerning the simulation of contaminant migration from an underground nuclear repository

COMPUTER TOOLS OF DYNAMIC MATHEMATIC SOFTWARE AND METHODICAL PROBLEMS OF THEIR USE

Directory of Open Access Journals (Sweden)

Olena V. Semenikhina

2014-08-01

Full Text Available The article presents results of analyses of standard computer tools of dynamic mathematic software which are used in solving tasks, and tools on which the teacher can support in the teaching of mathematics. Possibility of the organization of experimental investigating of mathematical objects on the basis of these tools and the wording of new tasks on the basis of the limited number of tools, fast automated check are specified. Some methodological comments on application of computer tools and methodological features of the use of interactive mathematical environments are presented. Problems, which are arising from the use of computer tools, among which rethinking forms and methods of training by teacher, the search for creative problems, the problem of rational choice of environment, check the e-solutions, common mistakes in the use of computer tools are selected.

Nutrition screening tools: Does one size fit all? A systematic review of screening tools for the hospital setting

NARCIS (Netherlands)

van Bokhorst-de van der Schueren, M.A.E.; Guaitoli, P.R.; Jansma, E.P.; de Vet, H.C.W.

2014-01-01

Background & aims: Numerous nutrition screening tools for the hospital setting have been developed. The aim of this systematic review is to study construct or criterion validity and predictive validity of nutrition screening tools for the general hospital setting. Methods: A systematic review of

Foundational Tools for Petascale Computing

Energy Technology Data Exchange (ETDEWEB)

Miller, Barton [Univ. of Wisconsin, Madison, WI (United States)

2014-05-19

The Paradyn project has a history of developing algorithms, techniques, and software that push the cutting edge of tool technology for high-end computing systems. Under this funding, we are working on a three-year agenda to make substantial new advances in support of new and emerging Petascale systems. The overall goal for this work is to address the steady increase in complexity of these petascale systems. Our work covers two key areas: (1) The analysis, instrumentation and control of binary programs. Work in this area falls under the general framework of the Dyninst API tool kits. (2) Infrastructure for building tools and applications at extreme scale. Work in this area falls under the general framework of the MRNet scalability framework. Note that work done under this funding is closely related to work done under a contemporaneous grant, “High-Performance Energy Applications and Systems”, SC0004061/FG02-10ER25972, UW PRJ36WV.

Computational tools for high-throughput discovery in biology

OpenAIRE

Jones, Neil Christopher

2007-01-01

High throughput data acquisition technology has inarguably transformed the landscape of the life sciences, in part by making possible---and necessary---the computational disciplines of bioinformatics and biomedical informatics. These fields focus primarily on developing tools for analyzing data and generating hypotheses about objects in nature, and it is in this context that we address three pressing problems in the fields of the computational life sciences which each require computing capaci...

Advanced Computing Tools and Models for Accelerator Physics

International Nuclear Information System (INIS)

Ryne, Robert; Ryne, Robert D.

2008-01-01

This paper is based on a transcript of my EPAC'08 presentation on advanced computing tools for accelerator physics. Following an introduction I present several examples, provide a history of the development of beam dynamics capabilities, and conclude with thoughts on the future of large scale computing in accelerator physics

Aligator: A computational tool for optimizing total chemical synthesis of large proteins.

Science.gov (United States)

Jacobsen, Michael T; Erickson, Patrick W; Kay, Michael S

2017-09-15

The scope of chemical protein synthesis (CPS) continues to expand, driven primarily by advances in chemical ligation tools (e.g., reversible solubilizing groups and novel ligation chemistries). However, the design of an optimal synthesis route can be an arduous and fickle task due to the large number of theoretically possible, and in many cases problematic, synthetic strategies. In this perspective, we highlight recent CPS tool advances and then introduce a new and easy-to-use program, Aligator (Automated Ligator), for analyzing and designing the most efficient strategies for constructing large targets using CPS. As a model set, we selected the E. coli ribosomal proteins and associated factors for computational analysis. Aligator systematically scores and ranks all feasible synthetic strategies for a particular CPS target. The Aligator script methodically evaluates potential peptide segments for a target using a scoring function that includes solubility, ligation site quality, segment lengths, and number of ligations to provide a ranked list of potential synthetic strategies. We demonstrate the utility of Aligator by analyzing three recent CPS projects from our lab: TNFα (157 aa), GroES (97 aa), and DapA (312 aa). As the limits of CPS are extended, we expect that computational tools will play an increasingly important role in the efficient execution of ambitious CPS projects such as production of a mirror-image ribosome. Copyright © 2017 Elsevier Ltd. All rights reserved.

Computer tools for systems engineering at LaRC

Science.gov (United States)

Walters, J. Milam

1994-01-01

The Systems Engineering Office (SEO) has been established to provide life cycle systems engineering support to Langley research Center projects. over the last two years, the computing market has been reviewed for tools which could enhance the effectiveness and efficiency of activities directed towards this mission. A group of interrelated applications have been procured, or are under development including a requirements management tool, a system design and simulation tool, and project and engineering data base. This paper will review the current configuration of these tools and provide information on future milestones and directions.

COMPUTER TOOLS OF DYNAMIC MATHEMATIC SOFTWARE AND METHODICAL PROBLEMS OF THEIR USE

OpenAIRE

Olena V. Semenikhina; Maryna H. Drushliak

2014-01-01

The article presents results of analyses of standard computer tools of dynamic mathematic software which are used in solving tasks, and tools on which the teacher can support in the teaching of mathematics. Possibility of the organization of experimental investigating of mathematical objects on the basis of these tools and the wording of new tasks on the basis of the limited number of tools, fast automated check are specified. Some methodological comments on application of computer tools and ...

Caesy: A software tool for computer-aided engineering

Science.gov (United States)

Wette, Matt

1993-01-01

A new software tool, Caesy, is described. This tool provides a strongly typed programming environment for research in the development of algorithms and software for computer-aided control system design. A description of the user language and its implementation as they currently stand are presented along with a description of work in progress and areas of future work.

Computational assessment of hemodynamics-based diagnostic tools using a database of virtual subjects: Application to three case studies.

Science.gov (United States)

Willemet, Marie; Vennin, Samuel; Alastruey, Jordi

2016-12-08

Many physiological indexes and algorithms based on pulse wave analysis have been suggested in order to better assess cardiovascular function. Because these tools are often computed from in-vivo hemodynamic measurements, their validation is time-consuming, challenging, and biased by measurement errors. Recently, a new methodology has been suggested to assess theoretically these computed tools: a database of virtual subjects generated using numerical 1D-0D modeling of arterial hemodynamics. The generated set of simulations encloses a wide selection of healthy cases that could be encountered in a clinical study. We applied this new methodology to three different case studies that demonstrate the potential of our new tool, and illustrated each of them with a clinically relevant example: (i) we assessed the accuracy of indexes estimating pulse wave velocity; (ii) we validated and refined an algorithm that computes central blood pressure; and (iii) we investigated theoretical mechanisms behind the augmentation index. Our database of virtual subjects is a new tool to assist the clinician: it provides insight into the physical mechanisms underlying the correlations observed in clinical practice. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Using the Eclipse Parallel Tools Platform to Assist Earth Science Model Development and Optimization on High Performance Computers

Science.gov (United States)

Alameda, J. C.

2011-12-01

Development and optimization of computational science models, particularly on high performance computers, and with the advent of ubiquitous multicore processor systems, practically on every system, has been accomplished with basic software tools, typically, command-line based compilers, debuggers, performance tools that have not changed substantially from the days of serial and early vector computers. However, model complexity, including the complexity added by modern message passing libraries such as MPI, and the need for hybrid code models (such as openMP and MPI) to be able to take full advantage of high performance computers with an increasing core count per shared memory node, has made development and optimization of such codes an increasingly arduous task. Additional architectural developments, such as many-core processors, only complicate the situation further. In this paper, we describe how our NSF-funded project, "SI2-SSI: A Productive and Accessible Development Workbench for HPC Applications Using the Eclipse Parallel Tools Platform" (WHPC) seeks to improve the Eclipse Parallel Tools Platform, an environment designed to support scientific code development targeted at a diverse set of high performance computing systems. Our WHPC project to improve Eclipse PTP takes an application-centric view to improve PTP. We are using a set of scientific applications, each with a variety of challenges, and using PTP to drive further improvements to both the scientific application, as well as to understand shortcomings in Eclipse PTP from an application developer perspective, to drive our list of improvements we seek to make. We are also partnering with performance tool providers, to drive higher quality performance tool integration. We have partnered with the Cactus group at Louisiana State University to improve Eclipse's ability to work with computational frameworks and extremely complex build systems, as well as to develop educational materials to incorporate into

Computer-based tools for decision support at the Hanford Site

International Nuclear Information System (INIS)

Doctor, P.G.; Mahaffey, J.A.; Cowley, P.J.; Freshley, M.D.; Hassig, N.L.; Brothers, J.W.; Glantz, C.S.; Strachan, D.M.

1992-11-01

To help integrate activities in the environmental restoration and waste management mission of the Hanford Site, the Hanford Integrated Planning Project (HIPP) was established and funded by the US Department of Energy. The project is divided into three key program elements, the first focusing on an explicit, defensible and comprehensive method for evaluating technical options. Based on the premise that computer technology can be used to support the decision-making process and facilitate integration among programs and activities, the Decision Support Tools Task was charged with assessing the status of computer technology for those purposes at the Site. The task addressed two types of tools: tools need to provide technical information and management support tools. Technical tools include performance and risk assessment models, information management systems, data and the computer infrastructure to supports models, data, and information management systems. Management decision support tools are used to synthesize information at a high' level to assist with making decisions. The major conclusions resulting from the assessment are that there is much technical information available, but it is not reaching the decision-makers in a form to be used. Many existing tools provide components that are needed to integrate site activities; however, some components are missing and, more importantly, the ''glue'' or connections to tie the components together to answer decision-makers questions is largely absent. Top priority should be given to decision support tools that support activities given in the TPA. Other decision tools are needed to facilitate and support the environmental restoration and waste management mission

Computer-based tools for decision support at the Hanford Site

Energy Technology Data Exchange (ETDEWEB)

Doctor, P.G.; Mahaffey, J.A.; Cowley, P.J.; Freshley, M.D.; Hassig, N.L.; Brothers, J.W.; Glantz, C.S.; Strachan, D.M.

1992-11-01

To help integrate activities in the environmental restoration and waste management mission of the Hanford Site, the Hanford Integrated Planning Project (HIPP) was established and funded by the US Department of Energy. The project is divided into three key program elements, the first focusing on an explicit, defensible and comprehensive method for evaluating technical options. Based on the premise that computer technology can be used to support the decision-making process and facilitate integration among programs and activities, the Decision Support Tools Task was charged with assessing the status of computer technology for those purposes at the Site. The task addressed two types of tools: tools need to provide technical information and management support tools. Technical tools include performance and risk assessment models, information management systems, data and the computer infrastructure to supports models, data, and information management systems. Management decision support tools are used to synthesize information at a high' level to assist with making decisions. The major conclusions resulting from the assessment are that there is much technical information available, but it is not reaching the decision-makers in a form to be used. Many existing tools provide components that are needed to integrate site activities; however, some components are missing and, more importantly, the glue'' or connections to tie the components together to answer decision-makers questions is largely absent. Top priority should be given to decision support tools that support activities given in the TPA. Other decision tools are needed to facilitate and support the environmental restoration and waste management mission.

Computer-based tools for decision support at the Hanford Site

Energy Technology Data Exchange (ETDEWEB)

Doctor, P.G.; Mahaffey, J.A.; Cowley, P.J.; Freshley, M.D.; Hassig, N.L.; Brothers, J.W.; Glantz, C.S.; Strachan, D.M.

1992-11-01

To help integrate activities in the environmental restoration and waste management mission of the Hanford Site, the Hanford Integrated Planning Project (HIPP) was established and funded by the US Department of Energy. The project is divided into three key program elements, the first focusing on an explicit, defensible and comprehensive method for evaluating technical options. Based on the premise that computer technology can be used to support the decision-making process and facilitate integration among programs and activities, the Decision Support Tools Task was charged with assessing the status of computer technology for those purposes at the Site. The task addressed two types of tools: tools need to provide technical information and management support tools. Technical tools include performance and risk assessment models, information management systems, data and the computer infrastructure to supports models, data, and information management systems. Management decision support tools are used to synthesize information at a high` level to assist with making decisions. The major conclusions resulting from the assessment are that there is much technical information available, but it is not reaching the decision-makers in a form to be used. Many existing tools provide components that are needed to integrate site activities; however, some components are missing and, more importantly, the ``glue`` or connections to tie the components together to answer decision-makers questions is largely absent. Top priority should be given to decision support tools that support activities given in the TPA. Other decision tools are needed to facilitate and support the environmental restoration and waste management mission.

Towards early software reliability prediction for computer forensic tools (case study).

Science.gov (United States)

Abu Talib, Manar

2016-01-01

Versatility, flexibility and robustness are essential requirements for software forensic tools. Researchers and practitioners need to put more effort into assessing this type of tool. A Markov model is a robust means for analyzing and anticipating the functioning of an advanced component based system. It is used, for instance, to analyze the reliability of the state machines of real time reactive systems. This research extends the architecture-based software reliability prediction model for computer forensic tools, which is based on Markov chains and COSMIC-FFP. Basically, every part of the computer forensic tool is linked to a discrete time Markov chain. If this can be done, then a probabilistic analysis by Markov chains can be performed to analyze the reliability of the components and of the whole tool. The purposes of the proposed reliability assessment method are to evaluate the tool's reliability in the early phases of its development, to improve the reliability assessment process for large computer forensic tools over time, and to compare alternative tool designs. The reliability analysis can assist designers in choosing the most reliable topology for the components, which can maximize the reliability of the tool and meet the expected reliability level specified by the end-user. The approach of assessing component-based tool reliability in the COSMIC-FFP context is illustrated with the Forensic Toolkit Imager case study.

A sampler of useful computational tools for applied geometry, computer graphics, and image processing foundations for computer graphics, vision, and image processing

CERN Document Server

Cohen-Or, Daniel; Ju, Tao; Mitra, Niloy J; Shamir, Ariel; Sorkine-Hornung, Olga; Zhang, Hao (Richard)

2015-01-01

A Sampler of Useful Computational Tools for Applied Geometry, Computer Graphics, and Image Processing shows how to use a collection of mathematical techniques to solve important problems in applied mathematics and computer science areas. The book discusses fundamental tools in analytical geometry and linear algebra. It covers a wide range of topics, from matrix decomposition to curvature analysis and principal component analysis to dimensionality reduction.Written by a team of highly respected professors, the book can be used in a one-semester, intermediate-level course in computer science. It

A computer-aided software-tool for sustainable process synthesis-intensification

DEFF Research Database (Denmark)

Kumar Tula, Anjan; Babi, Deenesh K.; Bottlaender, Jack

2017-01-01

and determine within the design space, the more sustainable processes. In this paper, an integrated computer-aided software-tool that searches the design space for hybrid/intensified more sustainable process options is presented. Embedded within the software architecture are process synthesis...... operations as well as reported hybrid/intensified unit operations is large and can be difficult to manually navigate in order to determine the best process flowsheet for the production of a desired chemical product. Therefore, it is beneficial to utilize computer-aided methods and tools to enumerate, analyze...... constraints while also matching the design targets, they are therefore more sustainable than the base case. The application of the software-tool to the production of biodiesel is presented, highlighting the main features of the computer-aided, multi-stage, multi-scale methods that are able to determine more...

Effects of Attitudes and Behaviours on Learning Mathematics with Computer Tools

Science.gov (United States)

Reed, Helen C.; Drijvers, Paul; Kirschner, Paul A.

2010-01-01

This mixed-methods study investigates the effects of student attitudes and behaviours on the outcomes of learning mathematics with computer tools. A computer tool was used to help students develop the mathematical concept of function. In the whole sample (N = 521), student attitudes could account for a 3.4 point difference in test scores between…

Idea: an integrated set of tools for sustainable nuclear decommissioning projects

International Nuclear Information System (INIS)

Detilleux, M.; Centner, B.; Vanderperre, S.; Wacquier, W.

2008-01-01

Decommissioning of nuclear installations constitutes an important challenge and shall prove to the public that the whole nuclear life cycle is fully mastered by the nuclear industry. This could lead to an easier public acceptance of the construction of new nuclear power plants. When ceasing operation, nuclear installations owners and operators are looking for solutions in order to assess and keep decommissioning costs at a reasonable level, to fully characterise waste streams (in particular radiological inventories of difficult-to-measure radionuclides) and to reduce personnel exposure during the decommissioning activities taking into account several project, site and country specific constraints. In response to this need, Tractebel Engineering has developed IDEA (Integrated DEcommissioning Application), an integrated set of computer tools, to support the engineering activities to be carried out in the frame of a decommissioning project. IDEA provides optimized solutions from an economical, environmental, social and safety perspective. (authors)

OPTHYLIC: An Optimised Tool for Hybrid Limits Computation

Science.gov (United States)

Busato, Emmanuel; Calvet, David; Theveneaux-Pelzer, Timothée

2018-05-01

A software tool, computing observed and expected upper limits on Poissonian process rates using a hybrid frequentist-Bayesian CLs method, is presented. This tool can be used for simple counting experiments where only signal, background and observed yields are provided or for multi-bin experiments where binned distributions of discriminating variables are provided. It allows the combination of several channels and takes into account statistical and systematic uncertainties, as well as correlations of systematic uncertainties between channels. It has been validated against other software tools and analytical calculations, for several realistic cases.

Nutrition screening tools: does one size fit all? A systematic review of screening tools for the hospital setting.

Science.gov (United States)

van Bokhorst-de van der Schueren, Marian A E; Guaitoli, Patrícia Realino; Jansma, Elise P; de Vet, Henrica C W

2014-02-01

Numerous nutrition screening tools for the hospital setting have been developed. The aim of this systematic review is to study construct or criterion validity and predictive validity of nutrition screening tools for the general hospital setting. A systematic review of English, French, German, Spanish, Portuguese and Dutch articles identified via MEDLINE, Cinahl and EMBASE (from inception to the 2nd of February 2012). Additional studies were identified by checking reference lists of identified manuscripts. Search terms included key words for malnutrition, screening or assessment instruments, and terms for hospital setting and adults. Data were extracted independently by 2 authors. Only studies expressing the (construct, criterion or predictive) validity of a tool were included. 83 studies (32 screening tools) were identified: 42 studies on construct or criterion validity versus a reference method and 51 studies on predictive validity on outcome (i.e. length of stay, mortality or complications). None of the tools performed consistently well to establish the patients' nutritional status. For the elderly, MNA performed fair to good, for the adults MUST performed fair to good. SGA, NRS-2002 and MUST performed well in predicting outcome in approximately half of the studies reviewed in adults, but not in older patients. Not one single screening or assessment tool is capable of adequate nutrition screening as well as predicting poor nutrition related outcome. Development of new tools seems redundant and will most probably not lead to new insights. New studies comparing different tools within one patient population are required. Copyright © 2013 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

System-level tools and reconfigurable computing for next-generation HWIL systems

Science.gov (United States)

Stark, Derek; McAulay, Derek; Cantle, Allan J.; Devlin, Malachy

2001-08-01

Previous work has been presented on the creation of computing architectures called DIME, which addressed the particular computing demands of hardware in the loop systems. These demands include low latency, high data rates and interfacing. While it is essential to have a capable platform for handling and processing of the data streams, the tools must also complement this so that a system's engineer is able to construct their final system. The paper will present the work in the area of integration of system level design tools, such as MATLAB and SIMULINK, with a reconfigurable computing platform. This will demonstrate how algorithms can be implemented and simulated in a familiar rapid application development environment before they are automatically transposed for downloading directly to the computing platform. This complements the established control tools, which handle the configuration and control of the processing systems leading to a tool suite for system development and implementation. As the development tools have evolved the core-processing platform has also been enhanced. These improved platforms are based on dynamically reconfigurable computing, utilizing FPGA technologies, and parallel processing methods that more than double the performance and data bandwidth capabilities. This offers support for the processing of images in Infrared Scene Projectors with 1024 X 1024 resolutions at 400 Hz frame rates. The processing elements will be using the latest generation of FPGAs, which implies that the presented systems will be rated in terms of Tera (1012) operations per second.

8th International Workshop on Parallel Tools for High Performance Computing

CERN Document Server

Gracia, José; Knüpfer, Andreas; Resch, Michael; Nagel, Wolfgang

2015-01-01

Numerical simulation and modelling using High Performance Computing has evolved into an established technique in academic and industrial research. At the same time, the High Performance Computing infrastructure is becoming ever more complex. For instance, most of the current top systems around the world use thousands of nodes in which classical CPUs are combined with accelerator cards in order to enhance their compute power and energy efficiency. This complexity can only be mastered with adequate development and optimization tools. Key topics addressed by these tools include parallelization on heterogeneous systems, performance optimization for CPUs and accelerators, debugging of increasingly complex scientific applications, and optimization of energy usage in the spirit of green IT. This book represents the proceedings of the 8th International Parallel Tools Workshop, held October 1-2, 2014 in Stuttgart, Germany – which is a forum to discuss the latest advancements in the parallel tools.

A validated set of tool pictures with matched objects and non-objects for laterality research.

Science.gov (United States)

Verma, Ark; Brysbaert, Marc

2015-01-01

Neuropsychological and neuroimaging research has established that knowledge related to tool use and tool recognition is lateralized to the left cerebral hemisphere. Recently, behavioural studies with the visual half-field technique have confirmed the lateralization. A limitation of this research was that different sets of stimuli had to be used for the comparison of tools to other objects and objects to non-objects. Therefore, we developed a new set of stimuli containing matched triplets of tools, other objects and non-objects. With the new stimulus set, we successfully replicated the findings of no visual field advantage for objects in an object recognition task combined with a significant right visual field advantage for tools in a tool recognition task. The set of stimuli is available as supplemental data to this article.

Computational tool for postoperative evaluation of cochlear implant patients

International Nuclear Information System (INIS)

Giacomini, Guilherme; Pavan, Ana Luiza M.; Pina, Diana R. de; Altemani, Joao M.C.; Castilho, Arthur M.

2016-01-01

The aim of this study was to develop a tool to calculate the insertion depth angle of cochlear implants, from computed tomography exams. The tool uses different image processing techniques, such as thresholding and active contour. Then, we compared the average insertion depth angle of three different implant manufacturers. The developed tool can be used, in the future, to compare the insertion depth angle of the cochlear implant with postoperative response of patient's hearing. (author)

Electronic circuit design with HEP computational tools

International Nuclear Information System (INIS)

Vaz, Mario

1996-01-01

CPSPICE is an electronic circuit statistical simulation program developed to run in a parallel environment under UNIX operating system and TCP/IP communications protocol, using CPS - Cooperative Processes Software , SPICE program and CERNLIB software package. It is part of a set of tools being develop, intended to help electronic engineers to design, model and simulate complex systems and circuits for High Energy Physics detectors, based on statistical methods, using the same software and methodology used by HEP physicists for data analysis. CPSPICE simulates electronic circuits by Monte Carlo method, through several different processes running simultaneously SPICE in UNIX parallel computers or workstation farms. Data transfer between CPS processes for a modified version of SPICE2G6 is done by RAM memory, but can also be done through hard disk files if no source files are available for the simulator, and for bigger simulation outputs files. Simulation results are written in a HBOOK file as a NTUPLE, to be examined by HBOOK in batch model or graphics, and analyzed by statistical procedures available. The HBOOK file be stored on hard disk for small amount of data, or into Exabyte tape file for large amount of data. HEP tools also helps circuit or component modeling, like MINUT program from CERNLIB, that implements Nelder and Mead Simplex and Gradient with or without derivatives algorithms, and can be used for design optimization.This paper presents CPSPICE program implementation. The scheme adopted is suitable to make parallel other electronic circuit simulators. (author)

Computing Convex Coverage Sets for Faster Multi-Objective Coordination

NARCIS (Netherlands)

Roijers, D.M.; Whiteson, S.; Oliehoek, F.A.

2015-01-01

In this article, we propose new algorithms for multi-objective coordination graphs (MO-CoGs). Key to the efficiency of these algorithms is that they compute a convex coverage set (CCS) instead of a Pareto coverage set (PCS). Not only is a CCS a sufficient solution set for a large class of problems,

CMS offline web tools

International Nuclear Information System (INIS)

Metson, S; Newbold, D; Belforte, S; Kavka, C; Bockelman, B; Dziedziniewicz, K; Egeland, R; Elmer, P; Eulisse, G; Tuura, L; Evans, D; Fanfani, A; Feichtinger, D; Kuznetsov, V; Lingen, F van; Wakefield, S

2008-01-01

We describe a relatively new effort within CMS to converge on a set of web based tools, using state of the art industry techniques, to engage with the CMS offline computing system. CMS collaborators require tools to monitor various components of the computing system and interact with the system itself. The current state of the various CMS web tools is described along side current planned developments. The CMS collaboration comprises of nearly 3000 people from all over the world. As well as its collaborators, its computing resources are spread all over globe and are accessed via the LHC grid to run analysis, large scale production and data transfer tasks. Due to the distributed nature of collaborators effective provision of collaborative tools is essential to maximise physics exploitation of the CMS experiment, especially when the size of the CMS data set is considered. CMS has chosen to provide such tools over the world wide web as a top level service, enabling all members of the collaboration to interact with the various offline computing components. Traditionally web interfaces have been added in HEP experiments as an afterthought. In the CMS offline we have decided to put web interfaces, and the development of a common CMS web framework, on an equal footing with the rest of the offline development. Tools exist within CMS to transfer and catalogue data (PhEDEx and DBS/DLS), run Monte Carlo production (ProdAgent) and submit analysis (CRAB). Effective human interfaces to these systems are required for users with different agendas and practical knowledge of the systems to effectively use the CMS computing system. The CMS web tools project aims to provide a consistent interface to all these tools

CMS offline web tools

Energy Technology Data Exchange (ETDEWEB)

Metson, S; Newbold, D [H.H. Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL (United Kingdom); Belforte, S; Kavka, C [INFN, Sezione di Trieste (Italy); Bockelman, B [University of Nebraska Lincoln, Lincoln, NE (United States); Dziedziniewicz, K [CERN, Geneva (Switzerland); Egeland, R [University of Minnesota Twin Cities, Minneapolis, MN (United States); Elmer, P [Princeton (United States); Eulisse, G; Tuura, L [Northeastern University, Boston, MA (United States); Evans, D [Fermilab MS234, Batavia, IL (United States); Fanfani, A [Universita degli Studi di Bologna (Italy); Feichtinger, D [PSI, Villigen (Switzerland); Kuznetsov, V [Cornell University, Ithaca, NY (United States); Lingen, F van [California Institute of Technology, Pasedena, CA (United States); Wakefield, S [Blackett Laboratory, Imperial College, London (United Kingdom)

2008-07-15

We describe a relatively new effort within CMS to converge on a set of web based tools, using state of the art industry techniques, to engage with the CMS offline computing system. CMS collaborators require tools to monitor various components of the computing system and interact with the system itself. The current state of the various CMS web tools is described along side current planned developments. The CMS collaboration comprises of nearly 3000 people from all over the world. As well as its collaborators, its computing resources are spread all over globe and are accessed via the LHC grid to run analysis, large scale production and data transfer tasks. Due to the distributed nature of collaborators effective provision of collaborative tools is essential to maximise physics exploitation of the CMS experiment, especially when the size of the CMS data set is considered. CMS has chosen to provide such tools over the world wide web as a top level service, enabling all members of the collaboration to interact with the various offline computing components. Traditionally web interfaces have been added in HEP experiments as an afterthought. In the CMS offline we have decided to put web interfaces, and the development of a common CMS web framework, on an equal footing with the rest of the offline development. Tools exist within CMS to transfer and catalogue data (PhEDEx and DBS/DLS), run Monte Carlo production (ProdAgent) and submit analysis (CRAB). Effective human interfaces to these systems are required for users with different agendas and practical knowledge of the systems to effectively use the CMS computing system. The CMS web tools project aims to provide a consistent interface to all these tools.

Design tools for computer-generated display of information to operators

International Nuclear Information System (INIS)

O'Brien, J.F.; Cain, D.G.; Sun, B.K.H.

1985-01-01

More and more computers are being used to process and display information to operators who control nuclear power plants. Implementation of computer-generated displays in power plant control rooms represents a considerable design challenge for industry designers. Over the last several years, the EPRI has conducted research aimed at providing industry designers tools to meet this new design challenge. These tools provide guidance in defining more 'intelligent' information for plant control and in developing effective displays to communicate this information to the operators. (orig./HP)

Principal Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool.

Science.gov (United States)

Clark, Neil R; Szymkiewicz, Maciej; Wang, Zichen; Monteiro, Caroline D; Jones, Matthew R; Ma'ayan, Avi

2015-11-01

Gene set analysis of differential expression, which identifies collectively differentially expressed gene sets, has become an important tool for biology. The power of this approach lies in its reduction of the dimensionality of the statistical problem and its incorporation of biological interpretation by construction. Many approaches to gene set analysis have been proposed, but benchmarking their performance in the setting of real biological data is difficult due to the lack of a gold standard. In a previously published work we proposed a geometrical approach to differential expression which performed highly in benchmarking tests and compared well to the most popular methods of differential gene expression. As reported, this approach has a natural extension to gene set analysis which we call Principal Angle Enrichment Analysis (PAEA). PAEA employs dimensionality reduction and a multivariate approach for gene set enrichment analysis. However, the performance of this method has not been assessed nor its implementation as a web-based tool. Here we describe new benchmarking protocols for gene set analysis methods and find that PAEA performs highly. The PAEA method is implemented as a user-friendly web-based tool, which contains 70 gene set libraries and is freely available to the community.

An integrated computational tool for precipitation simulation

Science.gov (United States)

Cao, W.; Zhang, F.; Chen, S.-L.; Zhang, C.; Chang, Y. A.

2011-07-01

Computer aided materials design is of increasing interest because the conventional approach solely relying on experimentation is no longer viable within the constraint of available resources. Modeling of microstructure and mechanical properties during precipitation plays a critical role in understanding the behavior of materials and thus accelerating the development of materials. Nevertheless, an integrated computational tool coupling reliable thermodynamic calculation, kinetic simulation, and property prediction of multi-component systems for industrial applications is rarely available. In this regard, we are developing a software package, PanPrecipitation, under the framework of integrated computational materials engineering to simulate precipitation kinetics. It is seamlessly integrated with the thermodynamic calculation engine, PanEngine, to obtain accurate thermodynamic properties and atomic mobility data necessary for precipitation simulation.

Scratch as a Computational Modelling Tool for Teaching Physics

Science.gov (United States)

Lopez, Victor; Hernandez, Maria Isabel

2015-01-01

The Scratch online authoring tool, which features a simple programming language that has been adapted to primary and secondary students, is being used more and more in schools as it offers students and teachers the opportunity to use a tool to build scientific models and evaluate their behaviour, just as can be done with computational modelling…

Final Report: Correctness Tools for Petascale Computing

Energy Technology Data Exchange (ETDEWEB)

Mellor-Crummey, John [Rice Univ., Houston, TX (United States)

2014-10-27

In the course of developing parallel programs for leadership computing systems, subtle programming errors often arise that are extremely difficult to diagnose without tools. To meet this challenge, University of Maryland, the University of Wisconsin—Madison, and Rice University worked to develop lightweight tools to help code developers pinpoint a variety of program correctness errors that plague parallel scientific codes. The aim of this project was to develop software tools that help diagnose program errors including memory leaks, memory access errors, round-off errors, and data races. Research at Rice University focused on developing algorithms and data structures to support efficient monitoring of multithreaded programs for memory access errors and data races. This is a final report about research and development work at Rice University as part of this project.

A tool for computing diversity and consideration on differences between diversity indices

OpenAIRE

Palaghianu, Ciprian

2016-01-01

Diversity represents a key concept in ecology, and there are various methods of assessing it. The multitude of diversity indices are quite puzzling and sometimes difficult to compute for a large volume of data. This paper promotes a computational tool used to assess the diversity of different entities. The BIODIV software is a user-friendly tool, developed using Microsoft Visual Basic. It is capable to compute several diversity indices such as: Shannon, Simpson, Pielou, Brillouin, Berger-Park...

MRUniNovo: an efficient tool for de novo peptide sequencing utilizing the hadoop distributed computing framework.

Science.gov (United States)

Li, Chuang; Chen, Tao; He, Qiang; Zhu, Yunping; Li, Kenli

2017-03-15

Tandem mass spectrometry-based de novo peptide sequencing is a complex and time-consuming process. The current algorithms for de novo peptide sequencing cannot rapidly and thoroughly process large mass spectrometry datasets. In this paper, we propose MRUniNovo, a novel tool for parallel de novo peptide sequencing. MRUniNovo parallelizes UniNovo based on the Hadoop compute platform. Our experimental results demonstrate that MRUniNovo significantly reduces the computation time of de novo peptide sequencing without sacrificing the correctness and accuracy of the results, and thus can process very large datasets that UniNovo cannot. MRUniNovo is an open source software tool implemented in java. The source code and the parameter settings are available at http://bioinfo.hupo.org.cn/MRUniNovo/index.php. s131020002@hnu.edu.cn ; taochen1019@163.com. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Problems and Issues in Using Computer- Based Support Tools to Enhance 'Soft' Systems Methodologies

Directory of Open Access Journals (Sweden)

Mark Stansfield

2001-11-01

Full Text Available This paper explores the issue of whether computer-based support tools can enhance the use of 'soft' systems methodologies as applied to real-world problem situations. Although work has been carried out by a number of researchers in applying computer-based technology to concepts and methodologies relating to 'soft' systems thinking such as Soft Systems Methodology (SSM, such attempts appear to be still in their infancy and have not been applied widely to real-world problem situations. This paper will highlight some of the problems that may be encountered in attempting to develop computer-based support tools for 'soft' systems methodologies. Particular attention will be paid to an attempt by the author to develop a computer-based support tool for a particular 'soft' systems method of inquiry known as the Appreciative Inquiry Method that is based upon Vickers' notion of 'appreciation' (Vickers, 196S and Checkland's SSM (Checkland, 1981. The final part of the paper will explore some of the lessons learnt from developing and applying the computer-based support tool to a real world problem situation, as well as considering the feasibility of developing computer-based support tools for 'soft' systems methodologies. This paper will put forward the point that a mixture of manual and computer-based tools should be employed to allow a methodology to be used in an unconstrained manner, but the benefits provided by computer-based technology should be utilised in supporting and enhancing the more mundane and structured tasks.

Geometric computations with interval and new robust methods applications in computer graphics, GIS and computational geometry

CERN Document Server

Ratschek, H

2003-01-01

This undergraduate and postgraduate text will familiarise readers with interval arithmetic and related tools to gain reliable and validated results and logically correct decisions for a variety of geometric computations plus the means for alleviating the effects of the errors. It also considers computations on geometric point-sets, which are neither robust nor reliable in processing with standard methods. The authors provide two effective tools for obtaining correct results: (a) interval arithmetic, and (b) ESSA the new powerful algorithm which improves many geometric computations and makes th

Validating the WHO maternal near miss tool: comparing high- and low-resource settings.

Science.gov (United States)

Witteveen, Tom; Bezstarosti, Hans; de Koning, Ilona; Nelissen, Ellen; Bloemenkamp, Kitty W; van Roosmalen, Jos; van den Akker, Thomas

2017-06-19

WHO proposed the WHO Maternal Near Miss (MNM) tool, classifying women according to several (potentially) life-threatening conditions, to monitor and improve quality of obstetric care. The objective of this study is to analyse merged data of one high- and two low-resource settings where this tool was applied and test whether the tool may be suitable for comparing severe maternal outcome (SMO) between these settings. Using three cohort studies that included SMO cases, during two-year time frames in the Netherlands, Tanzania and Malawi we reassessed all SMO cases (as defined by the original studies) with the WHO MNM tool (five disease-, four intervention- and seven organ dysfunction-based criteria). Main outcome measures were prevalence of MNM criteria and case fatality rates (CFR). A total of 3172 women were studied; 2538 (80.0%) from the Netherlands, 248 (7.8%) from Tanzania and 386 (12.2%) from Malawi. Total SMO detection was 2767 (87.2%) for disease-based criteria, 2504 (78.9%) for intervention-based criteria and 1211 (38.2%) for organ dysfunction-based criteria. Including every woman who received ≥1 unit of blood in low-resource settings as life-threatening, as defined by organ dysfunction criteria, led to more equally distributed populations. In one third of all Dutch and Malawian maternal death cases, organ dysfunction criteria could not be identified from medical records. Applying solely organ dysfunction-based criteria may lead to underreporting of SMO. Therefore, a tool based on defining MNM only upon establishing organ failure is of limited use for comparing settings with varying resources. In low-resource settings, lowering the threshold of transfused units of blood leads to a higher detection rate of MNM. We recommend refined disease-based criteria, accompanied by a limited set of intervention- and organ dysfunction-based criteria to set a measure of severity.

A new DoD initiative: the Computational Research and Engineering Acquisition Tools and Environments (CREATE) program

International Nuclear Information System (INIS)

Arevalo, S; Atwood, C; Bell, P; Blacker, T D; Dey, S; Fisher, D; Fisher, D A; Genalis, P; Gorski, J; Harris, A; Hill, K; Hurwitz, M; Kendall, R P; Meakin, R L; Morton, S; Moyer, E T; Post, D E; Strawn, R; Veldhuizen, D v; Votta, L G

2008-01-01

In FY2008, the U.S. Department of Defense (DoD) initiated the Computational Research and Engineering Acquisition Tools and Environments (CREATE) program, a $360M program with a two-year planning phase and a ten-year execution phase. CREATE will develop and deploy three computational engineering tool sets for DoD acquisition programs to use to design aircraft, ships and radio-frequency antennas. The planning and execution of CREATE are based on the 'lessons learned' from case studies of large-scale computational science and engineering projects. The case studies stress the importance of a stable, close-knit development team; a focus on customer needs and requirements; verification and validation; flexible and agile planning, management, and development processes; risk management; realistic schedules and resource levels; balanced short- and long-term goals and deliverables; and stable, long-term support by the program sponsor. Since it began in FY2008, the CREATE program has built a team and project structure, developed requirements and begun validating them, identified candidate products, established initial connections with the acquisition programs, begun detailed project planning and development, and generated the initial collaboration infrastructure necessary for success by its multi-institutional, multidisciplinary teams

A software package to construct polynomial sets over Z2 for determining the output of quantum computations

International Nuclear Information System (INIS)

Gerdt, Vladimir P.; Severyanov, Vasily M.

2006-01-01

A C package is presented that allows a user for an input quantum circuit to generate a set of multivariate polynomials over the finite field Z 2 whose total number of solutions in Z 2 determines the output of the quantum computation defined by the circuit. The generated polynomial system can further be converted to the canonical Grobner basis form which provides a universal algorithmic tool for counting the number of common roots of the polynomials

Answer Set Programming and Other Computing Paradigms

Science.gov (United States)

Meng, Yunsong

2013-01-01

Answer Set Programming (ASP) is one of the most prominent and successful knowledge representation paradigms. The success of ASP is due to its expressive non-monotonic modeling language and its efficient computational methods originating from building propositional satisfiability solvers. The wide adoption of ASP has motivated several extensions to…

Computer tool to evaluate the cue reactivity of chemically dependent individuals.

Science.gov (United States)

Silva, Meire Luci da; Frère, Annie France; Oliveira, Henrique Jesus Quintino de; Martucci Neto, Helio; Scardovelli, Terigi Augusto

2017-03-01

Anxiety is one of the major influences on the dropout of relapse and treatment of substance abuse treatment. Chemically dependent individuals need (CDI) to be aware of their emotional state in situations of risk during their treatment. Many patients do not agree with the diagnosis of the therapist when considering them vulnerable to environmental stimuli related to drugs. This research presents a cue reactivity detection tool based on a device acquiring physiological signals connected to personal computer. Depending on the variations of the emotional state of the drug addict, alteration of the physiological signals will be detected by the computer tool (CT) which will modify the displayed virtual sets without intervention of the therapist. Developed in 3ds Max® software, the CT is composed of scenarios and objects that are in the habit of marijuana and cocaine dependent individual's daily life. The interaction with the environment is accomplished using a Human-Computer Interface (HCI) that converts incoming physiological signals indicating anxiety state into commands that change the scenes. Anxiety was characterized by the average variability from cardiac and respiratory rate of 30 volunteers submitted stress environment situations. To evaluate the effectiveness of cue reactivity a total of 50 volunteers who were marijuana, cocaine or both dependent were accompanied. Prior to CT, the results demonstrated a poor correlation between the therapists' predictions and those of the chemically dependent individuals. After exposure to the CT, there was a significant increase of 73% in awareness of the risks of relapse. We confirmed the hypothesis that the CT, controlled only by physiological signals, increases the perception of vulnerability to risk situations of individuals with dependence on marijuana, cocaine or both. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Open environments to support systems engineering tool integration: A study using the Portable Common Tool Environment (PCTE)

Science.gov (United States)

Eckhardt, Dave E., Jr.; Jipping, Michael J.; Wild, Chris J.; Zeil, Steven J.; Roberts, Cathy C.

1993-01-01

A study of computer engineering tool integration using the Portable Common Tool Environment (PCTE) Public Interface Standard is presented. Over a 10-week time frame, three existing software products were encapsulated to work in the Emeraude environment, an implementation of the PCTE version 1.5 standard. The software products used were a computer-aided software engineering (CASE) design tool, a software reuse tool, and a computer architecture design and analysis tool. The tool set was then demonstrated to work in a coordinated design process in the Emeraude environment. The project and the features of PCTE used are described, experience with the use of Emeraude environment over the project time frame is summarized, and several related areas for future research are summarized.

A computer tool to support in design of industrial Ethernet.

Science.gov (United States)

Lugli, Alexandre Baratella; Santos, Max Mauro Dias; Franco, Lucia Regina Horta Rodrigues

2009-04-01

This paper presents a computer tool to support in the project and development of an industrial Ethernet network, verifying the physical layer (cables-resistance and capacitance, scan time, network power supply-POE's concept "Power Over Ethernet" and wireless), and occupation rate (amount of information transmitted to the network versus the controller network scan time). These functions are accomplished without a single physical element installed in the network, using only simulation. The computer tool has a software that presents a detailed vision of the network to the user, besides showing some possible problems in the network, and having an extremely friendly environment.

Cloud Computing as a Tool for Improving Business Competitiveness

Directory of Open Access Journals (Sweden)

Wišniewski Michał

2014-08-01

Full Text Available This article organizes knowledge on cloud computing presenting the classification of deployment models, characteristics and service models. The author, looking at the problem from the entrepreneur’s perspective, draws attention to the differences in the benefits depending on the cloud computing deployment models and considers an effective way of selection of cloud computing services according to the specificity of organization. Within this work, a thesis statement was considered that in economic terms the cloud computing is not always the best solution for your organization. This raises the question, “What kind of tools should be used to estimate the usefulness of the model cloud computing services in the enterprise?”

Automated planning target volume generation: an evaluation pitting a computer-based tool against human experts

International Nuclear Information System (INIS)

Ketting, Case H.; Austin-Seymour, Mary; Kalet, Ira; Jacky, Jon; Kromhout-Schiro, Sharon; Hummel, Sharon; Unger, Jonathan; Fagan, Lawrence M.; Griffin, Tom

1997-01-01

Purpose: Software tools are seeing increased use in three-dimensional treatment planning. However, the development of these tools frequently omits careful evaluation before placing them in clinical use. This study demonstrates the application of a rigorous evaluation methodology using blinded peer review to an automated software tool that produces ICRU-50 planning target volumes (PTVs). Methods and Materials: Seven physicians from three different institutions involved in three-dimensional treatment planning participated in the evaluation. Four physicians drew partial PTVs on nine test cases, consisting of four nasopharynx and five lung primaries. Using the same information provided to the human experts, the computer tool generated PTVs for comparison. The remaining three physicians, designated evaluators, individually reviewed the PTVs for acceptability. To exclude bias, the evaluators were blinded to the source (human or computer) of the PTVs they reviewed. Their scorings of the PTVs were statistically examined to determine if the computer tool performed as well as the human experts. Results: The computer tool was as successful as the human experts in generating PTVs. Failures were primarily attributable to insufficient margins around the clinical target volume and to encroachment upon critical structures. In a qualitative analysis, the human and computer experts displayed similar types and distributions of errors. Conclusions: Rigorous evaluation of computer-based radiotherapy tools requires comparison to current practice and can reveal areas for improvement before the tool enters clinical practice

Development and Evaluation of Computer-Based Laboratory Practical Learning Tool

Science.gov (United States)

Gandole, Y. B.

2006-01-01

Effective evaluation of educational software is a key issue for successful introduction of advanced tools in the curriculum. This paper details to developing and evaluating a tool for computer assisted learning of science laboratory courses. The process was based on the generic instructional system design model. Various categories of educational…

9th International Workshop on Parallel Tools for High Performance Computing

CERN Document Server

Hilbrich, Tobias; Niethammer, Christoph; Gracia, José; Nagel, Wolfgang; Resch, Michael

2016-01-01

High Performance Computing (HPC) remains a driver that offers huge potentials and benefits for science and society. However, a profound understanding of the computational matters and specialized software is needed to arrive at effective and efficient simulations. Dedicated software tools are important parts of the HPC software landscape, and support application developers. Even though a tool is by definition not a part of an application, but rather a supplemental piece of software, it can make a fundamental difference during the development of an application. Such tools aid application developers in the context of debugging, performance analysis, and code optimization, and therefore make a major contribution to the development of robust and efficient parallel software. This book introduces a selection of the tools presented and discussed at the 9th International Parallel Tools Workshop held in Dresden, Germany, September 2-3, 2015, which offered an established forum for discussing the latest advances in paral...

Development of computer-based analytical tool for assessing physical protection system

Science.gov (United States)

Mardhi, Alim; Pengvanich, Phongphaeth

2016-01-01

Assessment of physical protection system effectiveness is the priority for ensuring the optimum protection caused by unlawful acts against a nuclear facility, such as unauthorized removal of nuclear materials and sabotage of the facility itself. Since an assessment based on real exercise scenarios is costly and time-consuming, the computer-based analytical tool can offer the solution for approaching the likelihood threat scenario. There are several currently available tools that can be used instantly such as EASI and SAPE, however for our research purpose it is more suitable to have the tool that can be customized and enhanced further. In this work, we have developed a computer-based analytical tool by utilizing the network methodological approach for modelling the adversary paths. The inputs are multi-elements in security used for evaluate the effectiveness of the system's detection, delay, and response. The tool has capability to analyze the most critical path and quantify the probability of effectiveness of the system as performance measure.

Computer Tools for Construction, Modification and Analysis of Petri Nets

DEFF Research Database (Denmark)

Jensen, Kurt

1987-01-01

The practical use of Petri nets is — just as any other description technique — very dependent on the existence of adequate computer tools, which may assist the user to cope with the many details of a large description. For Petri nets there is a need for tools supporting construction of nets...

Approach and tool for computer animation of fields in electrical apparatus

International Nuclear Information System (INIS)

Miltchev, Radoslav; Yatchev, Ivan S.; Ritchie, Ewen

2002-01-01

The paper presents a technical approach and post-processing tool for creating and displaying computer animation. The approach enables handling of two- and three-dimensional physical field phenomena results obtained from finite element software or to display movement processes in electrical apparatus simulations. The main goal of this work is to extend auxiliary features built in general-purpose CAD software working in the Windows environment. Different storage techniques were examined and the one employing image capturing was chosen. The developed tool provides benefits of independent visualisation, creating scenarios and facilities for exporting animations in common file fon-nats for distribution on different computer platforms. It also provides a valuable educational tool.(Author)

10th International Workshop on Parallel Tools for High Performance Computing

CERN Document Server

Gracia, José; Hilbrich, Tobias; Knüpfer, Andreas; Resch, Michael; Nagel, Wolfgang

2017-01-01

This book presents the proceedings of the 10th International Parallel Tools Workshop, held October 4-5, 2016 in Stuttgart, Germany – a forum to discuss the latest advances in parallel tools. High-performance computing plays an increasingly important role for numerical simulation and modelling in academic and industrial research. At the same time, using large-scale parallel systems efficiently is becoming more difficult. A number of tools addressing parallel program development and analysis have emerged from the high-performance computing community over the last decade, and what may have started as collection of small helper script has now matured to production-grade frameworks. Powerful user interfaces and an extensive body of documentation allow easy usage by non-specialists. tools have been commercialized, but others are operated as open source by a growing research community.

Cost-effective cloud computing: a case study using the comparative genomics tool, roundup.

Science.gov (United States)

Kudtarkar, Parul; Deluca, Todd F; Fusaro, Vincent A; Tonellato, Peter J; Wall, Dennis P

2010-12-22

Comparative genomics resources, such as ortholog detection tools and repositories are rapidly increasing in scale and complexity. Cloud computing is an emerging technological paradigm that enables researchers to dynamically build a dedicated virtual cluster and may represent a valuable alternative for large computational tools in bioinformatics. In the present manuscript, we optimize the computation of a large-scale comparative genomics resource-Roundup-using cloud computing, describe the proper operating principles required to achieve computational efficiency on the cloud, and detail important procedures for improving cost-effectiveness to ensure maximal computation at minimal costs. Utilizing the comparative genomics tool, Roundup, as a case study, we computed orthologs among 902 fully sequenced genomes on Amazon's Elastic Compute Cloud. For managing the ortholog processes, we designed a strategy to deploy the web service, Elastic MapReduce, and maximize the use of the cloud while simultaneously minimizing costs. Specifically, we created a model to estimate cloud runtime based on the size and complexity of the genomes being compared that determines in advance the optimal order of the jobs to be submitted. We computed orthologous relationships for 245,323 genome-to-genome comparisons on Amazon's computing cloud, a computation that required just over 200 hours and cost $8,000 USD, at least 40% less than expected under a strategy in which genome comparisons were submitted to the cloud randomly with respect to runtime. Our cost savings projections were based on a model that not only demonstrates the optimal strategy for deploying RSD to the cloud, but also finds the optimal cluster size to minimize waste and maximize usage. Our cost-reduction model is readily adaptable for other comparative genomics tools and potentially of significant benefit to labs seeking to take advantage of the cloud as an alternative to local computing infrastructure.

Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming

Energy Technology Data Exchange (ETDEWEB)

Song, Hyun-Seob; Goldberg, Noam; Mahajan, Ashutosh; Ramkrishna, Doraiswami

2017-03-27

Elementary (flux) modes (EMs) have served as a valuable tool for investigating structural and functional properties of metabolic networks. Identification of the full set of EMs in genome-scale networks remains challenging due to combinatorial explosion of EMs in complex networks. It is often, however, that only a small subset of relevant EMs needs to be known, for which optimization-based sequential computation is a useful alternative. Most of the currently available methods along this line are based on the iterative use of mixed integer linear programming (MILP), the effectiveness of which significantly deteriorates as the number of iterations builds up. To alleviate the computational burden associated with the MILP implementation, we here present a novel optimization algorithm termed alternate integer linear programming (AILP). Results: Our algorithm was designed to iteratively solve a pair of integer programming (IP) and linear programming (LP) to compute EMs in a sequential manner. In each step, the IP identifies a minimal subset of reactions, the deletion of which disables all previously identified EMs. Thus, a subsequent LP solution subject to this reaction deletion constraint becomes a distinct EM. In cases where no feasible LP solution is available, IP-derived reaction deletion sets represent minimal cut sets (MCSs). Despite the additional computation of MCSs, AILP achieved significant time reduction in computing EMs by orders of magnitude. The proposed AILP algorithm not only offers a computational advantage in the EM analysis of genome-scale networks, but also improves the understanding of the linkage between EMs and MCSs.

On Computational Fluid Dynamics Tools in Architectural Design

DEFF Research Database (Denmark)

Kirkegaard, Poul Henning; Hougaard, Mads; Stærdahl, Jesper Winther

engineering computational fluid dynamics (CFD) simulation program ANSYS CFX and a CFD based representative program RealFlow are investigated. These two programs represent two types of CFD based tools available for use during phases of an architectural design process. However, as outlined in two case studies...

Nsite, NsiteH and NsiteM Computer Tools for Studying Tran-scription Regulatory Elements

KAUST Repository

Shahmuradov, Ilham

2015-07-02

Summary: Gene transcription is mostly conducted through interactions of various transcription factors and their binding sites on DNA (regulatory elements, REs). Today, we are still far from understanding the real regulatory content of promoter regions. Computer methods for identification of REs remain a widely used tool for studying and understanding transcriptional regulation mechanisms. The Nsite, NsiteH and NsiteM programs perform searches for statistically significant (non-random) motifs of known human, animal and plant one-box and composite REs in a single genomic sequence, in a pair of aligned homologous sequences and in a set of functionally related sequences, respectively.

Translation Memory and Computer Assisted Translation Tool for Medieval Texts

Directory of Open Access Journals (Sweden)

Törcsvári Attila

2013-05-01

Full Text Available Translation memories (TMs, as part of Computer Assisted Translation (CAT tools, support translators reusing portions of formerly translated text. Fencing books are good candidates for using TMs due to the high number of repeated terms. Medieval texts suffer a number of drawbacks that make hard even “simple” rewording to the modern version of the same language. The analyzed difficulties are: lack of systematic spelling, unusual word orders and typos in the original. A hypothesis is made and verified that even simple modernization increases legibility and it is feasible, also it is worthwhile to apply translation memories due to the numerous and even extremely long repeated terms. Therefore, methods and algorithms are presented 1. for automated transcription of medieval texts (when a limited training set is available, and 2. collection of repeated patterns. The efficiency of the algorithms is analyzed for recall and precision.

A Tool for Interactive Data Visualization: Application to Over 10,000 Brain Imaging and Phantom MRI Data Sets

Directory of Open Access Journals (Sweden)

Sandeep R Panta

2016-03-01

Full Text Available In this paper we propose a web-based approach for quick visualization of big data from brain magnetic resonance imaging (MRI scans using a combination of an automated image capture and processing system, nonlinear embedding, and interactive data visualization tools. We draw upon thousands of MRI scans captured via the COllaborative Imaging and Neuroinformatics Suite (COINS. We then interface the output of several analysis pipelines based on structural and functional data to a t-distributed stochastic neighbor embedding (t-SNE algorithm which reduces the number of dimensions for each scan in the input data set to two dimensions while preserving the local structure of data sets. Finally, we interactively display the output of this approach via a web-page, based on data driven documents (D3 JavaScript library. Two distinct approaches were used to visualize the data. In the first approach, we computed multiple quality control (QC values from pre-processed data, which were used as inputs to the t-SNE algorithm. This approach helps in assessing the quality of each data set relative to others. In the second case, computed variables of interest (e.g. brain volume or voxel values from segmented gray matter images were used as inputs to the t-SNE algorithm. This approach helps in identifying interesting patterns in the data sets. We demonstrate these approaches using multiple examples including 1 quality control measures calculated from phantom data over time, 2 quality control data from human functional MRI data across various studies, scanners, sites, 3 volumetric and density measures from human structural MRI data across various studies, scanners and sites. Results from (1 and (2 show the potential of our approach to combine t-SNE data reduction with interactive color coding of variables of interest to quickly identify visually unique clusters of data (i.e. data sets with poor QC, clustering of data by site quickly. Results from (3 demonstrate

Theory and computation of disturbance invariant sets for discrete-time linear systems

Directory of Open Access Journals (Sweden)

Kolmanovsky Ilya

1998-01-01

Full Text Available This paper considers the characterization and computation of invariant sets for discrete-time, time-invariant, linear systems with disturbance inputs whose values are confined to a specified compact set but are otherwise unknown. The emphasis is on determining maximal disturbance-invariant sets X that belong to a specified subset Γ of the state space. Such d-invariant sets have important applications in control problems where there are pointwise-in-time state constraints of the form χ ( t ∈ Γ . One purpose of the paper is to unite and extend in a rigorous way disparate results from the prior literature. In addition there are entirely new results. Specific contributions include: exploitation of the Pontryagin set difference to clarify conceptual matters and simplify mathematical developments, special properties of maximal invariant sets and conditions for their finite determination, algorithms for generating concrete representations of maximal invariant sets, practical computational questions, extension of the main results to general Lyapunov stable systems, applications of the computational techniques to the bounding of state and output response. Results on Lyapunov stable systems are applied to the implementation of a logic-based, nonlinear multimode regulator. For plants with disturbance inputs and state-control constraints it enlarges the constraint-admissible domain of attraction. Numerical examples illustrate the various theoretical and computational results.

Electronic structure of BN-aromatics: Choice of reliable computational tools

Science.gov (United States)

Mazière, Audrey; Chrostowska, Anna; Darrigan, Clovis; Dargelos, Alain; Graciaa, Alain; Chermette, Henry

2017-10-01

The importance of having reliable calculation tools to interpret and predict the electronic properties of BN-aromatics is directly linked to the growing interest for these very promising new systems in the field of materials science, biomedical research, or energy sustainability. Ionization energy (IE) is one of the most important parameters to approach the electronic structure of molecules. It can be theoretically estimated, but in order to evaluate their persistence and propose the most reliable tools for the evaluation of different electronic properties of existent or only imagined BN-containing compounds, we took as reference experimental values of ionization energies provided by ultra-violet photoelectron spectroscopy (UV-PES) in gas phase—the only technique giving access to the energy levels of filled molecular orbitals. Thus, a set of 21 aromatic molecules containing B-N bonds and B-N-B patterns has been merged for a comparison between experimental IEs obtained by UV-PES and various theoretical approaches for their estimation. Time-Dependent Density Functional Theory (TD-DFT) methods using B3LYP and long-range corrected CAM-B3LYP functionals are used, combined with the Δ SCF approach, and compared with electron propagator theory such as outer valence Green's function (OVGF, P3) and symmetry adapted cluster-configuration interaction ab initio methods. Direct Kohn-Sham estimation and "corrected" Kohn-Sham estimation are also given. The deviation between experimental and theoretical values is computed for each molecule, and a statistical study is performed over the average and the root mean square for the whole set and sub-sets of molecules. It is shown that (i) Δ SCF+TDDFT(CAM-B3LYP), OVGF, and P3 are the most efficient way for a good agreement with UV-PES values, (ii) a CAM-B3LYP range-separated hybrid functional is significantly better than B3LYP for the purpose, especially for extended conjugated systems, and (iii) the "corrected" Kohn-Sham result is a

REMOD: a computational tool for remodeling neuronal dendrites

Directory of Open Access Journals (Sweden)

Panagiotis Bozelos

2014-05-01

Full Text Available In recent years, several modeling studies have indicated that dendritic morphology is a key determinant of how individual neurons acquire a unique signal processing profile. The highly branched dendritic structure that originates from the cell body, explores the surrounding 3D space in a fractal-like manner, until it reaches a certain amount of complexity. Its shape undergoes significant alterations not only in various neuropathological conditions, but in physiological, too. Yet, despite the profound effect that these alterations can have on neuronal function, the causal relationship between structure and function remains largely elusive. The lack of a systematic approach for remodeling neuronal cells and their dendritic trees is a key limitation that contributes to this problem. In this context, we developed a computational tool that allows the remodeling of any type of neurons, given a set of exemplar morphologies. The tool is written in Python and provides a simple GUI that guides the user through various options to manipulate selected neuronal morphologies. It provides the ability to load one or more morphology files (.swc or .hoc and choose specific dendrites to operate one of the following actions: shrink, remove, extend or branch (as shown in Figure 1. The user retains complete control over the extent of each alteration and if a chosen action is not possible due to pre-existing structural constraints, appropriate warnings are produced. Importantly, the tool can also be used to extract morphology statistics for one or multiple morphologies, including features such as the total dendritic length, path length to the root, branch order, diameter tapering, etc. Finally, an experimental utility enables the user to remodel entire dendritic trees based on preloaded statistics from a database of cell-type specific neuronal morphologies. To our knowledge, this is the first tool that allows (a the remodeling of existing –as opposed to the de novo

Scalable space-time adaptive simulation tools for computational electrocardiology

OpenAIRE

Krause, Dorian; Krause, Rolf

2013-01-01

This work is concerned with the development of computational tools for the solution of reaction-diffusion equations from the field of computational electrocardiology. We designed lightweight spatially and space-time adaptive schemes for large-scale parallel simulations. We propose two different adaptive schemes based on locally structured meshes, managed either via a conforming coarse tessellation or a forest of shallow trees. A crucial ingredient of our approach is a non-conforming morta...

Interactive Computer Graphics

Science.gov (United States)

Kenwright, David

2000-01-01

Aerospace data analysis tools that significantly reduce the time and effort needed to analyze large-scale computational fluid dynamics simulations have emerged this year. The current approach for most postprocessing and visualization work is to explore the 3D flow simulations with one of a dozen or so interactive tools. While effective for analyzing small data sets, this approach becomes extremely time consuming when working with data sets larger than one gigabyte. An active area of research this year has been the development of data mining tools that automatically search through gigabyte data sets and extract the salient features with little or no human intervention. With these so-called feature extraction tools, engineers are spared the tedious task of manually exploring huge amounts of data to find the important flow phenomena. The software tools identify features such as vortex cores, shocks, separation and attachment lines, recirculation bubbles, and boundary layers. Some of these features can be extracted in a few seconds; others take minutes to hours on extremely large data sets. The analysis can be performed off-line in a batch process, either during or following the supercomputer simulations. These computations have to be performed only once, because the feature extraction programs search the entire data set and find every occurrence of the phenomena being sought. Because the important questions about the data are being answered automatically, interactivity is less critical than it is with traditional approaches.

An Open-Source Tool Set Enabling Analog-Digital-Software Co-Design

Directory of Open Access Journals (Sweden)

Michelle Collins

2016-02-01

Full Text Available This paper presents an analog-digital hardware-software co-design environment for simulating and programming reconfigurable systems. The tool simulates, designs, as well as enables experimental measurements after compiling to configurable systems in the same integrated design tool framework. High level software in Scilab/Xcos (open-source programs similar to MATLAB/Simulink that converts the high-level block description by the user to blif format (sci2blif, which acts as an input to the modified VPR tool, including the code v p r 2 s w c s , encoding the specific platform through specific architecture files, resulting in a targetable switch list on the resulting configurable analog–digital system. The resulting tool uses an analog and mixed-signal library of components, enabling users and future researchers access to the basic analog operations/computations that are possible.

Splitting Computation of Answer Set Program and Its Application on E-service

Directory of Open Access Journals (Sweden)

Bo Yang

2011-10-01

Full Text Available As a primary means for representing and reasoning about knowledge, Answer Set Programming (ASP has been applying in many areas such as planning, decision making, fault diagnosing and increasingly prevalent e-service. Based on the stable model semantics of logic programming, ASP can be used to solve various combinatorial search problems by finding the answer sets of logic programs which declaratively describe the problems. Itrs not an easy task to compute answer sets of a logic program using Gelfond and Lifschitzrs definition directly. In this paper, we show some results on characterization of answer sets of a logic program with constraints, and propose a way to split a program into several non-intersecting parts step by step, thus the computation of answer sets for every subprogram becomes relatively easy. To instantiate our splitting computation theory, an example about personalized product configuration in e-retailing is given to show the effectiveness of our method.

Improvement of visual debugging tool. Shortening the elapsed time for getting data and adding new functions to compare/combine a set of visualized data

International Nuclear Information System (INIS)

Matsuda, Katsuyuki; Takemiya, Hiroshi

2001-03-01

The visual debugging tool 'vdebug' has been improved, which was designed for the debugging of programs for scientific computing. Improved were the following two points; (1) shortening the elapsed time required for getting appropriate data to visualize; (2) adding new functions which enable to compare and/or combine a set of visualized data originated from two or more different programs. As for shortening elapsed time for getting data, with the improved version of 'vdebug', we could achieve the following results; over hundred times shortening the elapsed time with dbx, pdbx of SX-4 and over ten times with ndb of SR2201. As for the new functions to compare/combine visualized data, it was confirmed that we could easily checked the consistency between the computational results obtained in each calculational steps on two different computers: SP and ONYX. In this report, we illustrate how the tool 'vdebug' has been improved with an example. (author)

Computer Aided Design Tools for Extreme Environment Electronics, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — This project aims to provide Computer Aided Design (CAD) tools for radiation-tolerant, wide-temperature-range digital, analog, mixed-signal, and radio-frequency...

Computational Tool for Aerothermal Environment Around Transatmospheric Vehicles, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — The goal of this Project is to develop a high-fidelity computational tool for accurate prediction of aerothermal environment on transatmospheric vehicles. This...

Tools and approaches for simplifying serious games development in educational settings

OpenAIRE

Calvo, Antonio; Rotaru, Dan C.; Freire, Manuel; Fernandez-Manjon, Baltasar

2016-01-01

Serious Games can benefit from the commercial video games industry by taking advantage of current development tools. However, the economics and requirements of serious games and commercial games are very different. In this paper, we describe the factors that impact the total cost of ownership of serious games used in educational settings, review the specific requirements of games used as learning material, and analyze the different development tools available in the industry highlighting thei...

A least-squares computational ''tool kit''

International Nuclear Information System (INIS)

Smith, D.L.

1993-04-01

The information assembled in this report is intended to offer a useful computational ''tool kit'' to individuals who are interested in a variety of practical applications for the least-squares method of parameter estimation. The fundamental principles of Bayesian analysis are outlined first and these are applied to development of both the simple and the generalized least-squares conditions. Formal solutions that satisfy these conditions are given subsequently. Their application to both linear and non-linear problems is described in detail. Numerical procedures required to implement these formal solutions are discussed and two utility computer algorithms are offered for this purpose (codes LSIOD and GLSIOD written in FORTRAN). Some simple, easily understood examples are included to illustrate the use of these algorithms. Several related topics are then addressed, including the generation of covariance matrices, the role of iteration in applications of least-squares procedures, the effects of numerical precision and an approach that can be pursued in developing data analysis packages that are directed toward special applications

Computer graphics and research projects

International Nuclear Information System (INIS)

Ingtrakul, P.

1994-01-01

This report was prepared as an account of scientific visualization tools and application tools for scientists and engineers. It is provided a set of tools to create pictures and to interact with them in natural ways. It applied many techniques of computer graphics and computer animation through a number of full-color presentations as computer animated commercials, 3D computer graphics, dynamic and environmental simulations, scientific modeling and visualization, physically based modelling, and beavioral, skelatal, dynamics, and particle animation. It took in depth at original hardware and limitations of existing PC graphics adapters contain syste m performance, especially with graphics intensive application programs and user interfaces

Informed public choices for low-carbon electricity portfolios using a computer decision tool.

Science.gov (United States)

Mayer, Lauren A Fleishman; Bruine de Bruin, Wändi; Morgan, M Granger

2014-04-01

Reducing CO2 emissions from the electricity sector will likely require policies that encourage the widespread deployment of a diverse mix of low-carbon electricity generation technologies. Public discourse informs such policies. To make informed decisions and to productively engage in public discourse, citizens need to understand the trade-offs between electricity technologies proposed for widespread deployment. Building on previous paper-and-pencil studies, we developed a computer tool that aimed to help nonexperts make informed decisions about the challenges faced in achieving a low-carbon energy future. We report on an initial usability study of this interactive computer tool. After providing participants with comparative and balanced information about 10 electricity technologies, we asked them to design a low-carbon electricity portfolio. Participants used the interactive computer tool, which constrained portfolio designs to be realistic and yield low CO2 emissions. As they changed their portfolios, the tool updated information about projected CO2 emissions, electricity costs, and specific environmental impacts. As in the previous paper-and-pencil studies, most participants designed diverse portfolios that included energy efficiency, nuclear, coal with carbon capture and sequestration, natural gas, and wind. Our results suggest that participants understood the tool and used it consistently. The tool may be downloaded from http://cedmcenter.org/tools-for-cedm/informing-the-public-about-low-carbon-technologies/ .

A novel framework for diagnosing automatic tool changer and tool life based on cloud computing

Directory of Open Access Journals (Sweden)

Shang-Liang Chen

2016-03-01

Full Text Available Tool change is one among the most frequently performed machining processes, and if there is improper percussion as the tool’s position is changed, the spindle bearing can be damaged. A spindle malfunction can cause problems, such as a knife being dropped or bias in a machined hole. The measures currently taken to avoid such issues, which arose from the available machine tools, only involve determining whether the clapping knife’s state is correct using a spindle and the air adhesion method, which is also used to satisfy the high precision required from mechanical components. Therefore, it cannot be used with any type of machine tool; in addition, improper tapping of the spindle during an automatic tool change cannot be detected. Therefore, this study proposes a new type of diagnostic framework that combines cloud computing and vibration sensors, among of which, tool change is automatically diagnosed using an architecture to identify abnormalities and thereby enhances the reliability and productivity of the machine and equipment.

Computing the Feng-Rao distances for codes from order domains

DEFF Research Database (Denmark)

Ruano Benito, Diego

2007-01-01

We compute the Feng–Rao distance of a code coming from an order domain with a simplicial value semigroup. The main tool is the Apéry set of a semigroup that can be computed using a Gröbner basis.......We compute the Feng–Rao distance of a code coming from an order domain with a simplicial value semigroup. The main tool is the Apéry set of a semigroup that can be computed using a Gröbner basis....

Development of a New Data Tool for Computing Launch and Landing Availability with Respect to Surface Weather

Science.gov (United States)

Burns, K. Lee; Altino, Karen

2008-01-01

The Marshall Space Flight Center Natural Environments Branch has a long history of expertise in the modeling and computation of statistical launch availabilities with respect to weather conditions. Their existing data analysis product, the Atmospheric Parametric Risk Assessment (APRA) tool, computes launch availability given an input set of vehicle hardware and/or operational weather constraints by calculating the climatological probability of exceeding the specified constraint limits, APRA has been used extensively to provide the Space Shuttle program the ability to estimate impacts that various proposed design modifications would have to overall launch availability. The model accounts for both seasonal and diurnal variability at a single geographic location and provides output probabilities for a single arbitrary launch attempt. Recently, the Shuttle program has shown interest in having additional capabilities added to the APRA model, including analysis of humidity parameters, inclusion of landing site weather to produce landing availability, and concurrent analysis of multiple sites, to assist in operational landing site selection. In addition, the Constellation program has also expressed interest in the APRA tool, and has requested several additional capabilities to address some Constellation-specific issues, both in the specification and verification of design requirements and in the development of operations concepts. The combined scope of the requested capability enhancements suggests an evolution of the model beyond a simple revision process. Development has begun for a new data analysis tool that will satisfy the requests of both programs. This new tool, Probabilities of Atmospheric Conditions and Environmental Risk (PACER), will provide greater flexibility and significantly enhanced functionality compared to the currently existing tool.

Outsourcing Set Intersection Computation Based on Bloom Filter for Privacy Preservation in Multimedia Processing

Directory of Open Access Journals (Sweden)

Hongliang Zhu

2018-01-01

Full Text Available With the development of cloud computing, the advantages of low cost and high computation ability meet the demands of complicated computation of multimedia processing. Outsourcing computation of cloud could enable users with limited computing resources to store and process distributed multimedia application data without installing multimedia application software in local computer terminals, but the main problem is how to protect the security of user data in untrusted public cloud services. In recent years, the privacy-preserving outsourcing computation is one of the most common methods to solve the security problems of cloud computing. However, the existing computation cannot meet the needs for the large number of nodes and the dynamic topologies. In this paper, we introduce a novel privacy-preserving outsourcing computation method which combines GM homomorphic encryption scheme and Bloom filter together to solve this problem and propose a new privacy-preserving outsourcing set intersection computation protocol. Results show that the new protocol resolves the privacy-preserving outsourcing set intersection computation problem without increasing the complexity and the false positive probability. Besides, the number of participants, the size of input secret sets, and the online time of participants are not limited.

Sparse Image Reconstruction in Computed Tomography

DEFF Research Database (Denmark)

Jørgensen, Jakob Sauer

In recent years, increased focus on the potentially harmful effects of x-ray computed tomography (CT) scans, such as radiation-induced cancer, has motivated research on new low-dose imaging techniques. Sparse image reconstruction methods, as studied for instance in the field of compressed sensing...... applications. This thesis takes a systematic approach toward establishing quantitative understanding of conditions for sparse reconstruction to work well in CT. A general framework for analyzing sparse reconstruction methods in CT is introduced and two sets of computational tools are proposed: 1...... contributions to a general set of computational characterization tools. Thus, the thesis contributions help advance sparse reconstruction methods toward routine use in...

Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming.

Science.gov (United States)

Song, Hyun-Seob; Goldberg, Noam; Mahajan, Ashutosh; Ramkrishna, Doraiswami

2017-08-01

Elementary (flux) modes (EMs) have served as a valuable tool for investigating structural and functional properties of metabolic networks. Identification of the full set of EMs in genome-scale networks remains challenging due to combinatorial explosion of EMs in complex networks. It is often, however, that only a small subset of relevant EMs needs to be known, for which optimization-based sequential computation is a useful alternative. Most of the currently available methods along this line are based on the iterative use of mixed integer linear programming (MILP), the effectiveness of which significantly deteriorates as the number of iterations builds up. To alleviate the computational burden associated with the MILP implementation, we here present a novel optimization algorithm termed alternate integer linear programming (AILP). Our algorithm was designed to iteratively solve a pair of integer programming (IP) and linear programming (LP) to compute EMs in a sequential manner. In each step, the IP identifies a minimal subset of reactions, the deletion of which disables all previously identified EMs. Thus, a subsequent LP solution subject to this reaction deletion constraint becomes a distinct EM. In cases where no feasible LP solution is available, IP-derived reaction deletion sets represent minimal cut sets (MCSs). Despite the additional computation of MCSs, AILP achieved significant time reduction in computing EMs by orders of magnitude. The proposed AILP algorithm not only offers a computational advantage in the EM analysis of genome-scale networks, but also improves the understanding of the linkage between EMs and MCSs. The software is implemented in Matlab, and is provided as supplementary information . hyunseob.song@pnnl.gov. Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2017. This work is written by US Government employees and are in the public domain in the US.

DEVELOPMENT AND USE OF COMPUTER-AIDED PROCESS ENGINEERING TOOLS FOR POLLUTION PREVENTION

Science.gov (United States)

The use of Computer-Aided Process Engineering (CAPE) and process simulation tools has become established industry practice to predict simulation software, new opportunities are available for the creation of a wide range of ancillary tools that can be used from within multiple sim...

Theory and computation of disturbance invariant sets for discrete-time linear systems

Directory of Open Access Journals (Sweden)

Ilya Kolmanovsky

1998-01-01

. One purpose of the paper is to unite and extend in a rigorous way disparate results from the prior literature. In addition there are entirely new results. Specific contributions include: exploitation of the Pontryagin set difference to clarify conceptual matters and simplify mathematical developments, special properties of maximal invariant sets and conditions for their finite determination, algorithms for generating concrete representations of maximal invariant sets, practical computational questions, extension of the main results to general Lyapunov stable systems, applications of the computational techniques to the bounding of state and output response. Results on Lyapunov stable systems are applied to the implementation of a logic-based, nonlinear multimode regulator. For plants with disturbance inputs and state-control constraints it enlarges the constraint-admissible domain of attraction. Numerical examples illustrate the various theoretical and computational results.

Out-of-Core Computations of High-Resolution Level Sets by Means of Code Transformation

DEFF Research Database (Denmark)

Christensen, Brian Bunch; Nielsen, Michael Bang; Museth, Ken

2012-01-01

We propose a storage efficient, fast and parallelizable out-of-core framework for streaming computations of high resolution level sets. The fundamental techniques are skewing and tiling transformations of streamed level set computations which allow for the combination of interface propagation, re...... computations are now CPU bound and consequently the overall performance is unaffected by disk latency and bandwidth limitations. We demonstrate this with several benchmark tests that show sustained out-of-core throughputs close to that of in-core level set simulations....

The classification and evaluation of Computer-Aided Software Engineering tools

OpenAIRE

Manley, Gary W.

1990-01-01

Approved for public release; distribution unlimited. The use of Computer-Aided Software Engineering (CASE) tools has been viewed as a remedy for the software development crisis by achieving improved productivity and system quality via the automation of all or part of the software engineering process. The proliferation and tremendous variety of tools available have stretched the understanding of experienced practitioners and has had a profound impact on the software engineering process itse...

On Biblical Hebrew and Computer Science: Inspiration, Models, Tools, And Cross-fertilization

DEFF Research Database (Denmark)

Sandborg-Petersen, Ulrik

2011-01-01

Eep Talstra's work has been an inspiration to maby researchers, both within and outside of the field of Old Testament scholarship. Among others, Crist-Jan Doedens and the present author have been heavily influenced by Talstra in their own work within the field of computer science. The present...... of the present author. In addition, the tools surrounding Emdros, including SESB, Libronis, and the Emdros Query Tool, are described. Ecamples Biblical Hebrew scholar. Thus the inspiration of Talstra comes full-circle: from Biblical Hebrew databases to computer science and back into Biblical Hebrew scholarship....

Application of computer tools to the diagnosis of the combustion in motors

International Nuclear Information System (INIS)

Agudelo S, John R; Delgado M, Alvaro; Gutierrez V, Elkin

2001-01-01

This paper describes the fundamental topics concerning to analysis of combustion process in internal combustion engines, when latest generation computational tools are employed. For achieving this, it has been developed DIATERM using graphic programming languages. It is also described the thermo-dynamical model in which is based DIATERM. In the same way it is showed the potential of this computational tool when it is applied to analysis of pressure data in the combustion chamber of a turbo charged diesel engine, changing the load while rotational speed is maintained constant

HCI^2 Workbench: A Development Tool for Multimodal Human-Computer Interaction Systems

NARCIS (Netherlands)

Shen, Jie; Wenzhe, Shi; Pantic, Maja

In this paper, we present a novel software tool designed and implemented to simplify the development process of Multimodal Human-Computer Interaction (MHCI) systems. This tool, which is called the HCI^2 Workbench, exploits a Publish / Subscribe (P/S) architecture [13] [14] to facilitate efficient

A Tangible Programming Tool for Children to Cultivate Computational Thinking

Science.gov (United States)

Wang, Danli; Liu, Zhen

2014-01-01

Game and creation are activities which have good potential for computational thinking skills. In this paper we present T-Maze, an economical tangible programming tool for children aged 5–9 to build computer programs in maze games by placing wooden blocks. Through the use of computer vision technology, T-Maze provides a live programming interface with real-time graphical and voice feedback. We conducted a user study with 7 children using T-Maze to play two levels of maze-escape games and create their own mazes. The results show that T-Maze is not only easy to use, but also has the potential to help children cultivate computational thinking like abstraction, problem decomposition, and creativity. PMID:24719575

A Tangible Programming Tool for Children to Cultivate Computational Thinking

Directory of Open Access Journals (Sweden)

Danli Wang

2014-01-01

Full Text Available Game and creation are activities which have good potential for computational thinking skills. In this paper we present T-Maze, an economical tangible programming tool for children aged 5–9 to build computer programs in maze games by placing wooden blocks. Through the use of computer vision technology, T-Maze provides a live programming interface with real-time graphical and voice feedback. We conducted a user study with 7 children using T-Maze to play two levels of maze-escape games and create their own mazes. The results show that T-Maze is not only easy to use, but also has the potential to help children cultivate computational thinking like abstraction, problem decomposition, and creativity.

Natural language processing tools for computer assisted language learning

Directory of Open Access Journals (Sweden)

Vandeventer Faltin, Anne

2003-01-01

Full Text Available This paper illustrates the usefulness of natural language processing (NLP tools for computer assisted language learning (CALL through the presentation of three NLP tools integrated within a CALL software for French. These tools are (i a sentence structure viewer; (ii an error diagnosis system; and (iii a conjugation tool. The sentence structure viewer helps language learners grasp the structure of a sentence, by providing lexical and grammatical information. This information is derived from a deep syntactic analysis. Two different outputs are presented. The error diagnosis system is composed of a spell checker, a grammar checker, and a coherence checker. The spell checker makes use of alpha-codes, phonological reinterpretation, and some ad hoc rules to provide correction proposals. The grammar checker employs constraint relaxation and phonological reinterpretation as diagnosis techniques. The coherence checker compares the underlying "semantic" structures of a stored answer and of the learners' input to detect semantic discrepancies. The conjugation tool is a resource with enhanced capabilities when put on an electronic format, enabling searches from inflected and ambiguous verb forms.

Cumulative hierarchies and computability over universes of sets

Directory of Open Access Journals (Sweden)

Domenico Cantone

2008-05-01

Full Text Available Various metamathematical investigations, beginning with Fraenkel’s historical proof of the independence of the axiom of choice, called for suitable definitions of hierarchical universes of sets. This led to the discovery of such important cumulative structures as the one singled out by von Neumann (generally taken as the universe of all sets and Godel’s universe of the so-called constructibles. Variants of those are exploited occasionally in studies concerning the foundations of analysis (according to Abraham Robinson’s approach, or concerning non-well-founded sets. We hence offer a systematic presentation of these many structures, partly motivated by their relevance and pervasiveness in mathematics. As we report, numerous properties of hierarchy-related notions such as rank, have been verified with the assistance of the ÆtnaNova proof-checker.Through SETL and Maple implementations of procedures which effectively handle the Ackermann’s hereditarily finite sets, we illustrate a particularly significant case among those in which the entities which form a universe of sets can be algorithmically constructed and manipulated; hereby, the fruitful bearing on pure mathematics of cumulative set hierarchies ramifies into the realms of theoretical computer science and algorithmics.

Evolving Non-Dominated Parameter Sets for Computational Models from Multiple Experiments

Science.gov (United States)

Lane, Peter C. R.; Gobet, Fernand

2013-03-01

Creating robust, reproducible and optimal computational models is a key challenge for theorists in many sciences. Psychology and cognitive science face particular challenges as large amounts of data are collected and many models are not amenable to analytical techniques for calculating parameter sets. Particular problems are to locate the full range of acceptable model parameters for a given dataset, and to confirm the consistency of model parameters across different datasets. Resolving these problems will provide a better understanding of the behaviour of computational models, and so support the development of general and robust models. In this article, we address these problems using evolutionary algorithms to develop parameters for computational models against multiple sets of experimental data; in particular, we propose the `speciated non-dominated sorting genetic algorithm' for evolving models in several theories. We discuss the problem of developing a model of categorisation using twenty-nine sets of data and models drawn from four different theories. We find that the evolutionary algorithms generate high quality models, adapted to provide a good fit to all available data.

Evaluating online diagnostic decision support tools for the clinical setting.

Science.gov (United States)

Pryor, Marie; White, David; Potter, Bronwyn; Traill, Roger

2012-01-01

credibility of the clinical information. The evaluation methodology used here to assess the quality and comprehensiveness of clinical DDS tools was effective in identifying the most appropriate tool for the clinical setting. The use of clinical case scenarios is fundamental in determining the diagnostic accuracy and usability of the tools.

Automated and Assistive Tools for Accelerated Code migration of Scientific Computing on to Heterogeneous MultiCore Systems

Science.gov (United States)

2017-04-13

AFRL-AFOSR-UK-TR-2017-0029 Automated and Assistive Tools for Accelerated Code migration of Scientific Computing on to Heterogeneous MultiCore Systems ...2012, “ Automated and Assistive Tools for Accelerated Code migration of Scientific Computing on to Heterogeneous MultiCore Systems .” 2. The objective...2012 - 01/25/2015 4. TITLE AND SUBTITLE Automated and Assistive Tools for Accelerated Code migration of Scientific Computing on to Heterogeneous

Integrated modeling tool for performance engineering of complex computer systems

Science.gov (United States)

Wright, Gary; Ball, Duane; Hoyt, Susan; Steele, Oscar

1989-01-01

This report summarizes Advanced System Technologies' accomplishments on the Phase 2 SBIR contract NAS7-995. The technical objectives of the report are: (1) to develop an evaluation version of a graphical, integrated modeling language according to the specification resulting from the Phase 2 research; and (2) to determine the degree to which the language meets its objectives by evaluating ease of use, utility of two sets of performance predictions, and the power of the language constructs. The technical approach followed to meet these objectives was to design, develop, and test an evaluation prototype of a graphical, performance prediction tool. The utility of the prototype was then evaluated by applying it to a variety of test cases found in the literature and in AST case histories. Numerous models were constructed and successfully tested. The major conclusion of this Phase 2 SBIR research and development effort is that complex, real-time computer systems can be specified in a non-procedural manner using combinations of icons, windows, menus, and dialogs. Such a specification technique provides an interface that system designers and architects find natural and easy to use. In addition, PEDESTAL's multiview approach provides system engineers with the capability to perform the trade-offs necessary to produce a design that meets timing performance requirements. Sample system designs analyzed during the development effort showed that models could be constructed in a fraction of the time required by non-visual system design capture tools.

Software Tools: A One-Semester Secondary School Computer Course.

Science.gov (United States)

Bromley, John; Lakatos, John

1985-01-01

Provides a course outline, describes equipment and teacher requirements, discusses student evaluation and course outcomes, and details the computer programs used in a high school course. The course is designed to teach students use of the microcomputer as a tool through hands-on experience with a variety of commercial software programs. (MBR)

Development of Desktop Computing Applications and Engineering Tools on GPUs

DEFF Research Database (Denmark)

Sørensen, Hans Henrik Brandenborg; Glimberg, Stefan Lemvig; Hansen, Toke Jansen

(GPUs) for high-performance computing applications and software tools in science and engineering, inverse problems, visualization, imaging, dynamic optimization. The goals are to contribute to the development of new state-of-the-art mathematical models and algorithms for maximum throughout performance...

The MicroGrid: A Scientific Tool for Modeling Computational Grids

Directory of Open Access Journals (Sweden)

H.J. Song

2000-01-01

Full Text Available The complexity and dynamic nature of the Internet (and the emerging Computational Grid demand that middleware and applications adapt to the changes in configuration and availability of resources. However, to the best of our knowledge there are no simulation tools which support systematic exploration of dynamic Grid software (or Grid resource behavior. We describe our vision and initial efforts to build tools to meet these needs. Our MicroGrid simulation tools enable Globus applications to be run in arbitrary virtual grid resource environments, enabling broad experimentation. We describe the design of these tools, and their validation on micro-benchmarks, the NAS parallel benchmarks, and an entire Grid application. These validation experiments show that the MicroGrid can match actual experiments within a few percent (2% to 4%.

Field-programmable custom computing technology architectures, tools, and applications

CERN Document Server

Luk, Wayne; Pocek, Ken

2000-01-01

Field-Programmable Custom Computing Technology: Architectures, Tools, and Applications brings together in one place important contributions and up-to-date research results in this fast-moving area. In seven selected chapters, the book describes the latest advances in architectures, design methods, and applications of field-programmable devices for high-performance reconfigurable systems. The contributors to this work were selected from the leading researchers and practitioners in the field. It will be valuable to anyone working or researching in the field of custom computing technology. It serves as an excellent reference, providing insight into some of the most challenging issues being examined today.

Teachers' Use of Computational Tools to Construct and Explore Dynamic Mathematical Models

Science.gov (United States)

Santos-Trigo, Manuel; Reyes-Rodriguez, Aaron

2011-01-01

To what extent does the use of computational tools offer teachers the possibility of constructing dynamic models to identify and explore diverse mathematical relations? What ways of reasoning or thinking about the problems emerge during the model construction process that involves the use of the tools? These research questions guided the…

An examination of intrinsic errors in electronic structure methods using the Environmental Molecular Sciences Laboratory computational results database and the Gaussian-2 set

International Nuclear Information System (INIS)

Feller, D.; Peterson, K.A.

1998-01-01

The Gaussian-2 (G2) collection of atoms and molecules has been studied with Hartree endash Fock and correlated levels of theory, ranging from second-order perturbation theory to coupled cluster theory with noniterative inclusion of triple excitations. By exploiting the systematic convergence properties of the correlation consistent family of basis sets, complete basis set limits were estimated for a large number of the G2 energetic properties. Deviations with respect to experimentally derived energy differences corresponding to rigid molecules were obtained for 15 basis set/method combinations, as well as the estimated complete basis set limit. The latter values are necessary for establishing the intrinsic error for each method. In order to perform this analysis, the information generated in the present study was combined with the results of many previous benchmark studies in an electronic database, where it is available for use by other software tools. Such tools can assist users of electronic structure codes in making appropriate basis set and method choices that will increase the likelihood of achieving their accuracy goals without wasteful expenditures of computer resources. copyright 1998 American Institute of Physics

ESHOPPS: A COMPUTATIONAL TOOL TO AID THE TEACHING OF SHORTEST PATH ALGORITHMS

Directory of Open Access Journals (Sweden)

S. J. de A. LIMA

2015-07-01

Full Text Available The development of a computational tool called EShoPPS – Environment for Shortest Path Problem Solving, which is used to assist students in understanding the working of Dijkstra, Greedy search and A*(star algorithms is presented in this paper. Such algorithms are commonly taught in graduate and undergraduate courses of Engineering and Informatics and are used for solving many optimization problems that can be characterized as Shortest Path Problem. The EShoPPS is an interactive tool that allows students to create a graph representing the problem and also helps in developing their knowledge of each specific algorithm. Experiments performed with 155 students of undergraduate and graduate courses such as Industrial Engineering, Computer Science and Information Systems have shown that by using the EShoPPS tool students were able to improve their interpretation of investigated algorithms.

Teaching Computer Organization and Architecture Using Simulation and FPGA Applications

OpenAIRE

D. K.M. Al-Aubidy

2007-01-01

This paper presents the design concepts and realization of incorporating micro-operation simulation and FPGA implementation into a teaching tool for computer organization and architecture. This teaching tool helps computer engineering and computer science students to be familiarized practically with computer organization and architecture through the development of their own instruction set, computer programming and interfacing experiments. A two-pass assembler has been designed and implemente...

Common accounting system for monitoring the ATLAS distributed computing resources

International Nuclear Information System (INIS)

Karavakis, E; Andreeva, J; Campana, S; Saiz, P; Gayazov, S; Jezequel, S; Sargsyan, L; Schovancova, J; Ueda, I

2014-01-01

This paper covers in detail a variety of accounting tools used to monitor the utilisation of the available computational and storage resources within the ATLAS Distributed Computing during the first three years of Large Hadron Collider data taking. The Experiment Dashboard provides a set of common accounting tools that combine monitoring information originating from many different information sources; either generic or ATLAS specific. This set of tools provides quality and scalable solutions that are flexible enough to support the constantly evolving requirements of the ATLAS user community.

How to Fully Represent Expert Information about Imprecise Properties in a Computer System – Random Sets, Fuzzy Sets, and Beyond: An Overview

Science.gov (United States)

Nguyen, Hung T.; Kreinovich, Vladik

2014-01-01

To help computers make better decisions, it is desirable to describe all our knowledge in computer-understandable terms. This is easy for knowledge described in terms on numerical values: we simply store the corresponding numbers in the computer. This is also easy for knowledge about precise (well-defined) properties which are either true or false for each object: we simply store the corresponding “true” and “false” values in the computer. The challenge is how to store information about imprecise properties. In this paper, we overview different ways to fully store the expert information about imprecise properties. We show that in the simplest case, when the only source of imprecision is disagreement between different experts, a natural way to store all the expert information is to use random sets; we also show how fuzzy sets naturally appear in such random-set representation. We then show how the random-set representation can be extended to the general (“fuzzy”) case when, in addition to disagreements, experts are also unsure whether some objects satisfy certain properties or not. PMID:25386045

Computational Tools and Algorithms for Designing Customized Synthetic Genes

Energy Technology Data Exchange (ETDEWEB)

Gould, Nathan [Department of Computer Science, The College of New Jersey, Ewing, NJ (United States); Hendy, Oliver [Department of Biology, The College of New Jersey, Ewing, NJ (United States); Papamichail, Dimitris, E-mail: papamicd@tcnj.edu [Department of Computer Science, The College of New Jersey, Ewing, NJ (United States)

2014-10-06

Advances in DNA synthesis have enabled the construction of artificial genes, gene circuits, and genomes of bacterial scale. Freedom in de novo design of synthetic constructs provides significant power in studying the impact of mutations in sequence features, and verifying hypotheses on the functional information that is encoded in nucleic and amino acids. To aid this goal, a large number of software tools of variable sophistication have been implemented, enabling the design of synthetic genes for sequence optimization based on rationally defined properties. The first generation of tools dealt predominantly with singular objectives such as codon usage optimization and unique restriction site incorporation. Recent years have seen the emergence of sequence design tools that aim to evolve sequences toward combinations of objectives. The design of optimal protein-coding sequences adhering to multiple objectives is computationally hard, and most tools rely on heuristics to sample the vast sequence design space. In this review, we study some of the algorithmic issues behind gene optimization and the approaches that different tools have adopted to redesign genes and optimize desired coding features. We utilize test cases to demonstrate the efficiency of each approach, as well as identify their strengths and limitations.

Computational Tools and Algorithms for Designing Customized Synthetic Genes

International Nuclear Information System (INIS)

Gould, Nathan; Hendy, Oliver; Papamichail, Dimitris

2014-01-01

Advances in DNA synthesis have enabled the construction of artificial genes, gene circuits, and genomes of bacterial scale. Freedom in de novo design of synthetic constructs provides significant power in studying the impact of mutations in sequence features, and verifying hypotheses on the functional information that is encoded in nucleic and amino acids. To aid this goal, a large number of software tools of variable sophistication have been implemented, enabling the design of synthetic genes for sequence optimization based on rationally defined properties. The first generation of tools dealt predominantly with singular objectives such as codon usage optimization and unique restriction site incorporation. Recent years have seen the emergence of sequence design tools that aim to evolve sequences toward combinations of objectives. The design of optimal protein-coding sequences adhering to multiple objectives is computationally hard, and most tools rely on heuristics to sample the vast sequence design space. In this review, we study some of the algorithmic issues behind gene optimization and the approaches that different tools have adopted to redesign genes and optimize desired coding features. We utilize test cases to demonstrate the efficiency of each approach, as well as identify their strengths and limitations.

Computers and the internet: tools for youth empowerment.

Science.gov (United States)

Valaitis, Ruta K

2005-10-04

Youth are often disenfranchised in their communities and may feel they have little voice. Since computers are an important aspect of youth culture, they may offer solutions to increasing youth participation in communities. This qualitative case study investigated the perceptions of 19 (predominantly female) inner-city school youth about their use of computers and the Internet in a school-based community development project. Youth working with public health nurses in a school-based community development project communicated with local community members using computer-mediated communication, surveyed peers online, built websites, searched for information online, and prepared project materials using computers and the Internet. Participant observation, semistructured interviews, analysis of online messages, and online- and paper-based surveys were used to gather data about youth's and adults' perceptions and use of the technologies. Constant comparison method and between-method triangulation were used in the analysis to satisfy the existence of themes. Not all youth were interested in working with computers. Some electronic messages from adults were perceived to be critical, and writing to adults was intimidating for some youth. In addition, technical problems were experienced. Despite these barriers, most youth perceived that using computers and the Internet reduced their anxiety concerning communication with adults, increased their control when dealing with adults, raised their perception of their social status, increased participation within the community, supported reflective thought, increased efficiency, and improved their access to resources. Overall, youth perceived computers and the Internet to be empowering tools, and they should be encouraged to use such technology to support them in community initiatives.

Computer-aided system design

Science.gov (United States)

Walker, Carrie K.

1991-01-01

A technique has been developed for combining features of a systems architecture design and assessment tool and a software development tool. This technique reduces simulation development time and expands simulation detail. The Architecture Design and Assessment System (ADAS), developed at the Research Triangle Institute, is a set of computer-assisted engineering tools for the design and analysis of computer systems. The ADAS system is based on directed graph concepts and supports the synthesis and analysis of software algorithms mapped to candidate hardware implementations. Greater simulation detail is provided by the ADAS functional simulator. With the functional simulator, programs written in either Ada or C can be used to provide a detailed description of graph nodes. A Computer-Aided Software Engineering tool developed at the Charles Stark Draper Laboratory (CSDL CASE) automatically generates Ada or C code from engineering block diagram specifications designed with an interactive graphical interface. A technique to use the tools together has been developed, which further automates the design process.

The Multimorbidity Cluster Analysis Tool: Identifying Combinations and Permutations of Multiple Chronic Diseases Using a Record-Level Computational Analysis

Directory of Open Access Journals (Sweden)

Kathryn Nicholson

2017-12-01

Full Text Available Introduction: Multimorbidity, or the co-occurrence of multiple chronic health conditions within an individual, is an increasingly dominant presence and burden in modern health care systems.  To fully capture its complexity, further research is needed to uncover the patterns and consequences of these co-occurring health states.  As such, the Multimorbidity Cluster Analysis Tool and the accompanying Multimorbidity Cluster Analysis Toolkit have been created to allow researchers to identify distinct clusters that exist within a sample of participants or patients living with multimorbidity.  Development: The Tool and Toolkit were developed at Western University in London, Ontario, Canada.  This open-access computational program (JAVA code and executable file was developed and tested to support an analysis of thousands of individual records and up to 100 disease diagnoses or categories.  Application: The computational program can be adapted to the methodological elements of a research project, including type of data, type of chronic disease reporting, measurement of multimorbidity, sample size and research setting.  The computational program will identify all existing, and mutually exclusive, combinations and permutations within the dataset.  An application of this computational program is provided as an example, in which more than 75,000 individual records and 20 chronic disease categories resulted in the detection of 10,411 unique combinations and 24,647 unique permutations among female and male patients.  Discussion: The Tool and Toolkit are now available for use by researchers interested in exploring the complexities of multimorbidity.  Its careful use, and the comparison between results, will be valuable additions to the nuanced understanding of multimorbidity.

MAGMA: generalized gene-set analysis of GWAS data.

Science.gov (United States)

de Leeuw, Christiaan A; Mooij, Joris M; Heskes, Tom; Posthuma, Danielle

2015-04-01

By aggregating data for complex traits in a biologically meaningful way, gene and gene-set analysis constitute a valuable addition to single-marker analysis. However, although various methods for gene and gene-set analysis currently exist, they generally suffer from a number of issues. Statistical power for most methods is strongly affected by linkage disequilibrium between markers, multi-marker associations are often hard to detect, and the reliance on permutation to compute p-values tends to make the analysis computationally very expensive. To address these issues we have developed MAGMA, a novel tool for gene and gene-set analysis. The gene analysis is based on a multiple regression model, to provide better statistical performance. The gene-set analysis is built as a separate layer around the gene analysis for additional flexibility. This gene-set analysis also uses a regression structure to allow generalization to analysis of continuous properties of genes and simultaneous analysis of multiple gene sets and other gene properties. Simulations and an analysis of Crohn's Disease data are used to evaluate the performance of MAGMA and to compare it to a number of other gene and gene-set analysis tools. The results show that MAGMA has significantly more power than other tools for both the gene and the gene-set analysis, identifying more genes and gene sets associated with Crohn's Disease while maintaining a correct type 1 error rate. Moreover, the MAGMA analysis of the Crohn's Disease data was found to be considerably faster as well.

A Computational Tool for Testing Dose-related Trend Using an Age-adjusted Bootstrap-based Poly-k Test

Directory of Open Access Journals (Sweden)

Hojin Moon

2006-08-01

Full Text Available A computational tool for testing for a dose-related trend and/or a pairwise difference in the incidence of an occult tumor via an age-adjusted bootstrap-based poly-k test and the original poly-k test is presented in this paper. The poly-k test (Bailer and Portier 1988 is a survival-adjusted Cochran-Armitage test, which achieves robustness to effects of differential mortality across dose groups. The original poly-k test is asymptotically standard normal under the null hypothesis. However, the asymptotic normality is not valid if there is a deviation from the tumor onset distribution that is assumed in this test. Our age-adjusted bootstrap-based poly-k test assesses the significance of assumed asymptotic normal tests and investigates an empirical distribution of the original poly-k test statistic using an age-adjusted bootstrap method. A tumor of interest is an occult tumor for which the time to onset is not directly observable. Since most of the animal carcinogenicity studies are designed with a single terminal sacrifice, the present tool is applicable to rodent tumorigenicity assays that have a single terminal sacrifice. The present tool takes input information simply from a user screen and reports testing results back to the screen through a user-interface. The computational tool is implemented in C/C++ and is applied to analyze a real data set as an example. Our tool enables the FDA and the pharmaceutical industry to implement a statistical analysis of tumorigenicity data from animal bioassays via our age-adjusted bootstrap-based poly-k test and the original poly-k test which has been adopted by the National Toxicology Program as its standard statistical test.

On some methods for improving time of reachability sets computation for the dynamic system control problem

Science.gov (United States)

Zimovets, Artem; Matviychuk, Alexander; Ushakov, Vladimir

2016-12-01

The paper presents two different approaches to reduce the time of computer calculation of reachability sets. First of these two approaches use different data structures for storing the reachability sets in the computer memory for calculation in single-threaded mode. Second approach is based on using parallel algorithms with reference to the data structures from the first approach. Within the framework of this paper parallel algorithm of approximate reachability set calculation on computer with SMP-architecture is proposed. The results of numerical modelling are presented in the form of tables which demonstrate high efficiency of parallel computing technology and also show how computing time depends on the used data structure.

Am I getting an accurate picture: a tool to assess clinical handover in remote settings?

Directory of Open Access Journals (Sweden)

Malcolm Moore

2017-11-01

Full Text Available Abstract Background Good clinical handover is critical to safe medical care. Little research has investigated handover in rural settings. In a remote setting where nurses and medical students give telephone handover to an aeromedical retrieval service, we developed a tool by which the receiving clinician might assess the handover; and investigated factors impacting on the reliability and validity of that assessment. Methods Researchers consulted with clinicians to develop an assessment tool, based on the ISBAR handover framework, combining validity evidence and the existing literature. The tool was applied ‘live’ by receiving clinicians and from recorded handovers by academic assessors. The tool’s performance was analysed using generalisability theory. Receiving clinicians and assessors provided feedback. Results Reliability for assessing a call was good (G = 0.73 with 4 assessments. The scale had a single factor structure with good internal consistency (Cronbach’s alpha = 0.8. The group mean for the global score for nurses and students was 2.30 (SD 0.85 out of a maximum 3.0, with no difference between these sub-groups. Conclusions We have developed and evaluated a tool to assess high-stakes handover in a remote setting. It showed good reliability and was easy for working clinicians to use. Further investigation and use is warranted beyond this setting.

Computational Tools for RF Structure Design

CERN Document Server

Jensen, E

2004-01-01

The Finite Differences Method and the Finite Element Method are the two principally employed numerical methods in modern RF field simulation programs. The basic ideas behind these methods are explained, with regard to available simulation programs. We then go through a list of characteristic parameters of RF structures, explaining how they can be calculated using these tools. With the help of these parameters, we introduce the frequency-domain and the time-domain calculations, leading to impedances and wake-fields, respectively. Subsequently, we present some readily available computer programs, which are in use for RF structure design, stressing their distinctive features and limitations. One final example benchmarks the precision of different codes for calculating the eigenfrequency and Q of a simple cavity resonator.

Computational Tools and Algorithms for Designing Customized Synthetic Genes

Directory of Open Access Journals (Sweden)

Nathan eGould

2014-10-01

Full Text Available Advances in DNA synthesis have enabled the construction of artificial genes, gene circuits, and genomes of bacterial scale. Freedom in de-novo design of synthetic constructs provides significant power in studying the impact of mutations in sequence features, and verifying hypotheses on the functional information that is encoded in nucleic and amino acids. To aid this goal, a large number of software tools of variable sophistication have been implemented, enabling the design of synthetic genes for sequence optimization based on rationally defined properties. The first generation of tools dealt predominantly with singular objectives such as codon usage optimization and unique restriction site incorporation. Recent years have seen the emergence of sequence design tools that aim to evolve sequences toward combinations of objectives. The design of optimal protein coding sequences adhering to multiple objectives is computationally hard, and most tools rely on heuristics to sample the vast sequence design space. In this review we study some of the algorithmic issues behind gene optimization and the approaches that different tools have adopted to redesign genes and optimize desired coding features. We utilize test cases to demonstrate the efficiency of each approach, as well as identify their strengths and limitations.

The Manifestation of Stopping Sets and Absorbing Sets as Deviations on the Computation Trees of LDPC Codes

Directory of Open Access Journals (Sweden)

Eric Psota

2010-01-01

Full Text Available The error mechanisms of iterative message-passing decoders for low-density parity-check codes are studied. A tutorial review is given of the various graphical structures, including trapping sets, stopping sets, and absorbing sets that are frequently used to characterize the errors observed in simulations of iterative decoding of low-density parity-check codes. The connections between trapping sets and deviations on computation trees are explored in depth using the notion of problematic trapping sets in order to bridge the experimental and analytic approaches to these error mechanisms. A new iterative algorithm for finding low-weight problematic trapping sets is presented and shown to be capable of identifying many trapping sets that are frequently observed during iterative decoding of low-density parity-check codes on the additive white Gaussian noise channel. Finally, a new method is given for characterizing the weight of deviations that result from problematic trapping sets.

Systematic Methods and Tools for Computer Aided Modelling

DEFF Research Database (Denmark)

Fedorova, Marina

and processes can be faster, cheaper and very efficient. The developed modelling framework involves five main elements: 1) a modelling tool, that includes algorithms for model generation; 2) a template library, which provides building blocks for the templates (generic models previously developed); 3) computer......-format and COM-objects, are incorporated to allow the export and import of mathematical models; 5) a user interface that provides the work-flow and data-flow to guide the user through the different modelling tasks....

Computer- Aided Design in Power Engineering Application of Software Tools

CERN Document Server

Stojkovic, Zlatan

2012-01-01

This textbooks demonstrates the application of software tools in solving a series of problems from the field of designing power system structures and systems. It contains four chapters: The first chapter leads the reader through all the phases necessary in the procedures of computer aided modeling and simulation. It guides through the complex problems presenting on the basis of eleven original examples. The second chapter presents  application of software tools in power system calculations of power systems equipment design. Several design example calculations are carried out using engineering standards like MATLAB, EMTP/ATP, Excel & Access, AutoCAD and Simulink. The third chapters focuses on the graphical documentation using a collection of software tools (AutoCAD, EPLAN, SIMARIS SIVACON, SIMARIS DESIGN) which enable the complete automation of the development of graphical documentation of a power systems. In the fourth chapter, the application of software tools in the project management in power systems ...

Instructor's Perceptions towards the Use of an Online Instructional Tool in an Academic English Setting in Kuwait

Science.gov (United States)

Erguvan, Deniz

2014-01-01

This study sets out to explore the faculty members' perceptions of a specific web-based instruction tool (Achieve3000) in a private higher education institute in Kuwait. The online tool provides highly differentiated instruction, which is initiated with a level set at the beginning of the term. The program is used in two consecutive courses as…

Cybersecurity Assessment Parameter Profile (CAPP). A Tool for Making Sense of Cybersecurity Assessments

Science.gov (United States)

2018-03-28

statistical, mathematical , or computational techniques. Utility and limitations: The primary strength of qualitative analysis is the ability to...cybersecurity as “the prevention of damage to, protection of, and restoration of computers , electronic communications systems, electronic...lower. Modeled/Simulated assessment settings use tools like computer models or other stand-ins for live settings, and evaluate how that simulated

Evaluating the Utility of Web-Based Consumer Support Tools Using Rough Sets

Science.gov (United States)

Maciag, Timothy; Hepting, Daryl H.; Slezak, Dominik; Hilderman, Robert J.

On the Web, many popular e-commerce sites provide consumers with decision support tools to assist them in their commerce-related decision-making. Many consumers will rank the utility of these tools quite highly. Data obtained from web usage mining analyses, which may provide knowledge about a user's online experiences, could help indicate the utility of these tools. This type of analysis could provide insight into whether provided tools are adequately assisting consumers in conducting their online shopping activities or if new or additional enhancements need consideration. Although some research in this regard has been described in previous literature, there is still much that can be done. The authors of this paper hypothesize that a measurement of consumer decision accuracy, i.e. a measurement preferences, could help indicate the utility of these tools. This paper describes a procedure developed towards this goal using elements of rough set theory. The authors evaluated the procedure using two support tools, one based on a tool developed by the US-EPA and the other developed by one of the authors called cogito. Results from the evaluation did provide interesting insights on the utility of both support tools. Although it was shown that the cogito tool obtained slightly higher decision accuracy, both tools could be improved from additional enhancements. Details of the procedure developed and results obtained from the evaluation will be provided. Opportunities for future work are also discussed.

Design and Implementation of a Cloud Computing Adoption Decision Tool: Generating a Cloud Road

Science.gov (United States)

Bildosola, Iñaki; Río-Belver, Rosa; Cilleruelo, Ernesto; Garechana, Gaizka

2015-01-01

Migrating to cloud computing is one of the current enterprise challenges. This technology provides a new paradigm based on “on-demand payment” for information and communication technologies. In this sense, the small and medium enterprise is supposed to be the most interested, since initial investments are avoided and the technology allows gradual implementation. However, even if the characteristics and capacities have been widely discussed, entry into the cloud is still lacking in terms of practical, real frameworks. This paper aims at filling this gap, presenting a real tool already implemented and tested, which can be used as a cloud computing adoption decision tool. This tool uses diagnosis based on specific questions to gather the required information and subsequently provide the user with valuable information to deploy the business within the cloud, specifically in the form of Software as a Service (SaaS) solutions. This information allows the decision makers to generate their particular Cloud Road. A pilot study has been carried out with enterprises at a local level with a two-fold objective: to ascertain the degree of knowledge on cloud computing and to identify the most interesting business areas and their related tools for this technology. As expected, the results show high interest and low knowledge on this subject and the tool presented aims to readdress this mismatch, insofar as possible. PMID:26230400

Design and Implementation of a Cloud Computing Adoption Decision Tool: Generating a Cloud Road.

Directory of Open Access Journals (Sweden)

Iñaki Bildosola

Full Text Available Migrating to cloud computing is one of the current enterprise challenges. This technology provides a new paradigm based on "on-demand payment" for information and communication technologies. In this sense, the small and medium enterprise is supposed to be the most interested, since initial investments are avoided and the technology allows gradual implementation. However, even if the characteristics and capacities have been widely discussed, entry into the cloud is still lacking in terms of practical, real frameworks. This paper aims at filling this gap, presenting a real tool already implemented and tested, which can be used as a cloud computing adoption decision tool. This tool uses diagnosis based on specific questions to gather the required information and subsequently provide the user with valuable information to deploy the business within the cloud, specifically in the form of Software as a Service (SaaS solutions. This information allows the decision makers to generate their particular Cloud Road. A pilot study has been carried out with enterprises at a local level with a two-fold objective: to ascertain the degree of knowledge on cloud computing and to identify the most interesting business areas and their related tools for this technology. As expected, the results show high interest and low knowledge on this subject and the tool presented aims to readdress this mismatch, insofar as possible.

Design and Implementation of a Cloud Computing Adoption Decision Tool: Generating a Cloud Road.

Science.gov (United States)

Bildosola, Iñaki; Río-Belver, Rosa; Cilleruelo, Ernesto; Garechana, Gaizka

2015-01-01

Migrating to cloud computing is one of the current enterprise challenges. This technology provides a new paradigm based on "on-demand payment" for information and communication technologies. In this sense, the small and medium enterprise is supposed to be the most interested, since initial investments are avoided and the technology allows gradual implementation. However, even if the characteristics and capacities have been widely discussed, entry into the cloud is still lacking in terms of practical, real frameworks. This paper aims at filling this gap, presenting a real tool already implemented and tested, which can be used as a cloud computing adoption decision tool. This tool uses diagnosis based on specific questions to gather the required information and subsequently provide the user with valuable information to deploy the business within the cloud, specifically in the form of Software as a Service (SaaS) solutions. This information allows the decision makers to generate their particular Cloud Road. A pilot study has been carried out with enterprises at a local level with a two-fold objective: to ascertain the degree of knowledge on cloud computing and to identify the most interesting business areas and their related tools for this technology. As expected, the results show high interest and low knowledge on this subject and the tool presented aims to readdress this mismatch, insofar as possible.

TimeSet: A computer program that accesses five atomic time services on two continents

Science.gov (United States)

Petrakis, P. L.

1993-01-01

TimeSet is a shareware program for accessing digital time services by telephone. At its initial release, it was capable of capturing time signals only from the U.S. Naval Observatory to set a computer's clock. Later the ability to synchronize with the National Institute of Standards and Technology was added. Now, in Version 7.10, TimeSet is able to access three additional telephone time services in Europe - in Sweden, Austria, and Italy - making a total of five official services addressable by the program. A companion program, TimeGen, allows yet another source of telephone time data strings for callers equipped with TimeSet version 7.10. TimeGen synthesizes UTC time data strings in the Naval Observatory's format from an accurately set and maintained DOS computer clock, and transmits them to callers. This allows an unlimited number of 'freelance' time generating stations to be created. Timesetting from TimeGen is made feasible by the advent of Becker's RighTime, a shareware program that learns the drift characteristics of a computer's clock and continuously applies a correction to keep it accurate, and also brings .01 second resolution to the DOS clock. With clock regulation by RighTime and periodic update calls by the TimeGen station to an official time source via TimeSet, TimeGen offers the same degree of accuracy within the resolution of the computer clock as any official atomic time source.

On the sighting of unicorns: A variational approach to computing invariant sets in dynamical systems

Science.gov (United States)

Junge, Oliver; Kevrekidis, Ioannis G.

2017-06-01

We propose to compute approximations to invariant sets in dynamical systems by minimizing an appropriate distance between a suitably selected finite set of points and its image under the dynamics. We demonstrate, through computational experiments, that this approach can successfully converge to approximations of (maximal) invariant sets of arbitrary topology, dimension, and stability, such as, e.g., saddle type invariant sets with complicated dynamics. We further propose to extend this approach by adding a Lennard-Jones type potential term to the objective function, which yields more evenly distributed approximating finite point sets, and illustrate the procedure through corresponding numerical experiments.

How accurate are adolescents in portion-size estimation using the computer tool Young Adolescents' Nutrition Assessment on Computer (YANA-C)?

Science.gov (United States)

Vereecken, Carine; Dohogne, Sophie; Covents, Marc; Maes, Lea

2010-06-01

Computer-administered questionnaires have received increased attention for large-scale population research on nutrition. In Belgium-Flanders, Young Adolescents' Nutrition Assessment on Computer (YANA-C) has been developed. In this tool, standardised photographs are available to assist in portion-size estimation. The purpose of the present study is to assess how accurate adolescents are in estimating portion sizes of food using YANA-C. A convenience sample, aged 11-17 years, estimated the amounts of ten commonly consumed foods (breakfast cereals, French fries, pasta, rice, apple sauce, carrots and peas, crisps, creamy velouté, red cabbage, and peas). Two procedures were followed: (1) short-term recall: adolescents (n 73) self-served their usual portions of the ten foods and estimated the amounts later the same day; (2) real-time perception: adolescents (n 128) estimated two sets (different portions) of pre-weighed portions displayed near the computer. Self-served portions were, on average, 8 % underestimated; significant underestimates were found for breakfast cereals, French fries, peas, and carrots and peas. Spearman's correlations between the self-served and estimated weights varied between 0.51 and 0.84, with an average of 0.72. The kappa statistics were moderate (>0.4) for all but one item. Pre-weighed portions were, on average, 15 % underestimated, with significant underestimates for fourteen of the twenty portions. Photographs of food items can serve as a good aid in ranking subjects; however, to assess the actual intake at a group level, underestimation must be considered.

A set of tools for determining the LAT performance in specific applications

International Nuclear Information System (INIS)

Lott, B.; Ballet, J.; Chiang, J.; Lonjou, V.; Funk, S.

2007-01-01

The poster presents a set of simple tools being developed to predict GLAST's performance for specific cases, like the accumulation time needed to reach a given significance or statistical accuracy for a particular source. Different examples are given, like the generation of a full-sky sensitivity map

Computational Tools To Model Halogen Bonds in Medicinal Chemistry.

Science.gov (United States)

Ford, Melissa Coates; Ho, P Shing

2016-03-10

The use of halogens in therapeutics dates back to the earliest days of medicine when seaweed was used as a source of iodine to treat goiters. The incorporation of halogens to improve the potency of drugs is now fairly standard in medicinal chemistry. In the past decade, halogens have been recognized as direct participants in defining the affinity of inhibitors through a noncovalent interaction called the halogen bond or X-bond. Incorporating X-bonding into structure-based drug design requires computational models for the anisotropic distribution of charge and the nonspherical shape of halogens, which lead to their highly directional geometries and stabilizing energies. We review here current successes and challenges in developing computational methods to introduce X-bonding into lead compound discovery and optimization during drug development. This fast-growing field will push further development of more accurate and efficient computational tools to accelerate the exploitation of halogens in medicinal chemistry.

The Computer as a Tool for Learning through Reflection. Technical Report No. 376.

Science.gov (United States)

Collins, Allan; Brown, John Seely

Because of its ability to record and represent process, the computer can provide a powerful, motivating, and as yet untapped tool for focusing the students' attention directly on their own thought processes and learning through reflection. Properly abstracted and structured, the computational medium can capture the processes by which a novice or…

De-MetaST-BLAST: a tool for the validation of degenerate primer sets and data mining of publicly available metagenomes.

Directory of Open Access Journals (Sweden)

Christopher A Gulvik

Full Text Available Development and use of primer sets to amplify nucleic acid sequences of interest is fundamental to studies spanning many life science disciplines. As such, the validation of primer sets is essential. Several computer programs have been created to aid in the initial selection of primer sequences that may or may not require multiple nucleotide combinations (i.e., degeneracies. Conversely, validation of primer specificity has remained largely unchanged for several decades, and there are currently few available programs that allows for an evaluation of primers containing degenerate nucleotide bases. To alleviate this gap, we developed the program De-MetaST that performs an in silico amplification using user defined nucleotide sequence dataset(s and primer sequences that may contain degenerate bases. The program returns an output file that contains the in silico amplicons. When De-MetaST is paired with NCBI's BLAST (De-MetaST-BLAST, the program also returns the top 10 nr NCBI database hits for each recovered in silico amplicon. While the original motivation for development of this search tool was degenerate primer validation using the wealth of nucleotide sequences available in environmental metagenome and metatranscriptome databases, this search tool has potential utility in many data mining applications.

Older adult mistreatment risk screening: contribution to the validation of a screening tool in a domestic setting.

Science.gov (United States)

Lindenbach, Jeannette M; Larocque, Sylvie; Lavoie, Anne-Marise; Garceau, Marie-Luce

2012-06-01

ABSTRACTThe hidden nature of older adult mistreatment renders its detection in the domestic setting particularly challenging. A validated screening instrument that can provide a systematic assessment of risk factors can facilitate this detection. One such instrument, the "expanded Indicators of Abuse" tool, has been previously validated in the Hebrew language in a hospital setting. The present study has contributed to the validation of the "e-IOA" in an English-speaking community setting in Ontario, Canada. It consisted of two phases: (a) a content validity review and adaptation of the instrument by experts throughout Ontario, and (b) an inter-rater reliability assessment by home visiting nurses. The adaptation, the "Mistreatment of Older Adult Risk Factors" tool, offers a comprehensive tool for screening in the home setting. This instrument is significant to professional practice as practitioners working with older adults will be better equipped to assess for risk of mistreatment.

Computer-Assisted Visual Search/Decision Aids as a Training Tool for Mammography

National Research Council Canada - National Science Library

Nodine, Calvin

1999-01-01

The primary goal of the project is to develop a computer-assisted visual search (CAVS) mammography training tool that will improve the perceptual and cognitive skills of trainees leading to mammographic expertise...

Computer-Assisted Visual Search/Decision Aids as a Training Tool for Mammography

National Research Council Canada - National Science Library

Nodine, Calvin

1998-01-01

The primary goal of the project is to develop a computer-assisted visual search (CAVS) mammography training tool that will improve the perceptual and cognitive skills of trainees leading to mammographic expertise...

Computer-Assisted Visual Search/Decision Aids as a Training Tool for Mammography

National Research Council Canada - National Science Library

Nodine, Calvin

2000-01-01

The primary goal of the project is to develop a computer-assisted visual search (CAVS) mammography training tool that will improve the perceptual and cognitive skills of trainees leading to mammographic expertise...

Video analysis of projectile motion using tablet computers as experimental tools

Science.gov (United States)

Klein, P.; Gröber, S.; Kuhn, J.; Müller, A.

2014-01-01

Tablet computers were used as experimental tools to record and analyse the motion of a ball thrown vertically from a moving skateboard. Special applications plotted the measurement data component by component, allowing a simple determination of initial conditions and g in order to explore the underlying laws of motion. This experiment can easily be performed by students themselves, providing more autonomy in their problem-solving processes than traditional learning approaches. We believe that this autonomy and the authenticity of the experimental tool both foster their motivation.

Development of computer-based analytical tool for assessing physical protection system

Energy Technology Data Exchange (ETDEWEB)

Mardhi, Alim, E-mail: alim-m@batan.go.id [National Nuclear Energy Agency Indonesia, (BATAN), PUSPIPTEK area, Building 80, Serpong, Tangerang Selatan, Banten (Indonesia); Chulalongkorn University, Faculty of Engineering, Nuclear Engineering Department, 254 Phayathai Road, Pathumwan, Bangkok Thailand. 10330 (Thailand); Pengvanich, Phongphaeth, E-mail: ppengvan@gmail.com [Chulalongkorn University, Faculty of Engineering, Nuclear Engineering Department, 254 Phayathai Road, Pathumwan, Bangkok Thailand. 10330 (Thailand)

2016-01-22

Assessment of physical protection system effectiveness is the priority for ensuring the optimum protection caused by unlawful acts against a nuclear facility, such as unauthorized removal of nuclear materials and sabotage of the facility itself. Since an assessment based on real exercise scenarios is costly and time-consuming, the computer-based analytical tool can offer the solution for approaching the likelihood threat scenario. There are several currently available tools that can be used instantly such as EASI and SAPE, however for our research purpose it is more suitable to have the tool that can be customized and enhanced further. In this work, we have developed a computer–based analytical tool by utilizing the network methodological approach for modelling the adversary paths. The inputs are multi-elements in security used for evaluate the effectiveness of the system’s detection, delay, and response. The tool has capability to analyze the most critical path and quantify the probability of effectiveness of the system as performance measure.

Development of computer-based analytical tool for assessing physical protection system

International Nuclear Information System (INIS)

Mardhi, Alim; Pengvanich, Phongphaeth

2016-01-01

Assessment of physical protection system effectiveness is the priority for ensuring the optimum protection caused by unlawful acts against a nuclear facility, such as unauthorized removal of nuclear materials and sabotage of the facility itself. Since an assessment based on real exercise scenarios is costly and time-consuming, the computer-based analytical tool can offer the solution for approaching the likelihood threat scenario. There are several currently available tools that can be used instantly such as EASI and SAPE, however for our research purpose it is more suitable to have the tool that can be customized and enhanced further. In this work, we have developed a computer–based analytical tool by utilizing the network methodological approach for modelling the adversary paths. The inputs are multi-elements in security used for evaluate the effectiveness of the system’s detection, delay, and response. The tool has capability to analyze the most critical path and quantify the probability of effectiveness of the system as performance measure

Robust fault detection of linear systems using a computationally efficient set-membership method

DEFF Research Database (Denmark)

Tabatabaeipour, Mojtaba; Bak, Thomas

2014-01-01

In this paper, a computationally efficient set-membership method for robust fault detection of linear systems is proposed. The method computes an interval outer-approximation of the output of the system that is consistent with the model, the bounds on noise and disturbance, and the past measureme...... is trivially parallelizable. The method is demonstrated for fault detection of a hydraulic pitch actuator of a wind turbine. We show the effectiveness of the proposed method by comparing our results with two zonotope-based set-membership methods....

7th International Workshop on Parallel Tools for High Performance Computing

CERN Document Server

Gracia, José; Nagel, Wolfgang; Resch, Michael

2014-01-01

Current advances in High Performance Computing (HPC) increasingly impact efficient software development workflows. Programmers for HPC applications need to consider trends such as increased core counts, multiple levels of parallelism, reduced memory per core, and I/O system challenges in order to derive well performing and highly scalable codes. At the same time, the increasing complexity adds further sources of program defects. While novel programming paradigms and advanced system libraries provide solutions for some of these challenges, appropriate supporting tools are indispensable. Such tools aid application developers in debugging, performance analysis, or code optimization and therefore make a major contribution to the development of robust and efficient parallel software. This book introduces a selection of the tools presented and discussed at the 7th International Parallel Tools Workshop, held in Dresden, Germany, September 3-4, 2013.  

Assessing Affordances of Selected Cloud Computing Tools for Language Teacher Education in Nigeria

Science.gov (United States)

Ofemile, Abdulmalik Yusuf

2015-01-01

This paper reports part of a study that hoped to understand Teacher Educators' (TE) assessment of the affordances of selected cloud computing tools ranked among the top 100 for the year 2010. Research has shown that ICT and by extension cloud computing has positive impacts on daily life and this informed the Nigerian government's policy to…

Computing autocatalytic sets to unravel inconsistencies in metabolic network reconstructions

DEFF Research Database (Denmark)

Schmidt, R.; Waschina, S.; Boettger-Schmidt, D.

2015-01-01

, the method we report represents a powerful tool to identify inconsistencies in large-scale metabolic networks. AVAILABILITY AND IMPLEMENTATION: The method is available as source code on http://users.minet.uni-jena.de/ approximately m3kach/ASBIG/ASBIG.zip. CONTACT: christoph.kaleta@uni-jena.de SUPPLEMENTARY...... by inherent inconsistencies and gaps. RESULTS: Here we present a novel method to validate metabolic network reconstructions based on the concept of autocatalytic sets. Autocatalytic sets correspond to collections of metabolites that, besides enzymes and a growth medium, are required to produce all biomass...... components in a metabolic model. These autocatalytic sets are well-conserved across all domains of life, and their identification in specific genome-scale reconstructions allows us to draw conclusions about potential inconsistencies in these models. The method is capable of detecting inconsistencies, which...

Analytical bounds on SET charge sensitivity for qubit readout in a solid-state quantum computer

International Nuclear Information System (INIS)

Green, F.; Buehler, T.M.; Brenner, R.; Hamilton, A.R.; Dzurak, A.S.; Clark, R.G.

2002-01-01

Full text: Quantum Computing promises processing powers orders of magnitude beyond what is possible in conventional silicon-based computers. It harnesses the laws of quantum mechanics directly, exploiting the in built potential of a wave function for massively parallel information processing. Highly ordered and scaleable arrays of single donor atoms (quantum bits, or qubits), embedded in Si, are especially promising; they are a very natural fit to the existing, highly sophisticated, Si industry. The success of Si-based quantum computing depends on precisely initializing the quantum state of each qubit, and on precise reading out its final form. In the Kane architecture the qubit states are read out by detecting the spatial distribution of the donor's electron cloud using a sensitive electrometer. The single-electron transistor (SET) is an attractive candidate readout device for this, since the capacitive, or charging, energy of a SET's metallic central island is exquisitely sensitive to its electronic environment. Use of SETs as high-performance electrometers is therefore a key technology for data transfer in a solid-state quantum computer. We present an efficient analytical method to obtain bounds on the charge sensitivity of a single electron transistor (SET). Our classic Green-function analysis provides reliable estimates of SET sensitivity optimizing the design of the readout hardware. Typical calculations, and their physical meaning, are discussed. We compare them with the measured SET-response data

A computer tool for daily application of the linear quadratic model

International Nuclear Information System (INIS)

Macias Jaen, J.; Galan Montenegro, P.; Bodineau Gil, C.; Wals Zurita, A.; Serradilla Gil, A.M.

2001-01-01

The aim of this paper is to indicate the relevance of the criteria A.S.A.R.A. (As Short As Reasonably Achievable) in the optimization of a fractionated radiotherapy schedule and the presentation of a Windows computer program as an easy tool in order to: Evaluate the Biological Equivalent Dose (BED) in a fractionated schedule; Make comparison between different treatments; Compensate a treatment when a delay has been happened with a version of the Linear Quadratic model that has into account the factor of accelerated repopulation. Conclusions: Delays in the normal radiotherapy schedule are items that have to be controlled as much as possible because it is able to be a very important parameter in order to release a good application of treatment, principally when the tumour is fast growing. It is necessary to evaluate them. ASARA criteria is useful to indicate the relevance of this aspect. Also, computer tools like this one could help us in order to achieve this. (author)

Improving beam set-up using an online beam optics tool

International Nuclear Information System (INIS)

Richter, S.; Barth, W.; Franczak, B.; Scheeler, U.; Wilms, D.

2004-01-01

The GSI accelerator facility [1] consists of the Universal Linear Accelerator (Unilac), the heavy ion synchrotron SIS, and the Experimental Storage Ring (ESR). Two Unilac injectors with three ion source terminals provide ion species from the lightest such as hydrogen up to uranium. The High Current Injector (HSI) for low charge state ion beams provides mostly high intense but short pulses, whereas the High Charge State Injector (HLI) supplies long pulses with a high duty factor of up to 27%. Before entering the Alvarez section of the Unilac the ion beam from the HSI is stripped in a supersonic gas jet. Up to three different ion species can be accelerated for up to five experiments in a time-sharing mode. Frequent changes of beam energy and intensity during a single beam time period may result in time consuming set-up and tuning especially of the beam transport lines. To shorten these changeover times an online optics tool (MIRKO EXPERT) had been developed. Based on online emittance measurements at well-defined locations the beam envelopes are calculated using the actual magnet settings. With this input improved calculated magnet settings can be directly sent to the magnet power supplies. The program reads profile grid measurements, such that an atomized beam alignment is established and that steering times are minimized. Experiences on this tool will be reported. At the Unilac a special focus is put on high current operation with short but intense beam pulses. Limitations like missing non-destructive beam diagnostics, insufficient longitudinal beam diagnostics, insufficient longitudinal beam matching, and influence of the hard edged model for magnetic fields will be discussed. Special attention will be put on the limits due to high current effects with bunched beams. (author)

The Use of Computer Tools in the Design Process of Students’ Architectural Projects. Case Studies in Algeria

Science.gov (United States)

Saighi, Ouafa; Salah Zerouala, Mohamed

2017-12-01

This The paper particularly deals with the way in which computer tools are used by students in their design studio’s projects. Four institutions of architecture education in Algeria are considered as a case study to evaluate the impact of such tools on student design process. This aims to inspect in depth such use, to sort out its advantages and shortcomings in order to suggest some solutions. A field survey was undertaken on a sample of students and their teachers at the same institutions. The analysed results mainly show that computer tools are highly focusing on improving the quality of drawings representation and images seeking observers’ satisfaction hence influencing their decision. Some teachers are not very keen to overuse the computer during the design phase; they prefer the “traditional” approach. This is the present situation that Algerian university is facing which leads to conflict and disagreement between students and teachers. Meanwhile, there was no doubt that computer tools have effectively contributed to improve the competitive level among students.

Advanced computational tools and methods for nuclear analyses of fusion technology systems

International Nuclear Information System (INIS)

Fischer, U.; Chen, Y.; Pereslavtsev, P.; Simakov, S.P.; Tsige-Tamirat, H.; Loughlin, M.; Perel, R.L.; Petrizzi, L.; Tautges, T.J.; Wilson, P.P.H.

2005-01-01

An overview is presented of advanced computational tools and methods developed recently for nuclear analyses of Fusion Technology systems such as the experimental device ITER ('International Thermonuclear Experimental Reactor') and the intense neutron source IFMIF ('International Fusion Material Irradiation Facility'). These include Monte Carlo based computational schemes for the calculation of three-dimensional shut-down dose rate distributions, methods, codes and interfaces for the use of CAD geometry models in Monte Carlo transport calculations, algorithms for Monte Carlo based sensitivity/uncertainty calculations, as well as computational techniques and data for IFMIF neutronics and activation calculations. (author)

CRISIS2012: An Updated Tool to Compute Seismic Hazard

Science.gov (United States)

Ordaz, M.; Martinelli, F.; Meletti, C.; D'Amico, V.

2013-05-01

CRISIS is a computer tool for probabilistic seismic hazard analysis (PSHA), whose development started in the late 1980's at the Instituto de Ingeniería, UNAM, Mexico. It started circulating outside the Mexican borders at the beginning of the 1990's, when it was first distributed as part of SEISAN tools. Throughout the years, CRISIS has been used for seismic hazard studies in several countries in Latin America (Mexico, Guatemala, Belize, El Salvador, Honduras, Nicaragua, Costa Rica, Panama, Colombia, Venezuela, Ecuador, Peru, Argentina and Chile), and in many other countries of the World. CRISIS has always circulated free of charge for non-commercial applications. It is worth noting that CRISIS has been mainly written by people that are, at the same time, PSHA practitioners. Therefore, the development loop has been relatively short, and most of the modifications and improvements have been made to satisfy the needs of the developers themselves. CRISIS has evolved from a rather simple FORTRAN code to a relatively complex program with a friendly graphical interface, able to handle a variety of modeling possibilities for source geometries, seismicity descriptions and ground motion prediction models (GMPM). We will describe some of the improvements made for the newest version of the code: CRISIS 2012.These improvements, some of which were made in the frame of the Italian research project INGV-DPC S2 (http://nuovoprogettoesse2.stru.polimi.it/), funded by the Dipartimento della Protezione Civile (DPC; National Civil Protection Department), include: A wider variety of source geometries A wider variety of seismicity models, including the ability to handle non-Poissonian occurrence models and Poissonian smoothed-seismicity descriptions. Enhanced capabilities for using different kinds of GMPM: attenuation tables, built-in models and generalized attenuation models. In the case of built-in models, there is, by default, a set ready to use in CRISIS, but additional custom GMPMs

Mathematical tools for data mining set theory, partial orders, combinatorics

CERN Document Server

Simovici, Dan A

2014-01-01

Data mining essentially relies on several mathematical disciplines, many of which are presented in this second edition of this book. Topics include partially ordered sets, combinatorics, general topology, metric spaces, linear spaces, graph theory. To motivate the reader a significant number of applications of these mathematical tools are included ranging from association rules, clustering algorithms, classification, data constraints, logical data analysis, etc. The book is intended as a reference for researchers and graduate students. The current edition is a significant expansion of the firs

Assess/Mitigate Risk through the Use of Computer-Aided Software Engineering (CASE) Tools

Science.gov (United States)

Aguilar, Michael L.

2013-01-01

The NASA Engineering and Safety Center (NESC) was requested to perform an independent assessment of the mitigation of the Constellation Program (CxP) Risk 4421 through the use of computer-aided software engineering (CASE) tools. With the cancellation of the CxP, the assessment goals were modified to capture lessons learned and best practices in the use of CASE tools. The assessment goal was to prepare the next program for the use of these CASE tools. The outcome of the assessment is contained in this document.

Using Plickers as an Assessment Tool in Health and Physical Education Settings

Science.gov (United States)

Chng, Lena; Gurvitch, Rachel

2018-01-01

Written tests are one of the most common assessment tools classroom teachers use today. Despite its popularity, administering written tests or surveys, especially in health and physical education settings, is time consuming. In addition to the time taken to type and print out the tests or surveys, health and physical education teachers must grade…

Zebrafish Expression Ontology of Gene Sets (ZEOGS): A Tool to Analyze Enrichment of Zebrafish Anatomical Terms in Large Gene Sets

Science.gov (United States)

Marsico, Annalisa

2013-01-01

Abstract The zebrafish (Danio rerio) is an established model organism for developmental and biomedical research. It is frequently used for high-throughput functional genomics experiments, such as genome-wide gene expression measurements, to systematically analyze molecular mechanisms. However, the use of whole embryos or larvae in such experiments leads to a loss of the spatial information. To address this problem, we have developed a tool called Zebrafish Expression Ontology of Gene Sets (ZEOGS) to assess the enrichment of anatomical terms in large gene sets. ZEOGS uses gene expression pattern data from several sources: first, in situ hybridization experiments from the Zebrafish Model Organism Database (ZFIN); second, it uses the Zebrafish Anatomical Ontology, a controlled vocabulary that describes connected anatomical structures; and third, the available connections between expression patterns and anatomical terms contained in ZFIN. Upon input of a gene set, ZEOGS determines which anatomical structures are overrepresented in the input gene set. ZEOGS allows one for the first time to look at groups of genes and to describe them in terms of shared anatomical structures. To establish ZEOGS, we first tested it on random gene selections and on two public microarray datasets with known tissue-specific gene expression changes. These tests showed that ZEOGS could reliably identify the tissues affected, whereas only very few enriched terms to none were found in the random gene sets. Next we applied ZEOGS to microarray datasets of 24 and 72 h postfertilization zebrafish embryos treated with beclomethasone, a potent glucocorticoid. This analysis resulted in the identification of several anatomical terms related to glucocorticoid-responsive tissues, some of which were stage-specific. Our studies highlight the ability of ZEOGS to extract spatial information from datasets derived from whole embryos, indicating that ZEOGS could be a useful tool to automatically analyze gene

Zebrafish Expression Ontology of Gene Sets (ZEOGS): a tool to analyze enrichment of zebrafish anatomical terms in large gene sets.

Science.gov (United States)

Prykhozhij, Sergey V; Marsico, Annalisa; Meijsing, Sebastiaan H

2013-09-01

The zebrafish (Danio rerio) is an established model organism for developmental and biomedical research. It is frequently used for high-throughput functional genomics experiments, such as genome-wide gene expression measurements, to systematically analyze molecular mechanisms. However, the use of whole embryos or larvae in such experiments leads to a loss of the spatial information. To address this problem, we have developed a tool called Zebrafish Expression Ontology of Gene Sets (ZEOGS) to assess the enrichment of anatomical terms in large gene sets. ZEOGS uses gene expression pattern data from several sources: first, in situ hybridization experiments from the Zebrafish Model Organism Database (ZFIN); second, it uses the Zebrafish Anatomical Ontology, a controlled vocabulary that describes connected anatomical structures; and third, the available connections between expression patterns and anatomical terms contained in ZFIN. Upon input of a gene set, ZEOGS determines which anatomical structures are overrepresented in the input gene set. ZEOGS allows one for the first time to look at groups of genes and to describe them in terms of shared anatomical structures. To establish ZEOGS, we first tested it on random gene selections and on two public microarray datasets with known tissue-specific gene expression changes. These tests showed that ZEOGS could reliably identify the tissues affected, whereas only very few enriched terms to none were found in the random gene sets. Next we applied ZEOGS to microarray datasets of 24 and 72 h postfertilization zebrafish embryos treated with beclomethasone, a potent glucocorticoid. This analysis resulted in the identification of several anatomical terms related to glucocorticoid-responsive tissues, some of which were stage-specific. Our studies highlight the ability of ZEOGS to extract spatial information from datasets derived from whole embryos, indicating that ZEOGS could be a useful tool to automatically analyze gene expression

Computational Ecology and Open Science: Tools to Help Manage Lakes for Cyanobacteria in Lakes

Science.gov (United States)

Computational ecology is an interdisciplinary field that takes advantage of modern computation abilities to expand our ecological understanding. As computational ecologists, we use large data sets, which often cover large spatial extents, and advanced statistical/mathematical co...

Video Analysis of Projectile Motion Using Tablet Computers as Experimental Tools

Science.gov (United States)

Klein, P.; Gröber, S.; Kuhn, J.; Müller, A.

2014-01-01

Tablet computers were used as experimental tools to record and analyse the motion of a ball thrown vertically from a moving skateboard. Special applications plotted the measurement data component by component, allowing a simple determination of initial conditions and "g" in order to explore the underlying laws of motion. This experiment…

Computational Tool for Coupled Simulation of Nonequilibrium Hypersonic Flows with Ablation, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — The goal of this SBIR project is to develop a computational tool with unique predictive capabilities for the aerothermodynamic environment around ablation-cooled...

Computational Tool for Coupled Simulation of Nonequilibrium Hypersonic Flows with Ablation, Phase II

Data.gov (United States)

National Aeronautics and Space Administration — The goal of this SBIR project is to develop a predictive computational tool for the aerothermal environment around ablation-cooled hypersonic atmospheric entry...

Get set for computer science

CERN Document Server

Edwards, Alistair

2006-01-01

This book is aimed at students who are thinking of studying Computer Science or a related topic at university. Part One is a brief introduction to the topics that make up Computer Science, some of which you would expect to find as course modules in a Computer Science programme. These descriptions should help you to tell the difference between Computer Science as taught in different departments and so help you to choose a course that best suits you. Part Two builds on what you have learned about the nature of Computer Science by giving you guidance in choosing universities and making your appli

An integrated, open-source set of tools for urban vulnerability monitoring from Earth observation data

Science.gov (United States)

De Vecchi, Daniele; Harb, Mostapha; Dell'Acqua, Fabio; Aurelio Galeazzo, Daniel

2015-04-01

Aim: The paper introduces an integrated set of open-source tools designed to process medium and high-resolution imagery with the aim to extract vulnerability indicators [1]. Problem: In the context of risk monitoring [2], a series of vulnerability proxies can be defined, such as the extension of a built-up area or buildings regularity [3]. Different open-source C and Python libraries are already available for image processing and geospatial information (e.g. OrfeoToolbox, OpenCV and GDAL). They include basic processing tools but not vulnerability-oriented workflows. Therefore, it is of significant importance to provide end-users with a set of tools capable to return information at a higher level. Solution: The proposed set of python algorithms is a combination of low-level image processing and geospatial information handling tools along with high-level workflows. In particular, two main products are released under the GPL license: source code, developers-oriented, and a QGIS plugin. These tools were produced within the SENSUM project framework (ended December 2014) where the main focus was on earthquake and landslide risk. Further development and maintenance is guaranteed by the decision to include them in the platform designed within the FP 7 RASOR project . Conclusion: With the lack of a unified software suite for vulnerability indicators extraction, the proposed solution can provide inputs for already available models like the Global Earthquake Model. The inclusion of the proposed set of algorithms within the RASOR platforms can guarantee support and enlarge the community of end-users. Keywords: Vulnerability monitoring, remote sensing, optical imagery, open-source software tools References [1] M. Harb, D. De Vecchi, F. Dell'Acqua, "Remote sensing-based vulnerability proxies in the EU FP7 project SENSUM", Symposium on earthquake and landslide risk in Central Asia and Caucasus: exploiting remote sensing and geo-spatial information management, 29-30th January 2014

Computer-aided design in power engineering. Application of software tools

International Nuclear Information System (INIS)

Stojkovic, Zlatan

2012-01-01

Demonstrates the use software tools in the practice of design in the field of power systems. Presents many applications in the design in the field of power systems. Useful for educative purposes and practical work. This textbooks demonstrates the application of software tools in solving a series of problems from the field of designing power system structures and systems. It contains four chapters: The first chapter leads the reader through all the phases necessary in the procedures of computer aided modeling and simulation. It guides through the complex problems presenting on the basis of eleven original examples. The second chapter presents application of software tools in power system calculations of power systems equipment design. Several design example calculations are carried out using engineering standards like MATLAB, EMTP/ATP, Excel and Access, AutoCAD and Simulink. The third chapters focuses on the graphical documentation using a collection of software tools (AutoCAD, EPLAN, SIMARIS SIVACON, SIMARIS DESIGN) which enable the complete automation of the development of graphical documentation of a power systems. In the fourth chapter, the application of software tools in the project management in power systems is discussed. Here, the emphasis is put on the standard software MS Excel and MS Project.

Computer-aided design in power engineering. Application of software tools

Energy Technology Data Exchange (ETDEWEB)

Stojkovic, Zlatan

2012-07-01

Demonstrates the use software tools in the practice of design in the field of power systems. Presents many applications in the design in the field of power systems. Useful for educative purposes and practical work. This textbooks demonstrates the application of software tools in solving a series of problems from the field of designing power system structures and systems. It contains four chapters: The first chapter leads the reader through all the phases necessary in the procedures of computer aided modeling and simulation. It guides through the complex problems presenting on the basis of eleven original examples. The second chapter presents application of software tools in power system calculations of power systems equipment design. Several design example calculations are carried out using engineering standards like MATLAB, EMTP/ATP, Excel and Access, AutoCAD and Simulink. The third chapters focuses on the graphical documentation using a collection of software tools (AutoCAD, EPLAN, SIMARIS SIVACON, SIMARIS DESIGN) which enable the complete automation of the development of graphical documentation of a power systems. In the fourth chapter, the application of software tools in the project management in power systems is discussed. Here, the emphasis is put on the standard software MS Excel and MS Project.

Current-voltage curves for molecular junctions computed using all-electron basis sets

International Nuclear Information System (INIS)

Bauschlicher, Charles W.; Lawson, John W.

2006-01-01

We present current-voltage (I-V) curves computed using all-electron basis sets on the conducting molecule. The all-electron results are very similar to previous results obtained using effective core potentials (ECP). A hybrid integration scheme is used that keeps the all-electron calculations cost competitive with respect to the ECP calculations. By neglecting the coupling of states to the contacts below a fixed energy cutoff, the density matrix for the core electrons can be evaluated analytically. The full density matrix is formed by adding this core contribution to the valence part that is evaluated numerically. Expanding the definition of the core in the all-electron calculations significantly reduces the computational effort and, up to biases of about 2 V, the results are very similar to those obtained using more rigorous approaches. The convergence of the I-V curves and transmission coefficients with respect to basis set is discussed. The addition of diffuse functions is critical in approaching basis set completeness

Workplace wellness using online learning tools in a healthcare setting.

Science.gov (United States)

Blake, Holly; Gartshore, Emily

2016-09-01

The aim was to develop and evaluate an online learning tool for use with UK healthcare employees, healthcare educators and healthcare students, to increase knowledge of workplace wellness as an important public health issue. A 'Workplace Wellness' e-learning tool was developed and peer-reviewed by 14 topic experts. This focused on six key areas relating to workplace wellness: work-related stress, musculoskeletal disorders, diet and nutrition, physical activity, smoking and alcohol consumption. Each key area provided current evidence-based information on causes and consequences, access to UK government reports and national statistics, and guidance on actions that could be taken to improve health within a workplace setting. 188 users (93.1% female, age 18-60) completed online knowledge questionnaires before (n = 188) and after (n = 88) exposure to the online learning tool. Baseline knowledge of workplace wellness was poor (n = 188; mean accuracy 47.6%, s.d. 11.94). Knowledge significantly improved from baseline to post-intervention (mean accuracy = 77.5%, s.d. 13.71) (t(75) = -14.801, p online learning, indicating scope for development of further online packages relating to other important health parameters. Copyright © 2016 Elsevier Ltd. All rights reserved.

Planning Tools For Estimating Radiation Exposure At The National Ignition Facility

International Nuclear Information System (INIS)

Verbeke, J.; Young, M.; Brereton, S.; Dauffy, L.; Hall, J.; Hansen, L.; Khater, H.; Kim, S.; Pohl, B.; Sitaraman, S.

2010-01-01

A set of computational tools was developed to help estimate and minimize potential radiation exposure to workers from material activation in the National Ignition Facility (NIF). AAMI (Automated ALARA-MCNP Interface) provides an efficient, automated mechanism to perform the series of calculations required to create dose rate maps for the entire facility with minimal manual user input. NEET (NIF Exposure Estimation Tool) is a web application that combines the information computed by AAMI with a given shot schedule to compute and display the dose rate maps as a function of time. AAMI and NEET are currently used as work planning tools to determine stay-out times for workers following a given shot or set of shots, and to help in estimating integrated doses associated with performing various maintenance activities inside the target bay. Dose rate maps of the target bay were generated following a low-yield 10 16 D-T shot and will be presented in this paper.

Development and Assessment of a Chemistry-Based Computer Video Game as a Learning Tool

Science.gov (United States)

Martinez-Hernandez, Kermin Joel

2010-01-01

The chemistry-based computer video game is a multidisciplinary collaboration between chemistry and computer graphics and technology fields developed to explore the use of video games as a possible learning tool. This innovative approach aims to integrate elements of commercial video game and authentic chemistry context environments into a learning…

Validation of the TRUST tool in a Greek perioperative setting.

Science.gov (United States)

Chatzea, Vasiliki-Eirini; Sifaki-Pistolla, Dimitra; Dey, Nilanjan; Melidoniotis, Evangelos

2017-06-01

The aim of this study was to translate, culturally adapt and validate the TRUST questionnaire in a Greek perioperative setting. The TRUST questionnaire assesses the relationship between trust and performance. The study assessed the levels of trust and performance in the surgery and anaesthesiology department during a very stressful period for Greece (economic crisis) and offered a user friendly and robust assessment tool. The study concludes that the Greek version of the TRUST questionnaire is a reliable and valid instrument for measuring team performance among Greek perioperative teams. Copyright the Association for Perioperative Practice.

Computer Aided Methods & Tools for Separation & Purification of Fine Chemical & Pharmaceutical Products

DEFF Research Database (Denmark)

Afonso, Maria B.C.; Soni, Vipasha; Mitkowski, Piotr Tomasz

2006-01-01

An integrated approach that is particularly suitable for solving problems related to product-process design from the fine chemicals, agrochemicals, food and pharmaceutical industries is presented together with the corresponding methods and tools, which forms the basis for an integrated computer...

Predicting Structures of Ru-Centered Dyes: A Computational Screening Tool.

Science.gov (United States)

Fredin, Lisa A; Allison, Thomas C

2016-04-07

Dye-sensitized solar cells (DSCs) represent a means for harvesting solar energy to produce electrical power. Though a number of light harvesting dyes are in use, the search continues for more efficient and effective compounds to make commercially viable DSCs a reality. Computational methods have been increasingly applied to understand the dyes currently in use and to aid in the search for improved light harvesting compounds. Semiempirical quantum chemistry methods have a well-deserved reputation for giving good quality results in a very short amount of computer time. The most recent semiempirical models such as PM6 and PM7 are parametrized for a wide variety of molecule types, including organometallic complexes similar to DSC chromophores. In this article, the performance of PM6 is tested against a set of 20 molecules whose geometries were optimized using a density functional theory (DFT) method. It is found that PM6 gives geometries that are in good agreement with the optimized DFT structures. In order to reduce the differences between geometries optimized using PM6 and geometries optimized using DFT, the PM6 basis set parameters have been optimized for a subset of the molecules. It is found that it is sufficient to optimize the basis set for Ru alone to improve the agreement between the PM6 results and the DFT results. When this optimized Ru basis set is used, the mean unsigned error in Ru-ligand bond lengths is reduced from 0.043 to 0.017 Å in the set of 20 test molecules. Though the magnitude of these differences is small, the effect on the calculated UV/vis spectra is significant. These results clearly demonstrate the value of using PM6 to screen DSC chromophores as well as the value of optimizing PM6 basis set parameters for a specific set of molecules.

Utilizing of computational tools on the modelling of a simplified problem of neutron shielding

Energy Technology Data Exchange (ETDEWEB)

Lessa, Fabio da Silva Rangel; Platt, Gustavo Mendes; Alves Filho, Hermes [Universidade do Estado do Rio de Janeiro (UERJ), Nova Friburgo, RJ (Brazil). Inst. Politecnico]. E-mails: fsrlessa@gmail.com; gmplatt@iprj.uerj.br; halves@iprj.uerj.br

2007-07-01

In the current technology level, the investigation of several problems is studied through computational simulations whose results are in general satisfactory and much less expensive than the conventional forms of investigation (e.g., destructive tests, laboratory measures, etc.). Almost all of the modern scientific studies are executed using computational tools, as computers of superior capacity and their systems applications to make complex calculations, algorithmic iterations, etc. Besides the considerable economy in time and in space that the Computational Modelling provides, there is a financial economy to the scientists. The Computational Modelling is a modern methodology of investigation that asks for the theoretical study of the identified phenomena in the problem, a coherent mathematical representation of such phenomena, the generation of a numeric algorithmic system comprehensible for the computer, and finally the analysis of the acquired solution, or still getting use of pre-existent systems that facilitate the visualization of these results (editors of Cartesian graphs, for instance). In this work, was being intended to use many computational tools, implementation of numeric methods and a deterministic model in the study and analysis of a well known and simplified problem of nuclear engineering (the neutron transport), simulating a theoretical problem of neutron shielding with physical-material hypothetical parameters, of neutron flow in each space junction, programmed with Scilab version 4.0. (author)

Utilizing of computational tools on the modelling of a simplified problem of neutron shielding

International Nuclear Information System (INIS)

Lessa, Fabio da Silva Rangel; Platt, Gustavo Mendes; Alves Filho, Hermes

2007-01-01

In the current technology level, the investigation of several problems is studied through computational simulations whose results are in general satisfactory and much less expensive than the conventional forms of investigation (e.g., destructive tests, laboratory measures, etc.). Almost all of the modern scientific studies are executed using computational tools, as computers of superior capacity and their systems applications to make complex calculations, algorithmic iterations, etc. Besides the considerable economy in time and in space that the Computational Modelling provides, there is a financial economy to the scientists. The Computational Modelling is a modern methodology of investigation that asks for the theoretical study of the identified phenomena in the problem, a coherent mathematical representation of such phenomena, the generation of a numeric algorithmic system comprehensible for the computer, and finally the analysis of the acquired solution, or still getting use of pre-existent systems that facilitate the visualization of these results (editors of Cartesian graphs, for instance). In this work, was being intended to use many computational tools, implementation of numeric methods and a deterministic model in the study and analysis of a well known and simplified problem of nuclear engineering (the neutron transport), simulating a theoretical problem of neutron shielding with physical-material hypothetical parameters, of neutron flow in each space junction, programmed with Scilab version 4.0. (author)

Issues on the Development and Application of Computer Tools to Support Product Structuring and Configuring

DEFF Research Database (Denmark)

Hansen, Claus Thorp; Riitahuhta, A.

2001-01-01

The aim of this article is to make a balance on the results and challenges in the efforts to develop computer tools to support product structuring and configuring in product development projects. The balance will be made in two dimensions, a design science and an industrial dimension. The design ...... that there are large positive effects to be gained for industrial companies by conscious implementing computer tools based on the results of design science. The positive effects will be measured by e.g. predictable product quality, reduced lead time, and reuse of design solutions....

Information granularity, big data, and computational intelligence

CERN Document Server

Chen, Shyi-Ming

2015-01-01

The recent pursuits emerging in the realm of big data processing, interpretation, collection and organization have emerged in numerous sectors including business, industry, and government organizations. Data sets such as customer transactions for a mega-retailer, weather monitoring, intelligence gathering, quickly outpace the capacities of traditional techniques and tools of data analysis. The 3V (volume, variability and velocity) challenges led to the emergence of new techniques and tools in data visualization, acquisition, and serialization. Soft Computing being regarded as a plethora of technologies of fuzzy sets (or Granular Computing), neurocomputing and evolutionary optimization brings forward a number of unique features that might be instrumental to the development of concepts and algorithms to deal with big data. This carefully edited volume provides the reader with an updated, in-depth material on the emerging principles, conceptual underpinnings, algorithms and practice of Computational Intelligenc...

Fast Streaming 3D Level set Segmentation on the GPU for Smooth Multi-phase Segmentation

DEFF Research Database (Denmark)

Sharma, Ojaswa; Zhang, Qin; Anton, François

2011-01-01

Level set method based segmentation provides an efficient tool for topological and geometrical shape handling, but it is slow due to high computational burden. In this work, we provide a framework for streaming computations on large volumetric images on the GPU. A streaming computational model...

An Evaluation of the Webquest as a Computer-Based Learning Tool

Science.gov (United States)

Hassanien, Ahmed

2006-01-01

This paper explores the preparation and use of an internet activity for undergraduate learners in higher education (HE). It evaluates the effectiveness of using webquest as a computer-based learning (CBL) tool to support students to learn in HE. The evaluation undertaken offers insights into learner perceptions concerning the ease of use of the…

VLM Tool for IDS Integration

Directory of Open Access Journals (Sweden)

Cǎtǎlin NAE

2010-03-01

Full Text Available This paper is dedicated to a very specific type of analysis tool (VLM - Vortex Lattice Method to be integrated in a IDS - Integrated Design System, tailored for the usage of small aircraft industry. The major interest is to have the possibility to simulate at very low computational costs a preliminary set of aerodynamic characteristics for basic aerodynamic global characteristics (Lift, Drag, Pitching Moment and aerodynamic derivatives for longitudinal and lateral-directional stability analysis. This work enables fast investigations of the influence of configuration changes in a very efficient computational environment. Using experimental data and/or CFD information for a specific calibration of VLM method, reliability of the analysis may me increased so that a first type (iteration zero aerodynamic evaluation of the preliminary 3D configuration is possible. The output of this tool is basic state aerodynamic and associated stability and control derivatives, as well as a complete set of information on specific loads on major airframe components.The major interest in using and validating this type of methods is coming from the possibility to integrate it as a tool in an IDS system for conceptual design phase, as considered for development for CESAR project (IP, UE FP6.

Development and Evaluation of a Computer-Based, Self-Management Tool for People Recently Diagnosed with Type 2 Diabetes

Directory of Open Access Journals (Sweden)

Alison O. Booth

2016-01-01

Full Text Available Aim. The purpose of this study was to develop and evaluate a computer-based, dietary, and physical activity self-management program for people recently diagnosed with type 2 diabetes. Methods. The computer-based program was developed in conjunction with the target group and evaluated in a 12-week randomised controlled trial (RCT. Participants were randomised to the intervention (computer-program or control group (usual care. Primary outcomes were diabetes knowledge and goal setting (ADKnowl questionnaire, Diabetes Obstacles Questionnaire (DOQ measured at baseline and week 12. User feedback on the program was obtained via a questionnaire and focus groups. Results. Seventy participants completed the 12-week RCT (32 intervention, 38 control, mean age 59 (SD years. After completion there was a significant between-group difference in the “knowledge and beliefs scale” of the DOQ. Two-thirds of the intervention group rated the program as either good or very good, 92% would recommend the program to others, and 96% agreed that the information within the program was clear and easy to understand. Conclusions. The computer-program resulted in a small but statistically significant improvement in diet-related knowledge and user satisfaction was high. With some further development, this computer-based educational tool may be a useful adjunct to diabetes self-management. This trial is registered with clinicaltrials.gov NCT number NCT00877851.

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

Science.gov (United States)

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

2018-01-01

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

Tools for remote computing in accelerator control

International Nuclear Information System (INIS)

Anderssen, P.S.; Frammery, V.; Wilcke, R.

1990-01-01

In modern accelerator control systems, the intelligence of the equipment is distributed in the geographical and the logical sense. Control processes for a large variety of tasks reside in both the equipment and the control computers. Hence successful operation hinges on the availability and reliability of the communication infrastructure. The computers are interconnected by a communication system and use remote procedure calls and message passing for information exchange. These communication mechanisms need a well-defined convention, i.e. a protocol. They also require flexibility in both the setup and changes to the protocol specification. The network compiler is a tool which provides the programmer with a means of establishing such a protocol for his application. Input to the network compiler is a single interface description file provided by the programmer. This file is written according to a grammar, and completely specifies the interprocess communication interfaces. Passed through the network compiler, the interface description file automatically produces the additional source code needed for the protocol. Hence the programmer does not have to be concerned about the details of the communication calls. Any further additions and modifications are made easy, because all the information about the interface is kept in a single file. (orig.)

Data Intensive Computing on Amazon Web Services

Energy Technology Data Exchange (ETDEWEB)

Magana-Zook, S. A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2015-04-21

The Geophysical Monitoring Program (GMP) has spent the past few years building up the capability to perform data intensive computing using what have been referred to as “big data” tools. These big data tools would be used against massive archives of seismic signals (>300 TB) to conduct research not previously possible. Examples of such tools include Hadoop (HDFS, MapReduce), HBase, Hive, Storm, Spark, Solr, and many more by the day. These tools are useful for performing data analytics on datasets that exceed the resources of traditional analytic approaches. To this end, a research big data cluster (“Cluster A”) was set up as a collaboration between GMP and Livermore Computing (LC).

Development of a Computer-based Benchmarking and Analytical Tool. Benchmarking and Energy & Water Savings Tool in Dairy Plants (BEST-Dairy)

Energy Technology Data Exchange (ETDEWEB)

Xu, Tengfang [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Flapper, Joris [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Ke, Jing [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Kramer, Klaas [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Sathaye, Jayant [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

2012-02-01

The overall goal of the project is to develop a computer-based benchmarking and energy and water savings tool (BEST-Dairy) for use in the California dairy industry – including four dairy processes – cheese, fluid milk, butter, and milk powder.

Computational methods, tools and data for nuclear analyses of fusion technology systems

International Nuclear Information System (INIS)

Fischer, U.

2006-01-01

An overview is presented of the Research and Development work conducted at Forschungszentrum Karlsruhe in co-operation with other associations in the framework of the European Fusion Technology Programme on the development and qualification of computational tools and data for nuclear analyses of Fusion Technology systems. The focus is on the development of advanced methods and tools based on the Monte Carlo technique for particle transport simulations, and the evaluation and qualification of dedicated nuclear data to satisfy the needs of the ITER and the IFMIF projects. (author)

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

Science.gov (United States)

Kang, Congying

2012-04-01

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

Enabling Wide-Scale Computer Science Education through Improved Automated Assessment Tools

Science.gov (United States)

Boe, Bryce A.

There is a proliferating demand for newly trained computer scientists as the number of computer science related jobs continues to increase. University programs will only be able to train enough new computer scientists to meet this demand when two things happen: when there are more primary and secondary school students interested in computer science, and when university departments have the resources to handle the resulting increase in enrollment. To meet these goals, significant effort is being made to both incorporate computational thinking into existing primary school education, and to support larger university computer science class sizes. We contribute to this effort through the creation and use of improved automated assessment tools. To enable wide-scale computer science education we do two things. First, we create a framework called Hairball to support the static analysis of Scratch programs targeted for fourth, fifth, and sixth grade students. Scratch is a popular building-block language utilized to pique interest in and teach the basics of computer science. We observe that Hairball allows for rapid curriculum alterations and thus contributes to wide-scale deployment of computer science curriculum. Second, we create a real-time feedback and assessment system utilized in university computer science classes to provide better feedback to students while reducing assessment time. Insights from our analysis of student submission data show that modifications to the system configuration support the way students learn and progress through course material, making it possible for instructors to tailor assignments to optimize learning in growing computer science classes.

System capacity and economic modeling computer tool for satellite mobile communications systems

Science.gov (United States)

Wiedeman, Robert A.; Wen, Doong; Mccracken, Albert G.

1988-01-01

A unique computer modeling tool that combines an engineering tool with a financial analysis program is described. The resulting combination yields a flexible economic model that can predict the cost effectiveness of various mobile systems. Cost modeling is necessary in order to ascertain if a given system with a finite satellite resource is capable of supporting itself financially and to determine what services can be supported. Personal computer techniques using Lotus 123 are used for the model in order to provide as universal an application as possible such that the model can be used and modified to fit many situations and conditions. The output of the engineering portion of the model consists of a channel capacity analysis and link calculations for several qualities of service using up to 16 types of earth terminal configurations. The outputs of the financial model are a revenue analysis, an income statement, and a cost model validation section.

A browser-based 3D Visualization Tool designed for comparing CERES/CALIOP/CloudSAT level-2 data sets.

Science.gov (United States)

Chu, C.; Sun-Mack, S.; Chen, Y.; Heckert, E.; Doelling, D. R.

2017-12-01

In Langley NASA, Clouds and the Earth's Radiant Energy System (CERES) and Moderate Resolution Imaging Spectroradiometer (MODIS) are merged with Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) on the Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) and CloudSat Cloud Profiling Radar (CPR). The CERES merged product (C3M) matches up to three CALIPSO footprints with each MODIS pixel along its ground track. It then assigns the nearest CloudSat footprint to each of those MODIS pixels. The cloud properties from MODIS, retrieved using the CERES algorithms, are included in C3M with the matched CALIPSO and CloudSat products along with radiances from 18 MODIS channels. The dataset is used to validate the CERES retrieved MODIS cloud properties and the computed TOA and surface flux difference using MODIS or CALIOP/CloudSAT retrieved clouds. This information is then used to tune the computed fluxes to match the CERES observed TOA flux. A visualization tool will be invaluable to determine the cause of these large cloud and flux differences in order to improve the methodology. This effort is part of larger effort to allow users to order the CERES C3M product sub-setted by time and parameter as well as the previously mentioned visualization capabilities. This presentation will show a new graphical 3D-interface, 3D-CERESVis, that allows users to view both passive remote sensing satellites (MODIS and CERES) and active satellites (CALIPSO and CloudSat), such that the detailed vertical structures of cloud properties from CALIPSO and CloudSat are displayed side by side with horizontally retrieved cloud properties from MODIS and CERES. Similarly, the CERES computed profile fluxes whether using MODIS or CALIPSO and CloudSat clouds can also be compared. 3D-CERESVis is a browser-based visualization tool that makes uses of techniques such as multiple synchronized cursors, COLLADA format data and Cesium.

Computing the Pareto-Nash equilibrium set in finite multi-objective mixed-strategy games

Directory of Open Access Journals (Sweden)

Victoria Lozan

2013-10-01

Full Text Available The Pareto-Nash equilibrium set (PNES is described as intersection of graphs of efficient response mappings. The problem of PNES computing in finite multi-objective mixed-strategy games (Pareto-Nash games is considered. A method for PNES computing is studied. Mathematics Subject Classification 2010: 91A05, 91A06, 91A10, 91A43, 91A44.

How accurate are adolescents in portion-size estimation using the computer tool young adolescents' nutrition assessment on computer (YANA-C)?

OpenAIRE

Vereecken, Carine; Dohogne, Sophie; Covents, Marc; Maes, Lea

2010-01-01

Computer-administered questionnaires have received increased attention for large-scale population research on nutrition. In Belgium-Flanders, Young Adolescents' Nutrition Assessment on Computer (YANA-C) has been developed. In this tool, standardised photographs are available to assist in portion-size estimation. The purpose of the present study is to assess how accurate adolescents are in estimating portion sizes of food using YANA-C. A convenience sample, aged 11-17 years, estimated the amou...

AORN Ergonomic Tool 4: Solutions for Prolonged Standing in Perioperative Settings.

Science.gov (United States)

Hughes, Nancy L; Nelson, Audrey; Matz, Mary W; Lloyd, John

2011-06-01

Prolonged standing during surgical procedures poses a high risk of causing musculoskeletal disorders, including back, leg, and foot pain, which can be chronic or acute in nature. Ergonomic Tool 4: Solutions for Prolonged Standing in Perioperative Settings provides recommendations for relieving the strain of prolonged standing, including the use of antifatigue mats, supportive footwear, and sit/stand stools, that are based on well-accepted ergonomic safety concepts, current research, and access to new and emerging technology. Published by Elsevier Inc.

The GNEMRE Dendro Tool.

Energy Technology Data Exchange (ETDEWEB)

Merchant, Bion John

2007-10-01

The GNEMRE Dendro Tool provides a previously unrealized analysis capability in the field of nuclear explosion monitoring. Dendro Tool allows analysts to quickly and easily determine the similarity between seismic events using the waveform time-series for each of the events to compute cross-correlation values. Events can then be categorized into clusters of similar events. This analysis technique can be used to characterize historical archives of seismic events in order to determine many of the unique sources that are present. In addition, the source of any new events can be quickly identified simply by comparing the new event to the historical set.

Tools for studying dry-cured ham processing by using computed tomography.

Science.gov (United States)

Santos-Garcés, Eva; Muñoz, Israel; Gou, Pere; Sala, Xavier; Fulladosa, Elena

2012-01-11

An accurate knowledge and optimization of dry-cured ham elaboration processes could help to reduce operating costs and maximize product quality. The development of nondestructive tools to characterize chemical parameters such as salt and water contents and a(w) during processing is of special interest. In this paper, predictive models for salt content (R(2) = 0.960 and RMSECV = 0.393), water content (R(2) = 0.912 and RMSECV = 1.751), and a(w) (R(2) = 0.906 and RMSECV = 0.008), which comprise the whole elaboration process, were developed. These predictive models were used to develop analytical tools such as distribution diagrams, line profiles, and regions of interest (ROIs) from the acquired computed tomography (CT) scans. These CT analytical tools provided quantitative information on salt, water, and a(w) in terms of content but also distribution throughout the process. The information obtained was applied to two industrial case studies. The main drawback of the predictive models and CT analytical tools is the disturbance that fat produces in water content and a(w) predictions.

TACT: A Set of MSC/PATRAN- and MSC/NASTRAN- based Modal Correlation Tools

Science.gov (United States)

Marlowe, Jill M.; Dixon, Genevieve D.

1998-01-01

This paper describes the functionality and demonstrates the utility of the Test Analysis Correlation Tools (TACT), a suite of MSC/PATRAN Command Language (PCL) tools which automate the process of correlating finite element models to modal survey test data. The initial release of TACT provides a basic yet complete set of tools for performing correlation totally inside the PATRAN/NASTRAN environment. Features include a step-by-step menu structure, pre-test accelerometer set evaluation and selection, analysis and test result export/import in Universal File Format, calculation of frequency percent difference and cross-orthogonality correlation results using NASTRAN, creation and manipulation of mode pairs, and five different ways of viewing synchronized animations of analysis and test modal results. For the PATRAN-based analyst, TACT eliminates the repetitive, time-consuming and error-prone steps associated with transferring finite element data to a third-party modal correlation package, which allows the analyst to spend more time on the more challenging task of model updating. The usefulness of this software is presented using a case history, the correlation for a NASA Langley Research Center (LaRC) low aspect ratio research wind tunnel model. To demonstrate the improvements that TACT offers the MSC/PATRAN- and MSC/DIASTRAN- based structural analysis community, a comparison of the modal correlation process using TACT within PATRAN versus external third-party modal correlation packages is presented.

[Animal experimentation, computer simulation and surgical research].

Science.gov (United States)

Carpentier, Alain

2009-11-01

We live in a digital world In medicine, computers are providing new tools for data collection, imaging, and treatment. During research and development of complex technologies and devices such as artificial hearts, computer simulation can provide more reliable information than experimentation on large animals. In these specific settings, animal experimentation should serve more to validate computer models of complex devices than to demonstrate their reliability.

Tool set for distributed real-time machine control

Science.gov (United States)

Carrott, Andrew J.; Wright, Christopher D.; West, Andrew A.; Harrison, Robert; Weston, Richard H.

1997-01-01

Demands for increased control capabilities require next generation manufacturing machines to comprise intelligent building elements, physically located at the point where the control functionality is required. Networks of modular intelligent controllers are increasingly designed into manufacturing machines and usable standards are slowly emerging. To implement a control system using off-the-shelf intelligent devices from multi-vendor sources requires a number of well defined activities, including (a) the specification and selection of interoperable control system components, (b) device independent application programming and (c) device configuration, management, monitoring and control. This paper briefly discusses the support for the above machine lifecycle activities through the development of an integrated computing environment populated with an extendable software toolset. The toolset supports machine builder activities such as initial control logic specification, logic analysis, machine modeling, mechanical verification, application programming, automatic code generation, simulation/test, version control, distributed run-time support and documentation. The environment itself consists of system management tools and a distributed object-oriented database which provides storage for the outputs from machine lifecycle activities and specific target control solutions.

Decomposition recovery extension to the Computer Aided Prototyping System (CAPS) change-merge tool.

OpenAIRE

Keesling, William Ronald

1997-01-01

Approved for public release; distribution is unlimited A promising use of Computer Aided Prototyping System (CAPS) is to support concurrent design. Key to success in this context is the ability to automatically and reliably combine and integrate the prototypes produced in concurrent efforts. Thus, to be of practical use in this as well as most prototyping contexts, a CAPS tool must have a fast, automated, reliable prototype integration capability. The current CAPS Change Merge Tool is fast...

Open-source tools for data mining.

Science.gov (United States)

Zupan, Blaz; Demsar, Janez

2008-03-01

With a growing volume of biomedical databases and repositories, the need to develop a set of tools to address their analysis and support knowledge discovery is becoming acute. The data mining community has developed a substantial set of techniques for computational treatment of these data. In this article, we discuss the evolution of open-source toolboxes that data mining researchers and enthusiasts have developed over the span of a few decades and review several currently available open-source data mining suites. The approaches we review are diverse in data mining methods and user interfaces and also demonstrate that the field and its tools are ready to be fully exploited in biomedical research.

Computer assisted audit tools and techniques in real world: CAATT's applications and approaches in context

OpenAIRE

Pedrosa, I.; Costa, C. J.

2012-01-01

Nowadays, Computer Aided Audit Tools (and Techniques’) support almost all audit processes concerning data extraction and analysis. These tools were firstly aimed to support financial auditing processes. However, their scope is beyond this, therefore, we present case studies and good practices in an academic context. Although in large auditing companies Audit Tools to do data extraction and analysis are very common and applied in several contexts, we realized that is not easy to find practical...

Leveraging Python Interoperability Tools to Improve Sapphire's Usability

Energy Technology Data Exchange (ETDEWEB)

Gezahegne, A; Love, N S

2007-12-10

The Sapphire project at the Center for Applied Scientific Computing (CASC) develops and applies an extensive set of data mining algorithms for the analysis of large data sets. Sapphire's algorithms are currently available as a set of C++ libraries. However many users prefer higher level scripting languages such as Python for their ease of use and flexibility. In this report, we evaluate four interoperability tools for the purpose of wrapping Sapphire's core functionality with Python. Exposing Sapphire's functionality through a Python interface would increase its usability and connect its algorithms to existing Python tools.

The UEA Small RNA Workbench: A Suite of Computational Tools for Small RNA Analysis.

Science.gov (United States)

Mohorianu, Irina; Stocks, Matthew Benedict; Applegate, Christopher Steven; Folkes, Leighton; Moulton, Vincent

2017-01-01

RNA silencing (RNA interference, RNAi) is a complex, highly conserved mechanism mediated by short, typically 20-24 nt in length, noncoding RNAs known as small RNAs (sRNAs). They act as guides for the sequence-specific transcriptional and posttranscriptional regulation of target mRNAs and play a key role in the fine-tuning of biological processes such as growth, response to stresses, or defense mechanism.High-throughput sequencing (HTS) technologies are employed to capture the expression levels of sRNA populations. The processing of the resulting big data sets facilitated the computational analysis of the sRNA patterns of variation within biological samples such as time point experiments, tissue series or various treatments. Rapid technological advances enable larger experiments, often with biological replicates leading to a vast amount of raw data. As a result, in this fast-evolving field, the existing methods for sequence characterization and prediction of interaction (regulatory) networks periodically require adapting or in extreme cases, a complete redesign to cope with the data deluge. In addition, the presence of numerous tools focused only on particular steps of HTS analysis hinders the systematic parsing of the results and their interpretation.The UEA small RNA Workbench (v1-4), described in this chapter, provides a user-friendly, modular, interactive analysis in the form of a suite of computational tools designed to process and mine sRNA datasets for interesting characteristics that can be linked back to the observed phenotypes. First, we show how to preprocess the raw sequencing output and prepare it for downstream analysis. Then we review some quality checks that can be used as a first indication of sources of variability between samples. Next we show how the Workbench can provide a comparison of the effects of different normalization approaches on the distributions of expression, enhanced methods for the identification of differentially expressed

An expanded framework for the advanced computational testing and simulation toolkit

Energy Technology Data Exchange (ETDEWEB)

Marques, Osni A.; Drummond, Leroy A.

2003-11-09

The Advanced Computational Testing and Simulation (ACTS) Toolkit is a set of computational tools developed primarily at DOE laboratories and is aimed at simplifying the solution of common and important computational problems. The use of the tools reduces the development time for new codes and the tools provide functionality that might not otherwise be available. This document outlines an agenda for expanding the scope of the ACTS Project based on lessons learned from current activities. Highlights of this agenda include peer-reviewed certification of new tools; finding tools to solve problems that are not currently addressed by the Toolkit; working in collaboration with other software initiatives and DOE computer facilities; expanding outreach efforts; promoting interoperability, further development of the tools; and improving functionality of the ACTS Information Center, among other tasks. The ultimate goal is to make the ACTS tools more widely used and more effective in solving DOE's and the nation's scientific problems through the creation of a reliable software infrastructure for scientific computing.

A development of a quantitative situation awareness measurement tool: Computational Representation of Situation Awareness with Graphical Expressions (CoRSAGE)

International Nuclear Information System (INIS)

Yim, Ho Bin; Lee, Seung Min; Seong, Poong Hyun

2014-01-01

Highlights: • We proposed quantitative situation awareness (SA) evaluation technique. • We developed a computer based SA evaluation tool for NPPs training environment. • We introduced three rules and components to express more human-like results. • We conducted three sets of training with real plant operators. • Results showed that the tool could reasonably represent operator’s SA. - Abstract: Operator performance measures are used for multiple purposes, such as control room design, human system interface (HSI) evaluation, training, and so on. Performance measures are often focused on results; however, especially for a training purpose – at least in a nuclear industry, more detailed descriptions about processes are required. Situation awareness (SA) measurements have directly/indirectly played as a complimentary measure and provided descriptive insights on how to improve performance of operators for the next training. Unfortunately, most of the well-developed SA measurement techniques, such as Situation Awareness Global Assessment Technique (SAGAT) need an expert opinion which sometimes troubles easy spread of measurement’s application or usage. A quantitative SA measurement tool named Computational Representation of Situation Awareness with Graphical Expressions (CoRSAGE) is introduced to resolve some of these concerns. CoRSAGE is based on production rules to represent a human operator’s cognitive process of problem solving, and Bayesian inference to quantify it. Petri Net concept is also used for graphical expressions of SA flow. Three components – inference transition, volatile/non-volatile memory tokens – were newly developed to achieve required functions. Training data of a Loss of Coolant Accident (LOCA) scenario for an emergency condition and an earthquake scenario for an abnormal condition by real plant operators were used to validate the tool. The validation result showed that CoRSAGE performed a reasonable match to other performance

The Strategy Blueprint: A Strategy Process Computer-Aided Design Tool

OpenAIRE

Aldea, Adina Ioana; Febriani, Tania Rizki; Daneva, Maya; Iacob, Maria Eugenia

2017-01-01

Strategy has always been a main concern of organizations because it dictates their direction, and therefore determines their success. Thus, organizations need to have adequate support to guide them through their strategy formulation process. The goal of this research is to develop a computer-based tool, known as ‘the Strategy Blueprint’, consisting of a combination of nine strategy techniques, which can help organizations define the most suitable strategy, based on the internal and external f...

Atomdroid: a computational chemistry tool for mobile platforms.

Science.gov (United States)

Feldt, Jonas; Mata, Ricardo A; Dieterich, Johannes M

2012-04-23

We present the implementation of a new molecular mechanics program designed for use in mobile platforms, the first specifically built for these devices. The software is designed to run on Android operating systems and is compatible with several modern tablet-PCs and smartphones available in the market. It includes molecular viewer/builder capabilities with integrated routines for geometry optimizations and Monte Carlo simulations. These functionalities allow it to work as a stand-alone tool. We discuss some particular development aspects, as well as the overall feasibility of using computational chemistry software packages in mobile platforms. Benchmark calculations show that through efficient implementation techniques even hand-held devices can be used to simulate midsized systems using force fields.

Using open source computational tools for predicting human metabolic stability and additional absorption, distribution, metabolism, excretion, and toxicity properties.

Science.gov (United States)

Gupta, Rishi R; Gifford, Eric M; Liston, Ted; Waller, Chris L; Hohman, Moses; Bunin, Barry A; Ekins, Sean

2010-11-01

Ligand-based computational models could be more readily shared between researchers and organizations if they were generated with open source molecular descriptors [e.g., chemistry development kit (CDK)] and modeling algorithms, because this would negate the requirement for proprietary commercial software. We initially evaluated open source descriptors and model building algorithms using a training set of approximately 50,000 molecules and a test set of approximately 25,000 molecules with human liver microsomal metabolic stability data. A C5.0 decision tree model demonstrated that CDK descriptors together with a set of Smiles Arbitrary Target Specification (SMARTS) keys had good statistics [κ = 0.43, sensitivity = 0.57, specificity = 0.91, and positive predicted value (PPV) = 0.64], equivalent to those of models built with commercial Molecular Operating Environment 2D (MOE2D) and the same set of SMARTS keys (κ = 0.43, sensitivity = 0.58, specificity = 0.91, and PPV = 0.63). Extending the dataset to ∼193,000 molecules and generating a continuous model using Cubist with a combination of CDK and SMARTS keys or MOE2D and SMARTS keys confirmed this observation. When the continuous predictions and actual values were binned to get a categorical score we observed a similar κ statistic (0.42). The same combination of descriptor set and modeling method was applied to passive permeability and P-glycoprotein efflux data with similar model testing statistics. In summary, open source tools demonstrated predictive results comparable to those of commercial software with attendant cost savings. We discuss the advantages and disadvantages of open source descriptors and the opportunity for their use as a tool for organizations to share data precompetitively, avoiding repetition and assisting drug discovery.

Development of a multilevel health and safety climate survey tool within a mining setting.

Science.gov (United States)

Parker, Anthony W; Tones, Megan J; Ritchie, Gabrielle E

2017-09-01

This study aimed to design, implement and evaluate the reliability and validity of a multifactorial and multilevel health and safety climate survey (HSCS) tool with utility in the Australian mining setting. An 84-item questionnaire was developed and pilot tested on a sample of 302 Australian miners across two open cut sites. A 67-item, 10 factor solution was obtained via exploratory factor analysis (EFA) representing prioritization and attitudes to health and safety across multiple domains and organizational levels. Each factor demonstrated a high level of internal reliability, and a series of ANOVAs determined a high level of consistency in responses across the workforce, and generally irrespective of age, experience or job category. Participants tended to hold favorable views of occupational health and safety (OH&S) climate at the management, supervisor, workgroup and individual level. The survey tool demonstrated reliability and validity for use within an open cut Australian mining setting and supports a multilevel, industry specific approach to OH&S climate. Findings suggested a need for mining companies to maintain high OH&S standards to minimize risks to employee health and safety. Future research is required to determine the ability of this measure to predict OH&S outcomes and its utility within other mine settings. As this tool integrates health and safety, it may have benefits for assessment, monitoring and evaluation in the industry, and improving the understanding of how health and safety climate interact at multiple levels to influence OH&S outcomes. Copyright © 2017 National Safety Council and Elsevier Ltd. All rights reserved.

Modeling and evaluation of the influence of micro-EDM sparking state settings on the tool electrode wear behavior

DEFF Research Database (Denmark)

Puthumana, Govindan

2017-01-01

materials characterized by considerable wear ofthe tool used for material removal. This paper presents an investigation involving modeling and estimation of the effect of settings for generation of discharges in stable conditions of micro-EDM on the phenomenon of tool electrode wear. A stable sparking...... a condition for the minimum tool wear for this micro-EDM process configuration....

PACOM: A Versatile Tool for Integrating, Filtering, Visualizing, and Comparing Multiple Large Mass Spectrometry Proteomics Data Sets.

Science.gov (United States)

Martínez-Bartolomé, Salvador; Medina-Aunon, J Alberto; López-García, Miguel Ángel; González-Tejedo, Carmen; Prieto, Gorka; Navajas, Rosana; Salazar-Donate, Emilio; Fernández-Costa, Carolina; Yates, John R; Albar, Juan Pablo

2018-04-06

Mass-spectrometry-based proteomics has evolved into a high-throughput technology in which numerous large-scale data sets are generated from diverse analytical platforms. Furthermore, several scientific journals and funding agencies have emphasized the storage of proteomics data in public repositories to facilitate its evaluation, inspection, and reanalysis. (1) As a consequence, public proteomics data repositories are growing rapidly. However, tools are needed to integrate multiple proteomics data sets to compare different experimental features or to perform quality control analysis. Here, we present a new Java stand-alone tool, Proteomics Assay COMparator (PACOM), that is able to import, combine, and simultaneously compare numerous proteomics experiments to check the integrity of the proteomic data as well as verify data quality. With PACOM, the user can detect source of errors that may have been introduced in any step of a proteomics workflow and that influence the final results. Data sets can be easily compared and integrated, and data quality and reproducibility can be visually assessed through a rich set of graphical representations of proteomics data features as well as a wide variety of data filters. Its flexibility and easy-to-use interface make PACOM a unique tool for daily use in a proteomics laboratory. PACOM is available at https://github.com/smdb21/pacom .

Smartphone qualification & linux-based tools for CubeSat computing payloads

Science.gov (United States)

Bridges, C. P.; Yeomans, B.; Iacopino, C.; Frame, T. E.; Schofield, A.; Kenyon, S.; Sweeting, M. N.

Modern computers are now far in advance of satellite systems and leveraging of these technologies for space applications could lead to cheaper and more capable spacecraft. Together with NASA AMES's PhoneSat, the STRaND-1 nanosatellite team has been developing and designing new ways to include smart-phone technologies to the popular CubeSat platform whilst mitigating numerous risks. Surrey Space Centre (SSC) and Surrey Satellite Technology Ltd. (SSTL) have led in qualifying state-of-the-art COTS technologies and capabilities - contributing to numerous low-cost satellite missions. The focus of this paper is to answer if 1) modern smart-phone software is compatible for fast and low-cost development as required by CubeSats, and 2) if the components utilised are robust to the space environment. The STRaND-1 smart-phone payload software explored in this paper is united using various open-source Linux tools and generic interfaces found in terrestrial systems. A major result from our developments is that many existing software and hardware processes are more than sufficient to provide autonomous and operational payload object-to-object and file-based management solutions. The paper will provide methodologies on the software chains and tools used for the STRaND-1 smartphone computing platform, the hardware built with space qualification results (thermal, thermal vacuum, and TID radiation), and how they can be implemented in future missions.

Physics Education through Computational Tools: The Case of Geometrical and Physical Optics

Science.gov (United States)

Rodríguez, Y.; Santana, A.; Mendoza, L. M.

2013-01-01

Recently, with the development of more powerful and accurate computational tools, the inclusion of new didactic materials in the classroom is known to have increased. However, the form in which these materials can be used to enhance the learning process is still under debate. Many different methodologies have been suggested for constructing new…

The ZAP Project: Designing Interactive Computer Tools for Learning Psychology

Science.gov (United States)

Hulshof, Casper; Eysink, Tessa; de Jong, Ton

2006-01-01

In the ZAP project, a set of interactive computer programs called "ZAPs" was developed. The programs were designed in such a way that first-year students experience psychological phenomena in a vivid and self-explanatory way. Students can either take the role of participant in a psychological experiment, they can experience phenomena themselves,…

3D data processing with advanced computer graphics tools

Science.gov (United States)

Zhang, Song; Ekstrand, Laura; Grieve, Taylor; Eisenmann, David J.; Chumbley, L. Scott

2012-09-01

Often, the 3-D raw data coming from an optical profilometer contains spiky noises and irregular grid, which make it difficult to analyze and difficult to store because of the enormously large size. This paper is to address these two issues for an optical profilometer by substantially reducing the spiky noise of the 3-D raw data from an optical profilometer, and by rapidly re-sampling the raw data into regular grids at any pixel size and any orientation with advanced computer graphics tools. Experimental results will be presented to demonstrate the effectiveness of the proposed approach.

Hardware replacements and software tools for digital control computers

International Nuclear Information System (INIS)

Walker, R.A.P.; Wang, B-C.; Fung, J.

1996-01-01

computers which use 'Varian' technology. A new software program, Desk Top Tools, permits the designer greater flexibility in digital control computer software design and testing. This software development allows the user to emulate control of the CANDU reactor system by system. All discussions will highlight the ability of the replacements and the new developments to enhance the operation of the existing and 'repeat' plant digital control computers and will explore future applications of these developments. Examples of current use of all replacement components and software are provided. (author)

Transportable GPU (General Processor Units) chip set technology for standard computer architectures

Science.gov (United States)

Fosdick, R. E.; Denison, H. C.

1982-11-01

The USAFR-developed GPU Chip Set has been utilized by Tracor to implement both USAF and Navy Standard 16-Bit Airborne Computer Architectures. Both configurations are currently being delivered into DOD full-scale development programs. Leadless Hermetic Chip Carrier packaging has facilitated implementation of both architectures on single 41/2 x 5 substrates. The CMOS and CMOS/SOS implementations of the GPU Chip Set have allowed both CPU implementations to use less than 3 watts of power each. Recent efforts by Tracor for USAF have included the definition of a next-generation GPU Chip Set that will retain the application-proven architecture of the current chip set while offering the added cost advantages of transportability across ISO-CMOS and CMOS/SOS processes and across numerous semiconductor manufacturers using a newly-defined set of common design rules. The Enhanced GPU Chip Set will increase speed by an approximate factor of 3 while significantly reducing chip counts and costs of standard CPU implementations.

vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments

Directory of Open Access Journals (Sweden)

Demeter Lisa

2010-05-01

Full Text Available Abstract Background The replication rate (or fitness between viral variants has been investigated in vivo and in vitro for human immunodeficiency virus (HIV. HIV fitness plays an important role in the development and persistence of drug resistance. The accurate estimation of viral fitness relies on complicated computations based on statistical methods. This calls for tools that are easy to access and intuitive to use for various experiments of viral fitness. Results Based on a mathematical model and several statistical methods (least-squares approach and measurement error models, a Web-based computing tool has been developed for improving estimation of virus fitness in growth competition assays of human immunodeficiency virus type 1 (HIV-1. Conclusions Unlike the two-point calculation used in previous studies, the estimation here uses linear regression methods with all observed data in the competition experiment to more accurately estimate relative viral fitness parameters. The dilution factor is introduced for making the computational tool more flexible to accommodate various experimental conditions. This Web-based tool is implemented in C# language with Microsoft ASP.NET, and is publicly available on the Web at http://bis.urmc.rochester.edu/vFitness/.

What is needed to implement a computer-assisted health risk assessment tool? An exploratory concept mapping study

Directory of Open Access Journals (Sweden)

Ahmad Farah

2012-12-01

Full Text Available Abstract Background Emerging eHealth tools could facilitate the delivery of comprehensive care in time-constrained clinical settings. One such tool is interactive computer-assisted health-risk assessments (HRA, which may improve provider-patient communication at the point of care, particularly for psychosocial health concerns, which remain under-detected in clinical encounters. The research team explored the perspectives of healthcare providers representing a variety of disciplines (physicians, nurses, social workers, allied staff regarding the factors required for implementation of an interactive HRA on psychosocial health. Methods The research team employed a semi-qualitative participatory method known as Concept Mapping, which involved three distinct phases. First, in face-to-face and online brainstorming sessions, participants responded to an open-ended central question: “What factors should be in place within your clinical setting to support an effective computer-assisted screening tool for psychosocial risks?” The brainstormed items were consolidated by the research team. Then, in face-to-face and online sorting sessions, participants grouped the items thematically as ‘it made sense to them’. Participants also rated each item on a 5-point scale for its ‘importance’ and ‘action feasibility’ over the ensuing six month period. The sorted and rated data was analyzed using multidimensional scaling and hierarchical cluster analyses which produced visual maps. In the third and final phase, the face-to-face Interpretation sessions, the concept maps were discussed and illuminated by participants collectively. Results Overall, 54 providers participated (emergency care 48%; primary care 52%. Participants brainstormed 196 items thought to be necessary for the implementation of an interactive HRA emphasizing psychosocial health. These were consolidated by the research team into 85 items. After sorting and rating, cluster analysis

Computational Study on a PTAS for Planar Dominating Set Problem

Directory of Open Access Journals (Sweden)

Qian-Ping Gu

2013-01-01

Full Text Available The dominating set problem is a core NP-hard problem in combinatorial optimization and graph theory, and has many important applications. Baker [JACM 41,1994] introduces a k-outer planar graph decomposition-based framework for designing polynomial time approximation scheme (PTAS for a class of NP-hard problems in planar graphs. It is mentioned that the framework can be applied to obtain an O(2ckn time, c is a constant, (1+1/k-approximation algorithm for the planar dominating set problem. We show that the approximation ratio achieved by the mentioned application of the framework is not bounded by any constant for the planar dominating set problem. We modify the application of the framework to give a PTAS for the planar dominating set problem. With k-outer planar graph decompositions, the modified PTAS has an approximation ratio (1 + 2/k. Using 2k-outer planar graph decompositions, the modified PTAS achieves the approximation ratio (1+1/k in O(22ckn time. We report a computational study on the modified PTAS. Our results show that the modified PTAS is practical.

A computational tool to characterize particle tracking measurements in optical tweezers

International Nuclear Information System (INIS)

Taylor, Michael A; Bowen, Warwick P

2013-01-01

Here, we present a computational tool for optical tweezers which calculates the particle tracking signal measured with a quadrant detector and the shot-noise limit to position resolution. The tool is a piece of Matlab code which functions within the freely available Optical Tweezers Toolbox. It allows the measurements performed in most optical tweezer experiments to be theoretically characterized in a fast and easy manner. The code supports particles with arbitrary size, any optical fields and any combination of objective and condenser, and performs a full vector calculation of the relevant fields. Example calculations are presented which show the tracking signals for different particles, and the shot-noise limit to position sensitivity as a function of the effective condenser NA. (paper)

Nsite, NsiteH and NsiteM Computer Tools for Studying Tran-scription Regulatory Elements

KAUST Repository

Shahmuradov, Ilham; Solovyev, Victor

2015-01-01

regions. Computer methods for identification of REs remain a widely used tool for studying and understanding transcriptional regulation mechanisms. The Nsite, NsiteH and NsiteM programs perform searches for statistically significant (non-random) motifs

KeyWare: an open wireless distributed computing environment

Science.gov (United States)

Shpantzer, Isaac; Schoenfeld, Larry; Grindahl, Merv; Kelman, Vladimir

1995-12-01

Deployment of distributed applications in the wireless domain lack equivalent tools, methodologies, architectures, and network management that exist in LAN based applications. A wireless distributed computing environment (KeyWareTM) based on intelligent agents within a multiple client multiple server scheme was developed to resolve this problem. KeyWare renders concurrent application services to wireline and wireless client nodes encapsulated in multiple paradigms such as message delivery, database access, e-mail, and file transfer. These services and paradigms are optimized to cope with temporal and spatial radio coverage, high latency, limited throughput and transmission costs. A unified network management paradigm for both wireless and wireline facilitates seamless extensions of LAN- based management tools to include wireless nodes. A set of object oriented tools and methodologies enables direct asynchronous invocation of agent-based services supplemented by tool-sets matched to supported KeyWare paradigms. The open architecture embodiment of KeyWare enables a wide selection of client node computing platforms, operating systems, transport protocols, radio modems and infrastructures while maintaining application portability.

Identification and implementation of end-user needs during development of a state-of-the-art modeling tool-set - 59069

International Nuclear Information System (INIS)

Seitz, Roger; Williamson, Mark; Gerdes, Kurt; Freshley, Mark; Dixon, Paul; Collazo, Yvette T.; Hubbard, Susan

2012-01-01

The U.S. Department of Energy (US DOE) Office of Environmental Management, Technology Innovation and Development is supporting a multi-National Laboratory effort to develop the Advanced Simulation Capability for Environmental Management (ASCEM). ASCEM is an emerging state-of-the-art scientific approach and software infrastructure for understanding and predicting contaminant fate and transport in natural and engineered systems. These modular and open-source high performance computing tools and user interfaces will facilitate integrated approaches that enable standardized assessments of performance and risk for EM cleanup and closure decisions. The ASCEM team recognized that engaging end-users in the ASCEM development process would lead to enhanced development and implementation of the ASCEM tool-sets in the user community. End-user involvement in ASCEM covers a broad spectrum of perspectives, including: performance assessment (PA) and risk assessment practitioners, research scientists, decision-makers, oversight personnel, and regulators engaged in the US DOE cleanup mission. End-users are primarily engaged in ASCEM via the ASCEM User Steering Committee (USC) and the 'user needs interface' task. Future plans also include user involvement in demonstrations of the ASCEM tools. This paper will describe the details of how end users have been engaged in the ASCEM program and will demonstrate how this involvement has strengthened both the tool development and community confidence. ASCEM tools requested by end-users specifically target modeling challenges associated with US DOE cleanup activities. The demonstration activities involve application of ASCEM tools and capabilities to representative problems at DOE sites. Selected results from the ASCEM Phase 1 demonstrations are discussed to illustrate how capabilities requested by end-users were implemented in prototype versions of the ASCEM tool. The ASCEM team engaged a variety of interested parties early in the development

Solving large sets of coupled equations iteratively by vector processing on the CYBER 205 computer

International Nuclear Information System (INIS)

Tolsma, L.D.

1985-01-01

The set of coupled linear second-order differential equations which has to be solved for the quantum-mechanical description of inelastic scattering of atomic and nuclear particles can be rewritten as an equivalent set of coupled integral equations. When some type of functions is used as piecewise analytic reference solutions, the integrals that arise in this set can be evaluated analytically. The set of integral equations can be solved iteratively. For the results mentioned an inward-outward iteration scheme has been applied. A concept of vectorization of coupled-channel Fortran programs, based on this integral method, is presented for the use on the Cyber 205 computer. It turns out that, for two heavy ion nuclear scattering test cases, this vector algorithm gives an overall speed-up of about a factor of 2 to 3 compared to a highly optimized scalar algorithm for a one vector pipeline computer

Quantum computing on encrypted data.

Science.gov (United States)

Fisher, K A G; Broadbent, A; Shalm, L K; Yan, Z; Lavoie, J; Prevedel, R; Jennewein, T; Resch, K J

2014-01-01

The ability to perform computations on encrypted data is a powerful tool for protecting privacy. Recently, protocols to achieve this on classical computing systems have been found. Here, we present an efficient solution to the quantum analogue of this problem that enables arbitrary quantum computations to be carried out on encrypted quantum data. We prove that an untrusted server can implement a universal set of quantum gates on encrypted quantum bits (qubits) without learning any information about the inputs, while the client, knowing the decryption key, can easily decrypt the results of the computation. We experimentally demonstrate, using single photons and linear optics, the encryption and decryption scheme on a set of gates sufficient for arbitrary quantum computations. As our protocol requires few extra resources compared with other schemes it can be easily incorporated into the design of future quantum servers. These results will play a key role in enabling the development of secure distributed quantum systems.

Design of Intelligent Robot as A Tool for Teaching Media Based on Computer Interactive Learning and Computer Assisted Learning to Improve the Skill of University Student

Science.gov (United States)

Zuhrie, M. S.; Basuki, I.; Asto B, I. G. P.; Anifah, L.

2018-01-01

The focus of the research is the teaching module which incorporates manufacturing, planning mechanical designing, controlling system through microprocessor technology and maneuverability of the robot. Computer interactive and computer-assisted learning is strategies that emphasize the use of computers and learning aids (computer assisted learning) in teaching and learning activity. This research applied the 4-D model research and development. The model is suggested by Thiagarajan, et.al (1974). 4-D Model consists of four stages: Define Stage, Design Stage, Develop Stage, and Disseminate Stage. This research was conducted by applying the research design development with an objective to produce a tool of learning in the form of intelligent robot modules and kit based on Computer Interactive Learning and Computer Assisted Learning. From the data of the Indonesia Robot Contest during the period of 2009-2015, it can be seen that the modules that have been developed confirm the fourth stage of the research methods of development; disseminate method. The modules which have been developed for students guide students to produce Intelligent Robot Tool for Teaching Based on Computer Interactive Learning and Computer Assisted Learning. Results of students’ responses also showed a positive feedback to relate to the module of robotics and computer-based interactive learning.

The use of computer simulations in whole-class versus small-group settings

Science.gov (United States)

Smetana, Lara Kathleen

This study explored the use of computer simulations in a whole-class as compared to small-group setting. Specific consideration was given to the nature and impact of classroom conversations and interactions when computer simulations were incorporated into a high school chemistry course. This investigation fills a need for qualitative research that focuses on the social dimensions of actual classrooms. Participants included a novice chemistry teacher experienced in the use of educational technologies and two honors chemistry classes. The study was conducted in a rural school in the south-Atlantic United States at the end of the fall 2007 semester. The study took place during one instructional unit on atomic structure. Data collection allowed for triangulation of evidence from a variety of sources approximately 24 hours of video- and audio-taped classroom observations, supplemented with the researcher's field notes and analytic journal; miscellaneous classroom artifacts such as class notes, worksheets, and assignments; open-ended pre- and post-assessments; student exit interviews; teacher entrance, exit and informal interviews. Four web-based simulations were used, three of which were from the ExploreLearning collection. Assessments were analyzed using descriptive statistics and classroom observations, artifacts and interviews were analyzed using Erickson's (1986) guidelines for analytic induction. Conversational analysis was guided by methods outlined by Erickson (1982). Findings indicated (a) the teacher effectively incorporated simulations in both settings (b) students in both groups significantly improved their understanding of the chemistry concepts (c) there was no statistically significant difference between groups' achievement (d) there was more frequent exploratory talk in the whole-class group (e) there were more frequent and meaningful teacher-student interactions in the whole-class group (f) additional learning experiences not measured on the assessment

The Impact of Computer and Communications Technology on Recruiter Productivity and Quality of Life

National Research Council Canada - National Science Library

Blackstone, Tanja

2003-01-01

.... A test group of recruiters was given a set of tools, which included state of the art laptop computers, computer projection equipment, communications and database software, Internet and Intranet...

Barriers to the Integration of Computers in Early Childhood Settings: Teachers' Perceptions

Science.gov (United States)

Nikolopoulou, Kleopatra; Gialamas, Vasilis

2015-01-01

This study investigated teachers' perceptions of barriers to using - integrating computers in early childhood settings. A 26-item questionnaire was administered to 134 early childhood teachers in Greece. Lack of funding, lack of technical and administrative support, as well as inadequate training opportunities were among the major perceived…

PROACT user's guide: how to use the pallet recovery opportunity analysis computer tool

Science.gov (United States)

E. Bradley Hager; A.L. Hammett; Philip A. Araman

2003-01-01

Pallet recovery projects are environmentally responsible and offer promising business opportunities. The Pallet Recovery Opportunity Analysis Computer Tool (PROACT) assesses the operational and financial feasibility of potential pallet recovery projects. The use of project specific information supplied by the user increases the accuracy and the validity of the...

Visualization of unsteady computational fluid dynamics

Science.gov (United States)

Haimes, Robert

1994-11-01

A brief summary of the computer environment used for calculating three dimensional unsteady Computational Fluid Dynamic (CFD) results is presented. This environment requires a super computer as well as massively parallel processors (MPP's) and clusters of workstations acting as a single MPP (by concurrently working on the same task) provide the required computational bandwidth for CFD calculations of transient problems. The cluster of reduced instruction set computers (RISC) is a recent advent based on the low cost and high performance that workstation vendors provide. The cluster, with the proper software can act as a multiple instruction/multiple data (MIMD) machine. A new set of software tools is being designed specifically to address visualizing 3D unsteady CFD results in these environments. Three user's manuals for the parallel version of Visual3, pV3, revision 1.00 make up the bulk of this report.

Physics-Based Probabilistic Design Tool with System-Level Reliability Constraint, Phase II

Data.gov (United States)

National Aeronautics and Space Administration — The work proposed herein would develop a set of analytic methodologies and a computer tool suite enabling aerospace hardware designers to rapidly determine optimum...

An Exploration of the Effectiveness of an Audit Simulation Tool in a Classroom Setting

Science.gov (United States)

Zelin, Robert C., II

2010-01-01

The purpose of this study was to examine the effectiveness of using an audit simulation product in a classroom setting. Many students and professionals feel that a disconnect exists between learning auditing in the classroom and practicing auditing in the workplace. It was hoped that the introduction of an audit simulation tool would help to…

STARS software tool for analysis of reliability and safety

International Nuclear Information System (INIS)

Poucet, A.; Guagnini, E.

1989-01-01

This paper reports on the STARS (Software Tool for the Analysis of Reliability and Safety) project aims at developing an integrated set of Computer Aided Reliability Analysis tools for the various tasks involved in systems safety and reliability analysis including hazard identification, qualitative analysis, logic model construction and evaluation. The expert system technology offers the most promising perspective for developing a Computer Aided Reliability Analysis tool. Combined with graphics and analysis capabilities, it can provide a natural engineering oriented environment for computer assisted reliability and safety modelling and analysis. For hazard identification and fault tree construction, a frame/rule based expert system is used, in which the deductive (goal driven) reasoning and the heuristic, applied during manual fault tree construction, is modelled. Expert system can explain their reasoning so that the analyst can become aware of the why and the how results are being obtained. Hence, the learning aspect involved in manual reliability and safety analysis can be maintained and improved

Developmental screening tools: feasibility of use at primary healthcare level in low- and middle-income settings.

Science.gov (United States)

Fischer, Vinicius Jobim; Morris, Jodi; Martines, José

2014-06-01

An estimated 150 million children have a disability. Early identification of developmental disabilities is a high priority for the World Health Organization to allow action to reduce impairments through Gap Action Program on mental health. The study identified the feasibility of using the developmental screening and monitoring tools for children aged 0-3 year(s) by non-specialist primary healthcare providers in low-resource settings. A systematic review of the literature was conducted to identify the tools, assess their psychometric properties, and feasibility of use in low- and middle-income countries (LMICs). Key indicators to examine feasibility in LMICs were derived from a consultation with 23 international experts. We identified 426 studies from which 14 tools used in LMICs were extracted for further examination. Three tools reported adequate psychometric properties and met most of the feasibility criteria. Three tools appear promising for use in identifying and monitoring young children with disabilities at primary healthcare level in LMICs. Further research and development are needed to optimize these tools.

Computational protein design-the next generation tool to expand synthetic biology applications.

Science.gov (United States)

Gainza-Cirauqui, Pablo; Correia, Bruno Emanuel

2018-05-02

One powerful approach to engineer synthetic biology pathways is the assembly of proteins sourced from one or more natural organisms. However, synthetic pathways often require custom functions or biophysical properties not displayed by natural proteins, limitations that could be overcome through modern protein engineering techniques. Structure-based computational protein design is a powerful tool to engineer new functional capabilities in proteins, and it is beginning to have a profound impact in synthetic biology. Here, we review efforts to increase the capabilities of synthetic biology using computational protein design. We focus primarily on computationally designed proteins not only validated in vitro, but also shown to modulate different activities in living cells. Efforts made to validate computational designs in cells can illustrate both the challenges and opportunities in the intersection of protein design and synthetic biology. We also highlight protein design approaches, which although not validated as conveyors of new cellular function in situ, may have rapid and innovative applications in synthetic biology. We foresee that in the near-future, computational protein design will vastly expand the functional capabilities of synthetic cells. Copyright © 2018. Published by Elsevier Ltd.

Computational tools for genome-wide miRNA prediction and study

KAUST Repository

Malas, T.B.

2012-11-02

MicroRNAs (miRNAs) are single-stranded non-coding RNA susually of 22 nucleotidesin length that play an important post-transcriptional regulation role in many organisms. MicroRNAs bind a seed sequence to the 3-untranslated region (UTR) region of the target messenger RNA (mRNA), inducing degradation or inhibition of translation and resulting in a reduction in the protein level. This regulatory mechanism is central to many biological processes and perturbation could lead to diseases such as cancer. Given the biological importance, of miRNAs, there is a great need to identify and study their targets and functions. However, miRNAs are very difficult to clone in the lab and this has hindered the identification of novel miRNAs. Next-generation sequencing coupled with new computational tools has recently evolved to help researchers efficiently identify large numbers of novel miRNAs. In this review, we describe recent miRNA prediction tools and discuss their priorities, advantages and disadvantages. Malas and Ravasi.

Computational tools for genome-wide miRNA prediction and study

KAUST Repository

Malas, T.B.; Ravasi, Timothy

2012-01-01

MicroRNAs (miRNAs) are single-stranded non-coding RNA susually of 22 nucleotidesin length that play an important post-transcriptional regulation role in many organisms. MicroRNAs bind a seed sequence to the 3-untranslated region (UTR) region of the target messenger RNA (mRNA), inducing degradation or inhibition of translation and resulting in a reduction in the protein level. This regulatory mechanism is central to many biological processes and perturbation could lead to diseases such as cancer. Given the biological importance, of miRNAs, there is a great need to identify and study their targets and functions. However, miRNAs are very difficult to clone in the lab and this has hindered the identification of novel miRNAs. Next-generation sequencing coupled with new computational tools has recently evolved to help researchers efficiently identify large numbers of novel miRNAs. In this review, we describe recent miRNA prediction tools and discuss their priorities, advantages and disadvantages. Malas and Ravasi.

Principles for generation of time-dependent collimator settings during the LHC cycle

CERN Document Server

Bruce, R; Redaelli, S

2011-01-01

The settings of the LHC collimators have to be changed during the cycle of injection, ramp and squeeze to account for variations in the orbit, beam size and normalized distance to the beam center. We discuss the principles for how the settings are calculated and show a software tool that computes them as time-dependent functions from beambased data and theoretical optics models.

A computationally efficient tool for assessing the depth resolution in large-scale potential-field inversion

DEFF Research Database (Denmark)

Paoletti, Valeria; Hansen, Per Christian; Hansen, Mads Friis

2014-01-01

In potential-field inversion, careful management of singular value decomposition components is crucial for obtaining information about the source distribution with respect to depth. In principle, the depth-resolution plot provides a convenient visual tool for this analysis, but its computational...... on memory and computing time. We used the ApproxDRP to study retrievable depth resolution in inversion of the gravity field of the Neapolitan Volcanic Area. Our main contribution is the combined use of the Lanczos bidiagonalization algorithm, established in the scientific computing community, and the depth...

Basic data, computer codes and integral experiments: The tools for modelling in nuclear technology

International Nuclear Information System (INIS)

Sartori, E.

2001-01-01

When studying applications in nuclear technology we need to understand and be able to predict the behavior of systems manufactured by human enterprise. First, the underlying basic physical and chemical phenomena need to be understood. We have then to predict the results from the interplay of the large number of the different basic events: i.e. the macroscopic effects. In order to be able to build confidence in our modelling capability, we need then to compare these results against measurements carried out on such systems. The different levels of modelling require the solution of different types of equations using different type of parameters. The tools required for carrying out a complete validated analysis are: - The basic nuclear or chemical data; - The computer codes, and; - The integral experiments. This article describes the role each component plays in a computational scheme designed for modelling purposes. It describes also which tools have been developed and are internationally available. The role of the OECD/NEA Data Bank, the Radiation Shielding Information Computational Center (RSICC), and the IAEA Nuclear Data Section are playing in making these elements available to the community of scientists and engineers is described. (author)

Computability theory

CERN Document Server

Weber, Rebecca

2012-01-01

What can we compute--even with unlimited resources? Is everything within reach? Or are computations necessarily drastically limited, not just in practice, but theoretically? These questions are at the heart of computability theory. The goal of this book is to give the reader a firm grounding in the fundamentals of computability theory and an overview of currently active areas of research, such as reverse mathematics and algorithmic randomness. Turing machines and partial recursive functions are explored in detail, and vital tools and concepts including coding, uniformity, and diagonalization are described explicitly. From there the material continues with universal machines, the halting problem, parametrization and the recursion theorem, and thence to computability for sets, enumerability, and Turing reduction and degrees. A few more advanced topics round out the book before the chapter on areas of research. The text is designed to be self-contained, with an entire chapter of preliminary material including re...

Comparison of Property-Oriented Basis Sets for the Computation of Electronic and Nuclear Relaxation Hyperpolarizabilities.

Science.gov (United States)

Zaleśny, Robert; Baranowska-Łączkowska, Angelika; Medveď, Miroslav; Luis, Josep M

2015-09-08

In the present work, we perform an assessment of several property-oriented atomic basis sets in computing (hyper)polarizabilities with a focus on the vibrational contributions. Our analysis encompasses the Pol and LPol-ds basis sets of Sadlej and co-workers, the def2-SVPD and def2-TZVPD basis sets of Rappoport and Furche, and the ORP basis set of Baranowska-Łączkowska and Łączkowski. Additionally, we use the d-aug-cc-pVQZ and aug-cc-pVTZ basis sets of Dunning and co-workers to determine the reference estimates of the investigated electric properties for small- and medium-sized molecules, respectively. We combine these basis sets with ab initio post-Hartree-Fock quantum-chemistry approaches (including the coupled cluster method) to calculate electronic and nuclear relaxation (hyper)polarizabilities of carbon dioxide, formaldehyde, cis-diazene, and a medium-sized Schiff base. The primary finding of our study is that, among all studied property-oriented basis sets, only the def2-TZVPD and ORP basis sets yield nuclear relaxation (hyper)polarizabilities of small molecules with average absolute errors less than 5.5%. A similar accuracy for the nuclear relaxation (hyper)polarizabilites of the studied systems can also be reached using the aug-cc-pVDZ basis set (5.3%), although for more accurate calculations of vibrational contributions, i.e., average absolute errors less than 1%, the aug-cc-pVTZ basis set is recommended. It was also demonstrated that anharmonic contributions to first and second hyperpolarizabilities of a medium-sized Schiff base are particularly difficult to accurately predict at the correlated level using property-oriented basis sets. For instance, the value of the nuclear relaxation first hyperpolarizability computed at the MP2/def2-TZVPD level of theory is roughly 3 times larger than that determined using the aug-cc-pVTZ basis set. We link the failure of the def2-TZVPD basis set with the difficulties in predicting the first-order field

Visualization in simulation tools: requirements and a tool specification to support the teaching of dynamic biological processes.

Science.gov (United States)

Jørgensen, Katarina M; Haddow, Pauline C

2011-08-01

Simulation tools are playing an increasingly important role behind advances in the field of systems biology. However, the current generation of biological science students has either little or no experience with such tools. As such, this educational glitch is limiting both the potential use of such tools as well as the potential for tighter cooperation between the designers and users. Although some simulation tool producers encourage their use in teaching, little attempt has hitherto been made to analyze and discuss their suitability as an educational tool for noncomputing science students. In general, today's simulation tools assume that the user has a stronger mathematical and computing background than that which is found in most biological science curricula, thus making the introduction of such tools a considerable pedagogical challenge. This paper provides an evaluation of the pedagogical attributes of existing simulation tools for cell signal transduction based on Cognitive Load theory. Further, design recommendations for an improved educational simulation tool are provided. The study is based on simulation tools for cell signal transduction. However, the discussions are relevant to a broader biological simulation tool set.

Cloud Computing Adoption and Usage in Community Colleges

Science.gov (United States)

Behrend, Tara S.; Wiebe, Eric N.; London, Jennifer E.; Johnson, Emily C.

2011-01-01

Cloud computing is gaining popularity in higher education settings, but the costs and benefits of this tool have gone largely unexplored. The purpose of this study was to examine the factors that lead to technology adoption in a higher education setting. Specifically, we examined a range of predictors and outcomes relating to the acceptance of a…

Enhancing pediatric safety: assessing and improving resident competency in life-threatening events with a computer-based interactive resuscitation tool

International Nuclear Information System (INIS)

Lerner, Catherine; Gaca, Ana M.; Frush, Donald P.; Ancarana, Anjanette; Hohenhaus, Sue; Seelinger, Terry A.; Frush, Karen

2009-01-01

Though rare, allergic reactions occur as a result of administration of low osmolality nonionic iodinated contrast material to pediatric patients. Currently available resuscitation aids are inadequate in guiding radiologists' initial management of such reactions. To compare radiology resident competency with and without a computer-based interactive resuscitation tool in the management of life-threatening events in pediatric patients. The study was approved by the IRB. Radiology residents (n=19; 14 male, 5 female; 19 certified in basic life support/advanced cardiac life support; 1 certified in pediatric advanced life support) were videotaped during two simulated 5-min anaphylaxis scenarios involving 18-month-old and 8-year-old mannequins (order randomized). No advance warning was given. In half of the scenarios, a computer-based interactive resuscitation tool with a response-driven decision tree was available to residents (order randomized). Competency measures included: calling a code, administering oxygen and epinephrine, and correctly dosing epinephrine. Residents performed significantly more essential interventions with the computer-based resuscitation tool than without (72/76 vs. 49/76, P<0.001). Significantly more residents appropriately dosed epinephrine with the tool than without (17/19 vs. 1/19; P<0.001). More residents called a code with the tool than without (17/19 vs. 14/19; P = 0.08). A learning effect was present: average times to call a code, request oxygen, and administer epinephrine were shorter in the second scenario (129 vs. 93 s, P=0.24; 52 vs. 30 s, P<0.001; 152 vs. 82 s, P=0.025, respectively). All the trainees found the resuscitation tool helpful and potentially useful in a true pediatric emergency. A computer-based interactive resuscitation tool significantly improved resident performance in managing pediatric emergencies in the radiology department. (orig.)

Wigner functions and density matrices in curved spaces as computational tools

International Nuclear Information System (INIS)

Habib, S.; Kandrup, H.E.

1989-01-01

This paper contrasts two alternative approaches to statistical quantum field theory in curved spacetimes, namely (1) a canonical Hamiltonian approach, in which the basic object is a density matrix ρ characterizing the noncovariant, but globally defined, modes of the field; and (2) a Wigner function approach, in which the basic object is a Wigner function f defined quasilocally from the Hadamard, or correlation, function G 1 (x 1 , x 2 ). The key object is to isolate on the conceptual biases underlying each of these approaches and then to assess their utility and limitations in effecting concerete calculations. The following questions are therefore addressed and largely answered. What sort of spacetimes (e.g., de Sitter or Friedmann-Robertson-Walker) are comparatively eas to consider? What sorts of objects (e.g., average fields or renormalized stress energies) are easy to compute approximately? What, if anything, can be computed exactly? What approximations are intrinsic to each approach or convenient as computational tools? What sorts of ''field entropies'' are natural to define? copyright 1989 Academic Press, Inc

Color in Computer Vision Fundamentals and Applications

CERN Document Server

Gevers, Theo; van de Weijer, Joost; Geusebroek, Jan-Mark

2012-01-01

While the field of computer vision drives many of today’s digital technologies and communication networks, the topic of color has emerged only recently in most computer vision applications. One of the most extensive works to date on color in computer vision, this book provides a complete set of tools for working with color in the field of image understanding. Based on the authors’ intense collaboration for more than a decade and drawing on the latest thinking in the field of computer science, the book integrates topics from color science and computer vision, clearly linking theor

Implementation of a computer-aided detection tool for quantification of intracranial radiologic markers on brain CT images

Science.gov (United States)

Aghaei, Faranak; Ross, Stephen R.; Wang, Yunzhi; Wu, Dee H.; Cornwell, Benjamin O.; Ray, Bappaditya; Zheng, Bin

2017-03-01

Aneurysmal subarachnoid hemorrhage (aSAH) is a form of hemorrhagic stroke that affects middle-aged individuals and associated with significant morbidity and/or mortality especially those presenting with higher clinical and radiologic grades at the time of admission. Previous studies suggested that blood extravasated after aneurysmal rupture was a potentially clinical prognosis factor. But all such studies used qualitative scales to predict prognosis. The purpose of this study is to develop and test a new interactive computer-aided detection (CAD) tool to detect, segment and quantify brain hemorrhage and ventricular cerebrospinal fluid on non-contrasted brain CT images. First, CAD segments brain skull using a multilayer region growing algorithm with adaptively adjusted thresholds. Second, CAD assigns pixels inside the segmented brain region into one of three classes namely, normal brain tissue, blood and fluid. Third, to avoid "black-box" approach and increase accuracy in quantification of these two image markers using CT images with large noise variation in different cases, a graphic User Interface (GUI) was implemented and allows users to visually examine segmentation results. If a user likes to correct any errors (i.e., deleting clinically irrelevant blood or fluid regions, or fill in the holes inside the relevant blood or fluid regions), he/she can manually define the region and select a corresponding correction function. CAD will automatically perform correction and update the computed data. The new CAD tool is now being used in clinical and research settings to estimate various quantitatively radiological parameters/markers to determine radiological severity of aSAH at presentation and correlate the estimations with various homeostatic/metabolic derangements and predict clinical outcome.

PANDORA: keyword-based analysis of protein sets by integration of annotation sources.

Science.gov (United States)

Kaplan, Noam; Vaaknin, Avishay; Linial, Michal

2003-10-01

Recent advances in high-throughput methods and the application of computational tools for automatic classification of proteins have made it possible to carry out large-scale proteomic analyses. Biological analysis and interpretation of sets of proteins is a time-consuming undertaking carried out manually by experts. We have developed PANDORA (Protein ANnotation Diagram ORiented Analysis), a web-based tool that provides an automatic representation of the biological knowledge associated with any set of proteins. PANDORA uses a unique approach of keyword-based graphical analysis that focuses on detecting subsets of proteins that share unique biological properties and the intersections of such sets. PANDORA currently supports SwissProt keywords, NCBI Taxonomy, InterPro entries and the hierarchical classification terms from ENZYME, SCOP and GO databases. The integrated study of several annotation sources simultaneously allows a representation of biological relations of structure, function, cellular location, taxonomy, domains and motifs. PANDORA is also integrated into the ProtoNet system, thus allowing testing thousands of automatically generated clusters. We illustrate how PANDORA enhances the biological understanding of large, non-uniform sets of proteins originating from experimental and computational sources, without the need for prior biological knowledge on individual proteins.

Lessons learned developing a diagnostic tool for HIV-associated dementia feasible to implement in resource-limited settings: pilot testing in Kenya.

Directory of Open Access Journals (Sweden)

Judith Kwasa

Full Text Available To conduct a preliminary evaluation of the utility and reliability of a diagnostic tool for HIV-associated dementia (HAD for use by primary health care workers (HCW which would be feasible to implement in resource-limited settings.In resource-limited settings, HAD is an indication for anti-retroviral therapy regardless of CD4 T-cell count. Anti-retroviral therapy, the treatment for HAD, is now increasingly available in resource-limited settings. Nonetheless, HAD remains under-diagnosed likely because of limited clinical expertise and availability of diagnostic tests. Thus, a simple diagnostic tool which is practical to implement in resource-limited settings is an urgent need.A convenience sample of 30 HIV-infected outpatients was enrolled in Western Kenya. We assessed the sensitivity and specificity of a diagnostic tool for HAD as administered by a primary HCW. This was compared to an expert clinical assessment which included examination by a physician, neuropsychological testing, and in selected cases, brain imaging. Agreement between HCW and an expert examiner on certain tool components was measured using Kappa statistic.The sample was 57% male, mean age was 38.6 years, mean CD4 T-cell count was 323 cells/µL, and 54% had less than a secondary school education. Six (20% of the subjects were diagnosed with HAD by expert clinical assessment. The diagnostic tool was 63% sensitive and 67% specific for HAD. Agreement between HCW and expert examiners was poor for many individual items of the diagnostic tool (K = .03-.65. This diagnostic tool had moderate sensitivity and specificity for HAD. However, reliability was poor, suggesting that substantial training and formal evaluations of training adequacy will be critical to enable HCW to reliably administer a brief diagnostic tool for HAD.

Technology and Jobs: Computer-Aided Design. Numerical-Control Machine-Tool Operators. Office Automation.

Science.gov (United States)

Stanton, Michael; And Others

1985-01-01

Three reports on the effects of high technology on the nature of work include (1) Stanton on applications and implications of computer-aided design for engineers, drafters, and architects; (2) Nardone on the outlook and training of numerical-control machine tool operators; and (3) Austin and Drake on the future of clerical occupations in automated…

Minyoo Matata - The Vicious Worm - A Taenia solium Computer-Based Health-Education Tool - in Swahili

DEFF Research Database (Denmark)

Trevisan, Chiara; Fèvre, Eric M.; Owiny, Maurice

2017-01-01

Lack of knowledge is one of the main risk factors for the spread of the zoonotic parasite Taenia solium. The computer-based health-education tool 'The Vicious Worm' was developed to create awareness and provide evidence-based health education as a specific measure in control strategies. To increase...... the reach of the tool, a new version in Swahili was developed and can now be downloaded for free from http://theviciousworm.sites.ku.dk....

Comparison of High-Fidelity Computational Tools for Wing Design of a Distributed Electric Propulsion Aircraft

Science.gov (United States)

Deere, Karen A.; Viken, Sally A.; Carter, Melissa B.; Viken, Jeffrey K.; Derlaga, Joseph M.; Stoll, Alex M.

2017-01-01

A variety of tools, from fundamental to high order, have been used to better understand applications of distributed electric propulsion to aid the wing and propulsion system design of the Leading Edge Asynchronous Propulsion Technology (LEAPTech) project and the X-57 Maxwell airplane. Three high-fidelity, Navier-Stokes computational fluid dynamics codes used during the project with results presented here are FUN3D, STAR-CCM+, and OVERFLOW. These codes employ various turbulence models to predict fully turbulent and transitional flow. Results from these codes are compared for two distributed electric propulsion configurations: the wing tested at NASA Armstrong on the Hybrid-Electric Integrated Systems Testbed truck, and the wing designed for the X-57 Maxwell airplane. Results from these computational tools for the high-lift wing tested on the Hybrid-Electric Integrated Systems Testbed truck and the X-57 high-lift wing presented compare reasonably well. The goal of the X-57 wing and distributed electric propulsion system design achieving or exceeding the required ?? (sub L) = 3.95 for stall speed was confirmed with all of the computational codes.

Multimedia Instructional Tools' Impact on Student Motivation and Learning Strategies in Computer Applications Courses

Science.gov (United States)

Chapman, Debra; Wang, Shuyan

2015-01-01

Multimedia instructional tools (MMIT) have been identified as a way effectively and economically present instructional material. MMITs are commonly used in introductory computer applications courses as MMITs should be effective in increasing student knowledge and positively impact motivation and learning strategies, without increasing costs. This…

BACHSCORE. A tool for evaluating efficiently and reliably the quality of large sets of protein structures

Science.gov (United States)

Sarti, E.; Zamuner, S.; Cossio, P.; Laio, A.; Seno, F.; Trovato, A.

2013-12-01

In protein structure prediction it is of crucial importance, especially at the refinement stage, to score efficiently large sets of models by selecting the ones that are closest to the native state. We here present a new computational tool, BACHSCORE, that allows its users to rank different structural models of the same protein according to their quality, evaluated by using the BACH++ (Bayesian Analysis Conformation Hunt) scoring function. The original BACH statistical potential was already shown to discriminate with very good reliability the protein native state in large sets of misfolded models of the same protein. BACH++ features a novel upgrade in the solvation potential of the scoring function, now computed by adapting the LCPO (Linear Combination of Pairwise Orbitals) algorithm. This change further enhances the already good performance of the scoring function. BACHSCORE can be accessed directly through the web server: bachserver.pd.infn.it. Catalogue identifier: AEQD_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEQD_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 130159 No. of bytes in distributed program, including test data, etc.: 24 687 455 Distribution format: tar.gz Programming language: C++. Computer: Any computer capable of running an executable produced by a g++ compiler (4.6.3 version). Operating system: Linux, Unix OS-es. RAM: 1 073 741 824 bytes Classification: 3. Nature of problem: Evaluate the quality of a protein structural model, taking into account the possible “a priori” knowledge of a reference primary sequence that may be different from the amino-acid sequence of the model; the native protein structure should be recognized as the best model. Solution method: The contact potential scores the occurrence of any given type of residue pair in 5 possible

Qualification of integrated tool environments (QUITE) for the development of computer-based safety systems in NPP

International Nuclear Information System (INIS)

Miedl, Horst

2004-01-01

In NPP I et C systems are back fitted meanwhile increasingly by computer-based systems (I et C platforms). The corresponding safety functions are implemented by software, and this software is developed, configured and administrated with the help of integrated tool environments (ITE). An ITE offers a set of services which are used to construct an I et C system and consist typically of software packages for project control and documentation, specification and design, automatic code generation and so on. Commercial ITE are not necessarily conceived and qualified (type-tested) for nuclear specific applications but are used - and will increasingly be used - for the implementation of nuclear safety related I et C systems. Therefor, it is necessary to qualify commercial ITE with respect to their influence on the quality of the target system for each I et C platform (dependent on the safety category of the target system). Examples for commercial ITEs are I et C platforms like SPINLINE 3, TELEPERM XP, Common Q, TRICON, etc. (Author)

A review of computer tools for analysing the integration of renewable energy into various energy systems

DEFF Research Database (Denmark)

Connolly, D.; Lund, Henrik; Mathiesen, Brian Vad

2010-01-01

to integrating renewable energy, but instead the ‘ideal’ energy tool is highly dependent on the specific objectives that must be fulfilled. The typical applications for the 37 tools reviewed (from analysing single-building systems to national energy-systems), combined with numerous other factors......This paper includes a review of the different computer tools that can be used to analyse the integration of renewable energy. Initially 68 tools were considered, but 37 were included in the final analysis which was carried out in collaboration with the tool developers or recommended points...... of contact. The results in this paper provide the information necessary to identify a suitable energy tool for analysing the integration of renewable energy into various energy-systems under different objectives. It is evident from this paper that there is no energy tool that addresses all issues related...

Accurate Computation of Periodic Regions' Centers in the General M-Set with Integer Index Number

Directory of Open Access Journals (Sweden)

Wang Xingyuan

2010-01-01

Full Text Available This paper presents two methods for accurately computing the periodic regions' centers. One method fits for the general M-sets with integer index number, the other fits for the general M-sets with negative integer index number. Both methods improve the precision of computation by transforming the polynomial equations which determine the periodic regions' centers. We primarily discuss the general M-sets with negative integer index, and analyze the relationship between the number of periodic regions' centers on the principal symmetric axis and in the principal symmetric interior. We can get the centers' coordinates with at least 48 significant digits after the decimal point in both real and imaginary parts by applying the Newton's method to the transformed polynomial equation which determine the periodic regions' centers. In this paper, we list some centers' coordinates of general M-sets' k-periodic regions (k=3,4,5,6 for the index numbers α=−25,−24,…,−1 , all of which have highly numerical accuracy.

Ssecrett and neuroTrace: Interactive visualization and analysis tools for large-scale neuroscience data sets

KAUST Repository

Jeong, Wonki; Beyer, Johanna; Hadwiger, Markus; Blue, Rusty; Law, Charles; Vá zquez Reina, Amelio; Reid, Rollie Clay; Lichtman, Jeff W M D; Pfister, Hanspeter

2010-01-01

Recent advances in optical and electron microscopy let scientists acquire extremely high-resolution images for neuroscience research. Data sets imaged with modern electron microscopes can range between tens of terabytes to about one petabyte. These large data sizes and the high complexity of the underlying neural structures make it very challenging to handle the data at reasonably interactive rates. To provide neuroscientists flexible, interactive tools, the authors introduce Ssecrett and NeuroTrace, two tools they designed for interactive exploration and analysis of large-scale optical- and electron-microscopy images to reconstruct complex neural circuits of the mammalian nervous system. © 2010 IEEE.

Ssecrett and neuroTrace: Interactive visualization and analysis tools for large-scale neuroscience data sets

KAUST Repository

Jeong, Wonki

2010-05-01

Recent advances in optical and electron microscopy let scientists acquire extremely high-resolution images for neuroscience research. Data sets imaged with modern electron microscopes can range between tens of terabytes to about one petabyte. These large data sizes and the high complexity of the underlying neural structures make it very challenging to handle the data at reasonably interactive rates. To provide neuroscientists flexible, interactive tools, the authors introduce Ssecrett and NeuroTrace, two tools they designed for interactive exploration and analysis of large-scale optical- and electron-microscopy images to reconstruct complex neural circuits of the mammalian nervous system. © 2010 IEEE.

Peac – A set of tools to quickly enable Proof on a cluster

International Nuclear Information System (INIS)

Ganis, G; Vala, M

2012-01-01

With advent of the analysis phase of Lhcdata-processing, interest in Proof technology has considerably increased. While setting up a simple Proof cluster for basic usage is reasonably straightforward, exploiting the several new functionalities added in recent times may be complicated. Peac, standing for Proof Enabled Analysis Cluster, is a set of tools aiming to facilitate the setup and management of a Proof cluster. Peac is based on the experience made by setting up Proof for the Alice analysis facilities. It allows to easily build and configure Root and the additional software needed on the cluster, and may serve as distributor of binaries via Xrootd. Peac uses Proof-On-Demand (PoD) for resource management (start, stop or daemons). Finally, Peac sets-up and configures dataset management (using the Afdsmgrd daemon), as well as cluster monitoring (machine status and Proof query summaries) using MonAlisa. In this respect, a MonAlisa page has been dedicated to Peac users, so that a cluster managed by Peac can be automatically monitored. In this paper we present and describe the status and main components of Peac and show details about its usage.

Public Interest Energy Research (PIER) Program Development of a Computer-based Benchmarking and Analytical Tool. Benchmarking and Energy & Water Savings Tool in Dairy Plants (BEST-Dairy)

Energy Technology Data Exchange (ETDEWEB)

Xu, Tengfang [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Flapper, Joris [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Ke, Jing [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Kramer, Klaas [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Sathaye, Jayant [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

2012-02-01

The overall goal of the project is to develop a computer-based benchmarking and energy and water savings tool (BEST-Dairy) for use in the California dairy industry - including four dairy processes - cheese, fluid milk, butter, and milk powder. BEST-Dairy tool developed in this project provides three options for the user to benchmark each of the dairy product included in the tool, with each option differentiated based on specific detail level of process or plant, i.e., 1) plant level; 2) process-group level, and 3) process-step level. For each detail level, the tool accounts for differences in production and other variables affecting energy use in dairy processes. The dairy products include cheese, fluid milk, butter, milk powder, etc. The BEST-Dairy tool can be applied to a wide range of dairy facilities to provide energy and water savings estimates, which are based upon the comparisons with the best available reference cases that were established through reviewing information from international and national samples. We have performed and completed alpha- and beta-testing (field testing) of the BEST-Dairy tool, through which feedback from voluntary users in the U.S. dairy industry was gathered to validate and improve the tool's functionality. BEST-Dairy v1.2 was formally published in May 2011, and has been made available for free downloads from the internet (i.e., http://best-dairy.lbl.gov). A user's manual has been developed and published as the companion documentation for use with the BEST-Dairy tool. In addition, we also carried out technology transfer activities by engaging the dairy industry in the process of tool development and testing, including field testing, technical presentations, and technical assistance throughout the project. To date, users from more than ten countries in addition to those in the U.S. have downloaded the BEST-Dairy from the LBNL website. It is expected that the use of BEST-Dairy tool will advance understanding of energy and

Female Students' Experiences of Computer Technology in Single- versus Mixed-Gender School Settings

Science.gov (United States)

Burke, Lee-Ann; Murphy, Elizabeth

2006-01-01

This study explores how female students compare learning computer technology in a single- versus a mixed- gender school setting. Twelve females participated, all of whom were enrolled in a grade 12 course in Communications' Technology. Data collection included a questionnaire, a semi-structured interview and focus groups. Participants described…

Development of a transportation planning tool

International Nuclear Information System (INIS)

Funkhouser, B.R.; Moyer, J.W.; Ballweg, E.L.

1994-01-01

This paper describes the application of simulation modeling and logistics techniques to the development of a planning tool for the Department of Energy (DOE). The focus of the Transportation Planning Model (TPM) tool is to aid DOE and Sandia analysts in the planning of future fleet sizes, driver and support personnel sizes, base site locations, and resource balancing among the base sites. The design approach is to develop a rapid modeling environment which will allow analysts to easily set up a shipment scenario and perform multiple ''what if'' evaluations. The TPM is being developed on personal computers using commercial off-the shelf (COTS) software tools under the WINDOWS reg-sign operating environment. Prototype development of the TPM has been completed

Mobile computing in the humanitarian assistance setting: an introduction and some first steps.

Science.gov (United States)

Selanikio, Joel D; Kemmer, Teresa M; Bovill, Maria; Geisler, Karen

2002-04-01

We developed a Palm operating system-based handheld computer system for admin istering nutrition questionnaires and used it to gather nutritional information among the Burmese refugees in the Mae La refugee camp on the Thai-Burma border Our experience demonstrated that such technology can be easily adapted for such an austere setting and used to great advantage. Further, the technology showed tremendous potential to reduce both time required and errors commonly encountered when field staff collect information in the humanitarian setting. We also identified several areas needing further development.

Parallel analysis tools and new visualization techniques for ultra-large climate data set

Energy Technology Data Exchange (ETDEWEB)

Middleton, Don [National Center for Atmospheric Research, Boulder, CO (United States); Haley, Mary [National Center for Atmospheric Research, Boulder, CO (United States)

2014-12-10

ParVis was a project funded under LAB 10-05: “Earth System Modeling: Advanced Scientific Visualization of Ultra-Large Climate Data Sets”. Argonne was the lead lab with partners at PNNL, SNL, NCAR and UC-Davis. This report covers progress from January 1st, 2013 through Dec 1st, 2014. Two previous reports covered the period from Summer, 2010, through September 2011 and October 2011 through December 2012, respectively. While the project was originally planned to end on April 30, 2013, personnel and priority changes allowed many of the institutions to continue work through FY14 using existing funds. A primary focus of ParVis was introducing parallelism to climate model analysis to greatly reduce the time-to-visualization for ultra-large climate data sets. Work in the first two years was conducted on two tracks with different time horizons: one track to provide immediate help to climate scientists already struggling to apply their analysis to existing large data sets and another focused on building a new data-parallel library and tool for climate analysis and visualization that will give the field a platform for performing analysis and visualization on ultra-large datasets for the foreseeable future. In the final 2 years of the project, we focused mostly on the new data-parallel library and associated tools for climate analysis and visualization.

Chimera Grid Tools

Science.gov (United States)

Chan, William M.; Rogers, Stuart E.; Nash, Steven M.; Buning, Pieter G.; Meakin, Robert

2005-01-01

Chimera Grid Tools (CGT) is a software package for performing computational fluid dynamics (CFD) analysis utilizing the Chimera-overset-grid method. For modeling flows with viscosity about geometrically complex bodies in relative motion, the Chimera-overset-grid method is among the most computationally cost-effective methods for obtaining accurate aerodynamic results. CGT contains a large collection of tools for generating overset grids, preparing inputs for computer programs that solve equations of flow on the grids, and post-processing of flow-solution data. The tools in CGT include grid editing tools, surface-grid-generation tools, volume-grid-generation tools, utility scripts, configuration scripts, and tools for post-processing (including generation of animated images of flows and calculating forces and moments exerted on affected bodies). One of the tools, denoted OVERGRID, is a graphical user interface (GUI) that serves to visualize the grids and flow solutions and provides central access to many other tools. The GUI facilitates the generation of grids for a new flow-field configuration. Scripts that follow the grid generation process can then be constructed to mostly automate grid generation for similar configurations. CGT is designed for use in conjunction with a computer-aided-design program that provides the geometry description of the bodies, and a flow-solver program.

Applications of automatic differentiation in computational fluid dynamics

Science.gov (United States)

Green, Lawrence L.; Carle, A.; Bischof, C.; Haigler, Kara J.; Newman, Perry A.

1994-01-01

Automatic differentiation (AD) is a powerful computational method that provides for computing exact sensitivity derivatives (SD) from existing computer programs for multidisciplinary design optimization (MDO) or in sensitivity analysis. A pre-compiler AD tool for FORTRAN programs called ADIFOR has been developed. The ADIFOR tool has been easily and quickly applied by NASA Langley researchers to assess the feasibility and computational impact of AD in MDO with several different FORTRAN programs. These include a state-of-the-art three dimensional multigrid Navier-Stokes flow solver for wings or aircraft configurations in transonic turbulent flow. With ADIFOR the user specifies sets of independent and dependent variables with an existing computer code. ADIFOR then traces the dependency path throughout the code, applies the chain rule to formulate derivative expressions, and generates new code to compute the required SD matrix. The resulting codes have been verified to compute exact non-geometric and geometric SD for a variety of cases. in less time than is required to compute the SD matrix using centered divided differences.

Computer Forensic Function Testing: Media Preparation, Write Protection And Verification

Directory of Open Access Journals (Sweden)

Yinghua (David Guo

2010-06-01

Full Text Available Normal 0 false false false EN-US JA AR-SA The growth in the computer forensic field has created a demand for new software (or increased functionality to existing software and a means to verify that this software is truly forensic i.e. capable of meeting the requirements of the trier of fact. In this work, we review our previous work---a function oriented testing framework for validation and verification of computer forensic tools. This framework consists of three parts: function mapping, requirements specification and reference set development. Through function mapping, we give a scientific and systemical description of the fundamentals of computer forensic discipline, i.e. what functions are needed in the computer forensic investigation process. We focus this paper on the functions of media preparation, write protection and verification. Specifically, we complete the function mapping of these functions and specify their requirements. Based on this work, future work can be conducted to develop corresponding reference sets to test any tools that possess these functions.

The Potential of Computer-Based Expert Systems for Special Educators in Rural Settings.

Science.gov (United States)

Parry, James D.; Ferrara, Joseph M.

Knowledge-based expert computer systems are addressing issues relevant to all special educators, but are particularly relevant in rural settings where human experts are less available because of distance and cost. An expert system is an application of artificial intelligence (AI) that typically engages the user in a dialogue resembling the…

Basic elements of computational statistics

CERN Document Server

Härdle, Wolfgang Karl; Okhrin, Yarema

2017-01-01

This textbook on computational statistics presents tools and concepts of univariate and multivariate statistical data analysis with a strong focus on applications and implementations in the statistical software R. It covers mathematical, statistical as well as programming problems in computational statistics and contains a wide variety of practical examples. In addition to the numerous R sniplets presented in the text, all computer programs (quantlets) and data sets to the book are available on GitHub and referred to in the book. This enables the reader to fully reproduce as well as modify and adjust all examples to their needs. The book is intended for advanced undergraduate and first-year graduate students as well as for data analysts new to the job who would like a tour of the various statistical tools in a data analysis workshop. The experienced reader with a good knowledge of statistics and programming might skip some sections on univariate models and enjoy the various mathematical roots of multivariate ...

Improved mathematical and computational tools for modeling photon propagation in tissue

Science.gov (United States)

Calabro, Katherine Weaver

Light interacts with biological tissue through two predominant mechanisms: scattering and absorption, which are sensitive to the size and density of cellular organelles, and to biochemical composition (ex. hemoglobin), respectively. During the progression of disease, tissues undergo a predictable set of changes in cell morphology and vascularization, which directly affect their scattering and absorption properties. Hence, quantification of these optical property differences can be used to identify the physiological biomarkers of disease with interest often focused on cancer. Diffuse reflectance spectroscopy is a diagnostic tool, wherein broadband visible light is transmitted through a fiber optic probe into a turbid medium, and after propagating through the sample, a fraction of the light is collected at the surface as reflectance. The measured reflectance spectrum can be analyzed with appropriate mathematical models to extract the optical properties of the tissue, and from these, a set of physiological properties. A number of models have been developed for this purpose using a variety of approaches -- from diffusion theory, to computational simulations, and empirical observations. However, these models are generally limited to narrow ranges of tissue and probe geometries. In this thesis, reflectance models were developed for a much wider range of measurement parameters, and influences such as the scattering phase function and probe design were investigated rigorously for the first time. The results provide a comprehensive understanding of the factors that influence reflectance, with novel insights that, in some cases, challenge current assumptions in the field. An improved Monte Carlo simulation program, designed to run on a graphics processing unit (GPU), was built to simulate the data used in the development of the reflectance models. Rigorous error analysis was performed to identify how inaccuracies in modeling assumptions can be expected to affect the accuracy

ATLAS Distributed Computing Monitoring tools during the LHC Run I

Science.gov (United States)

Schovancová, J.; Campana, S.; Di Girolamo, A.; Jézéquel, S.; Ueda, I.; Wenaus, T.; Atlas Collaboration

2014-06-01

This contribution summarizes evolution of the ATLAS Distributed Computing (ADC) Monitoring project during the LHC Run I. The ADC Monitoring targets at the three groups of customers: ADC Operations team to early identify malfunctions and escalate issues to an activity or a service expert, ATLAS national contacts and sites for the real-time monitoring and long-term measurement of the performance of the provided computing resources, and the ATLAS Management for long-term trends and accounting information about the ATLAS Distributed Computing resources. During the LHC Run I a significant development effort has been invested in standardization of the monitoring and accounting applications in order to provide extensive monitoring and accounting suite. ADC Monitoring applications separate the data layer and the visualization layer. The data layer exposes data in a predefined format. The visualization layer is designed bearing in mind visual identity of the provided graphical elements, and re-usability of the visualization bits across the different tools. A rich family of various filtering and searching options enhancing available user interfaces comes naturally with the data and visualization layer separation. With a variety of reliable monitoring data accessible through standardized interfaces, the possibility of automating actions under well defined conditions correlating multiple data sources has become feasible. In this contribution we discuss also about the automated exclusion of degraded resources and their automated recovery in various activities.

HEP Computing Tools, Grid and Supercomputers for Genome Sequencing Studies

Science.gov (United States)

De, K.; Klimentov, A.; Maeno, T.; Mashinistov, R.; Novikov, A.; Poyda, A.; Tertychnyy, I.; Wenaus, T.

2017-10-01

PanDA - Production and Distributed Analysis Workload Management System has been developed to address ATLAS experiment at LHC data processing and analysis challenges. Recently PanDA has been extended to run HEP scientific applications on Leadership Class Facilities and supercomputers. The success of the projects to use PanDA beyond HEP and Grid has drawn attention from other compute intensive sciences such as bioinformatics. Recent advances of Next Generation Genome Sequencing (NGS) technology led to increasing streams of sequencing data that need to be processed, analysed and made available for bioinformaticians worldwide. Analysis of genomes sequencing data using popular software pipeline PALEOMIX can take a month even running it on the powerful computer resource. In this paper we will describe the adaptation the PALEOMIX pipeline to run it on a distributed computing environment powered by PanDA. To run pipeline we split input files into chunks which are run separately on different nodes as separate inputs for PALEOMIX and finally merge output file, it is very similar to what it done by ATLAS to process and to simulate data. We dramatically decreased the total walltime because of jobs (re)submission automation and brokering within PanDA. Using software tools developed initially for HEP and Grid can reduce payload execution time for Mammoths DNA samples from weeks to days.

Conducting Creativity Brainstorming Sessions in Small and Medium-Sized Enterprises Using Computer-Mediated Communication Tools

Science.gov (United States)

Murthy, Uday S.

A variety of Web-based low cost computer-mediated communication (CMC) tools are now available for use by small and medium-sized enterprises (SME). These tools invariably incorporate chat systems that facilitate simultaneous input in synchronous electronic meeting environments, allowing what is referred to as “electronic brainstorming.” Although prior research in information systems (IS) has established that electronic brainstorming can be superior to face-to-face brainstorming, there is a lack of detailed guidance regarding how CMC tools should be optimally configured to foster creativity in SMEs. This paper discusses factors to be considered in using CMC tools for creativity brainstorming and proposes recommendations for optimally configuring CMC tools to enhance creativity in SMEs. The recommendations are based on lessons learned from several recent experimental studies on the use of CMC tools for rich brainstorming tasks that require participants to invoke domain-specific knowledge. Based on a consideration of the advantages and disadvantages of the various configuration options, the recommendations provided can form the basis for selecting a CMC tool for creativity brainstorming or for creating an in-house CMC tool for the purpose.

Phenomenology tools on cloud infrastructures using OpenStack

International Nuclear Information System (INIS)

Campos, I.; Fernandez-del-Castillo, E.; Heinemeyer, S.; Lopez-Garcia, A.; Pahlen, F.; Borges, G.

2013-01-01

We present a new environment for computations in particle physics phenomenology employing recent developments in cloud computing. On this environment users can create and manage ''virtual'' machines on which the phenomenology codes/tools can be deployed easily in an automated way. We analyze the performance of this environment based on ''virtual'' machines versus the utilization of physical hardware. In this way we provide a qualitative result for the influence of the host operating system on the performance of a representative set of applications for phenomenology calculations. (orig.)

Phenomenology tools on cloud infrastructures using OpenStack

Science.gov (United States)

Campos, I.; Fernández-del-Castillo, E.; Heinemeyer, S.; Lopez-Garcia, A.; Pahlen, F.; Borges, G.

2013-04-01

We present a new environment for computations in particle physics phenomenology employing recent developments in cloud computing. On this environment users can create and manage "virtual" machines on which the phenomenology codes/tools can be deployed easily in an automated way. We analyze the performance of this environment based on "virtual" machines versus the utilization of physical hardware. In this way we provide a qualitative result for the influence of the host operating system on the performance of a representative set of applications for phenomenology calculations.

Development of computer-aided software engineering tool for sequential control of JT-60U

International Nuclear Information System (INIS)

Shimono, M.; Akasaka, H.; Kurihara, K.; Kimura, T.

1995-01-01

Discharge sequential control (DSC) is an essential control function for the intermittent and pulse discharge operation of a tokamak device, so that many subsystems may work with each other in correct order and/or synchronously. In the development of the DSC program, block diagrams of logical operation for sequential control are illustrated in its design at first. Then, the logical operators and I/O's which are involved in the block diagrams are compiled and converted to a certain particular form. Since the block diagrams of the sequential control amounts to about 50 sheets in the case of the JT-60 upgrade tokamak (JT-60U) high power discharge and the above steps of the development have been performed manually so far, a great effort has been required for the program development. In order to remove inefficiency in such development processes, a computer-aided software engineering (CASE) tool has been developed on a UNIX workstation. This paper reports how the authors design it for the development of the sequential control programs. The tool is composed of the following three tools: (1) Automatic drawing tool, (2) Editing tool, and (3) Trace tool. This CASE tool, an object-oriented programming tool having graphical formalism, can powerfully accelerate the cycle for the development of the sequential control function commonly associated with pulse discharge in a tokamak fusion device

A stability tool for use within TELEGRIP

International Nuclear Information System (INIS)

Son, W.H.; Trinkle, J.C.

1998-12-01

During the assembly of a product, it is vital that the partially-completed assembly be stable. To guarantee this, one must ensure that contacts among the parts and the fixtures are sufficient to stabilize the assembly. Thus, it would be desirable to have an efficient method for testing an assembly stability, and, if this is not possible, generating a set of additional fixture contact points, known as fixels, that will stabilize it. One can apply this method to the situation of safe handling of special nuclear material (SNM). To have these functionalities should help improve the safety and enhance the performance of special nuclear material (SNM) handling and storage operations, since some methods are needed for gripping objects in a stable manner. Also, one may need a way to find a pit-holding fixture inserted into containers. In this paper, the authors present a stability tool, which they call Stab Tool, which was developed to test the stability of objects grasped by robotic hands, objects placed in fixtures, or sets of objects piled randomly on top of one another. Stab Tool runs on top of a commercial software package, TELEGRIP, which is used for geometry modeling and motion creation. The successful development of the stability depends strongly on TELEGRIP's ability to compute the distances between pairs of three-dimensional bodies in the simulated environment. The interbody distance computation tool takes advantage of the polyhedral representations of bodies used by TELEGRIP and of linear programming techniques to yield an efficient algorithm

Verification of Simulation Tools

International Nuclear Information System (INIS)

Richard, Thierry

2015-01-01

Before qualifying a simulation tool, the requirements shall first be clearly identified, i.e.: - What type of study needs to be carried out? - What phenomena need to be modeled? This phase involves writing a precise technical specification. Once the requirements are defined, the most adapted product shall be selected from the various software options available on the market. Before using a particular version of a simulation tool to support the demonstration of nuclear safety studies, the following requirements shall be met. - An auditable quality assurance process complying with development international standards shall be developed and maintained, - A process of verification and validation (V and V) shall be implemented. This approach requires: writing a report and/or executive summary of the V and V activities, defining a validated domain (domain in which the difference between the results of the tools and those of another qualified reference is considered satisfactory for its intended use). - Sufficient documentation shall be available, - A detailed and formal description of the product (software version number, user configuration, other settings and parameters) in the targeted computing environment shall be available. - Source codes corresponding to the software shall be archived appropriately. When these requirements are fulfilled, the version of the simulation tool shall be considered qualified for a defined domain of validity, in a given computing environment. The functional verification shall ensure that: - the computer architecture of the tool does not include errors, - the numerical solver correctly represents the physical mathematical model, - equations are solved correctly. The functional verification can be demonstrated through certification or report of Quality Assurance. The functional validation shall allow the user to ensure that the equations correctly represent the physical phenomena in the perimeter of intended use. The functional validation can

Using brain-computer interfaces and brain-state dependent stimulation as tools in cognitive neuroscience

NARCIS (Netherlands)

Jensen, O.; Bahramisharif, A.; Oostenveld, R.; Klanke, S.; Hadjipapas, A.; Okazaki, Y.O.; Gerven, M.A.J. van

2011-01-01

Large efforts are currently being made to develop and improve online analysis of brain activity which can be used, e.g., for brain-computer interfacing (BCI). A BCI allows a subject to control a device by willfully changing his/her own brain activity. BCI therefore holds the promise as a tool for

Using brain-computer interfaces and brain-state dependent stimulation as tools in cognitive neuroscience

NARCIS (Netherlands)

Jensen, O.; Bahramisharif, A.; Oostenveld, R.; Klanke, S.; Hadjipapas, A.; Okazaki, Y.O.; Gerven, M.A.J. van

2011-01-01

Large efforts are currently being made to develop and improve online analysis of brain activity which can be used, e.g., for brain–computer interfacing (BCI). A BCI allows a subject to control a device by willfully changing his/her own brain activity. BCI therefore holds the promise as a tool for

Computer simulation tools for X-ray analysis scattering and diffraction methods

CERN Document Server

Morelhão, Sérgio Luiz

2016-01-01

The main goal of this book is to break down the huge barrier of difficulties faced by beginners from many fields (Engineering, Physics, Chemistry, Biology, Medicine, Material Science, etc.) in using X-rays as an analytical tool in their research. Besides fundamental concepts, MatLab routines are provided, showing how to test and implement the concepts. The major difficult in analyzing materials by X-ray techniques is that it strongly depends on simulation software. This book teaches the users on how to construct a library of routines to simulate scattering and diffraction by almost any kind of samples. It provides to a young student the knowledge that would take more than 20 years to acquire by working on X-rays and relying on the available textbooks. In this book, fundamental concepts in applied X-ray physics are demonstrated through available computer simulation tools. Using MatLab, more than eighty routines are developed for solving the proposed exercises, most of which can be directly used in experimental...

A Computable Plug-In Estimator of Minimum Volume Sets for Novelty Detection

KAUST Repository

Park, Chiwoo; Huang, Jianhua Z.; Ding, Yu

2010-01-01

A minimum volume set of a probability density is a region of minimum size among the regions covering a given probability mass of the density. Effective methods for finding the minimum volume sets are very useful for detecting failures or anomalies in commercial and security applications-a problem known as novelty detection. One theoretical approach of estimating the minimum volume set is to use a density level set where a kernel density estimator is plugged into the optimization problem that yields the appropriate level. Such a plug-in estimator is not of practical use because solving the corresponding minimization problem is usually intractable. A modified plug-in estimator was proposed by Hyndman in 1996 to overcome the computation difficulty of the theoretical approach but is not well studied in the literature. In this paper, we provide theoretical support to this estimator by showing its asymptotic consistency. We also show that this estimator is very competitive to other existing novelty detection methods through an extensive empirical study. ©2010 INFORMS.

A Computable Plug-In Estimator of Minimum Volume Sets for Novelty Detection

KAUST Repository

Park, Chiwoo

2010-10-01

A minimum volume set of a probability density is a region of minimum size among the regions covering a given probability mass of the density. Effective methods for finding the minimum volume sets are very useful for detecting failures or anomalies in commercial and security applications-a problem known as novelty detection. One theoretical approach of estimating the minimum volume set is to use a density level set where a kernel density estimator is plugged into the optimization problem that yields the appropriate level. Such a plug-in estimator is not of practical use because solving the corresponding minimization problem is usually intractable. A modified plug-in estimator was proposed by Hyndman in 1996 to overcome the computation difficulty of the theoretical approach but is not well studied in the literature. In this paper, we provide theoretical support to this estimator by showing its asymptotic consistency. We also show that this estimator is very competitive to other existing novelty detection methods through an extensive empirical study. ©2010 INFORMS.

THE ISSUE OF FORMING FUTURE MUSIC TEACHERS’ PROFESSIONAL COMPETENCE BY COMPUTER TECHNOLOGY TOOLS IN THE THEORY OF NATIONAL ART

Directory of Open Access Journals (Sweden)

Lyudmila Gavrilova

2017-04-01

Full Text Available The article deals with theoretical aspects of forming future music teachers’ professional competence by computer technology tools. The concept of professional competence has become a major criterion of preparing students for professional activities. The issue of the article is relevant as the competence approach has become a basis of implementing computer technologies into future music teachers’ training. The authors give a detailed analysis of implementing computer technologies into musical education. The special attention is paid to using a computer in musical education and making electronic pedagogical resources. The aim of the article is to outline the directions of national art research in the process of implementing computer tools that is one of the most efficient ways of updating process of future music teachers’ training. The article reveals theoretical aspects of forming future music teachers’ professional competence by computer technology tools. The authors point out that implementing musical and computer technologies into music art practice is realized in some directions: using a computer as a new musical instrument in composers, sound engineers, and arrangers’ activities; using a computer for studying the quality of music sound, analysing sounds and music compositions, spectral analysis of acoustic characteristics of singers’ voice; studying ancient music manuscripts due to digital technology; developing hardware and software for music education. A distinct direction of research is the pedagogical aspect of using a computer in music education (music and the use of special software for recording and editing music, the use of multimedia to enhance visibility in education, development of e-learning resources, etc.. The authors conclude that implementing computer technologies into future music teachers’ training makes this process more efficient. In the authors’ opinion the widespread introduction of distance learning

A benchmarking tool to evaluate computer tomography perfusion infarct core predictions against a DWI standard.

Science.gov (United States)

Cereda, Carlo W; Christensen, Søren; Campbell, Bruce Cv; Mishra, Nishant K; Mlynash, Michael; Levi, Christopher; Straka, Matus; Wintermark, Max; Bammer, Roland; Albers, Gregory W; Parsons, Mark W; Lansberg, Maarten G

2016-10-01

Differences in research methodology have hampered the optimization of Computer Tomography Perfusion (CTP) for identification of the ischemic core. We aim to optimize CTP core identification using a novel benchmarking tool. The benchmarking tool consists of an imaging library and a statistical analysis algorithm to evaluate the performance of CTP. The tool was used to optimize and evaluate an in-house developed CTP-software algorithm. Imaging data of 103 acute stroke patients were included in the benchmarking tool. Median time from stroke onset to CT was 185 min (IQR 180-238), and the median time between completion of CT and start of MRI was 36 min (IQR 25-79). Volumetric accuracy of the CTP-ROIs was optimal at an rCBF threshold of benchmarking tool can play an important role in optimizing CTP software as it provides investigators with a novel method to directly compare the performance of alternative CTP software packages. © The Author(s) 2015.

Computational tools for the construction of calibration curves for use in dose calculations in radiotherapy treatment planning

International Nuclear Information System (INIS)

Oliveira, Alex C.H.; Vieira, Jose W.; Escola Politecnica de Pernambuco , Recife, PE

2011-01-01

The realization of tissue inhomogeneity corrections in image-based treatment planning improves the accuracy of radiation dose calculations for patients undergoing external-beam radiotherapy. Before the tissue inhomogeneity correction can be applied, the relationship between the computed tomography (CT) numbers and density must be established. This relationship is typically established by a calibration curve empirically obtained from CT images of a phantom that has several inserts of tissue-equivalent materials, covering a wide range of densities. This calibration curve is scanner-dependent and allows the conversion of CT numbers in densities for use in dose calculations. This paper describes the implementation of computational tools necessary to construct calibration curves. These tools are used for reading and displaying of CT images in DICOM format, determination of the mean CT numbers (and their standard deviations) of each tissue-equivalent material and construction of calibration curves by fits with bilinear equations. All these tools have been implemented in the Microsoft Visual Studio 2010 in C≠ programming language. (author)

Sustainable computational science

DEFF Research Database (Denmark)

Rougier, Nicolas; Hinsen, Konrad; Alexandre, Frédéric

2017-01-01

Computer science offers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results, however computational science lags behind. In the best case, authors may provide their source code as a compressed archive and they may feel confident their research...... workflows, in particular in peer-reviews. Existing journals have been slow to adapt: source codes are rarely requested, hardly ever actually executed to check that they produce the results advertised in the article. ReScience is a peer-reviewed journal that targets computational research and encourages...... the explicit replication of already published research, promoting new and open-source implementations in order to ensure that the original research can be replicated from its description. To achieve this goal, the whole publishing chain is radically different from other traditional scientific journals. ReScience...

Development of tools and models for computational fracture assessment

International Nuclear Information System (INIS)

Talja, H.; Santaoja, K.

1998-01-01

The aim of the work presented in this paper has been to develop and test new computational tools and theoretically more sound methods for fracture mechanical analysis. The applicability of the engineering integrity assessment system MASI for evaluation of piping components has been extended. The most important motivation for the theoretical development have been the well-known fundamental limitations in the validity of J-integral, which limits its applicability in many important practical safety assessment cases. Examples are extensive plastic deformation, multimaterial structures and ascending loading paths (especially warm prestress, WPS). Further, the micromechanical Gurson model has been applied to several reactor pressure vessel materials. Special attention is paid to the transferability of Gurson model parameters from tensile test results to prediction of ductile failure behaviour of cracked structures. (author)

Instruction of Statistics via Computer-Based Tools: Effects on Statistics' Anxiety, Attitude, and Achievement

Science.gov (United States)

Ciftci, S. Koza; Karadag, Engin; Akdal, Pinar

2014-01-01

The purpose of this study was to determine the effect of statistics instruction using computer-based tools, on statistics anxiety, attitude, and achievement. This study was designed as quasi-experimental research and the pattern used was a matched pre-test/post-test with control group design. Data was collected using three scales: a Statistics…

Predicting Pt-195 NMR chemical shift using new relativistic all-electron basis set

NARCIS (Netherlands)

Paschoal, D.; Fonseca Guerra, C.; de Oliveira, M.A.L.; Ramalho, T.C.; Dos Santos, H.F.

2016-01-01

Predicting NMR properties is a valuable tool to assist the experimentalists in the characterization of molecular structure. For heavy metals, such as Pt-195, only a few computational protocols are available. In the present contribution, all-electron Gaussian basis sets, suitable to calculate the

A remote sensing computer-assisted learning tool developed using the unified modeling language

Science.gov (United States)

Friedrich, J.; Karslioglu, M. O.

The goal of this work has been to create an easy-to-use and simple-to-make learning tool for remote sensing at an introductory level. Many students struggle to comprehend what seems to be a very basic knowledge of digital images, image processing and image arithmetic, for example. Because professional programs are generally too complex and overwhelming for beginners and often not tailored to the specific needs of a course regarding functionality, a computer-assisted learning (CAL) program was developed based on the unified modeling language (UML), the present standard for object-oriented (OO) system development. A major advantage of this approach is an easier transition from modeling to coding of such an application, if modern UML tools are being used. After introducing the constructed UML model, its implementation is briefly described followed by a series of learning exercises. They illustrate how the resulting CAL tool supports students taking an introductory course in remote sensing at the author's institution.

FunGeneNet: a web tool to estimate enrichment of functional interactions in experimental gene sets.

Science.gov (United States)

Tiys, Evgeny S; Ivanisenko, Timofey V; Demenkov, Pavel S; Ivanisenko, Vladimir A

2018-02-09

Estimation of functional connectivity in gene sets derived from genome-wide or other biological experiments is one of the essential tasks of bioinformatics. A promising approach for solving this problem is to compare gene networks built using experimental gene sets with random networks. One of the resources that make such an analysis possible is CrossTalkZ, which uses the FunCoup database. However, existing methods, including CrossTalkZ, do not take into account individual types of interactions, such as protein/protein interactions, expression regulation, transport regulation, catalytic reactions, etc., but rather work with generalized types characterizing the existence of any connection between network members. We developed the online tool FunGeneNet, which utilizes the ANDSystem and STRING to reconstruct gene networks using experimental gene sets and to estimate their difference from random networks. To compare the reconstructed networks with random ones, the node permutation algorithm implemented in CrossTalkZ was taken as a basis. To study the FunGeneNet applicability, the functional connectivity analysis of networks constructed for gene sets involved in the Gene Ontology biological processes was conducted. We showed that the method sensitivity exceeds 0.8 at a specificity of 0.95. We found that the significance level of the difference between gene networks of biological processes and random networks is determined by the type of connections considered between objects. At the same time, the highest reliability is achieved for the generalized form of connections that takes into account all the individual types of connections. By taking examples of the thyroid cancer networks and the apoptosis network, it is demonstrated that key participants in these processes are involved in the interactions of those types by which these networks differ from random ones. FunGeneNet is a web tool aimed at proving the functionality of networks in a wide range of sizes of

GSAC - Generic Seismic Application Computing

Science.gov (United States)

Herrmann, R. B.; Ammon, C. J.; Koper, K. D.

2004-12-01

With the success of the IRIS data management center, the use of large data sets in seismological research has become common. Such data sets, and especially the significantly larger data sets expected from EarthScope, present challenges for analysis with existing tools developed over the last 30 years. For much of the community, the primary format for data analysis is the Seismic Analysis Code (SAC) format developed by Lawrence Livermore National Laboratory. Although somewhat restrictive in meta-data storage, the simplicity and stability of the format has established it as an important component of seismological research. Tools for working with SAC files fall into two categories - custom research quality processing codes and shared display - processing tools such as SAC2000, MatSeis,etc., which were developed primarily for the needs of individual seismic research groups. While the current graphics display and platform dependence of SAC2000 may be resolved if the source code is released, the code complexity and the lack of large-data set analysis or even introductory tutorials could preclude code improvements and development of expertise in its use. We believe that there is a place for new, especially open source, tools. The GSAC effort is an approach that focuses on ease of use, computational speed, transportability, rapid addition of new features and openness so that new and advanced students, researchers and instructors can quickly browse and process large data sets. We highlight several approaches toward data processing under this model. gsac - part of the Computer Programs in Seismology 3.30 distribution has much of the functionality of SAC2000 and works on UNIX/LINUX/MacOS-X/Windows (CYGWIN). This is completely programmed in C from scratch, is small, fast, and easy to maintain and extend. It is command line based and is easily included within shell processing scripts. PySAC is a set of Python functions that allow easy access to SAC files and enable efficient

A least-squares computational ``tool kit``. Nuclear data and measurements series

Energy Technology Data Exchange (ETDEWEB)

Smith, D.L.

1993-04-01

The information assembled in this report is intended to offer a useful computational ``tool kit`` to individuals who are interested in a variety of practical applications for the least-squares method of parameter estimation. The fundamental principles of Bayesian analysis are outlined first and these are applied to development of both the simple and the generalized least-squares conditions. Formal solutions that satisfy these conditions are given subsequently. Their application to both linear and non-linear problems is described in detail. Numerical procedures required to implement these formal solutions are discussed and two utility computer algorithms are offered for this purpose (codes LSIOD and GLSIOD written in FORTRAN). Some simple, easily understood examples are included to illustrate the use of these algorithms. Several related topics are then addressed, including the generation of covariance matrices, the role of iteration in applications of least-squares procedures, the effects of numerical precision and an approach that can be pursued in developing data analysis packages that are directed toward special applications.

A COMPUTATIONAL FRAMEWORK INVOLVING CFD AND DATA MINING TOOLS FOR ANALYZING DISEASE IN CAROTID ARTERY BIFURCATION

OpenAIRE

Tabib, Mandar; Rasheed, Adil; Fonn, Eivind

2017-01-01

Cardiovascular diseases, like Carotid Artery Disease and Coronary Artery Disease (CAD) are associated with the narrowing of artery due to build-up of fatty substances and cholesterol deposits (called plaque). Carotid Artery Disease increases the chances of brain stroke. Hence, the main objective of this work is to apply computational tools to help differentiate between the healthy and unhealthy artery (with 25% stenosis) using a combination of Computational Fluid Dynamics (CFD) and data minin...

Covariance Analysis Tool (G-CAT) for Computing Ascent, Descent, and Landing Errors

Science.gov (United States)

Boussalis, Dhemetrios; Bayard, David S.

2013-01-01

G-CAT is a covariance analysis tool that enables fast and accurate computation of error ellipses for descent, landing, ascent, and rendezvous scenarios, and quantifies knowledge error contributions needed for error budgeting purposes. Because GCAT supports hardware/system trade studies in spacecraft and mission design, it is useful in both early and late mission/ proposal phases where Monte Carlo simulation capability is not mature, Monte Carlo simulation takes too long to run, and/or there is a need to perform multiple parametric system design trades that would require an unwieldy number of Monte Carlo runs. G-CAT is formulated as a variable-order square-root linearized Kalman filter (LKF), typically using over 120 filter states. An important property of G-CAT is that it is based on a 6-DOF (degrees of freedom) formulation that completely captures the combined effects of both attitude and translation errors on the propagated trajectories. This ensures its accuracy for guidance, navigation, and control (GN&C) analysis. G-CAT provides the desired fast turnaround analysis needed for error budgeting in support of mission concept formulations, design trade studies, and proposal development efforts. The main usefulness of a covariance analysis tool such as G-CAT is its ability to calculate the performance envelope directly from a single run. This is in sharp contrast to running thousands of simulations to obtain similar information using Monte Carlo methods. It does this by propagating the "statistics" of the overall design, rather than simulating individual trajectories. G-CAT supports applications to lunar, planetary, and small body missions. It characterizes onboard knowledge propagation errors associated with inertial measurement unit (IMU) errors (gyro and accelerometer), gravity errors/dispersions (spherical harmonics, masscons), and radar errors (multiple altimeter beams, multiple Doppler velocimeter beams). G-CAT is a standalone MATLAB- based tool intended to

Phenomenology tools on cloud infrastructures using OpenStack

Energy Technology Data Exchange (ETDEWEB)

Campos, I.; Fernandez-del-Castillo, E.; Heinemeyer, S.; Lopez-Garcia, A. [Instituto de Fisica de Cantabria (CSIC-UC), Santander (Spain); Pahlen, F. [Instituto de Fisica de Cantabria (CSIC-UC), Santander (Spain); University of Zaragoza, Instituto de Biocomputacion y Fisica de Sistemas Complejos - BIFI, Zaragoza (Spain); Borges, G. [Laboratorio de Instrumentacao e Fisica Experimental de Particulas - LIP, Lisbon (Portugal)

2013-04-15

We present a new environment for computations in particle physics phenomenology employing recent developments in cloud computing. On this environment users can create and manage ''virtual'' machines on which the phenomenology codes/tools can be deployed easily in an automated way. We analyze the performance of this environment based on ''virtual'' machines versus the utilization of physical hardware. In this way we provide a qualitative result for the influence of the host operating system on the performance of a representative set of applications for phenomenology calculations. (orig.)

A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics.

Science.gov (United States)

Purawat, Shweta; Ieong, Pek U; Malmstrom, Robert D; Chan, Garrett J; Yeung, Alan K; Walker, Ross C; Altintas, Ilkay; Amaro, Rommie E

2017-06-20

With the drive toward high throughput molecular dynamics (MD) simulations involving ever-greater numbers of simulation replicates run for longer, biologically relevant timescales (microseconds), the need for improved computational methods that facilitate fully automated MD workflows gains more importance. Here we report the development of an automated workflow tool to perform AMBER GPU MD simulations. Our workflow tool capitalizes on the capabilities of the Kepler platform to deliver a flexible, intuitive, and user-friendly environment and the AMBER GPU code for a robust and high-performance simulation engine. Additionally, the workflow tool reduces user input time by automating repetitive processes and facilitates access to GPU clusters, whose high-performance processing power makes simulations of large numerical scale possible. The presented workflow tool facilitates the management and deployment of large sets of MD simulations on heterogeneous computing resources. The workflow tool also performs systematic analysis on the simulation outputs and enhances simulation reproducibility, execution scalability, and MD method development including benchmarking and validation. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Sampling and sensitivity analyses tools (SaSAT for computational modelling

Directory of Open Access Journals (Sweden)

Wilson David P

2008-02-01

Full Text Available Abstract SaSAT (Sampling and Sensitivity Analysis Tools is a user-friendly software package for applying uncertainty and sensitivity analyses to mathematical and computational models of arbitrary complexity and context. The toolbox is built in Matlab®, a numerical mathematical software package, and utilises algorithms contained in the Matlab® Statistics Toolbox. However, Matlab® is not required to use SaSAT as the software package is provided as an executable file with all the necessary supplementary files. The SaSAT package is also designed to work seamlessly with Microsoft Excel but no functionality is forfeited if that software is not available. A comprehensive suite of tools is provided to enable the following tasks to be easily performed: efficient and equitable sampling of parameter space by various methodologies; calculation of correlation coefficients; regression analysis; factor prioritisation; and graphical output of results, including response surfaces, tornado plots, and scatterplots. Use of SaSAT is exemplified by application to a simple epidemic model. To our knowledge, a number of the methods available in SaSAT for performing sensitivity analyses have not previously been used in epidemiological modelling and their usefulness in this context is demonstrated.

Constructing Bridges between Computational Tools in Heterogeneous and Homogeneous Catalysis

KAUST Repository

Falivene, Laura; Kozlov, Sergey M.; Cavallo, Luigi

2018-01-01

Better catalysts are needed to address numerous challenges faced by humanity. In this perspective, we review concepts and tools in theoretical and computational chemistry that can help to accelerate the rational design of homogeneous and heterogeneous catalysts. In particular, we focus on the following three topics: 1) identification of key intermediates and transition states in a reaction using the energetic span model, 2) disentanglement of factors influencing the relative stability of the key species using energy decomposition analysis and the activation strain model, and 3) discovery of new catalysts using volcano relationships. To facilitate wider use of these techniques across different areas, we illustrate their potentials and pitfalls when applied to the study of homogeneous and heterogeneous catalysts.

Constructing Bridges between Computational Tools in Heterogeneous and Homogeneous Catalysis

KAUST Repository

Falivene, Laura

2018-05-08

Better catalysts are needed to address numerous challenges faced by humanity. In this perspective, we review concepts and tools in theoretical and computational chemistry that can help to accelerate the rational design of homogeneous and heterogeneous catalysts. In particular, we focus on the following three topics: 1) identification of key intermediates and transition states in a reaction using the energetic span model, 2) disentanglement of factors influencing the relative stability of the key species using energy decomposition analysis and the activation strain model, and 3) discovery of new catalysts using volcano relationships. To facilitate wider use of these techniques across different areas, we illustrate their potentials and pitfalls when applied to the study of homogeneous and heterogeneous catalysts.

APERO, AN OPEN SOURCE BUNDLE ADJUSMENT SOFTWARE FOR AUTOMATIC CALIBRATION AND ORIENTATION OF SET OF IMAGES

Directory of Open Access Journals (Sweden)

M. Pierrot Deseilligny

2012-09-01

Full Text Available IGN has developed a set of photogrammetric tools, APERO and MICMAC, for computing 3D models from set of images. This software, developed initially for its internal needs are now delivered as open source code. This paper focuses on the presentation of APERO the orientation software. Compared to some other free software initiatives, it is probably more complex but also more complete, its targeted user is rather professionals (architects, archaeologist, geomophologist than people. APERO uses both computer vision approach for estimation of initial solution and photogrammetry for a rigorous compensation of the total error; it has a large library of parametric model of distortion allowing a precise modelization of all the kind of pinhole camera we know, including several model of fish-eye; there is also several tools for geo-referencing the result. The results are illustrated on various application, including the data-set of 3D-Arch workshop.

Fast Computation of Categorical Richness on Raster Data Sets and Related Problems

DEFF Research Database (Denmark)

de Berg, Mark; Tsirogiannis, Constantinos; Wilkinson, Bryan

2015-01-01

that runs in O(n) time and one for circular windows that runs in O((1+K/r)n) time, where K is the number of different categories appearing in G. The algorithms are not only very efficient in theory, but also in practice: our experiments show that our algorithms can handle raster data sets of hundreds...... of millions of cells. The categorical richness problem is related to colored range counting, where the goal is to preprocess a colored point set such that we can efficiently count the number of colors appearing inside a query range. We present a data structure for colored range counting in R^2 for the case......In many scientific fields, it is common to encounter raster data sets consisting of categorical data, such as soil type or land usage of a terrain. A problem that arises in the presence of such data is the following: given a raster G of n cells storing categorical data, compute for every cell c...

Simulation tools for scattering corrections in spectrally resolved x-ray computed tomography using McXtrace

Science.gov (United States)

Busi, Matteo; Olsen, Ulrik L.; Knudsen, Erik B.; Frisvad, Jeppe R.; Kehres, Jan; Dreier, Erik S.; Khalil, Mohamad; Haldrup, Kristoffer

2018-03-01

Spectral computed tomography is an emerging imaging method that involves using recently developed energy discriminating photon-counting detectors (PCDs). This technique enables measurements at isolated high-energy ranges, in which the dominating undergoing interaction between the x-ray and the sample is the incoherent scattering. The scattered radiation causes a loss of contrast in the results, and its correction has proven to be a complex problem, due to its dependence on energy, material composition, and geometry. Monte Carlo simulations can utilize a physical model to estimate the scattering contribution to the signal, at the cost of high computational time. We present a fast Monte Carlo simulation tool, based on McXtrace, to predict the energy resolved radiation being scattered and absorbed by objects of complex shapes. We validate the tool through measurements using a CdTe single PCD (Multix ME-100) and use it for scattering correction in a simulation of a spectral CT. We found the correction to account for up to 7% relative amplification in the reconstructed linear attenuation. It is a useful tool for x-ray CT to obtain a more accurate material discrimination, especially in the high-energy range, where the incoherent scattering interactions become prevailing (>50 keV).

Computational fluid dynamics simulation of indoor climate in low energy buildings: Computational set up

Directory of Open Access Journals (Sweden)

Risberg Daniel

2017-01-01

Full Text Available In this paper CFD was used for simulation of the indoor climate in a part of a low energy building. The focus of the work was on investigating the computational set up, such as grid size and boundary conditions in order to solve the indoor climate problems in an accurate way. Future work is to model a complete building, with reasonable calculation time and accuracy. A limited number of grid elements and knowledge of boundary settings are therefore essential. An accurate grid edge size of around 0.1 m was enough to predict the climate according to a grid independency study. Different turbulence models were compared with only small differences in the indoor air velocities and temperatures. The models show that radiation between building surfaces has a large impact on the temperature field inside the building, with the largest differences at the floor level. Simplifying the simulations by modelling the radiator as a surface in the outer wall of the room is appropriate for the calculations. The overall indoor climate is finally compared between three different cases for the outdoor air temperature. The results show a good indoor climate for a low energy building all around the year.

Computer Assessed Design – A Vehicle of Architectural Communication and a Design Tool

OpenAIRE

Petrovici, Liliana-Mihaela

2012-01-01

In comparison with the limits of the traditional representation tools, the development of the computer graphics constitutes an opportunity to assert architectural values. The differences between communication codes of the architects and public are diminished; the architectural ideas can be represented in a coherent, intelligible and attractive way, so that they get more chances to be materialized according to the thinking of the creator. Concurrently, the graphic software have been improving ...

Application of Bipolar Fuzzy Sets in Graph Structures

Directory of Open Access Journals (Sweden)

Muhammad Akram

2016-01-01

Full Text Available A graph structure is a useful tool in solving the combinatorial problems in different areas of computer science and computational intelligence systems. In this paper, we apply the concept of bipolar fuzzy sets to graph structures. We introduce certain notions, including bipolar fuzzy graph structure (BFGS, strong bipolar fuzzy graph structure, bipolar fuzzy Ni-cycle, bipolar fuzzy Ni-tree, bipolar fuzzy Ni-cut vertex, and bipolar fuzzy Ni-bridge, and illustrate these notions by several examples. We study ϕ-complement, self-complement, strong self-complement, and totally strong self-complement in bipolar fuzzy graph structures, and we investigate some of their interesting properties.

Dead time of dual detector tools

International Nuclear Information System (INIS)

Czubek, J.A.

1994-01-01

A theory of the dead time for the dual detector nuclear tool with the analogue signal transmission is given in the paper. At least two different times exist in such tools: the dead time of detectors (for final computation they assumed identical to each other) and the dead time of the signal transmission set-up. A method of two radioactive sources is proposed to measure these two different dead times. When the times used for measuring every countrate needed in the dead time determination algorithm are taken into account, the statistical accuracy of the dead time determination can be obtained. These estimations are performed by the computer simulation method. Two codes have been designed: DEADT2D (DEAD Time for 2 Detectors) and DEADT2DS (DEAD Time for 2 Detectors with Statistics). The first code calculates the dead time based on the recorded countrates only, the second is doing a 'simulation job' and provides information on the statistical distribution of the observed dead times. The theory and the numerical solutions were checked both by the simulation calculations and by the experiments performed with the ODSN-102 tool (the experiments were performed by T. Zorski). (Author)

Toward a VPH/Physiome ToolKit.

Science.gov (United States)

Garny, Alan; Cooper, Jonathan; Hunter, Peter J

2010-01-01

The Physiome Project was officially launched in 1997 and has since brought together teams from around the world to work on the development of a computational framework for the modeling of the human body. At the European level, this effort is focused around patient-specific solutions and is known as the Virtual Physiological Human (VPH) Initiative.Such modeling is both multiscale (in space and time) and multiphysics. This, therefore, requires careful interaction and collaboration between the teams involved in the VPH/Physiome effort, if we are to produce computer models that are not only quantitative, but also integrative and predictive.In that context, several technologies and solutions are already available, developed both by groups involved in the VPH/Physiome effort, and by others. They address areas such as data handling/fusion, markup languages, model repositories, ontologies, tools (for simulation, imaging, data fitting, etc.), as well as grid, middleware, and workflow.Here, we provide an overview of resources that should be considered for inclusion in the VPH/Physiome ToolKit (i.e., the set of tools that addresses the needs and requirements of the Physiome Project and VPH Initiative) and discuss some of the challenges that we are still facing.

High-resolution computational algorithms for simulating offshore wind turbines and farms: Model development and validation

Energy Technology Data Exchange (ETDEWEB)

Calderer, Antoni [Univ. of Minnesota, Minneapolis, MN (United States); Yang, Xiaolei [Stony Brook Univ., NY (United States); Angelidis, Dionysios [Univ. of Minnesota, Minneapolis, MN (United States); Feist, Chris [Univ. of Minnesota, Minneapolis, MN (United States); Guala, Michele [Univ. of Minnesota, Minneapolis, MN (United States); Ruehl, Kelley [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Guo, Xin [Univ. of Minnesota, Minneapolis, MN (United States); Boomsma, Aaron [Univ. of Minnesota, Minneapolis, MN (United States); Shen, Lian [Univ. of Minnesota, Minneapolis, MN (United States); Sotiropoulos, Fotis [Stony Brook Univ., NY (United States)

2015-10-30

The present project involves the development of modeling and analysis design tools for assessing offshore wind turbine technologies. The computational tools developed herein are able to resolve the effects of the coupled interaction of atmospheric turbulence and ocean waves on aerodynamic performance and structural stability and reliability of offshore wind turbines and farms. Laboratory scale experiments have been carried out to derive data sets for validating the computational models.

Quality assurance tool for organ at risk delineation in radiation therapy using a parametric statistical approach.

Science.gov (United States)

Hui, Cheukkai B; Nourzadeh, Hamidreza; Watkins, William T; Trifiletti, Daniel M; Alonso, Clayton E; Dutta, Sunil W; Siebers, Jeffrey V

2018-02-26

To develop a quality assurance (QA) tool that identifies inaccurate organ at risk (OAR) delineations. The QA tool computed volumetric features from prior OAR delineation data from 73 thoracic patients to construct a reference database. All volumetric features of the OAR delineation are computed in three-dimensional space. Volumetric features of a new OAR are compared with respect to those in the reference database to discern delineation outliers. A multicriteria outlier detection system warns users of specific delineation outliers based on combinations of deviant features. Fifteen independent experimental sets including automatic, propagated, and clinically approved manual delineation sets were used for verification. The verification OARs included manipulations to mimic common errors. Three experts reviewed the experimental sets to identify and classify errors, first without; and then 1 week after with the QA tool. In the cohort of manual delineations with manual manipulations, the QA tool detected 94% of the mimicked errors. Overall, it detected 37% of the minor and 85% of the major errors. The QA tool improved reviewer error detection sensitivity from 61% to 68% for minor errors (P = 0.17), and from 78% to 87% for major errors (P = 0.02). The QA tool assists users to detect potential delineation errors. QA tool integration into clinical procedures may reduce the frequency of inaccurate OAR delineation, and potentially improve safety and quality of radiation treatment planning. © 2018 American Association of Physicists in Medicine.

Causal Set Generator and Action Computer

OpenAIRE

Cunningham, William; Krioukov, Dmitri

2017-01-01

The causal set approach to quantum gravity has gained traction over the past three decades, but numerical experiments involving causal sets have been limited to relatively small scales. The software suite presented here provides a new framework for the generation and study of causal sets. Its efficiency surpasses previous implementations by several orders of magnitude. We highlight several important features of the code, including the compact data structures, the $O(N^2)$ causal set generatio...

Integrated Berth Allocation and Quay Crane Assignment Problem: Set partitioning models and computational results

DEFF Research Database (Denmark)

Iris, Cagatay; Pacino, Dario; Røpke, Stefan

2015-01-01

Most of the operational problems in container terminals are strongly interconnected. In this paper, we study the integrated Berth Allocation and Quay Crane Assignment Problem in seaport container terminals. We will extend the current state-of-the-art by proposing novel set partitioning models....... To improve the performance of the set partitioning formulations, a number of variable reduction techniques are proposed. Furthermore, we analyze the effects of different discretization schemes and the impact of using a time-variant/invariant quay crane allocation policy. Computational experiments show...

TRAC, a collaborative computer tool for tracer-test interpretation

Directory of Open Access Journals (Sweden)

Fécamp C.

2013-05-01

Full Text Available Artificial tracer tests are widely used by consulting engineers for demonstrating water circulation, proving the existence of leakage, or estimating groundwater velocity. However, the interpretation of such tests is often very basic, with the result that decision makers and professionals commonly face unreliable results through hasty and empirical interpretation. There is thus an increasing need for a reliable interpretation tool, compatible with the latest operating systems and available in several languages. BRGM, the French Geological Survey, has developed a project together with hydrogeologists from various other organizations to build software assembling several analytical solutions in order to comply with various field contexts. This computer program, called TRAC, is very light and simple, allowing the user to add his own analytical solution if the formula is not yet included. It aims at collaborative improvement by sharing the tool and the solutions. TRAC can be used for interpreting data recovered from a tracer test as well as for simulating the transport of a tracer in the saturated zone (for the time being. Calibration of a site operation is based on considering the hydrodynamic and hydrodispersive features of groundwater flow as well as the amount, nature and injection mode of the artificial tracer. The software is available in French, English and Spanish, and the latest version can be downloaded from the web site http://trac.brgm.fr.

Servicing HEP experiments with a complete set of ready integreated and configured common software components

International Nuclear Information System (INIS)

Roiser, Stefan; Gaspar, Ana; Perrin, Yves; Kruzelecki, Karol

2010-01-01

The LCG Applications Area at CERN provides basic software components for the LHC experiments such as ROOT, POOL, COOL which are developed in house and also a set of 'external' software packages (70) which are needed in addition such as Python, Boost, Qt, CLHEP, etc. These packages target many different areas of HEP computing such as data persistency, math, simulation, grid computing, databases, graphics, etc. Other packages provide tools for documentation, debugging, scripting languages and compilers. All these packages are provided in a consistent manner on different compilers, architectures and operating systems. The Software Process and Infrastructure project (SPI) [1] is responsible for the continous testing, coordination, release and deployment of these software packages. The main driving force for the actions carried out by SPI are the needs of the LHC experiments, but also other HEP experiments could profit from the set of consistent libraries provided and receive a stable and well tested foundation to build their experiment software frameworks. This presentation will first provide a brief description of the tools and services provided for the coordination, testing, release, deployment and presentation of LCG/AA software packages and then focus on a second set of tools provided for outside LHC experiments to deploy a stable set of HEP related software packages both as binary distribution or from source.

Servicing HEP experiments with a complete set of ready integreated and configured common software components

Energy Technology Data Exchange (ETDEWEB)

Roiser, Stefan; Gaspar, Ana; Perrin, Yves [CERN, CH-1211 Geneva 23, PH Department, SFT Group (Switzerland); Kruzelecki, Karol, E-mail: stefan.roiser@cern.c, E-mail: ana.gaspar@cern.c, E-mail: yves.perrin@cern.c, E-mail: karol.kruzelecki@cern.c [CERN, CH-1211 Geneva 23, PH Department, LBC Group (Switzerland)

2010-04-01

The LCG Applications Area at CERN provides basic software components for the LHC experiments such as ROOT, POOL, COOL which are developed in house and also a set of 'external' software packages (70) which are needed in addition such as Python, Boost, Qt, CLHEP, etc. These packages target many different areas of HEP computing such as data persistency, math, simulation, grid computing, databases, graphics, etc. Other packages provide tools for documentation, debugging, scripting languages and compilers. All these packages are provided in a consistent manner on different compilers, architectures and operating systems. The Software Process and Infrastructure project (SPI) [1] is responsible for the continous testing, coordination, release and deployment of these software packages. The main driving force for the actions carried out by SPI are the needs of the LHC experiments, but also other HEP experiments could profit from the set of consistent libraries provided and receive a stable and well tested foundation to build their experiment software frameworks. This presentation will first provide a brief description of the tools and services provided for the coordination, testing, release, deployment and presentation of LCG/AA software packages and then focus on a second set of tools provided for outside LHC experiments to deploy a stable set of HEP related software packages both as binary distribution or from source.

DDT: A Research Tool for Automatic Data Distribution in High Performance Fortran

Directory of Open Access Journals (Sweden)

Eduard AyguadÉ

1997-01-01

Full Text Available This article describes the main features and implementation of our automatic data distribution research tool. The tool (DDT accepts programs written in Fortran 77 and generates High Performance Fortran (HPF directives to map arrays onto the memories of the processors and parallelize loops, and executable statements to remap these arrays. DDT works by identifying a set of computational phases (procedures and loops. The algorithm builds a search space of candidate solutions for these phases which is explored looking for the combination that minimizes the overall cost; this cost includes data movement cost and computation cost. The movement cost reflects the cost of accessing remote data during the execution of a phase and the remapping costs that have to be paid in order to execute the phase with the selected mapping. The computation cost includes the cost of executing a phase in parallel according to the selected mapping and the owner computes rule. The tool supports interprocedural analysis and uses control flow information to identify how phases are sequenced during the execution of the application.

Porting of Bio-Informatics Tools for Plant Virology on a Computational Grid

International Nuclear Information System (INIS)

Lanzalone, G.; Lombardo, A.; Muoio, A.; Iacono-Manno, M.

2007-01-01

The goal of Tri Grid Project and PI2S2 is the creation of the first Sicilian regional computational Grid. In particular, it aims to build various software-hardware interfaces between the infrastructure and some scientific and industrial applications. In this context, we have integrated some among the most innovative computing applications in virology research inside these Grid infrastructure. Particularly, we have implemented in a complete work flow, various tools for pairwise or multiple sequence alignment and phylogeny tree construction (ClustalW-MPI), phylogenetic networks (Splits Tree), detection of recombination by phylogenetic methods (TOPALi) and prediction of DNA or RNA secondary consensus structures (KnetFold). This work will show how the ported applications decrease the execution time of the analysis programs, improve the accessibility to the data storage system and allow the use of metadata for data processing. (Author)

Computer-aided diagnosis of lung cancer: the effect of training data sets on classification accuracy of lung nodules

Science.gov (United States)

Gong, Jing; Liu, Ji-Yu; Sun, Xi-Wen; Zheng, Bin; Nie, Sheng-Dong

2018-02-01

This study aims to develop a computer-aided diagnosis (CADx) scheme for classification between malignant and benign lung nodules, and also assess whether CADx performance changes in detecting nodules associated with early and advanced stage lung cancer. The study involves 243 biopsy-confirmed pulmonary nodules. Among them, 76 are benign, 81 are stage I and 86 are stage III malignant nodules. The cases are separated into three data sets involving: (1) all nodules, (2) benign and stage I malignant nodules, and (3) benign and stage III malignant nodules. A CADx scheme is applied to segment lung nodules depicted on computed tomography images and we initially computed 66 3D image features. Then, three machine learning models namely, a support vector machine, naïve Bayes classifier and linear discriminant analysis, are separately trained and tested by using three data sets and a leave-one-case-out cross-validation method embedded with a Relief-F feature selection algorithm. When separately using three data sets to train and test three classifiers, the average areas under receiver operating characteristic curves (AUC) are 0.94, 0.90 and 0.99, respectively. When using the classifiers trained using data sets with all nodules, average AUC values are 0.88 and 0.99 for detecting early and advanced stage nodules, respectively. AUC values computed from three classifiers trained using the same data set are consistent without statistically significant difference (p  >  0.05). This study demonstrates (1) the feasibility of applying a CADx scheme to accurately distinguish between benign and malignant lung nodules, and (2) a positive trend between CADx performance and cancer progression stage. Thus, in order to increase CADx performance in detecting subtle and early cancer, training data sets should include more diverse early stage cancer cases.

Ratsnake: A Versatile Image Annotation Tool with Application to Computer-Aided Diagnosis

Directory of Open Access Journals (Sweden)

D. K. Iakovidis

2014-01-01

Full Text Available Image segmentation and annotation are key components of image-based medical computer-aided diagnosis (CAD systems. In this paper we present Ratsnake, a publicly available generic image annotation tool providing annotation efficiency, semantic awareness, versatility, and extensibility, features that can be exploited to transform it into an effective CAD system. In order to demonstrate this unique capability, we present its novel application for the evaluation and quantification of salient objects and structures of interest in kidney biopsy images. Accurate annotation identifying and quantifying such structures in microscopy images can provide an estimation of pathogenesis in obstructive nephropathy, which is a rather common disease with severe implication in children and infants. However a tool for detecting and quantifying the disease is not yet available. A machine learning-based approach, which utilizes prior domain knowledge and textural image features, is considered for the generation of an image force field customizing the presented tool for automatic evaluation of kidney biopsy images. The experimental evaluation of the proposed application of Ratsnake demonstrates its efficiency and effectiveness and promises its wide applicability across a variety of medical imaging domains.

MVPACK: a computer-aided design tool for multivariable control systems

International Nuclear Information System (INIS)

Mensah, S.; Frketich, G.

1985-10-01

The design and analysis of high-performance controllers for complex plants require a collection of interactive, powerful computer software. MVPACK, an open-ended package for the computer-aided design of control systems, has been developed in the Reactor Control Branch of the Chalk River Nuclear Laboratories. The package is fully interactive and includes a comprehensive state-of-the-art mathematical library to support development of complex, multivariable, control algorithms. Coded in RATFOR, MVPACK is portable with minimal changes. It operates with a flexible data structure which makes efficient use of minicomputer resources and provides a standard framework for program generation. The existence of a help mechanism enhances the simplicity of package utilization. This paper provides a brief tutorial overview of the package. It reviews the specifications used in the design and implementation of the package and briefly describes the database structure, supporting libraries and some design and analysis modules of MVPACK. Several application examples to illustrate the capability of the package are given. Experience with MVPACK shows that the package provides a synergistic environment for the design of control and regulation systems, and that it is a unique tool for training of control system engineers

Computer-aided engineering system for design of sequence arrays and lithographic masks

Science.gov (United States)

Hubbell, Earl A.; Morris, MacDonald S.; Winkler, James L.

1996-01-01

An improved set of computer tools for forming arrays. According to one aspect of the invention, a computer system (100) is used to select probes and design the layout of an array of DNA or other polymers with certain beneficial characteristics. According to another aspect of the invention, a computer system uses chip design files (104) to design and/or generate lithographic masks (110).

Implementation of a competency assessment tool for agency nurses working in an acute paediatric setting.

LENUS (Irish Health Repository)

Hennerby, Cathy

2012-02-01

AIM: This paper reports on the implementation of a competency assessment tool for registered general agency nurses working in an acute paediatric setting, using a change management framework. BACKGROUND: The increased number of registered general agency nurses working in an acute children\\'s hospital alerted concerns around their competency in working with children. These concerns were initially raised via informal complaints about \\'near misses\\

Human versus Computer Controlled Selection of Ventilator Settings: An Evaluation of Adaptive Support Ventilation and Mid-Frequency Ventilation

Directory of Open Access Journals (Sweden)

Eduardo Mireles-Cabodevila

2012-01-01

Full Text Available Background. There are modes of mechanical ventilation that can select ventilator settings with computer controlled algorithms (targeting schemes. Two examples are adaptive support ventilation (ASV and mid-frequency ventilation (MFV. We studied how different clinician-chosen ventilator settings are from these computer algorithms under different scenarios. Methods. A survey of critical care clinicians provided reference ventilator settings for a 70 kg paralyzed patient in five clinical/physiological scenarios. The survey-derived values for minute ventilation and minute alveolar ventilation were used as goals for ASV and MFV, respectively. A lung simulator programmed with each scenario’s respiratory system characteristics was ventilated using the clinician, ASV, and MFV settings. Results. Tidal volumes ranged from 6.1 to 8.3 mL/kg for the clinician, 6.7 to 11.9 mL/kg for ASV, and 3.5 to 9.9 mL/kg for MFV. Inspiratory pressures were lower for ASV and MFV. Clinician-selected tidal volumes were similar to the ASV settings for all scenarios except for asthma, in which the tidal volumes were larger for ASV and MFV. MFV delivered the same alveolar minute ventilation with higher end expiratory and lower end inspiratory volumes. Conclusions. There are differences and similarities among initial ventilator settings selected by humans and computers for various clinical scenarios. The ventilation outcomes are the result of the lung physiological characteristics and their interaction with the targeting scheme.

R Implementation of a Polyhedral Approximation to a 3D Set of Points Using the ?-Shape

Directory of Open Access Journals (Sweden)

Thomas Lafarge

2014-01-01

Full Text Available This work presents the implementation in R of the ?-shape of a finite set of points in the three-dimensional space R3. This geometric structure generalizes the convex hull and allows to recover the shape of non-convex and even non-connected sets in 3D, given a ran- dom sample of points taken into it. Besides the computation of the ?-shape, the R package alphashape3d provides users with tools to facilitate the three-dimensional graphical visu- alization of the estimated set as well as the computation of important characteristics such as the connected components or the volume, among others.

Use of a tool-set by Pan troglodytes troglodytes to obtain termites (Macrotermes) in the periphery of the Dja Biosphere Reserve, southeast Cameroon.

Science.gov (United States)

Deblauwe, Isra; Guislain, Patrick; Dupain, Jef; Van Elsacker, Linda

2006-12-01

At the northern periphery of the Dja Biosphere Reserve (southeastern Cameroon) we recorded a new use of a tool-set by Pan troglodytes troglodytes to prey on Macrotermes muelleri, M. renouxi, M. lilljeborgi, and M. nobilis. We recovered 79 puncturing sticks and 47 fishing probes at 17 termite nests between 2002 and 2005. The mean length of the puncturing sticks (n = 77) and fishing probes (n = 45) was 52 cm and 56 cm, respectively, and the mean diameter was 9 mm and 4.5 mm, respectively. Sixty-eight percent of 138 chimpanzee fecal samples contained major soldiers of four Macrotermes species. The chimpanzees in southeastern Cameroon appeared to be selective in their choice of plant material to make their tools. The tools found at our study site resemble those from other sites in this region. However, in southeastern Cameroon only one tool-set type was found, whereas two tool-set types have been reported in Congo. Our study suggests that, along with the different vegetation types and the availability of plant material around termite nests, the nest and gallery structure and foraging behavior of the different Macrotermes spp. at all Central African sites must be investigated before we can attribute differences in tool-use behavior to culture. (c) 2006 Wiley-Liss, Inc.

Performance of a computer-based assessment of cognitive function measures in two cohorts of seniors

Science.gov (United States)

Computer-administered assessment of cognitive function is being increasingly incorporated in clinical trials, however its performance in these settings has not been systematically evaluated. The Seniors Health and Activity Research Program (SHARP) pilot trial (N=73) developed a computer-based tool f...

Open source Modeling and optimization tools for Planning

Energy Technology Data Exchange (ETDEWEB)

Peles, S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2017-02-10

Open source modeling and optimization tools for planning The existing tools and software used for planning and analysis in California are either expensive, difficult to use, or not generally accessible to a large number of participants. These limitations restrict the availability of participants for larger scale energy and grid studies in the state. The proposed initiative would build upon federal and state investments in open source software, and create and improve open source tools for use in the state planning and analysis activities. Computational analysis and simulation frameworks in development at national labs and universities can be brought forward to complement existing tools. An open source platform would provide a path for novel techniques and strategies to be brought into the larger community and reviewed by a broad set of stakeholders.

Simulation tools for two-dimensional experiments in x-ray computed tomography using the FORBILD head phantom.

Science.gov (United States)

Yu, Zhicong; Noo, Frédéric; Dennerlein, Frank; Wunderlich, Adam; Lauritsch, Günter; Hornegger, Joachim

2012-07-07

Mathematical phantoms are essential for the development and early stage evaluation of image reconstruction algorithms in x-ray computed tomography (CT). This note offers tools for computer simulations using a two-dimensional (2D) phantom that models the central axial slice through the FORBILD head phantom. Introduced in 1999, in response to a need for a more robust test, the FORBILD head phantom is now seen by many as the gold standard. However, the simple Shepp-Logan phantom is still heavily used by researchers working on 2D image reconstruction. Universal acceptance of the FORBILD head phantom may have been prevented by its significantly higher complexity: software that allows computer simulations with the Shepp-Logan phantom is not readily applicable to the FORBILD head phantom. The tools offered here address this problem. They are designed for use with Matlab®, as well as open-source variants, such as FreeMat and Octave, which are all widely used in both academia and industry. To get started, the interested user can simply copy and paste the codes from this PDF document into Matlab® M-files.

Simulation tools for two-dimensional experiments in x-ray computed tomography using the FORBILD head phantom

International Nuclear Information System (INIS)

Yu Zhicong; Noo, Frédéric; Wunderlich, Adam; Dennerlein, Frank; Lauritsch, Günter; Hornegger, Joachim

2012-01-01

Mathematical phantoms are essential for the development and early stage evaluation of image reconstruction algorithms in x-ray computed tomography (CT). This note offers tools for computer simulations using a two-dimensional (2D) phantom that models the central axial slice through the FORBILD head phantom. Introduced in 1999, in response to a need for a more robust test, the FORBILD head phantom is now seen by many as the gold standard. However, the simple Shepp–Logan phantom is still heavily used by researchers working on 2D image reconstruction. Universal acceptance of the FORBILD head phantom may have been prevented by its significantly higher complexity: software that allows computer simulations with the Shepp–Logan phantom is not readily applicable to the FORBILD head phantom. The tools offered here address this problem. They are designed for use with Matlab®, as well as open-source variants, such as FreeMat and Octave, which are all widely used in both academia and industry. To get started, the interested user can simply copy and paste the codes from this PDF document into Matlab® M-files. (note)

A user's manual of Tools for Error Estimation of Complex Number Matrix Computation (Ver.1.0)

International Nuclear Information System (INIS)

Ichihara, Kiyoshi.

1997-03-01

'Tools for Error Estimation of Complex Number Matrix Computation' is a subroutine library which aids the users in obtaining the error ranges of the complex number linear system's solutions or the Hermitian matrices' eigen values. This library contains routines for both sequential computers and parallel computers. The subroutines for linear system error estimation calulate norms of residual vectors, matrices's condition numbers, error bounds of solutions and so on. The error estimation subroutines for Hermitian matrix eigen values' derive the error ranges of the eigen values according to the Korn-Kato's formula. This user's manual contains a brief mathematical background of error analysis on linear algebra and usage of the subroutines. (author)

A dataflow analysis tool for parallel processing of algorithms

Science.gov (United States)

Jones, Robert L., III

1993-01-01

A graph-theoretic design process and software tool is presented for selecting a multiprocessing scheduling solution for a class of computational problems. The problems of interest are those that can be described using a dataflow graph and are intended to be executed repetitively on a set of identical parallel processors. Typical applications include signal processing and control law problems. Graph analysis techniques are introduced and shown to effectively determine performance bounds, scheduling constraints, and resource requirements. The software tool is shown to facilitate the application of the design process to a given problem.

Seeking tools for image fusion between computed tomography, structural and functional magnetic resonance methods for applications in neurosurgery; Ferramentas para fusao de imagens dos metodos de tomografia computadorizada, ressonancia magnetica e ressonancia magnetica funcional para aplicacao pre-neurocirurgica

Energy Technology Data Exchange (ETDEWEB)

Rocha, Liana Guerra Sanches da, E-mail: liana@einstein.br [Departamento de Diagnostico por Imagem, Hospital Israelita Albert Einstein - HIAE, Sao Paulo (SP) (Brazil); Amaro Junior, Edson [Faculdade de Medicina, Universidade de Sao Paulo - USP, Sao Paulo, SP (Brazil). Deptartamento de Diagnostico por Imagem; Instituto do Cerebro - InCe, Hospital Israelita Albert Einstein - HIAE, Sao Paulo, SP (Brazil)

2012-04-15

To evaluate tools for the fusion of images generated by tomography and structural and functional magnetic resonance imaging. Methods: Magnetic resonance and functional magnetic resonance imaging were performed while a volunteer who had previously undergone cranial tomography performed motor and somatosensory tasks in a 3-Tesla scanner. Image data were analyzed with different programs, and the results were compared. Results: We constructed a flow chart of computational processes that allowed measurement of the spatial congruence between the methods. There was no single computational tool that contained the entire set of functions necessary to achieve the goal. Conclusion: The fusion of the images from the three methods proved to be feasible with the use of four free-access software programs (OsiriX, Register, MRIcro and FSL). Our results may serve as a basis for building software that will be useful as a virtual tool prior to neurosurgery. (author)

Unified, Cross-Platform, Open-Source Library Package for High-Performance Computing

Energy Technology Data Exchange (ETDEWEB)

Kozacik, Stephen [EM Photonics, Inc., Newark, DE (United States)

2017-05-15

Compute power is continually increasing, but this increased performance is largely found in sophisticated computing devices and supercomputer resources that are difficult to use, resulting in under-utilization. We developed a unified set of programming tools that will allow users to take full advantage of the new technology by allowing them to work at a level abstracted away from the platform specifics, encouraging the use of modern computing systems, including government-funded supercomputer facilities.

PLOT3D Export Tool for Tecplot

Science.gov (United States)

Alter, Stephen

2010-01-01

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

Google Sets, Google Suggest, and Google Search History: Three More Tools for the Reference Librarian's Bag of Tricks

OpenAIRE

Cirasella, Jill

2008-01-01

This article examines the features, quirks, and uses of Google Sets, Google Suggest, and Google Search History and argues that these three lesser-known Google tools warrant inclusion in the resourceful reference librarian’s bag of tricks.

A computer model for identifying security system upgrades

International Nuclear Information System (INIS)

Lamont, A.

1988-01-01

This paper describes a prototype safeguards analysis tool that automatically identifies system weaknesses against an insider adversary and suggest possible upgrades to improve the probability that the adversary will be detected. The tool is based on this premise: as the adversary acts, he or she creates a set of facts that can be detected by safeguards components. Whenever an adversary's planned set of actions create a set of facts which the security personnel would consider irregular or unusual, we can improve the security system by implementing safeguards that detect those facts. Therefore, an intelligent computer program can suggest upgrades to the facility if we construct a knowledge base that contains information about: (1) the facts created by each possible adversary action, (2) the facts that each possible safeguard can detect, and (3) groups of facts which will be considered irregular whenever they occur together. The authors describe the structure of the knowledge base and show how the above information can be represented in it. They also describe the procedures that a computer program can use to identify missing or weak safeguards and to suggest upgrades

Offline computing and networking

International Nuclear Information System (INIS)

Appel, J.A.; Avery, P.; Chartrand, G.

1985-01-01

This note summarizes the work of the Offline Computing and Networking Group. The report is divided into two sections; the first deals with the computing and networking requirements and the second with the proposed way to satisfy those requirements. In considering the requirements, we have considered two types of computing problems. The first is CPU-intensive activity such as production data analysis (reducing raw data to DST), production Monte Carlo, or engineering calculations. The second is physicist-intensive computing such as program development, hardware design, physics analysis, and detector studies. For both types of computing, we examine a variety of issues. These included a set of quantitative questions: how much CPU power (for turn-around and for through-put), how much memory, mass-storage, bandwidth, and so on. There are also very important qualitative issues: what features must be provided by the operating system, what tools are needed for program design, code management, database management, and for graphics

CERN School of Computing

CERN Multimedia

2007-01-01

The 2007 CERN School of Computing, organised by CERN in collaboration with the University of Split (FESB) will be held from 20 to 31 August 2007 in Dubrovnik, Croatia. It is aimed at postgraduate students and research workers with a few years' experience in scientific physics, computing or related fields. Special themes this year are: GRID Technologies: The Grid track delivers unique theoretical and hands-on education on some of the most advanced GRID topics; Software Technologies: The Software track addresses some of the most relevant modern techniques and tools for large scale distributed software development and handling as well as for computer security; Physics Computing: The Physics Computing track focuses on informatics topics specific to the HEP community. After setting-the-scene lectures, it addresses data acquisition and ROOT. Grants from the European Union Framework Programme 6 (FP6) are available to participants to cover part or all of the cost of the School. More information can be found at...

Self-learning computers for surgical planning and prediction of postoperative alignment.

Science.gov (United States)

Lafage, Renaud; Pesenti, Sébastien; Lafage, Virginie; Schwab, Frank J

2018-02-01

In past decades, the role of sagittal alignment has been widely demonstrated in the setting of spinal conditions. As several parameters can be affected, identifying the driver of the deformity is the cornerstone of a successful treatment approach. Despite the importance of restoring sagittal alignment for optimizing outcome, this task remains challenging. Self-learning computers and optimized algorithms are of great interest in spine surgery as in that they facilitate better planning and prediction of postoperative alignment. Nowadays, computer-assisted tools are part of surgeons' daily practice; however, the use of such tools remains to be time-consuming. NARRATIVE REVIEW AND RESULTS: Computer-assisted methods for the prediction of postoperative alignment consist of a three step analysis: identification of anatomical landmark, definition of alignment objectives, and simulation of surgery. Recently, complex rules for the prediction of alignment have been proposed. Even though this kind of work leads to more personalized objectives, the number of parameters involved renders it difficult for clinical use, stressing the importance of developing computer-assisted tools. The evolution of our current technology, including machine learning and other types of advanced algorithms, will provide powerful tools that could be useful in improving surgical outcomes and alignment prediction. These tools can combine different types of advanced technologies, such as image recognition and shape modeling, and using this technique, computer-assisted methods are able to predict spinal shape. The development of powerful computer-assisted methods involves the integration of several sources of information such as radiographic parameters (X-rays, MRI, CT scan, etc.), demographic information, and unusual non-osseous parameters (muscle quality, proprioception, gait analysis data). In using a larger set of data, these methods will aim to mimic what is actually done by spine surgeons, leading

A Proposal to Speed up the Computation of the Centroid of an Interval Type-2 Fuzzy Set

Directory of Open Access Journals (Sweden)

Carlos E. Celemin

2013-01-01

Full Text Available This paper presents two new algorithms that speed up the centroid computation of an interval type-2 fuzzy set. The algorithms include precomputation of the main operations and initialization based on the concept of uncertainty bounds. Simulations over different kinds of footprints of uncertainty reveal that the new algorithms achieve computation time reductions with respect to the Enhanced-Karnik algorithm, ranging from 40 to 70%. The results suggest that the initialization used in the new algorithms effectively reduces the number of iterations to compute the extreme points of the interval centroid while precomputation reduces the computational cost of each iteration.

Software Engineering for Scientific Computer Simulations

Science.gov (United States)

Post, Douglass E.; Henderson, Dale B.; Kendall, Richard P.; Whitney, Earl M.

2004-11-01

Computer simulation is becoming a very powerful tool for analyzing and predicting the performance of fusion experiments. Simulation efforts are evolving from including only a few effects to many effects, from small teams with a few people to large teams, and from workstations and small processor count parallel computers to massively parallel platforms. Successfully making this transition requires attention to software engineering issues. We report on the conclusions drawn from a number of case studies of large scale scientific computing projects within DOE, academia and the DoD. The major lessons learned include attention to sound project management including setting reasonable and achievable requirements, building a good code team, enforcing customer focus, carrying out verification and validation and selecting the optimum computational mathematics approaches.

Weight Estimation Tool for Children Aged 6 to 59 Months in Limited-Resource Settings.

Science.gov (United States)

Ralston, Mark E; Myatt, Mark A

2016-01-01

A simple, reliable anthropometric tool for rapid estimation of weight in children would be useful in limited-resource settings where current weight estimation tools are not uniformly reliable, nearly all global under-five mortality occurs, severe acute malnutrition is a significant contributor in approximately one-third of under-five mortality, and a weight scale may not be immediately available in emergencies to first-response providers. To determine the accuracy and precision of mid-upper arm circumference (MUAC) and height as weight estimation tools in children under five years of age in low-to-middle income countries. This was a retrospective observational study. Data were collected in 560 nutritional surveys during 1992-2006 using a modified Expanded Program of Immunization two-stage cluster sample design. Locations with high prevalence of acute and chronic malnutrition. A total of 453,990 children met inclusion criteria (age 6-59 months; weight ≤ 25 kg; MUAC 80-200 mm) and exclusion criteria (bilateral pitting edema; biologically implausible weight-for-height z-score (WHZ), weight-for-age z-score (WAZ), and height-for-age z-score (HAZ) values). Weight was estimated using Broselow Tape, Hong Kong formula, and database MUAC alone, height alone, and height and MUAC combined. Mean percentage difference between true and estimated weight, proportion of estimates accurate to within ± 25% and ± 10% of true weight, weighted Kappa statistic, and Bland-Altman bias were reported as measures of tool accuracy. Standard deviation of mean percentage difference and Bland-Altman 95% limits of agreement were reported as measures of tool precision. Database height was a more accurate and precise predictor of weight compared to Broselow Tape 2007 [B], Broselow Tape 2011 [A], and MUAC. Mean percentage difference between true and estimated weight was +0.49% (SD = 10.33%); proportion of estimates accurate to within ± 25% of true weight was 97.36% (95% CI 97.40%, 97.46%); and

Auditors’ Usage of Computer Assisted Audit Tools and Techniques: Empirical Evidence from Nigeria

OpenAIRE

Appah Ebimobowei; G.N. Ogbonna; Zuokemefa P. Enebraye

2013-01-01

This study examines use of computer assisted audit tool and techniques in audit practice in the Niger Delta of Nigeria. To achieve this objective, data was collected from primary and secondary sources. The secondary sources were from scholarly books and journals while the primary source involved a well structured questionnaire of three sections of thirty seven items with an average reliability of 0.838. The data collected from the questionnaire were analyzed using relevant descriptive statist...

Test Review for Preschool-Wide Evaluation Tool (PreSET) Manual: Assessing Universal Program-Wide Positive Behavior Support in Early Childhood

Science.gov (United States)

Rodriguez, Billie Jo

2013-01-01

The Preschool-Wide Evaluation Tool (PreSET; Steed & Pomerleau, 2012) is published by Paul H. Brookes Publishing Company in Baltimore, MD. The PreSET purports to measure universal and program-wide features of early childhood programs' implementation fidelity of program-wide positive behavior intervention and support (PW-PBIS) and is,…

BEAM EMITTANCE MEASUREMENT TOOL FOR CEBAF OPERATIONS

International Nuclear Information System (INIS)

Chevtsov, Pavel; Tiefenback, Michael

2008-01-01

A new software tool was created at Jefferson Lab to measure the emittance of the CEBAF electron beams. The tool consists of device control and data analysis applications. The device control application handles the work of wire scanners and writes their measurement results as well as the information about accelerator settings during these measurements into wire scanner data files. The data analysis application reads these files and calculates the beam emittance on the basis of a wire scanner data processing model. Both applications are computer platform independent but are mostly used on LINUX PCs recently installed in the accelerator control room. The new tool significantly simplifies beam emittance measurement procedures for accelerator operations and contributes to a very high availability of the CEBAF machine for the nuclear physics program at Jefferson Lab.

SALP-PC, a computer program for fault tree analysis on personal computers

International Nuclear Information System (INIS)

Contini, S.; Poucet, A.

1987-01-01

The paper presents the main characteristics of the SALP-PC computer code for fault tree analysis. The program has been developed in Fortran 77 on an Olivetti M24 personal computer (IBM compatible) in order to reach a high degree of portability. It is composed of six processors implementing the different phases of the analysis procedure. This particular structure presents some advantages like, for instance, the restart facility and the possibility to develop an event tree analysis code. The set of allowed logical operators, i.e. AND, OR, NOT, K/N, XOR, INH, together with the possibility to define boundary conditions, make the SALP-PC code a powerful tool for risk assessment. (orig.)

Ubiquitous information for ubiquitous computing: expressing clinical data sets with openEHR archetypes.

Science.gov (United States)

Garde, Sebastian; Hovenga, Evelyn; Buck, Jasmin; Knaup, Petra

2006-01-01

Ubiquitous computing requires ubiquitous access to information and knowledge. With the release of openEHR Version 1.0 there is a common model available to solve some of the problems related to accessing information and knowledge by improving semantic interoperability between clinical systems. Considerable work has been undertaken by various bodies to standardise Clinical Data Sets. Notwithstanding their value, several problems remain unsolved with Clinical Data Sets without the use of a common model underpinning them. This paper outlines these problems like incompatible basic data types and overlapping and incompatible definitions of clinical content. A solution to this based on openEHR archetypes is motivated and an approach to transform existing Clinical Data Sets into archetypes is presented. To avoid significant overlaps and unnecessary effort during archetype development, archetype development needs to be coordinated nationwide and beyond and also across the various health professions in a formalized process.

Implementation of a competency assessment tool for agency nurses working in an acute paediatric setting.

Science.gov (United States)

Hennerby, Cathy; Joyce, Pauline

2011-03-01

This paper reports on the implementation of a competency assessment tool for registered general agency nurses working in an acute paediatric setting, using a change management framework. The increased number of registered general agency nurses working in an acute children's hospital alerted concerns around their competency in working with children. These concerns were initially raised via informal complaints about 'near misses', parental dissatisfaction, perceived competency weaknesses and rising cost associated with their use. [Young's (2009) Journal of Organisational Change, 22, 524-548] nine-stage change framework was used to guide the implementation of the competency assessment tool within a paediatric acute care setting. The ongoing success of the initiative, from a nurse manager's perspective, relies on structured communication with the agency provider before employing competent agency nurses. Sustainability of the change will depend on nurse managers' persistence in attending the concerns of those resisting the change while simultaneously supporting those championing the change. These key communication and supporting roles highlight the pivotal role held by nurse managers, as gate keepers, in safe-guarding children while in hospital. Leadership qualities of nurse managers will also be challenged in continuing to manage and drive the change where resistance might prevail. © 2011 The Authors. Journal compilation © 2011 Blackwell Publishing Ltd.

Proceedings of the Workshop on Methods & Tools for Computer Supported Collaborative Creativity Process: Linking creativity & informal learning

NARCIS (Netherlands)

Retalis, Symeon; Sloep, Peter

2009-01-01

Retalis, S., & Sloep, P. B. (Eds.) (2009). Collection of 4 symposium papers at EC-TEL 2009. Proceedings of the Workshop on Methods & Tools for Computer Supported Collaborative Creativity Process: Linking creativity & informal learning. September, 30, 2009, Nice,

Computational models as predictors of HIV treatment outcomes for ...

African Journals Online (AJOL)

Background: Selecting the optimal combination of HIV drugs for an individual in resourcelimited settings is challenging because of the limited availability of drugs and genotyping. Objective: The evaluation as a potential treatment support tool of computational models that predict response to therapy without a genotype, ...

Severe accident management guidelines tool

International Nuclear Information System (INIS)

Gutierrez Varela, Javier; Tanarro Onrubia, Augustin; Martinez Fanegas, Rafael

2014-01-01

Severe Accident is addressed by means of a great number of documents such as guidelines, calculation aids and diagnostic trees. The response methodology often requires the use of several documents at the same time while Technical Support Centre members need to assess the appropriate set of equipment within the adequate mitigation strategies. In order to facilitate the response, TECNATOM has developed SAMG TOOL, initially named GGAS TOOL, which is an easy to use computer program that clearly improves and accelerates the severe accident management. The software is designed with powerful features that allow the users to focus on the decision-making process. Consequently, SAMG TOOL significantly improves the severe accident training, ensuring a better response under a real situation. The software is already installed in several Spanish Nuclear Power Plants and trainees claim that the methodology can be followed easier with it, especially because guidelines, calculation aids, equipment information and strategies availability can be accessed immediately (authors)

Tool vibration detection with eddy current sensors in machining process and computation of stability lobes using fuzzy classifiers

Science.gov (United States)

Devillez, Arnaud; Dudzinski, Daniel

2007-01-01

Today the knowledge of a process is very important for engineers to find optimal combination of control parameters warranting productivity, quality and functioning without defects and failures. In our laboratory, we carry out research in the field of high speed machining with modelling, simulation and experimental approaches. The aim of our investigation is to develop a software allowing the cutting conditions optimisation to limit the number of predictive tests, and the process monitoring to prevent any trouble during machining operations. This software is based on models and experimental data sets which constitute the knowledge of the process. In this paper, we deal with the problem of vibrations occurring during a machining operation. These vibrations may cause some failures and defects to the process, like workpiece surface alteration and rapid tool wear. To measure on line the tool micro-movements, we equipped a lathe with a specific instrumentation using eddy current sensors. Obtained signals were correlated with surface finish and a signal processing algorithm was used to determine if a test is stable or unstable. Then, a fuzzy classification method was proposed to classify the tests in a space defined by the width of cut and the cutting speed. Finally, it was shown that the fuzzy classification takes into account of the measurements incertitude to compute the stability limit or stability lobes of the process.

Exploiting volatile opportunistic computing resources with Lobster

Science.gov (United States)

Woodard, Anna; Wolf, Matthias; Mueller, Charles; Tovar, Ben; Donnelly, Patrick; Hurtado Anampa, Kenyi; Brenner, Paul; Lannon, Kevin; Hildreth, Mike; Thain, Douglas

2015-12-01

Analysis of high energy physics experiments using the Compact Muon Solenoid (CMS) at the Large Hadron Collider (LHC) can be limited by availability of computing resources. As a joint effort involving computer scientists and CMS physicists at Notre Dame, we have developed an opportunistic workflow management tool, Lobster, to harvest available cycles from university campus computing pools. Lobster consists of a management server, file server, and worker processes which can be submitted to any available computing resource without requiring root access. Lobster makes use of the Work Queue system to perform task management, while the CMS specific software environment is provided via CVMFS and Parrot. Data is handled via Chirp and Hadoop for local data storage and XrootD for access to the CMS wide-area data federation. An extensive set of monitoring and diagnostic tools have been developed to facilitate system optimisation. We have tested Lobster using the 20 000-core cluster at Notre Dame, achieving approximately 8-10k tasks running simultaneously, sustaining approximately 9 Gbit/s of input data and 340 Mbit/s of output data.

Discrete mathematics using a computer

CERN Document Server

Hall, Cordelia

2000-01-01

Several areas of mathematics find application throughout computer science, and all students of computer science need a practical working understanding of them. These core subjects are centred on logic, sets, recursion, induction, relations and functions. The material is often called discrete mathematics, to distinguish it from the traditional topics of continuous mathematics such as integration and differential equations. The central theme of this book is the connection between computing and discrete mathematics. This connection is useful in both directions: • Mathematics is used in many branches of computer science, in applica­ tions including program specification, datastructures,design and analysis of algorithms, database systems, hardware design, reasoning about the correctness of implementations, and much more; • Computers can help to make the mathematics easier to learn and use, by making mathematical terms executable, making abstract concepts more concrete, and through the use of software tools su...

DR2DI: a powerful computational tool for predicting novel drug-disease associations

Science.gov (United States)

Lu, Lu; Yu, Hua

2018-05-01

Finding the new related candidate diseases for known drugs provides an effective method for fast-speed and low-risk drug development. However, experimental identification of drug-disease associations is expensive and time-consuming. This motivates the need for developing in silico computational methods that can infer true drug-disease pairs with high confidence. In this study, we presented a novel and powerful computational tool, DR2DI, for accurately uncovering the potential associations between drugs and diseases using high-dimensional and heterogeneous omics data as information sources. Based on a unified and extended similarity kernel framework, DR2DI inferred the unknown relationships between drugs and diseases using Regularized Kernel Classifier. Importantly, DR2DI employed a semi-supervised and global learning algorithm which can be applied to uncover the diseases (drugs) associated with known and novel drugs (diseases). In silico global validation experiments showed that DR2DI significantly outperforms recent two approaches for predicting drug-disease associations. Detailed case studies further demonstrated that the therapeutic indications and side effects of drugs predicted by DR2DI could be validated by existing database records and literature, suggesting that DR2DI can be served as a useful bioinformatic tool for identifying the potential drug-disease associations and guiding drug repositioning. Our software and comparison codes are freely available at https://github.com/huayu1111/DR2DI.

DR2DI: a powerful computational tool for predicting novel drug-disease associations

Science.gov (United States)

Lu, Lu; Yu, Hua

2018-04-01

Finding the new related candidate diseases for known drugs provides an effective method for fast-speed and low-risk drug development. However, experimental identification of drug-disease associations is expensive and time-consuming. This motivates the need for developing in silico computational methods that can infer true drug-disease pairs with high confidence. In this study, we presented a novel and powerful computational tool, DR2DI, for accurately uncovering the potential associations between drugs and diseases using high-dimensional and heterogeneous omics data as information sources. Based on a unified and extended similarity kernel framework, DR2DI inferred the unknown relationships between drugs and diseases using Regularized Kernel Classifier. Importantly, DR2DI employed a semi-supervised and global learning algorithm which can be applied to uncover the diseases (drugs) associated with known and novel drugs (diseases). In silico global validation experiments showed that DR2DI significantly outperforms recent two approaches for predicting drug-disease associations. Detailed case studies further demonstrated that the therapeutic indications and side effects of drugs predicted by DR2DI could be validated by existing database records and literature, suggesting that DR2DI can be served as a useful bioinformatic tool for identifying the potential drug-disease associations and guiding drug repositioning. Our software and comparison codes are freely available at https://github.com/huayu1111/DR2DI.

Advances in type-2 fuzzy sets and systems theory and applications

CERN Document Server

Mendel, Jerry; Tahayori, Hooman

2013-01-01

This book explores recent developments in the theoretical foundations and novel applications of general and interval type-2 fuzzy sets and systems, including: algebraic properties of type-2 fuzzy sets, geometric-based definition of type-2 fuzzy set operators, generalizations of the continuous KM algorithm, adaptiveness and novelty of interval type-2 fuzzy logic controllers, relations between conceptual spaces and type-2 fuzzy sets, type-2 fuzzy logic systems versus perceptual computers; modeling human perception of real world concepts with type-2 fuzzy sets, different methods for generating membership functions of interval and general type-2 fuzzy sets, and applications of interval type-2 fuzzy sets to control, machine tooling, image processing and diet.  The applications demonstrate the appropriateness of using type-2 fuzzy sets and systems in real world problems that are characterized by different degrees of uncertainty.

On the development of a computer-based handwriting assessment tool to objectively quantify handwriting proficiency in children.

Science.gov (United States)

Falk, Tiago H; Tam, Cynthia; Schellnus, Heidi; Chau, Tom

2011-12-01

Standardized writing assessments such as the Minnesota Handwriting Assessment (MHA) can inform interventions for handwriting difficulties, which are prevalent among school-aged children. However, these tests usually involve the laborious task of subjectively rating the legibility of the written product, precluding their practical use in some clinical and educational settings. This study describes a portable computer-based handwriting assessment tool to objectively measure MHA quality scores and to detect handwriting difficulties in children. Several measures are proposed based on spatial, temporal, and grip force measurements obtained from a custom-built handwriting instrument. Thirty-five first and second grade students participated in the study, nine of whom exhibited handwriting difficulties. Students performed the MHA test and were subjectively scored based on speed and handwriting quality using five primitives: legibility, form, alignment, size, and space. Several spatial parameters are shown to correlate significantly (phandwriting legibility and speed, respectively. Using only size and space parameters, promising discrimination between proficient and non-proficient handwriting can be achieved. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Addressing unmet need for HIV testing in emergency care settings: a role for computer-facilitated rapid HIV testing?

Science.gov (United States)

Kurth, Ann E; Severynen, Anneleen; Spielberg, Freya

2013-08-01

HIV testing in emergency departments (EDs) remains underutilized. The authors evaluated a computer tool to facilitate rapid HIV testing in an urban ED. Randomly assigned nonacute adult ED patients were randomly assigned to a computer tool (CARE) and rapid HIV testing before a standard visit (n = 258) or to a standard visit (n = 259) with chart access. The authors assessed intervention acceptability and compared noted HIV risks. Participants were 56% nonWhite and 58% male; median age was 37 years. In the CARE arm, nearly all (251/258) of the patients completed the session and received HIV results; four declined to consent to the test. HIV risks were reported by 54% of users; one participant was confirmed HIV-positive, and two were confirmed false-positive (seroprevalence 0.4%, 95% CI [0.01, 2.2]). Half (55%) of the patients preferred computerized rather than face-to-face counseling for future HIV testing. In the standard arm, one HIV test and two referrals for testing occurred. Computer-facilitated HIV testing appears acceptable to ED patients. Future research should assess cost-effectiveness compared with staff-delivered approaches.

Performativity, Fabrication and Trust: Exploring Computer-Mediated Moderation

Science.gov (United States)

Clapham, Andrew

2013-01-01

Based on research conducted in an English secondary school, this paper explores computer-mediated moderation as a performative tool. The Module Assessment Meeting (MAM) was the moderation approach under investigation. I mobilise ethnographic data generated by a key informant, and triangulated with that from other actors in the setting, in order to…

SAGES: a suite of freely-available software tools for electronic disease surveillance in resource-limited settings.

Directory of Open Access Journals (Sweden)

Sheri L Lewis

Full Text Available Public health surveillance is undergoing a revolution driven by advances in the field of information technology. Many countries have experienced vast improvements in the collection, ingestion, analysis, visualization, and dissemination of public health data. Resource-limited countries have lagged behind due to challenges in information technology infrastructure, public health resources, and the costs of proprietary software. The Suite for Automated Global Electronic bioSurveillance (SAGES is a collection of modular, flexible, freely-available software tools for electronic disease surveillance in resource-limited settings. One or more SAGES tools may be used in concert with existing surveillance applications or the SAGES tools may be used en masse for an end-to-end biosurveillance capability. This flexibility allows for the development of an inexpensive, customized, and sustainable disease surveillance system. The ability to rapidly assess anomalous disease activity may lead to more efficient use of limited resources and better compliance with World Health Organization International Health Regulations.

A Hybrid Evaluation System Framework (Shell & Web) with Standardized Access to Climate Model Data and Verification Tools for a Clear Climate Science Infrastructure on Big Data High Performance Computers

Science.gov (United States)

Kadow, Christopher; Illing, Sebastian; Kunst, Oliver; Ulbrich, Uwe; Cubasch, Ulrich

2015-04-01

The project 'Integrated Data and Evaluation System for Decadal Scale Prediction' (INTEGRATION) as part of the German decadal prediction project MiKlip develops a central evaluation system. The fully operational hybrid features a HPC shell access and an user friendly web-interface. It employs one common system with a variety of verification tools and validation data from different projects in- and outside of MiKlip. The evaluation system is located at the German Climate Computing Centre (DKRZ) and has direct access to the bulk of its ESGF node including millions of climate model data sets, e.g. from CMIP5 and CORDEX. The database is organized by the international CMOR standard using the meta information of the self-describing model, reanalysis and observational data sets. Apache Solr is used for indexing the different data projects into one common search environment. This implemented meta data system with its advanced but easy to handle search tool supports users, developers and their tools to retrieve the required information. A generic application programming interface (API) allows scientific developers to connect their analysis tools with the evaluation system independently of the programming language used. Users of the evaluation techniques benefit from the common interface of the evaluation system without any need to understand the different scripting languages. Facilitating the provision and usage of tools and climate data increases automatically the number of scientists working with the data sets and identify discrepancies. Additionally, the history and configuration sub-system stores every analysis performed with the evaluation system in a MySQL database. Configurations and results of the tools can be shared among scientists via shell or web-system. Therefore, plugged-in tools gain automatically from transparency and reproducibility. Furthermore, when configurations match while starting a evaluation tool, the system suggests to use results already produced

Imprecision and uncertainty in information representation and processing new tools based on intuitionistic fuzzy sets and generalized nets

CERN Document Server

Sotirov, Sotir

2016-01-01

The book offers a comprehensive and timely overview of advanced mathematical tools for both uncertainty analysis and modeling of parallel processes, with a special emphasis on intuitionistic fuzzy sets and generalized nets. The different chapters, written by active researchers in their respective areas, are structured to provide a coherent picture of this interdisciplinary yet still evolving field of science. They describe key tools and give practical insights into and research perspectives on the use of Atanassov's intuitionistic fuzzy sets and logic, and generalized nets for describing and dealing with uncertainty in different areas of science, technology and business, in a single, to date unique book. Here, readers find theoretical chapters, dealing with intuitionistic fuzzy operators, membership functions and algorithms, among other topics, as well as application-oriented chapters, reporting on the implementation of methods and relevant case studies in management science, the IT industry, medicine and/or ...

A Standardized Needs Assessment Tool to Inform the Curriculum Development Process for Pediatric Resuscitation Simulation-Based Education in Resource-Limited Settings

Directory of Open Access Journals (Sweden)

Nicole Shilkofski

2018-02-01

Full Text Available IntroductionUnder five mortality rates (UFMR remain high for children in low- and middle-income countries (LMICs in the developing world. Education for practitioners in these environments is a key factor to improve outcomes that will address United Nations Sustainable Development Goals 3 and 10 (good health and well being and reduced inequalities. In order to appropriately contextualize a curriculum using simulation, it is necessary to first conduct a needs assessment of the target learner population. The World Health Organization (WHO has published a tool to assess capacity for emergency and surgical care in LMICs that is adaptable to this goal.Materials and methodsThe WHO Tool for Situational Analysis to Assess Emergency and Essential Surgical Care was modified to assess pediatric resuscitation capacity in clinical settings in two LMICs: Uganda and Myanmar. Modifications included assessment of self-identified learning needs, current practices, and perceived epidemiology of disease burden in each clinical setting, in addition to assessment of pediatric resuscitation capacity in regard to infrastructure, procedures, equipment, and supplies. The modified tool was administered to 94 respondents from the two settings who were target learners of a proposed simulation-based curriculum in pediatric and neonatal resuscitation.ResultsInfectious diseases (respiratory illnesses and diarrheal disease were cited as the most common causes of pediatric deaths in both countries. Self-identified learning needs included knowledge and skill development in pediatric airway/breathing topics, as well as general resuscitation topics such as CPR and fluid resuscitation in shock. Equipment and supply availability varied substantially between settings, and critical shortages were identified in each setting. Current practices and procedures were often limited by equipment availability or infrastructural considerations.Discussion and conclusionEpidemiology of disease

Data mining in soft computing framework: a survey.

Science.gov (United States)

Mitra, S; Pal, S K; Mitra, P

2002-01-01

The present article provides a survey of the available literature on data mining using soft computing. A categorization has been provided based on the different soft computing tools and their hybridizations used, the data mining function implemented, and the preference criterion selected by the model. The utility of the different soft computing methodologies is highlighted. Generally fuzzy sets are suitable for handling the issues related to understandability of patterns, incomplete/noisy data, mixed media information and human interaction, and can provide approximate solutions faster. Neural networks are nonparametric, robust, and exhibit good learning and generalization capabilities in data-rich environments. Genetic algorithms provide efficient search algorithms to select a model, from mixed media data, based on some preference criterion/objective function. Rough sets are suitable for handling different types of uncertainty in data. Some challenges to data mining and the application of soft computing methodologies are indicated. An extensive bibliography is also included.

Setting to earth for computer

International Nuclear Information System (INIS)

Gallego V, Luis Eduardo; Montana Ch, Johny Hernan; Tovar P, Andres Fernando; Amortegui, Francisco

2000-01-01

The program GMT allows the analysis of setting to earth for tensions DC and AC (of low frequency) of diverse configurations composed by cylindrical electrodes interconnected, in a homogeneous land or stratified (two layers). This analysis understands among other aspects: calculation of the setting resistance to earth, elevation of potential of the system (GPR), calculation of current densities in the conductors, potentials calculation in which point on the land surface (profile and surfaces), tensions calculation in passing and of contact, also, it carries out the interpretation of resistivity measures for Wenner and Schlumberger methods, finding a model of two layers

Variation of densitometry on computed tomography in COPD--influence of different software tools.

Directory of Open Access Journals (Sweden)

Mark O Wielpütz

Full Text Available Quantitative multidetector computed tomography (MDCT as a potential biomarker is increasingly used for severity assessment of emphysema in chronic obstructive pulmonary disease (COPD. Aim of this study was to evaluate the user-independent measurement variability between five different fully-automatic densitometry software tools.MDCT and full-body plethysmography incl. forced expiratory volume in 1s and total lung capacity were available for 49 patients with advanced COPD (age = 64±9 years, forced expiratory volume in 1 s = 31±6% predicted. Measurement variation regarding lung volume, emphysema volume, emphysema index, and mean lung density was evaluated for two scientific and three commercially available lung densitometry software tools designed to analyze MDCT from different scanner types.One scientific tool and one commercial tool failed to process most or all datasets, respectively, and were excluded. One scientific and another commercial tool analyzed 49, the remaining commercial tool 30 datasets. Lung volume, emphysema volume, emphysema index and mean lung density were significantly different amongst these three tools (p<0.001. Limits of agreement for lung volume were [-0.195, -0.052 l], [-0.305, -0.131 l], and [-0.123, -0.052 l] with correlation coefficients of r = 1.00 each. Limits of agreement for emphysema index were [-6.2, 2.9%], [-27.0, 16.9%], and [-25.5, 18.8%], with r = 0.79 to 0.98. Correlation of lung volume with total lung capacity was good to excellent (r = 0.77 to 0.91, p<0.001, but segmented lung volume (6.7±1.3-6.8±1.3 l were significantly lower than total lung capacity (7.7±1.7 l, p<0.001.Technical incompatibilities hindered evaluation of two of five tools. The remaining three showed significant measurement variation for emphysema, hampering quantitative MDCT as a biomarker in COPD. Follow-up studies should currently use identical software, and standardization efforts should encompass software as

Discovering highly informative feature set over high dimensions

KAUST Repository

Zhang, Chongsheng; Masseglia, Florent; Zhang, Xiangliang

2012-01-01

For many textual collections, the number of features is often overly large. These features can be very redundant, it is therefore desirable to have a small, succinct, yet highly informative collection of features that describes the key characteristics of a dataset. Information theory is one such tool for us to obtain this feature collection. With this paper, we mainly contribute to the improvement of efficiency for the process of selecting the most informative feature set over high-dimensional unlabeled data. We propose a heuristic theory for informative feature set selection from high dimensional data. Moreover, we design data structures that enable us to compute the entropies of the candidate feature sets efficiently. We also develop a simple pruning strategy that eliminates the hopeless candidates at each forward selection step. We test our method through experiments on real-world data sets, showing that our proposal is very efficient. © 2012 IEEE.

Discovering highly informative feature set over high dimensions

KAUST Repository

Zhang, Chongsheng

2012-11-01

For many textual collections, the number of features is often overly large. These features can be very redundant, it is therefore desirable to have a small, succinct, yet highly informative collection of features that describes the key characteristics of a dataset. Information theory is one such tool for us to obtain this feature collection. With this paper, we mainly contribute to the improvement of efficiency for the process of selecting the most informative feature set over high-dimensional unlabeled data. We propose a heuristic theory for informative feature set selection from high dimensional data. Moreover, we design data structures that enable us to compute the entropies of the candidate feature sets efficiently. We also develop a simple pruning strategy that eliminates the hopeless candidates at each forward selection step. We test our method through experiments on real-world data sets, showing that our proposal is very efficient. © 2012 IEEE.

N2A: a computational tool for modeling from neurons to algorithms

Directory of Open Access Journals (Sweden)

Fredrick eRothganger

2014-01-01

Full Text Available The exponential increase in available neural data has combined with the exponential growth in computing (Moore’s law to create new opportunities to understand neural systems at large scale and high detail. The ability to produce large and sophisticated simulations has introduced unique challenges to neuroscientists. Computational models in neuroscience are increasingly broad efforts, often involving the collaboration of experts in different domains. Furthermore, the size and detail of models have grown to levels for which understanding the implications of variability and assumptions is no longer trivial. Here, we introduce the model design platform N2A which aims to facilitate the design and validation of biologically realistic models. N2A uses a hierarchical representation of neural information to enable the integration of models from different users. N2A streamlines computational validation of a model by natively implementing standard tools in sensitivity analysis and uncertainty quantification. The part-relationship representation allows both network-level analysis and dynamical simulations. We will demonstrate how N2A can be used in a range of examples, including a simple Hodgkin-Huxley cable model, basic parameter sensitivity of an 80/20 network, and the expression of the structural plasticity of a growing dendrite and stem cell proliferation and differentiation.

BioSPICE: access to the most current computational tools for biologists.

Science.gov (United States)

Garvey, Thomas D; Lincoln, Patrick; Pedersen, Charles John; Martin, David; Johnson, Mark

2003-01-01

The goal of the BioSPICE program is to create a framework that provides biologists access to the most current computational tools. At the program midpoint, the BioSPICE member community has produced a software system that comprises contributions from approximately 20 participating laboratories integrated under the BioSPICE Dashboard and a methodology for continued software integration. These contributed software modules are the BioSPICE Dashboard, a graphical environment that combines Open Agent Architecture and NetBeans software technologies in a coherent, biologist-friendly user interface. The current Dashboard permits data sources, models, simulation engines, and output displays provided by different investigators and running on different machines to work together across a distributed, heterogeneous network. Among several other features, the Dashboard enables users to create graphical workflows by configuring and connecting available BioSPICE components. Anticipated future enhancements to BioSPICE include a notebook capability that will permit researchers to browse and compile data to support model building, a biological model repository, and tools to support the development, control, and data reduction of wet-lab experiments. In addition to the BioSPICE software products, a project website supports information exchange and community building.

The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production

Directory of Open Access Journals (Sweden)

Tilmann Weber

2016-06-01

Full Text Available Natural products are among the most important sources of lead molecules for drug discovery. With the development of affordable whole-genome sequencing technologies and other ‘omics tools, the field of natural products research is currently undergoing a shift in paradigms. While, for decades, mainly analytical and chemical methods gave access to this group of compounds, nowadays genomics-based methods offer complementary approaches to find, identify and characterize such molecules. This paradigm shift also resulted in a high demand for computational tools to assist researchers in their daily work. In this context, this review gives a summary of tools and databases that currently are available to mine, identify and characterize natural product biosynthesis pathways and their producers based on ‘omics data. A web portal called Secondary Metabolite Bioinformatics Portal (SMBP at http://www.secondarymetabolites.org is introduced to provide a one-stop catalog and links to these bioinformatics resources. In addition, an outlook is presented how the existing tools and those to be developed will influence synthetic biology approaches in the natural products field.

Advanced tools for smartphone-based experiments: phyphox

OpenAIRE

Staacks, Sebastian; Hütz, Simon; Heinke, Heidrun; Stampfer, Christoph

2018-01-01

The sensors in modern smartphones are a promising and cost-effective tool for experimentation in physics education, but many experiments face practical problems. Often the phone is inaccessible during the experiment and the data usually needs to be analyzed subsequently on a computer. We address both problems by introducing a new app, called "phyphox", which is specifically designed for utilizing experiments in physics teaching. The app is free and designed to offer the same set of features o...

Computer-aided tool for the teaching of relational algebra in data base courses

Directory of Open Access Journals (Sweden)

Johnny Villalobos Murillo

2016-03-01

Full Text Available This article describes the design and implementation of computer-aided tool called Relational Algebra Translator (RAT in data base courses, for the teaching of relational algebra. There was a problem when introducing the relational algebra topic in the course EIF 211 Design and Implementation of Databases, which belongs to the career of Engineering in Information Systems of the National University of Costa Rica, because students attending this course were lacking profound mathematical knowledge, which led to a learning problem, being this an important subject to understand what the data bases search and request do RAT comes along to enhance the teaching-learning process. It introduces the architectural and design principles required for its implementation, such as: the language symbol table, the gramatical rules and the basic algorithms that RAT uses to translate from relational algebra to SQL language. This tool has been used for one periods and has demonstrated to be effective in the learning-teaching process.  This urged investigators to publish it in the web site: www.slinfo.una.ac.cr in order for this tool to be used in other university courses.

Piloting a programme tool to evaluate malaria case investigation and reactive case detection activities: results from 3 settings in the Asia Pacific.

Science.gov (United States)

Cotter, Chris; Sudathip, Prayuth; Herdiana, Herdiana; Cao, Yuanyuan; Liu, Yaobao; Luo, Alex; Ranasinghe, Neil; Bennett, Adam; Cao, Jun; Gosling, Roly D

2017-08-22

Case investigation and reactive case detection (RACD) activities are widely-used in low transmission settings to determine the suspected origin of infection and identify and treat malaria infections nearby to the index patient household. Case investigation and RACD activities are time and resource intensive, include methodologies that vary across eliminating settings, and have no standardized metrics or tools available to monitor and evaluate them. In response to this gap, a simple programme tool was developed for monitoring and evaluating (M&E) RACD activities and piloted by national malaria programmes. During the development phase, four modules of the RACD M&E tool were created to assess and evaluate key case investigation and RACD activities and costs. A pilot phase was then carried out by programme implementers between 2013 and 2015, during which malaria surveillance teams in three different settings (China, Indonesia, Thailand) piloted the tool over a period of 3 months each. This study describes summary results of the pilots and feasibility and impact of the tool on programmes. All three study areas implemented the RACD M&E tool modules, and pilot users reported the tool and evaluation process were helpful to identify gaps in RACD programme activities. In the 45 health facilities evaluated, 71.8% (97/135; min 35.3-max 100.0%) of the proper notification and reporting forms and 20.0% (27/135; min 0.0-max 100.0%) of standard operating procedures (SOPs) were available to support malaria elimination activities. The tool highlighted gaps in reporting key data indicators on the completeness for malaria case reporting (98.8%; min 93.3-max 100.0%), case investigations (65.6%; min 61.8-max 78.4%) and RACD activities (70.0%; min 64.7-max 100.0%). Evaluation of the SOPs showed that knowledge and practices of malaria personnel varied within and between study areas. Average monthly costs for conducting case investigation and RACD activities showed variation between study

Computing and Displaying Isosurfaces in R

Directory of Open Access Journals (Sweden)

Dai Feng

2008-09-01

Full Text Available This paper presents R utilities for computing and displaying isosurfaces, or three-dimensional contour surfaces, from a three-dimensional array of function values. A version of the marching cubes algorithm that takes into account face and internal ambiguities is used to compute the isosurfaces. Vectorization is used to ensure adequate performance using only R code. Examples are presented showing contours of theoretical densities, density estimates, and medical imaging data. Rendering can use the rgl package or standard or grid graphics, and a set of tools for representing and rendering surfaces using standard or grid graphics is presented.

Radiation Mitigation and Power Optimization Design Tools for Reconfigurable Hardware in Orbit

Science.gov (United States)

French, Matthew; Graham, Paul; Wirthlin, Michael; Wang, Li; Larchev, Gregory

2005-01-01

The Reconfigurable Hardware in Orbit (RHinO)project is focused on creating a set of design tools that facilitate and automate design techniques for reconfigurable computing in space, using SRAM-based field-programmable-gate-array (FPGA) technology. In the second year of the project, design tools that leverage an established FPGA design environment have been created to visualize and analyze an FPGA circuit for radiation weaknesses and power inefficiencies. For radiation, a single event Upset (SEU) emulator, persistence analysis tool, and a half-latch removal tool for Xilinx/Virtex-II devices have been created. Research is underway on a persistence mitigation tool and multiple bit upsets (MBU) studies. For power, synthesis level dynamic power visualization and analysis tools have been completed. Power optimization tools are under development and preliminary test results are positive.

Feasibility of geometrical verification of patient set-up using body contours and computed tomography data

International Nuclear Information System (INIS)

Ploeger, Lennert S.; Betgen, Anja; Gilhuijs, Kenneth G.A.; Herk, Marcel van

2003-01-01

Background and purpose: Body contours can potentially be used for patient set-up verification in external-beam radiotherapy and might enable more accurate set-up of patients prior to irradiation. The aim of this study is to test the feasibility of patient set-up verification using a body contour scanner. Material and methods: Body contour scans of 33 lung cancer and 21 head-and-neck cancer patients were acquired on a simulator. We assume that this dataset is representative for the patient set-up on an accelerator. Shortly before acquisition of the body contour scan, a pair of orthogonal simulator images was taken as a reference. Both the body contour scan and the simulator images were matched in 3D to the planning computed tomography scan. Movement of skin with respect to bone was quantified based on an analysis of variance method. Results: Set-up errors determined with body-contours agreed reasonably well with those determined with simulator images. For the lung cancer patients, the average set-up errors (mm)±1 standard deviation (SD) for the left-right, cranio-caudal and anterior-posterior directions were 1.2±2.9, -0.8±5.0 and -2.3±3.1 using body contours, compared to -0.8±3.2, -1.0±4.1 and -1.2±2.4 using simulator images. For the head-and-neck cancer patients, the set-up errors were 0.5±1.8, 0.5±2.7 and -2.2±1.8 using body contours compared to -0.4±1.2, 0.1±2.1, -0.1±1.8 using simulator images. The SD of the set-up errors obtained from analysis of the body contours were not significantly different from those obtained from analysis of the simulator images. Movement of the skin with respect to bone (1 SD) was estimated at 2.3 mm for lung cancer patients and 1.7 mm for head-and-neck cancer patients. Conclusion: Measurement of patient set-up using a body-contouring device is possible. The accuracy, however, is limited by the movement of the skin with respect to the bone. In situations where the error in the patient set-up is relatively large, it is

TeraTools: Multiparameter data acquisition software for the Windows 95/NT OS

International Nuclear Information System (INIS)

Piercey, R.B.

1997-01-01

TeraTools, a general purpose, multiparameter, data acquisition application for Windows 95NT is described. It is based on the Kmax architecture which has been used since 1986 on the Macintosh computer at numerous industrial, education, and research sites world-wide. TeraTools includes high-level support for industry-standard modular instrumentation; a built-in scripting language; drivers for commercially available interfaces; hooks for external code extensions; event file sorting and replay; and a full set of histogramming and display tools. The environment is scalable and may be applied to problems involving a few parameters or many parameters

THE METHODICAL ASPECTS OF MAXIMA USING AS A TOOL FOR FUNDAMENTAL TRAINING OF BACHELORS OF COMPUTER SCIENCE