The SIMs Meet ESL Incorporating Authentic Computer Simulation Games into the Language Classroom

ERIC Educational Resources Information Center

Miller, Megan; Hegelheimer, Volker

2006-01-01

Despite their motivational appeal to learners, innovative and technologically advanced computer simulation games targeting native English speakers frequently remain beyond the competence of ESL learners as independent didactic tools. Guided by Chapelle's (2001) criteria for determining CALL task appropriateness, this paper illustrates how the…

Computer-Oriented Calculus Courses Using Finite Differences.

ERIC Educational Resources Information Center

Gordon, Sheldon P.

The so-called discrete approach in calculus instruction involves introducing topics from the calculus of finite differences and finite sums, both for motivation and as useful tools for applications of the calculus. In particular, it provides an ideal setting in which to incorporate computers into calculus courses. This approach has been…

Computer-Assisted Language Learning Authoring Issues

ERIC Educational Resources Information Center

Otto, Sue E. K.; Pusack, James P.

2009-01-01

Computer-assisted language learning (CALL) authoring refers to a wide variety of creative development activities using software tools that run the gamut from simple templates (easy-to-use predefined forms into which content is typed) to complex authoring environments (flexible but harder-to-use systems, requiring advanced skills and a great deal…

Iranian EFL Teachers' Perceptions of the Difficulties of Implementing CALL

ERIC Educational Resources Information Center

Hedayati, Hora; Marandi, S. Susan

2014-01-01

Despite the spread of reliable technological tools and the availability of computers in Iranian universities, as well as the mounting evidence of the effectiveness of blended learning, many Iranian language teachers are still reluctant to incorporate such tools in their English as a foreign language (EFL) classes. This study inspected the status…

A Comparative Study of Collaborative Learning in "Paper Scribbles" and "Group Scribbles"

ERIC Educational Resources Information Center

Hao, Chen Fang

2010-01-01

"Paper Scribbles" (PS) consisting of markers, vanguard sheets and 3M "Post-It" notes, is a pedagogical tool to harness collective intelligence of groups for collaborative learning in the classroom. Borrowing the key features of PS and yet avoiding some of their physical limitations, a computer-based tool called "Group…

Learning Mathematics by Designing, Programming, and Investigating with Interactive, Dynamic Computer-Based Objects

ERIC Educational Resources Information Center

Marshall, Neil; Buteau, Chantal

2014-01-01

As part of their undergraduate mathematics curriculum, students at Brock University learn to create and use computer-based tools with dynamic, visual interfaces, called Exploratory Objects, developed for the purpose of conducting pure or applied mathematical investigations. A student's Development Process Model of creating and using an Exploratory…

Tools and Trends in Self-Paced Language Instruction

ERIC Educational Resources Information Center

Godwin-Jones, Robert

2007-01-01

Ever since the PLATO system of the 1960's, CALL (computer assisted language learning) has had a major focus on providing self-paced, auto-correcting exercises for language learners to practice their skills and improve their knowledge of discrete areas of language learning. The computer has been recognized from the beginning as a patient and…

On the design of computer-based models for integrated environmental science.

PubMed

McIntosh, Brian S; Jeffrey, Paul; Lemon, Mark; Winder, Nick

2005-06-01

The current research agenda in environmental science is dominated by calls to integrate science and policy to better understand and manage links between social (human) and natural (nonhuman) processes. Freshwater resource management is one area where such calls can be heard. Designing computer-based models for integrated environmental science poses special challenges to the research community. At present it is not clear whether such tools, or their outputs, receive much practical policy or planning application. It is argued that this is a result of (1) a lack of appreciation within the research modeling community of the characteristics of different decision-making processes including policy, planning, and (2) participation, (3) a lack of appreciation of the characteristics of different decision-making contexts, (4) the technical difficulties in implementing the necessary support tool functionality, and (5) the socio-technical demands of designing tools to be of practical use. This article presents a critical synthesis of ideas from each of these areas and interprets them in terms of design requirements for computer-based models being developed to provide scientific information support for policy and planning. Illustrative examples are given from the field of freshwater resources management. Although computer-based diagramming and modeling tools can facilitate processes of dialogue, they lack adequate simulation capabilities. Component-based models and modeling frameworks provide such functionality and may be suited to supporting problematic or messy decision contexts. However, significant technical (implementation) and socio-technical (use) challenges need to be addressed before such ambition can be realized.

I'm a Useful NLP Tool--Get Me out of Here

ERIC Educational Resources Information Center

Ward, Monica

2015-01-01

Irish is a compulsory subject in Irish schools. However, there are several pedagogical issues with teaching and learning the language. Computer-Assisted Language Learning (CALL) is under-utilised in schools in Ireland and even more so in the case of Irish, as there are very few CALL resources for the language. This paper looks at the lessons…

Dynamic Load-Balancing for Distributed Heterogeneous Computing of Parallel CFD Problems

NASA Technical Reports Server (NTRS)

Ecer, A.; Chien, Y. P.; Boenisch, T.; Akay, H. U.

2000-01-01

The developed methodology is aimed at improving the efficiency of executing block-structured algorithms on parallel, distributed, heterogeneous computers. The basic approach of these algorithms is to divide the flow domain into many sub- domains called blocks, and solve the governing equations over these blocks. Dynamic load balancing problem is defined as the efficient distribution of the blocks among the available processors over a period of several hours of computations. In environments with computers of different architecture, operating systems, CPU speed, memory size, load, and network speed, balancing the loads and managing the communication between processors becomes crucial. Load balancing software tools for mutually dependent parallel processes have been created to efficiently utilize an advanced computation environment and algorithms. These tools are dynamic in nature because of the chances in the computer environment during execution time. More recently, these tools were extended to a second operating system: NT. In this paper, the problems associated with this application will be discussed. Also, the developed algorithms were combined with the load sharing capability of LSF to efficiently utilize workstation clusters for parallel computing. Finally, results will be presented on running a NASA based code ADPAC to demonstrate the developed tools for dynamic load balancing.

Computational Linguistic Assessment of Genre Differences Focusing on Text Cohesive Devices of Student Writing: Implications for Library Instruction

ERIC Educational Resources Information Center

Wang, Xin; Cho, Kwangsu

2010-01-01

This study examined two major academic genres of writing: argumentative and technical writing. Three hundred eighty-four undergraduate student-produced texts were parsed and analyzed through a computational tool called Coh-Metrix. The results inform the instructional librarians that students used genre-dependent cohesive devices in a limited way…

Using Palm Technology in Participatory Simulations of Complex Systems: A New Take on Ubiquitous and Accessible Mobile Computing

ERIC Educational Resources Information Center

Klopfer, Eric; Yoon, Susan; Perry, Judy

2005-01-01

This paper reports on teachers' perceptions of the educational affordances of a handheld application called Participatory Simulations. It presents evidence from five cases representing each of the populations who work with these computational tools. Evidence across multiple data sources yield similar results to previous research evaluations of…

The ZAP Project: Designing Interactive Computer Tools for Learning Psychology

ERIC Educational Resources Information Center

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,…

MENDEL: An Intelligent Computer Tutoring System for Genetics Problem-Solving, Conjecturing, and Understanding.

ERIC Educational Resources Information Center

Streibel, Michael; And Others

1987-01-01

Describes an advice-giving computer system being developed for genetics education called MENDEL that is based on research in learning, genetics problem solving, and expert systems. The value of MENDEL as a design tool and the tutorial function are stressed. Hypothesis testing, graphics, and experiential learning are also discussed. (Author/LRW)

Developing Strategic and Reasoning Abilities with Computer Games at Primary School Level

ERIC Educational Resources Information Center

Bottino, R. M.; Ferlino, L.; Ott, M.; Tavella, M.

2007-01-01

The paper reports a small-scale, long-term pilot project designed to foster strategic and reasoning abilities in young primary school pupils by engaging them in a number of computer games, mainly those usually called mind games (brainteasers, puzzlers, etc.). In this paper, the objectives, work methodology, experimental setting, and tools used in…

Symbolic-Graphical Calculators: Teaching Tools for Mathematics.

ERIC Educational Resources Information Center

Dick, Thomas P.

1992-01-01

Explores the role that symbolic-graphical calculators can play in the current calls for reform in the mathematics curriculum. Discusses symbolic calculators and graphing calculators in relation to problem solving, computational skills, and mathematics instruction. (MDH)

Pecha Kucha Style Powerpoint Presentation: An Innovative Call Approach to Developing Oral Presentation Skills of Tertiary Students

ERIC Educational Resources Information Center

Murugaiah, Puvaneswary

2016-01-01

In computer-assisted language learning (CALL), technological tools are often used both as an end and as a means to an end (Levy & Stockwell, 2006). Microsoft PowerPoint is an example of the latter as it is commonly used in oral presentations in classrooms. However, many student presentations are often boring as students generally read from…

DECONV-TOOL: An IDL based deconvolution software package

NASA Technical Reports Server (NTRS)

Varosi, F.; Landsman, W. B.

1992-01-01

There are a variety of algorithms for deconvolution of blurred images, each having its own criteria or statistic to be optimized in order to estimate the original image data. Using the Interactive Data Language (IDL), we have implemented the Maximum Likelihood, Maximum Entropy, Maximum Residual Likelihood, and sigma-CLEAN algorithms in a unified environment called DeConv_Tool. Most of the algorithms have as their goal the optimization of statistics such as standard deviation and mean of residuals. Shannon entropy, log-likelihood, and chi-square of the residual auto-correlation are computed by DeConv_Tool for the purpose of determining the performance and convergence of any particular method and comparisons between methods. DeConv_Tool allows interactive monitoring of the statistics and the deconvolved image during computation. The final results, and optionally, the intermediate results, are stored in a structure convenient for comparison between methods and review of the deconvolution computation. The routines comprising DeConv_Tool are available via anonymous FTP through the IDL Astronomy User's Library.

Multivariate Density Estimation and Remote Sensing

NASA Technical Reports Server (NTRS)

Scott, D. W.

1983-01-01

Current efforts to develop methods and computer algorithms to effectively represent multivariate data commonly encountered in remote sensing applications are described. While this may involve scatter diagrams, multivariate representations of nonparametric probability density estimates are emphasized. The density function provides a useful graphical tool for looking at data and a useful theoretical tool for classification. This approach is called a thunderstorm data analysis.

Searching for SNPs with cloud computing

PubMed Central

2009-01-01

As DNA sequencing outpaces improvements in computer speed, there is a critical need to accelerate tasks like alignment and SNP calling. Crossbow is a cloud-computing software tool that combines the aligner Bowtie and the SNP caller SOAPsnp. Executing in parallel using Hadoop, Crossbow analyzes data comprising 38-fold coverage of the human genome in three hours using a 320-CPU cluster rented from a cloud computing service for about $85. Crossbow is available from http://bowtie-bio.sourceforge.net/crossbow/. PMID:19930550

Open source bioimage informatics for cell biology.

PubMed

Swedlow, Jason R; Eliceiri, Kevin W

2009-11-01

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

The Effect of Length of Exposure to CALL Technology on Young Iranian EFL Learners' Grammar Gain

ERIC Educational Resources Information Center

Sadeghi, Karim; Dousti, Masoumeh

2013-01-01

In the twenty-first century, integration of technology into education is a force worthy of contemplation. Among all the possible technological tools that can be integrated into EFL classes, computers seem to have achieved a more dominant position. One of the outstanding features of computers is their potential to present educational games and to…

Management Tools

NASA Technical Reports Server (NTRS)

1987-01-01

Manugistics, Inc. (formerly AVYX, Inc.) has introduced a new programming language for IBM and IBM compatible computers called TREES-pls. It is a resource management tool originating from the space shuttle, that can be used in such applications as scheduling, resource allocation project control, information management, and artificial intelligence. Manugistics, Inc. was looking for a flexible tool that can be applied to many problems with minimal adaptation. Among the non-government markets are aerospace, other manufacturing, transportation, health care, food and beverage and professional services.

Genomics for Everyone

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

Chain, Patrick

Genomics — the genetic mapping and DNA sequencing of sets of genes or the complete genomes of organisms, along with related genome analysis and database work — is emerging as one of the transformative sciences of the 21st century. But current bioinformatics tools are not accessible to most biological researchers. Now, a new computational and web-based tool called EDGE Bioinformatics is working to fulfill the promise of democratizing genomics.

Conversion and Retrievability of Hard Copy and Digital Documents on Optical Disks

DTIC Science & Technology

1992-03-01

53 B. CURRENT THESIS PREPARATION TOOLS . ....... 54 1. Thesis Preparation using G-Thesis ..... 55 2. Thesis Preparation using Framemaker ...School mainframe. • Computer Science department students can use a software package called Framemaker , available on Sun work stations in their...by most thesis typists and students. For this reason, the discussion of thesis preparation tools will be limited to; G-thesis, Framemaker and

Applications of automatic differentiation in computational fluid dynamics

NASA Technical Reports Server (NTRS)

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.

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

PubMed Central

2010-01-01

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/. PMID:20482791

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

PubMed

Ma, Jingming; Dykes, Carrie; Wu, Tao; Huang, Yangxin; Demeter, Lisa; Wu, Hulin

2010-05-18

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. 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). 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/.

"Tennis elbow". A challenging call for computation and medicine

NASA Astrophysics Data System (ADS)

Sfetsioris, D.; Bontioti, E. N.

2014-10-01

An attempt to give an insight on the features composing this musculotendinous disorder. We address the issues of definition, pathophysiology and the mechanism underlying the onset and the occurrence of the disease, diagnosis and diagnostic tools as well as the methods of treatment. We focus mostly on conservative treatment protocols and we recognize the need for a more thorough investigation with the aid of computation.

Software Engineering Tools for Scientific Models

NASA Technical Reports Server (NTRS)

Abrams, Marc; Saboo, Pallabi; Sonsini, Mike

2013-01-01

Software tools were constructed to address issues the NASA Fortran development community faces, and they were tested on real models currently in use at NASA. These proof-of-concept tools address the High-End Computing Program and the Modeling, Analysis, and Prediction Program. Two examples are the NASA Goddard Earth Observing System Model, Version 5 (GEOS-5) atmospheric model in Cell Fortran on the Cell Broadband Engine, and the Goddard Institute for Space Studies (GISS) coupled atmosphere- ocean model called ModelE, written in fixed format Fortran.

A new tool called DISSECT for analysing large genomic data sets using a Big Data approach

PubMed Central

Canela-Xandri, Oriol; Law, Andy; Gray, Alan; Woolliams, John A.; Tenesa, Albert

2015-01-01

Large-scale genetic and genomic data are increasingly available and the major bottleneck in their analysis is a lack of sufficiently scalable computational tools. To address this problem in the context of complex traits analysis, we present DISSECT. DISSECT is a new and freely available software that is able to exploit the distributed-memory parallel computational architectures of compute clusters, to perform a wide range of genomic and epidemiologic analyses, which currently can only be carried out on reduced sample sizes or under restricted conditions. We demonstrate the usefulness of our new tool by addressing the challenge of predicting phenotypes from genotype data in human populations using mixed-linear model analysis. We analyse simulated traits from 470,000 individuals genotyped for 590,004 SNPs in ∼4 h using the combined computational power of 8,400 processor cores. We find that prediction accuracies in excess of 80% of the theoretical maximum could be achieved with large sample sizes. PMID:26657010

Open source bioimage informatics for cell biology

PubMed Central

Swedlow, Jason R.; Eliceiri, Kevin W.

2009-01-01

Significant technical advances in imaging, molecular biology and genomics have fueled a revolution in cell biology, in that the molecular and structural processes of the cell are now visualized and measured routinely. Driving much of this recent development has been the advent of computational tools for the acquisition, visualization, analysis and dissemination of these datasets. These tools collectively make up a new subfield of computational biology called bioimage informatics, which is facilitated by open source approaches. We discuss why open source tools for image informatics in cell biology are needed, some of the key general attributes of what make an open source imaging application successful, and point to opportunities for further operability that should greatly accelerate future cell biology discovery. PMID:19833518

Coordinating complex decision support activities across distributed applications

NASA Technical Reports Server (NTRS)

Adler, Richard M.

1994-01-01

Knowledge-based technologies have been applied successfully to automate planning and scheduling in many problem domains. Automation of decision support can be increased further by integrating task-specific applications with supporting database systems, and by coordinating interactions between such tools to facilitate collaborative activities. Unfortunately, the technical obstacles that must be overcome to achieve this vision of transparent, cooperative problem-solving are daunting. Intelligent decision support tools are typically developed for standalone use, rely on incompatible, task-specific representational models and application programming interfaces (API's), and run on heterogeneous computing platforms. Getting such applications to interact freely calls for platform independent capabilities for distributed communication, as well as tools for mapping information across disparate representations. Symbiotics is developing a layered set of software tools (called NetWorks! for integrating and coordinating heterogeneous distributed applications. he top layer of tools consists of an extensible set of generic, programmable coordination services. Developers access these services via high-level API's to implement the desired interactions between distributed applications.

A Computer-Aided Abstracting Tool Kit.

ERIC Educational Resources Information Center

Craven, Timothy C.

1993-01-01

Reports on the development of a prototype computerized abstractor's assistant called TEXNET, a text network management system. Features of the system discussed include semantic dependency links; displays of text structure; basic text editing; extracting; weighting methods; and listings of frequent words. (Contains 25 references.) (LRW)

Desktop Publishing: A Powerful Tool for Advanced Composition Courses.

ERIC Educational Resources Information Center

Sullivan, Patricia

1988-01-01

Examines the advantages of using desktop publishing in advanced writing classes. Explains how desktop publishing can spur creativity, call attention to the interaction between words and pictures, encourage the social dimensions of computing and composing, and provide students with practical skills. (MM)

Modular HPC I/O characterization with Darshan

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

Snyder, Shane; Carns, Philip; Harms, Kevin

2016-11-13

Contemporary high-performance computing (HPC) applications encompass a broad range of distinct I/O strategies and are often executed on a number of different compute platforms in their lifetime. These large-scale HPC platforms employ increasingly complex I/O subsystems to provide a suitable level of I/O performance to applications. Tuning I/O workloads for such a system is nontrivial, and the results generally are not portable to other HPC systems. I/O profiling tools can help to address this challenge, but most existing tools only instrument specific components within the I/O subsystem that provide a limited perspective on I/O performance. The increasing diversity of scientificmore » applications and computing platforms calls for greater flexibililty and scope in I/O characterization.« less

Genomics for Everyone

ScienceCinema

Chain, Patrick

2018-05-31

Genomics — the genetic mapping and DNA sequencing of sets of genes or the complete genomes of organisms, along with related genome analysis and database work — is emerging as one of the transformative sciences of the 21st century. But current bioinformatics tools are not accessible to most biological researchers. Now, a new computational and web-based tool called EDGE Bioinformatics is working to fulfill the promise of democratizing genomics.

Serious Games as New Educational Tools: How Effective Are They? A Meta-Analysis of Recent Studies

ERIC Educational Resources Information Center

Girard, C.; Ecalle, J.; Magnan, A.

2013-01-01

Computer-assisted learning is known to be an effective tool for improving learning in both adults and children. Recent years have seen the emergence of the so-called "serious games (SGs)" that are flooding the educational games market. In this paper, the term "serious games" is used to refer to video games (VGs) intended to serve a useful purpose.…

STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud.

PubMed

Karczewski, Konrad J; Fernald, Guy Haskin; Martin, Alicia R; Snyder, Michael; Tatonetti, Nicholas P; Dudley, Joel T

2014-01-01

The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5-10 hours to process a full exome sequence and $30 and 3-8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2.

Voice and gesture-based 3D multimedia presentation tool

NASA Astrophysics Data System (ADS)

Fukutake, Hiromichi; Akazawa, Yoshiaki; Okada, Yoshihiro

2007-09-01

This paper proposes a 3D multimedia presentation tool that allows the user to manipulate intuitively only through the voice input and the gesture input without using a standard keyboard or a mouse device. The authors developed this system as a presentation tool to be used in a presentation room equipped a large screen like an exhibition room in a museum because, in such a presentation environment, it is better to use voice commands and the gesture pointing input rather than using a keyboard or a mouse device. This system was developed using IntelligentBox, which is a component-based 3D graphics software development system. IntelligentBox has already provided various types of 3D visible, reactive functional components called boxes, e.g., a voice input component and various multimedia handling components. IntelligentBox also provides a dynamic data linkage mechanism called slot-connection that allows the user to develop 3D graphics applications by combining already existing boxes through direct manipulations on a computer screen. Using IntelligentBox, the 3D multimedia presentation tool proposed in this paper was also developed as combined components only through direct manipulations on a computer screen. The authors have already proposed a 3D multimedia presentation tool using a stage metaphor and its voice input interface. This time, we extended the system to make it accept the user gesture input besides voice commands. This paper explains details of the proposed 3D multimedia presentation tool and especially describes its component-based voice and gesture input interfaces.

SeqMule: automated pipeline for analysis of human exome/genome sequencing data.

PubMed

Guo, Yunfei; Ding, Xiaolei; Shen, Yufeng; Lyon, Gholson J; Wang, Kai

2015-09-18

Next-generation sequencing (NGS) technology has greatly helped us identify disease-contributory variants for Mendelian diseases. However, users are often faced with issues such as software compatibility, complicated configuration, and no access to high-performance computing facility. Discrepancies exist among aligners and variant callers. We developed a computational pipeline, SeqMule, to perform automated variant calling from NGS data on human genomes and exomes. SeqMule integrates computational-cluster-free parallelization capability built on top of the variant callers, and facilitates normalization/intersection of variant calls to generate consensus set with high confidence. SeqMule integrates 5 alignment tools, 5 variant calling algorithms and accepts various combinations all by one-line command, therefore allowing highly flexible yet fully automated variant calling. In a modern machine (2 Intel Xeon X5650 CPUs, 48 GB memory), when fast turn-around is needed, SeqMule generates annotated VCF files in a day from a 30X whole-genome sequencing data set; when more accurate calling is needed, SeqMule generates consensus call set that improves over single callers, as measured by both Mendelian error rate and consistency. SeqMule supports Sun Grid Engine for parallel processing, offers turn-key solution for deployment on Amazon Web Services, allows quality check, Mendelian error check, consistency evaluation, HTML-based reports. SeqMule is available at http://seqmule.openbioinformatics.org.

Muver, a computational framework for accurately calling accumulated mutations.

PubMed

Burkholder, Adam B; Lujan, Scott A; Lavender, Christopher A; Grimm, Sara A; Kunkel, Thomas A; Fargo, David C

2018-05-09

Identification of mutations from next-generation sequencing data typically requires a balance between sensitivity and accuracy. This is particularly true of DNA insertions and deletions (indels), that can impart significant phenotypic consequences on cells but are harder to call than substitution mutations from whole genome mutation accumulation experiments. To overcome these difficulties, we present muver, a computational framework that integrates established bioinformatics tools with novel analytical methods to generate mutation calls with the extremely low false positive rates and high sensitivity required for accurate mutation rate determination and comparison. Muver uses statistical comparison of ancestral and descendant allelic frequencies to identify variant loci and assigns genotypes with models that include per-sample assessments of sequencing errors by mutation type and repeat context. Muver identifies maximally parsimonious mutation pathways that connect these genotypes, differentiating potential allelic conversion events and delineating ambiguities in mutation location, type, and size. Benchmarking with a human gold standard father-son pair demonstrates muver's sensitivity and low false positive rates. In DNA mismatch repair (MMR) deficient Saccharomyces cerevisiae, muver detects multi-base deletions in homopolymers longer than the replicative polymerase footprint at rates greater than predicted for sequential single-base deletions, implying a novel multi-repeat-unit slippage mechanism. Benchmarking results demonstrate the high accuracy and sensitivity achieved with muver, particularly for indels, relative to available tools. Applied to an MMR-deficient Saccharomyces cerevisiae system, muver mutation calls facilitate mechanistic insights into DNA replication fidelity.

Usability analysis of 2D graphics software for designing technical clothing.

PubMed

Teodoroski, Rita de Cassia Clark; Espíndola, Edilene Zilma; Silva, Enéias; Moro, Antônio Renato Pereira; Pereira, Vera Lucia D V

2012-01-01

With the advent of technology, the computer became a working tool increasingly present in companies. Its purpose is to increase production and reduce the inherent errors in manual production. The aim of this study was to analyze the usability of 2D graphics software in creating clothing designs by a professional during his work. The movements of the mouse, keyboard and graphical tools were monitored in real time by software Camtasia 7® installed on the user's computer. To register the use of mouse and keyboard we used auxiliary software called MouseMeter®, which quantifies the number of times they pressed the right, middle and left mouse's buttons, the keyboard and also the distance traveled in meters by the cursor on the screen. Data was collected in periods of 15 minutes, 1 hour and 8 hours, consecutively. The results showed that the job is considered repetitive and high demands physical efforts, which can lead to the appearance of repetitive strain injuries. Thus, the goal of minimizing operator efforts and thereby enhance the usability of the examined tool, becomes imperative to replace the mouse by a device called tablet, which also offers an electronic pen and a drawing platform for design development.

The Effect of Age and Task Difficulty

ERIC Educational Resources Information Center

Mallo, Jason; Nordstrom, Cynthia R.; Bartels, Lynn K.; Traxler, Anthony

2007-01-01

Electronic Performance Monitoring (EPM) is a common technique used to record employee performance. EPM may include counting computer keystrokes, monitoring employees' phone calls or internet activity, or documenting time spent on work activities. Despite EPM's prevalence, no studies have examined how this management tool affects older workers--a…

Temporal Visualization for Legal Case Histories.

ERIC Educational Resources Information Center

Harris, Chanda; Allen, Robert B.; Plaisant, Catherine; Shneiderman, Ben

1999-01-01

Discusses visualization of legal information using a tool for temporal information called "LifeLines." Explores ways "LifeLines" could aid in viewing the links between original case and direct and indirect case histories. Uses the case of Apple Computer, Inc. versus Microsoft Corporation and Hewlett Packard Company to…

"Extreme Programming" in a Bioinformatics Class

ERIC Educational Resources Information Center

Kelley, Scott; Alger, Christianna; Deutschman, Douglas

2009-01-01

The importance of Bioinformatics tools and methodology in modern biological research underscores the need for robust and effective courses at the college level. This paper describes such a course designed on the principles of cooperative learning based on a computer software industry production model called "Extreme Programming" (EP).…

Framework for architecture-independent run-time reconfigurable applications

NASA Astrophysics Data System (ADS)

Lehn, David I.; Hudson, Rhett D.; Athanas, Peter M.

2000-10-01

Configurable Computing Machines (CCMs) have emerged as a technology with the computational benefits of custom ASICs as well as the flexibility and reconfigurability of general-purpose microprocessors. Significant effort from the research community has focused on techniques to move this reconfigurability from a rapid application development tool to a run-time tool. This requires the ability to change the hardware design while the application is executing and is known as Run-Time Reconfiguration (RTR). Widespread acceptance of run-time reconfigurable custom computing depends upon the existence of high-level automated design tools. Such tools must reduce the designers effort to port applications between different platforms as the architecture, hardware, and software evolves. A Java implementation of a high-level application framework, called Janus, is presented here. In this environment, developers create Java classes that describe the structural behavior of an application. The framework allows hardware and software modules to be freely mixed and interchanged. A compilation phase of the development process analyzes the structure of the application and adapts it to the target platform. Janus is capable of structuring the run-time behavior of an application to take advantage of the memory and computational resources available.

Simultaneous Aerodynamic and Structural Design Optimization (SASDO) for a 3-D Wing

NASA Technical Reports Server (NTRS)

Gumbert, Clyde R.; Hou, Gene J.-W.; Newman, Perry A.

2001-01-01

The formulation and implementation of an optimization method called Simultaneous Aerodynamic and Structural Design Optimization (SASDO) is shown as an extension of the Simultaneous Aerodynamic Analysis and Design Optimization (SAADO) method. It is extended by the inclusion of structure element sizing parameters as design variables and Finite Element Method (FEM) analysis responses as constraints. The method aims to reduce the computational expense. incurred in performing shape and sizing optimization using state-of-the-art Computational Fluid Dynamics (CFD) flow analysis, FEM structural analysis and sensitivity analysis tools. SASDO is applied to a simple. isolated, 3-D wing in inviscid flow. Results show that the method finds the saine local optimum as a conventional optimization method with some reduction in the computational cost and without significant modifications; to the analysis tools.

STORMSeq: An Open-Source, User-Friendly Pipeline for Processing Personal Genomics Data in the Cloud

PubMed Central

Karczewski, Konrad J.; Fernald, Guy Haskin; Martin, Alicia R.; Snyder, Michael; Tatonetti, Nicholas P.; Dudley, Joel T.

2014-01-01

The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5–10 hours to process a full exome sequence and $30 and 3–8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2. PMID:24454756

Cohesion Features in ESL Reading: Comparing Beginning, Intermediate and Advanced Textbooks

ERIC Educational Resources Information Center

Plakans, Lia; Bilki, Zeynep

2016-01-01

This study of English as a second language (ESL) reading textbooks investigates cohesion in reading passages from 27 textbooks. The guiding research questions were whether and how cohesion differs across textbooks written for beginning, intermediate, and advanced second language readers. Using a computational tool called Coh-Metrix, textual…

Proteinortho: detection of (co-)orthologs in large-scale analysis.

PubMed

Lechner, Marcus; Findeiss, Sven; Steiner, Lydia; Marz, Manja; Stadler, Peter F; Prohaska, Sonja J

2011-04-28

Orthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood of sequence data, and hence the rapidly increasing number of genomes that can be compared simultaneously, calls for efficient software tools as brute-force approaches with quadratic memory requirements become infeasible in practise. The rapid pace at which new data become available, furthermore, makes it desirable to compute genome-wide orthology relations for a given dataset rather than relying on relations listed in databases. The program Proteinortho described here is a stand-alone tool that is geared towards large datasets and makes use of distributed computing techniques when run on multi-core hardware. It implements an extended version of the reciprocal best alignment heuristic. We apply Proteinortho to compute orthologous proteins in the complete set of all 717 eubacterial genomes available at NCBI at the beginning of 2009. We identified thirty proteins present in 99% of all bacterial proteomes. Proteinortho significantly reduces the required amount of memory for orthology analysis compared to existing tools, allowing such computations to be performed on off-the-shelf hardware.

Computer Aided Method for System Safety and Reliability Assessments

DTIC Science & Technology

2008-09-01

program between 1998 and 2003. This tool was not marketed in the public domain after the CRV program ended. The other tool is called eXpress, and it...support Government reviewed and approved analyses methodologies which can 5 then be shared with other government agencies and industry partners...Documented for B&R, UP&L, EPRI 30 DEC 80 GO IBM Version Enhanced at UCC , Dallas, Descriptors, Facility to Alter Array Sizes, Explanation of Use 1 SEP 82

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

PubMed Central

Paley, Suzanne M.; Krummenacker, Markus; Latendresse, Mario; Dale, Joseph M.; Lee, Thomas J.; Kaipa, Pallavi; Gilham, Fred; Spaulding, Aaron; Popescu, Liviu; Altman, Tomer; Paulsen, Ian; Keseler, Ingrid M.; Caspi, Ron

2010-01-01

Pathway Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc integrates the evolving understanding of the genes, proteins, metabolic network and regulatory network of an organism. This article provides an overview of Pathway Tools capabilities. The software performs multiple computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers and prediction of operons. It enables interactive editing of PGDBs by DB curators. It supports web publishing of PGDBs, and provides a large number of query and visualization tools. The software also supports comparative analyses of PGDBs, and provides several systems biology analyses of PGDBs including reachability analysis of metabolic networks, and interactive tracing of metabolites through a metabolic network. More than 800 PGDBs have been created using Pathway Tools by scientists around the world, many of which are curated DBs for important model organisms. Those PGDBs can be exchanged using a peer-to-peer DB sharing system called the PGDB Registry. PMID:19955237

GAPIT: genome association and prediction integrated tool.

PubMed

Lipka, Alexander E; Tian, Feng; Wang, Qishan; Peiffer, Jason; Li, Meng; Bradbury, Peter J; Gore, Michael A; Buckler, Edward S; Zhang, Zhiwu

2012-09-15

Software programs that conduct genome-wide association studies and genomic prediction and selection need to use methodologies that maximize statistical power, provide high prediction accuracy and run in a computationally efficient manner. We developed an R package called Genome Association and Prediction Integrated Tool (GAPIT) that implements advanced statistical methods including the compressed mixed linear model (CMLM) and CMLM-based genomic prediction and selection. The GAPIT package can handle large datasets in excess of 10 000 individuals and 1 million single-nucleotide polymorphisms with minimal computational time, while providing user-friendly access and concise tables and graphs to interpret results. http://www.maizegenetics.net/GAPIT. zhiwu.zhang@cornell.edu Supplementary data are available at Bioinformatics online.

Conversion of Component-Based Point Definition to VSP Model and Higher Order Meshing

NASA Technical Reports Server (NTRS)

Ordaz, Irian

2011-01-01

Vehicle Sketch Pad (VSP) has become a powerful conceptual and parametric geometry tool with numerous export capabilities for third-party analysis codes as well as robust surface meshing capabilities for computational fluid dynamics (CFD) analysis. However, a capability gap currently exists for reconstructing a fully parametric VSP model of a geometry generated by third-party software. A computer code called GEO2VSP has been developed to close this gap and to allow the integration of VSP into a closed-loop geometry design process with other third-party design tools. Furthermore, the automated CFD surface meshing capability of VSP are demonstrated for component-based point definition geometries in a conceptual analysis and design framework.

A flexible tool for diagnosing water, energy, and entropy budgets in climate models

NASA Astrophysics Data System (ADS)

Lembo, Valerio; Lucarini, Valerio

2017-04-01

We have developed a new flexible software for studying the global energy budget, the hydrological cycle, and the material entropy production of global climate models. The program receives as input radiative, latent and sensible energy fluxes, with the requirement that the variable names are in agreement with the Climate and Forecast (CF) conventions for the production of NetCDF datasets. Annual mean maps, meridional sections and time series are computed by means of Climate Data Operators (CDO) collection of command line operators developed at Max-Planck Institute for Meteorology (MPI-M). If a land-sea mask is provided, the program also computes the required quantities separately on the continents and oceans. Depending on the user's choice, the program also calls the MATLAB software to compute meridional heat transports and location and intensities of the peaks in the two hemispheres. We are currently planning to adapt the program in order to be included in the Earth System Model eValuation Tool (ESMValTool) community diagnostics.

VARS-TOOL: A Comprehensive, Efficient, and Robust Sensitivity Analysis Toolbox

NASA Astrophysics Data System (ADS)

Razavi, S.; Sheikholeslami, R.; Haghnegahdar, A.; Esfahbod, B.

2016-12-01

VARS-TOOL is an advanced sensitivity and uncertainty analysis toolbox, applicable to the full range of computer simulation models, including Earth and Environmental Systems Models (EESMs). The toolbox was developed originally around VARS (Variogram Analysis of Response Surfaces), which is a general framework for Global Sensitivity Analysis (GSA) that utilizes the variogram/covariogram concept to characterize the full spectrum of sensitivity-related information, thereby providing a comprehensive set of "global" sensitivity metrics with minimal computational cost. VARS-TOOL is unique in that, with a single sample set (set of simulation model runs), it generates simultaneously three philosophically different families of global sensitivity metrics, including (1) variogram-based metrics called IVARS (Integrated Variogram Across a Range of Scales - VARS approach), (2) variance-based total-order effects (Sobol approach), and (3) derivative-based elementary effects (Morris approach). VARS-TOOL is also enabled with two novel features; the first one being a sequential sampling algorithm, called Progressive Latin Hypercube Sampling (PLHS), which allows progressively increasing the sample size for GSA while maintaining the required sample distributional properties. The second feature is a "grouping strategy" that adaptively groups the model parameters based on their sensitivity or functioning to maximize the reliability of GSA results. These features in conjunction with bootstrapping enable the user to monitor the stability, robustness, and convergence of GSA with the increase in sample size for any given case study. VARS-TOOL has been shown to achieve robust and stable results within 1-2 orders of magnitude smaller sample sizes (fewer model runs) than alternative tools. VARS-TOOL, available in MATLAB and Python, is under continuous development and new capabilities and features are forthcoming.

Sharing programming resources between Bio* projects through remote procedure call and native call stack strategies.

PubMed

Prins, Pjotr; Goto, Naohisa; Yates, Andrew; Gautier, Laurent; Willis, Scooter; Fields, Christopher; Katayama, Toshiaki

2012-01-01

Open-source software (OSS) encourages computer programmers to reuse software components written by others. In evolutionary bioinformatics, OSS comes in a broad range of programming languages, including C/C++, Perl, Python, Ruby, Java, and R. To avoid writing the same functionality multiple times for different languages, it is possible to share components by bridging computer languages and Bio* projects, such as BioPerl, Biopython, BioRuby, BioJava, and R/Bioconductor. In this chapter, we compare the two principal approaches for sharing software between different programming languages: either by remote procedure call (RPC) or by sharing a local call stack. RPC provides a language-independent protocol over a network interface; examples are RSOAP and Rserve. The local call stack provides a between-language mapping not over the network interface, but directly in computer memory; examples are R bindings, RPy, and languages sharing the Java Virtual Machine stack. This functionality provides strategies for sharing of software between Bio* projects, which can be exploited more often. Here, we present cross-language examples for sequence translation, and measure throughput of the different options. We compare calling into R through native R, RSOAP, Rserve, and RPy interfaces, with the performance of native BioPerl, Biopython, BioJava, and BioRuby implementations, and with call stack bindings to BioJava and the European Molecular Biology Open Software Suite. In general, call stack approaches outperform native Bio* implementations and these, in turn, outperform RPC-based approaches. To test and compare strategies, we provide a downloadable BioNode image with all examples, tools, and libraries included. The BioNode image can be run on VirtualBox-supported operating systems, including Windows, OSX, and Linux.

Flight test validation of a design procedure for digital autopilots

NASA Technical Reports Server (NTRS)

Bryant, W. H.

1983-01-01

Commercially available general aviation autopilots are currently in transition from an analogue circuit system to a computer implemented digital flight control system. Well known advantages of the digital autopilot include enhanced modes, self-test capacity, fault detection, and greater computational capacity. A digital autopilot's computational capacity can be used to full advantage by increasing the sophistication of the digital autopilot's chief function, stability and control. NASA's Langley Research Center has been pursuing the development of direct digital design tools for aircraft stabilization systems for several years. This effort has most recently been directed towards the development and realization of multi-mode digital autopilots for GA aircraft, conducted under a SPIFR-related program called the General Aviation Terminal Operations Research (GATOR) Program. This presentation focuses on the implementation and testing of a candidate multi-mode autopilot designed using these newly developed tools.

Final Report

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

Hollingsworth, Jeff

2014-07-31

The purpose of this project was to develop tools and techniques to improve the ability of computational scientists to investigate and correct problems (bugs) in their programs. Specifically, the University of Maryland component of this project focused on the problems associated with the finite number of bits available in a computer to represent numeric values. In large scale scientific computation, numbers are frequently added to and multiplied with each other billions of times. Thus even small errors due to the representation of numbers can accumulate into big errors. However, using too many bits to represent a number results in additionalmore » computation, memory, and energy costs. Thus it is critical to find the right size for numbers. This project focused on several aspects of this general problem. First, we developed a tool to look for cancelations, the catastrophic loss of precision in numbers due to the addition of two numbers whose actual values are close to each other, but whose representation in a computer is identical or nearly so. Second, we developed a suite of tools to allow programmers to identify exactly how much precision is required for each operation in their program. This tool allows programmers to both verify that enough precision is available, but more importantly find cases where extra precision could be eliminated to allow the program to use less memory, computer time, or energy. These tools use advanced binary modification techniques to allow the analysis of actual optimized code. The system, called Craft, has been applied to a number of benchmarks and real applications.« less

Tools Automate Spacecraft Testing, Operation

NASA Technical Reports Server (NTRS)

2010-01-01

"NASA began the Small Explorer (SMEX) program to develop spacecraft to advance astrophysics and space physics. As one of the entities supporting software development at Goddard Space Flight Center, the Hammers Company Inc. (tHC Inc.), of Greenbelt, Maryland, developed the Integrated Test and Operations System to support SMEX. Later, the company received additional Small Business Innovation Research (SBIR) funding from Goddard for a tool to facilitate the development of flight software called VirtualSat. NASA uses the tools to support 15 satellites, and the aerospace industry is using them to develop science instruments, spacecraft computer systems, and navigation and control software."

Gene calling and bacterial genome annotation with BG7.

PubMed

Tobes, Raquel; Pareja-Tobes, Pablo; Manrique, Marina; Pareja-Tobes, Eduardo; Kovach, Evdokim; Alekhin, Alexey; Pareja, Eduardo

2015-01-01

New massive sequencing technologies are providing many bacterial genome sequences from diverse taxa but a refined annotation of these genomes is crucial for obtaining scientific findings and new knowledge. Thus, bacterial genome annotation has emerged as a key point to investigate in bacteria. Any efficient tool designed specifically to annotate bacterial genomes sequenced with massively parallel technologies has to consider the specific features of bacterial genomes (absence of introns and scarcity of nonprotein-coding sequence) and of next-generation sequencing (NGS) technologies (presence of errors and not perfectly assembled genomes). These features make it convenient to focus on coding regions and, hence, on protein sequences that are the elements directly related with biological functions. In this chapter we describe how to annotate bacterial genomes with BG7, an open-source tool based on a protein-centered gene calling/annotation paradigm. BG7 is specifically designed for the annotation of bacterial genomes sequenced with NGS. This tool is sequence error tolerant maintaining their capabilities for the annotation of highly fragmented genomes or for annotating mixed sequences coming from several genomes (as those obtained through metagenomics samples). BG7 has been designed with scalability as a requirement, with a computing infrastructure completely based on cloud computing (Amazon Web Services).

Advanced tools for smartphone-based experiments: phyphox

NASA Astrophysics Data System (ADS)

Staacks, S.; Hütz, S.; Heinke, H.; Stampfer, C.

2018-07-01

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 on Android and iOS.

The PLATO System: A Study in the Diffusion of an Innovation.

ERIC Educational Resources Information Center

Driscoll, Francis D.; Wolf, W. C., Jr.

This study was designed to ascertain the relationships between the steps of a tool designed to link knowledge production and the needs of knowledge users (the Wolf-Welsh Linkage Methodology or WWLM) with milestones in the evolution of an innovative computer-assisted instructional system called PLATO (Programming Logic for Advanced Teaching…

An Authoring System for Creating Computer-Based Role-Performance Trainers.

ERIC Educational Resources Information Center

Guralnick, David; Kass, Alex

This paper describes a multimedia authoring system called MOPed-II. Like other authoring systems, MOPed-II reduces the time and expense of producing end-user applications by eliminating much of the programming effort they require. However, MOPed-II reflects an approach to authoring tools for educational multimedia which is different from most…

The Development of a Web-Based Virtual Environment for Teaching Qualitative Analysis of Structures

ERIC Educational Resources Information Center

O'Dwyer, D. W.; Logan-Phelan, T. M.; O'Neill, E. A.

2007-01-01

The current paper describes the design and development of a qualitative analysis course and an interactive web-based teaching and assessment tool called VSE (virtual structural environment). The widespread reliance on structural analysis programs requires engineers to be able to verify computer output by carrying out qualitative analyses.…

The Effects of Computer Assisted Mediating Prompts on EFL Learners' Writing Ability

ERIC Educational Resources Information Center

Damavandi, Zahra Mousazadeh; Hassaskhah, Jaleh; Zafarghandi, Amir Mahdavi

2018-01-01

This study aims to examine the EFL learners' perception and process of writing development through using a digital storytelling tool, called "Storyjumper." To do so, 15 intermediate-level students were participants of the study. The participants' writing development was frequently assessed through a series of repeated writing tests…

The Miller Motivation Scale: A New Counselling and Research Tool.

ERIC Educational Resources Information Center

Miller, Harold J.

The Miller Motivation Scale is a 160-item computer scored scale. It was developed to measure quickly and easily and display the motivational profile of the client. It has eight subscales. Five subscales measure encouragement, self-fulfillment and social interest. They are called Creative, Innovative, Productive, Cooperative, and Power. Three…

Electronic Mail Is One High-Tech Management Tool that Really Delivers.

ERIC Educational Resources Information Center

Parker, Donald C.

1987-01-01

Describes an electronic mail system used by the Horseheads (New York) Central School Distict's eight schools and central office that saves time and enhances productivity. This software calls up information from the district's computer network and sends it to other users' special files--electronic "mailboxes" set aside for messages and…

Integration of Wireless Technologies in Smart University Campus Environment: Framework Architecture

ERIC Educational Resources Information Center

Khamayseh, Yaser; Mardini, Wail; Aljawarneh, Shadi; Yassein, Muneer Bani

2015-01-01

In this paper, the authors are particularly interested in enhancing the education process by integrating new tools to the teaching environments. This enhancement is part of an emerging concept, called smart campus. Smart University Campus will come up with a new ubiquitous computing and communication field and change people's lives radically by…

Holy COW: Scaffolding Case Based Conferencing on the Web with Preservice Teachers.

ERIC Educational Resources Information Center

Bonk, Curtis J.; Angeli, Charoula; Malikowski, Steve R.; Supplee, Lauren

2001-01-01

This study on the effects of scaffolding electronic case-based learning on preservice teacher education explored the use of an asynchronous computer conferencing tool called COW (Conferencing on the Web) to determine whether open-ended learning environments that encouraged critical thinking could foster a greater degree of course connections and…

An innovative approach to compensator design

NASA Technical Reports Server (NTRS)

Mitchell, J. R.; Mcdaniel, W. L., Jr.

1973-01-01

The design is considered of a computer-aided-compensator for a control system from a frequency domain point of view. The design technique developed is based on describing the open loop frequency response by n discrete frequency points which result in n functions of the compensator coefficients. Several of these functions are chosen so that the system specifications are properly portrayed; then mathematical programming is used to improve all of these functions which have values below minimum standards. To do this, several definitions in regard to measuring the performance of a system in the frequency domain are given, e.g., relative stability, relative attenuation, proper phasing, etc. Next, theorems which govern the number of compensator coefficients necessary to make improvements in a certain number of functions are proved. After this a mathematical programming tool for aiding in the solution of the problem is developed. This tool is called the constraint improvement algorithm. Then for applying the constraint improvement algorithm generalized, gradients for the constraints are derived. Finally, the necessary theory is incorporated in a Computer program called CIP (compensator Improvement Program). The practical usefulness of CIP is demonstrated by two large system examples.

A Prototype of Pilot Knowledge Evaluation by an Intelligent CAI (Computer -Aided Instruction) System Using a Bayesian Diagnostic Model.

DTIC Science & Technology

1987-06-01

to a field of research called Computer-Aided Instruction (CAI). CAI is a powerful methodology for enhancing the overall quaiity and effectiveness of...provides a very powerful tool for statistical inference, especially when pooling informations from different source is appropriate. Thus. prior...04 , 2 ’ .. ."k, + ++ ,,;-+-,..,,..v ->’,0,,.’ I The power of the model lies in its ability to adapt a diagnostic session to the level of knowledge

Akuna: An Open Source User Environment for Managing Subsurface Simulation Workflows

NASA Astrophysics Data System (ADS)

Freedman, V. L.; Agarwal, D.; Bensema, K.; Finsterle, S.; Gable, C. W.; Keating, E. H.; Krishnan, H.; Lansing, C.; Moeglein, W.; Pau, G. S. H.; Porter, E.; Scheibe, T. D.

2014-12-01

The U.S. Department of Energy (DOE) is investing in development of a numerical modeling toolset called ASCEM (Advanced Simulation Capability for Environmental Management) to support modeling analyses at legacy waste sites. ASCEM is an open source and modular computing framework that incorporates new advances and tools for predicting contaminant fate and transport in natural and engineered systems. The ASCEM toolset includes both a Platform with Integrated Toolsets (called Akuna) and a High-Performance Computing multi-process simulator (called Amanzi). The focus of this presentation is on Akuna, an open-source user environment that manages subsurface simulation workflows and associated data and metadata. In this presentation, key elements of Akuna are demonstrated, which includes toolsets for model setup, database management, sensitivity analysis, parameter estimation, uncertainty quantification, and visualization of both model setup and simulation results. A key component of the workflow is in the automated job launching and monitoring capabilities, which allow a user to submit and monitor simulation runs on high-performance, parallel computers. Visualization of large outputs can also be performed without moving data back to local resources. These capabilities make high-performance computing accessible to the users who might not be familiar with batch queue systems and usage protocols on different supercomputers and clusters.

The Design of Modular Web-Based Collaboration

NASA Astrophysics Data System (ADS)

Intapong, Ploypailin; Settapat, Sittapong; Kaewkamnerdpong, Boonserm; Achalakul, Tiranee

Online collaborative systems are popular communication channels as the systems allow people from various disciplines to interact and collaborate with ease. The systems provide communication tools and services that can be integrated on the web; consequently, the systems are more convenient to use and easier to install. Nevertheless, most of the currently available systems are designed according to some specific requirements and cannot be straightforwardly integrated into various applications. This paper provides the design of a new collaborative platform, which is component-based and re-configurable. The platform is called the Modular Web-based Collaboration (MWC). MWC shares the same concept as computer supported collaborative work (CSCW) and computer-supported collaborative learning (CSCL), but it provides configurable tools for online collaboration. Each tool module can be integrated into users' web applications freely and easily. This makes collaborative system flexible, adaptable and suitable for online collaboration.

Knowledge-acquisition tools for medical knowledge-based systems.

PubMed

Lanzola, G; Quaglini, S; Stefanelli, M

1995-03-01

Knowledge-based systems (KBS) have been proposed to solve a large variety of medical problems. A strategic issue for KBS development and maintenance are the efforts required for both knowledge engineers and domain experts. The proposed solution is building efficient knowledge acquisition (KA) tools. This paper presents a set of KA tools we are developing within a European Project called GAMES II. They have been designed after the formulation of an epistemological model of medical reasoning. The main goal is that of developing a computational framework which allows knowledge engineers and domain experts to interact cooperatively in developing a medical KBS. To this aim, a set of reusable software components is highly recommended. Their design was facilitated by the development of a methodology for KBS construction. It views this process as comprising two activities: the tailoring of the epistemological model to the specific medical task to be executed and the subsequent translation of this model into a computational architecture so that the connections between computational structures and their knowledge level counterparts are maintained. The KA tools we developed are illustrated taking examples from the behavior of a KBS we are building for the management of children with acute myeloid leukemia.

Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses.

PubMed

Golosova, Olga; Henderson, Ross; Vaskin, Yuriy; Gabrielian, Andrei; Grekhov, German; Nagarajan, Vijayaraj; Oler, Andrew J; Quiñones, Mariam; Hurt, Darrell; Fursov, Mikhail; Huyen, Yentram

2014-01-01

The advent of Next Generation Sequencing (NGS) technologies has opened new possibilities for researchers. However, the more biology becomes a data-intensive field, the more biologists have to learn how to process and analyze NGS data with complex computational tools. Even with the availability of common pipeline specifications, it is often a time-consuming and cumbersome task for a bench scientist to install and configure the pipeline tools. We believe that a unified, desktop and biologist-friendly front end to NGS data analysis tools will substantially improve productivity in this field. Here we present NGS pipelines "Variant Calling with SAMtools", "Tuxedo Pipeline for RNA-seq Data Analysis" and "Cistrome Pipeline for ChIP-seq Data Analysis" integrated into the Unipro UGENE desktop toolkit. We describe the available UGENE infrastructure that helps researchers run these pipelines on different datasets, store and investigate the results and re-run the pipelines with the same parameters. These pipeline tools are included in the UGENE NGS package. Individual blocks of these pipelines are also available for expert users to create their own advanced workflows.

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

PubMed Central

2011-01-01

Background Orthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood of sequence data, and hence the rapidly increasing number of genomes that can be compared simultaneously, calls for efficient software tools as brute-force approaches with quadratic memory requirements become infeasible in practise. The rapid pace at which new data become available, furthermore, makes it desirable to compute genome-wide orthology relations for a given dataset rather than relying on relations listed in databases. Results The program Proteinortho described here is a stand-alone tool that is geared towards large datasets and makes use of distributed computing techniques when run on multi-core hardware. It implements an extended version of the reciprocal best alignment heuristic. We apply Proteinortho to compute orthologous proteins in the complete set of all 717 eubacterial genomes available at NCBI at the beginning of 2009. We identified thirty proteins present in 99% of all bacterial proteomes. Conclusions Proteinortho significantly reduces the required amount of memory for orthology analysis compared to existing tools, allowing such computations to be performed on off-the-shelf hardware. PMID:21526987

Smart Phones, a Powerful Tool in the Chemistry Classroom

ERIC Educational Resources Information Center

Williams, Antony J.; Pence, Harry E.

2011-01-01

Cell phones, especially "smart phones", seem to have become ubiquitous. Actually, it is misleading to call many of these devices phones, as they are actually a portable and powerful computer that can be very valuable in the chemistry classroom. Currently, there are three major ways in which smart phones can be used for education. Smart phones…

LamLum : a tool for evaluating the financial feasibility of laminated lumber plants

Treesearch

E.M. (Ted) Bilek; John F. Hunt

2006-01-01

A spreadsheet-based computer program called LamLum was created to analyze the economics of value- added laminated lumber manufacturing facilities. Such facilities manufacture laminations, typically from lower grades of structural lumber, then glue these laminations together to make various types of higher value laminated lumber products. This report provides the...

Tool Mediation in Focus on Form Activities: Case Studies in a Grammar-Exploring Environment

ERIC Educational Resources Information Center

Karlstrom, Petter; Cerratto-Pargman, Teresa; Lindstrom, Henrik; Knutsson, Ola

2007-01-01

We present two case studies of two different pedagogical tasks in a Computer Assisted Language Learning environment called Grim. The main design principle in Grim is to support "Focus on Form" in second language pedagogy. Grim contains several language technology-based features for exploring linguistic forms (static, rule-based and statistical),…

Visual management support system

Treesearch

Lee Anderson; Jerry Mosier; Geoffrey Chandler

1979-01-01

The Visual Management Support System (VMSS) is an extension of an existing computer program called VIEWIT, which has been extensively used by the U. S. Forest Service. The capabilities of this program lie in the rapid manipulation of large amounts of data, specifically opera-ting as a tool to overlay or merge one set of data with another. VMSS was conceived to...

The P.E.A.C.E. Pack: A Computerized Online Assessment of School Bullying

ERIC Educational Resources Information Center

Slee, Phillip T.; Mohyla, Jury

2014-01-01

School bullying is an international problem with harmful outcomes for those involved. This study describes the design and field testing of an innovative computer-based social learning tool for assessing student perceptions of bullying developed for an Australian intervention program called the P.E.A.C.E. Pack. Students rate their peer group…

High-order computational fluid dynamics tools for aircraft design

PubMed Central

Wang, Z. J.

2014-01-01

Most forecasts predict an annual airline traffic growth rate between 4.5 and 5% in the foreseeable future. To sustain that growth, the environmental impact of aircraft cannot be ignored. Future aircraft must have much better fuel economy, dramatically less greenhouse gas emissions and noise, in addition to better performance. Many technical breakthroughs must take place to achieve the aggressive environmental goals set up by governments in North America and Europe. One of these breakthroughs will be physics-based, highly accurate and efficient computational fluid dynamics and aeroacoustics tools capable of predicting complex flows over the entire flight envelope and through an aircraft engine, and computing aircraft noise. Some of these flows are dominated by unsteady vortices of disparate scales, often highly turbulent, and they call for higher-order methods. As these tools will be integral components of a multi-disciplinary optimization environment, they must be efficient to impact design. Ultimately, the accuracy, efficiency, robustness, scalability and geometric flexibility will determine which methods will be adopted in the design process. This article explores these aspects and identifies pacing items. PMID:25024419

Red-shouldered hawk broadcast surveys: Factors affecting detection of responses and population trends

USGS Publications Warehouse

McLeod, M.A.; Andersen, D.E.

1998-01-01

Forest-nesting raptors are often difficult to detect and monitor because they can be secretive, and their nests can be difficult to locate. Some species, however, respond to broadcasts of taped calls, and these responses may be useful both in monitoring population trends and in locating nests. We conducted broadcast surveys on roads and at active red-shouldered hawk (Buteo lineatus) nests in northcentral Minnesota to determine effects of type of call (conspecific or great horned owl [Bubo virginianus]), time of day, and phase of the breeding cycle on red-shouldered hawk response behavior and to evaluate usefulness of broadcasts as a population monitoring tool using area occupied-probability-of-detection techniques. During the breeding seasons of 1994 and 1995, we surveyed 4 10-station road transects 59 times and conducted 76 surveys at 24 active nests. Results of these surveys indicated conspecific calls broadcast prior to hatch and early in the day were the most effective method of detecting red-shouldered hawks. Probability of detection via conspecific calls averaged 0.25, and area occupied was 100%. Computer simulations using these field data indicated broadcast surveys have the potential to be used as a population monitoring tool.

Analyzing Spacecraft Telecommunication Systems

NASA Technical Reports Server (NTRS)

Kordon, Mark; Hanks, David; Gladden, Roy; Wood, Eric

2004-01-01

Multi-Mission Telecom Analysis Tool (MMTAT) is a C-language computer program for analyzing proposed spacecraft telecommunication systems. MMTAT utilizes parameterized input and computational models that can be run on standard desktop computers to perform fast and accurate analyses of telecommunication links. MMTAT is easy to use and can easily be integrated with other software applications and run as part of almost any computational simulation. It is distributed as either a stand-alone application program with a graphical user interface or a linkable library with a well-defined set of application programming interface (API) calls. As a stand-alone program, MMTAT provides both textual and graphical output. The graphs make it possible to understand, quickly and easily, how telecommunication performance varies with variations in input parameters. A delimited text file that can be read by any spreadsheet program is generated at the end of each run. The API in the linkable-library form of MMTAT enables the user to control simulation software and to change parameters during a simulation run. Results can be retrieved either at the end of a run or by use of a function call at any time step.

Functional magnetic resonance imaging examination of two modular architectures for switching multiple internal models.

PubMed

Imamizu, Hiroshi; Kuroda, Tomoe; Yoshioka, Toshinori; Kawato, Mitsuo

2004-02-04

An internal model is a neural mechanism that can mimic the input-output properties of a controlled object such as a tool. Recent research interests have moved on to how multiple internal models are learned and switched under a given context of behavior. Two representative computational models for task switching propose distinct neural mechanisms, thus predicting different brain activity patterns in the switching of internal models. In one model, called the mixture-of-experts architecture, switching is commanded by a single executive called a "gating network," which is different from the internal models. In the other model, called the MOSAIC (MOdular Selection And Identification for Control), the internal models themselves play crucial roles in switching. Consequently, the mixture-of-experts model predicts that neural activities related to switching and internal models can be temporally and spatially segregated, whereas the MOSAIC model predicts that they are closely intermingled. Here, we directly examined the two predictions by analyzing functional magnetic resonance imaging activities during the switching of one common tool (an ordinary computer mouse) and two novel tools: a rotated mouse, the cursor of which appears in a rotated position, and a velocity mouse, the cursor velocity of which is proportional to the mouse position. The switching and internal model activities temporally and spatially overlapped each other in the cerebellum and in the parietal cortex, whereas the overlap was very small in the frontal cortex. These results suggest that switching mechanisms in the frontal cortex can be explained by the mixture-of-experts architecture, whereas those in the cerebellum and the parietal cortex are explained by the MOSAIC model.

Software engineering methodologies and tools

NASA Technical Reports Server (NTRS)

Wilcox, Lawrence M.

1993-01-01

Over the years many engineering disciplines have developed, including chemical, electronic, etc. Common to all engineering disciplines is the use of rigor, models, metrics, and predefined methodologies. Recently, a new engineering discipline has appeared on the scene, called software engineering. For over thirty years computer software has been developed and the track record has not been good. Software development projects often miss schedules, are over budget, do not give the user what is wanted, and produce defects. One estimate is there are one to three defects per 1000 lines of deployed code. More and more systems are requiring larger and more complex software for support. As this requirement grows, the software development problems grow exponentially. It is believed that software quality can be improved by applying engineering principles. Another compelling reason to bring the engineering disciplines to software development is productivity. It has been estimated that productivity of producing software has only increased one to two percent a year in the last thirty years. Ironically, the computer and its software have contributed significantly to the industry-wide productivity, but computer professionals have done a poor job of using the computer to do their job. Engineering disciplines and methodologies are now emerging supported by software tools that address the problems of software development. This paper addresses some of the current software engineering methodologies as a backdrop for the general evaluation of computer assisted software engineering (CASE) tools from actual installation of and experimentation with some specific tools.

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

NASA Astrophysics Data System (ADS)

Delanoy, Richard L.

1996-03-01

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

Integrating interactive computational modeling in biology curricula.

PubMed

Helikar, Tomáš; Cutucache, Christine E; Dahlquist, Lauren M; Herek, Tyler A; Larson, Joshua J; Rogers, Jim A

2015-03-01

While the use of computer tools to simulate complex processes such as computer circuits is normal practice in fields like engineering, the majority of life sciences/biological sciences courses continue to rely on the traditional textbook and memorization approach. To address this issue, we explored the use of the Cell Collective platform as a novel, interactive, and evolving pedagogical tool to foster student engagement, creativity, and higher-level thinking. Cell Collective is a Web-based platform used to create and simulate dynamical models of various biological processes. Students can create models of cells, diseases, or pathways themselves or explore existing models. This technology was implemented in both undergraduate and graduate courses as a pilot study to determine the feasibility of such software at the university level. First, a new (In Silico Biology) class was developed to enable students to learn biology by "building and breaking it" via computer models and their simulations. This class and technology also provide a non-intimidating way to incorporate mathematical and computational concepts into a class with students who have a limited mathematical background. Second, we used the technology to mediate the use of simulations and modeling modules as a learning tool for traditional biological concepts, such as T cell differentiation or cell cycle regulation, in existing biology courses. Results of this pilot application suggest that there is promise in the use of computational modeling and software tools such as Cell Collective to provide new teaching methods in biology and contribute to the implementation of the "Vision and Change" call to action in undergraduate biology education by providing a hands-on approach to biology.

Towards a flexible middleware for context-aware pervasive and wearable systems.

PubMed

Muro, Marco; Amoretti, Michele; Zanichelli, Francesco; Conte, Gianni

2012-11-01

Ambient intelligence and wearable computing call for innovative hardware and software technologies, including a highly capable, flexible and efficient middleware, allowing for the reuse of existing pervasive applications when developing new ones. In the considered application domain, middleware should also support self-management, interoperability among different platforms, efficient communications, and context awareness. In the on-going "everything is networked" scenario scalability appears as a very important issue, for which the peer-to-peer (P2P) paradigm emerges as an appealing solution for connecting software components in an overlay network, allowing for efficient and balanced data distribution mechanisms. In this paper, we illustrate how all these concepts can be placed into a theoretical tool, called networked autonomic machine (NAM), implemented into a NAM-based middleware, and evaluated against practical problems of pervasive computing.

High-performance computational fluid dynamics: a custom-code approach

NASA Astrophysics Data System (ADS)

Fannon, James; Loiseau, Jean-Christophe; Valluri, Prashant; Bethune, Iain; Náraigh, Lennon Ó.

2016-07-01

We introduce a modified and simplified version of the pre-existing fully parallelized three-dimensional Navier-Stokes flow solver known as TPLS. We demonstrate how the simplified version can be used as a pedagogical tool for the study of computational fluid dynamics (CFDs) and parallel computing. TPLS is at its heart a two-phase flow solver, and uses calls to a range of external libraries to accelerate its performance. However, in the present context we narrow the focus of the study to basic hydrodynamics and parallel computing techniques, and the code is therefore simplified and modified to simulate pressure-driven single-phase flow in a channel, using only relatively simple Fortran 90 code with MPI parallelization, but no calls to any other external libraries. The modified code is analysed in order to both validate its accuracy and investigate its scalability up to 1000 CPU cores. Simulations are performed for several benchmark cases in pressure-driven channel flow, including a turbulent simulation, wherein the turbulence is incorporated via the large-eddy simulation technique. The work may be of use to advanced undergraduate and graduate students as an introductory study in CFDs, while also providing insight for those interested in more general aspects of high-performance computing.

Health Information Technology as a Universal Donor to Bioethics Education.

PubMed

Goodman, Kenneth W

2017-04-01

Health information technology, sometimes called biomedical informatics, is the use of computers and networks in the health professions. This technology has become widespread, from electronic health records to decision support tools to patient access through personal health records. These computational and information-based tools have engendered their own ethics literature and now present an opportunity to shape the standard medical and nursing ethics curricula. It is suggested that each of four core components in the professional education of clinicians-privacy, end-of-life care, access to healthcare and valid consent, and clinician-patient communication-offers an opportunity to leverage health information technology for curricular improvement. Using informatics in ethics education freshens ethics pedagogy and increases its utility, and does so without additional demands on overburdened curricula.

Verification of VLSI designs

NASA Technical Reports Server (NTRS)

Windley, P. J.

1991-01-01

In this paper we explore the specification and verification of VLSI designs. The paper focuses on abstract specification and verification of functionality using mathematical logic as opposed to low-level boolean equivalence verification such as that done using BDD's and Model Checking. Specification and verification, sometimes called formal methods, is one tool for increasing computer dependability in the face of an exponentially increasing testing effort.

Exploring Teacher Candidates' Experiences, Beliefs and Attitudes to Technology as an Instructional Learning Tool Following Instruction in a Technology-Rich Classroom

ERIC Educational Resources Information Center

DiPetta, Tony; Woloshyn, Vera

2009-01-01

The use of so-called, "smart-classrooms" or "e-classrooms" where students have wireless access to the internet, electronic projection and display systems, laptops and hand-held computers are increasingly seen as a means for instructors and students in higher education to create new and personalized understandings of traditional…

DaRT: A CALL System to Help Students Practice and Develop Reasoning Skills in Choosing English Articles.

ERIC Educational Resources Information Center

Yoshii, Rika; Milne, Alastair

1998-01-01

Describes DaRT, a computer assisted language-learning system for helping English-as-a-Second-Language students master English articles. DaRT uses a diagrammatic reasoning tool to present communicative contexts for exercises in choosing appropriate articles. This paper describes the development of DaRT and DaRT's system components and concludes…

Statistical Tools for Determining Fitness to Fly

DTIC Science & Technology

1981-09-01

program. (a) Number of Cards in file: 13 (b) Layout of Card 1: iIi Field Length a•e. Variable 1 8 Real EFAIL : Average # of failures for size of control...Method Compute Survival Probability and Frequency Tables 4-4 END 25P FLUW CHARTS 27 QSTART Input EFAIL ,CYEAR,NVAR,NAV,XINC BB~i i=1,3 name (1) i=1,4 Call

The Effectiveness of Computer-Based Spaced Repetition in Foreign Language Vocabulary Instruction: A Double-Blind Study

ERIC Educational Resources Information Center

Chukharev-Hudilainen, Evgeny; Klepikova, Tatiana A.

2016-01-01

The purpose of the present paper is twofold; first, we present an empirical study evaluating the effectiveness of a novel CALL tool for foreign language vocabulary instruction based on spaced repetition of target vocabulary items. The study demonstrates that by spending an average of three minutes each day on automatically generated vocabulary…

"I'm* Two Rabbits" / "J'ai un Rouge Pullover*". How Corrective Feedback Is Handled in Collaborative Exchange Programmes between Early Language Learners

ERIC Educational Resources Information Center

Choffat-Durr, Anne; Macaire, Dominique

2012-01-01

This article presents how, in the social dynamics of two classrooms involved in an exchange programme, young learners provide their peers with asynchronous feedback taking place in the digital medium. Within two Call Triangles that interact thanks to Computer Mediated Communication tools, teachers sharing the same methodological precept on…

A Security Monitoring Framework For Virtualization Based HEP Infrastructures

NASA Astrophysics Data System (ADS)

Gomez Ramirez, A.; Martinez Pedreira, M.; Grigoras, C.; Betev, L.; Lara, C.; Kebschull, U.; ALICE Collaboration

2017-10-01

High Energy Physics (HEP) distributed computing infrastructures require automatic tools to monitor, analyze and react to potential security incidents. These tools should collect and inspect data such as resource consumption, logs and sequence of system calls for detecting anomalies that indicate the presence of a malicious agent. They should also be able to perform automated reactions to attacks without administrator intervention. We describe a novel framework that accomplishes these requirements, with a proof of concept implementation for the ALICE experiment at CERN. We show how we achieve a fully virtualized environment that improves the security by isolating services and Jobs without a significant performance impact. We also describe a collected dataset for Machine Learning based Intrusion Prevention and Detection Systems on Grid computing. This dataset is composed of resource consumption measurements (such as CPU, RAM and network traffic), logfiles from operating system services, and system call data collected from production Jobs running in an ALICE Grid test site and a big set of malware samples. This malware set was collected from security research sites. Based on this dataset, we will proceed to develop Machine Learning algorithms able to detect malicious Jobs.

A preliminary study of a cloud-computing model for chronic illness self-care support in an underdeveloped country.

PubMed

Piette, John D; Mendoza-Avelares, Milton O; Ganser, Martha; Mohamed, Muhima; Marinec, Nicolle; Krishnan, Sheila

2011-06-01

Although interactive voice response (IVR) calls can be an effective tool for chronic disease management, many regions of the world lack the infrastructure to provide these services. This study evaluated the feasibility and potential impact of an IVR program using a cloud-computing model to improve diabetes management in Honduras. A single-group, pre-post study was conducted between June and August 2010. The telecommunications infrastructure was maintained on a U.S. server, and calls were directed to patients' cell phones using VoIP. Eighty-five diabetes patients in Honduras received weekly IVR disease management calls for 6 weeks, with automated follow-up e-mails to clinicians, and voicemail reports to family caregivers. Patients completed interviews at enrollment and a 6-week follow-up. Other measures included patients' glycemic control (HbA1c) and data from the IVR calling system. A total of 53% of participants completed at least half of their IVR calls and 23% of participants completed 80% or more. Higher baseline blood pressures, greater diabetes burden, greater distance from the clinic, and better medication adherence were related to higher call completion rates. Nearly all participants (98%) reported that because of the program, they improved in aspects of diabetes management such as glycemic control (56%) or foot care (89%). Mean HbA1c's decreased from 10.0% at baseline to 8.9% at follow-up (p<0.01). Most participants (92%) said that if the service were available in their clinic they would use it again. Cloud computing is a feasible strategy for providing IVR services globally. IVR self-care support may improve self-care and glycemic control for patients in underdeveloped countries. Published by Elsevier Inc.

A preliminary study of a cloud-computing model for chronic illness self-care support in an underdeveloped country

PubMed Central

Piette, John D.; Mendoza-Avelares, Milton O.; Ganser, Martha; Mohamed, Muhima; Marinec, Nicolle; Krishnan, Sheila

2013-01-01

Background Although interactive voice response (IVR) calls can be an effective tool for chronic disease management, many regions of the world lack the infrastructure to provide these services. Objective This study evaluated the feasibility and potential impact of an IVR program using a cloud-computing model to improve diabetes management in Honduras. Methods A single group, pre-post study was conducted between June and August 2010. The telecommunications infrastructure was maintained on a U.S. server, and calls were directed to patients’ cell phones using VoIP. Eighty-five diabetes patients in Honduras received weekly IVR disease management calls for six weeks, with automated follow-up emails to clinicians, and voicemail reports to family caregivers. Patients completed interviews at enrollment and a six week follow-up. Other measures included patients’ glycemic control (A1c) and data from the IVR calling system. Results 55% of participants completed the majority of their IVR calls and 33% completed 80% or more. Higher baseline blood pressures, greater diabetes burden, greater distance from the clinic, and better adherence were related to higher call completion rates. Nearly all participants (98%) reported that because of the program, they improved in aspects of diabetes management such as glycemic control (56%) or foot care (89%). Mean A1c’s decreased from 10.0% at baseline to 8.9% at follow-up (p<.01). Most participants (92%) said that if the service were available in their clinic they would use it again. Conclusions Cloud computing is a feasible strategy for providing IVR services globally. IVR self-care support may improve self-care and glycemic control for patients in under-developed countries. PMID:21565655

Computational thinking in life science education.

PubMed

Rubinstein, Amir; Chor, Benny

2014-11-01

We join the increasing call to take computational education of life science students a step further, beyond teaching mere programming and employing existing software tools. We describe a new course, focusing on enriching the curriculum of life science students with abstract, algorithmic, and logical thinking, and exposing them to the computational "culture." The design, structure, and content of our course are influenced by recent efforts in this area, collaborations with life scientists, and our own instructional experience. Specifically, we suggest that an effective course of this nature should: (1) devote time to explicitly reflect upon computational thinking processes, resisting the temptation to drift to purely practical instruction, (2) focus on discrete notions, rather than on continuous ones, and (3) have basic programming as a prerequisite, so students need not be preoccupied with elementary programming issues. We strongly recommend that the mere use of existing bioinformatics tools and packages should not replace hands-on programming. Yet, we suggest that programming will mostly serve as a means to practice computational thinking processes. This paper deals with the challenges and considerations of such computational education for life science students. It also describes a concrete implementation of the course and encourages its use by others.

PRO-Elicere: A Study for Create a New Process of Dependability Analysis of Space Computer Systems

NASA Astrophysics Data System (ADS)

da Silva, Glauco; Netto Lahoz, Carlos Henrique

2013-09-01

This paper presents the new approach to the computer system dependability analysis, called PRO-ELICERE, which introduces data mining concepts and intelligent mechanisms to decision support to analyze the potential hazards and failures of a critical computer system. Also, are presented some techniques and tools that support the traditional dependability analysis and briefly discusses the concept of knowledge discovery and intelligent databases for critical computer systems. After that, introduces the PRO-ELICERE process, an intelligent approach to automate the ELICERE, a process created to extract non-functional requirements for critical computer systems. The PRO-ELICERE can be used in the V&V activities in the projects of Institute of Aeronautics and Space, such as the Brazilian Satellite Launcher (VLS-1).

Identification of immunoglobulins using Chou's pseudo amino acid composition with feature selection technique.

PubMed

Tang, Hua; Chen, Wei; Lin, Hao

2016-04-01

Immunoglobulins, also called antibodies, are a group of cell surface proteins which are produced by the immune system in response to the presence of a foreign substance (called antigen). They play key roles in many medical, diagnostic and biotechnological applications. Correct identification of immunoglobulins is crucial to the comprehension of humoral immune function. With the avalanche of protein sequences identified in postgenomic age, it is highly desirable to develop computational methods to timely identify immunoglobulins. In view of this, we designed a predictor called "IGPred" by formulating protein sequences with the pseudo amino acid composition into which nine physiochemical properties of amino acids were incorporated. Jackknife cross-validated results showed that 96.3% of immunoglobulins and 97.5% of non-immunoglobulins can be correctly predicted, indicating that IGPred holds very high potential to become a useful tool for antibody analysis. For the convenience of most experimental scientists, a web-server for IGPred was established at http://lin.uestc.edu.cn/server/IGPred. We believe that the web-server will become a powerful tool to study immunoglobulins and to guide related experimental validations.

The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem.

PubMed

Phadungsukanan, Weerapong; Kraft, Markus; Townsend, Joe A; Murray-Rust, Peter

2012-08-07

: This paper introduces a subdomain chemistry format for storing computational chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (CML) by adding computational chemistry semantics on top of the CML Schema. The format allows a wide range of ab initio quantum chemistry calculations of individual molecules to be stored. These calculations include, for example, single point energy calculation, molecular geometry optimization, and vibrational frequency analysis. The paper also describes the supporting infrastructure, such as processing software, dictionaries, validation tools and database repositories. In addition, some of the challenges and difficulties in developing common computational chemistry dictionaries are discussed. The uses of CompChem are illustrated by two practical applications.

The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem

PubMed Central

2012-01-01

This paper introduces a subdomain chemistry format for storing computational chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (CML) by adding computational chemistry semantics on top of the CML Schema. The format allows a wide range of ab initio quantum chemistry calculations of individual molecules to be stored. These calculations include, for example, single point energy calculation, molecular geometry optimization, and vibrational frequency analysis. The paper also describes the supporting infrastructure, such as processing software, dictionaries, validation tools and database repositories. In addition, some of the challenges and difficulties in developing common computational chemistry dictionaries are discussed. The uses of CompChem are illustrated by two practical applications. PMID:22870956

User-Driven Sampling Strategies in Image Exploitation

DOE PAGES

Harvey, Neal R.; Porter, Reid B.

2013-12-23

Visual analytics and interactive machine learning both try to leverage the complementary strengths of humans and machines to solve complex data exploitation tasks. These fields overlap most significantly when training is involved: the visualization or machine learning tool improves over time by exploiting observations of the human-computer interaction. This paper focuses on one aspect of the human-computer interaction that we call user-driven sampling strategies. Unlike relevance feedback and active learning sampling strategies, where the computer selects which data to label at each iteration, we investigate situations where the user selects which data is to be labeled at each iteration. User-drivenmore » sampling strategies can emerge in many visual analytics applications but they have not been fully developed in machine learning. We discovered that in user-driven sampling strategies suggest new theoretical and practical research questions for both visualization science and machine learning. In this paper we identify and quantify the potential benefits of these strategies in a practical image analysis application. We find user-driven sampling strategies can sometimes provide significant performance gains by steering tools towards local minima that have lower error than tools trained with all of the data. Furthermore, in preliminary experiments we find these performance gains are particularly pronounced when the user is experienced with the tool and application domain.« less

User-driven sampling strategies in image exploitation

NASA Astrophysics Data System (ADS)

Harvey, Neal; Porter, Reid

2013-12-01

Visual analytics and interactive machine learning both try to leverage the complementary strengths of humans and machines to solve complex data exploitation tasks. These fields overlap most significantly when training is involved: the visualization or machine learning tool improves over time by exploiting observations of the human-computer interaction. This paper focuses on one aspect of the human-computer interaction that we call user-driven sampling strategies. Unlike relevance feedback and active learning sampling strategies, where the computer selects which data to label at each iteration, we investigate situations where the user selects which data is to be labeled at each iteration. User-driven sampling strategies can emerge in many visual analytics applications but they have not been fully developed in machine learning. User-driven sampling strategies suggest new theoretical and practical research questions for both visualization science and machine learning. In this paper we identify and quantify the potential benefits of these strategies in a practical image analysis application. We find user-driven sampling strategies can sometimes provide significant performance gains by steering tools towards local minima that have lower error than tools trained with all of the data. In preliminary experiments we find these performance gains are particularly pronounced when the user is experienced with the tool and application domain.

Computational Design and Discovery of Ni-Based Alloys and Coatings: Thermodynamic Approaches Validated by Experiments

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

Liu, Zi-Kui; Gleeson, Brian; Shang, Shunli

This project developed computational tools that can complement and support experimental efforts in order to enable discovery and more efficient development of Ni-base structural materials and coatings. The project goal was reached through an integrated computation-predictive and experimental-validation approach, including first-principles calculations, thermodynamic CALPHAD (CALculation of PHAse Diagram), and experimental investigations on compositions relevant to Ni-base superalloys and coatings in terms of oxide layer growth and microstructure stabilities. The developed description included composition ranges typical for coating alloys and, hence, allow for prediction of thermodynamic properties for these material systems. The calculation of phase compositions, phase fraction, and phase stabilities,more » which are directly related to properties such as ductility and strength, was a valuable contribution, along with the collection of computational tools that are required to meet the increasing demands for strong, ductile and environmentally-protective coatings. Specifically, a suitable thermodynamic description for the Ni-Al-Cr-Co-Si-Hf-Y system was developed for bulk alloy and coating compositions. Experiments were performed to validate and refine the thermodynamics from the CALPHAD modeling approach. Additionally, alloys produced using predictions from the current computational models were studied in terms of their oxidation performance. Finally, results obtained from experiments aided in the development of a thermodynamic modeling automation tool called ESPEI/pycalphad - for more rapid discovery and development of new materials.« less

Learning to Make Change Happen in Chinese Schools: Adapting a Problem-Based Computer Simulation for Developing School Leaders

ERIC Educational Resources Information Center

Hallinger, Philip; Shaobing, Tang; Jiafang, Lu

2017-01-01

School leader training has become a critical strategy in educational reform. However, in China, there still exists a big gap in terms of how to transfer leadership knowledge into practice. Thus, tools that can integrate formal knowledge into practice are called for urgently in school leader training. This paper presents the results of a research…

Computerized Biomechanical Man-Model

DTIC Science & Technology

1976-07-01

Force Systems Command Wright-Patterson AFB, Ohio ABSTRACT The COMputerized BIomechanical MAN-Model (called COMBIMAN) is a computer interactive graphics...concept was to build a mock- The use of mock-ups for biomechanical evalua- up which permitted the designer to visualize the tion has long been a tool...of the can become an obstacle to design change. Aerospace Medical Research Laboratory, we are developing a computerized biomechanical man-model

The APECS Virtual Poster Session: a virtual platform for science communication and discussion

NASA Astrophysics Data System (ADS)

Renner, A.; Jochum, K.; Jullion, L.; Pavlov, A.; Liggett, D.; Fugmann, G.; Baeseman, J. L.; Apecs Virtual Poster Session Working Group, T.

2011-12-01

The Virtual Poster Session (VPS) of the Association of Polar Early Career Scientists (APECS) was developed by early career scientists as an online tool for communicating and discussing science and research beyond the four walls of a conference venue. Poster sessions often are the backbone of a conference where especially early career scientists get a chance to communicate their research, discuss ideas, data, and scientific problems with their peers and senior scientists. There, they can hone their 'elevator pitch', discussion skills and presentation skills. APECS has taken the poster session one step further and created the VPS - the same idea but independent from conferences, travel, and location. All that is needed is a computer with internet access. Instead of letting their posters collect dust on the computer's hard drive, scientists can now upload them to the APECS website. There, others have the continuous opportunity to comment, give feedback and discuss the work. Currently, about 200 posters are accessible contributed by authors and co-authors from 34 countries. Since January 2010, researchers can discuss their poster with a broad international audience including fellow researchers, community members, potential colleagues and collaborators, policy makers and educators during monthly conference calls via an internet platform. Recordings of the calls are available online afterwards. Calls so far have included topical sessions on e.g. marine biology, glaciology, or social sciences, and interdisciplinary calls on Arctic sciences or polar research activities in a specific country, e.g. India or Romania. They attracted audiences of scientists at all career stages and from all continents, with on average about 15 persons participating per call. Online tools like the VPS open up new ways for creating collaborations and new research ideas and sharing different methodologies for future projects, pushing aside the boundaries of countries and nations, conferences, offices, and disciplines, and provide early career scientists with easily accessible training opportunities for their communication and outreach skills, independent of their location and funding situation.

Computational Modeling in Structural Materials Processing

NASA Technical Reports Server (NTRS)

Meyyappan, Meyya; Arnold, James O. (Technical Monitor)

1997-01-01

High temperature materials such as silicon carbide, a variety of nitrides, and ceramic matrix composites find use in aerospace, automotive, machine tool industries and in high speed civil transport applications. Chemical vapor deposition (CVD) is widely used in processing such structural materials. Variations of CVD include deposition on substrates, coating of fibers, inside cavities and on complex objects, and infiltration within preforms called chemical vapor infiltration (CVI). Our current knowledge of the process mechanisms, ability to optimize processes, and scale-up for large scale manufacturing is limited. In this regard, computational modeling of the processes is valuable since a validated model can be used as a design tool. The effort is similar to traditional chemically reacting flow modeling with emphasis on multicomponent diffusion, thermal diffusion, large sets of homogeneous reactions, and surface chemistry. In the case of CVI, models for pore infiltration are needed. In the present talk, examples of SiC nitride, and Boron deposition from the author's past work will be used to illustrate the utility of computational process modeling.

Coordinating complex problem-solving among distributed intelligent agents

NASA Technical Reports Server (NTRS)

Adler, Richard M.

1992-01-01

A process-oriented control model is described for distributed problem solving. The model coordinates the transfer and manipulation of information across independent networked applications, both intelligent and conventional. The model was implemented using SOCIAL, a set of object-oriented tools for distributing computing. Complex sequences of distributed tasks are specified in terms of high level scripts. Scripts are executed by SOCIAL objects called Manager Agents, which realize an intelligent coordination model that routes individual tasks to suitable server applications across the network. These tools are illustrated in a prototype distributed system for decision support of ground operations for NASA's Space Shuttle fleet.

ePORT, NASA's Computer Database Program for System Safety Risk Management Oversight (Electronic Project Online Risk Tool)

NASA Technical Reports Server (NTRS)

Johnson, Paul W.

2008-01-01

ePORT (electronic Project Online Risk Tool) provides a systematic approach to using an electronic database program to manage a program/project risk management processes. This presentation will briefly cover the standard risk management procedures, then thoroughly cover NASA's Risk Management tool called ePORT. This electronic Project Online Risk Tool (ePORT) is a web-based risk management program that provides a common framework to capture and manage risks, independent of a programs/projects size and budget. It is used to thoroughly cover the risk management paradigm providing standardized evaluation criterion for common management reporting, ePORT improves Product Line, Center and Corporate Management insight, simplifies program/project manager reporting, and maintains an archive of data for historical reference.

TOAD Editor

NASA Technical Reports Server (NTRS)

Bingle, Bradford D.; Shea, Anne L.; Hofler, Alicia S.

1993-01-01

Transferable Output ASCII Data (TOAD) computer program (LAR-13755), implements format designed to facilitate transfer of data across communication networks and dissimilar host computer systems. Any data file conforming to TOAD format standard called TOAD file. TOAD Editor is interactive software tool for manipulating contents of TOAD files. Commonly used to extract filtered subsets of data for visualization of results of computation. Also offers such user-oriented features as on-line help, clear English error messages, startup file, macroinstructions defined by user, command history, user variables, UNDO features, and full complement of mathematical statistical, and conversion functions. Companion program, TOAD Gateway (LAR-14484), converts data files from variety of other file formats to that of TOAD. TOAD Editor written in FORTRAN 77.

An application of artificial intelligence to the interpretation of mass spectra.

NASA Technical Reports Server (NTRS)

Buchanan, B. G.; Duffield, A. M.; Robertson, A. V.

1971-01-01

Description of the DENDRAL (Dendritic Algorithm) project, the objectives of which were to base the computer program on an alogorithm that generates an exhaustive, nonredundant list of all the structural isomers of a given chemical composition, and to devise a computer program that would perform an organic structure determination, given a molecular formula and a mass spectrum. This program is called 'Heuristic DENDRAL' and it operates by using the known structure/spectrum correlations to constrain the DENDRAL isomer generator to produce a single isomer for that composition. The collaboration of chemists and computer scientists has produced a tool of some practical utility from the chemical viewpoint, and an interesting program from the viewpoint of artificial intelligence.

A new approach for developing adjoint models

NASA Astrophysics Data System (ADS)

Farrell, P. E.; Funke, S. W.

2011-12-01

Many data assimilation algorithms rely on the availability of gradients of misfit functionals, which can be efficiently computed with adjoint models. However, the development of an adjoint model for a complex geophysical code is generally very difficult. Algorithmic differentiation (AD, also called automatic differentiation) offers one strategy for simplifying this task: it takes the abstraction that a model is a sequence of primitive instructions, each of which may be differentiated in turn. While extremely successful, this low-level abstraction runs into time-consuming difficulties when applied to the whole codebase of a model, such as differentiating through linear solves, model I/O, calls to external libraries, language features that are unsupported by the AD tool, and the use of multiple programming languages. While these difficulties can be overcome, it requires a large amount of technical expertise and an intimate familiarity with both the AD tool and the model. An alternative to applying the AD tool to the whole codebase is to assemble the discrete adjoint equations and use these to compute the necessary gradients. With this approach, the AD tool must be applied to the nonlinear assembly operators, which are typically small, self-contained units of the codebase. The disadvantage of this approach is that the assembly of the discrete adjoint equations is still very difficult to perform correctly, especially for complex multiphysics models that perform temporal integration; as it stands, this approach is as difficult and time-consuming as applying AD to the whole model. In this work, we have developed a library which greatly simplifies and automates the alternate approach of assembling the discrete adjoint equations. We propose a complementary, higher-level abstraction to that of AD: that a model is a sequence of linear solves. The developer annotates model source code with library calls that build a 'tape' of the operators involved and their dependencies, and supplies callbacks to compute the action of these operators. The library, called libadjoint, is then capable of symbolically manipulating the forward annotation to automatically assemble the adjoint equations. Libadjoint is open source, and is explicitly designed to be bolted-on to an existing discrete model. It can be applied to any discretisation, steady or time-dependent problems, and both linear and nonlinear systems. Using libadjoint has several advantages. It requires the application of an AD tool only to small pieces of code, making the use of AD far more tractable. As libadjoint derives the adjoint equations, the expertise required to develop an adjoint model is greatly diminished. One major advantage of this approach is that the model developer is freed from implementing complex checkpointing strategies for the adjoint model: libadjoint has sufficient information about the forward model to re-play the entire forward solve when necessary, and thus the checkpointing algorithm can be implemented entirely within the library itself. Examples are shown using the Fluidity/ICOM framework, a complex ocean model under development at Imperial College London.

National Combustion Code: A Multidisciplinary Combustor Design System

NASA Technical Reports Server (NTRS)

Stubbs, Robert M.; Liu, Nan-Suey

1997-01-01

The Internal Fluid Mechanics Division conducts both basic research and technology, and system technology research for aerospace propulsion systems components. The research within the division, which is both computational and experimental, is aimed at improving fundamental understanding of flow physics in inlets, ducts, nozzles, turbomachinery, and combustors. This article and the following three articles highlight some of the work accomplished in 1996. A multidisciplinary combustor design system is critical for optimizing the combustor design process. Such a system should include sophisticated computer-aided design (CAD) tools for geometry creation, advanced mesh generators for creating solid model representations, a common framework for fluid flow and structural analyses, modern postprocessing tools, and parallel processing. The goal of the present effort is to develop some of the enabling technologies and to demonstrate their overall performance in an integrated system called the National Combustion Code.

New computational tools for H/D determination in macromolecular structures from neutron data.

PubMed

Siliqi, Dritan; Caliandro, Rocco; Carrozzini, Benedetta; Cascarano, Giovanni Luca; Mazzone, Annamaria

2010-11-01

Two new computational methods dedicated to neutron crystallography, called n-FreeLunch and DNDM-NDM, have been developed and successfully tested. The aim in developing these methods is to determine hydrogen and deuterium positions in macromolecular structures by using information from neutron density maps. Of particular interest is resolving cases in which the geometrically predicted hydrogen or deuterium positions are ambiguous. The methods are an evolution of approaches that are already applied in X-ray crystallography: extrapolation beyond the observed resolution (known as the FreeLunch procedure) and a difference electron-density modification (DEDM) technique combined with the electron-density modification (EDM) tool (known as DEDM-EDM). It is shown that the two methods are complementary to each other and are effective in finding the positions of H and D atoms in neutron density maps.

S-MART, a software toolbox to aid RNA-Seq data analysis.

PubMed

Zytnicki, Matthias; Quesneville, Hadi

2011-01-01

High-throughput sequencing is now routinely performed in many experiments. But the analysis of the millions of sequences generated, is often beyond the expertise of the wet labs who have no personnel specializing in bioinformatics. Whereas several tools are now available to map high-throughput sequencing data on a genome, few of these can extract biological knowledge from the mapped reads. We have developed a toolbox called S-MART, which handles mapped RNA-Seq data. S-MART is an intuitive and lightweight tool which performs many of the tasks usually required for the analysis of mapped RNA-Seq reads. S-MART does not require any computer science background and thus can be used by all of the biologist community through a graphical interface. S-MART can run on any personal computer, yielding results within an hour even for Gb of data for most queries. S-MART may perform the entire analysis of the mapped reads, without any need for other ad hoc scripts. With this tool, biologists can easily perform most of the analyses on their computer for their RNA-Seq data, from the mapped data to the discovery of important loci.

S-MART, A Software Toolbox to Aid RNA-seq Data Analysis

PubMed Central

Zytnicki, Matthias; Quesneville, Hadi

2011-01-01

High-throughput sequencing is now routinely performed in many experiments. But the analysis of the millions of sequences generated, is often beyond the expertise of the wet labs who have no personnel specializing in bioinformatics. Whereas several tools are now available to map high-throughput sequencing data on a genome, few of these can extract biological knowledge from the mapped reads. We have developed a toolbox called S-MART, which handles mapped RNA-Seq data. S-MART is an intuitive and lightweight tool which performs many of the tasks usually required for the analysis of mapped RNA-Seq reads. S-MART does not require any computer science background and thus can be used by all of the biologist community through a graphical interface. S-MART can run on any personal computer, yielding results within an hour even for Gb of data for most queries. S-MART may perform the entire analysis of the mapped reads, without any need for other ad hoc scripts. With this tool, biologists can easily perform most of the analyses on their computer for their RNA-Seq data, from the mapped data to the discovery of important loci. PMID:21998740

Analytic and rule-based decision support tool for VDT workstation adjustment and computer accessories arrangement.

PubMed

Rurkhamet, Busagarin; Nanthavanij, Suebsak

2004-12-01

One important factor that leads to the development of musculoskeletal disorders (MSD) and cumulative trauma disorders (CTD) among visual display terminal (VDT) users is their work posture. While operating a VDT, a user's body posture is strongly influenced by the task, VDT workstation settings, and layout of computer accessories. This paper presents an analytic and rule-based decision support tool called EQ-DeX (an ergonomics and quantitative design expert system) that is developed to provide valid and practical recommendations regarding the adjustment of a VDT workstation and the arrangement of computer accessories. The paper explains the structure and components of EQ-DeX, input data, rules, and adjustment and arrangement algorithms. From input information such as gender, age, body height, task, etc., EQ-DeX uses analytic and rule-based algorithms to estimate quantitative settings of a computer table and a chair, as well as locations of computer accessories such as monitor, document holder, keyboard, and mouse. With the input and output screens that are designed using the concept of usability, the interactions between the user and EQ-DeX are convenient. Examples are also presented to demonstrate the recommendations generated by EQ-DeX.

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

NASA Astrophysics Data System (ADS)

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.

Body Imaging

NASA Technical Reports Server (NTRS)

1990-01-01

Magnetic Resonance Imaging (MRI) and Computer-aided Tomography (CT) images are often complementary. In most cases, MRI is good for viewing soft tissue but not bone, while CT images are good for bone but not always good for soft tissue discrimination. Physicians and engineers in the Department of Radiology at the University of Michigan Hospitals are developing a technique for combining the best features of MRI and CT scans to increase the accuracy of discriminating one type of body tissue from another. One of their research tools is a computer program called HICAP. The program can be used to distinguish between healthy and diseased tissue in body images.

Demonstration of Cost-Effective, High-Performance Computing at Performance and Reliability Levels Equivalent to a 1994 Vector Supercomputer

NASA Technical Reports Server (NTRS)

Babrauckas, Theresa

2000-01-01

The Affordable High Performance Computing (AHPC) project demonstrated that high-performance computing based on a distributed network of computer workstations is a cost-effective alternative to vector supercomputers for running CPU and memory intensive design and analysis tools. The AHPC project created an integrated system called a Network Supercomputer. By connecting computer work-stations through a network and utilizing the workstations when they are idle, the resulting distributed-workstation environment has the same performance and reliability levels as the Cray C90 vector Supercomputer at less than 25 percent of the C90 cost. In fact, the cost comparison between a Cray C90 Supercomputer and Sun workstations showed that the number of distributed networked workstations equivalent to a C90 costs approximately 8 percent of the C90.

Adaptation of a Control Center Development Environment for Industrial Process Control

NASA Technical Reports Server (NTRS)

Killough, Ronnie L.; Malik, James M.

1994-01-01

In the control center, raw telemetry data is received for storage, display, and analysis. This raw data must be combined and manipulated in various ways by mathematical computations to facilitate analysis, provide diversified fault detection mechanisms, and enhance display readability. A development tool called the Graphical Computation Builder (GCB) has been implemented which provides flight controllers with the capability to implement computations for use in the control center. The GCB provides a language that contains both general programming constructs and language elements specifically tailored for the control center environment. The GCB concept allows staff who are not skilled in computer programming to author and maintain computer programs. The GCB user is isolated from the details of external subsystem interfaces and has access to high-level functions such as matrix operators, trigonometric functions, and unit conversion macros. The GCB provides a high level of feedback during computation development that improves upon the often cryptic errors produced by computer language compilers. An equivalent need can be identified in the industrial data acquisition and process control domain: that of an integrated graphical development tool tailored to the application to hide the operating system, computer language, and data acquisition interface details. The GCB features a modular design which makes it suitable for technology transfer without significant rework. Control center-specific language elements can be replaced by elements specific to industrial process control.

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

PubMed

Kasahara, Kota; Kinoshita, Kengo

2016-01-01

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

Digitizing for Computer-Aided Finite Element Model Generation.

DTIC Science & Technology

1979-10-10

this approach is a collection of programs developed over the last eight years at the University of Arizona, and called the GIFTS system. This paper...briefly describes the latest version of the system, GIFTS -5, and demonstrates its suitability in a design environment by simple examples. The programs...constituting the GIFTS system were used as a tool for research in many areas, including mesh generation, finite element data base design, interactive

Learning with a Missing Sense: What Can We Learn from the Interaction of a Deaf Child with a Turtle?

ERIC Educational Resources Information Center

Miller, Paul

2009-01-01

This case study reports on the progress of Navon, a 13-year-old boy with prelingual deafness, over a 3-month period following exposure to Logo, a computer programming language that visualizes specific programming commands by means of a virtual drawing tool called the Turtle. Despite an almost complete lack of skills in spoken and sign language,…

FloCon 2005 Proceedings

DTIC Science & Technology

2005-09-01

from one subject to another [5, 6]. Since covert com - munication is very difficult to detect, most researchers resort to investigating methods that...situations (unlike our own) where traffic is not filtered (a darknet , for example). To prevent isolated anomalies during the learning pe- riod from...call to the computer running the flow tools. Then, using a standard R data input function, the wrapper function reads in the ASCII output of the com

Improved Load Alleviation Capability for the KC-135

DTIC Science & Technology

1997-09-01

software, such as Matlab, Mathematica, Simulink, and Robotica Front End for Mathematica available in the simulation laboratory Overview This thesis report is...outlined in Spong’s text in order to utilize the Robotica system development software which automates the process of calculating the kinematic and...kinematic and dynamic equations can be accomplished using a computer tool called Robotica Front End (RFE) [ 15], developed by Doctor Spong. Boom Root d3

Resilient Software Systems

DTIC Science & Technology

2015-06-01

and tools, called model-integrated computing ( MIC ) [3] relies on the use of domain-specific modeling languages for creating models of the system to be...hence giving reflective capabilities to it. We have followed the MIC method here: we designed a domain- specific modeling language for modeling...are produced one-off and not for the mass market , the scope for price reduction based on the market demands is non-existent. Processes to create

CoVaCS: a consensus variant calling system.

PubMed

Chiara, Matteo; Gioiosa, Silvia; Chillemi, Giovanni; D'Antonio, Mattia; Flati, Tiziano; Picardi, Ernesto; Zambelli, Federico; Horner, David Stephen; Pesole, Graziano; Castrignanò, Tiziana

2018-02-05

The advent and ongoing development of next generation sequencing technologies (NGS) has led to a rapid increase in the rate of human genome re-sequencing data, paving the way for personalized genomics and precision medicine. The body of genome resequencing data is progressively increasing underlining the need for accurate and time-effective bioinformatics systems for genotyping - a crucial prerequisite for identification of candidate causal mutations in diagnostic screens. Here we present CoVaCS, a fully automated, highly accurate system with a web based graphical interface for genotyping and variant annotation. Extensive tests on a gold standard benchmark data-set -the NA12878 Illumina platinum genome- confirm that call-sets based on our consensus strategy are completely in line with those attained by similar command line based approaches, and far more accurate than call-sets from any individual tool. Importantly our system exhibits better sensitivity and higher specificity than equivalent commercial software. CoVaCS offers optimized pipelines integrating state of the art tools for variant calling and annotation for whole genome sequencing (WGS), whole-exome sequencing (WES) and target-gene sequencing (TGS) data. The system is currently hosted at Cineca, and offers the speed of a HPC computing facility, a crucial consideration when large numbers of samples must be analysed. Importantly, all the analyses are performed automatically allowing high reproducibility of the results. As such, we believe that CoVaCS can be a valuable tool for the analysis of human genome resequencing studies. CoVaCS is available at: https://bioinformatics.cineca.it/covacs .

Combining qualitative and quantitative methods to analyze serious games outcomes: A pilot study for a new cognitive screening tool.

PubMed

Vallejo, Vanessa; Mitache, Andrei V; Tarnanas, Ioannis; Muri, Rene; Mosimann, Urs P; Nef, Tobias

2015-08-01

Computer games for a serious purpose - so called serious games can provide additional information for the screening and diagnosis of cognitive impairment. Moreover, they have the advantage of being an ecological tool by involving daily living tasks. However, there is a need for better comprehensive designs regarding the acceptance of this technology, as the target population is older adults that are not used to interact with novel technologies. Moreover given the complexity of the diagnosis and the need for precise assessment, an evaluation of the best approach to analyze the performance data is required. The present study examines the usability of a new screening tool and proposes several new outlines for data analysis.

compomics-utilities: an open-source Java library for computational proteomics.

PubMed

Barsnes, Harald; Vaudel, Marc; Colaert, Niklaas; Helsens, Kenny; Sickmann, Albert; Berven, Frode S; Martens, Lennart

2011-03-08

The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary significantly, they usually share a basic set of features, including the handling of protein and peptide sequences, the visualization of (and interaction with) spectra and chromatograms, and the parsing of results from various proteomics search engines. Developers typically spend considerable time and effort implementing these support structures, which detracts from working on the novel aspects of their tool. In order to simplify the development of proteomics tools, we have implemented an open-source support library for computational proteomics, called compomics-utilities. The library contains a broad set of features required for reading, parsing, and analyzing proteomics data. compomics-utilities is already used by a long list of existing software, ensuring library stability and continued support and development. As a user-friendly, well-documented and open-source library, compomics-utilities greatly simplifies the implementation of the basic features needed in most proteomics tools. Implemented in 100% Java, compomics-utilities is fully portable across platforms and architectures. Our library thus allows the developers to focus on the novel aspects of their tools, rather than on the basic functions, which can contribute substantially to faster development, and better tools for proteomics.

The SCEC Community Modeling Environment(SCEC/CME): A Collaboratory for Seismic Hazard Analysis

NASA Astrophysics Data System (ADS)

Maechling, P. J.; Jordan, T. H.; Minster, J. B.; Moore, R.; Kesselman, C.

2005-12-01

The SCEC Community Modeling Environment (SCEC/CME) Project is an NSF-supported Geosciences/IT partnership that is actively developing an advanced information infrastructure for system-level earthquake science in Southern California. This partnership includes SCEC, USC's Information Sciences Institute (ISI), the San Diego Supercomputer Center (SDSC), the Incorporated Institutions for Research in Seismology (IRIS), and the U.S. Geological Survey. The goal of the SCEC/CME is to develop seismological applications and information technology (IT) infrastructure to support the development of Seismic Hazard Analysis (SHA) programs and other geophysical simulations. The SHA application programs developed on the Project include a Probabilistic Seismic Hazard Analysis system called OpenSHA. OpenSHA computational elements that are currently available include a collection of attenuation relationships, and several Earthquake Rupture Forecasts (ERFs). Geophysicists in the collaboration have also developed Anelastic Wave Models (AWMs) using both finite-difference and finite-element approaches. Earthquake simulations using these codes have been run for a variety of earthquake sources. Rupture Dynamic Model (RDM) codes have also been developed that simulate friction-based fault slip. The SCEC/CME collaboration has also developed IT software and hardware infrastructure to support the development, execution, and analysis of these SHA programs. To support computationally expensive simulations, we have constructed a grid-based scientific workflow system. Using the SCEC grid, project collaborators can submit computations from the SCEC/CME servers to High Performance Computers at USC and TeraGrid High Performance Computing Centers. Data generated and archived by the SCEC/CME is stored in a digital library system, the Storage Resource Broker (SRB). This system provides a robust and secure system for maintaining the association between the data seta and their metadata. To provide an easy-to-use system for constructing SHA computations, a browser-based workflow assembly web portal has been developed. Users can compose complex SHA calculations, specifying SCEC/CME data sets as inputs to calculations, and calling SCEC/CME computational programs to process the data and the output. Knowledge-based software tools have been implemented that utilize ontological descriptions of SHA software and data can validate workflows created with this pathway assembly tool. Data visualization software developed by the collaboration supports analysis and validation of data sets. Several programs have been developed to visualize SCEC/CME data including GMT-based map making software for PSHA codes, 4D wavefield propagation visualization software based on OpenGL, and 3D Geowall-based visualization of earthquakes, faults, and seismic wave propagation. The SCEC/CME Project also helps to sponsor the SCEC UseIT Intern program. The UseIT Intern Program provides research opportunities in both Geosciences and Information Technology to undergraduate students in a variety of fields. The UseIT group has developed a 3D data visualization tool, called SCEC-VDO, as a part of this undergraduate research program.

Improving mapping and SNP-calling performance in multiplexed targeted next-generation sequencing

PubMed Central

2012-01-01

Background Compared to classical genotyping, targeted next-generation sequencing (tNGS) can be custom-designed to interrogate entire genomic regions of interest, in order to detect novel as well as known variants. To bring down the per-sample cost, one approach is to pool barcoded NGS libraries before sample enrichment. Still, we lack a complete understanding of how this multiplexed tNGS approach and the varying performance of the ever-evolving analytical tools can affect the quality of variant discovery. Therefore, we evaluated the impact of different software tools and analytical approaches on the discovery of single nucleotide polymorphisms (SNPs) in multiplexed tNGS data. To generate our own test model, we combined a sequence capture method with NGS in three experimental stages of increasing complexity (E. coli genes, multiplexed E. coli, and multiplexed HapMap BRCA1/2 regions). Results We successfully enriched barcoded NGS libraries instead of genomic DNA, achieving reproducible coverage profiles (Pearson correlation coefficients of up to 0.99) across multiplexed samples, with <10% strand bias. However, the SNP calling quality was substantially affected by the choice of tools and mapping strategy. With the aim of reducing computational requirements, we compared conventional whole-genome mapping and SNP-calling with a new faster approach: target-region mapping with subsequent ‘read-backmapping’ to the whole genome to reduce the false detection rate. Consequently, we developed a combined mapping pipeline, which includes standard tools (BWA, SAMtools, etc.), and tested it on public HiSeq2000 exome data from the 1000 Genomes Project. Our pipeline saved 12 hours of run time per Hiseq2000 exome sample and detected ~5% more SNPs than the conventional whole genome approach. This suggests that more potential novel SNPs may be discovered using both approaches than with just the conventional approach. Conclusions We recommend applying our general ‘two-step’ mapping approach for more efficient SNP discovery in tNGS. Our study has also shown the benefit of computing inter-sample SNP-concordances and inspecting read alignments in order to attain more confident results. PMID:22913592

RATT: Rapid Annotation Transfer Tool

PubMed Central

Otto, Thomas D.; Dillon, Gary P.; Degrave, Wim S.; Berriman, Matthew

2011-01-01

Second-generation sequencing technologies have made large-scale sequencing projects commonplace. However, making use of these datasets often requires gene function to be ascribed genome wide. Although tool development has kept pace with the changes in sequence production, for tasks such as mapping, de novo assembly or visualization, genome annotation remains a challenge. We have developed a method to rapidly provide accurate annotation for new genomes using previously annotated genomes as a reference. The method, implemented in a tool called RATT (Rapid Annotation Transfer Tool), transfers annotations from a high-quality reference to a new genome on the basis of conserved synteny. We demonstrate that a Mycobacterium tuberculosis genome or a single 2.5 Mb chromosome from a malaria parasite can be annotated in less than five minutes with only modest computational resources. RATT is available at http://ratt.sourceforge.net. PMID:21306991

A simple and inexpensive method of preoperative computer imaging for rhinoplasty.

PubMed

Ewart, Christopher J; Leonard, Christopher J; Harper, J Garrett; Yu, Jack

2006-01-01

GOALS/PURPOSE: Despite concerns of legal liability, preoperative computer imaging has become a popular tool for the plastic surgeon. The ability to project possible surgical outcomes can facilitate communication between the patient and surgeon. It can be an effective tool in the education and training of residents. Unfortunately, these imaging programs are expensive and have a steep learning curve. The purpose of this paper is to present a relatively inexpensive method of preoperative computer imaging with a reasonable learning curve. The price of currently available imaging programs was acquired through an online search, and inquiries were made to the software distributors. Their prices were compared to Adobe PhotoShop, which has special filters called "liquify" and "photocopy." It was used in the preoperative computer planning of 2 patients who presented for rhinoplasty at our institution. Projected images were created based on harmonious discussions between the patient and physician. Importantly, these images were presented to the patient as potential results, with no guarantees as to actual outcomes. Adobe PhotoShop can be purchased for 900-5800 dollars less than the leading computer imaging software for cosmetic rhinoplasty. Effective projected images were created using the "liquify" and "photocopy" filters in PhotoShop. Both patients had surgical planning and operations based on these images. They were satisfied with the results. Preoperative computer imaging can be a very effective tool for the plastic surgeon by providing improved physician-patient communication, increased patient confidence, and enhanced surgical planning. Adobe PhotoShop is a relatively inexpensive program that can provide these benefits using only 1 or 2 features.

Distributed data mining on grids: services, tools, and applications.

PubMed

Cannataro, Mario; Congiusta, Antonio; Pugliese, Andrea; Talia, Domenico; Trunfio, Paolo

2004-12-01

Data mining algorithms are widely used today for the analysis of large corporate and scientific datasets stored in databases and data archives. Industry, science, and commerce fields often need to analyze very large datasets maintained over geographically distributed sites by using the computational power of distributed and parallel systems. The grid can play a significant role in providing an effective computational support for distributed knowledge discovery applications. For the development of data mining applications on grids we designed a system called Knowledge Grid. This paper describes the Knowledge Grid framework and presents the toolset provided by the Knowledge Grid for implementing distributed knowledge discovery. The paper discusses how to design and implement data mining applications by using the Knowledge Grid tools starting from searching grid resources, composing software and data components, and executing the resulting data mining process on a grid. Some performance results are also discussed.

STRUTEX: A prototype knowledge-based system for initially configuring a structure to support point loads in two dimensions

NASA Technical Reports Server (NTRS)

Robers, James L.; Sobieszczanski-Sobieski, Jaroslaw

1989-01-01

Only recently have engineers begun making use of Artificial Intelligence (AI) tools in the area of conceptual design. To continue filling this void in the design process, a prototype knowledge-based system, called STRUTEX has been developed to initially configure a structure to support point loads in two dimensions. This prototype was developed for testing the application of AI tools to conceptual design as opposed to being a testbed for new methods for improving structural analysis and optimization. This system combines numerical and symbolic processing by the computer with interactive problem solving aided by the vision of the user. How the system is constructed to interact with the user is described. Of special interest is the information flow between the knowledge base and the data base under control of the algorithmic main program. Examples of computed and refined structures are presented during the explanation of the system.

Near-Infrared Neuroimaging with NinPy

PubMed Central

Strangman, Gary E.; Zhang, Quan; Zeffiro, Thomas

2009-01-01

There has been substantial recent growth in the use of non-invasive optical brain imaging in studies of human brain function in health and disease. Near-infrared neuroimaging (NIN) is one of the most promising of these techniques and, although NIN hardware continues to evolve at a rapid pace, software tools supporting optical data acquisition, image processing, statistical modeling, and visualization remain less refined. Python, a modular and computationally efficient development language, can support functional neuroimaging studies of diverse design and implementation. In particular, Python's easily readable syntax and modular architecture allow swift prototyping followed by efficient transition to stable production systems. As an introduction to our ongoing efforts to develop Python software tools for structural and functional neuroimaging, we discuss: (i) the role of non-invasive diffuse optical imaging in measuring brain function, (ii) the key computational requirements to support NIN experiments, (iii) our collection of software tools to support NIN, called NinPy, and (iv) future extensions of these tools that will allow integration of optical with other structural and functional neuroimaging data sources. Source code for the software discussed here will be made available at www.nmr.mgh.harvard.edu/Neural_SystemsGroup/software.html. PMID:19543449

An efficient framework for Java data processing systems in HPC environments

NASA Astrophysics Data System (ADS)

Fries, Aidan; Castañeda, Javier; Isasi, Yago; Taboada, Guillermo L.; Portell de Mora, Jordi; Sirvent, Raül

2011-11-01

Java is a commonly used programming language, although its use in High Performance Computing (HPC) remains relatively low. One of the reasons is a lack of libraries offering specific HPC functions to Java applications. In this paper we present a Java-based framework, called DpcbTools, designed to provide a set of functions that fill this gap. It includes a set of efficient data communication functions based on message-passing, thus providing, when a low latency network such as Myrinet is available, higher throughputs and lower latencies than standard solutions used by Java. DpcbTools also includes routines for the launching, monitoring and management of Java applications on several computing nodes by making use of JMX to communicate with remote Java VMs. The Gaia Data Processing and Analysis Consortium (DPAC) is a real case where scientific data from the ESA Gaia astrometric satellite will be entirely processed using Java. In this paper we describe the main elements of DPAC and its usage of the DpcbTools framework. We also assess the usefulness and performance of DpcbTools through its performance evaluation and the analysis of its impact on some DPAC systems deployed in the MareNostrum supercomputer (Barcelona Supercomputing Center).

Multimodal visualization interface for data management, self-learning and data presentation.

PubMed

Van Sint Jan, S; Demondion, X; Clapworthy, G; Louryan, S; Rooze, M; Cotten, A; Viceconti, M

2006-10-01

A multimodal visualization software, called the Data Manager (DM), has been developed to increase interdisciplinary communication around the topic of visualization and modeling of various aspects of the human anatomy. Numerous tools used in Radiology are integrated in the interface that runs on standard personal computers. The available tools, combined to hierarchical data management and custom layouts, allow analyzing of medical imaging data using advanced features outside radiological premises (for example, for patient review, conference presentation or tutorial preparation). The system is free, and based on an open-source software development architecture, and therefore updates of the system for custom applications are possible.

HRLSim: a high performance spiking neural network simulator for GPGPU clusters.

PubMed

Minkovich, Kirill; Thibeault, Corey M; O'Brien, Michael John; Nogin, Aleksey; Cho, Youngkwan; Srinivasa, Narayan

2014-02-01

Modeling of large-scale spiking neural models is an important tool in the quest to understand brain function and subsequently create real-world applications. This paper describes a spiking neural network simulator environment called HRL Spiking Simulator (HRLSim). This simulator is suitable for implementation on a cluster of general purpose graphical processing units (GPGPUs). Novel aspects of HRLSim are described and an analysis of its performance is provided for various configurations of the cluster. With the advent of inexpensive GPGPU cards and compute power, HRLSim offers an affordable and scalable tool for design, real-time simulation, and analysis of large-scale spiking neural networks.

A Latency-Tolerant Partitioner for Distributed Computing on the Information Power Grid

NASA Technical Reports Server (NTRS)

Das, Sajal K.; Harvey, Daniel J.; Biwas, Rupak; Kwak, Dochan (Technical Monitor)

2001-01-01

NASA's Information Power Grid (IPG) is an infrastructure designed to harness the power of graphically distributed computers, databases, and human expertise, in order to solve large-scale realistic computational problems. This type of a meta-computing environment is necessary to present a unified virtual machine to application developers that hides the intricacies of a highly heterogeneous environment and yet maintains adequate security. In this paper, we present a novel partitioning scheme. called MinEX, that dynamically balances processor workloads while minimizing data movement and runtime communication, for applications that are executed in a parallel distributed fashion on the IPG. We also analyze the conditions that are required for the IPG to be an effective tool for such distributed computations. Our results show that MinEX is a viable load balancer provided the nodes of the IPG are connected by a high-speed asynchronous interconnection network.

Long Range Plan for Embedded Computer Systems Support. Volume II

DTIC Science & Technology

1981-10-01

interface (pilot displays and controls plus visual system), and data collection (CMAC data, bus data and simulation data). Non-real time functions include...unless adequate upfront planning is implemented, the command will be controlled by the dynamics rather than controll - ing them. The upfront planning should...or should they be called manually? What amount and type of data should the various tools pass between each other? Under what conditions and controls

Human Subject Research Protocol: Computer-Aided Human Centric Cyber Situation Awareness: Understanding Cognitive Processes of Cyber Analysts

DTIC Science & Technology

2013-11-01

by existing cyber-attack detection tools far exceeds the analysts’ cognitive capabilities. Grounded in perceptual and cognitive theory , many visual...Processes Inspired by the sense-making theory discussed earlier, we model the analytical reasoning process of cyber analysts using three key...analyst are called “working hypotheses”); each hypothesis could trigger further actions to confirm or disconfirm it. New actions will lead to new

Improving Demonstration Using Better Interaction Techniques

DTIC Science & Technology

1997-01-14

Programming by demonstration (PBD) can be used to create tools and methods that eliminate the need to learn difficult computer languages. Gamut is a...do this, Gamut uses advanced interaction techniques that make it easier for a software author to express all needed aspects of one’s program. These...techniques include a simplified way to demonstrate new examples, called nudges, and a way to highlight objects to show they are important. Also, Gamut

Using Computational Modeling to Assess the Impact of Clinical Decision Support on Cancer Screening within Community Health Centers

PubMed Central

Carney, Timothy Jay; Morgan, Geoffrey P.; Jones, Josette; McDaniel, Anna M.; Weaver, Michael; Weiner, Bryan; Haggstrom, David A.

2014-01-01

Our conceptual model demonstrates our goal to investigate the impact of clinical decision support (CDS) utilization on cancer screening improvement strategies in the community health care (CHC) setting. We employed a dual modeling technique using both statistical and computational modeling to evaluate impact. Our statistical model used the Spearman’s Rho test to evaluate the strength of relationship between our proximal outcome measures (CDS utilization) against our distal outcome measure (provider self-reported cancer screening improvement). Our computational model relied on network evolution theory and made use of a tool called Construct-TM to model the use of CDS measured by the rate of organizational learning. We employed the use of previously collected survey data from community health centers Cancer Health Disparities Collaborative (HDCC). Our intent is to demonstrate the added valued gained by using a computational modeling tool in conjunction with a statistical analysis when evaluating the impact a health information technology, in the form of CDS, on health care quality process outcomes such as facility-level screening improvement. Significant simulated disparities in organizational learning over time were observed between community health centers beginning the simulation with high and low clinical decision support capability. PMID:24953241

A New Approach on the Long Term Dynamics of NEO's Under Yarkovsky Effect.

NASA Astrophysics Data System (ADS)

Peláez, Jesús; Urrutxua, Hodei; Bombardelli, Claudio; Perez-Grande, Isabel

2011-12-01

A classical approach to the many-body problem is that of using special perturbation methods. Nowadays and due to the availability of high-speed computers is an essential tool in Space Dynamics which exhibits a great advantage: it is applicable to any orbit involving any number of bodies and all sorts of astrodynamical problems, especially when these problems fall into regions in which general perturbation theories are absent. One such case is, for example, that Near Earth Objects (NEO's) dynamics. In this field, the Group of Tether Dynamics of UPM (GDT) has developed a new regularisation scheme - called DROMO - which is characterised by only 8 ODE. This new regularisation scheme allows a new approach to the dynamics of NEO's in the long term, specially appropriated to consider the influence of the anisotropic thermal emission (Yarkovsky and YORP effects) on the dynamics. A new project, called NEODROMO, has been started in GDT that aims to provide a reliable tool for the long term dynamics of NEO's.

Turbine Manufacture

NASA Technical Reports Server (NTRS)

1979-01-01

The machinery pictured is a set of Turbodyne steam turbines which power a sugar mill at Bell Glade, Florida. A NASA-developed computer program called NASTRAN aided development of these and other turbines manufactured by Turbodyne Corporation's Steam Turbine Division, Wellsville, New York. An acronym for NASA Structural Analysis Program, NASTRAN is a predictive tool which advises development teams how a structural design will perform under service use conditions. Turbodyne uses NASTRAN to analyze the dynamic behavior of steam turbine components, achieving substantial savings in development costs. One of the most widely used spinoffs, NASTRAN is made available to private industry through NASA's Computer Software Management Information Center (COSMIC) at the University of Georgia.

A Web Tool for Research in Nonlinear Optics

NASA Astrophysics Data System (ADS)

Prikhod'ko, Nikolay V.; Abramovsky, Viktor A.; Abramovskaya, Natalia V.; Demichev, Andrey P.; Kryukov, Alexandr P.; Polyakov, Stanislav P.

2016-02-01

This paper presents a project of developing the web platform called WebNLO for computer modeling of nonlinear optics phenomena. We discuss a general scheme of the platform and a model for interaction between the platform modules. The platform is built as a set of interacting RESTful web services (SaaS approach). Users can interact with the platform through a web browser or command line interface. Such a resource has no analogues in the field of nonlinear optics and will be created for the first time therefore allowing researchers to access high-performance computing resources that will significantly reduce the cost of the research and development process.

Constructing a logical, regular axis topology from an irregular topology

DOEpatents

Faraj, Daniel A.

2014-07-22

Constructing a logical regular topology from an irregular topology including, for each axial dimension and recursively, for each compute node in a subcommunicator until returning to a first node: adding to a logical line of the axial dimension a neighbor specified in a nearest neighbor list; calling the added compute node; determining, by the called node, whether any neighbor in the node's nearest neighbor list is available to add to the logical line; if a neighbor in the called compute node's nearest neighbor list is available to add to the logical line, adding, by the called compute node to the logical line, any neighbor in the called compute node's nearest neighbor list for the axial dimension not already added to the logical line; and, if no neighbor in the called compute node's nearest neighbor list is available to add to the logical line, returning to the calling compute node.

Constructing a logical, regular axis topology from an irregular topology

DOEpatents

Faraj, Daniel A.

2014-07-01

Constructing a logical regular topology from an irregular topology including, for each axial dimension and recursively, for each compute node in a subcommunicator until returning to a first node: adding to a logical line of the axial dimension a neighbor specified in a nearest neighbor list; calling the added compute node; determining, by the called node, whether any neighbor in the node's nearest neighbor list is available to add to the logical line; if a neighbor in the called compute node's nearest neighbor list is available to add to the logical line, adding, by the called compute node to the logical line, any neighbor in the called compute node's nearest neighbor list for the axial dimension not already added to the logical line; and, if no neighbor in the called compute node's nearest neighbor list is available to add to the logical line, returning to the calling compute node.

Validation of a Pressure-Based Combustion Simulation Tool Using a Single Element Injector Test Problem

NASA Technical Reports Server (NTRS)

Thakur, Siddarth; Wright, Jeffrey

2006-01-01

The traditional design and analysis practice for advanced propulsion systems, particularly chemical rocket engines, relies heavily on expensive full-scale prototype development and testing. Over the past decade, use of high-fidelity analysis and design tools such as CFD early in the product development cycle has been identified as one way to alleviate testing costs and to develop these devices better, faster and cheaper. Increased emphasis is being placed on developing and applying CFD models to simulate the flow field environments and performance of advanced propulsion systems. This necessitates the development of next generation computational tools which can be used effectively and reliably in a design environment by non-CFD specialists. A computational tool, called Loci-STREAM is being developed for this purpose. It is a pressure-based, Reynolds-averaged Navier-Stokes (RANS) solver for generalized unstructured grids, which is designed to handle all-speed flows (incompressible to hypersonic) and is particularly suitable for solving multi-species flow in fixed-frame combustion devices. Loci-STREAM integrates proven numerical methods for generalized grids and state-of-the-art physical models in a novel rule-based programming framework called Loci which allows: (a) seamless integration of multidisciplinary physics in a unified manner, and (b) automatic handling of massively parallel computing. The objective of the ongoing work is to develop a robust simulation capability for combustion problems in rocket engines. As an initial step towards validating this capability, a model problem is investigated in the present study which involves a gaseous oxygen/gaseous hydrogen (GO2/GH2) shear coaxial single element injector, for which experimental data are available. The sensitivity of the computed solutions to grid density, grid distribution, different turbulence models, and different near-wall treatments is investigated. A refined grid, which is clustered in the vicinity of the solid walls as well as the flame, is used to obtain a steady state solution which may be considered as the best solution attainable with the steady-state RANS methodology. From a design point of view, quick turnaround times are desirable; with this in mind, coarser grids are also employed and the resulting solutions are evaluated with respect to the fine grid solution.

THE NASA AMES PAH IR SPECTROSCOPIC DATABASE VERSION 2.00: UPDATED CONTENT, WEB SITE, AND ON(OFF)LINE TOOLS

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

Boersma, C.; Mattioda, A. L.; Allamandola, L. J.

A significantly updated version of the NASA Ames PAH IR Spectroscopic Database, the first major revision since its release in 2010, is presented. The current version, version 2.00, contains 700 computational and 75 experimental spectra compared, respectively, with 583 and 60 in the initial release. The spectra span the 2.5-4000 μm (4000-2.5 cm{sup -1}) range. New tools are available on the site that allow one to analyze spectra in the database and compare them with imported astronomical spectra as well as a suite of IDL object classes (a collection of programs utilizing IDL's object-oriented programming capabilities) that permit offline analysismore » called the AmesPAHdbIDLSuite. Most noteworthy among the additions are the extension of the computational spectroscopic database to include a number of significantly larger polycyclic aromatic hydrocarbons (PAHs), the ability to visualize the molecular atomic motions corresponding to each vibrational mode, and a new tool that allows one to perform a non-negative least-squares fit of an imported astronomical spectrum with PAH spectra in the computational database. Finally, a methodology is described in the Appendix, and implemented using the AmesPAHdbIDLSuite, that allows the user to enforce charge balance during the fitting procedure.« less

Object-oriented design and implementation of CFDLab: a computer-assisted learning tool for fluid dynamics using dual reciprocity boundary element methodology

NASA Astrophysics Data System (ADS)

Friedrich, J.

1999-08-01

As lecturers, our main concern and goal is to develop more attractive and efficient ways of communicating up-to-date scientific knowledge to our students and facilitate an in-depth understanding of physical phenomena. Computer-based instruction is very promising to help both teachers and learners in their difficult task, which involves complex cognitive psychological processes. This complexity is reflected in high demands on the design and implementation methods used to create computer-assisted learning (CAL) programs. Due to their concepts, flexibility, maintainability and extended library resources, object-oriented modeling techniques are very suitable to produce this type of pedagogical tool. Computational fluid dynamics (CFD) enjoys not only a growing importance in today's research, but is also very powerful for teaching and learning fluid dynamics. For this purpose, an educational PC program for university level called 'CFDLab 1.1' for Windows™ was developed with an interactive graphical user interface (GUI) for multitasking and point-and-click operations. It uses the dual reciprocity boundary element method as a versatile numerical scheme, allowing to handle a variety of relevant governing equations in two dimensions on personal computers due to its simple pre- and postprocessing including 2D Laplace, Poisson, diffusion, transient convection-diffusion.

Computational Model Tracking Primary Electrons, Secondary Electrons, and Ions in the Discharge Chamber of an Ion Engine

NASA Technical Reports Server (NTRS)

Mahalingam, Sudhakar; Menart, James A.

2005-01-01

Computational modeling of the plasma located in the discharge chamber of an ion engine is an important activity so that the development and design of the next generation of ion engines may be enhanced. In this work a computational tool called XOOPIC is used to model the primary electrons, secondary electrons, and ions inside the discharge chamber. The details of this computational tool are discussed in this paper. Preliminary results from XOOPIC are presented. The results presented include particle number density distributions for the primary electrons, the secondary electrons, and the ions. In addition the total number of a particular particle in the discharge chamber as a function of time, electric potential maps and magnetic field maps are presented. A primary electron number density plot from PRIMA is given in this paper so that the results of XOOPIC can be compared to it. PRIMA is a computer code that the present investigators have used in much of their previous work that provides results that compare well to experimental results. PRIMA only models the primary electrons in the discharge chamber. Modeling ions and secondary electrons, as well as the primary electrons, will greatly increase our ability to predict different characteristics of the plasma discharge used in an ion engine.

Advanced Doubling Adding Method for Radiative Transfer in Planetary Atmospheres

NASA Astrophysics Data System (ADS)

Liu, Quanhua; Weng, Fuzhong

2006-12-01

The doubling adding method (DA) is one of the most accurate tools for detailed multiple-scattering calculations. The principle of the method goes back to the nineteenth century in a problem dealing with reflection and transmission by glass plates. Since then the doubling adding method has been widely used as a reference tool for other radiative transfer models. The method has never been used in operational applications owing to tremendous demand on computational resources from the model. This study derives an analytical expression replacing the most complicated thermal source terms in the doubling adding method. The new development is called the advanced doubling adding (ADA) method. Thanks also to the efficiency of matrix and vector manipulations in FORTRAN 90/95, the advanced doubling adding method is about 60 times faster than the doubling adding method. The radiance (i.e., forward) computation code of ADA is easily translated into tangent linear and adjoint codes for radiance gradient calculations. The simplicity in forward and Jacobian computation codes is very useful for operational applications and for the consistency between the forward and adjoint calculations in satellite data assimilation.

Geant4 Computing Performance Benchmarking and Monitoring

DOE PAGES

Dotti, Andrea; Elvira, V. Daniel; Folger, Gunter; ...

2015-12-23

Performance evaluation and analysis of large scale computing applications is essential for optimal use of resources. As detector simulation is one of the most compute intensive tasks and Geant4 is the simulation toolkit most widely used in contemporary high energy physics (HEP) experiments, it is important to monitor Geant4 through its development cycle for changes in computing performance and to identify problems and opportunities for code improvements. All Geant4 development and public releases are being profiled with a set of applications that utilize different input event samples, physics parameters, and detector configurations. Results from multiple benchmarking runs are compared tomore » previous public and development reference releases to monitor CPU and memory usage. Observed changes are evaluated and correlated with code modifications. Besides the full summary of call stack and memory footprint, a detailed call graph analysis is available to Geant4 developers for further analysis. The set of software tools used in the performance evaluation procedure, both in sequential and multi-threaded modes, include FAST, IgProf and Open|Speedshop. In conclusion, the scalability of the CPU time and memory performance in multi-threaded application is evaluated by measuring event throughput and memory gain as a function of the number of threads for selected event samples.« less

FILTSoft: A computational tool for microstrip planar filter design

NASA Astrophysics Data System (ADS)

Elsayed, M. H.; Abidin, Z. Z.; Dahlan, S. H.; Cholan N., A.; Ngu, Xavier T. I.; Majid, H. A.

2017-09-01

Filters are key component of any communication system to control spectrum and suppress interferences. Designing a filter involves long process as well as good understanding of the basic hardware technology. Hence this paper introduces an automated design tool based on Matlab-GUI, called the FILTSoft (acronym for Filter Design Software) to ease the process. FILTSoft is a user friendly filter design tool to aid, guide and expedite calculations from lumped elements level to microstrip structure. Users just have to provide the required filter specifications as well as the material description. FILTSoft will calculate and display the lumped element details, the planar filter structure, and the expected filter's response. An example of a lowpass filter design was calculated using FILTSoft and the results were validated through prototype measurement for comparison purposes.

GrigoraSNPs: Optimized Analysis of SNPs for DNA Forensics.

PubMed

Ricke, Darrell O; Shcherbina, Anna; Michaleas, Adam; Fremont-Smith, Philip

2018-04-16

High-throughput sequencing (HTS) of single nucleotide polymorphisms (SNPs) enables additional DNA forensic capabilities not attainable using traditional STR panels. However, the inclusion of sets of loci selected for mixture analysis, extended kinship, phenotype, biogeographic ancestry prediction, etc., can result in large panel sizes that are difficult to analyze in a rapid fashion. GrigoraSNP was developed to address the allele-calling bottleneck that was encountered when analyzing SNP panels with more than 5000 loci using HTS. GrigoraSNPs uses a MapReduce parallel data processing on multiple computational threads plus a novel locus-identification hashing strategy leveraging target sequence tags. This tool optimizes the SNP calling module of the DNA analysis pipeline with runtimes that scale linearly with the number of HTS reads. Results are compared with SNP analysis pipelines implemented with SAMtools and GATK. GrigoraSNPs removes a computational bottleneck for processing forensic samples with large HTS SNP panels. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.

Interactive computer aided shift scheduling.

PubMed

Gaertner, J

2001-12-01

This paper starts with a discussion of computer aided shift scheduling. After a brief review of earlier approaches, two conceptualizations of this field are introduced: First, shift scheduling as a field that ranges from extremely stable rosters at one pole to rather market-like approaches on the other pole. Unfortunately, already small alterations of a scheduling problem (e.g., the number of groups, the number of shifts) may call for rather different approaches and tools. Second, their environment shapes scheduling problems and scheduling has to be done within idiosyncratic organizational settings. This calls for the amalgamation of scheduling with other tasks (e.g., accounting) and for reflections whether better solutions might become possible by changes in the problem definition (e.g., other service levels, organizational changes). Therefore shift scheduling should be understood as a highly connected problem. Building upon these two conceptualizations, a few examples of software that ease scheduling in some areas of this field are given and future research questions are outlined.

m-BIRCH: an online clustering approach for computer vision applications

NASA Astrophysics Data System (ADS)

Madan, Siddharth K.; Dana, Kristin J.

2015-03-01

We adapt a classic online clustering algorithm called Balanced Iterative Reducing and Clustering using Hierarchies (BIRCH), to incrementally cluster large datasets of features commonly used in multimedia and computer vision. We call the adapted version modified-BIRCH (m-BIRCH). The algorithm uses only a fraction of the dataset memory to perform clustering, and updates the clustering decisions when new data comes in. Modifications made in m-BIRCH enable data driven parameter selection and effectively handle varying density regions in the feature space. Data driven parameter selection automatically controls the level of coarseness of the data summarization. Effective handling of varying density regions is necessary to well represent the different density regions in data summarization. We use m-BIRCH to cluster 840K color SIFT descriptors, and 60K outlier corrupted grayscale patches. We use the algorithm to cluster datasets consisting of challenging non-convex clustering patterns. Our implementation of the algorithm provides an useful clustering tool and is made publicly available.

The TeraShake Computational Platform for Large-Scale Earthquake Simulations

NASA Astrophysics Data System (ADS)

Cui, Yifeng; Olsen, Kim; Chourasia, Amit; Moore, Reagan; Maechling, Philip; Jordan, Thomas

Geoscientific and computer science researchers with the Southern California Earthquake Center (SCEC) are conducting a large-scale, physics-based, computationally demanding earthquake system science research program with the goal of developing predictive models of earthquake processes. The computational demands of this program continue to increase rapidly as these researchers seek to perform physics-based numerical simulations of earthquake processes for larger meet the needs of this research program, a multiple-institution team coordinated by SCEC has integrated several scientific codes into a numerical modeling-based research tool we call the TeraShake computational platform (TSCP). A central component in the TSCP is a highly scalable earthquake wave propagation simulation program called the TeraShake anelastic wave propagation (TS-AWP) code. In this chapter, we describe how we extended an existing, stand-alone, wellvalidated, finite-difference, anelastic wave propagation modeling code into the highly scalable and widely used TS-AWP and then integrated this code into the TeraShake computational platform that provides end-to-end (initialization to analysis) research capabilities. We also describe the techniques used to enhance the TS-AWP parallel performance on TeraGrid supercomputers, as well as the TeraShake simulations phases including input preparation, run time, data archive management, and visualization. As a result of our efforts to improve its parallel efficiency, the TS-AWP has now shown highly efficient strong scaling on over 40K processors on IBM’s BlueGene/L Watson computer. In addition, the TSCP has developed into a computational system that is useful to many members of the SCEC community for performing large-scale earthquake simulations.

Model-Driven Useware Engineering

NASA Astrophysics Data System (ADS)

Meixner, Gerrit; Seissler, Marc; Breiner, Kai

User-oriented hardware and software development relies on a systematic development process based on a comprehensive analysis focusing on the users' requirements and preferences. Such a development process calls for the integration of numerous disciplines, from psychology and ergonomics to computer sciences and mechanical engineering. Hence, a correspondingly interdisciplinary team must be equipped with suitable software tools to allow it to handle the complexity of a multimodal and multi-device user interface development approach. An abstract, model-based development approach seems to be adequate for handling this complexity. This approach comprises different levels of abstraction requiring adequate tool support. Thus, in this chapter, we present the current state of our model-based software tool chain. We introduce the use model as the core model of our model-based process, transformation processes, and a model-based architecture, and we present different software tools that provide support for creating and maintaining the models or performing the necessary model transformations.

Cloud-Based Tools to Support High-Resolution Modeling (Invited)

NASA Astrophysics Data System (ADS)

Jones, N.; Nelson, J.; Swain, N.; Christensen, S.

2013-12-01

The majority of watershed models developed to support decision-making by water management agencies are simple, lumped-parameter models. Maturity in research codes and advances in the computational power from multi-core processors on desktop machines, commercial cloud-computing resources, and supercomputers with thousands of cores have created new opportunities for employing more accurate, high-resolution distributed models for routine use in decision support. The barriers for using such models on a more routine basis include massive amounts of spatial data that must be processed for each new scenario and lack of efficient visualization tools. In this presentation we will review a current NSF-funded project called CI-WATER that is intended to overcome many of these roadblocks associated with high-resolution modeling. We are developing a suite of tools that will make it possible to deploy customized web-based apps for running custom scenarios for high-resolution models with minimal effort. These tools are based on a software stack that includes 52 North, MapServer, PostGIS, HT Condor, CKAN, and Python. This open source stack provides a simple scripting environment for quickly configuring new custom applications for running high-resolution models as geoprocessing workflows. The HT Condor component facilitates simple access to local distributed computers or commercial cloud resources when necessary for stochastic simulations. The CKAN framework provides a powerful suite of tools for hosting such workflows in a web-based environment that includes visualization tools and storage of model simulations in a database to archival, querying, and sharing of model results. Prototype applications including land use change, snow melt, and burned area analysis will be presented. This material is based upon work supported by the National Science Foundation under Grant No. 1135482

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

Christoph, G.G; Jackson, K.A.; Neuman, M.C.

An effective method for detecting computer misuse is the automatic auditing and analysis of on-line user activity. This activity is reflected in the system audit record, by changes in the vulnerability posture of the system configuration, and in other evidence found through active testing of the system. In 1989 we started developing an automatic misuse detection system for the Integrated Computing Network (ICN) at Los Alamos National Laboratory. Since 1990 this system has been operational, monitoring a variety of network systems and services. We call it the Network Anomaly Detection and Intrusion Reporter, or NADIR. During the last year andmore » a half, we expanded NADIR to include processing of audit and activity records for the Cray UNICOS operating system. This new component is called the UNICOS Real-time NADIR, or UNICORN. UNICORN summarizes user activity and system configuration information in statistical profiles. In near real-time, it can compare current activity to historical profiles and test activity against expert rules that express our security policy and define improper or suspicious behavior. It reports suspicious behavior to security auditors and provides tools to aid in follow-up investigations. UNICORN is currently operational on four Crays in Los Alamos` main computing network, the ICN.« less

Multidisciplinary analysis of actively controlled large flexible spacecraft

NASA Technical Reports Server (NTRS)

Cooper, Paul A.; Young, John W.; Sutter, Thomas R.

1986-01-01

The control of Flexible Structures (COFS) program has supported the development of an analysis capability at the Langley Research Center called the Integrated Multidisciplinary Analysis Tool (IMAT) which provides an efficient data storage and transfer capability among commercial computer codes to aid in the dynamic analysis of actively controlled structures. IMAT is a system of computer programs which transfers Computer-Aided-Design (CAD) configurations, structural finite element models, material property and stress information, structural and rigid-body dynamic model information, and linear system matrices for control law formulation among various commercial applications programs through a common database. Although general in its formulation, IMAT was developed specifically to aid in the evaluation of the structures. A description of the IMAT system and results of an application of the system are given.

EEGNET: An Open Source Tool for Analyzing and Visualizing M/EEG Connectome.

PubMed

Hassan, Mahmoud; Shamas, Mohamad; Khalil, Mohamad; El Falou, Wassim; Wendling, Fabrice

2015-01-01

The brain is a large-scale complex network often referred to as the "connectome". Exploring the dynamic behavior of the connectome is a challenging issue as both excellent time and space resolution is required. In this context Magneto/Electroencephalography (M/EEG) are effective neuroimaging techniques allowing for analysis of the dynamics of functional brain networks at scalp level and/or at reconstructed sources. However, a tool that can cover all the processing steps of identifying brain networks from M/EEG data is still missing. In this paper, we report a novel software package, called EEGNET, running under MATLAB (Math works, inc), and allowing for analysis and visualization of functional brain networks from M/EEG recordings. EEGNET is developed to analyze networks either at the level of scalp electrodes or at the level of reconstructed cortical sources. It includes i) Basic steps in preprocessing M/EEG signals, ii) the solution of the inverse problem to localize / reconstruct the cortical sources, iii) the computation of functional connectivity among signals collected at surface electrodes or/and time courses of reconstructed sources and iv) the computation of the network measures based on graph theory analysis. EEGNET is the unique tool that combines the M/EEG functional connectivity analysis and the computation of network measures derived from the graph theory. The first version of EEGNET is easy to use, flexible and user friendly. EEGNET is an open source tool and can be freely downloaded from this webpage: https://sites.google.com/site/eegnetworks/.

EEGNET: An Open Source Tool for Analyzing and Visualizing M/EEG Connectome

PubMed Central

Hassan, Mahmoud; Shamas, Mohamad; Khalil, Mohamad; El Falou, Wassim; Wendling, Fabrice

2015-01-01

The brain is a large-scale complex network often referred to as the “connectome”. Exploring the dynamic behavior of the connectome is a challenging issue as both excellent time and space resolution is required. In this context Magneto/Electroencephalography (M/EEG) are effective neuroimaging techniques allowing for analysis of the dynamics of functional brain networks at scalp level and/or at reconstructed sources. However, a tool that can cover all the processing steps of identifying brain networks from M/EEG data is still missing. In this paper, we report a novel software package, called EEGNET, running under MATLAB (Math works, inc), and allowing for analysis and visualization of functional brain networks from M/EEG recordings. EEGNET is developed to analyze networks either at the level of scalp electrodes or at the level of reconstructed cortical sources. It includes i) Basic steps in preprocessing M/EEG signals, ii) the solution of the inverse problem to localize / reconstruct the cortical sources, iii) the computation of functional connectivity among signals collected at surface electrodes or/and time courses of reconstructed sources and iv) the computation of the network measures based on graph theory analysis. EEGNET is the unique tool that combines the M/EEG functional connectivity analysis and the computation of network measures derived from the graph theory. The first version of EEGNET is easy to use, flexible and user friendly. EEGNET is an open source tool and can be freely downloaded from this webpage: https://sites.google.com/site/eegnetworks/. PMID:26379232

pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms.

PubMed

Molnos, Sophie; Baumbach, Clemens; Wahl, Simone; Müller-Nurasyid, Martina; Strauch, Konstantin; Wang-Sattler, Rui; Waldenberger, Melanie; Meitinger, Thomas; Adamski, Jerzy; Kastenmüller, Gabi; Suhre, Karsten; Peters, Annette; Grallert, Harald; Theis, Fabian J; Gieger, Christian

2017-09-29

Genome-wide association studies allow us to understand the genetics of complex diseases. Human metabolism provides information about the disease-causing mechanisms, so it is usual to investigate the associations between genetic variants and metabolite levels. However, only considering genetic variants and their effects on one trait ignores the possible interplay between different "omics" layers. Existing tools only consider single-nucleotide polymorphism (SNP)-SNP interactions, and no practical tool is available for large-scale investigations of the interactions between pairs of arbitrary quantitative variables. We developed an R package called pulver to compute p-values for the interaction term in a very large number of linear regression models. Comparisons based on simulated data showed that pulver is much faster than the existing tools. This is achieved by using the correlation coefficient to test the null-hypothesis, which avoids the costly computation of inversions. Additional tricks are a rearrangement of the order, when iterating through the different "omics" layers, and implementing this algorithm in the fast programming language C++. Furthermore, we applied our algorithm to data from the German KORA study to investigate a real-world problem involving the interplay among DNA methylation, genetic variants, and metabolite levels. The pulver package is a convenient and rapid tool for screening huge numbers of linear regression models for significant interaction terms in arbitrary pairs of quantitative variables. pulver is written in R and C++, and can be downloaded freely from CRAN at https://cran.r-project.org/web/packages/pulver/ .

Digital Images on the DIME

NASA Technical Reports Server (NTRS)

2003-01-01

With NASA on its side, Positive Systems, Inc., of Whitefish, Montana, is veering away from the industry standards defined for producing and processing remotely sensed images. A top developer of imaging products for geographic information system (GIS) and computer-aided design (CAD) applications, Positive Systems is bucking traditional imaging concepts with a cost-effective and time-saving software tool called Digital Images Made Easy (DIME(trademark)). Like piecing a jigsaw puzzle together, DIME can integrate a series of raw aerial or satellite snapshots into a single, seamless panoramic image, known as a 'mosaic.' The 'mosaicked' images serve as useful backdrops to GIS maps - which typically consist of line drawings called 'vectors' - by allowing users to view a multidimensional map that provides substantially more geographic information.

Information Presentation and Control in a Modern Air Traffic Control Tower Simulator

NASA Technical Reports Server (NTRS)

Haines, Richard F.; Doubek, Sharon; Rabin, Boris; Harke, Stanton

1996-01-01

The proper presentation and management of information in America's largest and busiest (Level V) air traffic control towers calls for an in-depth understanding of many different human-computer considerations: user interface design for graphical, radar, and text; manual and automated data input hardware; information/display output technology; reconfigurable workstations; workload assessment; and many other related subjects. This paper discusses these subjects in the context of the Surface Development and Test Facility (SDTF) currently under construction at NASA's Ames Research Center, a full scale, multi-manned, air traffic control simulator which will provide the "look and feel" of an actual airport tower cab. Special emphasis will be given to the human-computer interfaces required for the different kinds of information displayed at the various controller and supervisory positions and to the computer-aided design (CAD) and other analytic, computer-based tools used to develop the facility.

a Discrete Mathematical Model to Simulate Malware Spreading

NASA Astrophysics Data System (ADS)

Del Rey, A. Martin; Sánchez, G. Rodriguez

2012-10-01

With the advent and worldwide development of Internet, the study and control of malware spreading has become very important. In this sense, some mathematical models to simulate malware propagation have been proposed in the scientific literature, and usually they are based on differential equations exploiting the similarities with mathematical epidemiology. The great majority of these models study the behavior of a particular type of malware called computer worms; indeed, to the best of our knowledge, no model has been proposed to simulate the spreading of a computer virus (the traditional type of malware which differs from computer worms in several aspects). In this sense, the purpose of this work is to introduce a new mathematical model not based on continuous mathematics tools but on discrete ones, to analyze and study the epidemic behavior of computer virus. Specifically, cellular automata are used in order to design such model.

Radiological interpretation of images displayed on tablet computers: a systematic review.

PubMed

Caffery, L J; Armfield, N R; Smith, A C

2015-06-01

To review the published evidence and to determine if radiological diagnostic accuracy is compromised when images are displayed on a tablet computer and thereby inform practice on using tablet computers for radiological interpretation by on-call radiologists. We searched the PubMed and EMBASE databases for studies on the diagnostic accuracy or diagnostic reliability of images interpreted on tablet computers. Studies were screened for inclusion based on pre-determined inclusion and exclusion criteria. Studies were assessed for quality and risk of bias using Quality Appraisal of Diagnostic Reliability Studies or the revised Quality Assessment of Diagnostic Accuracy Studies tool. Treatment of studies was reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). 11 studies met the inclusion criteria. 10 of these studies tested the Apple iPad(®) (Apple, Cupertino, CA). The included studies reported high sensitivity (84-98%), specificity (74-100%) and accuracy rates (98-100%) for radiological diagnosis. There was no statistically significant difference in accuracy between a tablet computer and a digital imaging and communication in medicine-calibrated control display. There was a near complete consensus from authors on the non-inferiority of diagnostic accuracy of images displayed on a tablet computer. All of the included studies were judged to be at risk of bias. Our findings suggest that the diagnostic accuracy of radiological interpretation is not compromised by using a tablet computer. This result is only relevant to the Apple iPad and to the modalities of CT, MRI and plain radiography. The iPad may be appropriate for an on-call radiologist to use for radiological interpretation.

The BioCyc collection of microbial genomes and metabolic pathways.

PubMed

Karp, Peter D; Billington, Richard; Caspi, Ron; Fulcher, Carol A; Latendresse, Mario; Kothari, Anamika; Keseler, Ingrid M; Krummenacker, Markus; Midford, Peter E; Ong, Quang; Ong, Wai Kit; Paley, Suzanne M; Subhraveti, Pallavi

2017-08-17

BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by biologist curators. BioCyc also provides an extensive range of query tools, visualization services and analysis software. Recent advances in BioCyc include an expansion in the content of BioCyc in terms of both the number of genomes and the types of information available for each genome; an expansion in the amount of curated content within BioCyc; and new developments in the BioCyc software tools including redesigned gene/protein pages and metabolite pages; new search tools; a new sequence-alignment tool; a new tool for visualizing groups of related metabolic pathways; and a facility called SmartTables, which enables biologists to perform analyses that previously would have required a programmer's assistance. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Actualities and Development of Heavy-Duty CNC Machine Tool Thermal Error Monitoring Technology

NASA Astrophysics Data System (ADS)

Zhou, Zu-De; Gui, Lin; Tan, Yue-Gang; Liu, Ming-Yao; Liu, Yi; Li, Rui-Ya

2017-09-01

Thermal error monitoring technology is the key technological support to solve the thermal error problem of heavy-duty CNC (computer numerical control) machine tools. Currently, there are many review literatures introducing the thermal error research of CNC machine tools, but those mainly focus on the thermal issues in small and medium-sized CNC machine tools and seldom introduce thermal error monitoring technologies. This paper gives an overview of the research on the thermal error of CNC machine tools and emphasizes the study of thermal error of the heavy-duty CNC machine tool in three areas. These areas are the causes of thermal error of heavy-duty CNC machine tool and the issues with the temperature monitoring technology and thermal deformation monitoring technology. A new optical measurement technology called the "fiber Bragg grating (FBG) distributed sensing technology" for heavy-duty CNC machine tools is introduced in detail. This technology forms an intelligent sensing and monitoring system for heavy-duty CNC machine tools. This paper fills in the blank of this kind of review articles to guide the development of this industry field and opens up new areas of research on the heavy-duty CNC machine tool thermal error.

Student Evaluation of CALL Tools during the Design Process

ERIC Educational Resources Information Center

Nesbitt, Dallas

2013-01-01

This article discusses the comparative effectiveness of student input at different times during the design of CALL tools for learning kanji, the Japanese characters of Chinese origin. The CALL software "package" consisted of tools to facilitate the writing, reading and practising of kanji characters in context. A pre-design questionnaire…

Interest in a digital health tool in veterans with epilepsy: results of a phone survey.

PubMed

Hixson, John D; Van Bebber, Stephanie L; Bertko, Kate M

2015-04-01

Online tools for managing chronic health conditions are becoming increasingly popular. Perceived benefits include ease of use, low costs, and availability but are contingent on patient engagement, Internet access, and digital literacy. This article describes data collected during the recruitment phase of a study evaluating an online self-management platform for epilepsy in a U.S. Veteran population. We used administrative data to identify and contact Veterans with a likely diagnosis of epilepsy in the Veterans Health Administration (VHA). Veterans who did not respond directly to a mailed invitation were recruited by phone to determine study interest and evaluate digital access. Of the 2,143 Veterans mailed study invitations, phone calls were made to 1,789 who did not specifically decline participation. Among those reached by phone (n = 1,053): 295 (28%) expressed interest in the study and an online tool, 333 (19%) reported a lack of computer and/or Internet access and 425 (40%) were not interested for other reasons. This study suggests an interest in online tools for managing health despite the fact that some Veterans lack computer and/or Internet access. As investment in digital health solutions grows, the VHA should prioritize the widespread provision of digital access to more Veterans. Reprint & Copyright © 2015 Association of Military Surgeons of the U.S.

Dynamics of flexible bodies in tree topology - A computer oriented approach

NASA Technical Reports Server (NTRS)

Singh, R. P.; Vandervoort, R. J.; Likins, P. W.

1984-01-01

An approach suited for automatic generation of the equations of motion for large mechanical systems (i.e., large space structures, mechanisms, robots, etc.) is presented. The system topology is restricted to a tree configuration. The tree is defined as an arbitrary set of rigid and flexible bodies connected by hinges characterizing relative translations and rotations of two adjoining bodies. The equations of motion are derived via Kane's method. The resulting equation set is of minimum dimension. Dynamical equations are imbedded in a computer program called TREETOPS. Extensive control simulation capability is built in the TREETOPS program. The simulation is driven by an interactive set-up program resulting in an easy to use analysis tool.

Building the Scientific Modeling Assistant: An interactive environment for specialized software design

NASA Technical Reports Server (NTRS)

Keller, Richard M.

1991-01-01

The construction of scientific software models is an integral part of doing science, both within NASA and within the scientific community at large. Typically, model-building is a time-intensive and painstaking process, involving the design of very large, complex computer programs. Despite the considerable expenditure of resources involved, completed scientific models cannot easily be distributed and shared with the larger scientific community due to the low-level, idiosyncratic nature of the implemented code. To address this problem, we have initiated a research project aimed at constructing a software tool called the Scientific Modeling Assistant. This tool provides automated assistance to the scientist in developing, using, and sharing software models. We describe the Scientific Modeling Assistant, and also touch on some human-machine interaction issues relevant to building a successful tool of this type.

2D Sub-Pixel Disparity Measurement Using QPEC / Medicis

NASA Astrophysics Data System (ADS)

Cournet, M.; Giros, A.; Dumas, L.; Delvit, J. M.; Greslou, D.; Languille, F.; Blanchet, G.; May, S.; Michel, J.

2016-06-01

In the frame of its earth observation missions, CNES created a library called QPEC, and one of its launcher called Medicis. QPEC / Medicis is a sub-pixel two-dimensional stereo matching algorithm that works on an image pair. This tool is a block matching algorithm, which means that it is based on a local method. Moreover it does not regularize the results found. It proposes several matching costs, such as the Zero mean Normalised Cross-Correlation or statistical measures (the Mutual Information being one of them), and different match validation flags. QPEC / Medicis is able to compute a two-dimensional dense disparity map with a subpixel precision. Hence, it is more versatile than disparity estimation methods found in computer vision literature, which often assume an epipolar geometry. CNES uses Medicis, among other applications, during the in-orbit image quality commissioning of earth observation satellites. For instance the Pléiades-HR 1A & 1B and the Sentinel-2 geometric calibrations are based on this block matching algorithm. Over the years, it has become a common tool in ground segments for in-flight monitoring purposes. For these two kinds of applications, the two-dimensional search and the local sub-pixel measure without regularization can be essential. This tool is also used to generate automatic digital elevation models, for which it was not initially dedicated. This paper deals with the QPEC / Medicis algorithm. It also presents some of its CNES applications (in-orbit commissioning, in flight monitoring or digital elevation model generation). Medicis software is distributed outside the CNES as well. This paper finally describes some of these external applications using Medicis, such as ground displacement measurement, or intra-oral scanner in the dental domain.

Direct-To Tool for En Route Controllers

NASA Technical Reports Server (NTRS)

Erzberger, Heinz; McNally, David; Foster, Michelle

2002-01-01

This paper describes a new automation tool for en route air traffic controllers, called the Direct-To Tool. The Tool is designed to reduce the time of flight and fuel consumption for aircraft flying in en route airspace. It provides each controller with the identities of aircraft in his/her sector, which can reduce their time en route by bypassing dog-legged route segments and flying "direct to" a waypoint closer to the destination airport. The Tool uses its build-in conflict probing capability to determine if the improved route is free of conflicts with other aircraft. The Tool's graphical computer interface enables the controller to enter a direct-to clearance by a simple point and click action. Because of its low workload and convenience, this method is strongly favored by controllers The Tool has been running since January with live radar data received at NASA from the Fort Worth Air Route Traffic Control Center. For aircraft operating in the Fort Worth Center, the Tool has the potential to save in excess of 500,000 in-flight minutes per year. A provisional patent application for this Tool has been filed. A field task in planned for the last quarter of this year.

3DRT-MPASS

NASA Technical Reports Server (NTRS)

Lickly, Ben

2005-01-01

Data from all current JPL missions are stored in files called SPICE kernels. At present, animators who want to use data from these kernels have to either read through the kernels looking for the desired data, or write programs themselves to retrieve information about all the needed objects for their animations. In this project, methods of automating the process of importing the data from the SPICE kernels were researched. In particular, tools were developed for creating basic scenes in Maya, a 3D computer graphics software package, from SPICE kernels.

Simulation of Etching in Chlorine Discharges Using an Integrated Feature Evolution-Plasma Model

NASA Technical Reports Server (NTRS)

Hwang, Helen H.; Bose, Deepak; Govindan, T. R.; Meyyappan, M.; Biegel, Bryan (Technical Monitor)

2002-01-01

To better utilize its vast collection of heterogeneous resources that are geographically distributed across the United States, NASA is constructing a computational grid called the Information Power Grid (IPG). This paper describes various tools and techniques that we are developing to measure and improve the performance of a broad class of NASA applications when run on the IPG. In particular, we are investigating the areas of grid benchmarking, grid monitoring, user-level application scheduling, and decentralized system-level scheduling.

On the importance of mathematical methods for analysis of MALDI-imaging mass spectrometry data.

PubMed

Trede, Dennis; Kobarg, Jan Hendrik; Oetjen, Janina; Thiele, Herbert; Maass, Peter; Alexandrov, Theodore

2012-03-21

In the last decade, matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS), also called as MALDI-imaging, has proven its potential in proteomics and was successfully applied to various types of biomedical problems, in particular to histopathological label-free analysis of tissue sections. In histopathology, MALDI-imaging is used as a general analytic tool revealing the functional proteomic structure of tissue sections, and as a discovery tool for detecting new biomarkers discriminating a region annotated by an experienced histologist, in particular, for cancer studies. A typical MALDI-imaging data set contains 10⁸ to 10⁹ intensity values occupying more than 1 GB. Analysis and interpretation of such huge amount of data is a mathematically, statistically and computationally challenging problem. In this paper we overview some computational methods for analysis of MALDI-imaging data sets. We discuss the importance of data preprocessing, which typically includes normalization, baseline removal and peak picking, and hightlight the importance of image denoising when visualizing IMS data.

On the Importance of Mathematical Methods for Analysis of MALDI-Imaging Mass Spectrometry Data.

PubMed

Trede, Dennis; Kobarg, Jan Hendrik; Oetjen, Janina; Thiele, Herbert; Maass, Peter; Alexandrov, Theodore

2012-03-01

In the last decade, matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS), also called as MALDI-imaging, has proven its potential in proteomics and was successfully applied to various types of biomedical problems, in particular to histopathological label-free analysis of tissue sections. In histopathology, MALDI-imaging is used as a general analytic tool revealing the functional proteomic structure of tissue sections, and as a discovery tool for detecting new biomarkers discriminating a region annotated by an experienced histologist, in particular, for cancer studies. A typical MALDI-imaging data set contains 108 to 109 intensity values occupying more than 1 GB. Analysis and interpretation of such huge amount of data is a mathematically, statistically and computationally challenging problem. In this paper we overview some computational methods for analysis of MALDI-imaging data sets. We discuss the importance of data preprocessing, which typically includes normalization, baseline removal and peak picking, and hightlight the importance of image denoising when visualizing IMS data.

Analytical simulation and PROFAT II: a new methodology and a computer automated tool for fault tree analysis in chemical process industries.

PubMed

Khan, F I; Abbasi, S A

2000-07-10

Fault tree analysis (FTA) is based on constructing a hypothetical tree of base events (initiating events) branching into numerous other sub-events, propagating the fault and eventually leading to the top event (accident). It has been a powerful technique used traditionally in identifying hazards in nuclear installations and power industries. As the systematic articulation of the fault tree is associated with assigning probabilities to each fault, the exercise is also sometimes called probabilistic risk assessment. But powerful as this technique is, it is also very cumbersome and costly, limiting its area of application. We have developed a new algorithm based on analytical simulation (named as AS-II), which makes the application of FTA simpler, quicker, and cheaper; thus opening up the possibility of its wider use in risk assessment in chemical process industries. Based on the methodology we have developed a computer-automated tool. The details are presented in this paper.

Development of hybrid computer plasma models for different pressure regimes

NASA Astrophysics Data System (ADS)

Hromadka, Jakub; Ibehej, Tomas; Hrach, Rudolf

2016-09-01

With increased performance of contemporary computers during last decades numerical simulations became a very powerful tool applicable also in plasma physics research. Plasma is generally an ensemble of mutually interacting particles that is out of the thermodynamic equilibrium and for this reason fluid computer plasma models give results with only limited accuracy. On the other hand, much more precise particle models are often limited only on 2D problems because of their huge demands on the computer resources. Our contribution is devoted to hybrid modelling techniques that combine advantages of both modelling techniques mentioned above, particularly to their so-called iterative version. The study is focused on mutual relations between fluid and particle models that are demonstrated on the calculations of sheath structures of low temperature argon plasma near a cylindrical Langmuir probe for medium and higher pressures. Results of a simple iterative hybrid plasma computer model are also given. The authors acknowledge the support of the Grant Agency of Charles University in Prague (project 220215).

Granular computing with multiple granular layers for brain big data processing.

PubMed

Wang, Guoyin; Xu, Ji

2014-12-01

Big data is the term for a collection of datasets so huge and complex that it becomes difficult to be processed using on-hand theoretical models and technique tools. Brain big data is one of the most typical, important big data collected using powerful equipments of functional magnetic resonance imaging, multichannel electroencephalography, magnetoencephalography, Positron emission tomography, near infrared spectroscopic imaging, as well as other various devices. Granular computing with multiple granular layers, referred to as multi-granular computing (MGrC) for short hereafter, is an emerging computing paradigm of information processing, which simulates the multi-granular intelligent thinking model of human brain. It concerns the processing of complex information entities called information granules, which arise in the process of data abstraction and derivation of information and even knowledge from data. This paper analyzes three basic mechanisms of MGrC, namely granularity optimization, granularity conversion, and multi-granularity joint computation, and discusses the potential of introducing MGrC into intelligent processing of brain big data.

Cloud Computing for Protein-Ligand Binding Site Comparison

PubMed Central

2013-01-01

The proteome-wide analysis of protein-ligand binding sites and their interactions with ligands is important in structure-based drug design and in understanding ligand cross reactivity and toxicity. The well-known and commonly used software, SMAP, has been designed for 3D ligand binding site comparison and similarity searching of a structural proteome. SMAP can also predict drug side effects and reassign existing drugs to new indications. However, the computing scale of SMAP is limited. We have developed a high availability, high performance system that expands the comparison scale of SMAP. This cloud computing service, called Cloud-PLBS, combines the SMAP and Hadoop frameworks and is deployed on a virtual cloud computing platform. To handle the vast amount of experimental data on protein-ligand binding site pairs, Cloud-PLBS exploits the MapReduce paradigm as a management and parallelizing tool. Cloud-PLBS provides a web portal and scalability through which biologists can address a wide range of computer-intensive questions in biology and drug discovery. PMID:23762824

Cloud computing for protein-ligand binding site comparison.

PubMed

Hung, Che-Lun; Hua, Guan-Jie

2013-01-01

The proteome-wide analysis of protein-ligand binding sites and their interactions with ligands is important in structure-based drug design and in understanding ligand cross reactivity and toxicity. The well-known and commonly used software, SMAP, has been designed for 3D ligand binding site comparison and similarity searching of a structural proteome. SMAP can also predict drug side effects and reassign existing drugs to new indications. However, the computing scale of SMAP is limited. We have developed a high availability, high performance system that expands the comparison scale of SMAP. This cloud computing service, called Cloud-PLBS, combines the SMAP and Hadoop frameworks and is deployed on a virtual cloud computing platform. To handle the vast amount of experimental data on protein-ligand binding site pairs, Cloud-PLBS exploits the MapReduce paradigm as a management and parallelizing tool. Cloud-PLBS provides a web portal and scalability through which biologists can address a wide range of computer-intensive questions in biology and drug discovery.

Pre-Service Teachers' Uses of and Barriers from Adopting Computer-Assisted Language Learning (CALL) Programs

ERIC Educational Resources Information Center

Samani, Ebrahim; Baki, Roselan; Razali, Abu Bakar

2014-01-01

Success in implementation of computer-assisted language learning (CALL) programs depends on the teachers' understanding of the roles of CALL programs in education. Consequently, it is also important to understand the barriers teachers face in the use of computer-assisted language learning (CALL) programs. The current study was conducted on 14…

Advances in Grid Computing for the FabrIc for Frontier Experiments Project at Fermialb

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

Herner, K.; Alba Hernandex, A. F.; Bhat, S.

The FabrIc for Frontier Experiments (FIFE) project is a major initiative within the Fermilab Scientic Computing Division charged with leading the computing model for Fermilab experiments. Work within the FIFE project creates close collaboration between experimenters and computing professionals to serve high-energy physics experiments of diering size, scope, and physics area. The FIFE project has worked to develop common tools for job submission, certicate management, software and reference data distribution through CVMFS repositories, robust data transfer, job monitoring, and databases for project tracking. Since the projects inception the experiments under the FIFE umbrella have signicantly matured, and present an increasinglymore » complex list of requirements to service providers. To meet these requirements, the FIFE project has been involved in transitioning the Fermilab General Purpose Grid cluster to support a partitionable slot model, expanding the resources available to experiments via the Open Science Grid, assisting with commissioning dedicated high-throughput computing resources for individual experiments, supporting the eorts of the HEP Cloud projects to provision a variety of back end resources, including public clouds and high performance computers, and developing rapid onboarding procedures for new experiments and collaborations. The larger demands also require enhanced job monitoring tools, which the project has developed using such tools as ElasticSearch and Grafana. in helping experiments manage their large-scale production work ows. This group in turn requires a structured service to facilitate smooth management of experiment requests, which FIFE provides in the form of the Production Operations Management Service (POMS). POMS is designed to track and manage requests from the FIFE experiments to run particular work ows, and support troubleshooting and triage in case of problems. Recently a new certicate management infrastructure called Distributed Computing Access with Federated Identities (DCAFI) has been put in place that has eliminated our dependence on a Fermilab-specic third-party Certicate Authority service and better accommodates FIFE collaborators without a Fermilab Kerberos account. DCAFI integrates the existing InCommon federated identity infrastructure, CILogon Basic CA, and a MyProxy service using a new general purpose open source tool. We will discuss the general FIFE onboarding strategy, progress in expanding FIFE experiments presence on the Open Science Grid, new tools for job monitoring, the POMS service, and the DCAFI project.« less

Advances in Grid Computing for the Fabric for Frontier Experiments Project at Fermilab

NASA Astrophysics Data System (ADS)

Herner, K.; Alba Hernandez, A. F.; Bhat, S.; Box, D.; Boyd, J.; Di Benedetto, V.; Ding, P.; Dykstra, D.; Fattoruso, M.; Garzoglio, G.; Kirby, M.; Kreymer, A.; Levshina, T.; Mazzacane, A.; Mengel, M.; Mhashilkar, P.; Podstavkov, V.; Retzke, K.; Sharma, N.; Teheran, J.

2017-10-01

The Fabric for Frontier Experiments (FIFE) project is a major initiative within the Fermilab Scientific Computing Division charged with leading the computing model for Fermilab experiments. Work within the FIFE project creates close collaboration between experimenters and computing professionals to serve high-energy physics experiments of differing size, scope, and physics area. The FIFE project has worked to develop common tools for job submission, certificate management, software and reference data distribution through CVMFS repositories, robust data transfer, job monitoring, and databases for project tracking. Since the projects inception the experiments under the FIFE umbrella have significantly matured, and present an increasingly complex list of requirements to service providers. To meet these requirements, the FIFE project has been involved in transitioning the Fermilab General Purpose Grid cluster to support a partitionable slot model, expanding the resources available to experiments via the Open Science Grid, assisting with commissioning dedicated high-throughput computing resources for individual experiments, supporting the efforts of the HEP Cloud projects to provision a variety of back end resources, including public clouds and high performance computers, and developing rapid onboarding procedures for new experiments and collaborations. The larger demands also require enhanced job monitoring tools, which the project has developed using such tools as ElasticSearch and Grafana. in helping experiments manage their large-scale production workflows. This group in turn requires a structured service to facilitate smooth management of experiment requests, which FIFE provides in the form of the Production Operations Management Service (POMS). POMS is designed to track and manage requests from the FIFE experiments to run particular workflows, and support troubleshooting and triage in case of problems. Recently a new certificate management infrastructure called Distributed Computing Access with Federated Identities (DCAFI) has been put in place that has eliminated our dependence on a Fermilab-specific third-party Certificate Authority service and better accommodates FIFE collaborators without a Fermilab Kerberos account. DCAFI integrates the existing InCommon federated identity infrastructure, CILogon Basic CA, and a MyProxy service using a new general purpose open source tool. We will discuss the general FIFE onboarding strategy, progress in expanding FIFE experiments presence on the Open Science Grid, new tools for job monitoring, the POMS service, and the DCAFI project.

Large-scale inverse model analyses employing fast randomized data reduction

NASA Astrophysics Data System (ADS)

Lin, Youzuo; Le, Ellen B.; O'Malley, Daniel; Vesselinov, Velimir V.; Bui-Thanh, Tan

2017-08-01

When the number of observations is large, it is computationally challenging to apply classical inverse modeling techniques. We have developed a new computationally efficient technique for solving inverse problems with a large number of observations (e.g., on the order of 107 or greater). Our method, which we call the randomized geostatistical approach (RGA), is built upon the principal component geostatistical approach (PCGA). We employ a data reduction technique combined with the PCGA to improve the computational efficiency and reduce the memory usage. Specifically, we employ a randomized numerical linear algebra technique based on a so-called "sketching" matrix to effectively reduce the dimension of the observations without losing the information content needed for the inverse analysis. In this way, the computational and memory costs for RGA scale with the information content rather than the size of the calibration data. Our algorithm is coded in Julia and implemented in the MADS open-source high-performance computational framework (http://mads.lanl.gov). We apply our new inverse modeling method to invert for a synthetic transmissivity field. Compared to a standard geostatistical approach (GA), our method is more efficient when the number of observations is large. Most importantly, our method is capable of solving larger inverse problems than the standard GA and PCGA approaches. Therefore, our new model inversion method is a powerful tool for solving large-scale inverse problems. The method can be applied in any field and is not limited to hydrogeological applications such as the characterization of aquifer heterogeneity.

Maestro: an orchestration framework for large-scale WSN simulations.

PubMed

Riliskis, Laurynas; Osipov, Evgeny

2014-03-18

Contemporary wireless sensor networks (WSNs) have evolved into large and complex systems and are one of the main technologies used in cyber-physical systems and the Internet of Things. Extensive research on WSNs has led to the development of diverse solutions at all levels of software architecture, including protocol stacks for communications. This multitude of solutions is due to the limited computational power and restrictions on energy consumption that must be accounted for when designing typical WSN systems. It is therefore challenging to develop, test and validate even small WSN applications, and this process can easily consume significant resources. Simulations are inexpensive tools for testing, verifying and generally experimenting with new technologies in a repeatable fashion. Consequently, as the size of the systems to be tested increases, so does the need for large-scale simulations. This article describes a tool called Maestro for the automation of large-scale simulation and investigates the feasibility of using cloud computing facilities for such task. Using tools that are built into Maestro, we demonstrate a feasible approach for benchmarking cloud infrastructure in order to identify cloud Virtual Machine (VM)instances that provide an optimal balance of performance and cost for a given simulation.

Maestro: An Orchestration Framework for Large-Scale WSN Simulations

PubMed Central

Riliskis, Laurynas; Osipov, Evgeny

2014-01-01

Contemporary wireless sensor networks (WSNs) have evolved into large and complex systems and are one of the main technologies used in cyber-physical systems and the Internet of Things. Extensive research on WSNs has led to the development of diverse solutions at all levels of software architecture, including protocol stacks for communications. This multitude of solutions is due to the limited computational power and restrictions on energy consumption that must be accounted for when designing typical WSN systems. It is therefore challenging to develop, test and validate even small WSN applications, and this process can easily consume significant resources. Simulations are inexpensive tools for testing, verifying and generally experimenting with new technologies in a repeatable fashion. Consequently, as the size of the systems to be tested increases, so does the need for large-scale simulations. This article describes a tool called Maestro for the automation of large-scale simulation and investigates the feasibility of using cloud computing facilities for such task. Using tools that are built into Maestro, we demonstrate a feasible approach for benchmarking cloud infrastructure in order to identify cloud Virtual Machine (VM)instances that provide an optimal balance of performance and cost for a given simulation. PMID:24647123

Designing computer learning environments for engineering and computer science: The scaffolded knowledge integration framework

NASA Astrophysics Data System (ADS)

Linn, Marcia C.

1995-06-01

Designing effective curricula for complex topics and incorporating technological tools is an evolving process. One important way to foster effective design is to synthesize successful practices. This paper describes a framework called scaffolded knowledge integration and illustrates how it guided the design of two successful course enhancements in the field of computer science and engineering. One course enhancement, the LISP Knowledge Integration Environment, improved learning and resulted in more gender-equitable outcomes. The second course enhancement, the spatial reasoning environment, addressed spatial reasoning in an introductory engineering course. This enhancement minimized the importance of prior knowledge of spatial reasoning and helped students develop a more comprehensive repertoire of spatial reasoning strategies. Taken together, the instructional research programs reinforce the value of the scaffolded knowledge integration framework and suggest directions for future curriculum reformers.

On modelling three-dimensional piezoelectric smart structures with boundary spectral element method

NASA Astrophysics Data System (ADS)

Zou, Fangxin; Aliabadi, M. H.

2017-05-01

The computational efficiency of the boundary element method in elastodynamic analysis can be significantly improved by employing high-order spectral elements for boundary discretisation. In this work, for the first time, the so-called boundary spectral element method is utilised to formulate the piezoelectric smart structures that are widely used in structural health monitoring (SHM) applications. The resultant boundary spectral element formulation has been validated by the finite element method (FEM) and physical experiments. The new formulation has demonstrated a lower demand on computational resources and a higher numerical stability than commercial FEM packages. Comparing to the conventional boundary element formulation, a significant reduction in computational expenses has been achieved. In summary, the boundary spectral element formulation presented in this paper provides a highly efficient and stable mathematical tool for the development of SHM applications.

Using Palm Technology in Participatory Simulations of Complex Systems: A New Take on Ubiquitous and Accessible Mobile Computing

NASA Astrophysics Data System (ADS)

Klopfer, Eric; Yoon, Susan; Perry, Judy

2005-09-01

This paper reports on teachers' perceptions of the educational affordances of a handheld application called Participatory Simulations. It presents evidence from five cases representing each of the populations who work with these computational tools. Evidence across multiple data sources yield similar results to previous research evaluations of handheld activities with respect to enhancing motivation, engagement and self-directed learning. Three additional themes are discussed that provide insight into understanding curricular applicability of Participatory Simulations that suggest a new take on ubiquitous and accessible mobile computing. These themes generally point to the multiple layers of social and cognitive flexibility intrinsic to their design: ease of adaptation to subject-matter content knowledge and curricular integration; facility in attending to teacher-individualized goals; and encouraging the adoption of learner-centered strategies.

Learning from Adverse Events in Obstetrics: Is a Standardized Computer Tool an Effective Strategy for Root Cause Analysis?

PubMed

Murray-Davis, Beth; McDonald, Helen; Cross-Sudworth, Fiona; Ahmed, Rashid; Simioni, Julia; Dore, Sharon; Marrin, Michael; DeSantis, Judy; Leyland, Nicholas; Gardosi, Jason; Hutton, Eileen; McDonald, Sarah

2015-08-01

Adverse events occur in up to 10% of obstetric cases, and up to one half of these could be prevented. Case reviews and root cause analysis using a structured tool may help health care providers to learn from adverse events and to identify trends and recurring systems issues. We sought to establish the reliability of a root cause analysis computer application called Standardized Clinical Outcome Review (SCOR). We designed a mixed methods study to evaluate the effectiveness of the tool. We conducted qualitative content analysis of five charts reviewed by both the traditional obstetric quality assurance methods and the SCOR tool. We also determined inter-rater reliability by having four health care providers review the same five cases using the SCOR tool. The comparative qualitative review revealed that the traditional quality assurance case review process used inconsistent language and made serious, personalized recommendations for those involved in the case. In contrast, the SCOR review provided a consistent format for recommendations, a list of action points, and highlighted systems issues. The mean percentage agreement between the four reviewers for the five cases was 75%. The different health care providers completed data entry and assessment of the case in a similar way. Missing data from the chart and poor wording of questions were identified as issues affecting percentage agreement. The SCOR tool provides a standardized, objective, obstetric-specific tool for root cause analysis that may improve identification of risk factors and dissemination of action plans to prevent future events.

Acoustic/seismic signal propagation and sensor performance modeling

NASA Astrophysics Data System (ADS)

Wilson, D. Keith; Marlin, David H.; Mackay, Sean

2007-04-01

Performance, optimal employment, and interpretation of data from acoustic and seismic sensors depend strongly and in complex ways on the environment in which they operate. Software tools for guiding non-expert users of acoustic and seismic sensors are therefore much needed. However, such tools require that many individual components be constructed and correctly connected together. These components include the source signature and directionality, representation of the atmospheric and terrain environment, calculation of the signal propagation, characterization of the sensor response, and mimicking of the data processing at the sensor. Selection of an appropriate signal propagation model is particularly important, as there are significant trade-offs between output fidelity and computation speed. Attenuation of signal energy, random fading, and (for array systems) variations in wavefront angle-of-arrival should all be considered. Characterization of the complex operational environment is often the weak link in sensor modeling: important issues for acoustic and seismic modeling activities include the temporal/spatial resolution of the atmospheric data, knowledge of the surface and subsurface terrain properties, and representation of ambient background noise and vibrations. Design of software tools that address these challenges is illustrated with two examples: a detailed target-to-sensor calculation application called the Sensor Performance Evaluator for Battlefield Environments (SPEBE) and a GIS-embedded approach called Battlefield Terrain Reasoning and Awareness (BTRA).

Construction of a combinatorial pipeline using two somatic variant  calling  methods  for whole exome sequence data of gastric cancer.

PubMed

Kohmoto, Tomohiro; Masuda, Kiyoshi; Naruto, Takuya; Tange, Shoichiro; Shoda, Katsutoshi; Hamada, Junichi; Saito, Masako; Ichikawa, Daisuke; Tajima, Atsushi; Otsuji, Eigo; Imoto, Issei

2017-01-01

High-throughput next-generation sequencing is a powerful tool to identify the genotypic landscapes of somatic variants and therapeutic targets in various cancers including gastric cancer, forming the basis for personalized medicine in the clinical setting. Although the advent of many computational algorithms leads to higher accuracy in somatic variant calling, no standard method exists due to the limitations of each method. Here, we constructed a new pipeline. We combined two different somatic variant callers with different algorithms, Strelka and VarScan 2, and evaluated performance using whole exome sequencing data obtained from 19 Japanese cases with gastric cancer (GC); then, we characterized these tumors based on identified driver molecular alterations. More single nucleotide variants (SNVs) and small insertions/deletions were detected by Strelka and VarScan 2, respectively. SNVs detected by both tools showed higher accuracy for estimating somatic variants compared with those detected by only one of the two tools and accurately showed the mutation signature and mutations of driver genes reported for GC. Our combinatorial pipeline may have an advantage in detection of somatic mutations in GC and may be useful for further genomic characterization of Japanese patients with GC to improve the efficacy of GC treatments. J. Med. Invest. 64: 233-240, August, 2017.

Electrophysiological signal analysis and visualization using Cloudwave for epilepsy clinical research.

PubMed

Jayapandian, Catherine P; Chen, Chien-Hung; Bozorgi, Alireza; Lhatoo, Samden D; Zhang, Guo-Qiang; Sahoo, Satya S

2013-01-01

Epilepsy is the most common serious neurological disorder affecting 50-60 million persons worldwide. Electrophysiological data recordings, such as electroencephalogram (EEG), are the gold standard for diagnosis and pre-surgical evaluation in epilepsy patients. The increasing trend towards multi-center clinical studies require signal visualization and analysis tools to support real time interaction with signal data in a collaborative environment, which cannot be supported by traditional desktop-based standalone applications. As part of the Prevention and Risk Identification of SUDEP Mortality (PRISM) project, we have developed a Web-based electrophysiology data visualization and analysis platform called Cloudwave using highly scalable open source cloud computing infrastructure. Cloudwave is integrated with the PRISM patient cohort identification tool called MEDCIS (Multi-modality Epilepsy Data Capture and Integration System). The Epilepsy and Seizure Ontology (EpSO) underpins both Cloudwave and MEDCIS to support query composition and result retrieval. Cloudwave is being used by clinicians and research staff at the University Hospital - Case Medical Center (UH-CMC) Epilepsy Monitoring Unit (EMU) and will be progressively deployed at four EMUs in the United States and the United Kingdomas part of the PRISM project.

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

NASA Astrophysics Data System (ADS)

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 computational science and engineering codes. Finally, we are partnering with the lead PTP developers at IBM, to ensure we are as effective as possible within the Eclipse community development. We are also conducting training and outreach to our user community, including conference BOF sessions, monthly user calls, and an annual user meeting, so that we can best inform the improvements we make to Eclipse PTP. With these activities we endeavor to encourage use of modern software engineering practices, as enabled through the Eclipse IDE, with computational science and engineering applications. These practices include proper use of source code repositories, tracking and rectifying issues, measuring and monitoring code performance changes against both optimizations as well as ever-changing software stacks and configurations on HPC systems, as well as ultimately encouraging development and maintenance of testing suites -- things that have become commonplace in many software endeavors, but have lagged in the development of science applications. We view that the challenge with the increased complexity of both HPC systems and science applications demands the use of better software engineering methods, preferably enabled by modern tools such as Eclipse PTP, to help the computational science community thrive as we evolve the HPC landscape.

A Research Roadmap for Computation-Based Human Reliability Analysis

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

Boring, Ronald; Mandelli, Diego; Joe, Jeffrey

2015-08-01

The United States (U.S.) Department of Energy (DOE) is sponsoring research through the Light Water Reactor Sustainability (LWRS) program to extend the life of the currently operating fleet of commercial nuclear power plants. The Risk Informed Safety Margin Characterization (RISMC) research pathway within LWRS looks at ways to maintain and improve the safety margins of these plants. The RISMC pathway includes significant developments in the area of thermalhydraulics code modeling and the development of tools to facilitate dynamic probabilistic risk assessment (PRA). PRA is primarily concerned with the risk of hardware systems at the plant; yet, hardware reliability is oftenmore » secondary in overall risk significance to human errors that can trigger or compound undesirable events at the plant. This report highlights ongoing efforts to develop a computation-based approach to human reliability analysis (HRA). This computation-based approach differs from existing static and dynamic HRA approaches in that it: (i) interfaces with a dynamic computation engine that includes a full scope plant model, and (ii) interfaces with a PRA software toolset. The computation-based HRA approach presented in this report is called the Human Unimodels for Nuclear Technology to Enhance Reliability (HUNTER) and incorporates in a hybrid fashion elements of existing HRA methods to interface with new computational tools developed under the RISMC pathway. The goal of this research effort is to model human performance more accurately than existing approaches, thereby minimizing modeling uncertainty found in current plant risk models.« less

Compute as Fast as the Engineers Can Think! ULTRAFAST COMPUTING TEAM FINAL REPORT

NASA Technical Reports Server (NTRS)

Biedron, R. T.; Mehrotra, P.; Nelson, M. L.; Preston, M. L.; Rehder, J. J.; Rogersm J. L.; Rudy, D. H.; Sobieski, J.; Storaasli, O. O.

1999-01-01

This report documents findings and recommendations by the Ultrafast Computing Team (UCT). In the period 10-12/98, UCT reviewed design case scenarios for a supersonic transport and a reusable launch vehicle to derive computing requirements necessary for support of a design process with efficiency so radically improved that human thought rather than the computer paces the process. Assessment of the present computing capability against the above requirements indicated a need for further improvement in computing speed by several orders of magnitude to reduce time to solution from tens of hours to seconds in major applications. Evaluation of the trends in computer technology revealed a potential to attain the postulated improvement by further increases of single processor performance combined with massively parallel processing in a heterogeneous environment. However, utilization of massively parallel processing to its full capability will require redevelopment of the engineering analysis and optimization methods, including invention of new paradigms. To that end UCT recommends initiation of a new activity at LaRC called Computational Engineering for development of new methods and tools geared to the new computer architectures in disciplines, their coordination, and validation and benefit demonstration through applications.

Economic Analysis of Complex Nuclear Fuel Cycles with NE-COST

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

Ganda, Francesco; Dixon, Brent; Hoffman, Edward

The purpose of this work is to present a new methodology, and associated computational tools, developed within the U.S. Department of Energy (U.S. DOE) Fuel Cycle Option Campaign to quantify the economic performance of complex nuclear fuel cycles. The levelized electricity cost at the busbar is generally chosen to quantify and compare the economic performance of different baseload generating technologies, including of nuclear: it is the cost of electricity which renders the risk-adjusted discounted net present value of the investment cash flow equal to zero. The work presented here is focused on the calculation of the levelized cost of electricitymore » of fuel cycles at mass balance equilibrium, which is termed LCAE (Levelized Cost of Electricity at Equilibrium). To alleviate the computational issues associated with the calculation of the LCAE for complex fuel cycles, a novel approach has been developed, which has been called the “island approach” because of its logical structure: a generic complex fuel cycle is subdivided into subsets of fuel cycle facilities, called islands, each containing one and only one type of reactor or blanket and an arbitrary number of fuel cycle facilities. A nuclear economic software tool, NE-COST, written in the commercial programming software MATLAB®, has been developed to calculate the LCAE of complex fuel cycles with the “island” computational approach. NE-COST has also been developed with the capability to handle uncertainty: the input parameters (both unit costs and fuel cycle characteristics) can have uncertainty distributions associated with them, and the output can be computed in terms of probability density functions of the LCAE. In this paper NE-COST will be used to quantify, as examples, the economic performance of (1) current Light Water Reactors (LWR) once-through systems; (2) continuous plutonium recycling in Fast Reactors (FR) with driver and blanket; (3) Recycling of plutonium bred in FR into LWR. For each fuel cycle, the contributions to the total LCAE of the main cost components will be identified.« less

Identifying Key Words in 9-1-1 Calls for Stroke: A Mixed Methods Approach.

PubMed

Richards, Christopher T; Wang, Baiyang; Markul, Eddie; Albarran, Frank; Rottman, Doreen; Aggarwal, Neelum T; Lindeman, Patricia; Stein-Spencer, Leslee; Weber, Joseph M; Pearlman, Kenneth S; Tataris, Katie L; Holl, Jane L; Klabjan, Diego; Prabhakaran, Shyam

2017-01-01

Identifying stroke during a 9-1-1 call is critical to timely prehospital care. However, emergency medical dispatchers (EMDs) recognize stroke in less than half of 9-1-1 calls, potentially due to the words used by callers to communicate stroke signs and symptoms. We hypothesized that callers do not typically use words and phrases considered to be classical descriptors of stroke, such as focal neurologic deficits, but that a mixed-methods approach can identify words and phrases commonly used by 9-1-1 callers to describe acute stroke victims. We performed a mixed-method, retrospective study of 9-1-1 call audio recordings for adult patients with confirmed stroke who were transported by ambulance in a large urban city. Content analysis, a qualitative methodology, and computational linguistics, a quantitative methodology, were used to identify key words and phrases used by 9-1-1 callers to describe acute stroke victims. Because a caller's level of emotional distress contributes to the communication during a 9-1-1 call, the Emotional Content and Cooperation Score was scored by a multidisciplinary team. A total of 110 9-1-1 calls, received between June and September 2013, were analyzed. EMDs recognized stroke in 48% of calls, and the emotional state of most callers (95%) was calm. In 77% of calls in which EMDs recognized stroke, callers specifically used the word "stroke"; however, the word "stroke" was used in only 38% of calls. Vague, non-specific words and phrases were used to describe stroke victims' symptoms in 55% of calls, and 45% of callers used distractor words and phrases suggestive of non-stroke emergencies. Focal neurologic symptoms were described in 39% of calls. Computational linguistics identified 9 key words that were more commonly used in calls where the EMD identified stroke. These words were concordant with terms identified through qualitative content analysis. Most 9-1-1 callers used vague, non-specific, or distractor words and phrases and infrequently provide classic stroke descriptions during 9-1-1 calls for stroke. Both qualitative and quantitative methodologies identified similar key words and phrases associated with accurate EMD stroke recognition. This study suggests that tools incorporating commonly used words and phrases could potentially improve EMD stroke recognition.

ANTLR Tree Grammar Generator and Extensions

NASA Technical Reports Server (NTRS)

Craymer, Loring

2005-01-01

A computer program implements two extensions of ANTLR (Another Tool for Language Recognition), which is a set of software tools for translating source codes between different computing languages. ANTLR supports predicated- LL(k) lexer and parser grammars, a notation for annotating parser grammars to direct tree construction, and predicated tree grammars. [ LL(k) signifies left-right, leftmost derivation with k tokens of look-ahead, referring to certain characteristics of a grammar.] One of the extensions is a syntax for tree transformations. The other extension is the generation of tree grammars from annotated parser or input tree grammars. These extensions can simplify the process of generating source-to-source language translators and they make possible an approach, called "polyphase parsing," to translation between computing languages. The typical approach to translator development is to identify high-level semantic constructs such as "expressions," "declarations," and "definitions" as fundamental building blocks in the grammar specification used for language recognition. The polyphase approach is to lump ambiguous syntactic constructs during parsing and then disambiguate the alternatives in subsequent tree transformation passes. Polyphase parsing is believed to be useful for generating efficient recognizers for C++ and other languages that, like C++, have significant ambiguities.

ORBIT: an integrated environment for user-customized bioinformatics tools.

PubMed

Bellgard, M I; Hiew, H L; Hunter, A; Wiebrands, M

1999-10-01

There are a large number of computational programs freely available to bioinformaticians via a client/server, web-based environment. However, the client interface to these tools (typically an html form page) cannot be customized from the client side as it is created by the service provider. The form page is usually generic enough to cater for a wide range of users. However, this implies that a user cannot set as 'default' advanced program parameters on the form or even customize the interface to his/her specific requirements or preferences. Currently, there is a lack of end-user interface environments that can be modified by the user when accessing computer programs available on a remote server running on an intranet or over the Internet. We have implemented a client/server system called ORBIT (Online Researcher's Bioinformatics Interface Tools) where individual clients can have interfaces created and customized to command-line-driven, server-side programs. Thus, Internet-based interfaces can be tailored to a user's specific bioinformatic needs. As interfaces are created on the client machine independent of the server, there can be different interfaces to the same server-side program to cater for different parameter settings. The interface customization is relatively quick (between 10 and 60 min) and all client interfaces are integrated into a single modular environment which will run on any computer platform supporting Java. The system has been developed to allow for a number of future enhancements and features. ORBIT represents an important advance in the way researchers gain access to bioinformatics tools on the Internet.

User's manual for tooth contact analysis of face-milled spiral bevel gears with given machine-tool settings

NASA Technical Reports Server (NTRS)

Litvin, Faydor L.; Zhang, YI; Chen, Jui-Sheng

1991-01-01

Research was performed to develop a computer program that will: (1) simulate the meshing and bearing contact for face milled spiral beval gears with given machine tool settings; and (2) to obtain the output, some of the data is required for hydrodynamic analysis. It is assumed that the machine tool settings and the blank data will be taken from the Gleason summaries. The theoretical aspects of the program are based on 'Local Synthesis and Tooth Contact Analysis of Face Mill Milled Spiral Bevel Gears'. The difference between the computer programs developed herein and the other one is as follows: (1) the mean contact point of tooth surfaces for gears with given machine tool settings must be determined iteratively, while parameters (H and V) are changed (H represents displacement along the pinion axis, V represents the gear displacement that is perpendicular to the plane drawn through the axes of the pinion and the gear of their initial positions), this means that when V differs from zero, the axis of the pionion and the gear are crossed but not intersected; (2) in addition to the regular output data (transmission errors and bearing contact), the new computer program provides information about the contacting force for each contact point and the sliding and the so-called rolling velocity. The following topics are covered: (1) instructions for the users as to how to insert the input data; (2) explanations regarding the output data; (3) numerical example; and (4) listing of the program.

Radiological interpretation of images displayed on tablet computers: a systematic review

PubMed Central

Armfield, N R; Smith, A C

2015-01-01

Objective: To review the published evidence and to determine if radiological diagnostic accuracy is compromised when images are displayed on a tablet computer and thereby inform practice on using tablet computers for radiological interpretation by on-call radiologists. Methods: We searched the PubMed and EMBASE databases for studies on the diagnostic accuracy or diagnostic reliability of images interpreted on tablet computers. Studies were screened for inclusion based on pre-determined inclusion and exclusion criteria. Studies were assessed for quality and risk of bias using Quality Appraisal of Diagnostic Reliability Studies or the revised Quality Assessment of Diagnostic Accuracy Studies tool. Treatment of studies was reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). Results: 11 studies met the inclusion criteria. 10 of these studies tested the Apple iPad® (Apple, Cupertino, CA). The included studies reported high sensitivity (84–98%), specificity (74–100%) and accuracy rates (98–100%) for radiological diagnosis. There was no statistically significant difference in accuracy between a tablet computer and a digital imaging and communication in medicine-calibrated control display. There was a near complete consensus from authors on the non-inferiority of diagnostic accuracy of images displayed on a tablet computer. All of the included studies were judged to be at risk of bias. Conclusion: Our findings suggest that the diagnostic accuracy of radiological interpretation is not compromised by using a tablet computer. This result is only relevant to the Apple iPad and to the modalities of CT, MRI and plain radiography. Advances in knowledge: The iPad may be appropriate for an on-call radiologist to use for radiological interpretation. PMID:25882691

Open Science in the Cloud: Towards a Universal Platform for Scientific and Statistical Computing

NASA Astrophysics Data System (ADS)

Chine, Karim

The UK, through the e-Science program, the US through the NSF-funded cyber infrastructure and the European Union through the ICT Calls aimed to provide "the technological solution to the problem of efficiently connecting data, computers, and people with the goal of enabling derivation of novel scientific theories and knowledge".1 The Grid (Foster, 2002; Foster; Kesselman, Nick, & Tuecke, 2002), foreseen as a major accelerator of discovery, didn't meet the expectations it had excited at its beginnings and was not adopted by the broad population of research professionals. The Grid is a good tool for particle physicists and it has allowed them to tackle the tremendous computational challenges inherent to their field. However, as a technology and paradigm for delivering computing on demand, it doesn't work and it can't be fixed. On one hand, "the abstractions that Grids expose - to the end-user, to the deployers and to application developers - are inappropriate and they need to be higher level" (Jha, Merzky, & Fox), and on the other hand, academic Grids are inherently economically unsustainable. They can't compete with a service outsourced to the Industry whose quality and price would be driven by market forces. The virtualization technologies and their corollary, the Infrastructure-as-a-Service (IaaS) style cloud, hold the promise to enable what the Grid failed to deliver: a sustainable environment for computational sciences that would lower the barriers for accessing federated computational resources, software tools and data; enable collaboration and resources sharing and provide the building blocks of a ubiquitous platform for traceable and reproducible computational research.

GCLAS: a graphical constituent loading analysis system

USGS Publications Warehouse

McKallip, T.E.; Koltun, G.F.; Gray, J.R.; Glysson, G.D.

2001-01-01

The U. S. Geological Survey has developed a program called GCLAS (Graphical Constituent Loading Analysis System) to aid in the computation of daily constituent loads transported in stream flow. Due to the relative paucity with which most water-quality data are collected, computation of daily constituent loads is moderately to highly dependent on human interpretation of the relation between stream hydraulics and constituent transport. GCLAS provides a visual environment for evaluating the relation between hydraulic and other covariate time series and the constituent chemograph. GCLAS replaces the computer program Sedcalc, which is the most recent USGS sanctioned tool for constructing sediment chemographs and computing suspended-sediment loads. Written in a portable language, GCLAS has an interactive graphical interface that permits easy entry of estimated values and provides new tools to aid in making those estimates. The use of a portable language for program development imparts a degree of computer platform independence that was difficult to obtain in the past, making implementation more straightforward within the USGS' s diverse computing environment. Some of the improvements introduced in GCLAS include (1) the ability to directly handle periods of zero or reverse flow, (2) the ability to analyze and apply coefficient adjustments to concentrations as a function of time, streamflow, or both, (3) the ability to compute discharges of constituents other than suspended sediment, (4) the ability to easily view data related to the chemograph at different levels of detail, and (5) the ability to readily display covariate time series data to provide enhanced visual cues for drawing the constituent chemograph.

AntiClustal: Multiple Sequence Alignment by antipole clustering and linear approximate 1-median computation.

PubMed

Di Pietro, C; Di Pietro, V; Emmanuele, G; Ferro, A; Maugeri, T; Modica, E; Pigola, G; Pulvirenti, A; Purrello, M; Ragusa, M; Scalia, M; Shasha, D; Travali, S; Zimmitti, V

2003-01-01

In this paper we present a new Multiple Sequence Alignment (MSA) algorithm called AntiClusAl. The method makes use of the commonly use idea of aligning homologous sequences belonging to classes generated by some clustering algorithm, and then continue the alignment process ina bottom-up way along a suitable tree structure. The final result is then read at the root of the tree. Multiple sequence alignment in each cluster makes use of the progressive alignment with the 1-median (center) of the cluster. The 1-median of set S of sequences is the element of S which minimizes the average distance from any other sequence in S. Its exact computation requires quadratic time. The basic idea of our proposed algorithm is to make use of a simple and natural algorithmic technique based on randomized tournaments which has been successfully applied to large size search problems in general metric spaces. In particular a clustering algorithm called Antipole tree and an approximate linear 1-median computation are used. Our algorithm compared with Clustal W, a widely used tool to MSA, shows a better running time results with fully comparable alignment quality. A successful biological application showing high aminoacid conservation during evolution of Xenopus laevis SOD2 is also cited.

VirSSPA- a virtual reality tool for surgical planning workflow.

PubMed

Suárez, C; Acha, B; Serrano, C; Parra, C; Gómez, T

2009-03-01

A virtual reality tool, called VirSSPA, was developed to optimize the planning of surgical processes. Segmentation algorithms for Computed Tomography (CT) images: a region growing procedure was used for soft tissues and a thresholding algorithm was implemented to segment bones. The algorithms operate semiautomati- cally since they only need seed selection with the mouse on each tissue segmented by the user. The novelty of the paper is the adaptation of an enhancement method based on histogram thresholding applied to CT images for surgical planning, which simplifies subsequent segmentation. A substantial improvement of the virtual reality tool VirSSPA was obtained with these algorithms. VirSSPA was used to optimize surgical planning, to decrease the time spent on surgical planning and to improve operative results. The success rate increases due to surgeons being able to see the exact extent of the patient's ailment. This tool can decrease operating room time, thus resulting in reduced costs. Virtual simulation was effective for optimizing surgical planning, which could, consequently, result in improved outcomes with reduced costs.

PLAT: An Automated Fault and Behavioural Anomaly Detection Tool for PLC Controlled Manufacturing Systems.

PubMed

Ghosh, Arup; Qin, Shiming; Lee, Jooyeoun; Wang, Gi-Nam

2016-01-01

Operational faults and behavioural anomalies associated with PLC control processes take place often in a manufacturing system. Real time identification of these operational faults and behavioural anomalies is necessary in the manufacturing industry. In this paper, we present an automated tool, called PLC Log-Data Analysis Tool (PLAT) that can detect them by using log-data records of the PLC signals. PLAT automatically creates a nominal model of the PLC control process and employs a novel hash table based indexing and searching scheme to satisfy those purposes. Our experiments show that PLAT is significantly fast, provides real time identification of operational faults and behavioural anomalies, and can execute within a small memory footprint. In addition, PLAT can easily handle a large manufacturing system with a reasonable computing configuration and can be installed in parallel to the data logging system to identify operational faults and behavioural anomalies effectively.

PLAT: An Automated Fault and Behavioural Anomaly Detection Tool for PLC Controlled Manufacturing Systems

PubMed Central

Ghosh, Arup; Qin, Shiming; Lee, Jooyeoun

2016-01-01

Operational faults and behavioural anomalies associated with PLC control processes take place often in a manufacturing system. Real time identification of these operational faults and behavioural anomalies is necessary in the manufacturing industry. In this paper, we present an automated tool, called PLC Log-Data Analysis Tool (PLAT) that can detect them by using log-data records of the PLC signals. PLAT automatically creates a nominal model of the PLC control process and employs a novel hash table based indexing and searching scheme to satisfy those purposes. Our experiments show that PLAT is significantly fast, provides real time identification of operational faults and behavioural anomalies, and can execute within a small memory footprint. In addition, PLAT can easily handle a large manufacturing system with a reasonable computing configuration and can be installed in parallel to the data logging system to identify operational faults and behavioural anomalies effectively. PMID:27974882

The PDA as a reference tool: libraries' role in enhancing nursing education.

PubMed

Scollin, Patrick; Callahan, John; Mehta, Apurva; Garcia, Elizabeth

2006-01-01

"The PDA as a Reference Tool: The Libraries' Role in Enhancing Nursing Education" is a pilot project funded by the University of Massachusetts President's Office Information Technology Council through their Professional Development Grant program in 2004. The project's goal is to offer faculty and students in nursing programs at two University of Massachusetts campuses access to an array of medical reference information, such as handbooks, dictionaries, calculators, and diagnostic tools, on small handheld computers called personal digital assistants. Through exposure to the variety of information resources in this digital format, participants can discover and explore these resources at no personal financial cost. Participants borrow handhelds from the University Library's circulation desks. The libraries provide support in routine resynchronizing of handhelds to update information. This report will discuss how the projects were administered, what we learned about what did and did not work, the problems and solutions, and where we hope to go from here.

Status of the Combustion Devices Injector Technology Program at the NASA MSFC

NASA Technical Reports Server (NTRS)

Jones, Gregg; Protz, Christopher; Trinh, Huu; Tucker, Kevin; Nesman, Tomas; Hulka, James

2005-01-01

To support the NASA Space Exploration Mission, an in-house program called Combustion Devices Injector Technology (CDIT) is being conducted at the NASA Marshall Space Flight Center (MSFC) for the fiscal year 2005. CDIT is focused on developing combustor technology and analysis tools to improve reliability and durability of upper-stage and in-space liquid propellant rocket engines. The three areas of focus include injector/chamber thermal compatibility, ignition, and combustion stability. In the compatibility and ignition areas, small-scale single- and multi-element hardware experiments will be conducted to demonstrate advanced technological concepts as well as to provide experimental data for validation of computational analysis tools. In addition, advanced analysis tools will be developed to eventually include 3-dimensional and multi- element effects and improve capability and validity to analyze heat transfer and ignition in large, multi-element injectors.

The braingraph.org database of high resolution structural connectomes and the brain graph tools.

PubMed

Kerepesi, Csaba; Szalkai, Balázs; Varga, Bálint; Grolmusz, Vince

2017-10-01

Based on the data of the NIH-funded Human Connectome Project, we have computed structural connectomes of 426 human subjects in five different resolutions of 83, 129, 234, 463 and 1015 nodes and several edge weights. The graphs are given in anatomically annotated GraphML format that facilitates better further processing and visualization. For 96 subjects, the anatomically classified sub-graphs can also be accessed, formed from the vertices corresponding to distinct lobes or even smaller regions of interests of the brain. For example, one can easily download and study the connectomes, restricted to the frontal lobes or just to the left precuneus of 96 subjects using the data. Partially directed connectomes of 423 subjects are also available for download. We also present a GitHub-deposited set of tools, called the Brain Graph Tools, for several processing tasks of the connectomes on the site http://braingraph.org.

The X-windows interactive navigation data editor

NASA Technical Reports Server (NTRS)

Rinker, G. C.

1992-01-01

A new computer program called the X-Windows Interactive Data Editor (XIDE) was developed and demonstrated as a prototype application for editing radio metric data in the orbit-determination process. The program runs on a variety of workstations and employs pull-down menus and graphical displays, which allow users to easily inspect and edit radio metric data in the orbit data files received from the Deep Space Network (DSN). The XIDE program is based on the Open Software Foundation OSF/Motif Graphical User Interface (GUI) and has proven to be an efficient tool for editing radio metric data in the navigation operations environment. It was adopted by the Magellan Navigation Team as their primary data-editing tool. Because the software was designed from the beginning to be portable, the prototype was successfully moved to new workstation environments. It was also itegrated into the design of the next-generation software tool for DSN multimission navigation interactive launch support.

A modified homogeneous relaxation model for CO2 two-phase flow in vapour ejector

NASA Astrophysics Data System (ADS)

Haida, M.; Palacz, M.; Smolka, J.; Nowak, A. J.; Hafner, A.; Banasiak, K.

2016-09-01

In this study, the homogenous relaxation model (HRM) for CO2 flow in a two-phase ejector was modified in order to increase the accuracy of the numerical simulations The two- phase flow model was implemented on the effective computational tool called ejectorPL for fully automated and systematic computations of various ejector shapes and operating conditions. The modification of the HRM was performed by a change of the relaxation time and the constants included in the relaxation time equation based on the experimental result under the operating conditions typical for the supermarket refrigeration system. The modified HRM was compared to the HEM results, which were performed based on the comparison of motive nozzle and suction nozzle mass flow rates.

Computer Animations as Astronomy Educational Tool: Immanuel Kant and the Island Universes Hypothesis

NASA Astrophysics Data System (ADS)

Mijic, M.; Park, D.; Zumaeta, J.; Simonian, V.; Levitin, S.; Sullivan, A.; Kang, E. Y. E.; Longson, T.

2008-11-01

Development of astronomy is based on well defined, watershed moments when an individual or a group of individuals make a discovery or a measurement that expand, and sometimes dramatically improve our knowledge of the Universe. The purpose of the Scientific Visualization project at Cal State Los Angeles is to bring these moments to life with the use of computer animations, the medium of the 21st century that appeals to the generations which grew up in Internet age. Our first story describes Immanuel Kant's remarkable the Island Universes hypothesis. Using elementary principles of then new Newtonian mechanics, Kant made bold and ultimately correct interpretation of the Milky Way and the objects that we now call galaxies.

Computer Animations as Astronomy Educational Tool: Immanuel Kant and The Island Universes Hypothesis

NASA Astrophysics Data System (ADS)

Mijic, Milan; Park, D.; Zumaeta, J.; Dong, H.; Simonian, V.; Levitin, S.; Sullivan, A.; Kang, E. Y. E.; Longson, T.; State LA SciVi Project, Cal

2008-05-01

Development of astronomy is based on well defined, watershed moments when an individual or a group of individuals make a discovery or a measurement that expand, and sometimes dramatically improve our knowledge of the Universe. The purpose of the Scientific Visualization project at Cal State LA is to bring these moments to life with the use of computer animations, the medium of the 21st century that appeals to the generations which grew up in Internet age. Our first story describes Immanuel Kant's remarkable the Island Universes hypothesis. Using elementary principles of then new Newtonian mechanics, Kant made bold and ultimately correct interpretation of the Milky Way and the objects that we now call galaxies

Precision Departure Release Capability (PDRC) Final Report

NASA Technical Reports Server (NTRS)

Engelland, Shawn A.; Capps, Richard; Day, Kevin Brian; Kistler, Matthew Stephen; Gaither, Frank; Juro, Greg

2013-01-01

After takeoff, aircraft must merge into en route (Center) airspace traffic flows that may be subject to constraints that create localized demand/capacity imbalances. When demand exceeds capacity, Traffic Management Coordinators (TMCs) and Frontline Managers (FLMs) often use tactical departure scheduling to manage the flow of departures into the constrained Center traffic flow. Tactical departure scheduling usually involves a Call for Release (CFR) procedure wherein the Tower must call the Center to coordinate a release time prior to allowing the flight to depart. In present-day operations release times are computed by the Center Traffic Management Advisor (TMA) decision support tool, based upon manual estimates of aircraft ready time verbally communicated from the Tower to the Center. The TMA-computed release time is verbally communicated from the Center back to the Tower where it is relayed to the Local controller as a release window that is typically three minutes wide. The Local controller will manage the departure to meet the coordinated release time window. Manual ready time prediction and verbal release time coordination are labor intensive and prone to inaccuracy. Also, use of release time windows adds uncertainty to the tactical departure process. Analysis of more than one million flights from January 2011 indicates that a significant number of tactically scheduled aircraft missed their en route slot due to ready time prediction uncertainty. Uncertainty in ready time estimates may result in missed opportunities to merge into constrained en route flows and lead to lost throughput. Next Generation Air Transportation System plans call for development of Tower automation systems capable of computing surface trajectory-based ready time estimates. NASA has developed the Precision Departure Release Capability (PDRC) concept that improves tactical departure scheduling by automatically communicating surface trajectory-based ready time predictions and departure runway assignments to the Center scheduling tool. The PDRC concept also incorporates earlier NASA and FAA research into automation-assisted CFR coordination. The PDRC concept reduces uncertainty by automatically communicating coordinated release times with seconds-level precision enabling TMCs and FLMs to work with target times rather than windows. NASA has developed a PDRC prototype system that integrates the Center's TMA system with a research prototype Tower decision support tool. A two-phase field evaluation was conducted at NASA's North Texas Research Station in Dallas/Fort Worth. The field evaluation validated the PDRC concept and demonstrated reduced release time uncertainty while being used for tactical departure scheduling of more than 230 operational flights over 29 weeks of operations. This paper presents research results from the PDRC research activity. Companion papers present the Concept of Operations and a Technology Description.

Precision Departure Release Capability (PDRC) Technology Description

NASA Technical Reports Server (NTRS)

Engelland, Shawn A.; Capps, Richard; Day, Kevin; Robinson, Corissia; Null, Jody R.

2013-01-01

After takeoff, aircraft must merge into en route (Center) airspace traffic flows which may be subject to constraints that create localized demand-capacity imbalances. When demand exceeds capacity, Traffic Management Coordinators (TMCs) often use tactical departure scheduling to manage the flow of departures into the constrained Center traffic flow. Tactical departure scheduling usually involves use of a Call for Release (CFR) procedure wherein the Tower must call the Center TMC to coordinate a release time prior to allowing the flight to depart. In present-day operations release times are computed by the Center Traffic Management Advisor (TMA) decision support tool based upon manual estimates of aircraft ready time verbally communicated from the Tower to the Center. The TMA-computed release is verbally communicated from the Center back to the Tower where it is relayed to the Local controller as a release window that is typically three minutes wide. The Local controller will manage the departure to meet the coordinated release time window. Manual ready time prediction and verbal release time coordination are labor intensive and prone to inaccuracy. Also, use of release time windows adds uncertainty to the tactical departure process. Analysis of more than one million flights from January 2011 indicates that a significant number of tactically scheduled aircraft missed their en route slot due to ready time prediction uncertainty. Uncertainty in ready time estimates may result in missed opportunities to merge into constrained en route flows and lead to lost throughput. Next Generation Air Transportation System (NextGen) plans call for development of Tower automation systems capable of computing surface trajectory-based ready time estimates. NASA has developed the Precision Departure Release Capability (PDRC) concept that uses this technology to improve tactical departure scheduling by automatically communicating surface trajectory-based ready time predictions to the Center scheduling tool. The PDRC concept also incorporates earlier NASA and FAA research into automation-assisted CFR coordination. The PDRC concept helps reduce uncertainty by automatically communicating coordinated release times with seconds-level precision enabling TMCs to work with target times rather than windows. NASA has developed a PDRC prototype system that integrates the Center's TMA system with a research prototype Tower decision support tool. A two-phase field evaluation was conducted at NASA's North Texas Research Station (NTX) in Dallas-Fort Worth. The field evaluation validated the PDRC concept and demonstrated reduced release time uncertainty while being used for tactical departure scheduling of more than 230 operational flights over 29 weeks of operations. This paper presents the Technology Description. Companion papers include the Final Report and a Concept of Operations.

Precision Departure Release Capability (PDRC): NASA to FAA Research Transition

NASA Technical Reports Server (NTRS)

Engelland, Shawn; Davis, Thomas J.

2013-01-01

After takeoff, aircraft must merge into en route (Center) airspace traffic flows which may be subject to constraints that create localized demand-capacity imbalances. When demand exceeds capacity, Traffic Management Coordinators (TMCs) and Frontline Managers (FLMs) often use tactical departure scheduling to manage the flow of departures into the constrained Center traffic flow. Tactical departure scheduling usually involves use of a Call for Release (CFR) procedure wherein the Tower must call the Center to coordinate a release time prior to allowing the flight to depart. In present-day operations release times are computed by the Center Traffic Management Advisor (TMA) decision support tool based upon manual estimates of aircraft ready time verbally communicated from the Tower to the Center. The TMA-computed release time is verbally communicated from the Center back to the Tower where it is relayed to the Local controller as a release window that is typically three minutes wide. The Local controller will manage the departure to meet the coordinated release time window. Manual ready time prediction and verbal release time coordination are labor intensive and prone to inaccuracy. Also, use of release time windows adds uncertainty to the tactical departure process. Analysis of more than one million flights from January 2011 indicates that a significant number of tactically scheduled aircraft missed their en route slot due to ready time prediction uncertainty. Uncertainty in ready time estimates may result in missed opportunities to merge into constrained en route flows and lead to lost throughput. Next Generation Air Transportation System plans call for development of Tower automation systems capable of computing surface trajectory-based ready time estimates. NASA has developed the Precision Departure Release Capability (PDRC) concept that improves tactical departure scheduling by automatically communicating surface trajectory-based ready time predictions and departure runway assignments to the Center scheduling tool. The PDRC concept also incorporates earlier NASA and FAA research into automation-assisted CFR coordination. The PDRC concept reduces uncertainty by automatically communicating coordinated release times with seconds-level precision enabling TMCs and FLMs to work with target times rather than windows. NASA has developed a PDRC prototype system that integrates the Center's TMA system with a research prototype Tower decision support tool. A two-phase field evaluation was conducted at NASA's North Texas Research Station in Dallas-Fort Worth. The field evaluation validated the PDRC concept and demonstrated reduced release time uncertainty while being used for tactical departure scheduling of more than 230 operational flights over 29 weeks of operations.

Precision Departure Release Capability (PDRC) Concept of Operations

NASA Technical Reports Server (NTRS)

Engelland, Shawn; Capps, Richard A.; Day, Kevin Brian

2013-01-01

After takeoff, aircraft must merge into en route (Center) airspace traffic flows which may be subject to constraints that create localized demandcapacity imbalances. When demand exceeds capacity Traffic Management Coordinators (TMCs) often use tactical departure scheduling to manage the flow of departures into the constrained Center traffic flow. Tactical departure scheduling usually involves use of a Call for Release (CFR) procedure wherein the Tower must call the Center TMC to coordinate a release time prior to allowing the flight to depart. In present-day operations release times are computed by the Center Traffic Management Advisor (TMA) decision support tool based upon manual estimates of aircraft ready time verbally communicated from the Tower to the Center. The TMA-computed release is verbally communicated from the Center back to the Tower where it is relayed to the Local controller as a release window that is typically three minutes wide. The Local controller will manage the departure to meet the coordinated release time window. Manual ready time prediction and verbal release time coordination are labor intensive and prone to inaccuracy. Also, use of release time windows adds uncertainty to the tactical departure process. Analysis of more than one million flights from January 2011 indicates that a significant number of tactically scheduled aircraft missed their en route slot due to ready time prediction uncertainty. Uncertainty in ready time estimates may result in missed opportunities to merge into constrained en route flows and lead to lost throughput. Next Generation Air Transportation System (NextGen) plans call for development of Tower automation systems capable of computing surface trajectory-based ready time estimates. NASA has developed the Precision Departure Release Capability (PDRC) concept that uses this technology to improve tactical departure scheduling by automatically communicating surface trajectory-based ready time predictions to the Center scheduling tool. The PDRC concept also incorporates earlier NASA and FAA research into automation-assisted CFR coordination. The PDRC concept helps reduce uncertainty by automatically communicating coordinated release times with seconds-level precision enabling TMCs to work with target times rather than windows. NASA has developed a PDRC prototype system that integrates the Center's TMA system with a research prototype Tower decision support tool. A two-phase field evaluation was conducted at NASA's North Texas Research Station (NTX) in DallasFort Worth. The field evaluation validated the PDRC concept and demonstrated reduced release time uncertainty while being used for tactical departure scheduling of more than 230 operational flights over 29 weeks of operations. This paper presents the Concept of Operations. Companion papers include the Final Report and a Technology Description. ? SUBJECT:

Integrating Computer-Assisted Language Learning in Saudi Schools: A Change Model

ERIC Educational Resources Information Center

Alresheed, Saleh; Leask, Marilyn; Raiker, Andrea

2015-01-01

Computer-assisted language learning (CALL) technology and pedagogy have gained recognition globally for their success in supporting second language acquisition (SLA). In Saudi Arabia, the government aims to provide most educational institutions with computers and networking for integrating CALL into classrooms. However, the recognition of CALL's…

Computer aided manufacturing for complex freeform optics

NASA Astrophysics Data System (ADS)

Wolfs, Franciscus; Fess, Ed; Johns, Dustin; LePage, Gabriel; Matthews, Greg

2017-10-01

Recently, the desire to use freeform optics has been increasing. Freeform optics can be used to expand the capabilities of optical systems and reduce the number of optics needed in an assembly. The traits that increase optical performance also present challenges in manufacturing. As tolerances on freeform optics become more stringent, it is necessary to continue to improve methods for how the grinding and polishing processes interact with metrology. To create these complex shapes, OptiPro has developed a computer aided manufacturing package called PROSurf. PROSurf generates tool paths required for grinding and polishing freeform optics with multiple axes of motion. It also uses metrology feedback for deterministic corrections. ProSurf handles 2 key aspects of the manufacturing process that most other CAM systems struggle with. The first is having the ability to support several input types (equations, CAD models, point clouds) and still be able to create a uniform high-density surface map useable for generating a smooth tool path. The second is to improve the accuracy of mapping a metrology file to the part surface. To perform this OptiPro is using 3D error maps instead of traditional 2D maps. The metrology error map drives the tool path adjustment applied during processing. For grinding, the error map adjusts the tool position to compensate for repeatable system error. For polishing, the error map drives the relative dwell times of the tool across the part surface. This paper will present the challenges associated with these issues and solutions that we have created.

Efficient Use of Distributed Systems for Scientific Applications

NASA Technical Reports Server (NTRS)

Taylor, Valerie; Chen, Jian; Canfield, Thomas; Richard, Jacques

2000-01-01

Distributed computing has been regarded as the future of high performance computing. Nationwide high speed networks such as vBNS are becoming widely available to interconnect high-speed computers, virtual environments, scientific instruments and large data sets. One of the major issues to be addressed with distributed systems is the development of computational tools that facilitate the efficient execution of parallel applications on such systems. These tools must exploit the heterogeneous resources (networks and compute nodes) in distributed systems. This paper presents a tool, called PART, which addresses this issue for mesh partitioning. PART takes advantage of the following heterogeneous system features: (1) processor speed; (2) number of processors; (3) local network performance; and (4) wide area network performance. Further, different finite element applications under consideration may have different computational complexities, different communication patterns, and different element types, which also must be taken into consideration when partitioning. PART uses parallel simulated annealing to partition the domain, taking into consideration network and processor heterogeneity. The results of using PART for an explicit finite element application executing on two IBM SPs (located at Argonne National Laboratory and the San Diego Supercomputer Center) indicate an increase in efficiency by up to 36% as compared to METIS, a widely used mesh partitioning tool. The input to METIS was modified to take into consideration heterogeneous processor performance; METIS does not take into consideration heterogeneous networks. The execution times for these applications were reduced by up to 30% as compared to METIS. These results are given in Figure 1 for four irregular meshes with number of elements ranging from 30,269 elements for the Barth5 mesh to 11,451 elements for the Barth4 mesh. Future work with PART entails using the tool with an integrated application requiring distributed systems. In particular this application, illustrated in the document entails an integration of finite element and fluid dynamic simulations to address the cooling of turbine blades of a gas turbine engine design. It is not uncommon to encounter high-temperature, film-cooled turbine airfoils with 1,000,000s of degrees of freedom. This results because of the complexity of the various components of the airfoils, requiring fine-grain meshing for accuracy. Additional information is contained in the original.

GDSCalc: A Web-Based Application for Evaluating Discrete Graph Dynamical Systems

PubMed Central

Elmeligy Abdelhamid, Sherif H.; Kuhlman, Chris J.; Marathe, Madhav V.; Mortveit, Henning S.; Ravi, S. S.

2015-01-01

Discrete dynamical systems are used to model various realistic systems in network science, from social unrest in human populations to regulation in biological networks. A common approach is to model the agents of a system as vertices of a graph, and the pairwise interactions between agents as edges. Agents are in one of a finite set of states at each discrete time step and are assigned functions that describe how their states change based on neighborhood relations. Full characterization of state transitions of one system can give insights into fundamental behaviors of other dynamical systems. In this paper, we describe a discrete graph dynamical systems (GDSs) application called GDSCalc for computing and characterizing system dynamics. It is an open access system that is used through a web interface. We provide an overview of GDS theory. This theory is the basis of the web application; i.e., an understanding of GDS provides an understanding of the software features, while abstracting away implementation details. We present a set of illustrative examples to demonstrate its use in education and research. Finally, we compare GDSCalc with other discrete dynamical system software tools. Our perspective is that no single software tool will perform all computations that may be required by all users; tools typically have particular features that are more suitable for some tasks. We situate GDSCalc within this space of software tools. PMID:26263006

GDSCalc: A Web-Based Application for Evaluating Discrete Graph Dynamical Systems.

PubMed

Elmeligy Abdelhamid, Sherif H; Kuhlman, Chris J; Marathe, Madhav V; Mortveit, Henning S; Ravi, S S

2015-01-01

Discrete dynamical systems are used to model various realistic systems in network science, from social unrest in human populations to regulation in biological networks. A common approach is to model the agents of a system as vertices of a graph, and the pairwise interactions between agents as edges. Agents are in one of a finite set of states at each discrete time step and are assigned functions that describe how their states change based on neighborhood relations. Full characterization of state transitions of one system can give insights into fundamental behaviors of other dynamical systems. In this paper, we describe a discrete graph dynamical systems (GDSs) application called GDSCalc for computing and characterizing system dynamics. It is an open access system that is used through a web interface. We provide an overview of GDS theory. This theory is the basis of the web application; i.e., an understanding of GDS provides an understanding of the software features, while abstracting away implementation details. We present a set of illustrative examples to demonstrate its use in education and research. Finally, we compare GDSCalc with other discrete dynamical system software tools. Our perspective is that no single software tool will perform all computations that may be required by all users; tools typically have particular features that are more suitable for some tasks. We situate GDSCalc within this space of software tools.

Implementing iRound: A Computer-Based Auditing Tool.

PubMed

Brady, Darcie

Many hospitals use rounding or auditing as a tool to help identify gaps and needs in quality and process performance. Some hospitals are also using rounding to help improve patient experience. It is known that purposeful rounding helps improve Hospital Consumer Assessment of Healthcare Providers and Systems scores by helping manage patient expectations, provide service recovery, and recognize quality caregivers. Rounding works when a standard method is used across the facility, where data are comparable and trustworthy. This facility had a pen-and-paper process in place that made data reporting difficult, created a silo culture between departments, and most audits and rounds were completed differently on each unit. It was recognized that this facility needed to standardize the rounding and auditing process. The tool created by the Advisory Board called iRound was chosen as the tool this facility would use for patient experience rounds as well as process and quality rounding. The success of the iRound tool in this facility depended on several factors that started many months before implementation to current everyday usage.

Development of a Robust and Efficient Parallel Solver for Unsteady Turbomachinery Flows

NASA Technical Reports Server (NTRS)

West, Jeff; Wright, Jeffrey; Thakur, Siddharth; Luke, Ed; Grinstead, Nathan

2012-01-01

The traditional design and analysis practice for advanced propulsion systems relies heavily on expensive full-scale prototype development and testing. Over the past decade, use of high-fidelity analysis and design tools such as CFD early in the product development cycle has been identified as one way to alleviate testing costs and to develop these devices better, faster and cheaper. In the design of advanced propulsion systems, CFD plays a major role in defining the required performance over the entire flight regime, as well as in testing the sensitivity of the design to the different modes of operation. Increased emphasis is being placed on developing and applying CFD models to simulate the flow field environments and performance of advanced propulsion systems. This necessitates the development of next generation computational tools which can be used effectively and reliably in a design environment. The turbomachinery simulation capability presented here is being developed in a computational tool called Loci-STREAM [1]. It integrates proven numerical methods for generalized grids and state-of-the-art physical models in a novel rule-based programming framework called Loci [2] which allows: (a) seamless integration of multidisciplinary physics in a unified manner, and (b) automatic handling of massively parallel computing. The objective is to be able to routinely simulate problems involving complex geometries requiring large unstructured grids and complex multidisciplinary physics. An immediate application of interest is simulation of unsteady flows in rocket turbopumps, particularly in cryogenic liquid rocket engines. The key components of the overall methodology presented in this paper are the following: (a) high fidelity unsteady simulation capability based on Detached Eddy Simulation (DES) in conjunction with second-order temporal discretization, (b) compliance with Geometric Conservation Law (GCL) in order to maintain conservative property on moving meshes for second-order time-stepping scheme, (c) a novel cloud-of-points interpolation method (based on a fast parallel kd-tree search algorithm) for interfaces between turbomachinery components in relative motion which is demonstrated to be highly scalable, and (d) demonstrated accuracy and parallel scalability on large grids (approx 250 million cells) in full turbomachinery geometries.

Demonstration of Automatically-Generated Adjoint Code for Use in Aerodynamic Shape Optimization

NASA Technical Reports Server (NTRS)

Green, Lawrence; Carle, Alan; Fagan, Mike

1999-01-01

Gradient-based optimization requires accurate derivatives of the objective function and constraints. These gradients may have previously been obtained by manual differentiation of analysis codes, symbolic manipulators, finite-difference approximations, or existing automatic differentiation (AD) tools such as ADIFOR (Automatic Differentiation in FORTRAN). Each of these methods has certain deficiencies, particularly when applied to complex, coupled analyses with many design variables. Recently, a new AD tool called ADJIFOR (Automatic Adjoint Generation in FORTRAN), based upon ADIFOR, was developed and demonstrated. Whereas ADIFOR implements forward-mode (direct) differentiation throughout an analysis program to obtain exact derivatives via the chain rule of calculus, ADJIFOR implements the reverse-mode counterpart of the chain rule to obtain exact adjoint form derivatives from FORTRAN code. Automatically-generated adjoint versions of the widely-used CFL3D computational fluid dynamics (CFD) code and an algebraic wing grid generation code were obtained with just a few hours processing time using the ADJIFOR tool. The codes were verified for accuracy and were shown to compute the exact gradient of the wing lift-to-drag ratio, with respect to any number of shape parameters, in about the time required for 7 to 20 function evaluations. The codes have now been executed on various computers with typical memory and disk space for problems with up to 129 x 65 x 33 grid points, and for hundreds to thousands of independent variables. These adjoint codes are now used in a gradient-based aerodynamic shape optimization problem for a swept, tapered wing. For each design iteration, the optimization package constructs an approximate, linear optimization problem, based upon the current objective function, constraints, and gradient values. The optimizer subroutines are called within a design loop employing the approximate linear problem until an optimum shape is found, the design loop limit is reached, or no further design improvement is possible due to active design variable bounds and/or constraints. The resulting shape parameters are then used by the grid generation code to define a new wing surface and computational grid. The lift-to-drag ratio and its gradient are computed for the new design by the automatically-generated adjoint codes. Several optimization iterations may be required to find an optimum wing shape. Results from two sample cases will be discussed. The reader should note that this work primarily represents a demonstration of use of automatically- generated adjoint code within an aerodynamic shape optimization. As such, little significance is placed upon the actual optimization results, relative to the method for obtaining the results.

Strategies for concurrent processing of complex algorithms in data driven architectures

NASA Technical Reports Server (NTRS)

Stoughton, John W.; Mielke, Roland R.

1988-01-01

The purpose is to document research to develop strategies for concurrent processing of complex algorithms in data driven architectures. The problem domain consists of decision-free algorithms having large-grained, computationally complex primitive operations. Such are often found in signal processing and control applications. The anticipated multiprocessor environment is a data flow architecture containing between two and twenty computing elements. Each computing element is a processor having local program memory, and which communicates with a common global data memory. A new graph theoretic model called ATAMM which establishes rules for relating a decomposed algorithm to its execution in a data flow architecture is presented. The ATAMM model is used to determine strategies to achieve optimum time performance and to develop a system diagnostic software tool. In addition, preliminary work on a new multiprocessor operating system based on the ATAMM specifications is described.

A Review of Enhanced Sampling Approaches for Accelerated Molecular Dynamics

NASA Astrophysics Data System (ADS)

Tiwary, Pratyush; van de Walle, Axel

Molecular dynamics (MD) simulations have become a tool of immense use and popularity for simulating a variety of systems. With the advent of massively parallel computer resources, one now routinely sees applications of MD to systems as large as hundreds of thousands to even several million atoms, which is almost the size of most nanomaterials. However, it is not yet possible to reach laboratory timescales of milliseconds and beyond with MD simulations. Due to the essentially sequential nature of time, parallel computers have been of limited use in solving this so-called timescale problem. Instead, over the years a large range of statistical mechanics based enhanced sampling approaches have been proposed for accelerating molecular dynamics, and accessing timescales that are well beyond the reach of the fastest computers. In this review we provide an overview of these approaches, including the underlying theory, typical applications, and publicly available software resources to implement them.

Simultaneous Aerodynamic Analysis and Design Optimization (SAADO) for a 3-D Flexible Wing

NASA Technical Reports Server (NTRS)

Gumbert, Clyde R.; Hou, Gene J.-W.

2001-01-01

The formulation and implementation of an optimization method called Simultaneous Aerodynamic Analysis and Design Optimization (SAADO) are extended from single discipline analysis (aerodynamics only) to multidisciplinary analysis - in this case, static aero-structural analysis - and applied to a simple 3-D wing problem. The method aims to reduce the computational expense incurred in performing shape optimization using state-of-the-art Computational Fluid Dynamics (CFD) flow analysis, Finite Element Method (FEM) structural analysis and sensitivity analysis tools. Results for this small problem show that the method reaches the same local optimum as conventional optimization. However, unlike its application to the win,, (single discipline analysis), the method. as I implemented here, may not show significant reduction in the computational cost. Similar reductions were seen in the two-design-variable (DV) problem results but not in the 8-DV results given here.

Inheritance on processes, exemplified on distributed termination detection

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

Thomsen, K.S.

1987-02-01

A multiple inheritance mechanism on processes is designed and presented within the framework of a small object oriented language. Processes are described in classes, and the different action parts of a process inherited from different classes are executed in a coroutine-like style called alternation. The inheritance mechanism is a useful tool for factorizing the description of common aspects of processes. This is demonstrated within the domain of distributed programming by using the inheritance mechanism to factorize the description of distributed termination detection algorithms from the description of the distributed main computations for which termination is to be detected. A clearmore » separation of concerns is obtained, and arbitrary combinations of terminations detection algorithms and main computations can be formed. The same termination detection classes can also be used for more general purposes within distributed programming, such as detecting termination of each phase in a multi-phase main computation.« less

Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics

PubMed Central

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

2015-01-01

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

Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics.

PubMed

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

2015-05-01

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

Nonequilibrium hypersonic flows simulations with asymptotic-preserving Monte Carlo methods

NASA Astrophysics Data System (ADS)

Ren, Wei; Liu, Hong; Jin, Shi

2014-12-01

In the rarefied gas dynamics, the DSMC method is one of the most popular numerical tools. It performs satisfactorily in simulating hypersonic flows surrounding re-entry vehicles and micro-/nano- flows. However, the computational cost is expensive, especially when Kn → 0. Even for flows in the near-continuum regime, pure DSMC simulations require a number of computational efforts for most cases. Albeit several DSMC/NS hybrid methods are proposed to deal with this, those methods still suffer from the boundary treatment, which may cause nonphysical solutions. Filbet and Jin [1] proposed a framework of new numerical methods of Boltzmann equation, called asymptotic preserving schemes, whose computational costs are affordable as Kn → 0. Recently, Ren et al. [2] realized the AP schemes with Monte Carlo methods (AP-DSMC), which have better performance than counterpart methods. In this paper, AP-DSMC is applied in simulating nonequilibrium hypersonic flows. Several numerical results are computed and analyzed to study the efficiency and capability of capturing complicated flow characteristics.

Programming with process groups: Group and multicast semantics

NASA Technical Reports Server (NTRS)

Birman, Kenneth P.; Cooper, Robert; Gleeson, Barry

1991-01-01

Process groups are a natural tool for distributed programming and are increasingly important in distributed computing environments. Discussed here is a new architecture that arose from an effort to simplify Isis process group semantics. The findings include a refined notion of how the clients of a group should be treated, what the properties of a multicast primitive should be when systems contain large numbers of overlapping groups, and a new construct called the causality domain. A system based on this architecture is now being implemented in collaboration with the Chorus and Mach projects.

77 FR 72830 - Request for Comments on Request for Continued Examination (RCE) Practice

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-06

... the submission of written comments using a Web-based collaboration tool called IdeaScale[supreg]; and... collaboration tool called IdeaScale[supreg]. The tool allows users to post comments on a topic, and view and...

Implementing Nonlinear Buoyancy and Excitation Forces in the WEC-Sim Wave Energy Converter Modeling Tool: Preprint

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

Lawson, M.; Yu, Y. H.; Nelessen, A.

2014-05-01

Wave energy converters (WECs) are commonly designed and analyzed using numerical models that combine multi-body dynamics with hydrodynamic models based on the Cummins Equation and linearized hydrodynamic coefficients. These modeling methods are attractive design tools because they are computationally inexpensive and do not require the use of high performance computing resources necessitated by high-fidelity methods, such as Navier Stokes computational fluid dynamics. Modeling hydrodynamics using linear coefficients assumes that the device undergoes small motions and that the wetted surface area of the devices is approximately constant. WEC devices, however, are typically designed to undergo large motions in order to maximizemore » power extraction, calling into question the validity of assuming that linear hydrodynamic models accurately capture the relevant fluid-structure interactions. In this paper, we study how calculating buoyancy and Froude-Krylov forces from the instantaneous position of a WEC device (referred to as instantaneous buoyancy and Froude-Krylov forces from herein) changes WEC simulation results compared to simulations that use linear hydrodynamic coefficients. First, we describe the WEC-Sim tool used to perform simulations and how the ability to model instantaneous forces was incorporated into WEC-Sim. We then use a simplified one-body WEC device to validate the model and to demonstrate how accounting for these instantaneously calculated forces affects the accuracy of simulation results, such as device motions, hydrodynamic forces, and power generation.« less

CERN alerter—RSS based system for information broadcast to all CERN offices

NASA Astrophysics Data System (ADS)

Otto, R.

2008-07-01

Nearly every large organization uses a tool to broadcast messages and information across the internal campus (messages like alerts announcing interruption in services or just information about upcoming events). These tools typically allow administrators (operators) to send 'targeted' messages which are sent only to specific groups of users or computers, e/g only those located in a specified building or connected to a particular computing service. CERN has a long history of such tools: CERNVMS's SPM_quotMESSAGE command, Zephyr [2] and the most recent the NICE Alerter based on the NNTP protocol. The NICE Alerter used on all Windows-based computers had to be phased out as a consequence of phasing out NNTP at CERN. The new solution to broadcast information messages on the CERN campus continues to provide the service based on cross-platform technologies, hence minimizing custom developments and relying on commercial software as much as possible. The new system, called CERN Alerter, is based on RSS (Really Simple Syndication) [9] for the transport protocol and uses Microsoft SharePoint as the backend for database and posting interface. The windows-based client relies on Internet Explorer 7.0 with custom code to trigger the window pop-ups and the notifications for new events. Linux and Mac OS X clients could also rely on any RSS readers to subscribe to targeted notifications. The paper covers the architecture and implementation aspects of the new system.

Research on CALL.

ERIC Educational Resources Information Center

Pederson, Kathleen Marshall

The status of research on computer-assisted language learning (CALL) is explored beginning with a historical perspective of research on the language laboratory, followed by analyses of applied research on CALL. A theoretical base is provided to illustrate the need for more basic research on CALL that considers computer capabilities, learner…

Computational Cellular Dynamics Based on the Chemical Master Equation: A Challenge for Understanding Complexity

PubMed Central

Liang, Jie; Qian, Hong

2010-01-01

Modern molecular biology has always been a great source of inspiration for computational science. Half a century ago, the challenge from understanding macromolecular dynamics has led the way for computations to be part of the tool set to study molecular biology. Twenty-five years ago, the demand from genome science has inspired an entire generation of computer scientists with an interest in discrete mathematics to join the field that is now called bioinformatics. In this paper, we shall lay out a new mathematical theory for dynamics of biochemical reaction systems in a small volume (i.e., mesoscopic) in terms of a stochastic, discrete-state continuous-time formulation, called the chemical master equation (CME). Similar to the wavefunction in quantum mechanics, the dynamically changing probability landscape associated with the state space provides a fundamental characterization of the biochemical reaction system. The stochastic trajectories of the dynamics are best known through the simulations using the Gillespie algorithm. In contrast to the Metropolis algorithm, this Monte Carlo sampling technique does not follow a process with detailed balance. We shall show several examples how CMEs are used to model cellular biochemical systems. We shall also illustrate the computational challenges involved: multiscale phenomena, the interplay between stochasticity and nonlinearity, and how macroscopic determinism arises from mesoscopic dynamics. We point out recent advances in computing solutions to the CME, including exact solution of the steady state landscape and stochastic differential equations that offer alternatives to the Gilespie algorithm. We argue that the CME is an ideal system from which one can learn to understand “complex behavior” and complexity theory, and from which important biological insight can be gained. PMID:24999297

Computational Cellular Dynamics Based on the Chemical Master Equation: A Challenge for Understanding Complexity.

PubMed

Liang, Jie; Qian, Hong

2010-01-01

Modern molecular biology has always been a great source of inspiration for computational science. Half a century ago, the challenge from understanding macromolecular dynamics has led the way for computations to be part of the tool set to study molecular biology. Twenty-five years ago, the demand from genome science has inspired an entire generation of computer scientists with an interest in discrete mathematics to join the field that is now called bioinformatics. In this paper, we shall lay out a new mathematical theory for dynamics of biochemical reaction systems in a small volume (i.e., mesoscopic) in terms of a stochastic, discrete-state continuous-time formulation, called the chemical master equation (CME). Similar to the wavefunction in quantum mechanics, the dynamically changing probability landscape associated with the state space provides a fundamental characterization of the biochemical reaction system. The stochastic trajectories of the dynamics are best known through the simulations using the Gillespie algorithm. In contrast to the Metropolis algorithm, this Monte Carlo sampling technique does not follow a process with detailed balance. We shall show several examples how CMEs are used to model cellular biochemical systems. We shall also illustrate the computational challenges involved: multiscale phenomena, the interplay between stochasticity and nonlinearity, and how macroscopic determinism arises from mesoscopic dynamics. We point out recent advances in computing solutions to the CME, including exact solution of the steady state landscape and stochastic differential equations that offer alternatives to the Gilespie algorithm. We argue that the CME is an ideal system from which one can learn to understand "complex behavior" and complexity theory, and from which important biological insight can be gained.

Accelerating Computation of DCM for ERP in MATLAB by External Function Calls to the GPU.

PubMed

Wang, Wei-Jen; Hsieh, I-Fan; Chen, Chun-Chuan

2013-01-01

This study aims to improve the performance of Dynamic Causal Modelling for Event Related Potentials (DCM for ERP) in MATLAB by using external function calls to a graphics processing unit (GPU). DCM for ERP is an advanced method for studying neuronal effective connectivity. DCM utilizes an iterative procedure, the expectation maximization (EM) algorithm, to find the optimal parameters given a set of observations and the underlying probability model. As the EM algorithm is computationally demanding and the analysis faces possible combinatorial explosion of models to be tested, we propose a parallel computing scheme using the GPU to achieve a fast estimation of DCM for ERP. The computation of DCM for ERP is dynamically partitioned and distributed to threads for parallel processing, according to the DCM model complexity and the hardware constraints. The performance efficiency of this hardware-dependent thread arrangement strategy was evaluated using the synthetic data. The experimental data were used to validate the accuracy of the proposed computing scheme and quantify the time saving in practice. The simulation results show that the proposed scheme can accelerate the computation by a factor of 155 for the parallel part. For experimental data, the speedup factor is about 7 per model on average, depending on the model complexity and the data. This GPU-based implementation of DCM for ERP gives qualitatively the same results as the original MATLAB implementation does at the group level analysis. In conclusion, we believe that the proposed GPU-based implementation is very useful for users as a fast screen tool to select the most likely model and may provide implementation guidance for possible future clinical applications such as online diagnosis.

Accelerating Computation of DCM for ERP in MATLAB by External Function Calls to the GPU

PubMed Central

Wang, Wei-Jen; Hsieh, I-Fan; Chen, Chun-Chuan

2013-01-01

This study aims to improve the performance of Dynamic Causal Modelling for Event Related Potentials (DCM for ERP) in MATLAB by using external function calls to a graphics processing unit (GPU). DCM for ERP is an advanced method for studying neuronal effective connectivity. DCM utilizes an iterative procedure, the expectation maximization (EM) algorithm, to find the optimal parameters given a set of observations and the underlying probability model. As the EM algorithm is computationally demanding and the analysis faces possible combinatorial explosion of models to be tested, we propose a parallel computing scheme using the GPU to achieve a fast estimation of DCM for ERP. The computation of DCM for ERP is dynamically partitioned and distributed to threads for parallel processing, according to the DCM model complexity and the hardware constraints. The performance efficiency of this hardware-dependent thread arrangement strategy was evaluated using the synthetic data. The experimental data were used to validate the accuracy of the proposed computing scheme and quantify the time saving in practice. The simulation results show that the proposed scheme can accelerate the computation by a factor of 155 for the parallel part. For experimental data, the speedup factor is about 7 per model on average, depending on the model complexity and the data. This GPU-based implementation of DCM for ERP gives qualitatively the same results as the original MATLAB implementation does at the group level analysis. In conclusion, we believe that the proposed GPU-based implementation is very useful for users as a fast screen tool to select the most likely model and may provide implementation guidance for possible future clinical applications such as online diagnosis. PMID:23840507

RSTensorFlow: GPU Enabled TensorFlow for Deep Learning on Commodity Android Devices

PubMed Central

Alzantot, Moustafa; Wang, Yingnan; Ren, Zhengshuang; Srivastava, Mani B.

2018-01-01

Mobile devices have become an essential part of our daily lives. By virtue of both their increasing computing power and the recent progress made in AI, mobile devices evolved to act as intelligent assistants in many tasks rather than a mere way of making phone calls. However, popular and commonly used tools and frameworks for machine intelligence are still lacking the ability to make proper use of the available heterogeneous computing resources on mobile devices. In this paper, we study the benefits of utilizing the heterogeneous (CPU and GPU) computing resources available on commodity android devices while running deep learning models. We leveraged the heterogeneous computing framework RenderScript to accelerate the execution of deep learning models on commodity Android devices. Our system is implemented as an extension to the popular open-source framework TensorFlow. By integrating our acceleration framework tightly into TensorFlow, machine learning engineers can now easily make benefit of the heterogeneous computing resources on mobile devices without the need of any extra tools. We evaluate our system on different android phones models to study the trade-offs of running different neural network operations on the GPU. We also compare the performance of running different models architectures such as convolutional and recurrent neural networks on CPU only vs using heterogeneous computing resources. Our result shows that although GPUs on the phones are capable of offering substantial performance gain in matrix multiplication on mobile devices. Therefore, models that involve multiplication of large matrices can run much faster (approx. 3 times faster in our experiments) due to GPU support. PMID:29629431

RSTensorFlow: GPU Enabled TensorFlow for Deep Learning on Commodity Android Devices.

PubMed

Alzantot, Moustafa; Wang, Yingnan; Ren, Zhengshuang; Srivastava, Mani B

2017-06-01

Mobile devices have become an essential part of our daily lives. By virtue of both their increasing computing power and the recent progress made in AI, mobile devices evolved to act as intelligent assistants in many tasks rather than a mere way of making phone calls. However, popular and commonly used tools and frameworks for machine intelligence are still lacking the ability to make proper use of the available heterogeneous computing resources on mobile devices. In this paper, we study the benefits of utilizing the heterogeneous (CPU and GPU) computing resources available on commodity android devices while running deep learning models. We leveraged the heterogeneous computing framework RenderScript to accelerate the execution of deep learning models on commodity Android devices. Our system is implemented as an extension to the popular open-source framework TensorFlow. By integrating our acceleration framework tightly into TensorFlow, machine learning engineers can now easily make benefit of the heterogeneous computing resources on mobile devices without the need of any extra tools. We evaluate our system on different android phones models to study the trade-offs of running different neural network operations on the GPU. We also compare the performance of running different models architectures such as convolutional and recurrent neural networks on CPU only vs using heterogeneous computing resources. Our result shows that although GPUs on the phones are capable of offering substantial performance gain in matrix multiplication on mobile devices. Therefore, models that involve multiplication of large matrices can run much faster (approx. 3 times faster in our experiments) due to GPU support.

Business continuity strategies for cyber defence: battling time and information overload.

PubMed

Streufert, John

2010-11-01

Can the same numbers and letters which are the life blood of modern business and government computer systems be harnessed to protect computers from attack against known information security risks? For the past seven years, Foreign Service officers and technicians of the US Government have sought to maintain diplomatic operations in the face of rising cyber attacks and test the hypothesis that an ounce of prevention is worth a pound of cure. As eight out of ten attacks leverage known computer security vulnerabilities or configuration setting weaknesses, a pound of cure would seem to be easy to come by. Yet modern security tools present an unusually consequential threat to business continuity - too much rather than too little information on cyber problems is presented, harking back to a phenomenon cited by social scientists in the 1960s called 'information overload'. Experience indicates that the longer the most serious cyber problems go untreated, the wider the attack surface adversaries can find. One technique used at the Department of State, called 'risk scoring', resulted in an 89 per cent overall reduction in measured risk over 12 months for the Department of State's servers and personal computers. Later refinements of risk scoring enabled technicians to correct unique security threats with unprecedented speed. This paper explores how the use of metrics, special care in presenting information to technicians and executives alike, as well as tactical use of organisational incentives can result in stronger cyber defences protecting modern organisations.

Clinical detection of deletion structural variants in whole-genome sequences

PubMed Central

Noll, Aaron C; Miller, Neil A; Smith, Laurie D; Yoo, Byunggil; Fiedler, Stephanie; Cooley, Linda D; Willig, Laurel K; Petrikin, Josh E; Cakici, Julie; Lesko, John; Newton, Angela; Detherage, Kali; Thiffault, Isabelle; Saunders, Carol J; Farrow, Emily G; Kingsmore, Stephen F

2016-01-01

Optimal management of acutely ill infants with monogenetic diseases requires rapid identification of causative haplotypes. Whole-genome sequencing (WGS) has been shown to identify pathogenic nucleotide variants in such infants. Deletion structural variants (DSVs, >50 nt) are implicated in many genetic diseases, and tools have been designed to identify DSVs using short-read WGS. Optimisation and integration of these tools into a WGS pipeline could improve diagnostic sensitivity and specificity of WGS. In addition, it may improve turnaround time when compared with current CNV assays, enhancing utility in acute settings. Here we describe DSV detection methods for use in WGS for rapid diagnosis in acutely ill infants: SKALD (Screening Konsensus and Annotation of Large Deletions) combines calls from two tools (Breakdancer and GenomeStrip) with calibrated filters and clinical interpretation rules. In four WGS runs, the average analytic precision (positive predictive value) of SKALD was 78%, and recall (sensitivity) was 27%, when compared with validated reference DSV calls. When retrospectively applied to a cohort of 36 families with acutely ill infants SKALD identified causative DSVs in two. The first was heterozygous deletion of exons 1–3 of MMP21 in trans with a heterozygous frame-shift deletion in two siblings with transposition of the great arteries and heterotaxy. In a newborn female with dysmorphic features, ventricular septal defect and persistent pulmonary hypertension, SKALD identified the breakpoints of a heterozygous, de novo 1p36.32p36.13 deletion. In summary, consensus DSV calling, implemented in an 8-h computational pipeline with parameterised filtering, has the potential to increase the diagnostic yield of WGS in acutely ill neonates and discover novel disease genes. PMID:29263817

Design Requirements for Communication-Intensive Interactive Applications

NASA Astrophysics Data System (ADS)

Bolchini, Davide; Garzotto, Franca; Paolini, Paolo

Online interactive applications call for new requirements paradigms to capture the growing complexity of computer-mediated communication. Crafting successful interactive applications (such as websites and multimedia) involves modeling the requirements for the user experience, including those leading to content design, usable information architecture and interaction, in profound coordination with the communication goals of all stakeholders involved, ranging from persuasion to social engagement, to call for action. To face this grand challenge, we propose a methodology for modeling communication requirements and provide a set of operational conceptual tools to be used in complex projects with multiple stakeholders. Through examples from real-life projects and lessons-learned from direct experience, we draw on the concepts of brand, value, communication goals, information and persuasion requirements to systematically guide analysts to master the multifaceted connections of these elements as drivers to inform successful communication designs.

Online System for Faster Multipoint Linkage Analysis via Parallel Execution on Thousands of Personal Computers

PubMed Central

Silberstein, M.; Tzemach, A.; Dovgolevsky, N.; Fishelson, M.; Schuster, A.; Geiger, D.

2006-01-01

Computation of LOD scores is a valuable tool for mapping disease-susceptibility genes in the study of Mendelian and complex diseases. However, computation of exact multipoint likelihoods of large inbred pedigrees with extensive missing data is often beyond the capabilities of a single computer. We present a distributed system called “SUPERLINK-ONLINE,” for the computation of multipoint LOD scores of large inbred pedigrees. It achieves high performance via the efficient parallelization of the algorithms in SUPERLINK, a state-of-the-art serial program for these tasks, and through the use of the idle cycles of thousands of personal computers. The main algorithmic challenge has been to efficiently split a large task for distributed execution in a highly dynamic, nondedicated running environment. Notably, the system is available online, which allows computationally intensive analyses to be performed with no need for either the installation of software or the maintenance of a complicated distributed environment. As the system was being developed, it was extensively tested by collaborating medical centers worldwide on a variety of real data sets, some of which are presented in this article. PMID:16685644

Performance Support Tools: Delivering Value when and where It Is Needed

ERIC Educational Resources Information Center

McManus, Paul; Rossett, Allison

2006-01-01

Some call them Electronic Performance Support Systems (EPSSs). Others prefer Performance Support Tools (PSTs) or decision support tools. One might call EPSSs or PSTs job aids on steroids, technological tools that provide critical information or advice needed to move forward at a particular moment in time. Characteristic advantages of an EPSS or a…

A WPS Based Architecture for Climate Data Analytic Services (CDAS) at NASA

NASA Astrophysics Data System (ADS)

Maxwell, T. P.; McInerney, M.; Duffy, D.; Carriere, L.; Potter, G. L.; Doutriaux, C.

2015-12-01

Faced with unprecedented growth in the Big Data domain of climate science, NASA has developed the Climate Data Analytic Services (CDAS) framework. This framework enables scientists to execute trusted and tested analysis operations in a high performance environment close to the massive data stores at NASA. The data is accessed in standard (NetCDF, HDF, etc.) formats in a POSIX file system and processed using trusted climate data analysis tools (ESMF, CDAT, NCO, etc.). The framework is structured as a set of interacting modules allowing maximal flexibility in deployment choices. The current set of module managers include: Staging Manager: Runs the computation locally on the WPS server or remotely using tools such as celery or SLURM. Compute Engine Manager: Runs the computation serially or distributed over nodes using a parallelization framework such as celery or spark. Decomposition Manger: Manages strategies for distributing the data over nodes. Data Manager: Handles the import of domain data from long term storage and manages the in-memory and disk-based caching architectures. Kernel manager: A kernel is an encapsulated computational unit which executes a processor's compute task. Each kernel is implemented in python exploiting existing analysis packages (e.g. CDAT) and is compatible with all CDAS compute engines and decompositions. CDAS services are accessed via a WPS API being developed in collaboration with the ESGF Compute Working Team to support server-side analytics for ESGF. The API can be executed using either direct web service calls, a python script or application, or a javascript-based web application. Client packages in python or javascript contain everything needed to make CDAS requests. The CDAS architecture brings together the tools, data storage, and high-performance computing required for timely analysis of large-scale data sets, where the data resides, to ultimately produce societal benefits. It is is currently deployed at NASA in support of the Collaborative REAnalysis Technical Environment (CREATE) project, which centralizes numerous global reanalysis datasets onto a single advanced data analytics platform. This service permits decision makers to investigate climate changes around the globe, inspect model trends, compare multiple reanalysis datasets, and variability.

groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data.

PubMed

Chae, Minho; Danko, Charles G; Kraus, W Lee

2015-07-16

Global run-on coupled with deep sequencing (GRO-seq) provides extensive information on the location and function of coding and non-coding transcripts, including primary microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and enhancer RNAs (eRNAs), as well as yet undiscovered classes of transcripts. However, few computational tools tailored toward this new type of sequencing data are available, limiting the applicability of GRO-seq data for identifying novel transcription units. Here, we present groHMM, a computational tool in R, which defines the boundaries of transcription units de novo using a two state hidden-Markov model (HMM). A systematic comparison of the performance between groHMM and two existing peak-calling methods tuned to identify broad regions (SICER and HOMER) favorably supports our approach on existing GRO-seq data from MCF-7 breast cancer cells. To demonstrate the broader utility of our approach, we have used groHMM to annotate a diverse array of transcription units (i.e., primary transcripts) from four GRO-seq data sets derived from cells representing a variety of different human tissue types, including non-transformed cells (cardiomyocytes and lung fibroblasts) and transformed cells (LNCaP and MCF-7 cancer cells), as well as non-mammalian cells (from flies and worms). As an example of the utility of groHMM and its application to questions about the transcriptome, we show how groHMM can be used to analyze cell type-specific enhancers as defined by newly annotated enhancer transcripts. Our results show that groHMM can reveal new insights into cell type-specific transcription by identifying novel transcription units, and serve as a complete and useful tool for evaluating functional genomic elements in cells.

Software architecture and design of the web services facilitating climate model diagnostic analysis

NASA Astrophysics Data System (ADS)

Pan, L.; Lee, S.; Zhang, J.; Tang, B.; Zhai, C.; Jiang, J. H.; Wang, W.; Bao, Q.; Qi, M.; Kubar, T. L.; Teixeira, J.

2015-12-01

Climate model diagnostic analysis is a computationally- and data-intensive task because it involves multiple numerical model outputs and satellite observation data that can both be high resolution. We have built an online tool that facilitates this process. The tool is called Climate Model Diagnostic Analyzer (CMDA). It employs the web service technology and provides a web-based user interface. The benefits of these choices include: (1) No installation of any software other than a browser, hence it is platform compatable; (2) Co-location of computation and big data on the server side, and small results and plots to be downloaded on the client side, hence high data efficiency; (3) multi-threaded implementation to achieve parallel performance on multi-core servers; and (4) cloud deployment so each user has a dedicated virtual machine. In this presentation, we will focus on the computer science aspects of this tool, namely the architectural design, the infrastructure of the web services, the implementation of the web-based user interface, the mechanism of provenance collection, the approach to virtualization, and the Amazon Cloud deployment. As an example, We will describe our methodology to transform an existing science application code into a web service using a Python wrapper interface and Python web service frameworks (i.e., Flask, Gunicorn, and Tornado). Another example is the use of Docker, a light-weight virtualization container, to distribute and deploy CMDA onto an Amazon EC2 instance. Our tool of CMDA has been successfully used in the 2014 Summer School hosted by the JPL Center for Climate Science. Students had positive feedbacks in general and we will report their comments. An enhanced version of CMDA with several new features, some requested by the 2014 students, will be used in the 2015 Summer School soon.

Cognitive simulation as a tool for cognitive task analysis.

PubMed

Roth, E M; Woods, D D; Pople, H E

1992-10-01

Cognitive simulations are runnable computer programs that represent models of human cognitive activities. We show how one cognitive simulation built as a model of some of the cognitive processes involved in dynamic fault management can be used in conjunction with small-scale empirical data on human performance to uncover the cognitive demands of a task, to identify where intention errors are likely to occur, and to point to improvements in the person-machine system. The simulation, called Cognitive Environment Simulation or CES, has been exercised on several nuclear power plant accident scenarios. Here we report one case to illustrate how a cognitive simulation tool such as CES can be used to clarify the cognitive demands of a problem-solving situation as part of a cognitive task analysis.

Spinoff from a Moon Tool

NASA Technical Reports Server (NTRS)

1981-01-01

Portable self-contained drill capable of extracting core samples as much as 10 feet below the surface was needed for the astronauts. Black & Decker used a specially developed computer program to optimize the design of the drill's motor and insure minimal power consumption. Refinement of the original technology led to the development of a cordless miniature vacuum cleaner called the Dustbuster. It has no hose, no cord, is 14 inches long, and also comes with a storage bracket that also serves as a recharger; plugs into a home outlet that charges the nickel cadmium batteries when not in use. Other home use cordless instruments include drills, shrub trimmers and grass shears. Company also manufactures a number of cordless tools used in the sheet metal automobile and construction industries, and a line of cordless orthopedic instruments.

Object-Oriented Multi-Disciplinary Design, Analysis, and Optimization Tool

NASA Technical Reports Server (NTRS)

Pak, Chan-gi

2011-01-01

An Object-Oriented Optimization (O3) tool was developed that leverages existing tools and practices, and allows the easy integration and adoption of new state-of-the-art software. At the heart of the O3 tool is the Central Executive Module (CEM), which can integrate disparate software packages in a cross platform network environment so as to quickly perform optimization and design tasks in a cohesive, streamlined manner. This object-oriented framework can integrate the analysis codes for multiple disciplines instead of relying on one code to perform the analysis for all disciplines. The CEM was written in FORTRAN and the script commands for each performance index were submitted through the use of the FORTRAN Call System command. In this CEM, the user chooses an optimization methodology, defines objective and constraint functions from performance indices, and provides starting and side constraints for continuous as well as discrete design variables. The structural analysis modules such as computations of the structural weight, stress, deflection, buckling, and flutter and divergence speeds have been developed and incorporated into the O3 tool to build an object-oriented Multidisciplinary Design, Analysis, and Optimization (MDAO) tool.

Development of the Assessment of Burden of COPD tool: an integrated tool to measure the burden of COPD.

PubMed

Slok, Annerika H M; in 't Veen, Johannes C C M; Chavannes, Niels H; van der Molen, Thys; Rutten-van Mölken, Maureen P M H; Kerstjens, Huib A M; Salomé, Philippe L; Holverda, Sebastiaan; Dekhuijzen, P N Richard; Schuiten, Denise; Asijee, Guus M; van Schayck, Onno C P

2014-07-10

In deciding on the treatment plan for patients with chronic obstructive pulmonary disease (COPD), the burden of COPD as experienced by patients should be the core focus. It is therefore important for daily practice to develop a tool that can both assess the burden of COPD and facilitate communication with patients in clinical practice. This paper describes the development of an integrated tool to assess the burden of COPD in daily practice. A definition of the burden of COPD was formulated by a Dutch expert team. Interviews showed that patients and health-care providers agreed on this definition. We found no existing instruments that fully measured burden of disease according to this definition. However, the Clinical COPD Questionnaire meets most requirements, and was therefore used and adapted. The adapted questionnaire is called the Assessment of Burden of COPD (ABC) scale. In addition, the ABC tool was developed, of which the ABC scale is the core part. The ABC tool is a computer program with an algorithm that visualises outcomes and provides treatment advice. The next step in the development of the tool is to test the validity and effectiveness of both the ABC scale and tool in daily practice.

Development of the Assessment of Burden of COPD tool: an integrated tool to measure the burden of COPD

PubMed Central

Slok, Annerika H M; in ’t Veen, Johannes C C M; Chavannes, Niels H; van der Molen, Thys; Rutten-van Mölken, Maureen P M H; Kerstjens, Huib A M; Salomé, Philippe L; Holverda, Sebastiaan; Dekhuijzen, PN Richard; Schuiten, Denise; Asijee, Guus M; van Schayck, Onno C P

2014-01-01

In deciding on the treatment plan for patients with chronic obstructive pulmonary disease (COPD), the burden of COPD as experienced by patients should be the core focus. It is therefore important for daily practice to develop a tool that can both assess the burden of COPD and facilitate communication with patients in clinical practice. This paper describes the development of an integrated tool to assess the burden of COPD in daily practice. A definition of the burden of COPD was formulated by a Dutch expert team. Interviews showed that patients and health-care providers agreed on this definition. We found no existing instruments that fully measured burden of disease according to this definition. However, the Clinical COPD Questionnaire meets most requirements, and was therefore used and adapted. The adapted questionnaire is called the Assessment of Burden of COPD (ABC) scale. In addition, the ABC tool was developed, of which the ABC scale is the core part. The ABC tool is a computer program with an algorithm that visualises outcomes and provides treatment advice. The next step in the development of the tool is to test the validity and effectiveness of both the ABC scale and tool in daily practice. PMID:25010353

Reflections of Computing Experiences in a Steel Factory in the Early 1960s

NASA Astrophysics Data System (ADS)

Järvinen, Pertti

We can best see many things from a historical perspective. What were the first pioneers doing in the information technology departments of Finnish manufacturing companies? In early 1960s, I had a special chance to work in a steel industry that had long traditions to use rather advanced tools and methods to intensify their productivity. The first computer in our company had such novel properties as movable disk packs making a direct access of stored data possible. In this paper, we describe the following issues and innovations in some depth. These include (a) transitioning from the punched card machines to a new computer era, (b) using advanced programming language to intensify production of new computer software, (c) drawing pictures by using a line printer, (d) supporting steel making with mathematical software, (e) storing executable programs to the disk memory and calling and moving them from there to the core memory for running, and (f) building a simple report generator. I will also pay attention to the breakthrough in those innovations and in this way demonstrate how some computing solutions were growing at that time.

Edge control in a computer controlled optical surfacing process using a heterocercal tool influence function.

PubMed

Hu, Haixiang; Zhang, Xin; Ford, Virginia; Luo, Xiao; Qi, Erhui; Zeng, Xuefeng; Zhang, Xuejun

2016-11-14

Edge effect is regarded as one of the most difficult technical issues in a computer controlled optical surfacing (CCOS) process. Traditional opticians have to even up the consequences of the two following cases. Operating CCOS in a large overhang condition affects the accuracy of material removal, while in a small overhang condition, it achieves a more accurate performance, but leaves a narrow rolled-up edge, which takes time and effort to remove. In order to control the edge residuals in the latter case, we present a new concept of the 'heterocercal' tool influence function (TIF). Generated from compound motion equipment, this type of TIF can 'transfer' the material removal from the inner place to the edge, meanwhile maintaining the high accuracy and efficiency of CCOS. We call it the 'heterocercal' TIF, because of the inspiration from the heterocercal tails of sharks, whose upper lobe provides most of the explosive power. The heterocercal TIF was theoretically analyzed, and physically realized in CCOS facilities. Experimental and simulation results showed good agreement. It enables significant control of the edge effect and convergence of entire surface errors in large tool-to-mirror size-ratio conditions. This improvement will largely help manufacturing efficiency in some extremely large optical system projects, like the tertiary mirror of the Thirty Meter Telescope.

CombiROC: an interactive web tool for selecting accurate marker combinations of omics data.

PubMed

Mazzara, Saveria; Rossi, Riccardo L; Grifantini, Renata; Donizetti, Simone; Abrignani, Sergio; Bombaci, Mauro

2017-03-30

Diagnostic accuracy can be improved considerably by combining multiple markers, whose performance in identifying diseased subjects is usually assessed via receiver operating characteristic (ROC) curves. The selection of multimarker signatures is a complicated process that requires integration of data signatures with sophisticated statistical methods. We developed a user-friendly tool, called CombiROC, to help researchers accurately determine optimal markers combinations from diverse omics methods. With CombiROC data from different domains, such as proteomics and transcriptomics, can be analyzed using sensitivity/specificity filters: the number of candidate marker panels rising from combinatorial analysis is easily optimized bypassing limitations imposed by the nature of different experimental approaches. Leaving to the user full control on initial selection stringency, CombiROC computes sensitivity and specificity for all markers combinations, performances of best combinations and ROC curves for automatic comparisons, all visualized in a graphic interface. CombiROC was designed without hard-coded thresholds, allowing a custom fit to each specific data: this dramatically reduces the computational burden and lowers the false negative rates given by fixed thresholds. The application was validated with published data, confirming the marker combination already originally described or even finding new ones. CombiROC is a novel tool for the scientific community freely available at http://CombiROC.eu.

A Decision Analysis Tool for Climate Impacts, Adaptations, and Vulnerabilities

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

Omitaomu, Olufemi A; Parish, Esther S; Nugent, Philip J

Climate change related extreme events (such as flooding, storms, and drought) are already impacting millions of people globally at a cost of billions of dollars annually. Hence, there are urgent needs for urban areas to develop adaptation strategies that will alleviate the impacts of these extreme events. However, lack of appropriate decision support tools that match local applications is limiting local planning efforts. In this paper, we present a quantitative analysis and optimization system with customized decision support modules built on geographic information system (GIS) platform to bridge this gap. This platform is called Urban Climate Adaptation Tool (Urban-CAT). Formore » all Urban-CAT models, we divide a city into a grid with tens of thousands of cells; then compute a list of metrics for each cell from the GIS data. These metrics are used as independent variables to predict climate impacts, compute vulnerability score, and evaluate adaptation options. Overall, the Urban-CAT system has three layers: data layer (that contains spatial data, socio-economic and environmental data, and analytic data), middle layer (that handles data processing, model management, and GIS operation), and application layer (that provides climate impacts forecast, adaptation optimization, and site evaluation). The Urban-CAT platform can guide city and county governments in identifying and planning for effective climate change adaptation strategies.« less

Patient-specific finite element modeling of bones.

PubMed

Poelert, Sander; Valstar, Edward; Weinans, Harrie; Zadpoor, Amir A

2013-04-01

Finite element modeling is an engineering tool for structural analysis that has been used for many years to assess the relationship between load transfer and bone morphology and to optimize the design and fixation of orthopedic implants. Due to recent developments in finite element model generation, for example, improved computed tomography imaging quality, improved segmentation algorithms, and faster computers, the accuracy of finite element modeling has increased vastly and finite element models simulating the anatomy and properties of an individual patient can be constructed. Such so-called patient-specific finite element models are potentially valuable tools for orthopedic surgeons in fracture risk assessment or pre- and intraoperative planning of implant placement. The aim of this article is to provide a critical overview of current themes in patient-specific finite element modeling of bones. In addition, the state-of-the-art in patient-specific modeling of bones is compared with the requirements for a clinically applicable patient-specific finite element method, and judgment is passed on the feasibility of application of patient-specific finite element modeling as a part of clinical orthopedic routine. It is concluded that further development in certain aspects of patient-specific finite element modeling are needed before finite element modeling can be used as a routine clinical tool.

A Microarray Tool Provides Pathway and GO Term Analysis.

PubMed

Koch, Martin; Royer, Hans-Dieter; Wiese, Michael

2011-12-01

Analysis of gene expression profiles is no longer exclusively a task for bioinformatic experts. However, gaining statistically significant results is challenging and requires both biological knowledge and computational know-how. Here we present a novel, user-friendly microarray reporting tool called maRt. The software provides access to bioinformatic resources, like gene ontology terms and biological pathways by use of the DAVID and the BioMart web-service. Results are summarized in structured HTML reports, each presenting a different layer of information. In these report, contents of diverse sources are integrated and interlinked. To speed up processing, maRt takes advantage of the multi-core technology of modern desktop computers by using parallel processing. Since the software is built upon a RCP infrastructure it might be an outset for developers aiming to integrate novel R based applications. Installer, documentation and various kinds of tutorials are available under LGPL license at the website of our institute http://www.pharma.uni-bonn.de/www/mart. This software is free for academic use. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Expert models and modeling processes associated with a computer-modeling tool

NASA Astrophysics Data System (ADS)

Zhang, Baohui; Liu, Xiufeng; Krajcik, Joseph S.

2006-07-01

Holding the premise that the development of expertise is a continuous process, this study concerns expert models and modeling processes associated with a modeling tool called Model-It. Five advanced Ph.D. students in environmental engineering and public health used Model-It to create and test models of water quality. Using think aloud technique and video recording, we captured their computer screen modeling activities and thinking processes. We also interviewed them the day following their modeling sessions to further probe the rationale of their modeling practices. We analyzed both the audio-video transcripts and the experts' models. We found the experts' modeling processes followed the linear sequence built in the modeling program with few instances of moving back and forth. They specified their goals up front and spent a long time thinking through an entire model before acting. They specified relationships with accurate and convincing evidence. Factors (i.e., variables) in expert models were clustered, and represented by specialized technical terms. Based on the above findings, we made suggestions for improving model-based science teaching and learning using Model-It.

Binding-Site Compatible Fragment Growing Applied to the Design of β2-Adrenergic Receptor Ligands.

PubMed

Chevillard, Florent; Rimmer, Helena; Betti, Cecilia; Pardon, Els; Ballet, Steven; van Hilten, Niek; Steyaert, Jan; Diederich, Wibke E; Kolb, Peter

2018-02-08

Fragment-based drug discovery is intimately linked to fragment extension approaches that can be accelerated using software for de novo design. Although computers allow for the facile generation of millions of suggestions, synthetic feasibility is however often neglected. In this study we computationally extended, chemically synthesized, and experimentally assayed new ligands for the β 2 -adrenergic receptor (β 2 AR) by growing fragment-sized ligands. In order to address the synthetic tractability issue, our in silico workflow aims at derivatized products based on robust organic reactions. The study started from the predicted binding modes of five fragments. We suggested a total of eight diverse extensions that were easily synthesized, and further assays showed that four products had an improved affinity (up to 40-fold) compared to their respective initial fragment. The described workflow, which we call "growing via merging" and for which the key tools are available online, can improve early fragment-based drug discovery projects, making it a useful creative tool for medicinal chemists during structure-activity relationship (SAR) studies.

Science in the cloud (SIC): A use case in MRI connectomics

PubMed Central

Gorgolewski, Krzysztof J.; Kleissas, Dean; Roncal, William Gray; Litt, Brian; Wandell, Brian; Poldrack, Russel A.; Wiener, Martin; Vogelstein, R. Jacob; Burns, Randal

2017-01-01

Abstract Modern technologies are enabling scientists to collect extraordinary amounts of complex and sophisticated data across a huge range of scales like never before. With this onslaught of data, we can allow the focal point to shift from data collection to data analysis. Unfortunately, lack of standardized sharing mechanisms and practices often make reproducing or extending scientific results very difficult. With the creation of data organization structures and tools that drastically improve code portability, we now have the opportunity to design such a framework for communicating extensible scientific discoveries. Our proposed solution leverages these existing technologies and standards, and provides an accessible and extensible model for reproducible research, called ‘science in the cloud’ (SIC). Exploiting scientific containers, cloud computing, and cloud data services, we show the capability to compute in the cloud and run a web service that enables intimate interaction with the tools and data presented. We hope this model will inspire the community to produce reproducible and, importantly, extensible results that will enable us to collectively accelerate the rate at which scientific breakthroughs are discovered, replicated, and extended. PMID:28327935

MINIVER upgrade for the AVID system. Volume 3: EXITS user's and input guide

NASA Technical Reports Server (NTRS)

Pond, J. E.; Schmitz, C. P.

1983-01-01

The successful design of thermal protection systems for vehicles operating in atmosphere and near-space environments requires accurate analyses of heating rate and temperature histories encountered along a trajectory. For preliminary design calculations, however, the requirement for accuracy must be tempered by the need for speed and versatility in computational tools used to determine thermal environments and structural thermal response. The MINIVER program was found to provide the proper balance between versatility, speed and accuracy for an aerothermal prediction tool. The advancement in computer aided design concepts at Langley Research Center (LaRC) in the past few years has made it desirable to incorporate the MINIVER program into the LaRC Advanced Vehicle Integrated Design, AVID, system. In order to effectively incorporate MINIVER into the AVID system, several changes to MINIVER were made. The thermal conduction options in MINIVER were removed and a new Explicit Interactive Thermal Structures (EXITS) code was developed. Many upgrades to the MINIVER code were made and a new Langley version of MINIVER called LANMIN was created.

MINIVER upgrade for the AVID system. Volume 1: LANMIN user's manual

NASA Technical Reports Server (NTRS)

Engel, C. D.; Praharaj, S. C.

1983-01-01

The successful design of thermal protection systems for vehicles operating in atmosphere and near space environments requires accurate analyses of heating rate and temperature histories encountered along a trajectory. For preliminary design calculations, however, the requirement for accuracy must be tempered by the need for speed and versatility in computational tools used to determine thermal environments and structural thermal response. The MINIVER program has been found to provide the proper balance between versatility, speed and accuracy for an aerothermal prediction tool. The advancement in computer aided design concepts at Langley Research Center (LaRC) in the past few years has made it desirable to incorporate the MINIVER program into the LaRC Advanced Vehicle Integrated Design, AVID, system. In order to effectively incorporate MINIVER into the AVID system, several changes to MINIVER were made. The thermal conduction options in MINIVER were removed and a new Explicit Interactive Thermal Structures (EXITS) code was developed. Many upgrades to the MINIVER code were made and a new Langley version of MINIVER called LANMIN was created. The theoretical methods and subroutine functions used in LANMIN are described.

Modeling protein structure at near atomic resolutions with Gorgon.

PubMed

Baker, Matthew L; Abeysinghe, Sasakthi S; Schuh, Stephen; Coleman, Ross A; Abrams, Austin; Marsh, Michael P; Hryc, Corey F; Ruths, Troy; Chiu, Wah; Ju, Tao

2011-05-01

Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions. Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details. With recent advances in cryo-EM, maps at near-atomic resolutions have been achieved for several macromolecular assemblies from which models have been manually constructed. In this work, we describe a new interactive modeling toolkit called Gorgon targeted at intermediate to near-atomic resolution density maps (10-3.5 Å), particularly from cryo-EM. Gorgon's de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models. Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes. Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure. Copyright © 2011 Elsevier Inc. All rights reserved.

Science in the cloud (SIC): A use case in MRI connectomics.

PubMed

Kiar, Gregory; Gorgolewski, Krzysztof J; Kleissas, Dean; Roncal, William Gray; Litt, Brian; Wandell, Brian; Poldrack, Russel A; Wiener, Martin; Vogelstein, R Jacob; Burns, Randal; Vogelstein, Joshua T

2017-05-01

Modern technologies are enabling scientists to collect extraordinary amounts of complex and sophisticated data across a huge range of scales like never before. With this onslaught of data, we can allow the focal point to shift from data collection to data analysis. Unfortunately, lack of standardized sharing mechanisms and practices often make reproducing or extending scientific results very difficult. With the creation of data organization structures and tools that drastically improve code portability, we now have the opportunity to design such a framework for communicating extensible scientific discoveries. Our proposed solution leverages these existing technologies and standards, and provides an accessible and extensible model for reproducible research, called 'science in the cloud' (SIC). Exploiting scientific containers, cloud computing, and cloud data services, we show the capability to compute in the cloud and run a web service that enables intimate interaction with the tools and data presented. We hope this model will inspire the community to produce reproducible and, importantly, extensible results that will enable us to collectively accelerate the rate at which scientific breakthroughs are discovered, replicated, and extended. © The Author 2017. Published by Oxford University Press.

Visualization techniques for computer network defense

NASA Astrophysics Data System (ADS)

Beaver, Justin M.; Steed, Chad A.; Patton, Robert M.; Cui, Xiaohui; Schultz, Matthew

2011-06-01

Effective visual analysis of computer network defense (CND) information is challenging due to the volume and complexity of both the raw and analyzed network data. A typical CND is comprised of multiple niche intrusion detection tools, each of which performs network data analysis and produces a unique alerting output. The state-of-the-practice in the situational awareness of CND data is the prevalent use of custom-developed scripts by Information Technology (IT) professionals to retrieve, organize, and understand potential threat events. We propose a new visual analytics framework, called the Oak Ridge Cyber Analytics (ORCA) system, for CND data that allows an operator to interact with all detection tool outputs simultaneously. Aggregated alert events are presented in multiple coordinated views with timeline, cluster, and swarm model analysis displays. These displays are complemented with both supervised and semi-supervised machine learning classifiers. The intent of the visual analytics framework is to improve CND situational awareness, to enable an analyst to quickly navigate and analyze thousands of detected events, and to combine sophisticated data analysis techniques with interactive visualization such that patterns of anomalous activities may be more easily identified and investigated.

Fast probabilistic file fingerprinting for big data

PubMed Central

2013-01-01

Background Biological data acquisition is raising new challenges, both in data analysis and handling. Not only is it proving hard to analyze the data at the rate it is generated today, but simply reading and transferring data files can be prohibitively slow due to their size. This primarily concerns logistics within and between data centers, but is also important for workstation users in the analysis phase. Common usage patterns, such as comparing and transferring files, are proving computationally expensive and are tying down shared resources. Results We present an efficient method for calculating file uniqueness for large scientific data files, that takes less computational effort than existing techniques. This method, called Probabilistic Fast File Fingerprinting (PFFF), exploits the variation present in biological data and computes file fingerprints by sampling randomly from the file instead of reading it in full. Consequently, it has a flat performance characteristic, correlated with data variation rather than file size. We demonstrate that probabilistic fingerprinting can be as reliable as existing hashing techniques, with provably negligible risk of collisions. We measure the performance of the algorithm on a number of data storage and access technologies, identifying its strengths as well as limitations. Conclusions Probabilistic fingerprinting may significantly reduce the use of computational resources when comparing very large files. Utilisation of probabilistic fingerprinting techniques can increase the speed of common file-related workflows, both in the data center and for workbench analysis. The implementation of the algorithm is available as an open-source tool named pfff, as a command-line tool as well as a C library. The tool can be downloaded from http://biit.cs.ut.ee/pfff. PMID:23445565

Implementing virtual reality interfaces for the geosciences

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

Bethel, W.; Jacobsen, J.; Austin, A.

1996-06-01

For the past few years, a multidisciplinary team of computer and earth scientists at Lawrence Berkeley National Laboratory has been exploring the use of advanced user interfaces, commonly called {open_quotes}Virtual Reality{close_quotes} (VR), coupled with visualization and scientific computing software. Working closely with industry, these efforts have resulted in an environment in which VR technology is coupled with existing visualization and computational tools. VR technology may be thought of as a user interface. It is useful to think of a spectrum, ranging the gamut from command-line interfaces to completely immersive environments. In the former, one uses the keyboard to enter threemore » or six-dimensional parameters. In the latter, three or six-dimensional information is provided by trackers contained either in hand-held devices or attached to the user in some fashion, e.g. attached to a head-mounted display. Rich, extensible and often complex languages are a vehicle whereby the user controls parameters to manipulate object position and location in a virtual world, but the keyboard is the obstacle in that typing is cumbersome, error-prone and typically slow. In the latter, the user can interact with these parameters by means of motor skills which are highly developed. Two specific geoscience application areas will be highlighted. In the first, we have used VR technology to manipulate three-dimensional input parameters, such as the spatial location of injection or production wells in a reservoir simulator. In the second, we demonstrate how VR technology has been used to manipulate visualization tools, such as a tool for computing streamlines via manipulation of a {open_quotes}rake.{close_quotes} The rake is presented to the user in the form of a {open_quotes}virtual well{close_quotes} icon, and provides parameters used by the streamlines algorithm.« less

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

The Profile Interface Generator (PIG) is a tool for loosely coupling applications and performance tools. It enables applications to write code that looks like standard C and Fortran functions calls, without requiring that applications link to specific implementations of those function calls. Performance tools can register with PIG in order to listen to only the calls that give information they care about. This interface reduces the build and configuration burden on application developers and allows semantic instrumentation to live in production codes without interfering with production runs.

Potential Paradigms and Possible Problems for CALL.

ERIC Educational Resources Information Center

Phillips, Martin

1987-01-01

Describes three models of CALL (computer assisted language learning) activity--games, the expert system, and the prosthetic approaches. A case is made for CALL development within a more instrumental view of the role of computers. (Author/CB)

OpenMP parallelization of a gridded SWAT (SWATG)

NASA Astrophysics Data System (ADS)

Zhang, Ying; Hou, Jinliang; Cao, Yongpan; Gu, Juan; Huang, Chunlin

2017-12-01

Large-scale, long-term and high spatial resolution simulation is a common issue in environmental modeling. A Gridded Hydrologic Response Unit (HRU)-based Soil and Water Assessment Tool (SWATG) that integrates grid modeling scheme with different spatial representations also presents such problems. The time-consuming problem affects applications of very high resolution large-scale watershed modeling. The OpenMP (Open Multi-Processing) parallel application interface is integrated with SWATG (called SWATGP) to accelerate grid modeling based on the HRU level. Such parallel implementation takes better advantage of the computational power of a shared memory computer system. We conducted two experiments at multiple temporal and spatial scales of hydrological modeling using SWATG and SWATGP on a high-end server. At 500-m resolution, SWATGP was found to be up to nine times faster than SWATG in modeling over a roughly 2000 km2 watershed with 1 CPU and a 15 thread configuration. The study results demonstrate that parallel models save considerable time relative to traditional sequential simulation runs. Parallel computations of environmental models are beneficial for model applications, especially at large spatial and temporal scales and at high resolutions. The proposed SWATGP model is thus a promising tool for large-scale and high-resolution water resources research and management in addition to offering data fusion and model coupling ability.

The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows

PubMed Central

O'Connor, Brian D.; Yuen, Denis; Chung, Vincent; Duncan, Andrew G.; Liu, Xiang Kun; Patricia, Janice; Paten, Benedict; Stein, Lincoln; Ferretti, Vincent

2017-01-01

As genomic datasets continue to grow, the feasibility of downloading data to a local organization and running analysis on a traditional compute environment is becoming increasingly problematic. Current large-scale projects, such as the ICGC PanCancer Analysis of Whole Genomes (PCAWG), the Data Platform for the U.S. Precision Medicine Initiative, and the NIH Big Data to Knowledge Center for Translational Genomics, are using cloud-based infrastructure to both host and perform analysis across large data sets. In PCAWG, over 5,800 whole human genomes were aligned and variant called across 14 cloud and HPC environments; the processed data was then made available on the cloud for further analysis and sharing. If run locally, an operation at this scale would have monopolized a typical academic data centre for many months, and would have presented major challenges for data storage and distribution. However, this scale is increasingly typical for genomics projects and necessitates a rethink of how analytical tools are packaged and moved to the data. For PCAWG, we embraced the use of highly portable Docker images for encapsulating and sharing complex alignment and variant calling workflows across highly variable environments. While successful, this endeavor revealed a limitation in Docker containers, namely the lack of a standardized way to describe and execute the tools encapsulated inside the container. As a result, we created the Dockstore ( https://dockstore.org), a project that brings together Docker images with standardized, machine-readable ways of describing and running the tools contained within. This service greatly improves the sharing and reuse of genomics tools and promotes interoperability with similar projects through emerging web service standards developed by the Global Alliance for Genomics and Health (GA4GH). PMID:28344774

The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows.

PubMed

O'Connor, Brian D; Yuen, Denis; Chung, Vincent; Duncan, Andrew G; Liu, Xiang Kun; Patricia, Janice; Paten, Benedict; Stein, Lincoln; Ferretti, Vincent

2017-01-01

As genomic datasets continue to grow, the feasibility of downloading data to a local organization and running analysis on a traditional compute environment is becoming increasingly problematic. Current large-scale projects, such as the ICGC PanCancer Analysis of Whole Genomes (PCAWG), the Data Platform for the U.S. Precision Medicine Initiative, and the NIH Big Data to Knowledge Center for Translational Genomics, are using cloud-based infrastructure to both host and perform analysis across large data sets. In PCAWG, over 5,800 whole human genomes were aligned and variant called across 14 cloud and HPC environments; the processed data was then made available on the cloud for further analysis and sharing. If run locally, an operation at this scale would have monopolized a typical academic data centre for many months, and would have presented major challenges for data storage and distribution. However, this scale is increasingly typical for genomics projects and necessitates a rethink of how analytical tools are packaged and moved to the data. For PCAWG, we embraced the use of highly portable Docker images for encapsulating and sharing complex alignment and variant calling workflows across highly variable environments. While successful, this endeavor revealed a limitation in Docker containers, namely the lack of a standardized way to describe and execute the tools encapsulated inside the container. As a result, we created the Dockstore ( https://dockstore.org), a project that brings together Docker images with standardized, machine-readable ways of describing and running the tools contained within. This service greatly improves the sharing and reuse of genomics tools and promotes interoperability with similar projects through emerging web service standards developed by the Global Alliance for Genomics and Health (GA4GH).

ICALL's Relevance to CALL

ERIC Educational Resources Information Center

Ward, Monica

2017-01-01

The term Intelligent Computer Assisted Language Learning (ICALL) covers many different aspects of CALL that add something extra to a CALL resource. This could be with the use of computational linguistics or Artificial Intelligence (AI). ICALL tends to be not very well understood within the CALL community. There may also be the slight fear factor…

Mining Software Usage with the Automatic Library Tracking Database (ALTD)

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

Hadri, Bilel; Fahey, Mark R

2013-01-01

Tracking software usage is important for HPC centers, computer vendors, code developers and funding agencies to provide more efficient and targeted software support, and to forecast needs and guide HPC software effort towards the Exascale era. However, accurately tracking software usage on HPC systems has been a challenging task. In this paper, we present a tool called Automatic Library Tracking Database (ALTD) that has been developed and put in production on several Cray systems. The ALTD infrastructure prototype automatically and transparently stores information about libraries linked into an application at compilation time and also the executables launched in a batchmore » job. We will illustrate the usage of libraries, compilers and third party software applications on a system managed by the National Institute for Computational Sciences.« less

Enhanced Electric Power Transmission by Hybrid Compensation Technique

NASA Astrophysics Data System (ADS)

Palanichamy, C.; Kiu, G. Q.

2015-04-01

In today's competitive environment, new power system engineers are likely to contribute immediately to the task, without years of seasoning via on-the-job training, mentoring, and rotation assignments. At the same time it is becoming obligatory to train power system engineering graduates for an increasingly quality-minded corporate environment. In order to achieve this, there is a need to make available better-quality tools for educating and training power system engineering students and in-service system engineers too. As a result of the swift advances in computer hardware and software, many windows-based computer software packages were developed for the purpose of educating and training. In line with those packages, a simulation package called Hybrid Series-Shunt Compensators (HSSC) has been developed and presented in this paper for educational purposes.

What Does CALL Have to Offer Computer Science and What Does Computer Science Have to Offer CALL?

ERIC Educational Resources Information Center

Cushion, Steve

2006-01-01

We will argue that CALL can usefully be viewed as a subset of computer software engineering and can profit from adopting some of the recent progress in software development theory. The unified modelling language has become the industry standard modelling technique and the accompanying unified process is rapidly gaining acceptance. The manner in…

On Undecidability Aspects of Resilient Computations and Implications to Exascale

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

Rao, Nageswara S

2014-01-01

Future Exascale computing systems with a large number of processors, memory elements and interconnection links, are expected to experience multiple, complex faults, which affect both applications and operating-runtime systems. A variety of algorithms, frameworks and tools are being proposed to realize and/or verify the resilience properties of computations that guarantee correct results on failure-prone computing systems. We analytically show that certain resilient computation problems in presence of general classes of faults are undecidable, that is, no algorithms exist for solving them. We first show that the membership verification in a generic set of resilient computations is undecidable. We describe classesmore » of faults that can create infinite loops or non-halting computations, whose detection in general is undecidable. We then show certain resilient computation problems to be undecidable by using reductions from the loop detection and halting problems under two formulations, namely, an abstract programming language and Turing machines, respectively. These two reductions highlight different failure effects: the former represents program and data corruption, and the latter illustrates incorrect program execution. These results call for broad-based, well-characterized resilience approaches that complement purely computational solutions using methods such as hardware monitors, co-designs, and system- and application-specific diagnosis codes.« less

COMPUTATIONAL TOXICOLOGY-WHERE IS THE DATA? ...

EPA Pesticide Factsheets

This talk will briefly describe the state of the data world for computational toxicology and one approach to improve the situation, called ACToR (Aggregated Computational Toxicology Resource). This talk will briefly describe the state of the data world for computational toxicology and one approach to improve the situation, called ACToR (Aggregated Computational Toxicology Resource).

Handheld Computer Use in U.S. Family Practice Residency Programs

PubMed Central

Criswell, Dan F.; Parchman, Michael L.

2002-01-01

Objective: The purpose of the study was to evaluate the uses of handheld computers (also called personal digital assistants, or PDAs) in family practice residency programs in the United States. Study Design: In November 2000, the authors mailed a questionnaire to the program directors of all American Academy of Family Physicians (AAFP) and American College of Osteopathic Family Practice (ACOFP) residency programs in the United States. Measurements: Data and patterns of the use and non-use of handheld computers were identified. Results: Approximately 50 percent (306 of 610) of the programs responded to the survey. Two thirds of the programs reported that handheld computers were used in their residencies, and an additional 14 percent had plans for implementation within 24 months. Both the Palm and the Windows CE operating systems were used, with the Palm operating system the most common. Military programs had the highest rate of use (8 of 10 programs, 80 percent), and osteopathic programs had the lowest (23 of 55 programs, 42 percent). Of programs that reported handheld computer use, 45 percent had required handheld computer applications that are used uniformly by all users. Funding for handheld computers and related applications was non-budgeted in 76percent of the programs in which handheld computers were used. In programs providing a budget for handheld computers, the average annual budget per user was $461.58. Interested faculty or residents, rather than computer information services personnel, performed upkeep and maintenance of handheld computers in 72 percent of the programs in which the computers are used. In addition to the installed calendar, memo pad, and address book, the most common clinical uses of handheld computers in the programs were as medication reference tools, electronic textbooks, and clinical computational or calculator-type programs. Conclusions: Handheld computers are widely used in family practice residency programs in the United States. Although handheld computers were designed as electronic organizers, in family practice residencies they are used as medication reference tools, electronic textbooks, and clinical computational programs and to track activities that were previously associated with desktop database applications. PMID:11751806

Handheld computer use in U.S. family practice residency programs.

PubMed

Criswell, Dan F; Parchman, Michael L

2002-01-01

The purpose of the study was to evaluate the uses of handheld computers (also called personal digital assistants, or PDAs) in family practice residency programs in the United States. In November 2000, the authors mailed a questionnaire to the program directors of all American Academy of Family Physicians (AAFP) and American College of Osteopathic Family Practice (ACOFP) residency programs in the United States. Data and patterns of the use and non-use of handheld computers were identified. Approximately 50 percent (306 of 610) of the programs responded to the survey. Two thirds of the programs reported that handheld computers were used in their residencies, and an additional 14 percent had plans for implementation within 24 months. Both the Palm and the Windows CE operating systems were used, with the Palm operating system the most common. Military programs had the highest rate of use (8 of 10 programs, 80 percent), and osteopathic programs had the lowest (23 of 55 programs, 42 percent). Of programs that reported handheld computer use, 45 percent had required handheld computer applications that are used uniformly by all users. Funding for handheld computers and related applications was non-budgeted in 76percent of the programs in which handheld computers were used. In programs providing a budget for handheld computers, the average annual budget per user was 461.58 dollars. Interested faculty or residents, rather than computer information services personnel, performed upkeep and maintenance of handheld computers in 72 percent of the programs in which the computers are used. In addition to the installed calendar, memo pad, and address book, the most common clinical uses of handheld computers in the programs were as medication reference tools, electronic textbooks, and clinical computational or calculator-type programs. Handheld computers are widely used in family practice residency programs in the United States. Although handheld computers were designed as electronic organizers, in family practice residencies they are used as medication reference tools, electronic textbooks, and clinical computational programs and to track activities that were previously associated with desktop database applications.

WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets

PubMed Central

2014-01-01

Background Sharing sets of chemical data (e.g., chemical properties, docking scores, etc.) among collaborators with diverse skill sets is a common task in computer-aided drug design and medicinal chemistry. The ability to associate this data with images of the relevant molecular structures greatly facilitates scientific communication. There is a need for a simple, free, open-source program that can automatically export aggregated reports of entire chemical data sets to files viewable on any computer, regardless of the operating system and without requiring the installation of additional software. Results We here present a program called WebChem Viewer that automatically generates these types of highly portable reports. Furthermore, in designing WebChem Viewer we have also created a useful online web application for remotely generating molecular structures from SMILES strings. We encourage the direct use of this online application as well as its incorporation into other software packages. Conclusions With these features, WebChem Viewer enables interdisciplinary collaborations that require the sharing and visualization of small molecule structures and associated sets of heterogeneous chemical data. The program is released under the FreeBSD license and can be downloaded from http://nbcr.ucsd.edu/WebChemViewer. The associated web application (called “Smiley2png 1.0”) can be accessed through freely available web services provided by the National Biomedical Computation Resource at http://nbcr.ucsd.edu. PMID:24886360

The Adaptation Study of the Questionnaires of the Attitude towards CALL (A-CALL), the Attitude towards CAL (A-CAL), the Attitude towards Foreign Language Learning (A-FLL) to Turkish Language

ERIC Educational Resources Information Center

Erdem, Cahit; Saykili, Abdullah; Kocyigit, Mehmet

2018-01-01

This study primarily aims to adapt the Foreign Language Learning (FLL), Computer assisted Learning (CAL) and Computer assisted Language Learning (CALL) scales developed by Vandewaetere and Desmet into Turkish context. The instrument consists of three scales which are "the attitude towards CALL questionnaire" ("A-CALL")…

The Objective Identification and Quantification of Interstitial Lung Abnormalities in Smokers.

PubMed

Ash, Samuel Y; Harmouche, Rola; Ross, James C; Diaz, Alejandro A; Hunninghake, Gary M; Putman, Rachel K; Onieva, Jorge; Martinez, Fernando J; Choi, Augustine M; Lynch, David A; Hatabu, Hiroto; Rosas, Ivan O; Estepar, Raul San Jose; Washko, George R

2017-08-01

Previous investigation suggests that visually detected interstitial changes in the lung parenchyma of smokers are highly clinically relevant and predict outcomes, including death. Visual subjective analysis to detect these changes is time-consuming, insensitive to subtle changes, and requires training to enhance reproducibility. Objective detection of such changes could provide a method of disease identification without these limitations. The goal of this study was to develop and test a fully automated image processing tool to objectively identify radiographic features associated with interstitial abnormalities in the computed tomography scans of a large cohort of smokers. An automated tool that uses local histogram analysis combined with distance from the pleural surface was used to detect radiographic features consistent with interstitial lung abnormalities in computed tomography scans from 2257 individuals from the Genetic Epidemiology of COPD study, a longitudinal observational study of smokers. The sensitivity and specificity of this tool was determined based on its ability to detect the visually identified presence of these abnormalities. The tool had a sensitivity of 87.8% and a specificity of 57.5% for the detection of interstitial lung abnormalities, with a c-statistic of 0.82, and was 100% sensitive and 56.7% specific for the detection of the visual subtype of interstitial abnormalities called fibrotic parenchymal abnormalities, with a c-statistic of 0.89. In smokers, a fully automated image processing tool is able to identify those individuals who have interstitial lung abnormalities with moderate sensitivity and specificity. Copyright © 2017 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

OPTIMIZING THROUGH CO-EVOLUTIONARY AVALANCHES

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

S. BOETTCHER; A. PERCUS

2000-08-01

We explore a new general-purpose heuristic for finding high-quality solutions to hard optimization problems. The method, called extremal optimization, is inspired by ''self-organized critically,'' a concept introduced to describe emergent complexity in many physical systems. In contrast to Genetic Algorithms which operate on an entire ''gene-pool'' of possible solutions, extremal optimization successively replaces extremely undesirable elements of a sub-optimal solution with new, random ones. Large fluctuations, called ''avalanches,'' ensue that efficiently explore many local optima. Drawing upon models used to simulate far-from-equilibrium dynamics, extremal optimization complements approximation methods inspired by equilibrium statistical physics, such as simulated annealing. With only onemore » adjustable parameter, its performance has proved competitive with more elaborate methods, especially near phase transitions. Those phase transitions are found in the parameter space of most optimization problems, and have recently been conjectured to be the origin of some of the hardest instances in computational complexity. We will demonstrate how extremal optimization can be implemented for a variety of combinatorial optimization problems. We believe that extremal optimization will be a useful tool in the investigation of phase transitions in combinatorial optimization problems, hence valuable in elucidating the origin of computational complexity.« less

Analytical Design Package (ADP2): A computer aided engineering tool for aircraft transparency design

NASA Technical Reports Server (NTRS)

Wuerer, J. E.; Gran, M.; Held, T. W.

1994-01-01

The Analytical Design Package (ADP2) is being developed as a part of the Air Force Frameless Transparency Program (FTP). ADP2 is an integrated design tool consisting of existing analysis codes and Computer Aided Engineering (CAE) software. The objective of the ADP2 is to develop and confirm an integrated design methodology for frameless transparencies, related aircraft interfaces, and their corresponding tooling. The application of this methodology will generate high confidence for achieving a qualified part prior to mold fabrication. ADP2 is a customized integration of analysis codes, CAE software, and material databases. The primary CAE integration tool for the ADP2 is P3/PATRAN, a commercial-off-the-shelf (COTS) software tool. The open architecture of P3/PATRAN allows customized installations with different applications modules for specific site requirements. Integration of material databases allows the engineer to select a material, and those material properties are automatically called into the relevant analysis code. The ADP2 materials database will be composed of four independent schemas: CAE Design, Processing, Testing, and Logistics Support. The design of ADP2 places major emphasis on the seamless integration of CAE and analysis modules with a single intuitive graphical interface. This tool is being designed to serve and be used by an entire project team, i.e., analysts, designers, materials experts, and managers. The final version of the software will be delivered to the Air Force in Jan. 1994. The Analytical Design Package (ADP2) will then be ready for transfer to industry. The package will be capable of a wide range of design and manufacturing applications.

NASA Tech Briefs, December 2005

NASA Technical Reports Server (NTRS)

2005-01-01

Topics covered include: Video Mosaicking for Inspection of Gas Pipelines; Shuttle-Data-Tape XML Translator; Highly Reliable, High-Speed, Unidirectional Serial Data Links; Data-Analysis System for Entry, Descent, and Landing; Hybrid UV Imager Containing Face-Up AlGaN/GaN Photodiodes; Multiple Embedded Processors for Fault-Tolerant Computing; Hybrid Power Management; Magnetometer Based on Optoelectronic Microwave Oscillator; Program Predicts Time Courses of Human/ Computer Interactions; Chimera Grid Tools; Astronomer's Proposal Tool; Conservative Patch Algorithm and Mesh Sequencing for PAB3D; Fitting Nonlinear Curves by Use of Optimization Techniques; Tool for Viewing Faults Under Terrain; Automated Synthesis of Long Communication Delays for Testing; Solving Nonlinear Euler Equations With Arbitrary Accuracy; Self-Organizing-Map Program for Analyzing Multivariate Data; Tool for Sizing Analysis of the Advanced Life Support System; Control Software for a High-Performance Telerobot; Java Radar Analysis Tool; Architecture for Verifiable Software; Tool for Ranking Research Options; Enhanced, Partially Redundant Emergency Notification System; Close-Call Action Log Form; Task Description Language; Improved Small-Particle Powders for Plasma Spraying; Bonding-Compatible Corrosion Inhibitor for Rinsing Metals; Wipes, Coatings, and Patches for Detecting Hydrazines; Rotating Vessels for Growing Protein Crystals; Oscillating-Linear-Drive Vacuum Compressor for CO2; Mechanically Biased, Hinged Pairs of Piezoelectric Benders; Apparatus for Precise Indium-Bump Bonding of Microchips; Radiation Dosimetry via Automated Fluorescence Microscopy; Multistage Magnetic Separator of Cells and Proteins; Elastic-Tether Suits for Artificial Gravity and Exercise; Multichannel Brain-Signal-Amplifying and Digitizing System; Ester-Based Electrolytes for Low-Temperature Li-Ion Cells; Hygrometer for Detecting Water in Partially Enclosed Volumes; Radio-Frequency Plasma Cleaning of a Penning Malmberg Trap; Reduction of Flap Side Edge Noise - the Blowing Flap; and Preventing Accidental Ignition of Upper-Stage Rocket Motors.

Runtime optimization of an application executing on a parallel computer

DOEpatents

None

2014-11-25

Identifying a collective operation within an application executing on a parallel computer; identifying a call site of the collective operation; determining whether the collective operation is root-based; if the collective operation is not root-based: establishing a tuning session and executing the collective operation in the tuning session; if the collective operation is root-based, determining whether all compute nodes executing the application identified the collective operation at the same call site; if all compute nodes identified the collective operation at the same call site, establishing a tuning session and executing the collective operation in the tuning session; and if all compute nodes executing the application did not identify the collective operation at the same call site, executing the collective operation without establishing a tuning session.

Runtime optimization of an application executing on a parallel computer

DOEpatents

Faraj, Daniel A; Smith, Brian E

2014-11-18

Identifying a collective operation within an application executing on a parallel computer; identifying a call site of the collective operation; determining whether the collective operation is root-based; if the collective operation is not root-based: establishing a tuning session and executing the collective operation in the tuning session; if the collective operation is root-based, determining whether all compute nodes executing the application identified the collective operation at the same call site; if all compute nodes identified the collective operation at the same call site, establishing a tuning session and executing the collective operation in the tuning session; and if all compute nodes executing the application did not identify the collective operation at the same call site, executing the collective operation without establishing a tuning session.

Runtime optimization of an application executing on a parallel computer

DOEpatents

Faraj, Daniel A.; Smith, Brian E.

2013-01-29

Identifying a collective operation within an application executing on a parallel computer; identifying a call site of the collective operation; determining whether the collective operation is root-based; if the collective operation is not root-based: establishing a tuning session and executing the collective operation in the tuning session; if the collective operation is root-based, determining whether all compute nodes executing the application identified the collective operation at the same call site; if all compute nodes identified the collective operation at the same call site, establishing a tuning session and executing the collective operation in the tuning session; and if all compute nodes executing the application did not identify the collective operation at the same call site, executing the collective operation without establishing a tuning session.

CT-assisted agile manufacturing

NASA Astrophysics Data System (ADS)

Stanley, James H.; Yancey, Robert N.

1996-11-01

The next century will witness at least two great revolutions in the way goods are produced. First, workers will use the medium of virtual reality in all aspects of marketing, research, development, prototyping, manufacturing, sales and service. Second, market forces will drive manufacturing towards small-lot production and just-in-time delivery. Already, we can discern the merging of these megatrends into what some are calling agile manufacturing. Under this new paradigm, parts and processes will be designed and engineered within the mind of a computer, tooled and manufactured by the offspring of today's rapid prototyping equipment, and evaluated for performance and reliability by advanced nondestructive evaluation (NDE) techniques and sophisticated computational models. Computed tomography (CT) is the premier example of an NDE method suitable for future agile manufacturing activities. It is the only modality that provides convenient access to the full suite of engineering data that users will need to avail themselves of computer- aided design, computer-aided manufacturing, and computer- aided engineering capabilities, as well as newly emerging reverse engineering, rapid prototyping and solid freeform fabrication technologies. As such, CT is assured a central, utilitarian role in future industrial operations. An overview of this exciting future for industrial CT is presented.

The 'last mile' of data handling: Fermilab's IFDH tools

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

Lyon, Adam L.; Mengel, Marc W.

2014-01-01

IFDH (Intensity Frontier Data Handling), is a suite of tools for data movement tasks for Fermilab experiments and is an important part of the FIFE[2] (Fabric for Intensity Frontier [1] Experiments) initiative described at this conference. IFDH encompasses moving input data from caches or storage elements to compute nodes (the 'last mile' of data movement) and moving output data potentially to those caches as part of the journey back to the user. IFDH also involves throttling and locking to ensure that large numbers of jobs do not cause data movement bottlenecks. IFDH is realized as an easy to use layermore » that users call in their job scripts (e.g. 'ifdh cp'), hiding the low level data movement tools. One advantage of this layer is that the underlying low level tools can be selected or changed without the need for the user to alter their scripts. Logging and performance monitoring can also be added easily. This system will be presented in detail as well as its impact on the ease of data handling at Fermilab experiments.« less

Practice Evaluation Strategies Among Social Workers: Why an Evidence-Informed Dual-Process Theory Still Matters.

PubMed

Davis, Thomas D

2017-01-01

Practice evaluation strategies range in style from the formal-analytic tools of single-subject designs, rapid assessment instruments, algorithmic steps in evidence-informed practice, and computer software applications, to the informal-interactive tools of clinical supervision, consultation with colleagues, use of client feedback, and clinical experience. The purpose of this article is to provide practice researchers in social work with an evidence-informed theory that is capable of explaining both how and why social workers use practice evaluation strategies to self-monitor the effectiveness of their interventions in terms of client change. The author delineates the theoretical contours and consequences of what is called dual-process theory. Drawing on evidence-informed advances in the cognitive and social neurosciences, the author identifies among everyday social workers a theoretically stable, informal-interactive tool preference that is a cognitively necessary, sufficient, and stand-alone preference that requires neither the supplementation nor balance of formal-analytic tools. The author's delineation of dual-process theory represents a theoretical contribution in the century-old attempt to understand how and why social workers evaluate their practice the way they do.

Documenting AUTOGEN and APGEN Model Files

NASA Technical Reports Server (NTRS)

Gladden, Roy E.; Khanampompan, Teerapat; Fisher, Forest W.; DelGuericio, Chris c.

2008-01-01

A computer program called "autogen hypertext map generator" satisfies a need for documenting and assisting in visualization of, and navigation through, model files used in the AUTOGEN and APGEN software mentioned in the two immediately preceding articles. This program parses autogen script files, autogen model files, PERL scripts, and apgen activity-definition files and produces a hypertext map of the files to aid in the navigation of the model. This program also provides a facility for adding notes and descriptions, beyond what is in the source model represented by the hypertext map. Further, this program provides access to a summary of the model through variable, function, sub routine, activity and resource declarations as well as providing full access to the source model and source code. The use of the tool enables easy access to the declarations and the ability to traverse routines and calls while analyzing the model.

Blind source computer device identification from recorded VoIP calls for forensic investigation.

PubMed

Jahanirad, Mehdi; Anuar, Nor Badrul; Wahab, Ainuddin Wahid Abdul

2017-03-01

The VoIP services provide fertile ground for criminal activity, thus identifying the transmitting computer devices from recorded VoIP call may help the forensic investigator to reveal useful information. It also proves the authenticity of the call recording submitted to the court as evidence. This paper extended the previous study on the use of recorded VoIP call for blind source computer device identification. Although initial results were promising but theoretical reasoning for this is yet to be found. The study suggested computing entropy of mel-frequency cepstrum coefficients (entropy-MFCC) from near-silent segments as an intrinsic feature set that captures the device response function due to the tolerances in the electronic components of individual computer devices. By applying the supervised learning techniques of naïve Bayesian, linear logistic regression, neural networks and support vector machines to the entropy-MFCC features, state-of-the-art identification accuracy of near 99.9% has been achieved on different sets of computer devices for both call recording and microphone recording scenarios. Furthermore, unsupervised learning techniques, including simple k-means, expectation-maximization and density-based spatial clustering of applications with noise (DBSCAN) provided promising results for call recording dataset by assigning the majority of instances to their correct clusters. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

PRANAS: A New Platform for Retinal Analysis and Simulation.

PubMed

Cessac, Bruno; Kornprobst, Pierre; Kraria, Selim; Nasser, Hassan; Pamplona, Daniela; Portelli, Geoffrey; Viéville, Thierry

2017-01-01

The retina encodes visual scenes by trains of action potentials that are sent to the brain via the optic nerve. In this paper, we describe a new free access user-end software allowing to better understand this coding. It is called PRANAS (https://pranas.inria.fr), standing for Platform for Retinal ANalysis And Simulation. PRANAS targets neuroscientists and modelers by providing a unique set of retina-related tools. PRANAS integrates a retina simulator allowing large scale simulations while keeping a strong biological plausibility and a toolbox for the analysis of spike train population statistics. The statistical method (entropy maximization under constraints) takes into account both spatial and temporal correlations as constraints, allowing to analyze the effects of memory on statistics. PRANAS also integrates a tool computing and representing in 3D (time-space) receptive fields. All these tools are accessible through a friendly graphical user interface. The most CPU-costly of them have been implemented to run in parallel.

Fractal characteristic in the wearing of cutting tool

NASA Astrophysics Data System (ADS)

Mei, Anhua; Wang, Jinghui

1995-11-01

This paper studies the cutting tool wear with fractal geometry. The wearing image of the flank has been collected by machine vision which consists of CCD camera and personal computer. After being processed by means of preserving smoothing, binary making and edge extracting, the clear boundary enclosing the worn area has been obtained. The fractal dimension of the worn surface is calculated by the methods called `Slit Island' and `Profile'. The experiments and calciating give the conclusion that the worn surface is enclosed by a irregular boundary curve with some fractal dimension and characteristics of self-similarity. Furthermore, the relation between the cutting velocity and the fractal dimension of the worn region has been submitted. This paper presents a series of methods for processing and analyzing the fractal information in the blank wear, which can be applied to research the projective relation between the fractal structure and the wear state, and establish the fractal model of the cutting tool wear.

CASAS: A tool for composing automatically and semantically astrophysical services

NASA Astrophysics Data System (ADS)

Louge, T.; Karray, M. H.; Archimède, B.; Knödlseder, J.

2017-07-01

Multiple astronomical datasets are available through internet and the astrophysical Distributed Computing Infrastructure (DCI) called Virtual Observatory (VO). Some scientific workflow technologies exist for retrieving and combining data from those sources. However selection of relevant services, automation of the workflows composition and the lack of user-friendly platforms remain a concern. This paper presents CASAS, a tool for semantic web services composition in astrophysics. This tool proposes automatic composition of astrophysical web services and brings a semantics-based, automatic composition of workflows. It widens the services choice and eases the use of heterogeneous services. Semantic web services composition relies on ontologies for elaborating the services composition; this work is based on Astrophysical Services ONtology (ASON). ASON had its structure mostly inherited from the VO services capacities. Nevertheless, our approach is not limited to the VO and brings VO plus non-VO services together without the need for premade recipes. CASAS is available for use through a simple web interface.

Ray tracing for inhomogeneous media applied to the human eye

NASA Astrophysics Data System (ADS)

Diaz-Gonzalez, G.; Iturbe-Castillo, M. D.; Juarez-Salazar, R.

2017-08-01

Inhomogeneous or gradient index media exhibit a refractive index varying with the position. This kind of media are very interesting because they can be found in both synthetic as well as real life optical devices such as the human lens. In this work we present the development of a computational tool for ray tracing in refractive optical systems. Particularly, the human eye is used as the optical system under study. An inhomogeneous medium with similar characteristics to the human lens is introduced and modeled by the so-called slices method. The useful of our proposal is illustrated by several graphical results.

Compression-based distance (CBD): a simple, rapid, and accurate method for microbiota composition comparison

PubMed Central

2013-01-01

Background Perturbations in intestinal microbiota composition have been associated with a variety of gastrointestinal tract-related diseases. The alleviation of symptoms has been achieved using treatments that alter the gastrointestinal tract microbiota toward that of healthy individuals. Identifying differences in microbiota composition through the use of 16S rRNA gene hypervariable tag sequencing has profound health implications. Current computational methods for comparing microbial communities are usually based on multiple alignments and phylogenetic inference, making them time consuming and requiring exceptional expertise and computational resources. As sequencing data rapidly grows in size, simpler analysis methods are needed to meet the growing computational burdens of microbiota comparisons. Thus, we have developed a simple, rapid, and accurate method, independent of multiple alignments and phylogenetic inference, to support microbiota comparisons. Results We create a metric, called compression-based distance (CBD) for quantifying the degree of similarity between microbial communities. CBD uses the repetitive nature of hypervariable tag datasets and well-established compression algorithms to approximate the total information shared between two datasets. Three published microbiota datasets were used as test cases for CBD as an applicable tool. Our study revealed that CBD recaptured 100% of the statistically significant conclusions reported in the previous studies, while achieving a decrease in computational time required when compared to similar tools without expert user intervention. Conclusion CBD provides a simple, rapid, and accurate method for assessing distances between gastrointestinal tract microbiota 16S hypervariable tag datasets. PMID:23617892

Computational prediction of hinge axes in proteins

PubMed Central

2014-01-01

Background A protein's function is determined by the wide range of motions exhibited by its 3D structure. However, current experimental techniques are not able to reliably provide the level of detail required for elucidating the exact mechanisms of protein motion essential for effective drug screening and design. Computational tools are instrumental in the study of the underlying structure-function relationship. We focus on a special type of proteins called "hinge proteins" which exhibit a motion that can be interpreted as a rotation of one domain relative to another. Results This work proposes a computational approach that uses the geometric structure of a single conformation to predict the feasible motions of the protein and is founded in recent work from rigidity theory, an area of mathematics that studies flexibility properties of general structures. Given a single conformational state, our analysis predicts a relative axis of motion between two specified domains. We analyze a dataset of 19 structures known to exhibit this hinge-like behavior. For 15, the predicted axis is consistent with a motion to a second, known conformation. We present a detailed case study for three proteins whose dynamics have been well-studied in the literature: calmodulin, the LAO binding protein and the Bence-Jones protein. Conclusions Our results show that incorporating rigidity-theoretic analyses can lead to effective computational methods for understanding hinge motions in macromolecules. This initial investigation is the first step towards a new tool for probing the structure-dynamics relationship in proteins. PMID:25080829

The next scientific revolution.

PubMed

Hey, Tony

2010-11-01

For decades, computer scientists have tried to teach computers to think like human experts. Until recently, most of those efforts have failed to come close to generating the creative insights and solutions that seem to come naturally to the best researchers, doctors, and engineers. But now, Tony Hey, a VP of Microsoft Research, says we're witnessing the dawn of a new generation of powerful computer tools that can "mash up" vast quantities of data from many sources, analyze them, and help produce revolutionary scientific discoveries. Hey and his colleagues call this new method of scientific exploration "machine learning." At Microsoft, a team has already used it to innovate a method of predicting with impressive accuracy whether a patient with congestive heart failure who is released from the hospital will be readmitted within 30 days. It was developed by directing a computer program to pore through hundreds of thousands of data points on 300,000 patients and "learn" the profiles of patients most likely to be rehospitalized. The economic impact of this prediction tool could be huge: If a hospital understands the likelihood that a patient will "bounce back," it can design programs to keep him stable and save thousands of dollars in health care costs. Similar efforts to uncover important correlations that could lead to scientific breakthroughs are under way in oceanography, conservation, and AIDS research. And in business, deep data exploration has the potential to unearth critical insights about customers, supply chains, advertising effectiveness, and more.

Compression-based distance (CBD): a simple, rapid, and accurate method for microbiota composition comparison.

PubMed

Yang, Fang; Chia, Nicholas; White, Bryan A; Schook, Lawrence B

2013-04-23

Perturbations in intestinal microbiota composition have been associated with a variety of gastrointestinal tract-related diseases. The alleviation of symptoms has been achieved using treatments that alter the gastrointestinal tract microbiota toward that of healthy individuals. Identifying differences in microbiota composition through the use of 16S rRNA gene hypervariable tag sequencing has profound health implications. Current computational methods for comparing microbial communities are usually based on multiple alignments and phylogenetic inference, making them time consuming and requiring exceptional expertise and computational resources. As sequencing data rapidly grows in size, simpler analysis methods are needed to meet the growing computational burdens of microbiota comparisons. Thus, we have developed a simple, rapid, and accurate method, independent of multiple alignments and phylogenetic inference, to support microbiota comparisons. We create a metric, called compression-based distance (CBD) for quantifying the degree of similarity between microbial communities. CBD uses the repetitive nature of hypervariable tag datasets and well-established compression algorithms to approximate the total information shared between two datasets. Three published microbiota datasets were used as test cases for CBD as an applicable tool. Our study revealed that CBD recaptured 100% of the statistically significant conclusions reported in the previous studies, while achieving a decrease in computational time required when compared to similar tools without expert user intervention. CBD provides a simple, rapid, and accurate method for assessing distances between gastrointestinal tract microbiota 16S hypervariable tag datasets.

Mobility analysis, simulation, and scale model testing for the design of wheeled planetary rovers

NASA Technical Reports Server (NTRS)

Lindemann, Randel A.; Eisen, Howard J.

1993-01-01

The use of computer based techniques to model and simulate wheeled rovers on rough natural terrains is considered. Physical models of a prototype vehicle can be used to test the correlation of the simulations in scaled testing. The computer approaches include a quasi-static planar or two dimensional analysis and design tool based on the traction necessary for the vehicle to have imminent mobility. The computer program modeled a six by six wheel drive vehicle of original kinematic configuration, called the Rocker Bogie. The Rocker Bogie was optimized using the quasi-static software with respect to its articulation parameters prior to fabrication of a prototype. In another approach used, the dynamics of the Rocker Bogie vehicle in 3-D space was modeled on an engineering workstation using commercial software. The model included the complex and nonlinear interaction of the tire and terrain. The results of the investigation yielded numerical and graphical results of the rover traversing rough terrain on the earth, moon, and Mars. In addition, animations of the rover excursions were also generated. A prototype vehicle was then used in a series of testbed and field experiments. Correspondence was then established between the computer models and the physical model. The results indicated the utility of the quasi-static tool for configurational design, as well as the predictive ability of the 3-D simulation to model the dynamic behavior of the vehicle over short traverses.

A pluggable framework for parallel pairwise sequence search.

PubMed

Archuleta, Jeremy; Feng, Wu-chun; Tilevich, Eli

2007-01-01

The current and near future of the computing industry is one of multi-core and multi-processor technology. Most existing sequence-search tools have been designed with a focus on single-core, single-processor systems. This discrepancy between software design and hardware architecture substantially hinders sequence-search performance by not allowing full utilization of the hardware. This paper presents a novel framework that will aid the conversion of serial sequence-search tools into a parallel version that can take full advantage of the available hardware. The framework, which is based on a software architecture called mixin layers with refined roles, enables modules to be plugged into the framework with minimal effort. The inherent modular design improves maintenance and extensibility, thus opening up a plethora of opportunities for advanced algorithmic features to be developed and incorporated while routine maintenance of the codebase persists.

The Electron Microscopy Outreach Program: A Web-based resource for research and education.

PubMed

Sosinsky, G E; Baker, T S; Hand, G; Ellisman, M H

1999-01-01

We have developed a centralized World Wide Web (WWW)-based environment that serves as a resource of software tools and expertise for biological electron microscopy. A major focus is molecular electron microscopy, but the site also includes information and links on structural biology at all levels of resolution. This site serves to help integrate or link structural biology techniques in accordance with user needs. The WWW site, called the Electron Microscopy (EM) Outreach Program (URL: http://emoutreach.sdsc.edu), provides scientists with computational and educational tools for their research and edification. In particular, we have set up a centralized resource containing course notes, references, and links to image analysis and three-dimensional reconstruction software for investigators wanting to learn about EM techniques either within or outside of their fields of expertise. Copyright 1999 Academic Press.

orthoFind Facilitates the Discovery of Homologous and Orthologous Proteins.

PubMed

Mier, Pablo; Andrade-Navarro, Miguel A; Pérez-Pulido, Antonio J

2015-01-01

Finding homologous and orthologous protein sequences is often the first step in evolutionary studies, annotation projects, and experiments of functional complementation. Despite all currently available computational tools, there is a requirement for easy-to-use tools that provide functional information. Here, a new web application called orthoFind is presented, which allows a quick search for homologous and orthologous proteins given one or more query sequences, allowing a recurrent and exhaustive search against reference proteomes, and being able to include user databases. It addresses the protein multidomain problem, searching for homologs with the same domain architecture, and gives a simple functional analysis of the results to help in the annotation process. orthoFind is easy to use and has been proven to provide accurate results with different datasets. Availability: http://www.bioinfocabd.upo.es/orthofind/.

Computational Enzymology and Organophosphorus Degrading Enzymes: Promising Approaches Toward Remediation Technologies of Warfare Agents and Pesticides

DOE PAGES

Ramalho, Teodorico C.; DeCastro, Alexandre A.; Silva, Daniela R.; ...

2015-08-26

The re-emergence of chemical weapons as a global threat in hands of terrorist groups, together with an increasing number of pesticides intoxications and environmental contaminations worldwide, has called the attention of the scientific community for the need of improvement in the technologies for detoxification of organophosphorus (OP) compounds. A compelling strategy is the use of bioremediation by enzymes that are able to hydrolyze these molecules to harmless chemical species. Several enzymes have been studied and engineered for this purpose. However, their mechanisms of action are not well understood. Theoretical investigations may help elucidate important aspects of these mechanisms and helpmore » in the development of more efficient bio-remediators. In this review, we point out the major contributions of computational methodologies applied to enzyme based detoxification of OPs. Furthermore, we highlight the use of PTE, PON, DFP, and BuChE as enzymes used in OP detoxification process and how computational tools such as molecular docking, molecular dynamics simulations and combined quantum mechanical/molecular mechanics have and will continue to contribute to this very important area of research.The re-emergence of chemical weapons as a global threat in hands of terrorist groups, together with an increasing number of pesticides intoxications and environmental contaminations worldwide, has called the attention of the scientific community for the need of improvement in the technologies for detoxification of organophosphorus (OP) compounds. A compelling strategy is the use of bioremediation by enzymes that are able to hydrolyze these molecules to harmless chemical species. Several enzymes have been studied and engineered for this purpose. However, their mechanisms of action are not well understood. Theoretical investigations may help elucidate important aspects of these mechanisms and help in the development of more efficient bio-remediators. In this review, we point out the major contributions of computational methodologies applied to enzyme based detoxification of OPs. Furthermore, we highlight the use of PTE, PON, DFP, and BuChE as enzymes used in OP detoxification process and how computational tools such as molecular docking, molecular dynamics simulations and combined quantum mechanical/molecular mechanics have and will continue to contribute to this very important area of research.« less

Computational Enzymology and Organophosphorus Degrading Enzymes: Promising Approaches Toward Remediation Technologies of Warfare Agents and Pesticides

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

Ramalho, Teodorico C.; DeCastro, Alexandre A.; Silva, Daniela R.

The re-emergence of chemical weapons as a global threat in hands of terrorist groups, together with an increasing number of pesticides intoxications and environmental contaminations worldwide, has called the attention of the scientific community for the need of improvement in the technologies for detoxification of organophosphorus (OP) compounds. A compelling strategy is the use of bioremediation by enzymes that are able to hydrolyze these molecules to harmless chemical species. Several enzymes have been studied and engineered for this purpose. However, their mechanisms of action are not well understood. Theoretical investigations may help elucidate important aspects of these mechanisms and helpmore » in the development of more efficient bio-remediators. In this review, we point out the major contributions of computational methodologies applied to enzyme based detoxification of OPs. Furthermore, we highlight the use of PTE, PON, DFP, and BuChE as enzymes used in OP detoxification process and how computational tools such as molecular docking, molecular dynamics simulations and combined quantum mechanical/molecular mechanics have and will continue to contribute to this very important area of research.The re-emergence of chemical weapons as a global threat in hands of terrorist groups, together with an increasing number of pesticides intoxications and environmental contaminations worldwide, has called the attention of the scientific community for the need of improvement in the technologies for detoxification of organophosphorus (OP) compounds. A compelling strategy is the use of bioremediation by enzymes that are able to hydrolyze these molecules to harmless chemical species. Several enzymes have been studied and engineered for this purpose. However, their mechanisms of action are not well understood. Theoretical investigations may help elucidate important aspects of these mechanisms and help in the development of more efficient bio-remediators. In this review, we point out the major contributions of computational methodologies applied to enzyme based detoxification of OPs. Furthermore, we highlight the use of PTE, PON, DFP, and BuChE as enzymes used in OP detoxification process and how computational tools such as molecular docking, molecular dynamics simulations and combined quantum mechanical/molecular mechanics have and will continue to contribute to this very important area of research.« less

Autonomous control systems: applications to remote sensing and image processing

NASA Astrophysics Data System (ADS)

Jamshidi, Mohammad

2001-11-01

One of the main challenges of any control (or image processing) paradigm is being able to handle complex systems under unforeseen uncertainties. A system may be called complex here if its dimension (order) is too high and its model (if available) is nonlinear, interconnected, and information on the system is uncertain such that classical techniques cannot easily handle the problem. Examples of complex systems are power networks, space robotic colonies, national air traffic control system, and integrated manufacturing plant, the Hubble Telescope, the International Space Station, etc. Soft computing, a consortia of methodologies such as fuzzy logic, neuro-computing, genetic algorithms and genetic programming, has proven to be powerful tools for adding autonomy and semi-autonomy to many complex systems. For such systems the size of soft computing control architecture will be nearly infinite. In this paper new paradigms using soft computing approaches are utilized to design autonomous controllers and image enhancers for a number of application areas. These applications are satellite array formations for synthetic aperture radar interferometry (InSAR) and enhancement of analog and digital images.

Uncertainty Aware Structural Topology Optimization Via a Stochastic Reduced Order Model Approach

NASA Technical Reports Server (NTRS)

Aguilo, Miguel A.; Warner, James E.

2017-01-01

This work presents a stochastic reduced order modeling strategy for the quantification and propagation of uncertainties in topology optimization. Uncertainty aware optimization problems can be computationally complex due to the substantial number of model evaluations that are necessary to accurately quantify and propagate uncertainties. This computational complexity is greatly magnified if a high-fidelity, physics-based numerical model is used for the topology optimization calculations. Stochastic reduced order model (SROM) methods are applied here to effectively 1) alleviate the prohibitive computational cost associated with an uncertainty aware topology optimization problem; and 2) quantify and propagate the inherent uncertainties due to design imperfections. A generic SROM framework that transforms the uncertainty aware, stochastic topology optimization problem into a deterministic optimization problem that relies only on independent calls to a deterministic numerical model is presented. This approach facilitates the use of existing optimization and modeling tools to accurately solve the uncertainty aware topology optimization problems in a fraction of the computational demand required by Monte Carlo methods. Finally, an example in structural topology optimization is presented to demonstrate the effectiveness of the proposed uncertainty aware structural topology optimization approach.

Computational imaging of light in flight

NASA Astrophysics Data System (ADS)

Hullin, Matthias B.

2014-10-01

Many computer vision tasks are hindered by image formation itself, a process that is governed by the so-called plenoptic integral. By averaging light falling into the lens over space, angle, wavelength and time, a great deal of information is irreversibly lost. The emerging idea of transient imaging operates on a time resolution fast enough to resolve non-stationary light distributions in real-world scenes. It enables the discrimination of light contributions by the optical path length from light source to receiver, a dimension unavailable in mainstream imaging to date. Until recently, such measurements used to require high-end optical equipment and could only be acquired under extremely restricted lab conditions. To address this challenge, we introduced a family of computational imaging techniques operating on standard time-of-flight image sensors, for the first time allowing the user to "film" light in flight in an affordable, practical and portable way. Just as impulse responses have proven a valuable tool in almost every branch of science and engineering, we expect light-in-flight analysis to impact a wide variety of applications in computer vision and beyond.

WAERS: an application for Web-assisted estimation of relative survival.

PubMed

Clèries, Ramon; Valls, Joan; Esteban, Laura; Gálvez, Jordi; Pareja, Laura; Sanz, Xavier; Alliste, Luisa; Martínez, José Miguel; Moreno, Víctor; Bosch, Xavier; Borràs, Josep Maria; Ribes, Josepa Maria

2007-09-01

Net cancer survival estimation is usually performed by computing relative survival (RS), which is defined as the ratio between observed and expected survival rates. The mortality of a reference population is required in order to compute the expected survival rate, which can be performed using a variety of statistical packages. A new Web interface to compute RS, called WAERS, has been developed by the Catalan Institute of Oncology. The reference population is first selected, and then the RS of a cohort is computed. A remote server is used for this purpose. A mock example serves to illustrate the use of the tool with a hypothetical cohort, for which RS is estimated based on three different reference populations (a province of Spain, an autonomous community (Region), and the entire Spanish population). At present, only mortality tables for different areas of Spain are available. Future improvements of this application will include mortality tables of Latin American and European Union countries, and stratified (control variable) analysis. This application can be also useful for cohort mortality studies and for registries of several diseases.

The next generation of command post computing

NASA Astrophysics Data System (ADS)

Arnold, Ross D.; Lieb, Aaron J.; Samuel, Jason M.; Burger, Mitchell A.

2015-05-01

The future of command post computing demands an innovative new solution to address a variety of challenging operational needs. The Command Post of the Future is the Army's primary command and control decision support system, providing situational awareness and collaborative tools for tactical decision making, planning, and execution management from Corps to Company level. However, as the U.S. Army moves towards a lightweight, fully networked battalion, disconnected operations, thin client architecture and mobile computing become increasingly essential. The Command Post of the Future is not designed to support these challenges in the coming decade. Therefore, research into a hybrid blend of technologies is in progress to address these issues. This research focuses on a new command and control system utilizing the rich collaboration framework afforded by Command Post of the Future coupled with a new user interface consisting of a variety of innovative workspace designs. This new system is called Tactical Applications. This paper details a brief history of command post computing, presents the challenges facing the modern Army, and explores the concepts under consideration for Tactical Applications that meet these challenges in a variety of innovative ways.

PCA method for automated detection of mispronounced words

NASA Astrophysics Data System (ADS)

Ge, Zhenhao; Sharma, Sudhendu R.; Smith, Mark J. T.

2011-06-01

This paper presents a method for detecting mispronunciations with the aim of improving Computer Assisted Language Learning (CALL) tools used by foreign language learners. The algorithm is based on Principle Component Analysis (PCA). It is hierarchical with each successive step refining the estimate to classify the test word as being either mispronounced or correct. Preprocessing before detection, like normalization and time-scale modification, is implemented to guarantee uniformity of the feature vectors input to the detection system. The performance using various features including spectrograms and Mel-Frequency Cepstral Coefficients (MFCCs) are compared and evaluated. Best results were obtained using MFCCs, achieving up to 99% accuracy in word verification and 93% in native/non-native classification. Compared with Hidden Markov Models (HMMs) which are used pervasively in recognition application, this particular approach is computational efficient and effective when training data is limited.

Computer-aided resource planning and scheduling for radiological services

NASA Astrophysics Data System (ADS)

Garcia, Hong-Mei C.; Yun, David Y.; Ge, Yiqun; Khan, Javed I.

1996-05-01

There exists tremendous opportunity in hospital-wide resource optimization based on system integration. This paper defines the resource planning and scheduling requirements integral to PACS, RIS and HIS integration. An multi-site case study is conducted to define the requirements. A well-tested planning and scheduling methodology, called Constrained Resource Planning model, has been applied to the chosen problem of radiological service optimization. This investigation focuses on resource optimization issues for minimizing the turnaround time to increase clinical efficiency and customer satisfaction, particularly in cases where the scheduling of multiple exams are required for a patient. How best to combine the information system efficiency and human intelligence in improving radiological services is described. Finally, an architecture for interfacing a computer-aided resource planning and scheduling tool with the existing PACS, HIS and RIS implementation is presented.

BALLIST: A computer program to empirically predict the bumper thickness required to prevent perforation of the Space Station by orbital debris

NASA Technical Reports Server (NTRS)

Rule, William Keith

1991-01-01

A computer program called BALLIST that is intended to be a design tool for engineers is described. BALLlST empirically predicts the bumper thickness required to prevent perforation of the Space Station pressure wall by a projectile (such as orbital debris) as a function of the projectile's velocity. 'Ballistic' limit curves (bumper thickness vs. projectile velocity) are calculated and are displayed on the screen as well as being stored in an ASCII file. A Whipple style of spacecraft wall configuration is assumed. The predictions are based on a database of impact test results. NASA/Marshall Space Flight Center currently has the capability to generate such test results. Numerical simulation results of impact conditions that can not be tested (high velocities or large particles) can also be used for predictions.

Computer simulation of the human respiratory system for educational purposes.

PubMed

Botsis, Taxiarhis; Halkiotis, Stelios-Chris; Kourlaba, Georgia

2004-01-01

The main objective of this study was the development of a computer simulation system for the human respiratory system, in order to educate students of nursing. This approach was based on existing mathematical models and on our own constructed specific functions. For the development of this educational tool the appropriate software packages were used according to the special demands of this process. This system is called ReSim (Respiratory Simulation) and consists of two parts: the first part deals with pulmonary volumes and the second one represents the mechanical behavior of lungs. The target group evaluated ReSim. The outcomes of the evaluation process were positive and helped us realize the system characteristics that needed improvements. Our basic conclusion is that the extended use of such systems supports the educational process and offers new potential for learning.

Computed myography: three-dimensional reconstruction of motor functions from surface EMG data

NASA Astrophysics Data System (ADS)

van den Doel, Kees; Ascher, Uri M.; Pai, Dinesh K.

2008-12-01

We describe a methodology called computed myography to qualitatively and quantitatively determine the activation level of individual muscles by voltage measurements from an array of voltage sensors on the skin surface. A finite element model for electrostatics simulation is constructed from morphometric data. For the inverse problem, we utilize a generalized Tikhonov regularization. This imposes smoothness on the reconstructed sources inside the muscles and suppresses sources outside the muscles using a penalty term. Results from experiments with simulated and human data are presented for activation reconstructions of three muscles in the upper arm (biceps brachii, bracialis and triceps). This approach potentially offers a new clinical tool to sensitively assess muscle function in patients suffering from neurological disorders (e.g., spinal cord injury), and could more accurately guide advances in the evaluation of specific rehabilitation training regimens.

Modeling of heterogeneous elastic materials by the multiscale hp-adaptive finite element method

NASA Astrophysics Data System (ADS)

Klimczak, Marek; Cecot, Witold

2018-01-01

We present an enhancement of the multiscale finite element method (MsFEM) by combining it with the hp-adaptive FEM. Such a discretization-based homogenization technique is a versatile tool for modeling heterogeneous materials with fast oscillating elasticity coefficients. No assumption on periodicity of the domain is required. In order to avoid direct, so-called overkill mesh computations, a coarse mesh with effective stiffness matrices is used and special shape functions are constructed to account for the local heterogeneities at the micro resolution. The automatic adaptivity (hp-type at the macro resolution and h-type at the micro resolution) increases efficiency of computation. In this paper details of the modified MsFEM are presented and a numerical test performed on a Fichera corner domain is presented in order to validate the proposed approach.

Hierarchical random cellular neural networks for system-level brain-like signal processing.

PubMed

Kozma, Robert; Puljic, Marko

2013-09-01

Sensory information processing and cognition in brains are modeled using dynamic systems theory. The brain's dynamic state is described by a trajectory evolving in a high-dimensional state space. We introduce a hierarchy of random cellular automata as the mathematical tools to describe the spatio-temporal dynamics of the cortex. The corresponding brain model is called neuropercolation which has distinct advantages compared to traditional models using differential equations, especially in describing spatio-temporal discontinuities in the form of phase transitions. Phase transitions demarcate singularities in brain operations at critical conditions, which are viewed as hallmarks of higher cognition and awareness experience. The introduced Monte-Carlo simulations obtained by parallel computing point to the importance of computer implementations using very large-scale integration (VLSI) and analog platforms. Copyright © 2013 Elsevier Ltd. All rights reserved.

Dialogue-Based CALL: An Overview of Existing Research

ERIC Educational Resources Information Center

Bibauw, Serge; François, Thomas; Desmet, Piet

2015-01-01

Dialogue-based Computer-Assisted Language Learning (CALL) covers applications and systems allowing a learner to practice the target language in a meaning-focused conversational activity with an automated agent. We first present a common definition for dialogue-based CALL, based on three features: dialogue as the activity unit, computer as the…

Pedagogy and Related Criteria: The Selection of Software for Computer Assisted Language Learning

ERIC Educational Resources Information Center

Samuels, Jeffrey D.

2013-01-01

Computer-Assisted Language Learning (CALL) is an established field of academic inquiry with distinct applications for second language teaching and learning. Many CALL professionals direct language labs or language resource centers (LRCs) in which CALL software applications and generic software applications support language learning programs and…

CALL Essentials: Principles and Practice in CALL Classrooms

ERIC Educational Resources Information Center

Egbert, Joy

2005-01-01

Computers and the Internet offer innovative teachers exciting ways to enhance their pedagogy and capture their students' attention. These technologies have created a growing field of inquiry, computer-assisted language learning (CALL). As new technologies have emerged, teaching professionals have adapted them to support teachers and learners in…

A Study of Multimedia Application-Based Vocabulary Acquisition

ERIC Educational Resources Information Center

Shao, Jing

2012-01-01

The development of computer-assisted language learning (CALL) has created the opportunity for exploring the effects of the multimedia application on foreign language vocabulary acquisition in recent years. This study provides an overview the computer-assisted language learning (CALL) and detailed a developing result of CALL--multimedia. With the…

[Application of virtual instrumentation technique in toxicological studies].

PubMed

Moczko, Jerzy A

2005-01-01

Research investigations require frequently direct connection of measuring equipment to the computer. Virtual instrumentation technique considerably facilitates programming of sophisticated acquisition-and-analysis procedures. In standard approach these two steps are performed subsequently with separate software tools. The acquired data are transfered with export / import procedures of particular program to the another one which executes next step of analysis. The described procedure is cumbersome, time consuming and may be potential source of the errors. In 1987 National Instruments Corporation introduced LabVIEW language based on the concept of graphical programming. Contrary to conventional textual languages it allows the researcher to concentrate on the resolved problem and omit all syntactical rules. Programs developed in LabVIEW are called as virtual instruments (VI) and are portable among different computer platforms as PCs, Macintoshes, Sun SPARCstations, Concurrent PowerMAX stations, HP PA/RISK workstations. This flexibility warrants that the programs prepared for one particular platform would be also appropriate to another one. In presented paper basic principles of connection of research equipment to computer systems were described.

Statistical Inference for Porous Materials using Persistent Homology.

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

Moon, Chul; Heath, Jason E.; Mitchell, Scott A.

2017-12-01

We propose a porous materials analysis pipeline using persistent homology. We rst compute persistent homology of binarized 3D images of sampled material subvolumes. For each image we compute sets of homology intervals, which are represented as summary graphics called persistence diagrams. We convert persistence diagrams into image vectors in order to analyze the similarity of the homology of the material images using the mature tools for image analysis. Each image is treated as a vector and we compute its principal components to extract features. We t a statistical model using the loadings of principal components to estimate material porosity, permeability,more » anisotropy, and tortuosity. We also propose an adaptive version of the structural similarity index (SSIM), a similarity metric for images, as a measure to determine the statistical representative elementary volumes (sREV) for persistence homology. Thus we provide a capability for making a statistical inference of the uid ow and transport properties of porous materials based on their geometry and connectivity.« less

Optimization Issues with Complex Rotorcraft Comprehensive Analysis

NASA Technical Reports Server (NTRS)

Walsh, Joanne L.; Young, Katherine C.; Tarzanin, Frank J.; Hirsh, Joel E.; Young, Darrell K.

1998-01-01

This paper investigates the use of the general purpose automatic differentiation (AD) tool called Automatic Differentiation of FORTRAN (ADIFOR) as a means of generating sensitivity derivatives for use in Boeing Helicopter's proprietary comprehensive rotor analysis code (VII). ADIFOR transforms an existing computer program into a new program that performs a sensitivity analysis in addition to the original analysis. In this study both the pros (exact derivatives, no step-size problems) and cons (more CPU, more memory) of ADIFOR are discussed. The size (based on the number of lines) of the VII code after ADIFOR processing increased by 70 percent and resulted in substantial computer memory requirements at execution. The ADIFOR derivatives took about 75 percent longer to compute than the finite-difference derivatives. However, the ADIFOR derivatives are exact and are not functions of step-size. The VII sensitivity derivatives generated by ADIFOR are compared with finite-difference derivatives. The ADIFOR and finite-difference derivatives are used in three optimization schemes to solve a low vibration rotor design problem.

A New Browser-based, Ontology-driven Tool for Generating Standardized, Deep Descriptions of Geoscience Models

NASA Astrophysics Data System (ADS)

Peckham, S. D.; Kelbert, A.; Rudan, S.; Stoica, M.

2016-12-01

Standardized metadata for models is the key to reliable and greatly simplified coupling in model coupling frameworks like CSDMS (Community Surface Dynamics Modeling System). This model metadata also helps model users to understand the important details that underpin computational models and to compare the capabilities of different models. These details include simplifying assumptions on the physics, governing equations and the numerical methods used to solve them, discretization of space (the grid) and time (the time-stepping scheme), state variables (input or output), model configuration parameters. This kind of metadata provides a "deep description" of a computational model that goes well beyond other types of metadata (e.g. author, purpose, scientific domain, programming language, digital rights, provenance, execution) and captures the science that underpins a model. While having this kind of standardized metadata for each model in a repository opens up a wide range of exciting possibilities, it is difficult to collect this information and a carefully conceived "data model" or schema is needed to store it. Automated harvesting and scraping methods can provide some useful information, but they often result in metadata that is inaccurate or incomplete, and this is not sufficient to enable the desired capabilities. In order to address this problem, we have developed a browser-based tool called the MCM Tool (Model Component Metadata) which runs on notebooks, tablets and smart phones. This tool was partially inspired by the TurboTax software, which greatly simplifies the necessary task of preparing tax documents. It allows a model developer or advanced user to provide a standardized, deep description of a computational geoscience model, including hydrologic models. Under the hood, the tool uses a new ontology for models built on the CSDMS Standard Names, expressed as a collection of RDF files (Resource Description Framework). This ontology is based on core concepts such as variables, objects, quantities, operations, processes and assumptions. The purpose of this talk is to present details of the new ontology and to then demonstrate the MCM Tool for several hydrologic models.

Easy Handling of Sensors and Actuators over TCP/IP Networks by Open Source Hardware/Software

PubMed Central

Mejías, Andrés; Herrera, Reyes S.; Márquez, Marco A.; Calderón, Antonio José; González, Isaías; Andújar, José Manuel

2017-01-01

There are several specific solutions for accessing sensors and actuators present in any process or system through a TCP/IP network, either local or a wide area type like the Internet. The usage of sensors and actuators of different nature and diverse interfaces (SPI, I2C, analogue, etc.) makes access to them from a network in a homogeneous and secure way more complex. A framework, including both software and hardware resources, is necessary to simplify and unify networked access to these devices. In this paper, a set of open-source software tools, specifically designed to cover the different issues concerning the access to sensors and actuators, and two proposed low-cost hardware architectures to operate with the abovementioned software tools are presented. They allow integrated and easy access to local or remote sensors and actuators. The software tools, integrated in the free authoring tool Easy Java and Javascript Simulations (EJS) solve the interaction issues between the subsystem that integrates sensors and actuators into the network, called convergence subsystem in this paper, and the Human Machine Interface (HMI)—this one designed using the intuitive graphical system of EJS—located on the user’s computer. The proposed hardware architectures and software tools are described and experimental implementations with the proposed tools are presented. PMID:28067801

Easy Handling of Sensors and Actuators over TCP/IP Networks by Open Source Hardware/Software.

PubMed

Mejías, Andrés; Herrera, Reyes S; Márquez, Marco A; Calderón, Antonio José; González, Isaías; Andújar, José Manuel

2017-01-05

There are several specific solutions for accessing sensors and actuators present in any process or system through a TCP/IP network, either local or a wide area type like the Internet. The usage of sensors and actuators of different nature and diverse interfaces (SPI, I2C, analogue, etc.) makes access to them from a network in a homogeneous and secure way more complex. A framework, including both software and hardware resources, is necessary to simplify and unify networked access to these devices. In this paper, a set of open-source software tools, specifically designed to cover the different issues concerning the access to sensors and actuators, and two proposed low-cost hardware architectures to operate with the abovementioned software tools are presented. They allow integrated and easy access to local or remote sensors and actuators. The software tools, integrated in the free authoring tool Easy Java and Javascript Simulations (EJS) solve the interaction issues between the subsystem that integrates sensors and actuators into the network, called convergence subsystem in this paper, and the Human Machine Interface (HMI)-this one designed using the intuitive graphical system of EJS-located on the user's computer. The proposed hardware architectures and software tools are described and experimental implementations with the proposed tools are presented.

DSC: software tool for simulation-based design of control strategies applied to wastewater treatment plants.

PubMed

Ruano, M V; Ribes, J; Seco, A; Ferrer, J

2011-01-01

This paper presents a computer tool called DSC (Simulation based Controllers Design) that enables an easy design of control systems and strategies applied to wastewater treatment plants. Although the control systems are developed and evaluated by simulation, this tool aims to facilitate the direct implementation of the designed control system to the PC of the full-scale WWTP (wastewater treatment plants). The designed control system can be programmed in a dedicated control application and can be connected to either the simulation software or the SCADA of the plant. To this end, the developed DSC incorporates an OPC server (OLE for process control) which facilitates an open-standard communication protocol for different industrial process applications. The potential capabilities of the DSC tool are illustrated through the example of a full-scale application. An aeration control system applied to a nutrient removing WWTP was designed, tuned and evaluated with the DSC tool before its implementation in the full scale plant. The control parameters obtained by simulation were suitable for the full scale plant with only few modifications to improve the control performance. With the DSC tool, the control systems performance can be easily evaluated by simulation. Once developed and tuned by simulation, the control systems can be directly applied to the full-scale WWTP.

NETIMIS: Dynamic Simulation of Health Economics Outcomes Using Big Data.

PubMed

Johnson, Owen A; Hall, Peter S; Hulme, Claire

2016-02-01

Many healthcare organizations are now making good use of electronic health record (EHR) systems to record clinical information about their patients and the details of their healthcare. Electronic data in EHRs is generated by people engaged in complex processes within complex environments, and their human input, albeit shaped by computer systems, is compromised by many human factors. These data are potentially valuable to health economists and outcomes researchers but are sufficiently large and complex enough to be considered part of the new frontier of 'big data'. This paper describes emerging methods that draw together data mining, process modelling, activity-based costing and dynamic simulation models. Our research infrastructure includes safe links to Leeds hospital's EHRs with 3 million secondary and tertiary care patients. We created a multidisciplinary team of health economists, clinical specialists, and data and computer scientists, and developed a dynamic simulation tool called NETIMIS (Network Tools for Intervention Modelling with Intelligent Simulation; http://www.netimis.com ) suitable for visualization of both human-designed and data-mined processes which can then be used for 'what-if' analysis by stakeholders interested in costing, designing and evaluating healthcare interventions. We present two examples of model development to illustrate how dynamic simulation can be informed by big data from an EHR. We found the tool provided a focal point for multidisciplinary team work to help them iteratively and collaboratively 'deep dive' into big data.

TRAC, a collaborative computer tool for tracer-test interpretation

NASA Astrophysics Data System (ADS)

Gutierrez, A.; Klinka, T.; Thiéry, D.; Buscarlet, E.; Binet, S.; Jozja, N.; Défarge, C.; Leclerc, B.; Fécamp, C.; Ahumada, Y.; Elsass, J.

2013-05-01

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">http://trac.brgm.fr.

Docker Container Manager: A Simple Toolkit for Isolated Work with Shared Computational, Storage, and Network Resources

NASA Astrophysics Data System (ADS)

Polyakov, S. P.; Kryukov, A. P.; Demichev, A. P.

2018-01-01

We present a simple set of command line interface tools called Docker Container Manager (DCM) that allow users to create and manage Docker containers with preconfigured SSH access while keeping the users isolated from each other and restricting their access to the Docker features that could potentially disrupt the work of the server. Users can access DCM server via SSH and are automatically redirected to DCM interface tool. From there, they can create new containers, stop, restart, pause, unpause, and remove containers and view the status of the existing containers. By default, the containers are also accessible via SSH using the same private key(s) but through different server ports. Additional publicly available ports can be mapped to the respective ports of a container, allowing for some network services to be run within it. The containers are started from read-only filesystem images. Some initial images must be provided by the DCM server administrators, and after containers are configured to meet one’s needs, the changes can be saved as new images. Users can see the available images and remove their own images. DCM server administrators are provided with commands to create and delete users. All commands were implemented as Python scripts. The tools allow to deploy and debug medium-sized distributed systems for simulation in different fields on one or several local computers.

Developing a Computational Environment for Coupling MOR Data, Maps, and Models: The Virtual Research Vessel (VRV) Prototype

NASA Astrophysics Data System (ADS)

Wright, D. J.; O'Dea, E.; Cushing, J. B.; Cuny, J. E.; Toomey, D. R.; Hackett, K.; Tikekar, R.

2001-12-01

The East Pacific Rise (EPR) from 9-10deg. N is currently our best-studied section of fast-spreading mid-ocean ridge. During several decades of investigation it has been explored by the full spectrum of ridge investigators, including chemists, biologists, geologists and geophysicists. These studies, and those that are ongoing, provide a wealth of observational data, results and data-driven theoretical (often numerical) studies that have not yet been fully utilized either by research scientists or by professional educators. While the situation is improving, a large amount of data, results, and related theoretical models still exist either in an inert, non-interactive form (e.g., journal publications) or as unlinked and currently incompatible computer data or algorithms. Infrastructure is needed not just for ready access to data, but linkage of disparate data sets (data to data) as well as data to models in order quantitatively evaluate hypotheses, refine numerical simulations, and explore new relations between observables. The prototype of a computational environment and toolset, called the Virtual Research Vessel (VRV), is being developed to provide scientists and educators with ready access to data, results and numerical models. While this effort is focused on the EPR 9N region, the resulting software tools and infrastructure should be helpful in establishing similar systems for other sections of the global mid-ocean ridge. Work in progress includes efforts to develop: (1) virtual database to incorporate diverse data types with domain-specific metadata into a global schema that allows web-query across different marine geology data sets, and an analogous declarative (database available) description of tools and models; (2) the ability to move data between GIS and the above DBMS, and tools to encourage data submission to archivesl (3) tools for finding and viewing archives, and translating between formats; (4) support for "computational steering" (tool composition) and model coupling (e.g., ability to run tool composition locally but access input data from the web, APIs to support coupling such as invoking programs that are running remotely, and help in writing data wrappers to publish programs); (5) support of migration paths for prototyped model coupling; and (6) export of marine geological data and data analysis to the undergraduate classroom (VRV-ET, "Educational Tool"). See the main VRV web site at http://oregonstate.edu/dept/vrv and the VRV-ET web site at: http://www.cs.uoregon.edu/research/vrv-et.

A high performance computing framework for physics-based modeling and simulation of military ground vehicles

NASA Astrophysics Data System (ADS)

Negrut, Dan; Lamb, David; Gorsich, David

2011-06-01

This paper describes a software infrastructure made up of tools and libraries designed to assist developers in implementing computational dynamics applications running on heterogeneous and distributed computing environments. Together, these tools and libraries compose a so called Heterogeneous Computing Template (HCT). The heterogeneous and distributed computing hardware infrastructure is assumed herein to be made up of a combination of CPUs and Graphics Processing Units (GPUs). The computational dynamics applications targeted to execute on such a hardware topology include many-body dynamics, smoothed-particle hydrodynamics (SPH) fluid simulation, and fluid-solid interaction analysis. The underlying theme of the solution approach embraced by HCT is that of partitioning the domain of interest into a number of subdomains that are each managed by a separate core/accelerator (CPU/GPU) pair. Five components at the core of HCT enable the envisioned distributed computing approach to large-scale dynamical system simulation: (a) the ability to partition the problem according to the one-to-one mapping; i.e., spatial subdivision, discussed above (pre-processing); (b) a protocol for passing data between any two co-processors; (c) algorithms for element proximity computation; and (d) the ability to carry out post-processing in a distributed fashion. In this contribution the components (a) and (b) of the HCT are demonstrated via the example of the Discrete Element Method (DEM) for rigid body dynamics with friction and contact. The collision detection task required in frictional-contact dynamics (task (c) above), is shown to benefit on the GPU of a two order of magnitude gain in efficiency when compared to traditional sequential implementations. Note: Reference herein to any specific commercial products, process, or service by trade name, trademark, manufacturer, or otherwise, does not imply its endorsement, recommendation, or favoring by the United States Army. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Army, and shall not be used for advertising or product endorsement purposes.

On the study of control effectiveness and computational efficiency of reduced Saint-Venant model in model predictive control of open channel flow

NASA Astrophysics Data System (ADS)

Xu, M.; van Overloop, P. J.; van de Giesen, N. C.

2011-02-01

Model predictive control (MPC) of open channel flow is becoming an important tool in water management. The complexity of the prediction model has a large influence on the MPC application in terms of control effectiveness and computational efficiency. The Saint-Venant equations, called SV model in this paper, and the Integrator Delay (ID) model are either accurate but computationally costly, or simple but restricted to allowed flow changes. In this paper, a reduced Saint-Venant (RSV) model is developed through a model reduction technique, Proper Orthogonal Decomposition (POD), on the SV equations. The RSV model keeps the main flow dynamics and functions over a large flow range but is easier to implement in MPC. In the test case of a modeled canal reach, the number of states and disturbances in the RSV model is about 45 and 16 times less than the SV model, respectively. The computational time of MPC with the RSV model is significantly reduced, while the controller remains effective. Thus, the RSV model is a promising means to balance the control effectiveness and computational efficiency.

Computational systems chemical biology.

PubMed

Oprea, Tudor I; May, Elebeoba E; Leitão, Andrei; Tropsha, Alexander

2011-01-01

There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology (SCB) (Nat Chem Biol 3: 447-450, 2007).The overarching goal of computational SCB is to develop tools for integrated chemical-biological data acquisition, filtering and processing, by taking into account relevant information related to interactions between proteins and small molecules, possible metabolic transformations of small molecules, as well as associated information related to genes, networks, small molecules, and, where applicable, mutants and variants of those proteins. There is yet an unmet need to develop an integrated in silico pharmacology/systems biology continuum that embeds drug-target-clinical outcome (DTCO) triplets, a capability that is vital to the future of chemical biology, pharmacology, and systems biology. Through the development of the SCB approach, scientists will be able to start addressing, in an integrated simulation environment, questions that make the best use of our ever-growing chemical and biological data repositories at the system-wide level. This chapter reviews some of the major research concepts and describes key components that constitute the emerging area of computational systems chemical biology.

Computational Systems Chemical Biology

PubMed Central

Oprea, Tudor I.; May, Elebeoba E.; Leitão, Andrei; Tropsha, Alexander

2013-01-01

There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically-based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology, SCB (Oprea et al., 2007). The overarching goal of computational SCB is to develop tools for integrated chemical-biological data acquisition, filtering and processing, by taking into account relevant information related to interactions between proteins and small molecules, possible metabolic transformations of small molecules, as well as associated information related to genes, networks, small molecules and, where applicable, mutants and variants of those proteins. There is yet an unmet need to develop an integrated in silico pharmacology / systems biology continuum that embeds drug-target-clinical outcome (DTCO) triplets, a capability that is vital to the future of chemical biology, pharmacology and systems biology. Through the development of the SCB approach, scientists will be able to start addressing, in an integrated simulation environment, questions that make the best use of our ever-growing chemical and biological data repositories at the system-wide level. This chapter reviews some of the major research concepts and describes key components that constitute the emerging area of computational systems chemical biology. PMID:20838980

User-Centered Computer Aided Language Learning

ERIC Educational Resources Information Center

Zaphiris, Panayiotis, Ed.; Zacharia, Giorgos, Ed.

2006-01-01

In the field of computer aided language learning (CALL), there is a need for emphasizing the importance of the user. "User-Centered Computer Aided Language Learning" presents methodologies, strategies, and design approaches for building interfaces for a user-centered CALL environment, creating a deeper understanding of the opportunities and…

Application for internal dosimetry using biokinetic distribution of photons based on nuclear medicine images.

PubMed

Leal Neto, Viriato; Vieira, José Wilson; Lima, Fernando Roberto de Andrade

2014-01-01

This article presents a way to obtain estimates of dose in patients submitted to radiotherapy with basis on the analysis of regions of interest on nuclear medicine images. A software called DoRadIo (Dosimetria das Radiações Ionizantes [Ionizing Radiation Dosimetry]) was developed to receive information about source organs and target organs, generating graphical and numerical results. The nuclear medicine images utilized in the present study were obtained from catalogs provided by medical physicists. The simulations were performed with computational exposure models consisting of voxel phantoms coupled with the Monte Carlo EGSnrc code. The software was developed with the Microsoft Visual Studio 2010 Service Pack and the project template Windows Presentation Foundation for C# programming language. With the mentioned tools, the authors obtained the file for optimization of Monte Carlo simulations using the EGSnrc; organization and compaction of dosimetry results with all radioactive sources; selection of regions of interest; evaluation of grayscale intensity in regions of interest; the file of weighted sources; and, finally, all the charts and numerical results. The user interface may be adapted for use in clinical nuclear medicine as a computer-aided tool to estimate the administered activity.

Camera Layout Design for the Upper Stage Thrust Cone

NASA Technical Reports Server (NTRS)

Wooten, Tevin; Fowler, Bart

2010-01-01

Engineers in the Integrated Design and Analysis Division (EV30) use a variety of different tools to aid in the design and analysis of the Ares I vehicle. One primary tool in use is Pro-Engineer. Pro-Engineer is a computer-aided design (CAD) software that allows designers to create computer generated structural models of vehicle structures. For the Upper State thrust cone, Pro-Engineer was used to assist in the design of a layout for two camera housings. These cameras observe the separation between the first and second stage of the Ares I vehicle. For the Ares I-X, one standard speed camera was used. The Ares I design calls for two separate housings, three cameras, and a lighting system. With previous design concepts and verification strategies in mind, a new layout for the two camera design concept was developed with members of the EV32 team. With the new design, Pro-Engineer was used to draw the layout to observe how the two camera housings fit with the thrust cone assembly. Future analysis of the camera housing design will verify the stability and clearance of the camera with other hardware present on the thrust cone.

Visualization Techniques for Computer Network Defense

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

Beaver, Justin M; Steed, Chad A; Patton, Robert M

2011-01-01

Effective visual analysis of computer network defense (CND) information is challenging due to the volume and complexity of both the raw and analyzed network data. A typical CND is comprised of multiple niche intrusion detection tools, each of which performs network data analysis and produces a unique alerting output. The state-of-the-practice in the situational awareness of CND data is the prevalent use of custom-developed scripts by Information Technology (IT) professionals to retrieve, organize, and understand potential threat events. We propose a new visual analytics framework, called the Oak Ridge Cyber Analytics (ORCA) system, for CND data that allows an operatormore » to interact with all detection tool outputs simultaneously. Aggregated alert events are presented in multiple coordinated views with timeline, cluster, and swarm model analysis displays. These displays are complemented with both supervised and semi-supervised machine learning classifiers. The intent of the visual analytics framework is to improve CND situational awareness, to enable an analyst to quickly navigate and analyze thousands of detected events, and to combine sophisticated data analysis techniques with interactive visualization such that patterns of anomalous activities may be more easily identified and investigated.« less

Common Analysis Tool Being Developed for Aeropropulsion: The National Cycle Program Within the Numerical Propulsion System Simulation Environment

NASA Technical Reports Server (NTRS)

Follen, Gregory J.; Naiman, Cynthia G.

1999-01-01

The NASA Lewis Research Center is developing an environment for analyzing and designing aircraft engines-the Numerical Propulsion System Simulation (NPSS). NPSS will integrate multiple disciplines, such as aerodynamics, structure, and heat transfer, and will make use of numerical "zooming" on component codes. Zooming is the coupling of analyses at various levels of detail. NPSS uses the latest computing and communication technologies to capture complex physical processes in a timely, cost-effective manner. The vision of NPSS is to create a "numerical test cell" enabling full engine simulations overnight on cost-effective computing platforms. Through the NASA/Industry Cooperative Effort agreement, NASA Lewis and industry partners are developing a new engine simulation called the National Cycle Program (NCP). NCP, which is the first step toward NPSS and is its initial framework, supports the aerothermodynamic system simulation process for the full life cycle of an engine. U.S. aircraft and airframe companies recognize NCP as the future industry standard common analysis tool for aeropropulsion system modeling. The estimated potential payoff for NCP is a $50 million/yr savings to industry through improved engineering productivity.

Computer-aided diagnosis software for vulvovaginal candidiasis detection from Pap smear images.

PubMed

Momenzadeh, Mohammadreza; Vard, Alireza; Talebi, Ardeshir; Mehri Dehnavi, Alireza; Rabbani, Hossein

2018-01-01

Vulvovaginal candidiasis (VVC) is a common gynecologic infection and it occurs when there is overgrowth of the yeast called Candida. VVC diagnosis is usually done by observing a Pap smear sample under a microscope and searching for the conidium and mycelium components of Candida. This manual method is time consuming, subjective and tedious. Any diagnosis tools that detect VVC, semi- or full-automatically, can be very helpful to pathologists. This article presents a computer aided diagnosis (CAD) software to improve human diagnosis of VVC from Pap smear samples. The proposed software is designed based on phenotypic and morphology features of the Candida in Pap smear sample images. This software provide a user-friendly interface which consists of a set of image processing tools and analytical results that helps to detect Candida and determine severity of illness. The software was evaluated on 200 Pap smear sample images and obtained specificity of 91.04% and sensitivity of 92.48% to detect VVC. As a result, the use of the proposed software reduces diagnostic time and can be employed as a second objective opinion for pathologists. © 2017 Wiley Periodicals, Inc.

Capturing remote mixing due to internal tides using multi-scale modeling tool: SOMAR-LES

NASA Astrophysics Data System (ADS)

Santilli, Edward; Chalamalla, Vamsi; Scotti, Alberto; Sarkar, Sutanu

2016-11-01

Internal tides that are generated during the interaction of an oscillating barotropic tide with the bottom bathymetry dissipate only a fraction of their energy near the generation region. The rest is radiated away in the form of low- high-mode internal tides. These internal tides dissipate energy at remote locations when they interact with the upper ocean pycnocline, continental slope, and large scale eddies. Capturing the wide range of length and time scales involved during the life-cycle of internal tides is computationally very expensive. A recently developed multi-scale modeling tool called SOMAR-LES combines the adaptive grid refinement features of SOMAR with the turbulence modeling features of a Large Eddy Simulation (LES) to capture multi-scale processes at a reduced computational cost. Numerical simulations of internal tide generation at idealized bottom bathymetries are performed to demonstrate this multi-scale modeling technique. Although each of the remote mixing phenomena have been considered independently in previous studies, this work aims to capture remote mixing processes during the life cycle of an internal tide in more realistic settings, by allowing multi-level (coarse and fine) grids to co-exist and exchange information during the time stepping process.

Visualization of particle interactions in granular media.

PubMed

Meier, Holger A; Schlemmer, Michael; Wagner, Christian; Kerren, Andreas; Hagen, Hans; Kuhl, Ellen; Steinmann, Paul

2008-01-01

Interaction between particles in so-called granular media, such as soil and sand, plays an important role in the context of geomechanical phenomena and numerous industrial applications. A two scale homogenization approach based on a micro and a macro scale level is briefly introduced in this paper. Computation of granular material in such a way gives a deeper insight into the context of discontinuous materials and at the same time reduces the computational costs. However, the description and the understanding of the phenomena in granular materials are not yet satisfactory. A sophisticated problem-specific visualization technique would significantly help to illustrate failure phenomena on the microscopic level. As main contribution, we present a novel 2D approach for the visualization of simulation data, based on the above outlined homogenization technique. Our visualization tool supports visualization on micro scale level as well as on macro scale level. The tool shows both aspects closely arranged in form of multiple coordinated views to give users the possibility to analyze the particle behavior effectively. A novel type of interactive rose diagrams was developed to represent the dynamic contact networks on the micro scale level in a condensed and efficient way.

Is CALL Obsolete? Language Acquisition and Language Learning Revisited in a Digital Age

ERIC Educational Resources Information Center

Jarvis, Huw; Krashen, Stephen

2014-01-01

In this article, Huw Jarvis and Stephen Krashen ask "Is CALL Obsolete?" When the term CALL (Computer-Assisted Language Learning) was introduced in the 1960s, the language education profession knew only about language learning, not language acquisition, and assumed the computer's primary contribution to second language acquisition…

Evaluating the Motivational Impact of CALL Systems: Current Practices and Future Directions

ERIC Educational Resources Information Center

Bodnar, Stephen; Cucchiarini, Catia; Strik, Helmer; van Hout, Roeland

2016-01-01

A major aim of computer-assisted language learning (CALL) is to create computer environments that facilitate students' second language (L2) acquisition. To achieve this aim, CALL employs technological innovations to create novel types of language practice. Evaluations of the new practice types serve the important role of distinguishing effective…

English Language Teachers' Perceptions of Computer-Assisted Language Learning

ERIC Educational Resources Information Center

Feng, Yu Lin

2012-01-01

A growing number of studies have reported the potential use of computer-assisted language learning (CALL) and other types of technology for ESL and EFL students. So far, most studies on CALL have focused on CALL-classroom comparisons (Chenoweth & Murday, 2003; Chenoweth, Ushida, & Murday, 2007; Fitze, 2006; Neri, Mich, Gerosa, &…

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

PubMed

Dinov, Ivo D; Rubin, Daniel; Lorensen, William; Dugan, Jonathan; Ma, Jeff; Murphy, Shawn; Kirschner, Beth; Bug, William; Sherman, Michael; Floratos, Aris; Kennedy, David; Jagadish, H V; Schmidt, Jeanette; Athey, Brian; Califano, Andrea; Musen, Mark; Altman, Russ; Kikinis, Ron; Kohane, Isaac; Delp, Scott; Parker, D Stott; Toga, Arthur W

2008-05-28

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-term resource management. We demonstrate several applications of iTools as a framework for integrated bioinformatics. iTools and the complete details about its specifications, usage and interfaces are available at the iTools web page http://iTools.ccb.ucla.edu.

iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources

PubMed Central

Dinov, Ivo D.; Rubin, Daniel; Lorensen, William; Dugan, Jonathan; Ma, Jeff; Murphy, Shawn; Kirschner, Beth; Bug, William; Sherman, Michael; Floratos, Aris; Kennedy, David; Jagadish, H. V.; Schmidt, Jeanette; Athey, Brian; Califano, Andrea; Musen, Mark; Altman, Russ; Kikinis, Ron; Kohane, Isaac; Delp, Scott; Parker, D. Stott; Toga, Arthur W.

2008-01-01

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-term resource management. We demonstrate several applications of iTools as a framework for integrated bioinformatics. iTools and the complete details about its specifications, usage and interfaces are available at the iTools web page http://iTools.ccb.ucla.edu. PMID:18509477

HCI∧2 framework: a software framework for multimodal human-computer interaction systems.

PubMed

Shen, Jie; Pantic, Maja

2013-12-01

This paper presents a novel software framework for the development and research in the area of multimodal human-computer interface (MHCI) systems. The proposed software framework, which is called the HCI∧2 Framework, is built upon publish/subscribe (P/S) architecture. It implements a shared-memory-based data transport protocol for message delivery and a TCP-based system management protocol. The latter ensures that the integrity of system structure is maintained at runtime. With the inclusion of bridging modules, the HCI∧2 Framework is interoperable with other software frameworks including Psyclone and ActiveMQ. In addition to the core communication middleware, we also present the integrated development environment (IDE) of the HCI∧2 Framework. It provides a complete graphical environment to support every step in a typical MHCI system development process, including module development, debugging, packaging, and management, as well as the whole system management and testing. The quantitative evaluation indicates that our framework outperforms other similar tools in terms of average message latency and maximum data throughput under a typical single PC scenario. To demonstrate HCI∧2 Framework's capabilities in integrating heterogeneous modules, we present several example modules working with a variety of hardware and software. We also present an example of a full system developed using the proposed HCI∧2 Framework, which is called the CamGame system and represents a computer game based on hand-held marker(s) and low-cost camera(s).

Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data

NASA Astrophysics Data System (ADS)

Sandmann, Sarah; de Graaf, Aniek O.; Karimi, Mohsen; van der Reijden, Bert A.; Hellström-Lindberg, Eva; Jansen, Joop H.; Dugas, Martin

2017-02-01

Valid variant calling results are crucial for the use of next-generation sequencing in clinical routine. However, there are numerous variant calling tools that usually differ in algorithms, filtering strategies, recommendations and thus, also in the output. We evaluated eight open-source tools regarding their ability to call single nucleotide variants and short indels with allelic frequencies as low as 1% in non-matched next-generation sequencing data: GATK HaplotypeCaller, Platypus, VarScan, LoFreq, FreeBayes, SNVer, SAMtools and VarDict. We analysed two real datasets from patients with myelodysplastic syndrome, covering 54 Illumina HiSeq samples and 111 Illumina NextSeq samples. Mutations were validated by re-sequencing on the same platform, on a different platform and expert based review. In addition we considered two simulated datasets with varying coverage and error profiles, covering 50 samples each. In all cases an identical target region consisting of 19 genes (42,322 bp) was analysed. Altogether, no tool succeeded in calling all mutations. High sensitivity was always accompanied by low precision. Influence of varying coverages- and background noise on variant calling was generally low. Taking everything into account, VarDict performed best. However, our results indicate that there is a need to improve reproducibility of the results in the context of multithreading.

A hybrid computational strategy to address WGS variant analysis in >5000 samples.

PubMed

Huang, Zhuoyi; Rustagi, Navin; Veeraraghavan, Narayanan; Carroll, Andrew; Gibbs, Richard; Boerwinkle, Eric; Venkata, Manjunath Gorentla; Yu, Fuli

2016-09-10

The decreasing costs of sequencing are driving the need for cost effective and real time variant calling of whole genome sequencing data. The scale of these projects are far beyond the capacity of typical computing resources available with most research labs. Other infrastructures like the cloud AWS environment and supercomputers also have limitations due to which large scale joint variant calling becomes infeasible, and infrastructure specific variant calling strategies either fail to scale up to large datasets or abandon joint calling strategies. We present a high throughput framework including multiple variant callers for single nucleotide variant (SNV) calling, which leverages hybrid computing infrastructure consisting of cloud AWS, supercomputers and local high performance computing infrastructures. We present a novel binning approach for large scale joint variant calling and imputation which can scale up to over 10,000 samples while producing SNV callsets with high sensitivity and specificity. As a proof of principle, we present results of analysis on Cohorts for Heart And Aging Research in Genomic Epidemiology (CHARGE) WGS freeze 3 dataset in which joint calling, imputation and phasing of over 5300 whole genome samples was produced in under 6 weeks using four state-of-the-art callers. The callers used were SNPTools, GATK-HaplotypeCaller, GATK-UnifiedGenotyper and GotCloud. We used Amazon AWS, a 4000-core in-house cluster at Baylor College of Medicine, IBM power PC Blue BioU at Rice and Rhea at Oak Ridge National Laboratory (ORNL) for the computation. AWS was used for joint calling of 180 TB of BAM files, and ORNL and Rice supercomputers were used for the imputation and phasing step. All other steps were carried out on the local compute cluster. The entire operation used 5.2 million core hours and only transferred a total of 6 TB of data across the platforms. Even with increasing sizes of whole genome datasets, ensemble joint calling of SNVs for low coverage data can be accomplished in a scalable, cost effective and fast manner by using heterogeneous computing platforms without compromising on the quality of variants.

Challenges and Security in Cloud Computing

NASA Astrophysics Data System (ADS)

Chang, Hyokyung; Choi, Euiin

People who live in this world want to solve any problems as they happen then. An IT technology called Ubiquitous computing should help the situations easier and we call a technology which makes it even better and powerful cloud computing. Cloud computing, however, is at the stage of the beginning to implement and use and it faces a lot of challenges in technical matters and security issues. This paper looks at the cloud computing security.

adwTools Developed: New Bulk Alloy and Surface Analysis Software for the Alloy Design Workbench

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Morse, Jeffrey A.; Noebe, Ronald D.; Abel, Phillip B.

2004-01-01

A suite of atomistic modeling software, called the Alloy Design Workbench, has been developed by the Computational Materials Group at the NASA Glenn Research Center and the Ohio Aerospace Institute (OAI). The main goal of this software is to guide and augment experimental materials research and development efforts by creating powerful, yet intuitive, software that combines a graphical user interface with an operating code suitable for real-time atomistic simulations of multicomponent alloy systems. Targeted for experimentalists, the interface is straightforward and requires minimum knowledge of the underlying theory, allowing researchers to focus on the scientific aspects of the work. The centerpiece of the Alloy Design Workbench suite is the adwTools module, which concentrates on the atomistic analysis of surfaces and bulk alloys containing an arbitrary number of elements. An additional module, adwParams, handles ab initio input for the parameterization used in adwTools. Future modules planned for the suite include adwSeg, which will provide numerical predictions for segregation profiles to alloy surfaces and interfaces, and adwReport, which will serve as a window into the database, providing public access to the parameterization data and a repository where users can submit their own findings from the rest of the suite. The entire suite is designed to run on desktop-scale computers. The adwTools module incorporates a custom OAI/Glenn-developed Fortran code based on the BFS (Bozzolo- Ferrante-Smith) method for alloys, ref. 1). The heart of the suite, this code is used to calculate the energetics of different compositions and configurations of atoms.

a Web-Based Interactive Tool for Multi-Resolution 3d Models of a Maya Archaeological Site

NASA Astrophysics Data System (ADS)

Agugiaro, G.; Remondino, F.; Girardi, G.; von Schwerin, J.; Richards-Rissetto, H.; De Amicis, R.

2011-09-01

Continuous technological advances in surveying, computing and digital-content delivery are strongly contributing to a change in the way Cultural Heritage is "perceived": new tools and methodologies for documentation, reconstruction and research are being created to assist not only scholars, but also to reach more potential users (e.g. students and tourists) willing to access more detailed information about art history and archaeology. 3D computer-simulated models, sometimes set in virtual landscapes, offer for example the chance to explore possible hypothetical reconstructions, while on-line GIS resources can help interactive analyses of relationships and change over space and time. While for some research purposes a traditional 2D approach may suffice, this is not the case for more complex analyses concerning spatial and temporal features of architecture, like for example the relationship of architecture and landscape, visibility studies etc. The project aims therefore at creating a tool, called "QueryArch3D" tool, which enables the web-based visualisation and queries of an interactive, multi-resolution 3D model in the framework of Cultural Heritage. More specifically, a complete Maya archaeological site, located in Copan (Honduras), has been chosen as case study to test and demonstrate the platform's capabilities. Much of the site has been surveyed and modelled at different levels of detail (LoD) and the geometric model has been semantically segmented and integrated with attribute data gathered from several external data sources. The paper describes the characteristics of the research work, along with its implementation issues and the initial results of the developed prototype.

Final Report: Quantification of Uncertainty in Extreme Scale Computations (QUEST)

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

Marzouk, Youssef; Conrad, Patrick; Bigoni, Daniele

QUEST (\\url{www.quest-scidac.org}) is a SciDAC Institute that is focused on uncertainty quantification (UQ) in large-scale scientific computations. Our goals are to (1) advance the state of the art in UQ mathematics, algorithms, and software; and (2) provide modeling, algorithmic, and general UQ expertise, together with software tools, to other SciDAC projects, thereby enabling and guiding a broad range of UQ activities in their respective contexts. QUEST is a collaboration among six institutions (Sandia National Laboratories, Los Alamos National Laboratory, the University of Southern California, Massachusetts Institute of Technology, the University of Texas at Austin, and Duke University) with a historymore » of joint UQ research. Our vision encompasses all aspects of UQ in leadership-class computing. This includes the well-founded setup of UQ problems; characterization of the input space given available data/information; local and global sensitivity analysis; adaptive dimensionality and order reduction; forward and inverse propagation of uncertainty; handling of application code failures, missing data, and hardware/software fault tolerance; and model inadequacy, comparison, validation, selection, and averaging. The nature of the UQ problem requires the seamless combination of data, models, and information across this landscape in a manner that provides a self-consistent quantification of requisite uncertainties in predictions from computational models. Accordingly, our UQ methods and tools span an interdisciplinary space across applied math, information theory, and statistics. The MIT QUEST effort centers on statistical inference and methods for surrogate or reduced-order modeling. MIT personnel have been responsible for the development of adaptive sampling methods, methods for approximating computationally intensive models, and software for both forward uncertainty propagation and statistical inverse problems. A key software product of the MIT QUEST effort is the MIT Uncertainty Quantification library, called MUQ (\\url{muq.mit.edu}).« less

A resilient and efficient CFD framework: Statistical learning tools for multi-fidelity and heterogeneous information fusion

NASA Astrophysics Data System (ADS)

Lee, Seungjoon; Kevrekidis, Ioannis G.; Karniadakis, George Em

2017-09-01

Exascale-level simulations require fault-resilient algorithms that are robust against repeated and expected software and/or hardware failures during computations, which may render the simulation results unsatisfactory. If each processor can share some global information about the simulation from a coarse, limited accuracy but relatively costless auxiliary simulator we can effectively fill-in the missing spatial data at the required times by a statistical learning technique - multi-level Gaussian process regression, on the fly; this has been demonstrated in previous work [1]. Based on the previous work, we also employ another (nonlinear) statistical learning technique, Diffusion Maps, that detects computational redundancy in time and hence accelerate the simulation by projective time integration, giving the overall computation a "patch dynamics" flavor. Furthermore, we are now able to perform information fusion with multi-fidelity and heterogeneous data (including stochastic data). Finally, we set the foundations of a new framework in CFD, called patch simulation, that combines information fusion techniques from, in principle, multiple fidelity and resolution simulations (and even experiments) with a new adaptive timestep refinement technique. We present two benchmark problems (the heat equation and the Navier-Stokes equations) to demonstrate the new capability that statistical learning tools can bring to traditional scientific computing algorithms. For each problem, we rely on heterogeneous and multi-fidelity data, either from a coarse simulation of the same equation or from a stochastic, particle-based, more "microscopic" simulation. We consider, as such "auxiliary" models, a Monte Carlo random walk for the heat equation and a dissipative particle dynamics (DPD) model for the Navier-Stokes equations. More broadly, in this paper we demonstrate the symbiotic and synergistic combination of statistical learning, domain decomposition, and scientific computing in exascale simulations.

Characterization of Protein Flexibility Using Small-Angle X-Ray Scattering and Amplified Collective Motion Simulations

PubMed Central

Wen, Bin; Peng, Junhui; Zuo, Xiaobing; Gong, Qingguo; Zhang, Zhiyong

2014-01-01

Large-scale flexibility within a multidomain protein often plays an important role in its biological function. Despite its inherent low resolution, small-angle x-ray scattering (SAXS) is well suited to investigate protein flexibility and determine, with the help of computational modeling, what kinds of protein conformations would coexist in solution. In this article, we develop a tool that combines SAXS data with a previously developed sampling technique called amplified collective motions (ACM) to elucidate structures of highly dynamic multidomain proteins in solution. We demonstrate the use of this tool in two proteins, bacteriophage T4 lysozyme and tandem WW domains of the formin-binding protein 21. The ACM simulations can sample the conformational space of proteins much more extensively than standard molecular dynamics (MD) simulations. Therefore, conformations generated by ACM are significantly better at reproducing the SAXS data than are those from MD simulations. PMID:25140431

Interactive Visualization of Computational Fluid Dynamics using Mosaic

NASA Technical Reports Server (NTRS)

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

1994-01-01

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

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

DOE PAGES

Kang, Dongwan D.; Froula, Jeff; Egan, Rob; ...

2015-01-01

Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. Because of the complex nature of these communities, existing metagenome binning methods often miss a large number of microbial species. In addition, most of the tools are not scalable to large datasets. Here we introduce automated software called MetaBAT that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency for accurate metagenome binning. MetaBAT outperforms alternative methods in accuracy and computational efficiency on both synthetic and real metagenome datasets. Lastly, it automatically formsmore » hundreds of high quality genome bins on a very large assembly consisting millions of contigs in a matter of hours on a single node. MetaBAT is open source software and available at https://bitbucket.org/berkeleylab/metabat.« less

Variable context Markov chains for HIV protease cleavage site prediction.

PubMed

Oğul, Hasan

2009-06-01

Deciphering the knowledge of HIV protease specificity and developing computational tools for detecting its cleavage sites in protein polypeptide chain are very desirable for designing efficient and specific chemical inhibitors to prevent acquired immunodeficiency syndrome. In this study, we developed a generative model based on a generalization of variable order Markov chains (VOMC) for peptide sequences and adapted the model for prediction of their cleavability by certain proteases. The new method, called variable context Markov chains (VCMC), attempts to identify the context equivalence based on the evolutionary similarities between individual amino acids. It was applied for HIV-1 protease cleavage site prediction problem and shown to outperform existing methods in terms of prediction accuracy on a common dataset. In general, the method is a promising tool for prediction of cleavage sites of all proteases and encouraged to be used for any kind of peptide classification problem as well.

Counter Action Procedure Generation in an Emergency Situation of Nuclear Power Plants

NASA Astrophysics Data System (ADS)

Gofuku, A.

2018-02-01

Lessons learned from the Fukushima Daiichi accident revealed various weak points in the design and operation of nuclear power plants at the time although there were many resilient activities made by the plant staff under difficult work environment. In order to reinforce the measures to make nuclear power plants more resilient, improvement of hardware and improvement of education and training of nuclear personnel are considered. In addition, considering the advancement of computer technology and artificial intelligence, it is a promising way to develop software tools to support the activities of plant staff.This paper focuses on the software tools to support the operations by human operators and introduces a concept of an intelligent operator support system that is called as co-operator. This paper also describes a counter operation generation technique the authors are studying as a core component of the co-operator.

Computer-Assisted Language Learning (CALL) in Support of (Re)-Learning Native Languages: The Case of Runyakitara

ERIC Educational Resources Information Center

Katushemererwe, Fridah; Nerbonne, John

2015-01-01

This study presents the results from a computer-assisted language learning (CALL) system of Runyakitara (RU_CALL). The major objective was to provide an electronic language learning environment that can enable learners with mother tongue deficiencies to enhance their knowledge of grammar and acquire writing skills in Runyakitara. The system…

PANGEA: pipeline for analysis of next generation amplicons

PubMed Central

Giongo, Adriana; Crabb, David B; Davis-Richardson, Austin G; Chauliac, Diane; Mobberley, Jennifer M; Gano, Kelsey A; Mukherjee, Nabanita; Casella, George; Roesch, Luiz FW; Walts, Brandon; Riva, Alberto; King, Gary; Triplett, Eric W

2010-01-01

High-throughput DNA sequencing can identify organisms and describe population structures in many environmental and clinical samples. Current technologies generate millions of reads in a single run, requiring extensive computational strategies to organize, analyze and interpret those sequences. A series of bioinformatics tools for high-throughput sequencing analysis, including preprocessing, clustering, database matching and classification, have been compiled into a pipeline called PANGEA. The PANGEA pipeline was written in Perl and can be run on Mac OSX, Windows or Linux. With PANGEA, sequences obtained directly from the sequencer can be processed quickly to provide the files needed for sequence identification by BLAST and for comparison of microbial communities. Two different sets of bacterial 16S rRNA sequences were used to show the efficiency of this workflow. The first set of 16S rRNA sequences is derived from various soils from Hawaii Volcanoes National Park. The second set is derived from stool samples collected from diabetes-resistant and diabetes-prone rats. The workflow described here allows the investigator to quickly assess libraries of sequences on personal computers with customized databases. PANGEA is provided for users as individual scripts for each step in the process or as a single script where all processes, except the χ2 step, are joined into one program called the ‘backbone’. PMID:20182525

PANGEA: pipeline for analysis of next generation amplicons.

PubMed

Giongo, Adriana; Crabb, David B; Davis-Richardson, Austin G; Chauliac, Diane; Mobberley, Jennifer M; Gano, Kelsey A; Mukherjee, Nabanita; Casella, George; Roesch, Luiz F W; Walts, Brandon; Riva, Alberto; King, Gary; Triplett, Eric W

2010-07-01

High-throughput DNA sequencing can identify organisms and describe population structures in many environmental and clinical samples. Current technologies generate millions of reads in a single run, requiring extensive computational strategies to organize, analyze and interpret those sequences. A series of bioinformatics tools for high-throughput sequencing analysis, including pre-processing, clustering, database matching and classification, have been compiled into a pipeline called PANGEA. The PANGEA pipeline was written in Perl and can be run on Mac OSX, Windows or Linux. With PANGEA, sequences obtained directly from the sequencer can be processed quickly to provide the files needed for sequence identification by BLAST and for comparison of microbial communities. Two different sets of bacterial 16S rRNA sequences were used to show the efficiency of this workflow. The first set of 16S rRNA sequences is derived from various soils from Hawaii Volcanoes National Park. The second set is derived from stool samples collected from diabetes-resistant and diabetes-prone rats. The workflow described here allows the investigator to quickly assess libraries of sequences on personal computers with customized databases. PANGEA is provided for users as individual scripts for each step in the process or as a single script where all processes, except the chi(2) step, are joined into one program called the 'backbone'.

An automated miniaturized Haploscope for testing binocular visual function

NASA Technical Reports Server (NTRS)

Decker, T. A.; Williams, R. E.; Kuether, C. L.; Wyman-Cornsweet, D.

1976-01-01

A computer-controlled binocular vision testing device has been developed as one part of a system designed for NASA to test the vision of astronauts during spaceflight. The device, called the Mark III Haploscope, utilizes semi-automated psychophysical test procedures to measure visual acuity, stereopsis, phorias, fixation disparity and accommodation/convergence relationships. All tests are self-administered, yield quantitative data and may be used repeatedly without subject memorization. Future applications of this programmable, compact device include its use as a clinical instrument to perform routine eye examinations or vision screening, and as a research tool to examine the effects of environment or work-cycle upon visual function.

Noise reduction in optically controlled quantum memory

NASA Astrophysics Data System (ADS)

Ma, Lijun; Slattery, Oliver; Tang, Xiao

2018-05-01

Quantum memory is an essential tool for quantum communications systems and quantum computers. An important category of quantum memory, called optically controlled quantum memory, uses a strong classical beam to control the storage and re-emission of a single-photon signal through an atomic ensemble. In this type of memory, the residual light from the strong classical control beam can cause severe noise and degrade the system performance significantly. Efficiently suppressing this noise is a requirement for the successful implementation of optically controlled quantum memories. In this paper, we briefly introduce the latest and most common approaches to quantum memory and review the various noise-reduction techniques used in implementing them.

Computational tools and lattice design for the PEP-II B-Factory

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

Cai, Y.; Irwin, J.; Nosochkov, Y.

1997-02-01

Several accelerator codes were used to design the PEP-II lattices, ranging from matrix-based codes, such as MAD and DIMAD, to symplectic-integrator codes, such as TRACY and DESPOT. In addition to element-by-element tracking, we constructed maps to determine aberration strengths. Furthermore, we have developed a fast and reliable method (nPB tracking) to track particles with a one-turn map. This new technique allows us to evaluate performance of the lattices on the entire tune-plane. Recently, we designed and implemented an object-oriented code in C++ called LEGO which integrates and expands upon TRACY and DESPOT. {copyright} {ital 1997 American Institute of Physics.}

Computational tools and lattice design for the PEP-II B-Factory

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

Cai Yunhai; Irwin, John; Nosochkov, Yuri

1997-02-01

Several accelerator codes were used to design the PEP-II lattices, ranging from matrix-based codes, such as MAD and DIMAD, to symplectic-integrator codes, such as TRACY and DESPOT. In addition to element-by-element tracking, we constructed maps to determine aberration strengths. Furthermore, we have developed a fast and reliable method (nPB tracking) to track particles with a one-turn map. This new technique allows us to evaluate performance of the lattices on the entire tune-plane. Recently, we designed and implemented an object-oriented code in C++ called LEGO which integrates and expands upon TRACY and DESPOT.

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

PubMed

Adolf-Bryfogle, Jared; Dunbrack, Roland L

2013-01-01

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

Method and apparatus for obtaining stack traceback data for multiple computing nodes of a massively parallel computer system

DOEpatents

Gooding, Thomas Michael; McCarthy, Patrick Joseph

2010-03-02

A data collector for a massively parallel computer system obtains call-return stack traceback data for multiple nodes by retrieving partial call-return stack traceback data from each node, grouping the nodes in subsets according to the partial traceback data, and obtaining further call-return stack traceback data from a representative node or nodes of each subset. Preferably, the partial data is a respective instruction address from each node, nodes having identical instruction address being grouped together in the same subset. Preferably, a single node of each subset is chosen and full stack traceback data is retrieved from the call-return stack within the chosen node.

A new approach to road accident rescue.

PubMed

Morales, Alejandro; González-Aguilera, Diego; López, Alfonso I; Gutiérrez, Miguel A

2016-01-01

This article develops and validates a new methodology and tool for rescue assistance in traffic accidents, with the aim of improving its efficiency and safety in the evacuation of people, reducing the number of victims in road accidents. Different tests supported by professionals and experts have been designed under different circumstances and with different categories of damaged vehicles coming from real accidents and simulated trapped victims in order to calibrate and refine the proposed methodology and tool. To validate this new approach, a tool called App_Rescue has been developed. This tool is based on the use of a computer system that allows an efficient access to the technical information of the vehicle and sanitary information of the common passengers. The time spent during rescue using the standard protocol and the proposed method was compared. This rescue assistance system allows us to make vital information accessible in posttrauma care services, improving the effectiveness of interventions by the emergency services, reducing the rescue time and therefore minimizing the consequences involved and the number of victims. This could often mean saving lives. In the different simulated rescue operations, the rescue time has been reduced an average of 14%.

From the desktop to the grid: scalable bioinformatics via workflow conversion.

PubMed

de la Garza, Luis; Veit, Johannes; Szolek, Andras; Röttig, Marc; Aiche, Stephan; Gesing, Sandra; Reinert, Knut; Kohlbacher, Oliver

2016-03-12

Reproducibility is one of the tenets of the scientific method. Scientific experiments often comprise complex data flows, selection of adequate parameters, and analysis and visualization of intermediate and end results. Breaking down the complexity of such experiments into the joint collaboration of small, repeatable, well defined tasks, each with well defined inputs, parameters, and outputs, offers the immediate benefit of identifying bottlenecks, pinpoint sections which could benefit from parallelization, among others. Workflows rest upon the notion of splitting complex work into the joint effort of several manageable tasks. There are several engines that give users the ability to design and execute workflows. Each engine was created to address certain problems of a specific community, therefore each one has its advantages and shortcomings. Furthermore, not all features of all workflow engines are royalty-free -an aspect that could potentially drive away members of the scientific community. We have developed a set of tools that enables the scientific community to benefit from workflow interoperability. We developed a platform-free structured representation of parameters, inputs, outputs of command-line tools in so-called Common Tool Descriptor documents. We have also overcome the shortcomings and combined the features of two royalty-free workflow engines with a substantial user community: the Konstanz Information Miner, an engine which we see as a formidable workflow editor, and the Grid and User Support Environment, a web-based framework able to interact with several high-performance computing resources. We have thus created a free and highly accessible way to design workflows on a desktop computer and execute them on high-performance computing resources. Our work will not only reduce time spent on designing scientific workflows, but also make executing workflows on remote high-performance computing resources more accessible to technically inexperienced users. We strongly believe that our efforts not only decrease the turnaround time to obtain scientific results but also have a positive impact on reproducibility, thus elevating the quality of obtained scientific results.

PAPST, a User Friendly and Powerful Java Platform for ChIP-Seq Peak Co-Localization Analysis and Beyond.

PubMed

Bible, Paul W; Kanno, Yuka; Wei, Lai; Brooks, Stephen R; O'Shea, John J; Morasso, Maria I; Loganantharaj, Rasiah; Sun, Hong-Wei

2015-01-01

Comparative co-localization analysis of transcription factors (TFs) and epigenetic marks (EMs) in specific biological contexts is one of the most critical areas of ChIP-Seq data analysis beyond peak calling. Yet there is a significant lack of user-friendly and powerful tools geared towards co-localization analysis based exploratory research. Most tools currently used for co-localization analysis are command line only and require extensive installation procedures and Linux expertise. Online tools partially address the usability issues of command line tools, but slow response times and few customization features make them unsuitable for rapid data-driven interactive exploratory research. We have developed PAPST: Peak Assignment and Profile Search Tool, a user-friendly yet powerful platform with a unique design, which integrates both gene-centric and peak-centric co-localization analysis into a single package. Most of PAPST's functions can be completed in less than five seconds, allowing quick cycles of data-driven hypothesis generation and testing. With PAPST, a researcher with or without computational expertise can perform sophisticated co-localization pattern analysis of multiple TFs and EMs, either against all known genes or a set of genomic regions obtained from public repositories or prior analysis. PAPST is a versatile, efficient, and customizable tool for genome-wide data-driven exploratory research. Creatively used, PAPST can be quickly applied to any genomic data analysis that involves a comparison of two or more sets of genomic coordinate intervals, making it a powerful tool for a wide range of exploratory genomic research. We first present PAPST's general purpose features then apply it to several public ChIP-Seq data sets to demonstrate its rapid execution and potential for cutting-edge research with a case study in enhancer analysis. To our knowledge, PAPST is the first software of its kind to provide efficient and sophisticated post peak-calling ChIP-Seq data analysis as an easy-to-use interactive application. PAPST is available at https://github.com/paulbible/papst and is a public domain work.

Predicting Minimum Control Speed on the Ground (VMCG) and Minimum Control Airspeed (VMCA) of Engine Inoperative Flight Using Aerodynamic Database and Propulsion Database Generators

NASA Astrophysics Data System (ADS)

Hadder, Eric Michael

There are many computer aided engineering tools and software used by aerospace engineers to design and predict specific parameters of an airplane. These tools help a design engineer predict and calculate such parameters such as lift, drag, pitching moment, takeoff range, maximum takeoff weight, maximum flight range and much more. However, there are very limited ways to predict and calculate the minimum control speeds of an airplane in engine inoperative flight. There are simple solutions, as well as complicated solutions, yet there is neither standard technique nor consistency throughout the aerospace industry. To further complicate this subject, airplane designers have the option of using an Automatic Thrust Control System (ATCS), which directly alters the minimum control speeds of an airplane. This work addresses this issue with a tool used to predict and calculate the Minimum Control Speed on the Ground (VMCG) as well as the Minimum Control Airspeed (VMCA) of any existing or design-stage airplane. With simple line art of an airplane, a program called VORLAX is used to generate an aerodynamic database used to calculate the stability derivatives of an airplane. Using another program called Numerical Propulsion System Simulation (NPSS), a propulsion database is generated to use with the aerodynamic database to calculate both VMCG and VMCA. This tool was tested using two airplanes, the Airbus A320 and the Lockheed Martin C130J-30 Super Hercules. The A320 does not use an Automatic Thrust Control System (ATCS), whereas the C130J-30 does use an ATCS. The tool was able to properly calculate and match known values of VMCG and VMCA for both of the airplanes. The fact that this tool was able to calculate the known values of VMCG and VMCA for both airplanes means that this tool would be able to predict the VMCG and VMCA of an airplane in the preliminary stages of design. This would allow design engineers the ability to use an Automatic Thrust Control System (ATCS) as part of the design of an airplane and still have the ability to predict the VMCG and VMCA of the airplane.

PAPST, a User Friendly and Powerful Java Platform for ChIP-Seq Peak Co-Localization Analysis and Beyond

PubMed Central

Bible, Paul W.; Kanno, Yuka; Wei, Lai; Brooks, Stephen R.; O’Shea, John J.; Morasso, Maria I.; Loganantharaj, Rasiah; Sun, Hong-Wei

2015-01-01

Comparative co-localization analysis of transcription factors (TFs) and epigenetic marks (EMs) in specific biological contexts is one of the most critical areas of ChIP-Seq data analysis beyond peak calling. Yet there is a significant lack of user-friendly and powerful tools geared towards co-localization analysis based exploratory research. Most tools currently used for co-localization analysis are command line only and require extensive installation procedures and Linux expertise. Online tools partially address the usability issues of command line tools, but slow response times and few customization features make them unsuitable for rapid data-driven interactive exploratory research. We have developed PAPST: Peak Assignment and Profile Search Tool, a user-friendly yet powerful platform with a unique design, which integrates both gene-centric and peak-centric co-localization analysis into a single package. Most of PAPST’s functions can be completed in less than five seconds, allowing quick cycles of data-driven hypothesis generation and testing. With PAPST, a researcher with or without computational expertise can perform sophisticated co-localization pattern analysis of multiple TFs and EMs, either against all known genes or a set of genomic regions obtained from public repositories or prior analysis. PAPST is a versatile, efficient, and customizable tool for genome-wide data-driven exploratory research. Creatively used, PAPST can be quickly applied to any genomic data analysis that involves a comparison of two or more sets of genomic coordinate intervals, making it a powerful tool for a wide range of exploratory genomic research. We first present PAPST’s general purpose features then apply it to several public ChIP-Seq data sets to demonstrate its rapid execution and potential for cutting-edge research with a case study in enhancer analysis. To our knowledge, PAPST is the first software of its kind to provide efficient and sophisticated post peak-calling ChIP-Seq data analysis as an easy-to-use interactive application. PAPST is available at https://github.com/paulbible/papst and is a public domain work. PMID:25970601

Advanced Simulation and Computing: A Summary Report to the Director's Review

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

McCoy, M G; Peck, T

2003-06-01

It has now been three years since the Advanced Simulation and Computing Program (ASCI), as managed by Defense and Nuclear Technologies (DNT) Directorate, has been reviewed by this Director's Review Committee (DRC). Since that time, there has been considerable progress for all components of the ASCI Program, and these developments will be highlighted in this document and in the presentations planned for June 9 and 10, 2003. There have also been some name changes. Today, the Program is called ''Advanced Simulation and Computing,'' Although it retains the familiar acronym ASCI, the initiative nature of the effort has given way tomore » sustained services as an integral part of the Stockpile Stewardship Program (SSP). All computing efforts at LLNL and the other two Defense Program (DP) laboratories are funded and managed under ASCI. This includes the so-called legacy codes, which remain essential tools in stockpile stewardship. The contract between the Department of Energy (DOE) and the University of California (UC) specifies an independent appraisal of Directorate technical work and programmatic management. Such represents the work of this DNT Review Committee. Beginning this year, the Laboratory is implementing a new review system. This process was negotiated between UC, the National Nuclear Security Administration (NNSA), and the Laboratory Directors. Central to this approach are eight performance objectives that focus on key programmatic and administrative goals. Associated with each of these objectives are a number of performance measures to more clearly characterize the attainment of the objectives. Each performance measure has a lead directorate and one or more contributing directorates. Each measure has an evaluation plan and has identified expected documentation to be included in the ''Assessment File''.« less

Chemical-Help Application for Classification and Identification of Stormwater Constituents

USGS Publications Warehouse

Granato, Gregory E.; Driskell, Timothy R.; Nunes, Catherine

2000-01-01

A computer application called Chemical Help was developed to facilitate review of reports for the National Highway Runoff Water-Quality Data and Methodology Synthesis (NDAMS). The application provides a tool to quickly find a proper classification for any constituent in the NDAMS review sheets. Chemical Help contents include the name of each water-quality property, constituent, or parameter, the section number within the NDAMS review sheet, the organizational levels within a classification hierarchy, the database number, and where appropriate, the chemical formula, the Chemical Abstract Service number, and a list of synonyms (for the organic chemicals). Therefore, Chemical Help provides information necessary to research available reference data for the water-quality properties and constituents of potential interest in stormwater studies. Chemical Help is implemented in the Microsoft help-system interface. (Computer files for the use and documentation of Chemical Help are included on an accompanying diskette.)

Automatic detection and severity measurement of eczema using image processing.

PubMed

Alam, Md Nafiul; Munia, Tamanna Tabassum Khan; Tavakolian, Kouhyar; Vasefi, Fartash; MacKinnon, Nick; Fazel-Rezai, Reza

2016-08-01

Chronic skin diseases like eczema may lead to severe health and financial consequences for patients if not detected and controlled early. Early measurement of disease severity, combined with a recommendation for skin protection and use of appropriate medication can prevent the disease from worsening. Current diagnosis can be costly and time-consuming. In this paper, an automatic eczema detection and severity measurement model are presented using modern image processing and computer algorithm. The system can successfully detect regions of eczema and classify the identified region as mild or severe based on image color and texture feature. Then the model automatically measures skin parameters used in the most common assessment tool called "Eczema Area and Severity Index (EASI)," by computing eczema affected area score, eczema intensity score, and body region score of eczema allowing both patients and physicians to accurately assess the affected skin.

Distributed and parallel Ada and the Ada 9X recommendations

NASA Technical Reports Server (NTRS)

Volz, Richard A.; Goldsack, Stephen J.; Theriault, R.; Waldrop, Raymond S.; Holzbacher-Valero, A. A.

1992-01-01

Recently, the DoD has sponsored work towards a new version of Ada, intended to support the construction of distributed systems. The revised version, often called Ada 9X, will become the new standard sometimes in the 1990s. It is intended that Ada 9X should provide language features giving limited support for distributed system construction. The requirements for such features are given. Many of the most advanced computer applications involve embedded systems that are comprised of parallel processors or networks of distributed computers. If Ada is to become the widely adopted language envisioned by many, it is essential that suitable compilers and tools be available to facilitate the creation of distributed and parallel Ada programs for these applications. The major languages issues impacting distributed and parallel programming are reviewed, and some principles upon which distributed/parallel language systems should be built are suggested. Based upon these, alternative language concepts for distributed/parallel programming are analyzed.

In Silico Identification of Novel APRIL Peptide Antagonists and Binding Insights by Molecular Modeling and Immunosorbent Assays.

PubMed

Silva, Joao H M da; Calmon-Hamaty, Flavia; Savino, Wilson; Hahne, Michael; Caffarena, Ernesto R

2015-01-01

The "A proliferation inducing ligand" protein (APRIL) is a cytokine over-expressed in many transformed and tumoral cells acting onto two distinct receptors of the Tumoral Necrosis Factor B cell maturation antigen (BCMA) and the transmembrane activator and calcium modulator and cyclophilin ligand interactor (TACI). We herein describe, through a detailed computational approach, the molecular interactions between TACI and its ligands APRIL and another structurally similar protein called B-cell activating factor (BAFF) by means of molecular dynamics. Dynamical analysis suggests R84 and D85 residues from TACI as possible mutation candidates, yielding increased affinity between TACI and APRIL. The association of computational simulations, site directed mutagenesis and peptide design could be a powerful tool, driving to better in vitro experiments. Our results contribute to the elucidation of APRIL signaling and help clarify the effects of blocking interaction between APRIL and its receptors through the use of particular peptides.

Gyroscope-driven mouse pointer with an EMOTIV® EEG headset and data analysis based on Empirical Mode Decomposition.

PubMed

Rosas-Cholula, Gerardo; Ramirez-Cortes, Juan Manuel; Alarcon-Aquino, Vicente; Gomez-Gil, Pilar; Rangel-Magdaleno, Jose de Jesus; Reyes-Garcia, Carlos

2013-08-14

This paper presents a project on the development of a cursor control emulating the typical operations of a computer-mouse, using gyroscope and eye-blinking electromyographic signals which are obtained through a commercial 16-electrode wireless headset, recently released by Emotiv. The cursor position is controlled using information from a gyroscope included in the headset. The clicks are generated through the user's blinking with an adequate detection procedure based on the spectral-like technique called Empirical Mode Decomposition (EMD). EMD is proposed as a simple and quick computational tool, yet effective, aimed to artifact reduction from head movements as well as a method to detect blinking signals for mouse control. Kalman filter is used as state estimator for mouse position control and jitter removal. The detection rate obtained in average was 94.9%. Experimental setup and some obtained results are presented.

Gyroscope-Driven Mouse Pointer with an EMOTIV® EEG Headset and Data Analysis Based on Empirical Mode Decomposition

PubMed Central

Rosas-Cholula, Gerardo; Ramirez-Cortes, Juan Manuel; Alarcon-Aquino, Vicente; Gomez-Gil, Pilar; Rangel-Magdaleno, Jose de Jesus; Reyes-Garcia, Carlos

2013-01-01

This paper presents a project on the development of a cursor control emulating the typical operations of a computer-mouse, using gyroscope and eye-blinking electromyographic signals which are obtained through a commercial 16-electrode wireless headset, recently released by Emotiv. The cursor position is controlled using information from a gyroscope included in the headset. The clicks are generated through the user's blinking with an adequate detection procedure based on the spectral-like technique called Empirical Mode Decomposition (EMD). EMD is proposed as a simple and quick computational tool, yet effective, aimed to artifact reduction from head movements as well as a method to detect blinking signals for mouse control. Kalman filter is used as state estimator for mouse position control and jitter removal. The detection rate obtained in average was 94.9%. Experimental setup and some obtained results are presented. PMID:23948873

NASA geometry data exchange specification for computational fluid dynamics (NASA IGES)

NASA Technical Reports Server (NTRS)

Blake, Matthew W.; Kerr, Patricia A.; Thorp, Scott A.; Jou, Jin J.

1994-01-01

This document specifies a subset of an existing product data exchange specification that is widely used in industry and government. The existing document is called the Initial Graphics Exchange Specification. This document, a subset of IGES, is intended for engineers analyzing product performance using tools such as computational fluid dynamics (CFD) software. This document specifies how to define mathematically and exchange the geometric model of an object. The geometry is represented utilizing nonuniform rational B-splines (NURBS) curves and surfaces. Only surface models are represented; no solid model representation is included. This specification does not include most of the other types of product information available in IGES (e.g., no material properties or surface finish properties) and does not provide all the specific file format details of IGES. The data exchange protocol specified in this document is fully conforming to the American National Standard (ANSI) IGES 5.2.

Software for biomedical engineering signal processing laboratory experiments.

PubMed

Tompkins, Willis J; Wilson, J

2009-01-01

In the early 1990's we developed a special computer program called UW DigiScope to provide a mechanism for anyone interested in biomedical digital signal processing to study the field without requiring any other instrument except a personal computer. There are many digital filtering and pattern recognition algorithms used in processing biomedical signals. In general, students have very limited opportunity to have hands-on access to the mechanisms of digital signal processing. In a typical course, the filters are designed non-interactively, which does not provide the student with significant understanding of the design constraints of such filters nor their actual performance characteristics. UW DigiScope 3.0 is the first major update since version 2.0 was released in 1994. This paper provides details on how the new version based on MATLAB! works with signals, including the filter design tool that is the programming interface between UW DigiScope and processing algorithms.

CAD Services: an Industry Standard Interface for Mechanical CAD Interoperability

NASA Technical Reports Server (NTRS)

Claus, Russell; Weitzer, Ilan

2002-01-01

Most organizations seek to design and develop new products in increasingly shorter time periods. At the same time, increased performance demands require a team-based multidisciplinary design process that may span several organizations. One approach to meet these demands is to use 'Geometry Centric' design. In this approach, design engineers team their efforts through one united representation of the design that is usually captured in a CAD system. Standards-based interfaces are critical to provide uniform, simple, distributed services that enable the 'Geometry Centric' design approach. This paper describes an industry-wide effort, under the Object Management Group's (OMG) Manufacturing Domain Task Force, to define interfaces that enable the interoperability of CAD, Computer Aided Manufacturing (CAM), and Computer Aided Engineering (CAE) tools. This critical link to enable 'Geometry Centric' design is called: Cad Services V1.0. This paper discusses the features of this standard and proposed application.

Retrieving the aerosol complex refractive index using PyMieScatt: A Mie computational package with visualization capabilities

NASA Astrophysics Data System (ADS)

Sumlin, Benjamin J.; Heinson, William R.; Chakrabarty, Rajan K.

2018-01-01

The complex refractive index m = n + ik of a particle is an intrinsic property which cannot be directly measured; it must be inferred from its extrinsic properties such as the scattering and absorption cross-sections. Bohren and Huffman called this approach "describing the dragon from its tracks", since the inversion of Lorenz-Mie theory equations is intractable without the use of computers. This article describes PyMieScatt, an open-source module for Python that contains functionality for solving the inverse problem for complex m using extensive optical and physical properties as input, and calculating regions where valid solutions may exist within the error bounds of laboratory measurements. Additionally, the module has comprehensive capabilities for studying homogeneous and coated single spheres, as well as ensembles of homogeneous spheres with user-defined size distributions, making it a complete tool for studying the optical behavior of spherical particles.

The semantic web and computer vision: old AI meets new AI

NASA Astrophysics Data System (ADS)

Mundy, J. L.; Dong, Y.; Gilliam, A.; Wagner, R.

2018-04-01

There has been vast process in linking semantic information across the billions of web pages through the use of ontologies encoded in the Web Ontology Language (OWL) based on the Resource Description Framework (RDF). A prime example is the Wikipedia where the knowledge contained in its more than four million pages is encoded in an ontological database called DBPedia http://wiki.dbpedia.org/. Web-based query tools can retrieve semantic information from DBPedia encoded in interlinked ontologies that can be accessed using natural language. This paper will show how this vast context can be used to automate the process of querying images and other geospatial data in support of report changes in structures and activities. Computer vision algorithms are selected and provided with context based on natural language requests for monitoring and analysis. The resulting reports provide semantically linked observations from images and 3D surface models.

Neural-network quantum state tomography

NASA Astrophysics Data System (ADS)

Torlai, Giacomo; Mazzola, Guglielmo; Carrasquilla, Juan; Troyer, Matthias; Melko, Roger; Carleo, Giuseppe

2018-05-01

The experimental realization of increasingly complex synthetic quantum systems calls for the development of general theoretical methods to validate and fully exploit quantum resources. Quantum state tomography (QST) aims to reconstruct the full quantum state from simple measurements, and therefore provides a key tool to obtain reliable analytics1-3. However, exact brute-force approaches to QST place a high demand on computational resources, making them unfeasible for anything except small systems4,5. Here we show how machine learning techniques can be used to perform QST of highly entangled states with more than a hundred qubits, to a high degree of accuracy. We demonstrate that machine learning allows one to reconstruct traditionally challenging many-body quantities—such as the entanglement entropy—from simple, experimentally accessible measurements. This approach can benefit existing and future generations of devices ranging from quantum computers to ultracold-atom quantum simulators6-8.

Web-based training: a new paradigm in computer-assisted instruction in medicine.

PubMed

Haag, M; Maylein, L; Leven, F J; Tönshoff, B; Haux, R

1999-01-01

Computer-assisted instruction (CAI) programs based on internet technologies, especially on the world wide web (WWW), provide new opportunities in medical education. The aim of this paper is to examine different aspects of such programs, which we call 'web-based training (WBT) programs', and to differentiate them from conventional CAI programs. First, we will distinguish five different interaction types: presentation; browsing; tutorial dialogue; drill and practice; and simulation. In contrast to conventional CAI, there are four architectural types of WBT programs: client-based; remote data and knowledge; distributed teaching; and server-based. We will discuss the implications of the different architectures for developing WBT software. WBT programs have to meet other requirements than conventional CAI programs. The most important tools and programming languages for developing WBT programs will be listed and assigned to the architecture types. For the future, we expect a trend from conventional CAI towards WBT programs.

The Overgrid Interface for Computational Simulations on Overset Grids

NASA Technical Reports Server (NTRS)

Chan, William M.; Kwak, Dochan (Technical Monitor)

2002-01-01

Computational simulations using overset grids typically involve multiple steps and a variety of software modules. A graphical interface called OVERGRID has been specially designed for such purposes. Data required and created by the different steps include geometry, grids, domain connectivity information and flow solver input parameters. The interface provides a unified environment for the visualization, processing, generation and diagnosis of such data. General modules are available for the manipulation of structured grids and unstructured surface triangulations. Modules more specific for the overset approach include surface curve generators, hyperbolic and algebraic surface grid generators, a hyperbolic volume grid generator, Cartesian box grid generators, and domain connectivity: pre-processing tools. An interface provides automatic selection and viewing of flow solver boundary conditions, and various other flow solver inputs. For problems involving multiple components in relative motion, a module is available to build the component/grid relationships and to prescribe and animate the dynamics of the different components.

Evolutionary fuzzy modeling human diagnostic decisions.

PubMed

Peña-Reyes, Carlos Andrés

2004-05-01

Fuzzy CoCo is a methodology, combining fuzzy logic and evolutionary computation, for constructing systems able to accurately predict the outcome of a human decision-making process, while providing an understandable explanation of the underlying reasoning. Fuzzy logic provides a formal framework for constructing systems exhibiting both good numeric performance (accuracy) and linguistic representation (interpretability). However, fuzzy modeling--meaning the construction of fuzzy systems--is an arduous task, demanding the identification of many parameters. To solve it, we use evolutionary computation techniques (specifically cooperative coevolution), which are widely used to search for adequate solutions in complex spaces. We have successfully applied the algorithm to model the decision processes involved in two breast cancer diagnostic problems, the WBCD problem and the Catalonia mammography interpretation problem, obtaining systems both of high performance and high interpretability. For the Catalonia problem, an evolved system was embedded within a Web-based tool-called COBRA-for aiding radiologists in mammography interpretation.

Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.

PubMed

Kisand, Veljo; Lettieri, Teresa

2013-04-01

De novo genome sequencing of previously uncharacterized microorganisms has the potential to open up new frontiers in microbial genomics by providing insight into both functional capabilities and biodiversity. Until recently, Roche 454 pyrosequencing was the NGS method of choice for de novo assembly because it generates hundreds of thousands of long reads (<450 bps), which are presumed to aid in the analysis of uncharacterized genomes. The array of tools for processing NGS data are increasingly free and open source and are often adopted for both their high quality and role in promoting academic freedom. The error rate of pyrosequencing the Alcanivorax borkumensis genome was such that thousands of insertions and deletions were artificially introduced into the finished genome. Despite a high coverage (~30 fold), it did not allow the reference genome to be fully mapped. Reads from regions with errors had low quality, low coverage, or were missing. The main defect of the reference mapping was the introduction of artificial indels into contigs through lower than 100% consensus and distracting gene calling due to artificial stop codons. No assembler was able to perform de novo assembly comparable to reference mapping. Automated annotation tools performed similarly on reference mapped and de novo draft genomes, and annotated most CDSs in the de novo assembled draft genomes. Free and open source software (FOSS) tools for assembly and annotation of NGS data are being developed rapidly to provide accurate results with less computational effort. Usability is not high priority and these tools currently do not allow the data to be processed without manual intervention. Despite this, genome assemblers now readily assemble medium short reads into long contigs (>97-98% genome coverage). A notable gap in pyrosequencing technology is the quality of base pair calling and conflicting base pairs between single reads at the same nucleotide position. Regardless, using draft whole genomes that are not finished and remain fragmented into tens of contigs allows one to characterize unknown bacteria with modest effort.

Halvade-RNA: Parallel variant calling from transcriptomic data using MapReduce.

PubMed

Decap, Dries; Reumers, Joke; Herzeel, Charlotte; Costanza, Pascal; Fostier, Jan

2017-01-01

Given the current cost-effectiveness of next-generation sequencing, the amount of DNA-seq and RNA-seq data generated is ever increasing. One of the primary objectives of NGS experiments is calling genetic variants. While highly accurate, most variant calling pipelines are not optimized to run efficiently on large data sets. However, as variant calling in genomic data has become common practice, several methods have been proposed to reduce runtime for DNA-seq analysis through the use of parallel computing. Determining the effectively expressed variants from transcriptomics (RNA-seq) data has only recently become possible, and as such does not yet benefit from efficiently parallelized workflows. We introduce Halvade-RNA, a parallel, multi-node RNA-seq variant calling pipeline based on the GATK Best Practices recommendations. Halvade-RNA makes use of the MapReduce programming model to create and manage parallel data streams on which multiple instances of existing tools such as STAR and GATK operate concurrently. Whereas the single-threaded processing of a typical RNA-seq sample requires ∼28h, Halvade-RNA reduces this runtime to ∼2h using a small cluster with two 20-core machines. Even on a single, multi-core workstation, Halvade-RNA can significantly reduce runtime compared to using multi-threading, thus providing for a more cost-effective processing of RNA-seq data. Halvade-RNA is written in Java and uses the Hadoop MapReduce 2.0 API. It supports a wide range of distributions of Hadoop, including Cloudera and Amazon EMR.

Getting the Best out of Excel

ERIC Educational Resources Information Center

Heys, Chris

2008-01-01

Excel, Microsoft's spreadsheet program, offers several tools which have proven useful in solving some optimization problems that arise in operations research. We will look at two such tools, the Excel modules called Solver and Goal Seek--this after deriving an equation, called the "cash accumulation equation", to be used in conjunction with them.

Systematic Propulsion Optimization Tools (SPOT)

NASA Technical Reports Server (NTRS)

Bower, Mark; Celestian, John

1992-01-01

This paper describes a computer program written by senior-level Mechanical Engineering students at the University of Alabama in Huntsville which is capable of optimizing user-defined delivery systems for carrying payloads into orbit. The custom propulsion system is designed by the user through the input of configuration, payload, and orbital parameters. The primary advantages of the software, called Systematic Propulsion Optimization Tools (SPOT), are a user-friendly interface and a modular FORTRAN 77 code designed for ease of modification. The optimization of variables in an orbital delivery system is of critical concern in the propulsion environment. The mass of the overall system must be minimized within the maximum stress, force, and pressure constraints. SPOT utilizes the Design Optimization Tools (DOT) program for the optimization techniques. The SPOT program is divided into a main program and five modules: aerodynamic losses, orbital parameters, liquid engines, solid engines, and nozzles. The program is designed to be upgraded easily and expanded to meet specific user needs. A user's manual and a programmer's manual are currently being developed to facilitate implementation and modification.

Transputer parallel processing at NASA Lewis Research Center

NASA Technical Reports Server (NTRS)

Ellis, Graham K.

1989-01-01

The transputer parallel processing lab at NASA Lewis Research Center (LeRC) consists of 69 processors (transputers) that can be connected into various networks for use in general purpose concurrent processing applications. The main goal of the lab is to develop concurrent scientific and engineering application programs that will take advantage of the computational speed increases available on a parallel processor over the traditional sequential processor. Current research involves the development of basic programming tools. These tools will help standardize program interfaces to specific hardware by providing a set of common libraries for applications programmers. The thrust of the current effort is in developing a set of tools for graphics rendering/animation. The applications programmer currently has two options for on-screen plotting. One option can be used for static graphics displays and the other can be used for animated motion. The option for static display involves the use of 2-D graphics primitives that can be called from within an application program. These routines perform the standard 2-D geometric graphics operations in real-coordinate space as well as allowing multiple windows on a single screen.

Climate Model Diagnostic Analyzer Web Service System

NASA Astrophysics Data System (ADS)

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

2013-12-01

The latest Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report stressed the need for the comprehensive and innovative evaluation of climate models with newly available global observations. The traditional approach to climate model evaluation, which compares a single parameter at a time, identifies symptomatic model biases and errors but fails to diagnose the model problems. The model diagnosis process requires physics-based multi-variable comparisons that typically involve large-volume and heterogeneous datasets, making them both computationally- and data-intensive. To address these challenges, we are developing a parallel, distributed web-service system that enables the physics-based multi-variable model performance evaluations and diagnoses through the comprehensive and synergistic use of multiple observational data, reanalysis data, and model outputs. We have developed a methodology to transform an existing science application code into a web service using a Python wrapper interface and Python web service frameworks (i.e., Flask, Gunicorn, and Tornado). The web-service system, called Climate Model Diagnostic Analyzer (CMDA), currently supports (1) all the datasets from Obs4MIPs and a few ocean datasets from NOAA and Argo, which can serve as observation-based reference data for model evaluation and (2) many of CMIP5 model outputs covering a broad range of atmosphere, ocean, and land variables from the CMIP5 specific historical runs and AMIP runs. Analysis capabilities currently supported by CMDA are (1) the calculation of annual and seasonal means of physical variables, (2) the calculation of time evolution of the means in any specified geographical region, (3) the calculation of correlation between two variables, and (4) the calculation of difference between two variables. A web user interface is chosen for CMDA because it not only lowers the learning curve and removes the adoption barrier of the tool but also enables instantaneous use, avoiding the hassle of local software installation and environment incompatibility. CMDA is planned to be used as an educational tool for the summer school organized by JPL's Center for Climate Science in 2014. The requirements of the educational tool are defined with the interaction with the school organizers, and CMDA is customized to meet the requirements accordingly. The tool needs to be production quality for 30+ simultaneous users. The summer school will thus serve as a valuable testbed for the tool development, preparing CMDA to serve the Earth-science modeling and model-analysis community at the end of the project. This work was funded by the NASA Earth Science Program called Computational Modeling Algorithms and Cyberinfrastructure (CMAC).

Performance Analysis of and Tool Support for Transactional Memory on BG/Q

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

Schindewolf, M

2011-12-08

Martin Schindewolf worked during his internship at the Lawrence Livermore National Laboratory (LLNL) under the guidance of Martin Schulz at the Computer Science Group of the Center for Applied Scientific Computing. We studied the performance of the TM subsystem of BG/Q as well as researched the possibilities for tool support for TM. To study the performance, we run CLOMP-TM. CLOMP-TM is a benchmark designed for the purpose to quantify the overhead of OpenMP and compare different synchronization primitives. To advance CLOMP-TM, we added Message Passing Interface (MPI) routines for a hybrid parallelization. This enables to run multiple MPI tasks, eachmore » running OpenMP, on one node. With these enhancements, a beneficial MPI task to OpenMP thread ratio is determined. Further, the synchronization primitives are ranked as a function of the application characteristics. To demonstrate the usefulness of these results, we investigate a real Monte Carlo simulation called Monte Carlo Benchmark (MCB). Applying the lessons learned yields the best task to thread ratio. Further, we were able to tune the synchronization by transactifying the MCB. Further, we develop tools that capture the performance of the TM run time system and present it to the application's developer. The performance of the TM run time system relies on the built-in statistics. These tools use the Blue Gene Performance Monitoring (BGPM) interface to correlate the statistics from the TM run time system with performance counter values. This combination provides detailed insights in the run time behavior of the application and enables to track down the cause of degraded performance. Further, one tool has been implemented that separates the performance counters in three categories: Successful Speculation, Unsuccessful Speculation and No Speculation. All of the tools are crafted around IBM's xlc compiler for C and C++ and have been run and tested on a Q32 early access system.« less

Digital Stratigraphy: Contextual Analysis of File System Traces in Forensic Science.

PubMed

Casey, Eoghan

2017-12-28

This work introduces novel methods for conducting forensic analysis of file allocation traces, collectively called digital stratigraphy. These in-depth forensic analysis methods can provide insight into the origin, composition, distribution, and time frame of strata within storage media. Using case examples and empirical studies, this paper illuminates the successes, challenges, and limitations of digital stratigraphy. This study also shows how understanding file allocation methods can provide insight into concealment activities and how real-world computer usage can complicate digital stratigraphy. Furthermore, this work explains how forensic analysts have misinterpreted traces of normal file system behavior as indications of concealment activities. This work raises awareness of the value of taking the overall context into account when analyzing file system traces. This work calls for further research in this area and for forensic tools to provide necessary information for such contextual analysis, such as highlighting mass deletion, mass copying, and potential backdating. © 2017 American Academy of Forensic Sciences.

Incorporating Manual and Autonomous Code Generation

NASA Technical Reports Server (NTRS)

McComas, David

1998-01-01

Code can be generated manually or using code-generated software tools, but how do you interpret the two? This article looks at a design methodology that combines object-oriented design with autonomic code generation for attitude control flight software. Recent improvements in space flight computers are allowing software engineers to spend more time engineering the applications software. The application developed was the attitude control flight software for an astronomical satellite called the Microwave Anisotropy Probe (MAP). The MAP flight system is being designed, developed, and integrated at NASA's Goddard Space Flight Center. The MAP controls engineers are using Integrated Systems Inc.'s MATRIXx for their controls analysis. In addition to providing a graphical analysis for an environment, MATRIXx includes an autonomic code generation facility called AutoCode. This article examines the forces that shaped the final design and describes three highlights of the design process: (1) Defining the manual to autonomic code interface; (2) Applying object-oriented design to the manual flight code; (3) Implementing the object-oriented design in C.

HELIOGate, a Portal for the Heliophysics Community

NASA Astrophysics Data System (ADS)

Pierantoni; Gabriele; Carley, Eoin

2014-10-01

Heliophysics is the branch of physics that investigates the interactions between the Sun and the other bodies of the solar system. Heliophysicists rely on data collected from numerous sources scattered across the Solar System. The data collected from these sources is processed to extract metadata and the metadata extracted in this fashion is then used to build indexes of features and events called catalogues. Heliophysicists also develop conceptual and mathematical models of the phenomena and the environment of the Solar System. More specifically, they investigate the physical characteristics of the phenomena and they simulate how they propagate throughout the Solar System with mathematical and physical abstractions called propagation models. HELIOGate aims at addressing the need to combine and orchestrate existing web services in a flexible and easily configurable fashion to tackle different scientific questions. HELIOGate also offers a tool capable of connecting to size! able computation and storage infrastructures to execute data processing codes that are needed to calibrate raw data and to extract metadata.

The Virtual Mission Operations Center

NASA Technical Reports Server (NTRS)

Moore, Mike; Fox, Jeffrey

1994-01-01

Spacecraft management is becoming more human intensive as spacecraft become more complex and as operations costs are growing accordingly. Several automation approaches have been proposed to lower these costs. However, most of these approaches are not flexible enough in the operations processes and levels of automation that they support. This paper presents a concept called the Virtual Mission Operations Center (VMOC) that provides highly flexible support for dynamic spacecraft management processes and automation. In a VMOC, operations personnel can be shared among missions, the operations team can change personnel and their locations, and automation can be added and removed as appropriate. The VMOC employs a form of on-demand supervisory control called management by exception to free operators from having to actively monitor their system. The VMOC extends management by exception, however, so that distributed, dynamic teams can work together. The VMOC uses work-group computing concepts and groupware tools to provide a team infrastructure, and it employs user agents to allow operators to define and control system automation.

Data communications in a parallel active messaging interface of a parallel computer

DOEpatents

Archer, Charles J; Blocksome, Michael A; Ratterman, Joseph D; Smith, Brian E

2013-11-12

Data communications in a parallel active messaging interface (`PAMI`) of a parallel computer composed of compute nodes that execute a parallel application, each compute node including application processors that execute the parallel application and at least one management processor dedicated to gathering information regarding data communications. The PAMI is composed of data communications endpoints, each endpoint composed of a specification of data communications parameters for a thread of execution on a compute node, including specifications of a client, a context, and a task, the compute nodes and the endpoints coupled for data communications through the PAMI and through data communications resources. Embodiments function by gathering call site statistics describing data communications resulting from execution of data communications instructions and identifying in dependence upon the call cite statistics a data communications algorithm for use in executing a data communications instruction at a call site in the parallel application.

A new method for computing the gyrocenter orbit in the tokamak configuration

NASA Astrophysics Data System (ADS)

Xu, Yingfeng

2013-10-01

Gyrokinetic theory is an important tool for studying the long-time behavior of magnetized plasmas in Tokamaks. The gyrocenter trajectory determined by the gyrocenter equations of motion can be computed by using a special kind of the Lie-transform perturbation method. The corresponding Lie-transform called I-transform makes that the transformed equations of motion have the same form as the unperturbed ones. The gyrocenter trajectory in short time is divided into two parts. One is along the unperturbed orbit. The other one, which is related to perturbation, is determined by the I-transform generating vector. The numerical gyrocenter orbit code based on this new method has been developed in the tokamak configuration and benchmarked with the other orbit code in some simple cases. Furthermore, it is clearly demonstrated that this new method for computing gyrocenter orbit is equivalent to the gyrocenter Hamilton equations of motion up to the second order in timestep. The new method can be applied to the gyrokinetic simulation. The gyrocenter orbit of the unperturbed part determined by the equilibrium fields can be computed previously in the gyrokinetic simulation, and the corresponding time consumption is neglectable.

Computational photography with plenoptic camera and light field capture: tutorial.

PubMed

Lam, Edmund Y

2015-11-01

Photography is a cornerstone of imaging. Ever since cameras became consumer products more than a century ago, we have witnessed great technological progress in optics and recording mediums, with digital sensors replacing photographic films in most instances. The latest revolution is computational photography, which seeks to make image reconstruction computation an integral part of the image formation process; in this way, there can be new capabilities or better performance in the overall imaging system. A leading effort in this area is called the plenoptic camera, which aims at capturing the light field of an object; proper reconstruction algorithms can then adjust the focus after the image capture. In this tutorial paper, we first illustrate the concept of plenoptic function and light field from the perspective of geometric optics. This is followed by a discussion on early attempts and recent advances in the construction of the plenoptic camera. We will then describe the imaging model and computational algorithms that can reconstruct images at different focus points, using mathematical tools from ray optics and Fourier optics. Last, but not least, we will consider the trade-off in spatial resolution and highlight some research work to increase the spatial resolution of the resulting images.

Flexible structure control experiments using a real-time workstation for computer-aided control engineering

NASA Technical Reports Server (NTRS)

Stieber, Michael E.

1989-01-01

A Real-Time Workstation for Computer-Aided Control Engineering has been developed jointly by the Communications Research Centre (CRC) and Ruhr-Universitaet Bochum (RUB), West Germany. The system is presently used for the development and experimental verification of control techniques for large space systems with significant structural flexibility. The Real-Time Workstation essentially is an implementation of RUB's extensive Computer-Aided Control Engineering package KEDDC on an INTEL micro-computer running under the RMS real-time operating system. The portable system supports system identification, analysis, control design and simulation, as well as the immediate implementation and test of control systems. The Real-Time Workstation is currently being used by CRC to study control/structure interaction on a ground-based structure called DAISY, whose design was inspired by a reflector antenna. DAISY emulates the dynamics of a large flexible spacecraft with the following characteristics: rigid body modes, many clustered vibration modes with low frequencies and extremely low damping. The Real-Time Workstation was found to be a very powerful tool for experimental studies, supporting control design and simulation, and conducting and evaluating tests withn one integrated environment.

The JPSS Ground Project Algorithm Verification, Test and Evaluation System

NASA Astrophysics Data System (ADS)

Vicente, G. A.; Jain, P.; Chander, G.; Nguyen, V. T.; Dixon, V.

2016-12-01

The Government Resource for Algorithm Verification, Independent Test, and Evaluation (GRAVITE) is an operational system that provides services to the Suomi National Polar-orbiting Partnership (S-NPP) Mission. It is also a unique environment for Calibration/Validation (Cal/Val) and Data Quality Assessment (DQA) of the Join Polar Satellite System (JPSS) mission data products. GRAVITE provides a fast and direct access to the data and products created by the Interface Data Processing Segment (IDPS), the NASA/NOAA operational system that converts Raw Data Records (RDR's) generated by sensors on the S-NPP into calibrated geo-located Sensor Data Records (SDR's) and generates Mission Unique Products (MUPS). It also facilitates algorithm investigation, integration, checkouts and tuning, instrument and product calibration and data quality support, monitoring and data/products distribution. GRAVITE is the portal for the latest S-NPP and JPSS baselined Processing Coefficient Tables (PCT's) and Look-Up-Tables (LUT's) and hosts a number DQA offline tools that takes advantage of the proximity to the near-real time data flows. It also contains a set of automated and ad-hoc Cal/Val tools used for algorithm analysis and updates, including an instance of the IDPS called GRAVITE Algorithm Development Area (G-ADA), that has the latest installation of the IDPS algorithms running in an identical software and hardware platforms. Two other important GRAVITE component are the Investigator-led Processing System (IPS) and the Investigator Computing Facility (ICF). The IPS is a dedicated environment where authorized users run automated scripts called Product Generation Executables (PGE's) to support Cal/Val and data quality assurance offline. This data-rich and data-driven service holds its own distribution system and allows operators to retrieve science data products. The ICF is a workspace where users can share computing applications and resources and have full access to libraries and science and sensor quality analysis tools. In this presentation we will describe the GRAVITE systems and subsystems, architecture, technical specifications, capabilities and resources, distributed data and products and the latest advances to support the JPSS science algorithm implementation, validation and testing.

Biomedical discovery acceleration, with applications to craniofacial development.

PubMed

Leach, Sonia M; Tipney, Hannah; Feng, Weiguo; Baumgartner, William A; Kasliwal, Priyanka; Schuyler, Ronald P; Williams, Trevor; Spritz, Richard A; Hunter, Lawrence

2009-03-01

The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning, and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or using biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data. An implementation of this approach, called the Hanalyzer, is demonstrated on a large-scale gene expression array dataset relevant to craniofacial development. The use of the tool was critical in the creation of hypotheses regarding the roles of four genes never previously characterized as involved in craniofacial development; each of these hypotheses was validated by further experimental work.

Variation of a Lightning NOx Indicator for National Climate Assessment

NASA Technical Reports Server (NTRS)

Koshak, William J.; McCaul, Eugene W., Jr.; Peterson, Harold S.; Vant-Hull, Brian

2014-01-01

During the past couple of years, an analysis tool was developed by the NASA Marshall Space Flight Center (MSFC) for the National Climate Assessment (NCA) program. The tool monitors and examines changes in lightning characteristics over the conterminous US (CONUS) on a continual basis. In this study, we have expanded the capability of the tool so that it can compute a new climate assessment variable that is called the Lightning NOx Indicator (LNI). Nitrogen oxides (NOx = NO + NO2) are known to indirectly influence our climate, and lightning NOx is the most important source of NOx in the upper troposphere (particularly in the tropics). The LNI is derived using Lightning Imaging Sensor (LIS) data and is computed by summing up the product of flash area x flash brightness over all flashes that occur in a particular region and period. Therefore, it is suggested that the LNI is a proxy to lightning NOx production. Specifically, larger flash areas are consistent with longer channel length and/or more energetic channels, and hence more NOx production. Brighter flashes are consistent with more energetic channels, and hence more NOx production. The location of the flash within the thundercloud and the optical scattering characteristics of the thundercloud are of course complicating factors. We analyze LIS data for the years 2003-2013 and provide geographical plots of the time-evolution of the LNI in order to determine if there are any significant changes or trends between like seasons, or from year to year.

ParticleCall: A particle filter for base calling in next-generation sequencing systems

PubMed Central

2012-01-01

Background Next-generation sequencing systems are capable of rapid and cost-effective DNA sequencing, thus enabling routine sequencing tasks and taking us one step closer to personalized medicine. Accuracy and lengths of their reads, however, are yet to surpass those provided by the conventional Sanger sequencing method. This motivates the search for computationally efficient algorithms capable of reliable and accurate detection of the order of nucleotides in short DNA fragments from the acquired data. Results In this paper, we consider Illumina’s sequencing-by-synthesis platform which relies on reversible terminator chemistry and describe the acquired signal by reformulating its mathematical model as a Hidden Markov Model. Relying on this model and sequential Monte Carlo methods, we develop a parameter estimation and base calling scheme called ParticleCall. ParticleCall is tested on a data set obtained by sequencing phiX174 bacteriophage using Illumina’s Genome Analyzer II. The results show that the developed base calling scheme is significantly more computationally efficient than the best performing unsupervised method currently available, while achieving the same accuracy. Conclusions The proposed ParticleCall provides more accurate calls than the Illumina’s base calling algorithm, Bustard. At the same time, ParticleCall is significantly more computationally efficient than other recent schemes with similar performance, rendering it more feasible for high-throughput sequencing data analysis. Improvement of base calling accuracy will have immediate beneficial effects on the performance of downstream applications such as SNP and genotype calling. ParticleCall is freely available at https://sourceforge.net/projects/particlecall. PMID:22776067

Quantum Walk Schemes for Universal Quantum Computation

NASA Astrophysics Data System (ADS)

Underwood, Michael S.

Random walks are a powerful tool for the efficient implementation of algorithms in classical computation. Their quantum-mechanical analogues, called quantum walks, hold similar promise. Quantum walks provide a model of quantum computation that has recently been shown to be equivalent in power to the standard circuit model. As in the classical case, quantum walks take place on graphs and can undergo discrete or continuous evolution, though quantum evolution is unitary and therefore deterministic until a measurement is made. This thesis considers the usefulness of continuous-time quantum walks to quantum computation from the perspectives of both their fundamental power under various formulations, and their applicability in practical experiments. In one extant scheme, logical gates are effected by scattering processes. The results of an exhaustive search for single-qubit operations in this model are presented. It is shown that the number of distinct operations increases exponentially with the number of vertices in the scattering graph. A catalogue of all graphs on up to nine vertices that implement single-qubit unitaries at a specific set of momenta is included in an appendix. I develop a novel scheme for universal quantum computation called the discontinuous quantum walk, in which a continuous-time quantum walker takes discrete steps of evolution via perfect quantum state transfer through small 'widget' graphs. The discontinuous quantum-walk scheme requires an exponentially sized graph, as do prior discrete and continuous schemes. To eliminate the inefficient vertex resource requirement, a computation scheme based on multiple discontinuous walkers is presented. In this model, n interacting walkers inhabiting a graph with 2n vertices can implement an arbitrary quantum computation on an input of length n, an exponential savings over previous universal quantum walk schemes. This is the first quantum walk scheme that allows for the application of quantum error correction. The many-particle quantum walk can be viewed as a single quantum walk undergoing perfect state transfer on a larger weighted graph, obtained via equitable partitioning. I extend this formalism to non-simple graphs. Examples of the application of equitable partitioning to the analysis of quantum walks and many-particle quantum systems are discussed.

The effect of introducing computers into an introductory physics problem-solving laboratory

NASA Astrophysics Data System (ADS)

McCullough, Laura Ellen

2000-10-01

Computers are appearing in every type of classroom across the country. Yet they often appear without benefit of studying their effects. The research that is available on computer use in classrooms has found mixed results, and often ignores the theoretical and instructional contexts of the computer in the classroom. The University of Minnesota's physics department employs a cooperative-group problem solving pedagogy, based on a cognitive apprenticeship instructional model, in its calculus-based introductory physics course. This study was designed to determine possible negative effects of introducing a computerized data-acquisition and analysis tool into this pedagogy as a problem-solving tool for students to use in laboratory. To determine the effects of the computer tool, two quasi-experimental treatment groups were selected. The computer-tool group (N = 170) used a tool, designed for this study (VideoTool), to collect and analyze motion data in the laboratory. The control group (N = 170) used traditional non-computer equipment (spark tapes and Polaroid(TM) film). The curriculum was kept as similar as possible for the two groups. During the ten week academic quarter, groups were examined for effects on performance on conceptual tests and grades, attitudes towards the laboratory and the laboratory tools, and behaviors within cooperative groups. Possible interactions with gender were also examined. Few differences were found between the control and computer-tool groups. The control group received slightly higher scores on one conceptual test, but this difference was not educationally significant. The computer-tool group had slightly more positive attitudes towards using the computer tool than their counterparts had towards the traditional tools. The computer-tool group also perceived that they spoke more frequently about physics misunderstandings, while the control group felt that they discussed equipment difficulties more often. This perceptual difference interacted with gender, with the men in the control group more likely to discuss equipment difficulties than any other group. Overall, the differences between the control and quasi-experimental groups were minimal. It was concluded that carefully replacing traditional data collection and analysis tools with a computer tool had no negative effects on achievement, attitude, group behavior, and did not interact with gender.

The use of computer assisted technology to enhance student psychiatric nurses learning during a practice placement.

PubMed

Denny, Margaret; Higgins, Agnes

2003-06-01

Despite the available literature that identifies the value of integrating computer-assisted learning into the curriculum, psychiatric nurse education lags behind in this area of curriculum development. The purpose of this paper is to report on a pilot project involving the use of a computer assisted learning (CAL) interactive multimedia (IMM) package called 'Admissions,' as a self-directed learning tool with two-second year psychiatric nursing students. The students were on a practice placement in an Irish mental health service. The aim of using the multimedia resource was to augment the students' learning during their practice placement and enable them to re-examine the issue of psychosis from a multiplicity of perspectives. This paper provides a brief description of the interactive multimedia package, together with a discussion on the support offered to the students during its use. experiential taxonomy is used as a framework to guide the discussion on the learning and evaluation process used. Feedback from the students suggests that the CAL package is easy to use, informative and promoted independence and self-directed study.

Computational Enzymology and Organophosphorus Degrading Enzymes: Promising Approaches Toward Remediation Technologies of Warfare Agents and Pesticides.

PubMed

Ramalho, Teodorico C; de Castro, Alexandre A; Silva, Daniela R; Silva, Maria Cristina; Franca, Tanos C C; Bennion, Brian J; Kuca, Kamil

2016-01-01

The re-emergence of chemical weapons as a global threat in hands of terrorist groups, together with an increasing number of pesticides intoxications and environmental contaminations worldwide, has called the attention of the scientific community for the need of improvement in the technologies for detoxification of organophosphorus (OP) compounds. A compelling strategy is the use of bioremediation by enzymes that are able to hydrolyze these molecules to harmless chemical species. Several enzymes have been studied and engineered for this purpose. However, their mechanisms of action are not well understood. Theoretical investigations may help elucidate important aspects of these mechanisms and help in the development of more efficient bio-remediators. In this review, we point out the major contributions of computational methodologies applied to enzyme based detoxification of OPs. Furthermore, we highlight the use of PTE, PON, DFP, and BuChE as enzymes used in OP detoxification process and how computational tools such as molecular docking, molecular dynamics simulations and combined quantum mechanical/molecular mechanics have and will continue to contribute to this very important area of research.

Associative architecture for image processing

NASA Astrophysics Data System (ADS)

Adar, Rutie; Akerib, Avidan

1997-09-01

This article presents a new generation in parallel processing architecture for real-time image processing. The approach is implemented in a real time image processor chip, called the XiumTM-2, based on combining a fully associative array which provides the parallel engine with a serial RISC core on the same die. The architecture is fully programmable and can be programmed to implement a wide range of color image processing, computer vision and media processing functions in real time. The associative part of the chip is based on patented pending methodology of Associative Computing Ltd. (ACL), which condenses 2048 associative processors, each of 128 'intelligent' bits. Each bit can be a processing bit or a memory bit. At only 33 MHz and 0.6 micron manufacturing technology process, the chip has a computational power of 3 billion ALU operations per second and 66 billion string search operations per second. The fully programmable nature of the XiumTM-2 chip enables developers to use ACL tools to write their own proprietary algorithms combined with existing image processing and analysis functions from ACL's extended set of libraries.

A theoretical analysis of the electromagnetic environment of the AS330 super Puma helicopter external and internal coupling

NASA Technical Reports Server (NTRS)

Flourens, F.; Morel, T.; Gauthier, D.; Serafin, D.

1991-01-01

Numerical techniques such as Finite Difference Time Domain (FDTD) computer programs, which were first developed to analyze the external electromagnetic environment of an aircraft during a wave illumination, a lightning event, or any kind of current injection, are now very powerful investigative tools. The program called GORFF-VE, was extended to compute the inner electromagnetic fields that are generated by the penetration of the outer fields through large apertures made in the all metallic body. Then, the internal fields can drive the electrical response of a cable network. The coupling between the inside and the outside of the helicopter is implemented using Huygen's principle. Moreover, the spectacular increase of computer resources, as calculations speed and memory capacity, allows the modellization structures as complex as these of helicopters with accuracy. This numerical model was exploited, first, to analyze the electromagnetic environment of an in-flight helicopter for several injection configurations, and second, to design a coaxial return path to simulate the lightning aircraft interaction with a strong current injection. The E field and current mappings are the result of these calculations.

2013 R&D 100 Award: ‘Miniapps’ Bolster High Performance Computing

ScienceCinema

Belak, Jim; Richards, David

2018-06-12

Two Livermore computer scientists served on a Sandia National Laboratories-led team that developed Mantevo Suite 1.0, the first integrated suite of small software programs, also called "miniapps," to be made available to the high performance computing (HPC) community. These miniapps facilitate the development of new HPC systems and the applications that run on them. Miniapps (miniature applications) serve as stripped down surrogates for complex, full-scale applications that can require a great deal of time and effort to port to a new HPC system because they often consist of hundreds of thousands of lines of code. The miniapps are a prototype that contains some or all of the essentials of the real application but with many fewer lines of code, making the miniapp more versatile for experimentation. This allows researchers to more rapidly explore options and optimize system design, greatly improving the chances the full-scale application will perform successfully. These miniapps have become essential tools for exploring complex design spaces because they can reliably predict the performance of full applications.

Mapping proteins in the presence of paralogs using units of coevolution

PubMed Central

2013-01-01

Background We study the problem of mapping proteins between two protein families in the presence of paralogs. This problem occurs as a difficult subproblem in coevolution-based computational approaches for protein-protein interaction prediction. Results Similar to prior approaches, our method is based on the idea that coevolution implies equal rates of sequence evolution among the interacting proteins, and we provide a first attempt to quantify this notion in a formal statistical manner. We call the units that are central to this quantification scheme the units of coevolution. A unit consists of two mapped protein pairs and its score quantifies the coevolution of the pairs. This quantification allows us to provide a maximum likelihood formulation of the paralog mapping problem and to cast it into a binary quadratic programming formulation. Conclusion CUPID, our software tool based on a Lagrangian relaxation of this formulation, makes it, for the first time, possible to compute state-of-the-art quality pairings in a few minutes of runtime. In summary, we suggest a novel alternative to the earlier available approaches, which is statistically sound and computationally feasible. PMID:24564758

Machine learning for a Toolkit for Image Mining

NASA Technical Reports Server (NTRS)

Delanoy, Richard L.

1995-01-01

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

Facility Composer (Trademark) and PACES (Trademark) Integration: Development of an XML Interface Based on Industry Foundation Classes

DTIC Science & Technology

2007-11-01

Engineer- ing Research Laboratory is currently developing a set of facility ‘architec- tural’ programming tools , called Facility ComposerTM (FC). FC...requirements in the early phases of project development. As the facility program, crite- ria, and requirements are chosen, these tools populate the IFC...developing a set of facility “ar- chitectural” programming tools , called Facility Composer (FC), to support the capture and tracking of facility criteria

Institutional computing (IC) information session

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

Koch, Kenneth R; Lally, Bryan R

2011-01-19

The LANL Institutional Computing Program (IC) will host an information session about the current state of unclassified Institutional Computing at Los Alamos, exciting plans for the future, and the current call for proposals for science and engineering projects requiring computing. Program representatives will give short presentations and field questions about the call for proposals and future planned machines, and discuss technical support available to existing and future projects. Los Alamos has started making a serious institutional investment in open computing available to our science projects, and that investment is expected to increase even more.

Applying AI tools to operational space environmental analysis

NASA Technical Reports Server (NTRS)

Krajnak, Mike; Jesse, Lisa; Mucks, John

1995-01-01

The U.S. Air Force and National Oceanic Atmospheric Agency (NOAA) space environmental operations centers are facing increasingly complex challenges meeting the needs of their growing user community. These centers provide current space environmental information and short term forecasts of geomagnetic activity. Recent advances in modeling and data access have provided sophisticated tools for making accurate and timely forecasts, but have introduced new problems associated with handling and analyzing large quantities of complex data. AI (Artificial Intelligence) techniques have been considered as potential solutions to some of these problems. Fielding AI systems has proven more difficult than expected, in part because of operational constraints. Using systems which have been demonstrated successfully in the operational environment will provide a basis for a useful data fusion and analysis capability. Our approach uses a general purpose AI system already in operational use within the military intelligence community, called the Temporal Analysis System (TAS). TAS is an operational suite of tools supporting data processing, data visualization, historical analysis, situation assessment and predictive analysis. TAS includes expert system tools to analyze incoming events for indications of particular situations and predicts future activity. The expert system operates on a knowledge base of temporal patterns encoded using a knowledge representation called Temporal Transition Models (TTM's) and an event database maintained by the other TAS tools. The system also includes a robust knowledge acquisition and maintenance tool for creating TTM's using a graphical specification language. The ability to manipulate TTM's in a graphical format gives non-computer specialists an intuitive way of accessing and editing the knowledge base. To support space environmental analyses, we used TAS's ability to define domain specific event analysis abstractions. The prototype system defines events covering reports of natural phenomena such as solar flares, bursts, geomagnetic storms, and five others pertinent to space environmental analysis. With our preliminary event definitions we experimented with TAS's support for temporal pattern analysis using X-ray flare and geomagnetic storm forecasts as case studies. We are currently working on a framework for integrating advanced graphics and space environmental models into this analytical environment.

Application for internal dosimetry using biokinetic distribution of photons based on nuclear medicine images*

PubMed Central

Leal Neto, Viriato; Vieira, José Wilson; Lima, Fernando Roberto de Andrade

2014-01-01

Objective This article presents a way to obtain estimates of dose in patients submitted to radiotherapy with basis on the analysis of regions of interest on nuclear medicine images. Materials and Methods A software called DoRadIo (Dosimetria das Radiações Ionizantes [Ionizing Radiation Dosimetry]) was developed to receive information about source organs and target organs, generating graphical and numerical results. The nuclear medicine images utilized in the present study were obtained from catalogs provided by medical physicists. The simulations were performed with computational exposure models consisting of voxel phantoms coupled with the Monte Carlo EGSnrc code. The software was developed with the Microsoft Visual Studio 2010 Service Pack and the project template Windows Presentation Foundation for C# programming language. Results With the mentioned tools, the authors obtained the file for optimization of Monte Carlo simulations using the EGSnrc; organization and compaction of dosimetry results with all radioactive sources; selection of regions of interest; evaluation of grayscale intensity in regions of interest; the file of weighted sources; and, finally, all the charts and numerical results. Conclusion The user interface may be adapted for use in clinical nuclear medicine as a computer-aided tool to estimate the administered activity. PMID:25741101

Evacuation simulation using Hybrid Space Discretisation and Application to Large Underground Rail Tunnel Station

NASA Astrophysics Data System (ADS)

Chooramun, N.; Lawrence, P. J.; Galea, E. R.

2017-08-01

In all evacuation simulation tools, the space through which agents navigate and interact is represented by one the following methods, namely Coarse regions, Fine nodes and Continuous regions. Each of the spatial representation methods has its benefits and limitations. For instance, the Coarse approach allows simulations to be processed very rapidly, but is unable to represent the interactions of the agents from an individual perspective; the Continuous approach provides a detailed representation of agent movement and interaction but suffers from relatively poor computational performance. The Fine nodal approach presents a compromise between the Continuous and Coarse approaches such that it allows agent interaction to be modelled while providing good computational performance. Our approach for representing space in an evacuation simulation tool differs such that it allows evacuation simulations to be run using a combination of Coarse regions, Fine nodes and Continuous regions. This approach, which we call Hybrid Spatial Discretisation (HSD), is implemented within the buildingEXODUS evacuation simulation software. The HSD incorporates the benefits of each of the spatial representation methods whilst providing an optimal environment for representing agent movement and interaction. In this work, we demonstrate the effectiveness of the HSD through its application to a moderately large case comprising of an underground rail tunnel station with a population of 2,000 agents.

Using an architectural approach to integrate heterogeneous, distributed software components

NASA Technical Reports Server (NTRS)

Callahan, John R.; Purtilo, James M.

1995-01-01

Many computer programs cannot be easily integrated because their components are distributed and heterogeneous, i.e., they are implemented in diverse programming languages, use different data representation formats, or their runtime environments are incompatible. In many cases, programs are integrated by modifying their components or interposing mechanisms that handle communication and conversion tasks. For example, remote procedure call (RPC) helps integrate heterogeneous, distributed programs. When configuring such programs, however, mechanisms like RPC must be used explicitly by software developers in order to integrate collections of diverse components. Each collection may require a unique integration solution. This paper describes improvements to the concepts of software packaging and some of our experiences in constructing complex software systems from a wide variety of components in different execution environments. Software packaging is a process that automatically determines how to integrate a diverse collection of computer programs based on the types of components involved and the capabilities of available translators and adapters in an environment. Software packaging provides a context that relates such mechanisms to software integration processes and reduces the cost of configuring applications whose components are distributed or implemented in different programming languages. Our software packaging tool subsumes traditional integration tools like UNIX make by providing a rule-based approach to software integration that is independent of execution environments.

ShatterProof: operational detection and quantification of chromothripsis.

PubMed

Govind, Shaylan K; Zia, Amin; Hennings-Yeomans, Pablo H; Watson, John D; Fraser, Michael; Anghel, Catalina; Wyatt, Alexander W; van der Kwast, Theodorus; Collins, Colin C; McPherson, John D; Bristow, Robert G; Boutros, Paul C

2014-03-19

Chromothripsis, a newly discovered type of complex genomic rearrangement, has been implicated in the evolution of several types of cancers. To date, it has been described in bone cancer, SHH-medulloblastoma and acute myeloid leukemia, amongst others, however there are still no formal or automated methods for detecting or annotating it in high throughput sequencing data. As such, findings of chromothripsis are difficult to compare and many cases likely escape detection altogether. We introduce ShatterProof, a software tool for detecting and quantifying chromothriptic events. ShatterProof takes structural variation calls (translocations, copy-number variations, short insertions and loss of heterozygosity) produced by any algorithm and using an operational definition of chromothripsis performs robust statistical tests to accurately predict the presence and location of chromothriptic events. Validation of our tool was conducted using clinical data sets including matched normal, prostate cancer samples in addition to the colorectal cancer and SCLC data sets used in the original description of chromothripsis. ShatterProof is computationally efficient, having low memory requirements and near linear computation time. This allows it to become a standard component of sequencing analysis pipelines, enabling researchers to routinely and accurately assess samples for chromothripsis. Source code and documentation can be found at http://search.cpan.org/~sgovind/Shatterproof.

An advanced artificial intelligence tool for menu design.

PubMed

Khan, Abdus Salam; Hoffmann, Achim

2003-01-01

The computer-assisted menu design still remains a difficult task. Usually knowledge that aids in menu design by a computer is hard-coded and because of that a computerised menu planner cannot handle the menu design problem for an unanticipated client. To address this problem we developed a menu design tool, MIKAS (menu construction using incremental knowledge acquisition system), an artificial intelligence system that allows the incremental development of a knowledge-base for menu design. We allow an incremental knowledge acquisition process in which the expert is only required to provide hints to the system in the context of actual problem instances during menu design using menus stored in a so-called Case Base. Our system incorporates Case-Based Reasoning (CBR), an Artificial Intelligence (AI) technique developed to mimic human problem solving behaviour. Ripple Down Rules (RDR) are a proven technique for the acquisition of classification knowledge from expert directly while they are using the system, which complement CBR in a very fruitful way. This combination allows the incremental improvement of the menu design system while it is already in routine use. We believe MIKAS allows better dietary practice by leveraging a dietitian's skills and expertise. As such MIKAS has the potential to be helpful for any institution where dietary advice is practised.

Applying Model-Based Reasoning to the FDIR of the Command and Data Handling Subsystem of the International Space Station

NASA Technical Reports Server (NTRS)

Robinson, Peter; Shirley, Mark; Fletcher, Daryl; Alena, Rick; Duncavage, Dan; Lee, Charles

2003-01-01

All of the International Space Station (ISS) systems which require computer control depend upon the hardware and software of the Command and Data Handling System (C&DH) system, currently a network of over 30 386-class computers called Multiplexor/Dimultiplexors (MDMs)[18]. The Caution and Warning System (C&W)[7], a set of software tasks that runs on the MDMs, is responsible for detecting, classifying, and reporting errors in all ISS subsystems including the C&DH. Fault Detection, Isolation and Recovery (FDIR) of these errors is typically handled with a combination of automatic and human effort. We are developing an Advanced Diagnostic System (ADS) to augment the C&W system with decision support tools to aid in root cause analysis as well as resolve differing human and machine C&DH state estimates. These tools which draw from sources in model-based reasoning[ 16,291, will improve the speed and accuracy of flight controllers by reducing the uncertainty in C&DH state estimation, allowing for a more complete assessment of risk. We have run tests with ISS telemetry and focus on those C&W events which relate to the C&DH system itself. This paper describes our initial results and subsequent plans.

Teaching and learning the Hodgkin-Huxley model based on software developed in NEURON's programming language hoc.

PubMed

Hernández, Oscar E; Zurek, Eduardo E

2013-05-15

We present a software tool called SENB, which allows the geometric and biophysical neuronal properties in a simple computational model of a Hodgkin-Huxley (HH) axon to be changed. The aim of this work is to develop a didactic and easy-to-use computational tool in the NEURON simulation environment, which allows graphical visualization of both the passive and active conduction parameters and the geometric characteristics of a cylindrical axon with HH properties. The SENB software offers several advantages for teaching and learning electrophysiology. First, SENB offers ease and flexibility in determining the number of stimuli. Second, SENB allows immediate and simultaneous visualization, in the same window and time frame, of the evolution of the electrophysiological variables. Third, SENB calculates parameters such as time and space constants, stimuli frequency, cellular area and volume, sodium and potassium equilibrium potentials, and propagation velocity of the action potentials. Furthermore, it allows the user to see all this information immediately in the main window. Finally, with just one click SENB can save an image of the main window as evidence. The SENB software is didactic and versatile, and can be used to improve and facilitate the teaching and learning of the underlying mechanisms in the electrical activity of an axon using the biophysical properties of the squid giant axon.

Geospatial Data as a Service: The GEOGLAM Rangelands and Pasture Productivity Map Experience

NASA Astrophysics Data System (ADS)

Evans, B. J. K.; Antony, J.; Guerschman, J. P.; Larraondo, P. R.; Richards, C. J.

2017-12-01

Empowering end-users like pastoralists, land management specialists and land policy makers in the use of earth observation data for both day-to-day and seasonal planning needs both interactive delivery of multiple geospatial datasets and the capability of supporting on-the-fly dynamic queries while simultaneously fostering a community around the effort. The use of and wide adoption of large data archives, like those produced by earth observation missions, are often limited by compute and storage capabilities of the remote user. We demonstrate that wide-scale use of large data archives can be facilitated by end-users dynamically requesting value-added products using open standards (WCS, WMS, WPS), with compute running in the cloud or dedicated data-centres and visualizing outputs on web-front ends. As an example, we will demonstrate how a tool called GSKY can empower a remote end-user by providing the data delivery and analytics capabilities for the GEOGLAM Rangelands and Pasture Productivity (RAPP) Map tool. The GEOGLAM RAPP initiative from the Group on Earth Observations (GEO) and its Agricultural Monitoring subgroup aims at providing practical tools to end-users focusing on the important role of rangelands and pasture systems in providing food production security from both agricultural crops and animal protein. Figure 1, is a screen capture from the RAPP Map interface for an important pasture area in the Namibian rangelands. The RAPP Map has been in production for six months and has garnered significant interest from groups and users all over the world. GSKY, being formulated around the theme of Open Geospatial Data-as-a-Service capabilities uses distributed computing and storage to facilitate this. It works behind the scenes, accepting OGC standard requests in WCS, WMS and WPS. Results from these requests are rendered on a web-front end. In this way, the complexities of data locality and compute execution are masked from an end user. On-the-fly computation of products such as NDVI, Leaf Area Index, vegetation cover and others from original source data including MODIS are achived, with Landsat and Sentinel-2 on the horizon. Innovative use of cloud computing and storage along with flexible front-ends, allow the democratization of data dissemination and we hope better outcomes for the planet.

Transient loads analysis for space flight applications

NASA Technical Reports Server (NTRS)

Thampi, S. K.; Vidyasagar, N. S.; Ganesan, N.

1992-01-01

A significant part of the flight readiness verification process involves transient analysis of the coupled Shuttle-payload system to determine the low frequency transient loads. This paper describes a methodology for transient loads analysis and its implementation for the Spacelab Life Sciences Mission. The analysis is carried out using two major software tools - NASTRAN and an external FORTRAN code called EZTRAN. This approach is adopted to overcome some of the limitations of NASTRAN's standard transient analysis capabilities. The method uses Data Recovery Matrices (DRM) to improve computational efficiency. The mode acceleration method is fully implemented in the DRM formulation to recover accurate displacements, stresses, and forces. The advantages of the method are demonstrated through a numerical example.

A Two-Layer Least Squares Support Vector Machine Approach to Credit Risk Assessment

NASA Astrophysics Data System (ADS)

Liu, Jingli; Li, Jianping; Xu, Weixuan; Shi, Yong

Least squares support vector machine (LS-SVM) is a revised version of support vector machine (SVM) and has been proved to be a useful tool for pattern recognition. LS-SVM had excellent generalization performance and low computational cost. In this paper, we propose a new method called two-layer least squares support vector machine which combines kernel principle component analysis (KPCA) and linear programming form of least square support vector machine. With this method sparseness and robustness is obtained while solving large dimensional and large scale database. A U.S. commercial credit card database is used to test the efficiency of our method and the result proved to be a satisfactory one.

A direct-inverse method for transonic and separated flows about airfoils

NASA Technical Reports Server (NTRS)

Carlson, K. D.

1985-01-01

A direct-inverse technique and computer program called TAMSEP that can be sued for the analysis of the flow about airfoils at subsonic and low transonic freestream velocities is presented. The method is based upon a direct-inverse nonconservative full potential inviscid method, a Thwaites laminar boundary layer technique, and the Barnwell turbulent momentum integral scheme; and it is formulated using Cartesian coordinates. Since the method utilizes inverse boundary conditions in regions of separated flow, it is suitable for predicing the flowfield about airfoils having trailing edge separated flow under high lift conditions. Comparisons with experimental data indicate that the method should be a useful tool for applied aerodynamic analyses.

Interdisciplinary analysis procedures in the modeling and control of large space-based structures

NASA Technical Reports Server (NTRS)

Cooper, Paul A.; Stockwell, Alan E.; Kim, Zeen C.

1987-01-01

The paper describes a computer software system called the Integrated Multidisciplinary Analysis Tool, IMAT, that has been developed at NASA Langley Research Center. IMAT provides researchers and analysts with an efficient capability to analyze satellite control systems influenced by structural dynamics. Using a menu-driven interactive executive program, IMAT links a relational database to commercial structural and controls analysis codes. The paper describes the procedures followed to analyze a complex satellite structure and control system. The codes used to accomplish the analysis are described, and an example is provided of an application of IMAT to the analysis of a reference space station subject to a rectangular pulse loading at its docking port.

A direct-inverse method for transonic and separated flows about airfoils

NASA Technical Reports Server (NTRS)

Carlson, Leland A.

1990-01-01

A direct-inverse technique and computer program called TAMSEP that can be used for the analysis of the flow about airfoils at subsonic and low transonic freestream velocities is presented. The method is based upon a direct-inverse nonconservative full potential inviscid method, a Thwaites laminar boundary layer technique, and the Barnwell turbulent momentum integral scheme; and it is formulated using Cartesian coordinates. Since the method utilizes inverse boundary conditions in regions of separated flow, it is suitable for predicting the flow field about airfoils having trailing edge separated flow under high lift conditions. Comparisons with experimental data indicate that the method should be a useful tool for applied aerodynamic analyses.

Closed-loop bird-computer interactions: a new method to study the role of bird calls.

PubMed

Lerch, Alexandre; Roy, Pierre; Pachet, François; Nagle, Laurent

2011-03-01

In the field of songbird research, many studies have shown the role of male songs in territorial defense and courtship. Calling, another important acoustic communication signal, has received much less attention, however, because calls are assumed to contain less information about the emitter than songs do. Birdcall repertoire is diverse, and the role of calls has been found to be significant in the area of social interaction, for example, in pair, family, and group cohesion. However, standard methods for studying calls do not allow precise and systematic study of their role in communication. We propose herein a new method to study bird vocal interaction. A closed-loop computer system interacts with canaries, Serinus canaria, by (1) automatically classifying two basic types of canary vocalization, single versus repeated calls, as they are produced by the subject, and (2) responding with a preprogrammed call type recorded from another bird. This computerized animal-machine interaction requires no human interference. We show first that the birds do engage in sustained interactions with the system, by studying the rate of single and repeated calls for various programmed protocols. We then show that female canaries differentially use single and repeated calls. First, they produce significantly more single than repeated calls, and second, the rate of single calls is associated with the context in which they interact, whereas repeated calls are context independent. This experiment is the first illustration of how closed-loop bird-computer interaction can be used productively to study social relationships. © Springer-Verlag 2010

Computer analysis of lighting style in fine art: steps towards inter-artist studies

NASA Astrophysics Data System (ADS)

Stork, David G.

2011-03-01

Stylometry in visual art-the mathematical description of artists' styles - has been based on a number of properties of works, such as color, brush stroke shape, visual texture, and measures of contours' curvatures. We introduce the concept of quantitative measures of lighting, such as statistical descriptions of spatial coherence, diuseness, and so forth, as properties of artistic style. Some artists of the high Renaissance, such as Leonardo, worked from nature and strove to render illumination "faithfully" photorealists, such as Richard Estes, worked from photographs and duplicated the "physics based" lighting accurately. As such, each had dierent motivations, methodologies, stagings, and "accuracies" in rendering lighting clues. Perceptual studies show that observers are poor judges of properties of lighting in photographs such as consistency (and thus by extension in paintings as well); computer methods such as rigorous cast-shadow analysis, occluding-contour analysis and spherical harmonic based estimation of light fields can be quite accurate. For this reasons, computer lighting analysis can provide a new tools for art historical studies. We review lighting analysis in paintings such as Vermeer's Girl with a pearl earring, de la Tour's Christ in the carpenter's studio, Caravaggio's Magdalen with the smoking flame and Calling of St. Matthew) and extend our corpus to works where lighting coherence is of interest to art historians, such as Caravaggio's Adoration of the Shepherds or Nativity (1609) in the Capuchin church of Santa Maria degli Angeli. Our measure of lighting coherence may help reveal the working methods of some artists and in diachronic studies of individual artists. We speculate on artists and art historical questions that may ultimately profit from future renements to these new computational tools.

Sense-making for intelligence analysis on social media data

NASA Astrophysics Data System (ADS)

Pritzkau, Albert

2016-05-01

Social networks, in particular online social networks as a subset, enable the analysis of social relationships which are represented by interaction, collaboration, or other sorts of influence between people. Any set of people and their internal social relationships can be modelled as a general social graph. These relationships are formed by exchanging emails, making phone calls, or carrying out a range of other activities that build up the network. This paper presents an overview of current approaches to utilizing social media as a ubiquitous sensor network in the context of national and global security. Exploitation of social media is usually an interdisciplinary endeavour, in which the relevant technologies and methods are identified and linked in order ultimately demonstrate selected applications. Effective and efficient intelligence is usually accomplished in a combined human and computer effort. Indeed, the intelligence process heavily depends on combining a human's flexibility, creativity, and cognitive ability with the bandwidth and processing power of today's computers. To improve the usability and accuracy of the intelligence analysis we will have to rely on data-processing tools at the level of natural language. Especially the collection and transformation of unstructured data into actionable, structured data requires scalable computational algorithms ranging from Artificial Intelligence, via Machine Learning, to Natural Language Processing (NLP). To support intelligence analysis on social media data, social media analytics is concerned with developing and evaluating computational tools and frameworks to collect, monitor, analyze, summarize, and visualize social media data. Analytics methods are employed to extract of significant patterns that might not be obvious. As a result, different data representations rendering distinct aspects of content and interactions serve as a means to adapt the focus of the intelligence analysis to specific information requests.

Fast multipurpose Monte Carlo simulation for proton therapy using multi- and many-core CPU architectures.

PubMed

Souris, Kevin; Lee, John Aldo; Sterpin, Edmond

2016-04-01

Accuracy in proton therapy treatment planning can be improved using Monte Carlo (MC) simulations. However the long computation time of such methods hinders their use in clinical routine. This work aims to develop a fast multipurpose Monte Carlo simulation tool for proton therapy using massively parallel central processing unit (CPU) architectures. A new Monte Carlo, called MCsquare (many-core Monte Carlo), has been designed and optimized for the last generation of Intel Xeon processors and Intel Xeon Phi coprocessors. These massively parallel architectures offer the flexibility and the computational power suitable to MC methods. The class-II condensed history algorithm of MCsquare provides a fast and yet accurate method of simulating heavy charged particles such as protons, deuterons, and alphas inside voxelized geometries. Hard ionizations, with energy losses above a user-specified threshold, are simulated individually while soft events are regrouped in a multiple scattering theory. Elastic and inelastic nuclear interactions are sampled from ICRU 63 differential cross sections, thereby allowing for the computation of prompt gamma emission profiles. MCsquare has been benchmarked with the gate/geant4 Monte Carlo application for homogeneous and heterogeneous geometries. Comparisons with gate/geant4 for various geometries show deviations within 2%-1 mm. In spite of the limited memory bandwidth of the coprocessor simulation time is below 25 s for 10(7) primary 200 MeV protons in average soft tissues using all Xeon Phi and CPU resources embedded in a single desktop unit. MCsquare exploits the flexibility of CPU architectures to provide a multipurpose MC simulation tool. Optimized code enables the use of accurate MC calculation within a reasonable computation time, adequate for clinical practice. MCsquare also simulates prompt gamma emission and can thus be used also for in vivo range verification.

A Practical Guide to the Technology and Adoption of Software Process Automation

DTIC Science & Technology

1994-03-01

IDE’s integration of Software through Pictures, CodeCenter, and FrameMaker ). However, successful use of in- tegrated tools, as reflected in actual...tool for a specific platform. Thus, when a Work Context calls for a word processor, the weaver.tis file can be set up to call FrameMaker for the Sun4

43 CFR 11.40 - What are type A procedures?

Code of Federal Regulations, 2010 CFR

2010-10-01

... 11.40 Public Lands: Interior Office of the Secretary of the Interior NATURAL RESOURCE DAMAGE... marine environments incorporates a computer model called the Natural Resource Damage Assessment Model for... environments incorporates a computer model called the Natural Resource Damage Assessment Model for Great Lakes...

43 CFR 11.40 - What are type A procedures?

Code of Federal Regulations, 2011 CFR

2011-10-01

... 11.40 Public Lands: Interior Office of the Secretary of the Interior NATURAL RESOURCE DAMAGE... marine environments incorporates a computer model called the Natural Resource Damage Assessment Model for... environments incorporates a computer model called the Natural Resource Damage Assessment Model for Great Lakes...

Identification of DNA-binding proteins by combining auto-cross covariance transformation and ensemble learning.

PubMed

Liu, Bin; Wang, Shanyi; Dong, Qiwen; Li, Shumin; Liu, Xuan

2016-04-20

DNA-binding proteins play a pivotal role in various intra- and extra-cellular activities ranging from DNA replication to gene expression control. With the rapid development of next generation of sequencing technique, the number of protein sequences is unprecedentedly increasing. Thus it is necessary to develop computational methods to identify the DNA-binding proteins only based on the protein sequence information. In this study, a novel method called iDNA-KACC is presented, which combines the Support Vector Machine (SVM) and the auto-cross covariance transformation. The protein sequences are first converted into profile-based protein representation, and then converted into a series of fixed-length vectors by the auto-cross covariance transformation with Kmer composition. The sequence order effect can be effectively captured by this scheme. These vectors are then fed into Support Vector Machine (SVM) to discriminate the DNA-binding proteins from the non DNA-binding ones. iDNA-KACC achieves an overall accuracy of 75.16% and Matthew correlation coefficient of 0.5 by a rigorous jackknife test. Its performance is further improved by employing an ensemble learning approach, and the improved predictor is called iDNA-KACC-EL. Experimental results on an independent dataset shows that iDNA-KACC-EL outperforms all the other state-of-the-art predictors, indicating that it would be a useful computational tool for DNA binding protein identification. .

elPrep: High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling

PubMed Central

Decap, Dries; Fostier, Jan; Reumers, Joke

2015-01-01

elPrep is a high-performance tool for preparing sequence alignment/map files for variant calling in sequencing pipelines. It can be used as a replacement for SAMtools and Picard for preparation steps such as filtering, sorting, marking duplicates, reordering contigs, and so on, while producing identical results. What sets elPrep apart is its software architecture that allows executing preparation pipelines by making only a single pass through the data, no matter how many preparation steps are used in the pipeline. elPrep is designed as a multithreaded application that runs entirely in memory, avoids repeated file I/O, and merges the computation of several preparation steps to significantly speed up the execution time. For example, for a preparation pipeline of five steps on a whole-exome BAM file (NA12878), we reduce the execution time from about 1:40 hours, when using a combination of SAMtools and Picard, to about 15 minutes when using elPrep, while utilising the same server resources, here 48 threads and 23GB of RAM. For the same pipeline on whole-genome data (NA12878), elPrep reduces the runtime from 24 hours to less than 5 hours. As a typical clinical study may contain sequencing data for hundreds of patients, elPrep can remove several hundreds of hours of computing time, and thus substantially reduce analysis time and cost. PMID:26182406

Differential morphology and image processing.

PubMed

Maragos, P

1996-01-01

Image processing via mathematical morphology has traditionally used geometry to intuitively understand morphological signal operators and set or lattice algebra to analyze them in the space domain. We provide a unified view and analytic tools for morphological image processing that is based on ideas from differential calculus and dynamical systems. This includes ideas on using partial differential or difference equations (PDEs) to model distance propagation or nonlinear multiscale processes in images. We briefly review some nonlinear difference equations that implement discrete distance transforms and relate them to numerical solutions of the eikonal equation of optics. We also review some nonlinear PDEs that model the evolution of multiscale morphological operators and use morphological derivatives. Among the new ideas presented, we develop some general 2-D max/min-sum difference equations that model the space dynamics of 2-D morphological systems (including the distance computations) and some nonlinear signal transforms, called slope transforms, that can analyze these systems in a transform domain in ways conceptually similar to the application of Fourier transforms to linear systems. Thus, distance transforms are shown to be bandpass slope filters. We view the analysis of the multiscale morphological PDEs and of the eikonal PDE solved via weighted distance transforms as a unified area in nonlinear image processing, which we call differential morphology, and briefly discuss its potential applications to image processing and computer vision.

NASA Accelerates SpaceCube Technology into Orbit

NASA Technical Reports Server (NTRS)

Petrick, David

2010-01-01

On May 11, 2009, STS-125 Space Shuttle Atlantis blasted off from Kennedy Space Center on a historic mission to service the Hubble Space Telescope (HST). In addition to sending up the hardware and tools required to repair the observatory, the servicing team at NASA's Goddard Space Flight Center also sent along a complex experimental payload called Relative Navigation Sensors (RNS). The main objective of the RNS payload was to provide real-time image tracking of HST during rendezvous and docking operations. RNS was a complete success, and was brought to life by four Xilinx FPGAs (Field Programmable Gate Arrays) tightly packed into one integrated computer called SpaceCube. SpaceCube is a compact, reconfigurable, multiprocessor computing platform for space applications demanding extreme processing capabilities based on Xilinx Virtex 4 FX60 FPGAs. In a matter of months, the concept quickly went from the white board to a fully funded flight project. The 4-inch by 4-inch SpaceCube processor card was prototyped by a group of Goddard engineers using internal research funding. Once engineers were able to demonstrate the processing power of SpaceCube to NASA, HST management stood behind the product and invested in a flight qualified version, inserting it into the heart of the RNS system. With the determination of putting Xilinx into space, the team strengthened to a small army and delivered a fully functional, space qualified system to the mission.

Group-based variant calling leveraging next-generation supercomputing for large-scale whole-genome sequencing studies.

PubMed

Standish, Kristopher A; Carland, Tristan M; Lockwood, Glenn K; Pfeiffer, Wayne; Tatineni, Mahidhar; Huang, C Chris; Lamberth, Sarah; Cherkas, Yauheniya; Brodmerkel, Carrie; Jaeger, Ed; Smith, Lance; Rajagopal, Gunaretnam; Curran, Mark E; Schork, Nicholas J

2015-09-22

Next-generation sequencing (NGS) technologies have become much more efficient, allowing whole human genomes to be sequenced faster and cheaper than ever before. However, processing the raw sequence reads associated with NGS technologies requires care and sophistication in order to draw compelling inferences about phenotypic consequences of variation in human genomes. It has been shown that different approaches to variant calling from NGS data can lead to different conclusions. Ensuring appropriate accuracy and quality in variant calling can come at a computational cost. We describe our experience implementing and evaluating a group-based approach to calling variants on large numbers of whole human genomes. We explore the influence of many factors that may impact the accuracy and efficiency of group-based variant calling, including group size, the biogeographical backgrounds of the individuals who have been sequenced, and the computing environment used. We make efficient use of the Gordon supercomputer cluster at the San Diego Supercomputer Center by incorporating job-packing and parallelization considerations into our workflow while calling variants on 437 whole human genomes generated as part of large association study. We ultimately find that our workflow resulted in high-quality variant calls in a computationally efficient manner. We argue that studies like ours should motivate further investigations combining hardware-oriented advances in computing systems with algorithmic developments to tackle emerging 'big data' problems in biomedical research brought on by the expansion of NGS technologies.

Factors influencing exemplary science teachers' levels of computer use

NASA Astrophysics Data System (ADS)

Hakverdi, Meral

This study examines exemplary science teachers' use of technology in science instruction, factors influencing their level of computer use, their level of knowledge/skills in using specific computer applications for science instruction, their use of computer-related applications/tools during their instruction, and their students' use of computer applications/tools in or for their science class. After a relevant review of the literature certain variables were selected for analysis. These variables included personal self-efficacy in teaching with computers, outcome expectancy, pupil-control ideology, level of computer use, age, gender, teaching experience, personal computer use, professional computer use and science teachers' level of knowledge/skills in using specific computer applications for science instruction. The sample for this study includes middle and high school science teachers who received the Presidential Award for Excellence in Science Teaching Award (sponsored by the White House and the National Science Foundation) between the years 1997 and 2003 from all 50 states and U.S. territories. Award-winning science teachers were contacted about the survey via e-mail or letter with an enclosed return envelope. Of the 334 award-winning science teachers, usable responses were received from 92 science teachers, which made a response rate of 27.5%. Analysis of the survey responses indicated that exemplary science teachers have a variety of knowledge/skills in using computer related applications/tools. The most commonly used computer applications/tools are information retrieval via the Internet, presentation tools, online communication, digital cameras, and data collection probes. Results of the study revealed that students' use of technology in their science classroom is highly correlated with the frequency of their science teachers' use of computer applications/tools. The results of the multiple regression analysis revealed that personal self-efficacy related to the exemplary science teachers' level of computer use suggesting that computer use is dependent on perceived abilities at using computers. The teachers' use of computer-related applications/tools during class, and their personal self-efficacy, age, and gender are highly related with their level of knowledge/skills in using specific computer applications for science instruction. The teachers' level of knowledge/skills in using specific computer applications for science instruction and gender related to their use of computer-related applications/tools during class and the students' use of computer-related applications/tools in or for their science class. In conclusion, exemplary science teachers need assistance in learning and using computer-related applications/tool in their science class.

Holmes: a graphical tool for development, simulation and analysis of Petri net based models of complex biological systems.

PubMed

Radom, Marcin; Rybarczyk, Agnieszka; Szawulak, Bartlomiej; Andrzejewski, Hubert; Chabelski, Piotr; Kozak, Adam; Formanowicz, Piotr

2017-12-01

Model development and its analysis is a fundamental step in systems biology. The theory of Petri nets offers a tool for such a task. Since the rapid development of computer science, a variety of tools for Petri nets emerged, offering various analytical algorithms. From this follows a problem of using different programs to analyse a single model. Many file formats and different representations of results make the analysis much harder. Especially for larger nets the ability to visualize the results in a proper form provides a huge help in the understanding of their significance. We present a new tool for Petri nets development and analysis called Holmes. Our program contains algorithms for model analysis based on different types of Petri nets, e.g. invariant generator, Maximum Common Transitions (MCT) sets and cluster modules, simulation algorithms or knockout analysis tools. A very important feature is the ability to visualize the results of almost all analytical modules. The integration of such modules into one graphical environment allows a researcher to fully devote his or her time to the model building and analysis. Available at http://www.cs.put.poznan.pl/mradom/Holmes/holmes.html. piotr@cs.put.poznan.pl. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

A life scientist's gateway to distributed data management and computing: the PathPort/ToolBus framework.

PubMed

Eckart, J Dana; Sobral, Bruno W S

2003-01-01

The emergent needs of the bioinformatics community challenge current information systems. The pace of biological data generation far outstrips Moore's Law. Therefore, a gap continues to widen between the capabilities to produce biological (molecular and cell) data sets and the capability to manage and analyze these data sets. As a result, Federal investments in large data set generation produces diminishing returns in terms of the community's capabilities of understanding biology and leveraging that understanding to make scientific and technological advances that improve society. We are building an open framework to address various data management issues including data and tool interoperability, nomenclature and data communication standardization, and database integration. PathPort, short for Pathogen Portal, employs a generic, web-services based framework to deal with some of the problems identified by the bioinformatics community. The motivating research goal of a scalable system to provide data management and analysis for key pathosystems, especially relating to molecular data, has resulted in a generic framework using two major components. On the server-side, we employ web-services. On the client-side, a Java application called ToolBus acts as a client-side "bus" for contacting data and tools and viewing results through a single, consistent user interface.

Adaptive awareness for personal and small group decision making.

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

Perano, Kenneth J.; Tucker, Steve; Pancerella, Carmen M.

2003-12-01

Many situations call for the use of sensors monitoring physiological and environmental data. In order to use the large amounts of sensor data to affect decision making, we are coupling heterogeneous sensors with small, light-weight processors, other powerful computers, wireless communications, and embedded intelligent software. The result is an adaptive awareness and warning tool, which provides both situation awareness and personal awareness to individuals and teams. Central to this tool is a sensor-independent architecture, which combines both software agents and a reusable core software framework that manages the available hardware resources and provides services to the agents. Agents can recognizemore » cues from the data, warn humans about situations, and act as decision-making aids. Within the agents, self-organizing maps (SOMs) are used to process physiological data in order to provide personal awareness. We have employed a novel clustering algorithm to train the SOM to discern individual body states and activities. This awareness tool has broad applicability to emergency teams, military squads, military medics, individual exercise and fitness monitoring, health monitoring for sick and elderly persons, and environmental monitoring in public places. This report discusses our hardware decisions, software framework, and a pilot awareness tool, which has been developed at Sandia National Laboratories.« less

A Fog Computing and Cloudlet Based Augmented Reality System for the Industry 4.0 Shipyard.

PubMed

Fernández-Caramés, Tiago M; Fraga-Lamas, Paula; Suárez-Albela, Manuel; Vilar-Montesinos, Miguel

2018-06-02

Augmented Reality (AR) is one of the key technologies pointed out by Industry 4.0 as a tool for enhancing the next generation of automated and computerized factories. AR can also help shipbuilding operators, since they usually need to interact with information (e.g., product datasheets, instructions, maintenance procedures, quality control forms) that could be handled easily and more efficiently through AR devices. This is the reason why Navantia, one of the 10 largest shipbuilders in the world, is studying the application of AR (among other technologies) in different shipyard environments in a project called "Shipyard 4.0". This article presents Navantia's industrial AR (IAR) architecture, which is based on cloudlets and on the fog computing paradigm. Both technologies are ideal for supporting physically-distributed, low-latency and QoS-aware applications that decrease the network traffic and the computational load of traditional cloud computing systems. The proposed IAR communications architecture is evaluated in real-world scenarios with payload sizes according to demanding Microsoft HoloLens applications and when using a cloud, a cloudlet and a fog computing system. The results show that, in terms of response delay, the fog computing system is the fastest when transferring small payloads (less than 128 KB), while for larger file sizes, the cloudlet solution is faster than the others. Moreover, under high loads (with many concurrent IAR clients), the cloudlet in some cases is more than four times faster than the fog computing system in terms of response delay.

Analysis of Sea Level Rise in Action

NASA Astrophysics Data System (ADS)

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

2016-12-01

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