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

DXRaySMCS: a user-friendly interface developed for prediction of diagnostic radiology X-ray spectra produced by Monte Carlo (MCNP-4C) simulation.

PubMed

Bahreyni Toossi, M T; Moradi, H; Zare, H

2008-01-01

In this work, the general purpose Monte Carlo N-particle radiation transport computer code (MCNP-4C) was used for the simulation of X-ray spectra in diagnostic radiology. The electron's path in the target was followed until its energy was reduced to 10 keV. A user-friendly interface named 'diagnostic X-ray spectra by Monte Carlo simulation (DXRaySMCS)' was developed to facilitate the application of MCNP-4C code for diagnostic radiology spectrum prediction. The program provides a user-friendly interface for: (i) modifying the MCNP input file, (ii) launching the MCNP program to simulate electron and photon transport and (iii) processing the MCNP output file to yield a summary of the results (relative photon number per energy bin). In this article, the development and characteristics of DXRaySMCS are outlined. As part of the validation process, output spectra for 46 diagnostic radiology system settings produced by DXRaySMCS were compared with the corresponding IPEM78. Generally, there is a good agreement between the two sets of spectra. No statistically significant differences have been observed between IPEM78 reported spectra and the simulated spectra generated in this study.

Computer-assisted instruction and diagnosis of radiographic findings.

PubMed

Harper, D; Butler, C; Hodder, R; Allman, R; Woods, J; Riordan, D

1984-04-01

Recent advances in computer technology, including high bit-density storage, digital imaging, and the ability to interface microprocessors with videodisk, create enormous opportunities in the field of medical education. This program, utilizing a personal computer, videodisk, BASIC language, a linked textfile system, and a triangulation approach to the interpretation of radiographs developed by Dr. W. L. Thompson, can enable the user to engage in a user-friendly, dynamic teaching program in radiology, applicable to various levels of expertise. Advantages include a relatively more compact and inexpensive system with rapid access and ease of revision which requires little instruction to the user.

Real-Time fMRI Pattern Decoding and Neurofeedback Using FRIEND: An FSL-Integrated BCI Toolbox

PubMed Central

Sato, João R.; Basilio, Rodrigo; Paiva, Fernando F.; Garrido, Griselda J.; Bramati, Ivanei E.; Bado, Patricia; Tovar-Moll, Fernanda; Zahn, Roland; Moll, Jorge

2013-01-01

The demonstration that humans can learn to modulate their own brain activity based on feedback of neurophysiological signals opened up exciting opportunities for fundamental and applied neuroscience. Although EEG-based neurofeedback has been long employed both in experimental and clinical investigation, functional MRI (fMRI)-based neurofeedback emerged as a promising method, given its superior spatial resolution and ability to gauge deep cortical and subcortical brain regions. In combination with improved computational approaches, such as pattern recognition analysis (e.g., Support Vector Machines, SVM), fMRI neurofeedback and brain decoding represent key innovations in the field of neuromodulation and functional plasticity. Expansion in this field and its applications critically depend on the existence of freely available, integrated and user-friendly tools for the neuroimaging research community. Here, we introduce FRIEND, a graphic-oriented user-friendly interface package for fMRI neurofeedback and real-time multivoxel pattern decoding. The package integrates routines for image preprocessing in real-time, ROI-based feedback (single-ROI BOLD level and functional connectivity) and brain decoding-based feedback using SVM. FRIEND delivers an intuitive graphic interface with flexible processing pipelines involving optimized procedures embedding widely validated packages, such as FSL and libSVM. In addition, a user-defined visual neurofeedback module allows users to easily design and run fMRI neurofeedback experiments using ROI-based or multivariate classification approaches. FRIEND is open-source and free for non-commercial use. Processing tutorials and extensive documentation are available. PMID:24312569

Acquisition of ICU data: concepts and demands.

PubMed

Imhoff, M

1992-12-01

As the issue of data overload is a problem in critical care today, it is of utmost importance to improve acquisition, storage, integration, and presentation of medical data, which appears only feasible with the help of bedside computers. The data originates from four major sources: (1) the bedside medical devices, (2) the local area network (LAN) of the ICU, (3) the hospital information system (HIS) and (4) manual input. All sources differ markedly in quality and quantity of data and in the demands of the interfaces between source of data and patient database. The demands for data acquisition from bedside medical devices, ICU-LAN and HIS concentrate on technical problems, such as computational power, storage capacity, real-time processing, interfacing with different devices and networks and the unmistakable assignment of data to the individual patient. The main problem of manual data acquisition is the definition and configuration of the user interface that must allow the inexperienced user to interact with the computer intuitively. Emphasis must be put on the construction of a pleasant, logical and easy-to-handle graphical user interface (GUI). Short response times will require high graphical processing capacity. Moreover, high computational resources are necessary in the future for additional interfacing devices such as speech recognition and 3D-GUI. Therefore, in an ICU environment the demands for computational power are enormous. These problems are complicated by the urgent need for friendly and easy-to-handle user interfaces. Both facts place ICU bedside computing at the vanguard of present and future workstation development leaving no room for solutions based on traditional concepts of personal computers.(ABSTRACT TRUNCATED AT 250 WORDS)

A user-friendly SSVEP-based brain-computer interface using a time-domain classifier.

PubMed

Luo, An; Sullivan, Thomas J

2010-04-01

We introduce a user-friendly steady-state visual evoked potential (SSVEP)-based brain-computer interface (BCI) system. Single-channel EEG is recorded using a low-noise dry electrode. Compared to traditional gel-based multi-sensor EEG systems, a dry sensor proves to be more convenient, comfortable and cost effective. A hardware system was built that displays four LED light panels flashing at different frequencies and synchronizes with EEG acquisition. The visual stimuli have been carefully designed such that potential risk to photosensitive people is minimized. We describe a novel stimulus-locked inter-trace correlation (SLIC) method for SSVEP classification using EEG time-locked to stimulus onsets. We studied how the performance of the algorithm is affected by different selection of parameters. Using the SLIC method, the average light detection rate is 75.8% with very low error rates (an 8.4% false positive rate and a 1.3% misclassification rate). Compared to a traditional frequency-domain-based method, the SLIC method is more robust (resulting in less annoyance to the users) and is also suitable for irregular stimulus patterns.

Evaluation and comparison of classical interatomic potentials through a user-friendly interactive web-interface

NASA Astrophysics Data System (ADS)

Choudhary, Kamal; Congo, Faical Yannick P.; Liang, Tao; Becker, Chandler; Hennig, Richard G.; Tavazza, Francesca

2017-01-01

Classical empirical potentials/force-fields (FF) provide atomistic insights into material phenomena through molecular dynamics and Monte Carlo simulations. Despite their wide applicability, a systematic evaluation of materials properties using such potentials and, especially, an easy-to-use user-interface for their comparison is still lacking. To address this deficiency, we computed energetics and elastic properties of variety of materials such as metals and ceramics using a wide range of empirical potentials and compared them to density functional theory (DFT) as well as to experimental data, where available. The database currently consists of 3248 entries including energetics and elastic property calculations, and it is still increasing. We also include computational tools for convex-hull plots for DFT and FF calculations. The data covers 1471 materials and 116 force-fields. In addition, both the complete database and the software coding used in the process have been released for public use online (presently at http://www.ctcms.nist.gov/˜knc6/periodic.html) in a user-friendly way designed to enable further material design and discovery.

Evaluation and comparison of classical interatomic potentials through a user-friendly interactive web-interface

PubMed Central

Choudhary, Kamal; Congo, Faical Yannick P.; Liang, Tao; Becker, Chandler; Hennig, Richard G.; Tavazza, Francesca

2017-01-01

Classical empirical potentials/force-fields (FF) provide atomistic insights into material phenomena through molecular dynamics and Monte Carlo simulations. Despite their wide applicability, a systematic evaluation of materials properties using such potentials and, especially, an easy-to-use user-interface for their comparison is still lacking. To address this deficiency, we computed energetics and elastic properties of variety of materials such as metals and ceramics using a wide range of empirical potentials and compared them to density functional theory (DFT) as well as to experimental data, where available. The database currently consists of 3248 entries including energetics and elastic property calculations, and it is still increasing. We also include computational tools for convex-hull plots for DFT and FF calculations. The data covers 1471 materials and 116 force-fields. In addition, both the complete database and the software coding used in the process have been released for public use online (presently at http://www.ctcms.nist.gov/∼knc6/periodic.html) in a user-friendly way designed to enable further material design and discovery. PMID:28140407

An Overview of U.S. Trends in Educational Software Design.

ERIC Educational Resources Information Center

Colvin, Linda B.

1989-01-01

Describes trends in educational software design in the United States for elementary and secondary education. Highlights include user-friendly software; learner control; interfacing the computer with other media, including television, telecommunications networks, and optical disk technology; microworlds; graphics; word processing; database…

Towards User-Friendly Spelling with an Auditory Brain-Computer Interface: The CharStreamer Paradigm

PubMed Central

Höhne, Johannes; Tangermann, Michael

2014-01-01

Realizing the decoding of brain signals into control commands, brain-computer interfaces (BCI) aim to establish an alternative communication pathway for locked-in patients. In contrast to most visual BCI approaches which use event-related potentials (ERP) of the electroencephalogram, auditory BCI systems are challenged with ERP responses, which are less class-discriminant between attended and unattended stimuli. Furthermore, these auditory approaches have more complex interfaces which imposes a substantial workload on their users. Aiming for a maximally user-friendly spelling interface, this study introduces a novel auditory paradigm: “CharStreamer”. The speller can be used with an instruction as simple as “please attend to what you want to spell”. The stimuli of CharStreamer comprise 30 spoken sounds of letters and actions. As each of them is represented by the sound of itself and not by an artificial substitute, it can be selected in a one-step procedure. The mental mapping effort (sound stimuli to actions) is thus minimized. Usability is further accounted for by an alphabetical stimulus presentation: contrary to random presentation orders, the user can foresee the presentation time of the target letter sound. Healthy, normal hearing users (n = 10) of the CharStreamer paradigm displayed ERP responses that systematically differed between target and non-target sounds. Class-discriminant features, however, varied individually from the typical N1-P2 complex and P3 ERP components found in control conditions with random sequences. To fully exploit the sequential presentation structure of CharStreamer, novel data analysis approaches and classification methods were introduced. The results of online spelling tests showed that a competitive spelling speed can be achieved with CharStreamer. With respect to user rating, it clearly outperforms a control setup with random presentation sequences. PMID:24886978

Bar-Code System for a Microbiological Laboratory

NASA Technical Reports Server (NTRS)

Law, Jennifer; Kirschner, Larry

2007-01-01

A bar-code system has been assembled for a microbiological laboratory that must examine a large number of samples. The system includes a commercial bar-code reader, computer hardware and software components, plus custom-designed database software. The software generates a user-friendly, menu-driven interface.

TmoleX--a graphical user interface for TURBOMOLE.

PubMed

Steffen, Claudia; Thomas, Klaus; Huniar, Uwe; Hellweg, Arnim; Rubner, Oliver; Schroer, Alexander

2010-12-01

We herein present the graphical user interface (GUI) TmoleX for the quantum chemical program package TURBOMOLE. TmoleX allows users to execute the complete workflow of a quantum chemical investigation from the initial building of a structure to the visualization of the results in a user friendly graphical front end. The purpose of TmoleX is to make TURBOMOLE easy to use and to provide a high degree of flexibility. Hence, it should be a valuable tool for most users from beginners to experts. The program is developed in Java and runs on Linux, Windows, and Mac platforms. It can be used to run calculations on local desktops as well as on remote computers. © 2010 Wiley Periodicals, Inc.

Effectiveness Evaluation of Force Protection Training Using Computer-Based Instruction and X3d Simulation

DTIC Science & Technology

2007-09-01

behavior libraries selection box, Savage Tactics behavior sub-folder and hostile behavior sub-folder that contains the behavior that is being assigned to...21) applications. The interface allows users to select models (locations, friendly assets, hostile assets, neutral assets, etc) that will be used in...altitude, etc.) for each model and define their behaviors (friendly patrol craft, hostile explosive-laden vessel, etc). Once the models and their

Constructing linkage maps in the genomics era with MapDisto 2.0.

PubMed

Heffelfinger, Christopher; Fragoso, Christopher A; Lorieux, Mathias

2017-07-15

Genotyping by sequencing (GBS) generates datasets that are challenging to handle by current genetic mapping software with graphical interface. Geneticists need new user-friendly computer programs that can analyze GBS data on desktop computers. This requires improvements in computation efficiency, both in terms of speed and use of random-access memory (RAM). MapDisto v.2.0 is a user-friendly computer program for construction of genetic linkage maps. It includes several new major features: (i) handling of very large genotyping datasets like the ones generated by GBS; (ii) direct importation and conversion of Variant Call Format (VCF) files; (iii) detection of linkage, i.e. construction of linkage groups in case of segregation distortion; (iv) data imputation on VCF files using a new approach, called LB-Impute. Features i to iv operate through inclusion of new Java modules that are used transparently by MapDisto; (v) QTL detection via a new R/qtl graphical interface. The program is available free of charge at mapdisto.free.fr. mapdisto@gmail.com. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

An Interactive, Web-based High Performance Modeling Environment for Computational Epidemiology.

PubMed

Deodhar, Suruchi; Bisset, Keith R; Chen, Jiangzhuo; Ma, Yifei; Marathe, Madhav V

2014-07-01

We present an integrated interactive modeling environment to support public health epidemiology. The environment combines a high resolution individual-based model with a user-friendly web-based interface that allows analysts to access the models and the analytics back-end remotely from a desktop or a mobile device. The environment is based on a loosely-coupled service-oriented-architecture that allows analysts to explore various counter factual scenarios. As the modeling tools for public health epidemiology are getting more sophisticated, it is becoming increasingly hard for non-computational scientists to effectively use the systems that incorporate such models. Thus an important design consideration for an integrated modeling environment is to improve ease of use such that experimental simulations can be driven by the users. This is achieved by designing intuitive and user-friendly interfaces that allow users to design and analyze a computational experiment and steer the experiment based on the state of the system. A key feature of a system that supports this design goal is the ability to start, stop, pause and roll-back the disease propagation and intervention application process interactively. An analyst can access the state of the system at any point in time and formulate dynamic interventions based on additional information obtained through state assessment. In addition, the environment provides automated services for experiment set-up and management, thus reducing the overall time for conducting end-to-end experimental studies. We illustrate the applicability of the system by describing computational experiments based on realistic pandemic planning scenarios. The experiments are designed to demonstrate the system's capability and enhanced user productivity.

An Interactive, Web-based High Performance Modeling Environment for Computational Epidemiology

PubMed Central

Deodhar, Suruchi; Bisset, Keith R.; Chen, Jiangzhuo; Ma, Yifei; Marathe, Madhav V.

2014-01-01

We present an integrated interactive modeling environment to support public health epidemiology. The environment combines a high resolution individual-based model with a user-friendly web-based interface that allows analysts to access the models and the analytics back-end remotely from a desktop or a mobile device. The environment is based on a loosely-coupled service-oriented-architecture that allows analysts to explore various counter factual scenarios. As the modeling tools for public health epidemiology are getting more sophisticated, it is becoming increasingly hard for non-computational scientists to effectively use the systems that incorporate such models. Thus an important design consideration for an integrated modeling environment is to improve ease of use such that experimental simulations can be driven by the users. This is achieved by designing intuitive and user-friendly interfaces that allow users to design and analyze a computational experiment and steer the experiment based on the state of the system. A key feature of a system that supports this design goal is the ability to start, stop, pause and roll-back the disease propagation and intervention application process interactively. An analyst can access the state of the system at any point in time and formulate dynamic interventions based on additional information obtained through state assessment. In addition, the environment provides automated services for experiment set-up and management, thus reducing the overall time for conducting end-to-end experimental studies. We illustrate the applicability of the system by describing computational experiments based on realistic pandemic planning scenarios. The experiments are designed to demonstrate the system's capability and enhanced user productivity. PMID:25530914

Improvements to the User Interface for LHCb's Software continuous integration system.

NASA Astrophysics Data System (ADS)

Clemencic, M.; Couturier, B.; Kyriazi, S.

2015-12-01

The purpose of this paper is to identify a set of steps leading to an improved interface for LHCb's Nightly Builds Dashboard. The goal is to have an efficient application that meets the needs of both the project developers, by providing them with a user friendly interface, as well as those of the computing team supporting the system, by providing them with a dashboard allowing for better monitoring of the build job themselves. In line with what is already used by LHCb, the web interface has been implemented with the Flask Python framework for future maintainability and code clarity. The Database chosen to host the data is the schema-less CouchDB[7], serving the purpose of flexibility in document form changes. To improve the user experience, we use JavaScript libraries such as JQuery[11].

The Helicopter Antenna Radiation Prediction Code (HARP)

NASA Technical Reports Server (NTRS)

Klevenow, F. T.; Lynch, B. G.; Newman, E. H.; Rojas, R. G.; Scheick, J. T.; Shamansky, H. T.; Sze, K. Y.

1990-01-01

The first nine months effort in the development of a user oriented computer code, referred to as the HARP code, for analyzing the radiation from helicopter antennas is described. The HARP code uses modern computer graphics to aid in the description and display of the helicopter geometry. At low frequencies the helicopter is modeled by polygonal plates, and the method of moments is used to compute the desired patterns. At high frequencies the helicopter is modeled by a composite ellipsoid and flat plates, and computations are made using the geometrical theory of diffraction. The HARP code will provide a user friendly interface, employing modern computer graphics, to aid the user to describe the helicopter geometry, select the method of computation, construct the desired high or low frequency model, and display the results.

CloudDOE: a user-friendly tool for deploying Hadoop clouds and analyzing high-throughput sequencing data with MapReduce.

PubMed

Chung, Wei-Chun; Chen, Chien-Chih; Ho, Jan-Ming; Lin, Chung-Yen; Hsu, Wen-Lian; Wang, Yu-Chun; Lee, D T; Lai, Feipei; Huang, Chih-Wei; Chang, Yu-Jung

2014-01-01

Explosive growth of next-generation sequencing data has resulted in ultra-large-scale data sets and ensuing computational problems. Cloud computing provides an on-demand and scalable environment for large-scale data analysis. Using a MapReduce framework, data and workload can be distributed via a network to computers in the cloud to substantially reduce computational latency. Hadoop/MapReduce has been successfully adopted in bioinformatics for genome assembly, mapping reads to genomes, and finding single nucleotide polymorphisms. Major cloud providers offer Hadoop cloud services to their users. However, it remains technically challenging to deploy a Hadoop cloud for those who prefer to run MapReduce programs in a cluster without built-in Hadoop/MapReduce. We present CloudDOE, a platform-independent software package implemented in Java. CloudDOE encapsulates technical details behind a user-friendly graphical interface, thus liberating scientists from having to perform complicated operational procedures. Users are guided through the user interface to deploy a Hadoop cloud within in-house computing environments and to run applications specifically targeted for bioinformatics, including CloudBurst, CloudBrush, and CloudRS. One may also use CloudDOE on top of a public cloud. CloudDOE consists of three wizards, i.e., Deploy, Operate, and Extend wizards. Deploy wizard is designed to aid the system administrator to deploy a Hadoop cloud. It installs Java runtime environment version 1.6 and Hadoop version 0.20.203, and initiates the service automatically. Operate wizard allows the user to run a MapReduce application on the dashboard list. To extend the dashboard list, the administrator may install a new MapReduce application using Extend wizard. CloudDOE is a user-friendly tool for deploying a Hadoop cloud. Its smart wizards substantially reduce the complexity and costs of deployment, execution, enhancement, and management. Interested users may collaborate to improve the source code of CloudDOE to further incorporate more MapReduce bioinformatics tools into CloudDOE and support next-generation big data open source tools, e.g., Hadoop BigTop and Spark. CloudDOE is distributed under Apache License 2.0 and is freely available at http://clouddoe.iis.sinica.edu.tw/.

CloudDOE: A User-Friendly Tool for Deploying Hadoop Clouds and Analyzing High-Throughput Sequencing Data with MapReduce

PubMed Central

Chung, Wei-Chun; Chen, Chien-Chih; Ho, Jan-Ming; Lin, Chung-Yen; Hsu, Wen-Lian; Wang, Yu-Chun; Lee, D. T.; Lai, Feipei; Huang, Chih-Wei; Chang, Yu-Jung

2014-01-01

Background Explosive growth of next-generation sequencing data has resulted in ultra-large-scale data sets and ensuing computational problems. Cloud computing provides an on-demand and scalable environment for large-scale data analysis. Using a MapReduce framework, data and workload can be distributed via a network to computers in the cloud to substantially reduce computational latency. Hadoop/MapReduce has been successfully adopted in bioinformatics for genome assembly, mapping reads to genomes, and finding single nucleotide polymorphisms. Major cloud providers offer Hadoop cloud services to their users. However, it remains technically challenging to deploy a Hadoop cloud for those who prefer to run MapReduce programs in a cluster without built-in Hadoop/MapReduce. Results We present CloudDOE, a platform-independent software package implemented in Java. CloudDOE encapsulates technical details behind a user-friendly graphical interface, thus liberating scientists from having to perform complicated operational procedures. Users are guided through the user interface to deploy a Hadoop cloud within in-house computing environments and to run applications specifically targeted for bioinformatics, including CloudBurst, CloudBrush, and CloudRS. One may also use CloudDOE on top of a public cloud. CloudDOE consists of three wizards, i.e., Deploy, Operate, and Extend wizards. Deploy wizard is designed to aid the system administrator to deploy a Hadoop cloud. It installs Java runtime environment version 1.6 and Hadoop version 0.20.203, and initiates the service automatically. Operate wizard allows the user to run a MapReduce application on the dashboard list. To extend the dashboard list, the administrator may install a new MapReduce application using Extend wizard. Conclusions CloudDOE is a user-friendly tool for deploying a Hadoop cloud. Its smart wizards substantially reduce the complexity and costs of deployment, execution, enhancement, and management. Interested users may collaborate to improve the source code of CloudDOE to further incorporate more MapReduce bioinformatics tools into CloudDOE and support next-generation big data open source tools, e.g., Hadoop BigTop and Spark. Availability: CloudDOE is distributed under Apache License 2.0 and is freely available at http://clouddoe.iis.sinica.edu.tw/. PMID:24897343

A Python-based interface to examine motions in time series of solar images

NASA Astrophysics Data System (ADS)

Campos-Rozo, J. I.; Vargas Domínguez, S.

2017-10-01

Python is considered to be a mature programming language, besides of being widely accepted as an engaging option for scientific analysis in multiple areas, as will be presented in this work for the particular case of solar physics research. SunPy is an open-source library based on Python that has been recently developed to furnish software tools to solar data analysis and visualization. In this work we present a graphical user interface (GUI) based on Python and Qt to effectively compute proper motions for the analysis of time series of solar data. This user-friendly computing interface, that is intended to be incorporated to the Sunpy library, uses a local correlation tracking technique and some extra tools that allows the selection of different parameters to calculate, vizualize and analyze vector velocity fields of solar data, i.e. time series of solar filtergrams and magnetograms.

ABrox-A user-friendly Python module for approximate Bayesian computation with a focus on model comparison.

PubMed

Mertens, Ulf Kai; Voss, Andreas; Radev, Stefan

2018-01-01

We give an overview of the basic principles of approximate Bayesian computation (ABC), a class of stochastic methods that enable flexible and likelihood-free model comparison and parameter estimation. Our new open-source software called ABrox is used to illustrate ABC for model comparison on two prominent statistical tests, the two-sample t-test and the Levene-Test. We further highlight the flexibility of ABC compared to classical Bayesian hypothesis testing by computing an approximate Bayes factor for two multinomial processing tree models. Last but not least, throughout the paper, we introduce ABrox using the accompanied graphical user interface.

Ecoupling server: A tool to compute and analyze electronic couplings.

PubMed

Cabeza de Vaca, Israel; Acebes, Sandra; Guallar, Victor

2016-07-05

Electron transfer processes are often studied through the evaluation and analysis of the electronic coupling (EC). Since most standard QM codes do not provide readily such a measure, additional, and user-friendly tools to compute and analyze electronic coupling from external wave functions will be of high value. The first server to provide a friendly interface for evaluation and analysis of electronic couplings under two different approximations (FDC and GMH) is presented in this communication. Ecoupling server accepts inputs from common QM and QM/MM software and provides useful plots to understand and analyze the results easily. The web server has been implemented in CGI-python using Apache and it is accessible at http://ecouplingserver.bsc.es. Ecoupling server is free and open to all users without login. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

An interactive program for pharmacokinetic modeling.

PubMed

Lu, D R; Mao, F

1993-05-01

A computer program, PharmK, was developed for pharmacokinetic modeling of experimental data. The program was written in C computer language based on the high-level user-interface Macintosh operating system. The intention was to provide a user-friendly tool for users of Macintosh computers. An interactive algorithm based on the exponential stripping method is used for the initial parameter estimation. Nonlinear pharmacokinetic model fitting is based on the maximum likelihood estimation method and is performed by the Levenberg-Marquardt method based on chi 2 criterion. Several methods are available to aid the evaluation of the fitting results. Pharmacokinetic data sets have been examined with the PharmK program, and the results are comparable with those obtained with other programs that are currently available for IBM PC-compatible and other types of computers.

[Real-time detection and processing of medical signals under windows using Lcard analog interfaces].

PubMed

Kuz'min, A A; Belozerov, A E; Pronin, T V

2008-01-01

Multipurpose modular software for an analog interface based on Lcard 761 is considered. Algorithms for pipeline processing of medical signals under Windows with dynamic control of computational resources are suggested. The software consists of user-friendly completable modifiable modules. The module hierarchy is based on object-oriented heritage principles, which make it possible to construct various real-time systems for long-term detection, processing, and imaging of multichannel medical signals.

Recent developments in the CCP-EM software suite.

PubMed

Burnley, Tom; Palmer, Colin M; Winn, Martyn

2017-06-01

As part of its remit to provide computational support to the cryo-EM community, the Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) has produced a software framework which enables easy access to a range of programs and utilities. The resulting software suite incorporates contributions from different collaborators by encapsulating them in Python task wrappers, which are then made accessible via a user-friendly graphical user interface as well as a command-line interface suitable for scripting. The framework includes tools for project and data management. An overview of the design of the framework is given, together with a survey of the functionality at different levels. The current CCP-EM suite has particular strength in the building and refinement of atomic models into cryo-EM reconstructions, which is described in detail.

Recent developments in the CCP-EM software suite

PubMed Central

Burnley, Tom

2017-01-01

As part of its remit to provide computational support to the cryo-EM community, the Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) has produced a software framework which enables easy access to a range of programs and utilities. The resulting software suite incorporates contributions from different collaborators by encapsulating them in Python task wrappers, which are then made accessible via a user-friendly graphical user interface as well as a command-line interface suitable for scripting. The framework includes tools for project and data management. An overview of the design of the framework is given, together with a survey of the functionality at different levels. The current CCP-EM suite has particular strength in the building and refinement of atomic models into cryo-EM reconstructions, which is described in detail. PMID:28580908

Applying graphics user interface ot group technology classification and coding at the Boeing aerospace company

NASA Astrophysics Data System (ADS)

Ness, P. H.; Jacobson, H.

1984-10-01

The thrust of 'group technology' is toward the exploitation of similarities in component design and manufacturing process plans to achieve assembly line flow cost efficiencies for small batch production. The systematic method devised for the identification of similarities in component geometry and processing steps is a coding and classification scheme implemented by interactive CAD/CAM systems. This coding and classification scheme has led to significant increases in computer processing power, allowing rapid searches and retrievals on the basis of a 30-digit code together with user-friendly computer graphics.

Nutrient Tracking Tool - A user-friendly tool for evaluating the water and air quality and quantity as affected by various agricultural management practices

NASA Astrophysics Data System (ADS)

Saleh, A.; Niraula, R.; Gallego, O.; Osei, E.; Kannan, N.

2017-12-01

The Nutrient Tracking Tool (NTT) is a user-friendly web-based computer program that estimate nutrient (nitrogen and phosphorus) and sediment losses from fields managed under a variety of cropping patterns and management practices. The NTT includes a user-friendly web-based interface and is linked to the Agricultural Policy Environmental eXtender (APEX) model. It also accesses USDA-NRCS's Web Soil Survey to obtain field, weather, and soil information. NTT provides producers, government officials, and other users with a fast and efficient method of estimating the nutrient, sediment, and atmosphoric gases (N2o, Co2, and NH4) losses, and crop production under different conservation practices regims at the farm-level. The information obtained from NTT can help producers to determine the most cost-effective conservation practice(s) to reduce the nutrient and sediment losses while optimizing the crop production. Also, the recent version of NTT (NTTg3) has been developed for those coutries without access to national databasis, such as soils and wether. The NTTg3 also has been designed as easy to use APEX interface. NTT is currently being evaluated for trading and other programs at Cheaseapea Bay regions and numerous states in US. During this presentation the new capabilities of NTTg3 will be described and demonstrated.

The power of pezonomics

NASA Technical Reports Server (NTRS)

Orr, Joel N.

1995-01-01

This reflection of human-computer interface and its requirements as virtual technology is advanced, proposes a new term: 'Pezonomics'. The term replaces the term ergonomics ('the law of work') with a definition pointing to 'the law of play.' The necessity of this term, the author reasons, comes from the need to 'capture the essence of play and calibrate our computer systems to its cadences.' Pezonomics will ensure that artificial environments, in particular virtual reality, are user friendly.

An Efficient User Interface Design for Nursing Information System Based on Integrated Patient Order Information.

PubMed

Chu, Chia-Hui; Kuo, Ming-Chuan; Weng, Shu-Hui; Lee, Ting-Ting

2016-01-01

A user friendly interface can enhance the efficiency of data entry, which is crucial for building a complete database. In this study, two user interfaces (traditional pull-down menu vs. check boxes) are proposed and evaluated based on medical records with fever medication orders by measuring the time for data entry, steps for each data entry record, and the complete rate of each medical record. The result revealed that the time for data entry is reduced from 22.8 sec/record to 3.2 sec/record. The data entry procedures also have reduced from 9 steps in the traditional one to 3 steps in the new one. In addition, the completeness of medical records is increased from 20.2% to 98%. All these results indicate that the new user interface provides a more user friendly and efficient approach for data entry than the traditional interface.

Ergatis: a web interface and scalable software system for bioinformatics workflows

PubMed Central

Orvis, Joshua; Crabtree, Jonathan; Galens, Kevin; Gussman, Aaron; Inman, Jason M.; Lee, Eduardo; Nampally, Sreenath; Riley, David; Sundaram, Jaideep P.; Felix, Victor; Whitty, Brett; Mahurkar, Anup; Wortman, Jennifer; White, Owen; Angiuoli, Samuel V.

2010-01-01

Motivation: The growth of sequence data has been accompanied by an increasing need to analyze data on distributed computer clusters. The use of these systems for routine analysis requires scalable and robust software for data management of large datasets. Software is also needed to simplify data management and make large-scale bioinformatics analysis accessible and reproducible to a wide class of target users. Results: We have developed a workflow management system named Ergatis that enables users to build, execute and monitor pipelines for computational analysis of genomics data. Ergatis contains preconfigured components and template pipelines for a number of common bioinformatics tasks such as prokaryotic genome annotation and genome comparisons. Outputs from many of these components can be loaded into a Chado relational database. Ergatis was designed to be accessible to a broad class of users and provides a user friendly, web-based interface. Ergatis supports high-throughput batch processing on distributed compute clusters and has been used for data management in a number of genome annotation and comparative genomics projects. Availability: Ergatis is an open-source project and is freely available at http://ergatis.sourceforge.net Contact: jorvis@users.sourceforge.net PMID:20413634

Algodoo: A Tool for Encouraging Creativity in Physics Teaching and Learning

NASA Astrophysics Data System (ADS)

Gregorcic, Bor; Bodin, Madelen

2017-01-01

Algodoo (http://www.algodoo.com) is a digital sandbox for physics 2D simulations. It allows students and teachers to easily create simulated "scenes" and explore physics through a user-friendly and visually attractive interface. In this paper, we present different ways in which students and teachers can use Algodoo to visualize and solve physics problems, investigate phenomena and processes, and engage in out-of-school activities and projects. Algodoo, with its approachable interface, inhabits a middle ground between computer games and "serious" computer modeling. It is suitable as an entry-level modeling tool for students of all ages and can facilitate discussions about the role of computer modeling in physics.

TIGER: A user-friendly interactive grid generation system for complicated turbomachinery and axis-symmetric configurations

NASA Technical Reports Server (NTRS)

Shih, Ming H.; Soni, Bharat K.

1993-01-01

The issue of time efficiency in grid generation is addressed by developing a user friendly graphical interface for interactive/automatic construction of structured grids around complex turbomachinery/axis-symmetric configurations. The accuracy of geometry modeling and its fidelity is accomplished by adapting the nonuniform rational b-spline (NURBS) representation. A customized interactive grid generation code, TIGER, has been developed to facilitate the grid generation process for complicated internal, external, and internal-external turbomachinery fields simulations. The FORMS Library is utilized to build user-friendly graphical interface. The algorithm allows a user to redistribute grid points interactively on curves/surfaces using NURBS formulation with accurate geometric definition. TIGER's features include multiblock, multiduct/shroud, multiblade row, uneven blade count, and patched/overlapping block interfaces. It has been applied to generate grids for various complicated turbomachinery geometries, as well as rocket and missile configurations.

The Georgetown University Library Information System (LIS): a minicomputer-based integrated library system.

PubMed Central

Broering, N C

1983-01-01

Georgetown University's Library Information System (LIS), an integrated library system designed and implemented at the Dahlgren Memorial Library, is broadly described from an administrative point of view. LIS' functional components consist of eight "user-friendly" modules: catalog, circulation, serials, bibliographic management (including Mini-MEDLINE), acquisitions, accounting, networking, and computer-assisted instruction. This article touches on emerging library services, user education, and computer information services, which are also changing the role of staff librarians. The computer's networking capability brings the library directly to users through personal or institutional computers at remote sites. The proposed Integrated Medical Center Information System at Georgetown University will include interface with LIS through a network mechanism. LIS is being replicated at other libraries, and a microcomputer version is being tested for use in a hospital setting. PMID:6688749

Computer programing for geosciences: Teach your students how to make tools

NASA Astrophysics Data System (ADS)

Grapenthin, Ronni

2011-12-01

When I announced my intention to pursue a Ph.D. in geophysics, some people gave me confused looks, because I was working on a master's degree in computer science at the time. My friends, like many incoming geoscience graduate students, have trouble linking these two fields. From my perspective, it is pretty straightforward: Much of geoscience evolves around novel analyses of large data sets that require custom tools—computer programs—to minimize the drudgery of manual data handling; other disciplines share this characteristic. While most faculty adapted to the need for tool development quite naturally, as they grew up around computer terminal interfaces, incoming graduate students lack intuitive understanding of programing concepts such as generalization and automation. I believe the major cause is the intuitive graphical user interfaces of modern operating systems and applications, which isolate the user from all technical details. Generally, current curricula do not recognize this gap between user and machine. For students to operate effectively, they require specialized courses teaching them the skills they need to make tools that operate on particular data sets and solve their specific problems. Courses in computer science departments are aimed at a different audience and are of limited help.

MOO in Your Face: Researching, Designing, and Programming a User-Friendly Interface.

ERIC Educational Resources Information Center

Haas, Mark; Gardner, Clinton

1999-01-01

Suggests the learning curve of a multi-user, object-oriented domain (MOO) blockades effective use. Discusses use of an IBM/PC-compatible interface that allows developers to modify the interface to provide a sense of presence for the user. Concludes that work in programming a variety of interfaces has led to a more intuitive environment for…

MASTRE trajectory code update to automate flight trajectory design, performance predictions, and vehicle sizing for support of shuttle and shuttle derived vehicles: Programmers manual

NASA Technical Reports Server (NTRS)

1993-01-01

The information required by a programmer using the Minimum Hamiltonian AScent Trajectory Evaluation (MASTRE) Program is provided. This document enables the programmer to either modify the program or convert the program to computers other than the VAX computer. Documentation for each subroutine or function based on providing the definitions of the variables and a source listing are included. Questions concerning the equations, techniques, or input requirements should be answered by either the Engineering or User's manuals. Three appendices are also included which provide a listing of the Root-Sum-Square (RSS) program, a listing of subroutine names and definitions used in the MASTRE User Friendly Interface Program, and listing of the subroutine names and definitions used in the Mass Properties Program. The RSS Program is used to aid in the performance of dispersion analyses. The RSS program reads a file generated by the MASTRE Program, calculates dispersion parameters, and generates output tables and output plot files. UFI Program provides a screen user interface to aid the user in providing input to the model. The Mass Properties Program defines the mass properties data for the MASTRE program through the use of user interface software.

Development of an imaging method for quantifying a large digital PCR droplet

NASA Astrophysics Data System (ADS)

Huang, Jen-Yu; Lee, Shu-Sheng; Hsu, Yu-Hsiang

2017-02-01

Portable devices have been recognized as the future linkage between end-users and lab-on-a-chip devices. It has a user friendly interface and provides apps to interface headphones, cameras, and communication duct, etc. In particular, the digital resolution of cameras installed in smartphones or pads already has a high imaging resolution with a high number of pixels. This unique feature has triggered researches to integrate optical fixtures with smartphone to provide microscopic imaging capabilities. In this paper, we report our study on developing a portable diagnostic tool based on the imaging system of a smartphone and a digital PCR biochip. A computational algorithm is developed to processing optical images taken from a digital PCR biochip with a smartphone in a black box. Each reaction droplet is recorded in pixels and is analyzed in a sRGB (red, green, and blue) color space. Multistep filtering algorithm and auto-threshold algorithm are adopted to minimize background noise contributed from ccd cameras and rule out false positive droplets, respectively. Finally, a size-filtering method is applied to identify the number of positive droplets to quantify target's concentration. Statistical analysis is then performed for diagnostic purpose. This process can be integrated in an app and can provide a user friendly interface without professional training.

Influence of Learning Styles on Graphical User Interface Preferences for e-Learners

ERIC Educational Resources Information Center

Dedic, Velimir; Markovic, Suzana

2012-01-01

Implementing Web-based educational environment requires not only developing appropriate architectures, but also incorporating human factors considerations. User interface becomes the major channel to convey information in e-learning context: a well-designed and friendly enough interface is thus the key element in helping users to get the best…

Virtual Diagnostic Interface: Aerospace Experimentation in the Synthetic Environment

NASA Technical Reports Server (NTRS)

Schwartz, Richard J.; McCrea, Andrew C.

2009-01-01

The Virtual Diagnostics Interface (ViDI) methodology combines two-dimensional image processing and three-dimensional computer modeling to provide comprehensive in-situ visualizations commonly utilized for in-depth planning of wind tunnel and flight testing, real time data visualization of experimental data, and unique merging of experimental and computational data sets in both real-time and post-test analysis. The preparation of such visualizations encompasses the realm of interactive three-dimensional environments, traditional and state of the art image processing techniques, database management and development of toolsets with user friendly graphical user interfaces. ViDI has been under development at the NASA Langley Research Center for over 15 years, and has a long track record of providing unique and insightful solutions to a wide variety of experimental testing techniques and validation of computational simulations. This report will address the various aspects of ViDI and how it has been applied to test programs as varied as NASCAR race car testing in NASA wind tunnels to real-time operations concerning Space Shuttle aerodynamic flight testing. In addition, future trends and applications will be outlined in the paper.

Virtual Diagnostic Interface: Aerospace Experimentation in the Synthetic Environment

NASA Technical Reports Server (NTRS)

Schwartz, Richard J.; McCrea, Andrew C.

2010-01-01

The Virtual Diagnostics Interface (ViDI) methodology combines two-dimensional image processing and three-dimensional computer modeling to provide comprehensive in-situ visualizations commonly utilized for in-depth planning of wind tunnel and flight testing, real time data visualization of experimental data, and unique merging of experimental and computational data sets in both real-time and post-test analysis. The preparation of such visualizations encompasses the realm of interactive three-dimensional environments, traditional and state of the art image processing techniques, database management and development of toolsets with user friendly graphical user interfaces. ViDI has been under development at the NASA Langley Research Center for over 15 years, and has a long track record of providing unique and insightful solutions to a wide variety of experimental testing techniques and validation of computational simulations. This report will address the various aspects of ViDI and how it has been applied to test programs as varied as NASCAR race car testing in NASA wind tunnels to real-time operations concerning Space Shuttle aerodynamic flight testing. In addition, future trends and applications will be outlined in the paper.

Pre- and postprocessing techniques for determining goodness of computational meshes

NASA Technical Reports Server (NTRS)

Oden, J. Tinsley; Westermann, T.; Bass, J. M.

1993-01-01

Research in error estimation, mesh conditioning, and solution enhancement for finite element, finite difference, and finite volume methods has been incorporated into AUDITOR, a modern, user-friendly code, which operates on 2D and 3D unstructured neutral files to improve the accuracy and reliability of computational results. Residual error estimation capabilities provide local and global estimates of solution error in the energy norm. Higher order results for derived quantities may be extracted from initial solutions. Within the X-MOTIF graphical user interface, extensive visualization capabilities support critical evaluation of results in linear elasticity, steady state heat transfer, and both compressible and incompressible fluid dynamics.

COPASI and its applications in biotechnology.

PubMed

Bergmann, Frank T; Hoops, Stefan; Klahn, Brian; Kummer, Ursula; Mendes, Pedro; Pahle, Jürgen; Sahle, Sven

2017-11-10

COPASI is software used for the creation, modification, simulation and computational analysis of kinetic models in various fields. It is open-source, available for all major platforms and provides a user-friendly graphical user interface, but is also controllable via the command line and scripting languages. These are likely reasons for its wide acceptance. We begin this review with a short introduction describing the general approaches and techniques used in computational modeling in the biosciences. Next we introduce the COPASI package, and its capabilities, before looking at typical applications of COPASI in biotechnology. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

AstrodyToolsWeb an e-Science project in Astrodynamics and Celestial Mechanics fields

NASA Astrophysics Data System (ADS)

López, R.; San-Juan, J. F.

2013-05-01

Astrodynamics Web Tools, AstrodyToolsWeb (http://tastrody.unirioja.es), is an ongoing collaborative Web Tools computing infrastructure project which has been specially designed to support scientific computation. AstrodyToolsWeb provides project collaborators with all the technical and human facilities in order to wrap, manage, and use specialized noncommercial software tools in Astrodynamics and Celestial Mechanics fields, with the aim of optimizing the use of resources, both human and material. However, this project is open to collaboration from the whole scientific community in order to create a library of useful tools and their corresponding theoretical backgrounds. AstrodyToolsWeb offers a user-friendly web interface in order to choose applications, introduce data, and select appropriate constraints in an intuitive and easy way for the user. After that, the application is executed in real time, whenever possible; then the critical information about program behavior (errors and logs) and output, including the postprocessing and interpretation of its results (graphical representation of data, statistical analysis or whatever manipulation therein), are shown via the same web interface or can be downloaded to the user's computer.

PPC750 Performance Monitor

NASA Technical Reports Server (NTRS)

Meyer, Donald; Uchenik, Igor

2007-01-01

The PPC750 Performance Monitor (Perfmon) is a computer program that helps the user to assess the performance characteristics of application programs running under the Wind River VxWorks real-time operating system on a PPC750 computer. Perfmon generates a user-friendly interface and collects performance data by use of performance registers provided by the PPC750 architecture. It processes and presents run-time statistics on a per-task basis over a repeating time interval (typically, several seconds or minutes) specified by the user. When the Perfmon software module is loaded with the user s software modules, it is available for use through Perfmon commands, without any modification of the user s code and at negligible performance penalty. Per-task run-time performance data made available by Perfmon include percentage time, number of instructions executed per unit time, dispatch ratio, stack high water mark, and level-1 instruction and data cache miss rates. The performance data are written to a file specified by the user or to the serial port of the computer

Chipster: user-friendly analysis software for microarray and other high-throughput data.

PubMed

Kallio, M Aleksi; Tuimala, Jarno T; Hupponen, Taavi; Klemelä, Petri; Gentile, Massimiliano; Scheinin, Ilari; Koski, Mikko; Käki, Janne; Korpelainen, Eija I

2011-10-14

The growth of high-throughput technologies such as microarrays and next generation sequencing has been accompanied by active research in data analysis methodology, producing new analysis methods at a rapid pace. While most of the newly developed methods are freely available, their use requires substantial computational skills. In order to enable non-programming biologists to benefit from the method development in a timely manner, we have created the Chipster software. Chipster (http://chipster.csc.fi/) brings a powerful collection of data analysis methods within the reach of bioscientists via its intuitive graphical user interface. Users can analyze and integrate different data types such as gene expression, miRNA and aCGH. The analysis functionality is complemented with rich interactive visualizations, allowing users to select datapoints and create new gene lists based on these selections. Importantly, users can save the performed analysis steps as reusable, automatic workflows, which can also be shared with other users. Being a versatile and easily extendable platform, Chipster can be used for microarray, proteomics and sequencing data. In this article we describe its comprehensive collection of analysis and visualization tools for microarray data using three case studies. Chipster is a user-friendly analysis software for high-throughput data. Its intuitive graphical user interface enables biologists to access a powerful collection of data analysis and integration tools, and to visualize data interactively. Users can collaborate by sharing analysis sessions and workflows. Chipster is open source, and the server installation package is freely available.

Chipster: user-friendly analysis software for microarray and other high-throughput data

PubMed Central

2011-01-01

Background The growth of high-throughput technologies such as microarrays and next generation sequencing has been accompanied by active research in data analysis methodology, producing new analysis methods at a rapid pace. While most of the newly developed methods are freely available, their use requires substantial computational skills. In order to enable non-programming biologists to benefit from the method development in a timely manner, we have created the Chipster software. Results Chipster (http://chipster.csc.fi/) brings a powerful collection of data analysis methods within the reach of bioscientists via its intuitive graphical user interface. Users can analyze and integrate different data types such as gene expression, miRNA and aCGH. The analysis functionality is complemented with rich interactive visualizations, allowing users to select datapoints and create new gene lists based on these selections. Importantly, users can save the performed analysis steps as reusable, automatic workflows, which can also be shared with other users. Being a versatile and easily extendable platform, Chipster can be used for microarray, proteomics and sequencing data. In this article we describe its comprehensive collection of analysis and visualization tools for microarray data using three case studies. Conclusions Chipster is a user-friendly analysis software for high-throughput data. Its intuitive graphical user interface enables biologists to access a powerful collection of data analysis and integration tools, and to visualize data interactively. Users can collaborate by sharing analysis sessions and workflows. Chipster is open source, and the server installation package is freely available. PMID:21999641

User Interface for the ESO Advanced Data Products Image Reduction Pipeline

NASA Astrophysics Data System (ADS)

Rité, C.; Delmotte, N.; Retzlaff, J.; Rosati, P.; Slijkhuis, R.; Vandame, B.

2006-07-01

The poster presents a friendly user interface for image reduction, totally written in Python and developed by the Advanced Data Products (ADP) group. The interface is a front-end to the ESO/MVM image reduction package, originally developed in the ESO Imaging Survey (EIS) project and used currently to reduce imaging data from several instruments such as WFI, ISAAC, SOFI and FORS1. As part of its scope, the interface produces high-level, VO-compliant, science images from raw data providing the astronomer with a complete monitoring system during the reduction, computing also statistical image properties for data quality assessment. The interface is meant to be used for VO services and it is free but un-maintained software and the intention of the authors is to share code and experience. The poster describes the interface architecture and current capabilities and give a description of the ESO/MVM engine for image reduction. The ESO/MVM engine should be released by the end of this year.

Program Aids Design Of Fluid-Circulating Systems

NASA Technical Reports Server (NTRS)

Bacskay, Allen; Dalee, Robert

1992-01-01

Computer Aided Systems Engineering and Analysis (CASE/A) program is interactive software tool for trade study and analysis, designed to increase productivity during all phases of systems engineering. Graphics-based command-driven software package provides user-friendly computing environment in which engineer analyzes performance and interface characteristics of ECLS/ATC system. Useful during all phases of spacecraft-design program, from initial conceptual design trade studies to actual flight, including pre-flight prediction and in-flight analysis of anomalies. Written in FORTRAN 77.

Jim Thomas, 1946-2010

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

Stone, Maureen; Kasik, David; Bailey, Mike

Jim Thomas, a visionary scientist and inspirational leader, died on 6 August 2010 in Richland, Washington. His impact on the fields of computer graphics, user interface software, and visualization was extraordinary, his ability to personally change people’s lives even more so. He is remembered for his enthusiasm, his mentorship, his generosity, and, most of all, his laughter. This collection of remembrances images him through the eyes of his many friends.

Assessing performance of an Electronic Health Record (EHR) using Cognitive Task Analysis.

PubMed

Saitwal, Himali; Feng, Xuan; Walji, Muhammad; Patel, Vimla; Zhang, Jiajie

2010-07-01

Many Electronic Health Record (EHR) systems fail to provide user-friendly interfaces due to the lack of systematic consideration of human-centered computing issues. Such interfaces can be improved to provide easy to use, easy to learn, and error-resistant EHR systems to the users. To evaluate the usability of an EHR system and suggest areas of improvement in the user interface. The user interface of the AHLTA (Armed Forces Health Longitudinal Technology Application) was analyzed using the Cognitive Task Analysis (CTA) method called GOMS (Goals, Operators, Methods, and Selection rules) and an associated technique called KLM (Keystroke Level Model). The GOMS method was used to evaluate the AHLTA user interface by classifying each step of a given task into Mental (Internal) or Physical (External) operators. This analysis was performed by two analysts independently and the inter-rater reliability was computed to verify the reliability of the GOMS method. Further evaluation was performed using KLM to estimate the execution time required to perform the given task through application of its standard set of operators. The results are based on the analysis of 14 prototypical tasks performed by AHLTA users. The results show that on average a user needs to go through 106 steps to complete a task. To perform all 14 tasks, they would spend about 22 min (independent of system response time) for data entry, of which 11 min are spent on more effortful mental operators. The inter-rater reliability analysis performed for all 14 tasks was 0.8 (kappa), indicating good reliability of the method. This paper empirically reveals and identifies the following finding related to the performance of AHLTA: (1) large number of average total steps to complete common tasks, (2) high average execution time and (3) large percentage of mental operators. The user interface can be improved by reducing (a) the total number of steps and (b) the percentage of mental effort, required for the tasks. 2010 Elsevier Ireland Ltd. All rights reserved.

Evaluation of the large scale computing needs of the energy research program and how to meet them. Final report

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

Miller, B.

The Energy Research program may be on the verge of abdicating an important role it has traditionally played in the development and use of state-of-the-art computer systems. The lack of easy access to Class VI systems coupled to the easy availability of local, user-friendly systems is conspiring to drive many investigators away from forefront research in computational science and in the use of state-of-the-art computers for more discipline-oriented problem solving. The survey conducted under the auspices of this contract clearly demonstrates a significant suppressed demand for actual Class VI hours totaling the full capacity of one such system. The currentmore » usage is about a factor of 15 below this level. There is also a need for about 50% more capacity in the current mini/midi availability. Meeting the needs of the ER community for this level of computing power and capacity is most probably best achieved through the establishment of a central Class VI capability at some site linked through a nationwide network to the various ER laboratories and universities and interfaced with the local user-friendly systems at those remote sites.« less

The development of an intelligent user interface for NASA's scientific databases

NASA Technical Reports Server (NTRS)

Campbell, William J.; Roelofs, Larry H.

1986-01-01

The National Space Science Data Center (NSSDC) has initiated an Intelligent Data Management (IDM) research effort which has as one of its components, the development of an Intelligent User Interface (IUI). The intent of the IUI effort is to develop a friendly and intelligent user interface service that is based on expert systems and natural language processing technologies. This paper presents the design concepts, development approach and evaluation of performance of a prototype Intelligent User Interface Subsystem (IUIS) supporting an operational database.

Comparing Text-based and Graphic User Interfaces for Novice and Expert Users

PubMed Central

Chen, Jung-Wei; Zhang, Jiajie

2007-01-01

Graphic User Interface (GUI) is commonly considered to be superior to Text-based User Interface (TUI). This study compares GUI and TUI in an electronic dental record system. Several usability analysis techniques compared the relative effectiveness of a GUI and a TUI. Expert users and novice users were evaluated in time required and steps needed to complete the task. A within-subject design was used to evaluate if the experience with either interface will affect task performance. The results show that the GUI interface was not better than the TUI for expert users. GUI interface was better for novice users. For novice users there was a learning transfer effect from TUI to GUI. This means a user interface is user-friendly or not depending on the mapping between the user interface and tasks. GUI by itself may or may not be better than TUI. PMID:18693811

Comparing Text-based and Graphic User Interfaces for novice and expert users.

PubMed

Chen, Jung-Wei; Zhang, Jiajie

2007-10-11

Graphic User Interface (GUI) is commonly considered to be superior to Text-based User Interface (TUI). This study compares GUI and TUI in an electronic dental record system. Several usability analysis techniques compared the relative effectiveness of a GUI and a TUI. Expert users and novice users were evaluated in time required and steps needed to complete the task. A within-subject design was used to evaluate if the experience with either interface will affect task performance. The results show that the GUI interface was not better than the TUI for expert users. GUI interface was better for novice users. For novice users there was a learning transfer effect from TUI to GUI. This means a user interface is user-friendly or not depending on the mapping between the user interface and tasks. GUI by itself may or may not be better than TUI.

iDrug: a web-accessible and interactive drug discovery and design platform

PubMed Central

2014-01-01

Background The progress in computer-aided drug design (CADD) approaches over the past decades accelerated the early-stage pharmaceutical research. Many powerful standalone tools for CADD have been developed in academia. As programs are developed by various research groups, a consistent user-friendly online graphical working environment, combining computational techniques such as pharmacophore mapping, similarity calculation, scoring, and target identification is needed. Results We presented a versatile, user-friendly, and efficient online tool for computer-aided drug design based on pharmacophore and 3D molecular similarity searching. The web interface enables binding sites detection, virtual screening hits identification, and drug targets prediction in an interactive manner through a seamless interface to all adapted packages (e.g., Cavity, PocketV.2, PharmMapper, SHAFTS). Several commercially available compound databases for hit identification and a well-annotated pharmacophore database for drug targets prediction were integrated in iDrug as well. The web interface provides tools for real-time molecular building/editing, converting, displaying, and analyzing. All the customized configurations of the functional modules can be accessed through featured session files provided, which can be saved to the local disk and uploaded to resume or update the history work. Conclusions iDrug is easy to use, and provides a novel, fast and reliable tool for conducting drug design experiments. By using iDrug, various molecular design processing tasks can be submitted and visualized simply in one browser without installing locally any standalone modeling softwares. iDrug is accessible free of charge at http://lilab.ecust.edu.cn/idrug. PMID:24955134

Development of the User Interface for AIR-Spec

NASA Astrophysics Data System (ADS)

Cervantes Alcala, E.; Guth, G.; Fedeler, S.; Samra, J.; Cheimets, P.; DeLuca, E.; Golub, L.

2016-12-01

The airborne infrared spectrometer (AIR-Spec) is an imaging spectrometer that will observe the solar corona during the 2017 total solar eclipse. This eclipse will provide a unique opportunity to observe infrared emission lines in the corona. Five spectral lines are of particular interest because they may eventually be used to measure the coronal magnetic field. To avoid infrared absorption from atmospheric water vapor, AIR-Spec will be placed on an NSF Gulfstream aircraft flying above 14.9 km. AIR-Spec must be capable of taking stable images while the plane moves. The instrument includes an image stabilization system, which uses fiber-optic gyroscopes to determine platform rotation, GPS to calculate the ephemeris of the sun, and a voltage-driven mirror to correct the line of sight. An operator monitors a white light image of the eclipse and manually corrects for residual drift. The image stabilization calculation is performed by a programmable automatic controller (PAC), which interfaces with the gyroscopes and mirror controller. The operator interfaces with a separate computer, which acquires images and computes the solar ephemeris. To ensure image stabilization is successful, a human machine interface (HMI) was developed to allow connection between the client and PAC. In order to make control of the instruments user friendly during the short eclipse observation, a graphical user interface (GUI) was also created. The GUI's functionality includes turning image stabilization on and off, allowing the user to input information about the geometric setup, calculating the solar ephemeris, refining estimates of the initial aircraft attitude, and storing data from the PAC on the operator's computer. It also displays time, location, attitude, ephemeris, gyro rates and mirror angles.

MrGrid: A Portable Grid Based Molecular Replacement Pipeline

PubMed Central

Reboul, Cyril F.; Androulakis, Steve G.; Phan, Jennifer M. N.; Whisstock, James C.; Goscinski, Wojtek J.; Abramson, David; Buckle, Ashley M.

2010-01-01

Background The crystallographic determination of protein structures can be computationally demanding and for difficult cases can benefit from user-friendly interfaces to high-performance computing resources. Molecular replacement (MR) is a popular protein crystallographic technique that exploits the structural similarity between proteins that share some sequence similarity. But the need to trial permutations of search models, space group symmetries and other parameters makes MR time- and labour-intensive. However, MR calculations are embarrassingly parallel and thus ideally suited to distributed computing. In order to address this problem we have developed MrGrid, web-based software that allows multiple MR calculations to be executed across a grid of networked computers, allowing high-throughput MR. Methodology/Principal Findings MrGrid is a portable web based application written in Java/JSP and Ruby, and taking advantage of Apple Xgrid technology. Designed to interface with a user defined Xgrid resource the package manages the distribution of multiple MR runs to the available nodes on the Xgrid. We evaluated MrGrid using 10 different protein test cases on a network of 13 computers, and achieved an average speed up factor of 5.69. Conclusions MrGrid enables the user to retrieve and manage the results of tens to hundreds of MR calculations quickly and via a single web interface, as well as broadening the range of strategies that can be attempted. This high-throughput approach allows parameter sweeps to be performed in parallel, improving the chances of MR success. PMID:20386612

A JAVA-based multimedia tool for clinical practice guidelines.

PubMed

Maojo, V; Herrero, C; Valenzuela, F; Crespo, J; Lazaro, P; Pazos, A

1997-01-01

We have developed a specific language for the representation of Clinical Practice Guidelines (CPGs) and Windows C++ and platform independent JAVA applications for multimedia presentation and edition of electronically stored CPGs. This approach facilitates translation of guidelines and protocols from paper to computer-based flowchart representations. Users can navigate through the algorithm with a friendly user interface and access related multimedia information within the context of each clinical problem. CPGs can be stored in a computer server and distributed over the World Wide Web, facilitating dissemination, local adaptation, and use as a reference element in medical care. We have chosen the Agency for Health Care and Policy Research's heart failure guideline to demonstrate the capabilities of our tool.

QuadBase2: web server for multiplexed guanine quadruplex mining and visualization

PubMed Central

Dhapola, Parashar; Chowdhury, Shantanu

2016-01-01

DNA guanine quadruplexes or G4s are non-canonical DNA secondary structures which affect genomic processes like replication, transcription and recombination. G4s are computationally identified by specific nucleotide motifs which are also called putative G4 (PG4) motifs. Despite the general relevance of these structures, there is currently no tool available that can allow batch queries and genome-wide analysis of these motifs in a user-friendly interface. QuadBase2 (quadbase.igib.res.in) presents a completely reinvented web server version of previously published QuadBase database. QuadBase2 enables users to mine PG4 motifs in up to 178 eukaryotes through the EuQuad module. This module interfaces with Ensembl Compara database, to allow users mine PG4 motifs in the orthologues of genes of interest across eukaryotes. PG4 motifs can be mined across genes and their promoter sequences in 1719 prokaryotes through ProQuad module. This module includes a feature that allows genome-wide mining of PG4 motifs and their visualization as circular histograms. TetraplexFinder, the module for mining PG4 motifs in user-provided sequences is now capable of handling up to 20 MB of data. QuadBase2 is a comprehensive PG4 motif mining tool that further expands the configurations and algorithms for mining PG4 motifs in a user-friendly way. PMID:27185890

Near infrared spectroscopy based brain-computer interface

NASA Astrophysics Data System (ADS)

Ranganatha, Sitaram; Hoshi, Yoko; Guan, Cuntai

2005-04-01

A brain-computer interface (BCI) provides users with an alternative output channel other than the normal output path of the brain. BCI is being given much attention recently as an alternate mode of communication and control for the disabled, such as patients suffering from Amyotrophic Lateral Sclerosis (ALS) or "locked-in". BCI may also find applications in military, education and entertainment. Most of the existing BCI systems which rely on the brain's electrical activity use scalp EEG signals. The scalp EEG is an inherently noisy and non-linear signal. The signal is detrimentally affected by various artifacts such as the EOG, EMG, ECG and so forth. EEG is cumbersome to use in practice, because of the need for applying conductive gel, and the need for the subject to be immobile. There is an urgent need for a more accessible interface that uses a more direct measure of cognitive function to control an output device. The optical response of Near Infrared Spectroscopy (NIRS) denoting brain activation can be used as an alternative to electrical signals, with the intention of developing a more practical and user-friendly BCI. In this paper, a new method of brain-computer interface (BCI) based on NIRS is proposed. Preliminary results of our experiments towards developing this system are reported.

Development of Web Interfaces for Analysis Codes

NASA Astrophysics Data System (ADS)

Emoto, M.; Watanabe, T.; Funaba, H.; Murakami, S.; Nagayama, Y.; Kawahata, K.

Several codes have been developed to analyze plasma physics. However, most of them are developed to run on supercomputers. Therefore, users who typically use personal computers (PCs) find it difficult to use these codes. In order to facilitate the widespread use of these codes, a user-friendly interface is required. The authors propose Web interfaces for these codes. To demonstrate the usefulness of this approach, the authors developed Web interfaces for two analysis codes. One of them is for FIT developed by Murakami. This code is used to analyze the NBI heat deposition, etc. Because it requires electron density profiles, electron temperatures, and ion temperatures as polynomial expressions, those unfamiliar with the experiments find it difficult to use this code, especially visitors from other institutes. The second one is for visualizing the lines of force in the LHD (large helical device) developed by Watanabe. This code is used to analyze the interference caused by the lines of force resulting from the various structures installed in the vacuum vessel of the LHD. This code runs on PCs; however, it requires that the necessary parameters be edited manually. Using these Web interfaces, users can execute these codes interactively.

QRev—Software for computation and quality assurance of acoustic doppler current profiler moving-boat streamflow measurements—User’s manual for version 2.8

USGS Publications Warehouse

Mueller, David S.

2016-05-12

The software program, QRev computes the discharge from moving-boat acoustic Doppler current profiler measurements using data collected with any of the Teledyne RD Instrument or SonTek bottom tracking acoustic Doppler current profilers. The computation of discharge is independent of the manufacturer of the acoustic Doppler current profiler because QRev applies consistent algorithms independent of the data source. In addition, QRev automates filtering and quality checking of the collected data and provides feedback to the user of potential quality issues with the measurement. Various statistics and characteristics of the measurement, in addition to a simple uncertainty assessment are provided to the user to assist them in properly rating the measurement. QRev saves an extensible markup language file that can be imported into databases or electronic field notes software. The user interacts with QRev through a tablet-friendly graphical user interface. This report is the manual for version 2.8 of QRev.

BATS: a Bayesian user-friendly software for analyzing time series microarray experiments.

PubMed

Angelini, Claudia; Cutillo, Luisa; De Canditiis, Daniela; Mutarelli, Margherita; Pensky, Marianna

2008-10-06

Gene expression levels in a given cell can be influenced by different factors, namely pharmacological or medical treatments. The response to a given stimulus is usually different for different genes and may depend on time. One of the goals of modern molecular biology is the high-throughput identification of genes associated with a particular treatment or a biological process of interest. From methodological and computational point of view, analyzing high-dimensional time course microarray data requires very specific set of tools which are usually not included in standard software packages. Recently, the authors of this paper developed a fully Bayesian approach which allows one to identify differentially expressed genes in a 'one-sample' time-course microarray experiment, to rank them and to estimate their expression profiles. The method is based on explicit expressions for calculations and, hence, very computationally efficient. The software package BATS (Bayesian Analysis of Time Series) presented here implements the methodology described above. It allows an user to automatically identify and rank differentially expressed genes and to estimate their expression profiles when at least 5-6 time points are available. The package has a user-friendly interface. BATS successfully manages various technical difficulties which arise in time-course microarray experiments, such as a small number of observations, non-uniform sampling intervals and replicated or missing data. BATS is a free user-friendly software for the analysis of both simulated and real microarray time course experiments. The software, the user manual and a brief illustrative example are freely available online at the BATS website: http://www.na.iac.cnr.it/bats.

Methods for Improving the User-Computer Interface. Technical Report.

ERIC Educational Resources Information Center

McCann, Patrick H.

This summary of methods for improving the user-computer interface is based on a review of the pertinent literature. Requirements of the personal computer user are identified and contrasted with computer designer perspectives towards the user. The user's psychological needs are described, so that the design of the user-computer interface may be…

JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing.

PubMed

Brown, David K; Penkler, David L; Musyoka, Thommas M; Bishop, Özlem Tastan

2015-01-01

Complex computational pipelines are becoming a staple of modern scientific research. Often these pipelines are resource intensive and require days of computing time. In such cases, it makes sense to run them over high performance computing (HPC) clusters where they can take advantage of the aggregated resources of many powerful computers. In addition to this, researchers often want to integrate their workflows into their own web servers. In these cases, software is needed to manage the submission of jobs from the web interface to the cluster and then return the results once the job has finished executing. We have developed the Job Management System (JMS), a workflow management system and web interface for high performance computing (HPC). JMS provides users with a user-friendly web interface for creating complex workflows with multiple stages. It integrates this workflow functionality with the resource manager, a tool that is used to control and manage batch jobs on HPC clusters. As such, JMS combines workflow management functionality with cluster administration functionality. In addition, JMS provides developer tools including a code editor and the ability to version tools and scripts. JMS can be used by researchers from any field to build and run complex computational pipelines and provides functionality to include these pipelines in external interfaces. JMS is currently being used to house a number of bioinformatics pipelines at the Research Unit in Bioinformatics (RUBi) at Rhodes University. JMS is an open-source project and is freely available at https://github.com/RUBi-ZA/JMS.

JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing

PubMed Central

Brown, David K.; Penkler, David L.; Musyoka, Thommas M.; Bishop, Özlem Tastan

2015-01-01

Complex computational pipelines are becoming a staple of modern scientific research. Often these pipelines are resource intensive and require days of computing time. In such cases, it makes sense to run them over high performance computing (HPC) clusters where they can take advantage of the aggregated resources of many powerful computers. In addition to this, researchers often want to integrate their workflows into their own web servers. In these cases, software is needed to manage the submission of jobs from the web interface to the cluster and then return the results once the job has finished executing. We have developed the Job Management System (JMS), a workflow management system and web interface for high performance computing (HPC). JMS provides users with a user-friendly web interface for creating complex workflows with multiple stages. It integrates this workflow functionality with the resource manager, a tool that is used to control and manage batch jobs on HPC clusters. As such, JMS combines workflow management functionality with cluster administration functionality. In addition, JMS provides developer tools including a code editor and the ability to version tools and scripts. JMS can be used by researchers from any field to build and run complex computational pipelines and provides functionality to include these pipelines in external interfaces. JMS is currently being used to house a number of bioinformatics pipelines at the Research Unit in Bioinformatics (RUBi) at Rhodes University. JMS is an open-source project and is freely available at https://github.com/RUBi-ZA/JMS. PMID:26280450

Improving the Usability of the User Interface for a Digital Textbook Platform for Elementary-School Students

ERIC Educational Resources Information Center

Lim, Cheolil; Song, Hae-Deok; Lee, Yekyung

2012-01-01

Usability is critical to the development of a user-friendly digital textbook platform interface, yet thorough research on interface development based on usability principles is in short supply. This study addresses that need by looking at usability attributes and corresponding design elements from a learning perspective. The researchers used a…

The GPRIME approach to finite element modeling

NASA Technical Reports Server (NTRS)

Wallace, D. R.; Mckee, J. H.; Hurwitz, M. M.

1983-01-01

GPRIME, an interactive modeling system, runs on the CDC 6000 computers and the DEC VAX 11/780 minicomputer. This system includes three components: (1) GPRIME, a user friendly geometric language and a processor to translate that language into geometric entities, (2) GGEN, an interactive data generator for 2-D models; and (3) SOLIDGEN, a 3-D solid modeling program. Each component has a computer user interface of an extensive command set. All of these programs make use of a comprehensive B-spline mathematics subroutine library, which can be used for a wide variety of interpolation problems and other geometric calculations. Many other user aids, such as automatic saving of the geometric and finite element data bases and hidden line removal, are available. This interactive finite element modeling capability can produce a complete finite element model, producing an output file of grid and element data.

Low Cost Desktop Image Analysis Workstation With Enhanced Interactive User Interface

NASA Astrophysics Data System (ADS)

Ratib, Osman M.; Huang, H. K.

1989-05-01

A multimodality picture archiving and communication system (PACS) is in routine clinical use in the UCLA Radiology Department. Several types workstations are currently implemented for this PACS. Among them, the Apple Macintosh II personal computer was recently chosen to serve as a desktop workstation for display and analysis of radiological images. This personal computer was selected mainly because of its extremely friendly user-interface, its popularity among the academic and medical community and its low cost. In comparison to other microcomputer-based systems the Macintosh II offers the following advantages: the extreme standardization of its user interface, file system and networking, and the availability of a very large variety of commercial software packages. In the current configuration the Macintosh II operates as a stand-alone workstation where images are imported from a centralized PACS server through an Ethernet network using a standard TCP-IP protocol, and stored locally on magnetic disk. The use of high resolution screens (1024x768 pixels x 8bits) offer sufficient performance for image display and analysis. We focused our project on the design and implementation of a variety of image analysis algorithms ranging from automated structure and edge detection to sophisticated dynamic analysis of sequential images. Specific analysis programs were developed for ultrasound images, digitized angiograms, MRI and CT tomographic images and scintigraphic images.

eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing

PubMed Central

2014-01-01

Background RNA sequencing (RNA-seq) is emerging as a critical approach in biological research. However, its high-throughput advantage is significantly limited by the capacity of bioinformatics tools. The research community urgently needs user-friendly tools to efficiently analyze the complicated data generated by high throughput sequencers. Results We developed a standalone tool with graphic user interface (GUI)-based analytic modules, known as eRNA. The capacity of performing parallel processing and sample management facilitates large data analyses by maximizing hardware usage and freeing users from tediously handling sequencing data. The module miRNA identification” includes GUIs for raw data reading, adapter removal, sequence alignment, and read counting. The module “mRNA identification” includes GUIs for reference sequences, genome mapping, transcript assembling, and differential expression. The module “Target screening” provides expression profiling analyses and graphic visualization. The module “Self-testing” offers the directory setups, sample management, and a check for third-party package dependency. Integration of other GUIs including Bowtie, miRDeep2, and miRspring extend the program’s functionality. Conclusions eRNA focuses on the common tools required for the mapping and quantification analysis of miRNA-seq and mRNA-seq data. The software package provides an additional choice for scientists who require a user-friendly computing environment and high-throughput capacity for large data analysis. eRNA is available for free download at https://sourceforge.net/projects/erna/?source=directory. PMID:24593312

eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing.

PubMed

Yuan, Tiezheng; Huang, Xiaoyi; Dittmar, Rachel L; Du, Meijun; Kohli, Manish; Boardman, Lisa; Thibodeau, Stephen N; Wang, Liang

2014-03-05

RNA sequencing (RNA-seq) is emerging as a critical approach in biological research. However, its high-throughput advantage is significantly limited by the capacity of bioinformatics tools. The research community urgently needs user-friendly tools to efficiently analyze the complicated data generated by high throughput sequencers. We developed a standalone tool with graphic user interface (GUI)-based analytic modules, known as eRNA. The capacity of performing parallel processing and sample management facilitates large data analyses by maximizing hardware usage and freeing users from tediously handling sequencing data. The module miRNA identification" includes GUIs for raw data reading, adapter removal, sequence alignment, and read counting. The module "mRNA identification" includes GUIs for reference sequences, genome mapping, transcript assembling, and differential expression. The module "Target screening" provides expression profiling analyses and graphic visualization. The module "Self-testing" offers the directory setups, sample management, and a check for third-party package dependency. Integration of other GUIs including Bowtie, miRDeep2, and miRspring extend the program's functionality. eRNA focuses on the common tools required for the mapping and quantification analysis of miRNA-seq and mRNA-seq data. The software package provides an additional choice for scientists who require a user-friendly computing environment and high-throughput capacity for large data analysis. eRNA is available for free download at https://sourceforge.net/projects/erna/?source=directory.

Back to BaySICS: a user-friendly program for Bayesian Statistical Inference from Coalescent Simulations.

PubMed

Sandoval-Castellanos, Edson; Palkopoulou, Eleftheria; Dalén, Love

2014-01-01

Inference of population demographic history has vastly improved in recent years due to a number of technological and theoretical advances including the use of ancient DNA. Approximate Bayesian computation (ABC) stands among the most promising methods due to its simple theoretical fundament and exceptional flexibility. However, limited availability of user-friendly programs that perform ABC analysis renders it difficult to implement, and hence programming skills are frequently required. In addition, there is limited availability of programs able to deal with heterochronous data. Here we present the software BaySICS: Bayesian Statistical Inference of Coalescent Simulations. BaySICS provides an integrated and user-friendly platform that performs ABC analyses by means of coalescent simulations from DNA sequence data. It estimates historical demographic population parameters and performs hypothesis testing by means of Bayes factors obtained from model comparisons. Although providing specific features that improve inference from datasets with heterochronous data, BaySICS also has several capabilities making it a suitable tool for analysing contemporary genetic datasets. Those capabilities include joint analysis of independent tables, a graphical interface and the implementation of Markov-chain Monte Carlo without likelihoods.

Development and application of GIS-based PRISM integration through a plugin approach

NASA Astrophysics Data System (ADS)

Lee, Woo-Seop; Chun, Jong Ahn; Kang, Kwangmin

2014-05-01

A PRISM (Parameter-elevation Regressions on Independent Slopes Model) QGIS-plugin was developed on Quantum GIS platform in this study. This Quantum GIS plugin system provides user-friendly graphic user interfaces (GUIs) so that users can obtain gridded meteorological data of high resolutions (1 km × 1 km). Also, this software is designed to run on a personal computer so that it does not require an internet access or a sophisticated computer system. This module is a user-friendly system that a user can generate PRISM data with ease. The proposed PRISM QGIS-plugin is a hybrid statistical-geographic model system that uses coarse resolution datasets (APHRODITE datasets in this study) with digital elevation data to generate the fine-resolution gridded precipitation. To validate the performance of the software, Prek Thnot River Basin in Kandal, Cambodia is selected for application. Overall statistical analysis shows promising outputs generated by the proposed plugin. Error measures such as RMSE (Root Mean Square Error) and MAPE (Mean Absolute Percentage Error) were used to evaluate the performance of the developed PRISM QGIS-plugin. Evaluation results using RMSE and MAPE were 2.76 mm and 4.2%, respectively. This study suggested that the plugin can be used to generate high resolution precipitation datasets for hydrological and climatological studies at a watershed where observed weather datasets are limited.

pROC: an open-source package for R and S+ to analyze and compare ROC curves.

PubMed

Robin, Xavier; Turck, Natacha; Hainard, Alexandre; Tiberti, Natalia; Lisacek, Frédérique; Sanchez, Jean-Charles; Müller, Markus

2011-03-17

Receiver operating characteristic (ROC) curves are useful tools to evaluate classifiers in biomedical and bioinformatics applications. However, conclusions are often reached through inconsistent use or insufficient statistical analysis. To support researchers in their ROC curves analysis we developed pROC, a package for R and S+ that contains a set of tools displaying, analyzing, smoothing and comparing ROC curves in a user-friendly, object-oriented and flexible interface. With data previously imported into the R or S+ environment, the pROC package builds ROC curves and includes functions for computing confidence intervals, statistical tests for comparing total or partial area under the curve or the operating points of different classifiers, and methods for smoothing ROC curves. Intermediary and final results are visualised in user-friendly interfaces. A case study based on published clinical and biomarker data shows how to perform a typical ROC analysis with pROC. pROC is a package for R and S+ specifically dedicated to ROC analysis. It proposes multiple statistical tests to compare ROC curves, and in particular partial areas under the curve, allowing proper ROC interpretation. pROC is available in two versions: in the R programming language or with a graphical user interface in the S+ statistical software. It is accessible at http://expasy.org/tools/pROC/ under the GNU General Public License. It is also distributed through the CRAN and CSAN public repositories, facilitating its installation.

Eruptive event generator based on the Gibson-Low magnetic configuration

NASA Astrophysics Data System (ADS)

Borovikov, D.; Sokolov, I. V.; Manchester, W. B.; Jin, M.; Gombosi, T. I.

2017-08-01

Coronal mass ejections (CMEs), a kind of energetic solar eruptions, are an integral subject of space weather research. Numerical magnetohydrodynamic (MHD) modeling, which requires powerful computational resources, is one of the primary means of studying the phenomenon. With increasing accessibility of such resources, grows the demand for user-friendly tools that would facilitate the process of simulating CMEs for scientific and operational purposes. The Eruptive Event Generator based on Gibson-Low flux rope (EEGGL), a new publicly available computational model presented in this paper, is an effort to meet this demand. EEGGL allows one to compute the parameters of a model flux rope driving a CME via an intuitive graphical user interface. We provide a brief overview of the physical principles behind EEGGL and its functionality. Ways toward future improvements of the tool are outlined.

Trace saver: A tool for network service improvement and personalised analysis of user centric statistics

NASA Astrophysics Data System (ADS)

Bilal, Muhammad; Asfand-e-Yar, Mockford, Steve; Khan, Wasiq; Awan, Irfan

2012-11-01

Mobile technology is among the fastest growing technologies in today's world with low cost and highly effective benefits. Most important and entertaining areas in mobile technology development and usage are location based services, user friendly networked applications and gaming applications. However, concern towards network operator service provision and improvement has been very low. The portable applications available for a range of mobile operating systems which help improve the network operator services are desirable by the mobile operators. This paper proposes a state of the art mobile application Tracesaver, which provides a great achievement over the barriers in gathering device and network related information, for network operators to improve their network service provision. Tracesaver is available for a broad range of mobile devices with different mobile operating systems and computational capabilities. The availability of Tracesaver in market has proliferated over the last year since it was published. The survey and results show that Tracesaver is being used by millions of mobile users and provides novel ways of network service improvement with its highly user friendly interface.

imDEV: a graphical user interface to R multivariate analysis tools in Microsoft Excel

USDA-ARS?s Scientific Manuscript database

Interactive modules for data exploration and visualization (imDEV) is a Microsoft Excel spreadsheet embedded application providing an integrated environment for the analysis of omics data sets with a user-friendly interface. Individual modules were designed to provide toolsets to enable interactive ...

Graphical User Interface Programming in Introductory Computer Science.

ERIC Educational Resources Information Center

Skolnick, Michael M.; Spooner, David L.

Modern computing systems exploit graphical user interfaces for interaction with users; as a result, introductory computer science courses must begin to teach the principles underlying such interfaces. This paper presents an approach to graphical user interface (GUI) implementation that is simple enough for beginning students to understand, yet…

ChimericSeq: An open-source, user-friendly interface for analyzing NGS data to identify and characterize viral-host chimeric sequences.

PubMed

Shieh, Fwu-Shan; Jongeneel, Patrick; Steffen, Jamin D; Lin, Selena; Jain, Surbhi; Song, Wei; Su, Ying-Hsiu

2017-01-01

Identification of viral integration sites has been important in understanding the pathogenesis and progression of diseases associated with particular viral infections. The advent of next-generation sequencing (NGS) has enabled researchers to understand the impact that viral integration has on the host, such as tumorigenesis. Current computational methods to analyze NGS data of virus-host junction sites have been limited in terms of their accessibility to a broad user base. In this study, we developed a software application (named ChimericSeq), that is the first program of its kind to offer a graphical user interface, compatibility with both Windows and Mac operating systems, and optimized for effectively identifying and annotating virus-host chimeric reads within NGS data. In addition, ChimericSeq's pipeline implements custom filtering to remove artifacts and detect reads with quantitative analytical reporting to provide functional significance to discovered integration sites. The improved accessibility of ChimericSeq through a GUI interface in both Windows and Mac has potential to expand NGS analytical support to a broader spectrum of the scientific community.

ChimericSeq: An open-source, user-friendly interface for analyzing NGS data to identify and characterize viral-host chimeric sequences

PubMed Central

Shieh, Fwu-Shan; Jongeneel, Patrick; Steffen, Jamin D.; Lin, Selena; Jain, Surbhi; Song, Wei

2017-01-01

Identification of viral integration sites has been important in understanding the pathogenesis and progression of diseases associated with particular viral infections. The advent of next-generation sequencing (NGS) has enabled researchers to understand the impact that viral integration has on the host, such as tumorigenesis. Current computational methods to analyze NGS data of virus-host junction sites have been limited in terms of their accessibility to a broad user base. In this study, we developed a software application (named ChimericSeq), that is the first program of its kind to offer a graphical user interface, compatibility with both Windows and Mac operating systems, and optimized for effectively identifying and annotating virus-host chimeric reads within NGS data. In addition, ChimericSeq’s pipeline implements custom filtering to remove artifacts and detect reads with quantitative analytical reporting to provide functional significance to discovered integration sites. The improved accessibility of ChimericSeq through a GUI interface in both Windows and Mac has potential to expand NGS analytical support to a broader spectrum of the scientific community. PMID:28829778

Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs.

PubMed

Lim, Chun Shen; Brown, Chris M

2017-01-01

Structured RNA elements may control virus replication, transcription and translation, and their distinct features are being exploited by novel antiviral strategies. Viral RNA elements continue to be discovered using combinations of experimental and computational analyses. However, the wealth of sequence data, notably from deep viral RNA sequencing, viromes, and metagenomes, necessitates computational approaches being used as an essential discovery tool. In this review, we describe practical approaches being used to discover functional RNA elements in viral genomes. In addition to success stories in new and emerging viruses, these approaches have revealed some surprising new features of well-studied viruses e.g., human immunodeficiency virus, hepatitis C virus, influenza, and dengue viruses. Some notable discoveries were facilitated by new comparative analyses of diverse viral genome alignments. Importantly, comparative approaches for finding RNA elements embedded in coding and non-coding regions differ. With the exponential growth of computer power we have progressed from stem-loop prediction on single sequences to cutting edge 3D prediction, and from command line to user friendly web interfaces. Despite these advances, many powerful, user friendly prediction tools and resources are underutilized by the virology community.

Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs

PubMed Central

Lim, Chun Shen; Brown, Chris M.

2018-01-01

Structured RNA elements may control virus replication, transcription and translation, and their distinct features are being exploited by novel antiviral strategies. Viral RNA elements continue to be discovered using combinations of experimental and computational analyses. However, the wealth of sequence data, notably from deep viral RNA sequencing, viromes, and metagenomes, necessitates computational approaches being used as an essential discovery tool. In this review, we describe practical approaches being used to discover functional RNA elements in viral genomes. In addition to success stories in new and emerging viruses, these approaches have revealed some surprising new features of well-studied viruses e.g., human immunodeficiency virus, hepatitis C virus, influenza, and dengue viruses. Some notable discoveries were facilitated by new comparative analyses of diverse viral genome alignments. Importantly, comparative approaches for finding RNA elements embedded in coding and non-coding regions differ. With the exponential growth of computer power we have progressed from stem-loop prediction on single sequences to cutting edge 3D prediction, and from command line to user friendly web interfaces. Despite these advances, many powerful, user friendly prediction tools and resources are underutilized by the virology community. PMID:29354101

A MATLAB-based graphical user interface for the identification of muscular activations from surface electromyography signals.

PubMed

Mengarelli, Alessandro; Cardarelli, Stefano; Verdini, Federica; Burattini, Laura; Fioretti, Sandro; Di Nardo, Francesco

2016-08-01

In this paper a graphical user interface (GUI) built in MATLAB® environment is presented. This interactive tool has been developed for the analysis of superficial electromyography (sEMG) signals and in particular for the assessment of the muscle activation time intervals. After the signal import, the tool performs a first analysis in a totally user independent way, providing a reliable computation of the muscular activation sequences. Furthermore, the user has the opportunity to modify each parameter of the on/off identification algorithm implemented in the presented tool. The presence of an user-friendly GUI allows the immediate evaluation of the effects that the modification of every single parameter has on the activation intervals recognition, through the real-time updating and visualization of the muscular activation/deactivation sequences. The possibility to accept the initial signal analysis or to modify the on/off identification with respect to each considered signal, with a real-time visual feedback, makes this GUI-based tool a valuable instrument in clinical, research applications and also in an educational perspective.

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research

PubMed Central

Yeung, Ka Yee

2016-01-01

Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface. PMID:27045593

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research.

PubMed

Hung, Ling-Hong; Kristiyanto, Daniel; Lee, Sung Bong; Yeung, Ka Yee

2016-01-01

Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface.

AlaScan: A Graphical User Interface for Alanine Scanning Free-Energy Calculations.

PubMed

Ramadoss, Vijayaraj; Dehez, François; Chipot, Christophe

2016-06-27

Computation of the free-energy changes that underlie molecular recognition and association has gained significant importance due to its considerable potential in drug discovery. The massive increase of computational power in recent years substantiates the application of more accurate theoretical methods for the calculation of binding free energies. The impact of such advances is the application of parent approaches, like computational alanine scanning, to investigate in silico the effect of amino-acid replacement in protein-ligand and protein-protein complexes, or probe the thermostability of individual proteins. Because human effort represents a significant cost that precludes the routine use of this form of free-energy calculations, minimizing manual intervention constitutes a stringent prerequisite for any such systematic computation. With this objective in mind, we propose a new plug-in, referred to as AlaScan, developed within the popular visualization program VMD to automate the major steps in alanine-scanning calculations, employing free-energy perturbation as implemented in the widely used molecular dynamics code NAMD. The AlaScan plug-in can be utilized upstream, to prepare input files for selected alanine mutations. It can also be utilized downstream to perform the analysis of different alanine-scanning calculations and to report the free-energy estimates in a user-friendly graphical user interface, allowing favorable mutations to be identified at a glance. The plug-in also assists the end-user in assessing the reliability of the calculation through rapid visual inspection.

UDATE1: A computer program for the calculation of uranium-series isotopic ages

USGS Publications Warehouse

Rosenbauer, R.J.

1991-01-01

UDATE1 is a FORTRAN-77 program with an interface for an Apple Macintosh computer that calculates isotope activities from measured count rates to date geologic materials by uranium-series disequilibria. Dates on pure samples can be determined directly by the accumulation of 230Th from 234U and of 231Pa from 235U. Dates for samples contaminated by clays containing abundant natural thorium can be corrected by the program using various mixing models. Input to the program and file management are made simple and user friendly by a series of Macintosh modal dialog boxes. ?? 1991.

Multiple-body simulation with emphasis on integrated Space Shuttle vehicle

NASA Technical Reports Server (NTRS)

Chiu, Ing-Tsau

1993-01-01

The program to obtain intergrid communications - Pegasus - was enhanced to make better use of computing resources. Periodic block tridiagonal and penta-diagonal diagonal routines in OVERFLOW were modified to use a better algorithm to speed up the calculation for grids with periodic boundary conditions. Several programs were added to collar grid tools and a user friendly shell script was developed to help users generate collar grids. User interface for HYPGEN was modified to cope with the changes in HYPGEN. ET/SRB attach hardware grids were added to the computational model for the space shuttle and is currently incorporated into the refined shuttle model jointly developed at Johnson Space Center and Ames Research Center. Flow simulation for the integrated space shuttle vehicle at flight Reynolds number was carried out and compared with flight data as well as the earlier simulation for wind tunnel Reynolds number.

HIV Therapy Simulator: a graphical user interface for comparing the effectiveness of novel therapy regimens.

PubMed

Lim, Huat Chye; Curlin, Marcel E; Mittler, John E

2011-11-01

Computer simulation models can be useful in exploring the efficacy of HIV therapy regimens in preventing the evolution of drug-resistant viruses. Current modeling programs, however, were designed by researchers with expertise in computational biology, limiting their accessibility to those who might lack such a background. We have developed a user-friendly graphical program, HIV Therapy Simulator (HIVSIM), that is accessible to non-technical users. The program allows clinicians and researchers to explore the effectiveness of various therapeutic strategies, such as structured treatment interruptions, booster therapies and induction-maintenance therapies. We anticipate that HIVSIM will be useful for evaluating novel drug-based treatment concepts in clinical research, and as an educational tool. HIV Therapy Simulator is freely available for Mac OS and Windows at http://sites.google.com/site/hivsimulator/. jmittler@uw.edu. Supplementary data are available at Bioinformatics online.

CovalentDock Cloud: a web server for automated covalent docking.

PubMed

Ouyang, Xuchang; Zhou, Shuo; Ge, Zemei; Li, Runtao; Kwoh, Chee Keong

2013-07-01

Covalent binding is an important mechanism for many drugs to gain its function. We developed a computational algorithm to model this chemical event and extended it to a web server, the CovalentDock Cloud, to make it accessible directly online without any local installation and configuration. It provides a simple yet user-friendly web interface to perform covalent docking experiments and analysis online. The web server accepts the structures of both the ligand and the receptor uploaded by the user or retrieved from online databases with valid access id. It identifies the potential covalent binding patterns, carries out the covalent docking experiments and provides visualization of the result for user analysis. This web server is free and open to all users at http://docking.sce.ntu.edu.sg/.

CovalentDock Cloud: a web server for automated covalent docking

PubMed Central

Ouyang, Xuchang; Zhou, Shuo; Ge, Zemei; Li, Runtao; Kwoh, Chee Keong

2013-01-01

Covalent binding is an important mechanism for many drugs to gain its function. We developed a computational algorithm to model this chemical event and extended it to a web server, the CovalentDock Cloud, to make it accessible directly online without any local installation and configuration. It provides a simple yet user-friendly web interface to perform covalent docking experiments and analysis online. The web server accepts the structures of both the ligand and the receptor uploaded by the user or retrieved from online databases with valid access id. It identifies the potential covalent binding patterns, carries out the covalent docking experiments and provides visualization of the result for user analysis. This web server is free and open to all users at http://docking.sce.ntu.edu.sg/. PMID:23677616

Development of a user-friendly system for image processing of electron microscopy by integrating a web browser and PIONE with Eos.

PubMed

Tsukamoto, Takafumi; Yasunaga, Takuo

2014-11-01

Eos (Extensible object-oriented system) is one of the powerful applications for image processing of electron micrographs. In usual cases, Eos works with only character user interfaces (CUI) under the operating systems (OS) such as OS-X or Linux, not user-friendly. Thus, users of Eos need to be expert at image processing of electron micrographs, and have a little knowledge of computer science, as well. However, all the persons who require Eos does not an expert for CUI. Thus we extended Eos to a web system independent of OS with graphical user interfaces (GUI) by integrating web browser.Advantage to use web browser is not only to extend Eos with GUI, but also extend Eos to work under distributed computational environment. Using Ajax (Asynchronous JavaScript and XML) technology, we implemented more comfortable user-interface on web browser. Eos has more than 400 commands related to image processing for electron microscopy, and the usage of each command is different from each other. Since the beginning of development, Eos has managed their user-interface by using the interface definition file of "OptionControlFile" written in CSV (Comma-Separated Value) format, i.e., Each command has "OptionControlFile", which notes information for interface and its usage generation. Developed GUI system called "Zephyr" (Zone for Easy Processing of HYpermedia Resources) also accessed "OptionControlFIle" and produced a web user-interface automatically, because its mechanism is mature and convenient,The basic actions of client side system was implemented properly and can supply auto-generation of web-form, which has functions of execution, image preview, file-uploading to a web server. Thus the system can execute Eos commands with unique options for each commands, and process image analysis. There remain problems of image file format for visualization and workspace for analysis: The image file format information is useful to check whether the input/output file is correct and we also need to provide common workspace for analysis because the client is physically separated from a server. We solved the file format problem by extension of rules of OptionControlFile of Eos. Furthermore, to solve workspace problems, we have developed two type of system. The first system is to use only local environments. The user runs a web server provided by Eos, access to a web client through a web browser, and manipulate the local files with GUI on the web browser. The second system is employing PIONE (Process-rule for Input/Output Negotiation Environment), which is our developing platform that works under heterogenic distributed environment. The users can put their resources, such as microscopic images, text files and so on, into the server-side environment supported by PIONE, and so experts can write PIONE rule definition, which defines a workflow of image processing. PIONE run each image processing on suitable computers, following the defined rule. PIONE has the ability of interactive manipulation, and user is able to try a command with various setting values. In this situation, we contribute to auto-generation of GUI for a PIONE workflow.As advanced functions, we have developed a module to log user actions. The logs include information such as setting values in image processing, procedure of commands and so on. If we use the logs effectively, we can get a lot of advantages. For example, when an expert may discover some know-how of image processing, other users can also share logs including his know-hows and so we may obtain recommendation workflow of image analysis, if we analyze logs. To implement social platform of image processing for electron microscopists, we have developed system infrastructure, as well. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

AIRMICS (U.S. Army Institute for Research in Management Information, Communications and Computer Sciences) Information Center Model Site Evaluation

DTIC Science & Technology

1986-10-01

34 syndrome . Five techniques for developing user self-sufficiency were discussed in-depth: (1) provide training at different proficiency levels, id provide...WY aba. 4 ’-a ’aba. @9 "a,.. I bJ~ V N- S ha. E-ii S ’a ’baa .4, .;y ’. ; . a.,. ~ ~ .: ;r YK’.- xYY I. r d’...da.4/ 4/ tq..ttf.%r./..v-./ - "cc~’ v,-r...data base, accessible through a user friendly interfaces, to correlate and deliver crime , traffic, vehicle, and personnel information to " / fixed and

Towards a user-friendly brain-computer interface: initial tests in ALS and PLS patients.

PubMed

Bai, Ou; Lin, Peter; Huang, Dandan; Fei, Ding-Yu; Floeter, Mary Kay

2010-08-01

Patients usually require long-term training for effective EEG-based brain-computer interface (BCI) control due to fatigue caused by the demands for focused attention during prolonged BCI operation. We intended to develop a user-friendly BCI requiring minimal training and less mental load. Testing of BCI performance was investigated in three patients with amyotrophic lateral sclerosis (ALS) and three patients with primary lateral sclerosis (PLS), who had no previous BCI experience. All patients performed binary control of cursor movement. One ALS patient and one PLS patient performed four-directional cursor control in a two-dimensional domain under a BCI paradigm associated with human natural motor behavior using motor execution and motor imagery. Subjects practiced for 5-10min and then participated in a multi-session study of either binary control or four-directional control including online BCI game over 1.5-2h in a single visit. Event-related desynchronization and event-related synchronization in the beta band were observed in all patients during the production of voluntary movement either by motor execution or motor imagery. The online binary control of cursor movement was achieved with an average accuracy about 82.1+/-8.2% with motor execution and about 80% with motor imagery, whereas offline accuracy was achieved with 91.4+/-3.4% with motor execution and 83.3+/-8.9% with motor imagery after optimization. In addition, four-directional cursor control was achieved with an accuracy of 50-60% with motor execution and motor imagery. Patients with ALS or PLS may achieve BCI control without extended training, and fatigue might be reduced during operation of a BCI associated with human natural motor behavior. The development of a user-friendly BCI will promote practical BCI applications in paralyzed patients. Copyright 2010 International Federation of Clinical Neurophysiology. All rights reserved.

Optimization of Residual Stresses in MMC's through Process Parameter Control and the use of Heterogeneous Compensating/Compliant Interfacial Layers. OPTCOMP2 User's Guide

NASA Technical Reports Server (NTRS)

Pindera, Marek-Jerzy; Salzar, Robert S.

1996-01-01

A user's guide for the computer program OPTCOMP2 is presented in this report. This program provides a capability to optimize the fabrication or service-induced residual stresses in unidirectional metal matrix composites subjected to combined thermomechanical axisymmetric loading by altering the processing history, as well as through the microstructural design of interfacial fiber coatings. The user specifies the initial architecture of the composite and the load history, with the constituent materials being elastic, plastic, viscoplastic, or as defined by the 'user-defined' constitutive model, in addition to the objective function and constraints, through a user-friendly data input interface. The optimization procedure is based on an efficient solution methodology for the inelastic response of a fiber/interface layer(s)/matrix concentric cylinder model where the interface layers can be either homogeneous or heterogeneous. The response of heterogeneous layers is modeled using Aboudi's three-dimensional method of cells micromechanics model. The commercial optimization package DOT is used for the nonlinear optimization problem. The solution methodology for the arbitrarily layered cylinder is based on the local-global stiffness matrix formulation and Mendelson's iterative technique of successive elastic solutions developed for elastoplastic boundary-value problems. The optimization algorithm employed in DOT is based on the method of feasible directions.

WebArray: an online platform for microarray data analysis

PubMed Central

Xia, Xiaoqin; McClelland, Michael; Wang, Yipeng

2005-01-01

Background Many cutting-edge microarray analysis tools and algorithms, including commonly used limma and affy packages in Bioconductor, need sophisticated knowledge of mathematics, statistics and computer skills for implementation. Commercially available software can provide a user-friendly interface at considerable cost. To facilitate the use of these tools for microarray data analysis on an open platform we developed an online microarray data analysis platform, WebArray, for bench biologists to utilize these tools to explore data from single/dual color microarray experiments. Results The currently implemented functions were based on limma and affy package from Bioconductor, the spacings LOESS histogram (SPLOSH) method, PCA-assisted normalization method and genome mapping method. WebArray incorporates these packages and provides a user-friendly interface for accessing a wide range of key functions of limma and others, such as spot quality weight, background correction, graphical plotting, normalization, linear modeling, empirical bayes statistical analysis, false discovery rate (FDR) estimation, chromosomal mapping for genome comparison. Conclusion WebArray offers a convenient platform for bench biologists to access several cutting-edge microarray data analysis tools. The website is freely available at . It runs on a Linux server with Apache and MySQL. PMID:16371165

Final Report: MaRSPlus Sensor System Electrical Cable Management and Distributed Motor Control Computer Interface

NASA Technical Reports Server (NTRS)

Reil, Robin

2011-01-01

The success of JPL's Next Generation Imaging Spectrometer (NGIS) in Earth remote sensing has inspired a follow-on instrument project, the MaRSPlus Sensor System (MSS). One of JPL's responsibilities in the MSS project involves updating the documentation from the previous JPL airborne imagers to provide all the information necessary for an outside customer to operate the instrument independently. As part of this documentation update, I created detailed electrical cabling diagrams to provide JPL technicians with clear and concise build instructions and a database to track the status of cables from order to build to delivery. Simultaneously, a distributed motor control system is being developed for potential use on the proposed 2018 Mars rover mission. This system would significantly reduce the mass necessary for rover motor control, making more mass space available to other important spacecraft systems. The current stage of the project consists of a desktop computer talking to a single "cold box" unit containing the electronics to drive a motor. In order to test the electronics, I developed a graphical user interface (GUI) using MATLAB to allow a user to send simple commands to the cold box and display the responses received in a user-friendly format.

VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences.

PubMed

Xu, Duo; Jaber, Yousef; Pavlidis, Pavlos; Gokcumen, Omer

2017-09-26

Constructing alignments and phylogenies for a given locus from large genome sequencing studies with relevant outgroups allow novel evolutionary and anthropological insights. However, no user-friendly tool has been developed to integrate thousands of recently available and anthropologically relevant genome sequences to construct complete sequence alignments and phylogenies. Here, we provide VCFtoTree, a user friendly tool with a graphical user interface that directly accesses online databases to download, parse and analyze genome variation data for regions of interest. Our pipeline combines popular sequence datasets and tree building algorithms with custom data parsing to generate accurate alignments and phylogenies using all the individuals from the 1000 Genomes Project, Neanderthal and Denisovan genomes, as well as reference genomes of Chimpanzee and Rhesus Macaque. It can also be applied to other phased human genomes, as well as genomes from other species. The output of our pipeline includes an alignment in FASTA format and a tree file in newick format. VCFtoTree fulfills the increasing demand for constructing alignments and phylogenies for a given loci from thousands of available genomes. Our software provides a user friendly interface for a wider audience without prerequisite knowledge in programming. VCFtoTree can be accessed from https://github.com/duoduoo/VCFtoTree_3.0.0 .

Analysis on laser plasma emission for characterization of colloids by video-based computer program

NASA Astrophysics Data System (ADS)

Putri, Kirana Yuniati; Lumbantoruan, Hendra Damos; Isnaeni

2016-02-01

Laser-induced breakdown detection (LIBD) is a sensitive technique for characterization of colloids with small size and low concentration. There are two types of detection, optical and acoustic. Optical LIBD employs CCD camera to capture the plasma emission and uses the information to quantify the colloids. This technique requires sophisticated technology which is often pricey. In order to build a simple, home-made LIBD system, a dedicated computer program based on MATLAB™ for analyzing laser plasma emission was developed. The analysis was conducted by counting the number of plasma emissions (breakdowns) during a certain period of time. Breakdown probability provided information on colloid size and concentration. Validation experiment showed that the computer program performed well on analyzing the plasma emissions. Optical LIBD has A graphical user interface (GUI) was also developed to make the program more user-friendly.

Distributed user interfaces for clinical ubiquitous computing applications.

PubMed

Bång, Magnus; Larsson, Anders; Berglund, Erik; Eriksson, Henrik

2005-08-01

Ubiquitous computing with multiple interaction devices requires new interface models that support user-specific modifications to applications and facilitate the fast development of active workspaces. We have developed NOSTOS, a computer-augmented work environment for clinical personnel to explore new user interface paradigms for ubiquitous computing. NOSTOS uses several devices such as digital pens, an active desk, and walk-up displays that allow the system to track documents and activities in the workplace. We present the distributed user interface (DUI) model that allows standalone applications to distribute their user interface components to several devices dynamically at run-time. This mechanism permit clinicians to develop their own user interfaces and forms to clinical information systems to match their specific needs. We discuss the underlying technical concepts of DUIs and show how service discovery, component distribution, events and layout management are dealt with in the NOSTOS system. Our results suggest that DUIs--and similar network-based user interfaces--will be a prerequisite of future mobile user interfaces and essential to develop clinical multi-device environments.

Computer Program for Analysis, Design and Optimization of Propulsion, Dynamics, and Kinematics of Multistage Rockets

NASA Astrophysics Data System (ADS)

Lali, Mehdi

2009-03-01

A comprehensive computer program is designed in MATLAB to analyze, design and optimize the propulsion, dynamics, thermodynamics, and kinematics of any serial multi-staging rocket for a set of given data. The program is quite user-friendly. It comprises two main sections: "analysis and design" and "optimization." Each section has a GUI (Graphical User Interface) in which the rocket's data are entered by the user and by which the program is run. The first section analyzes the performance of the rocket that is previously devised by the user. Numerous plots and subplots are provided to display the performance of the rocket. The second section of the program finds the "optimum trajectory" via billions of iterations and computations which are done through sophisticated algorithms using numerical methods and incremental integrations. Innovative techniques are applied to calculate the optimal parameters for the engine and designing the "optimal pitch program." This computer program is stand-alone in such a way that it calculates almost every design parameter in regards to rocket propulsion and dynamics. It is meant to be used for actual launch operations as well as educational and research purposes.

Toward More Critical Reviewing and Analysis of CD-ROM User Software Interfaces.

ERIC Educational Resources Information Center

Zink, Steven D.

1991-01-01

Criticizes reviews of library CD-ROM products as being uncritical of the user interface and advocates a more rigorous evaluation, not only to aid potential buyers, but as a way to influence manufacturers. Congressional Information Services' Masterfile 2 is evaluated in the context of Heckel's "Principles of Friendly Software Design." (24…

Optimization of Residual Stresses in MMC's Using Compensating/Compliant Interfacial Layers. Part 2: OPTCOMP User's Guide

NASA Technical Reports Server (NTRS)

Pindera, Marek-Jerzy; Salzar, Robert S.; Williams, Todd O.

1994-01-01

A user's guide for the computer program OPTCOMP is presented in this report. This program provides a capability to optimize the fabrication or service-induced residual stresses in uni-directional metal matrix composites subjected to combined thermo-mechanical axisymmetric loading using compensating or compliant layers at the fiber/matrix interface. The user specifies the architecture and the initial material parameters of the interfacial region, which can be either elastic or elastoplastic, and defines the design variables, together with the objective function, the associated constraints and the loading history through a user-friendly data input interface. The optimization procedure is based on an efficient solution methodology for the elastoplastic response of an arbitrarily layered multiple concentric cylinder model that is coupled to the commercial optimization package DOT. The solution methodology for the arbitrarily layered cylinder is based on the local-global stiffness matrix formulation and Mendelson's iterative technique of successive elastic solutions developed for elastoplastic boundary-value problems. The optimization algorithm employed in DOT is based on the method of feasible directions.

Gromita: a fully integrated graphical user interface to gromacs 4.

PubMed

Sellis, Diamantis; Vlachakis, Dimitrios; Vlassi, Metaxia

2009-09-07

Gromita is a fully integrated and efficient graphical user interface (GUI) to the recently updated molecular dynamics suite Gromacs, version 4. Gromita is a cross-platform, perl/tcl-tk based, interactive front end designed to break the command line barrier and introduce a new user-friendly environment to run molecular dynamics simulations through Gromacs. Our GUI features a novel workflow interface that guides the user through each logical step of the molecular dynamics setup process, making it accessible to both advanced and novice users. This tool provides a seamless interface to the Gromacs package, while providing enhanced functionality by speeding up and simplifying the task of setting up molecular dynamics simulations of biological systems. Gromita can be freely downloaded from http://bio.demokritos.gr/gromita/.

Alkahest NuclearBLAST : a user-friendly BLAST management and analysis system

PubMed Central

Diener, Stephen E; Houfek, Thomas D; Kalat, Sam E; Windham, DE; Burke, Mark; Opperman, Charles; Dean, Ralph A

2005-01-01

Background - Sequencing of EST and BAC end datasets is no longer limited to large research groups. Drops in per-base pricing have made high throughput sequencing accessible to individual investigators. However, there are few options available which provide a free and user-friendly solution to the BLAST result storage and data mining needs of biologists. Results - Here we describe NuclearBLAST, a batch BLAST analysis, storage and management system designed for the biologist. It is a wrapper for NCBI BLAST which provides a user-friendly web interface which includes a request wizard and the ability to view and mine the results. All BLAST results are stored in a MySQL database which allows for more advanced data-mining through supplied command-line utilities or direct database access. NuclearBLAST can be installed on a single machine or clustered amongst a number of machines to improve analysis throughput. NuclearBLAST provides a platform which eases data-mining of multiple BLAST results. With the supplied scripts, the program can export data into a spreadsheet-friendly format, automatically assign Gene Ontology terms to sequences and provide bi-directional best hits between two datasets. Users with SQL experience can use the database to ask even more complex questions and extract any subset of data they require. Conclusion - This tool provides a user-friendly interface for requesting, viewing and mining of BLAST results which makes the management and data-mining of large sets of BLAST analyses tractable to biologists. PMID:15958161

Remote Data Exploration with the Interactive Data Language (IDL)

NASA Technical Reports Server (NTRS)

Galloy, Michael

2013-01-01

A difficulty for many NASA researchers is that often the data to analyze is located remotely from the scientist and the data is too large to transfer for local analysis. Researchers have developed the Data Access Protocol (DAP) for accessing remote data. Presently one can use DAP from within IDL, but the IDL-DAP interface is both limited and cumbersome. A more powerful and user-friendly interface to DAP for IDL has been developed. Users are able to browse remote data sets graphically, select partial data to retrieve, import that data and make customized plots, and have an interactive IDL command line session simultaneous with the remote visualization. All of these IDL-DAP tools are usable easily and seamlessly for any IDL user. IDL and DAP are both widely used in science, but were not easily used together. The IDL DAP bindings were incomplete and had numerous bugs that prevented their serious use. For example, the existing bindings did not read DAP Grid data, which is the organization of nearly all NASA datasets currently served via DAP. This project uniquely provides a fully featured, user-friendly interface to DAP from IDL, both from the command line and a GUI application. The DAP Explorer GUI application makes browsing a dataset more user-friendly, while also providing the capability to run user-defined functions on specified data. Methods for running remote functions on the DAP server were investigated, and a technique for accomplishing this task was decided upon.

Gigwa-Genotype investigator for genome-wide analyses.

PubMed

Sempéré, Guilhem; Philippe, Florian; Dereeper, Alexis; Ruiz, Manuel; Sarah, Gautier; Larmande, Pierre

2016-06-06

Exploring the structure of genomes and analyzing their evolution is essential to understanding the ecological adaptation of organisms. However, with the large amounts of data being produced by next-generation sequencing, computational challenges arise in terms of storage, search, sharing, analysis and visualization. This is particularly true with regards to studies of genomic variation, which are currently lacking scalable and user-friendly data exploration solutions. Here we present Gigwa, a web-based tool that provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also on genotype patterns. The data storage relies on MongoDB, which offers good scalability properties. Gigwa can handle multiple databases and may be deployed in either single- or multi-user mode. In addition, it provides a wide range of popular export formats. The Gigwa application is suitable for managing large amounts of genomic variation data. Its user-friendly web interface makes such processing widely accessible. It can either be simply deployed on a workstation or be used to provide a shared data portal for a given community of researchers.

Combining factual and heuristic knowledge in knowledge acquisition

NASA Technical Reports Server (NTRS)

Gomez, Fernando; Hull, Richard; Karr, Clark; Hosken, Bruce; Verhagen, William

1992-01-01

A knowledge acquisition technique that combines heuristic and factual knowledge represented as two hierarchies is described. These ideas were applied to the construction of a knowledge acquisition interface to the Expert System Analyst (OPERA). The goal of OPERA is to improve the operations support of the computer network in the space shuttle launch processing system. The knowledge acquisition bottleneck lies in gathering knowledge from human experts and transferring it to OPERA. OPERA's knowledge acquisition problem is approached as a classification problem-solving task, combining this approach with the use of factual knowledge about the domain. The interface was implemented in a Symbolics workstation making heavy use of windows, pull-down menus, and other user-friendly devices.

EnviroNET: An on-line environment data base for LDEF data

NASA Technical Reports Server (NTRS)

Lauriente, Michael

1992-01-01

EnviroNET is an on-line, free form data base intended to provide a centralized depository for a wide range of technical information on environmentally induced interactions of use to Space Shuttle customers and spacecraft designers. It provides a user friendly, menu driven format on networks that are connected globally and is available twenty-four hours a day, every day. The information updated regularly, includes expository text, tabular numerical data, charts and graphs, and models. The system pools space data collected over the years by NASA, USAF, other government facilities, industry, universities, and ESA. The models accept parameter input from the user and calculate and display the derived values corresponding to that input. In addition to the archive, interactive graphics programs are also available on space debris, the neutral atmosphere, radiation, magnetic field, and ionosphere. A user friendly informative interface is standard for all the models with a pop-up window, help window with information on inputs, outputs, and caveats. The system will eventually simplify mission analysis with analytical tools and deliver solution for computational intense graphical applications to do 'What if' scenarios. A proposed plan for developing a repository of LDEF information for a user group concludes the presentation.

Open Source Live Distributions for Computer Forensics

NASA Astrophysics Data System (ADS)

Giustini, Giancarlo; Andreolini, Mauro; Colajanni, Michele

Current distributions of open source forensic software provide digital investigators with a large set of heterogeneous tools. Their use is not always focused on the target and requires high technical expertise. We present a new GNU/Linux live distribution, named CAINE (Computer Aided INvestigative Environment) that contains a collection of tools wrapped up into a user friendly environment. The CAINE forensic framework introduces novel important features, aimed at filling the interoperability gap across different forensic tools. Moreover, it provides a homogeneous graphical interface that drives digital investigators during the acquisition and analysis of electronic evidence, and it offers a semi-automatic mechanism for the creation of the final report.

shinyheatmap: Ultra fast low memory heatmap web interface for big data genomics.

PubMed

Khomtchouk, Bohdan B; Hennessy, James R; Wahlestedt, Claes

2017-01-01

Transcriptomics, metabolomics, metagenomics, and other various next-generation sequencing (-omics) fields are known for their production of large datasets, especially across single-cell sequencing studies. Visualizing such big data has posed technical challenges in biology, both in terms of available computational resources as well as programming acumen. Since heatmaps are used to depict high-dimensional numerical data as a colored grid of cells, efficiency and speed have often proven to be critical considerations in the process of successfully converting data into graphics. For example, rendering interactive heatmaps from large input datasets (e.g., 100k+ rows) has been computationally infeasible on both desktop computers and web browsers. In addition to memory requirements, programming skills and knowledge have frequently been barriers-to-entry for creating highly customizable heatmaps. We propose shinyheatmap: an advanced user-friendly heatmap software suite capable of efficiently creating highly customizable static and interactive biological heatmaps in a web browser. shinyheatmap is a low memory footprint program, making it particularly well-suited for the interactive visualization of extremely large datasets that cannot typically be computed in-memory due to size restrictions. Also, shinyheatmap features a built-in high performance web plug-in, fastheatmap, for rapidly plotting interactive heatmaps of datasets as large as 105-107 rows within seconds, effectively shattering previous performance benchmarks of heatmap rendering speed. shinyheatmap is hosted online as a freely available web server with an intuitive graphical user interface: http://shinyheatmap.com. The methods are implemented in R, and are available as part of the shinyheatmap project at: https://github.com/Bohdan-Khomtchouk/shinyheatmap. Users can access fastheatmap directly from within the shinyheatmap web interface, and all source code has been made publicly available on Github: https://github.com/Bohdan-Khomtchouk/fastheatmap.

DockingApp: a user friendly interface for facilitated docking simulations with AutoDock Vina.

PubMed

Di Muzio, Elena; Toti, Daniele; Polticelli, Fabio

2017-02-01

Molecular docking is a powerful technique that helps uncover the structural and energetic bases of the interaction between macromolecules and substrates, endogenous and exogenous ligands, and inhibitors. Moreover, this technique plays a pivotal role in accelerating the screening of large libraries of compounds for drug development purposes. The need to promote community-driven drug development efforts, especially as far as neglected diseases are concerned, calls for user-friendly tools to allow non-expert users to exploit the full potential of molecular docking. Along this path, here is described the implementation of DockingApp, a freely available, extremely user-friendly, platform-independent application for performing docking simulations and virtual screening tasks using AutoDock Vina. DockingApp sports an intuitive graphical user interface which greatly facilitates both the input phase and the analysis of the results, which can be visualized in graphical form using the embedded JMol applet. The application comes with the DrugBank set of more than 1400 ready-to-dock, FDA-approved drugs, to facilitate virtual screening and drug repurposing initiatives. Furthermore, other databases of compounds such as ZINC, available also in AutoDock format, can be readily and easily plugged in.

APM_GUI: analyzing particle movement on the cell membrane and determining confinement.

PubMed

Menchón, Silvia A; Martín, Mauricio G; Dotti, Carlos G

2012-02-20

Single-particle tracking is a powerful tool for tracking individual particles with high precision. It provides useful information that allows the study of diffusion properties as well as the dynamics of movement. Changes in particle movement behavior, such as transitions between Brownian motion and temporary confinement, can reveal interesting biophysical interactions. Although useful applications exist to determine the paths of individual particles, only a few software implementations are available to analyze these data, and these implementations are generally not user-friendly and do not have a graphical interface,. Here, we present APM_GUI (Analyzing Particle Movement), which is a MatLab-implemented application with a Graphical User Interface. This user-friendly application detects confined movement considering non-random confinement when a particle remains in a region longer than a Brownian diffusant would remain. In addition, APM_GUI exports the results, which allows users to analyze this information using software that they are familiar with. APM_GUI provides an open-source tool that quantifies diffusion coefficients and determines whether trajectories have non-random confinements. It also offers a simple and user-friendly tool that can be used by individuals without programming skills.

DockingApp: a user friendly interface for facilitated docking simulations with AutoDock Vina

NASA Astrophysics Data System (ADS)

Di Muzio, Elena; Toti, Daniele; Polticelli, Fabio

2017-02-01

Molecular docking is a powerful technique that helps uncover the structural and energetic bases of the interaction between macromolecules and substrates, endogenous and exogenous ligands, and inhibitors. Moreover, this technique plays a pivotal role in accelerating the screening of large libraries of compounds for drug development purposes. The need to promote community-driven drug development efforts, especially as far as neglected diseases are concerned, calls for user-friendly tools to allow non-expert users to exploit the full potential of molecular docking. Along this path, here is described the implementation of DockingApp, a freely available, extremely user-friendly, platform-independent application for performing docking simulations and virtual screening tasks using AutoDock Vina. DockingApp sports an intuitive graphical user interface which greatly facilitates both the input phase and the analysis of the results, which can be visualized in graphical form using the embedded JMol applet. The application comes with the DrugBank set of more than 1400 ready-to-dock, FDA-approved drugs, to facilitate virtual screening and drug repurposing initiatives. Furthermore, other databases of compounds such as ZINC, available also in AutoDock format, can be readily and easily plugged in.

MollDE: a homology modeling framework you can click with.

PubMed

Canutescu, Adrian A; Dunbrack, Roland L

2005-06-15

Molecular Integrated Development Environment (MolIDE) is an integrated application designed to provide homology modeling tools and protocols under a uniform, user-friendly graphical interface. Its main purpose is to combine the most frequent modeling steps in a semi-automatic, interactive way, guiding the user from the target protein sequence to the final three-dimensional protein structure. The typical basic homology modeling process is composed of building sequence profiles of the target sequence family, secondary structure prediction, sequence alignment with PDB structures, assisted alignment editing, side-chain prediction and loop building. All of these steps are available through a graphical user interface. MolIDE's user-friendly and streamlined interactive modeling protocol allows the user to focus on the important modeling questions, hiding from the user the raw data generation and conversion steps. MolIDE was designed from the ground up as an open-source, cross-platform, extensible framework. This allows developers to integrate additional third-party programs to MolIDE. http://dunbrack.fccc.edu/molide/molide.php rl_dunbrack@fccc.edu.

Interface design of VSOP'94 computer code for safety analysis

NASA Astrophysics Data System (ADS)

Natsir, Khairina; Yazid, Putranto Ilham; Andiwijayakusuma, D.; Wahanani, Nursinta Adi

2014-09-01

Today, most software applications, also in the nuclear field, come with a graphical user interface. VSOP'94 (Very Superior Old Program), was designed to simplify the process of performing reactor simulation. VSOP is a integrated code system to simulate the life history of a nuclear reactor that is devoted in education and research. One advantage of VSOP program is its ability to calculate the neutron spectrum estimation, fuel cycle, 2-D diffusion, resonance integral, estimation of reactors fuel costs, and integrated thermal hydraulics. VSOP also can be used to comparative studies and simulation of reactor safety. However, existing VSOP is a conventional program, which was developed using Fortran 65 and have several problems in using it, for example, it is only operated on Dec Alpha mainframe platforms and provide text-based output, difficult to use, especially in data preparation and interpretation of results. We develop a GUI-VSOP, which is an interface program to facilitate the preparation of data, run the VSOP code and read the results in a more user friendly way and useable on the Personal 'Computer (PC). Modifications include the development of interfaces on preprocessing, processing and postprocessing. GUI-based interface for preprocessing aims to provide a convenience way in preparing data. Processing interface is intended to provide convenience in configuring input files and libraries and do compiling VSOP code. Postprocessing interface designed to visualized the VSOP output in table and graphic forms. GUI-VSOP expected to be useful to simplify and speed up the process and analysis of safety aspects.

A data mining technique for discovering distinct patterns of hand signs: implications in user training and computer interface design.

PubMed

Ye, Nong; Li, Xiangyang; Farley, Toni

2003-01-15

Hand signs are considered as one of the important ways to enter information into computers for certain tasks. Computers receive sensor data of hand signs for recognition. When using hand signs as computer inputs, we need to (1) train computer users in the sign language so that their hand signs can be easily recognized by computers, and (2) design the computer interface to avoid the use of confusing signs for improving user input performance and user satisfaction. For user training and computer interface design, it is important to have a knowledge of which signs can be easily recognized by computers and which signs are not distinguishable by computers. This paper presents a data mining technique to discover distinct patterns of hand signs from sensor data. Based on these patterns, we derive a group of indistinguishable signs by computers. Such information can in turn assist in user training and computer interface design.

The GLOBE Visualization Project: Using WWW in the Classroom.

ERIC Educational Resources Information Center

de La Beaujardiere, J-F; And Others

1997-01-01

Describes a World Wide Web-based, user-friendly, language-independent graphical user interface providing access to visualizations created for GLOBE (Global Learning and Observations to Benefit the Environment), a multinational program of education and science. (DDR)

A memory efficient user interface for CLIPS micro-computer applications

NASA Technical Reports Server (NTRS)

Sterle, Mark E.; Mayer, Richard J.; Jordan, Janice A.; Brodale, Howard N.; Lin, Min-Jin

1990-01-01

The goal of the Integrated Southern Pine Beetle Expert System (ISPBEX) is to provide expert level knowledge concerning treatment advice that is convenient and easy to use for Forest Service personnel. ISPBEX was developed in CLIPS and delivered on an IBM PC AT class micro-computer, operating with an MS/DOS operating system. This restricted the size of the run time system to 640K. In order to provide a robust expert system, with on-line explanation, help, and alternative actions menus, as well as features that allow the user to back up or execute 'what if' scenarios, a memory efficient menuing system was developed to interface with the CLIPS programs. By robust, we mean an expert system that (1) is user friendly, (2) provides reasonable solutions for a wide variety of domain specific problems, (3) explains why some solutions were suggested but others were not, and (4) provides technical information relating to the problem solution. Several advantages were gained by using this type of user interface (UI). First, by storing the menus on the hard disk (instead of main memory) during program execution, a more robust system could be implemented. Second, since the menus were built rapidly, development time was reduced. Third, the user may try a new scenario by backing up to any of the input screens and revising segments of the original input without having to retype all the information. And fourth, asserting facts from the menus provided for a dynamic and flexible fact base. This UI technology has been applied successfully in expert systems applications in forest management, agriculture, and manufacturing. This paper discusses the architecture of the UI system, human factors considerations, and the menu syntax design.

Eye-gaze and intent: Application in 3D interface control

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

Schryver, J.C.; Goldberg, J.H.

1993-06-01

Computer interface control is typically accomplished with an input ``device`` such as keyboard, mouse, trackball, etc. An input device translates a users input actions, such as mouse clicks and key presses, into appropriate computer commands. To control the interface, the user must first convert intent into the syntax of the input device. A more natural means of computer control is possible when the computer can directly infer user intent, without need of intervening input devices. We describe an application of eye-gaze-contingent control of an interactive three-dimensional (3D) user interface. A salient feature of the user interface is natural input, withmore » a heightened impression of controlling the computer directly by the mind. With this interface, input of rotation and translation are intuitive, whereas other abstract features, such as zoom, are more problematic to match with user intent. This paper describes successes with implementation to date, and ongoing efforts to develop a more sophisticated intent inferencing methodology.« less

Eye-gaze and intent: Application in 3D interface control

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

Schryver, J.C.; Goldberg, J.H.

1993-01-01

Computer interface control is typically accomplished with an input device'' such as keyboard, mouse, trackball, etc. An input device translates a users input actions, such as mouse clicks and key presses, into appropriate computer commands. To control the interface, the user must first convert intent into the syntax of the input device. A more natural means of computer control is possible when the computer can directly infer user intent, without need of intervening input devices. We describe an application of eye-gaze-contingent control of an interactive three-dimensional (3D) user interface. A salient feature of the user interface is natural input, withmore » a heightened impression of controlling the computer directly by the mind. With this interface, input of rotation and translation are intuitive, whereas other abstract features, such as zoom, are more problematic to match with user intent. This paper describes successes with implementation to date, and ongoing efforts to develop a more sophisticated intent inferencing methodology.« less

The missing graphical user interface for genomics.

PubMed

Schatz, Michael C

2010-01-01

The Galaxy package empowers regular users to perform rich DNA sequence analysis through a much-needed and user-friendly graphical web interface. See research article http://genomebiology.com/2010/11/8/R86 RESEARCH HIGHLIGHT: With the advent of affordable and high-throughput DNA sequencing, sequencing is becoming an essential component in nearly every genetics lab. These data are being generated to probe sequence variations, to understand transcribed, regulated or methylated DNA elements, and to explore a host of other biological features across the tree of life and across a range of environments and conditions. Given this deluge of data, novices and experts alike are facing the daunting challenge of trying to analyze the raw sequence data computationally. With so many tools available and so many assays to analyze, how can one be expected to stay current with the state of the art? How can one be expected to learn to use each tool and construct robust end-to-end analysis pipelines, all while ensuring that input formats, command-line options, sequence databases and program libraries are set correctly? Finally, once the analysis is complete, how does one ensure the results are reproducible and transparent for others to scrutinize and study?In an article published in Genome Biology, Jeremy Goecks, Anton Nekrutenko, James Taylor and the rest of the Galaxy Team (Goecks et al. 1) make a great advance towards resolving these critical questions with the latest update to their Galaxy Project. The ambitious goal of Galaxy is to empower regular users to carry out their own computational analysis without having to be an expert in computational biology or computer science. Galaxy adds a desperately needed graphical user interface to genomics research, making data analysis universally accessible in a web browser, and freeing users from the minutiae of archaic command-line parameters, data formats and scripting languages. Data inputs and computational steps are selected from dynamic graphical menus, and the results are displayed in intuitive plots and summaries that encourage interactive workflows and the exploration of hypotheses. The underlying data analysis tools can be almost any piece of software, written in any language, but all their complexity is neatly hidden inside of Galaxy, allowing users to focus on scientific rather than technical questions.

RNAstructure: software for RNA secondary structure prediction and analysis.

PubMed

Reuter, Jessica S; Mathews, David H

2010-03-15

To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence. RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained. The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at http://rna.urmc.rochester.edu/RNAstructure.html.

An Object-Oriented Graphical User Interface for a Reusable Rocket Engine Intelligent Control System

NASA Technical Reports Server (NTRS)

Litt, Jonathan S.; Musgrave, Jeffrey L.; Guo, Ten-Huei; Paxson, Daniel E.; Wong, Edmond; Saus, Joseph R.; Merrill, Walter C.

1994-01-01

An intelligent control system for reusable rocket engines under development at NASA Lewis Research Center requires a graphical user interface to allow observation of the closed-loop system in operation. The simulation testbed consists of a real-time engine simulation computer, a controls computer, and several auxiliary computers for diagnostics and coordination. The system is set up so that the simulation computer could be replaced by the real engine and the change would be transparent to the control system. Because of the hard real-time requirement of the control computer, putting a graphical user interface on it was not an option. Thus, a separate computer used strictly for the graphical user interface was warranted. An object-oriented LISP-based graphical user interface has been developed on a Texas Instruments Explorer 2+ to indicate the condition of the engine to the observer through plots, animation, interactive graphics, and text.

BioImageXD: an open, general-purpose and high-throughput image-processing platform.

PubMed

Kankaanpää, Pasi; Paavolainen, Lassi; Tiitta, Silja; Karjalainen, Mikko; Päivärinne, Joacim; Nieminen, Jonna; Marjomäki, Varpu; Heino, Jyrki; White, Daniel J

2012-06-28

BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes. We demonstrate its performance in a study of integrin clustering in response to selected inhibitors.

Multidisciplinary propulsion simulation using NPSS

NASA Technical Reports Server (NTRS)

Claus, Russell W.; Evans, Austin L.; Follen, Gregory J.

1992-01-01

The current status of the Numerical Propulsion System Simulation (NPSS) program, a cooperative effort of NASA, industry, and universities to reduce the cost and time of advanced technology propulsion system development, is reviewed. The technologies required for this program include (1) interdisciplinary analysis to couple the relevant disciplines, such as aerodynamics, structures, heat transfer, combustion, acoustics, controls, and materials; (2) integrated systems analysis; (3) a high-performance computing platform, including massively parallel processing; and (4) a simulation environment providing a user-friendly interface. Several research efforts to develop these technologies are discussed.

HeatmapGenerator: high performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline.

PubMed

Khomtchouk, Bohdan B; Van Booven, Derek J; Wahlestedt, Claes

2014-01-01

The graphical visualization of gene expression data using heatmaps has become an integral component of modern-day medical research. Heatmaps are used extensively to plot quantitative differences in gene expression levels, such as those measured with RNAseq and microarray experiments, to provide qualitative large-scale views of the transcriptonomic landscape. Creating high-quality heatmaps is a computationally intensive task, often requiring considerable programming experience, particularly for customizing features to a specific dataset at hand. Software to create publication-quality heatmaps is developed with the R programming language, C++ programming language, and OpenGL application programming interface (API) to create industry-grade high performance graphics. We create a graphical user interface (GUI) software package called HeatmapGenerator for Windows OS and Mac OS X as an intuitive, user-friendly alternative to researchers with minimal prior coding experience to allow them to create publication-quality heatmaps using R graphics without sacrificing their desired level of customization. The simplicity of HeatmapGenerator is that it only requires the user to upload a preformatted input file and download the publicly available R software language, among a few other operating system-specific requirements. Advanced features such as color, text labels, scaling, legend construction, and even database storage can be easily customized with no prior programming knowledge. We provide an intuitive and user-friendly software package, HeatmapGenerator, to create high-quality, customizable heatmaps generated using the high-resolution color graphics capabilities of R. The software is available for Microsoft Windows and Apple Mac OS X. HeatmapGenerator is released under the GNU General Public License and publicly available at: http://sourceforge.net/projects/heatmapgenerator/. The Mac OS X direct download is available at: http://sourceforge.net/projects/heatmapgenerator/files/HeatmapGenerator_MAC_OSX.tar.gz/download. The Windows OS direct download is available at: http://sourceforge.net/projects/heatmapgenerator/files/HeatmapGenerator_WINDOWS.zip/download.

The System Dynamics Model User Sustainability Explorer (SD-MUSE) user interface: a user-friendly tool for interpreting system dynamic models

EPA Science Inventory

Sustainability-based decision making is a challenging process that requires balancing trade-offs among social, economic, and environmental components. System Dynamic (SD) models can be useful tools to inform sustainability-based decision making because they provide a holistic co...

A high performance scientific cloud computing environment for materials simulations

NASA Astrophysics Data System (ADS)

Jorissen, K.; Vila, F. D.; Rehr, J. J.

2012-09-01

We describe the development of a scientific cloud computing (SCC) platform that offers high performance computation capability. The platform consists of a scientific virtual machine prototype containing a UNIX operating system and several materials science codes, together with essential interface tools (an SCC toolset) that offers functionality comparable to local compute clusters. In particular, our SCC toolset provides automatic creation of virtual clusters for parallel computing, including tools for execution and monitoring performance, as well as efficient I/O utilities that enable seamless connections to and from the cloud. Our SCC platform is optimized for the Amazon Elastic Compute Cloud (EC2). We present benchmarks for prototypical scientific applications and demonstrate performance comparable to local compute clusters. To facilitate code execution and provide user-friendly access, we have also integrated cloud computing capability in a JAVA-based GUI. Our SCC platform may be an alternative to traditional HPC resources for materials science or quantum chemistry applications.

FRIEND: a brain-monitoring agent for adaptive and assistive systems.

PubMed

Morris, Alexis; Ulieru, Mihaela

2012-01-01

This paper presents an architectural design for adaptive-systems agents (FRIEND) that use brain state information to make more effective decisions on behalf of a user; measuring brain context versus situational demands. These systems could be useful for alerting users to cognitive workload levels or fatigue, and could attempt to compensate for higher cognitive activity by filtering noise information. In some cases such systems could also share control of devices, such as pulling over in an automated vehicle. These aim to assist people in everyday systems to perform tasks better and be more aware of internal states. Achieving a functioning system of this sort is a challenge, involving a unification of brain- computer-interfaces, human-computer-interaction, soft-computin deliberative multi-agent systems disciplines. Until recently, these were not able to be combined into a usable platform due largely to technological limitations (e.g., size, cost, and processing speed), insufficient research on extracting behavioral states from EEG signals, and lack of low-cost wireless sensing headsets. We aim to surpass these limitations and develop control architectures for making sense of brain state in applications by realizing an agent architecture for adaptive (human-aware) technology. In this paper we present an early, high-level design towards implementing a multi-purpose brain-monitoring agent system to improve user quality of life through the assistive applications of psycho-physiological monitoring, noise-filtering, and shared system control.

CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes

PubMed Central

Hestand, Matthew S; van Galen, Michiel; Villerius, Michel P; van Ommen, Gert-Jan B; den Dunnen, Johan T; 't Hoen, Peter AC

2008-01-01

Background The identification of transcription factor binding sites is difficult since they are only a small number of nucleotides in size, resulting in large numbers of false positives and false negatives in current approaches. Computational methods to reduce false positives are to look for over-representation of transcription factor binding sites in a set of similarly regulated promoters or to look for conservation in orthologous promoter alignments. Results We have developed a novel tool, "CORE_TF" (Conserved and Over-REpresented Transcription Factor binding sites) that identifies common transcription factor binding sites in promoters of co-regulated genes. To improve upon existing binding site predictions, the tool searches for position weight matrices from the TRANSFACR database that are over-represented in an experimental set compared to a random set of promoters and identifies cross-species conservation of the predicted transcription factor binding sites. The algorithm has been evaluated with expression and chromatin-immunoprecipitation on microarray data. We also implement and demonstrate the importance of matching the random set of promoters to the experimental promoters by GC content, which is a unique feature of our tool. Conclusion The program CORE_TF is accessible in a user friendly web interface at . It provides a table of over-represented transcription factor binding sites in the users input genes' promoters and a graphical view of evolutionary conserved transcription factor binding sites. In our test data sets it successfully predicts target transcription factors and their binding sites. PMID:19036135

VTGRAPH - GRAPHIC SOFTWARE TOOL FOR VT TERMINALS

NASA Technical Reports Server (NTRS)

Wang, C.

1994-01-01

VTGRAPH is a graphics software tool for DEC/VT or VT compatible terminals which are widely used by government and industry. It is a FORTRAN or C-language callable library designed to allow the user to deal with many computer environments which use VT terminals for window management and graphic systems. It also provides a PLOT10-like package plus color or shade capability for VT240, VT241, and VT300 terminals. The program is transportable to many different computers which use VT terminals. With this graphics package, the user can easily design more friendly user interface programs and design PLOT10 programs on VT terminals with different computer systems. VTGRAPH was developed using the ReGis Graphics set which provides a full range of graphics capabilities. The basic VTGRAPH capabilities are as follows: window management, PLOT10 compatible drawing, generic program routines for two and three dimensional plotting, and color graphics or shaded graphics capability. The program was developed in VAX FORTRAN in 1988. VTGRAPH requires a ReGis graphics set terminal and a FORTRAN compiler. The program has been run on a DEC MicroVAX 3600 series computer operating under VMS 5.0, and has a virtual memory requirement of 5KB.

cisTEM, user-friendly software for single-particle image processing.

PubMed

Grant, Timothy; Rohou, Alexis; Grigorieff, Nikolaus

2018-03-07

We have developed new open-source software called cis TEM (computational imaging system for transmission electron microscopy) for the processing of data for high-resolution electron cryo-microscopy and single-particle averaging. cis TEM features a graphical user interface that is used to submit jobs, monitor their progress, and display results. It implements a full processing pipeline including movie processing, image defocus determination, automatic particle picking, 2D classification, ab-initio 3D map generation from random parameters, 3D classification, and high-resolution refinement and reconstruction. Some of these steps implement newly-developed algorithms; others were adapted from previously published algorithms. The software is optimized to enable processing of typical datasets (2000 micrographs, 200 k - 300 k particles) on a high-end, CPU-based workstation in half a day or less, comparable to GPU-accelerated processing. Jobs can also be scheduled on large computer clusters using flexible run profiles that can be adapted for most computing environments. cis TEM is available for download from cistem.org. © 2018, Grant et al.

cisTEM, user-friendly software for single-particle image processing

PubMed Central

2018-01-01

We have developed new open-source software called cisTEM (computational imaging system for transmission electron microscopy) for the processing of data for high-resolution electron cryo-microscopy and single-particle averaging. cisTEM features a graphical user interface that is used to submit jobs, monitor their progress, and display results. It implements a full processing pipeline including movie processing, image defocus determination, automatic particle picking, 2D classification, ab-initio 3D map generation from random parameters, 3D classification, and high-resolution refinement and reconstruction. Some of these steps implement newly-developed algorithms; others were adapted from previously published algorithms. The software is optimized to enable processing of typical datasets (2000 micrographs, 200 k – 300 k particles) on a high-end, CPU-based workstation in half a day or less, comparable to GPU-accelerated processing. Jobs can also be scheduled on large computer clusters using flexible run profiles that can be adapted for most computing environments. cisTEM is available for download from cistem.org. PMID:29513216

Computer Assistance in Information Work. Part I: Conceptual Framework for Improving the Computer/User Interface in Information Work. Part II: Catalog of Acceleration, Augmentation, and Delegation Functions in Information Work.

ERIC Educational Resources Information Center

Paisley, William; Butler, Matilda

This study of the computer/user interface investigated the role of the computer in performing information tasks that users now perform without computer assistance. Users' perceptual/cognitive processes are to be accelerated or augmented by the computer; a long term goal is to delegate information tasks entirely to the computer. Cybernetic and…

PC Software graphics tool for conceptual design of space/planetary electrical power systems

NASA Technical Reports Server (NTRS)

Truong, Long V.

1995-01-01

This paper describes the Decision Support System (DSS), a personal computer software graphics tool for designing conceptual space and/or planetary electrical power systems. By using the DSS, users can obtain desirable system design and operating parameters, such as system weight, electrical distribution efficiency, and bus power. With this tool, a large-scale specific power system was designed in a matter of days. It is an excellent tool to help designers make tradeoffs between system components, hardware architectures, and operation parameters in the early stages of the design cycle. The DSS is a user-friendly, menu-driven tool with online help and a custom graphical user interface. An example design and results are illustrated for a typical space power system with multiple types of power sources, frequencies, energy storage systems, and loads.

SiteDB: Marshalling people and resources available to CMS

NASA Astrophysics Data System (ADS)

Metson, S.; Bonacorsi, D.; Dias Ferreira, M.; Egeland, R.

2010-04-01

In a collaboration the size of CMS (approx. 3000 users, and almost 100 computing centres of varying size) communication and accurate information about the sites it has access to is vital in co-ordinating the multitude of computing tasks required for smooth running. SiteDB is a tool developed by CMS to track sites available to the collaboration, the allocation to CMS of resources available at those sites and the associations between CMS members and the sites (as either a manager/operator of the site or a member of a group associated to the site). It is used to track the roles a person has for an associated site or group. SiteDB eases the coordination load for the operations teams by providing a consistent interface to manage communication with the people working at a site, by identifying who is responsible for a given task or service at a site and by offering a uniform interface to information on CMS contacts and sites. SiteDB provides api's and reports for other CMS tools to use to access the information it contains, for instance enabling CRAB to use "user friendly" names when black/white listing CE's, providing role based authentication and authorisation for other web based services and populating various troubleshooting squads in external ticketing systems in use daily by CMS Computing operations.

The Graphical User Interface: Crisis, Danger, and Opportunity.

ERIC Educational Resources Information Center

Boyd, L. H.; And Others

1990-01-01

This article describes differences between the graphical user interface and traditional character-based interface systems, identifies potential problems posed by graphic computing environments for blind computer users, and describes some programs and strategies that are being developed to provide access to those environments. (Author/JDD)

RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application.

PubMed

D'Antonio, Mattia; D'Onorio De Meo, Paolo; Pallocca, Matteo; Picardi, Ernesto; D'Erchia, Anna Maria; Calogero, Raffaele A; Castrignanò, Tiziana; Pesole, Graziano

2015-01-01

The study of RNA has been dramatically improved by the introduction of Next Generation Sequencing platforms allowing massive and cheap sequencing of selected RNA fractions, also providing information on strand orientation (RNA-Seq). The complexity of transcriptomes and of their regulative pathways make RNA-Seq one of most complex field of NGS applications, addressing several aspects of the expression process (e.g. identification and quantification of expressed genes and transcripts, alternative splicing and polyadenylation, fusion genes and trans-splicing, post-transcriptional events, etc.). In order to provide researchers with an effective and friendly resource for analyzing RNA-Seq data, we present here RAP (RNA-Seq Analysis Pipeline), a cloud computing web application implementing a complete but modular analysis workflow. This pipeline integrates both state-of-the-art bioinformatics tools for RNA-Seq analysis and in-house developed scripts to offer to the user a comprehensive strategy for data analysis. RAP is able to perform quality checks (adopting FastQC and NGS QC Toolkit), identify and quantify expressed genes and transcripts (with Tophat, Cufflinks and HTSeq), detect alternative splicing events (using SpliceTrap) and chimeric transcripts (with ChimeraScan). This pipeline is also able to identify splicing junctions and constitutive or alternative polyadenylation sites (implementing custom analysis modules) and call for statistically significant differences in genes and transcripts expression, splicing pattern and polyadenylation site usage (using Cuffdiff2 and DESeq). Through a user friendly web interface, the RAP workflow can be suitably customized by the user and it is automatically executed on our cloud computing environment. This strategy allows to access to bioinformatics tools and computational resources without specific bioinformatics and IT skills. RAP provides a set of tabular and graphical results that can be helpful to browse, filter and export analyzed data, according to the user needs.

Information management and analysis system for groundwater data in Thailand

NASA Astrophysics Data System (ADS)

Gill, D.; Luckananurung, P.

1992-01-01

The Ground Water Division of the Thai Department of Mineral Resources maintains a large archive of groundwater data with information on some 50,000 water wells. Each well file contains information on well location, well completion, borehole geology, water levels, water quality, and pumping tests. In order to enable efficient use of this information a computer-based system for information management and analysis was created. The project was sponsored by the United Nations Development Program and the Thai Department of Mineral Resources. The system was designed to serve users who lack prior training in automated data processing. Access is through a friendly user/system dialogue. Tasks are segmented into a number of logical steps, each of which is managed by a separate screen. Selective retrieval is possible by four different methods of area definition and by compliance with user-specified constraints on any combination of database variables. The main types of outputs are: (1) files of retrieved data, screened according to users' specifications; (2) an assortment of pre-formatted reports; (3) computed geochemical parameters and various diagrams of water chemistry derived therefrom; (4) bivariate scatter diagrams and linear regression analysis; (5) posting of data and computed results on maps; and (6) hydraulic aquifer characteristics as computed from pumping tests. Data are entered directly from formatted screens. Most records can be copied directly from hand-written documents. The database-management program performs data integrity checks in real time, enabling corrections at the time of input. The system software can be grouped into: (1) database administration and maintenance—these functions are carried out by the SIR/DBMS software package; (2) user communication interface for task definition and execution control—the interface is written in the operating system command language (VMS/DCL) and in FORTRAN 77; and (3) scientific data-processing programs, written in FORTRAN 77. The system was implemented on a DEC MicroVAX II computer.

CryoTran user's manual, version 1.0

NASA Technical Reports Server (NTRS)

Cowgill, Glenn R.; Chato, David J.; Saad, Ehab

1989-01-01

The development of cryogenic fluid management systems for space operation is a major portion of the efforts of the Cryogenic Fluids Technology Office (CFTO) at the NASA Lewis Research Center. Analytical models are a necessary part of experimental programs which are used to verify the results of experiments and are also used as a predictor for parametric studies. The CryoTran computer program is a bridge to obtain analytical results. The object of CryoTran is to coordinate these separate analyses into an integrated framework with a user-friendly interface and a common cryogenic property database. CryoTran is an integrated software system designed to help solve a diverse set of problems involving cryogenic fluid storage and transfer in both ground and low-g environments.

PC based temporary shielding administrative procedure (TSAP)

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

Olsen, D.E.; Pederson, G.E.; Hamby, P.N.

1995-03-01

A completely new Administrative Procedure for temporary shielding was developed for use at Commonwealth Edison`s six nuclear stations. This procedure promotes the use of shielding, and addresses industry requirements for the use and control of temporary shielding. The importance of an effective procedure has increased since more temporary shielding is being used as ALARA goals become more ambitious. To help implement the administrative procedure, a personal computer software program was written to incorporate the procedural requirements. This software incorporates the useability of a Windows graphical user interface with extensive help and database features. This combination of a comprehensive administrative proceduremore » and user friendly software promotes the effective use and management of temporary shielding while ensuring that industry requirements are met.« less

TLM-Tracker: software for cell segmentation, tracking and lineage analysis in time-lapse microscopy movies.

PubMed

Klein, Johannes; Leupold, Stefan; Biegler, Ilona; Biedendieck, Rebekka; Münch, Richard; Jahn, Dieter

2012-09-01

Time-lapse imaging in combination with fluorescence microscopy techniques enable the investigation of gene regulatory circuits and uncovered phenomena like culture heterogeneity. In this context, computational image processing for the analysis of single cell behaviour plays an increasing role in systems biology and mathematical modelling approaches. Consequently, we developed a software package with graphical user interface for the analysis of single bacterial cell behaviour. A new software called TLM-Tracker allows for the flexible and user-friendly interpretation for the segmentation, tracking and lineage analysis of microbial cells in time-lapse movies. The software package, including manual, tutorial video and examples, is available as Matlab code or executable binaries at http://www.tlmtracker.tu-bs.de.

EnviroNET: On-line information for LDEF

NASA Technical Reports Server (NTRS)

Lauriente, Michael

1993-01-01

EnviroNET is an on-line, free-form database intended to provide a centralized repository for a wide range of technical information on environmentally induced interactions of use to Space Shuttle customers and spacecraft designers. It provides a user-friendly, menu-driven format on networks that are connected globally and is available twenty-four hours a day - every day. The information, updated regularly, includes expository text, tabular numerical data, charts and graphs, and models. The system pools space data collected over the years by NASA, USAF, other government research facilities, industry, universities, and the European Space Agency. The models accept parameter input from the user, then calculate and display the derived values corresponding to that input. In addition to the archive, interactive graphics programs are also available on space debris, the neutral atmosphere, radiation, magnetic fields, and the ionosphere. A user-friendly, informative interface is standard for all the models and includes a pop-up help window with information on inputs, outputs, and caveats. The system will eventually simplify mission analysis with analytical tools and deliver solutions for computationally intense graphical applications to do 'What if...' scenarios. A proposed plan for developing a repository of information from the Long Duration Exposure Facility (LDEF) for a user group is presented.

Investigation and Implementation of a Tree Transformation System for User Friendly Programming.

DTIC Science & Technology

1984-12-01

systems have become an important area of research because of theiL direct impact on all areas of computer science such as software engineering ...RD-i52 716 INVESTIGTIN AND IMPLEMENTATION OF A TREE I/2TRANSFORMATION SYSTEM FOR USER FRIENDLY PROGRAMMING (U) NAVAL POSTGRADUATE SCHOOL MONTEREY CA...Implementation of a Master’s Thesis Tree Transformation System for User December 1984 Friendly Programming 6. PERFORMING ORG. REPORT NUMBER 7. AU~THOR(s) S

Development of the Software for 30 inch Telescope Control System at KHAO

NASA Astrophysics Data System (ADS)

Mun, B.-S.; Kim, S.-J.; Jang, M.; Min, S.-W.; Seol, K.-H.; Moon, K.-S.

2006-12-01

Even though 30inch optical telescope at Kyung Hee Astronomy Observatory has been used to produce a series of scientific achievements since its first light in 1992, numerous difficulties in the operation of the telescope have hindered the precise observations needed for further researches. Since the currently used PC-TCS (Personal Computer based Telescope Control system) software based on ISA-bus type is outdated, it doesn't have a user friendly interface and make it impossible to scale. Also accumulated errors which are generated by discordance from input and output signals into a motion controller required new control system. Thus we have improved the telescope control system by updating software and modifying mechanical parts. We applied a new BLDC (brushless DC) servo motor system to the mechanical parts of the telescope and developed a control software using Visual Basic 6.0. As a result, we could achieve a high accuracy in controlling of the telescope and use the userfriendly GUI (Graphic User Interface).

UCTM2: An updated User friendly Configurable Trigger, scaler and delay Module for nuclear and particle physics

NASA Astrophysics Data System (ADS)

Bourrion, O.; Boyer, B.; Derome, L.; Pignol, G.

2016-06-01

We developed a highly integrated and versatile electronic module to equip small nuclear physics experiments and lab teaching classes: the User friendly Configurable Trigger, scaler and delay Module for nuclear and particle physics (UCTM). It is configurable through a Graphical User Interface (GUI) and provides a large number of possible trigger conditions without any Hardware Description Language (HDL) required knowledge. This new version significantly enhances the previous capabilities by providing two additional features: signal digitization and time measurements. The design, performances and a typical application are presented.

Computer-Based Tools for Evaluating Graphical User Interfaces

NASA Technical Reports Server (NTRS)

Moore, Loretta A.

1997-01-01

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

Cooperative processing user interfaces for AdaNET

NASA Technical Reports Server (NTRS)

Gutzmann, Kurt M.

1991-01-01

A cooperative processing user interface (CUI) system shares the task of graphical display generation and presentation between the user's computer and a remote host. The communications link between the two computers is typically a modem or Ethernet. The two main purposes of a CUI are reduction of the amount of data transmitted between user and host machines, and provision of a graphical user interface system to make the system easier to use.

VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements.

PubMed

Christley, Scott; Scarborough, Walter; Salinas, Eddie; Rounds, William H; Toby, Inimary T; Fonner, John M; Levin, Mikhail K; Kim, Min; Mock, Stephen A; Jordan, Christopher; Ostmeyer, Jared; Buntzman, Adam; Rubelt, Florian; Davila, Marco L; Monson, Nancy L; Scheuermann, Richard H; Cowell, Lindsay G

2018-01-01

Recent technological advances in immune repertoire sequencing have created tremendous potential for advancing our understanding of adaptive immune response dynamics in various states of health and disease. Immune repertoire sequencing produces large, highly complex data sets, however, which require specialized methods and software tools for their effective analysis and interpretation. VDJServer is a cloud-based analysis portal for immune repertoire sequence data that provide access to a suite of tools for a complete analysis workflow, including modules for preprocessing and quality control of sequence reads, V(D)J gene segment assignment, repertoire characterization, and repertoire comparison. VDJServer also provides sophisticated visualizations for exploratory analysis. It is accessible through a standard web browser via a graphical user interface designed for use by immunologists, clinicians, and bioinformatics researchers. VDJServer provides a data commons for public sharing of repertoire sequencing data, as well as private sharing of data between users. We describe the main functionality and architecture of VDJServer and demonstrate its capabilities with use cases from cancer immunology and autoimmunity. VDJServer provides a complete analysis suite for human and mouse T-cell and B-cell receptor repertoire sequencing data. The combination of its user-friendly interface and high-performance computing allows large immune repertoire sequencing projects to be analyzed with no programming or software installation required. VDJServer is a web-accessible cloud platform that provides access through a graphical user interface to a data management infrastructure, a collection of analysis tools covering all steps in an analysis, and an infrastructure for sharing data along with workflows, results, and computational provenance. VDJServer is a free, publicly available, and open-source licensed resource.

ESPVI 4.0 ELECTROSTATIS PRECIPITATOR V-1 AND PERFORMANCE MODEL: USER'S MANUAL

EPA Science Inventory

The manual is the companion document for the microcomputer program ESPVI 4.0, Electrostatic Precipitation VI and Performance Model. The program was developed to provide a user- friendly interface to an advanced model of electrostatic precipitation (ESP) performance. The program i...

ProteoSign: an end-user online differential proteomics statistical analysis platform.

PubMed

Efstathiou, Georgios; Antonakis, Andreas N; Pavlopoulos, Georgios A; Theodosiou, Theodosios; Divanach, Peter; Trudgian, David C; Thomas, Benjamin; Papanikolaou, Nikolas; Aivaliotis, Michalis; Acuto, Oreste; Iliopoulos, Ioannis

2017-07-03

Profiling of proteome dynamics is crucial for understanding cellular behavior in response to intrinsic and extrinsic stimuli and maintenance of homeostasis. Over the last 20 years, mass spectrometry (MS) has emerged as the most powerful tool for large-scale identification and characterization of proteins. Bottom-up proteomics, the most common MS-based proteomics approach, has always been challenging in terms of data management, processing, analysis and visualization, with modern instruments capable of producing several gigabytes of data out of a single experiment. Here, we present ProteoSign, a freely available web application, dedicated in allowing users to perform proteomics differential expression/abundance analysis in a user-friendly and self-explanatory way. Although several non-commercial standalone tools have been developed for post-quantification statistical analysis of proteomics data, most of them are not end-user appealing as they often require very stringent installation of programming environments, third-party software packages and sometimes further scripting or computer programming. To avoid this bottleneck, we have developed a user-friendly software platform accessible via a web interface in order to enable proteomics laboratories and core facilities to statistically analyse quantitative proteomics data sets in a resource-efficient manner. ProteoSign is available at http://bioinformatics.med.uoc.gr/ProteoSign and the source code at https://github.com/yorgodillo/ProteoSign. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Social Circles: A 3D User Interface for Facebook

NASA Astrophysics Data System (ADS)

Rodrigues, Diego; Oakley, Ian

Online social network services are increasingly popular web applications which display large amounts of rich multimedia content: contacts, status updates, photos and event information. Arguing that this quantity of information overwhelms conventional user interfaces, this paper presents Social Circles, a rich interactive visualization designed to support real world users of social network services in everyday tasks such as keeping up with friends and organizing their network. It achieves this by using 3D UIs, fluid animations and a spatial metaphor to enable direct manipulation of a social network.

User interface support

NASA Technical Reports Server (NTRS)

Lewis, Clayton; Wilde, Nick

1989-01-01

Space construction will require heavy investment in the development of a wide variety of user interfaces for the computer-based tools that will be involved at every stage of construction operations. Using today's technology, user interface development is very expensive for two reasons: (1) specialized and scarce programming skills are required to implement the necessary graphical representations and complex control regimes for high-quality interfaces; (2) iteration on prototypes is required to meet user and task requirements, since these are difficult to anticipate with current (and foreseeable) design knowledge. We are attacking this problem by building a user interface development tool based on extensions to the spreadsheet model of computation. The tool provides high-level support for graphical user interfaces and permits dynamic modification of interfaces, without requiring conventional programming concepts and skills.

The Design of an Interactive Data Retrieval System for Casual Users.

ERIC Educational Resources Information Center

Radhakrishnan, T.; And Others

1982-01-01

Describes an interactive data retrieval system which was designed and implemented for casual users and which incorporates a user-friendly interface, aids to train beginners in use of the system, versatility in output, and error recovery protocols. A 14-item reference list and two figures illustrating system operation and output are included. (JL)

PointCom: semi-autonomous UGV control with intuitive interface

NASA Astrophysics Data System (ADS)

Rohde, Mitchell M.; Perlin, Victor E.; Iagnemma, Karl D.; Lupa, Robert M.; Rohde, Steven M.; Overholt, James; Fiorani, Graham

2008-04-01

Unmanned ground vehicles (UGVs) will play an important role in the nation's next-generation ground force. Advances in sensing, control, and computing have enabled a new generation of technologies that bridge the gap between manual UGV teleoperation and full autonomy. In this paper, we present current research on a unique command and control system for UGVs named PointCom (Point-and-Go Command). PointCom is a semi-autonomous command system for one or multiple UGVs. The system, when complete, will be easy to operate and will enable significant reduction in operator workload by utilizing an intuitive image-based control framework for UGV navigation and allowing a single operator to command multiple UGVs. The project leverages new image processing algorithms for monocular visual servoing and odometry to yield a unique, high-performance fused navigation system. Human Computer Interface (HCI) techniques from the entertainment software industry are being used to develop video-game style interfaces that require little training and build upon the navigation capabilities. By combining an advanced navigation system with an intuitive interface, a semi-autonomous control and navigation system is being created that is robust, user friendly, and less burdensome than many current generation systems. mand).

Extracting microtubule networks from superresolution single-molecule localization microscopy data

PubMed Central

Zhang, Zhen; Nishimura, Yukako; Kanchanawong, Pakorn

2017-01-01

Microtubule filaments form ubiquitous networks that specify spatial organization in cells. However, quantitative analysis of microtubule networks is hampered by their complex architecture, limiting insights into the interplay between their organization and cellular functions. Although superresolution microscopy has greatly facilitated high-resolution imaging of microtubule filaments, extraction of complete filament networks from such data sets is challenging. Here we describe a computational tool for automated retrieval of microtubule filaments from single-molecule-localization–based superresolution microscopy images. We present a user-friendly, graphically interfaced implementation and a quantitative analysis of microtubule network architecture phenotypes in fibroblasts. PMID:27852898

High-performance scientific computing in the cloud

NASA Astrophysics Data System (ADS)

Jorissen, Kevin; Vila, Fernando; Rehr, John

2011-03-01

Cloud computing has the potential to open up high-performance computational science to a much broader class of researchers, owing to its ability to provide on-demand, virtualized computational resources. However, before such approaches can become commonplace, user-friendly tools must be developed that hide the unfamiliar cloud environment and streamline the management of cloud resources for many scientific applications. We have recently shown that high-performance cloud computing is feasible for parallelized x-ray spectroscopy calculations. We now present benchmark results for a wider selection of scientific applications focusing on electronic structure and spectroscopic simulation software in condensed matter physics. These applications are driven by an improved portable interface that can manage virtual clusters and run various applications in the cloud. We also describe a next generation of cluster tools, aimed at improved performance and a more robust cluster deployment. Supported by NSF grant OCI-1048052.

A versatile program for the calculation of linear accelerator room shielding.

PubMed

Hassan, Zeinab El-Taher; Farag, Nehad M; Elshemey, Wael M

2018-03-22

This work aims at designing a computer program to calculate the necessary amount of shielding for a given or proposed linear accelerator room design in radiotherapy. The program (Shield Calculation in Radiotherapy, SCR) has been developed using Microsoft Visual Basic. It applies the treatment room shielding calculations of NCRP report no. 151 to calculate proper shielding thicknesses for a given linear accelerator treatment room design. The program is composed of six main user-friendly interfaces. The first enables the user to upload their choice of treatment room design and to measure the distances required for shielding calculations. The second interface enables the user to calculate the primary barrier thickness in case of three-dimensional conventional radiotherapy (3D-CRT), intensity modulated radiotherapy (IMRT) and total body irradiation (TBI). The third interface calculates the required secondary barrier thickness due to both scattered and leakage radiation. The fourth and fifth interfaces provide a means to calculate the photon dose equivalent for low and high energy radiation, respectively, in door and maze areas. The sixth interface enables the user to calculate the skyshine radiation for photons and neutrons. The SCR program has been successfully validated, precisely reproducing all of the calculated examples presented in NCRP report no. 151 in a simple and fast manner. Moreover, it easily performed the same calculations for a test design that was also calculated manually, and produced the same results. The program includes a new and important feature that is the ability to calculate required treatment room thickness in case of IMRT and TBI. It is characterised by simplicity, precision, data saving, printing and retrieval, in addition to providing a means for uploading and testing any proposed treatment room shielding design. The SCR program provides comprehensive, simple, fast and accurate room shielding calculations in radiotherapy.

PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization.

PubMed

Dogrusoz, U; Erson, E Z; Giral, E; Demir, E; Babur, O; Cetintas, A; Colak, R

2006-02-01

Patikaweb provides a Web interface for retrieving and analyzing biological pathways in the Patika database, which contains data integrated from various prominent public pathway databases. It features a user-friendly interface, dynamic visualization and automated layout, advanced graph-theoretic queries for extracting biologically important phenomena, local persistence capability and exporting facilities to various pathway exchange formats.

Space Communication Artificial Intelligence for Link Evaluation Terminal (SCAILET)

NASA Technical Reports Server (NTRS)

Shahidi, Anoosh K.; Schlegelmilch, Richard F.; Petrik, Edward J.; Walters, Jerry L.

1992-01-01

A software application to assist end-users of the high burst rate (HBR) link evaluation terminal (LET) for satellite communications is being developed. The HBR LET system developed at NASA Lewis Research Center is an element of the Advanced Communications Technology Satellite (ACTS) Project. The HBR LET is divided into seven major subsystems, each with its own expert. Programming scripts, test procedures defined by design engineers, set up the HBR LET system. These programming scripts are cryptic, hard to maintain and require a steep learning curve. These scripts were developed by the system engineers who will not be available for the end-users of the system. To increase end-user productivity a friendly interface needs to be added to the system. One possible solution is to provide the user with adequate documentation to perform the needed tasks. With the complexity of this system the vast amount of documentation needed would be overwhelming and the information would be hard to retrieve. With limited resources, maintenance is another reason for not using this form of documentation. An advanced form of interaction is being explored using current computer techniques. This application, which incorporates a combination of multimedia and artificial intelligence (AI) techniques to provided end-users with an intelligent interface to the HBR LET system, is comprised of an intelligent assistant, intelligent tutoring, and hypermedia documentation. The intelligent assistant and tutoring systems address the critical programming needs of the end-user.

RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application

PubMed Central

2015-01-01

Background The study of RNA has been dramatically improved by the introduction of Next Generation Sequencing platforms allowing massive and cheap sequencing of selected RNA fractions, also providing information on strand orientation (RNA-Seq). The complexity of transcriptomes and of their regulative pathways make RNA-Seq one of most complex field of NGS applications, addressing several aspects of the expression process (e.g. identification and quantification of expressed genes and transcripts, alternative splicing and polyadenylation, fusion genes and trans-splicing, post-transcriptional events, etc.). Moreover, the huge volume of data generated by NGS platforms introduces unprecedented computational and technological challenges to efficiently analyze and store sequence data and results. Methods In order to provide researchers with an effective and friendly resource for analyzing RNA-Seq data, we present here RAP (RNA-Seq Analysis Pipeline), a cloud computing web application implementing a complete but modular analysis workflow. This pipeline integrates both state-of-the-art bioinformatics tools for RNA-Seq analysis and in-house developed scripts to offer to the user a comprehensive strategy for data analysis. RAP is able to perform quality checks (adopting FastQC and NGS QC Toolkit), identify and quantify expressed genes and transcripts (with Tophat, Cufflinks and HTSeq), detect alternative splicing events (using SpliceTrap) and chimeric transcripts (with ChimeraScan). This pipeline is also able to identify splicing junctions and constitutive or alternative polyadenylation sites (implementing custom analysis modules) and call for statistically significant differences in genes and transcripts expression, splicing pattern and polyadenylation site usage (using Cuffdiff2 and DESeq). Results Through a user friendly web interface, the RAP workflow can be suitably customized by the user and it is automatically executed on our cloud computing environment. This strategy allows to access to bioinformatics tools and computational resources without specific bioinformatics and IT skills. RAP provides a set of tabular and graphical results that can be helpful to browse, filter and export analyzed data, according to the user needs. PMID:26046471

RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis.

PubMed

Afzal, Muhammad; Shahid, Ahmad Ali; Shehzadi, Abida; Nadeem, Shahid; Husnain, Tayyab

2012-01-01

RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available. http://www.cemb.edu.pk/sw.html RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language.

Interfacing modules for integrating discipline specific structural mechanics codes

NASA Technical Reports Server (NTRS)

Endres, Ned M.

1989-01-01

An outline of the organization and capabilities of the Engine Structures Computational Simulator (Simulator) at NASA Lewis Research Center is given. One of the goals of the research at Lewis is to integrate various discipline specific structural mechanics codes into a software system which can be brought to bear effectively on a wide range of engineering problems. This system must possess the qualities of being effective and efficient while still remaining user friendly. The simulator was initially designed for the finite element simulation of gas jet engine components. Currently, the simulator has been restricted to only the analysis of high pressure turbine blades and the accompanying rotor assembly, although the current installation can be expanded for other applications. The simulator presently assists the user throughout its procedures by performing information management tasks, executing external support tasks, organizing analysis modules and executing these modules in the user defined order while maintaining processing continuity.

Software to model AXAF-I image quality

NASA Technical Reports Server (NTRS)

Ahmad, Anees; Feng, Chen

1995-01-01

A modular user-friendly computer program for the modeling of grazing-incidence type x-ray optical systems has been developed. This comprehensive computer software GRAZTRACE covers the manipulation of input data, ray tracing with reflectivity and surface deformation effects, convolution with x-ray source shape, and x-ray scattering. The program also includes the capabilities for image analysis, detector scan modeling, and graphical presentation of the results. A number of utilities have been developed to interface the predicted Advanced X-ray Astrophysics Facility-Imaging (AXAF-I) mirror structural and thermal distortions with the ray-trace. This software is written in FORTRAN 77 and runs on a SUN/SPARC station. An interactive command mode version and a batch mode version of the software have been developed.

Human computer interface guide, revision A

NASA Technical Reports Server (NTRS)

1993-01-01

The Human Computer Interface Guide, SSP 30540, is a reference document for the information systems within the Space Station Freedom Program (SSFP). The Human Computer Interface Guide (HCIG) provides guidelines for the design of computer software that affects human performance, specifically, the human-computer interface. This document contains an introduction and subparagraphs on SSFP computer systems, users, and tasks; guidelines for interactions between users and the SSFP computer systems; human factors evaluation and testing of the user interface system; and example specifications. The contents of this document are intended to be consistent with the tasks and products to be prepared by NASA Work Package Centers and SSFP participants as defined in SSP 30000, Space Station Program Definition and Requirements Document. The Human Computer Interface Guide shall be implemented on all new SSFP contractual and internal activities and shall be included in any existing contracts through contract changes. This document is under the control of the Space Station Control Board, and any changes or revisions will be approved by the deputy director.

TRAP/SEE Code Users Manual for Predicting Trapped Radiation Environments

NASA Technical Reports Server (NTRS)

Armstrong, T. W.; Colborn, B. L.

2000-01-01

TRAP/SEE is a PC-based computer code with a user-friendly interface which predicts the ionizing radiation exposure of spacecraft having orbits in the Earth's trapped radiation belts. The code incorporates the standard AP8 and AE8 trapped proton and electron models but also allows application of an improved database interpolation method. The code treats low-Earth as well as highly-elliptical Earth orbits, taking into account trajectory perturbations due to gravitational forces from the Moon and Sun, atmospheric drag, and solar radiation pressure. Orbit-average spectra, peak spectra per orbit, and instantaneous spectra at points along the orbit trajectory are calculated. Described in this report are the features, models, model limitations and uncertainties, input and output descriptions, and example calculations and applications for the TRAP/SEE code.

A web-based information system for management and analysis of patient data after refractive eye surgery.

PubMed

Zuberbuhler, Bruno; Galloway, Peter; Reddy, Aravind; Saldana, Manuel; Gale, Richard

2007-12-01

The aim was to develop a software tool for refractive surgeons using a standard user-friendly web-based interface, providing the user with a secure environment to protect large volumes of patient data. The software application was named "Internet-based refractive analysis" (IBRA), and was programmed with the computer languages PHP, HTML and JavaScript, attached to the opensource MySQL database. IBRA facilitated internationally accepted presentation methods including the stability chart, the predictability chart and the safety chart; it was able to perform vector analysis for the course of a single patient or for group data. With the integrated nomogram calculation, treatment could be customised to reduce the postoperative refractive error. Multicenter functions permitted quality-control comparisons between different surgeons and laser units.

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

Da Rio, Nicola; Robberto, Massimo, E-mail: ndario@rssd.esa.int

We present the Tool for Astrophysical Data Analysis (TA-DA), a new software aimed to greatly simplify and improve the analysis of stellar photometric data in comparison with theoretical models, and allow the derivation of stellar parameters from multi-band photometry. Its flexibility allows one to address a number of such problems: from the interpolation of stellar models, or sets of stellar physical parameters in general, to the computation of synthetic photometry in arbitrary filters or units; from the analysis of observed color-magnitude diagrams to a Bayesian derivation of stellar parameters (and extinction) based on multi-band data. TA-DA is available as amore » pre-compiled Interactive Data Language widget-based application; its graphical user interface makes it considerably user-friendly. In this paper, we describe the software and its functionalities.« less

Human perceptual deficits as factors in computer interface test and evaluation

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

Bowser, S.E.

1992-06-01

Issues related to testing and evaluating human computer interfaces are usually based on the machine rather than on the human portion of the computer interface. Perceptual characteristics of the expected user are rarely investigated, and interface designers ignore known population perceptual limitations. For these reasons, environmental impacts on the equipment will more likely be defined than will user perceptual characteristics. The investigation of user population characteristics is most often directed toward intellectual abilities and anthropometry. This problem is compounded by the fact that some deficits capabilities tend to be found in higher-than-overall population distribution in some user groups. The testmore » and evaluation community can address the issue from two primary aspects. First, assessing user characteristics should be extended to include tests of perceptual capability. Secondly, interface designs should use multimode information coding.« less

Computation of Reacting Flows in Combustion Processes

NASA Technical Reports Server (NTRS)

Keith, Theo G., Jr.; Chen, Kuo-Huey

1997-01-01

The main objective of this research was to develop an efficient three-dimensional computer code for chemically reacting flows. The main computer code developed is ALLSPD-3D. The ALLSPD-3D computer program is developed for the calculation of three-dimensional, chemically reacting flows with sprays. The ALL-SPD code employs a coupled, strongly implicit solution procedure for turbulent spray combustion flows. A stochastic droplet model and an efficient method for treatment of the spray source terms in the gas-phase equations are used to calculate the evaporating liquid sprays. The chemistry treatment in the code is general enough that an arbitrary number of reaction and species can be defined by the users. Also, it is written in generalized curvilinear coordinates with both multi-block and flexible internal blockage capabilities to handle complex geometries. In addition, for general industrial combustion applications, the code provides both dilution and transpiration cooling capabilities. The ALLSPD algorithm, which employs the preconditioning and eigenvalue rescaling techniques, is capable of providing efficient solution for flows with a wide range of Mach numbers. Although written for three-dimensional flows in general, the code can be used for two-dimensional and axisymmetric flow computations as well. The code is written in such a way that it can be run in various computer platforms (supercomputers, workstations and parallel processors) and the GUI (Graphical User Interface) should provide a user-friendly tool in setting up and running the code.

Radiological Monitoring Equipment For Real-Time Quantification Of Area Contamination In Soils And Facility Decommissioning

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

M. V. Carpenter; Jay A. Roach; John R Giles

2005-09-01

The environmental restoration industry offers several sys¬tems that perform scan-type characterization of radiologically contaminated areas. The Idaho National Laboratory (INL) has developed and deployed a suite of field systems that rapidly scan, characterize, and analyse radiological contamination in surface soils. The base system consists of a detector, such as sodium iodide (NaI) spectrometers, a global positioning system (GPS), and an integrated user-friendly computer interface. This mobile concept was initially developed to provide precertifica¬tion analyses of soils contaminated with uranium, thorium, and radium at the Fernald Closure Project, near Cincinnati, Ohio. INL has expanded the functionality of this basic system tomore » create a suite of integrated field-deployable analytical systems. Using its engineering and radiation measurement expertise, aided by computer hardware and software support, INL has streamlined the data acquisition and analysis process to provide real-time information presented on wireless screens and in the form of coverage maps immediately available to field technicians. In addition, custom software offers a user-friendly interface with user-selectable alarm levels and automated data quality monitoring functions that validate the data. This system is deployed from various platforms, depending on the nature of the survey. The deployment platforms include a small all-terrain vehicle used to survey large, relatively flat areas, a hand-pushed unit for areas where manoeuvrability is important, an excavator-mounted system used to scan pits and trenches where personnel access is restricted, and backpack- mounted systems to survey rocky shoreline features and other physical settings that preclude vehicle-based deployment. Variants of the base system include sealed proportional counters for measuring actinides (i.e., plutonium-238 and americium-241) in building demolitions, soil areas, roadbeds, and process line routes at the Miamisburg Closure Project near Dayton, Ohio. In addition, INL supports decontamination operations at the Oak Ridge National Laboratory.« less

A real-time phoneme counting algorithm and application for speech rate monitoring.

PubMed

Aharonson, Vered; Aharonson, Eran; Raichlin-Levi, Katia; Sotzianu, Aviv; Amir, Ofer; Ovadia-Blechman, Zehava

2017-03-01

Adults who stutter can learn to control and improve their speech fluency by modifying their speaking rate. Existing speech therapy technologies can assist this practice by monitoring speaking rate and providing feedback to the patient, but cannot provide an accurate, quantitative measurement of speaking rate. Moreover, most technologies are too complex and costly to be used for home practice. We developed an algorithm and a smartphone application that monitor a patient's speaking rate in real time and provide user-friendly feedback to both patient and therapist. Our speaking rate computation is performed by a phoneme counting algorithm which implements spectral transition measure extraction to estimate phoneme boundaries. The algorithm is implemented in real time in a mobile application that presents its results in a user-friendly interface. The application incorporates two modes: one provides the patient with visual feedback of his/her speech rate for self-practice and another provides the speech therapist with recordings, speech rate analysis and tools to manage the patient's practice. The algorithm's phoneme counting accuracy was validated on ten healthy subjects who read a paragraph at slow, normal and fast paces, and was compared to manual counting of speech experts. Test-retest and intra-counter reliability were assessed. Preliminary results indicate differences of -4% to 11% between automatic and human phoneme counting. Differences were largest for slow speech. The application can thus provide reliable, user-friendly, real-time feedback for speaking rate control practice. Copyright © 2017 Elsevier Inc. All rights reserved.

MuSim, a Graphical User Interface for Multiple Simulation Programs

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

Roberts, Thomas; Cummings, Mary Anne; Johnson, Rolland

2016-06-01

MuSim is a new user-friendly program designed to interface to many different particle simulation codes, regardless of their data formats or geometry descriptions. It presents the user with a compelling graphical user interface that includes a flexible 3-D view of the simulated world plus powerful editing and drag-and-drop capabilities. All aspects of the design can be parametrized so that parameter scans and optimizations are easy. It is simple to create plots and display events in the 3-D viewer (with a slider to vary the transparency of solids), allowing for an effortless comparison of different simulation codes. Simulation codes: G4beamline, MAD-X,more » and MCNP; more coming. Many accelerator design tools and beam optics codes were written long ago, with primitive user interfaces by today's standards. MuSim is specifically designed to make it easy to interface to such codes, providing a common user experience for all, and permitting the construction and exploration of models with very little overhead. For today's technology-driven students, graphical interfaces meet their expectations far better than text-based tools, and education in accelerator physics is one of our primary goals.« less

The IVTANTHERMO-Online database for thermodynamic properties of individual substances with web interface

NASA Astrophysics Data System (ADS)

Belov, G. V.; Dyachkov, S. A.; Levashov, P. R.; Lomonosov, I. V.; Minakov, D. V.; Morozov, I. V.; Sineva, M. A.; Smirnov, V. N.

2018-01-01

The database structure, main features and user interface of an IVTANTHERMO-Online system are reviewed. This system continues the series of the IVTANTHERMO packages developed in JIHT RAS. It includes the database for thermodynamic properties of individual substances and related software for analysis of experimental results, data fitting, calculation and estimation of thermodynamical functions and thermochemistry quantities. In contrast to the previous IVTANTHERMO versions it has a new extensible database design, the client-server architecture, a user-friendly web interface with a number of new features for online and offline data processing.

Closed Loop Experiment Manager (CLEM)-An Open and Inexpensive Solution for Multichannel Electrophysiological Recordings and Closed Loop Experiments.

PubMed

Hazan, Hananel; Ziv, Noam E

2017-01-01

There is growing need for multichannel electrophysiological systems that record from and interact with neuronal systems in near real-time. Such systems are needed, for example, for closed loop, multichannel electrophysiological/optogenetic experimentation in vivo and in a variety of other neuronal preparations, or for developing and testing neuro-prosthetic devices, to name a few. Furthermore, there is a need for such systems to be inexpensive, reliable, user friendly, easy to set-up, open and expandable, and possess long life cycles in face of rapidly changing computing environments. Finally, they should provide powerful, yet reasonably easy to implement facilities for developing closed-loop protocols for interacting with neuronal systems. Here, we survey commercial and open source systems that address these needs to varying degrees. We then present our own solution, which we refer to as Closed Loop Experiments Manager (CLEM). CLEM is an open source, soft real-time, Microsoft Windows desktop application that is based on a single generic personal computer (PC) and an inexpensive, general-purpose data acquisition board. CLEM provides a fully functional, user-friendly graphical interface, possesses facilities for recording, presenting and logging electrophysiological data from up to 64 analog channels, and facilities for controlling external devices, such as stimulators, through digital and analog interfaces. Importantly, it includes facilities for running closed-loop protocols written in any programming language that can generate dynamic link libraries (DLLs). We describe the application, its architecture and facilities. We then demonstrate, using networks of cortical neurons growing on multielectrode arrays (MEA) that despite its reliance on generic hardware, its performance is appropriate for flexible, closed-loop experimentation at the neuronal network level.

Closed Loop Experiment Manager (CLEM)—An Open and Inexpensive Solution for Multichannel Electrophysiological Recordings and Closed Loop Experiments

PubMed Central

Hazan, Hananel; Ziv, Noam E.

2017-01-01

There is growing need for multichannel electrophysiological systems that record from and interact with neuronal systems in near real-time. Such systems are needed, for example, for closed loop, multichannel electrophysiological/optogenetic experimentation in vivo and in a variety of other neuronal preparations, or for developing and testing neuro-prosthetic devices, to name a few. Furthermore, there is a need for such systems to be inexpensive, reliable, user friendly, easy to set-up, open and expandable, and possess long life cycles in face of rapidly changing computing environments. Finally, they should provide powerful, yet reasonably easy to implement facilities for developing closed-loop protocols for interacting with neuronal systems. Here, we survey commercial and open source systems that address these needs to varying degrees. We then present our own solution, which we refer to as Closed Loop Experiments Manager (CLEM). CLEM is an open source, soft real-time, Microsoft Windows desktop application that is based on a single generic personal computer (PC) and an inexpensive, general-purpose data acquisition board. CLEM provides a fully functional, user-friendly graphical interface, possesses facilities for recording, presenting and logging electrophysiological data from up to 64 analog channels, and facilities for controlling external devices, such as stimulators, through digital and analog interfaces. Importantly, it includes facilities for running closed-loop protocols written in any programming language that can generate dynamic link libraries (DLLs). We describe the application, its architecture and facilities. We then demonstrate, using networks of cortical neurons growing on multielectrode arrays (MEA) that despite its reliance on generic hardware, its performance is appropriate for flexible, closed-loop experimentation at the neuronal network level. PMID:29093659

Computer systems and methods for the query and visualization of multidimensional databases

DOEpatents

Stolte, Chris; Tang, Diane L; Hanrahan, Patrick

2014-04-29

In response to a user request, a computer generates a graphical user interface on a computer display. A schema information region of the graphical user interface includes multiple operand names, each operand name associated with one or more fields of a multi-dimensional database. A data visualization region of the graphical user interface includes multiple shelves. Upon detecting a user selection of the operand names and a user request to associate each user-selected operand name with a respective shelf in the data visualization region, the computer generates a visual table in the data visualization region in accordance with the associations between the operand names and the corresponding shelves. The visual table includes a plurality of panes, each pane having at least one axis defined based on data for the fields associated with a respective operand name.

Computer systems and methods for the query and visualization of multidimensional databases

DOEpatents

Stolte, Chris [Palo Alto, CA; Tang, Diane L [Palo Alto, CA; Hanrahan, Patrick [Portola Valley, CA

2011-02-01

In response to a user request, a computer generates a graphical user interface on a computer display. A schema information region of the graphical user interface includes multiple operand names, each operand name associated with one or more fields of a multi-dimensional database. A data visualization region of the graphical user interface includes multiple shelves. Upon detecting a user selection of the operand names and a user request to associate each user-selected operand name with a respective shelf in the data visualization region, the computer generates a visual table in the data visualization region in accordance with the associations between the operand names and the corresponding shelves. The visual table includes a plurality of panes, each pane having at least one axis defined based on data for the fields associated with a respective operand name.

Computer systems and methods for the query and visualization of multidimensional databases

DOEpatents

Stolte, Chris [Palo Alto, CA; Tang, Diane L [Palo Alto, CA; Hanrahan, Patrick [Portola Valley, CA

2012-03-20

In response to a user request, a computer generates a graphical user interface on a computer display. A schema information region of the graphical user interface includes multiple operand names, each operand name associated with one or more fields of a multi-dimensional database. A data visualization region of the graphical user interface includes multiple shelves. Upon detecting a user selection of the operand names and a user request to associate each user-selected operand name with a respective shelf in the data visualization region, the computer generates a visual table in the data visualization region in accordance with the associations between the operand names and the corresponding shelves. The visual table includes a plurality of panes, each pane having at least one axis defined based on data for the fields associated with a respective operand name.

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches.

PubMed

Vaudel, Marc; Barsnes, Harald; Berven, Frode S; Sickmann, Albert; Martens, Lennart

2011-03-01

The identification of proteins by mass spectrometry is a standard technique in the field of proteomics, relying on search engines to perform the identifications of the acquired spectra. Here, we present a user-friendly, lightweight and open-source graphical user interface called SearchGUI (http://searchgui.googlecode.com), for configuring and running the freely available OMSSA (open mass spectrometry search algorithm) and X!Tandem search engines simultaneously. Freely available under the permissible Apache2 license, SearchGUI is supported on Windows, Linux and OSX. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The development of a prototype intelligent user interface subsystem for NASA's scientific database systems

NASA Technical Reports Server (NTRS)

Campbell, William J.; Roelofs, Larry H.; Short, Nicholas M., Jr.

1987-01-01

The National Space Science Data Center (NSSDC) has initiated an Intelligent Data Management (IDM) research effort which has as one of its components the development of an Intelligent User Interface (IUI).The intent of the latter is to develop a friendly and intelligent user interface service that is based on expert systems and natural language processing technologies. The purpose is to support the large number of potential scientific and engineering users presently having need of space and land related research and technical data but who have little or no experience in query languages or understanding of the information content or architecture of the databases involved. This technical memorandum presents prototype Intelligent User Interface Subsystem (IUIS) using the Crustal Dynamics Project Database as a test bed for the implementation of the CRUDDES (Crustal Dynamics Expert System). The knowledge base has more than 200 rules and represents a single application view and the architectural view. Operational performance using CRUDDES has allowed nondatabase users to obtain useful information from the database previously accessible only to an expert database user or the database designer.

76 FR 10628 - Self-Regulatory Organizations; the Depository Trust Company; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-25

... Change Regarding Providing Participants With a New Optional Settlement Web Interface February 22, 2011... Rule Change The proposed rule change will establish a new browser-based interface, the ``Settlement Web... Browser System (``PBS'').\\4\\ Based on request from its Participants, DTC has created a more user-friendly...

Assessing the Depth of Cognitive Processing as the Basis for Potential User-State Adaptation

PubMed Central

Nicolae, Irina-Emilia; Acqualagna, Laura; Blankertz, Benjamin

2017-01-01

Objective: Decoding neurocognitive processes on a single-trial basis with Brain-Computer Interface (BCI) techniques can reveal the user's internal interpretation of the current situation. Such information can potentially be exploited to make devices and interfaces more user aware. In this line of research, we took a further step by studying neural correlates of different levels of cognitive processes and developing a method that allows to quantify how deeply presented information is processed in the brain. Methods/Approach: Seventeen participants took part in an EEG study in which we evaluated different levels of cognitive processing (no processing, shallow, and deep processing) within three distinct domains (memory, language, and visual imagination). Our investigations showed gradual differences in the amplitudes of event-related potentials (ERPs) and in the extend and duration of event-related desynchronization (ERD) which both correlate with task difficulty. We performed multi-modal classification to map the measured correlates of neurocognitive processing to the corresponding level of processing. Results: Successful classification of the neural components was achieved, which reflects the level of cognitive processing performed by the participants. The results show performances above chance level for each participant and a mean performance of 70–90% for all conditions and classification pairs. Significance: The successful estimation of the level of cognition on a single-trial basis supports the feasibility of user-state adaptation based on ongoing neural activity. There is a variety of potential use cases such as: a user-friendly adaptive design of an interface or the development of assistance systems in safety critical workplaces. PMID:29046625

Assessing the Depth of Cognitive Processing as the Basis for Potential User-State Adaptation.

PubMed

Nicolae, Irina-Emilia; Acqualagna, Laura; Blankertz, Benjamin

2017-01-01

Objective: Decoding neurocognitive processes on a single-trial basis with Brain-Computer Interface (BCI) techniques can reveal the user's internal interpretation of the current situation. Such information can potentially be exploited to make devices and interfaces more user aware. In this line of research, we took a further step by studying neural correlates of different levels of cognitive processes and developing a method that allows to quantify how deeply presented information is processed in the brain. Methods/Approach: Seventeen participants took part in an EEG study in which we evaluated different levels of cognitive processing (no processing, shallow, and deep processing) within three distinct domains (memory, language, and visual imagination). Our investigations showed gradual differences in the amplitudes of event-related potentials (ERPs) and in the extend and duration of event-related desynchronization (ERD) which both correlate with task difficulty. We performed multi-modal classification to map the measured correlates of neurocognitive processing to the corresponding level of processing. Results: Successful classification of the neural components was achieved, which reflects the level of cognitive processing performed by the participants. The results show performances above chance level for each participant and a mean performance of 70-90% for all conditions and classification pairs. Significance: The successful estimation of the level of cognition on a single-trial basis supports the feasibility of user-state adaptation based on ongoing neural activity. There is a variety of potential use cases such as: a user-friendly adaptive design of an interface or the development of assistance systems in safety critical workplaces.

Student Preferences toward Microcomputer User Interfaces.

ERIC Educational Resources Information Center

Hazari, Sunil I.; Reaves, Rita R.

1994-01-01

Describes a study of undergraduates that was conducted to determine students' preferences toward Graphical User Interface versus Command Line Interface during computer-assisted instruction. Previous experience, comfort level, performance scores, and student attitudes are examined and compared, and the computer use survey is appended. (Contains 13…

Spatial issues in user interface design from a graphic design perspective

NASA Technical Reports Server (NTRS)

Marcus, Aaron

1989-01-01

The user interface of a computer system is a visual display that provides information about the status of operations on data within the computer and control options to the user that enable adjustments to these operations. From the very beginning of computer technology the user interface was a spatial display, although its spatial features were not necessarily complex or explicitly recognized by the users. All text and nonverbal signs appeared in a virtual space generally thought of as a single flat plane of symbols. Current technology of high performance workstations permits any element of the display to appear as dynamic, multicolor, 3-D signs in a virtual 3-D space. The complexity of appearance and the user's interaction with the display provide significant challenges to the graphic designer of current and future user interfaces. In particular, spatial depiction provides many opportunities for effective communication of objects, structures, processes, navigation, selection, and manipulation. Issues are presented that are relevant to the graphic designer seeking to optimize the user interface's spatial attributes for effective visual communication.

Manifest: A computer program for 2-D flow modeling in Stirling machines

NASA Technical Reports Server (NTRS)

Gedeon, David

1989-01-01

A computer program named Manifest is discussed. Manifest is a program one might want to use to model the fluid dynamics in the manifolds commonly found between the heat exchangers and regenerators of Stirling machines; but not just in the manifolds - in the regenerators as well. And in all sorts of other places too, such as: in heaters or coolers, or perhaps even in cylinder spaces. There are probably nonStirling uses for Manifest also. In broad strokes, Manifest will: (1) model oscillating internal compressible laminar fluid flow in a wide range of two-dimensional regions, either filled with porous materials or empty; (2) present a graphics-based user-friendly interface, allowing easy selection and modification of region shape and boundary condition specification; (3) run on a personal computer, or optionally (in the case of its number-crunching module) on a supercomputer; and (4) allow interactive examination of the solution output so the user can view vector plots of flow velocity, contour plots of pressure and temperature at various locations and tabulate energy-related integrals of interest.

Sharing Research Models: Using Software Engineering Practices for Facilitation

PubMed Central

Bryant, Stephanie P.; Solano, Eric; Cantor, Susanna; Cooley, Philip C.; Wagener, Diane K.

2011-01-01

Increasingly, researchers are turning to computational models to understand the interplay of important variables on systems’ behaviors. Although researchers may develop models that meet the needs of their investigation, application limitations—such as nonintuitive user interface features and data input specifications—may limit the sharing of these tools with other research groups. By removing these barriers, other research groups that perform related work can leverage these work products to expedite their own investigations. The use of software engineering practices can enable managed application production and shared research artifacts among multiple research groups by promoting consistent models, reducing redundant effort, encouraging rigorous peer review, and facilitating research collaborations that are supported by a common toolset. This report discusses three established software engineering practices— the iterative software development process, object-oriented methodology, and Unified Modeling Language—and the applicability of these practices to computational model development. Our efforts to modify the MIDAS TranStat application to make it more user-friendly are presented as an example of how computational models that are based on research and developed using software engineering practices can benefit a broader audience of researchers. PMID:21687780

Representing Graphical User Interfaces with Sound: A Review of Approaches

ERIC Educational Resources Information Center

Ratanasit, Dan; Moore, Melody M.

2005-01-01

The inability of computer users who are visually impaired to access graphical user interfaces (GUIs) has led researchers to propose approaches for adapting GUIs to auditory interfaces, with the goal of providing access for visually impaired people. This article outlines the issues involved in nonvisual access to graphical user interfaces, reviews…

Status and future of the 3D MAFIA group of codes

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

Ebeling, F.; Klatt, R.; Krawzcyk, F.

1988-12-01

The group of fully three dimensional computer codes for solving Maxwell's equations for a wide range of applications, MAFIA, is already well established. Extensive comparisons with measurements have demonstrated the accuracy of the computations. A large numer of components have been designed for accelerators, such as kicker magnets, non cyclindrical cavities, ferrite loaded cavities, vacuum chambers with slots and transitions, etc. The latest additions to the system include a new static solver that can calculate 3D magneto- and electrostatic fields, and a self consistent version of the 2D-BCI that solves the field equations and the equations of motion in parallel.more » Work on new eddy current modules has started, which will allow treatment of laminated and/or solid iron cores excited by low frequency currents. Based on our experience with the present releases 1 and 2, we have started a complete revision of the whole user interface and data structure, which will make the codes even more user-friendly and flexible.« less

User's Manual for the Object User Interface (OUI): An Environmental Resource Modeling Framework

USGS Publications Warehouse

Markstrom, Steven L.; Koczot, Kathryn M.

2008-01-01

The Object User Interface is a computer application that provides a framework for coupling environmental-resource models and for managing associated temporal and spatial data. The Object User Interface is designed to be easily extensible to incorporate models and data interfaces defined by the user. Additionally, the Object User Interface is highly configurable through the use of a user-modifiable, text-based control file that is written in the eXtensible Markup Language. The Object User Interface user's manual provides (1) installation instructions, (2) an overview of the graphical user interface, (3) a description of the software tools, (4) a project example, and (5) specifications for user configuration and extension.

Starting Over: Current Issues in Online Catalog User Interface Design.

ERIC Educational Resources Information Center

Crawford, Walt

1992-01-01

Discussion of online catalogs focuses on issues in interface design. Issues addressed include understanding the user base; common user access (CUA) with personal computers; common command language (CCL); hyperlinks; screen design issues; differences from card catalogs; indexes; graphic user interfaces (GUIs); color; online help; and remote users.…

A web-oriented software for the optimization of pooled experiments in NGS for detection of rare mutations.

PubMed

Evangelista, Daniela; Zuccaro, Antonio; Lančinskas, Algirdas; Žilinskas, Julius; Guarracino, Mario R

2016-02-17

The cost per patient of next generation sequencing for detection of rare mutations may be significantly reduced using pooled experiments. Recently, some techniques have been proposed for the planning of pooled experiments and for the optimal allocation of patients into pools. However, the lack of a user friendly resource for planning the design of pooled experiments forces the scientists to do frequent, complex and long computations. OPENDoRM is a powerful collection of novel mathematical algorithms usable via an intuitive graphical user interface. It enables researchers to speed up the planning of their routine experiments, as well as, to support scientists without specific bioinformatics expertises. Users can automatically carry out analysis in terms of costs associated with the optimal allocation of patients in pools. They are also able to choose between three distinct pooling mathematical methods, each of which also suggests the optimal configuration for the submitted experiment. Importantly, in order to keep track of the performed experiments, users can save and export the results of their experiments in standard tabular and charts contents. OPENDoRM is a freely available web-oriented application for the planning of pooled NGS experiments, available at: http://www-labgtp.na.icar.cnr.it/OPENDoRM. Its easy and intuitive graphical user interface enables researchers to plan theirs experiments using novel algorithms, and to interactively visualize the results.

Chemical and mineralogical data and processing methods management system prototype with application to study of the North Caucasus Blybsky Metamorphic Complexes metamorphism PT-condition

NASA Astrophysics Data System (ADS)

Ivanov, Stanislav; Kamzolkin, Vladimir; Konilov, Aleksandr; Aleshin, Igor

2014-05-01

There are many various methods of assessing the conditions of rocks formation based on determining the composition of the constituent minerals. Our objective was to create a universal tool for processing mineral's chemical analysis results and solving geothermobarometry problems by creating a database of existing sensors and providing a user-friendly standard interface. Similar computer assisted tools are based upon large collection of sensors (geothermometers and geobarometers) are known, for example, the project TPF (Konilov A.N., 1999) - text-based sensor collection tool written in PASCAL. The application contained more than 350 different sensors and has been used widely in petrochemical studies (see A.N. Konilov , A.A. Grafchikov, V.I. Fonarev 2010 for review). Our prototype uses the TPF project concept and is designed with modern application development techniques, which allows better flexibility. Main components of the designed system are 3 connected datasets: sensors collection (geothermometers, geobarometers, oxygen geobarometers, etc.), petrochemical data and modeling results. All data is maintained by special management and visualization tools and resides in sql database. System utilities allow user to import and export data in various file formats, edit records and plot graphs. Sensors database contains up to date collections of known methods. New sensors may be added by user. Measured database should be filled in by researcher. User friendly interface allows access to all available data and sensors, automates routine work, reduces the risk of common user mistakes and simplifies information exchange between research groups. We use prototype to evaluate peak pressure during the formation of garnet-amphibolite apoeclogites, gneisses and schists Blybsky metamorphic complex of the Front Range of the Northern Caucasus. In particular, our estimation of formation pressure range (18 ± 4 kbar) agrees on independent research results. The reported study was partially supported by RFBR, research project No. 14-05-00615.

Graphical Requirements for Force Level Planning. Volume 2

DTIC Science & Technology

1991-09-01

technology review includes graphics algorithms, computer hardware, computer software, and design methodologies. The technology can either exist today or...level graphics language. 7.4 User Interface Design Tools As user interfaces have become more sophisticated, they have become harder to develop. Xl...Setphen M. Pizer, editors. Proceedings 1986 Workshop on Interactive 31) Graphics , October 1986. 18 J. S. Dumas. Designing User Interface Software. Prentice

SWAT Check: A screening tool to assist users in the identification of potential model application problems

USDA-ARS?s Scientific Manuscript database

The Soil and Water Assessment Tool (SWAT) is a basin scale hydrologic model developed by the US Department of Agriculture-Agricultural Research Service. SWAT's broad applicability, user friendly model interfaces, and automatic calibration software have led to a rapid increase in the number of new u...

Documenting the Conversation: A Systematic Review of Library Discovery Layers

ERIC Educational Resources Information Center

Bossaller, Jenny S.; Sandy, Heather Moulaison

2017-01-01

This article describes the results of a systematic review of peer-reviewed, published research articles about "discovery layers," user-friendly interfaces or systems that provide single-search box access to library content. Focusing on articles in LISTA published 2009-2013, a set of 80 articles was coded for community of users, journal…

CRISPR Primer Designer: Design primers for knockout and chromosome imaging CRISPR-Cas system.

PubMed

Yan, Meng; Zhou, Shi-Rong; Xue, Hong-Wei

2015-07-01

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated system enables biologists to edit genomes precisely and provides a powerful tool for perturbing endogenous gene regulation, modulation of epigenetic markers, and genome architecture. However, there are concerns about the specificity of the system, especially the usages of knocking out a gene. Previous designing tools either were mostly built-in websites or ran as command-line programs, and none of them ran locally and acquired a user-friendly interface. In addition, with the development of CRISPR-derived systems, such as chromosome imaging, there were still no tools helping users to generate specific end-user spacers. We herein present CRISPR Primer Designer for researchers to design primers for CRISPR applications. The program has a user-friendly interface, can analyze the BLAST results by using multiple parameters, score for each candidate spacer, and generate the primers when using a certain plasmid. In addition, CRISPR Primer Designer runs locally and can be used to search spacer clusters, and exports primers for the CRISPR-Cas system-based chromosome imaging system. © 2014 Institute of Botany, Chinese Academy of Sciences.

A Multifunctional Brain-Computer Interface Intended for Home Use: An Evaluation with Healthy Participants and Potential End Users with Dry and Gel-Based Electrodes

PubMed Central

Käthner, Ivo; Halder, Sebastian; Hintermüller, Christoph; Espinosa, Arnau; Guger, Christoph; Miralles, Felip; Vargiu, Eloisa; Dauwalder, Stefan; Rafael-Palou, Xavier; Solà, Marc; Daly, Jean M.; Armstrong, Elaine; Martin, Suzanne; Kübler, Andrea

2017-01-01

Current brain-computer interface (BCIs) software is often tailored to the needs of scientists and technicians and therefore complex to allow for versatile use. To facilitate home use of BCIs a multifunctional P300 BCI with a graphical user interface intended for non-expert set-up and control was designed and implemented. The system includes applications for spelling, web access, entertainment, artistic expression and environmental control. In addition to new software, it also includes new hardware for the recording of electroencephalogram (EEG) signals. The EEG system consists of a small and wireless amplifier attached to a cap that can be equipped with gel-based or dry contact electrodes. The system was systematically evaluated with a healthy sample, and targeted end users of BCI technology, i.e., people with a varying degree of motor impairment tested the BCI in a series of individual case studies. Usability was assessed in terms of effectiveness, efficiency and satisfaction. Feedback of users was gathered with structured questionnaires. Two groups of healthy participants completed an experimental protocol with the gel-based and the dry contact electrodes (N = 10 each). The results demonstrated that all healthy participants gained control over the system and achieved satisfactory to high accuracies with both gel-based and dry electrodes (average error rates of 6 and 13%). Average satisfaction ratings were high, but certain aspects of the system such as the wearing comfort of the dry electrodes and design of the cap, and speed (in both groups) were criticized by some participants. Six potential end users tested the system during supervised sessions. The achieved accuracies varied greatly from no control to high control with accuracies comparable to that of healthy volunteers. Satisfaction ratings of the two end-users that gained control of the system were lower as compared to healthy participants. The advantages and disadvantages of the BCI and its applications are discussed and suggestions are presented for improvements to pave the way for user friendly BCIs intended to be used as assistive technology by persons with severe paralysis. PMID:28588442

A Multifunctional Brain-Computer Interface Intended for Home Use: An Evaluation with Healthy Participants and Potential End Users with Dry and Gel-Based Electrodes.

PubMed

Käthner, Ivo; Halder, Sebastian; Hintermüller, Christoph; Espinosa, Arnau; Guger, Christoph; Miralles, Felip; Vargiu, Eloisa; Dauwalder, Stefan; Rafael-Palou, Xavier; Solà, Marc; Daly, Jean M; Armstrong, Elaine; Martin, Suzanne; Kübler, Andrea

2017-01-01

Current brain-computer interface (BCIs) software is often tailored to the needs of scientists and technicians and therefore complex to allow for versatile use. To facilitate home use of BCIs a multifunctional P300 BCI with a graphical user interface intended for non-expert set-up and control was designed and implemented. The system includes applications for spelling, web access, entertainment, artistic expression and environmental control. In addition to new software, it also includes new hardware for the recording of electroencephalogram (EEG) signals. The EEG system consists of a small and wireless amplifier attached to a cap that can be equipped with gel-based or dry contact electrodes. The system was systematically evaluated with a healthy sample, and targeted end users of BCI technology, i.e., people with a varying degree of motor impairment tested the BCI in a series of individual case studies. Usability was assessed in terms of effectiveness, efficiency and satisfaction. Feedback of users was gathered with structured questionnaires. Two groups of healthy participants completed an experimental protocol with the gel-based and the dry contact electrodes ( N = 10 each). The results demonstrated that all healthy participants gained control over the system and achieved satisfactory to high accuracies with both gel-based and dry electrodes (average error rates of 6 and 13%). Average satisfaction ratings were high, but certain aspects of the system such as the wearing comfort of the dry electrodes and design of the cap, and speed (in both groups) were criticized by some participants. Six potential end users tested the system during supervised sessions. The achieved accuracies varied greatly from no control to high control with accuracies comparable to that of healthy volunteers. Satisfaction ratings of the two end-users that gained control of the system were lower as compared to healthy participants. The advantages and disadvantages of the BCI and its applications are discussed and suggestions are presented for improvements to pave the way for user friendly BCIs intended to be used as assistive technology by persons with severe paralysis.

Mask_explorer: A tool for exploring brain masks in fMRI group analysis.

PubMed

Gajdoš, Martin; Mikl, Michal; Mareček, Radek

2016-10-01

Functional magnetic resonance imaging (fMRI) studies of the human brain are appearing in increasing numbers, providing interesting information about this complex system. Unique information about healthy and diseased brains is inferred using many types of experiments and analyses. In order to obtain reliable information, it is necessary to conduct consistent experiments with large samples of subjects and to involve statistical methods to confirm or reject any tested hypotheses. Group analysis is performed for all voxels within a group mask, i.e. a common space where all of the involved subjects contribute information. To our knowledge, a user-friendly interface with the ability to visualize subject-specific details in a common analysis space did not yet exist. The purpose of our work is to develop and present such interface. Several pitfalls have to be avoided while preparing fMRI data for group analysis. One such pitfall is spurious non-detection, caused by inferring conclusions in the volume of a group mask that has been corrupted due to a preprocessing failure. We describe a MATLAB toolbox, called the mask_explorer, designed for prevention of this pitfall. The mask_explorer uses a graphical user interface, enables a user-friendly exploration of subject masks and is freely available. It is able to compute subject masks from raw data and create lists of subjects with potentially problematic data. It runs under MATLAB with the widely used SPM toolbox. Moreover, we present several practical examples where the mask_explorer is usefully applied. The mask_explorer is designed to quickly control the quality of the group fMRI analysis volume and to identify specific failures related to preprocessing steps and acquisition. It helps researchers detect subjects with potentially problematic data and consequently enables inspection of the data. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

The SubCons webserver: A user friendly web interface for state-of-the-art subcellular localization prediction.

PubMed

Salvatore, M; Shu, N; Elofsson, A

2018-01-01

SubCons is a recently developed method that predicts the subcellular localization of a protein. It combines predictions from four predictors using a Random Forest classifier. Here, we present the user-friendly web-interface implementation of SubCons. Starting from a protein sequence, the server rapidly predicts the subcellular localizations of an individual protein. In addition, the server accepts the submission of sets of proteins either by uploading the files or programmatically by using command line WSDL API scripts. This makes SubCons ideal for proteome wide analyses allowing the user to scan a whole proteome in few days. From the web page, it is also possible to download precalculated predictions for several eukaryotic organisms. To evaluate the performance of SubCons we present a benchmark of LocTree3 and SubCons using two recent mass-spectrometry based datasets of mouse and drosophila proteins. The server is available at http://subcons.bioinfo.se/. © 2017 The Protein Society.

BrainIACS: a system for web-based medical image processing

NASA Astrophysics Data System (ADS)

Kishore, Bhaskar; Bazin, Pierre-Louis; Pham, Dzung L.

2009-02-01

We describe BrainIACS, a web-based medical image processing system that permits and facilitates algorithm developers to quickly create extensible user interfaces for their algorithms. Designed to address the challenges faced by algorithm developers in providing user-friendly graphical interfaces, BrainIACS is completely implemented using freely available, open-source software. The system, which is based on a client-server architecture, utilizes an AJAX front-end written using the Google Web Toolkit (GWT) and Java Servlets running on Apache Tomcat as its back-end. To enable developers to quickly and simply create user interfaces for configuring their algorithms, the interfaces are described using XML and are parsed by our system to create the corresponding user interface elements. Most of the commonly found elements such as check boxes, drop down lists, input boxes, radio buttons, tab panels and group boxes are supported. Some elements such as the input box support input validation. Changes to the user interface such as addition and deletion of elements are performed by editing the XML file or by using the system's user interface creator. In addition to user interface generation, the system also provides its own interfaces for data transfer, previewing of input and output files, and algorithm queuing. As the system is programmed using Java (and finally Java-script after compilation of the front-end code), it is platform independent with the only requirements being that a Servlet implementation be available and that the processing algorithms can execute on the server platform.

Micromechanical combined stress analysis: MICSTRAN, a user manual

NASA Technical Reports Server (NTRS)

Naik, R. A.

1992-01-01

Composite materials are currently being used in aerospace and other applications. The ability to tailor the composite properties by the appropriate selection of its constituents, the fiber and matrix, is a major advantage of composite materials. The Micromechanical Combined Stress Analysis (MICSTRAN) code provides the materials engineer with a user-friendly personal computer (PC) based tool to calculate overall composite properties given the constituent fiber and matrix properties. To assess the ability of the composite to carry structural loads, the materials engineer also needs to calculate the internal stresses in the composite material. MICSTRAN is a simple tool to calculate such internal stresses with a composite ply under combined thermomechanical loading. It assumes that the fibers have a circular cross-section and are arranged either in a repeating square or diamond array pattern within a ply. It uses a classical elasticity solution technique that has been demonstrated to calculate accurate stress results. Input to the program consists of transversely isotropic fiber properties and isotropic matrix properties such as moduli, Poisson's ratios, coefficients of thermal expansion, and volume fraction. Output consists of overall thermoelastic constants and stresses. Stresses can be computed under the combined action of thermal, transverse, longitudinal, transverse shear, and longitudinal shear loadings. Stress output can be requested along the fiber-matrix interface, the model boundaries, circular arcs, or at user-specified points located anywhere in the model. The MICSTRAN program is Windows compatible and takes advantage of the Microsoft Windows graphical user interface which facilitates multitasking and extends memory access far beyond the limits imposed by the DOS operating system.

Assessment of the usability of a digital learning technology prototype for monitoring intracranial pressure 1

PubMed Central

de Carvalho, Lilian Regina; Évora, Yolanda Dora Martinez; Zem-Mascarenhas, Silvia Helena

2016-01-01

ABSTRACT Objective: to assess the usability of a digital learning technology prototype as a new method for minimally invasive monitoring of intracranial pressure. Method: descriptive study using a quantitative approach on assessing the usability of a prototype based on Nielsen's ten heuristics. Four experts in the area of Human-Computer interaction participated in the study. Results: the evaluation delivered eight violated heuristics and 31 usability problems in the 32 screens of the prototype. Conclusion: the suggestions of the evaluators were critical for developing an intuitive, user-friendly interface and will be included in the final version of the digital learning technology. PMID:27579932

A computationally efficient software application for calculating vibration from underground railways

NASA Astrophysics Data System (ADS)

Hussein, M. F. M.; Hunt, H. E. M.

2009-08-01

The PiP model is a software application with a user-friendly interface for calculating vibration from underground railways. This paper reports about the software with a focus on its latest version and the plans for future developments. The software calculates the Power Spectral Density of vibration due to a moving train on floating-slab track with track irregularity described by typical values of spectra for tracks with good, average and bad conditions. The latest version accounts for a tunnel embedded in a half space by employing a toolbox developed at K.U. Leuven which calculates Green's functions for a multi-layered half-space.

S3D: An interactive surface grid generation tool

NASA Technical Reports Server (NTRS)

Luh, Raymond Ching-Chung; Pierce, Lawrence E.; Yip, David

1992-01-01

S3D, an interactive software tool for surface grid generation, is described. S3D provides the means with which a geometry definition based either on a discretized curve set or a rectangular set can be quickly processed towards the generation of a surface grid for computational fluid dynamics (CFD) applications. This is made possible as a result of implementing commonly encountered surface gridding tasks in an environment with a highly efficient and user friendly graphical interface. Some of the more advanced features of S3D include surface-surface intersections, optimized surface domain decomposition and recomposition, and automated propagation of edge distributions to surrounding grids.

Intelligent Context-Aware and Adaptive Interface for Mobile LBS

PubMed Central

Liu, Yanhong

2015-01-01

Context-aware user interface plays an important role in many human-computer Interaction tasks of location based services. Although spatial models for context-aware systems have been studied extensively, how to locate specific spatial information for users is still not well resolved, which is important in the mobile environment where location based services users are impeded by device limitations. Better context-aware human-computer interaction models of mobile location based services are needed not just to predict performance outcomes, such as whether people will be able to find the information needed to complete a human-computer interaction task, but to understand human processes that interact in spatial query, which will in turn inform the detailed design of better user interfaces in mobile location based services. In this study, a context-aware adaptive model for mobile location based services interface is proposed, which contains three major sections: purpose, adjustment, and adaptation. Based on this model we try to describe the process of user operation and interface adaptation clearly through the dynamic interaction between users and the interface. Then we show how the model applies users' demands in a complicated environment and suggested the feasibility by the experimental results. PMID:26457077

Exploring a Net Centric Architecture Using the Net Warrior Airborne Early Warning and Control Node

DTIC Science & Technology

2007-12-01

implemented in different languages. Customisation Interfaces for customising components. User-friendly customisation tools will use these interfaces...Sun Enterprise Java Beans. Customisation Customisation in the context of components is defined in [Heineman & Councill 2001, p. 42] as ‘…the ability...of a consumer to adapt a component prior to its installation or use’. Customisation can be facilitated through the use of specialised interfaces

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics

PubMed Central

Brusniak, Mi-Youn; Bodenmiller, Bernd; Campbell, David; Cooke, Kelly; Eddes, James; Garbutt, Andrew; Lau, Hollis; Letarte, Simon; Mueller, Lukas N; Sharma, Vagisha; Vitek, Olga; Zhang, Ning; Aebersold, Ruedi; Watts, Julian D

2008-01-01

Background Quantitative proteomics holds great promise for identifying proteins that are differentially abundant between populations representing different physiological or disease states. A range of computational tools is now available for both isotopically labeled and label-free liquid chromatography mass spectrometry (LC-MS) based quantitative proteomics. However, they are generally not comparable to each other in terms of functionality, user interfaces, information input/output, and do not readily facilitate appropriate statistical data analysis. These limitations, along with the array of choices, present a daunting prospect for biologists, and other researchers not trained in bioinformatics, who wish to use LC-MS-based quantitative proteomics. Results We have developed Corra, a computational framework and tools for discovery-based LC-MS proteomics. Corra extends and adapts existing algorithms used for LC-MS-based proteomics, and statistical algorithms, originally developed for microarray data analyses, appropriate for LC-MS data analysis. Corra also adapts software engineering technologies (e.g. Google Web Toolkit, distributed processing) so that computationally intense data processing and statistical analyses can run on a remote server, while the user controls and manages the process from their own computer via a simple web interface. Corra also allows the user to output significantly differentially abundant LC-MS-detected peptide features in a form compatible with subsequent sequence identification via tandem mass spectrometry (MS/MS). We present two case studies to illustrate the application of Corra to commonly performed LC-MS-based biological workflows: a pilot biomarker discovery study of glycoproteins isolated from human plasma samples relevant to type 2 diabetes, and a study in yeast to identify in vivo targets of the protein kinase Ark1 via phosphopeptide profiling. Conclusion The Corra computational framework leverages computational innovation to enable biologists or other researchers to process, analyze and visualize LC-MS data with what would otherwise be a complex and not user-friendly suite of tools. Corra enables appropriate statistical analyses, with controlled false-discovery rates, ultimately to inform subsequent targeted identification of differentially abundant peptides by MS/MS. For the user not trained in bioinformatics, Corra represents a complete, customizable, free and open source computational platform enabling LC-MS-based proteomic workflows, and as such, addresses an unmet need in the LC-MS proteomics field. PMID:19087345

Designing the user interface: strategies for effective human-computer interaction

NASA Astrophysics Data System (ADS)

Shneiderman, B.

1998-03-01

In revising this popular book, Ben Shneiderman again provides a complete, current and authoritative introduction to user-interface design. The user interface is the part of every computer system that determines how people control and operate that system. When the interface is well designed, it is comprehensible, predictable, and controllable; users feel competent, satisfied, and responsible for their actions. Shneiderman discusses the principles and practices needed to design such effective interaction. Based on 20 years experience, Shneiderman offers readers practical techniques and guidelines for interface design. He also takes great care to discuss underlying issues and to support conclusions with empirical results. Interface designers, software engineers, and product managers will all find this book an invaluable resource for creating systems that facilitate rapid learning and performance, yield low error rates, and generate high user satisfaction. Coverage includes the human factors of interactive software (with a new discussion of diverse user communities), tested methods to develop and assess interfaces, interaction styles such as direct manipulation for graphical user interfaces, and design considerations such as effective messages, consistent screen design, and appropriate color.

User interface issues in supporting human-computer integrated scheduling

NASA Technical Reports Server (NTRS)

Cooper, Lynne P.; Biefeld, Eric W.

1991-01-01

The topics are presented in view graph form and include the following: characteristics of Operations Mission Planner (OMP) schedule domain; OMP architecture; definition of a schedule; user interface dimensions; functional distribution; types of users; interpreting user interaction; dynamic overlays; reactive scheduling; and transitioning the interface.

Development of interactive graphic user interfaces for modeling reaction-based biogeochemical processes in batch systems with BIOGEOCHEM

NASA Astrophysics Data System (ADS)

Chang, C.; Li, M.; Yeh, G.

2010-12-01

The BIOGEOCHEM numerical model (Yeh and Fang, 2002; Fang et al., 2003) was developed with FORTRAN for simulating reaction-based geochemical and biochemical processes with mixed equilibrium and kinetic reactions in batch systems. A complete suite of reactions including aqueous complexation, adsorption/desorption, ion-exchange, redox, precipitation/dissolution, acid-base reactions, and microbial mediated reactions were embodied in this unique modeling tool. Any reaction can be treated as fast/equilibrium or slow/kinetic reaction. An equilibrium reaction is modeled with an implicit finite rate governed by a mass action equilibrium equation or by a user-specified algebraic equation. A kinetic reaction is modeled with an explicit finite rate with an elementary rate, microbial mediated enzymatic kinetics, or a user-specified rate equation. None of the existing models has encompassed this wide array of scopes. To ease the input/output learning curve using the unique feature of BIOGEOCHEM, an interactive graphic user interface was developed with the Microsoft Visual Studio and .Net tools. Several user-friendly features, such as pop-up help windows, typo warning messages, and on-screen input hints, were implemented, which are robust. All input data can be real-time viewed and automated to conform with the input file format of BIOGEOCHEM. A post-processor for graphic visualizations of simulated results was also embedded for immediate demonstrations. By following data input windows step by step, errorless BIOGEOCHEM input files can be created even if users have little prior experiences in FORTRAN. With this user-friendly interface, the time effort to conduct simulations with BIOGEOCHEM can be greatly reduced.

R package MVR for Joint Adaptive Mean-Variance Regularization and Variance Stabilization

PubMed Central

Dazard, Jean-Eudes; Xu, Hua; Rao, J. Sunil

2015-01-01

We present an implementation in the R language for statistical computing of our recent non-parametric joint adaptive mean-variance regularization and variance stabilization procedure. The method is specifically suited for handling difficult problems posed by high-dimensional multivariate datasets (p ≫ n paradigm), such as in ‘omics’-type data, among which are that the variance is often a function of the mean, variable-specific estimators of variances are not reliable, and tests statistics have low powers due to a lack of degrees of freedom. The implementation offers a complete set of features including: (i) normalization and/or variance stabilization function, (ii) computation of mean-variance-regularized t and F statistics, (iii) generation of diverse diagnostic plots, (iv) synthetic and real ‘omics’ test datasets, (v) computationally efficient implementation, using C interfacing, and an option for parallel computing, (vi) manual and documentation on how to setup a cluster. To make each feature as user-friendly as possible, only one subroutine per functionality is to be handled by the end-user. It is available as an R package, called MVR (‘Mean-Variance Regularization’), downloadable from the CRAN. PMID:26819572

LabVIEW Graphical User Interface for a New High Sensitivity, High Resolution Micro-Angio-Fluoroscopic and ROI-CBCT System

PubMed Central

Keleshis, C; Ionita, CN; Yadava, G; Patel, V; Bednarek, DR; Hoffmann, KR; Verevkin, A; Rudin, S

2008-01-01

A graphical user interface based on LabVIEW software was developed to enable clinical evaluation of a new High-Sensitivity Micro-Angio-Fluoroscopic (HSMAF) system for real-time acquisition, display and rapid frame transfer of high-resolution region-of-interest images. The HSMAF detector consists of a CsI(Tl) phosphor, a light image intensifier (LII), and a fiber-optic taper coupled to a progressive scan, frame-transfer, charged-coupled device (CCD) camera which provides real-time 12 bit, 1k × 1k images capable of greater than 10 lp/mm resolution. Images can be captured in continuous or triggered mode, and the camera can be programmed by a computer using Camera Link serial communication. A graphical user interface was developed to control the camera modes such as gain and pixel binning as well as to acquire, store, display, and process the images. The program, written in LabVIEW, has the following capabilities: camera initialization, synchronized image acquisition with the x-ray pulses, roadmap and digital subtraction angiography acquisition (DSA), flat field correction, brightness and contrast control, last frame hold in fluoroscopy, looped playback of the acquired images in angiography, recursive temporal filtering and LII gain control. Frame rates can be up to 30 fps in full-resolution mode. The user friendly implementation of the interface along with the high framerate acquisition and display for this unique high-resolution detector should provide angiographers and interventionalists with a new capability for visualizing details of small vessels and endovascular devices such as stents and hence enable more accurate diagnoses and image guided interventions. (Support: NIH Grants R01NS43924, R01EB002873) PMID:18836570

LabVIEW Graphical User Interface for a New High Sensitivity, High Resolution Micro-Angio-Fluoroscopic and ROI-CBCT System.

PubMed

Keleshis, C; Ionita, Cn; Yadava, G; Patel, V; Bednarek, Dr; Hoffmann, Kr; Verevkin, A; Rudin, S

2008-01-01

A graphical user interface based on LabVIEW software was developed to enable clinical evaluation of a new High-Sensitivity Micro-Angio-Fluoroscopic (HSMAF) system for real-time acquisition, display and rapid frame transfer of high-resolution region-of-interest images. The HSMAF detector consists of a CsI(Tl) phosphor, a light image intensifier (LII), and a fiber-optic taper coupled to a progressive scan, frame-transfer, charged-coupled device (CCD) camera which provides real-time 12 bit, 1k × 1k images capable of greater than 10 lp/mm resolution. Images can be captured in continuous or triggered mode, and the camera can be programmed by a computer using Camera Link serial communication. A graphical user interface was developed to control the camera modes such as gain and pixel binning as well as to acquire, store, display, and process the images. The program, written in LabVIEW, has the following capabilities: camera initialization, synchronized image acquisition with the x-ray pulses, roadmap and digital subtraction angiography acquisition (DSA), flat field correction, brightness and contrast control, last frame hold in fluoroscopy, looped playback of the acquired images in angiography, recursive temporal filtering and LII gain control. Frame rates can be up to 30 fps in full-resolution mode. The user friendly implementation of the interface along with the high framerate acquisition and display for this unique high-resolution detector should provide angiographers and interventionalists with a new capability for visualizing details of small vessels and endovascular devices such as stents and hence enable more accurate diagnoses and image guided interventions. (Support: NIH Grants R01NS43924, R01EB002873).

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.

lncRNATargets: A platform for lncRNA target prediction based on nucleic acid thermodynamics.

PubMed

Hu, Ruifeng; Sun, Xiaobo

2016-08-01

Many studies have supported that long noncoding RNAs (lncRNAs) perform various functions in various critical biological processes. Advanced experimental and computational technologies allow access to more information on lncRNAs. Determining the functions and action mechanisms of these RNAs on a large scale is urgently needed. We provided lncRNATargets, which is a web-based platform for lncRNA target prediction based on nucleic acid thermodynamics. The nearest-neighbor (NN) model was used to calculate binging-free energy. The main principle of NN model for nucleic acid assumes that identity and orientation of neighbor base pairs determine stability of a given base pair. lncRNATargets features the following options: setting of a specific temperature that allow use not only for human but also for other animals or plants; processing all lncRNAs in high throughput without RNA size limitation that is superior to any other existing tool; and web-based, user-friendly interface, and colored result displays that allow easy access for nonskilled computer operators and provide better understanding of results. This technique could provide accurate calculation on the binding-free energy of lncRNA-target dimers to predict if these structures are well targeted together. lncRNATargets provides high accuracy calculations, and this user-friendly program is available for free at http://www.herbbol.org:8001/lrt/ .

Guide to the Stand-Damage Model interface management system

Treesearch

George Racin; J. J. Colbert

1995-01-01

This programmer's support document describes the Gypsy Moth Stand-Damage Model interface management system. Management of stand-damage data made it necessary to define structures to store data and provide the mechanisms to manipulate these data. The software provides a user-friendly means to manipulate files, graph and manage outputs, and edit input data. The...

The North Carolina State University Libraries Search Experience: Usability Testing Tabbed Search Interfaces for Academic Libraries

ERIC Educational Resources Information Center

Teague-Rector, Susan; Ballard, Angela; Pauley, Susan K.

2011-01-01

Creating a learnable, effective, and user-friendly library Web site hinges on providing easy access to search. Designing a search interface for academic libraries can be particularly challenging given the complexity and range of searchable library collections, such as bibliographic databases, electronic journals, and article search silos. Library…

Emotion Telepresence: Emotion Augmentation through Affective Haptics and Visual Stimuli

NASA Astrophysics Data System (ADS)

Tsetserukou, D.; Neviarouskaya, A.

2012-03-01

The paper focuses on a novel concept of emotional telepresence. The iFeel_IM! system which is in the vanguard of this technology integrates 3D virtual world Second Life, intelligent component for automatic emotion recognition from text messages, and innovative affective haptic interfaces providing additional nonverbal communication channels through simulation of emotional feedback and social touch (physical co-presence). Users can not only exchange messages but also emotionally and physically feel the presence of the communication partner (e.g., family member, friend, or beloved person). The next prototype of the system will include the tablet computer. The user can realize haptic interaction with avatar, and thus influence its mood and emotion of the partner. The finger gesture language will be designed for communication with avatar. This will bring new level of immersion of on-line communication.

Dynamic Distribution and Layouting of Model-Based User Interfaces in Smart Environments

NASA Astrophysics Data System (ADS)

Roscher, Dirk; Lehmann, Grzegorz; Schwartze, Veit; Blumendorf, Marco; Albayrak, Sahin

The developments in computer technology in the last decade change the ways of computer utilization. The emerging smart environments make it possible to build ubiquitous applications that assist users during their everyday life, at any time, in any context. But the variety of contexts-of-use (user, platform and environment) makes the development of such ubiquitous applications for smart environments and especially its user interfaces a challenging and time-consuming task. We propose a model-based approach, which allows adapting the user interface at runtime to numerous (also unknown) contexts-of-use. Based on a user interface modelling language, defining the fundamentals and constraints of the user interface, a runtime architecture exploits the description to adapt the user interface to the current context-of-use. The architecture provides automatic distribution and layout algorithms for adapting the applications also to contexts unforeseen at design time. Designers do not specify predefined adaptations for each specific situation, but adaptation constraints and guidelines. Furthermore, users are provided with a meta user interface to influence the adaptations according to their needs. A smart home energy management system serves as running example to illustrate the approach.

ESAP plus: a web-based server for EST-SSR marker development.

PubMed

Ponyared, Piyarat; Ponsawat, Jiradej; Tongsima, Sissades; Seresangtakul, Pusadee; Akkasaeng, Chutipong; Tantisuwichwong, Nathpapat

2016-12-22

Simple sequence repeats (SSRs) have become widely used as molecular markers in plant genetic studies due to their abundance, high allelic variation at each locus and simplicity to analyze using conventional PCR amplification. To study plants with unknown genome sequence, SSR markers from Expressed Sequence Tags (ESTs), which can be obtained from the plant mRNA (converted to cDNA), must be utilized. With the advent of high-throughput sequencing technology, huge EST sequence data have been generated and are now accessible from many public databases. However, SSR marker identification from a large in-house or public EST collection requires a computational pipeline that makes use of several standard bioinformatic tools to design high quality EST-SSR primers. Some of these computational tools are not users friendly and must be tightly integrated with reference genomic databases. A web-based bioinformatic pipeline, called EST Analysis Pipeline Plus (ESAP Plus), was constructed for assisting researchers to develop SSR markers from a large EST collection. ESAP Plus incorporates several bioinformatic scripts and some useful standard software tools necessary for the four main procedures of EST-SSR marker development, namely 1) pre-processing, 2) clustering and assembly, 3) SSR mining and 4) SSR primer design. The proposed pipeline also provides two alternative steps for reducing EST redundancy and identifying SSR loci. Using public sugarcane ESTs, ESAP Plus automatically executed the aforementioned computational pipeline via a simple web user interface, which was implemented using standard PHP, HTML, CSS and Java scripts. With ESAP Plus, users can upload raw EST data and choose various filtering options and parameters to analyze each of the four main procedures through this web interface. All input EST data and their predicted SSR results will be stored in the ESAP Plus MySQL database. Users will be notified via e-mail when the automatic process is completed and they can download all the results through the web interface. ESAP Plus is a comprehensive and convenient web-based bioinformatic tool for SSR marker development. ESAP Plus offers all necessary EST-SSR development processes with various adjustable options that users can easily use to identify SSR markers from a large EST collection. With familiar web interface, users can upload the raw EST using the data submission page and visualize/download the corresponding EST-SSR information from within ESAP Plus. ESAP Plus can handle considerably large EST datasets. This EST-SSR discovery tool can be accessed directly from: http://gbp.kku.ac.th/esap_plus/ .

Training leads to increased auditory brain-computer interface performance of end-users with motor impairments.

PubMed

Halder, S; Käthner, I; Kübler, A

2016-02-01

Auditory brain-computer interfaces are an assistive technology that can restore communication for motor impaired end-users. Such non-visual brain-computer interface paradigms are of particular importance for end-users that may lose or have lost gaze control. We attempted to show that motor impaired end-users can learn to control an auditory speller on the basis of event-related potentials. Five end-users with motor impairments, two of whom with additional visual impairments, participated in five sessions. We applied a newly developed auditory brain-computer interface paradigm with natural sounds and directional cues. Three of five end-users learned to select symbols using this method. Averaged over all five end-users the information transfer rate increased by more than 1800% from the first session (0.17 bits/min) to the last session (3.08 bits/min). The two best end-users achieved information transfer rates of 5.78 bits/min and accuracies of 92%. Our results show that an auditory BCI with a combination of natural sounds and directional cues, can be controlled by end-users with motor impairment. Training improves the performance of end-users to the level of healthy controls. To our knowledge, this is the first time end-users with motor impairments controlled an auditory brain-computer interface speller with such high accuracy and information transfer rates. Further, our results demonstrate that operating a BCI with event-related potentials benefits from training and specifically end-users may require more than one session to develop their full potential. Copyright © 2015 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

Neural Parallel Engine: A toolbox for massively parallel neural signal processing.

PubMed

Tam, Wing-Kin; Yang, Zhi

2018-05-01

Large-scale neural recordings provide detailed information on neuronal activities and can help elicit the underlying neural mechanisms of the brain. However, the computational burden is also formidable when we try to process the huge data stream generated by such recordings. In this study, we report the development of Neural Parallel Engine (NPE), a toolbox for massively parallel neural signal processing on graphical processing units (GPUs). It offers a selection of the most commonly used routines in neural signal processing such as spike detection and spike sorting, including advanced algorithms such as exponential-component-power-component (EC-PC) spike detection and binary pursuit spike sorting. We also propose a new method for detecting peaks in parallel through a parallel compact operation. Our toolbox is able to offer a 5× to 110× speedup compared with its CPU counterparts depending on the algorithms. A user-friendly MATLAB interface is provided to allow easy integration of the toolbox into existing workflows. Previous efforts on GPU neural signal processing only focus on a few rudimentary algorithms, are not well-optimized and often do not provide a user-friendly programming interface to fit into existing workflows. There is a strong need for a comprehensive toolbox for massively parallel neural signal processing. A new toolbox for massively parallel neural signal processing has been created. It can offer significant speedup in processing signals from large-scale recordings up to thousands of channels. Copyright © 2018 Elsevier B.V. All rights reserved.

Transportable Applications Environment Plus, Version 5.1

NASA Technical Reports Server (NTRS)

1994-01-01

Transportable Applications Environment Plus (TAE+) computer program providing integrated, portable programming environment for developing and running application programs based on interactive windows, text, and graphical objects. Enables both programmers and nonprogrammers to construct own custom application interfaces easily and to move interfaces and application programs to different computers. Used to define corporate user interface, with noticeable improvements in application developer's and end user's learning curves. Main components are; WorkBench, What You See Is What You Get (WYSIWYG) software tool for design and layout of user interface; and WPT (Window Programming Tools) Package, set of callable subroutines controlling user interface of application program. WorkBench and WPT's written in C++, and remaining code written in C.

DIANA-microT web server: elucidating microRNA functions through target prediction.

PubMed

Maragkakis, M; Reczko, M; Simossis, V A; Alexiou, P; Papadopoulos, G L; Dalamagas, T; Giannopoulos, G; Goumas, G; Koukis, E; Kourtis, K; Vergoulis, T; Koziris, N; Sellis, T; Tsanakas, P; Hatzigeorgiou, A G

2009-07-01

Computational microRNA (miRNA) target prediction is one of the key means for deciphering the role of miRNAs in development and disease. Here, we present the DIANA-microT web server as the user interface to the DIANA-microT 3.0 miRNA target prediction algorithm. The web server provides extensive information for predicted miRNA:target gene interactions with a user-friendly interface, providing extensive connectivity to online biological resources. Target gene and miRNA functions may be elucidated through automated bibliographic searches and functional information is accessible through Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The web server offers links to nomenclature, sequence and protein databases, and users are facilitated by being able to search for targeted genes using different nomenclatures or functional features, such as the genes possible involvement in biological pathways. The target prediction algorithm supports parameters calculated individually for each miRNA:target gene interaction and provides a signal-to-noise ratio and a precision score that helps in the evaluation of the significance of the predicted results. Using a set of miRNA targets recently identified through the pSILAC method, the performance of several computational target prediction programs was assessed. DIANA-microT 3.0 achieved there with 66% the highest ratio of correctly predicted targets over all predicted targets. The DIANA-microT web server is freely available at www.microrna.gr/microT.

Human/Computer Interfacing in Educational Environments.

ERIC Educational Resources Information Center

Sarti, Luigi

1992-01-01

This discussion of educational applications of user interfaces covers the benefits of adopting database techniques in organizing multimedia materials; the evolution of user interface technology, including teletype interfaces, analogic overlay graphics, window interfaces, and adaptive systems; application design problems, including the…

Developing a Cloud-Based Online Geospatial Information Sharing and Geoprocessing Platform to Facilitate Collaborative Education and Research

NASA Astrophysics Data System (ADS)

Yang, Z. L.; Cao, J.; Hu, K.; Gui, Z. P.; Wu, H. Y.; You, L.

2016-06-01

Efficient online discovering and applying geospatial information resources (GIRs) is critical in Earth Science domain as while for cross-disciplinary applications. However, to achieve it is challenging due to the heterogeneity, complexity and privacy of online GIRs. In this article, GeoSquare, a collaborative online geospatial information sharing and geoprocessing platform, was developed to tackle this problem. Specifically, (1) GIRs registration and multi-view query functions allow users to publish and discover GIRs more effectively. (2) Online geoprocessing and real-time execution status checking help users process data and conduct analysis without pre-installation of cumbersome professional tools on their own machines. (3) A service chain orchestration function enables domain experts to contribute and share their domain knowledge with community members through workflow modeling. (4) User inventory management allows registered users to collect and manage their own GIRs, monitor their execution status, and track their own geoprocessing histories. Besides, to enhance the flexibility and capacity of GeoSquare, distributed storage and cloud computing technologies are employed. To support interactive teaching and training, GeoSquare adopts the rich internet application (RIA) technology to create user-friendly graphical user interface (GUI). Results show that GeoSquare can integrate and foster collaboration between dispersed GIRs, computing resources and people. Subsequently, educators and researchers can share and exchange resources in an efficient and harmonious way.

Optimization of residual stresses in MMC's through the variation of interfacial layer architectures and processing parameters

NASA Technical Reports Server (NTRS)

Pindera, Marek-Jerzy; Salzar, Robert S.

1996-01-01

The objective of this work was the development of efficient, user-friendly computer codes for optimizing fabrication-induced residual stresses in metal matrix composites through the use of homogeneous and heterogeneous interfacial layer architectures and processing parameter variation. To satisfy this objective, three major computer codes have been developed and delivered to the NASA-Lewis Research Center, namely MCCM, OPTCOMP, and OPTCOMP2. MCCM is a general research-oriented code for investigating the effects of microstructural details, such as layered morphology of SCS-6 SiC fibers and multiple homogeneous interfacial layers, on the inelastic response of unidirectional metal matrix composites under axisymmetric thermomechanical loading. OPTCOMP and OPTCOMP2 combine the major analysis module resident in MCCM with a commercially-available optimization algorithm and are driven by user-friendly interfaces which facilitate input data construction and program execution. OPTCOMP enables the user to identify those dimensions, geometric arrangements and thermoelastoplastic properties of homogeneous interfacial layers that minimize thermal residual stresses for the specified set of constraints. OPTCOMP2 provides additional flexibility in the residual stress optimization through variation of the processing parameters (time, temperature, external pressure and axial load) as well as the microstructure of the interfacial region which is treated as a heterogeneous two-phase composite. Overviews of the capabilities of these codes are provided together with a summary of results that addresses the effects of various microstructural details of the fiber, interfacial layers and matrix region on the optimization of fabrication-induced residual stresses in metal matrix composites.

Large-scale feature searches of collections of medical imagery

NASA Astrophysics Data System (ADS)

Hedgcock, Marcus W.; Karshat, Walter B.; Levitt, Tod S.; Vosky, D. N.

1993-09-01

Large scale feature searches of accumulated collections of medical imagery are required for multiple purposes, including clinical studies, administrative planning, epidemiology, teaching, quality improvement, and research. To perform a feature search of large collections of medical imagery, one can either search text descriptors of the imagery in the collection (usually the interpretation), or (if the imagery is in digital format) the imagery itself. At our institution, text interpretations of medical imagery are all available in our VA Hospital Information System. These are downloaded daily into an off-line computer. The text descriptors of most medical imagery are usually formatted as free text, and so require a user friendly database search tool to make searches quick and easy for any user to design and execute. We are tailoring such a database search tool (Liveview), developed by one of the authors (Karshat). To further facilitate search construction, we are constructing (from our accumulated interpretation data) a dictionary of medical and radiological terms and synonyms. If the imagery database is digital, the imagery which the search discovers is easily retrieved from the computer archive. We describe our database search user interface, with examples, and compare the efficacy of computer assisted imagery searches from a clinical text database with manual searches. Our initial work on direct feature searches of digital medical imagery is outlined.

Hybrid 2-D and 3-D Immersive and Interactive User Interface for Scientific Data Visualization

DTIC Science & Technology

2017-08-01

visualization, 3-D interactive visualization, scientific visualization, virtual reality, real -time ray tracing 16. SECURITY CLASSIFICATION OF: 17...scientists to employ in the real world. Other than user-friendly software and hardware setup, scientists also need to be able to perform their usual...and scientific visualization communities mostly have different research priorities. For the VR community, the ability to support real -time user

A Framework and Implementation of User Interface and Human-Computer Interaction Instruction

ERIC Educational Resources Information Center

Peslak, Alan

2005-01-01

Researchers have suggested that up to 50 % of the effort in development of information systems is devoted to user interface development (Douglas, Tremaine, Leventhal, Wills, & Manaris, 2002; Myers & Rosson, 1992). Yet little study has been performed on the inclusion of important interface and human-computer interaction topics into a current…

75 FR 25853 - Agency Information Collection Activities; Submission to OMB for Review and Approval; Comment...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-10

....gov , to submit or view public comments, access the index listing of the contents of the docket, and...:8080/glas/login.htm . The Web-site will contain a user-friendly data entry interface for recipients to... series of screens containing pull-down menus and text boxes, where users can enter project specific...

OPAC: The Next Generation Placing an Encore Front End onto a SirsiDynix ILS

ERIC Educational Resources Information Center

Marcin, Susan; Morris, Peter

2008-01-01

Over the last few years, there has been a wealth of materials written and presented on next-generation library catalogs. These next-generation interfaces strive to turn "standard" integrated library systems (ILSs) into more nimble and robust search platforms that offer more user-friendly 2.0 enhancements for users. Rather than abandoning…

Textile electrodes and integrated smart textile for reliable biomonitoring.

PubMed

Paradiso, R; Pacelli, M

2011-01-01

Since birth the first and the most natural interface for the body is fabric, a soft, warm and reassuring material. Cloth is usually covering more than 80 % of the skin; which leads us to consider textile material as the most appropriate interface where new sensorial and interactive functions can be implemented. The new generation of personalised monitoring systems is based on this paradigm: functions like sensing, transmission and elaboration are implementable in the materials through the textile technology. Functional yarns and fibres are usable to realise garments where electrical and computing properties are combined with the traditional mechanical characteristics, giving rise to textile platforms that are comparable with the cloths that are normally used to produce our garments. The feel of the fabric is the same, but the functionality is augmented. Nowadays, consumers demand user-friendly connectivity and interactivity; sensing clothes are the most natural and ordinary interface able to follow us, everywhere in a non-intrusive way, in natural harmony with our body.

Development of wrist rehabilitation robot and interface system.

PubMed

Yamamoto, Ikuo; Matsui, Miki; Inagawa, Naohiro; Hachisuka, Kenji; Wada, Futoshi; Hachisuka, Akiko; Saeki, Satoru

2015-01-01

The authors have developed a practical wrist rehabilitation robot for hemiplegic patients. It consists of a mechanical rotation unit, sensor, grip, and computer system. A myoelectric sensor is used to monitor the extensor carpi radialis longus/brevis muscle and flexor carpi radialis muscle activity during training. The training robot can provoke training through myoelectric sensors, a biological signal detector and processor in advance, so that patients can undergo effective training of extention and flexion in an excited condition. In addition, both-wrist system has been developed for mirror effect training, which is the most effective function of the system, so that autonomous training using both wrists is possible. Furthermore, a user-friendly screen interface with easily recognizable touch panels has been developed to give effective training for patients. The developed robot is small size and easy to carry. The developed aspiring interface system is effective to motivate the training of patients. The effectiveness of the robot system has been verified in hospital trails.

The Impact of User Interface on Young Children's Computational Thinking

ERIC Educational Resources Information Center

Pugnali, Alex; Sullivan, Amanda; Bers, Marina Umaschi

2017-01-01

Aim/Purpose: Over the past few years, new approaches to introducing young children to computational thinking have grown in popularity. This paper examines the role that user interfaces have on children's mastery of computational thinking concepts and positive interpersonal behaviors. Background: There is a growing pressure to begin teaching…

Franklin: User Experiences

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

National Energy Research Supercomputing Center; He, Yun; Kramer, William T.C.

2008-05-07

The newest workhorse of the National Energy Research Scientific Computing Center is a Cray XT4 with 9,736 dual core nodes. This paper summarizes Franklin user experiences from friendly early user period to production period. Selected successful user stories along with top issues affecting user experiences are presented.

Open Astronomy Catalogs API

NASA Astrophysics Data System (ADS)

Guillochon, James; Cowperthwaite, Philip S.

2018-05-01

We announce the public release of the application program interface (API) for the Open Astronomy Catalogs (OACs), the OACAPI. The OACs serve near-complete collections of supernova, tidal disruption, kilonova, and fast stars data (including photometry, spectra, radio, and X-ray observations) via a user-friendly web interface that displays the data interactively and offers full data downloads. The OACAPI, by contrast, enables users to specifically download particular pieces of the OAC dataset via a flexible programmatic syntax, either via URL GET requests, or via a module within the astroquery Python package.

Avatars and virtual agents – relationship interfaces for the elderly

PubMed Central

2017-01-01

In the Digital Era, the authors witness a change in the relationship between the patient and the care-giver or Health Maintenance Organization's providing the health services. Another fact is the use of various technologies to increase the effectiveness and quality of health services across all primary and secondary users. These technologies range from telemedicine systems, decision making tools, online and self-services applications and virtual agents; all providing information and assistance. The common thread between all these digital implementations, is they all require human machine interfaces. These interfaces must be interactive, user friendly and inviting, to create user involvement and cooperation incentives. The challenge is to design interfaces which will best fit the target users and enable smooth interaction especially, for the elderly users. Avatars and Virtual Agents are one of the interfaces used for both home care monitoring and companionship. They are also inherently multimodal in nature and allow an intimate relation between the elderly users and the Avatar. This study discusses the need and nature of these relationship models, the challenges of designing for the elderly. The study proposes key features for the design and evaluation in the area of assistive applications using Avatar and Virtual agents for the elderly users. PMID:28706725

A MATLAB based 3D modeling and inversion code for MT data

NASA Astrophysics Data System (ADS)

Singh, Arun; Dehiya, Rahul; Gupta, Pravin K.; Israil, M.

2017-07-01

The development of a MATLAB based computer code, AP3DMT, for modeling and inversion of 3D Magnetotelluric (MT) data is presented. The code comprises two independent components: grid generator code and modeling/inversion code. The grid generator code performs model discretization and acts as an interface by generating various I/O files. The inversion code performs core computations in modular form - forward modeling, data functionals, sensitivity computations and regularization. These modules can be readily extended to other similar inverse problems like Controlled-Source EM (CSEM). The modular structure of the code provides a framework useful for implementation of new applications and inversion algorithms. The use of MATLAB and its libraries makes it more compact and user friendly. The code has been validated on several published models. To demonstrate its versatility and capabilities the results of inversion for two complex models are presented.

PAGANI Toolkit: Parallel graph-theoretical analysis package for brain network big data.

PubMed

Du, Haixiao; Xia, Mingrui; Zhao, Kang; Liao, Xuhong; Yang, Huazhong; Wang, Yu; He, Yong

2018-05-01

The recent collection of unprecedented quantities of neuroimaging data with high spatial resolution has led to brain network big data. However, a toolkit for fast and scalable computational solutions is still lacking. Here, we developed the PArallel Graph-theoretical ANalysIs (PAGANI) Toolkit based on a hybrid central processing unit-graphics processing unit (CPU-GPU) framework with a graphical user interface to facilitate the mapping and characterization of high-resolution brain networks. Specifically, the toolkit provides flexible parameters for users to customize computations of graph metrics in brain network analyses. As an empirical example, the PAGANI Toolkit was applied to individual voxel-based brain networks with ∼200,000 nodes that were derived from a resting-state fMRI dataset of 624 healthy young adults from the Human Connectome Project. Using a personal computer, this toolbox completed all computations in ∼27 h for one subject, which is markedly less than the 118 h required with a single-thread implementation. The voxel-based functional brain networks exhibited prominent small-world characteristics and densely connected hubs, which were mainly located in the medial and lateral fronto-parietal cortices. Moreover, the female group had significantly higher modularity and nodal betweenness centrality mainly in the medial/lateral fronto-parietal and occipital cortices than the male group. Significant correlations between the intelligence quotient and nodal metrics were also observed in several frontal regions. Collectively, the PAGANI Toolkit shows high computational performance and good scalability for analyzing connectome big data and provides a friendly interface without the complicated configuration of computing environments, thereby facilitating high-resolution connectomics research in health and disease. © 2018 Wiley Periodicals, Inc.

Evaluation of the Next-Gen Exercise Software Interface in the NEEMO Analog

NASA Technical Reports Server (NTRS)

Hanson, Andrea; Kalogera, Kent; Sandor, Aniko; Hardy, Marc; Frank, Andrew; English, Kirk; Williams, Thomas; Perera, Jeevan; Amonette, William

2017-01-01

NSBRI (National Space Biomedical Research Institute) funded research grant to develop the 'NextGen' exercise software for the NEEMO (NASA Extreme Environment Mission Operations) analog. Develop a software architecture to integrate instructional, motivational and socialization techniques into a common portal to enhance exercise countermeasures in remote environments. Increase user efficiency and satisfaction, and institute commonality across multiple exercise systems. Utilized GUI (Graphical User Interface) design principals focused on intuitive ease of use to minimize training time and realize early user efficiency. Project requirement to test the software in an analog environment. Top Level Project Aims: 1) Improve the usability of crew interface software to exercise CMS (Crew Management System) through common app-like interfaces. 2) Introduce virtual instructional motion training. 3) Use virtual environment to provide remote socialization with family and friends, improve exercise technique, adherence, motivation and ultimately performance outcomes.

TangibleCubes — Implementation of Tangible User Interfaces through the Usage of Microcontroller and Sensor Technology

NASA Astrophysics Data System (ADS)

Setscheny, Stephan

The interaction between human beings and technology builds a central aspect in human life. The most common form of this human-technology interface is the graphical user interface which is controlled through the mouse and the keyboard. In consequence of continuous miniaturization and the increasing performance of microcontrollers and sensors for the detection of human interactions, developers receive new possibilities for realising innovative interfaces. As far as this movement is concerned, the relevance of computers in the common sense and graphical user interfaces is decreasing. Especially in the area of ubiquitous computing and the interaction through tangible user interfaces a highly impact of this technical evolution can be seen. Apart from this, tangible and experience able interaction offers users the possibility of an interactive and intuitive method for controlling technical objects. The implementation of microcontrollers for control functions and sensors enables the realisation of these experience able interfaces. Besides the theories about tangible user interfaces, the consideration about sensors and the Arduino platform builds a main aspect of this work.

Human-computer interface including haptically controlled interactions

DOEpatents

Anderson, Thomas G.

2005-10-11

The present invention provides a method of human-computer interfacing that provides haptic feedback to control interface interactions such as scrolling or zooming within an application. Haptic feedback in the present method allows the user more intuitive control of the interface interactions, and allows the user's visual focus to remain on the application. The method comprises providing a control domain within which the user can control interactions. For example, a haptic boundary can be provided corresponding to scrollable or scalable portions of the application domain. The user can position a cursor near such a boundary, feeling its presence haptically (reducing the requirement for visual attention for control of scrolling of the display). The user can then apply force relative to the boundary, causing the interface to scroll the domain. The rate of scrolling can be related to the magnitude of applied force, providing the user with additional intuitive, non-visual control of scrolling.

Simple and Inexpensive 3D Printed Filter Fluorometer Designs: User-Friendly Instrument Models for Laboratory Learning and Outreach Activities

ERIC Educational Resources Information Center

Porter, Lon A., Jr.; Chapman, Cole A.; Alaniz, Jacob A.

2017-01-01

In this work, a versatile and user-friendly selection of stereolithography (STL) files and computer-aided design (CAD) models are shared to assist educators and students in the production of simple and inexpensive 3D printed filter fluorometer instruments. These devices are effective resources for supporting active learners in the exploration of…

iScreen: world's first cloud-computing web server for virtual screening and de novo drug design based on TCM database@Taiwan

NASA Astrophysics Data System (ADS)

Tsai, Tsung-Ying; Chang, Kai-Wei; Chen, Calvin Yu-Chian

2011-06-01

The rapidly advancing researches on traditional Chinese medicine (TCM) have greatly intrigued pharmaceutical industries worldwide. To take initiative in the next generation of drug development, we constructed a cloud-computing system for TCM intelligent screening system (iScreen) based on TCM Database@Taiwan. iScreen is compacted web server for TCM docking and followed by customized de novo drug design. We further implemented a protein preparation tool that both extract protein of interest from a raw input file and estimate the size of ligand bind site. In addition, iScreen is designed in user-friendly graphic interface for users who have less experience with the command line systems. For customized docking, multiple docking services, including standard, in-water, pH environment, and flexible docking modes are implemented. Users can download first 200 TCM compounds of best docking results. For TCM de novo drug design, iScreen provides multiple molecular descriptors for a user's interest. iScreen is the world's first web server that employs world's largest TCM database for virtual screening and de novo drug design. We believe our web server can lead TCM research to a new era of drug development. The TCM docking and screening server is available at http://iScreen.cmu.edu.tw/.

iScreen: world's first cloud-computing web server for virtual screening and de novo drug design based on TCM database@Taiwan.

PubMed

Tsai, Tsung-Ying; Chang, Kai-Wei; Chen, Calvin Yu-Chian

2011-06-01

The rapidly advancing researches on traditional Chinese medicine (TCM) have greatly intrigued pharmaceutical industries worldwide. To take initiative in the next generation of drug development, we constructed a cloud-computing system for TCM intelligent screening system (iScreen) based on TCM Database@Taiwan. iScreen is compacted web server for TCM docking and followed by customized de novo drug design. We further implemented a protein preparation tool that both extract protein of interest from a raw input file and estimate the size of ligand bind site. In addition, iScreen is designed in user-friendly graphic interface for users who have less experience with the command line systems. For customized docking, multiple docking services, including standard, in-water, pH environment, and flexible docking modes are implemented. Users can download first 200 TCM compounds of best docking results. For TCM de novo drug design, iScreen provides multiple molecular descriptors for a user's interest. iScreen is the world's first web server that employs world's largest TCM database for virtual screening and de novo drug design. We believe our web server can lead TCM research to a new era of drug development. The TCM docking and screening server is available at http://iScreen.cmu.edu.tw/.

ICT Services for Life Improvement for the Elderly.

PubMed

Sánchez-Rico, Alejandro; Garel, Pascal; Notarangelo, Isabella; Quintana, Marcos; Hernández, Gustavo; Asteriadis, Stylianos; Popa, Mirela; Vretos, Nicholas; Solachidis, Vassilis; Burgos, Marta; Girault, Ariane

2017-01-01

Integrated care ICT Platform to support patients, care-givers and health/social professionals in the care of dementia and Parkinson's disease with training, empowerment, sensor-based data analysis and cooperation services based on user-friendly interfaces.

Ubiquitous computing to support co-located clinical teams: using the semiotics of physical objects in system design.

PubMed

Bang, Magnus; Timpka, Toomas

2007-06-01

Co-located teams often use material objects to communicate messages in collaboration. Modern desktop computing systems with abstract graphical user interface (GUIs) fail to support this material dimension of inter-personal communication. The aim of this study is to investigate how tangible user interfaces can be used in computer systems to better support collaborative routines among co-located clinical teams. The semiotics of physical objects used in team collaboration was analyzed from data collected during 1 month of observations at an emergency room. The resulting set of communication patterns was used as a framework when designing an experimental system. Following the principles of augmented reality, physical objects were mapped into a physical user interface with the goal of maintaining the symbolic value of those objects. NOSTOS is an experimental ubiquitous computing environment that takes advantage of interaction devices integrated into the traditional clinical environment, including digital pens, walk-up displays, and a digital desk. The design uses familiar workplace tools to function as user interfaces to the computer in order to exploit established cognitive and collaborative routines. Paper-based tangible user interfaces and digital desks are promising technologies for co-located clinical teams. A key issue that needs to be solved before employing such solutions in practice is associated with limited feedback from the passive paper interfaces.

The Euler’s Graphical User Interface Spreadsheet Calculator for Solving Ordinary Differential Equations by Visual Basic for Application Programming

NASA Astrophysics Data System (ADS)

Gaik Tay, Kim; Cheong, Tau Han; Foong Lee, Ming; Kek, Sie Long; Abdul-Kahar, Rosmila

2017-08-01

In the previous work on Euler’s spreadsheet calculator for solving an ordinary differential equation, the Visual Basic for Application (VBA) programming was used, however, a graphical user interface was not developed to capture users input. This weakness may make users confuse on the input and output since those input and output are displayed in the same worksheet. Besides, the existing Euler’s spreadsheet calculator is not interactive as there is no prompt message if there is a mistake in inputting the parameters. On top of that, there are no users’ instructions to guide users to input the derivative function. Hence, in this paper, we improved previous limitations by developing a user-friendly and interactive graphical user interface. This improvement is aimed to capture users’ input with users’ instructions and interactive prompt error messages by using VBA programming. This Euler’s graphical user interface spreadsheet calculator is not acted as a black box as users can click on any cells in the worksheet to see the formula used to implement the numerical scheme. In this way, it could enhance self-learning and life-long learning in implementing the numerical scheme in a spreadsheet and later in any programming language.

A Question of Interface Design: How Do Online Service GUIs Measure Up?

ERIC Educational Resources Information Center

Head, Alison J.

1997-01-01

Describes recent improvements in graphical user interfaces (GUIs) offered by online services. Highlights include design considerations, including computer engineering capabilities and users' abilities; fundamental GUI design principles; user empowerment; visual communication and interaction; and an evaluation of online search interfaces. (LRW)

RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis

PubMed Central

Afzal, Muhammad; Shahid, Ahmad Ali; Shehzadi, Abida; Nadeem, Shahid; Husnain, Tayyab

2012-01-01

RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available. Availability http://www.cemb.edu.pk/sw.html Abbreviations RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language. PMID:23055611

SIFTER search: a web server for accurate phylogeny-based protein function prediction

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

Sahraeian, Sayed M.; Luo, Kevin R.; Brenner, Steven E.

We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access tomore » precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. Lastly, the SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.« less

An Assessment of IMPAC - Integrated Methodology for Propulsion and Airframe Controls

NASA Technical Reports Server (NTRS)

Walker, G. P.; Wagner, E. A.; Bodden, D. S.

1996-01-01

This report documents the work done under a NASA sponsored contract to transition to industry technologies developed under the NASA Lewis Research Center IMPAC (Integrated Methodology for Propulsion and Airframe Control) program. The critical steps in IMPAC are exercised on an example integrated flight/propulsion control design for linear airframe/engine models of a conceptual STOVL (Short Take-Off and Vertical Landing) aircraft, and MATRIXX (TM) executive files to implement each step are developed. The results from the example study are analyzed and lessons learned are listed along with recommendations that will improve the application of each design step. The end product of this research is a set of software requirements for developing a user-friendly control design tool which will automate the steps in the IMPAC methodology. Prototypes for a graphical user interface (GUI) are sketched to specify how the tool will interact with the user, and it is recommended to build the tool around existing computer aided control design software packages.

SIFTER search: a web server for accurate phylogeny-based protein function prediction

DOE PAGES

Sahraeian, Sayed M.; Luo, Kevin R.; Brenner, Steven E.

2015-05-15

We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access tomore » precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. Lastly, the SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.« less

Minimizing calibration time using inter-subject information of single-trial recognition of error potentials in brain-computer interfaces.

PubMed

Iturrate, Iñaki; Montesano, Luis; Chavarriaga, Ricardo; del R Millán, Jose; Minguez, Javier

2011-01-01

One of the main problems of both synchronous and asynchronous EEG-based BCIs is the need of an initial calibration phase before the system can be used. This phase is necessary due to the high non-stationarity of the EEG, since it changes between sessions and users. The calibration process limits the BCI systems to scenarios where the outputs are very controlled, and makes these systems non-friendly and exhausting for the users. Although it has been studied how to reduce calibration time for asynchronous signals, it is still an open issue for event-related potentials. Here, we propose the minimization of the calibration time on single-trial error potentials by using classifiers based on inter-subject information. The results show that it is possible to have a classifier with a high performance from the beginning of the experiment, and which is able to adapt itself making the calibration phase shorter and transparent to the user.

How to Create, Modify, and Interface Aspen In-House and User Databanks for System Configuration 1:

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

Camp, D W

2000-10-27

The goal of this document is to provide detailed instructions to create, modify, interface, and test Aspen User and In-House databanks with minimal frustration. The level of instructions are aimed at a novice Aspen Plus simulation user who is neither a programming nor computer-system expert. The instructions are tailored to Version 10.1 of Aspen Plus and the specific computing configuration summarized in the Title of this document and detailed in Section 2. Many details of setting up databanks depend on the computing environment specifics, such as the machines, operating systems, command languages, directory structures, inter-computer communications software, the version ofmore » the Aspen Engine and Graphical User Interface (GUI), and the directory structure of how these were installed.« less

Program For Generating Interactive Displays

NASA Technical Reports Server (NTRS)

Costenbader, Jay; Moleski, Walt; Szczur, Martha; Howell, David; Engelberg, Norm; Li, Tin P.; Misra, Dharitri; Miller, Philip; Neve, Leif; Wolf, Karl;

The Climate-G Portal: a Grid Enabled Scientifc Gateway for Climate Change

NASA Astrophysics Data System (ADS)

Fiore, Sandro; Negro, Alessandro; Aloisio, Giovanni

2010-05-01

Grid portals are web gateways aiming at concealing the underlying infrastructure through a pervasive, transparent, user-friendly, ubiquitous and seamless access to heterogeneous and geographical spread resources (i.e. storage, computational facilities, services, sensors, network, databases). Definitively they provide an enhanced problem-solving environment able to deal with modern, large scale scientific and engineering problems. Scientific gateways are able to introduce a revolution in the way scientists and researchers organize and carry out their activities. Access to distributed resources, complex workflow capabilities, and community-oriented functionalities are just some of the features that can be provided by such a web-based environment. In the context of the EGEE NA4 Earth Science Cluster, Climate-G is a distributed testbed focusing on climate change research topics. The Euro-Mediterranean Center for Climate Change (CMCC) is actively participating in the testbed providing the scientific gateway (Climate-G Portal) to access to the entire infrastructure. The Climate-G Portal has to face important and critical challenges as well as has to satisfy and address key requirements. In the following, the most relevant ones are presented and discussed. Transparency: the portal has to provide a transparent access to the underlying infrastructure preventing users from dealing with low level details and the complexity of a distributed grid environment. Security: users must be authenticated and authorized on the portal to access and exploit portal functionalities. A wide set of roles is needed to clearly assign the proper one to each user. The access to the computational grid must be completely secured, since the target infrastructure to run jobs is a production grid environment. A security infrastructure (based on X509v3 digital certificates) is strongly needed. Pervasivity and ubiquity: the access to the system must be pervasive and ubiquitous. This is easily true due to the nature of the needed web approach. Usability and simplicity: the portal has to provide simple, high level and user friendly interfaces to ease the access and exploitation of the entire system. Coexistence of general purpose and domain oriented services: along with general purpose services (file transfer, job submission, etc.), the portal has to provide domain based services and functionalities. Subsetting of data, visualization of 2D maps around a virtual globe, delivery of maps through OGC compliant interfaces (i.e. Web Map Service - WMS) are just some examples. Since april 2009, about 70 users (85% coming from the climate change community) got access to the portal. A key challenge of this work is the idea to provide users with an integrated working environment, that is a place where scientists can find huge amount of data, complete metadata support, a wide set of data access services, data visualization and analysis tools, easy access to the underlying grid infrastructure and advanced monitoring interfaces.

Mobile phones and elderly people: a noisy communication.

PubMed

Stamato, Cláudia; Moraes, Anamaria de

2012-01-01

Knowing the users is capital for building user-friendly digital interfaces. One way to think about the users is considering their familiarity with this technology. This article presents the results of twelve interviews with elderly people residing in the so-called South Zone of Rio de Janeiro (Brazil) who have used mobile phones over at least one year. It is part of the Doctor's Thesis "Mobile phones for elderly people - usability for social integration" ("Celulares para idosos - usabilidade a serviço da integração social"), which is targeted at ascertaining if the current mobile phones are user-friendly for elderly people. Through the technique of Guided Interviews, we found usage time, criteria for choice of phones, reasons for changes, preferences, and manners of use. Preliminarily, we have noticed differences in the behavior of the participating users and performed a qualitative analysis according to groups of age and gender.

visnormsc: A Graphical User Interface to Normalize Single-cell RNA Sequencing Data.

PubMed

Tang, Lijun; Zhou, Nan

2017-12-26

Single-cell RNA sequencing (RNA-seq) allows the analysis of gene expression with high resolution. The intrinsic defects of this promising technology imports technical noise into the single-cell RNA-seq data, increasing the difficulty of accurate downstream inference. Normalization is a crucial step in single-cell RNA-seq data pre-processing. SCnorm is an accurate and efficient method that can be used for this purpose. An R implementation of this method is currently available. On one hand, the R package possesses many excellent features from R. On the other hand, R programming ability is required, which prevents the biologists who lack the skills from learning to use it quickly. To make this method more user-friendly, we developed a graphical user interface, visnormsc, for normalization of single-cell RNA-seq data. It is implemented in Python and is freely available at https://github.com/solo7773/visnormsc . Although visnormsc is based on the existing method, it contributes to this field by offering a user-friendly alternative. The out-of-the-box and cross-platform features make visnormsc easy to learn and to use. It is expected to serve biologists by simplifying single-cell RNA-seq normalization.

WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data.

PubMed

Devlin, Joseph C; Battaglia, Thomas; Blaser, Martin J; Ruggles, Kelly V

2018-06-25

Exploration of large data sets, such as shotgun metagenomic sequence or expression data, by biomedical experts and medical professionals remains as a major bottleneck in the scientific discovery process. Although tools for this purpose exist for 16S ribosomal RNA sequencing analysis, there is a growing but still insufficient number of user-friendly interactive visualization workflows for easy data exploration and figure generation. The development of such platforms for this purpose is necessary to accelerate and streamline microbiome laboratory research. We developed the Workflow Hub for Automated Metagenomic Exploration (WHAM!) as a web-based interactive tool capable of user-directed data visualization and statistical analysis of annotated shotgun metagenomic and metatranscriptomic data sets. WHAM! includes exploratory and hypothesis-based gene and taxa search modules for visualizing differences in microbial taxa and gene family expression across experimental groups, and for creating publication quality figures without the need for command line interface or in-house bioinformatics. WHAM! is an interactive and customizable tool for downstream metagenomic and metatranscriptomic analysis providing a user-friendly interface allowing for easy data exploration by microbiome and ecological experts to facilitate discovery in multi-dimensional and large-scale data sets.

Bioclipse: an open source workbench for chemo- and bioinformatics.

PubMed

Spjuth, Ola; Helmus, Tobias; Willighagen, Egon L; Kuhn, Stefan; Eklund, Martin; Wagener, Johannes; Murray-Rust, Peter; Steinbeck, Christoph; Wikberg, Jarl E S

2007-02-22

There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no successful attempts have been made to integrate chemo- and bioinformatics into a single framework. Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL), an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at http://www.bioclipse.net.

Usability Evaluation Methods for Gesture-Based Games: A Systematic Review.

PubMed

Simor, Fernando Winckler; Brum, Manoela Rogofski; Schmidt, Jaison Dairon Ebertz; Rieder, Rafael; De Marchi, Ana Carolina Bertoletti

2016-10-04

Gestural interaction systems are increasingly being used, mainly in games, expanding the idea of entertainment and providing experiences with the purpose of promoting better physical and/or mental health. Therefore, it is necessary to establish mechanisms for evaluating the usability of these interfaces, which make gestures the basis of interaction, to achieve a balance between functionality and ease of use. This study aims to present the results of a systematic review focused on usability evaluation methods for gesture-based games, considering devices with motion-sensing capability. We considered the usability methods used, the common interface issues, and the strategies adopted to build good gesture-based games. The research was centered on four electronic databases: IEEE, Association for Computing Machinery (ACM), Springer, and Science Direct from September 4 to 21, 2015. Within 1427 studies evaluated, 10 matched the eligibility criteria. As a requirement, we considered studies about gesture-based games, Kinect and/or Wii as devices, and the use of a usability method to evaluate the user interface. In the 10 studies found, there was no standardization in the methods because they considered diverse analysis variables. Heterogeneously, authors used different instruments to evaluate gesture-based interfaces and no default approach was proposed. Questionnaires were the most used instruments (70%, 7/10), followed by interviews (30%, 3/10), and observation and video recording (20%, 2/10). Moreover, 60% (6/10) of the studies used gesture-based serious games to evaluate the performance of elderly participants in rehabilitation tasks. This highlights the need for creating an evaluation protocol for older adults to provide a user-friendly interface according to the user's age and limitations. Through this study, we conclude this field is in need of a usability evaluation method for serious games, especially games for older adults, and that the definition of a methodology and a test protocol may offer the user more comfort, welfare, and confidence.

SPIKY: a graphical user interface for monitoring spike train synchrony

PubMed Central

Mulansky, Mario; Bozanic, Nebojsa

2015-01-01

Techniques for recording large-scale neuronal spiking activity are developing very fast. This leads to an increasing demand for algorithms capable of analyzing large amounts of experimental spike train data. One of the most crucial and demanding tasks is the identification of similarity patterns with a very high temporal resolution and across different spatial scales. To address this task, in recent years three time-resolved measures of spike train synchrony have been proposed, the ISI-distance, the SPIKE-distance, and event synchronization. The Matlab source codes for calculating and visualizing these measures have been made publicly available. However, due to the many different possible representations of the results the use of these codes is rather complicated and their application requires some basic knowledge of Matlab. Thus it became desirable to provide a more user-friendly and interactive interface. Here we address this need and present SPIKY, a graphical user interface that facilitates the application of time-resolved measures of spike train synchrony to both simulated and real data. SPIKY includes implementations of the ISI-distance, the SPIKE-distance, and the SPIKE-synchronization (an improved and simplified extension of event synchronization) that have been optimized with respect to computation speed and memory demand. It also comprises a spike train generator and an event detector that makes it capable of analyzing continuous data. Finally, the SPIKY package includes additional complementary programs aimed at the analysis of large numbers of datasets and the estimation of significance levels. PMID:25744888

SPIKY: a graphical user interface for monitoring spike train synchrony.

PubMed

Kreuz, Thomas; Mulansky, Mario; Bozanic, Nebojsa

2015-05-01

Techniques for recording large-scale neuronal spiking activity are developing very fast. This leads to an increasing demand for algorithms capable of analyzing large amounts of experimental spike train data. One of the most crucial and demanding tasks is the identification of similarity patterns with a very high temporal resolution and across different spatial scales. To address this task, in recent years three time-resolved measures of spike train synchrony have been proposed, the ISI-distance, the SPIKE-distance, and event synchronization. The Matlab source codes for calculating and visualizing these measures have been made publicly available. However, due to the many different possible representations of the results the use of these codes is rather complicated and their application requires some basic knowledge of Matlab. Thus it became desirable to provide a more user-friendly and interactive interface. Here we address this need and present SPIKY, a graphical user interface that facilitates the application of time-resolved measures of spike train synchrony to both simulated and real data. SPIKY includes implementations of the ISI-distance, the SPIKE-distance, and the SPIKE-synchronization (an improved and simplified extension of event synchronization) that have been optimized with respect to computation speed and memory demand. It also comprises a spike train generator and an event detector that makes it capable of analyzing continuous data. Finally, the SPIKY package includes additional complementary programs aimed at the analysis of large numbers of datasets and the estimation of significance levels. Copyright © 2015 the American Physiological Society.

UTOPIA-User-Friendly Tools for Operating Informatics Applications.

PubMed

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

2004-01-01

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

An intelligent multi-media human-computer dialogue system

NASA Technical Reports Server (NTRS)

Neal, J. G.; Bettinger, K. E.; Byoun, J. S.; Dobes, Z.; Thielman, C. Y.

1988-01-01

Sophisticated computer systems are being developed to assist in the human decision-making process for very complex tasks performed under stressful conditions. The human-computer interface is a critical factor in these systems. The human-computer interface should be simple and natural to use, require a minimal learning period, assist the user in accomplishing his task(s) with a minimum of distraction, present output in a form that best conveys information to the user, and reduce cognitive load for the user. In pursuit of this ideal, the Intelligent Multi-Media Interfaces project is devoted to the development of interface technology that integrates speech, natural language text, graphics, and pointing gestures for human-computer dialogues. The objective of the project is to develop interface technology that uses the media/modalities intelligently in a flexible, context-sensitive, and highly integrated manner modelled after the manner in which humans converse in simultaneous coordinated multiple modalities. As part of the project, a knowledge-based interface system, called CUBRICON (CUBRC Intelligent CONversationalist) is being developed as a research prototype. The application domain being used to drive the research is that of military tactical air control.

Entrez Neuron RDFa: a pragmatic semantic web application for data integration in neuroscience research.

PubMed

Samwald, Matthias; Lim, Ernest; Masiar, Peter; Marenco, Luis; Chen, Huajun; Morse, Thomas; Mutalik, Pradeep; Shepherd, Gordon; Miller, Perry; Cheung, Kei-Hoi

2009-01-01

The amount of biomedical data available in Semantic Web formats has been rapidly growing in recent years. While these formats are machine-friendly, user-friendly web interfaces allowing easy querying of these data are typically lacking. We present "Entrez Neuron", a pilot neuron-centric interface that allows for keyword-based queries against a coherent repository of OWL ontologies. These ontologies describe neuronal structures, physiology, mathematical models and microscopy images. The returned query results are organized hierarchically according to brain architecture. Where possible, the application makes use of entities from the Open Biomedical Ontologies (OBO) and the 'HCLS knowledgebase' developed by the W3C Interest Group for Health Care and Life Science. It makes use of the emerging RDFa standard to embed ontology fragments and semantic annotations within its HTML-based user interface. The application and underlying ontologies demonstrate how Semantic Web technologies can be used for information integration within a curated information repository and between curated information repositories. It also demonstrates how information integration can be accomplished on the client side, through simple copying and pasting of portions of documents that contain RDFa markup.

Efficient detection of differentially methylated regions using DiMmeR.

PubMed

Almeida, Diogo; Skov, Ida; Silva, Artur; Vandin, Fabio; Tan, Qihua; Röttger, Richard; Baumbach, Jan

2017-02-15

Epigenome-wide association studies (EWAS) generate big epidemiological datasets. They aim for detecting differentially methylated DNA regions that are likely to influence transcriptional gene activity and, thus, the regulation of metabolic processes. The by far most widely used technology is the Illumina Methylation BeadChip, which measures the methylation levels of 450 (850) thousand cytosines, in the CpG dinucleotide context in a set of patients compared to a control group. Many bioinformatics tools exist for raw data analysis. However, most of them require some knowledge in the programming language R, have no user interface, and do not offer all necessary steps to guide users from raw data all the way down to statistically significant differentially methylated regions (DMRs) and the associated genes. Here, we present DiMmeR (Discovery of Multiple Differentially Methylated Regions), the first free standalone software that interactively guides with a user-friendly graphical user interface (GUI) scientists the whole way through EWAS data analysis. It offers parallelized statistical methods for efficiently identifying DMRs in both Illumina 450K and 850K EPIC chip data. DiMmeR computes empirical P -values through randomization tests, even for big datasets of hundreds of patients and thousands of permutations within a few minutes on a standard desktop PC. It is independent of any third-party libraries, computes regression coefficients, P -values and empirical P -values, and it corrects for multiple testing. DiMmeR is publicly available at http://dimmer.compbio.sdu.dk . diogoma@bmb.sdu.dk. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Visual Basic VPython Interface: Charged Particle in a Magnetic Field

NASA Astrophysics Data System (ADS)

Prayaga, Chandra

2006-12-01

A simple Visual Basic (VB) to VPython interface is described and illustrated with the example of a charged particle in a magnetic field. This interface allows data to be passed to Python through a text file read by Python. The first component of the interface is a user-friendly data entry screen designed in VB, in which the user can input values of the charge, mass, initial position and initial velocity of the particle, and the magnetic field. Next, a command button is coded to write these values to a text file. Another command button starts the VPython program, which reads the data from the text file, numerically solves the equation of motion, and provides the 3d graphics animation. Students can use the interface to run the program several times with different data and observe changes in the motion.

E-TALEN: a web tool to design TALENs for genome engineering.

PubMed

Heigwer, Florian; Kerr, Grainne; Walther, Nike; Glaeser, Kathrin; Pelz, Oliver; Breinig, Marco; Boutros, Michael

2013-11-01

Use of transcription activator-like effector nucleases (TALENs) is a promising new technique in the field of targeted genome engineering, editing and reverse genetics. Its applications span from introducing knockout mutations to endogenous tagging of proteins and targeted excision repair. Owing to this wide range of possible applications, there is a need for fast and user-friendly TALEN design tools. We developed E-TALEN (http://www.e-talen.org), a web-based tool to design TALENs for experiments of varying scale. E-TALEN enables the design of TALENs against a single target or a large number of target genes. We significantly extended previously published design concepts to consider genomic context and different applications. E-TALEN guides the user through an end-to-end design process of de novo TALEN pairs, which are specific to a certain sequence or genomic locus. Furthermore, E-TALEN offers a functionality to predict targeting and specificity for existing TALENs. Owing to the computational complexity of many of the steps in the design of TALENs, particular emphasis has been put on the implementation of fast yet accurate algorithms. We implemented a user-friendly interface, from the input parameters to the presentation of results. An additional feature of E-TALEN is the in-built sequence and annotation database available for many organisms, including human, mouse, zebrafish, Drosophila and Arabidopsis, which can be extended in the future.

Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses.

PubMed

Menegidio, Fabiano B; Jabes, Daniela L; Costa de Oliveira, Regina; Nunes, Luiz R

2018-02-01

This manuscript introduces and describes Dugong, a Docker image based on Ubuntu 16.04, which automates installation of more than 3500 bioinformatics tools (along with their respective libraries and dependencies), in alternative computational environments. The software operates through a user-friendly XFCE4 graphic interface that allows software management and installation by users not fully familiarized with the Linux command line and provides the Jupyter Notebook to assist in the delivery and exchange of consistent and reproducible protocols and results across laboratories, assisting in the development of open science projects. Source code and instructions for local installation are available at https://github.com/DugongBioinformatics, under the MIT open source license. Luiz.nunes@ufabc.edu.br. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

FRODOCK 2.0: fast protein-protein docking server.

PubMed

Ramírez-Aportela, Erney; López-Blanco, José Ramón; Chacón, Pablo

2016-08-01

The prediction of protein-protein complexes from the structures of unbound components is a challenging and powerful strategy to decipher the mechanism of many essential biological processes. We present a user-friendly protein-protein docking server based on an improved version of FRODOCK that includes a complementary knowledge-based potential. The web interface provides a very effective tool to explore and select protein-protein models and interactively screen them against experimental distance constraints. The competitive success rates and efficiency achieved allow the retrieval of reliable potential protein-protein binding conformations that can be further refined with more computationally demanding strategies. The server is free and open to all users with no login requirement at http://frodock.chaconlab.org pablo@chaconlab.org Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

Krishnamurthy, Dheepak

This paper is an overview of Power System Simulation Toolbox (psst). psst is an open-source Python application for the simulation and analysis of power system models. psst simulates the wholesale market operation by solving a DC Optimal Power Flow (DCOPF), Security Constrained Unit Commitment (SCUC) and a Security Constrained Economic Dispatch (SCED). psst also includes models for the various entities in a power system such as Generator Companies (GenCos), Load Serving Entities (LSEs) and an Independent System Operator (ISO). psst features an open modular object oriented architecture that will make it useful for researchers to customize, expand, experiment beyond solvingmore » traditional problems. psst also includes a web based Graphical User Interface (GUI) that allows for user friendly interaction and for implementation on remote High Performance Computing (HPCs) clusters for parallelized operations. This paper also provides an illustrative application of psst and benchmarks with standard IEEE test cases to show the advanced features and the performance of toolbox.« less

Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease

PubMed Central

Zhang, Qingzhou; Yang, Bo; Chen, Xujiao; Xu, Jing; Mei, Changlin; Mao, Zhiguo

2014-01-01

We present a bioinformatics database named Renal Gene Expression Database (RGED), which contains comprehensive gene expression data sets from renal disease research. The web-based interface of RGED allows users to query the gene expression profiles in various kidney-related samples, including renal cell lines, human kidney tissues and murine model kidneys. Researchers can explore certain gene profiles, the relationships between genes of interests and identify biomarkers or even drug targets in kidney diseases. The aim of this work is to provide a user-friendly utility for the renal disease research community to query expression profiles of genes of their own interest without the requirement of advanced computational skills. Availability and implementation: Website is implemented in PHP, R, MySQL and Nginx and freely available from http://rged.wall-eva.net. Database URL: http://rged.wall-eva.net PMID:25252782

Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease.

PubMed

Zhang, Qingzhou; Yang, Bo; Chen, Xujiao; Xu, Jing; Mei, Changlin; Mao, Zhiguo

2014-01-01

We present a bioinformatics database named Renal Gene Expression Database (RGED), which contains comprehensive gene expression data sets from renal disease research. The web-based interface of RGED allows users to query the gene expression profiles in various kidney-related samples, including renal cell lines, human kidney tissues and murine model kidneys. Researchers can explore certain gene profiles, the relationships between genes of interests and identify biomarkers or even drug targets in kidney diseases. The aim of this work is to provide a user-friendly utility for the renal disease research community to query expression profiles of genes of their own interest without the requirement of advanced computational skills. Website is implemented in PHP, R, MySQL and Nginx and freely available from http://rged.wall-eva.net. http://rged.wall-eva.net. © The Author(s) 2014. Published by Oxford University Press.

Spotsizer: High-throughput quantitative analysis of microbial growth.

PubMed

Bischof, Leanne; Převorovský, Martin; Rallis, Charalampos; Jeffares, Daniel C; Arzhaeva, Yulia; Bähler, Jürg

2016-10-01

Microbial colony growth can serve as a useful readout in assays for studying complex genetic interactions or the effects of chemical compounds. Although computational tools for acquiring quantitative measurements of microbial colonies have been developed, their utility can be compromised by inflexible input image requirements, non-trivial installation procedures, or complicated operation. Here, we present the Spotsizer software tool for automated colony size measurements in images of robotically arrayed microbial colonies. Spotsizer features a convenient graphical user interface (GUI), has both single-image and batch-processing capabilities, and works with multiple input image formats and different colony grid types. We demonstrate how Spotsizer can be used for high-throughput quantitative analysis of fission yeast growth. The user-friendly Spotsizer tool provides rapid, accurate, and robust quantitative analyses of microbial growth in a high-throughput format. Spotsizer is freely available at https://data.csiro.au/dap/landingpage?pid=csiro:15330 under a proprietary CSIRO license.

Basic concepts and architectural details of the Delphi trigger system

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

Bocci, V.; Booth, P.S.L.; Bozzo, M.

1995-08-01

Delphi (DEtector with Lepton, Photon and Hadron Identification) is one of the four experiments of the LEP (Large Electron Positron) collider at CERN. The detector is laid out to provide a nearly 4 {pi} coverage for charged particle tracking, electromagnetic, hadronic calorimetry and extended particle identification. The trigger system consists of four levels. The first two are synchronous with the BCO (Beam Cross Over) and rely on hardwired control units, while the last two are performed asynchronously with respect to the BCO and are driven by the Delphi host computers. The aim of this paper is to give a comprehensivemore » global view of the trigger system architecture, presenting in detail the first two levels, their various hardware components and the latest modifications introduced in order to improve their performance and make more user friendly the whole software user interface.« less

Embedded Process Modeling, Analogy-Based Option Generation and Analytical Graphic Interaction for Enhanced User-Computer Interaction: An Interactive Storyboard of Next Generation User-Computer Interface Technology. Phase 1

DTIC Science & Technology

1988-03-01

structure of the interface is a mapping from the physical world [for example, the use of icons, which S have inherent meaning to users but represent...design alternatives. Mechanisms for linking the user to the computer include physical devices (keyboards), actions taken with the devices (keystrokes...VALUATION AIDES TEMLATEI IITCOM1I LATOR IACTICAL KNOWLEDGE ACGIUISITION MICNnII t 1 Fig. 9. INTACVAL. * OtJiCTs ARE PHYSICAL ENTITIES OR CONCEPTUAL EN

Input data requirements for special processors in the computation system containing the VENTURE neutronics code. [LMFBR

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

Vondy, D.R.; Fowler, T.B.; Cunningham, G.W.

1979-07-01

User input data requirements are presented for certain special processors in a nuclear reactor computation system. These processors generally read data in formatted form and generate binary interface data files. Some data processing is done to convert from the user oriented form to the interface file forms. The VENTURE diffusion theory neutronics code and other computation modules in this system use the interface data files which are generated.

RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite.

PubMed

Fleishman, Sarel J; Leaver-Fay, Andrew; Corn, Jacob E; Strauch, Eva-Maria; Khare, Sagar D; Koga, Nobuyasu; Ashworth, Justin; Murphy, Paul; Richter, Florian; Lemmon, Gordon; Meiler, Jens; Baker, David

2011-01-01

Macromolecular modeling and design are increasingly useful in basic research, biotechnology, and teaching. However, the absence of a user-friendly modeling framework that provides access to a wide range of modeling capabilities is hampering the wider adoption of computational methods by non-experts. RosettaScripts is an XML-like language for specifying modeling tasks in the Rosetta framework. RosettaScripts provides access to protocol-level functionalities, such as rigid-body docking and sequence redesign, and allows fast testing and deployment of complex protocols without need for modifying or recompiling the underlying C++ code. We illustrate these capabilities with RosettaScripts protocols for the stabilization of proteins, the generation of computationally constrained libraries for experimental selection of higher-affinity binding proteins, loop remodeling, small-molecule ligand docking, design of ligand-binding proteins, and specificity redesign in DNA-binding proteins.

The PAWS and STEM reliability analysis programs

NASA Technical Reports Server (NTRS)

Butler, Ricky W.; Stevenson, Philip H.

1988-01-01

The PAWS and STEM programs are new design/validation tools. These programs provide a flexible, user-friendly, language-based interface for the input of Markov models describing the behavior of fault-tolerant computer systems. These programs produce exact solutions of the probability of system failure and provide a conservative estimate of the number of significant digits in the solution. PAWS uses a Pade approximation as a solution technique; STEM uses a Taylor series as a solution technique. Both programs have the capability to solve numerically stiff models. PAWS and STEM possess complementary properties with regard to their input space; and, an additional strength of these programs is that they accept input compatible with the SURE program. If used in conjunction with SURE, PAWS and STEM provide a powerful suite of programs to analyze the reliability of fault-tolerant computer systems.

DAMBE7: New and Improved Tools for Data Analysis in Molecular Biology and Evolution.

PubMed

Xia, Xuhua

2018-06-01

DAMBE is a comprehensive software package for genomic and phylogenetic data analysis on Windows, Linux, and Macintosh computers. New functions include imputing missing distances and phylogeny simultaneously (paving the way to build large phage and transposon trees), new bootstrapping/jackknifing methods for PhyPA (phylogenetics from pairwise alignments), and an improved function for fast and accurate estimation of the shape parameter of the gamma distribution for fitting rate heterogeneity over sites. Previous method corrects multiple hits for each site independently. DAMBE's new method uses all sites simultaneously for correction. DAMBE, featuring a user-friendly graphic interface, is freely available from http://dambe.bio.uottawa.ca (last accessed, April 17, 2018).

Meta-T: TetrisⓇ as an experimental paradigm for cognitive skills research.

PubMed

Lindstedt, John K; Gray, Wayne D

2015-12-01

Studies of human performance in complex tasks using video games are an attractive prospect, but many existing games lack a comprehensive way to modify the game and track performance beyond basic levels of analysis. Meta-T provides experimenters a tool to study behavior in a dynamic task environment with time-stressed decision-making and strong perceptual-motor elements, offering a host of experimental manipulations with a robust and detailed logging system for all user events, system events, and screen objects. Its experimenter-friendly interface provides control over detailed parameters of the task environment without need for programming expertise. Support for eye-tracking and computational cognitive modeling extend the paradigm's scope.

DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra

PubMed Central

2013-01-01

De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, their adoption threshold remains quite high. We here present a user-friendly and lightweight graphical user interface called DeNovoGUI for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics. Our platform-independent software is freely available under the permissible Apache2 open source license. Source code, binaries, and additional documentation are available at http://denovogui.googlecode.com. PMID:24295440

DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra.

PubMed

Muth, Thilo; Weilnböck, Lisa; Rapp, Erdmann; Huber, Christian G; Martens, Lennart; Vaudel, Marc; Barsnes, Harald

2014-02-07

De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, their adoption threshold remains quite high. We here present a user-friendly and lightweight graphical user interface called DeNovoGUI for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics. Our platform-independent software is freely available under the permissible Apache2 open source license. Source code, binaries, and additional documentation are available at http://denovogui.googlecode.com .

A user-friendly mathematical modelling web interface to assist local decision making in the fight against drug-resistant tuberculosis.

PubMed

Ragonnet, Romain; Trauer, James M; Denholm, Justin T; Marais, Ben J; McBryde, Emma S

2017-05-30

Multidrug-resistant and rifampicin-resistant tuberculosis (MDR/RR-TB) represent an important challenge for global tuberculosis (TB) control. The high rates of MDR/RR-TB observed among re-treatment cases can arise from diverse pathways: de novo amplification during initial treatment, inappropriate treatment of undiagnosed MDR/RR-TB, relapse despite appropriate treatment, or reinfection with MDR/RR-TB. Mathematical modelling allows quantification of the contribution made by these pathways in different settings. This information provides valuable insights for TB policy-makers, allowing better contextualised solutions. However, mathematical modelling outputs need to consider local data and be easily accessible to decision makers in order to improve their usefulness. We present a user-friendly web-based modelling interface, which can be used by people without technical knowledge. Users can input their own parameter values and produce estimates for their specific setting. This innovative tool provides easy access to mathematical modelling outputs that are highly relevant to national TB control programs. In future, the same approach could be applied to a variety of modelling applications, enhancing local decision making.

The Identification, Implementation, and Evaluation of Critical User Interface Design Features of Computer-Assisted Instruction Programs in Mathematics for Students with Learning Disabilities

ERIC Educational Resources Information Center

Seo, You-Jin; Woo, Honguk

2010-01-01

Critical user interface design features of computer-assisted instruction programs in mathematics for students with learning disabilities and corresponding implementation guidelines were identified in this study. Based on the identified features and guidelines, a multimedia computer-assisted instruction program, "Math Explorer", which delivers…

Numerical, Analytical, Experimental Study of Fluid Dynamic Forces in Seals Volume 6: Description of Scientific CFD Code SCISEAL

NASA Technical Reports Server (NTRS)

Athavale, Mahesh; Przekwas, Andrzej

2004-01-01

The objectives of the program were to develop computational fluid dynamics (CFD) codes and simpler industrial codes for analyzing and designing advanced seals for air-breathing and space propulsion engines. The CFD code SCISEAL is capable of producing full three-dimensional flow field information for a variety of cylindrical configurations. An implicit multidomain capability allow the division of complex flow domains to allow optimum use of computational cells. SCISEAL also has the unique capability to produce cross-coupled stiffness and damping coefficients for rotordynamic computations. The industrial codes consist of a series of separate stand-alone modules designed for expeditious parametric analyses and optimization of a wide variety of cylindrical and face seals. Coupled through a Knowledge-Based System (KBS) that provides a user-friendly Graphical User Interface (GUI), the industrial codes are PC based using an OS/2 operating system. These codes were designed to treat film seals where a clearance exists between the rotating and stationary components. Leakage is inhibited by surface roughness, small but stiff clearance films, and viscous pumping devices. The codes have demonstrated to be a valuable resource for seal development of future air-breathing and space propulsion engines.

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

DOE PAGES

Paez-Espino, David; Chen, I. -Min A.; Palaniappan, Krishna; ...

2016-10-30

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from > 6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs aremore » grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparingwith external sequences, thus serving as an essential resource in the viral genomics community.« less

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

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

Paez-Espino, David; Chen, I. -Min A.; Palaniappan, Krishna

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from > 6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs aremore » grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparingwith external sequences, thus serving as an essential resource in the viral genomics community.« less

Three-dimensional user interfaces for scientific visualization

NASA Technical Reports Server (NTRS)

Vandam, Andries

1995-01-01

The main goal of this project is to develop novel and productive user interface techniques for creating and managing visualizations of computational fluid dynamics (CFD) datasets. We have implemented an application framework in which we can visualize computational fluid dynamics user interfaces. This UI technology allows users to interactively place visualization probes in a dataset and modify some of their parameters. We have also implemented a time-critical scheduling system which strives to maintain a constant frame-rate regardless of the number of visualization techniques. In the past year, we have published parts of this research at two conferences, the research annotation system at Visualization 1994, and the 3D user interface at UIST 1994. The real-time scheduling system has been submitted to SIGGRAPH 1995 conference. Copies of these documents are included with this report.

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.

Real-time spectral analysis of HRV signals: an interactive and user-friendly PC system.

PubMed

Basano, L; Canepa, F; Ottonello, P

1998-01-01

We present a real-time system, built around a PC and a low-cost data acquisition board, for the spectral analysis of the heart rate variability signal. The Windows-like operating environment on which it is based makes the computer program very user-friendly even for non-specialized personnel. The Power Spectral Density is computed through the use of a hybrid method, in which a classical FFT analysis follows an autoregressive finite-extension of data; the stationarity of the sequence is continuously checked. The use of this algorithm gives a high degree of robustness of the spectral estimation. Moreover, always in real time, the FFT of every data block is computed and displayed in order to corroborate the results as well as to allow the user to interactively choose a proper AR model order.

Knob manager (KM) operators guide

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

NONE

1993-10-08

KM, Knob Manager, is a tool which enables the user to use the SUNDIALS knob box to adjust the settings of the control system. The followings are some features of KM: dynamic knob assignments with the user friendly interface; user-defined gain for individual knob; graphical displays for operating range and status of each process variable is assigned; backup and restore one or multiple process variable; save current settings to a file and recall the settings from that file in future.

Carbon footprint estimator, phase II : volume I - GASCAP model & volume II - technical appendices [technical brief].

DOT National Transportation Integrated Search

2014-03-01

This study resulted in the development of the GASCAP model (the Greenhouse Gas Assessment : Spreadsheet for Transportation Capital Projects). This spreadsheet model provides a user-friendly interface for determining the greenhouse gas (GHG) emissions...

Technobabble: Photoshop 6 Converges Web, Print Photograph-Editing Capabilities.

ERIC Educational Resources Information Center

Communication: Journalism Education Today, 2001

2001-01-01

Discusses the newly-released Adobe Photoshop 6, and its use in student publications. Notes its refined text-handling capabilities, a more user-friendly interface, integrated vector functions, easier preparation of Web images, and new and more powerful layer functions. (SR)

Determinants of user acceptance of a specific social platform for older adults: An empirical examination of user interface characteristics and behavioral intention.

PubMed

Tsai, Tsai-Hsuan; Chang, Hsien-Tsung; Chen, Yan-Jiun; Chang, Yung-Sheng

2017-01-01

The use of the Internet and social applications has many benefits for the elderly, but numerous investigations have shown that the elderly do not perceive online social networks as a friendly social environment. Therefore, TreeIt, a social application specifically designed for the elderly, was developed for this study. In the TreeIt application, seven mechanisms promoting social interaction were designed to allow older adults to use social networking sites (SNSs) to increase social connection, maintain the intensity of social connections and strengthen social experience. This study's main objective was to investigate how user interface design affects older people's intention and attitude related to using SNSs. Fourteen user interface evaluation heuristics proposed by Zhang et al. were adopted as the criteria to assess user interface usability and further grouped into three categories: system support, user interface design and navigation. The technology acceptance model was adopted to assess older people's intention and attitude related to using SNSs. One hundred and one elderly persons were enrolled in this study as subjects, and the results showed that all of the hypotheses proposed in this study were valid: system support and perceived usefulness had a significant effect on behavioral intention; user interface design and perceived ease of use were positively correlated with perceived usefulness; and navigation exerted an influence on perceived ease of use. The results of this study are valuable for the future development of social applications for the elderly.

CERESVis: A QC Tool for CERES that Leverages Browser Technology for Data Validation

NASA Astrophysics Data System (ADS)

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

2015-12-01

In this poster, we are going to present three user interfaces that CERES team uses to validate pixel-level data. Besides our home grown tools, we will aslo present the browser technology that we use to provide interactive interfaces, such as jquery, HighCharts and Google Earth. We pass data to the users' browsers and use the browsers to do some simple computations. The three user interfaces are: Thumbnails -- it displays hundrends images to allow users to browse 24-hour data files in few seconds. Multiple-synchronized cursors -- it allows users to compare multiple images side by side. Bounding Boxes and Histograms -- it allows users to draw multiple bounding boxes on an image and the browser computes/display the histograms.

Development of the Computer Interface Literacy Measure.

ERIC Educational Resources Information Center

Turner, G. Marc; Sweany, Noelle Wall; Husman, Jenefer

2000-01-01

Discussion of computer literacy and the rapidly changing face of technology focuses on a study that redefined computer literacy to include competencies for using graphical user interfaces for operating systems, hypermedia applications, and the Internet. Describes the development and testing of the Computer Interface Literacy Measure with…

MSIX - A general and user-friendly platform for RAM analysis

NASA Astrophysics Data System (ADS)

Pan, Z. J.; Blemel, Peter

The authors present a CAD (computer-aided design) platform supporting RAM (reliability, availability, and maintainability) analysis with efficient system description and alternative evaluation. The design concepts, implementation techniques, and application results are described. This platform is user-friendly because of its graphic environment, drawing facilities, object orientation, self-tutoring, and access to the operating system. The programs' independency and portability make them generally applicable to various analysis tasks.

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…

The User Interface: How Does Your Product Look and Feel?

ERIC Educational Resources Information Center

Strukhoff, Roger

1987-01-01

Discusses the importance of user cordial interfaces to the successful marketing of optical data disk products, and describes features of several online systems. The topics discussed include full text searching, indexed searching, menu driven interfaces, natural language interfaces, computer graphics, and possible future developments. (CLB)

Portable multiplicity counter

DOEpatents

Newell, Matthew R [Los Alamos, NM; Jones, David Carl [Los Alamos, NM

2009-09-01

A portable multiplicity counter has signal input circuitry, processing circuitry and a user/computer interface disposed in a housing. The processing circuitry, which can comprise a microcontroller integrated circuit operably coupled to shift register circuitry implemented in a field programmable gate array, is configured to be operable via the user/computer interface to count input signal pluses receivable at said signal input circuitry and record time correlations thereof in a total counting mode, coincidence counting mode and/or a multiplicity counting mode. The user/computer interface can be for example an LCD display/keypad and/or a USB interface. The counter can include a battery pack for powering the counter and low/high voltage power supplies for biasing external detectors so that the counter can be configured as a hand-held device for counting neutron events.

The Brainarium: An Interactive Immersive Tool for Brain Education, Art, and Neurotherapy

PubMed Central

2016-01-01

Recent theoretical and technological advances in neuroimaging techniques now allow brain electrical activity to be recorded using affordable and user-friendly equipment for nonscientist end-users. An increasing number of educators and artists have begun using electroencephalogram (EEG) to control multimedia and live artistic contents. In this paper, we introduce a new concept based on brain computer interface (BCI) technologies: the Brainarium. The Brainarium is a new pedagogical and artistic tool, which can deliver and illustrate scientific knowledge, as well as a new framework for scientific exploration. The Brainarium consists of a portable planetarium device that is being used as brain metaphor. This is done by projecting multimedia content on the planetarium dome and displaying EEG data recorded from a subject in real time using Brain Machine Interface (BMI) technologies. The system has been demonstrated through several performances involving an interaction between the subject controlling the BMI, a musician, and the audience during series of exhibitions and workshops in schools. We report here feedback from 134 participants who filled questionnaires to rate their experiences. Our results show improved subjective learning compared to conventional methods, improved entertainment value, improved absorption into the material being presented, and little discomfort. PMID:27698660

PELE web server: atomistic study of biomolecular systems at your fingertips.

PubMed

Madadkar-Sobhani, Armin; Guallar, Victor

2013-07-01

PELE, Protein Energy Landscape Exploration, our novel technology based on protein structure prediction algorithms and a Monte Carlo sampling, is capable of modelling the all-atom protein-ligand dynamical interactions in an efficient and fast manner, with two orders of magnitude reduced computational cost when compared with traditional molecular dynamics techniques. PELE's heuristic approach generates trial moves based on protein and ligand perturbations followed by side chain sampling and global/local minimization. The collection of accepted steps forms a stochastic trajectory. Furthermore, several processors may be run in parallel towards a collective goal or defining several independent trajectories; the whole procedure has been parallelized using the Message Passing Interface. Here, we introduce the PELE web server, designed to make the whole process of running simulations easier and more practical by minimizing input file demand, providing user-friendly interface and producing abstract outputs (e.g. interactive graphs and tables). The web server has been implemented in C++ using Wt (http://www.webtoolkit.eu) and MySQL (http://www.mysql.com). The PELE web server, accessible at http://pele.bsc.es, is free and open to all users with no login requirement.

The Neural-fuzzy Thermal Error Compensation Controller on CNC Machining Center

NASA Astrophysics Data System (ADS)

Tseng, Pai-Chung; Chen, Shen-Len

The geometric errors and structural thermal deformation are factors that influence the machining accuracy of Computer Numerical Control (CNC) machining center. Therefore, researchers pay attention to thermal error compensation technologies on CNC machine tools. Some real-time error compensation techniques have been successfully demonstrated in both laboratories and industrial sites. The compensation results still need to be enhanced. In this research, the neural-fuzzy theory has been conducted to derive a thermal prediction model. An IC-type thermometer has been used to detect the heat sources temperature variation. The thermal drifts are online measured by a touch-triggered probe with a standard bar. A thermal prediction model is then derived by neural-fuzzy theory based on the temperature variation and the thermal drifts. A Graphic User Interface (GUI) system is also built to conduct the user friendly operation interface with Insprise C++ Builder. The experimental results show that the thermal prediction model developed by neural-fuzzy theory methodology can improve machining accuracy from 80µm to 3µm. Comparison with the multi-variable linear regression analysis the compensation accuracy is increased from ±10µm to ±3µm.

The Brainarium: An Interactive Immersive Tool for Brain Education, Art, and Neurotherapy.

PubMed

Grandchamp, Romain; Delorme, Arnaud

2016-01-01

Recent theoretical and technological advances in neuroimaging techniques now allow brain electrical activity to be recorded using affordable and user-friendly equipment for nonscientist end-users. An increasing number of educators and artists have begun using electroencephalogram (EEG) to control multimedia and live artistic contents. In this paper, we introduce a new concept based on brain computer interface (BCI) technologies: the Brainarium. The Brainarium is a new pedagogical and artistic tool, which can deliver and illustrate scientific knowledge, as well as a new framework for scientific exploration. The Brainarium consists of a portable planetarium device that is being used as brain metaphor. This is done by projecting multimedia content on the planetarium dome and displaying EEG data recorded from a subject in real time using Brain Machine Interface (BMI) technologies. The system has been demonstrated through several performances involving an interaction between the subject controlling the BMI, a musician, and the audience during series of exhibitions and workshops in schools. We report here feedback from 134 participants who filled questionnaires to rate their experiences. Our results show improved subjective learning compared to conventional methods, improved entertainment value, improved absorption into the material being presented, and little discomfort.

The eNanoMapper database for nanomaterial safety information

PubMed Central

Chomenidis, Charalampos; Doganis, Philip; Fadeel, Bengt; Grafström, Roland; Hardy, Barry; Hastings, Janna; Hegi, Markus; Jeliazkov, Vedrin; Kochev, Nikolay; Kohonen, Pekka; Munteanu, Cristian R; Sarimveis, Haralambos; Smeets, Bart; Sopasakis, Pantelis; Tsiliki, Georgia; Vorgrimmler, David; Willighagen, Egon

2015-01-01

Summary Background: The NanoSafety Cluster, a cluster of projects funded by the European Commision, identified the need for a computational infrastructure for toxicological data management of engineered nanomaterials (ENMs). Ontologies, open standards, and interoperable designs were envisioned to empower a harmonized approach to European research in nanotechnology. This setting provides a number of opportunities and challenges in the representation of nanomaterials data and the integration of ENM information originating from diverse systems. Within this cluster, eNanoMapper works towards supporting the collaborative safety assessment for ENMs by creating a modular and extensible infrastructure for data sharing, data analysis, and building computational toxicology models for ENMs. Results: The eNanoMapper database solution builds on the previous experience of the consortium partners in supporting diverse data through flexible data storage, open source components and web services. We have recently described the design of the eNanoMapper prototype database along with a summary of challenges in the representation of ENM data and an extensive review of existing nano-related data models, databases, and nanomaterials-related entries in chemical and toxicogenomic databases. This paper continues with a focus on the database functionality exposed through its application programming interface (API), and its use in visualisation and modelling. Considering the preferred community practice of using spreadsheet templates, we developed a configurable spreadsheet parser facilitating user friendly data preparation and data upload. We further present a web application able to retrieve the experimental data via the API and analyze it with multiple data preprocessing and machine learning algorithms. Conclusion: We demonstrate how the eNanoMapper database is used to import and publish online ENM and assay data from several data sources, how the “representational state transfer” (REST) API enables building user friendly interfaces and graphical summaries of the data, and how these resources facilitate the modelling of reproducible quantitative structure–activity relationships for nanomaterials (NanoQSAR). PMID:26425413

The eNanoMapper database for nanomaterial safety information.

PubMed

Jeliazkova, Nina; Chomenidis, Charalampos; Doganis, Philip; Fadeel, Bengt; Grafström, Roland; Hardy, Barry; Hastings, Janna; Hegi, Markus; Jeliazkov, Vedrin; Kochev, Nikolay; Kohonen, Pekka; Munteanu, Cristian R; Sarimveis, Haralambos; Smeets, Bart; Sopasakis, Pantelis; Tsiliki, Georgia; Vorgrimmler, David; Willighagen, Egon

2015-01-01

The NanoSafety Cluster, a cluster of projects funded by the European Commision, identified the need for a computational infrastructure for toxicological data management of engineered nanomaterials (ENMs). Ontologies, open standards, and interoperable designs were envisioned to empower a harmonized approach to European research in nanotechnology. This setting provides a number of opportunities and challenges in the representation of nanomaterials data and the integration of ENM information originating from diverse systems. Within this cluster, eNanoMapper works towards supporting the collaborative safety assessment for ENMs by creating a modular and extensible infrastructure for data sharing, data analysis, and building computational toxicology models for ENMs. The eNanoMapper database solution builds on the previous experience of the consortium partners in supporting diverse data through flexible data storage, open source components and web services. We have recently described the design of the eNanoMapper prototype database along with a summary of challenges in the representation of ENM data and an extensive review of existing nano-related data models, databases, and nanomaterials-related entries in chemical and toxicogenomic databases. This paper continues with a focus on the database functionality exposed through its application programming interface (API), and its use in visualisation and modelling. Considering the preferred community practice of using spreadsheet templates, we developed a configurable spreadsheet parser facilitating user friendly data preparation and data upload. We further present a web application able to retrieve the experimental data via the API and analyze it with multiple data preprocessing and machine learning algorithms. We demonstrate how the eNanoMapper database is used to import and publish online ENM and assay data from several data sources, how the "representational state transfer" (REST) API enables building user friendly interfaces and graphical summaries of the data, and how these resources facilitate the modelling of reproducible quantitative structure-activity relationships for nanomaterials (NanoQSAR).

Coastal Modeling System: Dredging Module

DTIC Science & Technology

2016-06-01

nonuniform sediments, spatially variable placement thicknesses or depths, and a user-friendly interface within the SMS. ERDC/CHL CHETN-I-90 June...and W. Wu. 2011. Nonuniform sediment transport modeling and Grays Harbor, WA. In Proceedings of the Coastal Sediments’11. Jacksonville, FL. Stark, J

Visual design for the user interface, Part 1: Design fundamentals.

PubMed

Lynch, P J

1994-01-01

Digital audiovisual media and computer-based documents will be the dominant forms of professional communication in both clinical medicine and the biomedical sciences. The design of highly interactive multimedia systems will shortly become a major activity for biocommunications professionals. The problems of human-computer interface design are intimately linked with graphic design for multimedia presentations and on-line document systems. This article outlines the history of graphic interface design and the theories that have influenced the development of today's major graphic user interfaces.

TIGER: A graphically interactive grid system for turbomachinery applications

NASA Technical Reports Server (NTRS)

Shih, Ming-Hsin; Soni, Bharat K.

1992-01-01

Numerical grid generation algorithm associated with the flow field about turbomachinery geometries is presented. Graphical user interface is developed with FORMS Library to create an interactive, user-friendly working environment. This customized algorithm reduces the man-hours required to generate a grid associated with turbomachinery geometry, as compared to the use of general-purpose grid generation softwares. Bezier curves are utilized both interactively and automatically to accomplish grid line smoothness and orthogonality. Graphical User Interactions are provided in the algorithm, allowing the user to design and manipulate the grid lines with a mouse.

SimHap GUI: an intuitive graphical user interface for genetic association analysis.

PubMed

Carter, Kim W; McCaskie, Pamela A; Palmer, Lyle J

2008-12-25

Researchers wishing to conduct genetic association analysis involving single nucleotide polymorphisms (SNPs) or haplotypes are often confronted with the lack of user-friendly graphical analysis tools, requiring sophisticated statistical and informatics expertise to perform relatively straightforward tasks. Tools, such as the SimHap package for the R statistics language, provide the necessary statistical operations to conduct sophisticated genetic analysis, but lacks a graphical user interface that allows anyone but a professional statistician to effectively utilise the tool. We have developed SimHap GUI, a cross-platform integrated graphical analysis tool for conducting epidemiological, single SNP and haplotype-based association analysis. SimHap GUI features a novel workflow interface that guides the user through each logical step of the analysis process, making it accessible to both novice and advanced users. This tool provides a seamless interface to the SimHap R package, while providing enhanced functionality such as sophisticated data checking, automated data conversion, and real-time estimations of haplotype simulation progress. SimHap GUI provides a novel, easy-to-use, cross-platform solution for conducting a range of genetic and non-genetic association analyses. This provides a free alternative to commercial statistics packages that is specifically designed for genetic association analysis.

A tailored 200 parameter VME based data acquisition system for IBA at the Lund Ion Beam Analysis Facility - Hardware and software

NASA Astrophysics Data System (ADS)

Elfman, Mikael; Ros, Linus; Kristiansson, Per; Nilsson, E. J. Charlotta; Pallon, Jan

2016-03-01

With the recent advances towards modern Ion Beam Analysis (IBA), going from one- or few-parameter detector systems to multi-parameter systems, it has been necessary to expand and replace the more than twenty years old CAMAC based system. A new VME multi-parameter (presently up to 200 channels) data acquisition and control system has been developed and implemented at the Lund Ion Beam Analysis Facility (LIBAF). The system is based on the VX-511 Single Board Computer (SBC), acting as master with arbiter functionality and consists of standard VME modules like Analog to Digital Converters (ADC's), Charge to Digital Converters (QDC's), Time to Digital Converters (TDC's), scaler's, IO-cards, high voltage and waveform units. The modules have been specially selected to support all of the present detector systems in the laboratory, with the option of future expansion. Typically, the detector systems consist of silicon strip detectors, silicon drift detectors and scintillator detectors, for detection of charged particles, X-rays and γ-rays. The data flow of the raw data buffers out from the VME bus to the final storage place on a 16 terabyte network attached storage disc (NAS-disc) is described. The acquisition process, remotely controlled over one of the SBCs ethernet channels, is also discussed. The user interface is written in the Kmax software package, and is used to control the acquisition process as well as for advanced online and offline data analysis through a user-friendly graphical user interface (GUI). In this work the system implementation, layout and performance are presented. The user interface and possibilities for advanced offline analysis are also discussed and illustrated.

imDEV: a graphical user interface to R multivariate analysis tools in Microsoft Excel

PubMed Central

Grapov, Dmitry; Newman, John W.

2012-01-01

Summary: Interactive modules for Data Exploration and Visualization (imDEV) is a Microsoft Excel spreadsheet embedded application providing an integrated environment for the analysis of omics data through a user-friendly interface. Individual modules enables interactive and dynamic analyses of large data by interfacing R's multivariate statistics and highly customizable visualizations with the spreadsheet environment, aiding robust inferences and generating information-rich data visualizations. This tool provides access to multiple comparisons with false discovery correction, hierarchical clustering, principal and independent component analyses, partial least squares regression and discriminant analysis, through an intuitive interface for creating high-quality two- and a three-dimensional visualizations including scatter plot matrices, distribution plots, dendrograms, heat maps, biplots, trellis biplots and correlation networks. Availability and implementation: Freely available for download at http://sourceforge.net/projects/imdev/. Implemented in R and VBA and supported by Microsoft Excel (2003, 2007 and 2010). Contact: John.Newman@ars.usda.gov Supplementary Information: Installation instructions, tutorials and users manual are available at http://sourceforge.net/projects/imdev/. PMID:22815358

Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments.

PubMed

Castaño-Díez, Daniel; Kudryashev, Mikhail; Arheit, Marcel; Stahlberg, Henning

2012-05-01

Dynamo is a new software package for subtomogram averaging of cryo Electron Tomography (cryo-ET) data with three main goals: first, Dynamo allows user-transparent adaptation to a variety of high-performance computing platforms such as GPUs or CPU clusters. Second, Dynamo implements user-friendliness through GUI interfaces and scripting resources. Third, Dynamo offers user-flexibility through a plugin API. Besides the alignment and averaging procedures, Dynamo includes native tools for visualization and analysis of results and data, as well as support for third party visualization software, such as Chimera UCSF or EMAN2. As a demonstration of these functionalities, we studied bacterial flagellar motors and showed automatically detected classes with absent and present C-rings. Subtomogram averaging is a common task in current cryo-ET pipelines, which requires extensive computational resources and follows a well-established workflow. However, due to the data diversity, many existing packages offer slight variations of the same algorithm to improve results. One of the main purposes behind Dynamo is to provide explicit tools to allow the user the insertion of custom designed procedures - or plugins - to replace or complement the native algorithms in the different steps of the processing pipeline for subtomogram averaging without the burden of handling parallelization. Custom scripts that implement new approaches devised by the user are integrated into the Dynamo data management system, so that they can be controlled by the GUI or the scripting capacities. Dynamo executables do not require licenses for third party commercial software. Sources, executables and documentation are freely distributed on http://www.dynamo-em.org. Copyright © 2012 Elsevier Inc. All rights reserved.

Virtual button interface

DOEpatents

Jones, Jake S.

1999-01-01

An apparatus and method of issuing commands to a computer by a user interfacing with a virtual reality environment. To issue a command, the user directs gaze at a virtual button within the virtual reality environment, causing a perceptible change in the virtual button, which then sends a command corresponding to the virtual button to the computer, optionally after a confirming action is performed by the user, such as depressing a thumb switch.

The use of analytical models in human-computer interface design

NASA Technical Reports Server (NTRS)

Gugerty, Leo

1993-01-01

Recently, a large number of human-computer interface (HCI) researchers have investigated building analytical models of the user, which are often implemented as computer models. These models simulate the cognitive processes and task knowledge of the user in ways that allow a researcher or designer to estimate various aspects of an interface's usability, such as when user errors are likely to occur. This information can lead to design improvements. Analytical models can supplement design guidelines by providing designers rigorous ways of analyzing the information-processing requirements of specific tasks (i.e., task analysis). These models offer the potential of improving early designs and replacing some of the early phases of usability testing, thus reducing the cost of interface design. This paper describes some of the many analytical models that are currently being developed and evaluates the usefulness of analytical models for human-computer interface design. This paper will focus on computational, analytical models, such as the GOMS model, rather than less formal, verbal models, because the more exact predictions and task descriptions of computational models may be useful to designers. The paper also discusses some of the practical requirements for using analytical models in complex design organizations such as NASA.

FRIEND Engine Framework: a real time neurofeedback client-server system for neuroimaging studies

PubMed Central

Basilio, Rodrigo; Garrido, Griselda J.; Sato, João R.; Hoefle, Sebastian; Melo, Bruno R. P.; Pamplona, Fabricio A.; Zahn, Roland; Moll, Jorge

2015-01-01

In this methods article, we present a new implementation of a recently reported FSL-integrated neurofeedback tool, the standalone version of “Functional Real-time Interactive Endogenous Neuromodulation and Decoding” (FRIEND). We will refer to this new implementation as the FRIEND Engine Framework. The framework comprises a client-server cross-platform solution for real time fMRI and fMRI/EEG neurofeedback studies, enabling flexible customization or integration of graphical interfaces, devices, and data processing. This implementation allows a fast setup of novel plug-ins and frontends, which can be shared with the user community at large. The FRIEND Engine Framework is freely distributed for non-commercial, research purposes. PMID:25688193

Melanie II--a third-generation software package for analysis of two-dimensional electrophoresis images: I. Features and user interface.

PubMed

Appel, R D; Palagi, P M; Walther, D; Vargas, J R; Sanchez, J C; Ravier, F; Pasquali, C; Hochstrasser, D F

1997-12-01

Although two-dimensional electrophoresis (2-DE) computer analysis software packages have existed ever since 2-DE technology was developed, it is only now that the hardware and software technology allows large-scale studies to be performed on low-cost personal computers or workstations, and that setting up a 2-DE computer analysis system in a small laboratory is no longer considered a luxury. After a first attempt in the seventies and early eighties to develop 2-DE analysis software systems on hardware that had poor or even no graphical capabilities, followed in the late eighties by a wave of innovative software developments that were possible thanks to new graphical interface standards such as XWindows, a third generation of 2-DE analysis software packages has now come to maturity. It can be run on a variety of low-cost, general-purpose personal computers, thus making the purchase of a 2-DE analysis system easily attainable for even the smallest laboratory that is involved in proteome research. Melanie II 2-D PAGE, developed at the University Hospital of Geneva, is such a third-generation software system for 2-DE analysis. Based on unique image processing algorithms, this user-friendly object-oriented software package runs on multiple platforms, including Unix, MS-Windows 95 and NT, and Power Macintosh. It provides efficient spot detection and quantitation, state-of-the-art image comparison, statistical data analysis facilities, and is Internet-ready. Linked to proteome databases such as those available on the World Wide Web, it represents a valuable tool for the "Virtual Lab" of the post-genome area.

User interface development

NASA Technical Reports Server (NTRS)

Aggrawal, Bharat

1994-01-01

This viewgraph presentation describes the development of user interfaces for OS/2 versions of computer codes for the analysis of seals. Current status, new features, work in progress, and future plans are discussed.

SimRNAweb: a web server for RNA 3D structure modeling with optional restraints.

PubMed

Magnus, Marcin; Boniecki, Michał J; Dawson, Wayne; Bujnicki, Janusz M

2016-07-08

RNA function in many biological processes depends on the formation of three-dimensional (3D) structures. However, RNA structure is difficult to determine experimentally, which has prompted the development of predictive computational methods. Here, we introduce a user-friendly online interface for modeling RNA 3D structures using SimRNA, a method that uses a coarse-grained representation of RNA molecules, utilizes the Monte Carlo method to sample the conformational space, and relies on a statistical potential to describe the interactions in the folding process. SimRNAweb makes SimRNA accessible to users who do not normally use high performance computational facilities or are unfamiliar with using the command line tools. The simplest input consists of an RNA sequence to fold RNA de novo. Alternatively, a user can provide a 3D structure in the PDB format, for instance a preliminary model built with some other technique, to jump-start the modeling close to the expected final outcome. The user can optionally provide secondary structure and distance restraints, and can freeze a part of the starting 3D structure. SimRNAweb can be used to model single RNA sequences and RNA-RNA complexes (up to 52 chains). The webserver is available at http://genesilico.pl/SimRNAweb. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

GeMS: an advanced software package for designing synthetic genes.

PubMed

Jayaraj, Sebastian; Reid, Ralph; Santi, Daniel V

2005-01-01

A user-friendly, advanced software package for gene design is described. The software comprises an integrated suite of programs-also provided as stand-alone tools-that automatically performs the following tasks in gene design: restriction site prediction, codon optimization for any expression host, restriction site inclusion and exclusion, separation of long sequences into synthesizable fragments, T(m) and stem-loop determinations, optimal oligonucleotide component design and design verification/error-checking. The output is a complete design report and a list of optimized oligonucleotides to be prepared for subsequent gene synthesis. The user interface accommodates both inexperienced and experienced users. For inexperienced users, explanatory notes are provided such that detailed instructions are not necessary; for experienced users, a streamlined interface is provided without such notes. The software has been extensively tested in the design and successful synthesis of over 400 kb of genes, many of which exceeded 5 kb in length.

An Intuitive Dashboard for Bayesian Network Inference

NASA Astrophysics Data System (ADS)

Reddy, Vikas; Charisse Farr, Anna; Wu, Paul; Mengersen, Kerrie; Yarlagadda, Prasad K. D. V.

2014-03-01

Current Bayesian network software packages provide good graphical interface for users who design and develop Bayesian networks for various applications. However, the intended end-users of these networks may not necessarily find such an interface appealing and at times it could be overwhelming, particularly when the number of nodes in the network is large. To circumvent this problem, this paper presents an intuitive dashboard, which provides an additional layer of abstraction, enabling the end-users to easily perform inferences over the Bayesian networks. Unlike most software packages, which display the nodes and arcs of the network, the developed tool organises the nodes based on the cause-and-effect relationship, making the user-interaction more intuitive and friendly. In addition to performing various types of inferences, the users can conveniently use the tool to verify the behaviour of the developed Bayesian network. The tool has been developed using QT and SMILE libraries in C++.

Advanced display object selection methods for enhancing user-computer productivity

NASA Technical Reports Server (NTRS)

Osga, Glenn A.

1993-01-01

The User-Interface Technology Branch at NCCOSC RDT&E Division has been conducting a series of studies to address the suitability of commercial off-the-shelf (COTS) graphic user-interface (GUI) methods for efficiency and performance in critical naval combat systems. This paper presents an advanced selection algorithm and method developed to increase user performance when making selections on tactical displays. The method has also been applied with considerable success to a variety of cursor and pointing tasks. Typical GUI's allow user selection by: (1) moving a cursor with a pointing device such as a mouse, trackball, joystick, touchscreen; and (2) placing the cursor on the object. Examples of GUI objects are the buttons, icons, folders, scroll bars, etc. used in many personal computer and workstation applications. This paper presents an improved method of selection and the theoretical basis for the significant performance gains achieved with various input devices tested. The method is applicable to all GUI styles and display sizes, and is particularly useful for selections on small screens such as notebook computers. Considering the amount of work-hours spent pointing and clicking across all styles of available graphic user-interfaces, the cost/benefit in applying this method to graphic user-interfaces is substantial, with the potential for increasing productivity across thousands of users and applications.

Brainstorm: A User-Friendly Application for MEG/EEG Analysis

PubMed Central

Tadel, François; Baillet, Sylvain; Mosher, John C.; Pantazis, Dimitrios; Leahy, Richard M.

2011-01-01

Brainstorm is a collaborative open-source application dedicated to magnetoencephalography (MEG) and electroencephalography (EEG) data visualization and processing, with an emphasis on cortical source estimation techniques and their integration with anatomical magnetic resonance imaging (MRI) data. The primary objective of the software is to connect MEG/EEG neuroscience investigators with both the best-established and cutting-edge methods through a simple and intuitive graphical user interface (GUI). PMID:21584256

A User-Friendly, Keyword-Searchable Database of Geoscientific References Through 2007 for Afghanistan

USGS Publications Warehouse

Eppinger, Robert G.; Sipeki, Julianna; Scofield, M.L. Sco

2008-01-01

This report includes a document and accompanying Microsoft Access 2003 database of geoscientific references for the country of Afghanistan. The reference compilation is part of a larger joint study of Afghanistan?s energy, mineral, and water resources, and geologic hazards currently underway by the U.S. Geological Survey, the British Geological Survey, and the Afghanistan Geological Survey. The database includes both published (n = 2,489) and unpublished (n = 176) references compiled through calendar year 2007. The references comprise two separate tables in the Access database. The reference database includes a user-friendly, keyword-searchable interface and only minimum knowledge of the use of Microsoft Access is required.

Kinematics with the assistance of smartphones: Measuring data via GPS - Visualizing data with Google Earth

NASA Astrophysics Data System (ADS)

Gabriel, Patrik; Backhaus, Udo

2013-04-01

Nearly every smartphone is now GPS capable. The widespread use of GPS navigation has developed alongside less expensive hardware and user-friendly software interfaces, which may help to bring scientific research and teaching closer to real life.

Human-computer interface incorporating personal and application domains

DOEpatents

Anderson, Thomas G [Albuquerque, NM

2011-03-29

The present invention provides a human-computer interface. The interface includes provision of an application domain, for example corresponding to a three-dimensional application. The user is allowed to navigate and interact with the application domain. The interface also includes a personal domain, offering the user controls and interaction distinct from the application domain. The separation into two domains allows the most suitable interface methods in each: for example, three-dimensional navigation in the application domain, and two- or three-dimensional controls in the personal domain. Transitions between the application domain and the personal domain are under control of the user, and the transition method is substantially independent of the navigation in the application domain. For example, the user can fly through a three-dimensional application domain, and always move to the personal domain by moving a cursor near one extreme of the display.

Human-computer interface incorporating personal and application domains

DOEpatents

Anderson, Thomas G.

2004-04-20

The present invention provides a human-computer interface. The interface includes provision of an application domain, for example corresponding to a three-dimensional application. The user is allowed to navigate and interact with the application domain. The interface also includes a personal domain, offering the user controls and interaction distinct from the application domain. The separation into two domains allows the most suitable interface methods in each: for example, three-dimensional navigation in the application domain, and two- or three-dimensional controls in the personal domain. Transitions between the application domain and the personal domain are under control of the user, and the transition method is substantially independent of the navigation in the application domain. For example, the user can fly through a three-dimensional application domain, and always move to the personal domain by moving a cursor near one extreme of the display.

Development of a data mining and imaging informatics display tool for a multiple sclerosis e-folder system

NASA Astrophysics Data System (ADS)

Liu, Margaret; Loo, Jerry; Ma, Kevin; Liu, Brent

2011-03-01

Multiple sclerosis (MS) is a debilitating autoimmune disease of the central nervous system that damages axonal pathways through inflammation and demyelination. In order to address the need for a centralized application to manage and study MS patients, the MS e-Folder - a web-based, disease-specific electronic medical record system - was developed. The e-Folder has a PHP and MySQL based graphical user interface (GUI) that can serve as both a tool for clinician decision support and a data mining tool for researchers. This web-based GUI gives the e-Folder a user friendly interface that can be securely accessed through the internet and requires minimal software installation on the client side. The e-Folder GUI displays and queries patient medical records--including demographic data, social history, past medical history, and past MS history. In addition, DICOM format imaging data, and computer aided detection (CAD) results from a lesion load algorithm are also displayed. The GUI interface is dynamic and allows manipulation of the DICOM images, such as zoom, pan, and scrolling, and the ability to rotate 3D images. Given the complexity of clinical management and the need to bolster research in MS, the MS e-Folder system will improve patient care and provide MS researchers with a function-rich patient data hub.

PHREEQCI; a graphical user interface for the geochemical computer program PHREEQC

USGS Publications Warehouse

Charlton, Scott R.; Macklin, Clifford L.; Parkhurst, David L.

1997-01-01

PhreeqcI is a Windows-based graphical user interface for the geochemical computer program PHREEQC. PhreeqcI provides the capability to generate and edit input data files, run simulations, and view text files containing simulation results, all within the framework of a single interface. PHREEQC is a multipurpose geochemical program that can perform speciation, inverse, reaction-path, and 1D advective reaction-transport modeling. Interactive access to all of the capabilities of PHREEQC is available with PhreeqcI. The interface is written in Visual Basic and will run on personal computers under the Windows(3.1), Windows95, and WindowsNT operating systems.

Integrating Patient-Reported Outcomes into Spine Surgical Care through Visual Dashboards: Lessons Learned from Human-Centered Design.

PubMed

Hartzler, Andrea L; Chaudhuri, Shomir; Fey, Brett C; Flum, David R; Lavallee, Danielle

2015-01-01

The collection of patient-reported outcomes (PROs) draws attention to issues of importance to patients-physical function and quality of life. The integration of PRO data into clinical decisions and discussions with patients requires thoughtful design of user-friendly interfaces that consider user experience and present data in personalized ways to enhance patient care. Whereas most prior work on PROs focuses on capturing data from patients, little research details how to design effective user interfaces that facilitate use of this data in clinical practice. We share lessons learned from engaging health care professionals to inform design of visual dashboards, an emerging type of health information technology (HIT). We employed human-centered design (HCD) methods to create visual displays of PROs to support patient care and quality improvement. HCD aims to optimize the design of interactive systems through iterative input from representative users who are likely to use the system in the future. Through three major steps, we engaged health care professionals in targeted, iterative design activities to inform the development of a PRO Dashboard that visually displays patient-reported pain and disability outcomes following spine surgery. Design activities to engage health care administrators, providers, and staff guided our work from design concept to specifications for dashboard implementation. Stakeholder feedback from these health care professionals shaped user interface design features, including predefined overviews that illustrate at-a-glance trends and quarterly snapshots, granular data filters that enable users to dive into detailed PRO analytics, and user-defined views to share and reuse. Feedback also revealed important considerations for quality indicators and privacy-preserving sharing and use of PROs. Our work illustrates a range of engagement methods guided by human-centered principles and design recommendations for optimizing PRO Dashboards for patient care and quality improvement. Engaging health care professionals as stakeholders is a critical step toward the design of user-friendly HIT that is accepted, usable, and has the potential to enhance quality of care and patient outcomes.

RE-PLAN: An Extensible Software Architecture to Facilitate Disaster Response Planning

PubMed Central

O’Neill, Martin; Mikler, Armin R.; Indrakanti, Saratchandra; Tiwari, Chetan; Jimenez, Tamara

2014-01-01

Computational tools are needed to make data-driven disaster mitigation planning accessible to planners and policymakers without the need for programming or GIS expertise. To address this problem, we have created modules to facilitate quantitative analyses pertinent to a variety of different disaster scenarios. These modules, which comprise the REsponse PLan ANalyzer (RE-PLAN) framework, may be used to create tools for specific disaster scenarios that allow planners to harness large amounts of disparate data and execute computational models through a point-and-click interface. Bio-E, a user-friendly tool built using this framework, was designed to develop and analyze the feasibility of ad hoc clinics for treating populations following a biological emergency event. In this article, the design and implementation of the RE-PLAN framework are described, and the functionality of the modules used in the Bio-E biological emergency mitigation tool are demonstrated. PMID:25419503

PyFly: A fast, portable aerodynamics simulator

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

Garcia, Daniel; Ghommem, M.; Collier, Nathaniel O.

Here, we present a fast, user-friendly implementation of a potential flow solver based on the unsteady vortex lattice method (UVLM), namely PyFly. UVLM computes the aerodynamic loads applied on lifting surfaces while capturing the unsteady effects such as the added mass forces, the growth of bound circulation, and the wake while assuming that the flow separation location is known a priori. This method is based on discretizing the body surface into a lattice of vortex rings and relies on the Biot–Savart law to construct the velocity field at every point in the simulated domain. We introduce the pointwise approximation approachmore » to simulate the interactions of the far-field vortices to overcome the computational burden associated with the classical implementation of UVLM. The computational framework uses the Python programming language to provide an easy to handle user interface while the computational kernels are written in Fortran. The mixed language approach enables high performance regarding solution time and great flexibility concerning easiness of code adaptation to different system configurations and applications. The computational tool predicts the unsteady aerodynamic behavior of multiple moving bodies (e.g., flapping wings, rotating blades, suspension bridges) subject to incoming air. The aerodynamic simulator can also deal with enclosure effects, multi-body interactions, and B-spline representation of body shapes. Finally, we simulate different aerodynamic problems to illustrate the usefulness and effectiveness of PyFly.« less

Current And Future Directions Of Lens Design Software

NASA Astrophysics Data System (ADS)

Gustafson, Darryl E.

1983-10-01

The most effective environment for doing lens design continues to evolve as new computer hardware and software tools become available. Important recent hardware developments include: Low-cost but powerful interactive multi-user 32 bit computers with virtual memory that are totally software-compatible with prior larger and more expensive members of the family. A rapidly growing variety of graphics devices for both hard-copy and screen graphics, including many with color capability. In addition, with optical design software readily accessible in many forms, optical design has become a part-time activity for a large number of engineers instead of being restricted to a small number of full-time specialists. A designer interface that is friendly for the part-time user while remaining efficient for the full-time designer is thus becoming more important as well as more practical. Along with these developments, software tools in other scientific and engineering disciplines are proliferating. Thus, the optical designer is less and less unique in his use of computer-aided techniques and faces the challenge and opportunity of efficiently communicating his designs to other computer-aided-design (CAD), computer-aided-manufacturing (CAM), structural, thermal, and mechanical software tools. This paper will address the impact of these developments on the current and future directions of the CODE VTM optical design software package, its implementation, and the resulting lens design environment.

PyFly: A fast, portable aerodynamics simulator

DOE PAGES

Garcia, Daniel; Ghommem, M.; Collier, Nathaniel O.; ...

2018-03-14

Here, we present a fast, user-friendly implementation of a potential flow solver based on the unsteady vortex lattice method (UVLM), namely PyFly. UVLM computes the aerodynamic loads applied on lifting surfaces while capturing the unsteady effects such as the added mass forces, the growth of bound circulation, and the wake while assuming that the flow separation location is known a priori. This method is based on discretizing the body surface into a lattice of vortex rings and relies on the Biot–Savart law to construct the velocity field at every point in the simulated domain. We introduce the pointwise approximation approachmore » to simulate the interactions of the far-field vortices to overcome the computational burden associated with the classical implementation of UVLM. The computational framework uses the Python programming language to provide an easy to handle user interface while the computational kernels are written in Fortran. The mixed language approach enables high performance regarding solution time and great flexibility concerning easiness of code adaptation to different system configurations and applications. The computational tool predicts the unsteady aerodynamic behavior of multiple moving bodies (e.g., flapping wings, rotating blades, suspension bridges) subject to incoming air. The aerodynamic simulator can also deal with enclosure effects, multi-body interactions, and B-spline representation of body shapes. Finally, we simulate different aerodynamic problems to illustrate the usefulness and effectiveness of PyFly.« less

Rapid Prototyping of Hydrologic Model Interfaces with IPython

NASA Astrophysics Data System (ADS)

Farthing, M. W.; Winters, K. D.; Ahmadia, A. J.; Hesser, T.; Howington, S. E.; Johnson, B. D.; Tate, J.; Kees, C. E.

2014-12-01

A significant gulf still exists between the state of practice and state of the art in hydrologic modeling. Part of this gulf is due to the lack of adequate pre- and post-processing tools for newly developed computational models. The development of user interfaces has traditionally lagged several years behind the development of a particular computational model or suite of models. As a result, models with mature interfaces often lack key advancements in model formulation, solution methods, and/or software design and technology. Part of the problem has been a focus on developing monolithic tools to provide comprehensive interfaces for the entire suite of model capabilities. Such efforts require expertise in software libraries and frameworks for creating user interfaces (e.g., Tcl/Tk, Qt, and MFC). These tools are complex and require significant investment in project resources (time and/or money) to use. Moreover, providing the required features for the entire range of possible applications and analyses creates a cumbersome interface. For a particular site or application, the modeling requirements may be simplified or at least narrowed, which can greatly reduce the number and complexity of options that need to be accessible to the user. However, monolithic tools usually are not adept at dynamically exposing specific workflows. Our approach is to deliver highly tailored interfaces to users. These interfaces may be site and/or process specific. As a result, we end up with many, customized interfaces rather than a single, general-use tool. For this approach to be successful, it must be efficient to create these tailored interfaces. We need technology for creating quality user interfaces that is accessible and has a low barrier for integration into model development efforts. Here, we present efforts to leverage IPython notebooks as tools for rapid prototyping of site and application-specific user interfaces. We provide specific examples from applications in near-shore environments as well as levee analysis. We discuss our design decisions and methodology for developing customized interfaces, strategies for delivery of the interfaces to users in various computing environments, as well as implications for the design/implementation of simulation models.

Gender Differences between Graphical User Interfaces and Command Line Interfaces in Computer Instruction.

ERIC Educational Resources Information Center

Barker, Dan L.

This study focused primarily on two types of computer interfaces and the differences in academic performance that resulted from their use; it was secondarily designed to examine gender differences that may have existed before and after any change in interface. Much of the basic research in computer use was conducted with command line interface…

Transcriptator: An Automated Computational Pipeline to Annotate Assembled Reads and Identify Non Coding RNA.

PubMed

Tripathi, Kumar Parijat; Evangelista, Daniela; Zuccaro, Antonio; Guarracino, Mario Rosario

2015-01-01

RNA-seq is a new tool to measure RNA transcript counts, using high-throughput sequencing at an extraordinary accuracy. It provides quantitative means to explore the transcriptome of an organism of interest. However, interpreting this extremely large data into biological knowledge is a problem, and biologist-friendly tools are lacking. In our lab, we developed Transcriptator, a web application based on a computational Python pipeline with a user-friendly Java interface. This pipeline uses the web services available for BLAST (Basis Local Search Alignment Tool), QuickGO and DAVID (Database for Annotation, Visualization and Integrated Discovery) tools. It offers a report on statistical analysis of functional and Gene Ontology (GO) annotation's enrichment. It helps users to identify enriched biological themes, particularly GO terms, pathways, domains, gene/proteins features and protein-protein interactions related informations. It clusters the transcripts based on functional annotations and generates a tabular report for functional and gene ontology annotations for each submitted transcript to the web server. The implementation of QuickGo web-services in our pipeline enable the users to carry out GO-Slim analysis, whereas the integration of PORTRAIT (Prediction of transcriptomic non coding RNA (ncRNA) by ab initio methods) helps to identify the non coding RNAs and their regulatory role in transcriptome. In summary, Transcriptator is a useful software for both NGS and array data. It helps the users to characterize the de-novo assembled reads, obtained from NGS experiments for non-referenced organisms, while it also performs the functional enrichment analysis of differentially expressed transcripts/genes for both RNA-seq and micro-array experiments. It generates easy to read tables and interactive charts for better understanding of the data. The pipeline is modular in nature, and provides an opportunity to add new plugins in the future. Web application is freely available at: http://www-labgtp.na.icar.cnr.it/Transcriptator.

A hybrid brain-computer interface-based mail client.

PubMed

Yu, Tianyou; Li, Yuanqing; Long, Jinyi; Li, Feng

2013-01-01

Brain-computer interface-based communication plays an important role in brain-computer interface (BCI) applications; electronic mail is one of the most common communication tools. In this study, we propose a hybrid BCI-based mail client that implements electronic mail communication by means of real-time classification of multimodal features extracted from scalp electroencephalography (EEG). With this BCI mail client, users can receive, read, write, and attach files to their mail. Using a BCI mouse that utilizes hybrid brain signals, that is, motor imagery and P300 potential, the user can select and activate the function keys and links on the mail client graphical user interface (GUI). An adaptive P300 speller is employed for text input. The system has been tested with 6 subjects, and the experimental results validate the efficacy of the proposed method.

A Hybrid Brain-Computer Interface-Based Mail Client

PubMed Central

Yu, Tianyou; Li, Yuanqing; Long, Jinyi; Li, Feng

2013-01-01

Brain-computer interface-based communication plays an important role in brain-computer interface (BCI) applications; electronic mail is one of the most common communication tools. In this study, we propose a hybrid BCI-based mail client that implements electronic mail communication by means of real-time classification of multimodal features extracted from scalp electroencephalography (EEG). With this BCI mail client, users can receive, read, write, and attach files to their mail. Using a BCI mouse that utilizes hybrid brain signals, that is, motor imagery and P300 potential, the user can select and activate the function keys and links on the mail client graphical user interface (GUI). An adaptive P300 speller is employed for text input. The system has been tested with 6 subjects, and the experimental results validate the efficacy of the proposed method. PMID:23690880

CDROM User Interface Evaluation: The Appropriateness of GUIs.

ERIC Educational Resources Information Center

Bosch, Victoria Manglano; Hancock-Beaulieu, Micheline

1995-01-01

Assesses the appropriateness of GUIs (graphical user interfaces), more specifically Windows-based interfaces for CD-ROM. An evaluation model is described that was developed to carry out an expert evaluation of the interfaces of seven CD-ROM products. Results are discussed in light of HCI (human-computer interaction) usability criteria and design…

The crustal dynamics intelligent user interface anthology

NASA Technical Reports Server (NTRS)

Short, Nicholas M., Jr.; Campbell, William J.; Roelofs, Larry H.; Wattawa, Scott L.

1987-01-01

The National Space Science Data Center (NSSDC) has initiated an Intelligent Data Management (IDM) research effort which has, as one of its components, the development of an Intelligent User Interface (IUI). The intent of the IUI is to develop a friendly and intelligent user interface service based on expert systems and natural language processing technologies. The purpose of such a service is to support the large number of potential scientific and engineering users that have need of space and land-related research and technical data, but have little or no experience in query languages or understanding of the information content or architecture of the databases of interest. This document presents the design concepts, development approach and evaluation of the performance of a prototype IUI system for the Crustal Dynamics Project Database, which was developed using a microcomputer-based expert system tool (M. 1), the natural language query processor THEMIS, and the graphics software system GSS. The IUI design is based on a multiple view representation of a database from both the user and database perspective, with intelligent processes to translate between the views.

Linear Quadratic Gaussian Controller Design Using a Graphical User Interface: Application to the Beam-Waveguide Antennas

NASA Astrophysics Data System (ADS)

Maneri, E.; Gawronski, W.

1999-10-01

The linear quadratic Gaussian (LQG) design algorithms described in [2] and [5] have been used in the controller design of JPL's beam-waveguide [5] and 70-m [6] antennas. This algorithm significantly improves tracking precision in a windy environment. This article describes the graphical user interface (GUI) software for the design LQG controllers. It consists of two parts: the basic LQG design and the fine-tuning of the basic design using a constrained optimization algorithm. The presented GUI was developed to simplify the design process, to make the design process user-friendly, and to enable design of an LQG controller for one with a limited control engineering background. The user is asked to manipulate the GUI sliders and radio buttons to watch the antenna performance. Simple rules are given at the GUI display.

A review of existing and potential computer user interfaces for modern radiology.

PubMed

Iannessi, Antoine; Marcy, Pierre-Yves; Clatz, Olivier; Bertrand, Anne-Sophie; Sugimoto, Maki

2018-05-16

The digitalization of modern imaging has led radiologists to become very familiar with computers and their user interfaces (UI). New options for display and command offer expanded possibilities, but the mouse and keyboard remain the most commonly utilized, for usability reasons. In this work, we review and discuss different UI and their possible application in radiology. We consider two-dimensional and three-dimensional imaging displays in the context of interventional radiology, and discuss interest in touchscreens, kinetic sensors, eye detection, and augmented or virtual reality. We show that UI design specifically for radiologists is key for future use and adoption of such new interfaces. Next-generation UI must fulfil professional needs, while considering contextual constraints. • The mouse and keyboard remain the most utilized user interfaces for radiologists. • Touchscreen, holographic, kinetic sensors and eye tracking offer new possibilities for interaction. • 3D and 2D imaging require specific user interfaces. • Holographic display and augmented reality provide a third dimension to volume imaging. • Good usability is essential for adoption of new user interfaces by radiologists.

OPTIGRAMI V2 user's guide

Treesearch

Penny S. Lawson; R. Edward Thomas; Elizabeth S Walker

1996-01-01

OPTIGRAMI V2 is a computer program available for IBM persaonl computer with 80286 and higher processors. OPTIGRAMI V2 determines the least-cost lumber grade mix required to produce a given cutting order for clear parts from rough lumber of known grades in a crosscut-first rough mill operation. It is a user-friendly integrated application that includes optimization...

Determinants of user acceptance of a specific social platform for older adults: An empirical examination of user interface characteristics and behavioral intention

PubMed Central

Chang, Hsien-Tsung; Chen, Yan-Jiun; Chang, Yung-Sheng

2017-01-01

The use of the Internet and social applications has many benefits for the elderly, but numerous investigations have shown that the elderly do not perceive online social networks as a friendly social environment. Therefore, TreeIt, a social application specifically designed for the elderly, was developed for this study. In the TreeIt application, seven mechanisms promoting social interaction were designed to allow older adults to use social networking sites (SNSs) to increase social connection, maintain the intensity of social connections and strengthen social experience. This study’s main objective was to investigate how user interface design affects older people’s intention and attitude related to using SNSs. Fourteen user interface evaluation heuristics proposed by Zhang et al. were adopted as the criteria to assess user interface usability and further grouped into three categories: system support, user interface design and navigation. The technology acceptance model was adopted to assess older people’s intention and attitude related to using SNSs. One hundred and one elderly persons were enrolled in this study as subjects, and the results showed that all of the hypotheses proposed in this study were valid: system support and perceived usefulness had a significant effect on behavioral intention; user interface design and perceived ease of use were positively correlated with perceived usefulness; and navigation exerted an influence on perceived ease of use. The results of this study are valuable for the future development of social applications for the elderly. PMID:28837566

Entrez Neuron RDFa: a pragmatic Semantic Web application for data integration in neuroscience research

PubMed Central

Samwald, Matthias; Lim, Ernest; Masiar, Peter; Marenco, Luis; Chen, Huajun; Morse, Thomas; Mutalik, Pradeep; Shepherd, Gordon; Miller, Perry; Cheung, Kei-Hoi

2013-01-01

The amount of biomedical data available in Semantic Web formats has been rapidly growing in recent years. While these formats are machine-friendly, user-friendly web interfaces allowing easy querying of these data are typically lacking. We present “Entrez Neuron”, a pilot neuron-centric interface that allows for keyword-based queries against a coherent repository of OWL ontologies. These ontologies describe neuronal structures, physiology, mathematical models and microscopy images. The returned query results are organized hierarchically according to brain architecture. Where possible, the application makes use of entities from the Open Biomedical Ontologies (OBO) and the ‘HCLS knowledgebase’ developed by the W3C Interest Group for Health Care and Life Science. It makes use of the emerging RDFa standard to embed ontology fragments and semantic annotations within its HTML-based user interface. The application and underlying ontologies demonstrates how Semantic Web technologies can be used for information integration within a curated information repository and between curated information repositories. It also demonstrates how information integration can be accomplished on the client side, through simple copying and pasting of portions of documents that contain RDFa markup. PMID:19745321

Virtual button interface

DOEpatents

Jones, J.S.

1999-01-12

An apparatus and method of issuing commands to a computer by a user interfacing with a virtual reality environment are disclosed. To issue a command, the user directs gaze at a virtual button within the virtual reality environment, causing a perceptible change in the virtual button, which then sends a command corresponding to the virtual button to the computer, optionally after a confirming action is performed by the user, such as depressing a thumb switch. 4 figs.

The Digital Shoreline Analysis System (DSAS) Version 4.0 - An ArcGIS extension for calculating shoreline change

USGS Publications Warehouse

Thieler, E. Robert; Himmelstoss, Emily A.; Zichichi, Jessica L.; Ergul, Ayhan

2009-01-01

The Digital Shoreline Analysis System (DSAS) version 4.0 is a software extension to ESRI ArcGIS v.9.2 and above that enables a user to calculate shoreline rate-of-change statistics from multiple historic shoreline positions. A user-friendly interface of simple buttons and menus guides the user through the major steps of shoreline change analysis. Components of the extension and user guide include (1) instruction on the proper way to define a reference baseline for measurements, (2) automated and manual generation of measurement transects and metadata based on user-specified parameters, and (3) output of calculated rates of shoreline change and other statistical information. DSAS computes shoreline rates of change using four different methods: (1) endpoint rate, (2) simple linear regression, (3) weighted linear regression, and (4) least median of squares. The standard error, correlation coefficient, and confidence interval are also computed for the simple and weighted linear-regression methods. The results of all rate calculations are output to a table that can be linked to the transect file by a common attribute field. DSAS is intended to facilitate the shoreline change-calculation process and to provide rate-of-change information and the statistical data necessary to establish the reliability of the calculated results. The software is also suitable for any generic application that calculates positional change over time, such as assessing rates of change of glacier limits in sequential aerial photos, river edge boundaries, land-cover changes, and so on.

A computerized system based on an alternative pulse echo immersion technique for acoustic characterization of non-porous solid tissue mimicking materials

NASA Astrophysics Data System (ADS)

Nazihah Mat Daud, Anis; Jaafar, Rosly; Kadri Ayop, Shahrul; Supar Rohani, Md

2018-04-01

This paper discusses the development of a computerized acoustic characterization system of non-porous solid tissue mimicking materials. This system employs an alternative pulse echo immersion technique and consists of a pulser/receiver generator, a transducer used as both a transmitter and a receiver, a digital oscilloscope, and a personal computer with a custom-developed program installed. The program was developed on the LabVIEW 2012 platform and comprises two main components, a user interface and a block diagram. The user interface consists of three panels: a signal acquisition and selection panel, a display panel, and a calculation panel. The block diagram comprises four blocks: a signal acquisition block, a peak signal analysis block, an acoustic properties calculation and display block, and an additional block. Interestingly, the system can be operated in both online and offline modes. For the online mode, the measurements are performed by connecting the system with a Rigol DS2000 Series digital oscilloscope. In contrast, the measurements are carried out by processing the saved data on the computer for the offline mode. The accuracy and consistency of the developed system was validated by a KB-Aerotech Alpha Series transducer with 5 MHz center frequency and a Rigol DS2202 two-channel 200 MHz 2 GSa s-1 digital oscilloscope, based on the measurement of the acoustic properties of three poly(methyl methacrylate) samples immersed in a medium at a temperature of (24.0  ±  0.1) °C. The findings indicated that the accuracy and consistency of the developed system was exceptionally high, within a 1.04% margin of error compared to the reference values. As such, this computerized system can be efficiently used for the acoustic characterization of non-porous solid tissues, given its spontaneous display of results, user-friendly interface, and convenient hardware connection.

The Ndynamics package—Numerical analysis of dynamical systems and the fractal dimension of boundaries

NASA Astrophysics Data System (ADS)

Avellar, J.; Duarte, L. G. S.; da Mota, L. A. C. P.; de Melo, N.; Skea, J. E. F.

2012-09-01

A set of Maple routines is presented, fully compatible with the new releases of Maple (14 and higher). The package deals with the numerical evolution of dynamical systems and provide flexible plotting of the results. The package also brings an initial conditions generator, a numerical solver manager, and a focusing set of routines that allow for better analysis of the graphical display of the results. The novelty that the package presents an optional C interface is maintained. This allows for fast numerical integration, even for the totally inexperienced Maple user, without any C expertise being required. Finally, the package provides the routines to calculate the fractal dimension of boundaries (via box counting). New version program summary Program Title: Ndynamics Catalogue identifier: %Leave blank, supplied by Elsevier. Licensing provisions: no. Programming language: Maple, C. Computer: Intel(R) Core(TM) i3 CPU M330 @ 2.13 GHz. Operating system: Windows 7. RAM: 3.0 GB Keywords: Dynamical systems, Box counting, Fractal dimension, Symbolic computation, Differential equations, Maple. Classification: 4.3. Catalogue identifier of previous version: ADKH_v1_0. Journal reference of previous version: Comput. Phys. Commun. 119 (1999) 256. Does the new version supersede the previous version?: Yes. Nature of problem Computation and plotting of numerical solutions of dynamical systems and the determination of the fractal dimension of the boundaries. Solution method The default method of integration is a fifth-order Runge-Kutta scheme, but any method of integration present on the Maple system is available via an argument when calling the routine. A box counting [1] method is used to calculate the fractal dimension [2] of the boundaries. Reasons for the new version The Ndynamics package met a demand of our research community for a flexible and friendly environment for analyzing dynamical systems. All the user has to do is create his/her own Maple session, with the system to be studied, and use the commands on the package to (for instance) calculate the fractal dimension of a certain boundary, without knowing or worrying about a single line of C programming. So the package combines the flexibility and friendly aspect of Maple with the fast and robust numerical integration of the compiled (for example C) basin. The package is old, but the problems it was designed to dealt with are still there. Since Maple evolved, the package stopped working, and we felt compelled to produce this version, fully compatible with the latest version of Maple, to make it again available to the Maple user. Summary of revisions Deprecated Maple Packages and Commands: Paraphrasing the Maple in-built help files, "Some Maple commands and packages are deprecated. A command (or package) is deprecated when its functionality has been replaced by an improved implementation. The newer command is said to supersede the older one, and use of the newer command is strongly recommended". So, we have examined our code to see if some of these occurrences could be dangerous for it. For example, the "readlib" command is unnecessary, and we have removed its occurrences from our code. We have checked and changed all the necessary commands in order for us to be safe in respect to danger from this source. Another change we had to make was related to the tools we have implemented in order to use the interface for performing the numerical integration in C, externally, via the use of the Maple command "ssystem". In the past, we had used, for the external C integration, the DJGPP system. But now we present the package with (free) Borland distribution. The compilation and compiling commands are now slightly changed. For example, to compile only, we had used "gcc-c"; now, we use "bcc32-c", etc. All this installation (Borland) is explained on a "README" file we are submitting here to help the potential user. Restrictions Besides the inherent restrictions of numerical integration methods, this version of the package only deals with systems of first-order differential equations. Unusual features This package provides user-friendly software tools for analyzing the character of a dynamical system, whether it displays chaotic behaviour, and so on. Options within the package allow the user to specify characteristics that separate the trajectories into families of curves. In conjunction with the facilities for altering the user's viewpoint, this provides a graphical interface for the speedy and easy identification of regions with interesting dynamics. An unusual characteristic of the package is its interface for performing the numerical integrations in C using a fifth-order Runge-Kutta method (default). This potentially improves the speed of the numerical integration by some orders of magnitude and, in cases where it is necessary to calculate thousands of graphs in regions of difficult integration, this feature is very desirable. Besides that tool, somewhat more experienced users can produce their own C integrator and, by using the commands available in the package, use it as the C integrator provided with the package as long as the new integrator manages the input and output in the same format as the default one does. Running time This depends strongly on the dynamical system. With an Intel® Core™ i3 CPU M330 @ 2.13 GHz, the integration of 50 graphs, for a system of two first-order equations, typically takes less than a second to run (with the C integration interface). Without the C interface, it takes a few seconds. In order to calculate the fractal dimension, where we typically use 10,000 points to integrate, using the C interface it takes from 20 to 30 s. Without the C interface, it becomes really impractical, taking, sometimes, for the same case, almost an hour. For some cases, it takes many hours.

Hazardous materials information hotline using System 2000

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

Brower, J.E.; Fuchel, K.

1984-04-30

The Center for Assessment of Chemical and Physical Hazards (CACPH) at Brookhaven National Laboratory (BNL) has developed a computer hotline service for the Department of Energy (DOE) and its contractors. This service provides access to health and safety information for over 800 chemicals and hazardous materials. The data base uses System 2000 on a CDC 6600 and provides information on the chemical name and its synonyms, 17 categories of health and safety information, composition of chemical mixtures, categories of chemicals, use and hazards, and physical, chemical and toxicity attributes. In order to make this information available to people unfamiliar withmore » System 2000, a user-friendly interface was developed using a Fortran PLEX Program. 1 reference, 1 figure.« less

Integrated web-based viewing and secure remote access to a clinical data repository and diverse clinical systems.

PubMed

Duncan, R G; Saperia, D; Dulbandzhyan, R; Shabot, M M; Polaschek, J X; Jones, D T

2001-01-01

The advent of the World-Wide-Web protocols and client-server technology has made it easy to build low-cost, user-friendly, platform-independent graphical user interfaces to health information systems and to integrate the presentation of data from multiple systems. The authors describe a Web interface for a clinical data repository (CDR) that was moved from concept to production status in less than six months using a rapid prototyping approach, multi-disciplinary development team, and off-the-shelf hardware and software. The system has since been expanded to provide an integrated display of clinical data from nearly 20 disparate information systems.

A novel device for head gesture measurement system in combination with eye-controlled human machine interface

NASA Astrophysics Data System (ADS)

Lin, Chern-Sheng; Ho, Chien-Wa; Chang, Kai-Chieh; Hung, San-Shan; Shei, Hung-Jung; Yeh, Mau-Shiun

2006-06-01

This study describes the design and combination of an eye-controlled and a head-controlled human-machine interface system. This system is a highly effective human-machine interface, detecting head movement by changing positions and numbers of light sources on the head. When the users utilize the head-mounted display to browse a computer screen, the system will catch the images of the user's eyes with CCD cameras, which can also measure the angle and position of the light sources. In the eye-tracking system, the program in the computer will locate each center point of the pupils in the images, and record the information on moving traces and pupil diameters. In the head gesture measurement system, the user wears a double-source eyeglass frame, so the system catches images of the user's head by using a CCD camera in front of the user. The computer program will locate the center point of the head, transferring it to the screen coordinates, and then the user can control the cursor by head motions. We combine the eye-controlled and head-controlled human-machine interface system for the virtual reality applications.

MIGS-GPU: Microarray Image Gridding and Segmentation on the GPU.

PubMed

Katsigiannis, Stamos; Zacharia, Eleni; Maroulis, Dimitris

2017-05-01

Complementary DNA (cDNA) microarray is a powerful tool for simultaneously studying the expression level of thousands of genes. Nevertheless, the analysis of microarray images remains an arduous and challenging task due to the poor quality of the images that often suffer from noise, artifacts, and uneven background. In this study, the MIGS-GPU [Microarray Image Gridding and Segmentation on Graphics Processing Unit (GPU)] software for gridding and segmenting microarray images is presented. MIGS-GPU's computations are performed on the GPU by means of the compute unified device architecture (CUDA) in order to achieve fast performance and increase the utilization of available system resources. Evaluation on both real and synthetic cDNA microarray images showed that MIGS-GPU provides better performance than state-of-the-art alternatives, while the proposed GPU implementation achieves significantly lower computational times compared to the respective CPU approaches. Consequently, MIGS-GPU can be an advantageous and useful tool for biomedical laboratories, offering a user-friendly interface that requires minimum input in order to run.

User-Friendly Interface Developed for a Web-Based Service for SpaceCAL Emulations

NASA Technical Reports Server (NTRS)

Liszka, Kathy J.; Holtz, Allen P.

2004-01-01

A team at the NASA Glenn Research Center is developing a Space Communications Architecture Laboratory (SpaceCAL) for protocol development activities for coordinated satellite missions. SpaceCAL will provide a multiuser, distributed system to emulate space-based Internet architectures, backbone networks, formation clusters, and constellations. As part of a new effort in 2003, building blocks are being defined for an open distributed system to make the satellite emulation test bed accessible through an Internet connection. The first step in creating a Web-based service to control the emulation remotely is providing a user-friendly interface for encoding the data into a well-formed and complete Extensible Markup Language (XML) document. XML provides coding that allows data to be transferred between dissimilar systems. Scenario specifications include control parameters, network routes, interface bandwidths, delay, and bit error rate. Specifications for all satellite, instruments, and ground stations in a given scenario are also included in the XML document. For the SpaceCAL emulation, the XML document can be created using XForms, a Webbased forms language for data collection. Contrary to older forms technology, the interactive user interface makes the science prevalent, not the data representation. Required versus optional input fields, default values, automatic calculations, data validation, and reuse will help researchers quickly and accurately define missions. XForms can apply any XML schema defined for the test mission to validate data before forwarding it to the emulation facility. New instrument definitions, facilities, and mission types can be added to the existing schema. The first prototype user interface incorporates components for interactive input and form processing. Internet address, data rate, and the location of the facility are implemented with basic form controls with default values provided for convenience and efficiency using basic XForms operations. Because different emulation scenarios will vary widely in their component structure, more complex operations are used to add and delete facilities.

The simple rules of social contagion.

PubMed

Hodas, Nathan O; Lerman, Kristina

2014-03-11

It is commonly believed that information spreads between individuals like a pathogen, with each exposure by an informed friend potentially resulting in a naive individual becoming infected. However, empirical studies of social media suggest that individual response to repeated exposure to information is far more complex. As a proxy for intervention experiments, we compare user responses to multiple exposures on two different social media sites, Twitter and Digg. We show that the position of exposing messages on the user-interface strongly affects social contagion. Accounting for this visibility significantly simplifies the dynamics of social contagion. The likelihood an individual will spread information increases monotonically with exposure, while explicit feedback about how many friends have previously spread it increases the likelihood of a response. We provide a framework for unifying information visibility, divided attention, and explicit social feedback to predict the temporal dynamics of user behavior.

The Simple Rules of Social Contagion

NASA Astrophysics Data System (ADS)

Hodas, Nathan O.; Lerman, Kristina

2014-03-01

It is commonly believed that information spreads between individuals like a pathogen, with each exposure by an informed friend potentially resulting in a naive individual becoming infected. However, empirical studies of social media suggest that individual response to repeated exposure to information is far more complex. As a proxy for intervention experiments, we compare user responses to multiple exposures on two different social media sites, Twitter and Digg. We show that the position of exposing messages on the user-interface strongly affects social contagion. Accounting for this visibility significantly simplifies the dynamics of social contagion. The likelihood an individual will spread information increases monotonically with exposure, while explicit feedback about how many friends have previously spread it increases the likelihood of a response. We provide a framework for unifying information visibility, divided attention, and explicit social feedback to predict the temporal dynamics of user behavior.

Interactive Light Stimulus Generation with High Performance Real-Time Image Processing and Simple Scripting.

PubMed

Szécsi, László; Kacsó, Ágota; Zeck, Günther; Hantz, Péter

2017-01-01

Light stimulation with precise and complex spatial and temporal modulation is demanded by a series of research fields like visual neuroscience, optogenetics, ophthalmology, and visual psychophysics. We developed a user-friendly and flexible stimulus generating framework (GEARS GPU-based Eye And Retina Stimulation Software), which offers access to GPU computing power, and allows interactive modification of stimulus parameters during experiments. Furthermore, it has built-in support for driving external equipment, as well as for synchronization tasks, via USB ports. The use of GEARS does not require elaborate programming skills. The necessary scripting is visually aided by an intuitive interface, while the details of the underlying software and hardware components remain hidden. Internally, the software is a C++/Python hybrid using OpenGL graphics. Computations are performed on the GPU, and are defined in the GLSL shading language. However, all GPU settings, including the GPU shader programs, are automatically generated by GEARS. This is configured through a method encountered in game programming, which allows high flexibility: stimuli are straightforwardly composed using a broad library of basic components. Stimulus rendering is implemented solely in C++, therefore intermediary libraries for interfacing could be omitted. This enables the program to perform computationally demanding tasks like en-masse random number generation or real-time image processing by local and global operations.

User Friendly Processing of Sediment CT Data: Software and Application in High Resolution Non-Destructive Sediment Core Data Sets

NASA Astrophysics Data System (ADS)

Reilly, B. T.; Stoner, J. S.; Wiest, J.; Abbott, M. B.; Francus, P.; Lapointe, F.

2015-12-01

Computed Tomography (CT) of sediment cores allow for high resolution images, three dimensional volumes, and down core profiles, generated through the attenuation of X-rays as a function of density and atomic number. When using a medical CT-Scanner, these quantitative data are stored in pixels using the Hounsfield scale, which are relative to the attenuation of X-rays in water and air at standard temperature and pressure. Here we present MATLAB based software specifically designed for sedimentary applications with a user friendly graphical interface to process DICOM files and stitch overlapping CT scans. For visualization, the software allows easy generation of core slice images with grayscale and false color relative to a user defined Hounsfield number range. For comparison to other high resolution non-destructive methods, down core Hounsfield number profiles are extracted using a method robust to coring imperfections, like deformation, bowing, gaps, and gas expansion. We demonstrate the usefulness of this technique with lacustrine sediment cores from the Western United States and Canadian High Arctic, including Fish Lake, Oregon, and Sawtooth Lake, Ellesmere Island. These sites represent two different depositional environments and provide examples for a variety of common coring defects and lithologies. The Hounsfield profiles and images can be used in combination with other high resolution data sets, including sediment magnetic parameters, XRF core scans and many other types of data, to provide unique insights into how lithology influences paleoenvironmental and paleomagnetic records and their interpretations.

Development of a User Interface for a Regression Analysis Software Tool

NASA Technical Reports Server (NTRS)

Ulbrich, Norbert Manfred; Volden, Thomas R.

2010-01-01

An easy-to -use user interface was implemented in a highly automated regression analysis tool. The user interface was developed from the start to run on computers that use the Windows, Macintosh, Linux, or UNIX operating system. Many user interface features were specifically designed such that a novice or inexperienced user can apply the regression analysis tool with confidence. Therefore, the user interface s design minimizes interactive input from the user. In addition, reasonable default combinations are assigned to those analysis settings that influence the outcome of the regression analysis. These default combinations will lead to a successful regression analysis result for most experimental data sets. The user interface comes in two versions. The text user interface version is used for the ongoing development of the regression analysis tool. The official release of the regression analysis tool, on the other hand, has a graphical user interface that is more efficient to use. This graphical user interface displays all input file names, output file names, and analysis settings for a specific software application mode on a single screen which makes it easier to generate reliable analysis results and to perform input parameter studies. An object-oriented approach was used for the development of the graphical user interface. This choice keeps future software maintenance costs to a reasonable limit. Examples of both the text user interface and graphical user interface are discussed in order to illustrate the user interface s overall design approach.

P43-S Computational Biology Applications Suite for High-Performance Computing (BioHPC.net)

PubMed Central

Pillardy, J.

2007-01-01

One of the challenges of high-performance computing (HPC) is user accessibility. At the Cornell University Computational Biology Service Unit, which is also a Microsoft HPC institute, we have developed a computational biology application suite that allows researchers from biological laboratories to submit their jobs to the parallel cluster through an easy-to-use Web interface. Through this system, we are providing users with popular bioinformatics tools including BLAST, HMMER, InterproScan, and MrBayes. The system is flexible and can be easily customized to include other software. It is also scalable; the installation on our servers currently processes approximately 8500 job submissions per year, many of them requiring massively parallel computations. It also has a built-in user management system, which can limit software and/or database access to specified users. TAIR, the major database of the plant model organism Arabidopsis, and SGN, the international tomato genome database, are both using our system for storage and data analysis. The system consists of a Web server running the interface (ASP.NET C#), Microsoft SQL server (ADO.NET), compute cluster running Microsoft Windows, ftp server, and file server. Users can interact with their jobs and data via a Web browser, ftp, or e-mail. The interface is accessible at http://cbsuapps.tc.cornell.edu/.

WinPSSP : a revamp of the computer program PSSP and its performance solving the crystal structures of small organic compounds and solids of biological and pharmaceutical interest

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

Pagola, Silvina; Polymeros, Alekos; Kourkoumelis, Nikolaos

2017-02-01

The direct-space methods softwarePowder Structure Solution Program(PSSP) [Pagola & Stephens (2010).J. Appl. Cryst.43, 370–376] has been migrated to the Windows OS and the code has been optimized for fast runs.WinPSSPis a user-friendly graphical user interface that allows the input of preliminary crystal structure information, integrated intensities of the reflections and FWHM, the definition of structural parameters and a simulated annealing schedule, and the visualization of the calculated and experimental diffraction data overlaid for each individual solution. The solutions are reported as filename.cif files, which can be used to analyze packing motifs and chemical bonding, and to input the atomic coordinatesmore » into the Rietveld analysis softwareGSAS. WinPSSPperformance in straightforward crystal structure determinations has been evaluated using 18 molecular solids with 6–20 degrees of freedom. The free-distribution program as well as multimedia tutorials can be accessed at http://users.uoi.gr/nkourkou/winpssp/.« less

Young Children's Skill in Using a Mouse to Control a Graphical Computer Interface.

ERIC Educational Resources Information Center

Crook, Charles

1992-01-01

Describes a study that investigated the performance of preschoolers and children in the first three years of formal education on tasks that involved skills using a mouse-based control of a graphical computer interface. The children's performance is compared with that of novice adult users and expert users. (five references) (LRW)

Touch in Computer-Mediated Environments: An Analysis of Online Shoppers' Touch-Interface User Experiences

ERIC Educational Resources Information Center

Chung, Sorim

2016-01-01

Over the past few years, one of the most fundamental changes in current computer-mediated environments has been input devices, moving from mouse devices to touch interfaces. However, most studies of online retailing have not considered device environments as retail cues that could influence users' shopping behavior. In this research, I examine the…

The Use of Spatialized Speech in Auditory Interfaces for Computer Users Who Are Visually Impaired

ERIC Educational Resources Information Center

Sodnik, Jaka; Jakus, Grega; Tomazic, Saso

2012-01-01

Introduction: This article reports on a study that explored the benefits and drawbacks of using spatially positioned synthesized speech in auditory interfaces for computer users who are visually impaired (that is, are blind or have low vision). The study was a practical application of such systems--an enhanced word processing application compared…

Designing User-Computer Dialogues: Basic Principles and Guidelines.

ERIC Educational Resources Information Center

Harrell, Thomas H.

This discussion of the design of computerized psychological assessment or testing instruments stresses the importance of the well-designed computer-user interface. The principles underlying the three main functional elements of computer-user dialogue--data entry, data display, and sequential control--are discussed, and basic guidelines derived…

A new JAVA interface implementation of THESIAS: testing haplotype effects in association studies.

PubMed

Tregouet, D A; Garelle, V

2007-04-15

THESIAS (Testing Haplotype EffectS In Association Studies) is a popular software for carrying haplotype association analysis in unrelated individuals. In addition to the command line interface, a graphical JAVA interface is now proposed allowing one to run THESIAS in a user-friendly manner. Besides, new functionalities have been added to THESIAS including the possibility to analyze polychotomous phenotype and X-linked polymorphisms. The software package including documentation and example data files is freely available at http://genecanvas.ecgene.net. The source codes are also available upon request.

You've Come a Long Way, Baby, but...

ERIC Educational Resources Information Center

Fayen, Emily Gallup

An online library system is an example of a complex computer system in that it supports a variety of users, both patrons and staff, and is made up of many intricate programs with complex relationships among them. Certain features are essential to a user friendly system: (1) users cannot get lost in the system; (2) users cannot enter illegal…

Human-computer interface

DOEpatents

Anderson, Thomas G.

2004-12-21

The present invention provides a method of human-computer interfacing. Force feedback allows intuitive navigation and control near a boundary between regions in a computer-represented space. For example, the method allows a user to interact with a virtual craft, then push through the windshield of the craft to interact with the virtual world surrounding the craft. As another example, the method allows a user to feel transitions between different control domains of a computer representation of a space. The method can provide for force feedback that increases as a user's locus of interaction moves near a boundary, then perceptibly changes (e.g., abruptly drops or changes direction) when the boundary is traversed.

Customization of user interfaces to reduce errors and enhance user acceptance.

PubMed

Burkolter, Dina; Weyers, Benjamin; Kluge, Annette; Luther, Wolfram

2014-03-01

Customization is assumed to reduce error and increase user acceptance in the human-machine relation. Reconfiguration gives the operator the option to customize a user interface according to his or her own preferences. An experimental study with 72 computer science students using a simulated process control task was conducted. The reconfiguration group (RG) interactively reconfigured their user interfaces and used the reconfigured user interface in the subsequent test whereas the control group (CG) used a default user interface. Results showed significantly lower error rates and higher acceptance of the RG compared to the CG while there were no significant differences between the groups regarding situation awareness and mental workload. Reconfiguration seems to be promising and therefore warrants further exploration. Copyright © 2013 Elsevier Ltd and The Ergonomics Society. All rights reserved.

CAT 2 - An improved version of Cryogenic Analysis Tools for online and offline monitoring and analysis of large size cryostats

NASA Astrophysics Data System (ADS)

Pagliarone, C. E.; Uttaro, S.; Cappelli, L.; Fallone, M.; Kartal, S.

2017-02-01

CAT, Cryogenic Analysis Tools is a software package developed using LabVIEW and ROOT environments to analyze the performances of large size cryostats, where many parameters, input, and control variables need to be acquired and studied at the same time. The present paper describes how CAT works and which are the main improvements achieved in the new version: CAT 2. New Graphical User Interfaces have been developed in order to make the use of the full package more user-friendly as well as a process of resource optimization has been carried out. The offline analysis of the full cryostat performances is available both trough ROOT line command interface band also by using the new graphical interfaces.

Design guidelines for the use of audio cues in computer interfaces

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

Sumikawa, D.A.; Blattner, M.M.; Joy, K.I.

1985-07-01

A logical next step in the evolution of the computer-user interface is the incorporation of sound thereby using our senses of ''hearing'' in our communication with the computer. This allows our visual and auditory capacities to work in unison leading to a more effective and efficient interpretation of information received from the computer than by sight alone. In this paper we examine earcons, which are audio cues, used in the computer-user interface to provide information and feedback to the user about computer entities (these include messages and functions, as well as states and labels). The material in this paper ismore » part of a larger study that recommends guidelines for the design and use of audio cues in the computer-user interface. The complete work examines the disciplines of music, psychology, communication theory, advertising, and psychoacoustics to discover how sound is utilized and analyzed in those areas. The resulting information is organized according to the theory of semiotics, the theory of signs, into the syntax, semantics, and pragmatics of communication by sound. Here we present design guidelines for the syntax of earcons. Earcons are constructed from motives, short sequences of notes with a specific rhythm and pitch, embellished by timbre, dynamics, and register. Compound earcons and family earcons are introduced. These are related motives that serve to identify a family of related cues. Examples of earcons are given.« less

WHATIF: an open-source desktop application for extraction and management of the incidental findings from next-generation sequencing variant data

PubMed Central

Ye, Zhan; Kadolph, Christopher; Strenn, Robert; Wall, Daniel; McPherson, Elizabeth; Lin, Simon

2015-01-01

Background Identification and evaluation of incidental findings in patients following whole exome (WGS) or whole genome sequencing (WGS) is challenging for both practicing physicians and researchers. The American College of Medical Genetics and Genomics (ACMG) recently recommended a list of reportable incidental genetic findings. However, no informatics tools are currently available to support evaluation of incidental findings in next-generation sequencing data. Methods The Wisconsin Hierarchical Analysis Tool for Incidental Findings (WHATIF), was developed as a stand-alone Windows-based desktop executable, to support the interactive analysis of incidental findings in the context of the ACMG recommendations. WHATIF integrates the European Bioinformatics Institute Variant Effect Predictor (VEP) tool for biological interpretation and the National Center for Biotechnology Information ClinVar tool for clinical interpretation. Results An open-source desktop program was created to annotate incidental findings and present the results with a user-friendly interface. Further, a meaningful index (WHATIF Index) was devised for each gene to facilitate ranking of the relative importance of the variants and estimate the potential workload associated with further evaluation of the variants. Our WHATIF application is available at: http://tinyurl.com/WHATIF-SOFTWARE Conclusions The WHATIF application offers a user-friendly interface and allows users to investigate the extracted variant information efficiently and intuitively while always accessing the up to date information on variants via application programming interfaces (API) connections. WHATIF’s highly flexible design and straightforward implementation aids users in customizing the source code to meet their own special needs. PMID:25890833

Developing A Web-based User Interface for Semantic Information Retrieval

NASA Technical Reports Server (NTRS)

Berrios, Daniel C.; Keller, Richard M.

2003-01-01

While there are now a number of languages and frameworks that enable computer-based systems to search stored data semantically, the optimal design for effective user interfaces for such systems is still uncle ar. Such interfaces should mask unnecessary query detail from users, yet still allow them to build queries of arbitrary complexity without significant restrictions. We developed a user interface supporting s emantic query generation for Semanticorganizer, a tool used by scient ists and engineers at NASA to construct networks of knowledge and dat a. Through this interface users can select node types, node attribute s and node links to build ad-hoc semantic queries for searching the S emanticOrganizer network.

CLIPS application user interface for the PC

NASA Technical Reports Server (NTRS)

Jenkins, Jim; Holbrook, Rebecca; Shewhart, Mark; Crouse, Joey; Yarost, Stuart

1991-01-01

The majority of applications that utilize expert system development programs for their knowledge representation and inferencing capability require some form of interface with the end user. This interface is more than likely an interaction through the computer screen. When building an application the user interface can prove to be the most difficult and time consuming aspect to program. Commercial products currently exist which address this issue. To keep pace C Language Integrated Production System (CLIPS) will need to find a solution for their lack of an easy to use Application User Interface (AUI). This paper represents a survey of the DoD CLIPS' user community and provides the backbone of a possible solution.

User interface issues in supporting human-computer integrated scheduling

NASA Technical Reports Server (NTRS)

Cooper, Lynne P.; Biefeld, Eric W.

1991-01-01

Explored here is the user interface problems encountered with the Operations Missions Planner (OMP) project at the Jet Propulsion Laboratory (JPL). OMP uses a unique iterative approach to planning that places additional requirements on the user interface, particularly to support system development and maintenance. These requirements are necessary to support the concepts of heuristically controlled search, in-progress assessment, and iterative refinement of the schedule. The techniques used to address the OMP interface needs are given.

Usability Evaluation Methods for Gesture-Based Games: A Systematic Review

PubMed Central

Simor, Fernando Winckler; Brum, Manoela Rogofski; Schmidt, Jaison Dairon Ebertz; De Marchi, Ana Carolina Bertoletti

2016-01-01

Background Gestural interaction systems are increasingly being used, mainly in games, expanding the idea of entertainment and providing experiences with the purpose of promoting better physical and/or mental health. Therefore, it is necessary to establish mechanisms for evaluating the usability of these interfaces, which make gestures the basis of interaction, to achieve a balance between functionality and ease of use. Objective This study aims to present the results of a systematic review focused on usability evaluation methods for gesture-based games, considering devices with motion-sensing capability. We considered the usability methods used, the common interface issues, and the strategies adopted to build good gesture-based games. Methods The research was centered on four electronic databases: IEEE, Association for Computing Machinery (ACM), Springer, and Science Direct from September 4 to 21, 2015. Within 1427 studies evaluated, 10 matched the eligibility criteria. As a requirement, we considered studies about gesture-based games, Kinect and/or Wii as devices, and the use of a usability method to evaluate the user interface. Results In the 10 studies found, there was no standardization in the methods because they considered diverse analysis variables. Heterogeneously, authors used different instruments to evaluate gesture-based interfaces and no default approach was proposed. Questionnaires were the most used instruments (70%, 7/10), followed by interviews (30%, 3/10), and observation and video recording (20%, 2/10). Moreover, 60% (6/10) of the studies used gesture-based serious games to evaluate the performance of elderly participants in rehabilitation tasks. This highlights the need for creating an evaluation protocol for older adults to provide a user-friendly interface according to the user’s age and limitations. Conclusions Through this study, we conclude this field is in need of a usability evaluation method for serious games, especially games for older adults, and that the definition of a methodology and a test protocol may offer the user more comfort, welfare, and confidence. PMID:27702737

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

NASA Astrophysics Data System (ADS)

Kadow, C.; Illing, S.; Kunst, O.; Cubasch, U.

2014-12-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

Image Understanding and Intelligent Parallel Systems

DTIC Science & Technology

1991-05-09

a common user interface for the interactive , graphical manipulation of those histories, and...Circuits and Systems, August 1987. Yap, S.-K. and M.L. Scott, "PenGuin: A language for reactive graphical user interface programming," to appear, INTERACT 󈨞, Cambridge, United Kingdom, 1990. 74 ...of up to a factor of 100 over single-workstation implementations. User interfaces to large multiprocessor computers are a difficult issue addressed

Tavaxy: integrating Taverna and Galaxy workflows with cloud computing support.

PubMed

Abouelhoda, Mohamed; Issa, Shadi Alaa; Ghanem, Moustafa

2012-05-04

Over the past decade the workflow system paradigm has evolved as an efficient and user-friendly approach for developing complex bioinformatics applications. Two popular workflow systems that have gained acceptance by the bioinformatics community are Taverna and Galaxy. Each system has a large user-base and supports an ever-growing repository of application workflows. However, workflows developed for one system cannot be imported and executed easily on the other. The lack of interoperability is due to differences in the models of computation, workflow languages, and architectures of both systems. This lack of interoperability limits sharing of workflows between the user communities and leads to duplication of development efforts. In this paper, we present Tavaxy, a stand-alone system for creating and executing workflows based on using an extensible set of re-usable workflow patterns. Tavaxy offers a set of new features that simplify and enhance the development of sequence analysis applications: It allows the integration of existing Taverna and Galaxy workflows in a single environment, and supports the use of cloud computing capabilities. The integration of existing Taverna and Galaxy workflows is supported seamlessly at both run-time and design-time levels, based on the concepts of hierarchical workflows and workflow patterns. The use of cloud computing in Tavaxy is flexible, where the users can either instantiate the whole system on the cloud, or delegate the execution of certain sub-workflows to the cloud infrastructure. Tavaxy reduces the workflow development cycle by introducing the use of workflow patterns to simplify workflow creation. It enables the re-use and integration of existing (sub-) workflows from Taverna and Galaxy, and allows the creation of hybrid workflows. Its additional features exploit recent advances in high performance cloud computing to cope with the increasing data size and complexity of analysis.The system can be accessed either through a cloud-enabled web-interface or downloaded and installed to run within the user's local environment. All resources related to Tavaxy are available at http://www.tavaxy.org.

DDBJ read annotation pipeline: a cloud computing-based pipeline for high-throughput analysis of next-generation sequencing data.

PubMed

Nagasaki, Hideki; Mochizuki, Takako; Kodama, Yuichi; Saruhashi, Satoshi; Morizaki, Shota; Sugawara, Hideaki; Ohyanagi, Hajime; Kurata, Nori; Okubo, Kousaku; Takagi, Toshihisa; Kaminuma, Eli; Nakamura, Yasukazu

2013-08-01

High-performance next-generation sequencing (NGS) technologies are advancing genomics and molecular biological research. However, the immense amount of sequence data requires computational skills and suitable hardware resources that are a challenge to molecular biologists. The DNA Data Bank of Japan (DDBJ) of the National Institute of Genetics (NIG) has initiated a cloud computing-based analytical pipeline, the DDBJ Read Annotation Pipeline (DDBJ Pipeline), for a high-throughput annotation of NGS reads. The DDBJ Pipeline offers a user-friendly graphical web interface and processes massive NGS datasets using decentralized processing by NIG supercomputers currently free of charge. The proposed pipeline consists of two analysis components: basic analysis for reference genome mapping and de novo assembly and subsequent high-level analysis of structural and functional annotations. Users may smoothly switch between the two components in the pipeline, facilitating web-based operations on a supercomputer for high-throughput data analysis. Moreover, public NGS reads of the DDBJ Sequence Read Archive located on the same supercomputer can be imported into the pipeline through the input of only an accession number. This proposed pipeline will facilitate research by utilizing unified analytical workflows applied to the NGS data. The DDBJ Pipeline is accessible at http://p.ddbj.nig.ac.jp/.

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.

PubMed

Paez-Espino, David; Chen, I-Min A; Palaniappan, Krishna; Ratner, Anna; Chu, Ken; Szeto, Ernest; Pillay, Manoj; Huang, Jinghua; Markowitz, Victor M; Nielsen, Torben; Huntemann, Marcel; K Reddy, T B; Pavlopoulos, Georgios A; Sullivan, Matthew B; Campbell, Barbara J; Chen, Feng; McMahon, Katherine; Hallam, Steve J; Denef, Vincent; Cavicchioli, Ricardo; Caffrey, Sean M; Streit, Wolfgang R; Webster, John; Handley, Kim M; Salekdeh, Ghasem H; Tsesmetzis, Nicolas; Setubal, Joao C; Pope, Phillip B; Liu, Wen-Tso; Rivers, Adam R; Ivanova, Natalia N; Kyrpides, Nikos C

2017-01-04

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from >6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparing with external sequences, thus serving as an essential resource in the viral genomics community. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

DDBJ Read Annotation Pipeline: A Cloud Computing-Based Pipeline for High-Throughput Analysis of Next-Generation Sequencing Data

PubMed Central

Nagasaki, Hideki; Mochizuki, Takako; Kodama, Yuichi; Saruhashi, Satoshi; Morizaki, Shota; Sugawara, Hideaki; Ohyanagi, Hajime; Kurata, Nori; Okubo, Kousaku; Takagi, Toshihisa; Kaminuma, Eli; Nakamura, Yasukazu

2013-01-01

High-performance next-generation sequencing (NGS) technologies are advancing genomics and molecular biological research. However, the immense amount of sequence data requires computational skills and suitable hardware resources that are a challenge to molecular biologists. The DNA Data Bank of Japan (DDBJ) of the National Institute of Genetics (NIG) has initiated a cloud computing-based analytical pipeline, the DDBJ Read Annotation Pipeline (DDBJ Pipeline), for a high-throughput annotation of NGS reads. The DDBJ Pipeline offers a user-friendly graphical web interface and processes massive NGS datasets using decentralized processing by NIG supercomputers currently free of charge. The proposed pipeline consists of two analysis components: basic analysis for reference genome mapping and de novo assembly and subsequent high-level analysis of structural and functional annotations. Users may smoothly switch between the two components in the pipeline, facilitating web-based operations on a supercomputer for high-throughput data analysis. Moreover, public NGS reads of the DDBJ Sequence Read Archive located on the same supercomputer can be imported into the pipeline through the input of only an accession number. This proposed pipeline will facilitate research by utilizing unified analytical workflows applied to the NGS data. The DDBJ Pipeline is accessible at http://p.ddbj.nig.ac.jp/. PMID:23657089

SCNS: a graphical tool for reconstructing executable regulatory networks from single-cell genomic data.

PubMed

Woodhouse, Steven; Piterman, Nir; Wintersteiger, Christoph M; Göttgens, Berthold; Fisher, Jasmin

2018-05-25

Reconstruction of executable mechanistic models from single-cell gene expression data represents a powerful approach to understanding developmental and disease processes. New ambitious efforts like the Human Cell Atlas will soon lead to an explosion of data with potential for uncovering and understanding the regulatory networks which underlie the behaviour of all human cells. In order to take advantage of this data, however, there is a need for general-purpose, user-friendly and efficient computational tools that can be readily used by biologists who do not have specialist computer science knowledge. The Single Cell Network Synthesis toolkit (SCNS) is a general-purpose computational tool for the reconstruction and analysis of executable models from single-cell gene expression data. Through a graphical user interface, SCNS takes single-cell qPCR or RNA-sequencing data taken across a time course, and searches for logical rules that drive transitions from early cell states towards late cell states. Because the resulting reconstructed models are executable, they can be used to make predictions about the effect of specific gene perturbations on the generation of specific lineages. SCNS should be of broad interest to the growing number of researchers working in single-cell genomics and will help further facilitate the generation of valuable mechanistic insights into developmental, homeostatic and disease processes.

imDEV: a graphical user interface to R multivariate analysis tools in Microsoft Excel.

PubMed

Grapov, Dmitry; Newman, John W

2012-09-01

Interactive modules for Data Exploration and Visualization (imDEV) is a Microsoft Excel spreadsheet embedded application providing an integrated environment for the analysis of omics data through a user-friendly interface. Individual modules enables interactive and dynamic analyses of large data by interfacing R's multivariate statistics and highly customizable visualizations with the spreadsheet environment, aiding robust inferences and generating information-rich data visualizations. This tool provides access to multiple comparisons with false discovery correction, hierarchical clustering, principal and independent component analyses, partial least squares regression and discriminant analysis, through an intuitive interface for creating high-quality two- and a three-dimensional visualizations including scatter plot matrices, distribution plots, dendrograms, heat maps, biplots, trellis biplots and correlation networks. Freely available for download at http://sourceforge.net/projects/imdev/. Implemented in R and VBA and supported by Microsoft Excel (2003, 2007 and 2010).

Encoder-Decoder Optimization for Brain-Computer Interfaces

PubMed Central

Merel, Josh; Pianto, Donald M.; Cunningham, John P.; Paninski, Liam

2015-01-01

Neuroprosthetic brain-computer interfaces are systems that decode neural activity into useful control signals for effectors, such as a cursor on a computer screen. It has long been recognized that both the user and decoding system can adapt to increase the accuracy of the end effector. Co-adaptation is the process whereby a user learns to control the system in conjunction with the decoder adapting to learn the user's neural patterns. We provide a mathematical framework for co-adaptation and relate co-adaptation to the joint optimization of the user's control scheme ("encoding model") and the decoding algorithm's parameters. When the assumptions of that framework are respected, co-adaptation cannot yield better performance than that obtainable by an optimal initial choice of fixed decoder, coupled with optimal user learning. For a specific case, we provide numerical methods to obtain such an optimized decoder. We demonstrate our approach in a model brain-computer interface system using an online prosthesis simulator, a simple human-in-the-loop pyschophysics setup which provides a non-invasive simulation of the BCI setting. These experiments support two claims: that users can learn encoders matched to fixed, optimal decoders and that, once learned, our approach yields expected performance advantages. PMID:26029919

Encoder-decoder optimization for brain-computer interfaces.

PubMed

Merel, Josh; Pianto, Donald M; Cunningham, John P; Paninski, Liam

2015-06-01

Neuroprosthetic brain-computer interfaces are systems that decode neural activity into useful control signals for effectors, such as a cursor on a computer screen. It has long been recognized that both the user and decoding system can adapt to increase the accuracy of the end effector. Co-adaptation is the process whereby a user learns to control the system in conjunction with the decoder adapting to learn the user's neural patterns. We provide a mathematical framework for co-adaptation and relate co-adaptation to the joint optimization of the user's control scheme ("encoding model") and the decoding algorithm's parameters. When the assumptions of that framework are respected, co-adaptation cannot yield better performance than that obtainable by an optimal initial choice of fixed decoder, coupled with optimal user learning. For a specific case, we provide numerical methods to obtain such an optimized decoder. We demonstrate our approach in a model brain-computer interface system using an online prosthesis simulator, a simple human-in-the-loop pyschophysics setup which provides a non-invasive simulation of the BCI setting. These experiments support two claims: that users can learn encoders matched to fixed, optimal decoders and that, once learned, our approach yields expected performance advantages.

Analyzing large-scale spiking neural data with HRLAnalysis™

PubMed Central

Thibeault, Corey M.; O'Brien, Michael J.; Srinivasa, Narayan

2014-01-01

The additional capabilities provided by high-performance neural simulation environments and modern computing hardware has allowed for the modeling of increasingly larger spiking neural networks. This is important for exploring more anatomically detailed networks but the corresponding accumulation in data can make analyzing the results of these simulations difficult. This is further compounded by the fact that many existing analysis packages were not developed with large spiking data sets in mind. Presented here is a software suite developed to not only process the increased amount of spike-train data in a reasonable amount of time, but also provide a user friendly Python interface. We describe the design considerations, implementation and features of the HRLAnalysis™ suite. In addition, performance benchmarks demonstrating the speedup of this design compared to a published Python implementation are also presented. The result is a high-performance analysis toolkit that is not only usable and readily extensible, but also straightforward to interface with existing Python modules. PMID:24634655

A unified approach for composite cost reporting and prediction in the ACT program

NASA Technical Reports Server (NTRS)

Freeman, W. Tom; Vosteen, Louis F.; Siddiqi, Shahid

1991-01-01

The Structures Technology Program Office (STPO) at NASA Langley Research Center has held two workshops with representatives from the commercial airframe companies to establish a plan for development of a standard cost reporting format and a cost prediction tool for conceptual and preliminary designers. This paper reviews the findings of the workshop representatives with a plan for implementation of their recommendations. The recommendations of the cost tracking and reporting committee will be implemented by reinstituting the collection of composite part fabrication data in a format similar to the DoD/NASA Structural Composites Fabrication Guide. The process of data collection will be automated by taking advantage of current technology with user friendly computer interfaces and electronic data transmission. Development of a conceptual and preliminary designers' cost prediction model will be initiated. The model will provide a technically sound method for evaluating the relative cost of different composite structural designs, fabrication processes, and assembly methods that can be compared to equivalent metallic parts or assemblies. The feasibility of developing cost prediction software in a modular form for interfacing with state of the art preliminary design tools and computer aided design (CAD) programs is assessed.

A Graphical Database Interface for Casual, Naive Users.

ERIC Educational Resources Information Center

Burgess, Clifford; Swigger, Kathleen

1986-01-01

Describes the design of a database interface for infrequent users of computers which consists of a graphical display of a model of a database and a natural language query language. This interface was designed for and tested with physicians at the University of Texas Health Science Center in Dallas. (LRW)

Detecting Mental States by Machine Learning Techniques: The Berlin Brain-Computer Interface

NASA Astrophysics Data System (ADS)

Blankertz, Benjamin; Tangermann, Michael; Vidaurre, Carmen; Dickhaus, Thorsten; Sannelli, Claudia; Popescu, Florin; Fazli, Siamac; Danóczy, Márton; Curio, Gabriel; Müller, Klaus-Robert

The Berlin Brain-Computer Interface Brain-Computer Interface (BBCI) uses a machine learning approach to extract user-specific patterns from high-dimensional EEG-features optimized for revealing the user's mental state. Classical BCI applications are brain actuated tools for patients such as prostheses (see Section 4.1) or mental text entry systems ([1] and see [2-5] for an overview on BCI). In these applications, the BBCI uses natural motor skills of the users and specifically tailored pattern recognition algorithms for detecting the user's intent. But beyond rehabilitation, there is a wide range of possible applications in which BCI technology is used to monitor other mental states, often even covert ones (see also [6] in the fMRI realm). While this field is still largely unexplored, two examples from our studies are exemplified in Sections 4.3 and 4.4.

A graphical user interface for RAId, a knowledge integrated proteomics analysis suite with accurate statistics.

PubMed

Joyce, Brendan; Lee, Danny; Rubio, Alex; Ogurtsov, Aleksey; Alves, Gelio; Yu, Yi-Kuo

2018-03-15

RAId is a software package that has been actively developed for the past 10 years for computationally and visually analyzing MS/MS data. Founded on rigorous statistical methods, RAId's core program computes accurate E-values for peptides and proteins identified during database searches. Making this robust tool readily accessible for the proteomics community by developing a graphical user interface (GUI) is our main goal here. We have constructed a graphical user interface to facilitate the use of RAId on users' local machines. Written in Java, RAId_GUI not only makes easy executions of RAId but also provides tools for data/spectra visualization, MS-product analysis, molecular isotopic distribution analysis, and graphing the retrieval versus the proportion of false discoveries. The results viewer displays and allows the users to download the analyses results. Both the knowledge-integrated organismal databases and the code package (containing source code, the graphical user interface, and a user manual) are available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads/raid.html .

Development of a patient-specific dosimetry estimation system in nuclear medicine examination

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

Lin, H. H.; Dong, S. L.; Yang, H. J.

2011-07-01

The purpose of this study is to develop a patient-specific dosimetry estimation system in nuclear medicine examination using a SimSET-based Monte Carlo code. We added a dose deposition routine to store the deposited energy of the photons during their flights in SimSET and developed a user-friendly interface for reading PET and CT images. Dose calculated on ORNL phantom was used to validate the accuracy of this system. The S values for {sup 99m}Tc, {sup 18}F and {sup 131}I obtained by the system were compared to those from the MCNP4C code and OLINDA. The ratios of S values computed by thismore » system to those obtained with OLINDA for various organs were ranged from 0.93 to 1.18, which are comparable to that obtained from MCNP4C code (0.94 to 1.20). The average ratios of S value were 0.99{+-}0.04, 1.03{+-}0.05, and 1.00{+-}0.07 for isotopes {sup 131}I, {sup 18}F, and {sup 99m}Tc, respectively. The simulation time of SimSET was two times faster than MCNP4C's for various isotopes. A 3D dose calculation was also performed on a patient data set with PET/CT examination using this system. Results from the patient data showed that the estimated S values using this system differed slightly from those of OLINDA for ORNL phantom. In conclusion, this system can generate patient-specific dose distribution and display the isodose curves on top of the anatomic structure through a friendly graphic user interface. It may also provide a useful tool to establish an appropriate dose-reduction strategy to patients in nuclear medicine environments. (authors)« less

Automation of the CAS Document Delivery Service.

ERIC Educational Resources Information Center

Steensland, M. C.; Soukup, K. M.

1986-01-01

The automation of online order retrieval for Chemical Abstracts Service Document Delivery Service was accomplished by shifting to an order retrieval/dispatch process linked to a Unix network. The Unix-based environment, its terminal emulation, page-break, and user-friendly interface software, and later enhancements are reviewed. Resultant increase…

SimHap GUI: An intuitive graphical user interface for genetic association analysis

PubMed Central

Carter, Kim W; McCaskie, Pamela A; Palmer, Lyle J

2008-01-01

Background Researchers wishing to conduct genetic association analysis involving single nucleotide polymorphisms (SNPs) or haplotypes are often confronted with the lack of user-friendly graphical analysis tools, requiring sophisticated statistical and informatics expertise to perform relatively straightforward tasks. Tools, such as the SimHap package for the R statistics language, provide the necessary statistical operations to conduct sophisticated genetic analysis, but lacks a graphical user interface that allows anyone but a professional statistician to effectively utilise the tool. Results We have developed SimHap GUI, a cross-platform integrated graphical analysis tool for conducting epidemiological, single SNP and haplotype-based association analysis. SimHap GUI features a novel workflow interface that guides the user through each logical step of the analysis process, making it accessible to both novice and advanced users. This tool provides a seamless interface to the SimHap R package, while providing enhanced functionality such as sophisticated data checking, automated data conversion, and real-time estimations of haplotype simulation progress. Conclusion SimHap GUI provides a novel, easy-to-use, cross-platform solution for conducting a range of genetic and non-genetic association analyses. This provides a free alternative to commercial statistics packages that is specifically designed for genetic association analysis. PMID:19109877

PDSS/IMC CIS user's guide

NASA Technical Reports Server (NTRS)

1984-01-01

The Spacelab Payload Development Support System PDSS Image Motion Compensator (IMC) computer interface simulation (CIS) user's manual is given. The software provides a real time interface simulation for the following IMC subsystems: the Dry Rotor Reference Unit, the Advanced Star/Target Reference Optical sensor, the Ultra Violet imaging telescope, the Wisconson Ultraviolet Photopolarimetry Experiment, the Cruciform Power distributor, and the Spacelab Experiment Computer Operating System.

Computational design of RNAs with complex energy landscapes.

PubMed

Höner zu Siederdissen, Christian; Hammer, Stefan; Abfalter, Ingrid; Hofacker, Ivo L; Flamm, Christoph; Stadler, Peter F

2013-12-01

RNA has become an integral building material in synthetic biology. Dominated by their secondary structures, which can be computed efficiently, RNA molecules are amenable not only to in vitro and in vivo selection, but also to rational, computation-based design. While the inverse folding problem of constructing an RNA sequence with a prescribed ground-state structure has received considerable attention for nearly two decades, there have been few efforts to design RNAs that can switch between distinct prescribed conformations. We introduce a user-friendly tool for designing RNA sequences that fold into multiple target structures. The underlying algorithm makes use of a combination of graph coloring and heuristic local optimization to find sequences whose energy landscapes are dominated by the prescribed conformations. A flexible interface allows the specification of a wide range of design goals. We demonstrate that bi- and tri-stable "switches" can be designed easily with moderate computational effort for the vast majority of compatible combinations of desired target structures. RNAdesign is freely available under the GPL-v3 license. Copyright © 2013 Wiley Periodicals, Inc.

Automated platform for designing multiple robot work cells

NASA Astrophysics Data System (ADS)

Osman, N. S.; Rahman, M. A. A.; Rahman, A. A. Abdul; Kamsani, S. H.; Bali Mohamad, B. M.; Mohamad, E.; Zaini, Z. A.; Rahman, M. F. Ab; Mohamad Hatta, M. N. H.

2017-06-01

Designing the multiple robot work cells is very knowledge-intensive, intricate, and time-consuming process. This paper elaborates the development process of a computer-aided design program for generating the multiple robot work cells which offer a user-friendly interface. The primary purpose of this work is to provide a fast and easy platform for less cost and human involvement with minimum trial and errors adjustments. The automated platform is constructed based on the variant-shaped configuration concept with its mathematical model. A robot work cell layout, system components, and construction procedure of the automated platform are discussed in this paper where integration of these items will be able to automatically provide the optimum robot work cell design according to the information set by the user. This system is implemented on top of CATIA V5 software and utilises its Part Design, Assembly Design, and Macro tool. The current outcomes of this work provide a basis for future investigation in developing a flexible configuration system for the multiple robot work cells.

AP-IO: asynchronous pipeline I/O for hiding periodic output cost in CFD simulation.

PubMed

Xiaoguang, Ren; Xinhai, Xu

2014-01-01

Computational fluid dynamics (CFD) simulation often needs to periodically output intermediate results to files in the form of snapshots for visualization or restart, which seriously impacts the performance. In this paper, we present asynchronous pipeline I/O (AP-IO) optimization scheme for the periodically snapshot output on the basis of asynchronous I/O and CFD application characteristics. In AP-IO, dedicated background I/O processes or threads are in charge of handling the file write in pipeline mode, therefore the write overhead can be hidden with more calculation than classic asynchronous I/O. We design the framework of AP-IO and implement it in OpenFOAM, providing CFD users with a user-friendly interface. Experimental results on the Tianhe-2 supercomputer demonstrate that AP-IO can achieve a good optimization effect for the periodical snapshot output in CFD application, and the effect is especially better for massively parallel CFD simulations, which can reduce the total execution time up to about 40%.

pmx Webserver: A User Friendly Interface for Alchemistry.

PubMed

Gapsys, Vytautas; de Groot, Bert L

2017-02-27

With the increase of available computational power and improvements in simulation algorithms, alchemical molecular dynamics based free energy calculations have developed into routine usage. To further facilitate the usability of alchemical methods for amino acid mutations, we have developed a web based infrastructure for obtaining hybrid protein structures and topologies. The presented webserver allows amino acid mutation selection in five contemporary molecular mechanics force fields. In addition, a complete mutation scan with a user defined amino acid is supported. The output generated by the webserver is directly compatible with the Gromacs molecular dynamics engine and can be used with any of the alchemical free energy calculation setup. Furthermore, we present a database of input files and precalculated free energy differences for tripeptides approximating a disordered state of a protein, of particular use for protein stability studies. Finally, the usage of the webserver and its output is exemplified by performing an alanine scan and investigating thermodynamic stability of the Trp cage mini protein. The webserver is accessible at http://pmx.mpibpc.mpg.de.

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.

AP-IO: Asynchronous Pipeline I/O for Hiding Periodic Output Cost in CFD Simulation

PubMed Central

Xiaoguang, Ren; Xinhai, Xu

2014-01-01

Computational fluid dynamics (CFD) simulation often needs to periodically output intermediate results to files in the form of snapshots for visualization or restart, which seriously impacts the performance. In this paper, we present asynchronous pipeline I/O (AP-IO) optimization scheme for the periodically snapshot output on the basis of asynchronous I/O and CFD application characteristics. In AP-IO, dedicated background I/O processes or threads are in charge of handling the file write in pipeline mode, therefore the write overhead can be hidden with more calculation than classic asynchronous I/O. We design the framework of AP-IO and implement it in OpenFOAM, providing CFD users with a user-friendly interface. Experimental results on the Tianhe-2 supercomputer demonstrate that AP-IO can achieve a good optimization effect for the periodical snapshot output in CFD application, and the effect is especially better for massively parallel CFD simulations, which can reduce the total execution time up to about 40%. PMID:24955390

Output ordering and prioritisation system (OOPS): ranking biosynthetic gene clusters to enhance bioactive metabolite discovery.

PubMed

Peña, Alejandro; Del Carratore, Francesco; Cummings, Matthew; Takano, Eriko; Breitling, Rainer

2017-12-18

The rapid increase of publicly available microbial genome sequences has highlighted the presence of hundreds of thousands of biosynthetic gene clusters (BGCs) encoding valuable secondary metabolites. The experimental characterization of new BGCs is extremely laborious and struggles to keep pace with the in silico identification of potential BGCs. Therefore, the prioritisation of promising candidates among computationally predicted BGCs represents a pressing need. Here, we propose an output ordering and prioritisation system (OOPS) which helps sorting identified BGCs by a wide variety of custom-weighted biological and biochemical criteria in a flexible and user-friendly interface. OOPS facilitates a judicious prioritisation of BGCs using G+C content, coding sequence length, gene number, cluster self-similarity and codon bias parameters, as well as enabling the user to rank BGCs based upon BGC type, novelty, and taxonomic distribution. Effective prioritisation of BGCs will help to reduce experimental attrition rates and improve the breadth of bioactive metabolites characterized.

Pathview Web: user friendly pathway visualization and data integration

PubMed Central

Pant, Gaurav; Bhavnasi, Yeshvant K.; Blanchard, Steven G.; Brouwer, Cory

2017-01-01

Abstract Pathway analysis is widely used in omics studies. Pathway-based data integration and visualization is a critical component of the analysis. To address this need, we recently developed a novel R package called Pathview. Pathview maps, integrates and renders a large variety of biological data onto molecular pathway graphs. Here we developed the Pathview Web server, as to make pathway visualization and data integration accessible to all scientists, including those without the special computing skills or resources. Pathview Web features an intuitive graphical web interface and a user centered design. The server not only expands the core functions of Pathview, but also provides many useful features not available in the offline R package. Importantly, the server presents a comprehensive workflow for both regular and integrated pathway analysis of multiple omics data. In addition, the server also provides a RESTful API for programmatic access and conveniently integration in third-party software or workflows. Pathview Web is openly and freely accessible at https://pathview.uncc.edu/. PMID:28482075

Supervised interpretation of echocardiograms with a psychological model of expert supervision

NASA Astrophysics Data System (ADS)

Revankar, Shriram V.; Sher, David B.; Shalin, Valerie L.; Ramamurthy, Maya

1993-07-01

We have developed a collaborative scheme that facilitates active human supervision of the binary segmentation of an echocardiogram. The scheme complements the reliability of a human expert with the precision of segmentation algorithms. In the developed system, an expert user compares the computer generated segmentation with the original image in a user friendly graphics environment, and interactively indicates the incorrectly classified regions either by pointing or by circling. The precise boundaries of the indicated regions are computed by studying original image properties at that region, and a human visual attention distribution map obtained from the published psychological and psychophysical research. We use the developed system to extract contours of heart chambers from a sequence of two dimensional echocardiograms. We are currently extending this method to incorporate a richer set of inputs from the human supervisor, to facilitate multi-classification of image regions depending on their functionality. We are integrating into our system the knowledge related constraints that cardiologists use, to improve the capabilities of our existing system. This extension involves developing a psychological model of expert reasoning, functional and relational models of typical views in echocardiograms, and corresponding interface modifications to map the suggested actions to image processing algorithms.

BioSPICE: access to the most current computational tools for biologists.

PubMed

Garvey, Thomas D; Lincoln, Patrick; Pedersen, Charles John; Martin, David; Johnson, Mark

2003-01-01

The goal of the BioSPICE program is to create a framework that provides biologists access to the most current computational tools. At the program midpoint, the BioSPICE member community has produced a software system that comprises contributions from approximately 20 participating laboratories integrated under the BioSPICE Dashboard and a methodology for continued software integration. These contributed software modules are the BioSPICE Dashboard, a graphical environment that combines Open Agent Architecture and NetBeans software technologies in a coherent, biologist-friendly user interface. The current Dashboard permits data sources, models, simulation engines, and output displays provided by different investigators and running on different machines to work together across a distributed, heterogeneous network. Among several other features, the Dashboard enables users to create graphical workflows by configuring and connecting available BioSPICE components. Anticipated future enhancements to BioSPICE include a notebook capability that will permit researchers to browse and compile data to support model building, a biological model repository, and tools to support the development, control, and data reduction of wet-lab experiments. In addition to the BioSPICE software products, a project website supports information exchange and community building.

ARC SDK: A toolbox for distributed computing and data applications

NASA Astrophysics Data System (ADS)

Skou Andersen, M.; Cameron, D.; Lindemann, J.

2014-06-01

Grid middleware suites provide tools to perform the basic tasks of job submission and retrieval and data access, however these tools tend to be low-level, operating on individual jobs or files and lacking in higher-level concepts. User communities therefore generally develop their own application-layer software catering to their specific communities' needs on top of the Grid middleware. It is thus important for the Grid middleware to provide a friendly, well documented and simple to use interface for the applications to build upon. The Advanced Resource Connector (ARC), developed by NorduGrid, provides a Software Development Kit (SDK) which enables applications to use the middleware for job and data management. This paper presents the architecture and functionality of the ARC SDK along with an example graphical application developed with the SDK. The SDK consists of a set of libraries accessible through Application Programming Interfaces (API) in several languages. It contains extensive documentation and example code and is available on multiple platforms. The libraries provide generic interfaces and rely on plugins to support a given technology or protocol and this modular design makes it easy to add a new plugin if the application requires supporting additional technologies.The ARC Graphical Clients package is a graphical user interface built on top of the ARC SDK and the Qt toolkit and it is presented here as a fully functional example of an application. It provides a graphical interface to enable job submission and management at the click of a button, and allows data on any Grid storage system to be manipulated using a visual file system hierarchy, as if it were a regular file system.

Eye-gaze determination of user intent at the computer interface

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

Goldberg, J.H.; Schryver, J.C.

1993-12-31

Determination of user intent at the computer interface through eye-gaze monitoring can significantly aid applications for the disabled, as well as telerobotics and process control interfaces. Whereas current eye-gaze control applications are limited to object selection and x/y gazepoint tracking, a methodology was developed here to discriminate a more abstract interface operation: zooming-in or out. This methodology first collects samples of eve-gaze location looking at controlled stimuli, at 30 Hz, just prior to a user`s decision to zoom. The sample is broken into data frames, or temporal snapshots. Within a data frame, all spatial samples are connected into a minimummore » spanning tree, then clustered, according to user defined parameters. Each cluster is mapped to one in the prior data frame, and statistics are computed from each cluster. These characteristics include cluster size, position, and pupil size. A multiple discriminant analysis uses these statistics both within and between data frames to formulate optimal rules for assigning the observations into zooming, zoom-out, or no zoom conditions. The statistical procedure effectively generates heuristics for future assignments, based upon these variables. Future work will enhance the accuracy and precision of the modeling technique, and will empirically test users in controlled experiments.« less

Visual gene developer: a fully programmable bioinformatics software for synthetic gene optimization.

PubMed

Jung, Sang-Kyu; McDonald, Karen

2011-08-16

Direct gene synthesis is becoming more popular owing to decreases in gene synthesis pricing. Compared with using natural genes, gene synthesis provides a good opportunity to optimize gene sequence for specific applications. In order to facilitate gene optimization, we have developed a stand-alone software called Visual Gene Developer. The software not only provides general functions for gene analysis and optimization along with an interactive user-friendly interface, but also includes unique features such as programming capability, dedicated mRNA secondary structure prediction, artificial neural network modeling, network & multi-threaded computing, and user-accessible programming modules. The software allows a user to analyze and optimize a sequence using main menu functions or specialized module windows. Alternatively, gene optimization can be initiated by designing a gene construct and configuring an optimization strategy. A user can choose several predefined or user-defined algorithms to design a complicated strategy. The software provides expandable functionality as platform software supporting module development using popular script languages such as VBScript and JScript in the software programming environment. Visual Gene Developer is useful for both researchers who want to quickly analyze and optimize genes, and those who are interested in developing and testing new algorithms in bioinformatics. The software is available for free download at http://www.visualgenedeveloper.net.

Visual gene developer: a fully programmable bioinformatics software for synthetic gene optimization

PubMed Central

2011-01-01

Background Direct gene synthesis is becoming more popular owing to decreases in gene synthesis pricing. Compared with using natural genes, gene synthesis provides a good opportunity to optimize gene sequence for specific applications. In order to facilitate gene optimization, we have developed a stand-alone software called Visual Gene Developer. Results The software not only provides general functions for gene analysis and optimization along with an interactive user-friendly interface, but also includes unique features such as programming capability, dedicated mRNA secondary structure prediction, artificial neural network modeling, network & multi-threaded computing, and user-accessible programming modules. The software allows a user to analyze and optimize a sequence using main menu functions or specialized module windows. Alternatively, gene optimization can be initiated by designing a gene construct and configuring an optimization strategy. A user can choose several predefined or user-defined algorithms to design a complicated strategy. The software provides expandable functionality as platform software supporting module development using popular script languages such as VBScript and JScript in the software programming environment. Conclusion Visual Gene Developer is useful for both researchers who want to quickly analyze and optimize genes, and those who are interested in developing and testing new algorithms in bioinformatics. The software is available for free download at http://www.visualgenedeveloper.net. PMID:21846353

With whom do you feel most intimate?: Exploring the quality of Facebook friendships in relation to similarities and interaction behaviors.

PubMed

Wee, Jieun; Lee, Joonhwan

2017-01-01

It is widely accepted that people tend to associate more and feel closer to those who share similar attributes with themselves. Most of the research on the phenomenon has been carried out in face-to-face contexts. However, it is necessary to study the phenomenon in computer-mediated contexts as well. Exploring Facebook is important in that friendships within the network indicate a broader spectrum of friends, ranging from complete strangers to confiding relations. Also, since diverse communication methods are available on Facebook, which method a user adopts to interact with a "friend" could influence the quality of the relationship, i.e. intimacy. Thus, current research aims to test whether people in computer-mediated contexts do perceive more intimacy toward friends who share similar traits, and further, aims to examine which interaction methods influence the closeness of relationship by collecting activity data of users on Facebook. Results from current study show traits related to intimacy in the online context of Facebook. Moreover, in addition to the interaction type itself, direction of the interaction influenced how intimate users feel towards their friends. Overall findings suggest that further investigation on the dynamics of online communication methods used in developing and maintaining relationships is necessary.

DiversePathsJ: diverse shortest paths for bioimage analysis.

PubMed

Uhlmann, Virginie; Haubold, Carsten; Hamprecht, Fred A; Unser, Michael

2018-02-01

We introduce a formulation for the general task of finding diverse shortest paths between two end-points. Our approach is not linked to a specific biological problem and can be applied to a large variety of images thanks to its generic implementation as a user-friendly ImageJ/Fiji plugin. It relies on the introduction of additional layers in a Viterbi path graph, which requires slight modifications to the standard Viterbi algorithm rules. This layered graph construction allows for the specification of various constraints imposing diversity between solutions. The software allows obtaining a collection of diverse shortest paths under some user-defined constraints through a convenient and user-friendly interface. It can be used alone or be integrated into larger image analysis pipelines. http://bigwww.epfl.ch/algorithms/diversepathsj. michael.unser@epfl.ch or fred.hamprecht@iwr.uni-heidelberg.de. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

The Simple Rules of Social Contagion

PubMed Central

Hodas, Nathan O.; Lerman, Kristina

2014-01-01

It is commonly believed that information spreads between individuals like a pathogen, with each exposure by an informed friend potentially resulting in a naive individual becoming infected. However, empirical studies of social media suggest that individual response to repeated exposure to information is far more complex. As a proxy for intervention experiments, we compare user responses to multiple exposures on two different social media sites, Twitter and Digg. We show that the position of exposing messages on the user-interface strongly affects social contagion. Accounting for this visibility significantly simplifies the dynamics of social contagion. The likelihood an individual will spread information increases monotonically with exposure, while explicit feedback about how many friends have previously spread it increases the likelihood of a response. We provide a framework for unifying information visibility, divided attention, and explicit social feedback to predict the temporal dynamics of user behavior. PMID:24614301

Intelligent user interface concept for space station

NASA Technical Reports Server (NTRS)

Comer, Edward; Donaldson, Cameron; Bailey, Elizabeth; Gilroy, Kathleen

1986-01-01

The space station computing system must interface with a wide variety of users, from highly skilled operations personnel to payload specialists from all over the world. The interface must accommodate a wide variety of operations from the space platform, ground control centers and from remote sites. As a result, there is a need for a robust, highly configurable and portable user interface that can accommodate the various space station missions. The concept of an intelligent user interface executive, written in Ada, that would support a number of advanced human interaction techniques, such as windowing, icons, color graphics, animation, and natural language processing is presented. The user interface would provide intelligent interaction by understanding the various user roles, the operations and mission, the current state of the environment and the current working context of the users. In addition, the intelligent user interface executive must be supported by a set of tools that would allow the executive to be easily configured and to allow rapid prototyping of proposed user dialogs. This capability would allow human engineering specialists acting in the role of dialog authors to define and validate various user scenarios. The set of tools required to support development of this intelligent human interface capability is discussed and the prototyping and validation efforts required for development of the Space Station's user interface are outlined.

Comprehensive cluster analysis with Transitivity Clustering.

PubMed

Wittkop, Tobias; Emig, Dorothea; Truss, Anke; Albrecht, Mario; Böcker, Sebastian; Baumbach, Jan

2011-03-01

Transitivity Clustering is a method for the partitioning of biological data into groups of similar objects, such as genes, for instance. It provides integrated access to various functions addressing each step of a typical cluster analysis. To facilitate this, Transitivity Clustering is accessible online and offers three user-friendly interfaces: a powerful stand-alone version, a web interface, and a collection of Cytoscape plug-ins. In this paper, we describe three major workflows: (i) protein (super)family detection with Cytoscape, (ii) protein homology detection with incomplete gold standards and (iii) clustering of gene expression data. This protocol guides the user through the most important features of Transitivity Clustering and takes ∼1 h to complete.

GPU-based cloud service for Smith-Waterman algorithm using frequency distance filtration scheme.

PubMed

Lee, Sheng-Ta; Lin, Chun-Yuan; Hung, Che Lun

2013-01-01

As the conventional means of analyzing the similarity between a query sequence and database sequences, the Smith-Waterman algorithm is feasible for a database search owing to its high sensitivity. However, this algorithm is still quite time consuming. CUDA programming can improve computations efficiently by using the computational power of massive computing hardware as graphics processing units (GPUs). This work presents a novel Smith-Waterman algorithm with a frequency-based filtration method on GPUs rather than merely accelerating the comparisons yet expending computational resources to handle such unnecessary comparisons. A user friendly interface is also designed for potential cloud server applications with GPUs. Additionally, two data sets, H1N1 protein sequences (query sequence set) and human protein database (database set), are selected, followed by a comparison of CUDA-SW and CUDA-SW with the filtration method, referred to herein as CUDA-SWf. Experimental results indicate that reducing unnecessary sequence alignments can improve the computational time by up to 41%. Importantly, by using CUDA-SWf as a cloud service, this application can be accessed from any computing environment of a device with an Internet connection without time constraints.

SPARK: A Framework for Multi-Scale Agent-Based Biomedical Modeling.

PubMed

Solovyev, Alexey; Mikheev, Maxim; Zhou, Leming; Dutta-Moscato, Joyeeta; Ziraldo, Cordelia; An, Gary; Vodovotz, Yoram; Mi, Qi

2010-01-01

Multi-scale modeling of complex biological systems remains a central challenge in the systems biology community. A method of dynamic knowledge representation known as agent-based modeling enables the study of higher level behavior emerging from discrete events performed by individual components. With the advancement of computer technology, agent-based modeling has emerged as an innovative technique to model the complexities of systems biology. In this work, the authors describe SPARK (Simple Platform for Agent-based Representation of Knowledge), a framework for agent-based modeling specifically designed for systems-level biomedical model development. SPARK is a stand-alone application written in Java. It provides a user-friendly interface, and a simple programming language for developing Agent-Based Models (ABMs). SPARK has the following features specialized for modeling biomedical systems: 1) continuous space that can simulate real physical space; 2) flexible agent size and shape that can represent the relative proportions of various cell types; 3) multiple spaces that can concurrently simulate and visualize multiple scales in biomedical models; 4) a convenient graphical user interface. Existing ABMs of diabetic foot ulcers and acute inflammation were implemented in SPARK. Models of identical complexity were run in both NetLogo and SPARK; the SPARK-based models ran two to three times faster.

Visual Exploratory Search of Relationship Graphs on Smartphones

PubMed Central

Ouyang, Jianquan; Zheng, Hao; Kong, Fanbin; Liu, Tianming

2013-01-01

This paper presents a novel framework for Visual Exploratory Search of Relationship Graphs on Smartphones (VESRGS) that is composed of three major components: inference and representation of semantic relationship graphs on the Web via meta-search, visual exploratory search of relationship graphs through both querying and browsing strategies, and human-computer interactions via the multi-touch interface and mobile Internet on smartphones. In comparison with traditional lookup search methodologies, the proposed VESRGS system is characterized with the following perceived advantages. 1) It infers rich semantic relationships between the querying keywords and other related concepts from large-scale meta-search results from Google, Yahoo! and Bing search engines, and represents semantic relationships via graphs; 2) the exploratory search approach empowers users to naturally and effectively explore, adventure and discover knowledge in a rich information world of interlinked relationship graphs in a personalized fashion; 3) it effectively takes the advantages of smartphones’ user-friendly interfaces and ubiquitous Internet connection and portability. Our extensive experimental results have demonstrated that the VESRGS framework can significantly improve the users’ capability of seeking the most relevant relationship information to their own specific needs. We envision that the VESRGS framework can be a starting point for future exploration of novel, effective search strategies in the mobile Internet era. PMID:24223936

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration

PubMed Central

Ong, Edison; Xiang, Zuoshuang; Zhao, Bin; Liu, Yue; Lin, Yu; Zheng, Jie; Mungall, Chris; Courtot, Mélanie; Ruttenberg, Alan; He, Yongqun

2017-01-01

Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry.org) library. Ontobee currently hosts more than 180 ontologies (including 131 OBO Foundry Library ontologies) with over four million terms. Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term. Using the eXtensible Stylesheet Language Transformation (XSLT) technology, Ontobee is able to dereference a single ontology term URI, and then output RDF/eXtensible Markup Language (XML) for computer processing or display the HTML information on a web browser for human users. Statistics and detailed information are generated and displayed for each ontology listed in Ontobee. In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies. PMID:27733503

User's guide to resin infusion simulation program in the FORTRAN language

NASA Technical Reports Server (NTRS)

Weideman, Mark H.; Hammond, Vince H.; Loos, Alfred C.

1992-01-01

RTMCL is a user friendly computer code which simulates the manufacture of fabric composites by the resin infusion process. The computer code is based on the process simulation model described in reference 1. Included in the user's guide is a detailed step by step description of how to run the program and enter and modify the input data set. Sample input and output files are included along with an explanation of the results. Finally, a complete listing of the program is provided.

User interface design principles for the SSM/PMAD automated power system

NASA Technical Reports Server (NTRS)

Jakstas, Laura M.; Myers, Chris J.

1991-01-01

Martin Marietta has developed a user interface for the space station module power management and distribution (SSM/PMAD) automated power system testbed which provides human access to the functionality of the power system, as well as exemplifying current techniques in user interface design. The testbed user interface was designed to enable an engineer to operate the system easily without having significant knowledge of computer systems, as well as provide an environment in which the engineer can monitor and interact with the SSM/PMAD system hardware. The design of the interface supports a global view of the most important data from the various hardware and software components, as well as enabling the user to obtain additional or more detailed data when needed. The components and representations of the SSM/PMAD testbed user interface are examined. An engineer's interactions with the system are also described.

The New NASA Orbital Debris Engineering Model ORDEM2000

NASA Technical Reports Server (NTRS)

Liou, Jer-Chyi; Matney, Mark J.; Anz-Meador, Phillip D.; Kessler, Donald; Jansen, Mark; Theall, Jeffery R.

2002-01-01

The NASA Orbital Debris Program Office at Johnson Space Center has developed a new computer-based orbital debris engineering model, ORDEM2000, which describes the orbital debris environment in the low Earth orbit region between 200 and 2000 km altitude. The model is appropriate for those engineering solutions requiring knowledge and estimates of the orbital debris environment (debris spatial density, flux, etc.). ORDEM2000 can also be used as a benchmark for ground-based debris measurements and observations. We incorporated a large set of observational data, covering the object size range from 10 mm to 10 m, into the ORDEM2000 debris database, utilizing a maximum likelihood estimator to convert observations into debris population probability distribution functions. These functions then form the basis of debris populations. We developed a finite element model to process the debris populations to form the debris environment. A more capable input and output structure and a user-friendly graphical user interface are also implemented in the model. ORDEM2000 has been subjected to a significant verification and validation effort. This document describes ORDEM2000, which supersedes the previous model, ORDEM96. The availability of new sensor and in situ data, as well as new analytical techniques, has enabled the construction of this new model. Section 1 describes the general requirements and scope of an engineering model. Data analyses and the theoretical formulation of the model are described in Sections 2 and 3. Section 4 describes the verification and validation effort and the sensitivity and uncertainty analyses. Finally, Section 5 describes the graphical user interface, software installation, and test cases for the user.

The GENIUS Grid Portal and robot certificates: a new tool for e-Science

PubMed Central

Barbera, Roberto; Donvito, Giacinto; Falzone, Alberto; La Rocca, Giuseppe; Milanesi, Luciano; Maggi, Giorgio Pietro; Vicario, Saverio

2009-01-01

Background Grid technology is the computing model which allows users to share a wide pletora of distributed computational resources regardless of their geographical location. Up to now, the high security policy requested in order to access distributed computing resources has been a rather big limiting factor when trying to broaden the usage of Grids into a wide community of users. Grid security is indeed based on the Public Key Infrastructure (PKI) of X.509 certificates and the procedure to get and manage those certificates is unfortunately not straightforward. A first step to make Grids more appealing for new users has recently been achieved with the adoption of robot certificates. Methods Robot certificates have recently been introduced to perform automated tasks on Grids on behalf of users. They are extremely useful for instance to automate grid service monitoring, data processing production, distributed data collection systems. Basically these certificates can be used to identify a person responsible for an unattended service or process acting as client and/or server. Robot certificates can be installed on a smart card and used behind a portal by everyone interested in running the related applications in a Grid environment using a user-friendly graphic interface. In this work, the GENIUS Grid Portal, powered by EnginFrame, has been extended in order to support the new authentication based on the adoption of these robot certificates. Results The work carried out and reported in this manuscript is particularly relevant for all users who are not familiar with personal digital certificates and the technical aspects of the Grid Security Infrastructure (GSI). The valuable benefits introduced by robot certificates in e-Science can so be extended to users belonging to several scientific domains, providing an asset in raising Grid awareness to a wide number of potential users. Conclusion The adoption of Grid portals extended with robot certificates, can really contribute to creating transparent access to computational resources of Grid Infrastructures, enhancing the spread of this new paradigm in researchers' working life to address new global scientific challenges. The evaluated solution can of course be extended to other portals, applications and scientific communities. PMID:19534747

The GENIUS Grid Portal and robot certificates: a new tool for e-Science.

PubMed

Barbera, Roberto; Donvito, Giacinto; Falzone, Alberto; La Rocca, Giuseppe; Milanesi, Luciano; Maggi, Giorgio Pietro; Vicario, Saverio

2009-06-16

Grid technology is the computing model which allows users to share a wide pletora of distributed computational resources regardless of their geographical location. Up to now, the high security policy requested in order to access distributed computing resources has been a rather big limiting factor when trying to broaden the usage of Grids into a wide community of users. Grid security is indeed based on the Public Key Infrastructure (PKI) of X.509 certificates and the procedure to get and manage those certificates is unfortunately not straightforward. A first step to make Grids more appealing for new users has recently been achieved with the adoption of robot certificates. Robot certificates have recently been introduced to perform automated tasks on Grids on behalf of users. They are extremely useful for instance to automate grid service monitoring, data processing production, distributed data collection systems. Basically these certificates can be used to identify a person responsible for an unattended service or process acting as client and/or server. Robot certificates can be installed on a smart card and used behind a portal by everyone interested in running the related applications in a Grid environment using a user-friendly graphic interface. In this work, the GENIUS Grid Portal, powered by EnginFrame, has been extended in order to support the new authentication based on the adoption of these robot certificates. The work carried out and reported in this manuscript is particularly relevant for all users who are not familiar with personal digital certificates and the technical aspects of the Grid Security Infrastructure (GSI). The valuable benefits introduced by robot certificates in e-Science can so be extended to users belonging to several scientific domains, providing an asset in raising Grid awareness to a wide number of potential users. The adoption of Grid portals extended with robot certificates, can really contribute to creating transparent access to computational resources of Grid Infrastructures, enhancing the spread of this new paradigm in researchers' working life to address new global scientific challenges. The evaluated solution can of course be extended to other portals, applications and scientific communities.

MAGMA: analysis of two-channel microarrays made easy.

PubMed

Rehrauer, Hubert; Zoller, Stefan; Schlapbach, Ralph

2007-07-01

The web application MAGMA provides a simple and intuitive interface to identify differentially expressed genes from two-channel microarray data. While the underlying algorithms are not superior to those of similar web applications, MAGMA is particularly user friendly and can be used without prior training. The user interface guides the novice user through the most typical microarray analysis workflow consisting of data upload, annotation, normalization and statistical analysis. It automatically generates R-scripts that document MAGMA's entire data processing steps, thereby allowing the user to regenerate all results in his local R installation. The implementation of MAGMA follows the model-view-controller design pattern that strictly separates the R-based statistical data processing, the web-representation and the application logic. This modular design makes the application flexible and easily extendible by experts in one of the fields: statistical microarray analysis, web design or software development. State-of-the-art Java Server Faces technology was used to generate the web interface and to perform user input processing. MAGMA's object-oriented modular framework makes it easily extendible and applicable to other fields and demonstrates that modern Java technology is also suitable for rather small and concise academic projects. MAGMA is freely available at www.magma-fgcz.uzh.ch.

SVM Classifier - a comprehensive java interface for support vector machine classification of microarray data.

PubMed

Pirooznia, Mehdi; Deng, Youping

2006-12-12

Graphical user interface (GUI) software promotes novelty by allowing users to extend the functionality. SVM Classifier is a cross-platform graphical application that handles very large datasets well. The purpose of this study is to create a GUI application that allows SVM users to perform SVM training, classification and prediction. The GUI provides user-friendly access to state-of-the-art SVM methods embodied in the LIBSVM implementation of Support Vector Machine. We implemented the java interface using standard swing libraries. We used a sample data from a breast cancer study for testing classification accuracy. We achieved 100% accuracy in classification among the BRCA1-BRCA2 samples with RBF kernel of SVM. We have developed a java GUI application that allows SVM users to perform SVM training, classification and prediction. We have demonstrated that support vector machines can accurately classify genes into functional categories based upon expression data from DNA microarray hybridization experiments. Among the different kernel functions that we examined, the SVM that uses a radial basis kernel function provides the best performance. The SVM Classifier is available at http://mfgn.usm.edu/ebl/svm/.

WImpiBLAST: web interface for mpiBLAST to help biologists perform large-scale annotation using high performance computing.

PubMed

Sharma, Parichit; Mantri, Shrikant S

2014-01-01

The function of a newly sequenced gene can be discovered by determining its sequence homology with known proteins. BLAST is the most extensively used sequence analysis program for sequence similarity search in large databases of sequences. With the advent of next generation sequencing technologies it has now become possible to study genes and their expression at a genome-wide scale through RNA-seq and metagenome sequencing experiments. Functional annotation of all the genes is done by sequence similarity search against multiple protein databases. This annotation task is computationally very intensive and can take days to obtain complete results. The program mpiBLAST, an open-source parallelization of BLAST that achieves superlinear speedup, can be used to accelerate large-scale annotation by using supercomputers and high performance computing (HPC) clusters. Although many parallel bioinformatics applications using the Message Passing Interface (MPI) are available in the public domain, researchers are reluctant to use them due to lack of expertise in the Linux command line and relevant programming experience. With these limitations, it becomes difficult for biologists to use mpiBLAST for accelerating annotation. No web interface is available in the open-source domain for mpiBLAST. We have developed WImpiBLAST, a user-friendly open-source web interface for parallel BLAST searches. It is implemented in Struts 1.3 using a Java backbone and runs atop the open-source Apache Tomcat Server. WImpiBLAST supports script creation and job submission features and also provides a robust job management interface for system administrators. It combines script creation and modification features with job monitoring and management through the Torque resource manager on a Linux-based HPC cluster. Use case information highlights the acceleration of annotation analysis achieved by using WImpiBLAST. Here, we describe the WImpiBLAST web interface features and architecture, explain design decisions, describe workflows and provide a detailed analysis.

WImpiBLAST: Web Interface for mpiBLAST to Help Biologists Perform Large-Scale Annotation Using High Performance Computing

PubMed Central

Sharma, Parichit; Mantri, Shrikant S.

2014-01-01

The function of a newly sequenced gene can be discovered by determining its sequence homology with known proteins. BLAST is the most extensively used sequence analysis program for sequence similarity search in large databases of sequences. With the advent of next generation sequencing technologies it has now become possible to study genes and their expression at a genome-wide scale through RNA-seq and metagenome sequencing experiments. Functional annotation of all the genes is done by sequence similarity search against multiple protein databases. This annotation task is computationally very intensive and can take days to obtain complete results. The program mpiBLAST, an open-source parallelization of BLAST that achieves superlinear speedup, can be used to accelerate large-scale annotation by using supercomputers and high performance computing (HPC) clusters. Although many parallel bioinformatics applications using the Message Passing Interface (MPI) are available in the public domain, researchers are reluctant to use them due to lack of expertise in the Linux command line and relevant programming experience. With these limitations, it becomes difficult for biologists to use mpiBLAST for accelerating annotation. No web interface is available in the open-source domain for mpiBLAST. We have developed WImpiBLAST, a user-friendly open-source web interface for parallel BLAST searches. It is implemented in Struts 1.3 using a Java backbone and runs atop the open-source Apache Tomcat Server. WImpiBLAST supports script creation and job submission features and also provides a robust job management interface for system administrators. It combines script creation and modification features with job monitoring and management through the Torque resource manager on a Linux-based HPC cluster. Use case information highlights the acceleration of annotation analysis achieved by using WImpiBLAST. Here, we describe the WImpiBLAST web interface features and architecture, explain design decisions, describe workflows and provide a detailed analysis. PMID:24979410

Graphical User Interface Development for Representing Air Flow Patterns

NASA Technical Reports Server (NTRS)

Chaudhary, Nilika

2004-01-01

In the Turbine Branch, scientists carry out experimental and computational work to advance the efficiency and diminish the noise production of jet engine turbines. One way to do this is by decreasing the heat that the turbine blades receive. Most of the experimental work is carried out by taking a single turbine blade and analyzing the air flow patterns around it, because this data indicates the sections of the turbine blade that are getting too hot. Since the cost of doing turbine blade air flow experiments is very high, researchers try to do computational work that fits the experimental data. The goal of computational fluid dynamics is for scientists to find a numerical way to predict the complex flow patterns around different turbine blades without physically having to perform tests or costly experiments. When visualizing flow patterns, scientists need a way to represent the flow conditions around a turbine blade. A researcher will assign specific zones that surround the turbine blade. In a two-dimensional view, the zones are usually quadrilaterals. The next step is to assign boundary conditions which define how the flow enters or exits one side of a zone. way of setting up computational zones and grids, visualizing flow patterns, and storing all the flow conditions in a file on the computer for future computation. Such a program is necessary because the only method for creating flow pattern graphs is by hand, which is tedious and time-consuming. By using a computer program to create the zones and grids, the graph would be faster to make and easier to edit. Basically, the user would run a program that is an editable graph. The user could click and drag with the mouse to form various zones and grids, then edit the locations of these grids, add flow and boundary conditions, and finally save the graph for future use and analysis. My goal this summer is to create a graphical user interface (GUI) that incorporates all of these elements. I am writing the program in Java, a language that is portable among platforms, because it can run on different operating systems such as Windows and Unix without having to be rewritten. I had no prior experience of programming in Java at the start of my internship; I am continuously learning as I create the program. I have written the part of the program that enables a user to draw several zones, edit them, and store their locations. The next phase of my project is to allow the user to click on the side of a zone and create a boundary condition for it. A previous intern wrote a program that allows the user to input boundary conditions. I can integrate the two programs to create a larger, more usable program. After that, I will develop a way for the user to save the graph for future reference. Another eventual goal is to make the GUI capable of creating three-dimensional zones as well. Researchers such as my mentor, Dr. David Ashpis, need a quick, user-friendly

A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal.

PubMed

Eijssen, Lars M T; Goelela, Varshna S; Kelder, Thomas; Adriaens, Michiel E; Evelo, Chris T; Radonjic, Marijana

2015-06-30

Illumina whole-genome expression bead arrays are a widely used platform for transcriptomics. Most of the tools available for the analysis of the resulting data are not easily applicable by less experienced users. ArrayAnalysis.org provides researchers with an easy-to-use and comprehensive interface to the functionality of R and Bioconductor packages for microarray data analysis. As a modular open source project, it allows developers to contribute modules that provide support for additional types of data or extend workflows. To enable data analysis of Illumina bead arrays for a broad user community, we have developed a module for ArrayAnalysis.org that provides a free and user-friendly web interface for quality control and pre-processing for these arrays. This module can be used together with existing modules for statistical and pathway analysis to provide a full workflow for Illumina gene expression data analysis. The module accepts data exported from Illumina's GenomeStudio, and provides the user with quality control plots and normalized data. The outputs are directly linked to the existing statistics module of ArrayAnalysis.org, but can also be downloaded for further downstream analysis in third-party tools. The Illumina bead arrays analysis module is available at http://www.arrayanalysis.org . A user guide, a tutorial demonstrating the analysis of an example dataset, and R scripts are available. The module can be used as a starting point for statistical evaluation and pathway analysis provided on the website or to generate processed input data for a broad range of applications in life sciences research.

iPat: intelligent prediction and association tool for genomic research.

PubMed

Chen, Chunpeng James; Zhang, Zhiwu

2018-06-01

The ultimate goal of genomic research is to effectively predict phenotypes from genotypes so that medical management can improve human health and molecular breeding can increase agricultural production. Genomic prediction or selection (GS) plays a complementary role to genome-wide association studies (GWAS), which is the primary method to identify genes underlying phenotypes. Unfortunately, most computing tools cannot perform data analyses for both GWAS and GS. Furthermore, the majority of these tools are executed through a command-line interface (CLI), which requires programming skills. Non-programmers struggle to use them efficiently because of the steep learning curves and zero tolerance for data formats and mistakes when inputting keywords and parameters. To address these problems, this study developed a software package, named the Intelligent Prediction and Association Tool (iPat), with a user-friendly graphical user interface. With iPat, GWAS or GS can be performed using a pointing device to simply drag and/or click on graphical elements to specify input data files, choose input parameters and select analytical models. Models available to users include those implemented in third party CLI packages such as GAPIT, PLINK, FarmCPU, BLINK, rrBLUP and BGLR. Users can choose any data format and conduct analyses with any of these packages. File conversions are automatically conducted for specified input data and selected packages. A GWAS-assisted genomic prediction method was implemented to perform genomic prediction using any GWAS method such as FarmCPU. iPat was written in Java for adaptation to multiple operating systems including Windows, Mac and Linux. The iPat executable file, user manual, tutorials and example datasets are freely available at http://zzlab.net/iPat. zhiwu.zhang@wsu.edu.

Command and control interfaces for advanced neuroprosthetic applications.

PubMed

Scott, T R; Haugland, M

2001-10-01

Command and control interfaces permit the intention and situation of the user to influence the operation of the neural prosthesis. The wishes of the user are communicated via command interfaces to the neural prosthesis and the situation of the user by feedback control interfaces. Both these interfaces have been reviewed separately and are discussed in light of the current state of the art and projections for the future. It is apparent that as system functional complexity increases, the need for simpler command interfaces will increase. Such systems will demand more information to function effectively in order not to unreasonably increase user attention overhead. This will increase the need for bioelectric and biomechanical signals in a comprehensible form via elegant feedback control interfaces. Implementing such systems will also increase the computational demand on such neural prostheses.

BisQue: cloud-based system for management, annotation, visualization, analysis and data mining of underwater and remote sensing imagery

NASA Astrophysics Data System (ADS)

Fedorov, D.; Miller, R. J.; Kvilekval, K. G.; Doheny, B.; Sampson, S.; Manjunath, B. S.

2016-02-01

Logistical and financial limitations of underwater operations are inherent in marine science, including biodiversity observation. Imagery is a promising way to address these challenges, but the diversity of organisms thwarts simple automated analysis. Recent developments in computer vision methods, such as convolutional neural networks (CNN), are promising for automated classification and detection tasks but are typically very computationally expensive and require extensive training on large datasets. Therefore, managing and connecting distributed computation, large storage and human annotations of diverse marine datasets is crucial for effective application of these methods. BisQue is a cloud-based system for management, annotation, visualization, analysis and data mining of underwater and remote sensing imagery and associated data. Designed to hide the complexity of distributed storage, large computational clusters, diversity of data formats and inhomogeneous computational environments behind a user friendly web-based interface, BisQue is built around an idea of flexible and hierarchical annotations defined by the user. Such textual and graphical annotations can describe captured attributes and the relationships between data elements. Annotations are powerful enough to describe cells in fluorescent 4D images, fish species in underwater videos and kelp beds in aerial imagery. Presently we are developing BisQue-based analysis modules for automated identification of benthic marine organisms. Recent experiments with drop-out and CNN based classification of several thousand annotated underwater images demonstrated an overall accuracy above 70% for the 15 best performing species and above 85% for the top 5 species. Based on these promising results, we have extended bisque with a CNN-based classification system allowing continuous training on user-provided data.

Early evaluation of MDIS workstations at Madigan Army Medical Center

NASA Astrophysics Data System (ADS)

Leckie, Robert G.; Goeringer, Fred; Smith, Donald V.; Bender, Gregory N.; Choi, Hyung-Sik; Haynor, David R.; Kim, Yongmin

1993-06-01

The image viewing workstation is an all-important link in the PACS (Picture Archiving and Communications System) chain since it represents the interface between the system and the user. For PACS to function, the working environment and transfer of information to the user must be the same or better than the traditional film-based system. The important characteristics of a workstation from a clinical standpoint are acceptable image quality, rapid response time, a friendly user interface, and a well-integrated, highly-reliable, fault-tolerant system which provides the user ample functions to complete his tasks successfully. Since early 1992, the MDIS (Medical Diagnostic Imaging Support) system's diagnostic and clinical workstations have been installed at Madigan Army Medical Center. Various functionalities and performance characteristics of the MDIS workstations such as image display, response time, database, and ergonomics will be presented. User comments and early experience with the workstations as well as new functionality recommended for the future will be discussed.

"I'm Keeping Those There, Are You?": The Role of a New User Interface Paradigm--Separate Control of Shared Space (SCOSS)--in the Collaborative Decision-Making Process

ERIC Educational Resources Information Center

Kerawalla, Lucinda; Pearce, Darren; Yuill, Nicola; Luckin, Rosemary; Harris, Amanda

2008-01-01

We take a socio-cultural approach to comparing how dual control of a new user interface paradigm--Separate Control of Shared Space (SCOSS)--and dual control of a single user interface can work to mediate the collaborative decision-making process between pairs of children carrying out a multiple categorisation word task on a shared computer.…

A serial digital data communications device. [for real time flight simulation

NASA Technical Reports Server (NTRS)

Fetter, J. L.

1977-01-01

A general purpose computer peripheral device which is used to provide a full-duplex, serial, digital data transmission link between a Xerox Sigma computer and a wide variety of external equipment, including computers, terminals, and special purpose devices is reported. The interface has an extensive set of user defined options to assist the user in establishing the necessary data links. This report describes those options and other features of the serial communications interface and its performance by discussing its application to a particular problem.

User interface concerns

NASA Technical Reports Server (NTRS)

Redhed, D. D.

1978-01-01

Three possible goals for the Numerical Aerodynamic Simulation Facility (NASF) are: (1) a computational fluid dynamics (as opposed to aerodynamics) algorithm development tool; (2) a specialized research laboratory facility for nearly intractable aerodynamics problems that industry encounters; and (3) a facility for industry to use in its normal aerodynamics design work that requires high computing rates. The central system issue for industry use of such a computer is the quality of the user interface as implemented in some kind of a front end to the vector processor.

Development and implementation of an Integrated Water Resources Management System (IWRMS)

NASA Astrophysics Data System (ADS)

Flügel, W.-A.; Busch, C.

2011-04-01

One of the innovative objectives in the EC project BRAHMATWINN was the development of a stakeholder oriented Integrated Water Resources Management System (IWRMS). The toolset integrates the findings of the project and presents it in a user friendly way for decision support in sustainable integrated water resources management (IWRM) in river basins. IWRMS is a framework, which integrates different types of basin information and which supports the development of IWRM options for climate change mitigation. It is based on the River Basin Information System (RBIS) data models and delivers a graphical user interface for stakeholders. A special interface was developed for the integration of the enhanced DANUBIA model input and the NetSyMod model with its Mulino decision support system (mulino mDss) component. The web based IWRMS contains and combines different types of data and methods to provide river basin data and information for decision support. IWRMS is based on a three tier software framework which uses (i) html/javascript at the client tier, (ii) PHP programming language to realize the application tier, and (iii) a postgresql/postgis database tier to manage and storage all data, except the DANUBIA modelling raw data, which are file based and registered in the database tier. All three tiers can reside on one or different computers and are adapted to the local hardware infrastructure. IWRMS as well as RBIS are based on Open Source Software (OSS) components and flexible and time saving access to that database is guaranteed by web-based interfaces for data visualization and retrieval. The IWRMS is accessible via the BRAHMATWINN homepage: http://www.brahmatwinn.uni-jena.de and a user manual for the RBIS is available for download as well.

A FRAMEWORK TO DESIGN AND OPTIMIZE CHEMICAL FLOODING PROCESSES

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

Mojdeh Delshad; Gary A. Pope; Kamy Sepehrnoori

2005-07-01

The goal of this proposed research is to provide an efficient and user friendly simulation framework for screening and optimizing chemical/microbial enhanced oil recovery processes. The framework will include (1) a user friendly interface to identify the variables that have the most impact on oil recovery using the concept of experimental design and response surface maps, (2) UTCHEM reservoir simulator to perform the numerical simulations, and (3) an economic model that automatically imports the simulation production data to evaluate the profitability of a particular design. Such a reservoir simulation framework is not currently available to the oil industry. The objectivesmore » of Task 1 are to develop three primary modules representing reservoir, chemical, and well data. The modules will be interfaced with an already available experimental design model. The objective of the Task 2 is to incorporate UTCHEM reservoir simulator and the modules with the strategic variables and developing the response surface maps to identify the significant variables from each module. The objective of the Task 3 is to develop the economic model designed specifically for the chemical processes targeted in this proposal and interface the economic model with UTCHEM production output. Task 4 is on the validation of the framework and performing simulations of oil reservoirs to screen, design and optimize the chemical processes.« less

A Framework to Design and Optimize Chemical Flooding Processes

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

Mojdeh Delshad; Gary A. Pope; Kamy Sepehrnoori

2006-08-31

The goal of this proposed research is to provide an efficient and user friendly simulation framework for screening and optimizing chemical/microbial enhanced oil recovery processes. The framework will include (1) a user friendly interface to identify the variables that have the most impact on oil recovery using the concept of experimental design and response surface maps, (2) UTCHEM reservoir simulator to perform the numerical simulations, and (3) an economic model that automatically imports the simulation production data to evaluate the profitability of a particular design. Such a reservoir simulation framework is not currently available to the oil industry. The objectivesmore » of Task 1 are to develop three primary modules representing reservoir, chemical, and well data. The modules will be interfaced with an already available experimental design model. The objective of the Task 2 is to incorporate UTCHEM reservoir simulator and the modules with the strategic variables and developing the response surface maps to identify the significant variables from each module. The objective of the Task 3 is to develop the economic model designed specifically for the chemical processes targeted in this proposal and interface the economic model with UTCHEM production output. Task 4 is on the validation of the framework and performing simulations of oil reservoirs to screen, design and optimize the chemical processes.« less

A FRAMEWORK TO DESIGN AND OPTIMIZE CHEMICAL FLOODING PROCESSES

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

Mojdeh Delshad; Gary A. Pope; Kamy Sepehrnoori

2004-11-01

The goal of this proposed research is to provide an efficient and user friendly simulation framework for screening and optimizing chemical/microbial enhanced oil recovery processes. The framework will include (1) a user friendly interface to identify the variables that have the most impact on oil recovery using the concept of experimental design and response surface maps, (2) UTCHEM reservoir simulator to perform the numerical simulations, and (3) an economic model that automatically imports the simulation production data to evaluate the profitability of a particular design. Such a reservoir simulation framework is not currently available to the oil industry. The objectivesmore » of Task 1 are to develop three primary modules representing reservoir, chemical, and well data. The modules will be interfaced with an already available experimental design model. The objective of the Task 2 is to incorporate UTCHEM reservoir simulator and the modules with the strategic variables and developing the response surface maps to identify the significant variables from each module. The objective of the Task 3 is to develop the economic model designed specifically for the chemical processes targeted in this proposal and interface the economic model with UTCHEM production output. Task 4 is on the validation of the framework and performing simulations of oil reservoirs to screen, design and optimize the chemical processes.« less

XSEOS: An Open Software for Chemical Engineering Thermodynamics

ERIC Educational Resources Information Center

Castier, Marcelo

2008-01-01

An Excel add-in--XSEOS--that implements several excess Gibbs free energy models and equations of state has been developed for educational use. Several traditional and modern thermodynamic models are available in the package with a user-friendly interface. XSEOS has open code, is freely available, and should be useful for instructors and students…

SETAC Short Course: Introduction to interspecies toxicity extrapolation using EPA’s Web-ICE tool

EPA Science Inventory

The Web-ICE tool is a user friendly interface that contains modules to predict acute toxicity to over 500 species of aquatic (algae, invertebrates, fish) and terrestrial (birds and mammals) taxa. The tool contains a suite of over 3000 ICE models developed from a database of over ...

myPhyloDB: a local web server for the storage and analysis of metagenomics data

USDA-ARS?s Scientific Manuscript database

myPhyloDB is a user-friendly personal database with a browser-interface designed to facilitate the storage, processing, analysis, and distribution of metagenomics data. MyPhyloDB archives raw sequencing files, and allows for easy selection of project(s)/sample(s) of any combination from all availab...

WMI2, the Student's On-Line Symbolic Calculator

ERIC Educational Resources Information Center

Kovacs, Zoltan

2011-01-01

Student activities focused on discovering mathematics play an important role in the teaching and learning process. WebMathematics Interactive (WMI2) was developed to offer a fast and user-friendly on-line web interface to enhance the quality of both theoretical and applied mathematics courses. For the teacher, in the classroom, it provides…

An interactive information kiosk for the Adirondack Park Visitor Interpretive Center, Newcomb, NY

Treesearch

Lien Alpert; Lee P. Herrington

1998-01-01

Kiosks have traditionally been non-electronic, but today kiosks are being developed as interactive, electronic information centers to transmit information about government services, commercial products and recreational experiences. This project's objective was to develop and evaluate the usefulness of a user-friendly information interface for kiosks in the...

Corner Office: EBSCO's Tim Collins

ERIC Educational Resources Information Center

Fialkoff, Francine; Oder, Norman

2008-01-01

This article presents an interview with Tim Collins, president of EBSCO Publishing. The amiable Collins put EBSCO Publishing (EP) on the map through a combination of first-rate search and user-friendly interfaces, a long list of strategic acquisitions, and a dedicated, stable staff. Now, the company Collins has nurtured for over two decades ranks…

I-SAVE: AN INTERACTIVE REAL-TIME MONITOR AND CONTROLLER TO INFLUENCE ENERGY CONSERVATION BEHAVIOR BY IMPULSE SAVING

EPA Science Inventory

Simulation-based model to explore the benefits of monitoring and control to energy saving opportunities in residential homes; an adaptive algorithm to predict the type of electrical loads; a prototype user friendly interface monitoring and control device to save energy; a p...

Dialogue with an OPAC: How Visionary Was Swanson in 1964?

ERIC Educational Resources Information Center

Su, Shiao-Feng

1994-01-01

Traces the development of online public access catalogs (OPACs) and compares what has occurred with a 1964 article that outlined recommendations for a future card catalog. Subject access is emphasized, including Library of Congress Subject Headings, expansion of OPACs, user-friendly interfaces, new technologies, and current visions of the future…

GExplore: a web server for integrated queries of protein domains, gene expression and mutant phenotypes

PubMed Central

2009-01-01

Background The majority of the genes even in well-studied multi-cellular model organisms have not been functionally characterized yet. Mining the numerous genome wide data sets related to protein function to retrieve potential candidate genes for a particular biological process remains a challenge. Description GExplore has been developed to provide a user-friendly database interface for data mining at the gene expression/protein function level to help in hypothesis development and experiment design. It supports combinatorial searches for proteins with certain domains, tissue- or developmental stage-specific expression patterns, and mutant phenotypes. GExplore operates on a stand-alone database and has fast response times, which is essential for exploratory searches. The interface is not only user-friendly, but also modular so that it accommodates additional data sets in the future. Conclusion GExplore is an online database for quick mining of data related to gene and protein function, providing a multi-gene display of data sets related to the domain composition of proteins as well as expression and phenotype data. GExplore is publicly available at: http://genome.sfu.ca/gexplore/ PMID:19917126

Constructing Pairing-Friendly Elliptic Curves under Embedding Degree 1 for Securing Critical Infrastructures.

PubMed

Wang, Maocai; Dai, Guangming; Choo, Kim-Kwang Raymond; Jayaraman, Prem Prakash; Ranjan, Rajiv

2016-01-01

Information confidentiality is an essential requirement for cyber security in critical infrastructure. Identity-based cryptography, an increasingly popular branch of cryptography, is widely used to protect the information confidentiality in the critical infrastructure sector due to the ability to directly compute the user's public key based on the user's identity. However, computational requirements complicate the practical application of Identity-based cryptography. In order to improve the efficiency of identity-based cryptography, this paper presents an effective method to construct pairing-friendly elliptic curves with low hamming weight 4 under embedding degree 1. Based on the analysis of the Complex Multiplication(CM) method, the soundness of our method to calculate the characteristic of the finite field is proved. And then, three relative algorithms to construct pairing-friendly elliptic curve are put forward. 10 elliptic curves with low hamming weight 4 under 160 bits are presented to demonstrate the utility of our approach. Finally, the evaluation also indicates that it is more efficient to compute Tate pairing with our curves, than that of Bertoni et al.

User Centered System Design: Papers for the CHI '83 Conference on Human Factors in Computer Systems.

ERIC Educational Resources Information Center

California Univ., San Diego. Center for Human Information Processing.

Four papers from the University of California at San Diego (UCSD) Project on Human-Computer Interfaces are presented in this report. "Evaluation and Analysis of User's Activity Organization," by Liam Bannon, Allen Cypher, Steven Greenspan, and Melissa Monty, analyzes the activities performed by users of computer systems, develops a…

Experiments on Interfaces To Support Query Expansion.

ERIC Educational Resources Information Center

Beaulieu, M.

1997-01-01

Focuses on the user and human-computer interaction aspects of the research based on the Okapi text retrieval system. Three experiments implementing different approaches to query expansion are described, including the use of graphical user interfaces with different windowing techniques. (Author/LRW)

Estimating preferences for modes of drug administration: The case of US healthcare professionals.

PubMed

Tetteh, Ebenezer K; Morris, Steve; Titchener-Hooker, Nigel

2018-01-01

There are hidden drug administration costs that arise from a mismatch between end-user preferences and how manufacturers choose to formulate their drug products for delivery to patients. The corollary of this is: there are "intangible benefits" from considering end-user preferences in manufacturing patient-friendly medicines. It is important then to have some idea of what pharmaceutical manufacturers should consider in making patient-friendly medicines and of the magnitude of the indirect benefits from doing so. This study aimed to evaluate preferences of healthcare professionals in the US for the non-monetary attributes of different modes of drug administration. It uses these preference orderings to compute a monetary valuation of the indirect benefits from making patient-friendly medicines. A survey collected choice preferences of a sample of 210 healthcare professionals in the US for two unlabelled drug options. These drugs were identical except in the levels of attributes of drug administration. Using the choice data collected, statistical models were estimated to compute gross welfare benefits, measured by the expected compensating variation, from making drugs in a more patient-friendly manner. The monetary value of end-user benefits from developing patient-friendly drug delivery systems is: (1) as large as the annual acquisition costs per full treatment episode for some biologic drugs; and (2) likely to fall in the "high end" of the distribution of the direct monetary costs of drug administration. An examination of end-user preferences should help manufacturers make more effective and efficient use of limited resources for innovations in drug delivery system, or manufacturing research in general. Copyright © 2017 Elsevier Inc. All rights reserved.

Development and functional demonstration of a wireless intraoral inductive tongue computer interface for severely disabled persons.

PubMed

N S Andreasen Struijk, Lotte; Lontis, Eugen R; Gaihede, Michael; Caltenco, Hector A; Lund, Morten Enemark; Schioeler, Henrik; Bentsen, Bo

2017-08-01

Individuals with tetraplegia depend on alternative interfaces in order to control computers and other electronic equipment. Current interfaces are often limited in the number of available control commands, and may compromise the social identity of an individual due to their undesirable appearance. The purpose of this study was to implement an alternative computer interface, which was fully embedded into the oral cavity and which provided multiple control commands. The development of a wireless, intraoral, inductive tongue computer was described. The interface encompassed a 10-key keypad area and a mouse pad area. This system was embedded wirelessly into the oral cavity of the user. The functionality of the system was demonstrated in two tetraplegic individuals and two able-bodied individuals Results: The system was invisible during use and allowed the user to type on a computer using either the keypad area or the mouse pad. The maximal typing rate was 1.8 s for repetitively typing a correct character with the keypad area and 1.4 s for repetitively typing a correct character with the mouse pad area. The results suggest that this inductive tongue computer interface provides an esthetically acceptable and functionally efficient environmental control for a severely disabled user. Implications for Rehabilitation New Design, Implementation and detection methods for intra oral assistive devices. Demonstration of wireless, powering and encapsulation techniques suitable for intra oral embedment of assistive devices. Demonstration of the functionality of a rechargeable and fully embedded intra oral tongue controlled computer input device.

Fragment-Based Docking: Development of the CHARMMing Web User Interface as a Platform for Computer-Aided Drug Design

PubMed Central

2015-01-01

Web-based user interfaces to scientific applications are important tools that allow researchers to utilize a broad range of software packages with just an Internet connection and a browser.1 One such interface, CHARMMing (CHARMM interface and graphics), facilitates access to the powerful and widely used molecular software package CHARMM. CHARMMing incorporates tasks such as molecular structure analysis, dynamics, multiscale modeling, and other techniques commonly used by computational life scientists. We have extended CHARMMing’s capabilities to include a fragment-based docking protocol that allows users to perform molecular docking and virtual screening calculations either directly via the CHARMMing Web server or on computing resources using the self-contained job scripts generated via the Web interface. The docking protocol was evaluated by performing a series of “re-dockings” with direct comparison to top commercial docking software. Results of this evaluation showed that CHARMMing’s docking implementation is comparable to many widely used software packages and validates the use of the new CHARMM generalized force field for docking and virtual screening. PMID:25151852

Fragment-based docking: development of the CHARMMing Web user interface as a platform for computer-aided drug design.

PubMed

Pevzner, Yuri; Frugier, Emilie; Schalk, Vinushka; Caflisch, Amedeo; Woodcock, H Lee

2014-09-22

Web-based user interfaces to scientific applications are important tools that allow researchers to utilize a broad range of software packages with just an Internet connection and a browser. One such interface, CHARMMing (CHARMM interface and graphics), facilitates access to the powerful and widely used molecular software package CHARMM. CHARMMing incorporates tasks such as molecular structure analysis, dynamics, multiscale modeling, and other techniques commonly used by computational life scientists. We have extended CHARMMing's capabilities to include a fragment-based docking protocol that allows users to perform molecular docking and virtual screening calculations either directly via the CHARMMing Web server or on computing resources using the self-contained job scripts generated via the Web interface. The docking protocol was evaluated by performing a series of "re-dockings" with direct comparison to top commercial docking software. Results of this evaluation showed that CHARMMing's docking implementation is comparable to many widely used software packages and validates the use of the new CHARMM generalized force field for docking and virtual screening.

Practical experience with graphical user interfaces and object-oriented design in the clinical laboratory.

PubMed

Wells, I G; Cartwright, R Y; Farnan, L P

1993-12-15

The computing strategy in our laboratories evolved from research in Artificial Intelligence, and is based on powerful software tools running on high performance desktop computers with a graphical user interface. This allows most tasks to be regarded as design problems rather than implementation projects, and both rapid prototyping and an object-oriented approach to be employed during the in-house development and enhancement of the laboratory information systems. The practical application of this strategy is discussed, with particular reference to the system designer, the laboratory user and the laboratory customer. Routine operation covers five departments, and the systems are stable, flexible and well accepted by the users. Client-server computing, currently undergoing final trials, is seen as the key to further development, and this approach to Pathology computing has considerable potential for the future.

Development and deployment of a Desktop and Mobile application on grid for GPS studie

NASA Astrophysics Data System (ADS)

Ntumba, Patient; Lotoy, Vianney; Djungu, Saint Jean; Fleury, Rolland; Petitdidier, Monique; Gemünd, André; Schwichtenberg, Horst

2013-04-01

GPS networks for scientific studies are developed all other the world and large databases, regularly updated, like IGS are also available. Many GPS have been installed in West and Central Africa during AMMA (African Monsoon Multiplidisciplinary Analysis), IHY (International heliophysical Year)and many other projects since 2005. African scientists have been educated to use those data especially for meteorological and ionospheric studies. The annual variations of ionospheric parameters for a given station or map of a given region are very intensive computing. Then grid or cloud computing may be a solution to obtain results in a relatively short time. Real time At the University of Kinshasa the chosen solution is a grid of several PCs. It has been deployed by using Globus Toolkit on a Condor pool in order to support the processing of GPS data for ionospheric studies. To be user-friendly, graphical user interfaces(GUI) have been developed to help the user to prepare and submit jobs. One is a java GUI for desktop client, the other is an Android GUI for mobile client. The interest of a grid is the possibility to send a bunch of jobs with an adequate agent control in order to survey the job execution and result storage. After the feasibility study the grid will be extended to a larger number of PCs. Other solutions will be in parallel explored.

State-of-the-art Hydrology Education: Development of Windows-based and Web-based Interactive Teaching-Learning Software

NASA Astrophysics Data System (ADS)

Chu, X.

2011-12-01

This study, funded by the NSF CAREER program, focuses on developing new methods to quantify microtopography-controlled overland flow processes and integrating the cutting-edge hydrologic research with all-level education and outreach activities. To achieve the educational goal, an interactive teaching-learning software package has been developed. This software, with enhanced visualization capabilities, integrates the new modeling techniques, computer-guided learning processes, and education-oriented tools in a user-friendly interface. Both Windows-based and web-based versions have been developed. The software is specially designed for three major user levels: elementary level (Level 1: K-12 and outreach education), medium level (Level 2: undergraduate education), and advanced level (Level 3: graduate education). Depending on the levels, users are guided to different educational systems. Each system consists of a series of mini "libraries" featured with movies, pictures, and documentation that cover fundamental theories, varying scale experiments, and computer modeling of overland flow generation, surface runoff, and infiltration processes. Testing and practical use of this educational software in undergraduate and graduate teaching demonstrate its effectiveness to promote students' learning and interest in hydrologic sciences. This educational software also has been used as a hydrologic demonstration tool for K-12 students and Native American students through the Nurturing American Tribal Undergraduate Research Education (NATURE) program and Science, Technology, Engineering and Mathematics (STEM) outreach activities.

Online Statistical Modeling (Regression Analysis) for Independent Responses

NASA Astrophysics Data System (ADS)

Made Tirta, I.; Anggraeni, Dian; Pandutama, Martinus

2017-06-01

Regression analysis (statistical analmodelling) are among statistical methods which are frequently needed in analyzing quantitative data, especially to model relationship between response and explanatory variables. Nowadays, statistical models have been developed into various directions to model various type and complex relationship of data. Rich varieties of advanced and recent statistical modelling are mostly available on open source software (one of them is R). However, these advanced statistical modelling, are not very friendly to novice R users, since they are based on programming script or command line interface. Our research aims to developed web interface (based on R and shiny), so that most recent and advanced statistical modelling are readily available, accessible and applicable on web. We have previously made interface in the form of e-tutorial for several modern and advanced statistical modelling on R especially for independent responses (including linear models/LM, generalized linier models/GLM, generalized additive model/GAM and generalized additive model for location scale and shape/GAMLSS). In this research we unified them in the form of data analysis, including model using Computer Intensive Statistics (Bootstrap and Markov Chain Monte Carlo/ MCMC). All are readily accessible on our online Virtual Statistics Laboratory. The web (interface) make the statistical modeling becomes easier to apply and easier to compare them in order to find the most appropriate model for the data.

Analysis of User Interaction with a Brain-Computer Interface Based on Steady-State Visually Evoked Potentials: Case Study of a Game

PubMed Central

de Carvalho, Sarah Negreiros; Costa, Thiago Bulhões da Silva; Attux, Romis; Hornung, Heiko Horst; Arantes, Dalton Soares

2018-01-01

This paper presents a systematic analysis of a game controlled by a Brain-Computer Interface (BCI) based on Steady-State Visually Evoked Potentials (SSVEP). The objective is to understand BCI systems from the Human-Computer Interface (HCI) point of view, by observing how the users interact with the game and evaluating how the interface elements influence the system performance. The interactions of 30 volunteers with our computer game, named “Get Coins,” through a BCI based on SSVEP, have generated a database of brain signals and the corresponding responses to a questionnaire about various perceptual parameters, such as visual stimulation, acoustic feedback, background music, visual contrast, and visual fatigue. Each one of the volunteers played one match using the keyboard and four matches using the BCI, for comparison. In all matches using the BCI, the volunteers achieved the goals of the game. Eight of them achieved a perfect score in at least one of the four matches, showing the feasibility of the direct communication between the brain and the computer. Despite this successful experiment, adaptations and improvements should be implemented to make this innovative technology accessible to the end user. PMID:29849549

Analysis of User Interaction with a Brain-Computer Interface Based on Steady-State Visually Evoked Potentials: Case Study of a Game.

PubMed

Leite, Harlei Miguel de Arruda; de Carvalho, Sarah Negreiros; Costa, Thiago Bulhões da Silva; Attux, Romis; Hornung, Heiko Horst; Arantes, Dalton Soares

2018-01-01

This paper presents a systematic analysis of a game controlled by a Brain-Computer Interface (BCI) based on Steady-State Visually Evoked Potentials (SSVEP). The objective is to understand BCI systems from the Human-Computer Interface (HCI) point of view, by observing how the users interact with the game and evaluating how the interface elements influence the system performance. The interactions of 30 volunteers with our computer game, named "Get Coins," through a BCI based on SSVEP, have generated a database of brain signals and the corresponding responses to a questionnaire about various perceptual parameters, such as visual stimulation, acoustic feedback, background music, visual contrast, and visual fatigue. Each one of the volunteers played one match using the keyboard and four matches using the BCI, for comparison. In all matches using the BCI, the volunteers achieved the goals of the game. Eight of them achieved a perfect score in at least one of the four matches, showing the feasibility of the direct communication between the brain and the computer. Despite this successful experiment, adaptations and improvements should be implemented to make this innovative technology accessible to the end user.

Development of a Web Based Simulating System for Earthquake Modeling on the Grid

NASA Astrophysics Data System (ADS)

Seber, D.; Youn, C.; Kaiser, T.

2007-12-01

Existing cyberinfrastructure-based information, data and computational networks now allow development of state- of-the-art, user-friendly simulation environments that democratize access to high-end computational environments and provide new research opportunities for many research and educational communities. Within the Geosciences cyberinfrastructure network, GEON, we have developed the SYNSEIS (SYNthetic SEISmogram) toolkit to enable efficient computations of 2D and 3D seismic waveforms for a variety of research purposes especially for helping to analyze the EarthScope's USArray seismic data in a speedy and efficient environment. The underlying simulation software in SYNSEIS is a finite difference code, E3D, developed by LLNL (S. Larsen). The code is embedded within the SYNSEIS portlet environment and it is used by our toolkit to simulate seismic waveforms of earthquakes at regional distances (<1000km). Architecturally, SYNSEIS uses both Web Service and Grid computing resources in a portal-based work environment and has a built in access mechanism to connect to national supercomputer centers as well as to a dedicated, small-scale compute cluster for its runs. Even though Grid computing is well-established in many computing communities, its use among domain scientists still is not trivial because of multiple levels of complexities encountered. We grid-enabled E3D using our own dialect XML inputs that include geological models that are accessible through standard Web services within the GEON network. The XML inputs for this application contain structural geometries, source parameters, seismic velocity, density, attenuation values, number of time steps to compute, and number of stations. By enabling a portal based access to a such computational environment coupled with its dynamic user interface we enable a large user community to take advantage of such high end calculations in their research and educational activities. Our system can be used to promote an efficient and effective modeling environment to help scientists as well as educators in their daily activities and speed up the scientific discovery process.

Modeling Goal-Directed User Exploration in Human-Computer Interaction

DTIC Science & Technology

2011-02-01

scent, other factors including the layout position and grouping of options in the user-interface also affect user exploration and the likelihood of...grouping of options in the user-interface also affect user exploration and the likelihood of success. This dissertation contributes a new model of goal...better inform UI design. 1.1 RESEARCH GAPS IN MODELING In addition to infoscent, the layout of the UI also affects the choices made during

Formalisms for user interface specification and design

NASA Technical Reports Server (NTRS)

Auernheimer, Brent J.

1989-01-01

The application of formal methods to the specification and design of human-computer interfaces is described. A broad outline of human-computer interface problems, a description of the field of cognitive engineering and two relevant research results, the appropriateness of formal specification techniques, and potential NASA application areas are described.

Fast Risk Assessment Software For Natural Hazard Phenomena Using Georeference Population And Infrastructure Data Bases

NASA Astrophysics Data System (ADS)

Marrero, J. M.; Pastor Paz, J. E.; Erazo, C.; Marrero, M.; Aguilar, J.; Yepes, H. A.; Estrella, C. M.; Mothes, P. A.

2015-12-01

Disaster Risk Reduction (DRR) requires an integrated multi-hazard assessment approach towards natural hazard mitigation. In the case of volcanic risk, long term hazard maps are generally developed on a basis of the most probable scenarios (likelihood of occurrence) or worst cases. However, in the short-term, expected scenarios may vary substantially depending on the monitoring data or new knowledge. In this context, the time required to obtain and process data is critical for optimum decision making. Availability of up-to-date volcanic scenarios is as crucial as it is to have this data accompanied by efficient estimations of their impact among populations and infrastructure. To address this impact estimation during volcanic crises, or other natural hazards, a web interface has been developed to execute an ANSI C application. This application allows one to compute - in a matter of seconds - the demographic and infrastructure impact that any natural hazard may cause employing an overlay-layer approach. The web interface is tailored to users involved in the volcanic crises management of Cotopaxi volcano (Ecuador). The population data base and the cartographic basis used are of public domain, published by the National Office of Statistics of Ecuador (INEC, by its Spanish acronym). To run the application and obtain results the user is expected to upload a raster file containing information related to the volcanic hazard or any other natural hazard, and determine categories to group population or infrastructure potentially affected. The results are displayed in a user-friendly report.

VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites.

PubMed

Spinozzi, Giulio; Calabria, Andrea; Brasca, Stefano; Beretta, Stefano; Merelli, Ivan; Milanesi, Luciano; Montini, Eugenio

2017-11-25

Bioinformatics tools designed to identify lentiviral or retroviral vector insertion sites in the genome of host cells are used to address the safety and long-term efficacy of hematopoietic stem cell gene therapy applications and to study the clonal dynamics of hematopoietic reconstitution. The increasing number of gene therapy clinical trials combined with the increasing amount of Next Generation Sequencing data, aimed at identifying integration sites, require both highly accurate and efficient computational software able to correctly process "big data" in a reasonable computational time. Here we present VISPA2 (Vector Integration Site Parallel Analysis, version 2), the latest optimized computational pipeline for integration site identification and analysis with the following features: (1) the sequence analysis for the integration site processing is fully compliant with paired-end reads and includes a sequence quality filter before and after the alignment on the target genome; (2) an heuristic algorithm to reduce false positive integration sites at nucleotide level to reduce the impact of Polymerase Chain Reaction or trimming/alignment artifacts; (3) a classification and annotation module for integration sites; (4) a user friendly web interface as researcher front-end to perform integration site analyses without computational skills; (5) the time speedup of all steps through parallelization (Hadoop free). We tested VISPA2 performances using simulated and real datasets of lentiviral vector integration sites, previously obtained from patients enrolled in a hematopoietic stem cell gene therapy clinical trial and compared the results with other preexisting tools for integration site analysis. On the computational side, VISPA2 showed a > 6-fold speedup and improved precision and recall metrics (1 and 0.97 respectively) compared to previously developed computational pipelines. These performances indicate that VISPA2 is a fast, reliable and user-friendly tool for integration site analysis, which allows gene therapy integration data to be handled in a cost and time effective fashion. Moreover, the web access of VISPA2 ( http://openserver.itb.cnr.it/vispa/ ) ensures accessibility and ease of usage to researches of a complex analytical tool. We released the source code of VISPA2 in a public repository ( https://bitbucket.org/andreacalabria/vispa2 ).

MethLAB: a graphical user interface package for the analysis of array-based DNA methylation data.

PubMed

Kilaru, Varun; Barfield, Richard T; Schroeder, James W; Smith, Alicia K; Conneely, Karen N

2012-03-01

Recent evidence suggests that DNA methylation changes may underlie numerous complex traits and diseases. The advent of commercial, array-based methods to interrogate DNA methylation has led to a profusion of epigenetic studies in the literature. Array-based methods, such as the popular Illumina GoldenGate and Infinium platforms, estimate the proportion of DNA methylated at single-base resolution for thousands of CpG sites across the genome. These arrays generate enormous amounts of data, but few software resources exist for efficient and flexible analysis of these data. We developed a software package called MethLAB (http://genetics.emory.edu/conneely/MethLAB) using R, an open source statistical language that can be edited to suit the needs of the user. MethLAB features a graphical user interface (GUI) with a menu-driven format designed to efficiently read in and manipulate array-based methylation data in a user-friendly manner. MethLAB tests for association between methylation and relevant phenotypes by fitting a separate linear model for each CpG site. These models can incorporate both continuous and categorical phenotypes and covariates, as well as fixed or random batch or chip effects. MethLAB accounts for multiple testing by controlling the false discovery rate (FDR) at a user-specified level. Standard output includes a spreadsheet-ready text file and an array of publication-quality figures. Considering the growing interest in and availability of DNA methylation data, there is a great need for user-friendly open source analytical tools. With MethLAB, we present a timely resource that will allow users with no programming experience to implement flexible and powerful analyses of DNA methylation data.