PHYSICO2: an UNIX based standalone procedure for computation of physicochemical, window-dependent and substitution based evolutionary properties of protein sequences along with automated block preparation tool, version 2.

PubMed

Banerjee, Shyamashree; Gupta, Parth Sarthi Sen; Nayek, Arnab; Das, Sunit; Sur, Vishma Pratap; Seth, Pratyay; Islam, Rifat Nawaz Ul; Bandyopadhyay, Amal K

2015-01-01

Automated genome sequencing procedure is enriching the sequence database very fast. To achieve a balance between the entry of sequences in the database and their analyses, efficient software is required. In this end PHYSICO2, compare to earlier PHYSICO and other public domain tools, is most efficient in that it i] extracts physicochemical, window-dependent and homologousposition-based-substitution (PWS) properties including positional and BLOCK-specific diversity and conservation, ii] provides users with optional-flexibility in setting relevant input-parameters, iii] helps users to prepare BLOCK-FASTA-file by the use of Automated Block Preparation Tool of the program, iv] performs fast, accurate and user-friendly analyses and v] redirects itemized outputs in excel format along with detailed methodology. The program package contains documentation describing application of methods. Overall the program acts as efficient PWS-analyzer and finds application in sequence-bioinformatics. PHYSICO2: is freely available at http://sourceforge.net/projects/physico2/ along with its documentation at https://sourceforge.net/projects/physico2/files/Documentation.pdf/download for all users.

PHYSICO2: an UNIX based standalone procedure for computation of physicochemical, window-dependent and substitution based evolutionary properties of protein sequences along with automated block preparation tool, version 2

PubMed Central

Banerjee, Shyamashree; Gupta, Parth Sarthi Sen; Nayek, Arnab; Das, Sunit; Sur, Vishma Pratap; Seth, Pratyay; Islam, Rifat Nawaz Ul; Bandyopadhyay, Amal K

2015-01-01

Automated genome sequencing procedure is enriching the sequence database very fast. To achieve a balance between the entry of sequences in the database and their analyses, efficient software is required. In this end PHYSICO2, compare to earlier PHYSICO and other public domain tools, is most efficient in that it i] extracts physicochemical, window-dependent and homologousposition-based-substitution (PWS) properties including positional and BLOCK-specific diversity and conservation, ii] provides users with optional-flexibility in setting relevant input-parameters, iii] helps users to prepare BLOCK-FASTA-file by the use of Automated Block Preparation Tool of the program, iv] performs fast, accurate and user-friendly analyses and v] redirects itemized outputs in excel format along with detailed methodology. The program package contains documentation describing application of methods. Overall the program acts as efficient PWS-analyzer and finds application in sequence-bioinformatics. Availability PHYSICO2: is freely available at http://sourceforge.net/projects/physico2/ along with its documentation at https://sourceforge.net/projects/physico2/files/Documentation.pdf/download for all users. PMID:26339154

Three Applications of Automated Test Assembly within a User-Friendly Modeling Environment

ERIC Educational Resources Information Center

Cor, Ken; Alves, Cecilia; Gierl, Mark

2009-01-01

While linear programming is a common tool in business and industry, there have not been many applications in educational assessment and only a handful of individuals have been actively involved in conducting psychometric research in this area. Perhaps this is due, at least in part, to the complexity of existing software packages. This article…

3D-printed microfluidic automation.

PubMed

Au, Anthony K; Bhattacharjee, Nirveek; Horowitz, Lisa F; Chang, Tim C; Folch, Albert

2015-04-21

Microfluidic automation - the automated routing, dispensing, mixing, and/or separation of fluids through microchannels - generally remains a slowly-spreading technology because device fabrication requires sophisticated facilities and the technology's use demands expert operators. Integrating microfluidic automation in devices has involved specialized multi-layering and bonding approaches. Stereolithography is an assembly-free, 3D-printing technique that is emerging as an efficient alternative for rapid prototyping of biomedical devices. Here we describe fluidic valves and pumps that can be stereolithographically printed in optically-clear, biocompatible plastic and integrated within microfluidic devices at low cost. User-friendly fluid automation devices can be printed and used by non-engineers as replacement for costly robotic pipettors or tedious manual pipetting. Engineers can manipulate the designs as digital modules into new devices of expanded functionality. Printing these devices only requires the digital file and electronic access to a printer.

Application of Expert Systems for Diagnosing Equipment Failures at Central Energy Plants

DTIC Science & Technology

1993-12-01

package to create a "friendly" user interface. Real time data can be displayed in the familiar form of digital or analog gauges. Automated data...District ATTN: CETEC-tM-T ATTN: Libary (40) ATTN: CECC-R 22060 US Military Academy 1 096 ATTN: Egr Strategic Stwiliet Cr ATTN: MAE.-A US Anry EnVr

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.

Facilities Performance Indicators Report 2010-11: Tracking Your Facilities Vital Signs

ERIC Educational Resources Information Center

APPA: Association of Higher Education Facilities Officers, 2012

2012-01-01

APPA's Information and Research Committee's goal for this year was to enhance the survey and report tools by making them both more navigable, user friendly, and accurate. Significant progress has been made with all of these initiatives. APPA also automated many of the internal processes for the survey and report, which resulted in a…

User's operating procedures. Volume 2: Scout project financial analysis program

NASA Technical Reports Server (NTRS)

Harris, C. G.; Haris, D. K.

1985-01-01

A review is presented of the user's operating procedures for the Scout Project Automatic Data system, called SPADS. SPADS is the result of the past seven years of software development on a Prime mini-computer located at the Scout Project Office, NASA Langley Research Center, Hampton, Virginia. SPADS was developed as a single entry, multiple cross-reference data management and information retrieval system for the automation of Project office tasks, including engineering, financial, managerial, and clerical support. This volume, two (2) of three (3), provides the instructions to operate the Scout Project Financial Analysis program in data retrieval and file maintenance via the user friendly menu drivers.

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.

PRIMO: An Interactive Homology Modeling Pipeline.

PubMed

Hatherley, Rowan; Brown, David K; Glenister, Michael; Tastan Bishop, Özlem

2016-01-01

The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homology modeling of protein monomers. The pipeline eases the multi-step modeling process, and reduces the workload required by the user, while still allowing engagement from the user during every step. Default parameters are given for each step, which can either be modified or supplemented with additional external input. PRIMO has been designed for users of varying levels of experience with homology modeling. The pipeline incorporates a user-friendly interface that makes it easy to alter parameters used during modeling. During each stage of the modeling process, the site provides suggestions for novice users to improve the quality of their models. PRIMO provides functionality that allows users to also model ligands and ions in complex with their protein targets. Herein, we assess the accuracy of the fully automated capabilities of the server, including a comparative analysis of the available alignment programs, as well as of the refinement levels used during modeling. The tests presented here demonstrate the reliability of the PRIMO server when producing a large number of protein models. While PRIMO does focus on user involvement in the homology modeling process, the results indicate that in the presence of suitable templates, good quality models can be produced even without user intervention. This gives an idea of the base level accuracy of PRIMO, which users can improve upon by adjusting parameters in their modeling runs. The accuracy of PRIMO's automated scripts is being continuously evaluated by the CAMEO (Continuous Automated Model EvaluatiOn) project. The PRIMO site is free for non-commercial use and can be accessed at https://primo.rubi.ru.ac.za/.

PRIMO: An Interactive Homology Modeling Pipeline

PubMed Central

Glenister, Michael

2016-01-01

The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homology modeling of protein monomers. The pipeline eases the multi-step modeling process, and reduces the workload required by the user, while still allowing engagement from the user during every step. Default parameters are given for each step, which can either be modified or supplemented with additional external input. PRIMO has been designed for users of varying levels of experience with homology modeling. The pipeline incorporates a user-friendly interface that makes it easy to alter parameters used during modeling. During each stage of the modeling process, the site provides suggestions for novice users to improve the quality of their models. PRIMO provides functionality that allows users to also model ligands and ions in complex with their protein targets. Herein, we assess the accuracy of the fully automated capabilities of the server, including a comparative analysis of the available alignment programs, as well as of the refinement levels used during modeling. The tests presented here demonstrate the reliability of the PRIMO server when producing a large number of protein models. While PRIMO does focus on user involvement in the homology modeling process, the results indicate that in the presence of suitable templates, good quality models can be produced even without user intervention. This gives an idea of the base level accuracy of PRIMO, which users can improve upon by adjusting parameters in their modeling runs. The accuracy of PRIMO’s automated scripts is being continuously evaluated by the CAMEO (Continuous Automated Model EvaluatiOn) project. The PRIMO site is free for non-commercial use and can be accessed at https://primo.rubi.ru.ac.za/. PMID:27855192

Lab-on-a-Chip Device for Rapid Measurement of Vitamin D Levels.

PubMed

Peter, Harald; Bistolas, Nikitas; Schumacher, Soeren; Laurisch, Cecilia; Guest, Paul C; Höller, Ulrich; Bier, Frank F

2018-01-01

Lab-on-a-chip assays allow rapid analysis of one or more molecular analytes on an automated user-friendly platform. Here we describe a fully automated assay and readout for measurement of vitamin D levels in less than 15 min using the Fraunhofer in vitro diagnostics platform. Vitamin D (25-hydroxyvitamin D 3 [25(OH)D 3 ]) dilution series in buffer were successfully tested down to 2 ng/mL. This could be applied in the future as an inexpensive point-of-care analysis for patients suffering from a variety of conditions marked by vitamin D deficiencies.

3D-Printed Microfluidic Automation

PubMed Central

Au, Anthony K.; Bhattacharjee, Nirveek; Horowitz, Lisa F.; Chang, Tim C.; Folch, Albert

2015-01-01

Microfluidic automation – the automated routing, dispensing, mixing, and/or separation of fluids through microchannels – generally remains a slowly-spreading technology because device fabrication requires sophisticated facilities and the technology’s use demands expert operators. Integrating microfluidic automation in devices has involved specialized multi-layering and bonding approaches. Stereolithography is an assembly-free, 3D-printing technique that is emerging as an efficient alternative for rapid prototyping of biomedical devices. Here we describe fluidic valves and pumps that can be stereolithographically printed in optically-clear, biocompatible plastic and integrated within microfluidic devices at low cost. User-friendly fluid automation devices can be printed and used by non-engineers as replacement for costly robotic pipettors or tedious manual pipetting. Engineers can manipulate the designs as digital modules into new devices of expanded functionality. Printing these devices only requires the digital file and electronic access to a printer. PMID:25738695

AIRSAR Web-Based Data Processing

NASA Technical Reports Server (NTRS)

Chu, Anhua; Van Zyl, Jakob; Kim, Yunjin; Hensley, Scott; Lou, Yunling; Madsen, Soren; Chapman, Bruce; Imel, David; Durden, Stephen; Tung, Wayne

2007-01-01

The AIRSAR automated, Web-based data processing and distribution system is an integrated, end-to-end synthetic aperture radar (SAR) processing system. Designed to function under limited resources and rigorous demands, AIRSAR eliminates operational errors and provides for paperless archiving. Also, it provides a yearly tune-up of the processor on flight missions, as well as quality assurance with new radar modes and anomalous data compensation. The software fully integrates a Web-based SAR data-user request subsystem, a data processing system to automatically generate co-registered multi-frequency images from both polarimetric and interferometric data collection modes in 80/40/20 MHz bandwidth, an automated verification quality assurance subsystem, and an automatic data distribution system for use in the remote-sensor community. Features include Survey Automation Processing in which the software can automatically generate a quick-look image from an entire 90-GB SAR raw data 32-MB/s tape overnight without operator intervention. Also, the software allows product ordering and distribution via a Web-based user request system. To make AIRSAR more user friendly, it has been designed to let users search by entering the desired mission flight line (Missions Searching), or to search for any mission flight line by entering the desired latitude and longitude (Map Searching). For precision image automation processing, the software generates the products according to each data processing request stored in the database via a Queue management system. Users are able to have automatic generation of coregistered multi-frequency images as the software generates polarimetric and/or interferometric SAR data processing in ground and/or slant projection according to user processing requests for one of the 12 radar modes.

IFDOTMETER: A New Software Application for Automated Immunofluorescence Analysis.

PubMed

Rodríguez-Arribas, Mario; Pizarro-Estrella, Elisa; Gómez-Sánchez, Rubén; Yakhine-Diop, S M S; Gragera-Hidalgo, Antonio; Cristo, Alejandro; Bravo-San Pedro, Jose M; González-Polo, Rosa A; Fuentes, José M

2016-04-01

Most laboratories interested in autophagy use different imaging software for managing and analyzing heterogeneous parameters in immunofluorescence experiments (e.g., LC3-puncta quantification and determination of the number and size of lysosomes). One solution would be software that works on a user's laptop or workstation that can access all image settings and provide quick and easy-to-use analysis of data. Thus, we have designed and implemented an application called IFDOTMETER, which can run on all major operating systems because it has been programmed using JAVA (Sun Microsystems). Briefly, IFDOTMETER software has been created to quantify a variety of biological hallmarks, including mitochondrial morphology and nuclear condensation. The program interface is intuitive and user-friendly, making it useful for users not familiar with computer handling. By setting previously defined parameters, the software can automatically analyze a large number of images without the supervision of the researcher. Once analysis is complete, the results are stored in a spreadsheet. Using software for high-throughput cell image analysis offers researchers the possibility of performing comprehensive and precise analysis of a high number of images in an automated manner, making this routine task easier. © 2015 Society for Laboratory Automation and Screening.

Thermal depth profiling of vascular lesions: automated regularization of reconstruction algorithms

NASA Astrophysics Data System (ADS)

Verkruysse, Wim; Choi, Bernard; Zhang, Jenny R.; Kim, Jeehyun; Nelson, J. Stuart

2008-03-01

Pulsed photo-thermal radiometry (PPTR) is a non-invasive, non-contact diagnostic technique used to locate cutaneous chromophores such as melanin (epidermis) and hemoglobin (vascular structures). Clinical utility of PPTR is limited because it typically requires trained user intervention to regularize the inversion solution. Herein, the feasibility of automated regularization was studied. A second objective of this study was to depart from modeling port wine stain PWS, a vascular skin lesion frequently studied with PPTR, as strictly layered structures since this may influence conclusions regarding PPTR reconstruction quality. Average blood vessel depths, diameters and densities derived from histology of 30 PWS patients were used to generate 15 randomized lesion geometries for which we simulated PPTR signals. Reconstruction accuracy for subjective regularization was compared with that for automated regularization methods. The objective regularization approach performed better. However, the average difference was much smaller than the variation between the 15 simulated profiles. Reconstruction quality depended more on the actual profile to be reconstructed than on the reconstruction algorithm or regularization method. Similar, or better, accuracy reconstructions can be achieved with an automated regularization procedure which enhances prospects for user friendly implementation of PPTR to optimize laser therapy on an individual patient basis.

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.

Trust and reliance on an automated combat identification system.

PubMed

Wang, Lu; Jamieson, Greg A; Hollands, Justin G

2009-06-01

We examined the effects of aid reliability and reliability disclosure on human trust in and reliance on a combat identification (CID) aid. We tested whether trust acts as a mediating factor between belief in and reliance on a CID aid. Individual CID systems have been developed to reduce friendly fire incidents. However, these systems cannot positively identify a target that does not have a working transponder. Therefore, when the feedback is "unknown", the target could be hostile, neutral, or friendly. Soldiers have difficulty relying on this type of imperfect automation appropriately. In manual and aided conditions, 24 participants completed a simulated CID task. The reliability of the aid varied within participants, half of whom were told the aid reliability level. We used the difference in response bias values across conditions to measure automation reliance. Response bias varied more appropriately with the aid reliability level when it was disclosed than when not. Trust in aid feedback correlated with belief in aid reliability and reliance on aid feedback; however, belief was not correlated with reliance. To engender appropriate reliance on CID systems, users should be made aware of system reliability. The findings can be applied to the design of information displays for individual CID systems and soldier training.

ASPECTS: an automation-assisted SPE method development system.

PubMed

Li, Ming; Chou, Judy; King, Kristopher W; Yang, Liyu

2013-07-01

A typical conventional SPE method development (MD) process usually involves deciding the chemistry of the sorbent and eluent based on information about the analyte; experimentally preparing and trying out various combinations of adsorption chemistry and elution conditions; quantitatively evaluating the various conditions; and comparing quantitative results from all combination of conditions to select the best condition for method qualification. The second and fourth steps have mostly been performed manually until now. We developed an automation-assisted system that expedites the conventional SPE MD process by automating 99% of the second step, and expedites the fourth step by automatically processing the results data and presenting it to the analyst in a user-friendly format. The automation-assisted SPE MD system greatly saves the manual labor in SPE MD work, prevents analyst errors from causing misinterpretation of quantitative results, and shortens data analysis and interpretation time.

Combinatorial electrochemical synthesis and screening of Pt-WO3 catalysts for electro-oxidation of methanol

NASA Astrophysics Data System (ADS)

Jayaraman, Shrisudersan; Baeck, Sung-Hyeon; Jaramillo, Thomas F.; Kleiman-Shwarsctein, Alan; McFarland, Eric W.

2005-06-01

An automated system for high-throughput electrochemical synthesis and screening of fuel cell electro-oxidation catalysts is described. This system consists of an electrode probe that contains counter and reference electrodes that can be positioned inside an array of electrochemical cells created within a polypropylene block. The electrode probe is attached to an automated of X-Y-Z motion system. An externally controlled potentiostat is used to apply the electrochemical potential to the catalyst substrate. The motion and electrochemical control are integrated using a user-friendly software interface. During automated synthesis the deposition potential and/or current may be controlled by a pulse program triggered by the software using a data acquisition board. The screening includes automated experiments to obtain cyclic voltammograms. As an example, a platinum-tungsten oxide (Pt-WO3) library was synthesized and characterized for reactivity towards methanol electro-oxidation.

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

IDATEN and G-SITENNO: GUI-assisted software for coherent X-ray diffraction imaging experiments and data analyses at SACLA.

PubMed

Sekiguchi, Yuki; Yamamoto, Masaki; Oroguchi, Tomotaka; Takayama, Yuki; Suzuki, Shigeyuki; Nakasako, Masayoshi

2014-11-01

Using our custom-made diffraction apparatus KOTOBUKI-1 and two multiport CCD detectors, cryogenic coherent X-ray diffraction imaging experiments have been undertaken at the SPring-8 Angstrom Compact free electron LAser (SACLA) facility. To efficiently perform experiments and data processing, two software suites with user-friendly graphical user interfaces have been developed. The first is a program suite named IDATEN, which was developed to easily conduct four procedures during experiments: aligning KOTOBUKI-1, loading a flash-cooled sample into the cryogenic goniometer stage inside the vacuum chamber of KOTOBUKI-1, adjusting the sample position with respect to the X-ray beam using a pair of telescopes, and collecting diffraction data by raster scanning the sample with X-ray pulses. Named G-SITENNO, the other suite is an automated version of the original SITENNO suite, which was designed for processing diffraction data. These user-friendly software suites are now indispensable for collecting a large number of diffraction patterns and for processing the diffraction patterns immediately after collecting data within a limited beam time.

MareyMap Online: A User-Friendly Web Application and Database Service for Estimating Recombination Rates Using Physical and Genetic Maps.

PubMed

Siberchicot, Aurélie; Bessy, Adrien; Guéguen, Laurent; Marais, Gabriel A B

2017-10-01

Given the importance of meiotic recombination in biology, there is a need to develop robust methods to estimate meiotic recombination rates. A popular approach, called the Marey map approach, relies on comparing genetic and physical maps of a chromosome to estimate local recombination rates. In the past, we have implemented this approach in an R package called MareyMap, which includes many functionalities useful to get reliable recombination rate estimates in a semi-automated way. MareyMap has been used repeatedly in studies looking at the effect of recombination on genome evolution. Here, we propose a simpler user-friendly web service version of MareyMap, called MareyMap Online, which allows a user to get recombination rates from her/his own data or from a publicly available database that we offer in a few clicks. When the analysis is done, the user is asked whether her/his curated data can be placed in the database and shared with other users, which we hope will make meta-analysis on recombination rates including many species easy in the future. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Automated workflows for modelling chemical fate, kinetics and toxicity.

PubMed

Sala Benito, J V; Paini, Alicia; Richarz, Andrea-Nicole; Meinl, Thorsten; Berthold, Michael R; Cronin, Mark T D; Worth, Andrew P

2017-12-01

Automation is universal in today's society, from operating equipment such as machinery, in factory processes, to self-parking automobile systems. While these examples show the efficiency and effectiveness of automated mechanical processes, automated procedures that support the chemical risk assessment process are still in their infancy. Future human safety assessments will rely increasingly on the use of automated models, such as physiologically based kinetic (PBK) and dynamic models and the virtual cell based assay (VCBA). These biologically-based models will be coupled with chemistry-based prediction models that also automate the generation of key input parameters such as physicochemical properties. The development of automated software tools is an important step in harmonising and expediting the chemical safety assessment process. In this study, we illustrate how the KNIME Analytics Platform can be used to provide a user-friendly graphical interface for these biokinetic models, such as PBK models and VCBA, which simulates the fate of chemicals in vivo within the body and in vitro test systems respectively. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Extracting DNA from FFPE Tissue Biospecimens Using User-Friendly Automated Technology: Is There an Impact on Yield or Quality?

PubMed

Mathieson, William; Guljar, Nafia; Sanchez, Ignacio; Sroya, Manveer; Thomas, Gerry A

2018-05-03

DNA extracted from formalin-fixed, paraffin-embedded (FFPE) tissue blocks is amenable to analytical techniques, including sequencing. DNA extraction protocols are typically long and complex, often involving an overnight proteinase K digest. Automated platforms that shorten and simplify the process are therefore an attractive proposition for users wanting a faster turn-around or to process large numbers of biospecimens. It is, however, unclear whether automated extraction systems return poorer DNA yields or quality than manual extractions performed by experienced technicians. We extracted DNA from 42 FFPE clinical tissue biospecimens using the QiaCube (Qiagen) and ExScale (ExScale Biospecimen Solutions) automated platforms, comparing DNA yields and integrities with those from manual extractions. The QIAamp DNA FFPE Spin Column Kit was used for manual and QiaCube DNA extractions and the ExScale extractions were performed using two of the manufacturer's magnetic bead kits: one extracting DNA only and the other simultaneously extracting DNA and RNA. In all automated extraction methods, DNA yields and integrities (assayed using DNA Integrity Numbers from a 4200 TapeStation and the qPCR-based Illumina FFPE QC Assay) were poorer than in the manual method, with the QiaCube system performing better than the ExScale system. However, ExScale was fastest, offered the highest reproducibility when extracting DNA only, and required the least intervention or technician experience. Thus, the extraction methods have different strengths and weaknesses, would appeal to different users with different requirements, and therefore, we cannot recommend one method over another.

Specdata: Automated Analysis Software for Broadband Spectra

NASA Astrophysics Data System (ADS)

Oliveira, Jasmine N.; Martin-Drumel, Marie-Aline; McCarthy, Michael C.

2017-06-01

With the advancement of chirped-pulse techniques, broadband rotational spectra with a few tens to several hundred GHz of spectral coverage are now routinely recorded. When studying multi-component mixtures that might result, for example, with the use of an electrical discharge, lines of new chemical species are often obscured by those of known compounds, and analysis can be laborious. To address this issue, we have developed SPECdata, an open source, interactive tool which is designed to simplify and greatly accelerate the spectral analysis and discovery. Our software tool combines both automated and manual components that free the user from computation, while giving him/her considerable flexibility to assign, manipulate, interpret and export their analysis. The automated - and key - component of the new software is a database query system that rapidly assigns transitions of known species in an experimental spectrum. For each experiment, the software identifies spectral features, and subsequently assigns them to known molecules within an in-house database (Pickett .cat files, list of frequencies...), or those catalogued in Splatalogue (using automatic on-line queries). With suggested assignments, the control is then handed over to the user who can choose to accept, decline or add additional species. Data visualization, statistical information, and interactive widgets assist the user in making decisions about their data. SPECdata has several other useful features intended to improve the user experience. Exporting a full report of the analysis, or a peak file in which assigned lines are removed are among several options. A user may also save their progress to continue at another time. Additional features of SPECdata help the user to maintain and expand their database for future use. A user-friendly interface allows one to search, upload, edit or update catalog or experiment entries.

SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies

PubMed Central

2013-01-01

Background Surrogate variable analysis (SVA) is a powerful method to identify, estimate, and utilize the components of gene expression heterogeneity due to unknown and/or unmeasured technical, genetic, environmental, or demographic factors. These sources of heterogeneity are common in gene expression studies, and failing to incorporate them into the analysis can obscure results. Using SVA increases the biological accuracy and reproducibility of gene expression studies by identifying these sources of heterogeneity and correctly accounting for them in the analysis. Results Here we have developed a web application called SVAw (Surrogate variable analysis Web app) that provides a user friendly interface for SVA analyses of genome-wide expression studies. The software has been developed based on open source bioconductor SVA package. In our software, we have extended the SVA program functionality in three aspects: (i) the SVAw performs a fully automated and user friendly analysis workflow; (ii) It calculates probe/gene Statistics for both pre and post SVA analysis and provides a table of results for the regression of gene expression on the primary variable of interest before and after correcting for surrogate variables; and (iii) it generates a comprehensive report file, including graphical comparison of the outcome for the user. Conclusions SVAw is a web server freely accessible solution for the surrogate variant analysis of high-throughput datasets and facilitates removing all unwanted and unknown sources of variation. It is freely available for use at http://psychiatry.igm.jhmi.edu/sva. The executable packages for both web and standalone application and the instruction for installation can be downloaded from our web site. PMID:23497726

MIEC-SVM: automated pipeline for protein peptide/ligand interaction prediction.

PubMed

Li, Nan; Ainsworth, Richard I; Wu, Meixin; Ding, Bo; Wang, Wei

2016-03-15

MIEC-SVM is a structure-based method for predicting protein recognition specificity. Here, we present an automated MIEC-SVM pipeline providing an integrated and user-friendly workflow for construction and application of the MIEC-SVM models. This pipeline can handle standard amino acids and those with post-translational modifications (PTMs) or small molecules. Moreover, multi-threading and support to Sun Grid Engine (SGE) are implemented to significantly boost the computational efficiency. The program is available at http://wanglab.ucsd.edu/MIEC-SVM CONTACT: : wei-wang@ucsd.edu Supplementary data available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE

PubMed Central

Moriya, Toshio; Saur, Michael; Stabrin, Markus; Merino, Felipe; Voicu, Horatiu; Huang, Zhong; Penczek, Pawel A.; Raunser, Stefan; Gatsogiannis, Christos

2017-01-01

SPHIRE (SPARX for High-Resolution Electron Microscopy) is a novel open-source, user-friendly software suite for the semi-automated processing of single particle electron cryo-microscopy (cryo-EM) data. The protocol presented here describes in detail how to obtain a near-atomic resolution structure starting from cryo-EM micrograph movies by guiding users through all steps of the single particle structure determination pipeline. These steps are controlled from the new SPHIRE graphical user interface and require minimum user intervention. Using this protocol, a 3.5 Å structure of TcdA1, a Tc toxin complex from Photorhabdus luminescens, was derived from only 9500 single particles. This streamlined approach will help novice users without extensive processing experience and a priori structural information, to obtain noise-free and unbiased atomic models of their purified macromolecular complexes in their native state. PMID:28570515

An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products.

PubMed

Johnston, Chad W; Skinnider, Michael A; Wyatt, Morgan A; Li, Xiang; Ranieri, Michael R M; Yang, Lian; Zechel, David L; Ma, Bin; Magarvey, Nathan A

2015-09-28

Bacterial natural products are a diverse and valuable group of small molecules, and genome sequencing indicates that the vast majority remain undiscovered. The prediction of natural product structures from biosynthetic assembly lines can facilitate their discovery, but highly automated, accurate, and integrated systems are required to mine the broad spectrum of sequenced bacterial genomes. Here we present a genome-guided natural products discovery tool to automatically predict, combinatorialize and identify polyketides and nonribosomal peptides from biosynthetic assembly lines using LC-MS/MS data of crude extracts in a high-throughput manner. We detail the directed identification and isolation of six genetically predicted polyketides and nonribosomal peptides using our Genome-to-Natural Products platform. This highly automated, user-friendly programme provides a means of realizing the potential of genetically encoded natural products.

Development of a Software Tool to Automate ADCO Flight Controller Console Planning Tasks

NASA Technical Reports Server (NTRS)

Anderson, Mark G.

2011-01-01

This independent study project covers the development of the International Space Station (ISS) Attitude Determination and Control Officer (ADCO) Planning Exchange APEX Tool. The primary goal of the tool is to streamline existing manual and time-intensive planning tools into a more automated, user-friendly application that interfaces with existing products and allows the ADCO to produce accurate products and timelines more effectively. This paper will survey the current ISS attitude planning process and its associated requirements, goals, documentation and software tools and how a software tool could simplify and automate many of the planning actions which occur at the ADCO console. The project will be covered from inception through the initial prototype delivery in November 2011 and will include development of design requirements and software as well as design verification and testing.

ST Spot Detector: a web-based application for automatic spot and tissue detection for spatial Transcriptomics image datasets.

PubMed

Wong, Kim; Navarro, José Fernández; Bergenstråhle, Ludvig; Ståhl, Patrik L; Lundeberg, Joakim

2018-06-01

Spatial Transcriptomics (ST) is a method which combines high resolution tissue imaging with high troughput transcriptome sequencing data. This data must be aligned with the images for correct visualization, a process that involves several manual steps. Here we present ST Spot Detector, a web tool that automates and facilitates this alignment through a user friendly interface. jose.fernandez.navarro@scilifelab.se. Supplementary data are available at Bioinformatics online.

Advanced Cell Classifier: User-Friendly Machine-Learning-Based Software for Discovering Phenotypes in High-Content Imaging Data.

PubMed

Piccinini, Filippo; Balassa, Tamas; Szkalisity, Abel; Molnar, Csaba; Paavolainen, Lassi; Kujala, Kaisa; Buzas, Krisztina; Sarazova, Marie; Pietiainen, Vilja; Kutay, Ulrike; Smith, Kevin; Horvath, Peter

2017-06-28

High-content, imaging-based screens now routinely generate data on a scale that precludes manual verification and interrogation. Software applying machine learning has become an essential tool to automate analysis, but these methods require annotated examples to learn from. Efficiently exploring large datasets to find relevant examples remains a challenging bottleneck. Here, we present Advanced Cell Classifier (ACC), a graphical software package for phenotypic analysis that addresses these difficulties. ACC applies machine-learning and image-analysis methods to high-content data generated by large-scale, cell-based experiments. It features methods to mine microscopic image data, discover new phenotypes, and improve recognition performance. We demonstrate that these features substantially expedite the training process, successfully uncover rare phenotypes, and improve the accuracy of the analysis. ACC is extensively documented, designed to be user-friendly for researchers without machine-learning expertise, and distributed as a free open-source tool at www.cellclassifier.org. Copyright © 2017 Elsevier Inc. All rights reserved.

BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins.

PubMed

van Heel, Auke J; de Jong, Anne; Song, Chunxu; Viel, Jakob H; Kok, Jan; Kuipers, Oscar P

2018-05-21

Interest in secondary metabolites such as RiPPs (ribosomally synthesized and posttranslationally modified peptides) is increasing worldwide. To facilitate the research in this field we have updated our mining web server. BAGEL4 is faster than its predecessor and is now fully independent from ORF-calling. Gene clusters of interest are discovered using the core-peptide database and/or through HMM motifs that are present in associated context genes. The databases used for mining have been updated and extended with literature references and links to UniProt and NCBI. Additionally, we have included automated promoter and terminator prediction and the option to upload RNA expression data, which can be displayed along with the identified clusters. Further improvements include the annotation of the context genes, which is now based on a fast blast against the prokaryote part of the UniRef90 database, and the improved web-BLAST feature that dynamically loads structural data such as internal cross-linking from UniProt. Overall BAGEL4 provides the user with more information through a user-friendly web-interface which simplifies data evaluation. BAGEL4 is freely accessible at http://bagel4.molgenrug.nl.

AVR Microcontroller-based automated technique for analysis of DC motors

NASA Astrophysics Data System (ADS)

Kaur, P.; Chatterji, S.

2014-01-01

This paper provides essential information on the development of a 'dc motor test and analysis control card' using AVR series ATMega32 microcontroller. This card can be interfaced to PC and calculates parameters like motor losses, efficiency and plot characteristics for dc motors. Presently, there are different tests and methods available to evaluate motor parameters, but a single and universal user-friendly automated set-up has been discussed in this paper. It has been accomplished by designing a data acquisition and SCR bridge firing hardware based on AVR ATMega32 microcontroller. This hardware has the capability to drive the phase-controlled rectifiers and acquire real-time values of current, voltage, temperature and speed of motor. Various analyses feasible with the designed hardware are of immense importance for dc motor manufacturers and quality-sensitive users. Authors, through this paper aim to provide details of this AVR-based hardware which can be used for dc motor parameter analysis and also for motor control applications.

Developing a Ruggedized User-Friendly UAS for Monitoring Volcanic Emissions

NASA Astrophysics Data System (ADS)

Wardell, L. J.; Elston, J. S.; Stachura, M.

2017-12-01

Using lessons learned from a history of airborne volcano measurements and a range of UAS R&D, a reliable and ruggedized UAS is being developed specifically for volcano monitoring and response. A key feature is the user interface (UI) that allows for a menu of automated flight plans that will account for terrain and sensor requirements. Due to variation in response times of miniaturized airborne the sensors, flight plan options are extended to account for sensor lag when needed. By automating such complicating variables into the UI, the amount of background and training needed for operation is further minimized. Payload options include simultaneous in situ gas and particle sensors combined with downward-looking imagers to provide a wide range of data products. Currently under development by Black Swift Technologies, the latest updates and test results will be presented. Specifications of the Superswift airframe include a 6,000 m flight ceiling, 2.4 kg payload capacity, and 2 hr endurance.

Design and analysis on sorting blade for automated size-based sorting device

NASA Astrophysics Data System (ADS)

Razali, Zol Bahri; Kader, Mohamed Mydin M. Abdul; Samsudin, Yasser Suhaimi; Daud, Mohd Hisam

2017-09-01

Nowadays rubbish separating or recycling is a main problem of nation, where peoples dumped their rubbish into dumpsite without caring the value of the rubbish if it can be recycled and reused. Thus the author proposed an automated segregating device, purposely to teach people to separate their rubbish and value the rubbish that can be reused. The automated size-based mechanical segregating device provides significant improvements in terms of efficiency and consistency in this segregating process. This device is designed to make recycling easier, user friendly, in the hope that more people will take responsibility if it is less of an expense of time and effort. This paper discussed about redesign a blade for the sorting device which is to develop an efficient automated mechanical sorting device for the similar material but in different size. The machine is able to identify the size of waste and it depends to the coil inside the container to separate it out. The detail design and methodology is described in detail in this paper.

The closer the relationship, the more the interaction on facebook? Investigating the case of Taiwan users.

PubMed

Hsu, Chiung-Wen Julia; Wang, Ching-Chan; Tai, Yi-Ting

2011-01-01

This study argues for the necessity of applying offline contexts to social networking site research and the importance of distinguishing the relationship types of users' counterparts when studying Facebook users' behaviors. In an attempt to examine the relationship among users' behaviors, their counterparts' relationship types, and the users' perceived acquaintanceships after using Facebook, this study first investigated users' frequently used tools when interacting with different types of friends. Users tended to use less time- and effort-consuming and less privacy-concerned tools with newly acquired friends. This study further examined users' behaviors in terms of their closeness and intimacy and their perceived acquaintanceships toward four different types of friends. The study found that users gained more perceived acquaintanceships from less close friends with whom users have more frequent interaction but less intimate behaviors. As for closer friends, users tended to use more intimate activities to interact with them. However, these activities did not necessarily occur more frequently than the activities they employed with their less close friends. It was found that perceived acquaintanceships with closer friends were significantly lower than those with less close friends. This implies that Facebook is a mechanism for new friends, rather than close friends, to become more acquainted.

ASERA: A Spectrum Eye Recognition Assistant

NASA Astrophysics Data System (ADS)

Yuan, Hailong; Zhang, Haotong; Zhang, Yanxia; Lei, Yajuan; Dong, Yiqiao; Zhao, Yongheng

2018-04-01

ASERA, ASpectrum Eye Recognition Assistant, aids in quasar spectral recognition and redshift measurement and can also be used to recognize various types of spectra of stars, galaxies and AGNs (Active Galactic Nucleus). This interactive software allows users to visualize observed spectra, superimpose template spectra from the Sloan Digital Sky Survey (SDSS), and interactively access related spectral line information. ASERA is an efficient and user-friendly semi-automated toolkit for the accurate classification of spectra observed by LAMOST (the Large Sky Area Multi-object Fiber Spectroscopic Telescope) and is available as a standalone Java application and as a Java applet. The software offers several functions, including wavelength and flux scale settings, zoom in and out, redshift estimation, and spectral line identification.

BioTextQuest: a web-based biomedical text mining suite for concept discovery.

PubMed

Papanikolaou, Nikolas; Pafilis, Evangelos; Nikolaou, Stavros; Ouzounis, Christos A; Iliopoulos, Ioannis; Promponas, Vasilis J

2011-12-01

BioTextQuest combines automated discovery of significant terms in article clusters with structured knowledge annotation, via Named Entity Recognition services, offering interactive user-friendly visualization. A tag-cloud-based illustration of terms labeling each document cluster are semantically annotated according to the biological entity, and a list of document titles enable users to simultaneously compare terms and documents of each cluster, facilitating concept association and hypothesis generation. BioTextQuest allows customization of analysis parameters, e.g. clustering/stemming algorithms, exclusion of documents/significant terms, to better match the biological question addressed. http://biotextquest.biol.ucy.ac.cy vprobon@ucy.ac.cy; iliopj@med.uoc.gr Supplementary data are available at Bioinformatics online.

AutoCellSeg: robust automatic colony forming unit (CFU)/cell analysis using adaptive image segmentation and easy-to-use post-editing techniques.

PubMed

Khan, Arif Ul Maula; Torelli, Angelo; Wolf, Ivo; Gretz, Norbert

2018-05-08

In biological assays, automated cell/colony segmentation and counting is imperative owing to huge image sets. Problems occurring due to drifting image acquisition conditions, background noise and high variation in colony features in experiments demand a user-friendly, adaptive and robust image processing/analysis method. We present AutoCellSeg (based on MATLAB) that implements a supervised automatic and robust image segmentation method. AutoCellSeg utilizes multi-thresholding aided by a feedback-based watershed algorithm taking segmentation plausibility criteria into account. It is usable in different operation modes and intuitively enables the user to select object features interactively for supervised image segmentation method. It allows the user to correct results with a graphical interface. This publicly available tool outperforms tools like OpenCFU and CellProfiler in terms of accuracy and provides many additional useful features for end-users.

Time-Motion Analysis of Four Automated Systems for the Detection of Chlamydia trachomatis and Neisseria gonorrhoeae by Nucleic Acid Amplification Testing.

PubMed

Williams, James A; Eddleman, Laura; Pantone, Amy; Martinez, Regina; Young, Stephen; Van Der Pol, Barbara

2014-08-01

Next-generation diagnostics for Chlamydia trachomatis and Neisseria gonorrhoeae are available on semi- or fully-automated platforms. These systems require less hands-on time than older platforms and are user friendly. Four automated systems, the ABBOTT m2000 system, Becton Dickinson Viper System with XTR Technology, Gen-Probe Tigris DTS system, and Roche cobas 4800 system, were evaluated for total run time, hands-on time, and walk-away time. All of the systems evaluated in this time-motion study were able to complete a diagnostic test run within an 8-h work shift, instrument setup and operation were straightforward and uncomplicated, and walk-away time ranged from approximately 90 to 270 min in a head-to-head comparison of each system. All of the automated systems provide technical staff with increased time to perform other tasks during the run, offer easy expansion of the diagnostic test menu, and have the ability to increase specimen throughput. © 2013 Society for Laboratory Automation and Screening.

SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing.

PubMed

Sato, Yukuto; Kojima, Kaname; Nariai, Naoki; Yamaguchi-Kabata, Yumi; Kawai, Yosuke; Takahashi, Mamoru; Mimori, Takahiro; Nagasaki, Masao

2014-08-08

Next-generation sequencers (NGSs) have become one of the main tools for current biology. To obtain useful insights from the NGS data, it is essential to control low-quality portions of the data affected by technical errors such as air bubbles in sequencing fluidics. We develop a software SUGAR (subtile-based GUI-assisted refiner) which can handle ultra-high-throughput data with user-friendly graphical user interface (GUI) and interactive analysis capability. The SUGAR generates high-resolution quality heatmaps of the flowcell, enabling users to find possible signals of technical errors during the sequencing. The sequencing data generated from the error-affected regions of a flowcell can be selectively removed by automated analysis or GUI-assisted operations implemented in the SUGAR. The automated data-cleaning function based on sequence read quality (Phred) scores was applied to a public whole human genome sequencing data and we proved the overall mapping quality was improved. The detailed data evaluation and cleaning enabled by SUGAR would reduce technical problems in sequence read mapping, improving subsequent variant analysis that require high-quality sequence data and mapping results. Therefore, the software will be especially useful to control the quality of variant calls to the low population cells, e.g., cancers, in a sample with technical errors of sequencing procedures.

Cloud-Based Automated Design and Additive Manufacturing: A Usage Data-Enabled Paradigm Shift

PubMed Central

Lehmhus, Dirk; Wuest, Thorsten; Wellsandt, Stefan; Bosse, Stefan; Kaihara, Toshiya; Thoben, Klaus-Dieter; Busse, Matthias

2015-01-01

Integration of sensors into various kinds of products and machines provides access to in-depth usage information as basis for product optimization. Presently, this large potential for more user-friendly and efficient products is not being realized because (a) sensor integration and thus usage information is not available on a large scale and (b) product optimization requires considerable efforts in terms of manpower and adaptation of production equipment. However, with the advent of cloud-based services and highly flexible additive manufacturing techniques, these obstacles are currently crumbling away at rapid pace. The present study explores the state of the art in gathering and evaluating product usage and life cycle data, additive manufacturing and sensor integration, automated design and cloud-based services in manufacturing. By joining and extrapolating development trends in these areas, it delimits the foundations of a manufacturing concept that will allow continuous and economically viable product optimization on a general, user group or individual user level. This projection is checked against three different application scenarios, each of which stresses different aspects of the underlying holistic concept. The following discussion identifies critical issues and research needs by adopting the relevant stakeholder perspectives. PMID:26703606

Cloud-Based Automated Design and Additive Manufacturing: A Usage Data-Enabled Paradigm Shift.

PubMed

Lehmhus, Dirk; Wuest, Thorsten; Wellsandt, Stefan; Bosse, Stefan; Kaihara, Toshiya; Thoben, Klaus-Dieter; Busse, Matthias

2015-12-19

Integration of sensors into various kinds of products and machines provides access to in-depth usage information as basis for product optimization. Presently, this large potential for more user-friendly and efficient products is not being realized because (a) sensor integration and thus usage information is not available on a large scale and (b) product optimization requires considerable efforts in terms of manpower and adaptation of production equipment. However, with the advent of cloud-based services and highly flexible additive manufacturing techniques, these obstacles are currently crumbling away at rapid pace. The present study explores the state of the art in gathering and evaluating product usage and life cycle data, additive manufacturing and sensor integration, automated design and cloud-based services in manufacturing. By joining and extrapolating development trends in these areas, it delimits the foundations of a manufacturing concept that will allow continuous and economically viable product optimization on a general, user group or individual user level. This projection is checked against three different application scenarios, each of which stresses different aspects of the underlying holistic concept. The following discussion identifies critical issues and research needs by adopting the relevant stakeholder perspectives.

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.

Compact Microscope Imaging System Developed

NASA Technical Reports Server (NTRS)

McDowell, Mark

2001-01-01

The Compact Microscope Imaging System (CMIS) is a diagnostic tool with intelligent controls for use in space, industrial, medical, and security applications. The CMIS can be used in situ with a minimum amount of user intervention. This system, which was developed at the NASA Glenn Research Center, can scan, find areas of interest, focus, and acquire images automatically. Large numbers of multiple cell experiments require microscopy for in situ observations; this is only feasible with compact microscope systems. CMIS is a miniature machine vision system that combines intelligent image processing with remote control capabilities. The software also has a user-friendly interface that can be used independently of the hardware for post-experiment analysis. CMIS has potential commercial uses in the automated online inspection of precision parts, medical imaging, security industry (examination of currency in automated teller machines and fingerprint identification in secure entry locks), environmental industry (automated examination of soil/water samples), biomedical field (automated blood/cell analysis), and microscopy community. CMIS will improve research in several ways: It will expand the capabilities of MSD experiments utilizing microscope technology. It may be used in lunar and Martian experiments (Rover Robot). Because of its reduced size, it will enable experiments that were not feasible previously. It may be incorporated into existing shuttle orbiter and space station experiments, including glove-box-sized experiments as well as ground-based experiments.

StructRNAfinder: an automated pipeline and web server for RNA families prediction.

PubMed

Arias-Carrasco, Raúl; Vásquez-Morán, Yessenia; Nakaya, Helder I; Maracaja-Coutinho, Vinicius

2018-02-17

The function of many noncoding RNAs (ncRNAs) depend upon their secondary structures. Over the last decades, several methodologies have been developed to predict such structures or to use them to functionally annotate RNAs into RNA families. However, to fully perform this analysis, researchers should utilize multiple tools, which require the constant parsing and processing of several intermediate files. This makes the large-scale prediction and annotation of RNAs a daunting task even to researchers with good computational or bioinformatics skills. We present an automated pipeline named StructRNAfinder that predicts and annotates RNA families in transcript or genome sequences. This single tool not only displays the sequence/structural consensus alignments for each RNA family, according to Rfam database but also provides a taxonomic overview for each assigned functional RNA. Moreover, we implemented a user-friendly web service that allows researchers to upload their own nucleotide sequences in order to perform the whole analysis. Finally, we provided a stand-alone version of StructRNAfinder to be used in large-scale projects. The tool was developed under GNU General Public License (GPLv3) and is freely available at http://structrnafinder.integrativebioinformatics.me . The main advantage of StructRNAfinder relies on the large-scale processing and integrating the data obtained by each tool and database employed along the workflow, of which several files are generated and displayed in user-friendly reports, useful for downstream analyses and data exploration.

Dental Informatics tool "SOFPRO" for the study of oral submucous fibrosis.

PubMed

Erlewad, Dinesh Masajirao; Mundhe, Kalpana Anandrao; Hazarey, Vinay K

2016-01-01

Dental informatics is an evolving branch widely used in dental education and practice. Numerous applications that support clinical care, education and research have been developed. However, very few such applications are developed and utilized in the epidemiological studies of oral submucous fibrosis (OSF) which is affecting a significant population of Asian countries. To design and develop an user friendly software for the descriptive epidemiological study of OSF. With the help of a software engineer a computer program SOFPRO was designed and developed by using, Ms-Visual Basic 6.0 (VB), Ms-Access 2000, Crystal Report 7.0 and Ms-Paint in operating system XP. For the analysis purpose the available OSF data from the departmental precancer registry was fed into the SOFPRO. Known data, not known and null data are successfully accepted in data entry and represented in data analysis of OSF. Smooth working of SOFPRO and its correct data flow was tested against real-time data of OSF. SOFPRO was found to be a user friendly automated tool for easy data collection, retrieval, management and analysis of OSF patients.

Java Web Simulation (JWS); a web based database of kinetic models.

PubMed

Snoep, J L; Olivier, B G

2002-01-01

Software to make a database of kinetic models accessible via the internet has been developed and a core database has been set up at http://jjj.biochem.sun.ac.za/. This repository of models, available to everyone with internet access, opens a whole new way in which we can make our models public. Via the database, a user can change enzyme parameters and run time simulations or steady state analyses. The interface is user friendly and no additional software is necessary. The database currently contains 10 models, but since the generation of the program code to include new models has largely been automated the addition of new models is straightforward and people are invited to submit their models to be included in the database.

Cyber-Attack Methods, Why They Work on Us, and What to Do

NASA Technical Reports Server (NTRS)

Byrne, DJ

2015-01-01

Basic cyber-attack methods are well documented, and even automated with user-friendly GUIs (Graphical User Interfaces). Entire suites of attack tools are legal, conveniently packaged, and freely downloadable to anyone; more polished versions are sold with vendor support. Our team ran some of these against a selected set of projects within our organization to understand what the attacks do so that we can design and validate defenses against them. Some existing defenses were effective against the attacks, some less so. On average, every machine had twelve easily identifiable vulnerabilities, two of them "critical". Roughly 5% of passwords in use were easily crack-able. We identified a clear set of recommendations for each project, and some common patterns that emerged among them all.

Solving coiled-coil protein structures

DOE PAGES

Dauter, Zbigniew

2015-02-26

With the availability of more than 100,000 entries stored in the Protein Data Bank (PDB) that can be used as search models, molecular replacement (MR) is currently the most popular method of solving crystal structures of macromolecules. Significant methodological efforts have been directed in recent years towards making this approach more powerful and practical. This resulted in the creation of several computer programs, highly automated and user friendly, that are able to successfully solve many structures even by researchers who, although interested in structures of biomolecules, are not very experienced in crystallography.

Artificial intelligence, neural network, and Internet tool integration in a pathology workstation to improve information access

NASA Astrophysics Data System (ADS)

Sargis, J. C.; Gray, W. A.

1999-03-01

The APWS allows user friendly access to several legacy systems which would normally each demand domain expertise for proper utilization. The generalized model, including objects, classes, strategies and patterns is presented. The core components of the APWS are the Microsoft Windows 95 Operating System, Oracle, Oracle Power Objects, Artificial Intelligence tools, a medical hyperlibrary and a web site. The paper includes a discussion of how could be automated by taking advantage of the expert system, object oriented programming and intelligent relational database tools within the APWS.

A new mechatronic assistance system for the neurosurgical operating theatre: implementation, assessment of accuracy and application concepts.

PubMed

Rachinger, Jens; Bumm, Klaus; Wurm, Jochen; Bohr, Christopher; Nissen, Urs; Dannenmann, Tim; Buchfelder, Michael; Iro, Heinrich; Nimsky, Christopher

2007-01-01

To introduce a new robotic system to the field of neurosurgery and report on a preliminary assessment of accuracy as well as on envisioned application concepts. Based on experience with another system (Evolution 1, URS Inc., Schwerin, Germany), technical advancements are discussed. The basic module is an industrial 6 degrees of freedom robotic arm with a modified control element. The system combines frameless stereotaxy, robotics, and endoscopy. The robotic reproducibility error and the overall error were evaluated. For accuracy testing CT markers were placed on a cadaveric head and pinpointed with the robot's tool tip, both fully automated and telemanipulatory. Applicability in a clinical setting, user friendliness, safety and flexibility were assessed. The new system is suitable for use in the neurosurgical operating theatre. Hard- and software are user-friendly and flexible. The mean reproducibility error was 0.052-0.062 mm, the mean overall error was 0.816 mm. The system is less cumbersome and much easier to use than the Evolution 1. With its user-friendly interface and reliable safety features, its high application accuracy and flexibility, the new system is a versatile robotic platform for various neurosurgical applications. Adaptations for different applications are currently being realized. Copyright (c) 2007 S. Karger AG, Basel.

CANEapp: a user-friendly application for automated next generation transcriptomic data analysis.

PubMed

Velmeshev, Dmitry; Lally, Patrick; Magistri, Marco; Faghihi, Mohammad Ali

2016-01-13

Next generation sequencing (NGS) technologies are indispensable for molecular biology research, but data analysis represents the bottleneck in their application. Users need to be familiar with computer terminal commands, the Linux environment, and various software tools and scripts. Analysis workflows have to be optimized and experimentally validated to extract biologically meaningful data. Moreover, as larger datasets are being generated, their analysis requires use of high-performance servers. To address these needs, we developed CANEapp (application for Comprehensive automated Analysis of Next-generation sequencing Experiments), a unique suite that combines a Graphical User Interface (GUI) and an automated server-side analysis pipeline that is platform-independent, making it suitable for any server architecture. The GUI runs on a PC or Mac and seamlessly connects to the server to provide full GUI control of RNA-sequencing (RNA-seq) project analysis. The server-side analysis pipeline contains a framework that is implemented on a Linux server through completely automated installation of software components and reference files. Analysis with CANEapp is also fully automated and performs differential gene expression analysis and novel noncoding RNA discovery through alternative workflows (Cuffdiff and R packages edgeR and DESeq2). We compared CANEapp to other similar tools, and it significantly improves on previous developments. We experimentally validated CANEapp's performance by applying it to data derived from different experimental paradigms and confirming the results with quantitative real-time PCR (qRT-PCR). CANEapp adapts to any server architecture by effectively using available resources and thus handles large amounts of data efficiently. CANEapp performance has been experimentally validated on various biological datasets. CANEapp is available free of charge at http://psychiatry.med.miami.edu/research/laboratory-of-translational-rna-genomics/CANE-app . We believe that CANEapp will serve both biologists with no computational experience and bioinformaticians as a simple, timesaving but accurate and powerful tool to analyze large RNA-seq datasets and will provide foundations for future development of integrated and automated high-throughput genomics data analysis tools. Due to its inherently standardized pipeline and combination of automated analysis and platform-independence, CANEapp is an ideal for large-scale collaborative RNA-seq projects between different institutions and research groups.

A highly scalable information system as extendable framework solution for medical R&D projects.

PubMed

Holzmüller-Laue, Silke; Göde, Bernd; Stoll, Regina; Thurow, Kerstin

2009-01-01

For research projects in preventive medicine a flexible information management is needed that offers a free planning and documentation of project specific examinations. The system should allow a simple, preferably automated data acquisition from several distributed sources (e.g., mobile sensors, stationary diagnostic systems, questionnaires, manual inputs) as well as an effective data management, data use and analysis. An information system fulfilling these requirements has been developed at the Center for Life Science Automation (celisca). This system combines data of multiple investigations and multiple devices and displays them on a single screen. The integration of mobile sensor systems for comfortable, location-independent capture of time-based physiological parameter and the possibility of observation of these measurements directly by this system allow new scenarios. The web-based information system presented in this paper is configurable by user interfaces. It covers medical process descriptions, operative process data visualizations, a user-friendly process data processing, modern online interfaces (data bases, web services, XML) as well as a comfortable support of extended data analysis with third-party applications.

IDEOM: an Excel interface for analysis of LC-MS-based metabolomics data.

PubMed

Creek, Darren J; Jankevics, Andris; Burgess, Karl E V; Breitling, Rainer; Barrett, Michael P

2012-04-01

The application of emerging metabolomics technologies to the comprehensive investigation of cellular biochemistry has been limited by bottlenecks in data processing, particularly noise filtering and metabolite identification. IDEOM provides a user-friendly data processing application that automates filtering and identification of metabolite peaks, paying particular attention to common sources of noise and false identifications generated by liquid chromatography-mass spectrometry (LC-MS) platforms. Building on advanced processing tools such as mzMatch and XCMS, it allows users to run a comprehensive pipeline for data analysis and visualization from a graphical user interface within Microsoft Excel, a familiar program for most biological scientists. IDEOM is provided free of charge at http://mzmatch.sourceforge.net/ideom.html, as a macro-enabled spreadsheet (.xlsb). Implementation requires Microsoft Excel (2007 or later). R is also required for full functionality. michael.barrett@glasgow.ac.uk Supplementary data are available at Bioinformatics online.

COINS: A composites information database system

NASA Technical Reports Server (NTRS)

Siddiqi, Shahid; Vosteen, Louis F.; Edlow, Ralph; Kwa, Teck-Seng

1992-01-01

An automated data abstraction form (ADAF) was developed to collect information on advanced fabrication processes and their related costs. The information will be collected for all components being fabricated as part of the ACT program and include in a COmposites INformation System (COINS) database. The aim of the COINS development effort is to provide future airframe preliminary design and fabrication teams with a tool through which production cost can become a deterministic variable in the design optimization process. The effort was initiated by the Structures Technology Program Office (STPO) of the NASA LaRC to implement the recommendations of a working group comprised of representatives from the commercial airframe companies. The principal working group recommendation was to re-institute collection of composite part fabrication data in a format similar to the DOD/NASA Structural Composites Fabrication Guide. The fabrication information collection form was automated with current user friendly computer technology. This work in progress paper describes the new automated form and features that make the form easy to use by an aircraft structural design-manufacturing team.

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.

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

MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis.

PubMed

Lee, Dong-Yup; Yun, Hongsoek; Park, Sunwon; Lee, Sang Yup

2003-11-01

MetaFluxNet is a program package for managing information on the metabolic reaction network and for quantitatively analyzing metabolic fluxes in an interactive and customized way. It allows users to interpret and examine metabolic behavior in response to genetic and/or environmental modifications. As a result, quantitative in silico simulations of metabolic pathways can be carried out to understand the metabolic status and to design the metabolic engineering strategies. The main features of the program include a well-developed model construction environment, user-friendly interface for metabolic flux analysis (MFA), comparative MFA of strains having different genotypes under various environmental conditions, and automated pathway layout creation. http://mbel.kaist.ac.kr/ A manual for MetaFluxNet is available as PDF file.

FILTSoft: A computational tool for microstrip planar filter design

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

User-Friendly Tools for Random Matrices: An Introduction

DTIC Science & Technology

2012-12-03

T 2011 , Oliveira 2010, Mackey et al . 2012, ... Joel A. Tropp, User-Friendly Tools for Random Matrices, NIPS, 3 December 2012 47 To learn more... E...the matrix product Y = AΩ 3. Construct an orthonormal basis Q for the range of Y [Ref] Halko –Martinsson–T, SIAM Rev. 2011 . Joel A. Tropp, User-Friendly...concentration inequalities...” with L. Mackey et al .. Submitted 2012. § “User-Friendly Tools for Random Matrices: An Introduction.” 2012. See also

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

Dental Informatics tool “SOFPRO” for the study of oral submucous fibrosis

PubMed Central

Erlewad, Dinesh Masajirao; Mundhe, Kalpana Anandrao; Hazarey, Vinay K

2016-01-01

Background: Dental informatics is an evolving branch widely used in dental education and practice. Numerous applications that support clinical care, education and research have been developed. However, very few such applications are developed and utilized in the epidemiological studies of oral submucous fibrosis (OSF) which is affecting a significant population of Asian countries. Aims and Objectives: To design and develop an user friendly software for the descriptive epidemiological study of OSF. Materials and Methods: With the help of a software engineer a computer program SOFPRO was designed and developed by using, Ms-Visual Basic 6.0 (VB), Ms-Access 2000, Crystal Report 7.0 and Ms-Paint in operating system XP. For the analysis purpose the available OSF data from the departmental precancer registry was fed into the SOFPRO. Results: Known data, not known and null data are successfully accepted in data entry and represented in data analysis of OSF. Smooth working of SOFPRO and its correct data flow was tested against real-time data of OSF. Conclusion: SOFPRO was found to be a user friendly automated tool for easy data collection, retrieval, management and analysis of OSF patients. PMID:27601808

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.

StimDuino: an Arduino-based electrophysiological stimulus isolator.

PubMed

Sheinin, Anton; Lavi, Ayal; Michaelevski, Izhak

2015-03-30

Electrical stimulus isolator is a widely used device in electrophysiology. The timing of the stimulus application is usually automated and controlled by the external device or acquisition software; however, the intensity of the stimulus is adjusted manually. Inaccuracy, lack of reproducibility and no automation of the experimental protocol are disadvantages of the manual adjustment. To overcome these shortcomings, we developed StimDuino, an inexpensive Arduino-controlled stimulus isolator allowing highly accurate, reproducible automated setting of the stimulation current. The intensity of the stimulation current delivered by StimDuino is controlled by Arduino, an open-source microcontroller development platform. The automatic stimulation patterns are software-controlled and the parameters are set from Matlab-coded simple, intuitive and user-friendly graphical user interface. The software also allows remote control of the device over the network. Electrical current measurements showed that StimDuino produces the requested current output with high accuracy. In both hippocampal slice and in vivo recordings, the fEPSP measurements obtained with StimDuino and the commercial stimulus isolators showed high correlation. Commercial stimulus isolators are manually managed, while StimDuino generates automatic stimulation patterns with increasing current intensity. The pattern is utilized for the input-output relationship analysis, necessary for assessment of excitability. In contrast to StimuDuino, not all commercial devices are capable for remote control of the parameters and stimulation process. StimDuino-generated automation of the input-output relationship assessment eliminates need for the current intensity manually adjusting, improves stimulation reproducibility, accuracy and allows on-site and remote control of the stimulation parameters. Copyright © 2015 Elsevier B.V. All rights reserved.

Automating Phase Change Lines and Their Labels Using Microsoft Excel(R).

PubMed

Deochand, Neil

2017-09-01

Many researchers have rallied against drawn in graphical elements and offered ways to avoid them, especially regarding the insertion of phase change lines (Deochand, Costello, & Fuqua, 2015; Dubuque, 2015; Vanselow & Bourret, 2012). However, few have offered a solution to automating the phase labels, which are often utilized in behavior analytic graphical displays (Deochand et al., 2015). Despite the fact that Microsoft Excel® is extensively utilized by behavior analysts, solutions to resolve issues in our graphing practices are not always apparent or user-friendly. Considering the insertion of phase change lines and their labels constitute a repetitious and laborious endeavor, any minimization in the steps to accomplish these graphical elements could offer substantial time-savings to the field. The purpose of this report is to provide an updated way (and templates in the supplemental materials) to add phase change lines with their respective labels, which stay embedded to the graph when they are moved or updated.

[Modularization by the open standard. (I)].

PubMed

Hirano, H

2000-10-01

We are proceeding with the project called "Open LA21 Project" in the course of the clinical laboratory automation toward the 21st century. With the modular system that realizes integration, downsizing, a reasonable price, and is the future course in the clinical testing automation system as well, we aim to establish common standards among manufacturers as the only way to create user friendly market environments where the proper competition exists among the manufacturers. The common standards which are in preparation by the participating companies as "Open module system standards" are the standards which are going to be made public. They are intended to guarantee connection, compatibility of the products in conformity with the standards. In this project, we intend to realize the modular system that integrates each field, such as chemistry, hematology, coagulation/fibrinolysis, immunology, urinalysis in an early stage, and contribute positively to restructuring and upgrading the "raison d'etre" of the 21st century clinical testing.

A new, fast and semi-automated size determination method (SASDM) for studying multicellular tumor spheroids

PubMed Central

Monazzam, Azita; Razifar, Pasha; Lindhe, Örjan; Josephsson, Raymond; Långström, Bengt; Bergström, Mats

2005-01-01

Background Considering the width and importance of using Multicellular Tumor Spheroids (MTS) in oncology research, size determination of MTSs by an accurate and fast method is essential. In the present study an effective, fast and semi-automated method, SASDM, was developed to determinate the size of MTSs. The method was applied and tested in MTSs of three different cell-lines. Frozen section autoradiography and Hemotoxylin Eosin (H&E) staining was used for further confirmation. Results SASDM was shown to be effective, user-friendly, and time efficient, and to be more precise than the traditional methods and it was applicable for MTSs of different cell-lines. Furthermore, the results of image analysis showed high correspondence to the results of autoradiography and staining. Conclusion The combination of assessment of metabolic condition and image analysis in MTSs provides a good model to evaluate the effect of various anti-cancer treatments. PMID:16283948

Wet Lab Accelerator: A Web-Based Application Democratizing Laboratory Automation for Synthetic Biology.

PubMed

Bates, Maxwell; Berliner, Aaron J; Lachoff, Joe; Jaschke, Paul R; Groban, Eli S

2017-01-20

Wet Lab Accelerator (WLA) is a cloud-based tool that allows a scientist to conduct biology via robotic control without the need for any programming knowledge. A drag and drop interface provides a convenient and user-friendly method of generating biological protocols. Graphically developed protocols are turned into programmatic instruction lists required to conduct experiments at the cloud laboratory Transcriptic. Prior to the development of WLA, biologists were required to write in a programming language called "Autoprotocol" in order to work with Transcriptic. WLA relies on a new abstraction layer we call "Omniprotocol" to convert the graphical experimental description into lower level Autoprotocol language, which then directs robots at Transcriptic. While WLA has only been tested at Transcriptic, the conversion of graphically laid out experimental steps into Autoprotocol is generic, allowing extension of WLA into other cloud laboratories in the future. WLA hopes to democratize biology by bringing automation to general biologists.

Automated 3D structure composition for large RNAs

PubMed Central

Popenda, Mariusz; Szachniuk, Marta; Antczak, Maciej; Purzycka, Katarzyna J.; Lukasiak, Piotr; Bartol, Natalia; Blazewicz, Jacek; Adamiak, Ryszard W.

2012-01-01

Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues. PMID:22539264

Antibiogramj: A tool for analysing images from disk diffusion tests.

PubMed

Alonso, C A; Domínguez, C; Heras, J; Mata, E; Pascual, V; Torres, C; Zarazaga, M

2017-05-01

Disk diffusion testing, known as antibiogram, is widely applied in microbiology to determine the antimicrobial susceptibility of microorganisms. The measurement of the diameter of the zone of growth inhibition of microorganisms around the antimicrobial disks in the antibiogram is frequently performed manually by specialists using a ruler. This is a time-consuming and error-prone task that might be simplified using automated or semi-automated inhibition zone readers. However, most readers are usually expensive instruments with embedded software that require significant changes in laboratory design and workflow. Based on the workflow employed by specialists to determine the antimicrobial susceptibility of microorganisms, we have designed a software tool that, from images of disk diffusion tests, semi-automatises the process. Standard computer vision techniques are employed to achieve such an automatisation. We present AntibiogramJ, a user-friendly and open-source software tool to semi-automatically determine, measure and categorise inhibition zones of images from disk diffusion tests. AntibiogramJ is implemented in Java and deals with images captured with any device that incorporates a camera, including digital cameras and mobile phones. The fully automatic procedure of AntibiogramJ for measuring inhibition zones achieves an overall agreement of 87% with an expert microbiologist; moreover, AntibiogramJ includes features to easily detect when the automatic reading is not correct and fix it manually to obtain the correct result. AntibiogramJ is a user-friendly, platform-independent, open-source, and free tool that, up to the best of our knowledge, is the most complete software tool for antibiogram analysis without requiring any investment in new equipment or changes in the laboratory. Copyright © 2017 Elsevier B.V. All rights reserved.

URPD: a specific product primer design tool

PubMed Central

2012-01-01

Background Polymerase chain reaction (PCR) plays an important role in molecular biology. Primer design fundamentally determines its results. Here, we present a currently available software that is not located in analyzing large sequence but used for a rather straight-forward way of visualizing the primer design process for infrequent users. Findings URPD (yoUR Primer Design), a web-based specific product primer design tool, combines the NCBI Reference Sequences (RefSeq), UCSC In-Silico PCR, memetic algorithm (MA) and genetic algorithm (GA) primer design methods to obtain specific primer sets. A friendly user interface is accomplished by built-in parameter settings. The incorporated smooth pipeline operations effectively guide both occasional and advanced users. URPD contains an automated process, which produces feasible primer pairs that satisfy the specific needs of the experimental design with practical PCR amplifications. Visual virtual gel electrophoresis and in silico PCR provide a simulated PCR environment. The comparison of Practical gel electrophoresis comparison to virtual gel electrophoresis facilitates and verifies the PCR experiment. Wet-laboratory validation proved that the system provides feasible primers. Conclusions URPD is a user-friendly tool that provides specific primer design results. The pipeline design path makes it easy to operate for beginners. URPD also provides a high throughput primer design function. Moreover, the advanced parameter settings assist sophisticated researchers in performing experiential PCR. Several novel functions, such as a nucleotide accession number template sequence input, local and global specificity estimation, primer pair redesign, user-interactive sequence scale selection, and virtual and practical PCR gel electrophoresis discrepancies have been developed and integrated into URPD. The URPD program is implemented in JAVA and freely available at http://bio.kuas.edu.tw/urpd/. PMID:22713312

URPD: a specific product primer design tool.

PubMed

Chuang, Li-Yeh; Cheng, Yu-Huei; Yang, Cheng-Hong

2012-06-19

Polymerase chain reaction (PCR) plays an important role in molecular biology. Primer design fundamentally determines its results. Here, we present a currently available software that is not located in analyzing large sequence but used for a rather straight-forward way of visualizing the primer design process for infrequent users. URPD (yoUR Primer Design), a web-based specific product primer design tool, combines the NCBI Reference Sequences (RefSeq), UCSC In-Silico PCR, memetic algorithm (MA) and genetic algorithm (GA) primer design methods to obtain specific primer sets. A friendly user interface is accomplished by built-in parameter settings. The incorporated smooth pipeline operations effectively guide both occasional and advanced users. URPD contains an automated process, which produces feasible primer pairs that satisfy the specific needs of the experimental design with practical PCR amplifications. Visual virtual gel electrophoresis and in silico PCR provide a simulated PCR environment. The comparison of Practical gel electrophoresis comparison to virtual gel electrophoresis facilitates and verifies the PCR experiment. Wet-laboratory validation proved that the system provides feasible primers. URPD is a user-friendly tool that provides specific primer design results. The pipeline design path makes it easy to operate for beginners. URPD also provides a high throughput primer design function. Moreover, the advanced parameter settings assist sophisticated researchers in performing experiential PCR. Several novel functions, such as a nucleotide accession number template sequence input, local and global specificity estimation, primer pair redesign, user-interactive sequence scale selection, and virtual and practical PCR gel electrophoresis discrepancies have been developed and integrated into URPD. The URPD program is implemented in JAVA and freely available at http://bio.kuas.edu.tw/urpd/.

Screening_mgmt: a Python module for managing screening data.

PubMed

Helfenstein, Andreas; Tammela, Päivi

2015-02-01

High-throughput screening is an established technique in drug discovery and, as such, has also found its way into academia. High-throughput screening generates a considerable amount of data, which is why specific software is used for its analysis and management. The commercially available software packages are often beyond the financial limits of small-scale academic laboratories and, furthermore, lack the flexibility to fulfill certain user-specific requirements. We have developed a Python module, screening_mgmt, which is a lightweight tool for flexible data retrieval, analysis, and storage for different screening assays in one central database. The module reads custom-made analysis scripts and plotting instructions, and it offers a graphical user interface to import, modify, and display the data in a uniform manner. During the test phase, we used this module for the management of 10,000 data points of various origins. It has provided a practical, user-friendly tool for sharing and exchanging information between researchers. © 2014 Society for Laboratory Automation and Screening.

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

QCloud: A cloud-based quality control system for mass spectrometry-based proteomics laboratories

PubMed Central

Chiva, Cristina; Olivella, Roger; Borràs, Eva; Espadas, Guadalupe; Pastor, Olga; Solé, Amanda

2018-01-01

The increasing number of biomedical and translational applications in mass spectrometry-based proteomics poses new analytical challenges and raises the need for automated quality control systems. Despite previous efforts to set standard file formats, data processing workflows and key evaluation parameters for quality control, automated quality control systems are not yet widespread among proteomics laboratories, which limits the acquisition of high-quality results, inter-laboratory comparisons and the assessment of variability of instrumental platforms. Here we present QCloud, a cloud-based system to support proteomics laboratories in daily quality assessment using a user-friendly interface, easy setup, automated data processing and archiving, and unbiased instrument evaluation. QCloud supports the most common targeted and untargeted proteomics workflows, it accepts data formats from different vendors and it enables the annotation of acquired data and reporting incidences. A complete version of the QCloud system has successfully been developed and it is now open to the proteomics community (http://qcloud.crg.eu). QCloud system is an open source project, publicly available under a Creative Commons License Attribution-ShareAlike 4.0. PMID:29324744

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.

AMPA: an automated web server for prediction of protein antimicrobial regions.

PubMed

Torrent, Marc; Di Tommaso, Paolo; Pulido, David; Nogués, M Victòria; Notredame, Cedric; Boix, Ester; Andreu, David

2012-01-01

AMPA is a web application for assessing the antimicrobial domains of proteins, with a focus on the design on new antimicrobial drugs. The application provides fast discovery of antimicrobial patterns in proteins that can be used to develop new peptide-based drugs against pathogens. Results are shown in a user-friendly graphical interface and can be downloaded as raw data for later examination. AMPA is freely available on the web at http://tcoffee.crg.cat/apps/ampa. The source code is also available in the web. marc.torrent@upf.edu; david.andreu@upf.edu Supplementary data are available at Bioinformatics online.

Yleaf: Software for Human Y-Chromosomal Haplogroup Inference from Next-Generation Sequencing Data.

PubMed

Ralf, Arwin; Montiel González, Diego; Zhong, Kaiyin; Kayser, Manfred

2018-05-01

Next-generation sequencing (NGS) technologies offer immense possibilities given the large genomic data they simultaneously deliver. The human Y-chromosome serves as good example how NGS benefits various applications in evolution, anthropology, genealogy, and forensics. Prior to NGS, the Y-chromosome phylogenetic tree consisted of a few hundred branches, based on NGS data, it now contains many thousands. The complexity of both, Y tree and NGS data provide challenges for haplogroup assignment. For effective analysis and interpretation of Y-chromosome NGS data, we present Yleaf, a publically available, automated, user-friendly software for high-resolution Y-chromosome haplogroup inference independently of library and sequencing methods.

Gemi: PCR Primers Prediction from Multiple Alignments

PubMed Central

Sobhy, Haitham; Colson, Philippe

2012-01-01

Designing primers and probes for polymerase chain reaction (PCR) is a preliminary and critical step that requires the identification of highly conserved regions in a given set of sequences. This task can be challenging if the targeted sequences display a high level of diversity, as frequently encountered in microbiologic studies. We developed Gemi, an automated, fast, and easy-to-use bioinformatics tool with a user-friendly interface to design primers and probes based on multiple aligned sequences. This tool can be used for the purpose of real-time and conventional PCR and can deal efficiently with large sets of sequences of a large size. PMID:23316117

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.

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.

The Sargassum Early Advisory System (SEAS)

NASA Astrophysics Data System (ADS)

Armstrong, D.; Gallegos, S. C.

2016-02-01

The Sargassum Early Advisory System (SEAS) web-app was designed to automatically detect Sargassum at sea, forecast movement of the seaweed, and alert users of potential landings. Inspired to help address the economic hardships caused by large landings of Sargassum, the web app automates and enhances the manual tasks conducted by the SEAS group of Texas A&M University at Galveston. The SEAS web app is a modular, mobile-friendly tool that automates the entire workflow from data acquisition to user management. The modules include: 1) an Imagery Retrieval Module to automatically download Landsat-8 Operational Land Imagery (OLI) from the United States Geological Survey (USGS), 2) a Processing Module for automatic detection of Sargassum in the OLI imagery, and subsequent mapping of theses patches in the HYCOM grid, producing maps that show Sargassum clusters; 3) a Forecasting engine fed by the HYbrid Coordinate Ocean Model (HYCOM) model currents and winds from weather buoys; and 4) a mobile phone optimized geospatial user interface. The user can view the last known position of Sargassum clusters, trajectory and location projections for the next 24, 72 and 168 hrs. Users can also subscribe to alerts generated for particular areas. Currently, the SEAS web app produces advisories for Texas beaches. The forecasted Sargassum landing locations are validated by reports from Texas beach managers. However, the SEAS web app was designed to easily expand to other areas, and future plans call for extending the SEAS web app to Mexico and the Caribbean islands. The SEAS web app development is led by NASA, with participation by ASRC Federal/Computer Science Corporation, and the Naval Research Laboratory, all at Stennis Space Center, and Texas A&M University at Galveston.

Altering user' acceptance of automation through prior automation exposure.

PubMed

Bekier, Marek; Molesworth, Brett R C

2017-06-01

Air navigation service providers worldwide see increased use of automation as one solution to overcome the capacity constraints imbedded in the present air traffic management (ATM) system. However, increased use of automation within any system is dependent on user acceptance. The present research sought to determine if the point at which an individual is no longer willing to accept or cooperate with automation can be manipulated. Forty participants underwent training on a computer-based air traffic control programme, followed by two ATM exercises (order counterbalanced), one with and one without the aid of automation. Results revealed after exposure to a task with automation assistance, user acceptance of high(er) levels of automation ('tipping point') decreased; suggesting it is indeed possible to alter automation acceptance. Practitioner Summary: This paper investigates whether the point at which a user of automation rejects automation (i.e. 'tipping point') is constant or can be manipulated. The results revealed after exposure to a task with automation assistance, user acceptance of high(er) levels of automation decreased; suggesting it is possible to alter automation acceptance.

Remote Supervision and Control of Air Conditioning Systems in Different Modes

NASA Astrophysics Data System (ADS)

Rafeeq, Mohammed; Afzal, Asif; Rajendra, Sree

2018-01-01

In the era of automation, most of the application of engineering and science are interrelated with system for optimal operation. To get the efficient result of an operation and desired response, interconnected systems should be controlled by directing, regulating and commanding. Here, air conditioning (AC) system is considered for experimentation, to supervise and control its functioning in both, automated and manual mode. This paper reports the work intended to design and develop an automated and manual AC system working in remote and local mode, to increase the level of comfort, easy operation, reducing human intervention and faults occurring in the system. The Programmable Logical Controller (PLC) and Supervisory Control and Data Acquisition (SCADA) system were used for remote supervision and monitoring of AC systems using series ninety protocol and remote terminal unit modbus protocol as communication module to operate in remote mode. PLC was used as remote terminal for continuous supervision and control of AC system. SCADA software was used as a tool for designing user friendly graphical user interface. The proposed SCADA AC system successfully monitors and controls in accordance within the parameter limits like temperature, pressure, humidity and voltage. With all the features, this designed system is capable of efficient handling of the resources like the compressor, humidifier etc., with all the levels of safety and durability. This system also maintains the temperature and controls the humidity of the remote location and also looks after the health of the compressor.

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

Personal authentication using hand vein triangulation and knuckle shape.

PubMed

Kumar, Ajay; Prathyusha, K Venkata

2009-09-01

This paper presents a new approach to authenticate individuals using triangulation of hand vein images and simultaneous extraction of knuckle shape information. The proposed method is fully automated and employs palm dorsal hand vein images acquired from the low-cost, near infrared, contactless imaging. The knuckle tips are used as key points for the image normalization and extraction of region of interest. The matching scores are generated in two parallel stages: (i) hierarchical matching score from the four topologies of triangulation in the binarized vein structures and (ii) from the geometrical features consisting of knuckle point perimeter distances in the acquired images. The weighted score level combination from these two matching scores are used to authenticate the individuals. The achieved experimental results from the proposed system using contactless palm dorsal-hand vein images are promising (equal error rate of 1.14%) and suggest more user friendly alternative for user identification.

SpotCaliper: fast wavelet-based spot detection with accurate size estimation.

PubMed

Püspöki, Zsuzsanna; Sage, Daniel; Ward, John Paul; Unser, Michael

2016-04-15

SpotCaliper is a novel wavelet-based image-analysis software providing a fast automatic detection scheme for circular patterns (spots), combined with the precise estimation of their size. It is implemented as an ImageJ plugin with a friendly user interface. The user is allowed to edit the results by modifying the measurements (in a semi-automated way), extract data for further analysis. The fine tuning of the detections includes the possibility of adjusting or removing the original detections, as well as adding further spots. The main advantage of the software is its ability to capture the size of spots in a fast and accurate way. http://bigwww.epfl.ch/algorithms/spotcaliper/ zsuzsanna.puspoki@epfl.ch Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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.

PharmTeX: a LaTeX-Based Open-Source Platform for Automated Reporting Workflow.

PubMed

Rasmussen, Christian Hove; Smith, Mike K; Ito, Kaori; Sundararajan, Vijayakumar; Magnusson, Mats O; Niclas Jonsson, E; Fostvedt, Luke; Burger, Paula; McFadyen, Lynn; Tensfeldt, Thomas G; Nicholas, Timothy

2018-03-16

Every year, the pharmaceutical industry generates a large number of scientific reports related to drug research, development, and regulatory submissions. Many of these reports are created using text processing tools such as Microsoft Word. Given the large number of figures, tables, references, and other elements, this is often a tedious task involving hours of copying and pasting and substantial efforts in quality control (QC). In the present article, we present the LaTeX-based open-source reporting platform, PharmTeX, a community-based effort to make reporting simple, reproducible, and user-friendly. The PharmTeX creators put a substantial effort into simplifying the sometimes complex elements of LaTeX into user-friendly functions that rely on advanced LaTeX and Perl code running in the background. Using this setup makes LaTeX much more accessible for users with no prior LaTeX experience. A software collection was compiled for users not wanting to manually install the required software components. The PharmTeX templates allow for inclusion of tables directly from mathematical software output as well and figures from several formats. Code listings can be included directly from source. No previous experience and only a few hours of training are required to start writing reports using PharmTeX. PharmTeX significantly reduces the time required for creating a scientific report fully compliant with regulatory and industry expectations. QC is made much simpler, since there is a direct link between analysis output and report input. PharmTeX makes available to report authors the strengths of LaTeX document processing without the need for extensive training. Graphical Abstract ᅟ.

System for Automated Geoscientific Analyses (SAGA) v. 2.1.4

NASA Astrophysics Data System (ADS)

Conrad, O.; Bechtel, B.; Bock, M.; Dietrich, H.; Fischer, E.; Gerlitz, L.; Wehberg, J.; Wichmann, V.; Böhner, J.

2015-07-01

The System for Automated Geoscientific Analyses (SAGA) is an open source geographic information system (GIS), mainly licensed under the GNU General Public License. Since its first release in 2004, SAGA has rapidly developed from a specialized tool for digital terrain analysis to a comprehensive and globally established GIS platform for scientific analysis and modeling. SAGA is coded in C++ in an object oriented design and runs under several operating systems including Windows and Linux. Key functional features of the modular software architecture comprise an application programming interface for the development and implementation of new geoscientific methods, a user friendly graphical user interface with many visualization options, a command line interpreter, and interfaces to interpreted languages like R and Python. The current version 2.1.4 offers more than 600 tools, which are implemented in dynamically loadable libraries or shared objects and represent the broad scopes of SAGA in numerous fields of geoscientific endeavor and beyond. In this paper, we inform about the system's architecture, functionality, and its current state of development and implementation. Furthermore, we highlight the wide spectrum of scientific applications of SAGA in a review of published studies, with special emphasis on the core application areas digital terrain analysis, geomorphology, soil science, climatology and meteorology, as well as remote sensing.

Characterization of available automated external defibrillators in the market based on the product manuals in 2014

PubMed Central

Ho, Chik Leung; Cheng, Ka Wai; Ma, Tze Hang; Wong, Yau Hang; Cheng, Ka Lok; Kam, Chak Wah

2016-01-01

BACKGROUND: To popularize the wide-spread use of automated external defibrillator (AED) to save life in sudden cardiac arrest, we compared the strength and weakness of different types of AEDs to enable a sound selection based on regional requirement. METHODS: This was a retrospective descriptive study. Different types of AEDs were compared according to the information of AEDs from manuals and brochures provided by the manufacturers. Fifteen types of AEDs were divided into 3 groups, basic, intermediate and advanced. RESULTS: Lifeline™ AUTO AED had the best performance in price, portability and user-friendly among AEDs of basic level. It required less time for shock charging. Samaritan PAD defibrillator was superior in price, portability, durability and characteristic among AEDs of intermediate level. It had the longest warranty and highest protection against water and dust. Lifeline™ PRO AED had the best performance in most of the criteria among AEDs of advanced level and offered CPR video and manual mode for laypersons and clinicians respectively. CONCLUSION: Lifeline™ AUTO AED, Samaritan PAD defibrillator, Lifeline™ PRO AED are superior in AEDs of basic, intermediate and advanced levels, respectively. A feasible AED may be chosen by users according to the regional requirement and the current information about the best available products. PMID:27313810

SlugIn 1.0: A Free Tool for Automated Slug Test Analysis.

PubMed

Martos-Rosillo, Sergio; Guardiola-Albert, Carolina; Padilla Benítez, Alberto; Delgado Pastor, Joaquín; Azcón González, Antonio; Durán Valsero, Juan José

2018-05-01

The correct characterization of aquifer parameters is essential for water-supply and water-quality investigations. Slug tests are widely used for these purposes. While free software is available to interpret slug tests, some codes are not user-friendly, or do not include a wide range of methods to interpret the results, or do not include automatic, inverse solutions to the test data. The private sector has also generated several good programs to interpret slug test data, but they are not free of charge. The computer program SlugIn 1.0 is available online for free download, and is demonstrated to aid in the analysis of slug tests to estimate hydraulic parameters. The program provides an easy-to-use Graphical User Interface. SlugIn 1.0 incorporates automated parameter estimation and facilitates the visualization of several interpretations of the same test. It incorporates solutions for confined and unconfined aquifers, partially penetrating wells, skin effects, shape factor, anisotropy, high hydraulic conductivity formations and the Mace test for large-diameter wells. It is available in English and Spanish and can be downloaded from the web site of the Geological Survey of Spain. Two field examples are presented to illustrate how the software operates. © 2018, National Ground Water Association.

Retention payoff-based cost per day open regression equations: Application in a user-friendly decision support tool for investment analysis of automated estrus detection technologies.

PubMed

Dolecheck, K A; Heersche, G; Bewley, J M

2016-12-01

Assessing the economic implications of investing in automated estrus detection (AED) technologies can be overwhelming for dairy producers. The objectives of this study were to develop new regression equations for estimating the cost per day open (DO) and to apply the results to create a user-friendly, partial budget, decision support tool for investment analysis of AED technologies. In the resulting decision support tool, the end user can adjust herd-specific inputs regarding general management, current reproductive management strategies, and the proposed AED system. Outputs include expected DO, reproductive cull rate, net present value, and payback period for the proposed AED system. Utility of the decision support tool was demonstrated with an example dairy herd created using data from DairyMetrics (Dairy Records Management Systems, Raleigh, NC), Food and Agricultural Policy Research Institute (Columbia, MO), and published literature. Resulting herd size, rolling herd average milk production, milk price, and feed cost were 323 cows, 10,758kg, $0.41/kg, and $0.20/kg of dry matter, respectively. Automated estrus detection technologies with 2 levels of initial system cost (low: $5,000 vs. high: $10,000), tag price (low: $50 vs. high: $100), and estrus detection rate (low: 60% vs. high: 80%) were compared over a 7-yr investment period. Four scenarios were considered in a demonstration of the investment analysis tool: (1) a herd using 100% visual observation for estrus detection before adopting 100% AED, (2) a herd using 100% visual observation before adopting 75% AED and 25% visual observation, (3) a herd using 100% timed artificial insemination (TAI) before adopting 100% AED, and (4) a herd using 100% TAI before adopting 75% AED and 25% TAI. Net present value in scenarios 1 and 2 was always positive, indicating a positive investment situation. Net present value in scenarios 3 and 4 was always positive in combinations using a $50 tag price, and in scenario 4, the $5,000, $100, and 80% combination. Overall, the payback period ranged from 1.6 yr to greater than 10 yr. Investment analysis demonstration results were highly dependent on assumptions, especially AED system initial investment and labor costs. Dairy producers can use herd-specific inputs with the cost per day open regression equations and the decision support tool to estimate individual herd results. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Clinfo: A Research Data Management and Analysis System Acceptable to Physician Users

PubMed Central

Thompson, Howard K.; Baker, William R.; Christopher, T. Graham; Lacy, William; Groner, Gabriel

1977-01-01

Since 1972 a national consortium has studied the needs of clinical research investigators for automation support. After determining that the most pressing need was to provide a data storage retrieval, and analysis capability which the physician investigator himself would find convenient, easy to use, and “friendly,” a prototype minicomputer-based system was designed and implemented. The system (CLINFO) has been extensively tried out by numerous clinical investigators at three sites and found to be very much to the liking of the investigators. It greatly accelerates the time between the posing of a research question and an answer to that question. With the current availability of the CLINFO system and as automated medical record-keeping systems become available, it is reasonable to anticipate that it will soon be feasible for practicing physicians to carry out modest clinical research efforts on panels of their own patients, a valuable source of information which is rarely tapped for research purposes.

AEDs at your fingertips: automated external defibrillators on college campuses and a novel approach for increasing accessibility.

PubMed

Berger, Ryan J; O'Shea, Jesse G

2014-01-01

The use of automated external defibrillators (AEDs) increases survival in cardiac arrest events. Due to the success of previous efforts and free, readily available mobile mapping software, the discussion is to emphasize the importance of the use of AEDs to prevent sudden cardiac arrest-related deaths on college campuses and abroad, while suggesting a novel approach to aiding in access and awareness issues. A user-friendly mobile application (a low-cost iOS map) was developed at Florida State University to decrease AED retrieval distance and time. The development of mobile AED maps is feasible for a variety of universities and other entities, with the potential to save lives. Just having AEDs installed is not enough--they need to be easily locatable. Society increasingly relies on phones to provide information, and there are opportunities to use mobile technology to locate and share information about relevant emergency devices; these should be incorporated into the chain of survival.

CATCH/IT: a data warehouse to support comprehensive assessment for tracking community health.

PubMed Central

Berndt, D. J.; Hevner, A. R.; Studnicki, J.

1998-01-01

A systematic methodology, Comprehensive Assessment for Tracking Community Health (CATCH), for analyzing the health status of communities has been under development at the University of South Florida since the early 1990s. CATCH draws 226 health status indicators from multiple data sources and uses an innovative comparative framework and weighted evaluation criteria to produce a rank-ordered list of community health problems. CATCH has been applied successfully in many Florida counties; focusing attention on high priority health issues and measuring the impact of health expenditures on community health status outcomes. Previously performed manually, we are using information technology (IT) to automate the CATCH methodology with a full-scale data warehouse, user-friendly forms and reports, and extended analysis and data mining capabilities. The automated system, CATCH/IT, will reduce the time to prepare community health status reports from months to days. In this paper, we present the current status of the project, along with the principal research and development issues and future directions of the project. PMID:9929220

CATCH/IT: a data warehouse to support comprehensive assessment for tracking community health.

PubMed

Berndt, D J; Hevner, A R; Studnicki, J

1998-01-01

A systematic methodology, Comprehensive Assessment for Tracking Community Health (CATCH), for analyzing the health status of communities has been under development at the University of South Florida since the early 1990s. CATCH draws 226 health status indicators from multiple data sources and uses an innovative comparative framework and weighted evaluation criteria to produce a rank-ordered list of community health problems. CATCH has been applied successfully in many Florida counties; focusing attention on high priority health issues and measuring the impact of health expenditures on community health status outcomes. Previously performed manually, we are using information technology (IT) to automate the CATCH methodology with a full-scale data warehouse, user-friendly forms and reports, and extended analysis and data mining capabilities. The automated system, CATCH/IT, will reduce the time to prepare community health status reports from months to days. In this paper, we present the current status of the project, along with the principal research and development issues and future directions of the project.

ACME, a GIS tool for Automated Cirque Metric Extraction

NASA Astrophysics Data System (ADS)

Spagnolo, Matteo; Pellitero, Ramon; Barr, Iestyn D.; Ely, Jeremy C.; Pellicer, Xavier M.; Rea, Brice R.

2017-02-01

Regional scale studies of glacial cirque metrics provide key insights on the (palaeo) environment related to the formation of these erosional landforms. The growing availability of high resolution terrain models means that more glacial cirques can be identified and mapped in the future. However, the extraction of their metrics still largely relies on time consuming manual techniques or the combination of, more or less obsolete, GIS tools. In this paper, a newly coded toolbox is provided for the automated, and comparatively quick, extraction of 16 key glacial cirque metrics; including length, width, circularity, planar and 3D area, elevation, slope, aspect, plan closure and hypsometry. The set of tools, named ACME (Automated Cirque Metric Extraction), is coded in Python, runs in one of the most commonly used GIS packages (ArcGIS) and has a user friendly interface. A polygon layer of mapped cirques is required for all metrics, while a Digital Terrain Model and a point layer of cirque threshold midpoints are needed to run some of the tools. Results from ACME are comparable to those from other techniques and can be obtained rapidly, allowing large cirque datasets to be analysed and potentially important regional trends highlighted.

Automated Testing Experience of the Linear Aerospike SR-71 Experiment (LASRE) Controller

NASA Technical Reports Server (NTRS)

Larson, Richard R.

1999-01-01

System controllers must be fail-safe, low cost, flexible to software changes, able to output health and status words, and permit rapid retest qualification. The system controller designed and tested for the aerospike engine program was an attempt to meet these requirements. This paper describes (1) the aerospike controller design, (2) the automated simulation testing techniques, and (3) the real time monitoring data visualization structure. Controller cost was minimized by design of a single-string system that used an off-the-shelf 486 central processing unit (CPU). A linked-list architecture, with states (nodes) defined in a user-friendly state table, accomplished software changes to the controller. Proven to be fail-safe, this system reported the abort cause and automatically reverted to a safe condition for any first failure. A real time simulation and test system automated the software checkout and retest requirements. A program requirement to decode all abort causes in real time during all ground and flight tests assured the safety of flight decisions and the proper execution of mission rules. The design also included health and status words, and provided a real time analysis interpretation for all health and status data.

User Preferences and Design Recommendations for an mHealth App to Promote Cystic Fibrosis Self-Management

PubMed Central

Hilliard, Marisa E; Hahn, Amy; Ridge, Alana K; Eakin, Michelle N

2014-01-01

Background mHealth apps hold potential to provide automated, tailored support for treatment adherence among individuals with chronic medical conditions. Yet relatively little empirical research has guided app development and end users are infrequently involved in designing the app features or functions that would best suit their needs. Self-management apps may be particularly useful for people with chronic conditions like cystic fibrosis (CF) that have complex, demanding regimens. Objective The aim of this mixed-methods study was to involve individuals with CF in guiding the development of engaging, effective, user-friendly adherence promotion apps that meet their preferences and self-management needs. Methods Adults with CF (n=16, aged 21-48 years, 50% male) provided quantitative data via a secure Web survey and qualitative data via semi-structured telephone interviews regarding previous experiences using apps in general and for health, and preferred and unwanted features of potential future apps to support CF self-management. Results Participants were smartphone users who reported sending or receiving text messages (93%, 14/15) or emails (80%, 12/15) on their smartphone or device every day, and 87% (13/15) said it would be somewhat or very hard to give up their smartphone. Approximately one-half (53%, 8/15) reported having health apps, all diet/weight-related, yet many reported that existing nutrition apps were not well-suited for CF management. Participants wanted apps to support CF self-management with characteristics such as having multiple rather than single functions (eg, simple alarms), being specific to CF, and minimizing user burden. Common themes for desired CF app features were having information at one’s fingertips, automation of disease management activities such as pharmacy refills, integration with smartphones’ technological capabilities, enhancing communication with health care team, and facilitating socialization within the CF community. Opinions were mixed regarding gamification and earning rewards or prizes. Participants emphasized the need for customization options to meet individual preferences and disease management goals. Conclusions Unique capabilities of emerging smartphone technologies (eg, social networking integration, movement and location detection, integrated sensors, or electronic monitors) make many of these requests possible. Involving end users in all stages of mHealth app development and collaborating with technology experts and the health care system may result in apps that maintain engagement, improve integration and automation, and ultimately impact self-management and health outcomes. PMID:25344616

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

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.

Poster - 09: A MATLAB-based Program for Automated Quality Assurance of a Prostate Brachytherapy Ultrasound System

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

Poon, Justin; Sabondjian, Eric; Sankreacha, Raxa

Purpose: A robust Quality Assurance (QA) program is essential for prostate brachytherapy ultrasound systems due to the importance of imaging accuracy during treatment and planning. Task Group 128 of the American Association of Physicists in Medicine has recommended a set of QA tests covering grayscale visibility, depth of penetration, axial and lateral resolution, distance measurement, area measurement, volume measurement, and template/electronic grid alignment. Making manual measurements on the ultrasound system can be slow and inaccurate, so a MATLAB program was developed for automation of the described tests. Methods: Test images were acquired using a BK Medical Flex Focus 400 ultrasoundmore » scanner and 8848 transducer with the CIRS Brachytherapy QA Phantom – Model 045A. For each test, the program automatically segments the inputted image(s), makes the appropriate measurements, and indicates if the test passed or failed. The program was tested by analyzing two sets of images, where the measurements from the first set were used as baseline values. Results: The program successfully analyzed the images for each test and determined if any action limits were exceeded. All tests passed – the measurements made by the program were consistent and met the requirements outlined by Task Group 128. Conclusions: The MATLAB program we have developed can be used for automated QA of an ultrasound system for prostate brachytherapy. The GUI provides a user-friendly way to analyze images without the need for any manual measurement, potentially removing intra- and inter-user variability for more consistent results.« less

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

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.

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.

Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains.

PubMed

O'Farrell, Brian; Haase, Jana K; Velayudhan, Vimalkumar; Murphy, Ronan A; Achtman, Mark

2012-01-01

Microbial genotyping increasingly deals with large numbers of samples, and data are commonly evaluated by unstructured approaches, such as spread-sheets. The efficiency, reliability and throughput of genotyping would benefit from the automation of manual manipulations within the context of sophisticated data storage. We developed a medium- throughput genotyping pipeline for MultiLocus Sequence Typing (MLST) of bacterial pathogens. This pipeline was implemented through a combination of four automated liquid handling systems, a Laboratory Information Management System (LIMS) consisting of a variety of dedicated commercial operating systems and programs, including a Sample Management System, plus numerous Python scripts. All tubes and microwell racks were bar-coded and their locations and status were recorded in the LIMS. We also created a hierarchical set of items that could be used to represent bacterial species, their products and experiments. The LIMS allowed reliable, semi-automated, traceable bacterial genotyping from initial single colony isolation and sub-cultivation through DNA extraction and normalization to PCRs, sequencing and MLST sequence trace evaluation. We also describe robotic sequencing to facilitate cherrypicking of sequence dropouts. This pipeline is user-friendly, with a throughput of 96 strains within 10 working days at a total cost of < €25 per strain. Since developing this pipeline, >200,000 items were processed by two to three people. Our sophisticated automated pipeline can be implemented by a small microbiology group without extensive external support, and provides a general framework for semi-automated bacterial genotyping of large numbers of samples at low cost.

Transforming Microbial Genotyping: A Robotic Pipeline for Genotyping Bacterial Strains

PubMed Central

Velayudhan, Vimalkumar; Murphy, Ronan A.; Achtman, Mark

2012-01-01

Microbial genotyping increasingly deals with large numbers of samples, and data are commonly evaluated by unstructured approaches, such as spread-sheets. The efficiency, reliability and throughput of genotyping would benefit from the automation of manual manipulations within the context of sophisticated data storage. We developed a medium- throughput genotyping pipeline for MultiLocus Sequence Typing (MLST) of bacterial pathogens. This pipeline was implemented through a combination of four automated liquid handling systems, a Laboratory Information Management System (LIMS) consisting of a variety of dedicated commercial operating systems and programs, including a Sample Management System, plus numerous Python scripts. All tubes and microwell racks were bar-coded and their locations and status were recorded in the LIMS. We also created a hierarchical set of items that could be used to represent bacterial species, their products and experiments. The LIMS allowed reliable, semi-automated, traceable bacterial genotyping from initial single colony isolation and sub-cultivation through DNA extraction and normalization to PCRs, sequencing and MLST sequence trace evaluation. We also describe robotic sequencing to facilitate cherrypicking of sequence dropouts. This pipeline is user-friendly, with a throughput of 96 strains within 10 working days at a total cost of < €25 per strain. Since developing this pipeline, >200,000 items were processed by two to three people. Our sophisticated automated pipeline can be implemented by a small microbiology group without extensive external support, and provides a general framework for semi-automated bacterial genotyping of large numbers of samples at low cost. PMID:23144721

Integrated microfluidic technology for sub-lethal and behavioral marine ecotoxicity biotests

NASA Astrophysics Data System (ADS)

Huang, Yushi; Reyes Aldasoro, Constantino Carlos; Persoone, Guido; Wlodkowic, Donald

2015-06-01

Changes in behavioral traits exhibited by small aquatic invertebrates are increasingly postulated as ethically acceptable and more sensitive endpoints for detection of water-born ecotoxicity than conventional mortality assays. Despite importance of such behavioral biotests, their implementation is profoundly limited by the lack of appropriate biocompatible automation, integrated optoelectronic sensors, and the associated electronics and analysis algorithms. This work outlines development of a proof-of-concept miniaturized Lab-on-a-Chip (LOC) platform for rapid water toxicity tests based on changes in swimming patterns exhibited by Artemia franciscana (Artoxkit M™) nauplii. In contrast to conventionally performed end-point analysis based on counting numbers of dead/immobile specimens we performed a time-resolved video data analysis to dynamically assess impact of a reference toxicant on swimming pattern of A. franciscana. Our system design combined: (i) innovative microfluidic device keeping free swimming Artemia sp. nauplii under continuous microperfusion as a mean of toxin delivery; (ii) mechatronic interface for user-friendly fluidic actuation of the chip; and (iii) miniaturized video acquisition for movement analysis of test specimens. The system was capable of performing fully programmable time-lapse and video-microscopy of multiple samples for rapid ecotoxicity analysis. It enabled development of a user-friendly and inexpensive test protocol to dynamically detect sub-lethal behavioral end-points such as changes in speed of movement or distance traveled by each animal.

Creating the User-Friendly Library by Evaluating Patron Perception of Signage.

ERIC Educational Resources Information Center

Bosman, Ellen; Rusinek, Carol

1997-01-01

Librarians at Indiana University Northwest Library surveyed patrons on how to make the library's collection and services more accessible by improving signage. Examines the effectiveness of signage to instruct users, reduce difficulties and fears, ameliorate negative experiences, and contribute to a user-friendly environment. (AEF)

ROBOCAL: Gamma-ray isotopic hardware/software interface

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

Hurd, J.R.; Bonner, C.A.; Ostenak, C.A.

1989-01-01

ROBOCAL, presently being developed at the Los Alamos National Laboratory, is a full-scale prototypical robotic system for remotely performing calorimetric and gamma-ray isotopics measurements of nuclear materials. It features a fully automated vertical stacker-retriever for storing and retrieving packaged nuclear materials from a multi-drawer system, and a fully automated, uniquely integrated gantry robot for programmable selection and transfer of nuclear materials to calorimetric and gamma-ray isotopic measurement stations. Since ROBOCAL is to require almost no operator intervention, a mechanical control system is required in addition to a totally automated assay system. The assay system must be a completely integrated datamore » acquisition and isotopic analysis package fully capable of performing state-of-the-art homogeneous and heterogeneous analyses on many varied matrices. The TRIFID assay system being discussed at this conference by J. G. Fleissner of the Rocky Flats Plant has been adopted because of its many automated features. These include: MCA/ADC setup and acquisition; spectral storage and analysis utilizing an expert system formalism; report generation with internal measurement control printout; user friendly screens and menus. The mechanical control portion consists primarily of two detector platforms and a sample platform, each with independent movement. Some minor modifications and additions are needed with TRIFID to interface the assay and mechanical portions with the CimRoc 4000 software controlling the robot. 6 refs., 5 figs., 3 tabs.« less

ARIA: Delivering state-of-the-art InSAR products to end users

NASA Astrophysics Data System (ADS)

Agram, P. S.; Owen, S. E.; Hua, H.; Manipon, G.; Sacco, G. F.; Bue, B. D.; Fielding, E. J.; Yun, S. H.; Simons, M.; Webb, F.; Rosen, P. A.; Lundgren, P.; Liu, Z.

2016-12-01

Advanced Rapid Imaging and Analysis (ARIA) Center for Natural Hazards aims to bring state-of-the-art geodetic imaging capabilities to an operational level in support of local, national, and international hazard response communities. ARIA project's first foray into operational generation of InSAR products was with Calimap Project, in collaboration with ASI-CIDOT, using X-band data from the Cosmo-SkyMed constellation. Over the last year, ARIA's processing infrastructure has been significantly upgraded to exploit the free stream of high quality C-band SAR data from ESA's Sentinel-1 mission and related algorithmic improvements to the ISCE software. ARIA's data system can now operationally generate geocoded unwrapped phase and coherence products in GIS-friendly formats from Sentinel-1 TOPS mode data in an automated fashion, and this capability is currently being exercised various study sites across the United States including Hawaii, Central California, Iceland and South America. The ARIA team, building on the experience gained from handling X-band data and C-band data, has also built an automated machine learning-based classifier to label the auto-generated interferograms based on phase unwrapping quality. These high quality "time-series ready" InSAR products generated using state-of-the-art processing algorithms can be accessed by end users using two different mechanisms - 1) a Faceted-search interface that includes browse imagery for quick visualization and 2) an ElasticSearch-based API to enable bulk automated download, post-processing and time-series analysis. In this talk, we will present InSAR results from various global events that ARIA system has responded to. We will also discuss the set of geospatial big data tools including GIS libraries and API tools, that end users will need to familiarize themselves with in order to maximize the utilization of continuous stream of InSAR products from the Sentinel-1 and NISAR missions that the ARIA project will generate.

Hazardous Waste Generator Regulations: A User-Friendly Reference Document

EPA Pesticide Factsheets

User-friendly reference to assist EPA and state staff, industrial facilities generating and managing hazardous wastes as well as the general public, in locating and understanding RCRA hazardous waste generator regulations.

SmartHome: a domotic framework based on smart sensing and actuator network to reduce energy wastes

NASA Astrophysics Data System (ADS)

Santamaria, Amilcare Francesco; De Rango, Floriano; Falbo, Domenico; Barletta, Domenico

2014-05-01

Domestic environment and human interaction with services supplied by domotic devices is going to be a very interesting application field. With a domotic system is possible to achieve great interaction between human beings, environments and smart devices. The enhancing of these interactions is the main goal of this work whose intent is to improve the classic concept of domotics. The framework we developed can be used for several application fields such as lighting, heating, conditioning or water management and energy consumption. In particular, the proposed system can optimize energy consumptions by rising awareness to users that have full control of their house and the possibility to save money and reduce the impact of the energetic consumes to the earth, matching the new "green" motto requirements. In this way, the overall system wants to match the central concept of Internet Of Things (IoT) as well. From this point of view a complex automation system with smart devices make possible a more efficient way to produce, follow and manage domotic policies. Following the spread of IoT, for this work we designed and implemented new plug-and-play and ready-to-use smart devices that are part of a complex automation system that offers a user-friendly web application and allows users to control and interact with different plans of their house in order to make life more comfortable and be aware of their energy consumptions. Control and awareness arc the two key points that led us to develop the proposed system.

Deep Interactive Learning with Sharkzor

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

None

Sharkzor is a web application for machine-learning assisted image sort and summary. Deep learning algorithms are leveraged to infer, augment, and automate the user’s mental model. Initially, images uploaded by the user are spread out on a canvas. The user then interacts with the images to impute their mental model into the applications algorithmic underpinnings. Methods of interaction within Sharkzor’s user interface and user experience support three primary user tasks: triage, organize and automate. The user triages the large pile of overlapping images by moving images of interest into proximity. The user then organizes said images into meaningful groups. Aftermore » interacting with the images and groups, deep learning helps to automate the user’s interactions. The loop of interaction, automation, and response by the user allows the system to quickly make sense of large amounts of data.« less

Inferring tie strength from online directed behavior.

PubMed

Jones, Jason J; Settle, Jaime E; Bond, Robert M; Fariss, Christopher J; Marlow, Cameron; Fowler, James H

2013-01-01

Some social connections are stronger than others. People have not only friends, but also best friends. Social scientists have long recognized this characteristic of social connections and researchers frequently use the term tie strength to refer to this concept. We used online interaction data (specifically, Facebook interactions) to successfully identify real-world strong ties. Ground truth was established by asking users themselves to name their closest friends in real life. We found the frequency of online interaction was diagnostic of strong ties, and interaction frequency was much more useful diagnostically than were attributes of the user or the user's friends. More private communications (messages) were not necessarily more informative than public communications (comments, wall posts, and other interactions).

Friend suggestion in social network based on user log

NASA Astrophysics Data System (ADS)

Kaviya, R.; Vanitha, M.; Sumaiya Thaseen, I.; Mangaiyarkarasi, R.

2017-11-01

Simple friend recommendation algorithms such as similarity, popularity and social aspects is the basic requirement to be explored to methodically form high-performance social friend recommendation. Suggestion of friends is followed. No tags of character were followed. In the proposed system, we use an algorithm for network correlation-based social friend recommendation (NC-based SFR).It includes user activities like where one lives and works. A new friend recommendation method, based on network correlation, by considering the effect of different social roles. To model the correlation between different networks, we develop a method that aligns these networks through important feature selection. We consider by preserving the network structure for a more better recommendations so that it significantly improves the accuracy for better friend-recommendation.

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

Sun, Z. J.; Wells, D.; Green, J.

Photon Activation Analysis (PAA) of environmental, archaeological and industrial samples requires extensive data analysis that is susceptible to error. For the purpose of saving time, manpower and minimizing error, a computer program was designed, built and implemented using SQL, Access 2007 and asp.net technology to automate this process. Based on the peak information of the spectrum and assisted by its PAA library, the program automatically identifies elements in the samples and calculates their concentrations and respective uncertainties. The software also could be operated in browser/server mode, which gives the possibility to use it anywhere the internet is accessible. By switchingmore » the nuclide library and the related formula behind, the new software can be easily expanded to neutron activation analysis (NAA), charged particle activation analysis (CPAA) or proton-induced X-ray emission (PIXE). Implementation of this would standardize the analysis of nuclear activation data. Results from this software were compared to standard PAA analysis with excellent agreement. With minimum input from the user, the software has proven to be fast, user-friendly and reliable.« less

Effective electron-density map improvement and structure validation on a Linux multi-CPU web cluster: The TB Structural Genomics Consortium Bias Removal Web Service.

PubMed

Reddy, Vinod; Swanson, Stanley M; Segelke, Brent; Kantardjieff, Katherine A; Sacchettini, James C; Rupp, Bernhard

2003-12-01

Anticipating a continuing increase in the number of structures solved by molecular replacement in high-throughput crystallography and drug-discovery programs, a user-friendly web service for automated molecular replacement, map improvement, bias removal and real-space correlation structure validation has been implemented. The service is based on an efficient bias-removal protocol, Shake&wARP, and implemented using EPMR and the CCP4 suite of programs, combined with various shell scripts and Fortran90 routines. The service returns improved maps, converted data files and real-space correlation and B-factor plots. User data are uploaded through a web interface and the CPU-intensive iteration cycles are executed on a low-cost Linux multi-CPU cluster using the Condor job-queuing package. Examples of map improvement at various resolutions are provided and include model completion and reconstruction of absent parts, sequence correction, and ligand validation in drug-target structures.

Control and materials characterization System for 6T Superconducting Cryogen Free Magnet Facility at IUAC, New Delhi

NASA Astrophysics Data System (ADS)

Dutt, R. N.; Meena, D. K.; Kar, S.; Soni, V.; Nadaf, A.; Das, A.; Singh, F.; Datta, T. S.

2017-02-01

A system for carrying out automatic experimental measurements of various electrical transport characteristics and their relation to magnetic fields for samples mounted on the sample holder on a Variable Temperature Insert (VTI) of the Cryogen Free Superconducting Magnet System (CFMS) has been developed. The control and characterization system is capable of monitoring, online plotting and history logging in real-time of cryogenic temperatures with the Silicon (Si) Diode and Zirconium Oxy-Nitride sensors installed inside the magnet facility. Electrical transport property measurements have been automated with implementation of current reversal resistance measurements and automatic temperature set-point ramping with the parameters of interest available in real-time as well as for later analysis. The Graphical User Interface (GUI) based system is user friendly to facilitate operations. An ingenious electronics for reading Zirconium Oxy-Nitride temperature sensors has been used. Price to performance ratio has been optimized by using in house developed measurement techniques mixed with specialized commercial cryogenic measurement / control equipment.

Polytobacco, marijuana, and alcohol use patterns in college students: A latent class analysis.

PubMed

Haardörfer, Regine; Berg, Carla J; Lewis, Michael; Payne, Jackelyn; Pillai, Drishti; McDonald, Bennett; Windle, Michael

2016-08-01

Limited research has examined polysubstance use profiles among young adults focusing on the various tobacco products currently available. We examined use patterns of various tobacco products, marijuana, and alcohol using data from the baseline survey of a multiwave longitudinal study of 3418 students aged 18-25 recruited from seven U.S. college campuses. We assessed sociodemographics, individual-level factors (depression; perceptions of harm and addictiveness,), and sociocontextual factors (parental/friend use). We conducted a latent class analysis and multivariable logistic regression to examine correlates of class membership (Abstainers were referent group). Results indicated five classes: Abstainers (26.1% per past 4-month use), Alcohol only users (38.9%), Heavy polytobacco users (7.3%), Light polytobacco users (17.3%), and little cigar and cigarillo (LCC)/hookah/marijuana co-users (10.4%). The most stable was LCC/hookah/marijuana co-users (77.3% classified as such in past 30-day and 4-month timeframes), followed by Heavy polytobacco users (53.2% classified consistently). Relative to Abstainers, Heavy polytobacco users were less likely to be Black and have no friends using alcohol and perceived harm of tobacco and marijuana use lower. Light polytobacco users were older, more likely to have parents using tobacco, and less likely to have friends using tobacco. LCC/hookah/marijuana co-users were older and more likely to have parents using tobacco. Alcohol only users perceived tobacco and marijuana use to be less socially acceptable, were more likely to have parents using alcohol and friends using marijuana, but less likely to have friends using tobacco. These findings may inform substance use prevention and recovery programs by better characterizing polysubstance use patterns. Copyright © 2016 Elsevier Ltd. All rights reserved.

Polytobacco, marijuana, and alcohol use patterns in college students: A latent class analysis

PubMed Central

Haardörfer, Regine; Berg, Carla J.; Lewis, Michael; Payne, Jackelyn; Pillai, Drishti; McDonald, Bennett; Windle, Michael

2016-01-01

Limited research has examined polysubstance use profiles among young adults focusing on the various tobacco products currently available. We examined use patterns of various tobacco products, marijuana, and alcohol using data from the baseline survey of a multiwave longitudinal study of 3418 students aged 18-25 recruited from seven U.S. college campuses. We assessed sociodemographics, individual-level factors (depression; perceptions of harm and addictiveness,), and sociocontextual factors (parental/friend use). We conducted a latent class analysis and multivariable logistic regression to examine correlates of class membership (Abstainers were referent group). Results indicated five classes: Abstainers (26.1% per past 4-month use), Alcohol only users (38.9%), Heavy polytobacco users (7.3%), Light polytobacco users (17.3%), and little cigar and cigarillo (LCC)/hookah/marijuana co-users (10.4%). The most stable was LCC/hookah/marijuana co-users (77.3% classified as such in past 30-day and 4-month timeframes), followed by Heavy polytobacco users (53.2% classified consistently). Relative to Abstainers, Heavy polytobacco users were less likely to be Black and have no friends using alcohol and perceived harm of tobacco and marijuana use lower. Light polytobacco users were older, more likely to have parents using tobacco, and less likely to have friends using tobacco. LCC/hookah/marijuana co-users were older and more likely to have parents using tobacco. Alcohol only users perceived tobacco and marijuana use to be less socially acceptable, were more likely to have parents using alcohol and friends using marijuana, but less likely to have friends using tobacco. These findings may inform substance use prevention and recovery programs by better characterizing polysubstance use patterns. PMID:27074202

Virtual Observatory and Colitec Software: Modules, Features, Methods

NASA Astrophysics Data System (ADS)

Pohorelov, A. V.; Khlamov, S. V.; Savanevych, V. E.; Briukhovetskyi, A. B.; Vlasenko, V. P.

In this article we described complex processing system created by the CoLiTec project. This system includes features, user-friendly tools for processing control, results reviewing, integration with online catalogs and a lot of different computational modules that are based on the developed methods. Some of them are described in the article.The main directions of the CoLiTec software development are the Virtual Observatory, software for automated asteroids and comets detection and software for brightness equalization.The CoLiTec software is widely used in a number of observatories in the CIS. It has been used in about 700 000 observations, during which 1560 asteroids, including 5 NEO, 21 Trojan asteroids of Jupiter, 1 Centaur and four comets were discovered.

Systems Maintenance Automated Repair Tasks (SMART)

NASA Technical Reports Server (NTRS)

2008-01-01

SMART is an interactive decision analysis and refinement software system that uses evaluation criteria for discrepant conditions to automatically provide and populate a document/procedure with predefined steps necessary to repair a discrepancy safely, effectively, and efficiently. SMART can store the tacit (corporate) knowledge merging the hardware specification requirements with the actual "how to" repair methods, sequences, and required equipment, all within a user-friendly interface. Besides helping organizations retain repair knowledge in streamlined procedures and sequences, SMART can also help them in saving processing time and expense, increasing productivity, improving quality, and adhering more closely to safety and other guidelines. Though SMART was developed for Space Shuttle applications, its interface is easily adaptable to any hardware that can be broken down by component, subcomponent, discrepancy, and repair.

GoIFISH: a system for the quantification of single cell heterogeneity from IFISH images.

PubMed

Trinh, Anne; Rye, Inga H; Almendro, Vanessa; Helland, Aslaug; Russnes, Hege G; Markowetz, Florian

2014-08-26

Molecular analysis has revealed extensive intra-tumor heterogeneity in human cancer samples, but cannot identify cell-to-cell variations within the tissue microenvironment. In contrast, in situ analysis can identify genetic aberrations in phenotypically defined cell subpopulations while preserving tissue-context specificity. GoIFISHGoIFISH is a widely applicable, user-friendly system tailored for the objective and semi-automated visualization, detection and quantification of genomic alterations and protein expression obtained from fluorescence in situ analysis. In a sample set of HER2-positive breast cancers GoIFISHGoIFISH is highly robust in visual analysis and its accuracy compares favorably to other leading image analysis methods. GoIFISHGoIFISH is freely available at www.sourceforge.net/projects/goifish/.

MilxXplore: a web-based system to explore large imaging datasets.

PubMed

Bourgeat, P; Dore, V; Villemagne, V L; Rowe, C C; Salvado, O; Fripp, J

2013-01-01

As large-scale medical imaging studies are becoming more common, there is an increasing reliance on automated software to extract quantitative information from these images. As the size of the cohorts keeps increasing with large studies, there is a also a need for tools that allow results from automated image processing and analysis to be presented in a way that enables fast and efficient quality checking, tagging and reporting on cases in which automatic processing failed or was problematic. MilxXplore is an open source visualization platform, which provides an interface to navigate and explore imaging data in a web browser, giving the end user the opportunity to perform quality control and reporting in a user friendly, collaborative and efficient way. Compared to existing software solutions that often provide an overview of the results at the subject's level, MilxXplore pools the results of individual subjects and time points together, allowing easy and efficient navigation and browsing through the different acquisitions of a subject over time, and comparing the results against the rest of the population. MilxXplore is fast, flexible and allows remote quality checks of processed imaging data, facilitating data sharing and collaboration across multiple locations, and can be easily integrated into a cloud computing pipeline. With the growing trend of open data and open science, such a tool will become increasingly important to share and publish results of imaging analysis.

BioCluster: tool for identification and clustering of Enterobacteriaceae based on biochemical data.

PubMed

Abdullah, Ahmed; Sabbir Alam, S M; Sultana, Munawar; Hossain, M Anwar

2015-06-01

Presumptive identification of different Enterobacteriaceae species is routinely achieved based on biochemical properties. Traditional practice includes manual comparison of each biochemical property of the unknown sample with known reference samples and inference of its identity based on the maximum similarity pattern with the known samples. This process is labor-intensive, time-consuming, error-prone, and subjective. Therefore, automation of sorting and similarity in calculation would be advantageous. Here we present a MATLAB-based graphical user interface (GUI) tool named BioCluster. This tool was designed for automated clustering and identification of Enterobacteriaceae based on biochemical test results. In this tool, we used two types of algorithms, i.e., traditional hierarchical clustering (HC) and the Improved Hierarchical Clustering (IHC), a modified algorithm that was developed specifically for the clustering and identification of Enterobacteriaceae species. IHC takes into account the variability in result of 1-47 biochemical tests within this Enterobacteriaceae family. This tool also provides different options to optimize the clustering in a user-friendly way. Using computer-generated synthetic data and some real data, we have demonstrated that BioCluster has high accuracy in clustering and identifying enterobacterial species based on biochemical test data. This tool can be freely downloaded at http://microbialgen.du.ac.bd/biocluster/. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

Comparison Analysis among Large Amount of SNS Sites

NASA Astrophysics Data System (ADS)

Toriumi, Fujio; Yamamoto, Hitoshi; Suwa, Hirohiko; Okada, Isamu; Izumi, Kiyoshi; Hashimoto, Yasuhiro

In recent years, application of Social Networking Services (SNS) and Blogs are growing as new communication tools on the Internet. Several large-scale SNS sites are prospering; meanwhile, many sites with relatively small scale are offering services. Such small-scale SNSs realize small-group isolated type of communication while neither mixi nor MySpace can do that. However, the studies on SNS are almost about particular large-scale SNSs and cannot analyze whether their results apply for general features or for special characteristics on the SNSs. From the point of view of comparison analysis on SNS, comparison with just several types of those cannot reach a statistically significant level. We analyze many SNS sites with the aim of classifying them by using some approaches. Our paper classifies 50,000 sites for small-scale SNSs and gives their features from the points of network structure, patterns of communication, and growth rate of SNS. The result of analysis for network structure shows that many SNS sites have small-world attribute with short path lengths and high coefficients of their cluster. Distribution of degrees of the SNS sites is close to power law. This result indicates the small-scale SNS sites raise the percentage of users with many friends than mixi. According to the analysis of their coefficients of assortativity, those SNS sites have negative values of assortativity, and that means users with high degree tend to connect users with small degree. Next, we analyze the patterns of user communication. A friend network of SNS is explicit while users' communication behaviors are defined as an implicit network. What kind of relationships do these networks have? To address this question, we obtain some characteristics of users' communication structure and activation patterns of users on the SNS sites. By using new indexes, friend aggregation rate and friend coverage rate, we show that SNS sites with high value of friend coverage rate activate diary postings and their comments. Besides, they become activated when hub users with high degree do not behave actively on the sites with high value of friend aggregation rate and high value of friend coverage rate. On the other hand, activation emerges when hub users behave actively on the sites with low value of friend aggregation rate and high value of friend coverage rate. Finally, we observe SNS sites which are increasing the number of users considerably, from the viewpoint of network structure, and extract characteristics of high growth SNS sites. As a result of discrimination on the basis of the decision tree analysis, we can recognize the high growth SNS sites with a high degree of accuracy. Besides, this approach suggests mixi and the other small-scale SNS sites have different character trait.

Automated DICOM metadata and volumetric anatomical information extraction for radiation dosimetry

NASA Astrophysics Data System (ADS)

Papamichail, D.; Ploussi, A.; Kordolaimi, S.; Karavasilis, E.; Papadimitroulas, P.; Syrgiamiotis, V.; Efstathopoulos, E.

2015-09-01

Patient-specific dosimetry calculations based on simulation techniques have as a prerequisite the modeling of the modality system and the creation of voxelized phantoms. This procedure requires the knowledge of scanning parameters and patients’ information included in a DICOM file as well as image segmentation. However, the extraction of this information is complicated and time-consuming. The objective of this study was to develop a simple graphical user interface (GUI) to (i) automatically extract metadata from every slice image of a DICOM file in a single query and (ii) interactively specify the regions of interest (ROI) without explicit access to the radiology information system. The user-friendly application developed in Matlab environment. The user can select a series of DICOM files and manage their text and graphical data. The metadata are automatically formatted and presented to the user as a Microsoft Excel file. The volumetric maps are formed by interactively specifying the ROIs and by assigning a specific value in every ROI. The result is stored in DICOM format, for data and trend analysis. The developed GUI is easy, fast and and constitutes a very useful tool for individualized dosimetry. One of the future goals is to incorporate a remote access to a PACS server functionality.

PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface.

PubMed

Uszkoreit, Julian; Maerkens, Alexandra; Perez-Riverol, Yasset; Meyer, Helmut E; Marcus, Katrin; Stephan, Christian; Kohlbacher, Oliver; Eisenacher, Martin

2015-07-02

Protein inference connects the peptide spectrum matches (PSMs) obtained from database search engines back to proteins, which are typically at the heart of most proteomics studies. Different search engines yield different PSMs and thus different protein lists. Analysis of results from one or multiple search engines is often hampered by different data exchange formats and lack of convenient and intuitive user interfaces. We present PIA, a flexible software suite for combining PSMs from different search engine runs and turning these into consistent results. PIA can be integrated into proteomics data analysis workflows in several ways. A user-friendly graphical user interface can be run either locally or (e.g., for larger core facilities) from a central server. For automated data processing, stand-alone tools are available. PIA implements several established protein inference algorithms and can combine results from different search engines seamlessly. On several benchmark data sets, we show that PIA can identify a larger number of proteins at the same protein FDR when compared to that using inference based on a single search engine. PIA supports the majority of established search engines and data in the mzIdentML standard format. It is implemented in Java and freely available at https://github.com/mpc-bioinformatics/pia.

Hands-On Universe: A Global Program for Education and Public Outreach in Astronomy

NASA Astrophysics Data System (ADS)

Boër, M.; Thiébaut, C.; Pack, H.; Pennypaker, C.; Isaac, M.; Melchior, A.-L.; Faye, S.; Ebisuzaki, T.

Hands-On Universe (HOU) is an educational program that enables students to investigate the Universe while applying tools and concepts from science, math, and technology. Using the Internet, HOU participants around the world request observations from an automated telescope, download images from a large image archive, and analyze them with the aid of user-friendly image processing software. This program is now in many countries, including the USA, France, Germany, Sweden, Japan, and Australia. A network of telescopes has been established, many of them remotely operated. Students in the classroom are able to make night observations during the day, using a telescope in another country. An archive of images taken on large telescopes is also accessible, as well as resources for teachers. Students deal with real research projects, e.g., the search for asteroids, which resulted in the discovery of a Kuiper Belt object by high-school students. Not only does Hands-On Universe give the general public access to professional astronomy, it also demonstrates the use of a complex automated system, data processing techniques, and automation. Using telescopes located in many countries over the globe, a powerful and genuine cooperation between teachers and children from various countries is promoted, with a clear educational goal.

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.

Step-by-step guide to building an inexpensive 3D printed motorized positioning stage for automated high-content screening microscopy.

PubMed

Schneidereit, Dominik; Kraus, Larissa; Meier, Jochen C; Friedrich, Oliver; Gilbert, Daniel F

2017-06-15

High-content screening microscopy relies on automation infrastructure that is typically proprietary, non-customizable, costly and requires a high level of skill to use and maintain. The increasing availability of rapid prototyping technology makes it possible to quickly engineer alternatives to conventional automation infrastructure that are low-cost and user-friendly. Here, we describe a 3D printed inexpensive open source and scalable motorized positioning stage for automated high-content screening microscopy and provide detailed step-by-step instructions to re-building the device, including a comprehensive parts list, 3D design files in STEP (Standard for the Exchange of Product model data) and STL (Standard Tessellation Language) format, electronic circuits and wiring diagrams as well as software code. System assembly including 3D printing requires approx. 30h. The fully assembled device is light-weight (1.1kg), small (33×20×8cm) and extremely low-cost (approx. EUR 250). We describe positioning characteristics of the stage, including spatial resolution, accuracy and repeatability, compare imaging data generated with our device to data obtained using a commercially available microplate reader, demonstrate its suitability to high-content microscopy in 96-well high-throughput screening format and validate its applicability to automated functional Cl - - and Ca 2+ -imaging with recombinant HEK293 cells as a model system. A time-lapse video of the stage during operation and as part of a custom assembled screening robot can be found at https://vimeo.com/158813199. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

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.

@Note: a workbench for biomedical text mining.

PubMed

Lourenço, Anália; Carreira, Rafael; Carneiro, Sónia; Maia, Paulo; Glez-Peña, Daniel; Fdez-Riverola, Florentino; Ferreira, Eugénio C; Rocha, Isabel; Rocha, Miguel

2009-08-01

Biomedical Text Mining (BioTM) is providing valuable approaches to the automated curation of scientific literature. However, most efforts have addressed the benchmarking of new algorithms rather than user operational needs. Bridging the gap between BioTM researchers and biologists' needs is crucial to solve real-world problems and promote further research. We present @Note, a platform for BioTM that aims at the effective translation of the advances between three distinct classes of users: biologists, text miners and software developers. Its main functional contributions are the ability to process abstracts and full-texts; an information retrieval module enabling PubMed search and journal crawling; a pre-processing module with PDF-to-text conversion, tokenisation and stopword removal; a semantic annotation schema; a lexicon-based annotator; a user-friendly annotation view that allows to correct annotations and a Text Mining Module supporting dataset preparation and algorithm evaluation. @Note improves the interoperability, modularity and flexibility when integrating in-home and open-source third-party components. Its component-based architecture allows the rapid development of new applications, emphasizing the principles of transparency and simplicity of use. Although it is still on-going, it has already allowed the development of applications that are currently being used.

Point Analysis in Java applied to histological images of the perforant pathway: a user's account.

PubMed

Scorcioni, Ruggero; Wright, Susan N; Patrick Card, J; Ascoli, Giorgio A; Barrionuevo, Germán

2008-01-01

The freeware Java tool Point Analysis in Java (PAJ), created to perform 3D point analysis, was tested in an independent laboratory setting. The input data consisted of images of the hippocampal perforant pathway from serial immunocytochemical localizations of the rat brain in multiple views at different resolutions. The low magnification set (x2 objective) comprised the entire perforant pathway, while the high magnification set (x100 objective) allowed the identification of individual fibers. A preliminary stereological study revealed a striking linear relationship between the fiber count at high magnification and the optical density at low magnification. PAJ enabled fast analysis for down-sampled data sets and a friendly interface with automated plot drawings. Noted strengths included the multi-platform support as well as the free availability of the source code, conducive to a broad user base and maximum flexibility for ad hoc requirements. PAJ has great potential to extend its usability by (a) improving its graphical user interface, (b) increasing its input size limit, (c) improving response time for large data sets, and (d) potentially being integrated with other Java graphical tools such as ImageJ.

PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data.

PubMed

Anslan, Sten; Bahram, Mohammad; Hiiesalu, Indrek; Tedersoo, Leho

2017-11-01

High-throughput sequencing methods have become a routine analysis tool in environmental sciences as well as in public and private sector. These methods provide vast amount of data, which need to be analysed in several steps. Although the bioinformatics may be applied using several public tools, many analytical pipelines allow too few options for the optimal analysis for more complicated or customized designs. Here, we introduce PipeCraft, a flexible and handy bioinformatics pipeline with a user-friendly graphical interface that links several public tools for analysing amplicon sequencing data. Users are able to customize the pipeline by selecting the most suitable tools and options to process raw sequences from Illumina, Pacific Biosciences, Ion Torrent and Roche 454 sequencing platforms. We described the design and options of PipeCraft and evaluated its performance by analysing the data sets from three different sequencing platforms. We demonstrated that PipeCraft is able to process large data sets within 24 hr. The graphical user interface and the automated links between various bioinformatics tools enable easy customization of the workflow. All analytical steps and options are recorded in log files and are easily traceable. © 2017 John Wiley & Sons Ltd.

A Simple Automated Method for the Determination of Nitrate and Nitrite in Infant Formula and Milk Powder Using Sequential Injection Analysis

PubMed Central

Pistón, Mariela; Mollo, Alicia; Knochen, Moisés

2011-01-01

A fast and efficient automated method using a sequential injection analysis (SIA) system, based on the Griess, reaction was developed for the determination of nitrate and nitrite in infant formulas and milk powder. The system enables to mix a measured amount of sample (previously constituted in the liquid form and deproteinized) with the chromogenic reagent to produce a colored substance whose absorbance was recorded. For nitrate determination, an on-line prereduction step was added by passing the sample through a Cd minicolumn. The system was controlled from a PC by means of a user-friendly program. Figures of merit include linearity (r2 > 0.999 for both analytes), limits of detection (0.32 mg kg−1 NO3-N, and 0.05 mg kg−1 NO2-N), and precision (sr%) 0.8–3.0. Results were statistically in good agreement with those obtained with the reference ISO-IDF method. The sampling frequency was 30 hour−1 (nitrate) and 80 hour−1 (nitrite) when performed separately. PMID:21960750

Automated management for pavement inspection system (AMPIS)

NASA Astrophysics Data System (ADS)

Chung, Hung Chi; Girardello, Roberto; Soeller, Tony; Shinozuka, Masanobu

2003-08-01

An automated in-situ road surface distress surveying and management system, AMPIS, has been developed on the basis of video images within the framework of GIS software. Video image processing techniques are introduced to acquire, process and analyze the road surface images obtained from a moving vehicle. ArcGIS platform is used to integrate the routines of image processing and spatial analysis in handling the full-scale metropolitan highway surface distress detection and data fusion/management. This makes it possible to present user-friendly interfaces in GIS and to provide efficient visualizations of surveyed results not only for the use of transportation engineers to manage road surveying documentations, data acquisition, analysis and management, but also for financial officials to plan maintenance and repair programs and further evaluate the socio-economic impacts of highway degradation and deterioration. A review performed in this study on fundamental principle of Pavement Management System (PMS) and its implementation indicates that the proposed approach of using GIS concept and its tools for PMS application will reshape PMS into a new information technology-based system providing a convenient and efficient pavement inspection and management.

GIS-based automated management of highway surface crack inspection system

NASA Astrophysics Data System (ADS)

Chung, Hung-Chi; Shinozuka, Masanobu; Soeller, Tony; Girardello, Roberto

2004-07-01

An automated in-situ road surface distress surveying and management system, AMPIS, has been developed on the basis of video images within the framework of GIS software. Video image processing techniques are introduced to acquire, process and analyze the road surface images obtained from a moving vehicle. ArcGIS platform is used to integrate the routines of image processing and spatial analysis in handling the full-scale metropolitan highway surface distress detection and data fusion/management. This makes it possible to present user-friendly interfaces in GIS and to provide efficient visualizations of surveyed results not only for the use of transportation engineers to manage road surveying documentations, data acquisition, analysis and management, but also for financial officials to plan maintenance and repair programs and further evaluate the socio-economic impacts of highway degradation and deterioration. A review performed in this study on fundamental principle of Pavement Management System (PMS) and its implementation indicates that the proposed approach of using GIS concept and its tools for PMS application will reshape PMS into a new information technology-based system that can provide convenient and efficient pavement inspection and management.

Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra.

PubMed

Tolić, Nikola; Liu, Yina; Liyu, Andrey; Shen, Yufeng; Tfaily, Malak M; Kujawinski, Elizabeth B; Longnecker, Krista; Kuo, Li-Jung; Robinson, Errol W; Paša-Tolić, Ljiljana; Hess, Nancy J

2017-12-05

Ultrahigh resolution mass spectrometry, such as Fourier transform ion cyclotron resonance mass spectrometry (FT ICR MS), can resolve thousands of molecular ions in complex organic matrices. A Compound Identification Algorithm (CIA) was previously developed for automated elemental formula assignment for natural organic matter (NOM). In this work, we describe software Formularity with a user-friendly interface for CIA function and newly developed search function Isotopic Pattern Algorithm (IPA). While CIA assigns elemental formulas for compounds containing C, H, O, N, S, and P, IPA is capable of assigning formulas for compounds containing other elements. We used halogenated organic compounds (HOC), a chemical class that is ubiquitous in nature as well as anthropogenic systems, as an example to demonstrate the capability of Formularity with IPA. A HOC standard mix was used to evaluate the identification confidence of IPA. Tap water and HOC spike in Suwannee River NOM were used to assess HOC identification in complex environmental samples. Strategies for reconciliation of CIA and IPA assignments were discussed. Software and sample databases with documentation are freely available.

Particle tracking in drug and gene delivery research: State-of-the-art applications and methods.

PubMed

Schuster, Benjamin S; Ensign, Laura M; Allan, Daniel B; Suk, Jung Soo; Hanes, Justin

2015-08-30

Particle tracking is a powerful microscopy technique to quantify the motion of individual particles at high spatial and temporal resolution in complex fluids and biological specimens. Particle tracking's applications and impact in drug and gene delivery research have greatly increased during the last decade. Thanks to advances in hardware and software, this technique is now more accessible than ever, and can be reliably automated to enable rapid processing of large data sets, thereby further enhancing the role that particle tracking will play in drug and gene delivery studies in the future. We begin this review by discussing particle tracking-based advances in characterizing extracellular and cellular barriers to therapeutic nanoparticles and in characterizing nanoparticle size and stability. To facilitate wider adoption of the technique, we then present a user-friendly review of state-of-the-art automated particle tracking algorithms and methods of analysis. We conclude by reviewing technological developments for next-generation particle tracking methods, and we survey future research directions in drug and gene delivery where particle tracking may be useful. Copyright © 2015 Elsevier B.V. All rights reserved.

The virtual case: a new method to completely digitize cytological and histological slides.

PubMed

Demichelis, F; Barbareschi, M; Dalla Palma, P; Forti, S

2002-08-01

The purpose of this study was to present a new method for handling histological/cytological cases. Thanks to the introduction of information technology in pathology, including the amenities afforded by robotic microscopes and digital imaging, tissue slides can be represented and evaluated using digital techniques in order to construct virtual cases through completely automated procedures. A virtual case (VC) is composed of a collection of digital images representing a histological/cytological slide at all magnification levels together with all relevant clinical data. In the present study, we describe an automated system to manage robotic microscope and image acquisition for the proper construction of VCs. These can then be viewed on a computer by means of an interface ("user-friendly") that allows one to select the more appropriate fields and to examine them at different magnifications, rapidly going from panoramic views to high resolution and vice versa. In comparison with glass slides, VCs have several advantages arising from their digital nature and can be considered a common platform for a wide range of applications such as teleconsultation, education, research, and quality control and proficiency tests.

Automated Help System For A Supercomputer

NASA Technical Reports Server (NTRS)

Callas, George P.; Schulbach, Catherine H.; Younkin, Michael

1994-01-01

Expert-system software developed to provide automated system of user-helping displays in supercomputer system at Ames Research Center Advanced Computer Facility. Users located at remote computer terminals connected to supercomputer and each other via gateway computers, local-area networks, telephone lines, and satellite links. Automated help system answers routine user inquiries about how to use services of computer system. Available 24 hours per day and reduces burden on human experts, freeing them to concentrate on helping users with complicated problems.

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.

Cognitive consequences of clumsy automation on high workload, high consequence human performance

NASA Technical Reports Server (NTRS)

Cook, Richard I.; Woods, David D.; Mccolligan, Elizabeth; Howie, Michael B.

1991-01-01

The growth of computational power has fueled attempts to automate more of the human role in complex problem solving domains, especially those where system faults have high consequences and where periods of high workload may saturate the performance capacity of human operators. Examples of these domains include flightdecks, space stations, air traffic control, nuclear power operation, ground satellite control rooms, and surgical operating rooms. Automation efforts may have unanticipated effects on human performance, particularly if they increase the workload at peak workload times or change the practitioners' strategies for coping with workload. Smooth and effective changes in automation requires detailed understanding of the congnitive tasks confronting the user: it has been called user centered automation. The introduction of a new computerized technology in a group of hospital operating rooms used for heart surgery was observed. The study revealed how automation, especially 'clumsy automation', effects practitioner work patterns and suggest that clumsy automation constrains users in specific and significant ways. Users tailor both the new system and their tasks in order to accommodate the needs of process and production. The study of this tailoring may prove a powerful tool for exposing previously hidden patterns of user data processing, integration, and decision making which may, in turn, be useful in the design of more effective human-machine systems.

Humans: still vital after all these years of automation.

PubMed

Parasuraman, Raja; Wickens, Christopher D

2008-06-01

The authors discuss empirical studies of human-automation interaction and their implications for automation design. Automation is prevalent in safety-critical systems and increasingly in everyday life. Many studies of human performance in automated systems have been conducted over the past 30 years. Developments in three areas are examined: levels and stages of automation, reliance on and compliance with automation, and adaptive automation. Automation applied to information analysis or decision-making functions leads to differential system performance benefits and costs that must be considered in choosing appropriate levels and stages of automation. Human user dependence on automated alerts and advisories reflects two components of operator trust, reliance and compliance, which are in turn determined by the threshold designers use to balance automation misses and false alarms. Finally, adaptive automation can provide additional benefits in balancing workload and maintaining the user's situation awareness, although more research is required to identify when adaptation should be user controlled or system driven. The past three decades of empirical research on humans and automation has provided a strong science base that can be used to guide the design of automated systems. This research can be applied to most current and future automated systems.

A study into the automation of cognitive assessment tasks for delivery via the telephone: lessons for developing remote monitoring applications for the elderly.

PubMed

D'Arcy, Shona; Rapcan, Viliam; Gali, Alessandra; Burke, Nicola; O'Connell, Gloria Crispino; Robertson, Ian H; Reilly, Richard B

2013-01-01

Cognitive assessments are valuable tools in assessing neurological conditions. They are critical in measuring deficits in cognitive function in an array of neurological disorders and during the ageing process. Automation of cognitive assessments is one way to address the increasing burden on medical resources for an ever increasing ageing population. This study investigated the suitability of using automated Interactive Voice Response (IVR) technology to deliver a suite of cognitive assessments to older adults using speech as the input modality. Several clinically valid and gold-standard cognitive assessments were selected for implementation in the IVR application. The IVR application was designed using human centred design principles to ensure the experience was as user friendly as possible. Sixty one participants completed two IVR assessments and one face to face (FF) assessment with a neuropsychologist. Completion rates for individual tests were inspected to identify those tests that are most suitable for administration via IVR technology. Interclass correlations were calculated to assess the reliability of the automated administration of the cognitive assessments across delivery modes. While all participants successfully completed all automated assessments, variability in the completion rates for different cognitive tests was observed. Statistical analysis found significant interclass correlations for certain cognitive tests between the different modes of administration. Analysis also suggests that an initial FF assessment reduces the variability in cognitive test scores when introducing automation into such an assessment. [corrected] This study has demonstrated the functional and cognitive reliability of administering specific cognitive tests using an automated, speech driven application. This study has defined the characteristics of existing cognitive tests that are suitable for such an automated delivery system and also informs on the limitations of other cognitive tests for this modality. This study presents recommendations for developing future large scale cognitive assessments.

Living Lab as an Agile Approach in Developing User-Friendly Welfare Technology.

PubMed

Holappa, Niina; Sirkka, Andrew

2017-01-01

This paper discusses living lab as a method of developing user-friendly welfare technology, and presents a qualitative evaluation research of how living lab tested technologies impacted on the life of healthcare customers and professionals over test periods.

SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals

PubMed Central

Damienikan, Aliaksandr U.

2016-01-01

The majority of bacterial genome annotations are currently automated and based on a ‘gene by gene’ approach. Regulatory signals and operon structures are rarely taken into account which often results in incomplete and even incorrect gene function assignments. Here we present SigmoID, a cross-platform (OS X, Linux and Windows) open-source application aiming at simplifying the identification of transcription regulatory sites (promoters, transcription factor binding sites and terminators) in bacterial genomes and providing assistance in correcting annotations in accordance with regulatory information. SigmoID combines a user-friendly graphical interface to well known command line tools with a genome browser for visualising regulatory elements in genomic context. Integrated access to online databases with regulatory information (RegPrecise and RegulonDB) and web-based search engines speeds up genome analysis and simplifies correction of genome annotation. We demonstrate some features of SigmoID by constructing a series of regulatory protein binding site profiles for two groups of bacteria: Soft Rot Enterobacteriaceae (Pectobacterium and Dickeya spp.) and Pseudomonas spp. Furthermore, we inferred over 900 transcription factor binding sites and alternative sigma factor promoters in the annotated genome of Pectobacterium atrosepticum. These regulatory signals control putative transcription units covering about 40% of the P. atrosepticum chromosome. Reviewing the annotation in cases where it didn’t fit with regulatory information allowed us to correct product and gene names for over 300 loci. PMID:27257541

Optical tracking of embryonic vertebrates behavioural responses using automated time-resolved video-microscopy system

NASA Astrophysics Data System (ADS)

Walpitagama, Milanga; Kaslin, Jan; Nugegoda, Dayanthi; Wlodkowic, Donald

2016-12-01

The fish embryo toxicity (FET) biotest performed on embryos of zebrafish (Danio rerio) has gained significant popularity as a rapid and inexpensive alternative approach in chemical hazard and risk assessment. The FET was designed to evaluate acute toxicity on embryonic stages of fish exposed to the test chemical. The current standard, similar to most traditional methods for evaluating aquatic toxicity provides, however, little understanding of effects of environmentally relevant concentrations of chemical stressors. We postulate that significant environmental effects such as altered motor functions, physiological alterations reflected in heart rate, effects on development and reproduction can occur at sub-lethal concentrations well below than LC10. Behavioral studies can, therefore, provide a valuable integrative link between physiological and ecological effects. Despite the advantages of behavioral analysis development of behavioral toxicity, biotests is greatly hampered by the lack of dedicated laboratory automation, in particular, user-friendly and automated video microscopy systems. In this work we present a proof-of-concept development of an optical system capable of tracking embryonic vertebrates behavioral responses using automated and vastly miniaturized time-resolved video-microscopy. We have employed miniaturized CMOS cameras to perform high definition video recording and analysis of earliest vertebrate behavioral responses. The main objective was to develop a biocompatible embryo positioning structures that were suitable for high-throughput imaging as well as video capture and video analysis algorithms. This system should support the development of sub-lethal and behavioral markers for accelerated environmental monitoring.

I trust it, but I don't know why: effects of implicit attitudes toward automation on trust in an automated system.

PubMed

Merritt, Stephanie M; Heimbaugh, Heather; LaChapell, Jennifer; Lee, Deborah

2013-06-01

This study is the first to examine the influence of implicit attitudes toward automation on users' trust in automation. Past empirical work has examined explicit (conscious) influences on user level of trust in automation but has not yet measured implicit influences. We examine concurrent effects of explicit propensity to trust machines and implicit attitudes toward automation on trust in an automated system. We examine differential impacts of each under varying automation performance conditions (clearly good, ambiguous, clearly poor). Participants completed both a self-report measure of propensity to trust and an Implicit Association Test measuring implicit attitude toward automation, then performed an X-ray screening task. Automation performance was manipulated within-subjects by varying the number and obviousness of errors. Explicit propensity to trust and implicit attitude toward automation did not significantly correlate. When the automation's performance was ambiguous, implicit attitude significantly affected automation trust, and its relationship with propensity to trust was additive: Increments in either were related to increases in trust. When errors were obvious, a significant interaction between the implicit and explicit measures was found, with those high in both having higher trust. Implicit attitudes have important implications for automation trust. Users may not be able to accurately report why they experience a given level of trust. To understand why users trust or fail to trust automation, measurements of implicit and explicit predictors may be necessary. Furthermore, implicit attitude toward automation might be used as a lever to effectively calibrate trust.

Analysis of Environmental Friendly Library Based on the Satisfaction and Service Quality: study at Library “X”

NASA Astrophysics Data System (ADS)

Herdiansyah, Herdis; Satriya Utama, Andre; Safruddin; Hidayat, Heri; Gema Zuliana Irawan, Angga; Immanuel Tjandra Muliawan, R.; Mutia Pratiwi, Diana

2017-10-01

One of the factor that influenced the development of science is the existence of the library, which in this case is the college libraries. Library, which is located in the college environment, aims to supply collections of literatures to support research activities as well as educational for students of the college. Conceptually, every library now starts to practice environmental principles. For example, “X” library as a central library claims to be an environmental friendly library for practicing environmental friendly management, but the X library has not inserted the satisfaction and service aspect to the users, including whether it is true that environmental friendly process is perceived by library users. Satisfaction can be seen from the comparison between expectations and reality of library users. This paper analyzes the level of library user satisfaction with library services in the campus area and the gap between expectations and reality felt by the library users. The result of the research shows that there is a disparity between the hope of library management, which is sustainable and environmentally friendly with the reality in the management of the library, so that it has not given satisfaction to the users yet. The gap value of satisfaction that has the biggest difference is in the library collection with the value of 1.57; while for the smallest gap value is in the same service to all students with a value of 0.67.

Adversarial reasoning and resource allocation: the LG approach

NASA Astrophysics Data System (ADS)

Stilman, Boris; Yakhnis, Vladimir; Umanskiy, Oleg; Boyd, Ron

2005-05-01

Many existing automated tools purporting to model the intelligent enemy utilize a fixed battle plan for the enemy while using flexible decisions of human players for the friendly side. According to the Naval Studies Board, "It is an open secret and a point of distress ... that too much of the substantive content of such M&S has its origin in anecdote, ..., or a narrow construction tied to stereotypical current practices of 'doctrinally correct behavior.'" Clearly, such runs lack objectivity by being heavily skewed in favor of the friendly forces. Presently, the military branches employ a variety of game-based simulators and synthetic environments, with manual (i.e., user-based) decision-making, for training and other purposes. However, without an ability to automatically generate the best strategies, tactics, and COA, the games serve mostly to display the current situation rather than form a basis for automated decision-making and effective training. We solve the problem of adversarial reasoning as a gaming problem employing Linguistic Geometry (LG), a new type of game theory demonstrating significant increase in size in gaming problems solvable in real and near-real time. It appears to be a viable approach for solving such practical problems as mission planning and battle management. Essentially, LG may be structured into two layers: game construction and game solving. Game construction includes construction of a game called an LG hypergame based on a hierarchy of Abstract Board Games (ABG). Game solving includes resource allocation for constructing an advantageous initial game state and strategy generation to reach a desirable final game state in the course of the game.

QuickRNASeq lifts large-scale RNA-seq data analyses to the next level of automation and interactive visualization.

PubMed

Zhao, Shanrong; Xi, Li; Quan, Jie; Xi, Hualin; Zhang, Ying; von Schack, David; Vincent, Michael; Zhang, Baohong

2016-01-08

RNA sequencing (RNA-seq), a next-generation sequencing technique for transcriptome profiling, is being increasingly used, in part driven by the decreasing cost of sequencing. Nevertheless, the analysis of the massive amounts of data generated by large-scale RNA-seq remains a challenge. Multiple algorithms pertinent to basic analyses have been developed, and there is an increasing need to automate the use of these tools so as to obtain results in an efficient and user friendly manner. Increased automation and improved visualization of the results will help make the results and findings of the analyses readily available to experimental scientists. By combing the best open source tools developed for RNA-seq data analyses and the most advanced web 2.0 technologies, we have implemented QuickRNASeq, a pipeline for large-scale RNA-seq data analyses and visualization. The QuickRNASeq workflow consists of three main steps. In Step #1, each individual sample is processed, including mapping RNA-seq reads to a reference genome, counting the numbers of mapped reads, quality control of the aligned reads, and SNP (single nucleotide polymorphism) calling. Step #1 is computationally intensive, and can be processed in parallel. In Step #2, the results from individual samples are merged, and an integrated and interactive project report is generated. All analyses results in the report are accessible via a single HTML entry webpage. Step #3 is the data interpretation and presentation step. The rich visualization features implemented here allow end users to interactively explore the results of RNA-seq data analyses, and to gain more insights into RNA-seq datasets. In addition, we used a real world dataset to demonstrate the simplicity and efficiency of QuickRNASeq in RNA-seq data analyses and interactive visualizations. The seamless integration of automated capabilites with interactive visualizations in QuickRNASeq is not available in other published RNA-seq pipelines. The high degree of automation and interactivity in QuickRNASeq leads to a substantial reduction in the time and effort required prior to further downstream analyses and interpretation of the analyses findings. QuickRNASeq advances primary RNA-seq data analyses to the next level of automation, and is mature for public release and adoption.

Evaluation of an alternative extraction procedure for enterotoxin determination in dairy products.

PubMed

Meyrand, A; Atrache, V; Bavai, C; Montet, M P; Vernozy-Rozand, C

1999-06-01

A concentration protocol based on trichloroacetic acid precipitation was evaluated and compared with the reference method using dialysis concentration. Different quantities of purified staphylococcal enterotoxins were added to pasteurized Camembert-type cheeses. Detection of enterotoxins in these cheeses was performed using an automated detection system. Raw goat milk Camembert-type cheeses involved in a staphylococcal food poisoning were also tested. Both enterotoxin extraction methods allowed detection of the lowest enterotoxin concentration level used in this study (0.5 ng g-1). Compared with the dialysis concentration method, TCA precipitation of staphylococcal enterotoxins was 'user-friendly' and less time-consuming. These results suggest that TCA precipitation is a rapid (1 h), simple and reliable method of extracting enterotoxin from food which gives excellent recovery from dairy products.

Progress in the development of paper-based diagnostics for low-resource point-of-care settings

PubMed Central

Byrnes, Samantha; Thiessen, Gregory; Fu, Elain

2014-01-01

This Review focuses on recent work in the field of paper microfluidics that specifically addresses the goal of translating the multistep processes that are characteristic of gold-standard laboratory tests to low-resource point-of-care settings. A major challenge is to implement multistep processes with the robust fluid control required to achieve the necessary sensitivity and specificity of a given application in a user-friendly package that minimizes equipment. We review key work in the areas of fluidic controls for automation in paper-based devices, readout methods that minimize dedicated equipment, and power and heating methods that are compatible with low-resource point-of-care settings. We also highlight a focused set of recent applications and discuss future challenges. PMID:24256361

Editorial: Bayesian benefits for child psychology and psychiatry researchers.

PubMed

Oldehinkel, Albertine J

2016-09-01

For many scientists, performing statistical tests has become an almost automated routine. However, p-values are frequently used and interpreted incorrectly; and even when used appropriately, p-values tend to provide answers that do not match researchers' questions and hypotheses well. Bayesian statistics present an elegant and often more suitable alternative. The Bayesian approach has rarely been applied in child psychology and psychiatry research so far, but the development of user-friendly software packages and tutorials has placed it well within reach now. Because Bayesian analyses require a more refined definition of hypothesized probabilities of possible outcomes than the classical approach, going Bayesian may offer the additional benefit of sparkling the development and refinement of theoretical models in our field. © 2016 Association for Child and Adolescent Mental Health.

Not all trust is created equal: dispositional and history-based trust in human-automation interactions.

PubMed

Merritt, Stephanie M; Ilgen, Daniel R

2008-04-01

We provide an empirical demonstration of the importance of attending to human user individual differences in examinations of trust and automation use. Past research has generally supported the notions that machine reliability predicts trust in automation, and trust in turn predicts automation use. However, links between user personality and perceptions of the machine with trust in automation have not been empirically established. On our X-ray screening task, 255 students rated trust and made automation use decisions while visually searching for weapons in X-ray images of luggage. We demonstrate that individual differences affect perceptions of machine characteristics when actual machine characteristics are constant, that perceptions account for 52% of trust variance above the effects of actual characteristics, and that perceptions mediate the effects of actual characteristics on trust. Importantly, we also demonstrate that when administered at different times, the same six trust items reflect two types of trust (dispositional trust and history-based trust) and that these two trust constructs are differentially related to other variables. Interactions were found among user characteristics, machine characteristics, and automation use. Our results suggest that increased specificity in the conceptualization and measurement of trust is required, future researchers should assess user perceptions of machine characteristics in addition to actual machine characteristics, and incorporation of user extraversion and propensity to trust machines can increase prediction of automation use decisions. Potential applications include the design of flexible automation training programs tailored to individuals who differ in systematic ways.

IBM Watson Analytics: Automating Visualization, Descriptive, and Predictive Statistics

PubMed Central

2016-01-01

Background We live in an era of explosive data generation that will continue to grow and involve all industries. One of the results of this explosion is the need for newer and more efficient data analytics procedures. Traditionally, data analytics required a substantial background in statistics and computer science. In 2015, International Business Machines Corporation (IBM) released the IBM Watson Analytics (IBMWA) software that delivered advanced statistical procedures based on the Statistical Package for the Social Sciences (SPSS). The latest entry of Watson Analytics into the field of analytical software products provides users with enhanced functions that are not available in many existing programs. For example, Watson Analytics automatically analyzes datasets, examines data quality, and determines the optimal statistical approach. Users can request exploratory, predictive, and visual analytics. Using natural language processing (NLP), users are able to submit additional questions for analyses in a quick response format. This analytical package is available free to academic institutions (faculty and students) that plan to use the tools for noncommercial purposes. Objective To report the features of IBMWA and discuss how this software subjectively and objectively compares to other data mining programs. Methods The salient features of the IBMWA program were examined and compared with other common analytical platforms, using validated health datasets. Results Using a validated dataset, IBMWA delivered similar predictions compared with several commercial and open source data mining software applications. The visual analytics generated by IBMWA were similar to results from programs such as Microsoft Excel and Tableau Software. In addition, assistance with data preprocessing and data exploration was an inherent component of the IBMWA application. Sensitivity and specificity were not included in the IBMWA predictive analytics results, nor were odds ratios, confidence intervals, or a confusion matrix. Conclusions IBMWA is a new alternative for data analytics software that automates descriptive, predictive, and visual analytics. This program is very user-friendly but requires data preprocessing, statistical conceptual understanding, and domain expertise. PMID:27729304

Closha: bioinformatics workflow system for the analysis of massive sequencing data.

PubMed

Ko, GunHwan; Kim, Pan-Gyu; Yoon, Jongcheol; Han, Gukhee; Park, Seong-Jin; Song, Wangho; Lee, Byungwook

2018-02-19

While next-generation sequencing (NGS) costs have fallen in recent years, the cost and complexity of computation remain substantial obstacles to the use of NGS in bio-medical care and genomic research. The rapidly increasing amounts of data available from the new high-throughput methods have made data processing infeasible without automated pipelines. The integration of data and analytic resources into workflow systems provides a solution to the problem by simplifying the task of data analysis. To address this challenge, we developed a cloud-based workflow management system, Closha, to provide fast and cost-effective analysis of massive genomic data. We implemented complex workflows making optimal use of high-performance computing clusters. Closha allows users to create multi-step analyses using drag and drop functionality and to modify the parameters of pipeline tools. Users can also import the Galaxy pipelines into Closha. Closha is a hybrid system that enables users to use both analysis programs providing traditional tools and MapReduce-based big data analysis programs simultaneously in a single pipeline. Thus, the execution of analytics algorithms can be parallelized, speeding up the whole process. We also developed a high-speed data transmission solution, KoDS, to transmit a large amount of data at a fast rate. KoDS has a file transfer speed of up to 10 times that of normal FTP and HTTP. The computer hardware for Closha is 660 CPU cores and 800 TB of disk storage, enabling 500 jobs to run at the same time. Closha is a scalable, cost-effective, and publicly available web service for large-scale genomic data analysis. Closha supports the reliable and highly scalable execution of sequencing analysis workflows in a fully automated manner. Closha provides a user-friendly interface to all genomic scientists to try to derive accurate results from NGS platform data. The Closha cloud server is freely available for use from http://closha.kobic.re.kr/ .

Standardized Access and Processing of Multi-Source Earth Observation Time-Series Data within a Regional Data Middleware

NASA Astrophysics Data System (ADS)

Eberle, J.; Schmullius, C.

2017-12-01

Increasing archives of global satellite data present a new challenge to handle multi-source satellite data in a user-friendly way. Any user is confronted with different data formats and data access services. In addition the handling of time-series data is complex as an automated processing and execution of data processing steps is needed to supply the user with the desired product for a specific area of interest. In order to simplify the access to data archives of various satellite missions and to facilitate the subsequent processing, a regional data and processing middleware has been developed. The aim of this system is to provide standardized and web-based interfaces to multi-source time-series data for individual regions on Earth. For further use and analysis uniform data formats and data access services are provided. Interfaces to data archives of the sensor MODIS (NASA) as well as the satellites Landsat (USGS) and Sentinel (ESA) have been integrated in the middleware. Various scientific algorithms, such as the calculation of trends and breakpoints of time-series data, can be carried out on the preprocessed data on the basis of uniform data management. Jupyter Notebooks are linked to the data and further processing can be conducted directly on the server using Python and the statistical language R. In addition to accessing EO data, the middleware is also used as an intermediary between the user and external databases (e.g., Flickr, YouTube). Standardized web services as specified by OGC are provided for all tools of the middleware. Currently, the use of cloud services is being researched to bring algorithms to the data. As a thematic example, an operational monitoring of vegetation phenology is being implemented on the basis of various optical satellite data and validation data from the German Weather Service. Other examples demonstrate the monitoring of wetlands focusing on automated discovery and access of Landsat and Sentinel data for local areas.

IBM Watson Analytics: Automating Visualization, Descriptive, and Predictive Statistics.

PubMed

Hoyt, Robert Eugene; Snider, Dallas; Thompson, Carla; Mantravadi, Sarita

2016-10-11

We live in an era of explosive data generation that will continue to grow and involve all industries. One of the results of this explosion is the need for newer and more efficient data analytics procedures. Traditionally, data analytics required a substantial background in statistics and computer science. In 2015, International Business Machines Corporation (IBM) released the IBM Watson Analytics (IBMWA) software that delivered advanced statistical procedures based on the Statistical Package for the Social Sciences (SPSS). The latest entry of Watson Analytics into the field of analytical software products provides users with enhanced functions that are not available in many existing programs. For example, Watson Analytics automatically analyzes datasets, examines data quality, and determines the optimal statistical approach. Users can request exploratory, predictive, and visual analytics. Using natural language processing (NLP), users are able to submit additional questions for analyses in a quick response format. This analytical package is available free to academic institutions (faculty and students) that plan to use the tools for noncommercial purposes. To report the features of IBMWA and discuss how this software subjectively and objectively compares to other data mining programs. The salient features of the IBMWA program were examined and compared with other common analytical platforms, using validated health datasets. Using a validated dataset, IBMWA delivered similar predictions compared with several commercial and open source data mining software applications. The visual analytics generated by IBMWA were similar to results from programs such as Microsoft Excel and Tableau Software. In addition, assistance with data preprocessing and data exploration was an inherent component of the IBMWA application. Sensitivity and specificity were not included in the IBMWA predictive analytics results, nor were odds ratios, confidence intervals, or a confusion matrix. IBMWA is a new alternative for data analytics software that automates descriptive, predictive, and visual analytics. This program is very user-friendly but requires data preprocessing, statistical conceptual understanding, and domain expertise.

A Meta-Analysis of Factors Influencing the Development of Trust in Automation: Implications for Human-Robot Interaction

DTIC Science & Technology

2014-07-01

Submoderating factors were examined and reported for human-related (i.e., age, cognitive factors, emotive factors) and automation- related (i.e., features and...capabilities) effects. Analyses were also conducted for type of automated aid: cognitive, control, and perceptual automation aids. Automated cognitive...operator, user) action. Perceptual aids are used to assist the operator or user by providing warnings or to assist with pattern recognition. All

Trial, Adoption, Usage and Diffusion of Social Media

DTIC Science & Technology

2011-12-01

Gaming Users Online Forums Users Podcasting Users Ease of use 15 20 3 0 0 0 To stay in contact 11 0 1 0 0 0 Pressure from friends 10 1 2 0 0 0...focused 2 0 0 0 0 0 Ease of use 2 3 0 0 0 0 Kill boredom 2 0 0 0 0 0 Content (self- expression) 1 0 1 0 0 0 Catch people’s attention 1 0 0 0 0 0...Users Online Forums Users Podcasting Users Stay in contact with friends 20 0 0 0 0 0 Ease of use 6 2 0 0 0 0 Technology features 6 8 0 0

MilxXplore: a web-based system to explore large imaging datasets

PubMed Central

Bourgeat, P; Dore, V; Villemagne, V L; Rowe, C C; Salvado, O; Fripp, J

2013-01-01

Objective As large-scale medical imaging studies are becoming more common, there is an increasing reliance on automated software to extract quantitative information from these images. As the size of the cohorts keeps increasing with large studies, there is a also a need for tools that allow results from automated image processing and analysis to be presented in a way that enables fast and efficient quality checking, tagging and reporting on cases in which automatic processing failed or was problematic. Materials and methods MilxXplore is an open source visualization platform, which provides an interface to navigate and explore imaging data in a web browser, giving the end user the opportunity to perform quality control and reporting in a user friendly, collaborative and efficient way. Discussion Compared to existing software solutions that often provide an overview of the results at the subject's level, MilxXplore pools the results of individual subjects and time points together, allowing easy and efficient navigation and browsing through the different acquisitions of a subject over time, and comparing the results against the rest of the population. Conclusions MilxXplore is fast, flexible and allows remote quality checks of processed imaging data, facilitating data sharing and collaboration across multiple locations, and can be easily integrated into a cloud computing pipeline. With the growing trend of open data and open science, such a tool will become increasingly important to share and publish results of imaging analysis. PMID:23775173

A LabVIEW based template for user created experiment automation.

PubMed

Kim, D J; Fisk, Z

2012-12-01

We have developed an expandable software template to automate user created experiments. The LabVIEW based template is easily modifiable to add together user created measurements, controls, and data logging with virtually any type of laboratory equipment. We use reentrant sequential selection to implement sequence script making it possible to wrap a long series of the user created experiments and execute them in sequence. Details of software structure and application examples for scanning probe microscope and automated transport experiments using custom built laboratory electronics and a cryostat are described.

Human Resources Planning for Office Automation.

ERIC Educational Resources Information Center

Munoz, Judith T.

1985-01-01

Examination of the transition to automated offices revealed that the prospect can be anxiety-producing for potential users, most users did not receive adequate training, lack of training may cause equipment underutilization, administrators are often not prepared to manage the change, and most experienced job satisfaction after automation. (MSE)

Ion channel pharmacology under flow: automation via well-plate microfluidics.

PubMed

Spencer, C Ian; Li, Nianzhen; Chen, Qin; Johnson, Juliette; Nevill, Tanner; Kammonen, Juha; Ionescu-Zanetti, Cristian

2012-08-01

Automated patch clamping addresses the need for high-throughput screening of chemical entities that alter ion channel function. As a result, there is considerable utility in the pharmaceutical screening arena for novel platforms that can produce relevant data both rapidly and consistently. Here we present results that were obtained with an innovative microfluidic automated patch clamp system utilizing a well-plate that eliminates the necessity of internal robotic liquid handling. Continuous recording from cell ensembles, rapid solution switching, and a bench-top footprint enable a number of assay formats previously inaccessible to automated systems. An electro-pneumatic interface was employed to drive the laminar flow of solutions in a microfluidic network that delivered cells in suspension to ensemble recording sites. Whole-cell voltage clamp was applied to linear arrays of 20 cells in parallel utilizing a 64-channel voltage clamp amplifier. A number of unique assays requiring sequential compound applications separated by a second or less, such as rapid determination of the agonist EC(50) for a ligand-gated ion channel or the kinetics of desensitization recovery, are enabled by the system. In addition, the system was validated via electrophysiological characterizations of both voltage-gated and ligand-gated ion channel targets: hK(V)2.1 and human Ether-à-go-go-related gene potassium channels, hNa(V)1.7 and 1.8 sodium channels, and (α1) hGABA(A) and (α1) human nicotinic acetylcholine receptor receptors. Our results show that the voltage dependence, kinetics, and interactions of these channels with pharmacological agents were matched to reference data. The results from these IonFlux™ experiments demonstrate that the system provides high-throughput automated electrophysiology with enhanced reliability and consistency, in a user-friendly format.

Standardizing Activation Analysis: New Software for Photon Activation Analysis

NASA Astrophysics Data System (ADS)

Sun, Z. J.; Wells, D.; Segebade, C.; Green, J.

2011-06-01

Photon Activation Analysis (PAA) of environmental, archaeological and industrial samples requires extensive data analysis that is susceptible to error. For the purpose of saving time, manpower and minimizing error, a computer program was designed, built and implemented using SQL, Access 2007 and asp.net technology to automate this process. Based on the peak information of the spectrum and assisted by its PAA library, the program automatically identifies elements in the samples and calculates their concentrations and respective uncertainties. The software also could be operated in browser/server mode, which gives the possibility to use it anywhere the internet is accessible. By switching the nuclide library and the related formula behind, the new software can be easily expanded to neutron activation analysis (NAA), charged particle activation analysis (CPAA) or proton-induced X-ray emission (PIXE). Implementation of this would standardize the analysis of nuclear activation data. Results from this software were compared to standard PAA analysis with excellent agreement. With minimum input from the user, the software has proven to be fast, user-friendly and reliable.

A technical description of a novel pharmacological anesthesia robot.

PubMed

Wehbe, Mohamad; Arbeid, Erik; Cyr, Shantale; Mathieu, Pierre A; Taddei, Riccardo; Morse, Joshua; Hemmerling, Thomas M

2014-02-01

To control the three components of general anesthesia (hypnosis, analgesia, and neuromuscular blockade), an automated closed-loop, anesthesia-drug delivery system (McSleepy) was developed. Bispectral index was used as the control variable for hypnosis, the analgoscore for analgesia, and phonomyography for neuromuscular blockade. McSleepy can be used to control the induction, maintenance and emergence from general anesthesia. To do so, a large touch screen is used to provide a user friendly interface, permitting bidirectional communication: the user giving information about the different stages of anesthesia, and the system prompting the anesthesiologist to perform certain actions such as mask ventilation, intubation or waking-up the patient using audio clips with voice commands. Several safety features were implemented to provide a secure and reliable anesthesia. Preliminary results of 15 patients are presented in this paper. Evaluation of McSleepy was done through an assessment of its clinical performance and using Varvel's performance indices. The system was found to be clinically useful by providing good precision in drug administration and reliable results for the duration of a general anesthesia.

SCALE Code System

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

Rearden, Bradley T.; Jessee, Matthew Anderson

The SCALE Code System is a widely-used modeling and simulation suite for nuclear safety analysis and design that is developed, maintained, tested, and managed by the Reactor and Nuclear Systems Division (RNSD) of Oak Ridge National Laboratory (ORNL). SCALE provides a comprehensive, verified and validated, user-friendly tool set for criticality safety, reactor and lattice physics, radiation shielding, spent fuel and radioactive source term characterization, and sensitivity and uncertainty analysis. Since 1980, regulators, licensees, and research institutions around the world have used SCALE for safety analysis and design. SCALE provides an integrated framework with dozens of computational modules including three deterministicmore » and three Monte Carlo radiation transport solvers that are selected based on the desired solution strategy. SCALE includes current nuclear data libraries and problem-dependent processing tools for continuous-energy (CE) and multigroup (MG) neutronics and coupled neutron-gamma calculations, as well as activation, depletion, and decay calculations. SCALE includes unique capabilities for automated variance reduction for shielding calculations, as well as sensitivity and uncertainty analysis. SCALE’s graphical user interfaces assist with accurate system modeling, visualization of nuclear data, and convenient access to desired results.« less

SCALE Code System 6.2.1

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

Rearden, Bradley T.; Jessee, Matthew Anderson

The SCALE Code System is a widely-used modeling and simulation suite for nuclear safety analysis and design that is developed, maintained, tested, and managed by the Reactor and Nuclear Systems Division (RNSD) of Oak Ridge National Laboratory (ORNL). SCALE provides a comprehensive, verified and validated, user-friendly tool set for criticality safety, reactor and lattice physics, radiation shielding, spent fuel and radioactive source term characterization, and sensitivity and uncertainty analysis. Since 1980, regulators, licensees, and research institutions around the world have used SCALE for safety analysis and design. SCALE provides an integrated framework with dozens of computational modules including three deterministicmore » and three Monte Carlo radiation transport solvers that are selected based on the desired solution strategy. SCALE includes current nuclear data libraries and problem-dependent processing tools for continuous-energy (CE) and multigroup (MG) neutronics and coupled neutron-gamma calculations, as well as activation, depletion, and decay calculations. SCALE includes unique capabilities for automated variance reduction for shielding calculations, as well as sensitivity and uncertainty analysis. SCALE’s graphical user interfaces assist with accurate system modeling, visualization of nuclear data, and convenient access to desired results.« less

'We are always in some form of contact': friendships among homeless drug and alcohol users living in hostels.

PubMed

Neale, Joanne; Brown, Caral

2016-09-01

Homeless drug and alcohol users are one of the most marginalised groups in society. They frequently have complex needs and limited social support. In this paper, we explore the role of friendship in the lives of homeless drug and alcohol users living in hostels, using the concepts of 'social capital' and 'recovery capital' to frame the analyses. The study was undertaken in three hostels, each in a different English city, during 2013-2014. Audio recorded semi-structured interviews were conducted with 30 residents (9 females; 21 males) who self-reported drink and/or drug problems; follow-up interviews were completed 4-6 weeks later with 22 participants (6 females; 16 males). Data were transcribed verbatim, coded using the software package MAXQDA, and analysed using Framework. Only 21 participants reported current friends at interview 1, and friendship networks were small and changeable. Despite this, participants desired friendships that were culturally normative. Eight categories of friend emerged from the data: family-like friends; using friends; homeless friends; childhood friends; online-only friends; drug treatment friends; work friends; and mutual interest friends. Routine and regular contact was highly valued, with family-like friends appearing to offer the most constant practical and emotional support. The use of information and communication technologies (ICTs) was central to many participants' friendships, keeping them connected to social support and recovery capital outside homelessness and substance-using worlds. We conclude that those working with homeless drug and alcohol users - and potentially other marginalised populations - could beneficially encourage their clients to identify and build upon their most positive and reliable relationships. Additionally, they might explore ways of promoting the use of ICTs to combat loneliness and isolation. Texting, emailing, online mutual aid meetings, chatrooms, Internet penpals, skyping and other social media all offer potentially valuable opportunities for building friendships that can bolster otherwise limited social and recovery capital. © 2015 The Authors. Health and Social Care in the Community Published by John Wiley & Sons Ltd.

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.

Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information

NASA Astrophysics Data System (ADS)

Sushko, Iurii; Novotarskyi, Sergii; Körner, Robert; Pandey, Anil Kumar; Rupp, Matthias; Teetz, Wolfram; Brandmaier, Stefan; Abdelaziz, Ahmed; Prokopenko, Volodymyr V.; Tanchuk, Vsevolod Y.; Todeschini, Roberto; Varnek, Alexandre; Marcou, Gilles; Ertl, Peter; Potemkin, Vladimir; Grishina, Maria; Gasteiger, Johann; Schwab, Christof; Baskin, Igor I.; Palyulin, Vladimir A.; Radchenko, Eugene V.; Welsh, William J.; Kholodovych, Vladyslav; Chekmarev, Dmitriy; Cherkasov, Artem; Aires-de-Sousa, Joao; Zhang, Qing-You; Bender, Andreas; Nigsch, Florian; Patiny, Luc; Williams, Antony; Tkachenko, Valery; Tetko, Igor V.

2011-06-01

The Online Chemical Modeling Environment is a web-based platform that aims to automate and simplify the typical steps required for QSAR modeling. The platform consists of two major subsystems: the database of experimental measurements and the modeling framework. A user-contributed database contains a set of tools for easy input, search and modification of thousands of records. The OCHEM database is based on the wiki principle and focuses primarily on the quality and verifiability of the data. The database is tightly integrated with the modeling framework, which supports all the steps required to create a predictive model: data search, calculation and selection of a vast variety of molecular descriptors, application of machine learning methods, validation, analysis of the model and assessment of the applicability domain. As compared to other similar systems, OCHEM is not intended to re-implement the existing tools or models but rather to invite the original authors to contribute their results, make them publicly available, share them with other users and to become members of the growing research community. Our intention is to make OCHEM a widely used platform to perform the QSPR/QSAR studies online and share it with other users on the Web. The ultimate goal of OCHEM is collecting all possible chemoinformatics tools within one simple, reliable and user-friendly resource. The OCHEM is free for web users and it is available online at http://www.ochem.eu.

Bridging the Gap - Networking Educators using Real-Time Seismic Data

NASA Astrophysics Data System (ADS)

Ortiz, A. M.; Renwald, M. D.; Baldwin, T. K.; Hall, M. K.

2004-12-01

After nearly a decade, the seismology community has made critical advances in identifying what is effective and what is needed for success in incorporating real-time seismic data in the classroom. Today's K-16 classroom teachers have many options and opportunities for incorporating short- and long-term inquiry activities for monitoring earthquakes and analyzing seismic data in their daily instruction. Through the SpiNet program, we are providing web-based tools that support educators working with real-time seismic data (http://www.scieds.com/spinet/). Our site includes a Recent Seismicity section, which allows users to share seismic data in real-time, and provides near real-time information about global seismicity. Our Activities section provides data and lessons to assist educators who wish to integrate seismology into their classroom. The Research section, currently under development, will allow educators to share general information about how they teach seismology in their classroom through a discussion board and by posting lesson plans. In addition, we are developing a user-friendly tool for students to post results of their research projects. Designing a website which targets a range of users requires a working knowledge of both user needs and website programming and design. User needs include providing a logical navigational structure and accounting for differences in browser functionality, internet access, and users' abilities. Using website development tools, such as PHP, MySQL, RDF feeds, and specialized geoscience applications, we are automating site maintenance; incorporating databases for information storage and retrieval; and providing accessibility for users with a range of skills and physical limitations. By incorporating these features, we have built a dynamic interface for a broad range of users interested in educational seismology.

ANGIOCARE: an automated system for fast three-dimensional coronary reconstruction by integrating angiographic and intracoronary ultrasound data.

PubMed

Bourantas, Christos V; Kalatzis, Fanis G; Papafaklis, Michail I; Fotiadis, Dimitrios I; Tweddel, Ann C; Kourtis, Iraklis C; Katsouras, Christos S; Michalis, Lampros K

2008-08-01

The development of an automated, user-friendly system (ANGIOCARE), for rapid three-dimensional (3D) coronary reconstruction, integrating angiographic and, intracoronary ultrasound (ICUS) data. Biplane angiographic and ICUS sequence images are imported into the system where a prevalidated method is used for coronary reconstruction. This incorporates extraction of the catheter path from two end-diastolic X-ray images and detection of regions of interest (lumen, outer vessel wall) in the ICUS sequence by an automated border detection algorithm. The detected borders are placed perpendicular to the catheter path and established algorithms used to estimate their absolute orientation. The resulting 3D object is imported into an advanced visualization module with which the operator can interact, examine plaque distribution (depicted as a color coded map) and assess plaque burden by virtual endoscopy. Data from 19 patients (27 vessels) undergoing biplane angiography and ICUS were examined. The reconstructed vessels were 21.3-80.2 mm long. The mean difference was 0.9 +/- 2.9% between the plaque volumes measured using linear 3D ICUS analysis and the volumes, estimated by taking into account the curvature of the vessel. The time required to reconstruct a luminal narrowing of 25 mm was approximately 10 min. The ANGIOCARE system provides rapid coronary reconstruction allowing the operator accurately to estimate the length of the lesion and determine plaque distribution and volume. (c) 2008 Wiley-Liss, Inc.

MR efficiency using automated MRI-desktop eProtocol

NASA Astrophysics Data System (ADS)

Gao, Fei; Xu, Yanzhe; Panda, Anshuman; Zhang, Min; Hanson, James; Su, Congzhe; Wu, Teresa; Pavlicek, William; James, Judy R.

2017-03-01

MRI protocols are instruction sheets that radiology technologists use in routine clinical practice for guidance (e.g., slice position, acquisition parameters etc.). In Mayo Clinic Arizona (MCA), there are over 900 MR protocols (ranging across neuro, body, cardiac, breast etc.) which makes maintaining and updating the protocol instructions a labor intensive effort. The task is even more challenging given different vendors (Siemens, GE etc.). This is a universal problem faced by all the hospitals and/or medical research institutions. To increase the efficiency of the MR practice, we designed and implemented a web-based platform (eProtocol) to automate the management of MRI protocols. It is built upon a database that automatically extracts protocol information from DICOM compliant images and provides a user-friendly interface to the technologists to create, edit and update the protocols. Advanced operations such as protocol migrations from scanner to scanner and capability to upload Multimedia content were also implemented. To the best of our knowledge, eProtocol is the first MR protocol automated management tool used clinically. It is expected that this platform will significantly improve the radiology operations efficiency including better image quality and exam consistency, fewer repeat examinations and less acquisition errors. These protocols instructions will be readily available to the technologists during scans. In addition, this web-based platform can be extended to other imaging modalities such as CT, Mammography, and Interventional Radiology and different vendors for imaging protocol management.

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

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

One Size Fits All: Evaluation of the Transferability of a New "Learning" Histologic Image Analysis Application.

PubMed

Arlt, Janine; Homeyer, André; Sänger, Constanze; Dahmen, Uta; Dirsch, Olaf

2016-01-01

Quantitative analysis of histologic slides is of importance for pathology and also to address surgical questions. Recently, a novel application was developed for the automated quantification of whole-slide images. The aim of this study was to test and validate the underlying image analysis algorithm with respect to user friendliness, accuracy, and transferability to different histologic scenarios. The algorithm splits the images into tiles of a predetermined size and identifies the tissue class of each tile. In the training procedure, the user specifies example tiles of the different tissue classes. In the subsequent analysis procedure, the algorithm classifies each tile into the previously specified classes. User friendliness was evaluated by recording training time and testing reproducibility of the training procedure of users with different background. Accuracy was determined with respect to single and batch analysis. Transferability was demonstrated by analyzing tissue of different organs (rat liver, kidney, small bowel, and spleen) and with different stainings (glutamine synthetase and hematoxylin-eosin). Users of different educational background could apply the program efficiently after a short introduction. When analyzing images with similar properties, accuracy of >90% was reached in single images as well as in batch mode. We demonstrated that the novel application is user friendly and very accurate. With the "training" procedure the application can be adapted to novel image characteristics simply by giving examples of relevant tissue structures. Therefore, it is suitable for the fast and efficient analysis of high numbers of fully digitalized histologic sections, potentially allowing "high-throughput" quantitative "histomic" analysis.

CRIM-TRACK: sensor system for detection of criminal chemical substances

NASA Astrophysics Data System (ADS)

Munk, Jens K.; Buus, Ole T.; Larsen, Jan; Dossi, Eleftheria; Tatlow, Sol; Lässig, Lina; Sandström, Lars; Jakobsen, Mogens H.

2015-10-01

Detection of illegal compounds requires a reliable, selective and sensitive detection device. The successful device features automated target acquisition, identification and signal processing. It is portable, fast, user friendly, sensitive, specific, and cost efficient. LEAs are in need of such technology. CRIM-TRACK is developing a sensing device based on these requirements. We engage highly skilled specialists from research institutions, industry, SMEs and LEAs and rely on a team of end users to benefit maximally from our prototypes. Currently we can detect minute quantities of drugs, explosives and precursors thereof in laboratory settings. Using colorimetric technology we have developed prototypes that employ disposable sensing chips. Ease of operation and intuitive sensor response are highly prioritized features that we implement as we gather data to feed into machine learning. With machine learning our ability to detect threat compounds amidst harmless substances improves. Different end users prefer their equipment optimized for their specific field. In an explosives-detecting scenario, the end user may prefer false positives over false negatives, while the opposite may be true in a drug-detecting scenario. Such decisions will be programmed to match user preference. Sensor output can be as detailed as the sensor allows. The user can be informed of the statistics behind the detection, identities of all detected substances, and quantities thereof. The response can also be simplified to "yes" vs. "no". The technology under development in CRIM-TRACK will provide custom officers, police and other authorities with an effective tool to control trafficking of illegal drugs and drug precursors.

Utilizing Facebook and Automated Telephone Calls to Increase Adoption of a Local Smoke Alarm Installation Program.

PubMed

Frattaroli, Shannon; Schulman, Eric; McDonald, Eileen M; Omaki, Elise C; Shields, Wendy C; Jones, Vanya; Brewer, William

2018-05-17

Innovative strategies are needed to improve the prevalence of working smoke alarms in homes. To our knowledge, this is the first study to report on the effectiveness of Facebook advertising and automated telephone calls as population-level strategies to encourage an injury prevention behavior. We examine the effectiveness of Facebook advertising and automated telephone calls as strategies to enroll individuals in Baltimore City's Fire Department's free smoke alarm installation program. We directed our advertising efforts toward Facebook users eligible for the Baltimore City Fire Department's free smoke alarm installation program and all homes with a residential phone line included in Baltimore City's automated call system. The Facebook campaign targeted Baltimore City residents 18 years of age and older. In total, an estimated 300 000 Facebook users met the eligibility criteria. Facebook advertisements were delivered to users' desktop and mobile device newsfeeds. A prerecorded message was sent to all residential landlines listed in the city's automated call system. By the end of the campaign, the 3 advertisements generated 456 666 impressions reaching 130 264 Facebook users. Of the users reached, 4367 individuals (1.3%) clicked the advertisement. The automated call system included approximately 90 000 residential phone numbers. Participants attributed 25 smoke alarm installation requests to Facebook and 458 to the automated call. Facebook advertisements are a novel approach to promoting smoke alarms and appear to be effective in exposing individuals to injury prevention messages. However, converting Facebook message recipients to users of a smoke alarm installation program occurred infrequently in this study. Residents who participated in the smoke alarm installation program were more likely to cite the automated call as the impetus for their participation. Additional research is needed to understand the circumstances and strategies to effectively use the social networking site as a tool to convert passive users into active participants.

w4CSeq: software and web application to analyze 4C-seq data.

PubMed

Cai, Mingyang; Gao, Fan; Lu, Wange; Wang, Kai

2016-11-01

Circularized Chromosome Conformation Capture followed by deep sequencing (4C-Seq) is a powerful technique to identify genome-wide partners interacting with a pre-specified genomic locus. Here, we present a computational and statistical approach to analyze 4C-Seq data generated from both enzyme digestion and sonication fragmentation-based methods. We implemented a command line software tool and a web interface called w4CSeq, which takes in the raw 4C sequencing data (FASTQ files) as input, performs automated statistical analysis and presents results in a user-friendly manner. Besides providing users with the list of candidate interacting sites/regions, w4CSeq generates figures showing genome-wide distribution of interacting regions, and sketches the enrichment of key features such as TSSs, TTSs, CpG sites and DNA replication timing around 4C sites. Users can establish their own web server by downloading source codes at https://github.com/WGLab/w4CSeq Additionally, a demo web server is available at http://w4cseq.wglab.org CONTACT: kaiwang@usc.edu or wangelu@usc.eduSupplementary information: 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.

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.

Improving medical stores management through automation and effective communication.

PubMed

Kumar, Ashok; Cariappa, M P; Marwaha, Vishal; Sharma, Mukti; Arora, Manu

2016-01-01

Medical stores management in hospitals is a tedious and time consuming chore with limited resources tasked for the purpose and poor penetration of Information Technology. The process of automation is slow paced due to various inherent factors and is being challenged by the increasing inventory loads and escalating budgets for procurement of drugs. We carried out an indepth case study at the Medical Stores of a tertiary care health care facility. An iterative six step Quality Improvement (QI) process was implemented based on the Plan-Do-Study-Act (PDSA) cycle. The QI process was modified as per requirement to fit the medical stores management model. The results were evaluated after six months. After the implementation of QI process, 55 drugs of the medical store inventory which had expired since 2009 onwards were replaced with fresh stock by the suppliers as a result of effective communication through upgraded database management. Various pending audit objections were dropped due to the streamlined documentation and processes. Inventory management improved drastically due to automation, with disposal orders being initiated four months prior to the expiry of drugs and correct demands being generated two months prior to depletion of stocks. The monthly expense summary of drugs was now being done within ten days of the closing month. Improving communication systems within the hospital with vendor database management and reaching out to clinicians is important. Automation of inventory management requires to be simple and user-friendly, utilizing existing hardware. Physical stores monitoring is indispensable, especially due to the scattered nature of stores. Staff training and standardized documentation protocols are the other keystones for optimal medical store management.

EpHLA: an innovative and user-friendly software automating the HLAMatchmaker algorithm for antibody analysis.

PubMed

Sousa, Luiz Cláudio Demes da Mata; Filho, Herton Luiz Alves Sales; Von Glehn, Cristina de Queiroz Carrascosa; da Silva, Adalberto Socorro; Neto, Pedro de Alcântara dos Santos; de Castro, José Adail Fonseca; do Monte, Semíramis Jamil Hadad

2011-12-01

The global challenge for solid organ transplantation programs is to distribute organs to the highly sensitized recipients. The purpose of this work is to describe and test the functionality of the EpHLA software, a program that automates the analysis of acceptable and unacceptable HLA epitopes on the basis of the HLAMatchmaker algorithm. HLAMatchmaker considers small configurations of polymorphic residues referred to as eplets as essential components of HLA-epitopes. Currently, the analyses require the creation of temporary files and the manual cut and paste of laboratory tests results between electronic spreadsheets, which is time-consuming and prone to administrative errors. The EpHLA software was developed in Object Pascal programming language and uses the HLAMatchmaker algorithm to generate histocompatibility reports. The automated generation of reports requires the integration of files containing the results of laboratory tests (HLA typing, anti-HLA antibody signature) and public data banks (NMDP, IMGT). The integration and the access to this data were accomplished by means of the framework called eDAFramework. The eDAFramework was developed in Object Pascal and PHP and it provides data access functionalities for software developed in these languages. The tool functionality was successfully tested in comparison to actual, manually derived reports of patients from a renal transplantation program with related donors. We successfully developed software, which enables the automated definition of the epitope specificities of HLA antibodies. This new tool will benefit the management of recipient/donor pairs selection for highly sensitized patients. Copyright © 2011 Elsevier B.V. All rights reserved.

Automatic Camera Calibration for Cultural Heritage Applications Using Unstructured Planar Objects

NASA Astrophysics Data System (ADS)

Adam, K.; Kalisperakis, I.; Grammatikopoulos, L.; Karras, G.; Petsa, E.

2013-07-01

As a rule, image-based documentation of cultural heritage relies today on ordinary digital cameras and commercial software. As such projects often involve researchers not familiar with photogrammetry, the question of camera calibration is important. Freely available open-source user-friendly software for automatic camera calibration, often based on simple 2D chess-board patterns, are an answer to the demand for simplicity and automation. However, such tools cannot respond to all requirements met in cultural heritage conservation regarding possible imaging distances and focal lengths. Here we investigate the practical possibility of camera calibration from unknown planar objects, i.e. any planar surface with adequate texture; we have focused on the example of urban walls covered with graffiti. Images are connected pair-wise with inter-image homographies, which are estimated automatically through a RANSAC-based approach after extracting and matching interest points with the SIFT operator. All valid points are identified on all images on which they appear. Provided that the image set includes a "fronto-parallel" view, inter-image homographies with this image are regarded as emulations of image-to-world homographies and allow computing initial estimates for the interior and exterior orientation elements. Following this initialization step, the estimates are introduced into a final self-calibrating bundle adjustment. Measures are taken to discard unsuitable images and verify object planarity. Results from practical experimentation indicate that this method may produce satisfactory results. The authors intend to incorporate the described approach into their freely available user-friendly software tool, which relies on chess-boards, to assist non-experts in their projects with image-based approaches.

Advanced shortwave infrared and Raman hyperspectral sensors for homeland security and law enforcement operations

NASA Astrophysics Data System (ADS)

Klueva, Oksana; Nelson, Matthew P.; Gardner, Charles W.; Gomer, Nathaniel R.

2015-05-01

Proliferation of chemical and explosive threats as well as illicit drugs continues to be an escalating danger to civilian and military personnel. Conventional means of detecting and identifying hazardous materials often require the use of reagents and/or physical sampling, which is a time-consuming, costly and often dangerous process. Stand-off detection allows the operator to detect threat residues from a safer distance minimizing danger to people and equipment. Current fielded technologies for standoff detection of chemical and explosive threats are challenged by low area search rates, poor targeting efficiency, lack of sensitivity and specificity or use of costly and potentially unsafe equipment such as lasers. A demand exists for stand-off systems that are fast, safe, reliable and user-friendly. To address this need, ChemImage Sensor Systems™ (CISS) has developed reagent-less, non-contact, non-destructive sensors for the real-time detection of hazardous materials based on widefield shortwave infrared (SWIR) and Raman hyperspectral imaging (HSI). Hyperspectral imaging enables automated target detection displayed in the form of image making result analysis intuitive and user-friendly. Application of the CISS' SWIR-HSI and Raman sensing technologies to Homeland Security and Law Enforcement for standoff detection of homemade explosives and illicit drugs and their precursors in vehicle and personnel checkpoints is discussed. Sensing technologies include a portable, robot-mounted and standalone variants of the technology. Test data is shown that supports the use of SWIR and Raman HSI for explosive and drug screening at checkpoints as well as screening for explosives and drugs at suspected clandestine manufacturing facilities.

A software platform for the analysis of dermatology images

NASA Astrophysics Data System (ADS)

Vlassi, Maria; Mavraganis, Vlasios; Asvestas, Panteleimon

2017-11-01

The purpose of this paper is to present a software platform developed in Python programming environment that can be used for the processing and analysis of dermatology images. The platform provides the capability for reading a file that contains a dermatology image. The platform supports image formats such as Windows bitmaps, JPEG, JPEG2000, portable network graphics, TIFF. Furthermore, it provides suitable tools for selecting, either manually or automatically, a region of interest (ROI) on the image. The automated selection of a ROI includes filtering for smoothing the image and thresholding. The proposed software platform has a friendly and clear graphical user interface and could be a useful second-opinion tool to a dermatologist. Furthermore, it could be used to classify images including from other anatomical parts such as breast or lung, after proper re-training of the classification algorithms.

Use of the World Wide Web for multisite data collection.

PubMed

Subramanian, A K; McAfee, A T; Getzinger, J P

1997-08-01

As access to the Internet becomes increasingly available, research applications in medicine will increase. This paper describes the use of the Internet, and, more specifically, the World Wide Web (WWW), as a channel of communication between EDs throughout the world and investigators who are interested in facilitating the collection of data from multiple sites. Data entered into user-friendly electronic surveys can be transmitted over the Internet to a database located at the site of the study, rendering geographic separation less of a barrier to the conduction of multisite studies. The electronic format of the data can enable real-time statistical processing while data are stored using existing database technologies. In theory, automated processing of variables within such a database enables early identification of data trends. Methods of ensuring validity, security, and compliance are discussed.

US Topo Maps 2014: Program updates and research

USGS Publications Warehouse

Fishburn, Kristin A.

2014-01-01

The U. S. Geological Survey (USGS) US Topo map program is now in year two of its second three-year update cycle. Since the program was launched in 2009, the product and the production system tools and processes have undergone enhancements that have made the US Topo maps a popular success story. Research and development continues with structural and content product enhancements, streamlined and more fully automated workflows, and the evaluation of a GIS-friendly US Topo GIS Packet. In addition, change detection methodologies are under evaluation to further streamline product maintenance and minimize resource expenditures for production in the future. The US Topo map program will continue to evolve in the years to come, providing traditional map users and Geographic Information System (GIS) analysts alike with a convenient, freely available product incorporating nationally consistent data that are quality assured to high standards.

ARES (Automated Residential Energy Standard) 1.2: User`s guide, in support of proposed interim energy conservation voluntary performance standards for new non-federal residential buildings: Volume 1

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

NONE

The ARES (Automated Residential Energy Standard) User`s Guide is designed to the user successfully operate the ARES computer program. This guide assumes that the user is familiar with basic PC skills such as using a keyboard and loading a disk drive. The ARES computer program was designed to assist building code officials in creating a residential energy standard based on local climate and costs.

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 .

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 Focinator v2-0 - Graphical Interface, Four Channels, Colocalization Analysis and Cell Phase Identification.

PubMed

Oeck, Sebastian; Malewicz, Nathalie M; Hurst, Sebastian; Al-Refae, Klaudia; Krysztofiak, Adam; Jendrossek, Verena

2017-07-01

The quantitative analysis of foci plays an important role in various cell biological methods. In the fields of radiation biology and experimental oncology, the effect of ionizing radiation, chemotherapy or molecularly targeted drugs on DNA damage induction and repair is frequently performed by the analysis of protein clusters or phosphorylated proteins recruited to so called repair foci at DNA damage sites, involving for example γ-H2A.X, 53BP1 or RAD51. We recently developed "The Focinator" as a reliable and fast tool for automated quantitative and qualitative analysis of nuclei and DNA damage foci. The refined software is now even more user-friendly due to a graphical interface and further features. Thus, we included an R-script-based mode for automated image opening, file naming, progress monitoring and an error report. Consequently, the evaluation no longer required the attendance of the operator after initial parameter definition. Moreover, the Focinator v2-0 is now able to perform multi-channel analysis of four channels and evaluation of protein-protein colocalization by comparison of up to three foci channels. This enables for example the quantification of foci in cells of a specific cell cycle phase.

Computer-assisted analysis of the vascular endothelial cell motile response to injury.

PubMed

Askey, D B; Herman, I M

1988-12-01

We have developed an automated, user-friendly method to track vascular endothelial cell migration in vitro using an IBM PC/XT with MS DOS. Analog phase-contrast images of the bovine aortic endothelial cells are converted into digital images (8 bit, 250 x 240 pixel resolution) using a Tecmar Video VanGogh A/D board. Digitized images are stored at selected time points following mechanical injury in vitro. FORTRAN and assembly language subroutines have been implemented to automatically detect the wound edge and the edge of each cell nucleus in the phase-contrast, light-microscope field. Detection of the wound edge is accomplished by intensity thresholding following noise reduction in the image and subsequent sampling of the wound. After the range of wound intensities is determined, the entire image is sampled and a histogram of intensities is formed. The histogram peak corresponding to the wound intensities is subtracted, leaving a histogram peak that gives the range of intensities corresponding to the cell nuclei. Rates of cell migration, as well as cellular trajectories and cell surface areas, can be automatically quantitated and analyzed. This inexpensive, automated cell-tracking system should be widely applicable in a variety of cell biologic applications.

SBMLmod: a Python-based web application and web service for efficient data integration and model simulation.

PubMed

Schäuble, Sascha; Stavrum, Anne-Kristin; Bockwoldt, Mathias; Puntervoll, Pål; Heiland, Ines

2017-06-24

Systems Biology Markup Language (SBML) is the standard model representation and description language in systems biology. Enriching and analysing systems biology models by integrating the multitude of available data, increases the predictive power of these models. This may be a daunting task, which commonly requires bioinformatic competence and scripting. We present SBMLmod, a Python-based web application and service, that automates integration of high throughput data into SBML models. Subsequent steady state analysis is readily accessible via the web service COPASIWS. We illustrate the utility of SBMLmod by integrating gene expression data from different healthy tissues as well as from a cancer dataset into a previously published model of mammalian tryptophan metabolism. SBMLmod is a user-friendly platform for model modification and simulation. The web application is available at http://sbmlmod.uit.no , whereas the WSDL definition file for the web service is accessible via http://sbmlmod.uit.no/SBMLmod.wsdl . Furthermore, the entire package can be downloaded from https://github.com/MolecularBioinformatics/sbml-mod-ws . We envision that SBMLmod will make automated model modification and simulation available to a broader research community.

Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra

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

Tolić, Nikola; Liu, Yina; Liyu, Andrey

Ultrahigh-resolution mass spectrometry, such as Fourier transform ion-cyclotron resonance mass spectrometry (FT-ICR MS), can resolve thousands of molecular ions in complex organic matrices. A Compound Identification Algorithm (CIA) was previously developed for automated elemental formula assignment for natural organic matter (NOM). In this work we describe a user friendly interface for CIA, titled Formularity, which includes an additional functionality to perform search of formulas based on an Isotopic Pattern Algorithm (IPA). While CIA assigns elemental formulas for compounds containing C, H, O, N, S, and P, IPA is capable of assigning formulas for compounds containing other elements. We used halogenatedmore » organic compounds (HOC), a chemical class that is ubiquitous in nature as well as anthropogenic systems, as an example to demonstrate the capability of Formularity with IPA. A HOC standard mix was used to evaluate the identification confidence of IPA. The HOC spike in NOM and tap water were used to assess HOC identification in natural and anthropogenic matrices. Strategies for reconciliation of CIA and IPA assignments are discussed. Software and sample databases with documentation are freely available from the PNNL OMICS software repository https://omics.pnl.gov/software/formularity.« less

Automated inference procedure for the determination of cell growth parameters

NASA Astrophysics Data System (ADS)

Harris, Edouard A.; Koh, Eun Jee; Moffat, Jason; McMillen, David R.

2016-01-01

The growth rate and carrying capacity of a cell population are key to the characterization of the population's viability and to the quantification of its responses to perturbations such as drug treatments. Accurate estimation of these parameters necessitates careful analysis. Here, we present a rigorous mathematical approach for the robust analysis of cell count data, in which all the experimental stages of the cell counting process are investigated in detail with the machinery of Bayesian probability theory. We advance a flexible theoretical framework that permits accurate estimates of the growth parameters of cell populations and of the logical correlations between them. Moreover, our approach naturally produces an objective metric of avoidable experimental error, which may be tracked over time in a laboratory to detect instrumentation failures or lapses in protocol. We apply our method to the analysis of cell count data in the context of a logistic growth model by means of a user-friendly computer program that automates this analysis, and present some samples of its output. Finally, we note that a traditional least squares fit can provide misleading estimates of parameter values, because it ignores available information with regard to the way in which the data have actually been collected.

Trajectory Optimization: OTIS 4

NASA Technical Reports Server (NTRS)

Riehl, John P.; Sjauw, Waldy K.; Falck, Robert D.; Paris, Stephen W.

2010-01-01

The latest release of the Optimal Trajectories by Implicit Simulation (OTIS4) allows users to simulate and optimize aerospace vehicle trajectories. With OTIS4, one can seamlessly generate optimal trajectories and parametric vehicle designs simultaneously. New features also allow OTIS4 to solve non-aerospace continuous time optimal control problems. The inputs and outputs of OTIS4 have been updated extensively from previous versions. Inputs now make use of objectoriented constructs, including one called a metastring. Metastrings use a greatly improved calculator and common nomenclature to reduce the user s workload. They allow for more flexibility in specifying vehicle physical models, boundary conditions, and path constraints. The OTIS4 calculator supports common mathematical functions, Boolean operations, and conditional statements. This allows users to define their own variables for use as outputs, constraints, or objective functions. The user-defined outputs can directly interface with other programs, such as spreadsheets, plotting packages, and visualization programs. Internally, OTIS4 has more explicit and implicit integration procedures, including high-order collocation methods, the pseudo-spectral method, and several variations of multiple shooting. Users may switch easily between the various methods. Several unique numerical techniques such as automated variable scaling and implicit integration grid refinement, support the integration methods. OTIS4 is also significantly more user friendly than previous versions. The installation process is nearly identical on various platforms, including Microsoft Windows, Apple OS X, and Linux operating systems. Cross-platform scripts also help make the execution of OTIS and post-processing of data easier. OTIS4 is supplied free by NASA and is subject to ITAR (International Traffic in Arms Regulations) restrictions. Users must have a Fortran compiler, and a Python interpreter is highly recommended.

CARE 3 user-friendly interface user's guide

NASA Technical Reports Server (NTRS)

Martensen, A. L.

1987-01-01

CARE 3 predicts the unreliability of highly reliable reconfigurable fault-tolerant systems that include redundant computers or computer systems. CARE3MENU is a user-friendly interface used to create an input for the CARE 3 program. The CARE3MENU interface has been designed to minimize user input errors. Although a CARE3MENU session may be successfully completed and all parameters may be within specified limits or ranges, the CARE 3 program is not guaranteed to produce meaningful results if the user incorrectly interprets the CARE 3 stochastic model. The CARE3MENU User Guide provides complete information on how to create a CARE 3 model with the interface. The CARE3MENU interface runs under the VAX/VMS operating system.

Binge drinking, marijuana use, and friendships: the relationship between similar and dissimilar usage and friendship quality.

PubMed

Boman, John H; Stogner, John; Miller, Bryan Lee

2013-01-01

While it is commonly understood that the substance use of peers influences an individual's substance use, much less is understood about the interplay between substance use and friendship quality. Using a sample of 2,148 emerging adults nested within 1,074 dyadic friendships, this study separately investigates how concordance and discordance in binge drinking and marijuana use between friends is related to each friend's perceptions of friendship quality. Because "friendship quality" is a complex construct, we employ a measure containing five sub-elements--companionship, a lack of conflict, willingness to help a friend, relationship security, and closeness. Results for both binge drinking and marijuana use reveal that individuals in friendship pairs who are concordant in their substance use perceive significantly higher perceptions of friendship quality than individuals in dyads who are dissimilar in substance use. Specifically, concordant binge drinkers estimate significantly higher levels of companionship, relationship security, and willingness to help their friend than concordant non-users, discordant users, and discordant non-users. However, the highest amount of conflict in friendships is found when both friends engage in binge drinking and marijuana use. Several interpretations of these findings are discussed. Overall, concordance between friends' binge drinking and marijuana use appears to help some elements of friendship quality and harm others.

Library Automation Alternatives in 1996 and User Satisfaction Ratings of Library Users by Operating System.

ERIC Educational Resources Information Center

Cibbarelli, Pamela

1996-01-01

Examines library automation product introductions and conversions to new operating systems. Compares user satisfaction ratings of the following library software packages: DOS/Windows, UNIX, Macintosh, and DEC VAX/VMS. Software is rated according to documentation, service/support, training, product reliability, product capabilities, ease of use,…

Automated diagnostic kiosk for diagnosing diseases

DOEpatents

Regan, John Frederick; Birch, James Michael

2014-02-11

An automated and autonomous diagnostic apparatus that is capable of dispensing collection vials and collections kits to users interesting in collecting a biological sample and submitting their collected sample contained within a collection vial into the apparatus for automated diagnostic services. The user communicates with the apparatus through a touch-screen monitor. A user is able to enter personnel information into the apparatus including medical history, insurance information, co-payment, and answer a series of questions regarding their illness, which is used to determine the assay most likely to yield a positive result. Remotely-located physicians can communicate with users of the apparatus using video tele-medicine and request specific assays to be performed. The apparatus archives submitted samples for additional testing. Users may receive their assay results electronically. Users may allow the uploading of their diagnoses into a central databank for disease surveillance purposes.

Flexible software architecture for user-interface and machine control in laboratory automation.

PubMed

Arutunian, E B; Meldrum, D R; Friedman, N A; Moody, S E

1998-10-01

We describe a modular, layered software architecture for automated laboratory instruments. The design consists of a sophisticated user interface, a machine controller and multiple individual hardware subsystems, each interacting through a client-server architecture built entirely on top of open Internet standards. In our implementation, the user-interface components are built as Java applets that are downloaded from a server integrated into the machine controller. The user-interface client can thereby provide laboratory personnel with a familiar environment for experiment design through a standard World Wide Web browser. Data management and security are seamlessly integrated at the machine-controller layer using QNX, a real-time operating system. This layer also controls hardware subsystems through a second client-server interface. This architecture has proven flexible and relatively easy to implement and allows users to operate laboratory automation instruments remotely through an Internet connection. The software architecture was implemented and demonstrated on the Acapella, an automated fluid-sample-processing system that is under development at the University of Washington.

For Professors, "Friending" Can Be Fraught

ERIC Educational Resources Information Center

Lipka, Sara

2007-01-01

People connect on Facebook by asking to "friend" one another. A typical user lists at least 100 such connections, while newbies are informed, "You don't have any friends yet." A humbling statement. It might make one want to find some. But friending students can be even dicier than befriending them. In the real world, casual professors may ask…

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…

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

Inferring Tie Strength from Online Directed Behavior

PubMed Central

Jones, Jason J.; Settle, Jaime E.; Bond, Robert M.; Fariss, Christopher J.; Marlow, Cameron; Fowler, James H.

2013-01-01

Some social connections are stronger than others. People have not only friends, but also best friends. Social scientists have long recognized this characteristic of social connections and researchers frequently use the term tie strength to refer to this concept. We used online interaction data (specifically, Facebook interactions) to successfully identify real-world strong ties. Ground truth was established by asking users themselves to name their closest friends in real life. We found the frequency of online interaction was diagnostic of strong ties, and interaction frequency was much more useful diagnostically than were attributes of the user or the user’s friends. More private communications (messages) were not necessarily more informative than public communications (comments, wall posts, and other interactions). PMID:23300964

Preliminary evaluation of user terminals for an automated pilot briefing system

DOT National Transportation Integrated Search

1976-08-01

This report describes a preliminary evaluation of various user terminal concepts for an automated aviation pilot weather briefing and flight plan filing system. Terminals embodying differing operational concepts were used by volunteer general aviatio...

Iterative User Interface Design for Automated Sequential Organ Failure Assessment Score Calculator in Sepsis Detection

PubMed Central

Herasevich, Vitaly

2017-01-01

Background The new sepsis definition has increased the need for frequent sequential organ failure assessment (SOFA) score recalculation and the clerical burden of information retrieval makes this score ideal for automated calculation. Objective The aim of this study was to (1) estimate the clerical workload of manual SOFA score calculation through a time-motion analysis and (2) describe a user-centered design process for an electronic medical record (EMR) integrated, automated SOFA score calculator with subsequent usability evaluation study. Methods First, we performed a time-motion analysis by recording time-to-task-completion for the manual calculation of 35 baseline and 35 current SOFA scores by 14 internal medicine residents over a 2-month period. Next, we used an agile development process to create a user interface for a previously developed automated SOFA score calculator. The final user interface usability was evaluated by clinician end users with the Computer Systems Usability Questionnaire. Results The overall mean (standard deviation, SD) time-to-complete manual SOFA score calculation time was 61.6 s (33). Among the 24% (12/50) usability survey respondents, our user-centered user interface design process resulted in >75% favorability of survey items in the domains of system usability, information quality, and interface quality. Conclusions Early stakeholder engagement in our agile design process resulted in a user interface for an automated SOFA score calculator that reduced clinician workload and met clinicians’ needs at the point of care. Emerging interoperable platforms may facilitate dissemination of similarly useful clinical score calculators and decision support algorithms as “apps.” A user-centered design process and usability evaluation should be considered during creation of these tools. PMID:28526675

Iterative User Interface Design for Automated Sequential Organ Failure Assessment Score Calculator in Sepsis Detection.

PubMed

Aakre, Christopher Ansel; Kitson, Jaben E; Li, Man; Herasevich, Vitaly

2017-05-18

The new sepsis definition has increased the need for frequent sequential organ failure assessment (SOFA) score recalculation and the clerical burden of information retrieval makes this score ideal for automated calculation. The aim of this study was to (1) estimate the clerical workload of manual SOFA score calculation through a time-motion analysis and (2) describe a user-centered design process for an electronic medical record (EMR) integrated, automated SOFA score calculator with subsequent usability evaluation study. First, we performed a time-motion analysis by recording time-to-task-completion for the manual calculation of 35 baseline and 35 current SOFA scores by 14 internal medicine residents over a 2-month period. Next, we used an agile development process to create a user interface for a previously developed automated SOFA score calculator. The final user interface usability was evaluated by clinician end users with the Computer Systems Usability Questionnaire. The overall mean (standard deviation, SD) time-to-complete manual SOFA score calculation time was 61.6 s (33). Among the 24% (12/50) usability survey respondents, our user-centered user interface design process resulted in >75% favorability of survey items in the domains of system usability, information quality, and interface quality. Early stakeholder engagement in our agile design process resulted in a user interface for an automated SOFA score calculator that reduced clinician workload and met clinicians' needs at the point of care. Emerging interoperable platforms may facilitate dissemination of similarly useful clinical score calculators and decision support algorithms as "apps." A user-centered design process and usability evaluation should be considered during creation of these tools. ©Christopher Ansel Aakre, Jaben E Kitson, Man Li, Vitaly Herasevich. Originally published in JMIR Human Factors (http://humanfactors.jmir.org), 18.05.2017.

National Helpline for Problem Gambling: A Profile of Its Users' Characteristics

PubMed Central

Bastiani, Luca; Fea, Maurizio; Potente, Roberta; Luppi, Claudia; Lucchini, Fabio; Molinaro, Sabrina

2015-01-01

Gambling has seen a significant increase in Italy in the last 10 years and has rapidly become a public health issue, and for these reasons the first National Helpline for Problem Gambling (GR-Helpline) has been established. The aims of this study are to describe the GR-Helpline users' characteristics and to compare the prevalence rates of the users with those of moderate-risk/problematic gamblers obtained from the national survey (IPSAD 2010-2011). Statistical analysis was performed on data obtained from the counselling sessions (phone/e-mail/chat) carried out on 5,805 users (57.5% gamblers; 42.5% families/friends). This confirms that the problems related to gambling concern not only the gamblers but also their families and friends. Significant differences were found between gamblers and families/friends involving gender (74% of gamblers were male; 76.9% of families/friends were female), as well as age-classes and geographical area. Female gamblers had a higher mean age (47.3 versus 40.2 years) and preferred nonstrategy-based games. Prevalence rates of GR-Helpline users and of moderate risk/problematic gamblers were correlated (Rho = 0.58; p = 0.0113). The results highlight the fact that remote access to counselling can be an effective means of promoting treatment for problem gamblers who do not otherwise appeal directly for services. PMID:26064772

A web-server of cell type discrimination system.

PubMed

Wang, Anyou; Zhong, Yan; Wang, Yanhua; He, Qianchuan

2014-01-01

Discriminating cell types is a daily request for stem cell biologists. However, there is not a user-friendly system available to date for public users to discriminate the common cell types, embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), and somatic cells (SCs). Here, we develop WCTDS, a web-server of cell type discrimination system, to discriminate the three cell types and their subtypes like fetal versus adult SCs. WCTDS is developed as a top layer application of our recent publication regarding cell type discriminations, which employs DNA-methylation as biomarkers and machine learning models to discriminate cell types. Implemented by Django, Python, R, and Linux shell programming, run under Linux-Apache web server, and communicated through MySQL, WCTDS provides a friendly framework to efficiently receive the user input and to run mathematical models for analyzing data and then to present results to users. This framework is flexible and easy to be expended for other applications. Therefore, WCTDS works as a user-friendly framework to discriminate cell types and subtypes and it can also be expended to detect other cell types like cancer cells.

A Web-Server of Cell Type Discrimination System

PubMed Central

Zhong, Yan

2014-01-01

Discriminating cell types is a daily request for stem cell biologists. However, there is not a user-friendly system available to date for public users to discriminate the common cell types, embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), and somatic cells (SCs). Here, we develop WCTDS, a web-server of cell type discrimination system, to discriminate the three cell types and their subtypes like fetal versus adult SCs. WCTDS is developed as a top layer application of our recent publication regarding cell type discriminations, which employs DNA-methylation as biomarkers and machine learning models to discriminate cell types. Implemented by Django, Python, R, and Linux shell programming, run under Linux-Apache web server, and communicated through MySQL, WCTDS provides a friendly framework to efficiently receive the user input and to run mathematical models for analyzing data and then to present results to users. This framework is flexible and easy to be expended for other applications. Therefore, WCTDS works as a user-friendly framework to discriminate cell types and subtypes and it can also be expended to detect other cell types like cancer cells. PMID:24578634

Factors associated with tobacco use among adolescents in India: results from the Global Youth Tobacco Survey, India (2000-2003).

PubMed

Oswal, Kunal C

2015-03-01

To differentiate between the different types of tobacco users and analyze the association between types of tobacco users and factors like pocket money and peer and parental influence across most of the state in India using the data obtained from Global Youth Tobacco Survey (GYTS) between 2000 and 2004. The GYTS data encompassed a representative 2-stage probability sample of students aged 13 to 15 years across 24 states and 2 union territories in India. These students were interviewed using an anonymous, self-administered questionnaire. A very strong association between users and pocket money was found in most of the states, with northeastern states having a very strong association-Sikkim, odds ratio (OR) = 8.43 (confidence interval [CI] = 6.08-11.69), and Manipur, OR = 5.58 (CI = 3.60-8.65)-after adjusting for close friend being smoker, close friend being smokeless tobacco user, parental influence, age, and gender. This study found a strong association between tobacco use by adolescents and having pocket money and close friends being tobacco users. © 2012 APJPH.

MASH Suite: a user-friendly and versatile software interface for high-resolution mass spectrometry data interpretation and visualization.

PubMed

Guner, Huseyin; Close, Patrick L; Cai, Wenxuan; Zhang, Han; Peng, Ying; Gregorich, Zachery R; Ge, Ying

2014-03-01

The rapid advancements in mass spectrometry (MS) instrumentation, particularly in Fourier transform (FT) MS, have made the acquisition of high-resolution and high-accuracy mass measurements routine. However, the software tools for the interpretation of high-resolution MS data are underdeveloped. Although several algorithms for the automatic processing of high-resolution MS data are available, there is still an urgent need for a user-friendly interface with functions that allow users to visualize and validate the computational output. Therefore, we have developed MASH Suite, a user-friendly and versatile software interface for processing high-resolution MS data. MASH Suite contains a wide range of features that allow users to easily navigate through data analysis, visualize complex high-resolution MS data, and manually validate automatically processed results. Furthermore, it provides easy, fast, and reliable interpretation of top-down, middle-down, and bottom-up MS data. MASH Suite is convenient, easily operated, and freely available. It can greatly facilitate the comprehensive interpretation and validation of high-resolution MS data with high accuracy and reliability.

MySpace and Facebook: applying the uses and gratifications theory to exploring friend-networking sites.

PubMed

Raacke, John; Bonds-Raacke, Jennifer

2008-04-01

The increased use of the Internet as a new tool in communication has changed the way people interact. This fact is even more evident in the recent development and use of friend-networking sites. However, no research has evaluated these sites and their impact on college students. Therefore, the present study was conducted to evaluate: (a) why people use these friend-networking sites, (b) what the characteristics are of the typical college user, and (c) what uses and gratifications are met by using these sites. Results indicated that the vast majority of college students are using these friend-networking sites for a significant portion of their day for reasons such as making new friends and locating old friends. Additionally, both men and women of traditional college age are equally engaging in this form of online communication with this result holding true for nearly all ethnic groups. Finally, results showed that many uses and gratifications are met by users (e.g., "keeping in touch with friends"). Results are discussed in light of the impact that friend-networking sites have on communication and social needs of college students.

Development of a user-friendly delivery method for the fungus Metarhizium anisopliac to control the ectoparasitic mite Varroa destructor in honey bee, Apis mellifera, colonies

USDA-ARS?s Scientific Manuscript database

A user-friendly method to deliver Metarhizium spores to honey bee colonies for control of Varroa mites was developed and tested. Patty blend formulations protected the fungal spores at brood nest temperatures and served as an improved delivery system of the fungus to bee hives. Field trials conducte...

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.

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.

The Facebook paths to happiness: effects of the number of Facebook friends and self-presentation on subjective well-being.

PubMed

Kim, Junghyun; Lee, Jong-Eun Roselyn

2011-06-01

The current study investigates whether and how Facebook increases college-age users' subjective well-being by focusing on the number of Facebook friends and self-presentation strategies (positive vs. honest). A structural equation modeling analysis of cross-sectional survey data of college student Facebook users (N=391) revealed that the number of Facebook friends had a positive association with subjective well-being, but this association was not mediated by perceived social support. Additionally, we found that there was a negative curvilinear (inverted U-shape curve) relationship between Facebook friends and perceived social support. As for self-presentation strategies, whereas positive self-presentation had a direct effect on subjective well-being, honest self-presentation had a significant indirect effect on subjective well-being through perceived social support. Our study suggests that the number of Facebook friends and positive self-presentation may enhance users' subjective well-being, but this portion of happiness may not be grounded in perceived social support. On the other hand, honest self-presentation may enhance happiness rooted in social support provided by Facebook friends. Implications of our findings are discussed in light of affirmation of self-worth, time and effort required for building and maintaining friendships, and the important role played by self-disclosure in signaling one's need for social support.

Correction of spin diffusion during iterative automated NOE assignment

NASA Astrophysics Data System (ADS)

Linge, Jens P.; Habeck, Michael; Rieping, Wolfgang; Nilges, Michael

2004-04-01

Indirect magnetization transfer increases the observed nuclear Overhauser enhancement (NOE) between two protons in many cases, leading to an underestimation of target distances. Wider distance bounds are necessary to account for this error. However, this leads to a loss of information and may reduce the quality of the structures generated from the inter-proton distances. Although several methods for spin diffusion correction have been published, they are often not employed to derive distance restraints. This prompted us to write a user-friendly and CPU-efficient method to correct for spin diffusion that is fully integrated in our program ambiguous restraints for iterative assignment (ARIA). ARIA thus allows automated iterative NOE assignment and structure calculation with spin diffusion corrected distances. The method relies on numerical integration of the coupled differential equations which govern relaxation by matrix squaring and sparse matrix techniques. We derive a correction factor for the distance restraints from calculated NOE volumes and inter-proton distances. To evaluate the impact of our spin diffusion correction, we tested the new calibration process extensively with data from the Pleckstrin homology (PH) domain of Mus musculus β-spectrin. By comparing structures refined with and without spin diffusion correction, we show that spin diffusion corrected distance restraints give rise to structures of higher quality (notably fewer NOE violations and a more regular Ramachandran map). Furthermore, spin diffusion correction permits the use of tighter error bounds which improves the distinction between signal and noise in an automated NOE assignment scheme.

Human Papillomavirus Genotyping Using an Automated Film-Based Chip Array

PubMed Central

Erali, Maria; Pattison, David C.; Wittwer, Carl T.; Petti, Cathy A.

2009-01-01

The INFINITI HPV-QUAD assay is a commercially available genotyping platform for human papillomavirus (HPV) that uses multiplex PCR, followed by automated processing for primer extension, hybridization, and detection. The analytical performance of the HPV-QUAD assay was evaluated using liquid cervical cytology specimens, and the results were compared with those results obtained using the digene High-Risk HPV hc2 Test (HC2). The specimen types included Surepath and PreservCyt transport media, as well as residual SurePath and HC2 transport media from the HC2 assay. The overall concordance of positive and negative results following the resolution of indeterminate and intermediate results was 83% among the 197 specimens tested. HC2 positive (+) and HPV-QUAD negative (−) results were noted in 24 specimens that were shown by real-time PCR and sequence analysis to contain no HPV, HPV types that were cross-reactive in the HC2 assay, or low virus levels. Conversely, HC2 (−) and HPV-QUAD (+) results were noted in four specimens and were subsequently attributed to cross-contamination. The most common HPV types to be identified in this study were HPV16, HPV18, HPV52/58, and HPV39/56. We show that the HPV-QUAD assay is a user friendly, automated system for the identification of distinct HPV genotypes. Based on its analytical performance, future studies with this platform are warranted to assess its clinical utility for HPV detection and genotyping. PMID:19644025

Human papillomavirus genotyping using an automated film-based chip array.

PubMed

Erali, Maria; Pattison, David C; Wittwer, Carl T; Petti, Cathy A

2009-09-01

The INFINITI HPV-QUAD assay is a commercially available genotyping platform for human papillomavirus (HPV) that uses multiplex PCR, followed by automated processing for primer extension, hybridization, and detection. The analytical performance of the HPV-QUAD assay was evaluated using liquid cervical cytology specimens, and the results were compared with those results obtained using the digene High-Risk HPV hc2 Test (HC2). The specimen types included Surepath and PreservCyt transport media, as well as residual SurePath and HC2 transport media from the HC2 assay. The overall concordance of positive and negative results following the resolution of indeterminate and intermediate results was 83% among the 197 specimens tested. HC2 positive (+) and HPV-QUAD negative (-) results were noted in 24 specimens that were shown by real-time PCR and sequence analysis to contain no HPV, HPV types that were cross-reactive in the HC2 assay, or low virus levels. Conversely, HC2 (-) and HPV-QUAD (+) results were noted in four specimens and were subsequently attributed to cross-contamination. The most common HPV types to be identified in this study were HPV16, HPV18, HPV52/58, and HPV39/56. We show that the HPV-QUAD assay is a user friendly, automated system for the identification of distinct HPV genotypes. Based on its analytical performance, future studies with this platform are warranted to assess its clinical utility for HPV detection and genotyping.

Design and implementation of relational databases relevant to the diverse needs of a tuberculosis case contact study in the Gambia.

PubMed

Jeffries, D J; Donkor, S; Brookes, R H; Fox, A; Hill, P C

2004-09-01

The data requirements of a large multidisciplinary tuberculosis case contact study are complex. We describe an ACCESS-based relational database system that meets our rigorous requirements for data entry and validation, while being user-friendly, flexible, exportable, and easy to install on a network or stand alone system. This includes the development of a double data entry package for epidemiology and laboratory data, semi-automated entry of ELISPOT data directly from the plate reader, and a suite of new programmes for the manipulation and integration of flow cytometry data. The double entered epidemiology and immunology databases are combined into a separate database, providing a near-real-time analysis of immuno-epidemiological data, allowing important trends to be identified early and major decisions about the study to be made and acted on. This dynamic data management model is portable and can easily be applied to other studies.

Usability evaluation of an experimental text summarization system and three search engines: implications for the reengineering of health care interfaces.

PubMed

Kushniruk, Andre W; Kan, Min-Yem; McKeown, Kathleen; Klavans, Judith; Jordan, Desmond; LaFlamme, Mark; Patel, Vimia L

2002-01-01

This paper describes the comparative evaluation of an experimental automated text summarization system, Centrifuser and three conventional search engines - Google, Yahoo and About.com. Centrifuser provides information to patients and families relevant to their questions about specific health conditions. It then produces a multidocument summary of articles retrieved by a standard search engine, tailored to the user's question. Subjects, consisting of friends or family of hospitalized patients, were asked to "think aloud" as they interacted with the four systems. The evaluation involved audio- and video recording of subject interactions with the interfaces in situ at a hospital. Results of the evaluation show that subjects found Centrifuser's summarization capability useful and easy to understand. In comparing Centrifuser to the three search engines, subjects' ratings varied; however, specific interface features were deemed useful across interfaces. We conclude with a discussion of the implications for engineering Web-based retrieval systems.

shinyGISPA: A web application for characterizing phenotype by gene sets using multiple omics data combinations.

PubMed

Dwivedi, Bhakti; Kowalski, Jeanne

2018-01-01

While many methods exist for integrating multi-omics data or defining gene sets, there is no one single tool that defines gene sets based on merging of multiple omics data sets. We present shinyGISPA, an open-source application with a user-friendly web-based interface to define genes according to their similarity in several molecular changes that are driving a disease phenotype. This tool was developed to help facilitate the usability of a previously published method, Gene Integrated Set Profile Analysis (GISPA), among researchers with limited computer-programming skills. The GISPA method allows the identification of multiple gene sets that may play a role in the characterization, clinical application, or functional relevance of a disease phenotype. The tool provides an automated workflow that is highly scalable and adaptable to applications that go beyond genomic data merging analysis. It is available at http://shinygispa.winship.emory.edu/shinyGISPA/.

shinyGISPA: A web application for characterizing phenotype by gene sets using multiple omics data combinations

PubMed Central

Dwivedi, Bhakti

2018-01-01

While many methods exist for integrating multi-omics data or defining gene sets, there is no one single tool that defines gene sets based on merging of multiple omics data sets. We present shinyGISPA, an open-source application with a user-friendly web-based interface to define genes according to their similarity in several molecular changes that are driving a disease phenotype. This tool was developed to help facilitate the usability of a previously published method, Gene Integrated Set Profile Analysis (GISPA), among researchers with limited computer-programming skills. The GISPA method allows the identification of multiple gene sets that may play a role in the characterization, clinical application, or functional relevance of a disease phenotype. The tool provides an automated workflow that is highly scalable and adaptable to applications that go beyond genomic data merging analysis. It is available at http://shinygispa.winship.emory.edu/shinyGISPA/. PMID:29415010

Emergency Management Computer-Aided Trainer (EMCAT)

NASA Technical Reports Server (NTRS)

Rodriguez, R. C.; Johnson, R. P.

1986-01-01

The Emergency Management Computer-Aided Trainer (EMCAT) developed by Essex Corporation or NASA and the Federal Emergency Management Administration's (FEMA) National Fire Academy (NFA) is described. It is a computer based training system for fire fighting personnel. A prototype EMCAT system was developed by NASA first using video tape images and then video disk images when the technology became available. The EMCAT system is meant to fill the training needs of the fire fighting community with affordable state-of-the-art technologies. An automated real time simulation of the fire situation was needed to replace the outdated manual training methods currently being used. In order to be successful, this simulator had to provide realism, be user friendly, be affordable, and support multiple scenarios. The EMCAT system meets these requirements and therefore represents an innovative training tool, not only for the fire fighting community, but also for the needs of other disciplines.

The application of integrated knowledge-based systems for the Biomedical Risk Assessment Intelligent Network (BRAIN)

NASA Technical Reports Server (NTRS)

Loftin, Karin C.; Ly, Bebe; Webster, Laurie; Verlander, James; Taylor, Gerald R.; Riley, Gary; Culbert, Chris

1992-01-01

One of NASA's goals for long duration space flight is to maintain acceptable levels of crew health, safety, and performance. One way of meeting this goal is through BRAIN, an integrated network of both human and computer elements. BRAIN will function as an advisor to mission managers by assessing the risk of inflight biomedical problems and recommending appropriate countermeasures. Described here is a joint effort among various NASA elements to develop BRAIN and the Infectious Disease Risk Assessment (IDRA) prototype. The implementation of this effort addresses the technological aspects of knowledge acquisition, integration of IDRA components, the use of expert systems to automate the biomedical prediction process, development of a user friendly interface, and integration of IDRA and ExerCISys systems. Because C language, CLIPS and the X-Window System are portable and easily integrated, they were chosen ss the tools for the initial IDRA prototype.

Novel numerical techniques for magma dynamics

NASA Astrophysics Data System (ADS)

Rhebergen, S.; Katz, R. F.; Wathen, A.; Alisic, L.; Rudge, J. F.; Wells, G.

2013-12-01

We discuss the development of finite element techniques and solvers for magma dynamics computations. These are implemented within the FEniCS framework. This approach allows for user-friendly, expressive, high-level code development, but also provides access to powerful, scalable numerical solvers and a large family of finite element discretisations. With the recent addition of dolfin-adjoint, FeniCS supports automated adjoint and tangent-linear models, enabling the rapid development of Generalised Stability Analysis. The ability to easily scale codes to three dimensions with large meshes, and/or to apply intricate adjoint calculations means that efficiency of the numerical algorithms is vital. We therefore describe our development and analysis of preconditioners designed specifically for finite element discretizations of equations governing magma dynamics. The preconditioners are based on Elman-Silvester-Wathen methods for the Stokes equation, and we extend these to flows with compaction. Our simulations are validated by comparison of results with laboratory experiments on partially molten aggregates.

Automated novel high-accuracy miniaturized positioning system for use in analytical instrumentation

NASA Astrophysics Data System (ADS)

Siomos, Konstadinos; Kaliakatsos, John; Apostolakis, Manolis; Lianakis, John; Duenow, Peter

1996-01-01

The development of three-dimensional automotive devices (micro-robots) for applications in analytical instrumentation, clinical chemical diagnostics and advanced laser optics, depends strongly on the ability of such a device: firstly to be positioned with high accuracy, reliability, and automatically, by means of user friendly interface techniques; secondly to be compact; and thirdly to operate under vacuum conditions, free of most of the problems connected with conventional micropositioners using stepping-motor gear techniques. The objective of this paper is to develop and construct a mechanically compact computer-based micropositioning system for coordinated motion in the X-Y-Z directions with: (1) a positioning accuracy of less than 1 micrometer, (the accuracy of the end-position of the system is controlled by a hard/software assembly using a self-constructed optical encoder); (2) a heat-free propulsion mechanism for vacuum operation; and (3) synchronized X-Y motion.

Analysing trends and forecasting malaria epidemics in Madagascar using a sentinel surveillance network: a web-based application.

PubMed

Girond, Florian; Randrianasolo, Laurence; Randriamampionona, Lea; Rakotomanana, Fanjasoa; Randrianarivelojosia, Milijaona; Ratsitorahina, Maherisoa; Brou, Télesphore Yao; Herbreteau, Vincent; Mangeas, Morgan; Zigiumugabe, Sixte; Hedje, Judith; Rogier, Christophe; Piola, Patrice

2017-02-13

The use of a malaria early warning system (MEWS) to trigger prompt public health interventions is a key step in adding value to the epidemiological data routinely collected by sentinel surveillance systems. This study describes a system using various epidemic thresholds and a forecasting component with the support of new technologies to improve the performance of a sentinel MEWS. Malaria-related data from 21 sentinel sites collected by Short Message Service are automatically analysed to detect malaria trends and malaria outbreak alerts with automated feedback reports. Roll Back Malaria partners can, through a user-friendly web-based tool, visualize potential outbreaks and generate a forecasting model. The system already demonstrated its ability to detect malaria outbreaks in Madagascar in 2014. This approach aims to maximize the usefulness of a sentinel surveillance system to predict and detect epidemics in limited-resource environments.

Scalable synthesis of sequence-defined, unimolecular macromolecules by Flow-IEG

PubMed Central

Leibfarth, Frank A.; Johnson, Jeremiah A.; Jamison, Timothy F.

2015-01-01

We report a semiautomated synthesis of sequence and architecturally defined, unimolecular macromolecules through a marriage of multistep flow synthesis and iterative exponential growth (Flow-IEG). The Flow-IEG system performs three reactions and an in-line purification in a total residence time of under 10 min, effectively doubling the molecular weight of an oligomeric species in an uninterrupted reaction sequence. Further iterations using the Flow-IEG system enable an exponential increase in molecular weight. Incorporating a variety of monomer structures and branching units provides control over polymer sequence and architecture. The synthesis of a uniform macromolecule with a molecular weight of 4,023 g/mol is demonstrated. The user-friendly nature, scalability, and modularity of Flow-IEG provide a general strategy for the automated synthesis of sequence-defined, unimolecular macromolecules. Flow-IEG is thus an enabling tool for theory validation, structure–property studies, and advanced applications in biotechnology and materials science. PMID:26269573

Accelerated Enveloping Distribution Sampling: Enabling Sampling of Multiple End States while Preserving Local Energy Minima.

PubMed

Perthold, Jan Walther; Oostenbrink, Chris

2018-05-17

Enveloping distribution sampling (EDS) is an efficient approach to calculate multiple free-energy differences from a single molecular dynamics (MD) simulation. However, the construction of an appropriate reference-state Hamiltonian that samples all states efficiently is not straightforward. We propose a novel approach for the construction of the EDS reference-state Hamiltonian, related to a previously described procedure to smoothen energy landscapes. In contrast to previously suggested EDS approaches, our reference-state Hamiltonian preserves local energy minima of the combined end-states. Moreover, we propose an intuitive, robust and efficient parameter optimization scheme to tune EDS Hamiltonian parameters. We demonstrate the proposed method with established and novel test systems and conclude that our approach allows for the automated calculation of multiple free-energy differences from a single simulation. Accelerated EDS promises to be a robust and user-friendly method to compute free-energy differences based on solid statistical mechanics.

Feasibility study of a take-home array-based functional electrical stimulation system with automated setup for current functional electrical stimulation users with foot-drop.

PubMed

Prenton, Sarah; Kenney, Laurence P; Stapleton, Claire; Cooper, Glen; Reeves, Mark L; Heller, Ben W; Sobuh, Mohammad; Barker, Anthony T; Healey, Jamie; Good, Timothy R; Thies, Sibylle B; Howard, David; Williamson, Tracey

2014-10-01

To investigate the feasibility of unsupervised community use of an array-based automated setup functional electrical stimulator for current foot-drop functional electrical stimulation (FES) users. Feasibility study. Gait laboratory and community use. Participants (N=7) with diagnosis of unilateral foot-drop of central neurologic origin (>6mo) who were regular users of a foot-drop FES system (>3mo). Array-based automated setup FES system for foot-drop (ShefStim). Logged usage, logged automated setup times for the array-based automated setup FES system and diary recording of problems experienced, all collected in the community environment. Walking speed, ankle angles at initial contact, foot clearance during swing, and the Quebec User Evaluation of Satisfaction with Assistive Technology version 2.0 (QUEST version 2.0) questionnaire, all collected in the gait laboratory. All participants were able to use the array-based automated setup FES system. Total setup time took longer than participants' own FES systems, and automated setup time was longer than in a previous study of a similar system. Some problems were experienced, but overall, participants were as satisfied with this system as their own FES system. The increase in walking speed (N=7) relative to no stimulation was comparable between both systems, and appropriate ankle angles at initial contact (N=7) and foot clearance during swing (n=5) were greater with the array-based automated setup FES system. This study demonstrates that an array-based automated setup FES system for foot-drop can be successfully used unsupervised. Despite setup's taking longer and some problems, users are satisfied with the system and it would appear as effective, if not better, at addressing the foot-drop impairment. Further product development of this unique system, followed by a larger-scale and longer-term study, is required before firm conclusions about its efficacy can be reached. Copyright © 2014 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Integrated Analysis Platform: An Open-Source Information System for High-Throughput Plant Phenotyping1[C][W][OPEN

PubMed Central

Klukas, Christian; Chen, Dijun; Pape, Jean-Michel

2014-01-01

High-throughput phenotyping is emerging as an important technology to dissect phenotypic components in plants. Efficient image processing and feature extraction are prerequisites to quantify plant growth and performance based on phenotypic traits. Issues include data management, image analysis, and result visualization of large-scale phenotypic data sets. Here, we present Integrated Analysis Platform (IAP), an open-source framework for high-throughput plant phenotyping. IAP provides user-friendly interfaces, and its core functions are highly adaptable. Our system supports image data transfer from different acquisition environments and large-scale image analysis for different plant species based on real-time imaging data obtained from different spectra. Due to the huge amount of data to manage, we utilized a common data structure for efficient storage and organization of data for both input data and result data. We implemented a block-based method for automated image processing to extract a representative list of plant phenotypic traits. We also provide tools for build-in data plotting and result export. For validation of IAP, we performed an example experiment that contains 33 maize (Zea mays ‘Fernandez’) plants, which were grown for 9 weeks in an automated greenhouse with nondestructive imaging. Subsequently, the image data were subjected to automated analysis with the maize pipeline implemented in our system. We found that the computed digital volume and number of leaves correlate with our manually measured data in high accuracy up to 0.98 and 0.95, respectively. In summary, IAP provides a multiple set of functionalities for import/export, management, and automated analysis of high-throughput plant phenotyping data, and its analysis results are highly reliable. PMID:24760818

An automated microfluidic DNA microarray platform for genetic variant detection in inherited arrhythmic diseases.

PubMed

Huang, Shu-Hong; Chang, Yu-Shin; Juang, Jyh-Ming Jimmy; Chang, Kai-Wei; Tsai, Mong-Hsun; Lu, Tzu-Pin; Lai, Liang-Chuan; Chuang, Eric Y; Huang, Nien-Tsu

2018-03-12

In this study, we developed an automated microfluidic DNA microarray (AMDM) platform for point mutation detection of genetic variants in inherited arrhythmic diseases. The platform allows for automated and programmable reagent sequencing under precise conditions of hybridization flow and temperature control. It is composed of a commercial microfluidic control system, a microfluidic microarray device, and a temperature control unit. The automated and rapid hybridization process can be performed in the AMDM platform using Cy3 labeled oligonucleotide exons of SCN5A genetic DNA, which produces proteins associated with sodium channels abundant in the heart (cardiac) muscle cells. We then introduce a graphene oxide (GO)-assisted DNA microarray hybridization protocol to enable point mutation detection. In this protocol, a GO solution is added after the staining step to quench dyes bound to single-stranded DNA or non-perfectly matched DNA, which can improve point mutation specificity. As proof-of-concept we extracted the wild-type and mutant of exon 12 and exon 17 of SCN5A genetic DNA from patients with long QT syndrome or Brugada syndrome by touchdown PCR and performed a successful point mutation discrimination in the AMDM platform. Overall, the AMDM platform can greatly reduce laborious and time-consuming hybridization steps and prevent potential contamination. Furthermore, by introducing the reciprocating flow into the microchannel during the hybridization process, the total assay time can be reduced to 3 hours, which is 6 times faster than the conventional DNA microarray. Given the automatic assay operation, shorter assay time, and high point mutation discrimination, we believe that the AMDM platform has potential for low-cost, rapid and sensitive genetic testing in a simple and user-friendly manner, which may benefit gene screening in medical practice.

Improving medical stores management through automation and effective communication

PubMed Central

Kumar, Ashok; Cariappa, M.P.; Marwaha, Vishal; Sharma, Mukti; Arora, Manu

2016-01-01

Background Medical stores management in hospitals is a tedious and time consuming chore with limited resources tasked for the purpose and poor penetration of Information Technology. The process of automation is slow paced due to various inherent factors and is being challenged by the increasing inventory loads and escalating budgets for procurement of drugs. Methods We carried out an indepth case study at the Medical Stores of a tertiary care health care facility. An iterative six step Quality Improvement (QI) process was implemented based on the Plan–Do–Study–Act (PDSA) cycle. The QI process was modified as per requirement to fit the medical stores management model. The results were evaluated after six months. Results After the implementation of QI process, 55 drugs of the medical store inventory which had expired since 2009 onwards were replaced with fresh stock by the suppliers as a result of effective communication through upgraded database management. Various pending audit objections were dropped due to the streamlined documentation and processes. Inventory management improved drastically due to automation, with disposal orders being initiated four months prior to the expiry of drugs and correct demands being generated two months prior to depletion of stocks. The monthly expense summary of drugs was now being done within ten days of the closing month. Conclusion Improving communication systems within the hospital with vendor database management and reaching out to clinicians is important. Automation of inventory management requires to be simple and user-friendly, utilizing existing hardware. Physical stores monitoring is indispensable, especially due to the scattered nature of stores. Staff training and standardized documentation protocols are the other keystones for optimal medical store management. PMID:26900225

Batch calculations in CalcHEP

NASA Astrophysics Data System (ADS)

Pukhov, A.

2003-04-01

CalcHEP is a clone of the CompHEP project which is developed by the author outside of the CompHEP group. CompHEP/CalcHEP are packages for automatic calculations of elementary particle decay and collision properties in the lowest order of perturbation theory. The main idea prescribed into the packages is to make available passing on from the Lagrangian to the final distributions effectively with a high level of automation. According to this, the packages were created as a menu driven user friendly programs for calculations in the interactive mode. From the other side, long-time calculations should be done in the non-interactive regime. Thus, from the beginning CompHEP has a problem of batch calculations. In CompHEP 33.23 the batch session was realized by mean of interactive menu which allows to the user to formulate the task for batch. After that the not-interactive session was launched. This way is too restricted, not flexible, and leads to doubling in programming. In this article I discuss another approach how one can force an interactive program to work in non-interactive mode. This approach was realized in CalcHEP 2.1 disposed on http://theory.sinp.msu.ru/~pukhov/calchep.html.

Towards high-throughput automated targeted femtosecond laser-based transfection of adherent cells

NASA Astrophysics Data System (ADS)

Antkowiak, Maciej; Torres-Mapa, Maria Leilani; Gunn-Moore, Frank; Dholakia, Kishan

2011-03-01

Femtosecond laser induced cell membrane poration has proven to be an attractive alternative to the classical methods of drug and gene delivery. It is a selective, sterile, non-contact technique that offers a highly localized operation, low toxicity and consistent performance. However, its broader application still requires the development of robust, high-throughput and user-friendly systems. We present a system capable of unassisted enhanced targeted optoinjection and phototransfection of adherent mammalian cells with a femtosecond laser. We demonstrate the advantages of a dynamic diffractive optical element, namely a spatial light modulator (SLM) for precise three dimensional positioning of the beam. It enables the implementation of a "point-and-shoot" system in which using the software interface a user simply points at the cell and a predefined sequence of precisely positioned doses can be applied. We show that irradiation in three axial positions alleviates the problem of exact beam positioning on the cell membrane and doubles the number of viably optoinjected cells when compared with a single dose. The presented system enables untargeted raster scan irradiation which provides transfection of adherent cells at the throughput of 1 cell per second.

RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants.

PubMed

Li, Pingchuan; Quan, Xiande; Jia, Gaofeng; Xiao, Jin; Cloutier, Sylvie; You, Frank M

2016-11-02

Resistance gene analogs (RGAs), such as NBS-encoding proteins, receptor-like protein kinases (RLKs) and receptor-like proteins (RLPs), are potential R-genes that contain specific conserved domains and motifs. Thus, RGAs can be predicted based on their conserved structural features using bioinformatics tools. Computer programs have been developed for the identification of individual domains and motifs from the protein sequences of RGAs but none offer a systematic assessment of the different types of RGAs. A user-friendly and efficient pipeline is needed for large-scale genome-wide RGA predictions of the growing number of sequenced plant genomes. An integrative pipeline, named RGAugury, was developed to automate RGA prediction. The pipeline first identifies RGA-related protein domains and motifs, namely nucleotide binding site (NB-ARC), leucine rich repeat (LRR), transmembrane (TM), serine/threonine and tyrosine kinase (STTK), lysin motif (LysM), coiled-coil (CC) and Toll/Interleukin-1 receptor (TIR). RGA candidates are identified and classified into four major families based on the presence of combinations of these RGA domains and motifs: NBS-encoding, TM-CC, and membrane associated RLP and RLK. All time-consuming analyses of the pipeline are paralleled to improve performance. The pipeline was evaluated using the well-annotated Arabidopsis genome. A total of 98.5, 85.2, and 100 % of the reported NBS-encoding genes, membrane associated RLPs and RLKs were validated, respectively. The pipeline was also successfully applied to predict RGAs for 50 sequenced plant genomes. A user-friendly web interface was implemented to ease command line operations, facilitate visualization and simplify result management for multiple datasets. RGAugury is an efficiently integrative bioinformatics tool for large scale genome-wide identification of RGAs. It is freely available at Bitbucket: https://bitbucket.org/yaanlpc/rgaugury .

Biblio-MetReS for user-friendly mining of genes and biological processes in scientific documents.

PubMed

Usie, Anabel; Karathia, Hiren; Teixidó, Ivan; Alves, Rui; Solsona, Francesc

2014-01-01

One way to initiate the reconstruction of molecular circuits is by using automated text-mining techniques. Developing more efficient methods for such reconstruction is a topic of active research, and those methods are typically included by bioinformaticians in pipelines used to mine and curate large literature datasets. Nevertheless, experimental biologists have a limited number of available user-friendly tools that use text-mining for network reconstruction and require no programming skills to use. One of these tools is Biblio-MetReS. Originally, this tool permitted an on-the-fly analysis of documents contained in a number of web-based literature databases to identify co-occurrence of proteins/genes. This approach ensured results that were always up-to-date with the latest live version of the databases. However, this 'up-to-dateness' came at the cost of large execution times. Here we report an evolution of the application Biblio-MetReS that permits constructing co-occurrence networks for genes, GO processes, Pathways, or any combination of the three types of entities and graphically represent those entities. We show that the performance of Biblio-MetReS in identifying gene co-occurrence is as least as good as that of other comparable applications (STRING and iHOP). In addition, we also show that the identification of GO processes is on par to that reported in the latest BioCreAtIvE challenge. Finally, we also report the implementation of a new strategy that combines on-the-fly analysis of new documents with preprocessed information from documents that were encountered in previous analyses. This combination simultaneously decreases program run time and maintains 'up-to-dateness' of the results. http://metres.udl.cat/index.php/downloads, metres.cmb@gmail.com.

Trial Promoter: A Web-Based Tool for Boosting the Promotion of Clinical Research Through Social Media.

PubMed

Reuter, Katja; Ukpolo, Francis; Ward, Edward; Wilson, Melissa L; Angyan, Praveen

2016-06-29

Scarce information about clinical research, in particular clinical trials, is among the top reasons why potential participants do not take part in clinical studies. Without volunteers, on the other hand, clinical research and the development of novel approaches to preventing, diagnosing, and treating disease are impossible. Promising digital options such as social media have the potential to work alongside traditional methods to boost the promotion of clinical research. However, investigators and research institutions are challenged to leverage these innovations while saving time and resources. To develop and test the efficiency of a Web-based tool that automates the generation and distribution of user-friendly social media messages about clinical trials. Trial Promoter is developed in Ruby on Rails, HTML, cascading style sheet (CSS), and JavaScript. In order to test the tool and the correctness of the generated messages, clinical trials (n=46) were randomized into social media messages and distributed via the microblogging social media platform Twitter and the social network Facebook. The percent correct was calculated to determine the probability with which Trial Promoter generates accurate messages. During a 10-week testing phase, Trial Promoter automatically generated and published 525 user-friendly social media messages on Twitter and Facebook. On average, Trial Promoter correctly used the message templates and substituted the message parameters (text, URLs, and disease hashtags) 97.7% of the time (1563/1600). Trial Promoter may serve as a promising tool to render clinical trial promotion more efficient while requiring limited resources. It supports the distribution of any research or other types of content. The Trial Promoter code and installation instructions are freely available online.

iMet-Q: A User-Friendly Tool for Label-Free Metabolomics Quantitation Using Dynamic Peak-Width Determination

PubMed Central

Chang, Hui-Yin; Chen, Ching-Tai; Lih, T. Mamie; Lynn, Ke-Shiuan; Juo, Chiun-Gung; Hsu, Wen-Lian; Sung, Ting-Yi

2016-01-01

Efficient and accurate quantitation of metabolites from LC-MS data has become an important topic. Here we present an automated tool, called iMet-Q (intelligent Metabolomic Quantitation), for label-free metabolomics quantitation from high-throughput MS1 data. By performing peak detection and peak alignment, iMet-Q provides a summary of quantitation results and reports ion abundance at both replicate level and sample level. Furthermore, it gives the charge states and isotope ratios of detected metabolite peaks to facilitate metabolite identification. An in-house standard mixture and a public Arabidopsis metabolome data set were analyzed by iMet-Q. Three public quantitation tools, including XCMS, MetAlign, and MZmine 2, were used for performance comparison. From the mixture data set, seven standard metabolites were detected by the four quantitation tools, for which iMet-Q had a smaller quantitation error of 12% in both profile and centroid data sets. Our tool also correctly determined the charge states of seven standard metabolites. By searching the mass values for those standard metabolites against Human Metabolome Database, we obtained a total of 183 metabolite candidates. With the isotope ratios calculated by iMet-Q, 49% (89 out of 183) metabolite candidates were filtered out. From the public Arabidopsis data set reported with two internal standards and 167 elucidated metabolites, iMet-Q detected all of the peaks corresponding to the internal standards and 167 metabolites. Meanwhile, our tool had small abundance variation (≤0.19) when quantifying the two internal standards and had higher abundance correlation (≥0.92) when quantifying the 167 metabolites. iMet-Q provides user-friendly interfaces and is publicly available for download at http://ms.iis.sinica.edu.tw/comics/Software_iMet-Q.html. PMID:26784691

Trial Promoter: A Web-Based Tool for Boosting the Promotion of Clinical Research Through Social Media

PubMed Central

Ukpolo, Francis; Ward, Edward; Wilson, Melissa L

2016-01-01

Background Scarce information about clinical research, in particular clinical trials, is among the top reasons why potential participants do not take part in clinical studies. Without volunteers, on the other hand, clinical research and the development of novel approaches to preventing, diagnosing, and treating disease are impossible. Promising digital options such as social media have the potential to work alongside traditional methods to boost the promotion of clinical research. However, investigators and research institutions are challenged to leverage these innovations while saving time and resources. Objective To develop and test the efficiency of a Web-based tool that automates the generation and distribution of user-friendly social media messages about clinical trials. Methods Trial Promoter is developed in Ruby on Rails, HTML, cascading style sheet (CSS), and JavaScript. In order to test the tool and the correctness of the generated messages, clinical trials (n=46) were randomized into social media messages and distributed via the microblogging social media platform Twitter and the social network Facebook. The percent correct was calculated to determine the probability with which Trial Promoter generates accurate messages. Results During a 10-week testing phase, Trial Promoter automatically generated and published 525 user-friendly social media messages on Twitter and Facebook. On average, Trial Promoter correctly used the message templates and substituted the message parameters (text, URLs, and disease hashtags) 97.7% of the time (1563/1600). Conclusions Trial Promoter may serve as a promising tool to render clinical trial promotion more efficient while requiring limited resources. It supports the distribution of any research or other types of content. The Trial Promoter code and installation instructions are freely available online. PMID:27357424

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.

Self-descriptions on LinkedIn: Recruitment or friendship identity?

PubMed

Garcia, Danilo; Cloninger, Kevin M; Granjard, Alexandre; Molander-Söderholm, Kristian; Amato, Clara; Sikström, Sverker

2018-04-26

We used quantitative semantics to find clusters of words in LinkedIn users' self-descriptions to an employer or a friend. Some of these clusters discriminated between worker and friend conditions (e.g., flexible vs. caring) and between LinkedIn users with high and low education (e.g., analytical vs. messy). © 2018 The Institute of Psychology, Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

Genetic algorithm and graph theory based matrix factorization method for online friend recommendation.

PubMed

Li, Qu; Yao, Min; Yang, Jianhua; Xu, Ning

2014-01-01

Online friend recommendation is a fast developing topic in web mining. In this paper, we used SVD matrix factorization to model user and item feature vector and used stochastic gradient descent to amend parameter and improve accuracy. To tackle cold start problem and data sparsity, we used KNN model to influence user feature vector. At the same time, we used graph theory to partition communities with fairly low time and space complexity. What is more, matrix factorization can combine online and offline recommendation. Experiments showed that the hybrid recommendation algorithm is able to recommend online friends with good accuracy.

A Visual Guide to Sorting Electrophysiological Recordings Using 'SpikeSorter'.

PubMed

Swindale, Nicholas V; Mitelut, Catalin; Murphy, Timothy H; Spacek, Martin A

2017-02-10

Few stand-alone software applications are available for sorting spikes from recordings made with multi-electrode arrays. Ideally, an application should be user friendly with a graphical user interface, able to read data files in a variety of formats, and provide users with a flexible set of tools giving them the ability to detect and sort extracellular voltage waveforms from different units with some degree of reliability. Previously published spike sorting methods are now available in a software program, SpikeSorter, intended to provide electrophysiologists with a complete set of tools for sorting, starting from raw recorded data file and ending with the export of sorted spikes times. Procedures are automated to the extent this is currently possible. The article explains and illustrates the use of the program. A representative data file is opened, extracellular traces are filtered, events are detected and then clustered. A number of problems that commonly occur during sorting are illustrated, including the artefactual over-splitting of units due to the tendency of some units to fire spikes in pairs where the second spike is significantly smaller than the first, and over-splitting caused by slow variation in spike height over time encountered in some units. The accuracy of SpikeSorter's performance has been tested with surrogate ground truth data and found to be comparable to that of other algorithms in current development.

A Comparison of Three-Dimensional Simulations of Traveling-Wave Tube Cold-Test Characteristics Using CST MICROWAVE STUDIO and MAFIA

NASA Technical Reports Server (NTRS)

Chevalier, C. T.; Herrmann, K. A.; Kory, C. L.; Wilson, J. D.; Cross, A. W.; Williams, W. D. (Technical Monitor)

2001-01-01

Previously, it was shown that MAFIA (solutions of Maxwell's equations by the Finite Integration Algorithm), a three-dimensional simulation code, can be used to produce accurate cold-test characteristics including frequency-phase dispersion, interaction impedance, and attenuation for traveling-wave tube (TWT) slow-wave structures. In an effort to improve user-friendliness and simulation time, a model was developed to compute the cold-test parameters using the electromagnetic field simulation software package CST MICROWAVE STUDIO (MWS). Cold-test parameters were calculated for several slow-wave circuits including a ferruled coupled-cavity, a folded waveguide, and a novel finned-ladder circuit using both MWS and MAFIA. Comparisons indicate that MWS provides more accurate cold-test data with significantly reduced simulation times. Both MAFIA and MWS are based on the finite integration (FI) method; however, MWS has several advantages over MAFIA. First, it has a Windows based interface for PC operation, making it very user-friendly, whereas MAFIA is UNIX based. MWS uses a new Perfect Boundary Approximation (PBA), which increases the accuracy of the simulations by avoiding stair step approximations associated with MAFIA's representation of structures. Finally, MWS includes a Visual Basic for Applications (VBA) compatible macro language that enables the simulation process to be automated and allows for the optimization of user-defined goal functions, such as interaction impedance.

The new NCPSS BL19U2 beamline at the SSRF for small-angle X-ray scattering from biological macromolecules in solution.

PubMed

Li, Na; Li, Xiuhong; Wang, Yuzhu; Liu, Guangfeng; Zhou, Ping; Wu, Hongjin; Hong, Chunxia; Bian, Fenggang; Zhang, Rongguang

2016-10-01

The beamline BL19U2 is located in the Shanghai Synchrotron Radiation Facility (SSRF) and is its first beamline dedicated to biological material small-angle X-ray scattering (BioSAXS). The electrons come from an undulator which can provide high brilliance for the BL19U2 end stations. A double flat silicon crystal (111) monochromator is used in BL19U2, with a tunable monochromatic photon energy ranging from 7 to 15 keV. To meet the rapidly growing demands of crystallographers, biochemists and structural biologists, the BioSAXS beamline allows manual and automatic sample loading/unloading. A Pilatus 1M detector (Dectris) is employed for data collection, characterized by a high dynamic range and a short readout time. The highly automated data processing pipeline SASFLOW was integrated into BL19U2, with help from the BioSAXS group of the European Molecular Biology Laboratory (EMBL, Hamburg), which provides a user-friendly interface for data processing. The BL19U2 beamline was officially opened to users in March 2015. To date, feedback from users has been positive and the number of experimental proposals at BL19U2 is increasing. A description of the new BioSAXS beamline and the setup characteristics is given, together with examples of data obtained.

Research on the Application of Persona in Book Recommendation System

NASA Astrophysics Data System (ADS)

Gao, Baozhong; Du, Shouyan; Li, Xinzhi; Liu, Fangai

2017-10-01

Currently, there still exists a host of problems in the book recommendation system, such as low accuracy, weak correlation and poor pertinence. Aiming to unravel these problems, this paper based on the theory of big data and data mining technology, through analyzing internet user behavior and the “5C” model of personal credit evaluation, combined with joint impact weight calculation method, which involves user grade, borrowing credit, book friend recommendation degree, book friend recommended adoption degree, borrowing frequency, borrowing number, and borrowing time interval. User activity and credit are also taken into account in the process of establishing user tagging system so as to build classified book recommendation service. This method is of universal meaning to the book recommendation service of smart campus with user as the core under big data environment.

Effects of Automated Tier 2 Storybook Intervention on Vocabulary and Comprehension Learning in Preschool Children with Limited Oral Language Skills

ERIC Educational Resources Information Center

Kelley, Elizabeth Spencer; Goldstein, Howard; Spencer, Trina D.; Sherman, Amber

2015-01-01

This early efficacy study examined the effects of an automated storybook intervention designed to promote school readiness among at-risk prekindergarten children. Story Friends is a small-group intervention in which vocabulary and question-answering lessons are embedded in a series of storybooks.A randomized group design with an embedded…

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.

Automated Tracking of Cell Migration with Rapid Data Analysis.

PubMed

DuChez, Brian J

2017-09-01

Cell migration is essential for many biological processes including development, wound healing, and metastasis. However, studying cell migration often requires the time-consuming and labor-intensive task of manually tracking cells. To accelerate the task of obtaining coordinate positions of migrating cells, we have developed a graphical user interface (GUI) capable of automating the tracking of fluorescently labeled nuclei. This GUI provides an intuitive user interface that makes automated tracking accessible to researchers with no image-processing experience or familiarity with particle-tracking approaches. Using this GUI, users can interactively determine a minimum of four parameters to identify fluorescently labeled cells and automate acquisition of cell trajectories. Additional features allow for batch processing of numerous time-lapse images, curation of unwanted tracks, and subsequent statistical analysis of tracked cells. Statistical outputs allow users to evaluate migratory phenotypes, including cell speed, distance, displacement, and persistence, as well as measures of directional movement, such as forward migration index (FMI) and angular displacement. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Heuristic automation for decluttering tactical displays.

PubMed

St John, Mark; Smallman, Harvey S; Manes, Daniel I; Feher, Bela A; Morrison, Jeffrey G

2005-01-01

Tactical displays can quickly become cluttered with large numbers of symbols that can compromise effective monitoring. Here, we studied how heuristic automation can aid users by intelligently "decluttering" the display. In a realistic simulated naval air defense task, 27 experienced U.S. Navy users monitored a cluttered airspace and executed defensive responses against significant threats. An algorithm continuously evaluated aircraft for their levels of threat and decluttered the less threatening ones by dimming their symbols. Users appropriately distrusted and spot-checked the automation's assessments, and decluttering had very little effect on which aircraft were judged as significantly threatening. Nonetheless, decluttering improved the timeliness of responses to threatening aircraft by 25% as compared with a baseline display with no decluttering; it was especially beneficial for threats in more peripheral locations, and 25 of 27 participants preferred decluttering. Heuristic automation, when properly designed to guide users' attention by decluttering less important objects, may prove valuable in many cluttered monitoring situations, including air traffic management, crisis team management, and tactical situation awareness in general.

On Abstractions and Simplifications in the Design of Human-Automation Interfaces

NASA Technical Reports Server (NTRS)

Heymann, Michael; Degani, Asaf; Shafto, Michael; Meyer, George; Clancy, Daniel (Technical Monitor)

2001-01-01

This report addresses the design of human-automation interaction from a formal perspective that focuses on the information content of the interface, rather than the design of the graphical user interface. It also addresses the, issue of the information provided to the user (e.g., user-manuals, training material, and all other resources). In this report, we propose a formal procedure for generating interfaces and user-manuals. The procedure is guided by two criteria: First, the interface must be correct, i.e., that with the given interface the user will be able to perform the specified tasks correctly. Second, the interface should be as succinct as possible. The report discusses the underlying concepts and the formal methods for this approach. Several examples are used to illustrate the procedure. The algorithm for constructing interfaces can be automated, and a preliminary software system for its implementation has been developed.

On Abstractions and Simplifications in the Design of Human-Automation Interfaces

NASA Technical Reports Server (NTRS)

Heymann, Michael; Degani, Asaf; Clancy, Daniel (Technical Monitor)

2002-01-01

This report addresses the design of human-automation interaction from a formal perspective that focuses on the information content of the interface, rather than the design of the graphical user interface. It also addresses the issue of the information provided to the user (e.g., user-manuals, training material, and all other resources). In this report, we propose a formal procedure for generating interfaces and user-manuals. The procedure is guided by two criteria: First, the interface must be correct, that is, with the given interface the user will be able to perform the specified tasks correctly. Second, the interface should be succinct. The report discusses the underlying concepts and the formal methods for this approach. Two examples are used to illustrate the procedure. The algorithm for constructing interfaces can be automated, and a preliminary software system for its implementation has been developed.

Automated Test Case Generation for an Autopilot Requirement Prototype

NASA Technical Reports Server (NTRS)

Giannakopoulou, Dimitra; Rungta, Neha; Feary, Michael

2011-01-01

Designing safety-critical automation with robust human interaction is a difficult task that is susceptible to a number of known Human-Automation Interaction (HAI) vulnerabilities. It is therefore essential to develop automated tools that provide support both in the design and rapid evaluation of such automation. The Automation Design and Evaluation Prototyping Toolset (ADEPT) enables the rapid development of an executable specification for automation behavior and user interaction. ADEPT supports a number of analysis capabilities, thus enabling the detection of HAI vulnerabilities early in the design process, when modifications are less costly. In this paper, we advocate the introduction of a new capability to model-based prototyping tools such as ADEPT. The new capability is based on symbolic execution that allows us to automatically generate quality test suites based on the system design. Symbolic execution is used to generate both user input and test oracles user input drives the testing of the system implementation, and test oracles ensure that the system behaves as designed. We present early results in the context of a component in the Autopilot system modeled in ADEPT, and discuss the challenges of test case generation in the HAI domain.

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.

Automation and decision support in interactive consumer products.

PubMed

Sauer, J; Rüttinger, B

2007-06-01

This article presents two empirical studies (n = 30, n = 48) that are concerned with different forms of automation in interactive consumer products. The goal of the studies was to evaluate the effectiveness of two types of automation: perceptual augmentation (i.e. supporting users' information acquisition and analysis); and control integration (i.e. supporting users' action selection and implementation). Furthermore, the effectiveness of on-product information (i.e. labels attached to product) in supporting automation design was evaluated. The findings suggested greater benefits for automation in control integration than in perceptual augmentation alone, which may be partly due to the specific requirements of consumer product usage. If employed appropriately, on-product information can be a helpful means of information conveyance. The article discusses the implications of automation design in interactive consumer products while drawing on automation models from the work environment.

Recommendations from Friends Anytime and Anywhere: Toward a Model of Contextual Offer and Consumption Values

PubMed Central

Shen, Xiao-Liang; Wang, Nan

2013-01-01

Abstract The ubiquity and portability of mobile devices provide additional opportunities for information retrieval. People can easily access mobile applications anytime and anywhere when they need to acquire specific context-aware recommendations (contextual offer) from their friends. This study, thus, represents an initial attempt to understand users' acceptance of a mobile-based social reviews platform, where recommendations from friends can be obtained with mobile devices. Based on the consumption value theory, a theoretical model is proposed and empirically examined using survey data from 218 mobile users. The findings demonstrate that contextual offers based on users' profiles, access time, and geographic positions significantly predict their value perceptions (utilitarian, hedonic, and social), which, in turn, affect their intention to use a mobile social reviews platform. This study is also believed to provide some useful insights to both research and practice. PMID:23530548

Improvement of the insertion axis for cochlear implantation with a robot-based system.

PubMed

Torres, Renato; Kazmitcheff, Guillaume; De Seta, Daniele; Ferrary, Evelyne; Sterkers, Olivier; Nguyen, Yann

2017-02-01

It has previously reported that alignment of the insertion axis along the basal turn of the cochlea was depending on surgeon' experience. In this experimental study, we assessed technological assistances, such as navigation or a robot-based system, to improve the insertion axis during cochlear implantation. A preoperative cone beam CT and a mastoidectomy with a posterior tympanotomy were performed on four temporal bones. The optimal insertion axis was defined as the closest axis to the scala tympani centerline avoiding the facial nerve. A neuronavigation system, a robot assistance prototype, and software allowing a semi-automated alignment of the robot were used to align an insertion tool with an optimal insertion axis. Four procedures were performed and repeated three times in each temporal bone: manual, manual navigation-assisted, robot-based navigation-assisted, and robot-based semi-automated. The angle between the optimal and the insertion tool axis was measured in the four procedures. The error was 8.3° ± 2.82° for the manual procedure (n = 24), 8.6° ± 2.83° for the manual navigation-assisted procedure (n = 24), 5.4° ± 3.91° for the robot-based navigation-assisted procedure (n = 24), and 3.4° ± 1.56° for the robot-based semi-automated procedure (n = 12). A higher accuracy was observed with the semi-automated robot-based technique than manual and manual navigation-assisted (p < 0.01). Combination of a navigation system and a manual insertion does not improve the alignment accuracy due to the lack of friendly user interface. On the contrary, a semi-automated robot-based system reduces both the error and the variability of the alignment with a defined optimal axis.

FRAME (Force Review Automation Environment): MATLAB-based AFM data processor.

PubMed

Partola, Kostyantyn R; Lykotrafitis, George

2016-05-03

Data processing of force-displacement curves generated by atomic force microscopes (AFMs) for elastic moduli and unbinding event measurements is very time consuming and susceptible to user error or bias. There is an evident need for consistent, dependable, and easy-to-use AFM data processing software. We have developed an open-source software application, the force review automation environment (or FRAME), that provides users with an intuitive graphical user interface, automating data processing, and tools for expediting manual processing. We did not observe a significant difference between manually processed and automatically processed results from the same data sets. Copyright © 2016 Elsevier Ltd. All rights reserved.

Innovative approach towards understanding optics

NASA Astrophysics Data System (ADS)

Garg, Amit; Bharadwaj, Sadashiv Raj; Kumar, Raj; Shudhanshu, Avinash Kumar; Verma, Deepak Kumar

2016-01-01

Over the last few years, there has been a decline in the students’ interest towards Science and Optics. Use of technology in the form of various types of sensors and data acquisition systems has come as a saviour. Till date, manual routine tools and techniques are used to perform various experimental procedures in most of the science/optics laboratories in our country. The manual tools are cumbersome whereas the automated ones are costly. It does not enthuse young researchers towards the science laboratories. There is a need to develop applications which can be easily integrated, tailored at school and undergraduate level laboratories and are economical at the same time. Equipments with advanced technologies are available but they are uneconomical and have complicated working principle with a black box approach. The present work describes development of portable tools and applications which are user-friendly. This is being implemented using open-source physical computing platform based on a simple low cost microcontroller board and a development environment for writing software. The present paper reports the development of an automated spectrometer, an instrument used in almost all optics experiments at undergraduate level, and students’ response to this innovation. These tools will inspire young researchers towards science and facilitate development of advance low cost equipments making life easier for Indian as well as developing nations.

Computer-automated ABCD versus dermatologists with different degrees of experience in dermoscopy.

PubMed

Piccolo, Domenico; Crisman, Giuliana; Schoinas, Spyridon; Altamura, Davide; Peris, Ketty

2014-01-01

Dermoscopy is a very useful and non-invasive technique for in vivo observation and preoperative diagnosis of pigmented skin lesions (PSLs) inasmuch as it enables analysis of surface and subsurface structures that are not discernible to the naked eye. The authors used the ABCD rule of dermoscopy to test the accuracy of melanoma diagnosis with respect to a panel of 165 PSLs and the intra- and inter-observer diagnostic agreement obtained between three dermatologists with different degrees of experience, one General Practitioner and a DDA for computer-assisted diagnosis (Nevuscreen(®), Arkè s.a.s., Avezzano, Italy). 165 Pigmented Skin Lesions from 165 patients were selected. Histopathological examination revealed 132 benign melanocytic skin lesions and 33 melanomas. The kappa statistic, sensitivity, specificity and predictive positive and negative values were calculated to measure agreement between all the human observers and in comparison with the automated DDA. Our results revealed poor reproducibility of the semi-quantitative algorithm devised by Stolz et al. independently of observers' experience in dermoscopy. Nevuscreen(®) (Arkè s.a.s., Avezzano, Italy) proved to be 'user friendly' to all observers, thus enabling a more critical evaluation of each lesion and representing a helpful tool for clinicians without significant experience in dermoscopy in improving and achieving more accurate diagnosis of PSLs.

clubber: removing the bioinformatics bottleneck in big data analyses.

PubMed

Miller, Maximilian; Zhu, Chengsheng; Bromberg, Yana

2017-06-13

With the advent of modern day high-throughput technologies, the bottleneck in biological discovery has shifted from the cost of doing experiments to that of analyzing results. clubber is our automated cluster-load balancing system developed for optimizing these "big data" analyses. Its plug-and-play framework encourages re-use of existing solutions for bioinformatics problems. clubber's goals are to reduce computation times and to facilitate use of cluster computing. The first goal is achieved by automating the balance of parallel submissions across available high performance computing (HPC) resources. Notably, the latter can be added on demand, including cloud-based resources, and/or featuring heterogeneous environments. The second goal of making HPCs user-friendly is facilitated by an interactive web interface and a RESTful API, allowing for job monitoring and result retrieval. We used clubber to speed up our pipeline for annotating molecular functionality of metagenomes. Here, we analyzed the Deepwater Horizon oil-spill study data to quantitatively show that the beach sands have not yet entirely recovered. Further, our analysis of the CAMI-challenge data revealed that microbiome taxonomic shifts do not necessarily correlate with functional shifts. These examples (21 metagenomes processed in 172 min) clearly illustrate the importance of clubber in the everyday computational biology environment.

Innovative IT system for material management in warehouses

NASA Astrophysics Data System (ADS)

Papoutsidakis, Michael; Sigala, Maria; Simeonaki, Eleni; Tseles, Dimitrios

2017-09-01

Nowadays through the rapid development of technology in all areas there is a constant effort to introduce technological solutions in everyday life with emphasis on materials management information systems (Enterprise Resource Planning). During the last few years the variety of these systems has been increased for small business or for SMEs as well as for larger companies and industries. In the field of material management and main management operations with automated processes, ERP applications have only recently begun to make their appearance. In this paper will be presented the development of a system for automated material storage process in a system built through specific roles that will manage materials using an integrated barcode scanner. In addition we will analyse and describe the operation and modules of other systems that have been created for the same usage. The aim of this project is to create a prototype application that will be innovative with a flexible nature that will give solutions, with low cost and it will be user friendly. This application will allow quick and proper materials management for storage. The expected result is that the application can be used by smart devices in android environment and computers without an external barcode scanner, making the application accessible to the buyer at low cost.

clubber: removing the bioinformatics bottleneck in big data analyses

PubMed Central

Miller, Maximilian; Zhu, Chengsheng; Bromberg, Yana

2018-01-01

With the advent of modern day high-throughput technologies, the bottleneck in biological discovery has shifted from the cost of doing experiments to that of analyzing results. clubber is our automated cluster-load balancing system developed for optimizing these “big data” analyses. Its plug-and-play framework encourages re-use of existing solutions for bioinformatics problems. clubber’s goals are to reduce computation times and to facilitate use of cluster computing. The first goal is achieved by automating the balance of parallel submissions across available high performance computing (HPC) resources. Notably, the latter can be added on demand, including cloud-based resources, and/or featuring heterogeneous environments. The second goal of making HPCs user-friendly is facilitated by an interactive web interface and a RESTful API, allowing for job monitoring and result retrieval. We used clubber to speed up our pipeline for annotating molecular functionality of metagenomes. Here, we analyzed the Deepwater Horizon oil-spill study data to quantitatively show that the beach sands have not yet entirely recovered. Further, our analysis of the CAMI-challenge data revealed that microbiome taxonomic shifts do not necessarily correlate with functional shifts. These examples (21 metagenomes processed in 172 min) clearly illustrate the importance of clubber in the everyday computational biology environment. PMID:28609295

The influence of personal networks on the use and abuse of alcohol and drugs.

PubMed

Calafat, Amador; Cajal, Berta; Juan, Montse; Mendes, Fernando; Kokkevi, Anna; Blay, Nicole; Palmer, Alfonso; Duch, Maria Angels

2010-01-01

Party networks of young people are very important for socialization, but can also influence their involvement in risk behaviours or they can be protective. The influence of nightlife network of friends in using alcohol/ drugs is investigated through a survey. We explore the individual-centred networks (7.360 friends) of 1.363 recreational nightlife users in 9 European cities in 2006, through 22 friend characteristics. Statistical analysis utilised factorial analysis with varimax rotation and analysis of variance. The 69% of the sample had been drunk during the last month and more than half of them had used illicit drugs. Most of the respondents use to have a stable group of friends with whom to go out. Networks main characteristics were being more or less deviant and/or prosocial. Having not network or a less prosocial network is related to be low consumers. Having a non deviant, but prosocial network is related to being a person who gets drunk without using illegal drugs. Users of illegal drugs have a deviant and prosocial network. Finally ex users have less deviant networks, but at the same time a helper and prosocial network. Males drug use patterns appear to be less affected by the characteristics of their networks. Some preventive consequences coming from these results are already known as the importance of having less deviant friends. But some other issues are less known: to enhance certain prosocial skills may have counter preventive effects among recreational users and to influence the network for preventative purposes may be more effective among females.

Automated Instructional Management Systems (AIMS) Version III, Users Manual.

ERIC Educational Resources Information Center

New York Inst. of Tech., Old Westbury.

This document sets forth the procedures necessary to utilize and understand the operating characteristics of the Automated Instructional Management System - Version III, a computer-based system for management of educational processes. Directions for initialization, including internal and user files; system and operational input requirements;…

Development of an Automated Precipitation Processing Model and Applications in Hydrologic Investigations

NASA Astrophysics Data System (ADS)

Milewski, A. M.; Markondiah Jayaprakash, S.; Sultan, M.; Becker, R.

2006-12-01

Given the advances in new technologies, more and more scientists are beginning to utilize remote sensing or satellite imagery in their research applications. Remote sensing data offer a synoptic view and observational quantitative parameters over large domains and thus provide cost-effective solutions by reducing the labor involved in collecting extensive field observations. One of the valuable data sets that can be extracted from remote sensing observations is precipitation. Prior to the deployment of the relevant satellite-based sensors, users had to resort to rainfall stations to obtain precipitation data. Currently, users can freely download digital Tropical Rainfall Measuring Mission (TRMM) and Special Spectral Measuring Imager (SSM/I) precipitation data, however, the process of data extraction is not user friendly as it requires computer programming to fully utilize these datasets. We have developed the Automated Precipitation Processing Module (APPM) to simplify the tedious manual process needed to retrieve rainfall estimates via satellite measurements. The function of the APPM is to process the TRMM and SSM/I data according to the user's spatial and temporal inputs. Using APPM, we processed all available TRMM and SSM/I data for six continents (processed data is available on six compact discs: one/continent: refer to www.esrs.wmich.edu). The input data includes global SSM/I (1987-1998) and TRMM (1998-2005) covering an area extending from 50 degrees North to 50 degrees South. Advantages of using our software include: (1) user friendly technology, (2) reduction in processing time (e.g., processing of the entire TRMM & SSM/I dataset (1987-2005) for Africa was reduced from one year to one week), and (3) reduction in required computer resources (original TRMM & SSM/I data: 1.5 terabytes; processed: 300 megabytes). The APPM reads raw binary data and allows for: (1) sub-setting global dataset given user-defined boundaries (latitude and longitude), (2) selection of temporal range of interest, (3) Definition of minimum threshold precipitation value, (4) plotting of rainfall events versus time and recording events that exceed a specified threshold value, and (5) merge outputs of SSM/I and TRMM data into one continuous record. The maximum allowable temporal range is from 1987 to 2005, which is the time frame during which precipitation sensors were deployed. Most hydrologic investigations require dense networks of hydrologic monitoring systems that are expensive which makes this situation difficult in many parts of the world. Through the use of the APPM and the Soil Water and Assessment Tool (SWAT) model the ground water recharge and surface water runoff was computed for the past 18 years in several arid areas of the world (Egypt, Sinai, and Israel). Results include 13 watersheds in Egypt, 10 watersheds in Sinai, and 2 watersheds in Israel. The selected watersheds provide ample calibration data (rain gauges, stream flow) on a continuous basis for the duration of the model (1987- 2005). The average precipitation amounts (35mm/yr) in these areas are controlled by extreme rainfall events (~15) where precipitation exceeds 20mm/day. Implications for utilizing temporal global remote sensing data for calculating continuous rainfall/runoff models on global and regional scales for the past two decades are now within reach.

PANDA: a pipeline toolbox for analyzing brain diffusion images.

PubMed

Cui, Zaixu; Zhong, Suyu; Xu, Pengfei; He, Yong; Gong, Gaolang

2013-01-01

Diffusion magnetic resonance imaging (dMRI) is widely used in both scientific research and clinical practice in in-vivo studies of the human brain. While a number of post-processing packages have been developed, fully automated processing of dMRI datasets remains challenging. Here, we developed a MATLAB toolbox named "Pipeline for Analyzing braiN Diffusion imAges" (PANDA) for fully automated processing of brain diffusion images. The processing modules of a few established packages, including FMRIB Software Library (FSL), Pipeline System for Octave and Matlab (PSOM), Diffusion Toolkit and MRIcron, were employed in PANDA. Using any number of raw dMRI datasets from different subjects, in either DICOM or NIfTI format, PANDA can automatically perform a series of steps to process DICOM/NIfTI to diffusion metrics [e.g., fractional anisotropy (FA) and mean diffusivity (MD)] that are ready for statistical analysis at the voxel-level, the atlas-level and the Tract-Based Spatial Statistics (TBSS)-level and can finish the construction of anatomical brain networks for all subjects. In particular, PANDA can process different subjects in parallel, using multiple cores either in a single computer or in a distributed computing environment, thus greatly reducing the time cost when dealing with a large number of datasets. In addition, PANDA has a friendly graphical user interface (GUI), allowing the user to be interactive and to adjust the input/output settings, as well as the processing parameters. As an open-source package, PANDA is freely available at http://www.nitrc.org/projects/panda/. This novel toolbox is expected to substantially simplify the image processing of dMRI datasets and facilitate human structural connectome studies.

PANDA: a pipeline toolbox for analyzing brain diffusion images

PubMed Central

Cui, Zaixu; Zhong, Suyu; Xu, Pengfei; He, Yong; Gong, Gaolang

2013-01-01

Diffusion magnetic resonance imaging (dMRI) is widely used in both scientific research and clinical practice in in-vivo studies of the human brain. While a number of post-processing packages have been developed, fully automated processing of dMRI datasets remains challenging. Here, we developed a MATLAB toolbox named “Pipeline for Analyzing braiN Diffusion imAges” (PANDA) for fully automated processing of brain diffusion images. The processing modules of a few established packages, including FMRIB Software Library (FSL), Pipeline System for Octave and Matlab (PSOM), Diffusion Toolkit and MRIcron, were employed in PANDA. Using any number of raw dMRI datasets from different subjects, in either DICOM or NIfTI format, PANDA can automatically perform a series of steps to process DICOM/NIfTI to diffusion metrics [e.g., fractional anisotropy (FA) and mean diffusivity (MD)] that are ready for statistical analysis at the voxel-level, the atlas-level and the Tract-Based Spatial Statistics (TBSS)-level and can finish the construction of anatomical brain networks for all subjects. In particular, PANDA can process different subjects in parallel, using multiple cores either in a single computer or in a distributed computing environment, thus greatly reducing the time cost when dealing with a large number of datasets. In addition, PANDA has a friendly graphical user interface (GUI), allowing the user to be interactive and to adjust the input/output settings, as well as the processing parameters. As an open-source package, PANDA is freely available at http://www.nitrc.org/projects/panda/. This novel toolbox is expected to substantially simplify the image processing of dMRI datasets and facilitate human structural connectome studies. PMID:23439846

How gamma radiation processing systems are benefiting from the latest advances in information technology

NASA Astrophysics Data System (ADS)

Gibson, Wayne H.; Levesque, Daniel

2000-03-01

This paper discusses how gamma irradiation plants are putting the latest advances in computer and information technology to use for better process control, cost savings, and strategic advantages. Some irradiator operations are gaining significant benefits by integrating computer technology and robotics with real-time information processing, multi-user databases, and communication networks. The paper reports on several irradiation facilities that are making good use of client/server LANs, user-friendly graphics interfaces, supervisory control and data acquisition (SCADA) systems, distributed I/O with real-time sensor devices, trending analysis, real-time product tracking, dynamic product scheduling, and automated dosimetry reading. These plants are lowering costs by fast and reliable reconciliation of dosimetry data, easier validation to GMP requirements, optimizing production flow, and faster release of sterilized products to market. There is a trend in the manufacturing sector towards total automation using "predictive process control". Real-time verification of process parameters "on-the-run" allows control parameters to be adjusted appropriately, before the process strays out of limits. Applying this technology to the gamma radiation process, control will be based on monitoring the key parameters such as time, and making adjustments during the process to optimize quality and throughput. Dosimetry results will be used as a quality control measurement rather than as a final monitor for the release of the product. Results are correlated with the irradiation process data to quickly and confidently reconcile variations. Ultimately, a parametric process control system utilizing responsive control, feedback and verification will not only increase productivity and process efficiency, but can also result in operating within tighter dose control set points.

Data processing and in-flight calibration systems for OMI-EOS-Aura

NASA Astrophysics Data System (ADS)

van den Oord, G. H. J.; Dobber, M.; van de Vegte, J.; van der Neut, I.; Som de Cerff, W.; Rozemeijer, N. C.; Schenkelaars, V.; ter Linden, M.

2006-08-01

The OMI instrument that flies on the EOS Aura mission was launched in July 2004. OMI is a UV-VIS imaging spectrometer that measures in the 270 - 500 nm wavelength range. OMI provides daily global coverage with high spatial resolution. Every orbit of 100 minutes OMI generates about 0.5 GB of Level 0 data and 1.2 GB of Level 1 data. About half of the Level 1 data consists of in-flight calibration measurements. These data rates make it necessary to automate the process of in-flight calibration. For that purpose two facilities have been developed at KNMI in the Netherlands: the OMI Dutch Processing System (ODPS) and the Trend Monitoring and In-flight Calibration Facility (TMCF). A description of these systems is provided with emphasis on the use for radiometric, spectral and detector calibration and characterization. With the advance of detector technology and the need for higher spatial resolution, data rates will become even higher for future missions. To make effective use of automated systems like the TMCF, it is of paramount importance to integrate the instrument operations concept, the information contained in the Level 1 (meta-)data products and the inflight calibration software and system databases. In this way a robust but also flexible end-to-end system can be developed that serves the needs of the calibration staff, the scientific data users and the processing staff. The way this has been implemented for OMI may serve as an example of a cost-effective and user friendly solution for future missions. The basic system requirements for in-flight calibration are discussed and examples are given how these requirements have been implemented for OMI. Special attention is paid to the aspect of supporting the Level 0 - 1 processing with timely and accurate calibration constants.

Fireballs in the Sky

NASA Astrophysics Data System (ADS)

Day, B. H.; Bland, P.

2016-12-01

Fireballs in the Sky is an innovative Australian citizen science program that connects the public with the research of the Desert Fireball Network (DFN). This research aims to understand the early workings of the solar system, and Fireballs in the Sky invites people around the world to learn about this science, contributing fireball sightings via a user-friendly app. To date, more than 23,000 people have downloaded the app world-wide and participated in planetary science. The Fireballs in the Sky app allows users to get involved with the Desert Fireball Network research, supplementing DFN observations and providing enhanced coverage by reporting their own meteor sightings to DFN scientists. Fireballs in the Sky reports are used to track the trajectories of meteors - from their orbit in space to where they might have landed on Earth. Led by Phil Bland at Curtin University in Australia, the Desert Fireball Network (DFN) uses automated observatories across Australia to triangulate trajectories of meteorites entering the atmosphere, determine pre-entry orbits, and pinpoint their fall positions. Each observatory is an autonomous intelligent imaging system, taking 1000×36Megapixel all-sky images throughout the night, using neural network algorithms to recognize events. They are capable of operating for 12 months in a harsh environment, and store all imagery collected. We developed a completely automated software pipeline for data reduction, and built a supercomputer database for storage, allowing us to process our entire archive. The DFN currently stands at 50 stations distributed across the Australian continent, covering an area of 2.5 million km^2. Working with DFN's partners at NASA's Solar System Exploration Research Virtual Institute, the team is expanding the network beyond Australia to locations around the world. Fireballs in the Sky allows a growing public base to learn about and participate in this exciting research.

PDB Editor: a user-friendly Java-based Protein Data Bank file editor with a GUI.

PubMed

Lee, Jonas; Kim, Sung Hou

2009-04-01

The Protein Data Bank file format is the format most widely used by protein crystallographers and biologists to disseminate and manipulate protein structures. Despite this, there are few user-friendly software packages available to efficiently edit and extract raw information from PDB files. This limitation often leads to many protein crystallographers wasting significant time manually editing PDB files. PDB Editor, written in Java Swing GUI, allows the user to selectively search, select, extract and edit information in parallel. Furthermore, the program is a stand-alone application written in Java which frees users from the hassles associated with platform/operating system-dependent installation and usage. PDB Editor can be downloaded from http://sourceforge.net/projects/pdbeditorjl/.

Effect of descriptive information and experience on automation reliance.

PubMed

Yuviler-Gavish, Nirit; Gopher, Daniel

2011-06-01

The present research addresses the issue of reliance on decision support systems for the long-term (DSSLT), which help users develop decision-making strategies and long-term planning. It is argued that providing information about a system's future performance in an experiential manner, as compared with a descriptive manner, encourages users to increase their reliance level. Establishing appropriate reliance on DSSLT is contingent on the system developer's ability to provide users with information about the system's future performance. A sequence of three studies contrasts the effect on automation reliance of providing descriptive information versus experience for DSSLT with two different positive expected values of recommendations. Study I demonstrated that when automation reliance was determined solely on the basis of description, it was relatively low, but it increased significantly when a decision was made after experience with 50 training simulations. Participants were able to learn to increase their automation reliance levels when they encountered the same type of recommendation again. Study 2 showed that the absence of preliminary descriptive information did not affect the automation reliance levels obtained after experience. Study 3 demonstrated that participants were able to generalize their learning about increasing reliance levels to new recommendations. Using experience rather than description to give users information about future performance in DSSLT can help increase automation reliance levels. Implications for designing DSSLT and decision support systems in general are discussed.

Automating Relational Database Design for Microcomputer Users.

ERIC Educational Resources Information Center

Pu, Hao-Che

1991-01-01

Discusses issues involved in automating the relational database design process for microcomputer users and presents a prototype of a microcomputer-based system (RA, Relation Assistant) that is based on expert systems technology and helps avoid database maintenance problems. Relational database design is explained and the importance of easy input…

18 CFR 37.8 - Obligations of OASIS users.

Code of Federal Regulations, 2010 CFR

2010-04-01

..., DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT OPEN ACCESS SAME-TIME INFORMATION SYSTEMS § 37.8... initiating a significant amount of automated queries. The OASIS user must also notify the Responsible Party one month in advance of expected significant increases in the volume of automated queries. [Order 605...

Structural diversity effect on hashtag adoption in Twitter

NASA Astrophysics Data System (ADS)

Zhang, Aihua; Zheng, Mingxing; Pang, Bowen

2018-03-01

With online social network developing rapidly these years, user' behavior in online social network has attracted a lot of attentions to it. In this paper, we study Twitter user's behavior of hashtag adoption from the perspective of social contagion and focus on "structure diversity" effect on individual's behavior in Twitter. We achieve data through Twitter's API by crawling and build a users' network to carry on empirical research. The Girvan-Newman (G-N) algorithm is used to analyze the structural diversity of user's ego network, and Logistic regression model is adopted to examine the hypothesis. The findings of our empirical study indicate that user' behavior in online social network is indeed influenced by his friends and his decision is significantly affected by the number of groups that these friends belong to, which we call structural diversity.

Virtual socialization in adults with spina bifida.

PubMed

Chan, Wendy M; Dicianno, Brad E

2011-03-01

To use spina bifida (SB) as a model of chronic physical disability to study the associations of virtual socialization, friendships, and quality of life (QOL) in adults. Cross-sectional survey. Subjects were recruited from residential living facilities, outpatient clinics, and the University of Pittsburgh Medical Center (UPMC) research registry. Inclusion criteria were age between 18 and 80 years and clinical diagnoses of SB cystica (myelomeningocele) and hydrocephalus. The exclusion criterion was the diagnosis of SB occulta. Sixty-three eligible adults were enrolled, and all completed the study. The survey via questionnaire was performed in person or over the telephone. Data collected included the World Health Organization's Medical Outcomes Study 26-item Short Form, Economic Self-Sufficiency from the Craig Handicap Assessment and Reporting Technique Short Form, virtual socializing habits, and number of friends. Three linear regression models were performed, each with a unique dependent variable: number of friends, psychological QOL, or social QOL. The following independent variables were included in all models: age, gender, ethnicity, economic self-sufficiency, marital status, education level, lesion level, health status, user group, collection method, and time spent virtually socializing. In addition, each regression model included the dependent variables from the other 2 models in its independent variables. Increased degree of virtual socialization (VS) was associated with a greater number of friends (P = .003, r = .684). Mean (standard deviation) numbers of friends by VS groups were the following: users, n = 4.9 ± 2.7; semi-users, n = 3.8 ± 2.7; and nonusers, n = 2.1 ± 2.3, which represent a 2.3 times greater number of friends between the users and nonusers. The effect of virtual socialization on QOL was also positive, however, not statistically significant. People with chronic physical disabilities, such as SB, are at high risk for peer rejection and long-term social avoidance. Users of the most immersive forms of virtual socialization, have more real world friends than both semi-users and nonusers. Any form of VS, whether immersive or real time, may improve the opportunity for meaningful social encounters. Prospective intervention studies are needed to elucidate whether a causal positive relationship between virtual socialization and friendships exists. Further research is needed to clarify virtual socialization's impact on QOL; however, the upward trend in all 4 domains of QOL across user groups suggests similar potential benefits. Copyright © 2011 American Academy of Physical Medicine and Rehabilitation. Published by Elsevier Inc. All rights reserved.

A Comprehensive Software and Database Management System for Glomerular Filtration Rate Estimation by Radionuclide Plasma Sampling and Serum Creatinine Methods.

PubMed

Jha, Ashish Kumar

2015-01-01

Glomerular filtration rate (GFR) estimation by plasma sampling method is considered as the gold standard. However, this method is not widely used because the complex technique and cumbersome calculations coupled with the lack of availability of user-friendly software. The routinely used Serum Creatinine method (SrCrM) of GFR estimation also requires the use of online calculators which cannot be used without internet access. We have developed user-friendly software "GFR estimation software" which gives the options to estimate GFR by plasma sampling method as well as SrCrM. We have used Microsoft Windows(®) as operating system and Visual Basic 6.0 as the front end and Microsoft Access(®) as database tool to develop this software. We have used Russell's formula for GFR calculation by plasma sampling method. GFR calculations using serum creatinine have been done using MIRD, Cockcroft-Gault method, Schwartz method, and Counahan-Barratt methods. The developed software is performing mathematical calculations correctly and is user-friendly. This software also enables storage and easy retrieval of the raw data, patient's information and calculated GFR for further processing and comparison. This is user-friendly software to calculate the GFR by various plasma sampling method and blood parameter. This software is also a good system for storing the raw and processed data for future analysis.

ASERA: A spectrum eye recognition assistant for quasar spectra

NASA Astrophysics Data System (ADS)

Yuan, Hailong; Zhang, Haotong; Zhang, Yanxia; Lei, Yajuan; Dong, Yiqiao; Zhao, Yongheng

2013-11-01

Spectral type recognition is an important and fundamental step of large sky survey projects in the data reduction for further scientific research, like parameter measurement and statistic work. It tends out to be a huge job to manually inspect the low quality spectra produced from the massive spectroscopic survey, where the automatic pipeline may not provide confident type classification results. In order to improve the efficiency and effectiveness of spectral classification, we develop a semi-automated toolkit named ASERA, ASpectrum Eye Recognition Assistant. The main purpose of ASERA is to help the user in quasar spectral recognition and redshift measurement. Furthermore it can also be used to recognize various types of spectra of stars, galaxies and AGNs (Active Galactic Nucleus). It is an interactive software allowing the user to visualize observed spectra, superimpose template spectra from the Sloan Digital Sky Survey (SDSS), and interactively access related spectral line information. It is an efficient and user-friendly toolkit for the accurate classification of spectra observed by LAMOST (the Large Sky Area Multi-object Fiber Spectroscopic Telescope). The toolkit is available in two modes: a Java standalone application and a Java applet. ASERA has a few functions, such as wavelength and flux scale setting, zoom in and out, redshift estimation, spectral line identification, which helps user to improve the spectral classification accuracy especially for low quality spectra and reduce the labor of eyeball check. The function and performance of this tool is displayed through the recognition of several quasar spectra and a late type stellar spectrum from the LAMOST Pilot survey. Its future expansion capabilities are discussed.

Old and new techniques mixed up into optical photomask measurement method

NASA Astrophysics Data System (ADS)

Fukui, Jumpei; Tachibana, Yusaku; Osanai, Makoto

2017-07-01

It has been still highly required for cost efficient solution with easy operation for full-automated CD measurement for line width about 500nm up to 5μm on photomask, because it is frequently use such photomask in the process of manufacturing MEMS sensor for IoT and some devices made in BCD (Bipola CMOS DMOS). As reply to such demand in photomask manufacturing field, we try to take a low noise digital camera technology and LED light source for i-line, which are recently developed, into new measuring tool in order to achieve 1nm (3σ) repeatability for line width measurement between 300nm to 10μm. In addition, for the purpose of full-automated operation, it is very important to find where an initial target line in dense pattern. To achieve such auto line detection precisely, we have improved accuracy of high precision stage (20nm as 3σ) and an alignment algorithm of MEMS Stepper to combine with this tool. As for user-friendly interface, Windows based software helps a lot for not only the operation but also recipe creation or edition in Excel. Actually, in the MEMS manufacturing process, there are various photomasks which need to be check and measure frequently therefore various recipe files are also have to be created and edited frequently.. In order to meet such a requirement in photomask management, we try to make it true by mixing old and new techniques together into one system, which comes to fully automated and cost efficient tool with 1nm repeatability in CD measurement.

Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks

PubMed Central

Beal, Jacob; Lu, Ting; Weiss, Ron

2011-01-01

Background The field of synthetic biology promises to revolutionize our ability to engineer biological systems, providing important benefits for a variety of applications. Recent advances in DNA synthesis and automated DNA assembly technologies suggest that it is now possible to construct synthetic systems of significant complexity. However, while a variety of novel genetic devices and small engineered gene networks have been successfully demonstrated, the regulatory complexity of synthetic systems that have been reported recently has somewhat plateaued due to a variety of factors, including the complexity of biology itself and the lag in our ability to design and optimize sophisticated biological circuitry. Methodology/Principal Findings To address the gap between DNA synthesis and circuit design capabilities, we present a platform that enables synthetic biologists to express desired behavior using a convenient high-level biologically-oriented programming language, Proto. The high level specification is compiled, using a regulatory motif based mechanism, to a gene network, optimized, and then converted to a computational simulation for numerical verification. Through several example programs we illustrate the automated process of biological system design with our platform, and show that our compiler optimizations can yield significant reductions in the number of genes () and latency of the optimized engineered gene networks. Conclusions/Significance Our platform provides a convenient and accessible tool for the automated design of sophisticated synthetic biological systems, bridging an important gap between DNA synthesis and circuit design capabilities. Our platform is user-friendly and features biologically relevant compiler optimizations, providing an important foundation for the development of sophisticated biological systems. PMID:21850228

Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks.

PubMed

Beal, Jacob; Lu, Ting; Weiss, Ron

2011-01-01

The field of synthetic biology promises to revolutionize our ability to engineer biological systems, providing important benefits for a variety of applications. Recent advances in DNA synthesis and automated DNA assembly technologies suggest that it is now possible to construct synthetic systems of significant complexity. However, while a variety of novel genetic devices and small engineered gene networks have been successfully demonstrated, the regulatory complexity of synthetic systems that have been reported recently has somewhat plateaued due to a variety of factors, including the complexity of biology itself and the lag in our ability to design and optimize sophisticated biological circuitry. To address the gap between DNA synthesis and circuit design capabilities, we present a platform that enables synthetic biologists to express desired behavior using a convenient high-level biologically-oriented programming language, Proto. The high level specification is compiled, using a regulatory motif based mechanism, to a gene network, optimized, and then converted to a computational simulation for numerical verification. Through several example programs we illustrate the automated process of biological system design with our platform, and show that our compiler optimizations can yield significant reductions in the number of genes (~ 50%) and latency of the optimized engineered gene networks. Our platform provides a convenient and accessible tool for the automated design of sophisticated synthetic biological systems, bridging an important gap between DNA synthesis and circuit design capabilities. Our platform is user-friendly and features biologically relevant compiler optimizations, providing an important foundation for the development of sophisticated biological systems.

TWIST User Presentation

EPA Pesticide Factsheets

The Wastewater Information System Tool (TWIST) is downloadable, user-friendly management tool that will allow state and local health departments to effectively inventory and manage small wastewater treatment systems in their jurisdictions.

Developing Automated Feedback Materials for a Training Simulator: An Interaction between Users and Researchers.

ERIC Educational Resources Information Center

Shlechter, Theodore M.; And Others

This paper focuses upon the research and development (R&D) process associated with developing automated feedback materials for the SIMulation NETworking (SIMNET) training system. This R&D process involved a partnership among instructional developers, practitioners, and researchers. Users' input has been utilized to help: (1) design the…

ARES: automated response function code. Users manual. [HPGAM and LSQVM

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

Maung, T.; Reynolds, G.M.

This ARES user's manual provides detailed instructions for a general understanding of the Automated Response Function Code and gives step by step instructions for using the complete code package on a HP-1000 system. This code is designed to calculate response functions of NaI gamma-ray detectors, with cylindrical or rectangular geometries.

The use of Graphic User Interface for development of a user-friendly CRS-Stack software

NASA Astrophysics Data System (ADS)

Sule, Rachmat; Prayudhatama, Dythia; Perkasa, Muhammad D.; Hendriyana, Andri; Fatkhan; Sardjito; Adriansyah

2017-04-01

The development of a user-friendly Common Reflection Surface (CRS) Stack software that has been built by implementing Graphical User Interface (GUI) is described in this paper. The original CRS-Stack software developed by WIT Consortium is compiled in the unix/linux environment, which is not a user-friendly software, so that a user must write the commands and parameters manually in a script file. Due to this limitation, the CRS-Stack become a non popular method, although applying this method is actually a promising way in order to obtain better seismic sections, which have better reflector continuity and S/N ratio. After obtaining successful results that have been tested by using several seismic data belong to oil companies in Indonesia, it comes to an idea to develop a user-friendly software in our own laboratory. Graphical User Interface (GUI) is a type of user interface that allows people to interact with computer programs in a better way. Rather than typing commands and module parameters, GUI allows the users to use computer programs in much simple and easy. Thus, GUI can transform the text-based interface into graphical icons and visual indicators. The use of complicated seismic unix shell script can be avoided. The Java Swing GUI library is used to develop this CRS-Stack GUI. Every shell script that represents each seismic process is invoked from Java environment. Besides developing interactive GUI to perform CRS-Stack processing, this CRS-Stack GUI is design to help geophysicists to manage a project with complex seismic processing procedures. The CRS-Stack GUI software is composed by input directory, operators, and output directory, which are defined as a seismic data processing workflow. The CRS-Stack processing workflow involves four steps; i.e. automatic CMP stack, initial CRS-Stack, optimized CRS-Stack, and CRS-Stack Supergather. Those operations are visualized in an informative flowchart with self explanatory system to guide the user inputting the parameter values for each operation. The knowledge of CRS-Stack processing procedure is still preserved in the software, which is easy and efficient to be learned. The software will still be developed in the future. Any new innovative seismic processing workflow will also be added into this GUI software.

Developing an automated water emitting-sensing system, based on integral tensiometers placed in homogenous environment.

NASA Astrophysics Data System (ADS)

Dabach, Sharon; Shani, Uri

2010-05-01

As the population grows, irrigated agriculture is using more water and fertilizers to supply the growing food demand. However, the uptake by various plants is only 30 to 50% of the water applied. The remaining water flows to surface water and groundwater and causes their contamination by fertilizers or other toxins such as herbicides or pesticides. To improve the water use efficiency of crops and decrease the drainage below the root zone, irrigation water should be applied according to the plant demand. The aim of this work is to develop an automated irrigation system based on real-time feedback from an inexpensive and reliable integrated sensing system. This system will supply water to plants according to their demand, without any user interference during the entire growth season. To achieve this goal a sensor (Geo-Tensiometer) was designed and tested. This sensor has better contact with the surrounding soil, is more reliable and much cheaper than the ceramic cup tensiometer. A lysimeter experiment was conducted to evaluate a subsurface drip irrigation regime based on the Geo-Tensiometer and compare it to a daily irrigation regime. All of the drippers were wrapped in Geo-textile. By integrating the Geo-Tensiometer within the Geo-textile which surrounds the drippers, we created a homogenous media in the entire lysimeter in which the reading of the matric potential takes place. This media, the properties of which are set and known to us, encourages root growth therein. Root density in this media is very high; therefore most of the plant water uptake is from this area. The irrigation system in treatment A irrigated when the matric potential reached a threshold which was set every morning automatically by the system. The daily treatment included a single irrigation each morning that was set to return 120% of the evapotranspiration of the previous day. All Geo-Tensiometers were connected to an automated washing system, that flushed air trapped in the Geo-Tensiometers. In treatment A, the system discharge changed according to the plant water demand. The discharge changes followed the water uptake changes during the day and during the entire growth period without any user interference. The integration of Geo-Tensiometer into the emitter system, together with the irrigation regime, maintained high and constant water content in the root zone in comparison to other irrigation methods, such as daily drip irrigation. Reading the matric potential in this media yielded better indication of water availability to the plants than sensors placed 3 cm from the emitters. In addition, the amount of water drainage below the root zone decreased significantly and therefore the threat of polluting groundwater. Furthermore, the automated flushing system eliminated the need for manual maintenance of the tensiometers creating a user friendly system.

Assessing user acceptance towards automated and conventional sink use for hand decontamination using the technology acceptance model.

PubMed

Dawson, Carolyn H; Mackrill, Jamie B; Cain, Rebecca

2017-12-01

Hand hygiene (HH) prevents harmful contaminants spreading in settings including domestic, health care and food handling. Strategies to improve HH range from behavioural techniques through to automated sinks that ensure hand surface cleaning. This study aimed to assess user experience and acceptance towards a new automated sink, compared to a normal sink. An adapted version of the technology acceptance model (TAM) assessed each mode of handwashing. A within-subjects design enabled N = 46 participants to evaluate both sinks. Perceived Ease of Use and Satisfaction of Use were significantly lower for the automated sink, compared to the conventional sink (p < 0.005). Across the remaining TAM factors, there was no significant difference. Participants suggested design features including jet strength, water temperature and device affordance may improve HH technology. We provide recommendations for future HH technology development to contribute a positive user experience, relevant to technology developers, ergonomists and those involved in HH across all sectors. Practitioner Summary: The need to facilitate timely, effective hand hygiene to prevent illness has led to a rise in automated handwashing systems across different contexts. User acceptance is a key factor in system uptake. This paper applies the technology acceptance model as a means to explore and optimise the design of such systems.

Analysis of Delays in Transmitting Time Code Using an Automated Computer Time Distribution System

DTIC Science & Technology

1999-12-01

jlevine@clock. bldrdoc.gov Abstract An automated computer time distribution system broadcasts standard tune to users using computers and modems via...contributed to &lays - sofhareplatform (50% of the delay), transmission speed of time- codes (25OA), telephone network (lS%), modem and others (10’4). The... modems , and telephone lines. Users dial the ACTS server to receive time traceable to the national time scale of Singapore, UTC(PSB). The users can in

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.

A Helping Hand.

ERIC Educational Resources Information Center

Renner, Jason M.

2000-01-01

Discusses how designing a hand washing-friendly environment can help to reduce the spread of germs in school restrooms. Use of electronic faucets, surface risk management, traffic flow, and user- friendly hand washing systems that are convenient and maximally hygienic are examined. (GR)

Web-Based Family Life Education: Spotlight on User Experience

ERIC Educational Resources Information Center

Doty, Jennifer; Doty, Matthew; Dwrokin, Jodi

2011-01-01

Family Life Education (FLE) websites can benefit from the field of user experience, which makes technology easy to use. A heuristic evaluation of five FLE sites was performed using Neilson's heuristics, guidelines for making sites user friendly. Greater site complexity resulted in more potential user problems. Sites most frequently had problems…

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.

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.

Automated information retrieval using CLIPS

NASA Technical Reports Server (NTRS)

Raines, Rodney Doyle, III; Beug, James Lewis

1991-01-01

Expert systems have considerable potential to assist computer users in managing the large volume of information available to them. One possible use of an expert system is to model the information retrieval interests of a human user and then make recommendations to the user as to articles of interest. At Cal Poly, a prototype expert system written in the C Language Integrated Production System (CLIPS) serves as an Automated Information Retrieval System (AIRS). AIRS monitors a user's reading preferences, develops a profile of the user, and then evaluates items returned from the information base. When prompted by the user, AIRS returns a list of items of interest to the user. In order to minimize the impact on system resources, AIRS is designed to run in the background during periods of light system use.

Quora.com: Another Place for Users to Ask Questions

ERIC Educational Resources Information Center

Ovadia, Steven

2011-01-01

Quora (www.quora.com) is a contemporary, web-based take on reference. Users post questions within Quora and other users answer the questions. Users can vote for and against answers (or not vote at all). It is users asking questions of friends and strangers and then sorting through the results. If the model sounds familiar, it's because it is.…

Evaluation of rapid readout biological indicators for 132 degrees C gravity and 132 degrees C vacuum-assisted steam sterilization cycles using a new automated fluorescent reader.

PubMed

Alfa, Michelle J; Olson, Nancy; DeGagne, Pat; Jackson, Michele

2002-07-01

The primary objective of this study was to evaluate fluorescent readout results of Attest 1291 Biological Indicators (BIs) (3M Health Care, St. Paul, MN) and Attest 1296 BI test packs (containing Attest 1292 BIs) using full and fractional cycles compared with the growth data when prolonged incubation (7 days) was included. Gravity displacement and vacuum-assisted steam sterilization cycles were evaluated. A secondary objective of this study was to evaluate the new automated rapid fluorescent reader (Attest 290 Auto Reader). The rapid readout BIs for gravity displacement and vacuum-assisted steam autoclave cycles at 132 degrees C were processed using full (4 minutes) and four fractional cycles that provided 30% to 80% positive results for growth after 24 hours of incubation (48 hours of incubation for Attest 1292 BIs from the Attest 1296 test packs). Sixty of each type of BI were tested for each cycle (300 of each BI type in total). For all full steam sterilization cycles, results of the rapid fluorescent readout and the 24-hour, 48-hour, and 7-day growth tests were negative for all Attest 1291 and 1292 BIs tested. For all fractional cycles, the 24- and 48-hour growth results for the Attest 1291 and 1292 BIs, respectively, were the same as the 7-day growth results. The fractional cycle data indicated that fluorescent rapid readout was a more sensitive indicator than growth. There were rare (0.9%) false-negative results for BIs under fractional cycle conditions and these all correlated with short fractional cycle exposure times. The fluorescent rapid readout results of the 1291 BIs and 1296 BI test packs reliably predict both 24- and 48-hour and 7-day growth. These data support the value of rapid readout BIs for sterilizer monitoring for both the vacuum-assisted and the gravity displacement steam sterilization cycles. The new automated reader requires less manipulation of the BI and makes monitoring user friendly and less prone to user errors.

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.

Stage Evolution of Office Automation Technological Change and Organizational Learning.

ERIC Educational Resources Information Center

Sumner, Mary

1985-01-01

A study was conducted to identify stage characteristics in terms of technology, applications, the role and responsibilities of the office automation organization, and planning and control strategies; and to describe the respective roles of data processing professionals, office automation analysts, and users in office automation systems development…

Implementing a low-cost web-based clinical trial management system for community studies: a case study.

PubMed

Geyer, John; Myers, Kathleen; Vander Stoep, Ann; McCarty, Carolyn; Palmer, Nancy; DeSalvo, Amy

2011-10-01

Clinical trials with multiple intervention locations and a single research coordinating center can be logistically difficult to implement. Increasingly, web-based systems are used to provide clinical trial support with many commercial, open source, and proprietary systems in use. New web-based tools are available which can be customized without programming expertise to deliver web-based clinical trial management and data collection functions. To demonstrate the feasibility of utilizing low-cost configurable applications to create a customized web-based data collection and study management system for a five intervention site randomized clinical trial establishing the efficacy of providing evidence-based treatment via teleconferencing to children with attention-deficit hyperactivity disorder. The sites are small communities that would not usually be included in traditional randomized trials. A major goal was to develop database that participants could access from computers in their home communities for direct data entry. Discussed is the selection process leading to the identification and utilization of a cost-effective and user-friendly set of tools capable of customization for data collection and study management tasks. An online assessment collection application, template-based web portal creation application, and web-accessible Access 2007 database were selected and customized to provide the following features: schedule appointments, administer and monitor online secure assessments, issue subject incentives, and securely transmit electronic documents between sites. Each tool was configured by users with limited programming expertise. As of June 2011, the system has successfully been used with 125 participants in 5 communities, who have completed 536 sets of assessment questionnaires, 8 community therapists, and 11 research staff at the research coordinating center. Total automation of processes is not possible with the current set of tools as each is loosely affiliated, creating some inefficiency. This system is best suited to investigations with a single data source e.g., psychosocial questionnaires. New web-based applications can be used by investigators with limited programming experience to implement user-friendly, efficient, and cost-effective tools for multi-site clinical trials with small distant communities. Such systems allow the inclusion in research of populations that are not usually involved in clinical trials.

NaviSE: superenhancer navigator integrating epigenomics signal algebra.

PubMed

Ascensión, Alex M; Arrospide-Elgarresta, Mikel; Izeta, Ander; Araúzo-Bravo, Marcos J

2017-06-06

Superenhancers are crucial structural genomic elements determining cell fate, and they are also involved in the determination of several diseases, such as cancer or neurodegeneration. Although there are pipelines which use independent pieces of software to predict the presence of superenhancers from genome-wide chromatin marks or DNA-interaction protein binding sites, there is not yet an integrated software tool that processes automatically algebra combinations of raw data sequencing into a comprehensive final annotated report of predicted superenhancers. We have developed NaviSE, a user-friendly streamlined tool which performs a fully-automated parallel processing of genome-wide epigenomics data from sequencing files into a final report, built with a comprehensive set of annotated files that are navigated through a graphic user interface dynamically generated by NaviSE. NaviSE also implements an 'epigenomics signal algebra' that allows the combination of multiple activation and repression epigenomics signals. NaviSE provides an interactive chromosomal landscaping of the locations of superenhancers, which can be navigated to obtain annotated information about superenhancer signal profile, associated genes, gene ontology enrichment analysis, motifs of transcription factor binding sites enriched in superenhancers, graphs of the metrics evaluating the superenhancers quality, protein-protein interaction networks and enriched metabolic pathways among other features. We have parallelised the most time-consuming tasks achieving a reduction up to 30% for a 15 CPUs machine. We have optimized the default parameters of NaviSE to facilitate its use. NaviSE allows different entry levels of data processing, from sra-fastq files to bed files; and unifies the processing of multiple replicates. NaviSE outperforms the more time-consuming processes required in a non-integrated pipeline. Alongside its high performance, NaviSE is able to provide biological insights, predicting cell type specific markers, such as SOX2 and ZIC3 in embryonic stem cells, CDK5R1 and REST in neurons and CD86 and TLR2 in monocytes. NaviSE is a user-friendly streamlined solution for superenhancer analysis, annotation and navigation, requiring only basic computer and next generation sequencing knowledge. NaviSE binaries and documentation are available at: https://sourceforge.net/projects/navise-superenhancer/ .

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.

Automated Glacier Surface Velocity using Multi-Image/Multi-Chip (MIMC) Feature Tracking

NASA Astrophysics Data System (ADS)

Ahn, Y.; Howat, I. M.

2009-12-01

Remote sensing from space has enabled effective monitoring of remote and inhospitable polar regions. Glacier velocity, and its variation in time, is one of the most important parameters needed to understand glacier dynamics, glacier mass balance and contribution to sea level rise. Regular measurements of ice velocity are possible from large and accessible satellite data set archives, such as ASTER and LANDSAT-7. Among satellite imagery, optical imagery (i.e. passive, visible to near-infrared band sensors) provides abundant data with optimal spatial resolution and repeat interval for tracking glacier motion at high temporal resolution. Due to massive amounts of data, computation of ice velocity from feature tracking requires 1) user-friendly interface, 2) minimum local/user parameter inputs and 3) results that need minimum editing. We focus on robust feature tracking, applicable to all currently available optical satellite imagery, that is ASTER, SPOT and LANDSAT etc. We introduce the MIMC (multiple images/multiple chip sizes) matching approach that does not involve any user defined local/empirical parameters except approximate average glacier speed. We also introduce a method for extracting velocity from LANDSAT-7 SLC-off data, which has 22 percent of scene data missing in slanted strips due to failure of the scan line corrector. We apply our approach to major outlet glaciers in west/east Greenland and assess our MIMC feature tracking technique by comparison with conventional correlation matching and other methods (e.g. InSAR).

Toward intelligent information system

NASA Astrophysics Data System (ADS)

Komatsu, Sanzo

NASA/RECON, the predecessor of DIALOG System, was originally designed as a user friendly system for astronauts, so that they should not miss-operate the machine in spite of tension in the outer space. Since then, DIALOG has endeavoured to develop a series of user friendly systems, such as knowledge index, inbound gateway, as well as Version II. In this so-called end user searching era, DIALOG has released a series of front end systems successively; DIALOG Business Connection, DIALOG Medical Connection and OneSearch in 1986, early and late 1987 respectively. They are all called expert systems. In this paper, the features of each system are described in some detail and the remaining critical issues are also discussed.

Electric-powered indoor/outdoor wheelchairs (EPIOCs): users' views of influence on family, friends and carers.

PubMed

Frank, Andrew; Neophytou, Claudius; Frank, Julia; de Souza, Lorraine

2010-01-01

This study explored the effects of electric-powered indoor/outdoor wheelchair (EPIOC) provision to users on their family and carers. EPIOC users receiving their chairs between February and November 2002 (N = 74) were invited to participate in a telephone questionnaire/interview, and 64 agreed. This study examined the responses to the question 'Has the use of your EPIOC affected your family or friends in any way?' and related comments. Interviews were analysed using a qualitative framework approach to identify emergent themes. In addition, the proportion of individuals raising issues related to each theme was determined. Participants were interviewed 10-19 (mean = 14.3) months after chair delivery. The following themes emerged: reduced physical burden on family/friends and increased independence and freedom. However, an EPIOC does not eliminate other practical problems particularly during transportation and negotiating kerbs and slopes. Users also reported anxiety/worry in relationship to EPIOC use, e.g., weather conditions, personal safety (muggings), use of ramps and kerbs. There are considerable benefits to families and carers associated with powered wheelchair use. A reduction in the physical demand for pushing and increased freedom were identified. These benefits appear to outweigh the residual practical difficulties and worries.

Millikelvin cryocooler for space- and ground-based detector systems

NASA Astrophysics Data System (ADS)

Bartlett, J.; Hardy, G.; Hepburn, I.; Milward, S.; Coker, P.; Theobald, C.

2012-09-01

This paper describes the design of a continuously operating millikelvin cryocooler (mKCC) and its origins. It takes heritage from the double adiabatic demagnetization refrigerator (dADR) which was built for the European Space Agency (ESA). The compact design is based on a tandem configuration continuous ADR which alternately cycles two dADRs. The mKCC is a single module (dimensions 355 x 56 x120 mm) which operates from a 4 K bath (liquid or cryocooler) and provides an interface to the user which is settable from < 100 mK to 4 K. Predicted maximum cooling power at 100 mK is 7μW. It will use only single crystal tungsten magnetoresistive heat switches (the first ADR cooler to do so) and the measured thermal performance of these heat switches is presented. The mKCC uses ten shielded 2 Tesla superconducting magnets capable of ramping to full field in 20 - 30 seconds. This has been demonstrated in the lab and the results are given for the successful performance of a prototype Chromium Potassium Alum (CPA) pill using one of these magnets. The mKCC has been designed to be fully automated and user friendly with the aim of expanding the use of millikelvin cryogenics and providing a good testing and operating platform for detector systems.

Towards adaptive, streaming analysis of x-ray tomography data

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

Thomas, Mathew; Kleese van Dam, Kerstin; Marshall, Matthew J.

2015-03-04

Temporal and spatial resolution of chemical imaging methodologies such as x-ray tomography are rapidly increasing, leading to more complex experimental procedures and fast growing data volumes. Automated analysis pipelines and big data analytics are becoming essential to effectively evaluate the results of such experiments. Offering those data techniques in an adaptive, streaming environment can further substantially improve the scientific discovery process, by enabling experimental control and steering based on the evaluation of emerging phenomena as they are observed by the experiment. Pacific Northwest National Laboratory (PNNL)’ Chemical Imaging Initiative (CII - http://imaging.pnnl.gov/ ) has worked since 2011 towards developing amore » framework that allows users to rapidly compose and customize high throughput experimental analysis pipelines for multiple instrument types. The framework, named ‘Rapid Experimental Analysis’ (REXAN) Framework [1], is based on the idea of reusable component libraries and utilizes the PNNL developed collaborative data management and analysis environment ‘Velo’, to provide a user friendly analysis and data management environment for experimental facilities. This article will, discuss the capabilities established for X-Ray tomography, discuss lessons learned, and provide an overview of our more recent work in the Analysis in Motion Initiative (AIM - http://aim.pnnl.gov/ ) at PNNL to provide REXAN capabilities in a streaming environment.« less

PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways.

PubMed

Demir, E; Babur, O; Dogrusoz, U; Gursoy, A; Nisanci, G; Cetin-Atalay, R; Ozturk, M

2002-07-01

Availability of the sequences of entire genomes shifts the scientific curiosity towards the identification of function of the genomes in large scale as in genome studies. In the near future, data produced about cellular processes at molecular level will accumulate with an accelerating rate as a result of proteomics studies. In this regard, it is essential to develop tools for storing, integrating, accessing, and analyzing this data effectively. We define an ontology for a comprehensive representation of cellular events. The ontology presented here enables integration of fragmented or incomplete pathway information and supports manipulation and incorporation of the stored data, as well as multiple levels of abstraction. Based on this ontology, we present the architecture of an integrated environment named Patika (Pathway Analysis Tool for Integration and Knowledge Acquisition). Patika is composed of a server-side, scalable, object-oriented database and client-side editors to provide an integrated, multi-user environment for visualizing and manipulating network of cellular events. This tool features automated pathway layout, functional computation support, advanced querying and a user-friendly graphical interface. We expect that Patika will be a valuable tool for rapid knowledge acquisition, microarray generated large-scale data interpretation, disease gene identification, and drug development. A prototype of Patika is available upon request from the authors.

SCALE Code System 6.2.2

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

Rearden, Bradley T.; Jessee, Matthew Anderson

The SCALE Code System is a widely used modeling and simulation suite for nuclear safety analysis and design that is developed, maintained, tested, and managed by the Reactor and Nuclear Systems Division (RNSD) of Oak Ridge National Laboratory (ORNL). SCALE provides a comprehensive, verified and validated, user-friendly tool set for criticality safety, reactor physics, radiation shielding, radioactive source term characterization, and sensitivity and uncertainty analysis. Since 1980, regulators, licensees, and research institutions around the world have used SCALE for safety analysis and design. SCALE provides an integrated framework with dozens of computational modules including 3 deterministic and 3 Monte Carlomore » radiation transport solvers that are selected based on the desired solution strategy. SCALE includes current nuclear data libraries and problem-dependent processing tools for continuous-energy (CE) and multigroup (MG) neutronics and coupled neutron-gamma calculations, as well as activation, depletion, and decay calculations. SCALE includes unique capabilities for automated variance reduction for shielding calculations, as well as sensitivity and uncertainty analysis. SCALE’s graphical user interfaces assist with accurate system modeling, visualization of nuclear data, and convenient access to desired results. SCALE 6.2 represents one of the most comprehensive revisions in the history of SCALE, providing several new capabilities and significant improvements in many existing features.« less

User-friendly freehand ultrasound calibration using Lego bricks and automatic registration.

PubMed

Xiao, Yiming; Yan, Charles Xiao Bo; Drouin, Simon; De Nigris, Dante; Kochanowska, Anna; Collins, D Louis

2016-09-01

As an inexpensive, noninvasive, and portable clinical imaging modality, ultrasound (US) has been widely employed in many interventional procedures for monitoring potential tissue deformation, surgical tool placement, and locating surgical targets. The application requires the spatial mapping between 2D US images and 3D coordinates of the patient. Although positions of the devices (i.e., ultrasound transducer) and the patient can be easily recorded by a motion tracking system, the spatial relationship between the US image and the tracker attached to the US transducer needs to be estimated through an US calibration procedure. Previously, various calibration techniques have been proposed, where a spatial transformation is computed to match the coordinates of corresponding features in a physical phantom and those seen in the US scans. However, most of these methods are difficult to use for novel users. We proposed an ultrasound calibration method by constructing a phantom from simple Lego bricks and applying an automated multi-slice 2D-3D registration scheme without volumetric reconstruction. The method was validated for its calibration accuracy and reproducibility. Our method yields a calibration accuracy of [Formula: see text] mm and a calibration reproducibility of 1.29 mm. We have proposed a robust, inexpensive, and easy-to-use ultrasound calibration method.

UManSysProp: an online facility for molecular property prediction and atmospheric aerosol calculations

NASA Astrophysics Data System (ADS)

Topping, D.; Barley, M. H.; Bane, M.; Higham, N.; Aumont, B.; McFiggans, G.

2015-11-01

In this paper we describe the development and application of a new web based facility, UManSysProp (http://umansysprop.seaes.manchester.ac.uk), for automating predictions of molecular and atmospheric aerosol properties. Current facilities include: pure component vapour pressures, critical properties and sub-cooled densities of organic molecules; activity coefficient predictions for mixed inorganic-organic liquid systems; hygroscopic growth factors and CCN activation potential of mixed inorganic/organic aerosol particles; absorptive partitioning calculations with/without a treatment of non-ideality. The aim of this new facility is to provide a single point of reference for all properties relevant to atmospheric aerosol that have been checked for applicability to atmospheric compounds where possible. The group contribution approach allows users to upload molecular information in the form of SMILES strings and UManSysProp will automatically extract the relevant information for calculations. Built using open source chemical informatics, and hosted at the University of Manchester, the facilities are provided via a browser and device-friendly web-interface, or can be accessed using the user's own code via a JSON API. In this paper we demonstrate its use with specific examples that can be simulated using the web-browser interface.

EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries

PubMed Central

Smith, Robin P; Buchser, William J; Lemmon, Marcus B; Pardinas, Jose R; Bixby, John L; Lemmon, Vance P

2008-01-01

Background Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. Results We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization. Conclusion EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects. PMID:18402700

QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts

PubMed Central

Ribeiro, João V.; Bernardi, Rafael C.; Rudack, Till; Stone, John E.; Phillips, James C.; Freddolino, Peter L.; Schulten, Klaus

2016-01-01

The proper functioning of biomolecules in living cells requires them to assume particular structures and to undergo conformational changes. Both biomolecular structure and motion can be studied using a wide variety of techniques, but none offers the level of detail as do molecular dynamics (MD) simulations. Integrating two widely used modeling programs, namely NAMD and VMD, we have created a robust, user-friendly software, QwikMD, which enables novices and experts alike to address biomedically relevant questions, where often only molecular dynamics simulations can provide answers. Performing both simple and advanced MD simulations interactively, QwikMD automates as many steps as necessary for preparing, carrying out, and analyzing simulations while checking for common errors and enabling reproducibility. QwikMD meets also the needs of experts in the field, increasing the efficiency and quality of their work by carrying out tedious or repetitive tasks while enabling easy control of every step. Whether carrying out simulations within the live view mode on a small laptop or performing complex and large simulations on supercomputers or Cloud computers, QwikMD uses the same steps and user interface. QwikMD is freely available by download on group and personal computers. It is also available on the cloud at Amazon Web Services. PMID:27216779

EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries.

PubMed

Smith, Robin P; Buchser, William J; Lemmon, Marcus B; Pardinas, Jose R; Bixby, John L; Lemmon, Vance P

2008-04-10

Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization. EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects.

QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts

NASA Astrophysics Data System (ADS)

Ribeiro, João V.; Bernardi, Rafael C.; Rudack, Till; Stone, John E.; Phillips, James C.; Freddolino, Peter L.; Schulten, Klaus

2016-05-01

The proper functioning of biomolecules in living cells requires them to assume particular structures and to undergo conformational changes. Both biomolecular structure and motion can be studied using a wide variety of techniques, but none offers the level of detail as do molecular dynamics (MD) simulations. Integrating two widely used modeling programs, namely NAMD and VMD, we have created a robust, user-friendly software, QwikMD, which enables novices and experts alike to address biomedically relevant questions, where often only molecular dynamics simulations can provide answers. Performing both simple and advanced MD simulations interactively, QwikMD automates as many steps as necessary for preparing, carrying out, and analyzing simulations while checking for common errors and enabling reproducibility. QwikMD meets also the needs of experts in the field, increasing the efficiency and quality of their work by carrying out tedious or repetitive tasks while enabling easy control of every step. Whether carrying out simulations within the live view mode on a small laptop or performing complex and large simulations on supercomputers or Cloud computers, QwikMD uses the same steps and user interface. QwikMD is freely available by download on group and personal computers. It is also available on the cloud at Amazon Web Services.

Intelligent Agent Technology

NASA Technical Reports Server (NTRS)

1996-01-01

Open Sesame! is the first commercial software product that learns user's behavior, and offers automation and coaching suggestions to the user. The neural learning module looks for repetitive patterns that have not been automated; when it finds one, it creates an observation and, upon approval, automates the task. The manufacturer, Charles River Analytics, credits Langley Research Center and Johnson Space Center Small Business Innovation Research grants and the time the president and vice president spent at the two centers in the 1970s as being essential to the development of their product line.

Designing for flexible interaction between humans and automation: delegation interfaces for supervisory control.

PubMed

Miller, Christopher A; Parasuraman, Raja

2007-02-01

To develop a method enabling human-like, flexible supervisory control via delegation to automation. Real-time supervisory relationships with automation are rarely as flexible as human task delegation to other humans. Flexibility in human-adaptable automation can provide important benefits, including improved situation awareness, more accurate automation usage, more balanced mental workload, increased user acceptance, and improved overall performance. We review problems with static and adaptive (as opposed to "adaptable") automation; contrast these approaches with human-human task delegation, which can mitigate many of the problems; and revise the concept of a "level of automation" as a pattern of task-based roles and authorizations. We argue that delegation requires a shared hierarchical task model between supervisor and subordinates, used to delegate tasks at various levels, and offer instruction on performing them. A prototype implementation called Playbook is described. On the basis of these analyses, we propose methods for supporting human-machine delegation interactions that parallel human-human delegation in important respects. We develop an architecture for machine-based delegation systems based on the metaphor of a sports team's "playbook." Finally, we describe a prototype implementation of this architecture, with an accompanying user interface and usage scenario, for mission planning for uninhabited air vehicles. Delegation offers a viable method for flexible, multilevel human-automation interaction to enhance system performance while maintaining user workload at a manageable level. Most applications of adaptive automation (aviation, air traffic control, robotics, process control, etc.) are potential avenues for the adaptable, delegation approach we advocate. We present an extended example for uninhabited air vehicle mission planning.

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…

Enhancing reproducibility of ultrasonic measurements by new users

NASA Astrophysics Data System (ADS)

Pramanik, Manojit; Gupta, Madhumita; Krishnan, Kajoli Banerjee

2013-03-01

Perception of operator influences ultrasound image acquisition and processing. Lower costs are attracting new users to medical ultrasound. Anticipating an increase in this trend, we conducted a study to quantify the variability in ultrasonic measurements made by novice users and identify methods to reduce it. We designed a protocol with four presets and trained four new users to scan and manually measure the head circumference of a fetal phantom with an ultrasound scanner. In the first phase, the users followed this protocol in seven distinct sessions. They then received feedback on the quality of the scans from an expert. In the second phase, two of the users repeated the entire protocol aided by visual cues provided to them during scanning. We performed off-line measurements on all the images using a fully automated algorithm capable of measuring the head circumference from fetal phantom images. The ground truth (198.1±1.6 mm) was based on sixteen scans and measurements made by an expert. Our analysis shows that: (1) the inter-observer variability of manual measurements was 5.5 mm, whereas the inter-observer variability of automated measurements was only 0.6 mm in the first phase (2) consistency of image appearance improved and mean manual measurements was 4-5 mm closer to the ground truth in the second phase (3) automated measurements were more precise, accurate and less sensitive to different presets compared to manual measurements in both phases. Our results show that visual aids and automation can bring more reproducibility to ultrasonic measurements made by new users.

Intelligence Preparation of the Battlefield (Automated) IPB(A).

DTIC Science & Technology

1980-02-14

courses of action as the basis for friendly operations planninq. The commander’s intelligence system must handle timely combat information...through A8 represent the series of snapshots developed for Option A. Snapshots would be developed for each ontion, and stored in an automated file for ...process throughout a battle situation demands local ability to modify the IPB products stored in the system, and to develop new ones as enemy courses

Development and preliminary data on the use of a mobile app specifically designed to increase community awareness of invasive pneumococcal disease and its prevention.

PubMed

Panatto, Donatella; Domnich, Alexander; Gasparini, Roberto; Bonanni, Paolo; Icardi, Giancarlo; Amicizia, Daniela; Arata, Lucia; Bragazzi, Nicola Luigi; Signori, Alessio; Landa, Paolo; Bechini, Angela; Boccalini, Sara

2016-04-02

Given the growing use and great potential of mobile apps, this project aimed to develop and implement a user-friendly app to increase laypeople's knowledge and awareness of invasive pneumococcal disease (IPD). Despite the heavy burden of IPD, the documented low awareness of IPD among both laypeople and healthcare professionals and far from optimal pneumococcal vaccination coverage, no app specifically targeting IPD has been developed so far. The app was designed to be maximally functional and conceived in accordance with user-centered design. Its content, layout and usability were discussed and formally tested during several workshops that involved the principal stakeholders, including experts in IPD and information technology and potential end-users. Following several workshops, it was decided that, in order to make the app more interactive, its core should be a personal "checker" of the risk of contracting IPD and a user-friendly risk-communication strategy. The checker was populated with risk factors identified through both Italian and international official guidelines. Formal evaluation of the app revealed its good readability and usability properties. A sister web site with the same content was created to achieve higher population exposure. Seven months after being launched in a price- and registration-free modality, the app, named "Pneumo Rischio," averaged 20.9 new users/day and 1.3 sessions/user. The first in-field results suggest that "Pneumo Rischio" is a promising tool for increasing the population's awareness of IPD and its prevention through a user-friendly risk checker.

Video conferencing made easy

NASA Technical Reports Server (NTRS)

Larsen, D. Gail; Schwieder, Paul R.

1993-01-01

Network video conferencing is advancing rapidly throughout the nation, and the Idaho National Engineering Laboratory (INEL), a Department of Energy (DOE) facility, is at the forefront of the development. Engineers at INEL/EG&G designed and installed a very unique DOE videoconferencing system, offering many outstanding features, that include true multipoint conferencing, user-friendly design and operation with no full-time operators required, and the potential for cost effective expansion of the system. One area where INEL/EG&G engineers made a significant contribution to video conferencing was in the development of effective, user-friendly, end station driven scheduling software. A PC at each user site is used to schedule conferences via a windows package. This software interface provides information to the users concerning conference availability, scheduling, initiation, and termination. The menus are 'mouse' controlled. Once a conference is scheduled, a workstation at the hubs monitors the network to initiate all scheduled conferences. No active operator participation is required once a user schedules a conference through the local PC; the workstation automatically initiates and terminates the conference as scheduled. As each conference is scheduled, hard copy notification is also printed at each participating site. Video conferencing is the wave of the future. The use of these user-friendly systems will save millions in lost productivity and travel cost throughout the nation. The ease of operation and conference scheduling will play a key role on the extent industry uses this new technology. The INEL/EG&G has developed a prototype scheduling system for both commercial and federal government use.

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.

Video conferencing made easy

NASA Astrophysics Data System (ADS)

Larsen, D. Gail; Schwieder, Paul R.

1993-02-01

Network video conferencing is advancing rapidly throughout the nation, and the Idaho National Engineering Laboratory (INEL), a Department of Energy (DOE) facility, is at the forefront of the development. Engineers at INEL/EG&G designed and installed a very unique DOE videoconferencing system, offering many outstanding features, that include true multipoint conferencing, user-friendly design and operation with no full-time operators required, and the potential for cost effective expansion of the system. One area where INEL/EG&G engineers made a significant contribution to video conferencing was in the development of effective, user-friendly, end station driven scheduling software. A PC at each user site is used to schedule conferences via a windows package. This software interface provides information to the users concerning conference availability, scheduling, initiation, and termination. The menus are 'mouse' controlled. Once a conference is scheduled, a workstation at the hubs monitors the network to initiate all scheduled conferences. No active operator participation is required once a user schedules a conference through the local PC; the workstation automatically initiates and terminates the conference as scheduled. As each conference is scheduled, hard copy notification is also printed at each participating site. Video conferencing is the wave of the future. The use of these user-friendly systems will save millions in lost productivity and travel cost throughout the nation. The ease of operation and conference scheduling will play a key role on the extent industry uses this new technology. The INEL/EG&G has developed a prototype scheduling system for both commercial and federal government use.

Video conferencing made easy

NASA Astrophysics Data System (ADS)

Larsen, D. G.; Schwieder, P. R.

Network video conferencing is advancing rapidly throughout the nation, and the Idaho National Engineering Laboratory (INEL), a Department of Energy (DOE) facility, is at the forefront of the development. Engineers at INEL/EG&G designed and installed a very unique DOE video conferencing system, offering many outstanding features, that include true multipoint conferencing, user-friendly design and operation with no full-time operators required, and the potential for cost effective expansion of the system. One area where INEL/EG&G engineers made a significant contribution to video conferencing was in the development of effective, user-friendly, end station driven scheduling software. A PC at each user site is used to schedule conferences via a windows package. This software interface provides information to the users concerning conference availability, scheduling, initiation, and termination. The menus are 'mouse' controlled. Once a conference is scheduled, a workstation at the hub monitors the network to initiate all scheduled conferences. No active operator participation is required once a user schedules a conference through the local PC; the workstation automatically initiates and terminates the conference as scheduled. As each conference is scheduled, hard copy notification is also printed at each participating site. Video conferencing is the wave of the future. The use of these user-friendly systems will save millions in lost productivity and travel costs throughout the nation. The ease of operation and conference scheduling will play a key role on the extent industry uses this new technology. The INEL/EG&G has developed a prototype scheduling system for both commercial and federal government use.

Fast and straightforward analysis approach of charge transport data in single molecule junctions.

PubMed

Zhang, Qian; Liu, Chenguang; Tao, Shuhui; Yi, Ruowei; Su, Weitao; Zhao, Cezhou; Zhao, Chun; Dappe, Yannick J; Nichols, Richard J; Yang, Li

2018-08-10

In this study, we introduce an efficient data sorting algorithm, including filters for noisy signals, conductance mapping for analyzing the most dominant conductance group and sub-population groups. The capacity of our data analysis process has also been corroborated on real experimental data sets of Au-1,6-hexanedithiol-Au and Au-1,8-octanedithiol-Au molecular junctions. The fully automated and unsupervised program requires less than one minute on a standard PC to sort the data and generate histograms. The resulting one-dimensional and two-dimensional log histograms give conductance values in good agreement with previous studies. Our algorithm is a straightforward, fast and user-friendly tool for single molecule charge transport data analysis. We also analyze the data in a form of a conductance map which can offer evidence for diversity in molecular conductance. The code for automatic data analysis is openly available, well-documented and ready to use, thereby offering a useful new tool for single molecule electronics.

[Clinical application of mass spectrometry in the pediatric field: current topics].

PubMed

Yamaguchi, Seiji

2013-09-01

Mass spectrometry, including tandem mass spectrometry (MS/MS) and gas chromatography-mass spectrometry (GC/MS), is becoming prominent in the diagnosis of metabolic disorders in the pediatric field. It enables biochemical diagnosis of metabolic disorders from the metabolic profiles obtained by MS/MS and/or GC/MS. In neonatal mass screening for inherited metabolic disease (IMD) using MS/MS, amino acids and acylcarnitines on dried blood spots are analyzed. The target diseases include amino acidemia, urea cycle disorder, organic acidemia, and fatty acid oxidation disorder. In the MS/MS screening, organic acid analysis using GC/MS is required for differential and/or definite diagnosis of the IMDs. GC/MS data processing, however, is difficult, and metabolic diagnosis often requires the necessary skills and expertize. We developed an automated system of GC/MS data processing and autodiagnosis, and the biochemical diagnosis using GC/MS became markedly easier and user-friendly. Mass spectrometric techniques will expand from research laboratories to clinical laboratories in the near future.

A data-based conservation planning tool for Florida panthers

USGS Publications Warehouse

Murrow, Jennifer L.; Thatcher, Cindy A.; Van Manen, Frank T.; Clark, Joseph D.

2013-01-01

Habitat loss and fragmentation are the greatest threats to the endangered Florida panther (Puma concolor coryi). We developed a data-based habitat model and user-friendly interface so that land managers can objectively evaluate Florida panther habitat. We used a geographic information system (GIS) and the Mahalanobis distance statistic (D2) to develop a model based on broad-scale landscape characteristics associated with panther home ranges. Variables in our model were Euclidean distance to natural land cover, road density, distance to major roads, human density, amount of natural land cover, amount of semi-natural land cover, amount of permanent or semi-permanent flooded area–open water, and a cost–distance variable. We then developed a Florida Panther Habitat Estimator tool, which automates and replicates the GIS processes used to apply the statistical habitat model. The estimator can be used by persons with moderate GIS skills to quantify effects of land-use changes on panther habitat at local and landscape scales. Example applications of the tool are presented.

AncestrySNPminer: A bioinformatics tool to retrieve and develop ancestry informative SNP panels

PubMed Central

Amirisetty, Sushil; Khurana Hershey, Gurjit K.; Baye, Tesfaye M.

2012-01-01

A wealth of genomic information is available in public and private databases. However, this information is underutilized for uncovering population specific and functionally relevant markers underlying complex human traits. Given the huge amount of SNP data available from the annotation of human genetic variation, data mining is a faster and cost effective approach for investigating the number of SNPs that are informative for ancestry. In this study, we present AncestrySNPminer, the first web-based bioinformatics tool specifically designed to retrieve Ancestry Informative Markers (AIMs) from genomic data sets and link these informative markers to genes and ontological annotation classes. The tool includes an automated and simple “scripting at the click of a button” functionality that enables researchers to perform various population genomics statistical analyses methods with user friendly querying and filtering of data sets across various populations through a single web interface. AncestrySNPminer can be freely accessed at https://research.cchmc.org/mershalab/AncestrySNPminer/login.php. PMID:22584067

Development of an optoelectronic holographic platform for otolaryngology applications

NASA Astrophysics Data System (ADS)

Harrington, Ellery; Dobrev, Ivo; Bapat, Nikhil; Flores, Jorge Mauricio; Furlong, Cosme; Rosowski, John; Cheng, Jeffery Tao; Scarpino, Chris; Ravicz, Michael

2010-08-01

In this paper, we present advances on our development of an optoelectronic holographic computing platform with the ability to quantitatively measure full-field-of-view nanometer-scale movements of the tympanic membrane (TM). These measurements can facilitate otologists' ability to study and diagnose hearing disorders in humans. The holographic platform consists of a laser delivery system and an otoscope. The control software, called LaserView, is written in Visual C++ and handles communication and synchronization between hardware components. It provides a user-friendly interface to allow viewing of holographic images with several tools to automate holography-related tasks and facilitate hardware communication. The software uses a series of concurrent threads to acquire images, control the hardware, and display quantitative holographic data at video rates and in two modes of operation: optoelectronic holography and lensless digital holography. The holographic platform has been used to perform experiments on several live and post-mortem specimens, and is to be deployed in a medical research environment with future developments leading to its eventual clinical use.

3D-Lab: a collaborative web-based platform for molecular modeling.

PubMed

Grebner, Christoph; Norrby, Magnus; Enström, Jonatan; Nilsson, Ingemar; Hogner, Anders; Henriksson, Jonas; Westin, Johan; Faramarzi, Farzad; Werner, Philip; Boström, Jonas

2016-09-01

The use of 3D information has shown impact in numerous applications in drug design. However, it is often under-utilized and traditionally limited to specialists. We want to change that, and present an approach making 3D information and molecular modeling accessible and easy-to-use 'for the people'. A user-friendly and collaborative web-based platform (3D-Lab) for 3D modeling, including a blazingly fast virtual screening capability, was developed. 3D-Lab provides an interface to automatic molecular modeling, like conformer generation, ligand alignments, molecular dockings and simple quantum chemistry protocols. 3D-Lab is designed to be modular, and to facilitate sharing of 3D-information to promote interactions between drug designers. Recent enhancements to our open-source virtual reality tool Molecular Rift are described. The integrated drug-design platform allows drug designers to instantaneously access 3D information and readily apply advanced and automated 3D molecular modeling tasks, with the aim to improve decision-making in drug design projects.

Advanced radiology information system.

PubMed

Kolovou, L; Vatousi, M; Lymperopoulos, D; Koukias, M

2005-01-01

The innovative features of an advanced Radiology Information System (RIS) are presented in this paper. The interoperability of RIS with the other Intra-hospital Information Systems that interacts with, dealing with the compatibility and open architecture issues, are accomplished by two novel mechanisms [1]. The first one is the particular message handling system that is applied for the exchange of information, according to the Health Level Seven (HL7) protocol's specifications and serves the transfer of medical and administrative data among the RIS applications and data store unit. The same mechanism allows the secure and HL7-compatible interactions with the Hospital Information System (HIS) too. The second one implements the translation of information between the formats that HL7 and Digital Imaging and Communication in Medicine (DICOM) protocols specify, providing the communication between RIS and Picture and Archive Communication System (PACS). The whole structure ensures the automation of the every-day procedures that the ;medical protocol' specifies and provides its services through a friendly and easy to manage graphical user interface.

"Plasmo2D": an ancillary proteomic tool to aid identification of proteins from Plasmodium falciparum.

PubMed

Khachane, Amit; Kumar, Ranjit; Jain, Sanyam; Jain, Samta; Banumathy, Gowrishankar; Singh, Varsha; Nagpal, Saurabh; Tatu, Utpal

2005-01-01

Bioinformatics tools to aid gene and protein sequence analysis have become an integral part of biology in the post-genomic era. Release of the Plasmodium falciparum genome sequence has allowed biologists to define the gene and the predicted protein content as well as their sequences in the parasite. Using pI and molecular weight as characteristics unique to each protein, we have developed a bioinformatics tool to aid identification of proteins from Plasmodium falciparum. The tool makes use of a Virtual 2-DE generated by plotting all of the proteins from the Plasmodium database on a pI versus molecular weight scale. Proteins are identified by comparing the position of migration of desired protein spots from an experimental 2-DE and that on a virtual 2-DE. The procedure has been automated in the form of user-friendly software called "Plasmo2D". The tool can be downloaded from http://144.16.89.25/Plasmo2D.zip.

CASAS: A tool for composing automatically and semantically astrophysical services

NASA Astrophysics Data System (ADS)

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

2017-07-01

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

An in silico pipeline to filter the Toxoplasma gondii proteome for proteins that could traffic to the host cell nucleus and influence host cell epigenetic regulation.

PubMed

Syn, Genevieve; Blackwell, Jenefer M; Jamieson, Sarra E; Francis, Richard W

2018-01-01

Toxoplasma gondii uses epigenetic mechanisms to regulate both endogenous and host cell gene expression. To identify genes with putative epigenetic functions, we developed an in silico pipeline to interrogate the T. gondii proteome of 8313 proteins. Step 1 employs PredictNLS and NucPred to identify genes predicted to target eukaryotic nuclei. Step 2 uses GOLink to identify proteins of epigenetic function based on Gene Ontology terms. This resulted in 611 putative nuclear localised proteins with predicted epigenetic functions. Step 3 filtered for secretory proteins using SignalP, SecretomeP, and experimental data. This identified 57 of the 611 putative epigenetic proteins as likely to be secreted. The pipeline is freely available online, uses open access tools and software with user-friendly Perl scripts to automate and manage the results, and is readily adaptable to undertake any such in silico search for genes contributing to particular functions.

Couldn't or wouldn't? The influence of privacy concerns and self-efficacy in privacy management on privacy protection.

PubMed

Chen, Hsuan-Ting; Chen, Wenghong

2015-01-01

Sampling 515 college students, this study investigates how privacy protection, including profile visibility, self-disclosure, and friending, are influenced by privacy concerns and efficacy regarding one's own ability to manage privacy settings, a factor that researchers have yet to give a great deal of attention to in the context of social networking sites (SNSs). The results of this study indicate an inconsistency in adopting strategies to protect privacy, a disconnect from limiting profile visibility and friending to self-disclosure. More specifically, privacy concerns lead SNS users to limit their profile visibility and discourage them from expanding their network. However, they do not constrain self-disclosure. Similarly, while self-efficacy in privacy management encourages SNS users to limit their profile visibility, it facilitates self-disclosure. This suggests that if users are limiting their profile visibility and constraining their friending behaviors, it does not necessarily mean they will reduce self-disclosure on SNSs because these behaviors are predicted by different factors. In addition, the study finds an interaction effect between privacy concerns and self-efficacy in privacy management on friending. It points to the potential problem of increased risk-taking behaviors resulting from high self-efficacy in privacy management and low privacy concerns.

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.

Accessibility Testing of Social Websites

NASA Astrophysics Data System (ADS)

Lányi, Cecilia Sik

There is no doubt that social websites have become one of the greatest inventions of the twenty-first century. Maintaining social connections, getting new and new friends, online entertainment: these are the very things we expect a good portal to provide. The concept of the social websites is that upon registration users share a desired amount of personal data with other users and after that they build a so called friend network using their acquaintances as building elements. The more acquaintances are present the more information is accessible during a certain period of time.

USER'S GUIDE FOR GLOED VERSION 1.0 - THE GLOBAL EMISSIONS DATABASE

EPA Science Inventory

The document is a user's guide for the EPA-developed, powerful software package, Global Emissions Database (GloED). GloED is a user-friendly, menu-driven tool for storing and retrieving emissions factors and activity data on a country-specific basis. Data can be selected from dat...

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...

You Don't De-Friend the Dead: An Analysis of Grief Communication by College Students through Facebook Profiles

ERIC Educational Resources Information Center

Pennington, Natalie

2013-01-01

This research examined how various members of a social network interact with the Facebook (FB) profile page of a friend who has died. From 43 in-depth qualitative interviews, FB friends of deceased FB users maintained their FB connection with the deceased. Most participants who visited the profile found it helpful to look at pictures; a few wrote…

Social Networks as a Critical Pathway for Public Education in IYA2009

NASA Astrophysics Data System (ADS)

Plait, P.; Gay, P. L.

2008-11-01

Social networks are websites (or software that distributes media over the Internet) where users can share content to either a list of friends on that site or to anyone who surfs onto their page, and where those friends can interact and discuss the content. By linking to friends online, the users' personal content (pictures, songs, favorite movies, diaries, websites, and so on) is dynamically distributed, and can ``become viral,'' that is, get spread rapidly as more people see it and spread it themselves. Social networks are immensely popular around the planet, especially with teens, and by tapping into these networks IYA can excite and inspire a younger audience. IYA already has a small but growing presence on several of the larger social networks, and more are planned.

A Java-based tool for creating KML files from GPS waypoints

NASA Astrophysics Data System (ADS)

Kinnicutt, P. G.; Rivard, C.; Rimer, S.

2008-12-01

Google Earth provides a free tool with powerful capabilities for visualizing geoscience images and data. Commercial software tools exist for doing sophisticated digitizing and spatial modeling , but for the purposes of presentation, visualization and overlaying aerial images with data Google Earth provides much of the functionality. Likewise, with current technologies in GPS (Global Positioning System) systems and with Google Earth Plus, it is possible to upload GPS waypoints, tracks and routes directly into Google Earth for visualization. However, older technology GPS units and even low-cost GPS units found today may lack the necessary communications interface to a computer (e.g. no Bluetooth, no WiFi, no USB, no Serial, etc.) or may have an incompatible interface, such as a Serial port but no USB adapter available. In such cases, any waypoints, tracks and routes saved in the GPS unit or recorded in a field notebook must be manually transferred to a computer for use in a GIS system or other program. This presentation describes a Java-based tool developed by the author which enables users to enter GPS coordinates in a user-friendly manner, then save these coordinates in a Keyhole MarkUp Language (KML) file format, for visualization in Google Earth. This tool either accepts user-interactive input or accepts input from a CSV (Comma Separated Value) file, which can be generated from any spreadsheet program. This tool accepts input in the form of lat/long or UTM (Universal Transverse Mercator) coordinates. This presentation describes this system's applicability through several small case studies. This free and lightweight tool simplifies the task of manually inputting GPS data into Google Earth for people working in the field without an automated mechanism for uploading the data; for instance, the user may not have internet connectivity or may not have the proper hardware or software. Since it is a Java application and not a web- based tool, it can be installed on one's field laptop and the GPS data can be manually entered without the need for internet connectivity. This tool provides a table view of the GPS data, but lacks a KML viewer to view the data overlain on top of an aerial view, as this viewer functionality is provided in Google Earth. The tool's primary contribution lies in its more convenient method for entering the GPS data manually when automated technologies are not available.

GeoBrain Computational Cyber-laboratory for Earth Science Studies

NASA Astrophysics Data System (ADS)

Deng, M.; di, L.

2009-12-01

Computational approaches (e.g., computer-based data visualization, analysis and modeling) are critical for conducting increasingly data-intensive Earth science (ES) studies to understand functions and changes of the Earth system. However, currently Earth scientists, educators, and students have met two major barriers that prevent them from being effectively using computational approaches in their learning, research and application activities. The two barriers are: 1) difficulties in finding, obtaining, and using multi-source ES data; and 2) lack of analytic functions and computing resources (e.g., analysis software, computing models, and high performance computing systems) to analyze the data. Taking advantages of recent advances in cyberinfrastructure, Web service, and geospatial interoperability technologies, GeoBrain, a project funded by NASA, has developed a prototype computational cyber-laboratory to effectively remove the two barriers. The cyber-laboratory makes ES data and computational resources at large organizations in distributed locations available to and easily usable by the Earth science community through 1) enabling seamless discovery, access and retrieval of distributed data, 2) federating and enhancing data discovery with a catalogue federation service and a semantically-augmented catalogue service, 3) customizing data access and retrieval at user request with interoperable, personalized, and on-demand data access and services, 4) automating or semi-automating multi-source geospatial data integration, 5) developing a large number of analytic functions as value-added, interoperable, and dynamically chainable geospatial Web services and deploying them in high-performance computing facilities, 6) enabling the online geospatial process modeling and execution, and 7) building a user-friendly extensible web portal for users to access the cyber-laboratory resources. Users can interactively discover the needed data and perform on-demand data analysis and modeling through the web portal. The GeoBrain cyber-laboratory provides solutions to meet common needs of ES research and education, such as, distributed data access and analysis services, easy access to and use of ES data, and enhanced geoprocessing and geospatial modeling capability. It greatly facilitates ES research, education, and applications. The development of the cyber-laboratory provides insights, lessons-learned, and technology readiness to build more capable computing infrastructure for ES studies, which can meet wide-range needs of current and future generations of scientists, researchers, educators, and students for their formal or informal educational training, research projects, career development, and lifelong learning.

Quantitative comparisons of three automated methods for estimating intracranial volume: A study of 270 longitudinal magnetic resonance images.

PubMed

Shang, Xiaoyan; Carlson, Michelle C; Tang, Xiaoying

2018-04-30

Total intracranial volume (TIV) is often used as a measure of brain size to correct for individual variability in magnetic resonance imaging (MRI) based morphometric studies. An adjustment of TIV can greatly increase the statistical power of brain morphometry methods. As such, an accurate and precise TIV estimation is of great importance in MRI studies. In this paper, we compared three automated TIV estimation methods (multi-atlas likelihood fusion (MALF), Statistical Parametric Mapping 8 (SPM8) and FreeSurfer (FS)) using longitudinal T1-weighted MR images in a cohort of 70 older participants at elevated sociodemographic risk for Alzheimer's disease. Statistical group comparisons in terms of four different metrics were performed. Furthermore, sex, education level, and intervention status were investigated separately for their impacts on the TIV estimation performance of each method. According to our experimental results, MALF was the least susceptible to atrophy, while SPM8 and FS suffered a loss in precision. In group-wise analysis, MALF was the least sensitive method to group variation, whereas SPM8 was particularly sensitive to sex and FS was unstable with respect to education level. In terms of effectiveness, both MALF and SPM8 delivered a user-friendly performance, while FS was relatively computationally intensive. Copyright © 2018 Elsevier B.V. All rights reserved.

Developing a Business Intelligence Process for a Training Module in SharePoint 2010

NASA Technical Reports Server (NTRS)

Schmidtchen, Bryce; Solano, Wanda M.; Albasini, Colby

2015-01-01

Prior to this project, training information for the employees of the National Center for Critical Processing and Storage (NCCIPS) was stored in an array of unrelated spreadsheets and SharePoint lists that had to be manually updated. By developing a content management system through a web application platform named SharePoint, this training system is now highly automated and provides a much less intensive method of storing training data and scheduling training courses. This system was developed by using SharePoint Designer and laying out the data structure for the interaction between different lists of data about the employees. The automation of data population inside of the lists was accomplished by implementing SharePoint workflows which essentially lay out the logic for how data is connected and calculated between certain lists. The resulting training system is constructed from a combination of five lists of data with a single list acting as the user-friendly interface. This interface is populated with the courses required for each employee and includes past and future information about course requirements. The employees of NCCIPS now have the ability to view, log, and schedule their training information and courses with much more ease. This system will relieve a significant amount of manual input and serve as a powerful informational resource for the employees of NCCIPS in the future.

GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR.

PubMed

Gubelmann, Carine; Gattiker, Alexandre; Massouras, Andreas; Hens, Korneel; David, Fabrice; Decouttere, Frederik; Rougemont, Jacques; Deplancke, Bart

2011-01-01

The vast majority of genes in humans and other organisms undergo alternative splicing, yet the biological function of splice variants is still very poorly understood in large part because of the lack of simple tools that can map the expression profiles and patterns of these variants with high sensitivity. High-throughput quantitative real-time polymerase chain reaction (qPCR) is an ideal technique to accurately quantify nucleic acid sequences including splice variants. However, currently available primer design programs do not distinguish between splice variants and also differ substantially in overall quality, functionality or throughput mode. Here, we present GETPrime, a primer database supported by a novel platform that uniquely combines and automates several features critical for optimal qPCR primer design. These include the consideration of all gene splice variants to enable either gene-specific (covering the majority of splice variants) or transcript-specific (covering one splice variant) expression profiling, primer specificity validation, automated best primer pair selection according to strict criteria and graphical visualization of the latter primer pairs within their genomic context. GETPrime primers have been extensively validated experimentally, demonstrating high transcript specificity in complex samples. Thus, the free-access, user-friendly GETPrime database allows fast primer retrieval and visualization for genes or groups of genes of most common model organisms, and is available at http://updepla1srv1.epfl.ch/getprime/. Database URL: http://deplanckelab.epfl.ch.

GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR

PubMed Central

Gubelmann, Carine; Gattiker, Alexandre; Massouras, Andreas; Hens, Korneel; David, Fabrice; Decouttere, Frederik; Rougemont, Jacques; Deplancke, Bart

2011-01-01

The vast majority of genes in humans and other organisms undergo alternative splicing, yet the biological function of splice variants is still very poorly understood in large part because of the lack of simple tools that can map the expression profiles and patterns of these variants with high sensitivity. High-throughput quantitative real-time polymerase chain reaction (qPCR) is an ideal technique to accurately quantify nucleic acid sequences including splice variants. However, currently available primer design programs do not distinguish between splice variants and also differ substantially in overall quality, functionality or throughput mode. Here, we present GETPrime, a primer database supported by a novel platform that uniquely combines and automates several features critical for optimal qPCR primer design. These include the consideration of all gene splice variants to enable either gene-specific (covering the majority of splice variants) or transcript-specific (covering one splice variant) expression profiling, primer specificity validation, automated best primer pair selection according to strict criteria and graphical visualization of the latter primer pairs within their genomic context. GETPrime primers have been extensively validated experimentally, demonstrating high transcript specificity in complex samples. Thus, the free-access, user-friendly GETPrime database allows fast primer retrieval and visualization for genes or groups of genes of most common model organisms, and is available at http://updepla1srv1.epfl.ch/getprime/. Database URL: http://deplanckelab.epfl.ch. PMID:21917859

Standardized 3D Bioprinting of Soft Tissue Models with Human Primary Cells.

PubMed

Rimann, Markus; Bono, Epifania; Annaheim, Helene; Bleisch, Matthias; Graf-Hausner, Ursula

2016-08-01

Cells grown in 3D are more physiologically relevant than cells cultured in 2D. To use 3D models in substance testing and regenerative medicine, reproducibility and standardization are important. Bioprinting offers not only automated standardizable processes but also the production of complex tissue-like structures in an additive manner. We developed an all-in-one bioprinting solution to produce soft tissue models. The holistic approach included (1) a bioprinter in a sterile environment, (2) a light-induced bioink polymerization unit, (3) a user-friendly software, (4) the capability to print in standard labware for high-throughput screening, (5) cell-compatible inkjet-based printheads, (6) a cell-compatible ready-to-use BioInk, and (7) standard operating procedures. In a proof-of-concept study, skin as a reference soft tissue model was printed. To produce dermal equivalents, primary human dermal fibroblasts were printed in alternating layers with BioInk and cultured for up to 7 weeks. During long-term cultures, the models were remodeled and fully populated with viable and spreaded fibroblasts. Primary human dermal keratinocytes were seeded on top of dermal equivalents, and epidermis-like structures were formed as verified with hematoxylin and eosin staining and immunostaining. However, a fully stratified epidermis was not achieved. Nevertheless, this is one of the first reports of an integrative bioprinting strategy for industrial routine application. © 2015 Society for Laboratory Automation and Screening.

Automation and Intensity Modulated Radiation Therapy for Individualized High-Quality Tangent Breast Treatment Plans

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

Purdie, Thomas G., E-mail: Tom.Purdie@rmp.uhn.on.ca; Department of Radiation Oncology, University of Toronto, Toronto, Ontario; Techna Institute, University Health Network, Toronto, Ontario

Purpose: To demonstrate the large-scale clinical implementation and performance of an automated treatment planning methodology for tangential breast intensity modulated radiation therapy (IMRT). Methods and Materials: Automated planning was used to prospectively plan tangential breast IMRT treatment for 1661 patients between June 2009 and November 2012. The automated planning method emulates the manual steps performed by the user during treatment planning, including anatomical segmentation, beam placement, optimization, dose calculation, and plan documentation. The user specifies clinical requirements of the plan to be generated through a user interface embedded in the planning system. The automated method uses heuristic algorithms to definemore » and simplify the technical aspects of the treatment planning process. Results: Automated planning was used in 1661 of 1708 patients receiving tangential breast IMRT during the time interval studied. Therefore, automated planning was applicable in greater than 97% of cases. The time for treatment planning using the automated process is routinely 5 to 6 minutes on standard commercially available planning hardware. We have shown a consistent reduction in plan rejections from plan reviews through the standard quality control process or weekly quality review multidisciplinary breast rounds as we have automated the planning process for tangential breast IMRT. Clinical plan acceptance increased from 97.3% using our previous semiautomated inverse method to 98.9% using the fully automated method. Conclusions: Automation has become the routine standard method for treatment planning of tangential breast IMRT at our institution and is clinically feasible on a large scale. The method has wide clinical applicability and can add tremendous efficiency, standardization, and quality to the current treatment planning process. The use of automated methods can allow centers to more rapidly adopt IMRT and enhance access to the documented improvements in care for breast cancer patients, using technologies that are widely available and already in clinical use.« less

Automation and intensity modulated radiation therapy for individualized high-quality tangent breast treatment plans.

PubMed

Purdie, Thomas G; Dinniwell, Robert E; Fyles, Anthony; Sharpe, Michael B

2014-11-01

To demonstrate the large-scale clinical implementation and performance of an automated treatment planning methodology for tangential breast intensity modulated radiation therapy (IMRT). Automated planning was used to prospectively plan tangential breast IMRT treatment for 1661 patients between June 2009 and November 2012. The automated planning method emulates the manual steps performed by the user during treatment planning, including anatomical segmentation, beam placement, optimization, dose calculation, and plan documentation. The user specifies clinical requirements of the plan to be generated through a user interface embedded in the planning system. The automated method uses heuristic algorithms to define and simplify the technical aspects of the treatment planning process. Automated planning was used in 1661 of 1708 patients receiving tangential breast IMRT during the time interval studied. Therefore, automated planning was applicable in greater than 97% of cases. The time for treatment planning using the automated process is routinely 5 to 6 minutes on standard commercially available planning hardware. We have shown a consistent reduction in plan rejections from plan reviews through the standard quality control process or weekly quality review multidisciplinary breast rounds as we have automated the planning process for tangential breast IMRT. Clinical plan acceptance increased from 97.3% using our previous semiautomated inverse method to 98.9% using the fully automated method. Automation has become the routine standard method for treatment planning of tangential breast IMRT at our institution and is clinically feasible on a large scale. The method has wide clinical applicability and can add tremendous efficiency, standardization, and quality to the current treatment planning process. The use of automated methods can allow centers to more rapidly adopt IMRT and enhance access to the documented improvements in care for breast cancer patients, using technologies that are widely available and already in clinical use. Copyright © 2014 Elsevier Inc. All rights reserved.

Development of design principles for automated systems in transport control.

PubMed

Balfe, Nora; Wilson, John R; Sharples, Sarah; Clarke, Theresa

2012-01-01

This article reports the results of a qualitative study investigating attitudes towards and opinions of an advanced automation system currently used in UK rail signalling. In-depth interviews were held with 10 users, key issues associated with automation were identified and the automation's impact on the signalling task investigated. The interview data highlighted the importance of the signallers' understanding of the automation and their (in)ability to predict its outputs. The interviews also covered the methods used by signallers to interact with and control the automation, and the perceived effects on their workload. The results indicate that despite a generally low level of understanding and ability to predict the actions of the automation system, signallers have developed largely successful coping mechanisms that enable them to use the technology effectively. These findings, along with parallel work identifying desirable attributes of automation from the literature in the area, were used to develop 12 principles of automation which can be used to help design new systems which better facilitate cooperative working. The work reported in this article was completed with the active involvement of operational rail staff who regularly use automated systems in rail signalling. The outcomes are currently being used to inform decisions on the extent and type of automation and user interfaces in future generations of rail control systems.

An Automated, High-Throughput System for GISAXS and GIWAXS Measurements of Thin Films

NASA Astrophysics Data System (ADS)

Schaible, Eric; Jimenez, Jessica; Church, Matthew; Lim, Eunhee; Stewart, Polite; Hexemer, Alexander

Grazing incidence small-angle X-ray scattering (GISAXS) and grazing incidence wide-angle X-ray scattering (GIWAXS) are important techniques for characterizing thin films. In order to meet rapidly increasing demand, the SAXSWAXS beamline at the Advanced Light Source (beamline 7.3.3) has implemented a fully automated, high-throughput system to conduct SAXS, GISAXS and GIWAXS measurements. An automated robot arm transfers samples from a holding tray to a measurement stage. Intelligent software aligns each sample in turn, and measures each according to user-defined specifications. Users mail in trays of samples on individually barcoded pucks, and can download and view their data remotely. Data will be pipelined to the NERSC supercomputing facility, and will be available to users via a web portal that facilitates highly parallelized analysis.

"Hyperstat": an educational and working tool in epidemiology.

PubMed

Nicolosi, A

1995-01-01

The work of a researcher in epidemiology is based on studying literature, planning studies, gathering data, analyzing data and writing results. Therefore he has need for performing, more or less, simple calculations, the need for consulting or quoting literature, the need for consulting textbooks about certain issues or procedures, and the need for looking at a specific formula. There are no programs conceived as a workstation to assist the different aspects of researcher work in an integrated fashion. A hypertextual system was developed which supports different stages of the epidemiologist's work. It combines database management, statistical analysis or planning, and literature searches. The software was developed on Apple Macintosh by using Hypercard 2.1 as a database and HyperTalk as a programming language. The program is structured in 7 "stacks" or files: Procedures; Statistical Tables; Graphs; References; Text; Formulas; Help. Each stack has its own management system with an automated Table of Contents. Stacks contain "cards" which make up the databases and carry executable programs. The programs are of four kinds: association; statistical procedure; formatting (input/output); database management. The system performs general statistical procedures, procedures applicable to epidemiological studies only (follow-up and case-control), and procedures for clinical trials. All commands are given by clicking the mouse on self-explanatory "buttons". In order to perform calculations, the user only needs to enter the data into the appropriate cells and then click on the selected procedure's button. The system has a hypertextual structure. The user can go from a procedure to other cards following the preferred order of succession and according to built-in associations. The user can access different levels of knowledge or information from any stack he is consulting or operating. From every card, the user can go to a selected procedure to perform statistical calculations, to the reference database management system, to the textbook in which all procedures and issues are discussed in detail, to the database of statistical formulas with automated table of contents, to statistical tables with automated table of contents, or to the help module. he program has a very user-friendly interface and leaves the user free to use the same format he would use on paper. The interface does not require special skills. It reflects the Macintosh philosophy of using windows, buttons and mouse. This allows the user to perform complicated calculations without losing the "feel" of data, weight alternatives, and simulations. This program shares many features in common with hypertexts. It has an underlying network database where the nodes consist of text, graphics, executable procedures, and combinations of these; the nodes in the database correspond to windows on the screen; the links between the nodes in the database are visible as "active" text or icons in the windows; the text is read by following links and opening new windows. The program is especially useful as an educational tool, directed to medical and epidemiology students. The combination of computing capabilities with a textbook and databases of formulas and literature references, makes the program versatile and attractive as a learning tool. The program is also helpful in the work done at the desk, where the researcher examines results, consults literature, explores different analytic approaches, plans new studies, or writes grant proposals or scientific articles.

General Tool for Evaluating High-Contrast Coronagraphic Telescope Performance Error Budgets

NASA Technical Reports Server (NTRS)

Marchen, Luis F.

2011-01-01

The Coronagraph Performance Error Budget (CPEB) tool automates many of the key steps required to evaluate the scattered starlight contrast in the dark hole of a space-based coronagraph. The tool uses a Code V prescription of the optical train, and uses MATLAB programs to call ray-trace code that generates linear beam-walk and aberration sensitivity matrices for motions of the optical elements and line-of-sight pointing, with and without controlled fine-steering mirrors (FSMs). The sensitivity matrices are imported by macros into Excel 2007, where the error budget is evaluated. The user specifies the particular optics of interest, and chooses the quality of each optic from a predefined set of PSDs. The spreadsheet creates a nominal set of thermal and jitter motions, and combines that with the sensitivity matrices to generate an error budget for the system. CPEB also contains a combination of form and ActiveX controls with Visual Basic for Applications code to allow for user interaction in which the user can perform trade studies such as changing engineering requirements, and identifying and isolating stringent requirements. It contains summary tables and graphics that can be instantly used for reporting results in view graphs. The entire process to obtain a coronagraphic telescope performance error budget has been automated into three stages: conversion of optical prescription from Zemax or Code V to MACOS (in-house optical modeling and analysis tool), a linear models process, and an error budget tool process. The first process was improved by developing a MATLAB package based on the Class Constructor Method with a number of user-defined functions that allow the user to modify the MACOS optical prescription. The second process was modified by creating a MATLAB package that contains user-defined functions that automate the process. The user interfaces with the process by utilizing an initialization file where the user defines the parameters of the linear model computations. Other than this, the process is fully automated. The third process was developed based on the Terrestrial Planet Finder coronagraph Error Budget Tool, but was fully automated by using VBA code, form, and ActiveX controls.

Automatic and continuous landslide monitoring: the Rotolon Web-based platform

NASA Astrophysics Data System (ADS)

Frigerio, Simone; Schenato, Luca; Mantovani, Matteo; Bossi, Giulia; Marcato, Gianluca; Cavalli, Marco; Pasuto, Alessandro

2013-04-01

Mount Rotolon (Eastern Italian Alps) is affected by a complex landslide that, since 1985, is threatening the nearby village of Recoaro Terme. The first written proof of a landslide occurrence dated back to 1798. After the last re-activation on November 2010 (637 mm of intense rainfall recorded in the 12 days prior the event), a mass of approximately 320.000 m3 detached from the south flank of Mount Rotolon and evolved into a fast debris flow that ran for about 3 km along the stream bed. A real-time monitoring system was required to detect early indication of rapid movements, potentially saving lives and property. A web-based platform for automatic and continuous monitoring was designed as a first step in the implementation of an early-warning system. Measurements collected by the automated geotechnical and topographic instrumentation, deployed over the landslide body, are gathered in a central box station. After the calibration process, they are transmitted by web services on a local server, where graphs, maps, reports and alert announcement are automatically generated and updated. All the processed information are available by web browser with different access rights. The web environment provides the following advantages: 1) data is collected from different data sources and matched on a single server-side frame 2) a remote user-interface allows regular technical maintenance and direct access to the instruments 3) data management system is synchronized and automatically tested 4) a graphical user interface on browser provides a user-friendly tool for decision-makers to interact with a system continuously updated. On this site two monitoring systems are actually on course: 1) GB-InSAR radar interferometer (University of Florence - Department of Earth Science) and 2) Automated Total Station (ATS) combined with extensometers network in a Web-based solution (CNR-IRPI Padova). This work deals with details on methodology, services and techniques adopted for the second monitoring solution. The activity directly interfaces with local Civil Protection agency, Regional Geological Service and local authorities with integrated roles and aims.

A Compilation of MATLAB Scripts and Functions for MACGMC Analyses

NASA Technical Reports Server (NTRS)

Murthy, Pappu L. N.; Bednarcyk, Brett A.; Mital, Subodh K.

2017-01-01

The primary aim of the current effort is to provide scripts that automate many of the repetitive pre- and post-processing tasks associated with composite materials analyses using the Micromechanics Analysis Code with the Generalized Method of Cells. This document consists of a compilation of hundreds of scripts that were developed in MATLAB (The Mathworks, Inc., Natick, MA) programming language and consolidated into 16 MATLAB functions. (MACGMC). MACGMC is a composite material and laminate analysis software code developed at NASA Glenn Research Center. The software package has been built around the generalized method of cells (GMC) family of micromechanics theories. The computer code is developed with a user-friendly framework, along with a library of local inelastic, damage, and failure models. Further, application of simulated thermo-mechanical loading, generation of output results, and selection of architectures to represent the composite material have been automated to increase the user friendliness, as well as to make it more robust in terms of input preparation and code execution. Finally, classical lamination theory has been implemented within the software, wherein GMC is used to model the composite material response of each ply. Thus, the full range of GMC composite material capabilities is available for analysis of arbitrary laminate configurations as well. The pre-processing tasks include generation of a multitude of different repeating unit cells (RUCs) for CMCs and PMCs, visualization of RUCs from MACGMC input and output files and generation of the RUC section of a MACGMC input file. The post-processing tasks include visualization of the predicted composite response, such as local stress and strain contours, damage initiation and progression, stress-strain behavior, and fatigue response. In addition to the above, several miscellaneous scripts have been developed that can be used to perform repeated Monte-Carlo simulations to enable probabilistic simulations with minimal manual intervention. This document is formatted to provide MATLAB source files and descriptions of how to utilize them. It is assumed that the user has a basic understanding of how MATLAB scripts work and some MATLAB programming experience.

MAC/GMC 4.0 User's Manual: Example Problem Manual. Volume 3

NASA Technical Reports Server (NTRS)

Bednarcyk, Brett A.; Arnold, Steven M.

2002-01-01

This document is the third volume in the three volume set of User's Manuals for the Micromechanics Analysis Code with Generalized Method of Cells Version 4.0 (MAC/GMC 4.0). Volume 1 is the Theory Manual, Volume 2 is the Keywords Manual, and this document is the Example Problems Manual. MAC/GMC 4.0 is a composite material and laminate analysis software program developed at the NASA Glenn Research Center. It is based on the generalized method of cells (GMC) micromechanics theory, which provides access to the local stress and strain fields in the composite material. This access grants GMC the ability to accommodate arbitrary local models for inelastic material behavior and various types of damage and failure analysis. MAC/GMC 4.0 has been built around GMC to provide the theory with a user-friendly framework, along with a library of local inelastic, damage, and failure models. Further, application of simulated thermo-mechanical loading, generation of output results, and selection of architectures to represent the composite material, have been automated in MAC/GMC 4.0. Finally, classical lamination theory has been implemented within MAC/GMC 4.0 wherein GMC is used to model the composite material response of each ply. Consequently, the full range of GMC composite material capabilities is available for analysis of arbitrary laminate configurations as well. This volume provides in-depth descriptions of 43 example problems, which were specially designed to highlight many of the most important capabilities of the code. The actual input files associated with each example problem are distributed with the MAC/GMC 4.0 software; thus providing the user with a convenient starting point for their own specialized problems of interest.

Development of a handheld widefield hyperspectral imaging (HSI) sensor for standoff detection of explosive, chemical, and narcotic residues

NASA Astrophysics Data System (ADS)

Nelson, Matthew P.; Basta, Andrew; Patil, Raju; Klueva, Oksana; Treado, Patrick J.

2013-05-01

The utility of Hyper Spectral Imaging (HSI) passive chemical detection employing wide field, standoff imaging continues to be advanced in detection applications. With a drive for reduced SWaP (Size, Weight, and Power), increased speed of detection and sensitivity, developing a handheld platform that is robust and user-friendly increases the detection capabilities of the end user. In addition, easy to use handheld detectors could improve the effectiveness of locating and identifying threats while reducing risks to the individual. ChemImage Sensor Systems (CISS) has developed the HSI Aperio™ sensor for real time, wide area surveillance and standoff detection of explosives, chemical threats, and narcotics for use in both government and commercial contexts. Employing liquid crystal tunable filter technology, the HSI system has an intuitive user interface that produces automated detections and real-time display of threats with an end user created library of threat signatures that is easily updated allowing for new hazardous materials. Unlike existing detection technologies that often require close proximity for sensing and so endanger operators and costly equipment, the handheld sensor allows the individual operator to detect threats from a safe distance. Uses of the sensor include locating production facilities of illegal drugs or IEDs by identification of materials on surfaces such as walls, floors, doors, deposits on production tools and residue on individuals. In addition, the sensor can be used for longer-range standoff applications such as hasty checkpoint or vehicle inspection of residue materials on surfaces or bulk material identification. The CISS Aperio™ sensor has faster data collection, faster image processing, and increased detection capability compared to previous sensors.

A User Study: Keyboard and Applications to Simplify Smartphone Adoption for Seniors.

PubMed

Austad, Hanne O; Liverud, Anders E; Chan, Richard; Røhne, Mette

2017-01-01

The aim of the user study was to evaluate how the developed assistive physical keyboard, the Ezi-PAD, and integrated senior friendly applications, can encourage non-smartphone seniors to start using the smartphone and enable senior smartphone users to continue using a smartphone in spite of increasing motoric or visual impairment. A number of seniors with different experience and impairment, aged 64 to 86, were equipped with a smartphone and an Ezi-PAD assembly. After basic training, their use of the smartphone was monitored for up to 2 months. Five out of nine participants used the system for 2 months, and found the Ezi-PAD easy to use. The senior friendly applications gave extra utilitarian value to the phone.

The Human Response to Library Automation.

ERIC Educational Resources Information Center

Kirkland, Janice, Ed.

1989-01-01

Eleven articles discuss the response of library users and personnel to automation. Topics covered include computerized reference services, online public access catalogs, paraprofessional staff perceptions of technology, organizational and managerial impacts of automation, workshops on new technology, gender differences in motivation to manage and…

Continuous Calibration of Trust in Automated Systems

DTIC Science & Technology

2014-01-01

Airlines Flight 214 in San Francisco. Therefore, understanding how users form, lose, and recover trust in imperfect automation is of critical...1997). Misuse and disuse can have fatal consequences; for example, inappropriate automation reliance has been implicated in the recent crash of Asiana

Kinematic synthesis of adjustable robotic mechanisms

NASA Astrophysics Data System (ADS)

Chuenchom, Thatchai

1993-01-01

Conventional hard automation, such as a linkage-based or a cam-driven system, provides high speed capability and repeatability but not the flexibility required in many industrial applications. The conventional mechanisms, that are typically single-degree-of-freedom systems, are being increasingly replaced by multi-degree-of-freedom multi-actuators driven by logic controllers. Although this new trend in sophistication provides greatly enhanced flexibility, there are many instances where the flexibility needs are exaggerated and the associated complexity is unnecessary. Traditional mechanism-based hard automation, on the other hand, neither can fulfill multi-task requirements nor are cost-effective mainly due to lack of methods and tools to design-in flexibility. This dissertation attempts to bridge this technological gap by developing Adjustable Robotic Mechanisms (ARM's) or 'programmable mechanisms' as a middle ground between high speed hard automation and expensive serial jointed-arm robots. This research introduces the concept of adjustable robotic mechanisms towards cost-effective manufacturing automation. A generalized analytical synthesis technique has been developed to support the computational design of ARM's that lays the theoretical foundation for synthesis of adjustable mechanisms. The synthesis method developed in this dissertation, called generalized adjustable dyad and triad synthesis, advances the well-known Burmester theory in kinematics to a new level. While this method provides planar solutions, a novel patented scheme is utilized for converting prescribed three-dimensional motion specifications into sets of planar projections. This provides an analytical and a computational tool for designing adjustable mechanisms that satisfy multiple sets of three-dimensional motion specifications. Several design issues were addressed, including adjustable parameter identification, branching defect, and mechanical errors. An efficient mathematical scheme for identification of adjustable member was also developed. The analytical synthesis techniques developed in this dissertation were successfully implemented in a graphic-intensive user-friendly computer program. A physical prototype of a general purpose adjustable robotic mechanism has been constructed to serve as a proof-of-concept model.

A semi-automated region of interest detection method in the scintigraphic glomerular filtration rate determination for patients with abnormal low renal function.

PubMed

Tian, Cancan; Zheng, Xiujuan; Han, Yuan; Sun, Xiaoguang; Chen, Kewei; Huang, Qiu

2013-11-01

This work presents a novel semi-automated renal region-of-interest (ROI) determination method that is user friendly, time saving, and yet provides a robust glomerular filtration rate (GFR) estimation highly consistent with the reference method. We reviewed data from 57 patients who underwent (99m)Tc-diethylenetriaminepentaacetic acid renal scintigraphy and were diagnosed with abnormal renal function. The renal and background ROIs were delineated by the proposed multi-step, semi-automated method, which integrates temporal/morphologic information via visual inspection and computer-aided calculations. The total GFR was estimated using the proposed method (sGFR) performed by 2 junior clinicians (A and B) with 1 and 3 years of experience, respectively (sGFR_a, sGFR_b), and compared with the reference total GFR (rGFR) estimated by a senior clinician with 20 years of experience who manually delineated the kidney and background ROIs. All GFR calculations herein were conducted using the Gates method. Data from 10 patients with unilateral or non-functioning kidneys were excluded from the analysis. For the remaining patients, sGFR correlated well with rGFR (r(s/rGFR_a) = 0.957, P < 0.001 and r(s/rGFR_b) = 0.951, P < 0.001) and sGFR_a correlated well with sGFR_b (r(a/b) = 0.997, P < 0.001). Moreover, the Bland-Altman plots for sGFR_a and sGFR_b confirm the high reproducibility of the proposed method between different operators. Finally, the proposed procedure is almost 3 times faster than the routinely used procedure in clinical practice. The results suggest that this method is easy to use, highly reproducible, and accurate in measuring the GFR of patients with low renal function. The method is being further extended to a fully automated procedure.

Quantification of Dynamic Morphological Drug Responses in 3D Organotypic Cell Cultures by Automated Image Analysis

PubMed Central

Härmä, Ville; Schukov, Hannu-Pekka; Happonen, Antti; Ahonen, Ilmari; Virtanen, Johannes; Siitari, Harri; Åkerfelt, Malin; Lötjönen, Jyrki; Nees, Matthias

2014-01-01

Glandular epithelial cells differentiate into complex multicellular or acinar structures, when embedded in three-dimensional (3D) extracellular matrix. The spectrum of different multicellular morphologies formed in 3D is a sensitive indicator for the differentiation potential of normal, non-transformed cells compared to different stages of malignant progression. In addition, single cells or cell aggregates may actively invade the matrix, utilizing epithelial, mesenchymal or mixed modes of motility. Dynamic phenotypic changes involved in 3D tumor cell invasion are sensitive to specific small-molecule inhibitors that target the actin cytoskeleton. We have used a panel of inhibitors to demonstrate the power of automated image analysis as a phenotypic or morphometric readout in cell-based assays. We introduce a streamlined stand-alone software solution that supports large-scale high-content screens, based on complex and organotypic cultures. AMIDA (Automated Morphometric Image Data Analysis) allows quantitative measurements of large numbers of images and structures, with a multitude of different spheroid shapes, sizes, and textures. AMIDA supports an automated workflow, and can be combined with quality control and statistical tools for data interpretation and visualization. We have used a representative panel of 12 prostate and breast cancer lines that display a broad spectrum of different spheroid morphologies and modes of invasion, challenged by a library of 19 direct or indirect modulators of the actin cytoskeleton which induce systematic changes in spheroid morphology and differentiation versus invasion. These results were independently validated by 2D proliferation, apoptosis and cell motility assays. We identified three drugs that primarily attenuated the invasion and formation of invasive processes in 3D, without affecting proliferation or apoptosis. Two of these compounds block Rac signalling, one affects cellular cAMP/cGMP accumulation. Our approach supports the growing needs for user-friendly, straightforward solutions that facilitate large-scale, cell-based 3D assays in basic research, drug discovery, and target validation. PMID:24810913

Automated imaging system for single molecules

DOEpatents

Schwartz, David Charles; Runnheim, Rodney; Forrest, Daniel

2012-09-18

There is provided a high throughput automated single molecule image collection and processing system that requires minimal initial user input. The unique features embodied in the present disclosure allow automated collection and initial processing of optical images of single molecules and their assemblies. Correct focus may be automatically maintained while images are collected. Uneven illumination in fluorescence microscopy is accounted for, and an overall robust imaging operation is provided yielding individual images prepared for further processing in external systems. Embodiments described herein are useful in studies of any macromolecules such as DNA, RNA, peptides and proteins. The automated image collection and processing system and method of same may be implemented and deployed over a computer network, and may be ergonomically optimized to facilitate user interaction.

Industrial Wireless Sensors: A User's Perspective on the Impact of Standards on Wide-spread Deployment

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

Taft, Cyrus W.; Manges, Wayne W; Sorge, John N

2012-01-01

The role of wireless sensing technologies in industrial instrumentation will undoubtedly become more important in the years ahead. . Deployment of such instrumentation in an industrial setting with its heightened security and robustness criteria hinges on user acceptance of verified performance as well as meeting cost requirements. Today, industrial users face many choices when specifying a wireless sensor network, including radio performance, battery life, interoperability, security, and standards compliance. The potential market for industrial wireless sensors is literally millions of wireless instruments and it is imperative that accurate information for applying the technology to real-world applications be available to themore » end-user so that they can make informed deployment decisions. The majority of industrial wireless automation designs now being deployed or being considered for deployment are based on three different standards . The HART Communications Foundation s WirelessHART (IEC 62591), the International Society of Automation s ISA100.11a, and the offering from the Industrial Wireless Alliance of China known as WIA-PA (IEC 62601). Aside from these industrial automation standards, users must also be cognizant of the underlying wireless network standards IEEE 802.11, IEEE 802.15.4, and IEEE 802.15.3a and their interactions with the three principal industrial automation protocols mentioned previously. The crucial questions being asked by end users revolve around sensor network performance, interoperability, reliability, and security. This paper will discuss potential wireless sensor applications in power plants, barriers to the acceptance of wireless technology, concerns related to standards, and provide an end user prospective on the issues affecting wide-spread deployment of wireless sensors. Finally, the authors conclude with a discussion of a recommended path forward including how standards organizations can better facilitate end user decision making and how end users can locate and use objective information for decision making.« less

Living with an autonomous spatiotemporal home heating system: Exploration of the user experiences (UX) through a longitudinal technology intervention-based mixed-methods approach.

PubMed

Kruusimagi, Martin; Sharples, Sarah; Robinson, Darren

2017-11-01

Rising energy demands place pressure on domestic energy consumption, but savings can be delivered through home automation and engaging users with their heating and energy behaviours. The aim of this paper is to explore user experiences (UX) of living with an automated heating system regarding experiences of control, understanding of the system, emerging thermal behaviours, and interactions with the system as this area is not sufficiently researched in the existing homes setting through extended deployment. We present a longitudinal deployment of a quasi-autonomous spatiotemporal home heating system in three homes. Users were provided with a smartphone control application linked to a self-learning heating algorithm. Rich qualitative and quantitative data presented here enabled a holistic exploration of UX. The paper's contribution focuses on highlighting key aspects of UX living with an automated heating systems including (i) adoption of the control interface into the social context, (ii) how users' vigilance in maintaining preferred conditions prevailed as a better indicator of system over-ride than gross deviation from thermal comfort, (iii) limited but motivated proactivity in system-initiated communications as best strategy for soliciting user feedback when inference fails, and (iv) two main motivations for interacting with the interface - managing irregularities when absent from the house and maintaining immediate comfort, latter compromising of a checking behaviour that can transit to a system state alteration behaviour depending on mismatches. We conclude by highlighting the complex socio-technical context in which thermal decisions are made in a situated action manner, and by calling for a more holistic, UX-focused approach in the design of automated home systems involving user experiences. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Automated Identification of Medically Important Bacteria by 16S rRNA Gene Sequencing Using a Novel Comprehensive Database, 16SpathDB▿

PubMed Central

Woo, Patrick C. Y.; Teng, Jade L. L.; Yeung, Juilian M. Y.; Tse, Herman; Lau, Susanna K. P.; Yuen, Kwok-Yung

2011-01-01

Despite the increasing use of 16S rRNA gene sequencing, interpretation of 16S rRNA gene sequence results is one of the most difficult problems faced by clinical microbiologists and technicians. To overcome the problems we encountered in the existing databases during 16S rRNA gene sequence interpretation, we built a comprehensive database, 16SpathDB (http://147.8.74.24/16SpathDB) based on the 16S rRNA gene sequences of all medically important bacteria listed in the Manual of Clinical Microbiology and evaluated its use for automated identification of these bacteria. Among 91 nonduplicated bacterial isolates collected in our clinical microbiology laboratory, 71 (78%) were reported by 16SpathDB as a single bacterial species having >98.0% nucleotide identity with the query sequence, 19 (20.9%) were reported as more than one bacterial species having >98.0% nucleotide identity with the query sequence, and 1 (1.1%) was reported as no match. For the 71 bacterial isolates reported as a single bacterial species, all results were identical to their true identities as determined by a polyphasic approach. For the 19 bacterial isolates reported as more than one bacterial species, all results contained their true identities as determined by a polyphasic approach and all of them had their true identities as the “best match in 16SpathDB.” For the isolate (Gordonibacter pamelaeae) reported as no match, the bacterium has never been reported to be associated with human disease and was not included in the Manual of Clinical Microbiology. 16SpathDB is an automated, user-friendly, efficient, accurate, and regularly updated database for 16S rRNA gene sequence interpretation in clinical microbiology laboratories. PMID:21389154

Development of an online morbidity, mortality, and near-miss reporting system to identify patterns of adverse events in surgical patients.

PubMed

Bilimoria, Karl Y; Kmiecik, Thomas E; DaRosa, Debra A; Halverson, Amy; Eskandari, Mark K; Bell, Richard H; Soper, Nathaniel J; Wayne, Jeffrey D

2009-04-01

To design a Web-based system to track adverse and near-miss events, to establish an automated method to identify patterns of events, and to assess the adverse event reporting behavior of physicians. A Web-based system was designed to collect physician-reported adverse events including weekly Morbidity and Mortality (M&M) entries and anonymous adverse/near-miss events. An automated system was set up to help identify event patterns. Adverse event frequency was compared with hospital databases to assess reporting completeness. A metropolitan tertiary care center. Identification of adverse event patterns and completeness of reporting. From September 2005 to August 2007, 15,524 surgical patients were reported including 957 (6.2%) adverse events and 34 (0.2%) anonymous reports. The automated pattern recognition system helped identify 4 event patterns from M&M reports and 3 patterns from anonymous/near-miss reporting. After multidisciplinary meetings and expert reviews, the patterns were addressed with educational initiatives, correction of systems issues, and/or intensive quality monitoring. Only 25% of complications and 42% of inpatient deaths were reported. A total of 75.2% of adverse events resulting in permanent disability or death were attributed to the nature of the disease. Interventions to improve reporting were largely unsuccessful. We have developed a user-friendly Web-based system to track complications and identify patterns of adverse events. Underreporting of adverse events and attributing the complication to the nature of the disease represent a problem in reporting culture among surgeons at our institution. Similar systems should be used by surgery departments, particularly those affiliated with teaching hospitals, to identify quality improvement opportunities.

lumpR 2.0.0: an R package facilitating landscape discretisation for hillslope-based hydrological models

NASA Astrophysics Data System (ADS)

Pilz, Tobias; Francke, Till; Bronstert, Axel

2017-08-01

The characteristics of a landscape pose essential factors for hydrological processes. Therefore, an adequate representation of the landscape of a catchment in hydrological models is vital. However, many of such models exist differing, amongst others, in spatial concept and discretisation. The latter constitutes an essential pre-processing step, for which many different algorithms along with numerous software implementations exist. In that context, existing solutions are often model specific, commercial, or depend on commercial back-end software, and allow only a limited or no workflow automation at all. Consequently, a new package for the scientific software and scripting environment R, called lumpR, was developed. lumpR employs an algorithm for hillslope-based landscape discretisation directed to large-scale application via a hierarchical multi-scale approach. The package addresses existing limitations as it is free and open source, easily extendible to other hydrological models, and the workflow can be fully automated. Moreover, it is user-friendly as the direct coupling to a GIS allows for immediate visual inspection and manual adjustment. Sufficient control is furthermore retained via parameter specification and the option to include expert knowledge. Conversely, completely automatic operation also allows for extensive analysis of aspects related to landscape discretisation. In a case study, the application of the package is presented. A sensitivity analysis of the most important discretisation parameters demonstrates its efficient workflow automation. Considering multiple streamflow metrics, the employed model proved reasonably robust to the discretisation parameters. However, parameters determining the sizes of subbasins and hillslopes proved to be more important than the others, including the number of representative hillslopes, the number of attributes employed for the lumping algorithm, and the number of sub-discretisations of the representative hillslopes.

Automated analysis of information processing, kinetic independence and modular architecture in biochemical networks using MIDIA.

PubMed

Bowsher, Clive G

2011-02-15

Understanding the encoding and propagation of information by biochemical reaction networks and the relationship of such information processing properties to modular network structure is of fundamental importance in the study of cell signalling and regulation. However, a rigorous, automated approach for general biochemical networks has not been available, and high-throughput analysis has therefore been out of reach. Modularization Identification by Dynamic Independence Algorithms (MIDIA) is a user-friendly, extensible R package that performs automated analysis of how information is processed by biochemical networks. An important component is the algorithm's ability to identify exact network decompositions based on both the mass action kinetics and informational properties of the network. These modularizations are visualized using a tree structure from which important dynamic conditional independence properties can be directly read. Only partial stoichiometric information needs to be used as input to MIDIA, and neither simulations nor knowledge of rate parameters are required. When applied to a signalling network, for example, the method identifies the routes and species involved in the sequential propagation of information between its multiple inputs and outputs. These routes correspond to the relevant paths in the tree structure and may be further visualized using the Input-Output Path Matrix tool. MIDIA remains computationally feasible for the largest network reconstructions currently available and is straightforward to use with models written in Systems Biology Markup Language (SBML). The package is distributed under the GNU General Public License and is available, together with a link to browsable Supplementary Material, at http://code.google.com/p/midia. Further information is at www.maths.bris.ac.uk/~macgb/Software.html.

Automated water analyser computer supported system (AWACSS) Part I: Project objectives, basic technology, immunoassay development, software design and networking.

PubMed

Tschmelak, Jens; Proll, Guenther; Riedt, Johannes; Kaiser, Joachim; Kraemmer, Peter; Bárzaga, Luis; Wilkinson, James S; Hua, Ping; Hole, J Patrick; Nudd, Richard; Jackson, Michael; Abuknesha, Ram; Barceló, Damià; Rodriguez-Mozaz, Sara; de Alda, Maria J López; Sacher, Frank; Stien, Jan; Slobodník, Jaroslav; Oswald, Peter; Kozmenko, Helena; Korenková, Eva; Tóthová, Lívia; Krascsenits, Zoltan; Gauglitz, Guenter

2005-02-15

A novel analytical system AWACSS (automated water analyser computer-supported system) based on immunochemical technology has been developed that can measure several organic pollutants at low nanogram per litre level in a single few-minutes analysis without any prior sample pre-concentration nor pre-treatment steps. Having in mind actual needs of water-sector managers related to the implementation of the Drinking Water Directive (DWD) (98/83/EC, 1998) and Water Framework Directive WFD (2000/60/EC, 2000), drinking, ground, surface, and waste waters were major media used for the evaluation of the system performance. The instrument was equipped with remote control and surveillance facilities. The system's software allows for the internet-based networking between the measurement and control stations, global management, trend analysis, and early-warning applications. The experience of water laboratories has been utilised at the design of the instrument's hardware and software in order to make the system rugged and user-friendly. Several market surveys were conducted during the project to assess the applicability of the final system. A web-based AWACSS database was created for automated evaluation and storage of the obtained data in a format compatible with major databases of environmental organic pollutants in Europe. This first part article gives the reader an overview of the aims and scope of the AWACSS project as well as details about basic technology, immunoassays, software, and networking developed and utilised within the research project. The second part article reports on the system performance, first real sample measurements, and an international collaborative trial (inter-laboratory tests) to compare the biosensor with conventional anayltical methods.

CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota

PubMed Central

2013-01-01

Background Besides the development of comprehensive tools for high-throughput 16S ribosomal RNA amplicon sequence analysis, there exists a growing need for protocols emphasizing alternative phylogenetic markers such as those representing eukaryotic organisms. Results Here we introduce CloVR-ITS, an automated pipeline for comparative analysis of internal transcribed spacer (ITS) pyrosequences amplified from metagenomic DNA isolates and representing fungal species. This pipeline performs a variety of steps similar to those commonly used for 16S rRNA amplicon sequence analysis, including preprocessing for quality, chimera detection, clustering of sequences into operational taxonomic units (OTUs), taxonomic assignment (at class, order, family, genus, and species levels) and statistical analysis of sample groups of interest based on user-provided information. Using ITS amplicon pyrosequencing data from a previous human gastric fluid study, we demonstrate the utility of CloVR-ITS for fungal microbiota analysis and provide runtime and cost examples, including analysis of extremely large datasets on the cloud. We show that the largest fractions of reads from the stomach fluid samples were assigned to Dothideomycetes, Saccharomycetes, Agaricomycetes and Sordariomycetes but that all samples were dominated by sequences that could not be taxonomically classified. Representatives of the Candida genus were identified in all samples, most notably C. quercitrusa, while sequence reads assigned to the Aspergillus genus were only identified in a subset of samples. CloVR-ITS is made available as a pre-installed, automated, and portable software pipeline for cloud-friendly execution as part of the CloVR virtual machine package (http://clovr.org). Conclusion The CloVR-ITS pipeline provides fungal microbiota analysis that can be complementary to bacterial 16S rRNA and total metagenome sequence analysis allowing for more comprehensive studies of environmental and host-associated microbial communities. PMID:24451270

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)

FACTOR FINDER CD-ROM

EPA Science Inventory

The Factor Finder CD-ROM is a user-friendly, searchable tool used to locate exposure factors and sociodemographic data for user-defined populations. Factor Finder improves the exposure assessors and risk assessors (etc.) ability to efficiently locate exposure-related informatio...

HWNOISE program users' guide

DOT National Transportation Integrated Search

1992-02-01

HWNOISE is a VNTSC-developed user friendly program written in : Microsoft Fortran version 4.01 for the IBM PC/AT and : compatibles to analyze acoustic data. This program is an : integral part of the Federal Highway Administration's Mobile : Noise Dat...

HWINPUT program users' guide

DOT National Transportation Integrated Search

1992-02-01

HWINPUT is a VNTSC-developed user friendly program written in : Microsoft Fortran version 4.01 for the IBM PC/AT. This program : is an integral part of the Federal Highway Administration's : Mobile Noise Data Gathering and Analysis Laboratory and is ...

ROCOPT: A user friendly interactive code to optimize rocket structural components

NASA Technical Reports Server (NTRS)

Rule, William K.

1989-01-01

ROCOPT is a user-friendly, graphically-interfaced, microcomputer-based computer program (IBM compatible) that optimizes rocket components by minimizing the structural weight. The rocket components considered are ring stiffened truncated cones and cylinders. The applied loading is static, and can consist of any combination of internal or external pressure, axial force, bending moment, and torque. Stress margins are calculated by means of simple closed form strength of material type equations. Stability margins are determined by approximate, orthotropic-shell, closed-form equations. A modified form of Powell's method, in conjunction with a modified form of the external penalty method, is used to determine the minimum weight of the structure subject to stress and stability margin constraints, as well as user input constraints on the structural dimensions. The graphical interface guides the user through the required data prompts, explains program options and graphically displays results for easy interpretation.

Software systems for modeling articulated figures

NASA Technical Reports Server (NTRS)

Phillips, Cary B.

1989-01-01

Research in computer animation and simulation of human task performance requires sophisticated geometric modeling and user interface tools. The software for a research environment should present the programmer with a powerful but flexible substrate of facilities for displaying and manipulating geometric objects, yet insure that future tools have a consistent and friendly user interface. Jack is a system which provides a flexible and extensible programmer and user interface for displaying and manipulating complex geometric figures, particularly human figures in a 3D working environment. It is a basic software framework for high-performance Silicon Graphics IRIS workstations for modeling and manipulating geometric objects in a general but powerful way. It provides a consistent and user-friendly interface across various applications in computer animation and simulation of human task performance. Currently, Jack provides input and control for applications including lighting specification and image rendering, anthropometric modeling, figure positioning, inverse kinematics, dynamic simulation, and keyframe animation.

Automation Applications in an Advanced Air Traffic Management System : Volume 5A. DELTA Simulation Model - User's Guide

DOT National Transportation Integrated Search

1974-08-01

Volume 4 describes the automation requirements. A presentation of automation requirements is made for an advanced air traffic management system in terms of controller work for-e, computer resources, controller productivity, system manning, failure ef...

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…

User Vulnerability and its Reduction on a Social Networking Site

DTIC Science & Technology

2014-01-01

social networking sites bring about new...and explore other users’ profiles and friend networks. Social networking sites have reshaped business models [Vayner- chuk 2009], provided platform... social networking sites is to enable users to be more social, user privacy and security issues cannot be ignored. On one hand, most social networking sites

A generic template for automated bioanalytical ligand-binding assays using modular robotic scripts in support of discovery biotherapeutic programs.

PubMed

Duo, Jia; Dong, Huijin; DeSilva, Binodh; Zhang, Yan J

2013-07-01

Sample dilution and reagent pipetting are time-consuming steps in ligand-binding assays (LBAs). Traditional automation-assisted LBAs use assay-specific scripts that require labor-intensive script writing and user training. Five major script modules were developed on Tecan Freedom EVO liquid handling software to facilitate the automated sample preparation and LBA procedure: sample dilution, sample minimum required dilution, standard/QC minimum required dilution, standard/QC/sample addition, and reagent addition. The modular design of automation scripts allowed the users to assemble an automated assay with minimal script modification. The application of the template was demonstrated in three LBAs to support discovery biotherapeutic programs. The results demonstrated that the modular scripts provided the flexibility in adapting to various LBA formats and the significant time saving in script writing and scientist training. Data generated by the automated process were comparable to those by manual process while the bioanalytical productivity was significantly improved using the modular robotic scripts.

Application of multi-factorial design of experiments to successfully optimize immunoassays for robust measurements of therapeutic proteins.

PubMed

Ray, Chad A; Patel, Vimal; Shih, Judy; Macaraeg, Chris; Wu, Yuling; Thway, Theingi; Ma, Mark; Lee, Jean W; Desilva, Binodh

2009-02-20

Developing a process that generates robust immunoassays that can be used to support studies with tight timelines is a common challenge for bioanalytical laboratories. Design of experiments (DOEs) is a tool that has been used by many industries for the purpose of optimizing processes. The approach is capable of identifying critical factors and their interactions with a minimal number of experiments. The challenge for implementing this tool in the bioanalytical laboratory is to develop a user-friendly approach that scientists can understand and apply. We have successfully addressed these challenges by eliminating the screening design, introducing automation, and applying a simple mathematical approach for the output parameter. A modified central composite design (CCD) was applied to three ligand binding assays. The intra-plate factors selected were coating, detection antibody concentration, and streptavidin-HRP concentrations. The inter-plate factors included incubation times for each step. The objective was to maximize the logS/B (S/B) of the low standard to the blank. The maximum desirable conditions were determined using JMP 7.0. To verify the validity of the predictions, the logS/B prediction was compared against the observed logS/B during pre-study validation experiments. The three assays were optimized using the multi-factorial DOE. The total error for all three methods was less than 20% which indicated method robustness. DOE identified interactions in one of the methods. The model predictions for logS/B were within 25% of the observed pre-study validation values for all methods tested. The comparison between the CCD and hybrid screening design yielded comparable parameter estimates. The user-friendly design enables effective application of multi-factorial DOE to optimize ligand binding assays for therapeutic proteins. The approach allows for identification of interactions between factors, consistency in optimal parameter determination, and reduced method development time.

Students' Facebook "Friends": Public and Private Spheres

ERIC Educational Resources Information Center

West, Anne; Lewis, Jane; Currie, Peter

2009-01-01

Friendship is highly significant during the university years. Facebook, widely used by students, is designed to facilitate communication with different groups of "friends". This exploratory study involved interviewing a sample of student users of Facebook: it focuses on the extent to which older adults, especially parents, are accepted as Facebook…

Workflow efficiency of two 1.5 T MR scanners with and without an automated user interface for head examinations.

PubMed

Moenninghoff, Christoph; Umutlu, Lale; Kloeters, Christian; Ringelstein, Adrian; Ladd, Mark E; Sombetzki, Antje; Lauenstein, Thomas C; Forsting, Michael; Schlamann, Marc

2013-06-01

Workflow efficiency and workload of radiological technologists (RTs) were compared in head examinations performed with two 1.5 T magnetic resonance (MR) scanners equipped with or without an automated user interface called "day optimizing throughput" (Dot) workflow engine. Thirty-four patients with known intracranial pathology were examined with a 1.5 T MR scanner with Dot workflow engine (Siemens MAGNETOM Aera) and with a 1.5 T MR scanner with conventional user interface (Siemens MAGNETOM Avanto) using four standardized examination protocols. The elapsed time for all necessary work steps, which were performed by 11 RTs within the total examination time, was compared for each examination at both MR scanners. The RTs evaluated the user-friendliness of both scanners by a questionnaire. Normality of distribution was checked for all continuous variables by use of the Shapiro-Wilk test. Normally distributed variables were analyzed by Student's paired t-test, otherwise Wilcoxon signed-rank test was used to compare means. Total examination time of MR examinations performed with Dot engine was reduced from 24:53 to 20:01 minutes (P < .001) and the necessary RT intervention decreased by 61% (P < .001). The Dot engine's automated choice of MR protocols was significantly better assessed by the RTs than the conventional user interface (P = .001). According to this preliminary study, the Dot workflow engine is a time-saving user assistance software, which decreases the RTs' effort significantly and may help to automate neuroradiological examinations for a higher workflow efficiency. Copyright © 2013 AUR. Published by Elsevier Inc. All rights reserved.

High School and Beyond: Twins and Siblings' File Users' Manual, User's Manual for Teacher Comment File, Friends File Users' Manual.

ERIC Educational Resources Information Center

National Center for Education Statistics (ED), Washington, DC.

These three users' manuals are for specific files of the High School and Beyond Study, a national longitudinal study of high school sophomores and seniors in 1980. The three files are computerized databases that are available on magnetic tape. As one component of base year data collection, information identifying twins, triplets, and some non-twin…

Automated Data Handling And Instrument Control Using Low-Cost Desktop Computers And An IEEE 488 Compatible Version Of The ODETA V.

NASA Astrophysics Data System (ADS)

van Leunen, J. A. J.; Dreessen, J.

1984-05-01

The result of a measurement of the modulation transfer function is only useful as long as it is accompanied by a complete description of all relevant measuring conditions involved. For this reason it is necessary to file a full description of the relevant measuring conditions together with the results. In earlier times some of our results were rendered useless because some of the relevant measuring conditions were accidentally not written down and were forgotten. This was mainly due to the lack of concensus about which measuring conditions had to be filed together with the result of a measurement. One way to secure uniform and complete archiving of measuring conditions and results is to automate the data handling. An attendent advantage of automation of data handling is that it does away with the time-consuming correction of rough measuring results. The automation of the data handling was accomplished with rather cheap desktop computers, which were powerfull enough, however, to allow us to automate the measurement as well. After automation of the data handling we started with automatic collection of rough measurement data. Step by step we extended the automation by letting the desktop computer control more and more of the measuring set-up. At present the desktop computer controls all the electrical and most of the mechanical measuring conditions. Further it controls and reads the MTF measuring instrument. Focussing and orientation optimization can be fully automatic, semi-automatic or completely manual. MTF measuring results can be collected automatically but they can also be typed in by hand. Due to the automation we are able to implement proper archival of measuring results together with all necessary measuring conditions. The improved measuring efficiency made it possible to increase the number of routine measurements done in the same time period by an order of magnitude. To our surprise the measuring accuracy also improved by a factor of two. This was due to the much better reproducibility of the automatic optimization, which resulted in better reproducibility of the measurement result. Another advantage of the automation is that the programs that control the data handling and the automatic measurement are "user friendly". They guide the operator through the measuring procedure using information from earlier measurements of equivalent test specimens. This makes it possible to let routine measurements be done by much less skilled assistants. It also removes much of the tedious routine labour normally involved in MTF measurements. It can be concluded that automation of MTF measurements as described in the foregoing enhances the usefulness of MTF results as well as reducing the cost of MTF measurements.

Assessment of newborn screening parent education materials.

PubMed

Arnold, Connie L; Davis, Terry C; Frempong, Janet Ohene; Humiston, Sharon G; Bocchini, Anna; Kennen, Estela M; Lloyd-Puryear, Michele

2006-05-01

The purpose of this study was to measure the readability and user-friendliness (clarity, complexity, organization, appearance, and cultural appropriateness of materials) of parent education brochures on newborn screening. We studied English-language versions of the brochures that state newborn screening programs prepare and distribute. We obtained brochures from 48 states and Puerto Rico. We evaluated each brochure for readability with the Flesch reading ease formula. User-friendliness of the brochures was assessed with an instrument we created that contained 22 specific criteria grouped into 5 categories, ie, layout, illustrations, message, manageable information, and cultural appropriateness. Most current newborn screening brochures should be revised to make them more readable and user-friendly for parents. Ninety-two percent of brochures were written at a reading level that is higher than the average reading level of US adults (eighth-grade level). In most brochures, the essential information for parents was buried. Although all brochures were brief and focused on the newborn screening tests being performed, 81% needed improvement in getting to the point quickly and making it easy for parents to identify what they needed to know or to do. None of the brochures scored high in all 22 criteria on the user-friendliness checklist. Parent education materials about newborn screening should be revised to be easier to read and more user-friendly, by lowering the reading difficulty to eighth-grade level and focusing on issues such as layout, illustrations, message, information, and cultural appropriateness. It is important that state newborn screening programs and organizations work with parents to develop and to evaluate materials to ensure that they are user-friendly.

Virtual reality for intelligent and interactive operating, training, and visualization systems

NASA Astrophysics Data System (ADS)

Freund, Eckhard; Rossmann, Juergen; Schluse, Michael

2000-10-01

Virtual Reality Methods allow a new and intuitive way of communication between man and machine. The basic idea of Virtual Reality (VR) is the generation of artificial computer simulated worlds, which the user not only can look at but also can interact with actively using data glove and data helmet. The main emphasis for the use of such techniques at the IRF is the development of a new generation of operator interfaces for the control of robots and other automation components and for intelligent training systems for complex tasks. The basic idea of the methods developed at the IRF for the realization of Projective Virtual Reality is to let the user work in the virtual world as he would act in reality. The user actions are recognized by the Virtual reality System and by means of new and intelligent control software projected onto the automation components like robots which afterwards perform the necessary actions in reality to execute the users task. In this operation mode the user no longer has to be a robot expert to generate tasks for robots or to program them, because intelligent control software recognizes the users intention and generated automatically the commands for nearly every automation component. Now, Virtual Reality Methods are ideally suited for universal man-machine-interfaces for the control and supervision of a big class of automation components, interactive training and visualization systems. The Virtual Reality System of the IRF-COSIMIR/VR- forms the basis for different projects starting with the control of space automation systems in the projects CIROS, VITAL and GETEX, the realization of a comprehensive development tool for the International Space Station and last but not least with the realistic simulation fire extinguishing, forest machines and excavators which will be presented in the final paper in addition to the key ideas of this Virtual Reality System.

User-friendly design approach for analog layout design

NASA Astrophysics Data System (ADS)

Li, Yongfu; Lee, Zhao Chuan; Tripathi, Vikas; Perez, Valerio; Ong, Yoong Seang; Hui, Chiu Wing

2017-03-01

Analog circuits are sensitives to the changes in the layout environment conditions, manufacturing processes, and variations. This paper presents analog verification flow with five types of analogfocused layout constraint checks to assist engineers in identifying any potential device mismatch and layout drawing mistakes. Compared to several solutions, our approach only requires layout design, which is sufficient to recognize all the matched devices. Our approach simplifies the data preparation and allows seamless integration into the layout environment with minimum disruption to the custom layout flow. Our user-friendly analog verification flow provides the engineer with more confident with their layouts quality.

The automated multi-stage substructuring system for NASTRAN

NASA Technical Reports Server (NTRS)

Field, E. I.; Herting, D. N.; Herendeen, D. L.; Hoesly, R. L.

1975-01-01

The substructuring capability developed for eventual installation in Level 16 is now operational in a test version of NASTRAN. Its features are summarized. These include the user-oriented, Case Control type control language, the automated multi-stage matrix processing, the independent direct access data storage facilities, and the static and normal modes solution capabilities. A complete problem analysis sequence is presented with card-by-card description of the user input.

Automated processing of thermal infrared images of Osservatorio Vesuviano permanent surveillance network by using Matlab code

NASA Astrophysics Data System (ADS)

Sansivero, Fabio; Vilardo, Giuseppe; Caputo, Teresa

2017-04-01

The permanent thermal infrared surveillance network of Osservatorio Vesuviano (INGV) is composed of 6 stations which acquire IR frames of fumarole fields in the Campi Flegrei caldera and inside the Vesuvius crater (Italy). The IR frames are uploaded to a dedicated server in the Surveillance Center of Osservatorio Vesuviano in order to process the infrared data and to excerpt all the information contained. In a first phase the infrared data are processed by an automated system (A.S.I.R.A. Acq- Automated System of IR Analysis and Acquisition) developed in Matlab environment and with a user-friendly graphic user interface (GUI). ASIRA daily generates time-series of residual temperature values of the maximum temperatures observed in the IR scenes after the removal of seasonal effects. These time-series are displayed in the Surveillance Room of Osservatorio Vesuviano and provide information about the evolution of shallow temperatures field of the observed areas. In particular the features of ASIRA Acq include: a) efficient quality selection of IR scenes, b) IR images co-registration in respect of a reference frame, c) seasonal correction by using a background-removal methodology, a) filing of IR matrices and of the processed data in shared archives accessible to interrogation. The daily archived records can be also processed by ASIRA Plot (Matlab code with GUI) to visualize IR data time-series and to help in evaluating inputs parameters for further data processing and analysis. Additional processing features are accomplished in a second phase by ASIRA Tools which is Matlab code with GUI developed to extract further information from the dataset in automated way. The main functions of ASIRA Tools are: a) the analysis of temperature variations of each pixel of the IR frame in a given time interval, b) the removal of seasonal effects from temperature of every pixel in the IR frames by using an analytic approach (removal of sinusoidal long term seasonal component by using a polynomial fit Matlab function - LTFC_SCOREF), c) the export of data in different raster formats (i.e. Surfer grd). An interesting example of elaborations of the data produced by ASIRA Tools is the map of the temperature changing rate, which provide remarkable information about the potential migration of fumarole activity. The high efficiency of Matlab in processing matrix data from IR scenes and the flexibility of this code-developing tool proved to be very useful to produce applications to use in volcanic surveillance aimed to monitor the evolution of surface temperatures field in diffuse degassing volcanic areas.

A System for Distributing Real-Time Customized (NEXRAD-Radar) Geosciences Data

NASA Astrophysics Data System (ADS)

Singh, Satpreet; McWhirter, Jeff; Krajewski, Witold; Kruger, Anton; Goska, Radoslaw; Seo, Bongchul; Domaszczynski, Piotr; Weber, Jeff

2010-05-01

Hydrometeorologists and hydrologists can benefit from (weather) radar derived rain products, including rain rates and accumulations. The Hydro-NEXRAD system (HNX1) has been in operation since 2006 at IIHR-Hydroscience and Engineering at The University of Iowa. It provides rapid and user-friendly access to such user-customized products, generated using archived Weather Surveillance Doppler Radar (WSR-88D) data from the NEXRAD weather radar network in the United States. HNX1 allows researchers to deal directly with radar-derived rain products, without the burden of the details of radar data collection, quality control, processing, and format conversion. A number of hydrologic applications can benefit from a continuous real-time feed of customized radar-derived rain products. We are currently developing such a system, Hydro-NEXRAD 2 (HNX2). HNX2 collects real-time, unprocessed data from multiple NEXRAD radars as they become available, processes them through a user-configurable pipeline of data-processing modules, and then publishes processed products at regular intervals. Modules in the data processing pipeline encapsulate algorithms such as non-meteorological echo detection, range correction, radar-reflectivity-rain rate (Z-R) conversion, advection correction, merging products from multiple radars, and grid transformations. HNX2's implementation presents significant challenges, including quality-control, error-handling, time-synchronization of data from multiple asynchronous sources, generation of multiple-radar metadata products, distribution of products to a user base with diverse needs and constraints, and scalability. For content management and distribution, HNX2 uses RAMADDA (Repository for Archiving, Managing and Accessing Diverse Data), developed by the UCAR/Unidata Program Center in the Unites States. RAMADDA allows HNX2 to publish products through automation and gives users multiple access methods to the published products, including simple web-browser based access, and OpenDAP access. The latter allows a user to set up automation at his/her end, and fetch new data from HNX2 at regular intervals. HNX2 uses a two-dimensional metadata structure called a mosaic for managing metadata of the rain products. Currently, HNX2 is in pre-production state and is serving near real-time rain-rate map data-products for individual radars and merged data-products from seven radars covering the state of Iowa in the United States. These products then drive a rainfall-runoff model called CUENCAS, which is used as part of the Iowa Flood Center (housed at The University of Iowa) real-time flood forecasting system. We are currently developing a generalized scalable framework that will run on inexpensive hardware and will provide products for basins anywhere in the continental United States.

Two Types of Well Followed Users in the Followership Networks of Twitter

PubMed Central

Saito, Kodai; Masuda, Naoki

2014-01-01

In the Twitter blogosphere, the number of followers is probably the most basic and succinct quantity for measuring popularity of users. However, the number of followers can be manipulated in various ways; we can even buy follows. Therefore, alternative popularity measures for Twitter users on the basis of, for example, users' tweets and retweets, have been developed. In the present work, we take a purely network approach to this fundamental question. First, we find that two relatively distinct types of users possessing a large number of followers exist, in particular for Japanese, Russian, and Korean users among the seven language groups that we examined. A first type of user follows a small number of other users. A second type of user follows approximately the same number of other users as the number of follows that the user receives. Then, we compare local (i.e., egocentric) followership networks around the two types of users with many followers. We show that the second type, which is presumably uninfluential users despite its large number of followers, is characterized by high link reciprocity, a large number of friends (i.e., those whom a user follows) for the followers, followers' high link reciprocity, large clustering coefficient, large fraction of the second type of users among the followers, and a small PageRank. Our network-based results support that the number of followers used alone is a misleading measure of user's popularity. We propose that the number of friends, which is simple to measure, also helps us to assess the popularity of Twitter users. PMID:24416209

A user-friendly means to scale from the biochemistry of photosynthesis to whole crop canopies and production in time and space - development of Java WIMOVAC.

PubMed

Song, Qingfeng; Chen, Dairui; Long, Stephen P; Zhu, Xin-Guang

2017-01-01

Windows Intuitive Model of Vegetation response to Atmosphere and Climate Change (WIMOVAC) has been used widely as a generic modular mechanistically rich model of plant production. It can predict the responses of leaf and canopy carbon balance, as well as production in different environmental conditions, in particular those relevant to global change. Here, we introduce an open source Java user-friendly version of WIMOVAC. This software is platform independent and can be easily downloaded to a laptop and used without any prior programming skills. In this article, we describe the structure, equations and user guide and illustrate some potential applications of WIMOVAC. © 2016 The Authors Plant, Cell & Environment Published by John Wiley & Sons Ltd.

The Change to Administrative Computing in Schools.

ERIC Educational Resources Information Center

Brown, Daniel J.

1984-01-01

Describes a study of the process of school office automation which focuses on personnel reactions to administrative computing, what users view as advantages and disadvantages of the automation, perceived barriers and facilitators of the change to automation, school personnel view of long term effects, and implications for school computer policy.…

Automating Document Delivery: A Conference Report.

ERIC Educational Resources Information Center

Ensor, Pat

1992-01-01

Describes presentations made at a forum on automation, interlibrary loan (ILL), and document delivery sponsored by the Houston Area Library Consortium. Highlights include access versus ownership; software for ILL; fee-based services; automated management systems for ILL; and electronic mail and online systems for end-user-generated ILL requests.…

Automation Applications in an Advanced Air Traffic Management System : Volume 5B. DELTA Simulation Model - Programmer's Guide.

DOT National Transportation Integrated Search

1974-08-01

Volume 5 describes the DELTA Simulation Model. It includes all documentation of the DELTA (Determine Effective Levels of Task Automation) computer simulation developed by TRW for use in the Automation Applications Study. Volume 5A includes a user's m...

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.

Semi-automated Neuron Boundary Detection and Nonbranching Process Segmentation in Electron Microscopy Images

PubMed Central

Jurrus, Elizabeth; Watanabe, Shigeki; Giuly, Richard J.; Paiva, Antonio R. C.; Ellisman, Mark H.; Jorgensen, Erik M.; Tasdizen, Tolga

2013-01-01

Neuroscientists are developing new imaging techniques and generating large volumes of data in an effort to understand the complex structure of the nervous system. The complexity and size of this data makes human interpretation a labor-intensive task. To aid in the analysis, new segmentation techniques for identifying neurons in these feature rich datasets are required. This paper presents a method for neuron boundary detection and nonbranching process segmentation in electron microscopy images and visualizing them in three dimensions. It combines both automated segmentation techniques with a graphical user interface for correction of mistakes in the automated process. The automated process first uses machine learning and image processing techniques to identify neuron membranes that deliniate the cells in each two-dimensional section. To segment nonbranching processes, the cell regions in each two-dimensional section are connected in 3D using correlation of regions between sections. The combination of this method with a graphical user interface specially designed for this purpose, enables users to quickly segment cellular processes in large volumes. PMID:22644867

Semi-Automated Neuron Boundary Detection and Nonbranching Process Segmentation in Electron Microscopy Images

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

Jurrus, Elizabeth R.; Watanabe, Shigeki; Giuly, Richard J.

2013-01-01

Neuroscientists are developing new imaging techniques and generating large volumes of data in an effort to understand the complex structure of the nervous system. The complexity and size of this data makes human interpretation a labor-intensive task. To aid in the analysis, new segmentation techniques for identifying neurons in these feature rich datasets are required. This paper presents a method for neuron boundary detection and nonbranching process segmentation in electron microscopy images and visualizing them in three dimensions. It combines both automated segmentation techniques with a graphical user interface for correction of mistakes in the automated process. The automated processmore » first uses machine learning and image processing techniques to identify neuron membranes that deliniate the cells in each two-dimensional section. To segment nonbranching processes, the cell regions in each two-dimensional section are connected in 3D using correlation of regions between sections. The combination of this method with a graphical user interface specially designed for this purpose, enables users to quickly segment cellular processes in large volumes.« less

A two-dimensionally coincident second difference cosmic ray spike removal method for the fully automated processing of Raman spectra.

PubMed

Schulze, H Georg; Turner, Robin F B

2014-01-01

Charge-coupled device detectors are vulnerable to cosmic rays that can contaminate Raman spectra with positive going spikes. Because spikes can adversely affect spectral processing and data analyses, they must be removed. Although both hardware-based and software-based spike removal methods exist, they typically require parameter and threshold specification dependent on well-considered user input. Here, we present a fully automated spike removal algorithm that proceeds without requiring user input. It is minimally dependent on sample attributes, and those that are required (e.g., standard deviation of spectral noise) can be determined with other fully automated procedures. At the core of the method is the identification and location of spikes with coincident second derivatives along both the spectral and spatiotemporal dimensions of two-dimensional datasets. The method can be applied to spectra that are relatively inhomogeneous because it provides fairly effective and selective targeting of spikes resulting in minimal distortion of spectra. Relatively effective spike removal obtained with full automation could provide substantial benefits to users where large numbers of spectra must be processed.

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)

Tweeting the Friendly Skies: Investigating Information Exchange among Twitter Users about Airlines

ERIC Educational Resources Information Center

Sreenivasan, Nirupama Dharmavaram; Lee, Chei Sian; Goh, Dion Hoe-Lian

2012-01-01

Purpose: The purpose of this study is to investigate airline users' microblog postings pertaining to their travel-related information exchange so as to assess their wants, preferences and feedback about airline products and services. Examining such real-time information exchange is important as users rely on this for various purposes such as…

What Friends Are For: Collaborative Intelligence Analysis and Search

DTIC Science & Technology

2014-06-01

14. SUBJECT TERMS Intelligence Community, information retrieval, recommender systems , search engines, social networks, user profiling, Lucene...improvements over existing search systems . The improvements are shown to be robust to high levels of human error and low similarity between users ...precision NOLH nearly orthogonal Latin hypercubes P@ precision at documents RS recommender systems TREC Text REtrieval Conference USM user

ConcreteWorks v3 training/user manual (P1) : ConcreteWorks software (P2).

DOT National Transportation Integrated Search

2017-04-01

ConcreteWorks is designed to be a user-friendly software package that can help concrete : professionals optimize concrete mixture proportioning, perform a concrete thermal analysis, and : increase the chloride diffusion service life. The software pac...

UManSysProp v1.0: an online and open-source facility for molecular property prediction and atmospheric aerosol calculations

NASA Astrophysics Data System (ADS)

Topping, David; Barley, Mark; Bane, Michael K.; Higham, Nicholas; Aumont, Bernard; Dingle, Nicholas; McFiggans, Gordon

2016-03-01

In this paper we describe the development and application of a new web-based facility, UManSysProp (http://umansysprop.seaes.manchester.ac.uk), for automating predictions of molecular and atmospheric aerosol properties. Current facilities include pure component vapour pressures, critical properties, and sub-cooled densities of organic molecules; activity coefficient predictions for mixed inorganic-organic liquid systems; hygroscopic growth factors and CCN (cloud condensation nuclei) activation potential of mixed inorganic-organic aerosol particles; and absorptive partitioning calculations with/without a treatment of non-ideality. The aim of this new facility is to provide a single point of reference for all properties relevant to atmospheric aerosol that have been checked for applicability to atmospheric compounds where possible. The group contribution approach allows users to upload molecular information in the form of SMILES (Simplified Molecular Input Line Entry System) strings and UManSysProp will automatically extract the relevant information for calculations. Built using open-source chemical informatics, and hosted at the University of Manchester, the facilities are provided via a browser and device-friendly web interface, or can be accessed using the user's own code via a JSON API (application program interface). We also provide the source code for all predictive techniques provided on the site, covered by the GNU GPL (General Public License) license to encourage development of a user community. We have released this via a Github repository (doi:10.5281/zenodo.45143). In this paper we demonstrate its use with specific examples that can be simulated using the web-browser interface.

MAC/GMC 4.0 User's Manual: Keywords Manual. Volume 2

NASA Technical Reports Server (NTRS)

Bednarcyk, Brett A.; Arnold, Steven M.

2002-01-01

This document is the second volume in the three volume set of User's Manuals for the Micromechanics Analysis Code with Generalized Method of Cells Version 4.0 (MAC/GMC 4.0). Volume 1 is the Theory Manual, this document is the Keywords Manual, and Volume 3 is the Example Problem Manual. MAC/GMC 4.0 is a composite material and laminate analysis software program developed at the NASA Glenn Research Center. It is based on the generalized method of cells (GMC) micromechanics theory, which provides access to the local stress and strain fields in the composite material. This access grants GMC the ability to accommodate arbitrary local models for inelastic material behavior and various types of damage and failure analysis. MAC/GMC 4.0 has been built around GMC to provide the theory with a user-friendly framework, along with a library of local inelastic, damage, and failure models. Further, applications of simulated thermo-mechanical loading, generation of output results, and selection of architectures to represent the composite material have been automated in MAC/GMC 4.0. Finally, classical lamination theory has been implemented within MAC/GMC 4.0 wherein GMC is used to model the composite material response of each ply. Consequently, the full range of GMC composite material capabilities is available for analysis of arbitrary laminate configurations as well. This volume describes the basic information required to use the MAC/GMC 4.0 software, including a 'Getting Started' section, and an in-depth description of each of the 22 keywords used in the input file to control the execution of the code.

myPhyloDB: a local web server for the storage and analysis of metagenomic data.

PubMed

Manter, Daniel K; Korsa, Matthew; Tebbe, Caleb; Delgado, Jorge A

2016-01-01

myPhyloDB v.1.1.2 is a user-friendly personal database with a browser-interface designed to facilitate the storage, processing, analysis, and distribution of microbial community populations (e.g. 16S metagenomics data). MyPhyloDB archives raw sequencing files, and allows for easy selection of project(s)/sample(s) of any combination from all available data in the database. The data processing capabilities of myPhyloDB are also flexible enough to allow the upload and storage of pre-processed data, or use the built-in Mothur pipeline to automate the processing of raw sequencing data. myPhyloDB provides several analytical (e.g. analysis of covariance,t-tests, linear regression, differential abundance (DESeq2), and principal coordinates analysis (PCoA)) and normalization (rarefaction, DESeq2, and proportion) tools for the comparative analysis of taxonomic abundance, species richness and species diversity for projects of various types (e.g. human-associated, human gut microbiome, air, soil, and water) for any taxonomic level(s) desired. Finally, since myPhyloDB is a local web-server, users can quickly distribute data between colleagues and end-users by simply granting others access to their personal myPhyloDB database. myPhyloDB is available athttp://www.ars.usda.gov/services/software/download.htm?softwareid=472 and more information along with tutorials can be found on our websitehttp://www.myphylodb.org. Database URL:http://www.myphylodb.org. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the United States.

A Full-Featured User Friendly CO 2-EOR and Sequestration Planning Software

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

Savage, Bill

A Full-Featured, User Friendly CO 2-EOR and Sequestration Planning Software This project addressed the development of an integrated software solution that includes a graphical user interface, numerical simulation, visualization tools and optimization processes for reservoir simulation modeling of CO 2-EOR. The objective was to assist the industry in the development of domestic energy resources by expanding the application of CO 2-EOR technologies, and ultimately to maximize the CO 2} sequestration capacity of the U.S. The software resulted in a field-ready application for the industry to address the current CO 2-EOR technologies. The software has been made available to the publicmore » without restrictions and with user friendly operating documentation and tutorials. The software (executable only) can be downloaded from NITEC’s website at www.nitecllc.com. This integrated solution enables the design, optimization and operation of CO 2-EOR processes for small and mid-sized operators, who currently cannot afford the expensive, time intensive solutions that the major oil companies enjoy. Based on one estimate, small oil fields comprise 30% of the of total economic resource potential for the application of CO 2-EOR processes in the U.S. This corresponds to 21.7 billion barrels of incremental, technically recoverable oil using the current “best practices”, and 31.9 billion barrels using “next-generation” CO 2-EOR techniques. The project included a Case Study of a prospective CO 2-EOR candidate field in Wyoming by a small independent, Linc Energy Petroleum Wyoming, Inc. NITEC LLC has an established track record of developing innovative and user friendly software. The Principle Investigator is an experienced manager and engineer with expertise in software development, numerical techniques, and GUI applications. Unique, presently-proprietary NITEC technologies have been integrated into this application to further its ease of use and technical functionality.« less

"Friending Facebook?" A Minicourse on the Use of Social Media by Health Professionals

ERIC Educational Resources Information Center

George, Daniel R.

2011-01-01

Introduction: Health professionals are working in an era of social technologies that empower users to generate content in real time. This article describes a 3-part continuing education minicourse called "Friending Facebook?" undertaken at Penn State Hershey Medical Center that aimed to model the functionality of current technologies in…

Automated Engineering Design (AED); An approach to automated documentation

NASA Technical Reports Server (NTRS)

Mcclure, C. W.

1970-01-01

The automated engineering design (AED) is reviewed, consisting of a high level systems programming language, a series of modular precoded subroutines, and a set of powerful software machine tools that effectively automate the production and design of new languages. AED is used primarily for development of problem and user-oriented languages. Software production phases are diagramed, and factors which inhibit effective documentation are evaluated.

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.

SoRS: Social recommendation using global rating reputation and local rating similarity

NASA Astrophysics Data System (ADS)

Qian, Fulan; Zhao, Shu; Tang, Jie; Zhang, Yanping

2016-11-01

Recommendation is an important and also challenging problem in online social networks. It needs to consider not only users' personalized interests, but also social relations between users. Indeed, in practice, users are often inclined to accept recommendations from friends or opinion leaders (users with high reputations). In this paper, we present a novel recommendation framework, social recommendation using global rating reputation and local rating similarity, which combine user reputation and social similarity based on ratings. User reputation can be obtained by iteratively calculating the correlation of historical ratings of user and intrinsic qualities of items. We view the user reputation as the user's global influence and the similarity based on rating of social relation as the user's local influence, introduce it in the basic social recommender model. Thus users with high reputation have a strong influence on the others, and on the other hand, the effect of a user with low reputation has been weakened. The recommendation accuracy of proposed framework can be improved by effectively removing nature noise because of less rigorous user ratings and strengthening the effect of user influence with high reputation. We also improve the similarity based on ratings by avoiding the high similarity with the less common ratings between friends. We evaluate our approach on three datasets including Movielens, Epinions and Douban. Empirical results demonstrate that proposed framework achieves significant improvements on recommendation accuracy. User reputation and local similarity which are both based on ratings have a lot of helpful in improvement of prediction accuracy. The reputation also can help to improve the recommendation precision with the small training sets.

Early Detection of Clinically Significant Prostate Cancer Using Ultrasonic Acoustic Radiation Force Impulse (ARFI) Imaging

DTIC Science & Technology

2017-10-01

Toolkit for rapid 3D visualization and image volume interpretation, followed by automated transducer positioning in a user-selected image plane for... Toolkit (IGSTK) to enable rapid 3D visualization and image volume interpretation followed by automated transducer positioning in the user-selected... careers in science, technology, and the humanities. What do you plan to do during the next reporting period to accomplish the goals? If this

Improvement of Computer Software Quality through Software Automated Tools.

DTIC Science & Technology

1986-08-30

information that are returned from the tools to the human user, and the forms in which these outputs are presented. Page 2 of 4 STAGE OF DEVELOPMENT: What... AUTOMIATED SOFTWARE TOOL MONITORING SYSTEM APPENDIX 2 2-1 INTRODUCTION This document and Automated Software Tool Monitoring Program (Appendix 1) are...t Output Output features provide links from the tool to both the human user and the target machine (where applicable). They describe the types

Fireballs in the Sky: an Augmented Reality Citizen Science Program

NASA Astrophysics Data System (ADS)

Day, B. H.; Bland, P.; Sayers, R.

2017-12-01

Fireballs in the Sky is an innovative Australian citizen science program that connects the public with the research of the Desert Fireball Network (DFN). This research aims to understand the early workings of the solar system, and Fireballs in the Sky invites people around the world to learn about this science, contributing fireball sightings via a user-friendly augmented reality mobile app. Tens of thousands of people have downloaded the app world-wide and participated in the science of meteoritics. The Fireballs in the Sky app allows users to get involved with the Desert Fireball Network research, supplementing DFN observations and providing enhanced coverage by reporting their own meteor sightings to DFN scientists. Fireballs in the Sky reports are used to track the trajectories of meteors - from their orbit in space to where they might have landed on Earth. Led by Phil Bland at Curtin University in Australia, the Desert Fireball Network (DFN) uses automated observatories across Australia to triangulate trajectories of meteorites entering the atmosphere, determine pre-entry orbits, and pinpoint their fall positions. Each observatory is an autonomous intelligent imaging system, taking 1000×36Megapixel all-sky images throughout the night, using neural network algorithms to recognize events. They are capable of operating for 12 months in a harsh environment, and store all imagery collected. We developed a completely automated software pipeline for data reduction, and built a supercomputer database for storage, allowing us to process our entire archive. The DFN currently stands at 50 stations distributed across the Australian continent, covering an area of 2.5 million km^2. Working with DFN's partners at NASA's Solar System Exploration Research Virtual Institute, the team is expanding the network beyond Australia to locations around the world. Fireballs in the Sky allows a growing public base to learn about and participate in this exciting research.

Fireballs in the Sky: An Augmented Reality Citizen Science Program

NASA Technical Reports Server (NTRS)

Day, Brian

2017-01-01

Fireballs in the Sky is an innovative Australian citizen science program that connects the public with the research of the Desert Fireball Network (DFN). This research aims to understand the early workings of the solar system, and Fireballs in the Sky invites people around the world to learn about this science, contributing fireball sightings via a user-friendly augmented reality mobile app. Tens of thousands of people have downloaded the app world-wide and participated in the science of meteoritics. The Fireballs in the Sky app allows users to get involved with the Desert Fireball Network research, supplementing DFN observations and providing enhanced coverage by reporting their own meteor sightings to DFN scientists. Fireballs in the Sky reports are used to track the trajectories of meteors - from their orbit in space to where they might have landed on Earth. Led by Phil Bland at Curtin University in Australia, the Desert Fireball Network (DFN) uses automated observatories across Australia to triangulate trajectories of meteorites entering the atmosphere, determine pre-entry orbits, and pinpoint their fall positions. Each observatory is an autonomous intelligent imaging system, taking 1000 by 36 megapixel all-sky images throughout the night, using neural network algorithms to recognize events. They are capable of operating for 12 months in a harsh environment, and store all imagery collected. We developed a completely automated software pipeline for data reduction, and built a supercomputer database for storage, allowing us to process our entire archive. The DFN currently stands at 50 stations distributed across the Australian continent, covering an area of 2.5 million square kilometers. Working with DFN's partners at NASA's Solar System Exploration Research Virtual Institute, the team is expanding the network beyond Australia to locations around the world. Fireballs in the Sky allows a growing public base to learn about and participate in this exciting research.

The more friends, the less political talk? Predictors of Facebook discussions among college students.

PubMed

Jang, S Mo; Lee, Hoon; Park, Yong Jin

2014-05-01

Although previous research has indicated that Facebook users, especially young adults, can cultivate their civic values by talking about public matters with their Facebook friends, little research has examined the predictors of political discussion on Facebook. Using survey data from 442 college students in the United States, this study finds that individual characteristics and network size influence college students' expressive behavior on Facebook related to two controversial topics: gay rights issues and politics. In line with previous studies about offline political discussion, the results show that conflict avoidance and ambivalence about target issues are negatively associated with Facebook discussions. Perhaps the most interesting finding is that users who have a large number of Facebook friends are less likely to talk about politics and gay rights issues on Facebook despite having access to increasing human and information resources. Theoretical implications of these findings and future directions are addressed.

Mathematical imaging methods for mitosis analysis in live-cell phase contrast microscopy.

PubMed

Grah, Joana Sarah; Harrington, Jennifer Alison; Koh, Siang Boon; Pike, Jeremy Andrew; Schreiner, Alexander; Burger, Martin; Schönlieb, Carola-Bibiane; Reichelt, Stefanie

2017-02-15

In this paper we propose a workflow to detect and track mitotic cells in time-lapse microscopy image sequences. In order to avoid the requirement for cell lines expressing fluorescent markers and the associated phototoxicity, phase contrast microscopy is often preferred over fluorescence microscopy in live-cell imaging. However, common specific image characteristics complicate image processing and impede use of standard methods. Nevertheless, automated analysis is desirable due to manual analysis being subjective, biased and extremely time-consuming for large data sets. Here, we present the following workflow based on mathematical imaging methods. In the first step, mitosis detection is performed by means of the circular Hough transform. The obtained circular contour subsequently serves as an initialisation for the tracking algorithm based on variational methods. It is sub-divided into two parts: in order to determine the beginning of the whole mitosis cycle, a backwards tracking procedure is performed. After that, the cell is tracked forwards in time until the end of mitosis. As a result, the average of mitosis duration and ratios of different cell fates (cell death, no division, division into two or more daughter cells) can be measured and statistics on cell morphologies can be obtained. All of the tools are featured in the user-friendly MATLAB®Graphical User Interface MitosisAnalyser. Copyright © 2017. Published by Elsevier Inc.

Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences.

PubMed

Zhang, Jianwei; Kudrna, Dave; Mu, Ting; Li, Weiming; Copetti, Dario; Yu, Yeisoo; Goicoechea, Jose Luis; Lei, Yang; Wing, Rod A

2016-10-15

Next generation sequencing technologies have revolutionized our ability to rapidly and affordably generate vast quantities of sequence data. Once generated, raw sequences are assembled into contigs or scaffolds. However, these assemblies are mostly fragmented and inaccurate at the whole genome scale, largely due to the inability to integrate additional informative datasets (e.g. physical, optical and genetic maps). To address this problem, we developed a semi-automated software tool-Genome Puzzle Master (GPM)-that enables the integration of additional genomic signposts to edit and build 'new-gen-assemblies' that result in high-quality 'annotation-ready' pseudomolecules. With GPM, loaded datasets can be connected to each other via their logical relationships which accomplishes tasks to 'group,' 'merge,' 'order and orient' sequences in a draft assembly. Manual editing can also be performed with a user-friendly graphical interface. Final pseudomolecules reflect a user's total data package and are available for long-term project management. GPM is a web-based pipeline and an important part of a Laboratory Information Management System (LIMS) which can be easily deployed on local servers for any genome research laboratory. The GPM (with LIMS) package is available at https://github.com/Jianwei-Zhang/LIMS CONTACTS: jzhang@mail.hzau.edu.cn or rwing@mail.arizona.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Dose response explorer: an integrated open-source tool for exploring and modelling radiotherapy dose volume outcome relationships

NASA Astrophysics Data System (ADS)

El Naqa, I.; Suneja, G.; Lindsay, P. E.; Hope, A. J.; Alaly, J. R.; Vicic, M.; Bradley, J. D.; Apte, A.; Deasy, J. O.

2006-11-01

Radiotherapy treatment outcome models are a complicated function of treatment, clinical and biological factors. Our objective is to provide clinicians and scientists with an accurate, flexible and user-friendly software tool to explore radiotherapy outcomes data and build statistical tumour control or normal tissue complications models. The software tool, called the dose response explorer system (DREES), is based on Matlab, and uses a named-field structure array data type. DREES/Matlab in combination with another open-source tool (CERR) provides an environment for analysing treatment outcomes. DREES provides many radiotherapy outcome modelling features, including (1) fitting of analytical normal tissue complication probability (NTCP) and tumour control probability (TCP) models, (2) combined modelling of multiple dose-volume variables (e.g., mean dose, max dose, etc) and clinical factors (age, gender, stage, etc) using multi-term regression modelling, (3) manual or automated selection of logistic or actuarial model variables using bootstrap statistical resampling, (4) estimation of uncertainty in model parameters, (5) performance assessment of univariate and multivariate analyses using Spearman's rank correlation and chi-square statistics, boxplots, nomograms, Kaplan-Meier survival plots, and receiver operating characteristics curves, and (6) graphical capabilities to visualize NTCP or TCP prediction versus selected variable models using various plots. DREES provides clinical researchers with a tool customized for radiotherapy outcome modelling. DREES is freely distributed. We expect to continue developing DREES based on user feedback.

Development and Feasibility Testing of a Smartphone Intervention to Improve Adherence to Antipsychotic Medications.

PubMed

Kreyenbuhl, Julie; Record, Elizabeth J; Himelhoch, Seth; Charlotte, Melanie; Palmer-Bacon, Jessica; Dixon, Lisa B; Medoff, Deborah R; Li, Lan

2016-07-25

Approximately 60% of individuals with schizophrenia do not take their antipsychotic medications as prescribed, and nonadherence is associated with exacerbation of psychotic symptoms, increased hospital and emergency room use, and increased healthcare costs. Behavioral-tailoring strategies that incorporate medication taking into the daily routine and use environmental supports have shown promise as adherence-enhancing interventions. Informed by the Information-Motivation-Behavioral (IMB) Skills Model and using the iterative process of user-centered design, we collaborated with individuals with schizophrenia and psychiatrists to develop an interactive smartphone application and web-based clinician interface, MedActive, for improving adherence to oral antipsychotic treatment. MedActive facilitates the active involvement of individuals with schizophrenia in managing their antipsychotic medication regimen by providing automated reminders for medication administration and tailored motivational feedback to encourage adherence, and by displaying user-friendly results of daily ecological momentary assessments (EMAs) of medication adherence, positive psychotic symptoms, and medication side effects for individuals and their psychiatrists. In a 2-week open trial completed by 7 individuals with schizophrenia and their psychiatrists, MedActive was determined to be both feasible and acceptable, with patient participants responding to 80% of all scheduled EMAs and providing positive evaluations of their use of the application. Psychiatrist participants were interested in viewing the information provided on the MedActive clinician interface, but cited practical barriers to regularly accessing it and integrating into their daily practice.

PHYSICO: An UNIX based Standalone Procedure for Computation of Individual and Group Properties of Protein Sequences.

PubMed

Gupta, Parth Sarthi Sen; Banerjee, Shyamashree; Islam, Rifat Nawaz Ul; Mondal, Sudipta; Mondal, Buddhadev; Bandyopadhyay, Amal K

2014-01-01

In the genomic and proteomic era, efficient and automated analyses of sequence properties of protein have become an important task in bioinformatics. There are general public licensed (GPL) software tools to perform a part of the job. However, computations of mean properties of large number of orthologous sequences are not possible from the above mentioned GPL sets. Further, there is no GPL software or server which can calculate window dependent sequence properties for a large number of sequences in a single run. With a view to overcome above limitations, we have developed a standalone procedure i.e. PHYSICO, which performs various stages of computation in a single run based on the type of input provided either in RAW-FASTA or BLOCK-FASTA format and makes excel output for: a) Composition, Class composition, Mean molecular weight, Isoelectic point, Aliphatic index and GRAVY, b) column based compositions, variability and difference matrix, c) 25 kinds of window dependent sequence properties. The program is fast, efficient, error free and user friendly. Calculation of mean and standard deviation of homologous sequences sets, for comparison purpose when relevant, is another attribute of the program; a property seldom seen in existing GPL softwares. PHYSICO is freely available for non-commercial/academic user in formal request to the corresponding author akbanerjee@biotech.buruniv.ac.in.

PHYSICO: An UNIX based Standalone Procedure for Computation of Individual and Group Properties of Protein Sequences

PubMed Central

Gupta, Parth Sarthi Sen; Banerjee, Shyamashree; Islam, Rifat Nawaz Ul; Mondal, Sudipta; Mondal, Buddhadev; Bandyopadhyay, Amal K

2014-01-01

In the genomic and proteomic era, efficient and automated analyses of sequence properties of protein have become an important task in bioinformatics. There are general public licensed (GPL) software tools to perform a part of the job. However, computations of mean properties of large number of orthologous sequences are not possible from the above mentioned GPL sets. Further, there is no GPL software or server which can calculate window dependent sequence properties for a large number of sequences in a single run. With a view to overcome above limitations, we have developed a standalone procedure i.e. PHYSICO, which performs various stages of computation in a single run based on the type of input provided either in RAW-FASTA or BLOCK-FASTA format and makes excel output for: a) Composition, Class composition, Mean molecular weight, Isoelectic point, Aliphatic index and GRAVY, b) column based compositions, variability and difference matrix, c) 25 kinds of window dependent sequence properties. The program is fast, efficient, error free and user friendly. Calculation of mean and standard deviation of homologous sequences sets, for comparison purpose when relevant, is another attribute of the program; a property seldom seen in existing GPL softwares. Availability PHYSICO is freely available for non-commercial/academic user in formal request to the corresponding author akbanerjee@biotech.buruniv.ac.in PMID:24616564

CMS Connect

NASA Astrophysics Data System (ADS)

Balcas, J.; Bockelman, B.; Gardner, R., Jr.; Hurtado Anampa, K.; Jayatilaka, B.; Aftab Khan, F.; Lannon, K.; Larson, K.; Letts, J.; Marra Da Silva, J.; Mascheroni, M.; Mason, D.; Perez-Calero Yzquierdo, A.; Tiradani, A.

2017-10-01

The CMS experiment collects and analyzes large amounts of data coming from high energy particle collisions produced by the Large Hadron Collider (LHC) at CERN. This involves a huge amount of real and simulated data processing that needs to be handled in batch-oriented platforms. The CMS Global Pool of computing resources provide +100K dedicated CPU cores and another 50K to 100K CPU cores from opportunistic resources for these kind of tasks and even though production and event processing analysis workflows are already managed by existing tools, there is still a lack of support to submit final stage condor-like analysis jobs familiar to Tier-3 or local Computing Facilities users into these distributed resources in an integrated (with other CMS services) and friendly way. CMS Connect is a set of computing tools and services designed to augment existing services in the CMS Physics community focusing on these kind of condor analysis jobs. It is based on the CI-Connect platform developed by the Open Science Grid and uses the CMS GlideInWMS infrastructure to transparently plug CMS global grid resources into a virtual pool accessed via a single submission machine. This paper describes the specific developments and deployment of CMS Connect beyond the CI-Connect platform in order to integrate the service with CMS specific needs, including specific Site submission, accounting of jobs and automated reporting to standard CMS monitoring resources in an effortless way to their users.

Efficient Segmentation of a Breast in B-Mode Ultrasound Tomography Using Three-Dimensional GrabCut (GC3D)

PubMed Central

Wu, Shibin; Zhuang, Ling; Wei, Xinhua; Sak, Mark; Neb, Duric; Hu, Jiani; Xie, Yaoqin

2017-01-01

As an emerging modality for whole breast imaging, ultrasound tomography (UST), has been adopted for diagnostic purposes. Efficient segmentation of an entire breast in UST images plays an important role in quantitative tissue analysis and cancer diagnosis, while major existing methods suffer from considerable time consumption and intensive user interaction. This paper explores three-dimensional GrabCut (GC3D) for breast isolation in thirty reflection (B-mode) UST volumetric images. The algorithm can be conveniently initialized by localizing points to form a polygon, which covers the potential breast region. Moreover, two other variations of GrabCut and an active contour method were compared. Algorithm performance was evaluated from volume overlap ratios (TO, target overlap; MO, mean overlap; FP, false positive; FN, false negative) and time consumption. Experimental results indicate that GC3D considerably reduced the work load and achieved good performance (TO = 0.84; MO = 0.91; FP = 0.006; FN = 0.16) within an average of 1.2 min per volume. Furthermore, GC3D is not only user friendly, but also robust to various inputs, suggesting its great potential to facilitate clinical applications during whole-breast UST imaging. In the near future, the implemented GC3D can be easily automated to tackle B-mode UST volumetric images acquired from the updated imaging system. PMID:28786946

Reliability of an Automated High-Resolution Manometry Analysis Program across Expert Users, Novice Users, and Speech-Language Pathologists

ERIC Educational Resources Information Center

Jones, Corinne A.; Hoffman, Matthew R.; Geng, Zhixian; Abdelhalim, Suzan M.; Jiang, Jack J.; McCulloch, Timothy M.

2014-01-01

Purpose: The purpose of this study was to investigate inter- and intrarater reliability among expert users, novice users, and speech-language pathologists with a semiautomated high-resolution manometry analysis program. We hypothesized that all users would have high intrarater reliability and high interrater reliability. Method: Three expert…

webPOISONCONTROL: can poison control be automated?

PubMed

Litovitz, Toby; Benson, Blaine E; Smolinske, Susan

2016-08-01

A free webPOISONCONTROL app allows the public to determine the appropriate triage of poison ingestions without calling poison control. If accepted and safe, this alternative expands access to reliable poison control services to those who prefer the Internet over the telephone. This study assesses feasibility, safety, and user-acceptance of automated online triage of asymptomatic, nonsuicidal poison ingestion cases. The user provides substance name, amount, age, and weight in an automated online tool or downloadable app, and is given a specific triage recommendation to stay home, go to the emergency department, or call poison control for further guidance. Safety was determined by assessing outcomes of consecutive home-triaged cases with follow-up and by confirming the correct application of algorithms. Case completion times and user perceptions of speed and ease of use were measures of user-acceptance. Of 9256 cases, 73.3% were triaged to home, 2.1% to an emergency department, and 24.5% directed to call poison control. Children younger than 6 years were involved in 75.2% of cases. Automated follow-up was done in 31.2% of home-triaged cases; 82.3% of these had no effect. No major or fatal outcomes were reported. More than 91% of survey respondents found the tool quick and easy to use. Median case completion time was 4.1 minutes. webPOISONCONTROL augments traditional poison control services by providing automated, accurate online access to case-specific triage and first aid guidance for poison ingestions. It is safe, quick, and easy to use. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Investing in the Future: Automation Marketplace 2009

ERIC Educational Resources Information Center

Breeding, Marshall

2009-01-01

In a year where the general economy presented enormous challenges, libraries continued to make investments in automation, especially in products that help improve what and how they deliver to their end users. Access to electronic content remains a key driver. In response to anticipated needs for new approaches to library automation, many companies…

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.

Improving Information Exchange and Coordination amongst Homeland Security Organizations (Briefing Charts)

DTIC Science & Technology

2005-06-01

need for user-defined dashboard • automated monitoring of web data sources • task driven data aggregation and display Working toward automated processing of task, resource, and intelligence updates

National Space Science Data Center data archive and distribution service (NDADS) automated retrieval mail system user's guide

NASA Technical Reports Server (NTRS)

Perry, Charleen M.; Vansteenberg, Michael E.

1992-01-01

The National Space Science Data Center (NSSDC) has developed an automated data retrieval request service utilizing our Data Archive and Distribution Service (NDADS) computer system. NDADS currently has selected project data written to optical disk platters with the disks residing in a robotic 'jukebox' near-line environment. This allows for rapid and automated access to the data with no staff intervention required. There are also automated help information and user services available that can be accessed. The request system permits an average-size data request to be completed within minutes of the request being sent to NSSDC. A mail message, in the format described in this document, retrieves the data and can send it to a remote site. Also listed in this document are the data currently available.

Automating spectral measurements

NASA Astrophysics Data System (ADS)

Goldstein, Fred T.

2008-09-01

This paper discusses the architecture of software utilized in spectroscopic measurements. As optical coatings become more sophisticated, there is mounting need to automate data acquisition (DAQ) from spectrophotometers. Such need is exacerbated when 100% inspection is required, ancillary devices are utilized, cost reduction is crucial, or security is vital. While instrument manufacturers normally provide point-and-click DAQ software, an application programming interface (API) may be missing. In such cases automation is impossible or expensive. An API is typically provided in libraries (*.dll, *.ocx) which may be embedded in user-developed applications. Users can thereby implement DAQ automation in several Windows languages. Another possibility, developed by FTG as an alternative to instrument manufacturers' software, is the ActiveX application (*.exe). ActiveX, a component of many Windows applications, provides means for programming and interoperability. This architecture permits a point-and-click program to act as automation client and server. Excel, for example, can control and be controlled by DAQ applications. Most importantly, ActiveX permits ancillary devices such as barcode readers and XY-stages to be easily and economically integrated into scanning procedures. Since an ActiveX application has its own user-interface, it can be independently tested. The ActiveX application then runs (visibly or invisibly) under DAQ software control. Automation capabilities are accessed via a built-in spectro-BASIC language with industry-standard (VBA-compatible) syntax. Supplementing ActiveX, spectro-BASIC also includes auxiliary serial port commands for interfacing programmable logic controllers (PLC). A typical application is automatic filter handling.

Measuring Individual Differences in the Perfect Automation Schema.

PubMed

Merritt, Stephanie M; Unnerstall, Jennifer L; Lee, Deborah; Huber, Kelli

2015-08-01

A self-report measure of the perfect automation schema (PAS) is developed and tested. Researchers have hypothesized that the extent to which users possess a PAS is associated with greater decreases in trust after users encounter automation errors. However, no measure of the PAS currently exists. We developed a self-report measure assessing two proposed PAS factors: high expectations and all-or-none thinking about automation performance. In two studies, participants responded to our PAS measure, interacted with imperfect automated aids, and reported trust. Each of the two PAS measure factors demonstrated fit to the hypothesized factor structure and convergent and discriminant validity when compared with propensity to trust machines and trust in a specific aid. However, the high expectations and all-or-none thinking scales showed low intercorrelations and differential relationships with outcomes, suggesting that they might best be considered two separate constructs rather than two subfactors of the PAS. All-or-none thinking had significant associations with decreases in trust following aid errors, whereas high expectations did not. Results therefore suggest that the all-or-none thinking scale may best represent the PAS construct. Our PAS measure (specifically, the all-or-none thinking scale) significantly predicted the severe trust decreases thought to be associated with high PAS. Further, it demonstrated acceptable psychometric properties across two samples. This measure may be used in future work to assess levels of PAS in users of automated systems in either research or applied settings. © 2015, Human Factors and Ergonomics Society.

MIROS: A Hybrid Real-Time Energy-Efficient Operating System for the Resource-Constrained Wireless Sensor Nodes

PubMed Central

Liu, Xing; Hou, Kun Mean; de Vaulx, Christophe; Shi, Hongling; Gholami, Khalid El

2014-01-01

Operating system (OS) technology is significant for the proliferation of the wireless sensor network (WSN). With an outstanding OS; the constrained WSN resources (processor; memory and energy) can be utilized efficiently. Moreover; the user application development can be served soundly. In this article; a new hybrid; real-time; memory-efficient; energy-efficient; user-friendly and fault-tolerant WSN OS MIROS is designed and implemented. MIROS implements the hybrid scheduler and the dynamic memory allocator. Real-time scheduling can thus be achieved with low memory consumption. In addition; it implements a mid-layer software EMIDE (Efficient Mid-layer Software for User-Friendly Application Development Environment) to decouple the WSN application from the low-level system. The application programming process can consequently be simplified and the application reprogramming performance improved. Moreover; it combines both the software and the multi-core hardware techniques to conserve the energy resources; improve the node reliability; as well as achieve a new debugging method. To evaluate the performance of MIROS; it is compared with the other WSN OSes (TinyOS; Contiki; SOS; openWSN and mantisOS) from different OS concerns. The final evaluation results prove that MIROS is suitable to be used even on the tight resource-constrained WSN nodes. It can support the real-time WSN applications. Furthermore; it is energy efficient; user friendly and fault tolerant. PMID:25248069

MIROS: a hybrid real-time energy-efficient operating system for the resource-constrained wireless sensor nodes.

PubMed

Liu, Xing; Hou, Kun Mean; de Vaulx, Christophe; Shi, Hongling; El Gholami, Khalid

2014-09-22

Operating system (OS) technology is significant for the proliferation of the wireless sensor network (WSN). With an outstanding OS; the constrained WSN resources (processor; memory and energy) can be utilized efficiently. Moreover; the user application development can be served soundly. In this article; a new hybrid; real-time; memory-efficient; energy-efficient; user-friendly and fault-tolerant WSN OS MIROS is designed and implemented. MIROS implements the hybrid scheduler and the dynamic memory allocator. Real-time scheduling can thus be achieved with low memory consumption. In addition; it implements a mid-layer software EMIDE (Efficient Mid-layer Software for User-Friendly Application Development Environment) to decouple the WSN application from the low-level system. The application programming process can consequently be simplified and the application reprogramming performance improved. Moreover; it combines both the software and the multi-core hardware techniques to conserve the energy resources; improve the node reliability; as well as achieve a new debugging method. To evaluate the performance of MIROS; it is compared with the other WSN OSes (TinyOS; Contiki; SOS; openWSN and mantisOS) from different OS concerns. The final evaluation results prove that MIROS is suitable to be used even on the tight resource-constrained WSN nodes. It can support the real-time WSN applications. Furthermore; it is energy efficient; user friendly and fault tolerant.

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.

Usability Testing, User-Centered Design, and LibGuides Subject Guides: A Case Study

ERIC Educational Resources Information Center

Sonsteby, Alec; DeJonghe, Jennifer

2013-01-01

Usability testing has become a routine way for many libraries to ensure that their Web presence is user-friendly and accessible. At the same time, popular subject guide creation systems, such as LibGuides, decentralize Web content creation and put authorship into the hands of librarians who may not be trained in user-centered design principles. At…

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…

Services for Graduate Students: A Review of Academic Library Web Sites

ERIC Educational Resources Information Center

Rempel, Hannah Gascho

2010-01-01

A library's Web site is well recognized as the gateway to the library for the vast majority of users. Choosing the most user-friendly Web architecture to reflect the many services libraries offer is a complex process, and librarians are still experimenting to find what works best for their users. As part of a redesign of the Oregon State…

Collective iteration behavior for online social networks

NASA Astrophysics Data System (ADS)

Liu, Jian-Guo; Li, Ren-De; Guo, Qiang; Zhang, Yi-Cheng

2018-06-01

Understanding the patterns of collective behavior in online social network (OSNs) is critical to expanding the knowledge of human behavior and tie relationship. In this paper, we investigate a specific pattern called social signature in Facebook and Wiki users' online communication behaviors, capturing the distribution of frequency of interactions between different alters over time in the ego network. The empirical results show that there are robust social signatures of interactions no matter how friends change over time, which indicates that a stable commutation pattern exists in online communication. By comparing a random null model, we find the that commutation pattern is heterogeneous between ego and alters. Furthermore, in order to regenerate the pattern of the social signature, we present a preferential interaction model, which assumes that new users intend to look for the old users with strong ties while old users have tendency to interact with new friends. The experimental results show that the presented model can reproduce the heterogeneity of social signature by adjusting 2 parameters, the number of communicating targets m and the max number of interactions n, for Facebook users, m = n = 5, for Wiki users, m = 2 and n = 8. This work helps in deeply understanding the regularity of social signature.

Logistics Automation Master Plan (LAMP). Better Logistics Support through Automation.

DTIC Science & Technology

1983-06-01

office micro-computers, positioned throughout the command chain , by providing real time links between LCA and all users: 2. Goals: Assist HQDA staff in...field i.e., Airland Battle 2000. IV-27 Section V: CONCEPT OF EXECUTION Suply (Retail) A. SRstem Description. I. The Division Logistics Property Book...7. Divisional Direct Support Unit Automated Supply System (DDASS)/Direct pport Level Suply Automation (DLSA). DDASS and DLSA are system development

The Clinical Ethnographic Interview: A user-friendly guide to the cultural formulation of distress and help seeking

PubMed Central

Arnault, Denise Saint; Shimabukuro, Shizuka

2013-01-01

Transcultural nursing, psychiatry, and medical anthropology have theorized that practitioners and researchers need more flexible instruments to gather culturally relevant illness experience, meaning, and help seeking. The state of the science is sufficiently developed to allow standardized yet ethnographically sound protocols for assessment. However, vigorous calls for culturally adapted assessment models have yielded little real change in routine practice. This paper describes the conversion of the Diagnostic and Statistical Manual IV, Appendix I Outline for Cultural Formulation into a user-friendly Clinical Ethnographic Interview (CEI), and provides clinical examples of its use in a sample of highly distressed Japanese women. PMID:22194348

A user-friendly application for the extraction of kubios hrv output to an optimal format for statistical analysis - biomed 2011.

PubMed

Johnsen Lind, Andreas; Helge Johnsen, Bjorn; Hill, Labarron K; Sollers Iii, John J; Thayer, Julian F

2011-01-01

The aim of the present manuscript is to present a user-friendly and flexible platform for transforming Kubios HRV output files to an .xls-file format, used by MS Excel. The program utilizes either native or bundled Java and is platform-independent and mobile. This means that it can run without being installed on a computer. It also has an option of continuous transferring of data indicating that it can run in the background while Kubios produces output files. The program checks for changes in the file structure and automatically updates the .xls- output file.

Laser Signature Prediction Using The VALUE Computer Program

NASA Astrophysics Data System (ADS)

Akerman, Alexander; Hoffman, George A.; Patton, Ronald

1989-09-01

A variety of enhancements are being made to the 1976-vintage LASERX computer code. These include: - Surface characterization with BDRF tabular data - Specular reflection from transparent surfaces - Generation of glint direction maps - Generation of relative range imagery - Interface to the LOWTRAN atmospheric transmission code - Interface to the LEOPS laser sensor code - User friendly menu prompting for easy setup Versions of VALUE have been written for both VAX/VMS and PC/DOS computer environments. Outputs have also been revised to be user friendly and include tables, plots, and images for (1) intensity, (2) cross section,(3) reflectance, (4) relative range, (5) region type, and (6) silhouette.

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.

Exploring the Attractiveness of New Psychoactive Substances (NPS) among Experienced Drug Users.

PubMed

van Amsterdam, Jan G C; Nabben, Ton; Keiman, Daan; Haanschoten, Gijs; Korf, Dirk

2015-01-01

A growing number of New Psychoactive Substances (NPS) appear yearly on the European market (81 for the first time in 2013, adding to a total of over 350 NPS). Using semi-structured interviews with 25 Dutch experienced recreational drug users, the role of the Internet and friends in gathering and exchanging information about NPS was elaborated. Furthermore, we investigated how NPS were acquired and which aspects make NPS more or less attractive, including their legal status. It appeared that the Internet was an important source of information about NPS in general. Personal experiences with NPS were preferably shared face-to-face with friends, as for privacy reasons users were cautious to post their experiences on web sites and forums. NPS were usually obtained or bought from friends or-to a lesser extent-purchased via the Internet. The preference for a specific NPS depended on the desired effects (mostly stimulant or psychedelic), price (similar to MDMA or amphetamine), duration of effect (preferably around four hours), and setting (at home, at festivals, or in nightlife). Legal status was not relevant for the decision to use NPS. Most NPS are not superior to the already marketed drugs, and do not displace conventional illicit drugs.

Social Network Infiltration

NASA Astrophysics Data System (ADS)

Plait, Philip

2008-05-01

Social networks are websites (or software that distributes media online) where users can distribute content to either a list of friends on that site or to anyone who surfs onto their page, and where those friends can interact and discuss the content. By linking to friends online, the users’ personal content (pictures, songs, favorite movies, diaries, websites, and so on) is dynamically distributed, and can "become viral", that is, get spread rapidly as more people see it and spread it themselves. Social networks are immensely popular around the planet, especially with younger users. The biggest social networks are Facebook and MySpace; an IYA2009 user already exists on Facebook, and one will be created for MySpace (in fact, several NASA satellites such as GLAST and Swift already have successful MySpace pages). Twitter is another network where data distribution is more limited; it is more like a mini-blog, but is very popular. IYA2009 already has a Twitter page, and will be updated more often with relevant information. In this talk I will review the existing social networks, show people how and why they are useful, and give them the tools they need to contribute meaningfully to IYA's online reach.

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.

A user friendly system for ultrasound carotid intima-media thickness image interpretation

NASA Astrophysics Data System (ADS)

Zhu, Xiangjun; Kendall, Christopher B.; Hurst, R. Todd; Liang, Jianming

2011-03-01

Assessment of Carotid Intima-Media Thickness (CIMT) by B-mode ultrasound is a technically mature and reproducible technology. Given the high morbidity, mortality and the large societal burden associated with CV diseases, as a safe yet inexpensive tool, CIMT is increasingly utilized for cardiovascular (CV) risk stratification. However, CIMT requires a precise measure of the thickness of the intima and media layers of the carotid artery that can be tedious, time consuming, and demand specialized expertise and experience. To this end, we have developed a highly user-friendly system for semiautomatic CIMT image interpretation. Our contribution is the application of active contour models (snake models) with hard constraints, leading to an accurate, adaptive and user-friendly border detection algorithm. A comparison study with the CIMT measurement software in Siemens Syngo® Arterial Health Package shows that our system gives a small bias in mean (0.049 +/-0.051mm) and maximum (0.010 +/- 0.083 mm) CIMT measures and offers a higher reproducibility (average correlation coefficients were 0.948 and 0.844 in mean and maximum CIMT respectively (P <0.001)). This superior performance is attributed to our novel interface design for hard constraints in the snake models.

Quantitative comparison and evaluation of software packages for assessment of abdominal adipose tissue distribution by magnetic resonance imaging.

PubMed

Bonekamp, S; Ghosh, P; Crawford, S; Solga, S F; Horska, A; Brancati, F L; Diehl, A M; Smith, S; Clark, J M

2008-01-01

To examine five available software packages for the assessment of abdominal adipose tissue with magnetic resonance imaging, compare their features and assess the reliability of measurement results. Feature evaluation and test-retest reliability of softwares (NIHImage, SliceOmatic, Analyze, HippoFat and EasyVision) used in manual, semi-automated or automated segmentation of abdominal adipose tissue. A random sample of 15 obese adults with type 2 diabetes. Axial T1-weighted spin echo images centered at vertebral bodies of L2-L3 were acquired at 1.5 T. Five software packages were evaluated (NIHImage, SliceOmatic, Analyze, HippoFat and EasyVision), comparing manual, semi-automated and automated segmentation approaches. Images were segmented into cross-sectional area (CSA), and the areas of visceral (VAT) and subcutaneous adipose tissue (SAT). Ease of learning and use and the design of the graphical user interface (GUI) were rated. Intra-observer accuracy and agreement between the software packages were calculated using intra-class correlation. Intra-class correlation coefficient was used to obtain test-retest reliability. Three of the five evaluated programs offered a semi-automated technique to segment the images based on histogram values or a user-defined threshold. One software package allowed manual delineation only. One fully automated program demonstrated the drawbacks of uncritical automated processing. The semi-automated approaches reduced variability and measurement error, and improved reproducibility. There was no significant difference in the intra-observer agreement in SAT and CSA. The VAT measurements showed significantly lower test-retest reliability. There were some differences between the software packages in qualitative aspects, such as user friendliness. Four out of five packages provided essentially the same results with respect to the inter- and intra-rater reproducibility. Our results using SliceOmatic, Analyze or NIHImage were comparable and could be used interchangeably. Newly developed fully automated approaches should be compared to one of the examined software packages.

Quantitative comparison and evaluation of software packages for assessment of abdominal adipose tissue distribution by magnetic resonance imaging

PubMed Central

Bonekamp, S; Ghosh, P; Crawford, S; Solga, SF; Horska, A; Brancati, FL; Diehl, AM; Smith, S; Clark, JM

2009-01-01

Objective To examine five available software packages for the assessment of abdominal adipose tissue with magnetic resonance imaging, compare their features and assess the reliability of measurement results. Design Feature evaluation and test–retest reliability of softwares (NIHImage, SliceOmatic, Analyze, HippoFat and EasyVision) used in manual, semi-automated or automated segmentation of abdominal adipose tissue. Subjects A random sample of 15 obese adults with type 2 diabetes. Measurements Axial T1-weighted spin echo images centered at vertebral bodies of L2–L3 were acquired at 1.5 T. Five software packages were evaluated (NIHImage, SliceOmatic, Analyze, HippoFat and EasyVision), comparing manual, semi-automated and automated segmentation approaches. Images were segmented into cross-sectional area (CSA), and the areas of visceral (VAT) and subcutaneous adipose tissue (SAT). Ease of learning and use and the design of the graphical user interface (GUI) were rated. Intra-observer accuracy and agreement between the software packages were calculated using intra-class correlation. Intra-class correlation coefficient was used to obtain test–retest reliability. Results Three of the five evaluated programs offered a semi-automated technique to segment the images based on histogram values or a user-defined threshold. One software package allowed manual delineation only. One fully automated program demonstrated the drawbacks of uncritical automated processing. The semi-automated approaches reduced variability and measurement error, and improved reproducibility. There was no significant difference in the intra-observer agreement in SAT and CSA. The VAT measurements showed significantly lower test–retest reliability. There were some differences between the software packages in qualitative aspects, such as user friendliness. Conclusion Four out of five packages provided essentially the same results with respect to the inter- and intra-rater reproducibility. Our results using SliceOmatic, Analyze or NIHImage were comparable and could be used interchangeably. Newly developed fully automated approaches should be compared to one of the examined software packages. PMID:17700582

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.

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.

The ESA/ESO/NASA Photoshop FITS Liberator 3: Have your say on new features

NASA Astrophysics Data System (ADS)

Nielsen, L. H.; Christensen, L. L.; Hurt, R. L.; Nielsen, K.; Johansen, T.

2008-06-01

The popular, free ESA/ESO/NASA Photoshop FITS Liberator image processing software (a plugin for Adobe Photoshop) is about to get simpler, faster and more user-friendly! Here we would like to solicit inputs from the community of users.

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...