ISPAN (Interactive Stiffened Panel Analysis): A tool for quick concept evaluation and design trade studies

NASA Technical Reports Server (NTRS)

Hairr, John W.; Dorris, William J.; Ingram, J. Edward; Shah, Bharat M.

1993-01-01

Interactive Stiffened Panel Analysis (ISPAN) modules, written in FORTRAN, were developed to provide an easy to use tool for creating finite element models of composite material stiffened panels. The modules allow the user to interactively construct, solve and post-process finite element models of four general types of structural panel configurations using only the panel dimensions and properties as input data. Linear, buckling and post-buckling solution capability is provided. This interactive input allows rapid model generation and solution by non finite element users. The results of a parametric study of a blade stiffened panel are presented to demonstrate the usefulness of the ISPAN modules. Also, a non-linear analysis of a test panel was conducted and the results compared to measured data and previous correlation analysis.

C-SPADE: a web-tool for interactive analysis and visualization of drug screening experiments through compound-specific bioactivity dendrograms

PubMed Central

Alam, Zaid; Peddinti, Gopal

2017-01-01

Abstract The advent of polypharmacology paradigm in drug discovery calls for novel chemoinformatic tools for analyzing compounds’ multi-targeting activities. Such tools should provide an intuitive representation of the chemical space through capturing and visualizing underlying patterns of compound similarities linked to their polypharmacological effects. Most of the existing compound-centric chemoinformatics tools lack interactive options and user interfaces that are critical for the real-time needs of chemical biologists carrying out compound screening experiments. Toward that end, we introduce C-SPADE, an open-source exploratory web-tool for interactive analysis and visualization of drug profiling assays (biochemical, cell-based or cell-free) using compound-centric similarity clustering. C-SPADE allows the users to visually map the chemical diversity of a screening panel, explore investigational compounds in terms of their similarity to the screening panel, perform polypharmacological analyses and guide drug-target interaction predictions. C-SPADE requires only the raw drug profiling data as input, and it automatically retrieves the structural information and constructs the compound clusters in real-time, thereby reducing the time required for manual analysis in drug development or repurposing applications. The web-tool provides a customizable visual workspace that can either be downloaded as figure or Newick tree file or shared as a hyperlink with other users. C-SPADE is freely available at http://cspade.fimm.fi/. PMID:28472495

SpirPro: A Spirulina proteome database and web-based tools for the analysis of protein-protein interactions at the metabolic level in Spirulina (Arthrospira) platensis C1.

PubMed

Senachak, Jittisak; Cheevadhanarak, Supapon; Hongsthong, Apiradee

2015-07-29

Spirulina (Arthrospira) platensis is the only cyanobacterium that in addition to being studied at the molecular level and subjected to gene manipulation, can also be mass cultivated in outdoor ponds for commercial use as a food supplement. Thus, encountering environmental changes, including temperature stresses, is common during the mass production of Spirulina. The use of cyanobacteria as an experimental platform, especially for photosynthetic gene manipulation in plants and bacteria, is becoming increasingly important. Understanding the mechanisms and protein-protein interaction networks that underlie low- and high-temperature responses is relevant to Spirulina mass production. To accomplish this goal, high-throughput techniques such as OMICs analyses are used. Thus, large datasets must be collected, managed and subjected to information extraction. Therefore, databases including (i) proteomic analysis and protein-protein interaction (PPI) data and (ii) domain/motif visualization tools are required for potential use in temperature response models for plant chloroplasts and photosynthetic bacteria. A web-based repository was developed including an embedded database, SpirPro, and tools for network visualization. Proteome data were analyzed integrated with protein-protein interactions and/or metabolic pathways from KEGG. The repository provides various information, ranging from raw data (2D-gel images) to associated results, such as data from interaction and/or pathway analyses. This integration allows in silico analyses of protein-protein interactions affected at the metabolic level and, particularly, analyses of interactions between and within the affected metabolic pathways under temperature stresses for comparative proteomic analysis. The developed tool, which is coded in HTML with CSS/JavaScript and depicted in Scalable Vector Graphics (SVG), is designed for interactive analysis and exploration of the constructed network. SpirPro is publicly available on the web at http://spirpro.sbi.kmutt.ac.th . SpirPro is an analysis platform containing an integrated proteome and PPI database that provides the most comprehensive data on this cyanobacterium at the systematic level. As an integrated database, SpirPro can be applied in various analyses, such as temperature stress response networking analysis in cyanobacterial models and interacting domain-domain analysis between proteins of interest.

Using Coupled Energy, Airflow and IAQ Software (TRNSYS/CONTAM) to Evaluate Building Ventilation Strategies.

PubMed

Dols, W Stuart; Emmerich, Steven J; Polidoro, Brian J

2016-03-01

Building energy analysis tools are available in many forms that provide the ability to address a broad spectrum of energy-related issues in various combinations. Often these tools operate in isolation from one another, making it difficult to evaluate the interactions between related phenomena and interacting systems, forcing oversimplified assumptions to be made about various phenomena that could otherwise be addressed directly with another tool. One example of such interdependence is the interaction between heat transfer, inter-zone airflow and indoor contaminant transport. In order to better address these interdependencies, the National Institute of Standards and Technology (NIST) has developed an updated version of the multi-zone airflow and contaminant transport modelling tool, CONTAM, along with a set of utilities to enable coupling of the full CONTAM model with the TRNSYS simulation tool in a more seamless manner and with additional capabilities that were previously not available. This paper provides an overview of these new capabilities and applies them to simulating a medium-size office building. These simulations address the interaction between whole-building energy, airflow and contaminant transport in evaluating various ventilation strategies including natural and demand-controlled ventilation. CONTAM has been in practical use for many years allowing building designers, as well as IAQ and ventilation system analysts, to simulate the complex interactions between building physical layout and HVAC system configuration in determining building airflow and contaminant transport. It has been widely used to design and analyse smoke management systems and evaluate building performance in response to chemical, biological and radiological events. While CONTAM has been used to address design and performance of buildings implementing energy conserving ventilation systems, e.g., natural and hybrid, this new coupled simulation capability will enable users to apply the tool to couple CONTAM with existing energy analysis software to address the interaction between indoor air quality considerations and energy conservation measures in building design and analysis. This paper presents two practical case studies using the coupled modelling tool to evaluate IAQ performance of a CO 2 -based demand-controlled ventilation system under different levels of building envelope airtightness and the design and analysis of a natural ventilation system.

Using Coupled Energy, Airflow and IAQ Software (TRNSYS/CONTAM) to Evaluate Building Ventilation Strategies

PubMed Central

Dols, W. Stuart.; Emmerich, Steven J.; Polidoro, Brian J.

2016-01-01

Building energy analysis tools are available in many forms that provide the ability to address a broad spectrum of energy-related issues in various combinations. Often these tools operate in isolation from one another, making it difficult to evaluate the interactions between related phenomena and interacting systems, forcing oversimplified assumptions to be made about various phenomena that could otherwise be addressed directly with another tool. One example of such interdependence is the interaction between heat transfer, inter-zone airflow and indoor contaminant transport. In order to better address these interdependencies, the National Institute of Standards and Technology (NIST) has developed an updated version of the multi-zone airflow and contaminant transport modelling tool, CONTAM, along with a set of utilities to enable coupling of the full CONTAM model with the TRNSYS simulation tool in a more seamless manner and with additional capabilities that were previously not available. This paper provides an overview of these new capabilities and applies them to simulating a medium-size office building. These simulations address the interaction between whole-building energy, airflow and contaminant transport in evaluating various ventilation strategies including natural and demand-controlled ventilation. Practical Application CONTAM has been in practical use for many years allowing building designers, as well as IAQ and ventilation system analysts, to simulate the complex interactions between building physical layout and HVAC system configuration in determining building airflow and contaminant transport. It has been widely used to design and analyse smoke management systems and evaluate building performance in response to chemical, biological and radiological events. While CONTAM has been used to address design and performance of buildings implementing energy conserving ventilation systems, e.g., natural and hybrid, this new coupled simulation capability will enable users to apply the tool to couple CONTAM with existing energy analysis software to address the interaction between indoor air quality considerations and energy conservation measures in building design and analysis. This paper presents two practical case studies using the coupled modelling tool to evaluate IAQ performance of a CO2-based demand-controlled ventilation system under different levels of building envelope airtightness and the design and analysis of a natural ventilation system. PMID:27099405

Interactive Visual Analysis within Dynamic Ocean Models

NASA Astrophysics Data System (ADS)

Butkiewicz, T.

2012-12-01

The many observation and simulation based ocean models available today can provide crucial insights for all fields of marine research and can serve as valuable references when planning data collection missions. However, the increasing size and complexity of these models makes leveraging their contents difficult for end users. Through a combination of data visualization techniques, interactive analysis tools, and new hardware technologies, the data within these models can be made more accessible to domain scientists. We present an interactive system that supports exploratory visual analysis within large-scale ocean flow models. The currents and eddies within the models are illustrated using effective, particle-based flow visualization techniques. Stereoscopic displays and rendering methods are employed to ensure that the user can correctly perceive the complex 3D structures of depth-dependent flow patterns. Interactive analysis tools are provided which allow the user to experiment through the introduction of their customizable virtual dye particles into the models to explore regions of interest. A multi-touch interface provides natural, efficient interaction, with custom multi-touch gestures simplifying the otherwise challenging tasks of navigating and positioning tools within a 3D environment. We demonstrate the potential applications of our visual analysis environment with two examples of real-world significance: Firstly, an example of using customized particles with physics-based behaviors to simulate pollutant release scenarios, including predicting the oil plume path for the 2010 Deepwater Horizon oil spill disaster. Secondly, an interactive tool for plotting and revising proposed autonomous underwater vehicle mission pathlines with respect to the surrounding flow patterns predicted by the model; as these survey vessels have extremely limited energy budgets, designing more efficient paths allows for greater survey areas.

Control/structure interaction conceptual design tool

NASA Technical Reports Server (NTRS)

Briggs, Hugh C.

1990-01-01

The JPL Control/Structure Interaction Program is developing new analytical methods for designing micro-precision spacecraft with controlled structures. One of these, the Conceptual Design Tool, will illustrate innovative new approaches to the integration of multi-disciplinary analysis and design methods. The tool will be used to demonstrate homogeneity of presentation, uniform data representation across analytical methods, and integrated systems modeling. The tool differs from current 'integrated systems' that support design teams most notably in its support for the new CSI multi-disciplinary engineer. The design tool will utilize a three dimensional solid model of the spacecraft under design as the central data organization metaphor. Various analytical methods, such as finite element structural analysis, control system analysis, and mechanical configuration layout, will store and retrieve data from a hierarchical, object oriented data structure that supports assemblies of components with associated data and algorithms. In addition to managing numerical model data, the tool will assist the designer in organizing, stating, and tracking system requirements.

Tools to Support Human Factors and Systems Engineering Interactions During Early Analysis

NASA Technical Reports Server (NTRS)

Thronesbery, Carroll; Malin, Jane T.; Holden, Kritina; Smith, Danielle Paige

2005-01-01

We describe an approach and existing software tool support for effective interactions between human factors engineers and systems engineers in early analysis activities during system acquisition. We examine the tasks performed during this stage, emphasizing those tasks where system engineers and human engineers interact. The Concept of Operations (ConOps) document is an important product during this phase, and particular attention is paid to its influences on subsequent acquisition activities. Understanding this influence helps ConOps authors describe a complete system concept that guides subsequent acquisition activities. We identify commonly used system engineering and human engineering tools and examine how they can support the specific tasks associated with system definition. We identify possible gaps in the support of these tasks, the largest of which appears to be creating the ConOps document itself. Finally, we outline the goals of our future empirical investigations of tools to support system concept definition.

Tools to Support Human Factors and Systems Engineering Interactions During Early Analysis

NASA Technical Reports Server (NTRS)

Thronesbery, Carroll; Malin, Jane T.; Holden, Kritina; Smith, Danielle Paige

2006-01-01

We describe an approach and existing software tool support for effective interactions between human factors engineers and systems engineers in early analysis activities during system acquisition. We examine the tasks performed during this stage, emphasizing those tasks where system engineers and human engineers interact. The Concept of Operations (ConOps) document is an important product during this phase, and particular attention is paid to its influences on subsequent acquisition activities. Understanding this influence helps ConOps authors describe a complete system concept that guides subsequent acquisition activities. We identify commonly used system engineering and human engineering tools and examine how they can support the specific tasks associated with system definition. We identify possible gaps in the support of these tasks, the largest of which appears to be creating the ConOps document itself. Finally, we outline the goals of our future empirical investigations of tools to support system concept definition.

Interactive visualization to advance earthquake simulation

USGS Publications Warehouse

Kellogg, L.H.; Bawden, G.W.; Bernardin, T.; Billen, M.; Cowgill, E.; Hamann, B.; Jadamec, M.; Kreylos, O.; Staadt, O.; Sumner, D.

2008-01-01

The geological sciences are challenged to manage and interpret increasing volumes of data as observations and simulations increase in size and complexity. For example, simulations of earthquake-related processes typically generate complex, time-varying data sets in two or more dimensions. To facilitate interpretation and analysis of these data sets, evaluate the underlying models, and to drive future calculations, we have developed methods of interactive visualization with a special focus on using immersive virtual reality (VR) environments to interact with models of Earth's surface and interior. Virtual mapping tools allow virtual "field studies" in inaccessible regions. Interactive tools allow us to manipulate shapes in order to construct models of geological features for geodynamic models, while feature extraction tools support quantitative measurement of structures that emerge from numerical simulation or field observations, thereby enabling us to improve our interpretation of the dynamical processes that drive earthquakes. VR has traditionally been used primarily as a presentation tool, albeit with active navigation through data. Reaping the full intellectual benefits of immersive VR as a tool for scientific analysis requires building on the method's strengths, that is, using both 3D perception and interaction with observed or simulated data. This approach also takes advantage of the specialized skills of geological scientists who are trained to interpret, the often limited, geological and geophysical data available from field observations. ?? Birkhaueser 2008.

Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data

PubMed Central

Fernandez, Nicolas F.; Gundersen, Gregory W.; Rahman, Adeeb; Grimes, Mark L.; Rikova, Klarisa; Hornbeck, Peter; Ma’ayan, Avi

2017-01-01

Most tools developed to visualize hierarchically clustered heatmaps generate static images. Clustergrammer is a web-based visualization tool with interactive features such as: zooming, panning, filtering, reordering, sharing, performing enrichment analysis, and providing dynamic gene annotations. Clustergrammer can be used to generate shareable interactive visualizations by uploading a data table to a web-site, or by embedding Clustergrammer in Jupyter Notebooks. The Clustergrammer core libraries can also be used as a toolkit by developers to generate visualizations within their own applications. Clustergrammer is demonstrated using gene expression data from the cancer cell line encyclopedia (CCLE), original post-translational modification data collected from lung cancer cells lines by a mass spectrometry approach, and original cytometry by time of flight (CyTOF) single-cell proteomics data from blood. Clustergrammer enables producing interactive web based visualizations for the analysis of diverse biological data. PMID:28994825

The Blue DRAGON--a system for monitoring the kinematics and the dynamics of endoscopic tools in minimally invasive surgery for objective laparoscopic skill assessment.

PubMed

Rosen, Jacob; Brown, Jeffrey D; Barreca, Marco; Chang, Lily; Hannaford, Blake; Sinanan, Mika

2002-01-01

Minimally invasive surgeiy (MIS) involves a multi-dimensional series of tasks requiring a synthesis between visual information and the kinematics and dynamics of the surgical tools. Analysis of these sources of information is a key step in mastering MIS surgery but may also be used to define objective criteria for characterizing surgical performance. The BIueDRAGON is a new system for acquiring the kinematics and the dynamics of two endoscopic tools along with the visual view of the surgical scene. It includes two four-bar mechanisms equipped with position and force torque sensors for measuring the positions and the orientations (P/O) of two endoscopic tools along with the forces and torques applied by the surgeons hands. The methodology of decomposing the surgical task is based on a fully connected, finite-states (28 states) Markov model where each states corresponded to a fundamental tool/tissue interaction based on the tool kinematics and associated with unique F/T signatures. The experimental protocol included seven MIS tasks performed on an animal model (pig) by 30 surgeons at different levels of their residency training. Preliminary analysis of these data showed that major differences between residents at different skill levels were: (i) the types of tool/tissue interactions being used, (ii) the transitions between tool/tissue interactions being applied by each hand, (iii) time spent while perfonning each tool/tissue interaction, (iv) the overall completion time, and (v) the variable F/T magnitudes being applied by the subjects through the endoscopic tools. Systems like surgical robots or virtual reality simulators that inherently measure the kinematics and the dynamics of the surgical tool may benefit from inclusion of the proposed methodology for analysis of efficacy and objective evaluation of surgical skills during training.

Tools and Equipment Modeling for Automobile Interactive Assembling Operating Simulation

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

Wu Dianliang; Zhu Hongmin; Shanghai Key Laboratory of Advance Manufacturing Environment

Tools and equipment play an important role in the simulation of virtual assembly, especially in the assembly process simulation and plan. Because of variety in function and complexity in structure and manipulation, the simulation of tools and equipments remains to be a challenge for interactive assembly operation. Based on analysis of details and characteristics of interactive operations for automobile assembly, the functional requirement for tools and equipments of automobile assembly is given. Then, a unified modeling method for information expression and function realization of general tools and equipments is represented, and the handling methods of manual, semi-automatic, automatic tools andmore » equipments are discussed. Finally, the application in assembly simulation of rear suspension and front suspension of Roewe 750 automobile is given. The result shows that the modeling and handling methods are applicable in the interactive simulation of various tools and equipments, and can also be used for supporting assembly process planning in virtual environment.« less

ISS Mini AERCam Radio Frequency (RF) Coverage Analysis Using iCAT Development Tool

NASA Technical Reports Server (NTRS)

Bolen, Steve; Vazquez, Luis; Sham, Catherine; Fredrickson, Steven; Fink, Patrick; Cox, Jan; Phan, Chau; Panneton, Robert

2003-01-01

The long-term goals of the National Aeronautics and Space Administration's (NASA's) Human Exploration and Development of Space (HEDS) enterprise may require the development of autonomous free-flier (FF) robotic devices to operate within the vicinity of low-Earth orbiting spacecraft to supplement human extravehicular activities (EVAs) in space. Future missions could require external visual inspection of the spacecraft that would be difficult, or dangerous, for humans to perform. Under some circumstance, it may be necessary to employ an un-tethered communications link between the FF and the users. The interactive coverage analysis tool (ICAT) is a software tool that has been developed to perform critical analysis of the communications link performance for a FF operating in the vicinity of the International Space Station (ISS) external environment. The tool allows users to interactively change multiple parameters of the communications link parameters to efficiently perform systems engineering trades on network performance. These trades can be directly translated into design and requirements specifications. This tool significantly reduces the development time in determining a communications network topology by allowing multiple parameters to be changed, and the results of link coverage to be statistically characterized and plotted interactively.

An interactive distance solution for stroke rehabilitation in the home setting - A feasibility study.

PubMed

Palmcrantz, Susanne; Borg, Jörgen; Sommerfeld, Disa; Plantin, Jeanette; Wall, Anneli; Ehn, Maria; Sjölinder, Marie; Boman, Inga-Lill

2017-09-01

In this study an interactive distance solution (called the DISKO tool) was developed to enable home-based motor training after stroke. The overall aim was to explore the feasibility and safety of using the DISKO-tool, customized for interactive stroke rehabilitation in the home setting, in different rehabilitation phases after stroke. Fifteen patients in three different stages in the continuum of rehabilitation after stroke participated in a home-based training program using the DISKO-tool. The program included 15 training sessions with recurrent follow-ups by the integrated application for video communication with a physiotherapist. Safety and feasibility were assessed from patients, physiotherapists, and a technician using logbooks, interviews, and a questionnaire. Qualitative content analysis and descriptive statistics were used in the analysis. Fourteen out of 15 patients finalized the training period with a mean of 19.5 minutes spent on training at each session. The DISKO-tool was found to be useful and safe by patients and physiotherapists. This study demonstrates the feasibility and safety of the DISKO-tool and provides guidance in further development and testing of interactive distance technology for home rehabilitation, to be used by health care professionals and patients in different phases of rehabilitation after stroke.

Applying Pragmatics Principles for Interaction with Visual Analytics.

PubMed

Hoque, Enamul; Setlur, Vidya; Tory, Melanie; Dykeman, Isaac

2018-01-01

Interactive visual data analysis is most productive when users can focus on answering the questions they have about their data, rather than focusing on how to operate the interface to the analysis tool. One viable approach to engaging users in interactive conversations with their data is a natural language interface to visualizations. These interfaces have the potential to be both more expressive and more accessible than other interaction paradigms. We explore how principles from language pragmatics can be applied to the flow of visual analytical conversations, using natural language as an input modality. We evaluate the effectiveness of pragmatics support in our system Evizeon, and present design considerations for conversation interfaces to visual analytics tools.

Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis

DOE PAGES

Pavlopoulos, Georgios A.; Paez-Espino, David; Kyrpides, Nikos C.; ...

2017-07-18

Gene expression, signal transduction, protein/chemical interactions, biomedical literature cooccurrences, and other concepts are often captured in biological network representations where nodes represent a certain bioentity and edges the connections between them. While many tools to manipulate, visualize, and interactively explore such networks already exist, only few of them can scale up and follow today’s indisputable information growth. In this review, we shortly list a catalog of available network visualization tools and, from a user-experience point of view, we identify four candidate tools suitable for larger-scale network analysis, visualization, and exploration. Lastly, we comment on their strengths and their weaknesses andmore » empirically discuss their scalability, user friendliness, and postvisualization capabilities.« less

Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis

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

Pavlopoulos, Georgios A.; Paez-Espino, David; Kyrpides, Nikos C.

Gene expression, signal transduction, protein/chemical interactions, biomedical literature cooccurrences, and other concepts are often captured in biological network representations where nodes represent a certain bioentity and edges the connections between them. While many tools to manipulate, visualize, and interactively explore such networks already exist, only few of them can scale up and follow today’s indisputable information growth. In this review, we shortly list a catalog of available network visualization tools and, from a user-experience point of view, we identify four candidate tools suitable for larger-scale network analysis, visualization, and exploration. Lastly, we comment on their strengths and their weaknesses andmore » empirically discuss their scalability, user friendliness, and postvisualization capabilities.« less

A drill-soil system modelization for future Mars exploration

NASA Astrophysics Data System (ADS)

Finzi, A. E.; Lavagna, M.; Rocchitelli, G.

2004-01-01

This paper presents a first approach to the problem of modeling a drilling process to be carried on in the space environment by a dedicated payload. Systems devoted to work in space present very strict requirements in many different fields such as thermal response, electric power demand, reliability and so on. Thus, models devoted to the operational behaviour simulation represent a fundamental help in the design phase and give a great improvement in the final product quality. As the required power is the crucial constraint within drilling devices, the tool-soil interaction modelization and simulation are finalized to the computation of the power demand as a function of both the drill and the soil parameters. An accurate study of the tool and the soil separately has been firstly carried on and, secondly their interaction has been analyzed. The Dee-Dri system, designed by Tecnospazio and to be part of the lander components in the NASA's Mars Sample Return Mission, has been taken as the tool reference. The Deep-Drill system is a complex rotary tool devoted to the soil perforation and sample collection; it has to operate in a Martian zone made of rocks similar to the terrestrial basalt, then the modelization is restricted to the interaction analysis between the tool and materials belonging to the rock set. The tool geometric modelization has been faced by a finite element approach with a Langrangian formulation: for the static analysis a refined model is assumed considering both the actual geometry of the head and the rod screws; a simplified model has been used to deal with the dynamic analysis. The soil representation is based on the Mohr-Coulomb crack criterion and an Eulerian approach has been selected to model it. However, software limitations in dealing with the tool-soil interface definition required assuming a Langrangian formulation for the soil too. The interaction between the soil and the tool has been modeled by extending the two-dimensional Nishimatsu's theory for rock cutting for rotating perforation tools. A fine analysis on f.e.m. element choice for each part of the tool is presented together with static analysis results. The dynamic analysis results are limited to the first impact phenomenon between the rock and the tool head. The validity of both the theoretical and numerical models is confirmed by the good agreement between simulation results and data coming from the experiments done within the Tecnospazio facilities.

SACA: Software Assisted Call Analysis--an interactive tool supporting content exploration, online guidance and quality improvement of counseling dialogues.

PubMed

Trinkaus, Hans L; Gaisser, Andrea E

2010-09-01

Nearly 30,000 individual inquiries are answered annually by the telephone cancer information service (CIS, KID) of the German Cancer Research Center (DKFZ). The aim was to develop a tool for evaluating these calls, and to support the complete counseling process interactively. A novel software tool is introduced, based on a structure similar to a music score. Treating the interaction as a "duet", guided by the CIS counselor, the essential contents of the dialogue are extracted automatically. For this, "trained speech recognition" is applied to the (known) counselor's part, and "keyword spotting" is used on the (unknown) client's part to pick out specific items from the "word streams". The outcomes fill an abstract score representing the dialogue. Pilot tests performed on a prototype of SACA (Software Assisted Call Analysis) resulted in a basic proof of concept: Demographic data as well as information regarding the situation of the caller could be identified. The study encourages following up on the vision of an integrated SACA tool for supporting calls online and performing statistics on its knowledge database offline. Further research perspectives are to check SACA's potential in comparison with established interaction analysis systems like RIAS. Copyright (c) 2010 Elsevier Ireland Ltd. All rights reserved.

Interactive Visualization to Advance Earthquake Simulation

NASA Astrophysics Data System (ADS)

Kellogg, Louise H.; Bawden, Gerald W.; Bernardin, Tony; Billen, Magali; Cowgill, Eric; Hamann, Bernd; Jadamec, Margarete; Kreylos, Oliver; Staadt, Oliver; Sumner, Dawn

2008-04-01

The geological sciences are challenged to manage and interpret increasing volumes of data as observations and simulations increase in size and complexity. For example, simulations of earthquake-related processes typically generate complex, time-varying data sets in two or more dimensions. To facilitate interpretation and analysis of these data sets, evaluate the underlying models, and to drive future calculations, we have developed methods of interactive visualization with a special focus on using immersive virtual reality (VR) environments to interact with models of Earth’s surface and interior. Virtual mapping tools allow virtual “field studies” in inaccessible regions. Interactive tools allow us to manipulate shapes in order to construct models of geological features for geodynamic models, while feature extraction tools support quantitative measurement of structures that emerge from numerical simulation or field observations, thereby enabling us to improve our interpretation of the dynamical processes that drive earthquakes. VR has traditionally been used primarily as a presentation tool, albeit with active navigation through data. Reaping the full intellectual benefits of immersive VR as a tool for scientific analysis requires building on the method’s strengths, that is, using both 3D perception and interaction with observed or simulated data. This approach also takes advantage of the specialized skills of geological scientists who are trained to interpret, the often limited, geological and geophysical data available from field observations.

Visualization tool for three-dimensional plasma velocity distributions (ISEE_3D) as a plug-in for SPEDAS

NASA Astrophysics Data System (ADS)

Keika, Kunihiro; Miyoshi, Yoshizumi; Machida, Shinobu; Ieda, Akimasa; Seki, Kanako; Hori, Tomoaki; Miyashita, Yukinaga; Shoji, Masafumi; Shinohara, Iku; Angelopoulos, Vassilis; Lewis, Jim W.; Flores, Aaron

2017-12-01

This paper introduces ISEE_3D, an interactive visualization tool for three-dimensional plasma velocity distribution functions, developed by the Institute for Space-Earth Environmental Research, Nagoya University, Japan. The tool provides a variety of methods to visualize the distribution function of space plasma: scatter, volume, and isosurface modes. The tool also has a wide range of functions, such as displaying magnetic field vectors and two-dimensional slices of distributions to facilitate extensive analysis. The coordinate transformation to the magnetic field coordinates is also implemented in the tool. The source codes of the tool are written as scripts of a widely used data analysis software language, Interactive Data Language, which has been widespread in the field of space physics and solar physics. The current version of the tool can be used for data files of the plasma distribution function from the Geotail satellite mission, which are publicly accessible through the Data Archives and Transmission System of the Institute of Space and Astronautical Science (ISAS)/Japan Aerospace Exploration Agency (JAXA). The tool is also available in the Space Physics Environment Data Analysis Software to visualize plasma data from the Magnetospheric Multiscale and the Time History of Events and Macroscale Interactions during Substorms missions. The tool is planned to be applied to data from other missions, such as Arase (ERG) and Van Allen Probes after replacing or adding data loading plug-ins. This visualization tool helps scientists understand the dynamics of space plasma better, particularly in the regions where the magnetohydrodynamic approximation is not valid, for example, the Earth's inner magnetosphere, magnetopause, bow shock, and plasma sheet.

Hydrogen Financial Analysis Scenario Tool (H2FAST). Web Tool User's Manual

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

Bush, B.; Penev, M.; Melaina, M.

The Hydrogen Financial Analysis Scenario Tool (H2FAST) provides a quick and convenient indepth financial analysis for hydrogen fueling stations. This manual describes how to use the H2FAST web tool, which is one of three H2FAST formats developed by the National Renewable Energy Laboratory (NREL). Although all of the formats are based on the same financial computations and conform to generally accepted accounting principles (FASAB 2014, Investopedia 2014), each format provides a different level of complexity and user interactivity.

Using Enabling Technologies to Facilitate the Comparison of Satellite Observations with the Model Forecasts for Hurricane Study

NASA Astrophysics Data System (ADS)

Li, P.; Knosp, B.; Hristova-Veleva, S. M.; Niamsuwan, N.; Johnson, M. P.; Shen, T. P. J.; Tanelli, S.; Turk, J.; Vu, Q. A.

2014-12-01

Due to their complexity and volume, the satellite data are underutilized in today's hurricane research and operations. To better utilize these data, we developed the JPL Tropical Cyclone Information System (TCIS) - an Interactive Data Portal providing fusion between Near-Real-Time satellite observations and model forecasts to facilitate model evaluation and improvement. We have collected satellite observations and model forecasts in the Atlantic Basin and the East Pacific for the hurricane seasons since 2010 and supported the NASA Airborne Campaigns for Hurricane Study such as the Genesis and Rapid Intensification Processes (GRIP) in 2010 and the Hurricane and Severe Storm Sentinel (HS3) from 2012 to 2014. To enable the direct inter-comparisons of the satellite observations and the model forecasts, the TCIS was integrated with the NASA Earth Observing System Simulator Suite (NEOS3) to produce synthetic observations (e.g. simulated passive microwave brightness temperatures) from a number of operational hurricane forecast models (HWRF and GFS). An automated process was developed to trigger NEOS3 simulations via web services given the location and time of satellite observations, monitor the progress of the NEOS3 simulations, display the synthetic observation and ingest them into the TCIS database when they are done. In addition, three analysis tools, the joint PDF analysis of the brightness temperatures, ARCHER for finding the storm-center and the storm organization and the Wave Number Analysis tool for storm asymmetry and morphology analysis were integrated into TCIS to provide statistical and structural analysis on both observed and synthetic data. Interactive tools were built in the TCIS visualization system to allow the spatial and temporal selections of the datasets, the invocation of the tools with user specified parameters, and the display and the delivery of the results. In this presentation, we will describe the key enabling technologies behind the design of the TCIS interactive data portal and analysis tools, including the spatial database technology for the representation and query of the level 2 satellite data, the automatic process flow using web services, the interactive user interface using the Google Earth API, and a common and expandable Python wrapper to invoke the analysis tools.

Quantitative Imaging In Pathology (QUIP) | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

This site hosts web accessible applications, tools and data designed to support analysis, management, and exploration of whole slide tissue images for cancer research. The following tools are included: caMicroscope: A digital pathology data management and visualization plaform that enables interactive viewing of whole slide tissue images and segmentation results. caMicroscope can be also used independently of QUIP. FeatureExplorer: An interactive tool to allow patient-level feature exploration across multiple dimensions.

Query2Question: Translating Visualization Interaction into Natural Language.

PubMed

Nafari, Maryam; Weaver, Chris

2015-06-01

Richly interactive visualization tools are increasingly popular for data exploration and analysis in a wide variety of domains. Existing systems and techniques for recording provenance of interaction focus either on comprehensive automated recording of low-level interaction events or on idiosyncratic manual transcription of high-level analysis activities. In this paper, we present the architecture and translation design of a query-to-question (Q2Q) system that automatically records user interactions and presents them semantically using natural language (written English). Q2Q takes advantage of domain knowledge and uses natural language generation (NLG) techniques to translate and transcribe a progression of interactive visualization states into a visual log of styled text that complements and effectively extends the functionality of visualization tools. We present Q2Q as a means to support a cross-examination process in which questions rather than interactions are the focus of analytic reasoning and action. We describe the architecture and implementation of the Q2Q system, discuss key design factors and variations that effect question generation, and present several visualizations that incorporate Q2Q for analysis in a variety of knowledge domains.

Data Analysis Tools and Methods for Improving the Interaction Design in E-Learning

ERIC Educational Resources Information Center

Popescu, Paul Stefan

2015-01-01

In this digital era, learning from data gathered from different software systems may have a great impact on the quality of the interaction experience. There are two main directions that come to enhance this emerging research domain, Intelligent Data Analysis (IDA) and Human Computer Interaction (HCI). HCI specific research methodologies can be…

Interactive Planning under Uncertainty with Casual Modeling and Analysis

DTIC Science & Technology

2006-01-01

Tool ( CAT ), a system for creating and analyzing causal models similar to Bayes networks. In order to use CAT as a tool for planning, users go through...an iterative process in which they use CAT to create and an- alyze alternative plans. One of the biggest difficulties is that the number of possible...Causal Analysis Tool ( CAT ), which is a tool for representing and analyzing causal networks sim- ilar to Bayesian networks. In order to represent plans

New generation of exploration tools: interactive modeling software and microcomputers

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

Krajewski, S.A.

1986-08-01

Software packages offering interactive modeling techniques are now available for use on microcomputer hardware systems. These packages are reasonably priced for both company and independent explorationists; they do not require users to have high levels of computer literacy; they are capable of rapidly completing complex ranges of sophisticated geologic and geophysical modeling tasks; and they can produce presentation-quality output for comparison with real-world data. For example, interactive packages are available for mapping, log analysis, seismic modeling, reservoir studies, and financial projects as well as for applying a variety of statistical and geostatistical techniques to analysis of exploration data. More importantly,more » these packages enable explorationists to directly apply their geologic expertise when developing and fine-tuning models for identifying new prospects and for extending producing fields. As a result of these features, microcomputers and interactive modeling software are becoming common tools in many exploration offices. Gravity and magnetics software programs illustrate some of the capabilities of such exploration tools.« less

Analysis of yield and oil from a series of canola breeding trials. Part II. Exploring variety by environment interaction using factor analysis.

PubMed

Cullis, B R; Smith, A B; Beeck, C P; Cowling, W A

2010-11-01

Exploring and exploiting variety by environment (V × E) interaction is one of the major challenges facing plant breeders. In paper I of this series, we presented an approach to modelling V × E interaction in the analysis of complex multi-environment trials using factor analytic models. In this paper, we develop a range of statistical tools which explore V × E interaction in this context. These tools include graphical displays such as heat-maps of genetic correlation matrices as well as so-called E-scaled uniplots that are a more informative alternative to the classical biplot for large plant breeding multi-environment trials. We also present a new approach to prediction for multi-environment trials that include pedigree information. This approach allows meaningful selection indices to be formed either for potential new varieties or potential parents.

atBioNet--an integrated network analysis tool for genomics and biomarker discovery.

PubMed

Ding, Yijun; Chen, Minjun; Liu, Zhichao; Ding, Don; Ye, Yanbin; Zhang, Min; Kelly, Reagan; Guo, Li; Su, Zhenqiang; Harris, Stephen C; Qian, Feng; Ge, Weigong; Fang, Hong; Xu, Xiaowei; Tong, Weida

2012-07-20

Large amounts of mammalian protein-protein interaction (PPI) data have been generated and are available for public use. From a systems biology perspective, Proteins/genes interactions encode the key mechanisms distinguishing disease and health, and such mechanisms can be uncovered through network analysis. An effective network analysis tool should integrate different content-specific PPI databases into a comprehensive network format with a user-friendly platform to identify key functional modules/pathways and the underlying mechanisms of disease and toxicity. atBioNet integrates seven publicly available PPI databases into a network-specific knowledge base. Knowledge expansion is achieved by expanding a user supplied proteins/genes list with interactions from its integrated PPI network. The statistically significant functional modules are determined by applying a fast network-clustering algorithm (SCAN: a Structural Clustering Algorithm for Networks). The functional modules can be visualized either separately or together in the context of the whole network. Integration of pathway information enables enrichment analysis and assessment of the biological function of modules. Three case studies are presented using publicly available disease gene signatures as a basis to discover new biomarkers for acute leukemia, systemic lupus erythematosus, and breast cancer. The results demonstrated that atBioNet can not only identify functional modules and pathways related to the studied diseases, but this information can also be used to hypothesize novel biomarkers for future analysis. atBioNet is a free web-based network analysis tool that provides a systematic insight into proteins/genes interactions through examining significant functional modules. The identified functional modules are useful for determining underlying mechanisms of disease and biomarker discovery. It can be accessed at: http://www.fda.gov/ScienceResearch/BioinformaticsTools/ucm285284.htm.

An experiment with interactive planning models

NASA Technical Reports Server (NTRS)

Beville, J.; Wagner, J. H.; Zannetos, Z. S.

1970-01-01

Experiments on decision making in planning problems are described. Executives were tested in dealing with capital investments and competitive pricing decisions under conditions of uncertainty. A software package, the interactive risk analysis model system, was developed, and two controlled experiments were conducted. It is concluded that planning models can aid management, and predicted uses of the models are as a central tool, as an educational tool, to improve consistency in decision making, to improve communications, and as a tool for consensus decision making.

SHAPA: An interactive software tool for protocol analysis applied to aircrew communications and workload

NASA Technical Reports Server (NTRS)

James, Jeffrey M.; Sanderson, Penelope M.; Seidler, Karen S.

1990-01-01

As modern transport environments become increasingly complex, issues such as crew communication, interaction with automation, and workload management have become crucial. Much research is being focused on holistic aspects of social and cognitive behavior, such as the strategies used to handle workload, the flow of information, the scheduling of tasks, the verbal and non-verbal interactions between crew members. Traditional laboratory performance measures no longer sufficiently meet the needs of researchers addressing these issues. However observational techniques are better equipped to capture the type of data needed and to build models of the requisite level of sophistication. Presented here is SHAPA, an interactive software tool for performing both verbal and non-verbal protocol analysis. It has been developed with the idea of affording the researchers the closest possible degree of engagement with protocol data. The researcher can configure SHAPA to encode protocols using any theoretical framework or encoding vocabulary that is desired. SHAPA allows protocol analysis to be performed at any level of analysis, and it supplies a wide variety of tools for data aggregation, manipulation. The output generated by SHAPA can be used alone or in combination with other performance variables to get a rich picture of the influences on sequences of verbal or nonverbal behavior.

A Survey of Educational Games as Interaction Design Tools for Affective Learning: Thematic Analysis Taxonomy

ERIC Educational Resources Information Center

Yusoff, Zarwina; Kamsin, Amirrudin; Shamshirband, Shahaboddin; Chronopoulos, Anthony T.

2018-01-01

A Computer game is the new platform in generating learning experiences for educational purposes. There are many educational games that have been used as an interaction design tool in a learning environment to enhance students learning outcomes. However, research also claims that playing video games can have a negative impact on student behavior,…

Scalable Visual Analytics of Massive Textual Datasets

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

Krishnan, Manoj Kumar; Bohn, Shawn J.; Cowley, Wendy E.

2007-04-01

This paper describes the first scalable implementation of text processing engine used in Visual Analytics tools. These tools aid information analysts in interacting with and understanding large textual information content through visual interfaces. By developing parallel implementation of the text processing engine, we enabled visual analytics tools to exploit cluster architectures and handle massive dataset. The paper describes key elements of our parallelization approach and demonstrates virtually linear scaling when processing multi-gigabyte data sets such as Pubmed. This approach enables interactive analysis of large datasets beyond capabilities of existing state-of-the art visual analytics tools.

Evaluation of a computerized aid for creating human behavioral representations of human-computer interaction.

PubMed

Williams, Kent E; Voigt, Jeffrey R

2004-01-01

The research reported herein presents the results of an empirical evaluation that focused on the accuracy and reliability of cognitive models created using a computerized tool: the cognitive analysis tool for human-computer interaction (CAT-HCI). A sample of participants, expert in interacting with a newly developed tactical display for the U.S. Army's Bradley Fighting Vehicle, individually modeled their knowledge of 4 specific tasks employing the CAT-HCI tool. Measures of the accuracy and consistency of task models created by these task domain experts using the tool were compared with task models created by a double expert. The findings indicated a high degree of consistency and accuracy between the different "single experts" in the task domain in terms of the resultant models generated using the tool. Actual or potential applications of this research include assessing human-computer interaction complexity, determining the productivity of human-computer interfaces, and analyzing an interface design to determine whether methods can be automated.

modPDZpep: a web resource for structure based analysis of human PDZ-mediated interaction networks.

PubMed

Sain, Neetu; Mohanty, Debasisa

2016-09-21

PDZ domains recognize short sequence stretches usually present in C-terminal of their interaction partners. Because of the involvement of PDZ domains in many important biological processes, several attempts have been made for developing bioinformatics tools for genome-wide identification of PDZ interaction networks. Currently available tools for prediction of interaction partners of PDZ domains utilize machine learning approach. Since, they have been trained using experimental substrate specificity data for specific PDZ families, their applicability is limited to PDZ families closely related to the training set. These tools also do not allow analysis of PDZ-peptide interaction interfaces. We have used a structure based approach to develop modPDZpep, a program to predict the interaction partners of human PDZ domains and analyze structural details of PDZ interaction interfaces. modPDZpep predicts interaction partners by using structural models of PDZ-peptide complexes and evaluating binding energy scores using residue based statistical pair potentials. Since, it does not require training using experimental data on peptide binding affinity, it can predict substrates for diverse PDZ families. Because of the use of simple scoring function for binding energy, it is also fast enough for genome scale structure based analysis of PDZ interaction networks. Benchmarking using artificial as well as real negative datasets indicates good predictive power with ROC-AUC values in the range of 0.7 to 0.9 for a large number of human PDZ domains. Another novel feature of modPDZpep is its ability to map novel PDZ mediated interactions in human protein-protein interaction networks, either by utilizing available experimental phage display data or by structure based predictions. In summary, we have developed modPDZpep, a web-server for structure based analysis of human PDZ domains. It is freely available at http://www.nii.ac.in/modPDZpep.html or http://202.54.226.235/modPDZpep.html . This article was reviewed by Michael Gromiha and Zoltán Gáspári.

Analyses of track shift under high-speed vehicle-track interaction : safety of high speed ground transportation systems

DOT National Transportation Integrated Search

1997-06-01

This report describes analysis tools to predict shift under high-speed vehicle- : track interaction. The analysis approach is based on two fundamental models : developed (as part of this research); the first model computes the track lateral : residua...

Using Interactive Visualization to Analyze Solid Earth Data and Geodynamics Models

NASA Astrophysics Data System (ADS)

Kellogg, L. H.; Kreylos, O.; Billen, M. I.; Hamann, B.; Jadamec, M. A.; Rundle, J. B.; van Aalsburg, J.; Yikilmaz, M. B.

2008-12-01

The geological sciences are challenged to manage and interpret increasing volumes of data as observations and simulations increase in size and complexity. Major projects such as EarthScope and GeoEarthScope are producing the data needed to characterize the structure and kinematics of Earth's surface and interior at unprecedented resolution. At the same time, high-performance computing enables high-precision and fine- detail simulation of geodynamics processes, complementing the observational data. To facilitate interpretation and analysis of these datasets, to evaluate models, and to drive future calculations, we have developed methods of interactive visualization with a special focus on using immersive virtual reality (VR) environments to interact with models of Earth's surface and interior. VR has traditionally been used primarily as a presentation tool allowing active navigation through data. Reaping the full intellectual benefits of immersive VR as a tool for accelerated scientific analysis requires building on the method's strengths, that is, using both 3D perception and interaction with observed or simulated data. Our approach to VR takes advantage of the specialized skills of geoscientists who are trained to interpret geological and geophysical data generated from field observations. Interactive tools allow the scientist to explore and interpret geodynamic models, tomographic models, and topographic observations, while feature extraction tools support quantitative measurement of structures that emerge from numerical simulations or field observations. The use of VR technology enables us to improve our interpretation of crust and mantle structure and of geodynamical processes. Mapping tools based on computer visualization allow virtual "field studies" in inaccessible regions, and an interactive tool allows us to construct digital fault models for use in numerical models. Using the interactive tools on a high-end platform such as an immersive virtual reality room known as a Cave Automatic Virtual Environment (CAVE), enables the scientist to stand in data three-dimensional dataset while taking measurements. The CAVE involves three or more projection surfaces arranged as walls in a room. Stereo projectors combined with a motion tracking system and immersion recreates the experience of carrying out research in the field. This high-end system provides significant advantages for scientists working with complex volumetric data. The interactive tools also work on low-cost platforms that provide stereo views and the potential for interactivity such as a Geowall or a 3D enabled TV. The Geowall is also a well-established tool for education, and in combination with the tools we have developed, enables the rapid transfer of research data and new knowledge to the classroom. The interactive visualization tools can also be used on a desktop or laptop with or without stereo capability. Further information about the Virtual Reality User Interface (VRUI), the 3DVisualizer, the Virtual mapping tools, and the LIDAR viewer, can be found on the KeckCAVES website, www.keckcaves.org.

TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks.

PubMed

Lepoivre, Cyrille; Bergon, Aurélie; Lopez, Fabrice; Perumal, Narayanan B; Nguyen, Catherine; Imbert, Jean; Puthier, Denis

2012-01-31

Deciphering gene regulatory networks by in silico approaches is a crucial step in the study of the molecular perturbations that occur in diseases. The development of regulatory maps is a tedious process requiring the comprehensive integration of various evidences scattered over biological databases. Thus, the research community would greatly benefit from having a unified database storing known and predicted molecular interactions. Furthermore, given the intrinsic complexity of the data, the development of new tools offering integrated and meaningful visualizations of molecular interactions is necessary to help users drawing new hypotheses without being overwhelmed by the density of the subsequent graph. We extend the previously developed TranscriptomeBrowser database with a set of tables containing 1,594,978 human and mouse molecular interactions. The database includes: (i) predicted regulatory interactions (computed by scanning vertebrate alignments with a set of 1,213 position weight matrices), (ii) potential regulatory interactions inferred from systematic analysis of ChIP-seq experiments, (iii) regulatory interactions curated from the literature, (iv) predicted post-transcriptional regulation by micro-RNA, (v) protein kinase-substrate interactions and (vi) physical protein-protein interactions. In order to easily retrieve and efficiently analyze these interactions, we developed In-teractomeBrowser, a graph-based knowledge browser that comes as a plug-in for Transcriptome-Browser. The first objective of InteractomeBrowser is to provide a user-friendly tool to get new insight into any gene list by providing a context-specific display of putative regulatory and physical interactions. To achieve this, InteractomeBrowser relies on a "cell compartments-based layout" that makes use of a subset of the Gene Ontology to map gene products onto relevant cell compartments. This layout is particularly powerful for visual integration of heterogeneous biological information and is a productive avenue in generating new hypotheses. The second objective of InteractomeBrowser is to fill the gap between interaction databases and dynamic modeling. It is thus compatible with the network analysis software Cytoscape and with the Gene Interaction Network simulation software (GINsim). We provide examples underlying the benefits of this visualization tool for large gene set analysis related to thymocyte differentiation. The InteractomeBrowser plugin is a powerful tool to get quick access to a knowledge database that includes both predicted and validated molecular interactions. InteractomeBrowser is available through the TranscriptomeBrowser framework and can be found at: http://tagc.univ-mrs.fr/tbrowser/. Our database is updated on a regular basis.

The Spectral Image Processing System (SIPS) - Interactive visualization and analysis of imaging spectrometer data

NASA Technical Reports Server (NTRS)

Kruse, F. A.; Lefkoff, A. B.; Boardman, J. W.; Heidebrecht, K. B.; Shapiro, A. T.; Barloon, P. J.; Goetz, A. F. H.

1993-01-01

The Center for the Study of Earth from Space (CSES) at the University of Colorado, Boulder, has developed a prototype interactive software system called the Spectral Image Processing System (SIPS) using IDL (the Interactive Data Language) on UNIX-based workstations. SIPS is designed to take advantage of the combination of high spectral resolution and spatial data presentation unique to imaging spectrometers. It streamlines analysis of these data by allowing scientists to rapidly interact with entire datasets. SIPS provides visualization tools for rapid exploratory analysis and numerical tools for quantitative modeling. The user interface is X-Windows-based, user friendly, and provides 'point and click' operation. SIPS is being used for multidisciplinary research concentrating on use of physically based analysis methods to enhance scientific results from imaging spectrometer data. The objective of this continuing effort is to develop operational techniques for quantitative analysis of imaging spectrometer data and to make them available to the scientific community prior to the launch of imaging spectrometer satellite systems such as the Earth Observing System (EOS) High Resolution Imaging Spectrometer (HIRIS).

PIVOT: platform for interactive analysis and visualization of transcriptomics data.

PubMed

Zhu, Qin; Fisher, Stephen A; Dueck, Hannah; Middleton, Sarah; Khaladkar, Mugdha; Kim, Junhyong

2018-01-05

Many R packages have been developed for transcriptome analysis but their use often requires familiarity with R and integrating results of different packages requires scripts to wrangle the datatypes. Furthermore, exploratory data analyses often generate multiple derived datasets such as data subsets or data transformations, which can be difficult to track. Here we present PIVOT, an R-based platform that wraps open source transcriptome analysis packages with a uniform user interface and graphical data management that allows non-programmers to interactively explore transcriptomics data. PIVOT supports more than 40 popular open source packages for transcriptome analysis and provides an extensive set of tools for statistical data manipulations. A graph-based visual interface is used to represent the links between derived datasets, allowing easy tracking of data versions. PIVOT further supports automatic report generation, publication-quality plots, and program/data state saving, such that all analysis can be saved, shared and reproduced. PIVOT will allow researchers with broad background to easily access sophisticated transcriptome analysis tools and interactively explore transcriptome datasets.

OpenPrescribing: normalised data and software tool to research trends in English NHS primary care prescribing 1998-2016.

PubMed

Curtis, Helen J; Goldacre, Ben

2018-02-23

We aimed to compile and normalise England's national prescribing data for 1998-2016 to facilitate research on long-term time trends and create an open-data exploration tool for wider use. We compiled data from each individual year's national statistical publications and normalised them by mapping each drug to its current classification within the national formulary where possible. We created a freely accessible, interactive web tool to allow anyone to interact with the processed data. We downloaded all available annual prescription cost analysis datasets, which include cost and quantity for all prescription items dispensed in the community in England. Medical devices and appliances were excluded. We measured the extent of normalisation of data and aimed to produce a functioning accessible analysis tool. All data were imported successfully. 87.5% of drugs were matched exactly on name to the current formulary and a further 6.5% to similar drug names. All drugs in core clinical chapters were reconciled to their current location in the data schema, with only 1.26% of drugs not assigned a current chemical code. We created an openly accessible interactive tool to facilitate wider use of these data. Publicly available data can be made accessible through interactive online tools to help researchers and policy-makers explore time trends in prescribing. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

ULg Spectra: An Interactive Software Tool to Improve Undergraduate Students' Structural Analysis Skills

ERIC Educational Resources Information Center

Agnello, Armelinda; Carre, Cyril; Billen, Roland; Leyh, Bernard; De Pauw, Edwin; Damblon, Christian

2018-01-01

The analysis of spectroscopic data to solve chemical structures requires practical skills and drills. In this context, we have developed ULg Spectra, a computer-based tool designed to improve the ability of learners to perform complex reasoning. The identification of organic chemical compounds involves gathering and interpreting complementary…

ExAtlas: An interactive online tool for meta-analysis of gene expression data.

PubMed

Sharov, Alexei A; Schlessinger, David; Ko, Minoru S H

2015-12-01

We have developed ExAtlas, an on-line software tool for meta-analysis and visualization of gene expression data. In contrast to existing software tools, ExAtlas compares multi-component data sets and generates results for all combinations (e.g. all gene expression profiles versus all Gene Ontology annotations). ExAtlas handles both users' own data and data extracted semi-automatically from the public repository (GEO/NCBI database). ExAtlas provides a variety of tools for meta-analyses: (1) standard meta-analysis (fixed effects, random effects, z-score, and Fisher's methods); (2) analyses of global correlations between gene expression data sets; (3) gene set enrichment; (4) gene set overlap; (5) gene association by expression profile; (6) gene specificity; and (7) statistical analysis (ANOVA, pairwise comparison, and PCA). ExAtlas produces graphical outputs, including heatmaps, scatter-plots, bar-charts, and three-dimensional images. Some of the most widely used public data sets (e.g. GNF/BioGPS, Gene Ontology, KEGG, GAD phenotypes, BrainScan, ENCODE ChIP-seq, and protein-protein interaction) are pre-loaded and can be used for functional annotations.

SEURAT: visual analytics for the integrated analysis of microarray data.

PubMed

Gribov, Alexander; Sill, Martin; Lück, Sonja; Rücker, Frank; Döhner, Konstanze; Bullinger, Lars; Benner, Axel; Unwin, Antony

2010-06-03

In translational cancer research, gene expression data is collected together with clinical data and genomic data arising from other chip based high throughput technologies. Software tools for the joint analysis of such high dimensional data sets together with clinical data are required. We have developed an open source software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data together with associated clinical data, array CGH data and SNP array data. The different data types are organized by a comprehensive data manager. Interactive tools are provided for all graphics: heatmaps, dendrograms, barcharts, histograms, eventcharts and a chromosome browser, which displays genetic variations along the genome. All graphics are dynamic and fully linked so that any object selected in a graphic will be highlighted in all other graphics. For exploratory data analysis the software provides unsupervised data analytics like clustering, seriation algorithms and biclustering algorithms. The SEURAT software meets the growing needs of researchers to perform joint analysis of gene expression, genomical and clinical data.

Fair Use Education for the Twenty-First Century: A Comparative Study of Students' Use of an Interactive Tool to Guide Decision Making

ERIC Educational Resources Information Center

Greenhow, Christine; Walker, J. D.; Donnelly, Dan; Cohen, Brad

2008-01-01

Christine Greenhow, J. D. Walker, Dan Donnelly, and Brad Cohen describe the implementation and evaluation of the University of Minnesota's Fair Use Analysis (FUA) tool, an interactive online application intended to educate users and foster defensible fair use practice in accordance with copyright law by guiding users through a robust,…

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

USDA-ARS?s Scientific Manuscript database

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

Computer-Based Interaction Analysis with DEGREE Revisited

ERIC Educational Resources Information Center

Barros, B.; Verdejo, M. F.

2016-01-01

We review our research with "DEGREE" and analyse how our work has impacted the collaborative learning community since 2000. Our research is framed within the context of computer-based interaction analysis and the development of computer-supported collaborative learning (CSCL) tools. We identify some aspects of our work which have been…

Patient-oriented interactive E-health tools on U.S. hospital Web sites.

PubMed

Huang, Edgar; Chang, Chiu-Chi Angela

2012-01-01

The purpose of this study is to provide evidence for strategic planning regarding e-health development in U.S. hospitals. A content analysis of a representative sample of the U.S. hospital Web sites has revealed how U.S. hospitals have taken advantage of the 21 patient-oriented interactive tools identified in this study. Significant gaps between various types of hospitals have also been found. It is concluded that although the majority of the U.S. hospitals have adopted traditional functional tools, they need to make significant inroad in implementing the core e-business tools to serve their patients/users, making their Web sites more efficient marketing tools.

The Environment-Power System Analysis Tool development program. [for spacecraft power supplies

NASA Technical Reports Server (NTRS)

Jongeward, Gary A.; Kuharski, Robert A.; Kennedy, Eric M.; Wilcox, Katherine G.; Stevens, N. John; Putnam, Rand M.; Roche, James C.

1989-01-01

The Environment Power System Analysis Tool (EPSAT) is being developed to provide engineers with the ability to assess the effects of a broad range of environmental interactions on space power systems. A unique user-interface-data-dictionary code architecture oversees a collection of existing and future environmental modeling codes (e.g., neutral density) and physical interaction models (e.g., sheath ionization). The user-interface presents the engineer with tables, graphs, and plots which, under supervision of the data dictionary, are automatically updated in response to parameter change. EPSAT thus provides the engineer with a comprehensive and responsive environmental assessment tool and the scientist with a framework into which new environmental or physical models can be easily incorporated.

Toward an Efficient Icing CFD Process Using an Interactive Software Toolkit: Smagglce 2D

NASA Technical Reports Server (NTRS)

Vickerman, Mary B.; Choo, Yung K.; Schilling, Herbert W.; Baez, Marivell; Braun, Donald C.; Cotton, Barbara J.

2001-01-01

Two-dimensional CID analysis for iced airfoils can be a labor-intensive task. The software toolkit SmaggIce 2D is being developed to help streamline the CID process and provide the unique features needed for icing. When complete, it will include a combination of partially automated and fully interactive tools for all aspects of the tasks leading up to the flow analysis: geometry preparation, domain decomposition. block boundary demoralization. gridding, and linking with a flow solver. It also includes tools to perform ice shape characterization, an important aid in determining the relationship between ice characteristics and their effects on aerodynamic performance. Completed tools, work-in-progress, and planned features of the software toolkit are presented here.

Interactive, open source, travel time scenario modelling: tools to facilitate participation in health service access analysis.

PubMed

Fisher, Rohan; Lassa, Jonatan

2017-04-18

Modelling travel time to services has become a common public health tool for planning service provision but the usefulness of these analyses is constrained by the availability of accurate input data and limitations inherent in the assumptions and parameterisation. This is particularly an issue in the developing world where access to basic data is limited and travel is often complex and multi-modal. Improving the accuracy and relevance in this context requires greater accessibility to, and flexibility in, travel time modelling tools to facilitate the incorporation of local knowledge and the rapid exploration of multiple travel scenarios. The aim of this work was to develop simple open source, adaptable, interactive travel time modelling tools to allow greater access to and participation in service access analysis. Described are three interconnected applications designed to reduce some of the barriers to the more wide-spread use of GIS analysis of service access and allow for complex spatial and temporal variations in service availability. These applications are an open source GIS tool-kit and two geo-simulation models. The development of these tools was guided by health service issues from a developing world context but they present a general approach to enabling greater access to and flexibility in health access modelling. The tools demonstrate a method that substantially simplifies the process for conducting travel time assessments and demonstrate a dynamic, interactive approach in an open source GIS format. In addition this paper provides examples from empirical experience where these tools have informed better policy and planning. Travel and health service access is complex and cannot be reduced to a few static modeled outputs. The approaches described in this paper use a unique set of tools to explore this complexity, promote discussion and build understanding with the goal of producing better planning outcomes. The accessible, flexible, interactive and responsive nature of the applications described has the potential to allow complex environmental social and political considerations to be incorporated and visualised. Through supporting evidence-based planning the innovative modelling practices described have the potential to help local health and emergency response planning in the developing world.

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.

Usability testing of Avoiding Diabetes Thru Action Plan Targeting (ADAPT) decision support for integrating care-based counseling of pre-diabetes in an electronic health record.

PubMed

Chrimes, Dillon; Kitos, Nicole R; Kushniruk, Andre; Mann, Devin M

2014-09-01

Usability testing can be used to evaluate human-computer interaction (HCI) and communication in shared decision making (SDM) for patient-provider behavioral change and behavioral contracting. Traditional evaluations of usability using scripted or mock patient scenarios with think-aloud protocol analysis provide a way to identify HCI issues. In this paper we describe the application of these methods in the evaluation of the Avoiding Diabetes Thru Action Plan Targeting (ADAPT) tool, and test the usability of the tool to support the ADAPT framework for integrated care counseling of pre-diabetes. The think-aloud protocol analysis typically does not provide an assessment of how patient-provider interactions are effected in "live" clinical workflow or whether a tool is successful. Therefore, "Near-live" clinical simulations involving applied simulation methods were used to compliment the think-aloud results. This complementary usability technique was used to test the end-user HCI and tool performance by more closely mimicking the clinical workflow and capturing interaction sequences along with assessing the functionality of computer module prototypes on clinician workflow. We expected this method to further complement and provide different usability findings as compared to think-aloud analysis. Together, this mixed method evaluation provided comprehensive and realistic feedback for iterative refinement of the ADAPT system prior to implementation. The study employed two phases of testing of a new interactive ADAPT tool that embedded an evidence-based shared goal setting component into primary care workflow for dealing with pre-diabetes counseling within a commercial physician office electronic health record (EHR). Phase I applied usability testing that involved "think-aloud" protocol analysis of eight primary care providers interacting with several scripted clinical scenarios. Phase II used "near-live" clinical simulations of five providers interacting with standardized trained patient actors enacting the clinical scenario of counseling for pre-diabetes, each of whom had a pedometer that recorded the number of steps taken over a week. In both phases, all sessions were audio-taped and motion screen-capture software was activated for onscreen recordings. Transcripts were coded using iterative qualitative content analysis methods. In Phase I, the impact of the components and layout of ADAPT on user's Navigation, Understandability, and Workflow were associated with the largest volume of negative comments (i.e. approximately 80% of end-user commentary), while Usability and Content of ADAPT were representative of more positive than negative user commentary. The heuristic category of Usability had a positive-to-negative comment ratio of 2.1, reflecting positive perception of the usability of the tool, its functionality, and overall co-productive utilization of ADAPT. However, there were mixed perceptions about content (i.e., how the information was displayed, organized and described in the tool). In Phase II, the duration of patient encounters was approximately 10 min with all of the Patient Instructions (prescriptions) and behavioral contracting being activated at the end of each visit. Upon activation, providers accepted the pathway prescribed by the tool 100% of the time and completed all the fields in the tool in the simulation cases. Only 14% of encounter time was spent using the functionality of the ADAPT tool in terms of keystrokes and entering relevant data. The rest of the time was spent on communication and dialog to populate the patient instructions. In all cases, the interaction sequence of reviewing and discussing exercise and diet of the patient was linked to the functionality of the ADAPT tool in terms of monitoring, response-efficacy, self-efficacy, and negotiation in the patient-provider dialog. There was a change from one-way dialog to two-way dialog and negotiation that ended in a behavioral contract. This change demonstrated the tool's sequence, which supported recording current exercise and diet followed by a diet and exercise goal setting procedure to reduce the risk of diabetes onset. This study demonstrated that "think-aloud" protocol analysis with "near-live" clinical simulations provided a successful usability evaluation of a new primary care pre-diabetes shared goal setting tool. Each phase of the study provided complementary observations on problems with the new onscreen tool and was used to show the influence of the ADAPT framework on the usability, workflow integration, and communication between the patient and provider. The think-aloud tests with the provider showed the tool can be used according to the ADAPT framework (exercise-to-diet behavior change and tool utilization), while the clinical simulations revealed the ADAPT framework to realistically support patient-provider communication to obtain behavioral change contract. SDM interactions and mechanisms affecting protocol-based care can be more completely captured by combining "near-live" clinical simulations with traditional "think-aloud analysis" which augments clinician utilization. More analysis is required to verify if the rich communication actions found in Phase II compliment clinical workflows. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Modeling Tools for Propulsion Analysis and Computational Fluid Dynamics on the Internet

NASA Technical Reports Server (NTRS)

Muss, J. A.; Johnson, C. W.; Gotchy, M. B.

2000-01-01

The existing RocketWeb(TradeMark) Internet Analysis System (httr)://www.iohnsonrockets.com/rocketweb) provides an integrated set of advanced analysis tools that can be securely accessed over the Internet. Since these tools consist of both batch and interactive analysis codes, the system includes convenient methods for creating input files and evaluating the resulting data. The RocketWeb(TradeMark) system also contains many features that permit data sharing which, when further developed, will facilitate real-time, geographically diverse, collaborative engineering within a designated work group. Adding work group management functionality while simultaneously extending and integrating the system's set of design and analysis tools will create a system providing rigorous, controlled design development, reducing design cycle time and cost.

Supporting secure programming in web applications through interactive static analysis.

PubMed

Zhu, Jun; Xie, Jing; Lipford, Heather Richter; Chu, Bill

2014-07-01

Many security incidents are caused by software developers' failure to adhere to secure programming practices. Static analysis tools have been used to detect software vulnerabilities. However, their wide usage by developers is limited by the special training required to write rules customized to application-specific logic. Our approach is interactive static analysis, to integrate static analysis into Integrated Development Environment (IDE) and provide in-situ secure programming support to help developers prevent vulnerabilities during code construction. No additional training is required nor are there any assumptions on ways programs are built. Our work is motivated in part by the observation that many vulnerabilities are introduced due to failure to practice secure programming by knowledgeable developers. We implemented a prototype interactive static analysis tool as a plug-in for Java in Eclipse. Our technical evaluation of our prototype detected multiple zero-day vulnerabilities in a large open source project. Our evaluations also suggest that false positives may be limited to a very small class of use cases.

Supporting secure programming in web applications through interactive static analysis

PubMed Central

Zhu, Jun; Xie, Jing; Lipford, Heather Richter; Chu, Bill

2013-01-01

Many security incidents are caused by software developers’ failure to adhere to secure programming practices. Static analysis tools have been used to detect software vulnerabilities. However, their wide usage by developers is limited by the special training required to write rules customized to application-specific logic. Our approach is interactive static analysis, to integrate static analysis into Integrated Development Environment (IDE) and provide in-situ secure programming support to help developers prevent vulnerabilities during code construction. No additional training is required nor are there any assumptions on ways programs are built. Our work is motivated in part by the observation that many vulnerabilities are introduced due to failure to practice secure programming by knowledgeable developers. We implemented a prototype interactive static analysis tool as a plug-in for Java in Eclipse. Our technical evaluation of our prototype detected multiple zero-day vulnerabilities in a large open source project. Our evaluations also suggest that false positives may be limited to a very small class of use cases. PMID:25685513

Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks

PubMed Central

Ulitsky, Igor; Shamir, Ron

2007-01-01

The biological interpretation of genetic interactions is a major challenge. Recently, Kelley and Ideker proposed a method to analyze together genetic and physical networks, which explains many of the known genetic interactions as linking different pathways in the physical network. Here, we extend this method and devise novel analytic tools for interpreting genetic interactions in a physical context. Applying these tools on a large-scale Saccharomyces cerevisiae data set, our analysis reveals 140 between-pathway models that explain 3765 genetic interactions, roughly doubling those that were previously explained. Model genes tend to have short mRNA half-lives and many phosphorylation sites, suggesting that their stringent regulation is linked to pathway redundancy. We also identify ‘pivot' proteins that have many physical interactions with both pathways in our models, and show that pivots tend to be essential and highly conserved. Our analysis of models and pivots sheds light on the organization of the cellular machinery as well as on the roles of individual proteins. PMID:17437029

An Interactive Tool for Discrete Phase Analysis in Two-Phase Flows

NASA Technical Reports Server (NTRS)

Dejong, Frederik J.; Thoren, Stephen J.

1993-01-01

Under a NASA MSFC SBIR Phase 1 effort an interactive software package has been developed for the analysis of discrete (particulate) phase dynamics in two-phase flows in which the discrete phase does not significantly affect the continuous phase. This package contains a Graphical User Interface (based on the X Window system and the Motif tool kit) coupled to a particle tracing program, which allows the user to interactively set up and run a case for which a continuous phase grid and flow field are available. The software has been applied to a solid rocket motor problem, to demonstrate its ease of use and its suitability for problems of engineering interest, and has been delivered to NASA Marshall Space Flight Center.

An Unsupervised Anomalous Event Detection and Interactive Analysis Framework for Large-scale Satellite Data

NASA Astrophysics Data System (ADS)

LIU, Q.; Lv, Q.; Klucik, R.; Chen, C.; Gallaher, D. W.; Grant, G.; Shang, L.

2016-12-01

Due to the high volume and complexity of satellite data, computer-aided tools for fast quality assessments and scientific discovery are indispensable for scientists in the era of Big Data. In this work, we have developed a framework for automated anomalous event detection in massive satellite data. The framework consists of a clustering-based anomaly detection algorithm and a cloud-based tool for interactive analysis of detected anomalies. The algorithm is unsupervised and requires no prior knowledge of the data (e.g., expected normal pattern or known anomalies). As such, it works for diverse data sets, and performs well even in the presence of missing and noisy data. The cloud-based tool provides an intuitive mapping interface that allows users to interactively analyze anomalies using multiple features. As a whole, our framework can (1) identify outliers in a spatio-temporal context, (2) recognize and distinguish meaningful anomalous events from individual outliers, (3) rank those events based on "interestingness" (e.g., rareness or total number of outliers) defined by users, and (4) enable interactively query, exploration, and analysis of those anomalous events. In this presentation, we will demonstrate the effectiveness and efficiency of our framework in the application of detecting data quality issues and unusual natural events using two satellite datasets. The techniques and tools developed in this project are applicable for a diverse set of satellite data and will be made publicly available for scientists in early 2017.

Analysis of Java Client/Server and Web Programming Tools for Development of Educational Systems.

ERIC Educational Resources Information Center

Muldner, Tomasz

This paper provides an analysis of old and new programming tools for development of client/server programs, particularly World Wide Web-based programs. The focus is on development of educational systems that use interactive shared workspaces to provide portable and expandable solutions. The paper begins with a short description of relevant terms.…

ISAC - A tool for aeroservoelastic modeling and analysis. [Interaction of Structures, Aerodynamics, and Control

NASA Technical Reports Server (NTRS)

Adams, William M., Jr.; Hoadley, Sherwood T.

1993-01-01

This paper discusses the capabilities of the Interaction of Structures, Aerodynamics, and Controls (ISAC) system of program modules. The major modeling, analysis, and data management components of ISAC are identified. Equations of motion are displayed for a Laplace-domain representation of the unsteady aerodynamic forces. Options for approximating a frequency-domain representation of unsteady aerodynamic forces with rational functions of the Laplace variable are shown. Linear time invariant state-space equations of motion that result are discussed. Model generation and analyses of stability and dynamic response characteristics are shown for an aeroelastic vehicle which illustrate some of the capabilities of ISAC as a modeling and analysis tool for aeroelastic applications.

Developing Interactional Competence through Video-Based Computer-Mediated Conversations: Beginning Learners of Spanish

ERIC Educational Resources Information Center

Tecedor Cabrero, Marta

2013-01-01

This dissertation examines the discourse produced by beginning learners of Spanish using social media. Specifically, it looks at the use and development of interactional resources during two video-mediated conversations. Through a combination of Conversation Analysis tools and quantitative data analysis, the use of turn-taking strategies, repair…

COINGRAD; Control Oriented Interactive Graphical Analysis and Design.

ERIC Educational Resources Information Center

Volz, Richard A.; And Others

The computer is currently a vital tool in engineering analysis and design. With the introduction of moderately priced graphics terminals, it will become even more important in the future as rapid graphic interaction between the engineer and the computer becomes more feasible in computer-aided design (CAD). To provide a vehicle for introducing…

Interactive Digital Signal Processor

NASA Technical Reports Server (NTRS)

Mish, W. H.

1985-01-01

Interactive Digital Signal Processor, IDSP, consists of set of time series analysis "operators" based on various algorithms commonly used for digital signal analysis. Processing of digital signal time series to extract information usually achieved by applications of number of fairly standard operations. IDSP excellent teaching tool for demonstrating application for time series operators to artificially generated signals.

Configuration Analysis Tool (CAT). System Description and users guide (revision 1)

NASA Technical Reports Server (NTRS)

Decker, W.; Taylor, W.; Mcgarry, F. E.; Merwarth, P.

1982-01-01

A system description of, and user's guide for, the Configuration Analysis Tool (CAT) are presented. As a configuration management tool, CAT enhances the control of large software systems by providing a repository for information describing the current status of a project. CAT provides an editing capability to update the information and a reporting capability to present the information. CAT is an interactive program available in versions for the PDP-11/70 and VAX-11/780 computers.

Data Independent Acquisition analysis in ProHits 4.0.

PubMed

Liu, Guomin; Knight, James D R; Zhang, Jian Ping; Tsou, Chih-Chiang; Wang, Jian; Lambert, Jean-Philippe; Larsen, Brett; Tyers, Mike; Raught, Brian; Bandeira, Nuno; Nesvizhskii, Alexey I; Choi, Hyungwon; Gingras, Anne-Claude

2016-10-21

Affinity purification coupled with mass spectrometry (AP-MS) is a powerful technique for the identification and quantification of physical interactions. AP-MS requires careful experimental design, appropriate control selection and quantitative workflows to successfully identify bona fide interactors amongst a large background of contaminants. We previously introduced ProHits, a Laboratory Information Management System for interaction proteomics, which tracks all samples in a mass spectrometry facility, initiates database searches and provides visualization tools for spectral counting-based AP-MS approaches. More recently, we implemented Significance Analysis of INTeractome (SAINT) within ProHits to provide scoring of interactions based on spectral counts. Here, we provide an update to ProHits to support Data Independent Acquisition (DIA) with identification software (DIA-Umpire and MSPLIT-DIA), quantification tools (through DIA-Umpire, or externally via targeted extraction), and assessment of quantitative enrichment (through mapDIA) and scoring of interactions (through SAINT-intensity). With additional improvements, notably support of the iProphet pipeline, facilitated deposition into ProteomeXchange repositories and enhanced export and viewing functions, ProHits 4.0 offers a comprehensive suite of tools to facilitate affinity proteomics studies. It remains challenging to score, annotate and analyze proteomics data in a transparent manner. ProHits was previously introduced as a LIMS to enable storing, tracking and analysis of standard AP-MS data. In this revised version, we expand ProHits to include integration with a number of identification and quantification tools based on Data-Independent Acquisition (DIA). ProHits 4.0 also facilitates data deposition into public repositories, and the transfer of data to new visualization tools. Copyright © 2016 Elsevier B.V. All rights reserved.

Computational Tools and Facilities for the Next-Generation Analysis and Design Environment

NASA Technical Reports Server (NTRS)

Noor, Ahmed K. (Compiler); Malone, John B. (Compiler)

1997-01-01

This document contains presentations from the joint UVA/NASA Workshop on Computational Tools and Facilities for the Next-Generation Analysis and Design Environment held at the Virginia Consortium of Engineering and Science Universities in Hampton, Virginia on September 17-18, 1996. The presentations focused on the computational tools and facilities for analysis and design of engineering systems, including, real-time simulations, immersive systems, collaborative engineering environment, Web-based tools and interactive media for technical training. Workshop attendees represented NASA, commercial software developers, the aerospace industry, government labs, and academia. The workshop objectives were to assess the level of maturity of a number of computational tools and facilities and their potential for application to the next-generation integrated design environment.

Supporting Scientific Analysis within Collaborative Problem Solving Environments

NASA Technical Reports Server (NTRS)

Watson, Velvin R.; Kwak, Dochan (Technical Monitor)

2000-01-01

Collaborative problem solving environments for scientists should contain the analysis tools the scientists require in addition to the remote collaboration tools used for general communication. Unfortunately, most scientific analysis tools have been designed for a "stand-alone mode" and cannot be easily modified to work well in a collaborative environment. This paper addresses the questions, "What features are desired in a scientific analysis tool contained within a collaborative environment?", "What are the tool design criteria needed to provide these features?", and "What support is required from the architecture to support these design criteria?." First, the features of scientific analysis tools that are important for effective analysis in collaborative environments are listed. Next, several design criteria for developing analysis tools that will provide these features are presented. Then requirements for the architecture to support these design criteria are listed. Sonic proposed architectures for collaborative problem solving environments are reviewed and their capabilities to support the specified design criteria are discussed. A deficiency in the most popular architecture for remote application sharing, the ITU T. 120 architecture, prevents it from supporting highly interactive, dynamic, high resolution graphics. To illustrate that the specified design criteria can provide a highly effective analysis tool within a collaborative problem solving environment, a scientific analysis tool that contains the specified design criteria has been integrated into a collaborative environment and tested for effectiveness. The tests were conducted in collaborations between remote sites in the US and between remote sites on different continents. The tests showed that the tool (a tool for the visual analysis of computer simulations of physics) was highly effective for both synchronous and asynchronous collaborative analyses. The important features provided by the tool (and made possible by the specified design criteria) are: 1. The tool provides highly interactive, dynamic, high resolution, 3D graphics. 2. All remote scientists can view the same dynamic, high resolution, 3D scenes of the analysis as the analysis is being conducted. 3. The responsiveness of the tool is nearly identical to the responsiveness of the tool in a stand-alone mode. 4. The scientists can transfer control of the analysis between themselves. 5. Any analysis session or segment of an analysis session, whether done individually or collaboratively, can be recorded and posted on the Web for other scientists or students to download and play in either a collaborative or individual mode. 6. The scientist or student who downloaded the session can, individually or collaboratively, modify or extend the session with his/her own "what if" analysis of the data and post his/her version of the analysis back onto the Web. 7. The peak network bandwidth used in the collaborative sessions is only 1K bit/second even though the scientists at all sites are viewing high resolution (1280 x 1024 pixels), dynamic, 3D scenes of the analysis. The links between the specified design criteria and these performance features are presented.

Application of SOJA and InforMatrix in practice: interactive web and workshop tools.

PubMed

Brenninkmeijer, Rob; Janknegt, Robert

2007-10-01

System of Objectified Judgement Analysis (SOJA) and InforMatrix are decision-matrix techniques designed to support a rational selection of drugs. Both SOJA and InforMatrix can be considered as strategic tools in the practical implementation of rational pharmacotherapy. In order to apply the matrix techniques to drug selection, strategic navigation through essential information (with the aim of reaching consensus in pharmacotherapy) is required. The consensus has to be reached in an interactive, communicative, collegial manner, within a professional environment. This environment is realised in the form of interactive applications in workshops and on the internet. Such interactive applications are illustrated and discussed in this article.

Interactive metagenomic visualization in a Web browser.

PubMed

Ondov, Brian D; Bergman, Nicholas H; Phillippy, Adam M

2011-09-30

A critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. The inherent uncertainty in assignments to these groups makes it important to consider both their hierarchical contexts and their prediction confidence. The current tools for visualizing metagenomic data, however, omit or distort quantitative hierarchical relationships and lack the facility for displaying secondary variables. Here we present Krona, a new visualization tool that allows intuitive exploration of relative abundances and confidences within the complex hierarchies of metagenomic classifications. Krona combines a variant of radial, space-filling displays with parametric coloring and interactive polar-coordinate zooming. The HTML5 and JavaScript implementation enables fully interactive charts that can be explored with any modern Web browser, without the need for installed software or plug-ins. This Web-based architecture also allows each chart to be an independent document, making them easy to share via e-mail or post to a standard Web server. To illustrate Krona's utility, we describe its application to various metagenomic data sets and its compatibility with popular metagenomic analysis tools. Krona is both a powerful metagenomic visualization tool and a demonstration of the potential of HTML5 for highly accessible bioinformatic visualizations. Its rich and interactive displays facilitate more informed interpretations of metagenomic analyses, while its implementation as a browser-based application makes it extremely portable and easily adopted into existing analysis packages. Both the Krona rendering code and conversion tools are freely available under a BSD open-source license, and available from: http://krona.sourceforge.net.

Scientific Platform as a Service - Tools and solutions for efficient access to and analysis of oceanographic data

NASA Astrophysics Data System (ADS)

Vines, Aleksander; Hansen, Morten W.; Korosov, Anton

2017-04-01

Existing infrastructure international and Norwegian projects, e.g., NorDataNet, NMDC and NORMAP, provide open data access through the OPeNDAP protocol following the conventions for CF (Climate and Forecast) metadata, designed to promote the processing and sharing of files created with the NetCDF application programming interface (API). This approach is now also being implemented in the Norwegian Sentinel Data Hub (satellittdata.no) to provide satellite EO data to the user community. Simultaneously with providing simplified and unified data access, these projects also seek to use and establish common standards for use and discovery metadata. This then allows development of standardized tools for data search and (subset) streaming over the internet to perform actual scientific analysis. A combinnation of software tools, which we call a Scientific Platform as a Service (SPaaS), will take advantage of these opportunities to harmonize and streamline the search, retrieval and analysis of integrated satellite and auxiliary observations of the oceans in a seamless system. The SPaaS is a cloud solution for integration of analysis tools with scientific datasets via an API. The core part of the SPaaS is a distributed metadata catalog to store granular metadata describing the structure, location and content of available satellite, model, and in situ datasets. The analysis tools include software for visualization (also online), interactive in-depth analysis, and server-based processing chains. The API conveys search requests between system nodes (i.e., interactive and server tools) and provides easy access to the metadata catalog, data repositories, and the tools. The SPaaS components are integrated in virtual machines, of which provisioning and deployment are automatized using existing state-of-the-art open-source tools (e.g., Vagrant, Ansible, Docker). The open-source code for scientific tools and virtual machine configurations is under version control at https://github.com/nansencenter/, and is coupled to an online continuous integration system (e.g., Travis CI).

An integrative system biology approach to unravel potential drug candidates for multiple age related disorders.

PubMed

Srivastava, Isha; Khurana, Pooja; Yadav, Mohini; Hasija, Yasha

2017-12-01

Aging, though an inevitable part of life, is becoming a worldwide social and economic problem. Healthy aging is usually marked by low probability of age related disorders. Good therapeutic approaches are still in need to cure age related disorders. Occurrence of more than one ARD in an individual, expresses the need of discovery of such target proteins, which can affect multiple ARDs. Advanced scientific and medical research technologies throughout last three decades have arrived to the point where lots of key molecular determinants affect human disorders can be examined thoroughly. In this study, we designed and executed an approach to prioritize drugs that may target multiple age related disorders. Our methodology, focused on the analysis of biological pathways and protein protein interaction networks that may contribute to the pharmacology of age related disorders, included various steps such as retrieval and analysis of data, protein-protein interaction network analysis, and statistical and comparative analysis of topological coefficients, pathway, and functional enrichment analysis, and identification of drug-target proteins. We assume that the identified molecular determinants may be prioritized for further screening as novel drug targets to cure multiple ARDs. Based on the analysis, an online tool named as 'ARDnet' has been developed to construct and demonstrate ARD interactions at the level of PPI, ARDs and ARDs protein interaction, ARDs pathway interaction and drug-target interaction. The tool is freely made available at http://genomeinformatics.dtu.ac.in/ARDNet/Index.html. Copyright © 2017 Elsevier B.V. All rights reserved.

BIND: the Biomolecular Interaction Network Database

PubMed Central

Bader, Gary D.; Betel, Doron; Hogue, Christopher W. V.

2003-01-01

The Biomolecular Interaction Network Database (BIND: http://bind.ca) archives biomolecular interaction, complex and pathway information. A web-based system is available to query, view and submit records. BIND continues to grow with the addition of individual submissions as well as interaction data from the PDB and a number of large-scale interaction and complex mapping experiments using yeast two hybrid, mass spectrometry, genetic interactions and phage display. We have developed a new graphical analysis tool that provides users with a view of the domain composition of proteins in interaction and complex records to help relate functional domains to protein interactions. An interaction network clustering tool has also been developed to help focus on regions of interest. Continued input from users has helped further mature the BIND data specification, which now includes the ability to store detailed information about genetic interactions. The BIND data specification is available as ASN.1 and XML DTD. PMID:12519993

MAPPI-DAT: data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform.

PubMed

Gupta, Surya; De Puysseleyr, Veronic; Van der Heyden, José; Maddelein, Davy; Lemmens, Irma; Lievens, Sam; Degroeve, Sven; Tavernier, Jan; Martens, Lennart

2017-05-01

Protein-protein interaction (PPI) studies have dramatically expanded our knowledge about cellular behaviour and development in different conditions. A multitude of high-throughput PPI techniques have been developed to achieve proteome-scale coverage for PPI studies, including the microarray based Mammalian Protein-Protein Interaction Trap (MAPPIT) system. Because such high-throughput techniques typically report thousands of interactions, managing and analysing the large amounts of acquired data is a challenge. We have therefore built the MAPPIT cell microArray Protein Protein Interaction-Data management & Analysis Tool (MAPPI-DAT) as an automated data management and analysis tool for MAPPIT cell microarray experiments. MAPPI-DAT stores the experimental data and metadata in a systematic and structured way, automates data analysis and interpretation, and enables the meta-analysis of MAPPIT cell microarray data across all stored experiments. MAPPI-DAT is developed in Python, using R for data analysis and MySQL as data management system. MAPPI-DAT is cross-platform and can be ran on Microsoft Windows, Linux and OS X/macOS. The source code and a Microsoft Windows executable are freely available under the permissive Apache2 open source license at https://github.com/compomics/MAPPI-DAT. jan.tavernier@vib-ugent.be or lennart.martens@vib-ugent.be. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data

PubMed Central

Schweppe, Devin K.; Zheng, Chunxiang; Chavez, Juan D.; Navare, Arti T.; Wu, Xia; Eng, Jimmy K.; Bruce, James E.

2016-01-01

Motivation: Large-scale chemical cross-linking with mass spectrometry (XL-MS) analyses are quickly becoming a powerful means for high-throughput determination of protein structural information and protein–protein interactions. Recent studies have garnered thousands of cross-linked interactions, yet the field lacks an effective tool to compile experimental data or access the network and structural knowledge for these large scale analyses. We present XLinkDB 2.0 which integrates tools for network analysis, Protein Databank queries, modeling of predicted protein structures and modeling of docked protein structures. The novel, integrated approach of XLinkDB 2.0 enables the holistic analysis of XL-MS protein interaction data without limitation to the cross-linker or analytical system used for the analysis. Availability and Implementation: XLinkDB 2.0 can be found here, including documentation and help: http://xlinkdb.gs.washington.edu/. Contact: jimbruce@uw.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153666

Nonverbal communication in doctor-elderly patient transactions (NDEPT): development of a tool.

PubMed

Gorawara-Bhat, Rita; Cook, Mary Ann; Sachs, Greg A

2007-05-01

There are several measurement tools to assess verbal dimensions in clinical encounters; in contrast, there is no established tool to evaluate physical nonverbal dimensions in geriatric encounters. The present paper describes the development of a tool to assess the physical context of exam rooms in doctor-older patient visits. Salient features of the tool were derived from the medical literature and systematic observations of videotapes and refined during current research. The tool consists of two main dimensions of exam rooms: (1) physical dimensions comprising static and dynamic attributes that become operational through the spatial configuration and can influence the manifestation of (2) kinesic attributes. Details of the coding form and inter-rater reliability are presented. The usefulness of the tool is demonstrated through an analysis of 50 National Institute of Aging videotapes. Physicians in exam rooms with no desk in the interaction, no height difference and optimal interaction distance were observed to have greater eye contact and touch than physicians' in exam rooms with a desk, similar height difference and interaction distance. The tool can enable physicians to assess the spatial configuration of exam rooms (through Parts A and B) and thus facilitate the structuring of kinesic attributes (Part C).

TreeQ-VISTA: An Interactive Tree Visualization Tool withFunctional Annotation Query Capabilities

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

Gu, Shengyin; Anderson, Iain; Kunin, Victor

2007-05-07

Summary: We describe a general multiplatform exploratorytool called TreeQ-Vista, designed for presenting functional annotationsin a phylogenetic context. Traits, such as phenotypic and genomicproperties, are interactively queried from a relational database with auser-friendly interface which provides a set of tools for users with orwithout SQL knowledge. The query results are projected onto aphylogenetic tree and can be displayed in multiple color groups. A richset of browsing, grouping and query tools are provided to facilitatetrait exploration, comparison and analysis.Availability: The program,detailed tutorial and examples are available online athttp://genome-test.lbl.gov/vista/TreeQVista.

Negotiating Sequential Boundaries and Learning Opportunities: A Case from a Japanese Language Classroom

ERIC Educational Resources Information Center

Mori, Junko

2004-01-01

Using the methodological framework of conversation analysis (CA) as a central tool for analysis, this study examines a peer interactive task that occurred in a Japanese as a foreign language classroom. During the short segment of interaction, the students shifted back and forth between the development of an assigned task and the management of…

A Guide to Analyzing Message-Response Sequences and Group Interaction Patterns in Computer-Mediated Communication

ERIC Educational Resources Information Center

Jeong, Allan

2005-01-01

This paper proposes a set of methods and a framework for evaluating, modeling, and predicting group interactions in computer-mediated communication. The method of sequential analysis is described along with specific software tools and techniques to facilitate the analysis of message-response sequences. In addition, the Dialogic Theory and its…

I PASS: an interactive policy analysis simulation system.

Treesearch

Doug Olson; Con Schallau; Wilbur Maki

1984-01-01

This paper describes an interactive policy analysis simulation system(IPASS) that can be used to analyze the long-term economic and demographic effects of alternative forest resource management policies. The IPASS model is a dynamic analytical tool that forecasts growth and development of an economy. It allows the user to introduce changes in selected parameters based...

Computational Tools for Probing Interactions in Multiple Linear Regression, Multilevel Modeling, and Latent Curve Analysis

ERIC Educational Resources Information Center

Preacher, Kristopher J.; Curran, Patrick J.; Bauer, Daniel J.

2006-01-01

Simple slopes, regions of significance, and confidence bands are commonly used to evaluate interactions in multiple linear regression (MLR) models, and the use of these techniques has recently been extended to multilevel or hierarchical linear modeling (HLM) and latent curve analysis (LCA). However, conducting these tests and plotting the…

SEURAT: Visual analytics for the integrated analysis of microarray data

PubMed Central

2010-01-01

Background In translational cancer research, gene expression data is collected together with clinical data and genomic data arising from other chip based high throughput technologies. Software tools for the joint analysis of such high dimensional data sets together with clinical data are required. Results We have developed an open source software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data together with associated clinical data, array CGH data and SNP array data. The different data types are organized by a comprehensive data manager. Interactive tools are provided for all graphics: heatmaps, dendrograms, barcharts, histograms, eventcharts and a chromosome browser, which displays genetic variations along the genome. All graphics are dynamic and fully linked so that any object selected in a graphic will be highlighted in all other graphics. For exploratory data analysis the software provides unsupervised data analytics like clustering, seriation algorithms and biclustering algorithms. Conclusions The SEURAT software meets the growing needs of researchers to perform joint analysis of gene expression, genomical and clinical data. PMID:20525257

HYPATIA--An Online Tool for ATLAS Event Visualization

ERIC Educational Resources Information Center

Kourkoumelis, C.; Vourakis, S.

2014-01-01

This paper describes an interactive tool for analysis of data from the ATLAS experiment taking place at the world's highest energy particle collider at CERN. The tool, called HYPATIA/applet, enables students of various levels to become acquainted with particle physics and look for discoveries in a similar way to that of real research.

ReliefSeq: A Gene-Wise Adaptive-K Nearest-Neighbor Feature Selection Tool for Finding Gene-Gene Interactions and Main Effects in mRNA-Seq Gene Expression Data

PubMed Central

McKinney, Brett A.; White, Bill C.; Grill, Diane E.; Li, Peter W.; Kennedy, Richard B.; Poland, Gregory A.; Oberg, Ann L.

2013-01-01

Relief-F is a nonparametric, nearest-neighbor machine learning method that has been successfully used to identify relevant variables that may interact in complex multivariate models to explain phenotypic variation. While several tools have been developed for assessing differential expression in sequence-based transcriptomics, the detection of statistical interactions between transcripts has received less attention in the area of RNA-seq analysis. We describe a new extension and assessment of Relief-F for feature selection in RNA-seq data. The ReliefSeq implementation adapts the number of nearest neighbors (k) for each gene to optimize the Relief-F test statistics (importance scores) for finding both main effects and interactions. We compare this gene-wise adaptive-k (gwak) Relief-F method with standard RNA-seq feature selection tools, such as DESeq and edgeR, and with the popular machine learning method Random Forests. We demonstrate performance on a panel of simulated data that have a range of distributional properties reflected in real mRNA-seq data including multiple transcripts with varying sizes of main effects and interaction effects. For simulated main effects, gwak-Relief-F feature selection performs comparably to standard tools DESeq and edgeR for ranking relevant transcripts. For gene-gene interactions, gwak-Relief-F outperforms all comparison methods at ranking relevant genes in all but the highest fold change/highest signal situations where it performs similarly. The gwak-Relief-F algorithm outperforms Random Forests for detecting relevant genes in all simulation experiments. In addition, Relief-F is comparable to the other methods based on computational time. We also apply ReliefSeq to an RNA-Seq study of smallpox vaccine to identify gene expression changes between vaccinia virus-stimulated and unstimulated samples. ReliefSeq is an attractive tool for inclusion in the suite of tools used for analysis of mRNA-Seq data; it has power to detect both main effects and interaction effects. Software Availability: http://insilico.utulsa.edu/ReliefSeq.php. PMID:24339943

Translating statistical species-habitat models to interactive decision support tools

USGS Publications Warehouse

Wszola, Lyndsie S.; Simonsen, Victoria L.; Stuber, Erica F.; Gillespie, Caitlyn R.; Messinger, Lindsey N.; Decker, Karie L.; Lusk, Jeffrey J.; Jorgensen, Christopher F.; Bishop, Andrew A.; Fontaine, Joseph J.

2017-01-01

Understanding species-habitat relationships is vital to successful conservation, but the tools used to communicate species-habitat relationships are often poorly suited to the information needs of conservation practitioners. Here we present a novel method for translating a statistical species-habitat model, a regression analysis relating ring-necked pheasant abundance to landcover, into an interactive online tool. The Pheasant Habitat Simulator combines the analytical power of the R programming environment with the user-friendly Shiny web interface to create an online platform in which wildlife professionals can explore the effects of variation in local landcover on relative pheasant habitat suitability within spatial scales relevant to individual wildlife managers. Our tool allows users to virtually manipulate the landcover composition of a simulated space to explore how changes in landcover may affect pheasant relative habitat suitability, and guides users through the economic tradeoffs of landscape changes. We offer suggestions for development of similar interactive applications and demonstrate their potential as innovative science delivery tools for diverse professional and public audiences.

Translating statistical species-habitat models to interactive decision support tools.

PubMed

Wszola, Lyndsie S; Simonsen, Victoria L; Stuber, Erica F; Gillespie, Caitlyn R; Messinger, Lindsey N; Decker, Karie L; Lusk, Jeffrey J; Jorgensen, Christopher F; Bishop, Andrew A; Fontaine, Joseph J

2017-01-01

Understanding species-habitat relationships is vital to successful conservation, but the tools used to communicate species-habitat relationships are often poorly suited to the information needs of conservation practitioners. Here we present a novel method for translating a statistical species-habitat model, a regression analysis relating ring-necked pheasant abundance to landcover, into an interactive online tool. The Pheasant Habitat Simulator combines the analytical power of the R programming environment with the user-friendly Shiny web interface to create an online platform in which wildlife professionals can explore the effects of variation in local landcover on relative pheasant habitat suitability within spatial scales relevant to individual wildlife managers. Our tool allows users to virtually manipulate the landcover composition of a simulated space to explore how changes in landcover may affect pheasant relative habitat suitability, and guides users through the economic tradeoffs of landscape changes. We offer suggestions for development of similar interactive applications and demonstrate their potential as innovative science delivery tools for diverse professional and public audiences.

Translating statistical species-habitat models to interactive decision support tools

PubMed Central

Simonsen, Victoria L.; Stuber, Erica F.; Gillespie, Caitlyn R.; Messinger, Lindsey N.; Decker, Karie L.; Lusk, Jeffrey J.; Jorgensen, Christopher F.; Bishop, Andrew A.; Fontaine, Joseph J.

2017-01-01

Understanding species-habitat relationships is vital to successful conservation, but the tools used to communicate species-habitat relationships are often poorly suited to the information needs of conservation practitioners. Here we present a novel method for translating a statistical species-habitat model, a regression analysis relating ring-necked pheasant abundance to landcover, into an interactive online tool. The Pheasant Habitat Simulator combines the analytical power of the R programming environment with the user-friendly Shiny web interface to create an online platform in which wildlife professionals can explore the effects of variation in local landcover on relative pheasant habitat suitability within spatial scales relevant to individual wildlife managers. Our tool allows users to virtually manipulate the landcover composition of a simulated space to explore how changes in landcover may affect pheasant relative habitat suitability, and guides users through the economic tradeoffs of landscape changes. We offer suggestions for development of similar interactive applications and demonstrate their potential as innovative science delivery tools for diverse professional and public audiences. PMID:29236707

A Sample Data Publication: Interactive Access, Analysis and Display of Remotely Stored Datasets From Hurricane Charley

NASA Astrophysics Data System (ADS)

Weber, J.; Domenico, B.

2004-12-01

This paper is an example of what we call data interactive publications. With a properly configured workstation, the readers can click on "hotspots" in the document that launches an interactive analysis tool called the Unidata Integrated Data Viewer (IDV). The IDV will enable the readers to access, analyze and display datasets on remote servers as well as documents describing them. Beyond the parameters and datasets initially configured into the paper, the analysis tool will have access to all the other dataset parameters as well as to a host of other datasets on remote servers. These data interactive publications are built on top of several data delivery, access, discovery, and visualization tools developed by Unidata and its partner organizations. For purposes of illustrating this integrative technology, we will use data from the event of Hurricane Charley over Florida from August 13-15, 2004. This event illustrates how components of this process fit together. The Local Data Manager (LDM), Open-source Project for a Network Data Access Protocol (OPeNDAP) and Abstract Data Distribution Environment (ADDE) services, Thematic Realtime Environmental Distributed Data Service (THREDDS) cataloging services, and the IDV are highlighted in this example of a publication with embedded pointers for accessing and interacting with remote datasets. An important objective of this paper is to illustrate how these integrated technologies foster the creation of documents that allow the reader to learn the scientific concepts by direct interaction with illustrative datasets, and help build a framework for integrated Earth System science.

FunRich proteomics software analysis, let the fun begin!

PubMed

Benito-Martin, Alberto; Peinado, Héctor

2015-08-01

Protein MS analysis is the preferred method for unbiased protein identification. It is normally applied to a large number of both small-scale and high-throughput studies. However, user-friendly computational tools for protein analysis are still needed. In this issue, Mathivanan and colleagues (Proteomics 2015, 15, 2597-2601) report the development of FunRich software, an open-access software that facilitates the analysis of proteomics data, providing tools for functional enrichment and interaction network analysis of genes and proteins. FunRich is a reinterpretation of proteomic software, a standalone tool combining ease of use with customizable databases, free access, and graphical representations. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Usability testing of Avoiding Diabetes Thru Action Plan Targeting (ADAPT) decision support for integrating care-based counseling of pre-diabetes in an electronic health record

PubMed Central

Chrimes, Dillon; Kushniruk, Andre; Kitos, Nicole R.

2014-01-01

Purpose Usability testing can be used to evaluate human computer interaction (HCI) and communication in shared decision making (SDM) for patient-provider behavioral change and behavioral contracting. Traditional evaluations of usability using scripted or mock patient scenarios with think-aloud protocol analysis provide a to identify HCI issues. In this paper we describe the application of these methods in the evaluation of the Avoiding Diabetes Thru Action Plan Targeting (ADAPT) tool, and test the usability of the tool to support the ADAPT framework for integrated care counseling of pre-diabetes. The think-aloud protocol analysis typically does not provide an assessment of how patient-provider interactions are effected in “live” clinical workflow or whether a tool is successful. Therefore, “Near-live” clinical simulations involving applied simulation methods were used to compliment the think-aloud results. This complementary usability technique was used to test the end-user HCI and tool performance by more closely mimicking the clinical workflow and capturing interaction sequences along with assessing the functionality of computer module prototypes on clinician workflow. We expected this method to further complement and provide different usability findings as compared to think-aloud analysis. Together, this mixed method evaluation provided comprehensive and realistic feedback for iterative refinement of the ADAPT system prior to implementation. Methods The study employed two phases of testing of a new interactive ADAPT tool that embedded an evidence-based shared goal setting component into primary care workflow for dealing with pre-diabetes counseling within a commercial physician office electronic health record (EHR). Phase I applied usability testing that involved “think-aloud” protocol analysis of 8 primary care providers interacting with several scripted clinical scenarios. Phase II used “near-live” clinical simulations of 5 providers interacting with standardized trained patient actors enacting the clinical scenario of counseling for pre-diabetes, each of whom had a pedometer that recorded the number of steps taken over a week. In both phases, all sessions were audio-taped and motion screen-capture software was activated for onscreen recordings. Transcripts were coded using iterative qualitative content analysis methods. Results In Phase I, the impact of the components and layout of ADAPT on user’s Navigation, Understandability, and Workflow were associated with the largest volume of negative comments (i.e. approximately 80% of end-user commentary), while Usability and Content of ADAPT were representative of more positive than negative user commentary. The heuristic category of Usability had a positive-to-negative comment ratio of 2.1, reflecting positive perception of the usability of the tool, its functionality, and overall co-productive utilization of ADAPT. However, there were mixed perceptions about content (i.e., how the information was displayed, organized and described in the tool). In Phase II, the duration of patient encounters was approximately 10 minutes with all of the Patient Instructions (prescriptions) and behavioral contracting being activated at the end of each visit. Upon activation, providers accepted the pathway prescribed by the tool 100% of the time and completed all the fields in the tool in the simulation cases. Only 14% of encounter time was spent using the functionality of the ADAPT tool in terms of keystrokes and entering relevant data. The rest of the time was spent on communication and dialogue to populate the patient instructions. In all cases, the interaction sequence of reviewing and discussing exercise and diet of the patient was linked to the functionality of the ADAPT tool in terms of monitoring, response-efficacy, self-efficacy, and negotiation in the patient-provider dialogue. There was a change from one-way dialogue to two-way dialogue and negotiation that ended in a behavioral contract. This change demonstrated the tool’s sequence, which supported recording current exercise and diet followed by a diet and exercise goal setting procedure to reduce the risk of diabetes onset. Conclusions This study demonstrated that “think-aloud” protocol analysis with “near-live” clinical simulations provided a successful usability evaluation of a new primary care pre-diabetes shared goal setting tool. Each phase of the study provided complementary observations on problems with the new onscreen tool and was used to show the influence of the ADAPT framework on the usability, workflow integration, and communication between the patient and provider. The think-aloud tests with the provider showed the tool can be used according to the ADAPT framework (exercise-to-diet behavior change and tool utilization), while the clinical simulations revealed the ADAPT framework to realistically support patient-provider communication to obtain behavioral change contract. SDM interactions and mechanisms affecting protocol-based care can be more completely captured by combining “near-live” clinical simulations with traditional “think-aloud analysis” which augments clinician utilization. More analysis is required to verify if the rich communication actions found in Phase II compliment clinical workflows. PMID:24981988

Explorative visual analytics on interval-based genomic data and their metadata.

PubMed

Jalili, Vahid; Matteucci, Matteo; Masseroli, Marco; Ceri, Stefano

2017-12-04

With the wide-spreading of public repositories of NGS processed data, the availability of user-friendly and effective tools for data exploration, analysis and visualization is becoming very relevant. These tools enable interactive analytics, an exploratory approach for the seamless "sense-making" of data through on-the-fly integration of analysis and visualization phases, suggested not only for evaluating processing results, but also for designing and adapting NGS data analysis pipelines. This paper presents abstractions for supporting the early analysis of NGS processed data and their implementation in an associated tool, named GenoMetric Space Explorer (GeMSE). This tool serves the needs of the GenoMetric Query Language, an innovative cloud-based system for computing complex queries over heterogeneous processed data. It can also be used starting from any text files in standard BED, BroadPeak, NarrowPeak, GTF, or general tab-delimited format, containing numerical features of genomic regions; metadata can be provided as text files in tab-delimited attribute-value format. GeMSE allows interactive analytics, consisting of on-the-fly cycling among steps of data exploration, analysis and visualization that help biologists and bioinformaticians in making sense of heterogeneous genomic datasets. By means of an explorative interaction support, users can trace past activities and quickly recover their results, seamlessly going backward and forward in the analysis steps and comparative visualizations of heatmaps. GeMSE effective application and practical usefulness is demonstrated through significant use cases of biological interest. GeMSE is available at http://www.bioinformatics.deib.polimi.it/GeMSE/ , and its source code is available at https://github.com/Genometric/GeMSE under GPLv3 open-source license.

ISAAC - InterSpecies Analysing Application using Containers.

PubMed

Baier, Herbert; Schultz, Jörg

2014-01-15

Information about genes, transcripts and proteins is spread over a wide variety of databases. Different tools have been developed using these databases to identify biological signals in gene lists from large scale analysis. Mostly, they search for enrichments of specific features. But, these tools do not allow an explorative walk through different views and to change the gene lists according to newly upcoming stories. To fill this niche, we have developed ISAAC, the InterSpecies Analysing Application using Containers. The central idea of this web based tool is to enable the analysis of sets of genes, transcripts and proteins under different biological viewpoints and to interactively modify these sets at any point of the analysis. Detailed history and snapshot information allows tracing each action. Furthermore, one can easily switch back to previous states and perform new analyses. Currently, sets can be viewed in the context of genomes, protein functions, protein interactions, pathways, regulation, diseases and drugs. Additionally, users can switch between species with an automatic, orthology based translation of existing gene sets. As todays research usually is performed in larger teams and consortia, ISAAC provides group based functionalities. Here, sets as well as results of analyses can be exchanged between members of groups. ISAAC fills the gap between primary databases and tools for the analysis of large gene lists. With its highly modular, JavaEE based design, the implementation of new modules is straight forward. Furthermore, ISAAC comes with an extensive web-based administration interface including tools for the integration of third party data. Thus, a local installation is easily feasible. In summary, ISAAC is tailor made for highly explorative interactive analyses of gene, transcript and protein sets in a collaborative environment.

Mars Trek: An Interactive Web Portal for Current and Future Missions to Mars

NASA Technical Reports Server (NTRS)

Law, E.; Day, B.

2017-01-01

NASA's Mars Trek (https://marstrek.jpl.nasa.gov) provides a web-based Portal and a suite of interactive visualization and analysis tools to enable mission planners, lunar scientists, and engineers to access mapped data products from past and current missions to Mars. During the past year, the capabilities and data served by Mars Trek have been significantly expanded beyond its original design as a public outreach tool. At the request of NASA's Science Mission Directorate and Human Exploration Operations Mission Directorate, Mars Trek's technology and capabilities are now being extended to support site selection and analysis activities for the first human missions to Mars.

Frontal affinity chromatography: A unique research tool for biospecific interaction that promotes glycobiology

PubMed Central

KASAI, Kenichi

2014-01-01

Combination of bioaffinity and chromatography gave birth to affinity chromatography. A further combination with frontal analysis resulted in creation of frontal affinity chromatography (FAC). This new versatile research tool enabled detailed analysis of weak interactions that play essential roles in living systems, especially those between complex saccharides and saccharide-binding proteins. FAC now becomes the best method for the investigation of saccharide-binding proteins (lectins) from viewpoints of sensitivity, accuracy, and efficiency, and is contributing greatly to the development of glycobiology. It opened a door leading to deeper understanding of the significance of saccharide recognition in life. The theory is also concisely described. PMID:25169774

Mars Trek: An Interactive Web Portal for Current and Future Missions to Mars

NASA Astrophysics Data System (ADS)

Law, E.; Day, B.

2017-09-01

NASA's Mars Trek (https://marstrek.jpl.nasa.gov) provides a web-based Portal and a suite of interactive visualization and analysis tools to enable mission planners, lunar scientists, and engineers to access mapped data products from past and current missions to Mars. During the past year, the capabilities and data served by Mars Trek have been significantly expanded beyond its original design as a public outreach tool. At the request of NASA's Science Mission Directorate and Human Exploration Operations Mission Directorate, Mars Trek's technology and capabilities are now being extended to support site selection and analysis activities for the first human missions to Mars.

Feasibility of lane closures using probe data : technical brief.

DOT National Transportation Integrated Search

2017-04-01

This study developed an on-line system analysis tool called the Work Zone Interactive : Management Application - Planning (WIMAP-P), an easy-to-use and easy-to-learn tool for : predicting the traffic impact caused by work zone lane closures on freewa...

Explaining reaction mechanisms using the dual descriptor: a complementary tool to the molecular electrostatic potential.

PubMed

Martínez-Araya, Jorge Ignacio

2013-07-01

The intrinsic reactivity of cyanide when interacting with a silver cation was rationalized using the dual descriptor (DD) as a complement to the molecular electrostatic potential (MEP) in order to predict interactions at the local level. It was found that DD accurately explains covalent interactions that cannot be explained by MEP, which focuses on essentially ionic interactions. This allowed the rationalization of the reaction mechanism that yields silver cyanide in the gas phase. Other similar reaction mechanisms involving a silver cation interacting with water, ammonia, and thiosulfate were also explained by the combination of MEP and DD. This analysis provides another example of the usefulness of DD as a tool for gaining a deeper understanding of any reaction mechanism that is mainly governed by covalent interactions.

Functional Analysis of OMICs Data and Small Molecule Compounds in an Integrated "Knowledge-Based" Platform.

PubMed

Dubovenko, Alexey; Nikolsky, Yuri; Rakhmatulin, Eugene; Nikolskaya, Tatiana

2017-01-01

Analysis of NGS and other sequencing data, gene variants, gene expression, proteomics, and other high-throughput (OMICs) data is challenging because of its biological complexity and high level of technical and biological noise. One way to deal with both problems is to perform analysis with a high fidelity annotated knowledgebase of protein interactions, pathways, and functional ontologies. This knowledgebase has to be structured in a computer-readable format and must include software tools for managing experimental data, analysis, and reporting. Here, we present MetaCore™ and Key Pathway Advisor (KPA), an integrated platform for functional data analysis. On the content side, MetaCore and KPA encompass a comprehensive database of molecular interactions of different types, pathways, network models, and ten functional ontologies covering human, mouse, and rat genes. The analytical toolkit includes tools for gene/protein list enrichment analysis, statistical "interactome" tool for the identification of over- and under-connected proteins in the dataset, and a biological network analysis module made up of network generation algorithms and filters. The suite also features Advanced Search, an application for combinatorial search of the database content, as well as a Java-based tool called Pathway Map Creator for drawing and editing custom pathway maps. Applications of MetaCore and KPA include molecular mode of action of disease research, identification of potential biomarkers and drug targets, pathway hypothesis generation, analysis of biological effects for novel small molecule compounds and clinical applications (analysis of large cohorts of patients, and translational and personalized medicine).

Portfolio: a prototype workstation for development and evaluation of tools for analysis and management of digital portal images.

PubMed

Boxwala, A A; Chaney, E L; Fritsch, D S; Friedman, C P; Rosenman, J G

1998-09-01

The purpose of this investigation was to design and implement a prototype physician workstation, called PortFolio, as a platform for developing and evaluating, by means of controlled observer studies, user interfaces and interactive tools for analyzing and managing digital portal images. The first observer study was designed to measure physician acceptance of workstation technology, as an alternative to a view box, for inspection and analysis of portal images for detection of treatment setup errors. The observer study was conducted in a controlled experimental setting to evaluate physician acceptance of the prototype workstation technology exemplified by PortFolio. PortFolio incorporates a windows user interface, a compact kit of carefully selected image analysis tools, and an object-oriented data base infrastructure. The kit evaluated in the observer study included tools for contrast enhancement, registration, and multimodal image visualization. Acceptance was measured in the context of performing portal image analysis in a structured protocol designed to simulate clinical practice. The acceptability and usage patterns were measured from semistructured questionnaires and logs of user interactions. Radiation oncologists, the subjects for this study, perceived the tools in PortFolio to be acceptable clinical aids. Concerns were expressed regarding user efficiency, particularly with respect to the image registration tools. The results of our observer study indicate that workstation technology is acceptable to radiation oncologists as an alternative to a view box for clinical detection of setup errors from digital portal images. Improvements in implementation, including more tools and a greater degree of automation in the image analysis tasks, are needed to make PortFolio more clinically practical.

Graphics Flutter Analysis Methods, an interactive computing system at Lockheed-California Company

NASA Technical Reports Server (NTRS)

Radovcich, N. A.

1975-01-01

An interactive computer graphics system, Graphics Flutter Analysis Methods (GFAM), was developed to complement FAMAS, a matrix-oriented batch computing system, and other computer programs in performing complex numerical calculations using a fully integrated data management system. GFAM has many of the matrix operation capabilities found in FAMAS, but on a smaller scale, and is utilized when the analysis requires a high degree of interaction between the engineer and computer, and schedule constraints exclude the use of batch entry programs. Applications of GFAM to a variety of preliminary design, development design, and project modification programs suggest that interactive flutter analysis using matrix representations is a feasible and cost effective computing tool.

NMRPro: an integrated web component for interactive processing and visualization of NMR spectra.

PubMed

Mohamed, Ahmed; Nguyen, Canh Hao; Mamitsuka, Hiroshi

2016-07-01

The popularity of using NMR spectroscopy in metabolomics and natural products has driven the development of an array of NMR spectral analysis tools and databases. Particularly, web applications are well used recently because they are platform-independent and easy to extend through reusable web components. Currently available web applications provide the analysis of NMR spectra. However, they still lack the necessary processing and interactive visualization functionalities. To overcome these limitations, we present NMRPro, a web component that can be easily incorporated into current web applications, enabling easy-to-use online interactive processing and visualization. NMRPro integrates server-side processing with client-side interactive visualization through three parts: a python package to efficiently process large NMR datasets on the server-side, a Django App managing server-client interaction, and SpecdrawJS for client-side interactive visualization. Demo and installation instructions are available at http://mamitsukalab.org/tools/nmrpro/ mohamed@kuicr.kyoto-u.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Visual analytics in cheminformatics: user-supervised descriptor selection for QSAR methods.

PubMed

Martínez, María Jimena; Ponzoni, Ignacio; Díaz, Mónica F; Vazquez, Gustavo E; Soto, Axel J

2015-01-01

The design of QSAR/QSPR models is a challenging problem, where the selection of the most relevant descriptors constitutes a key step of the process. Several feature selection methods that address this step are concentrated on statistical associations among descriptors and target properties, whereas the chemical knowledge is left out of the analysis. For this reason, the interpretability and generality of the QSAR/QSPR models obtained by these feature selection methods are drastically affected. Therefore, an approach for integrating domain expert's knowledge in the selection process is needed for increase the confidence in the final set of descriptors. In this paper a software tool, which we named Visual and Interactive DEscriptor ANalysis (VIDEAN), that combines statistical methods with interactive visualizations for choosing a set of descriptors for predicting a target property is proposed. Domain expertise can be added to the feature selection process by means of an interactive visual exploration of data, and aided by statistical tools and metrics based on information theory. Coordinated visual representations are presented for capturing different relationships and interactions among descriptors, target properties and candidate subsets of descriptors. The competencies of the proposed software were assessed through different scenarios. These scenarios reveal how an expert can use this tool to choose one subset of descriptors from a group of candidate subsets or how to modify existing descriptor subsets and even incorporate new descriptors according to his or her own knowledge of the target property. The reported experiences showed the suitability of our software for selecting sets of descriptors with low cardinality, high interpretability, low redundancy and high statistical performance in a visual exploratory way. Therefore, it is possible to conclude that the resulting tool allows the integration of a chemist's expertise in the descriptor selection process with a low cognitive effort in contrast with the alternative of using an ad-hoc manual analysis of the selected descriptors. Graphical abstractVIDEAN allows the visual analysis of candidate subsets of descriptors for QSAR/QSPR. In the two panels on the top, users can interactively explore numerical correlations as well as co-occurrences in the candidate subsets through two interactive graphs.

Network Analysis Tools: from biological networks to clusters and pathways.

PubMed

Brohée, Sylvain; Faust, Karoline; Lima-Mendez, Gipsi; Vanderstocken, Gilles; van Helden, Jacques

2008-01-01

Network Analysis Tools (NeAT) is a suite of computer tools that integrate various algorithms for the analysis of biological networks: comparison between graphs, between clusters, or between graphs and clusters; network randomization; analysis of degree distribution; network-based clustering and path finding. The tools are interconnected to enable a stepwise analysis of the network through a complete analytical workflow. In this protocol, we present a typical case of utilization, where the tasks above are combined to decipher a protein-protein interaction network retrieved from the STRING database. The results returned by NeAT are typically subnetworks, networks enriched with additional information (i.e., clusters or paths) or tables displaying statistics. Typical networks comprising several thousands of nodes and arcs can be analyzed within a few minutes. The complete protocol can be read and executed in approximately 1 h.

Correction tool for Active Shape Model based lumbar muscle segmentation.

PubMed

Valenzuela, Waldo; Ferguson, Stephen J; Ignasiak, Dominika; Diserens, Gaelle; Vermathen, Peter; Boesch, Chris; Reyes, Mauricio

2015-08-01

In the clinical environment, accuracy and speed of the image segmentation process plays a key role in the analysis of pathological regions. Despite advances in anatomic image segmentation, time-effective correction tools are commonly needed to improve segmentation results. Therefore, these tools must provide faster corrections with a low number of interactions, and a user-independent solution. In this work we present a new interactive correction method for correcting the image segmentation. Given an initial segmentation and the original image, our tool provides a 2D/3D environment, that enables 3D shape correction through simple 2D interactions. Our scheme is based on direct manipulation of free form deformation adapted to a 2D environment. This approach enables an intuitive and natural correction of 3D segmentation results. The developed method has been implemented into a software tool and has been evaluated for the task of lumbar muscle segmentation from Magnetic Resonance Images. Experimental results show that full segmentation correction could be performed within an average correction time of 6±4 minutes and an average of 68±37 number of interactions, while maintaining the quality of the final segmentation result within an average Dice coefficient of 0.92±0.03.

PAINT: a promoter analysis and interaction network generation tool for gene regulatory network identification.

PubMed

Vadigepalli, Rajanikanth; Chakravarthula, Praveen; Zak, Daniel E; Schwaber, James S; Gonye, Gregory E

2003-01-01

We have developed a bioinformatics tool named PAINT that automates the promoter analysis of a given set of genes for the presence of transcription factor binding sites. Based on coincidence of regulatory sites, this tool produces an interaction matrix that represents a candidate transcriptional regulatory network. This tool currently consists of (1) a database of promoter sequences of known or predicted genes in the Ensembl annotated mouse genome database, (2) various modules that can retrieve and process the promoter sequences for binding sites of known transcription factors, and (3) modules for visualization and analysis of the resulting set of candidate network connections. This information provides a substantially pruned list of genes and transcription factors that can be examined in detail in further experimental studies on gene regulation. Also, the candidate network can be incorporated into network identification methods in the form of constraints on feasible structures in order to render the algorithms tractable for large-scale systems. The tool can also produce output in various formats suitable for use in external visualization and analysis software. In this manuscript, PAINT is demonstrated in two case studies involving analysis of differentially regulated genes chosen from two microarray data sets. The first set is from a neuroblastoma N1E-115 cell differentiation experiment, and the second set is from neuroblastoma N1E-115 cells at different time intervals following exposure to neuropeptide angiotensin II. PAINT is available for use as an agent in BioSPICE simulation and analysis framework (www.biospice.org), and can also be accessed via a WWW interface at www.dbi.tju.edu/dbi/tools/paint/.

Vids: Version 2.0 Alpha Visualization Engine

DTIC Science & Technology

2018-04-25

fidelity than existing efforts. Vids is a project aimed at producing more dynamic and interactive visualization tools using modern computer game ...move through and interact with the data to improve informational understanding. The Vids software leverages off-the-shelf modern game development...analysis and correlations. Recently, an ARL-pioneered project named Virtual Reality Data Analysis Environment (VRDAE) used VR and a modern game engine

Investigating the Magnetic Interaction with Geomag and Tracker Video Analysis: Static Equilibrium and Anharmonic Dynamics

ERIC Educational Resources Information Center

Onorato, P.; Mascheretti, P.; DeAmbrosis, A.

2012-01-01

In this paper, we describe how simple experiments realizable by using easily found and low-cost materials allow students to explore quantitatively the magnetic interaction thanks to the help of an Open Source Physics tool, the Tracker Video Analysis software. The static equilibrium of a "column" of permanents magnets is carefully investigated by…

The role of 3-D interactive visualization in blind surveys of H I in galaxies

NASA Astrophysics Data System (ADS)

Punzo, D.; van der Hulst, J. M.; Roerdink, J. B. T. M.; Oosterloo, T. A.; Ramatsoku, M.; Verheijen, M. A. W.

2015-09-01

Upcoming H I surveys will deliver large datasets, and automated processing using the full 3-D information (two positional dimensions and one spectral dimension) to find and characterize H I objects is imperative. In this context, visualization is an essential tool for enabling qualitative and quantitative human control on an automated source finding and analysis pipeline. We discuss how Visual Analytics, the combination of automated data processing and human reasoning, creativity and intuition, supported by interactive visualization, enables flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities helping the discovery and analysis of subtle structures in the 3-D domain. The requirements for a fully interactive visualization tool are: coupled 1-D/2-D/3-D visualization, quantitative and comparative capabilities, combined with supervised semi-automated analysis. Moreover, the source code must have the following characteristics for enabling collaborative work: open, modular, well documented, and well maintained. We review four state of-the-art, 3-D visualization packages assessing their capabilities and feasibility for use in the case of 3-D astronomical data.

STATWIZ - AN ELECTRONIC STATISTICAL TOOL (ABSTRACT)

EPA Science Inventory

StatWiz is a web-based, interactive, and dynamic statistical tool for researchers. It will allow researchers to input information and/or data and then receive experimental design options, or outputs from data analysis. StatWiz is envisioned as an expert system that will walk rese...

GAC: Gene Associations with Clinical, a web based application.

PubMed

Zhang, Xinyan; Rupji, Manali; Kowalski, Jeanne

2017-01-01

We present GAC, a shiny R based tool for interactive visualization of clinical associations based on high-dimensional data. The tool provides a web-based suite to perform supervised principal component analysis (SuperPC), an approach that uses both high-dimensional data, such as gene expression, combined with clinical data to infer clinical associations. We extended the approach to address binary outcomes, in addition to continuous and time-to-event data in our package, thereby increasing the use and flexibility of SuperPC.  Additionally, the tool provides an interactive visualization for summarizing results based on a forest plot for both binary and time-to-event data.  In summary, the GAC suite of tools provide a one stop shop for conducting statistical analysis to identify and visualize the association between a clinical outcome of interest and high-dimensional data types, such as genomic data. Our GAC package has been implemented in R and is available via http://shinygispa.winship.emory.edu/GAC/. The developmental repository is available at https://github.com/manalirupji/GAC.

CASAS: Cancer Survival Analysis Suite, a web based application

PubMed Central

Rupji, Manali; Zhang, Xinyan; Kowalski, Jeanne

2017-01-01

We present CASAS, a shiny R based tool for interactive survival analysis and visualization of results. The tool provides a web-based one stop shop to perform the following types of survival analysis:  quantile, landmark and competing risks, in addition to standard survival analysis.  The interface makes it easy to perform such survival analyses and obtain results using the interactive Kaplan-Meier and cumulative incidence plots.  Univariate analysis can be performed on one or several user specified variable(s) simultaneously, the results of which are displayed in a single table that includes log rank p-values and hazard ratios along with their significance. For several quantile survival analyses from multiple cancer types, a single summary grid is constructed. The CASAS package has been implemented in R and is available via http://shinygispa.winship.emory.edu/CASAS/. The developmental repository is available at https://github.com/manalirupji/CASAS/. PMID:28928946

CASAS: Cancer Survival Analysis Suite, a web based application.

PubMed

Rupji, Manali; Zhang, Xinyan; Kowalski, Jeanne

2017-01-01

We present CASAS, a shiny R based tool for interactive survival analysis and visualization of results. The tool provides a web-based one stop shop to perform the following types of survival analysis:  quantile, landmark and competing risks, in addition to standard survival analysis.  The interface makes it easy to perform such survival analyses and obtain results using the interactive Kaplan-Meier and cumulative incidence plots.  Univariate analysis can be performed on one or several user specified variable(s) simultaneously, the results of which are displayed in a single table that includes log rank p-values and hazard ratios along with their significance. For several quantile survival analyses from multiple cancer types, a single summary grid is constructed. The CASAS package has been implemented in R and is available via http://shinygispa.winship.emory.edu/CASAS/. The developmental repository is available at https://github.com/manalirupji/CASAS/.

PAPST, a User Friendly and Powerful Java Platform for ChIP-Seq Peak Co-Localization Analysis and Beyond.

PubMed

Bible, Paul W; Kanno, Yuka; Wei, Lai; Brooks, Stephen R; O'Shea, John J; Morasso, Maria I; Loganantharaj, Rasiah; Sun, Hong-Wei

2015-01-01

Comparative co-localization analysis of transcription factors (TFs) and epigenetic marks (EMs) in specific biological contexts is one of the most critical areas of ChIP-Seq data analysis beyond peak calling. Yet there is a significant lack of user-friendly and powerful tools geared towards co-localization analysis based exploratory research. Most tools currently used for co-localization analysis are command line only and require extensive installation procedures and Linux expertise. Online tools partially address the usability issues of command line tools, but slow response times and few customization features make them unsuitable for rapid data-driven interactive exploratory research. We have developed PAPST: Peak Assignment and Profile Search Tool, a user-friendly yet powerful platform with a unique design, which integrates both gene-centric and peak-centric co-localization analysis into a single package. Most of PAPST's functions can be completed in less than five seconds, allowing quick cycles of data-driven hypothesis generation and testing. With PAPST, a researcher with or without computational expertise can perform sophisticated co-localization pattern analysis of multiple TFs and EMs, either against all known genes or a set of genomic regions obtained from public repositories or prior analysis. PAPST is a versatile, efficient, and customizable tool for genome-wide data-driven exploratory research. Creatively used, PAPST can be quickly applied to any genomic data analysis that involves a comparison of two or more sets of genomic coordinate intervals, making it a powerful tool for a wide range of exploratory genomic research. We first present PAPST's general purpose features then apply it to several public ChIP-Seq data sets to demonstrate its rapid execution and potential for cutting-edge research with a case study in enhancer analysis. To our knowledge, PAPST is the first software of its kind to provide efficient and sophisticated post peak-calling ChIP-Seq data analysis as an easy-to-use interactive application. PAPST is available at https://github.com/paulbible/papst and is a public domain work.

PAPST, a User Friendly and Powerful Java Platform for ChIP-Seq Peak Co-Localization Analysis and Beyond

PubMed Central

Bible, Paul W.; Kanno, Yuka; Wei, Lai; Brooks, Stephen R.; O’Shea, John J.; Morasso, Maria I.; Loganantharaj, Rasiah; Sun, Hong-Wei

2015-01-01

Comparative co-localization analysis of transcription factors (TFs) and epigenetic marks (EMs) in specific biological contexts is one of the most critical areas of ChIP-Seq data analysis beyond peak calling. Yet there is a significant lack of user-friendly and powerful tools geared towards co-localization analysis based exploratory research. Most tools currently used for co-localization analysis are command line only and require extensive installation procedures and Linux expertise. Online tools partially address the usability issues of command line tools, but slow response times and few customization features make them unsuitable for rapid data-driven interactive exploratory research. We have developed PAPST: Peak Assignment and Profile Search Tool, a user-friendly yet powerful platform with a unique design, which integrates both gene-centric and peak-centric co-localization analysis into a single package. Most of PAPST’s functions can be completed in less than five seconds, allowing quick cycles of data-driven hypothesis generation and testing. With PAPST, a researcher with or without computational expertise can perform sophisticated co-localization pattern analysis of multiple TFs and EMs, either against all known genes or a set of genomic regions obtained from public repositories or prior analysis. PAPST is a versatile, efficient, and customizable tool for genome-wide data-driven exploratory research. Creatively used, PAPST can be quickly applied to any genomic data analysis that involves a comparison of two or more sets of genomic coordinate intervals, making it a powerful tool for a wide range of exploratory genomic research. We first present PAPST’s general purpose features then apply it to several public ChIP-Seq data sets to demonstrate its rapid execution and potential for cutting-edge research with a case study in enhancer analysis. To our knowledge, PAPST is the first software of its kind to provide efficient and sophisticated post peak-calling ChIP-Seq data analysis as an easy-to-use interactive application. PAPST is available at https://github.com/paulbible/papst and is a public domain work. PMID:25970601

Interactive metagenomic visualization in a Web browser

PubMed Central

2011-01-01

Background A critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. The inherent uncertainty in assignments to these groups makes it important to consider both their hierarchical contexts and their prediction confidence. The current tools for visualizing metagenomic data, however, omit or distort quantitative hierarchical relationships and lack the facility for displaying secondary variables. Results Here we present Krona, a new visualization tool that allows intuitive exploration of relative abundances and confidences within the complex hierarchies of metagenomic classifications. Krona combines a variant of radial, space-filling displays with parametric coloring and interactive polar-coordinate zooming. The HTML5 and JavaScript implementation enables fully interactive charts that can be explored with any modern Web browser, without the need for installed software or plug-ins. This Web-based architecture also allows each chart to be an independent document, making them easy to share via e-mail or post to a standard Web server. To illustrate Krona's utility, we describe its application to various metagenomic data sets and its compatibility with popular metagenomic analysis tools. Conclusions Krona is both a powerful metagenomic visualization tool and a demonstration of the potential of HTML5 for highly accessible bioinformatic visualizations. Its rich and interactive displays facilitate more informed interpretations of metagenomic analyses, while its implementation as a browser-based application makes it extremely portable and easily adopted into existing analysis packages. Both the Krona rendering code and conversion tools are freely available under a BSD open-source license, and available from: http://krona.sourceforge.net. PMID:21961884

The experiences of undergraduate nursing students with bots in Second LifeRTM

NASA Astrophysics Data System (ADS)

Rose, Lesele H.

As technology continues to transform education from the status quo of traditional lecture-style instruction to an interactive engaging learning experience, students' experiences within the learning environment continues to change as well. This dissertation addressed the need for continuing research in advancing implementation of technology in higher education. The purpose of this phenomenological study was to discover more about the experiences of undergraduate nursing students using standardized geriatric evaluation tools when interacting with scripted geriatric patient bots tools in a simulated instructional intake setting. Data was collected through a Demographics questionnaire, an Experiential questionnaire, and a Reflection questionnaire. Triangulation of data collection occurred through an automatically created log of the interactions with the two bots, and by an automatically recorded log of the participants' movements while in the simulated geriatric intake interview. The data analysis consisted of an iterative review of the questionnaires and the participants' logs in an effort to identify common themes, recurring comments, and issues which would benefit from further exploration. Findings revealed that the interactions with the bots were perceived as a valuable experience for the participants from the perspective of interacting with the Geriatric Evaluation Tools in the role of an intake nurse. Further research is indicated to explore instructional interactions with bots in effectively mastering the use of established Geriatric Evaluation Tools.

Interactive Parallel Data Analysis within Data-Centric Cluster Facilities using the IPython Notebook

NASA Astrophysics Data System (ADS)

Pascoe, S.; Lansdowne, J.; Iwi, A.; Stephens, A.; Kershaw, P.

2012-12-01

The data deluge is making traditional analysis workflows for many researchers obsolete. Support for parallelism within popular tools such as matlab, IDL and NCO is not well developed and rarely used. However parallelism is necessary for processing modern data volumes on a timescale conducive to curiosity-driven analysis. Furthermore, for peta-scale datasets such as the CMIP5 archive, it is no longer practical to bring an entire dataset to a researcher's workstation for analysis, or even to their institutional cluster. Therefore, there is an increasing need to develop new analysis platforms which both enable processing at the point of data storage and which provides parallelism. Such an environment should, where possible, maintain the convenience and familiarity of our current analysis environments to encourage curiosity-driven research. We describe how we are combining the interactive python shell (IPython) with our JASMIN data-cluster infrastructure. IPython has been specifically designed to bridge the gap between the HPC-style parallel workflows and the opportunistic curiosity-driven analysis usually carried out using domain specific languages and scriptable tools. IPython offers a web-based interactive environment, the IPython notebook, and a cluster engine for parallelism all underpinned by the well-respected Python/Scipy scientific programming stack. JASMIN is designed to support the data analysis requirements of the UK and European climate and earth system modeling community. JASMIN, with its sister facility CEMS focusing the earth observation community, has 4.5 PB of fast parallel disk storage alongside over 370 computing cores provide local computation. Through the IPython interface to JASMIN, users can make efficient use of JASMIN's multi-core virtual machines to perform interactive analysis on all cores simultaneously or can configure IPython clusters across multiple VMs. Larger-scale clusters can be provisioned through JASMIN's batch scheduling system. Outputs can be summarised and visualised using the full power of Python's many scientific tools, including Scipy, Matplotlib, Pandas and CDAT. This rich user experience is delivered through the user's web browser; maintaining the interactive feel of a workstation-based environment with the parallel power of a remote data-centric processing facility.

Interactive Graphics Analysis for Aircraft Design

NASA Technical Reports Server (NTRS)

Townsend, J. C.

1983-01-01

Program uses higher-order far field drag minimization. Computer program WDES WDEM preliminary aerodynamic design tool for one or two interacting, subsonic lifting surfaces. Subcritical wing design code employs higher-order far-field drag minimization technique. Linearized aerodynamic theory used. Program written in FORTRAN IV.

Molecular Dynamics Visualization (MDV): Stereoscopic 3D Display of Biomolecular Structure and Interactions Using the Unity Game Engine.

PubMed

Wiebrands, Michael; Malajczuk, Chris J; Woods, Andrew J; Rohl, Andrew L; Mancera, Ricardo L

2018-06-21

Molecular graphics systems are visualization tools which, upon integration into a 3D immersive environment, provide a unique virtual reality experience for research and teaching of biomolecular structure, function and interactions. We have developed a molecular structure and dynamics application, the Molecular Dynamics Visualization tool, that uses the Unity game engine combined with large scale, multi-user, stereoscopic visualization systems to deliver an immersive display experience, particularly with a large cylindrical projection display. The application is structured to separate the biomolecular modeling and visualization systems. The biomolecular model loading and analysis system was developed as a stand-alone C# library and provides the foundation for the custom visualization system built in Unity. All visual models displayed within the tool are generated using Unity-based procedural mesh building routines. A 3D user interface was built to allow seamless dynamic interaction with the model while being viewed in 3D space. Biomolecular structure analysis and display capabilities are exemplified with a range of complex systems involving cell membranes, protein folding and lipid droplets.

OmicsNet: a web-based tool for creation and visual analysis of biological networks in 3D space.

PubMed

Zhou, Guangyan; Xia, Jianguo

2018-06-07

Biological networks play increasingly important roles in omics data integration and systems biology. Over the past decade, many excellent tools have been developed to support creation, analysis and visualization of biological networks. However, important limitations remain: most tools are standalone programs, the majority of them focus on protein-protein interaction (PPI) or metabolic networks, and visualizations often suffer from 'hairball' effects when networks become large. To help address these limitations, we developed OmicsNet - a novel web-based tool that allows users to easily create different types of molecular interaction networks and visually explore them in a three-dimensional (3D) space. Users can upload one or multiple lists of molecules of interest (genes/proteins, microRNAs, transcription factors or metabolites) to create and merge different types of biological networks. The 3D network visualization system was implemented using the powerful Web Graphics Library (WebGL) technology that works natively in most major browsers. OmicsNet supports force-directed layout, multi-layered perspective layout, as well as spherical layout to help visualize and navigate complex networks. A rich set of functions have been implemented to allow users to perform coloring, shading, topology analysis, and enrichment analysis. OmicsNet is freely available at http://www.omicsnet.ca.

PANDA-view: An easy-to-use tool for statistical analysis and visualization of quantitative proteomics data.

PubMed

Chang, Cheng; Xu, Kaikun; Guo, Chaoping; Wang, Jinxia; Yan, Qi; Zhang, Jian; He, Fuchu; Zhu, Yunping

2018-05-22

Compared with the numerous software tools developed for identification and quantification of -omics data, there remains a lack of suitable tools for both downstream analysis and data visualization. To help researchers better understand the biological meanings in their -omics data, we present an easy-to-use tool, named PANDA-view, for both statistical analysis and visualization of quantitative proteomics data and other -omics data. PANDA-view contains various kinds of analysis methods such as normalization, missing value imputation, statistical tests, clustering and principal component analysis, as well as the most commonly-used data visualization methods including an interactive volcano plot. Additionally, it provides user-friendly interfaces for protein-peptide-spectrum representation of the quantitative proteomics data. PANDA-view is freely available at https://sourceforge.net/projects/panda-view/. 1987ccpacer@163.com and zhuyunping@gmail.com. Supplementary data are available at Bioinformatics online.

Metabolomic Analysis and Visualization Engine for LC–MS Data

PubMed Central

Melamud, Eugene; Vastag, Livia; Rabinowitz, Joshua D.

2017-01-01

Metabolomic analysis by liquid chromatography–high-resolution mass spectrometry results in data sets with thousands of features arising from metabolites, fragments, isotopes, and adducts. Here we describe a software package, Metabolomic Analysis and Visualization ENgine (MAVEN), designed for efficient interactive analysis of LC–MS data, including in the presence of isotope labeling. The software contains tools for all aspects of the data analysis process, from feature extraction to pathway-based graphical data display. To facilitate data validation, a machine learning algorithm automatically assesses peak quality. Users interact with raw data primarily in the form of extracted ion chromatograms, which are displayed with overlaid circles indicating peak quality, and bar graphs of peak intensities for both unlabeled and isotope-labeled metabolite forms. Click-based navigation leads to additional information, such as raw data for specific isotopic forms or for metabolites changing significantly between conditions. Fast data processing algorithms result in nearly delay-free browsing. Drop-down menus provide tools for the overlay of data onto pathway maps. These tools enable animating series of pathway graphs, e.g., to show propagation of labeled forms through a metabolic network. MAVEN is released under an open source license at http://maven.princeton.edu. PMID:21049934

Geometric modeling for computer aided design

NASA Technical Reports Server (NTRS)

Schwing, James L.; Olariu, Stephen

1995-01-01

The primary goal of this grant has been the design and implementation of software to be used in the conceptual design of aerospace vehicles particularly focused on the elements of geometric design, graphical user interfaces, and the interaction of the multitude of software typically used in this engineering environment. This has resulted in the development of several analysis packages and design studies. These include two major software systems currently used in the conceptual level design of aerospace vehicles. These tools are SMART, the Solid Modeling Aerospace Research Tool, and EASIE, the Environment for Software Integration and Execution. Additional software tools were designed and implemented to address the needs of the engineer working in the conceptual design environment. SMART provides conceptual designers with a rapid prototyping capability and several engineering analysis capabilities. In addition, SMART has a carefully engineered user interface that makes it easy to learn and use. Finally, a number of specialty characteristics have been built into SMART which allow it to be used efficiently as a front end geometry processor for other analysis packages. EASIE provides a set of interactive utilities that simplify the task of building and executing computer aided design systems consisting of diverse, stand-alone, analysis codes. Resulting in a streamlining of the exchange of data between programs reducing errors and improving the efficiency. EASIE provides both a methodology and a collection of software tools to ease the task of coordinating engineering design and analysis codes.

Analysis of Learning Tools in the study of Developmental of Interactive Multimedia Based Physic Learning Charged in Problem Solving

NASA Astrophysics Data System (ADS)

Manurung, Sondang; Demonta Pangabean, Deo

2017-05-01

The main purpose of this study is to produce needs analysis, literature review, and learning tools in the study of developmental of interactive multimedia based physic learning charged in problem solving to improve thinking ability of physic prospective student. The first-year result of the study is: result of the draft based on a needs analysis of the facts on the ground, the conditions of existing learning and literature studies. Following the design of devices and instruments performed as well the development of media. Result of the second study is physics learning device -based interactive multimedia charged problem solving in the form of textbooks and scientific publications. Previous learning models tested in a limited sample, then in the evaluation and repair. Besides, the product of research has an economic value on the grounds: (1) a virtual laboratory to offer this research provides a solution purchases physics laboratory equipment is expensive; (2) address the shortage of teachers of physics in remote areas as a learning tool can be accessed offline and online; (3). reducing material or consumables as tutorials can be done online; Targeted research is the first year: i.e story board learning physics that have been scanned in a web form CD (compact disk) and the interactive multimedia of gas Kinetic Theory concept. This draft is based on a needs analysis of the facts on the ground, the existing learning conditions, and literature studies. Previous learning models tested in a limited sample, then in the evaluation and repair.

Improved Design of Tunnel Supports : Volume 1 : Simplified Analysis for Ground-Structure Interaction in Tunneling

DOT National Transportation Integrated Search

1980-06-01

The purpose of this report is to provide the tunneling profession with improved practical tools in the technical or design area, which provide more accurate representations of the ground-structure interaction in tunneling. The design methods range fr...

Sight Application Analysis Tool

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

Bronevetsky, G.

2014-09-17

The scale and complexity of scientific applications makes it very difficult to optimize, debug and extend them to support new capabilities. We have developed a tool that supports developers’ efforts to understand the logical flow of their applications and interactions between application components and hardware in a way that scales with application complexity and parallelism.

Activity Theory and Qualitative Research in Digital Domains

ERIC Educational Resources Information Center

Sam, Cecile

2012-01-01

Understanding the interactions between people, computer-mediated communication, and online life requires that researchers appropriate a set of methodological tools that would be best suited for capturing and analyzing the phenomenon. However, these tools are not limited to relevant technological forms of data collections and analysis programs; it…

Aerospace Systems Design in NASA's Collaborative Engineering Environment

NASA Technical Reports Server (NTRS)

Monell, Donald W.; Piland, William M.

1999-01-01

Past designs of complex aerospace systems involved an environment consisting of collocated design teams with project managers, technical discipline experts, and other experts (e.g. manufacturing and systems operations). These experts were generally qualified only on the basis of past design experience and typically had access to a limited set of integrated analysis tools. These environments provided less than desirable design fidelity, often lead to the inability of assessing critical programmatic and technical issues (e.g., cost risk, technical impacts), and generally derived a design that was not necessarily optimized across the entire system. The continually changing, modern aerospace industry demands systems design processes that involve the best talent available (no matter where it resides) and access to the best design and analysis tools. A solution to these demands involves a design environment referred to as collaborative engineering. The collaborative engineering environment evolving within the National Aeronautics and Space Administration (NASA) is a capability that enables the Agency's engineering infrastructure to interact and use the best state-of-the-art tools and data across organizational boundaries. Using collaborative engineering, the collocated team is replaced with an interactive team structure where the team members are geographically distributed and the best engineering talent can be applied to the design effort regardless of physical location. In addition, a more efficient, higher quality design product is delivered by bringing together the best engineering talent with more up-to-date design and analysis tools. These tools are focused on interactive, multidisciplinary design and analysis with emphasis on the complete life cycle of the system, and they include nontraditional, integrated tools for life cycle cost estimation and risk assessment. NASA has made substantial progress during the last two years in developing a collaborative engineering environment. NASA is planning to use this collaborative engineering infrastructure to provide better aerospace systems life cycle design and analysis, which includes analytical assessment of the technical and programmatic aspects of a system from "cradle to grave." This paper describes the recent NASA developments in the area of collaborative engineering, the benefits (realized and anticipated) of using the developed capability, and the long-term plans for implementing this capability across the Agency.

Aerospace Systems Design in NASA's Collaborative Engineering Environment

NASA Technical Reports Server (NTRS)

Monell, Donald W.; Piland, William M.

2000-01-01

Past designs of complex aerospace systems involved an environment consisting of collocated design teams with project managers, technical discipline experts, and other experts (e.g., manufacturing and systems operation). These experts were generally qualified only on the basis of past design experience and typically had access to a limited set of integrated analysis tools. These environments provided less than desirable design fidelity, often lead to the inability of assessing critical programmatic and technical issues (e.g., cost, risk, technical impacts), and generally derived a design that was not necessarily optimized across the entire system. The continually changing, modern aerospace industry demands systems design processes that involve the best talent available (no matter where it resides) and access to the the best design and analysis tools. A solution to these demands involves a design environment referred to as collaborative engineering. The collaborative engineering environment evolving within the National Aeronautics and Space Administration (NASA) is a capability that enables the Agency's engineering infrastructure to interact and use the best state-of-the-art tools and data across organizational boundaries. Using collaborative engineering, the collocated team is replaced with an interactive team structure where the team members are geographical distributed and the best engineering talent can be applied to the design effort regardless of physical location. In addition, a more efficient, higher quality design product is delivered by bringing together the best engineering talent with more up-to-date design and analysis tools. These tools are focused on interactive, multidisciplinary design and analysis with emphasis on the complete life cycle of the system, and they include nontraditional, integrated tools for life cycle cost estimation and risk assessment. NASA has made substantial progress during the last two years in developing a collaborative engineering environment. NASA is planning to use this collaborative engineering engineering infrastructure to provide better aerospace systems life cycle design and analysis, which includes analytical assessment of the technical and programmatic aspects of a system from "cradle to grave." This paper describes the recent NASA developments in the area of collaborative engineering, the benefits (realized and anticipated) of using the developed capability, and the long-term plans for implementing this capability across Agency.

Aerospace Systems Design in NASA's Collaborative Engineering Environment

NASA Astrophysics Data System (ADS)

Monell, Donald W.; Piland, William M.

2000-07-01

Past designs of complex aerospace systems involved an environment consisting of collocated design teams with project managers, technical discipline experts, and other experts (e.g., manufacturing and systems operations). These experts were generally qualified only on the basis of past design experience and typically had access to a limited set of integrated analysis tools. These environments provided less than desirable design fidelity, often led to the inability of assessing critical programmatic and technical issues (e.g., cost, risk, technical impacts), and generally derived a design that was not necessarily optimized across the entire system. The continually changing, modern aerospace industry demands systems design processes that involve the best talent available (no matter where it resides) and access to the best design and analysis tools. A solution to these demands involves a design environment referred to as collaborative engineering. The collaborative engineering environment evolving within the National Aeronautics and Space Administration (NASA) is a capability that enables the Agency's engineering infrastructure to interact and use the best state-of-the-art tools and data across organizational boundaries. Using collaborative engineering, the collocated team is replaced with an interactive team structure where the team members are geographically distributed and the best engineering talent can be applied to the design effort regardless of physical location. In addition, a more efficient, higher quality design product is delivered by bringing together the best engineering talent with more up-to-date design and analysis tools. These tools are focused on interactive, multidisciplinary design and analysis with emphasis on the complete life cycle of the system, and they include nontraditional, integrated tools for life cycle cost estimation and risk assessment. NASA has made substantial progress during the last two years in developing a collaborative engineering environment. NASA is planning to use this collaborative engineering infrastructure to provide better aerospace systems life cycle design and analysis, which includes analytical assessment of the technical and programmatic aspects of a system from "cradle to grave." This paper describes the recent NASA developments in the area of collaborative engineering, the benefits (realized and anticipated) of using the developed capability, and the long-term plans for implementing this capability across the Agency.

A Simple Tool for the Design and Analysis of Multiple-Reflector Antennas in a Multi-Disciplinary Environment

NASA Technical Reports Server (NTRS)

Katz, Daniel S.; Cwik, Tom; Fu, Chuigang; Imbriale, William A.; Jamnejad, Vahraz; Springer, Paul L.; Borgioli, Andrea

2000-01-01

The process of designing and analyzing a multiple-reflector system has traditionally been time-intensive, requiring large amounts of both computational and human time. At many frequencies, a discrete approximation of the radiation integral may be used to model the system. The code which implements this physical optics (PO) algorithm was developed at the Jet Propulsion Laboratory. It analyzes systems of antennas in pairs, and for each pair, the analysis can be computationally time-consuming. Additionally, the antennas must be described using a local coordinate system for each antenna, which makes it difficult to integrate the design into a multi-disciplinary framework in which there is traditionally one global coordinate system, even before considering deforming the antenna as prescribed by external structural and/or thermal factors. Finally, setting up the code to correctly analyze all the antenna pairs in the system can take a fair amount of time, and introduces possible human error. The use of parallel computing to reduce the computational time required for the analysis of a given pair of antennas has been previously discussed. This paper focuses on the other problems mentioned above. It will present a methodology and examples of use of an automated tool that performs the analysis of a complete multiple-reflector system in an integrated multi-disciplinary environment (including CAD modeling, and structural and thermal analysis) at the click of a button. This tool, named MOD Tool (Millimeter-wave Optics Design Tool), has been designed and implemented as a distributed tool, with a client that runs almost identically on Unix, Mac, and Windows platforms, and a server that runs primarily on a Unix workstation and can interact with parallel supercomputers with simple instruction from the user interacting with the client.

The effect of introducing computers into an introductory physics problem-solving laboratory

NASA Astrophysics Data System (ADS)

McCullough, Laura Ellen

2000-10-01

Computers are appearing in every type of classroom across the country. Yet they often appear without benefit of studying their effects. The research that is available on computer use in classrooms has found mixed results, and often ignores the theoretical and instructional contexts of the computer in the classroom. The University of Minnesota's physics department employs a cooperative-group problem solving pedagogy, based on a cognitive apprenticeship instructional model, in its calculus-based introductory physics course. This study was designed to determine possible negative effects of introducing a computerized data-acquisition and analysis tool into this pedagogy as a problem-solving tool for students to use in laboratory. To determine the effects of the computer tool, two quasi-experimental treatment groups were selected. The computer-tool group (N = 170) used a tool, designed for this study (VideoTool), to collect and analyze motion data in the laboratory. The control group (N = 170) used traditional non-computer equipment (spark tapes and Polaroid(TM) film). The curriculum was kept as similar as possible for the two groups. During the ten week academic quarter, groups were examined for effects on performance on conceptual tests and grades, attitudes towards the laboratory and the laboratory tools, and behaviors within cooperative groups. Possible interactions with gender were also examined. Few differences were found between the control and computer-tool groups. The control group received slightly higher scores on one conceptual test, but this difference was not educationally significant. The computer-tool group had slightly more positive attitudes towards using the computer tool than their counterparts had towards the traditional tools. The computer-tool group also perceived that they spoke more frequently about physics misunderstandings, while the control group felt that they discussed equipment difficulties more often. This perceptual difference interacted with gender, with the men in the control group more likely to discuss equipment difficulties than any other group. Overall, the differences between the control and quasi-experimental groups were minimal. It was concluded that carefully replacing traditional data collection and analysis tools with a computer tool had no negative effects on achievement, attitude, group behavior, and did not interact with gender.

Space Earthquake Perturbation Simulation (SEPS) an application based on Geant4 tools to model and simulate the interaction between the Earthquake and the particle trapped on the Van Allen belt

NASA Astrophysics Data System (ADS)

Ambroglini, Filippo; Jerome Burger, William; Battiston, Roberto; Vitale, Vincenzo; Zhang, Yu

2014-05-01

During last decades, few space experiments revealed anomalous bursts of charged particles, mainly electrons with energy larger than few MeV. A possible source of these bursts are the low-frequency seismo-electromagnetic emissions, which can cause the precipitation of the electrons from the lower boundary of their inner belt. Studies of these bursts reported also a short-term pre-seismic excess. Starting from simulation tools traditionally used on high energy physics we developed a dedicated application SEPS (Space Perturbation Earthquake Simulation), based on the Geant4 tool and PLANETOCOSMICS program, able to model and simulate the electromagnetic interaction between the earthquake and the particles trapped in the inner Van Allen belt. With SEPS one can study the transport of particles trapped in the Van Allen belts through the Earth's magnetic field also taking into account possible interactions with the Earth's atmosphere. SEPS provides the possibility of: testing different models of interaction between electromagnetic waves and trapped particles, defining the mechanism of interaction as also shaping the area in which this takes place,assessing the effects of perturbations in the magnetic field on the particles path, performing back-tracking analysis and also modelling the interaction with electric fields. SEPS is in advanced development stage, so that it could be already exploited to test in details the results of correlation analysis between particle bursts and earthquakes based on NOAA and SAMPEX data. The test was performed both with a full simulation analysis, (tracing from the position of the earthquake and going to see if there were paths compatible with the burst revealed) and with a back-tracking analysis (tracing from the burst detection point and checking the compatibility with the position of associated earthquake).

SERVING EPA'S MISSION: POTENTIAL ROLES OF ENGERETIC TOOLS

EPA Science Inventory

Effective environmental protection requires an understanding of environmental systems dynamics that includes socioeconomic activity along with its interactions with environmental processes. Some forms of scientific analysis, such as emergy analysis, do seek to account for the ...

D-VASim: an interactive virtual laboratory environment for the simulation and analysis of genetic circuits.

PubMed

Baig, Hasan; Madsen, Jan

2017-01-15

Simulation and behavioral analysis of genetic circuits is a standard approach of functional verification prior to their physical implementation. Many software tools have been developed to perform in silico analysis for this purpose, but none of them allow users to interact with the model during runtime. The runtime interaction gives the user a feeling of being in the lab performing a real world experiment. In this work, we present a user-friendly software tool named D-VASim (Dynamic Virtual Analyzer and Simulator), which provides a virtual laboratory environment to simulate and analyze the behavior of genetic logic circuit models represented in an SBML (Systems Biology Markup Language). Hence, SBML models developed in other software environments can be analyzed and simulated in D-VASim. D-VASim offers deterministic as well as stochastic simulation; and differs from other software tools by being able to extract and validate the Boolean logic from the SBML model. D-VASim is also capable of analyzing the threshold value and propagation delay of a genetic circuit model. D-VASim is available for Windows and Mac OS and can be downloaded from bda.compute.dtu.dk/downloads/. haba@dtu.dk, jama@dtu.dk. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Sports teams as superorganisms: implications of sociobiological models of behaviour for research and practice in team sports performance analysis.

PubMed

Duarte, Ricardo; Araújo, Duarte; Correia, Vanda; Davids, Keith

2012-08-01

Significant criticisms have emerged on the way that collective behaviours in team sports have been traditionally evaluated. A major recommendation has been for future research and practice to focus on the interpersonal relationships developed between team players during performance. Most research has typically investigated team game performance in subunits (attack or defence), rather than considering the interactions of performers within the whole team. In this paper, we offer the view that team performance analysis could benefit from the adoption of biological models used to explain how repeated interactions between grouping individuals scale to emergent social collective behaviours. We highlight the advantages of conceptualizing sports teams as functional integrated 'super-organisms' and discuss innovative measurement tools, which might be used to capture the superorganismic properties of sports teams. These tools are suitable for revealing the idiosyncratic collective behaviours underlying the cooperative and competitive tendencies of different sports teams, particularly their coordination of labour and the most frequent channels of communication and patterns of interaction between team players. The principles and tools presented here can serve as the basis for novel approaches and applications of performance analysis devoted to understanding sports teams as cohesive, functioning, high-order organisms exhibiting their own peculiar behavioural patterns.

Animated analysis of geoscientific datasets: An interactive graphical application

NASA Astrophysics Data System (ADS)

Morse, Peter; Reading, Anya; Lueg, Christopher

2017-12-01

Geoscientists are required to analyze and draw conclusions from increasingly large volumes of data. There is a need to recognise and characterise features and changing patterns of Earth observables within such large datasets. It is also necessary to identify significant subsets of the data for more detailed analysis. We present an innovative, interactive software tool and workflow to visualise, characterise, sample and tag large geoscientific datasets from both local and cloud-based repositories. It uses an animated interface and human-computer interaction to utilise the capacity of human expert observers to identify features via enhanced visual analytics. 'Tagger' enables users to analyze datasets that are too large in volume to be drawn legibly on a reasonable number of single static plots. Users interact with the moving graphical display, tagging data ranges of interest for subsequent attention. The tool provides a rapid pre-pass process using fast GPU-based OpenGL graphics and data-handling and is coded in the Quartz Composer visual programing language (VPL) on Mac OSX. It makes use of interoperable data formats, and cloud-based (or local) data storage and compute. In a case study, Tagger was used to characterise a decade (2000-2009) of data recorded by the Cape Sorell Waverider Buoy, located approximately 10 km off the west coast of Tasmania, Australia. These data serve as a proxy for the understanding of Southern Ocean storminess, which has both local and global implications. This example shows use of the tool to identify and characterise 4 different types of storm and non-storm events during this time. Events characterised in this way are compared with conventional analysis, noting advantages and limitations of data analysis using animation and human interaction. Tagger provides a new ability to make use of humans as feature detectors in computer-based analysis of large-volume geosciences and other data.

Analysis of Interactive Conflict Resolution Tool Usage in a Mixed Equipage Environment

NASA Technical Reports Server (NTRS)

Homola, Jeffrey; Morey, Susan; Cabrall, Christopher; Martin, Lynne; Mercer, Joey; Prevot, Thomas

2013-01-01

A human-in-the-loop simulation was conducted that examined separation assurance concepts in varying levels of traffic density with mixtures of aircraft equipage and automation. This paper's analysis focuses on one of the experimental conditions in which traffic levels were approximately fifty percent higher than today, and approximately fifty percent of the traffic within the test area were equipped with data communications (data comm) capabilities. The other fifty percent of the aircraft required control by voice much like today. Within this environment, the air traffic controller participants were provided access to tools and automation designed to support the primary task of separation assurance that are currently unavailable. Two tools were selected for analysis in this paper: 1) a pre-probed altitude fly-out menu that provided instant feedback of conflict probe results for a range of altitudes, and 2) an interactive auto resolver that provided on-demand access to an automation-generated conflict resolution trajectory. Although encouraged, use of the support tools was not required; the participants were free to use the tools as they saw fit, and they were also free to accept, reject, or modify the resolutions offered by the automation. This mode of interaction provided a unique opportunity to examine exactly when and how these tools were used, as well as how acceptable the resolutions were. Results showed that the participants used the pre-probed altitude fly-out menu in 14% of conflict cases and preferred to use it in a strategic timeframe on data comm equipped and level flight aircraft. The interactive auto resolver was also used in a primarily strategic timeframe on 22% of conflicts and that their preference was to use it on conflicts involving data comm equipped aircraft as well. Of the 258 resolutions displayed, 46% were implemented and 54% were not. The auto resolver was rated highly by participants in terms of confidence and preference. Factors such as aircraft equipage, ownership, and location of predicted separation loss appeared to play a role in the decision of controllers to accept or reject the auto resolver's resolutions.

A Contextual Analysis of Classroom Interaction at the University Level: An Operations Research Approach.

ERIC Educational Resources Information Center

Hester, Paul H.

This study sought to demonstrate how an interactive model can be used as a "semiotic" tool to reconcile contrasting views of the role of the college professor. The study used concepts of group dynamics to study classroom leadership, climate, and expectations and a social-psychological perspective was used to analyze group interaction patterns as…

Contact: Effects of an Intervention Program To Foster Harmonious Interactions between Deaf-Blind Children and Their Educators.

ERIC Educational Resources Information Center

Janssen, Marleen J.; Riksen-Walraven, J. Marianne; Van Dijk, Jan P. M.

2003-01-01

This study examined the effects of an intervention program to improve the quality of daily interaction between six congenitally deaf-blind children and their 14 educators (teachers, caregivers, and mothers). With video analysis as the most important tool, the interaction coaches trained the educators to recognize the children's signals and attune…

Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format.

PubMed

Webb, Ryan L; Ma'ayan, Avi

2011-03-21

The World Wide Web plays a critical role in enabling molecular, cell, systems and computational biologists to exchange, search, visualize, integrate, and analyze experimental data. Such efforts can be further enhanced through the development of semantic web concepts. The semantic web idea is to enable machines to understand data through the development of protocol free data exchange formats such as Resource Description Framework (RDF) and the Web Ontology Language (OWL). These standards provide formal descriptors of objects, object properties and their relationships within a specific knowledge domain. However, the overhead of converting datasets typically stored in data tables such as Excel, text or PDF into RDF or OWL formats is not trivial for non-specialists and as such produces a barrier to seamless data exchange between researchers, databases and analysis tools. This problem is particularly of importance in the field of network systems biology where biochemical interactions between genes and their protein products are abstracted to networks. For the purpose of converting biochemical interactions into the BioPAX format, which is the leading standard developed by the computational systems biology community, we developed an open-source command line tool that takes as input tabular data describing different types of molecular biochemical interactions. The tool converts such interactions into the BioPAX level 3 OWL format. We used the tool to convert several existing and new mammalian networks of protein interactions, signalling pathways, and transcriptional regulatory networks into BioPAX. Some of these networks were deposited into PathwayCommons, a repository for consolidating and organizing biochemical networks. The software tool Sig2BioPAX is a resource that enables experimental and computational systems biologists to contribute their identified networks and pathways of molecular interactions for integration and reuse with the rest of the research community.

Interactive cutting path analysis programs

NASA Technical Reports Server (NTRS)

Weiner, J. M.; Williams, D. S.; Colley, S. R.

1975-01-01

The operation of numerically controlled machine tools is interactively simulated. Four programs were developed to graphically display the cutting paths for a Monarch lathe, Cintimatic mill, Strippit sheet metal punch, and the wiring path for a Standard wire wrap machine. These programs are run on a IMLAC PDS-ID graphic display system under the DOS-3 disk operating system. The cutting path analysis programs accept input via both paper tape and disk file.

Identifying key sources of uncertainty in the modelling of greenhouse gas emissions from wastewater treatment.

PubMed

Sweetapple, Christine; Fu, Guangtao; Butler, David

2013-09-01

This study investigates sources of uncertainty in the modelling of greenhouse gas emissions from wastewater treatment, through the use of local and global sensitivity analysis tools, and contributes to an in-depth understanding of wastewater treatment modelling by revealing critical parameters and parameter interactions. One-factor-at-a-time sensitivity analysis is used to screen model parameters and identify those with significant individual effects on three performance indicators: total greenhouse gas emissions, effluent quality and operational cost. Sobol's method enables identification of parameters with significant higher order effects and of particular parameter pairs to which model outputs are sensitive. Use of a variance-based global sensitivity analysis tool to investigate parameter interactions enables identification of important parameters not revealed in one-factor-at-a-time sensitivity analysis. These interaction effects have not been considered in previous studies and thus provide a better understanding wastewater treatment plant model characterisation. It was found that uncertainty in modelled nitrous oxide emissions is the primary contributor to uncertainty in total greenhouse gas emissions, due largely to the interaction effects of three nitrogen conversion modelling parameters. The higher order effects of these parameters are also shown to be a key source of uncertainty in effluent quality. Copyright © 2013 Elsevier Ltd. All rights reserved.

Pelagic Habitat Analysis Module (PHAM) for GIS Based Fisheries Decision Support

NASA Technical Reports Server (NTRS)

Kiefer, D. A.; Armstrong, Edward M.; Harrison, D. P.; Hinton, M. G.; Kohin, S.; Snyder, S.; O'Brien, F. J.

2011-01-01

We have assembled a system that integrates satellite and model output with fisheries data We have developed tools that allow analysis of the interaction between species and key environmental variables Demonstrated the capacity to accurately map habitat of Thresher Sharks Alopias vulpinus & pelagicus. Their seasonal migration along the California Current is at least partly driven by the seasonal migration of sardine, key prey of the sharks.We have assembled a system that integrates satellite and model output with fisheries data We have developed tools that allow analysis of the interaction between species and key environmental variables Demonstrated the capacity to accurately map habitat of Thresher Sharks Alopias vulpinus nd pelagicus. Their seasonal migration along the California Current is at least partly driven by the seasonal migration of sardine, key prey of the sharks.

Developing tools for digital radar image data evaluation

NASA Technical Reports Server (NTRS)

Domik, G.; Leberl, F.; Raggam, J.

1986-01-01

The refinement of radar image analysis methods has led to a need for a systems approach to radar image processing software. Developments stimulated through satellite radar are combined with standard image processing techniques to create a user environment to manipulate and analyze airborne and satellite radar images. One aim is to create radar products for the user from the original data to enhance the ease of understanding the contents. The results are called secondary image products and derive from the original digital images. Another aim is to support interactive SAR image analysis. Software methods permit use of a digital height model to create ortho images, synthetic images, stereo-ortho images, radar maps or color combinations of different component products. Efforts are ongoing to integrate individual tools into a combined hardware/software environment for interactive radar image analysis.

Use of Electronic Health Record Tools to Facilitate and Audit Infliximab Prescribing.

PubMed

Sharpless, Bethany R; Del Rosario, Fernando; Molle-Rios, Zarela; Hilmas, Elora

2018-01-01

The objective of this project was to assess a pediatric institution's use of infliximab and develop and evaluate electronic health record tools to improve safety and efficiency of infliximab ordering through auditing and improved communication. Best use of infliximab was defined through a literature review, analysis of baseline use of infliximab at our institution, and distribution and analysis of a national survey. Auditing and order communication were optimized through implementation of mandatory indications in the infliximab orderable and creation of an interactive flowsheet that collects discrete and free-text data. The value of the implemented electronic health record tools was assessed at the conclusion of the project. Baseline analysis determined that 93.8% of orders were dosed appropriately according to the findings of a literature review. After implementation of the flowsheet and indications, the time to perform an audit of use was reduced from 60 minutes to 5 minutes per month. Four months post implementation, data were entered by 60% of the pediatric gastroenterologists at our institution on 15.3% of all encounters for infliximab. Users were surveyed on the value of the tools, with 100% planning to continue using the workflow, and 82% stating the tools frequently improve the efficiency and safety of infliximab prescribing. Creation of a standard workflow by using an interactive flowsheet has improved auditing ability and facilitated the communication of important order information surrounding infliximab. Providers and pharmacists feel these tools improve the safety and efficiency of infliximab ordering, and auditing data reveal that the tools are being used.

Patient-specific surgical planning and hemodynamic computational fluid dynamics optimization through free-form haptic anatomy editing tool (SURGEM).

PubMed

Pekkan, Kerem; Whited, Brian; Kanter, Kirk; Sharma, Shiva; de Zelicourt, Diane; Sundareswaran, Kartik; Frakes, David; Rossignac, Jarek; Yoganathan, Ajit P

2008-11-01

The first version of an anatomy editing/surgical planning tool (SURGEM) targeting anatomical complexity and patient-specific computational fluid dynamics (CFD) analysis is presented. Novel three-dimensional (3D) shape editing concepts and human-shape interaction technologies have been integrated to facilitate interactive surgical morphology alterations, grid generation and CFD analysis. In order to implement "manual hemodynamic optimization" at the surgery planning phase for patients with congenital heart defects, these tools are applied to design and evaluate possible modifications of patient-specific anatomies. In this context, anatomies involve complex geometric topologies and tortuous 3D blood flow pathways with multiple inlets and outlets. These tools make it possible to freely deform the lumen surface and to bend and position baffles through real-time, direct manipulation of the 3D models with both hands, thus eliminating the tedious and time-consuming phase of entering the desired geometry using traditional computer-aided design (CAD) systems. The 3D models of the modified anatomies are seamlessly exported and meshed for patient-specific CFD analysis. Free-formed anatomical modifications are quantified using an in-house skeletization based cross-sectional geometry analysis tool. Hemodynamic performance of the systematically modified anatomies is compared with the original anatomy using CFD. CFD results showed the relative importance of the various surgically created features such as pouch size, vena cave to pulmonary artery (PA) flare and PA stenosis. An interactive surgical-patch size estimator is also introduced. The combined design/analysis cycle time is used for comparing and optimizing surgical plans and improvements are tabulated. The reduced cost of patient-specific shape design and analysis process, made it possible to envision large clinical studies to assess the validity of predictive patient-specific CFD simulations. In this paper, model anatomical design studies are performed on a total of eight different complex patient specific anatomies. Using SURGEM, more than 30 new anatomical designs (or candidate configurations) are created, and the corresponding user times presented. CFD performances for eight of these candidate configurations are also presented.

Interactive, technology-enhanced self-regulated learning tools in healthcare education: a literature review.

PubMed

Petty, Julia

2013-01-01

Learning technology is increasingly being implemented for programmes of blended learning within nurse education. With a growing emphasis on self-directed study particularly in post-basic education, there is a need for learners to be guided in their learning away from practice and limited classroom time. Technology-enabled (TE) tools which engage learners actively can play a part in this. The effectiveness and value of interactive TE learning strategies within healthcare is the focus of this paper. To identify literature that explores the effectiveness of interactive, TE tools on knowledge acquisition and learner satisfaction within healthcare with a view to evaluating their use for post-basic nurse education. A Literature Review was performed focusing on papers exploring the comparative value and perceived benefit of TE tools compared to traditional modes of learning within healthcare. The Databases identified as most suitable due to their relevance to healthcare were accessed through EBSCOhost. Primary, Boolean and advanced searches on key terms were undertaken. Inclusion and exclusion criteria were applied which resulted in a final selection of 11 studies for critique. Analysis of the literature found that knowledge acquisition in most cases was enhanced and measured learner satisfaction was generally positive for interactive, self-regulated TE tools. However, TE education may not suit all learners and this is critiqued in the light of the identified limitations. Interactive self regulation and/or testing can be a valuable learning strategy that can be incorporated into self-directed programmes of study for post-registration learners. Whilst acknowledging the learning styles not suited to such tools, the concurrent use of self-directed TE tools with those learning strategies necessitating a more social presence can work together to support enhancement of knowledge required to deliver rationale for nursing practice. Copyright © 2012 Elsevier Ltd. All rights reserved.

Multi-Spacecraft Analysis with Generic Visualization Tools

NASA Astrophysics Data System (ADS)

Mukherjee, J.; Vela, L.; Gonzalez, C.; Jeffers, S.

2010-12-01

To handle the needs of scientists today and in the future, software tools are going to have to take better advantage of the currently available hardware. Specifically, computing power, memory, and disk space have become cheaper, while bandwidth has become more expensive due to the explosion of online applications. To overcome these limitations, we have enhanced our Southwest Data Display and Analysis System (SDDAS) to take better advantage of the hardware by utilizing threads and data caching. Furthermore, the system was enhanced to support a framework for adding data formats and data visualization methods without costly rewrites. Visualization tools can speed analysis of many common scientific tasks and we will present a suite of tools that encompass the entire process of retrieving data from multiple data stores to common visualizations of the data. The goals for the end user are ease of use and interactivity with the data and the resulting plots. The data can be simultaneously plotted in a variety of formats and/or time and spatial resolutions. The software will allow one to slice and separate data to achieve other visualizations. Furthermore, one can interact with the data using the GUI or through an embedded language based on the Lua scripting language. The data presented will be primarily from the Cluster and Mars Express missions; however, the tools are data type agnostic and can be used for virtually any type of data.

Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure.

PubMed

Olechnovic, Kliment; Margelevicius, Mindaugas; Venclovas, Ceslovas

2011-03-01

We present Voroprot, an interactive cross-platform software tool that provides a unique set of capabilities for exploring geometric features of protein structure. Voroprot allows the construction and visualization of the Apollonius diagram (also known as the additively weighted Voronoi diagram), the Apollonius graph, protein alpha shapes, interatomic contact surfaces, solvent accessible surfaces, pockets and cavities inside protein structure. Voroprot is available for Windows, Linux and Mac OS X operating systems and can be downloaded from http://www.ibt.lt/bioinformatics/voroprot/.

Analysis of Carbohydrate-Carbohydrate Interactions Using Sugar-Functionalized Silicon Nanoparticles for Cell Imaging.

PubMed

Lai, Chian-Hui; Hütter, Julia; Hsu, Chien-Wei; Tanaka, Hidenori; Varela-Aramburu, Silvia; De Cola, Luisa; Lepenies, Bernd; Seeberger, Peter H

2016-01-13

Protein-carbohydrate binding depends on multivalent ligand display that is even more important for low affinity carbohydrate-carbohydrate interactions. Detection and analysis of these low affinity multivalent binding events are technically challenging. We describe the synthesis of dual-fluorescent sugar-capped silicon nanoparticles that proved to be an attractive tool for the analysis of low affinity interactions. These ultrasmall NPs with sizes of around 4 nm can be used for NMR quantification of coupled sugars. The silicon nanoparticles are employed to measure the interaction between the cancer-associated glycosphingolipids GM3 and Gg3 and the associated kD value by surface plasmon resonance experiments. Cell binding studies, to investigate the biological relevance of these carbohydrate-carbohydrate interactions, also benefit from these fluorescent sugar-capped nanoparticles.

A Software Tool for Integrated Optical Design Analysis

NASA Technical Reports Server (NTRS)

Moore, Jim; Troy, Ed; DePlachett, Charles; Montgomery, Edward (Technical Monitor)

2001-01-01

Design of large precision optical systems requires multi-disciplinary analysis, modeling, and design. Thermal, structural and optical characteristics of the hardware must be accurately understood in order to design a system capable of accomplishing the performance requirements. The interactions between each of the disciplines become stronger as systems are designed lighter weight for space applications. This coupling dictates a concurrent engineering design approach. In the past, integrated modeling tools have been developed that attempt to integrate all of the complex analysis within the framework of a single model. This often results in modeling simplifications and it requires engineering specialist to learn new applications. The software described in this presentation addresses the concurrent engineering task using a different approach. The software tool, Integrated Optical Design Analysis (IODA), uses data fusion technology to enable a cross discipline team of engineering experts to concurrently design an optical system using their standard validated engineering design tools.

Students' Conceptions of Congruency through the Use of Dynamic Geometry Software

ERIC Educational Resources Information Center

Gonzalez, Gloriana; Herbst, Patricio G.

2009-01-01

This paper describes students' interactions with dynamic diagrams in the context of an American geometry class. Students used the dragging tool and the measuring tool in Cabri Geometry to make mathematical conjectures. The analysis, using the cK[cent sign] model of conceptions, suggests that incorporating technology in mathematics classrooms…

GAC: Gene Associations with Clinical, a web based application

PubMed Central

Zhang, Xinyan; Rupji, Manali; Kowalski, Jeanne

2018-01-01

We present GAC, a shiny R based tool for interactive visualization of clinical associations based on high-dimensional data. The tool provides a web-based suite to perform supervised principal component analysis (SuperPC), an approach that uses both high-dimensional data, such as gene expression, combined with clinical data to infer clinical associations. We extended the approach to address binary outcomes, in addition to continuous and time-to-event data in our package, thereby increasing the use and flexibility of SuperPC.  Additionally, the tool provides an interactive visualization for summarizing results based on a forest plot for both binary and time-to-event data.  In summary, the GAC suite of tools provide a one stop shop for conducting statistical analysis to identify and visualize the association between a clinical outcome of interest and high-dimensional data types, such as genomic data. Our GAC package has been implemented in R and is available via http://shinygispa.winship.emory.edu/GAC/. The developmental repository is available at https://github.com/manalirupji/GAC. PMID:29263780

A Sociocultural Analysis of Social Interaction and Collaboration within the Cooking Practices of Children

ERIC Educational Resources Information Center

Bligh, Caroline Adele; Fathima, Monalisa

2017-01-01

This article applies sociocultural theorizing as a tool to analyze children's collaborative cooking practices through the key sociocultural concepts of social interaction and collaboration within a school cooking club. The "everyday" activity of cooking is examined using field notes gathered through participant observations, diary…

The Role of Research in Making Interactive Products Effective.

ERIC Educational Resources Information Center

Rossi, Robert J.

1986-01-01

Argues that research and development (R&D) methods should be utilized to develop new technologies for training and retailing and describes useful research tools--critical incident methodology, task analysis, performance recording. Discussion covers R&D applications to interactive systems development in the areas of product need, customer…

State Analysis Database Tool

NASA Technical Reports Server (NTRS)

Rasmussen, Robert; Bennett, Matthew

2006-01-01

The State Analysis Database Tool software establishes a productive environment for collaboration among software and system engineers engaged in the development of complex interacting systems. The tool embodies State Analysis, a model-based system engineering methodology founded on a state-based control architecture (see figure). A state represents a momentary condition of an evolving system, and a model may describe how a state evolves and is affected by other states. The State Analysis methodology is a process for capturing system and software requirements in the form of explicit models and states, and defining goal-based operational plans consistent with the models. Requirements, models, and operational concerns have traditionally been documented in a variety of system engineering artifacts that address different aspects of a mission s lifecycle. In State Analysis, requirements, models, and operations information are State Analysis artifacts that are consistent and stored in a State Analysis Database. The tool includes a back-end database, a multi-platform front-end client, and Web-based administrative functions. The tool is structured to prompt an engineer to follow the State Analysis methodology, to encourage state discovery and model description, and to make software requirements and operations plans consistent with model descriptions.

Analyzing Human-Landscape Interactions: Tools That Integrate

NASA Astrophysics Data System (ADS)

Zvoleff, Alex; An, Li

2014-01-01

Humans have transformed much of Earth's land surface, giving rise to loss of biodiversity, climate change, and a host of other environmental issues that are affecting human and biophysical systems in unexpected ways. To confront these problems, environmental managers must consider human and landscape systems in integrated ways. This means making use of data obtained from a broad range of methods (e.g., sensors, surveys), while taking into account new findings from the social and biophysical science literatures. New integrative methods (including data fusion, simulation modeling, and participatory approaches) have emerged in recent years to address these challenges, and to allow analysts to provide information that links qualitative and quantitative elements for policymakers. This paper brings attention to these emergent tools while providing an overview of the tools currently in use for analysis of human-landscape interactions. Analysts are now faced with a staggering array of approaches in the human-landscape literature—in an attempt to bring increased clarity to the field, we identify the relative strengths of each tool, and provide guidance to analysts on the areas to which each tool is best applied. We discuss four broad categories of tools: statistical methods (including survival analysis, multi-level modeling, and Bayesian approaches), GIS and spatial analysis methods, simulation approaches (including cellular automata, agent-based modeling, and participatory modeling), and mixed-method techniques (such as alternative futures modeling and integrated assessment). For each tool, we offer an example from the literature of its application in human-landscape research. Among these tools, participatory approaches are gaining prominence for analysts to make the broadest possible array of information available to researchers, environmental managers, and policymakers. Further development of new approaches of data fusion and integration across sites or disciplines pose an important challenge for future work in integrating human and landscape components.

FoodMicrobionet: A database for the visualisation and exploration of food bacterial communities based on network analysis.

PubMed

Parente, Eugenio; Cocolin, Luca; De Filippis, Francesca; Zotta, Teresa; Ferrocino, Ilario; O'Sullivan, Orla; Neviani, Erasmo; De Angelis, Maria; Cotter, Paul D; Ercolini, Danilo

2016-02-16

Amplicon targeted high-throughput sequencing has become a popular tool for the culture-independent analysis of microbial communities. Although the data obtained with this approach are portable and the number of sequences available in public databases is increasing, no tool has been developed yet for the analysis and presentation of data obtained in different studies. This work describes an approach for the development of a database for the rapid exploration and analysis of data on food microbial communities. Data from seventeen studies investigating the structure of bacterial communities in dairy, meat, sourdough and fermented vegetable products, obtained by 16S rRNA gene targeted high-throughput sequencing, were collated and analysed using Gephi, a network analysis software. The resulting database, which we named FoodMicrobionet, was used to analyse nodes and network properties and to build an interactive web-based visualisation. The latter allows the visual exploration of the relationships between Operational Taxonomic Units (OTUs) and samples and the identification of core- and sample-specific bacterial communities. It also provides additional search tools and hyperlinks for the rapid selection of food groups and OTUs and for rapid access to external resources (NCBI taxonomy, digital versions of the original articles). Microbial interaction network analysis was carried out using CoNet on datasets extracted from FoodMicrobionet: the complexity of interaction networks was much lower than that found for other bacterial communities (human microbiome, soil and other environments). This may reflect both a bias in the dataset (which was dominated by fermented foods and starter cultures) and the lower complexity of food bacterial communities. Although some technical challenges exist, and are discussed here, the net result is a valuable tool for the exploration of food bacterial communities by the scientific community and food industry. Copyright © 2015. Published by Elsevier B.V.

CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures.

PubMed

Kozlikova, Barbora; Sebestova, Eva; Sustr, Vilem; Brezovsky, Jan; Strnad, Ondrej; Daniel, Lukas; Bednar, David; Pavelka, Antonin; Manak, Martin; Bezdeka, Martin; Benes, Petr; Kotry, Matus; Gora, Artur; Damborsky, Jiri; Sochor, Jiri

2014-09-15

The transport of ligands, ions or solvent molecules into proteins with buried binding sites or through the membrane is enabled by protein tunnels and channels. CAVER Analyst is a software tool for calculation, analysis and real-time visualization of access tunnels and channels in static and dynamic protein structures. It provides an intuitive graphic user interface for setting up the calculation and interactive exploration of identified tunnels/channels and their characteristics. CAVER Analyst is a multi-platform software written in JAVA. Binaries and documentation are freely available for non-commercial use at http://www.caver.cz. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Genetic interaction analysis of point mutations enables interrogation of gene function at a residue-level resolution

PubMed Central

Braberg, Hannes; Moehle, Erica A.; Shales, Michael; Guthrie, Christine; Krogan, Nevan J.

2014-01-01

We have achieved a residue-level resolution of genetic interaction mapping – a technique that measures how the function of one gene is affected by the alteration of a second gene – by analyzing point mutations. Here, we describe how to interpret point mutant genetic interactions, and outline key applications for the approach, including interrogation of protein interaction interfaces and active sites, and examination of post-translational modifications. Genetic interaction analysis has proven effective for characterizing cellular processes; however, to date, systematic high-throughput genetic interaction screens have relied on gene deletions or knockdowns, which limits the resolution of gene function analysis and poses problems for multifunctional genes. Our point mutant approach addresses these issues, and further provides a tool for in vivo structure-function analysis that complements traditional biophysical methods. We also discuss the potential for genetic interaction mapping of point mutations in human cells and its application to personalized medicine. PMID:24842270

Review: visual analytics of climate networks

NASA Astrophysics Data System (ADS)

Nocke, T.; Buschmann, S.; Donges, J. F.; Marwan, N.; Schulz, H.-J.; Tominski, C.

2015-09-01

Network analysis has become an important approach in studying complex spatiotemporal behaviour within geophysical observation and simulation data. This new field produces increasing numbers of large geo-referenced networks to be analysed. Particular focus lies currently on the network analysis of the complex statistical interrelationship structure within climatological fields. The standard procedure for such network analyses is the extraction of network measures in combination with static standard visualisation methods. Existing interactive visualisation methods and tools for geo-referenced network exploration are often either not known to the analyst or their potential is not fully exploited. To fill this gap, we illustrate how interactive visual analytics methods in combination with geovisualisation can be tailored for visual climate network investigation. Therefore, the paper provides a problem analysis relating the multiple visualisation challenges to a survey undertaken with network analysts from the research fields of climate and complex systems science. Then, as an overview for the interested practitioner, we review the state-of-the-art in climate network visualisation and provide an overview of existing tools. As a further contribution, we introduce the visual network analytics tools CGV and GTX, providing tailored solutions for climate network analysis, including alternative geographic projections, edge bundling, and 3-D network support. Using these tools, the paper illustrates the application potentials of visual analytics for climate networks based on several use cases including examples from global, regional, and multi-layered climate networks.

Review: visual analytics of climate networks

NASA Astrophysics Data System (ADS)

Nocke, T.; Buschmann, S.; Donges, J. F.; Marwan, N.; Schulz, H.-J.; Tominski, C.

2015-04-01

Network analysis has become an important approach in studying complex spatiotemporal behaviour within geophysical observation and simulation data. This new field produces increasing amounts of large geo-referenced networks to be analysed. Particular focus lies currently on the network analysis of the complex statistical interrelationship structure within climatological fields. The standard procedure for such network analyses is the extraction of network measures in combination with static standard visualisation methods. Existing interactive visualisation methods and tools for geo-referenced network exploration are often either not known to the analyst or their potential is not fully exploited. To fill this gap, we illustrate how interactive visual analytics methods in combination with geovisualisation can be tailored for visual climate network investigation. Therefore, the paper provides a problem analysis, relating the multiple visualisation challenges with a survey undertaken with network analysts from the research fields of climate and complex systems science. Then, as an overview for the interested practitioner, we review the state-of-the-art in climate network visualisation and provide an overview of existing tools. As a further contribution, we introduce the visual network analytics tools CGV and GTX, providing tailored solutions for climate network analysis, including alternative geographic projections, edge bundling, and 3-D network support. Using these tools, the paper illustrates the application potentials of visual analytics for climate networks based on several use cases including examples from global, regional, and multi-layered climate networks.

NASTRAN analysis of Tokamak vacuum vessel using interactive graphics

NASA Technical Reports Server (NTRS)

Miller, A.; Badrian, M.

1978-01-01

Isoparametric quadrilateral and triangular elements were used to represent the vacuum vessel shell structure. For toroidally symmetric loadings, MPCs were employed across model boundaries and rigid format 24 was invoked. Nonsymmetric loadings required the use of the cyclic symmetry analysis available with rigid format 49. NASTRAN served as an important analysis tool in the Tokamak design effort by providing a reliable means for assessing structural integrity. Interactive graphics were employed in the finite element model generation and in the post-processing of results. It was felt that model generation and checkout with interactive graphics reduced the modelling effort and debugging man-hours significantly.

Negotiation Process Analysis: A Research and Training Tool.

ERIC Educational Resources Information Center

Williams, Timothy

This paper proposes the use of interaction process analysis to study negotiation behaviors. Following a review of current literature in the field, the paper presents a theoretical framework for the analysis of both labor/management and social negotiation processes. Central to the framework described are two systems of activities that together…

Chandra Interactive Analysis of Observations (CIAO)

NASA Technical Reports Server (NTRS)

Dobrzycki, Adam

2000-01-01

The Chandra (formerly AXAF) telescope, launched on July 23, 1999, provides X-rays data with unprecedented spatial and spectral resolution. As part of the Chandra scientific support, the Chandra X-ray Observatory Center provides a new data analysis system, CIAO ("Chandra Interactive Analysis of Observations"). We will present the main components of the system: "First Look" analysis; SHERPA: a multi-dimensional, multi-mission modeling and fitting application; Chandra Imaging and Plotting System; Detect package-source detection algorithms; and DM package generic data manipulation tools, We will set up a demonstration of the portable version of the system and show examples of Chandra Data Analysis.

Control system design and analysis using the INteractive Controls Analysis (INCA) program

NASA Technical Reports Server (NTRS)

Bauer, Frank H.; Downing, John P.

1987-01-01

The INteractive Controls Analysis (INCA) program was developed at the Goddard Space Flight Center to provide a user friendly efficient environment for the design and analysis of linear control systems. Since its inception, INCA has found extensive use in the design, development, and analysis of control systems for spacecraft, instruments, robotics, and pointing systems. Moreover, the results of the analytic tools imbedded in INCA have been flight proven with at least three currently orbiting spacecraft. This paper describes the INCA program and illustrates, using a flight proven example, how the package can perform complex design analyses with relative ease.

AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis

PubMed Central

Badidi, Elarbi; De Sousa, Cristina; Lang, B Franz; Burger, Gertraud

2003-01-01

Background Sequence data analyses such as gene identification, structure modeling or phylogenetic tree inference involve a variety of bioinformatics software tools. Due to the heterogeneity of bioinformatics tools in usage and data requirements, scientists spend much effort on technical issues including data format, storage and management of input and output, and memorization of numerous parameters and multi-step analysis procedures. Results In this paper, we present the design and implementation of AnaBench, an interactive, Web-based bioinformatics Analysis workBench allowing streamlined data analysis. Our philosophy was to minimize the technical effort not only for the scientist who uses this environment to analyze data, but also for the administrator who manages and maintains the workbench. With new bioinformatics tools published daily, AnaBench permits easy incorporation of additional tools. This flexibility is achieved by employing a three-tier distributed architecture and recent technologies including CORBA middleware, Java, JDBC, and JSP. A CORBA server permits transparent access to a workbench management database, which stores information about the users, their data, as well as the description of all bioinformatics applications that can be launched from the workbench. Conclusion AnaBench is an efficient and intuitive interactive bioinformatics environment, which offers scientists application-driven, data-driven and protocol-driven analysis approaches. The prototype of AnaBench, managed by a team at the Université de Montréal, is accessible on-line at: . Please contact the authors for details about setting up a local-network AnaBench site elsewhere. PMID:14678565

Novel integrative genomic tool for interrogating lithium response in bipolar disorder

PubMed Central

Hunsberger, J G; Chibane, F L; Elkahloun, A G; Henderson, R; Singh, R; Lawson, J; Cruceanu, C; Nagarajan, V; Turecki, G; Squassina, A; Medeiros, C D; Del Zompo, M; Rouleau, G A; Alda, M; Chuang, D-M

2015-01-01

We developed a novel integrative genomic tool called GRANITE (Genetic Regulatory Analysis of Networks Investigational Tool Environment) that can effectively analyze large complex data sets to generate interactive networks. GRANITE is an open-source tool and invaluable resource for a variety of genomic fields. Although our analysis is confined to static expression data, GRANITE has the capability of evaluating time-course data and generating interactive networks that may shed light on acute versus chronic treatment, as well as evaluating dose response and providing insight into mechanisms that underlie therapeutic versus sub-therapeutic doses or toxic doses. As a proof-of-concept study, we investigated lithium (Li) response in bipolar disorder (BD). BD is a severe mood disorder marked by cycles of mania and depression. Li is one of the most commonly prescribed and decidedly effective treatments for many patients (responders), although its mode of action is not yet fully understood, nor is it effective in every patient (non-responders). In an in vitro study, we compared vehicle versus chronic Li treatment in patient-derived lymphoblastoid cells (LCLs) (derived from either responders or non-responders) using both microRNA (miRNA) and messenger RNA gene expression profiling. We present both Li responder and non-responder network visualizations created by our GRANITE analysis in BD. We identified by network visualization that the Let-7 family is consistently downregulated by Li in both groups where this miRNA family has been implicated in neurodegeneration, cell survival and synaptic development. We discuss the potential of this analysis for investigating treatment response and even providing clinicians with a tool for predicting treatment response in their patients, as well as for providing the industry with a tool for identifying network nodes as targets for novel drug discovery. PMID:25646593

Novel integrative genomic tool for interrogating lithium response in bipolar disorder.

PubMed

Hunsberger, J G; Chibane, F L; Elkahloun, A G; Henderson, R; Singh, R; Lawson, J; Cruceanu, C; Nagarajan, V; Turecki, G; Squassina, A; Medeiros, C D; Del Zompo, M; Rouleau, G A; Alda, M; Chuang, D-M

2015-02-03

We developed a novel integrative genomic tool called GRANITE (Genetic Regulatory Analysis of Networks Investigational Tool Environment) that can effectively analyze large complex data sets to generate interactive networks. GRANITE is an open-source tool and invaluable resource for a variety of genomic fields. Although our analysis is confined to static expression data, GRANITE has the capability of evaluating time-course data and generating interactive networks that may shed light on acute versus chronic treatment, as well as evaluating dose response and providing insight into mechanisms that underlie therapeutic versus sub-therapeutic doses or toxic doses. As a proof-of-concept study, we investigated lithium (Li) response in bipolar disorder (BD). BD is a severe mood disorder marked by cycles of mania and depression. Li is one of the most commonly prescribed and decidedly effective treatments for many patients (responders), although its mode of action is not yet fully understood, nor is it effective in every patient (non-responders). In an in vitro study, we compared vehicle versus chronic Li treatment in patient-derived lymphoblastoid cells (LCLs) (derived from either responders or non-responders) using both microRNA (miRNA) and messenger RNA gene expression profiling. We present both Li responder and non-responder network visualizations created by our GRANITE analysis in BD. We identified by network visualization that the Let-7 family is consistently downregulated by Li in both groups where this miRNA family has been implicated in neurodegeneration, cell survival and synaptic development. We discuss the potential of this analysis for investigating treatment response and even providing clinicians with a tool for predicting treatment response in their patients, as well as for providing the industry with a tool for identifying network nodes as targets for novel drug discovery.

Genome-wide gene–gene interaction analysis for next-generation sequencing

PubMed Central

Zhao, Jinying; Zhu, Yun; Xiong, Momiao

2016-01-01

The critical barrier in interaction analysis for next-generation sequencing (NGS) data is that the traditional pairwise interaction analysis that is suitable for common variants is difficult to apply to rare variants because of their prohibitive computational time, large number of tests and low power. The great challenges for successful detection of interactions with NGS data are (1) the demands in the paradigm of changes in interaction analysis; (2) severe multiple testing; and (3) heavy computations. To meet these challenges, we shift the paradigm of interaction analysis between two SNPs to interaction analysis between two genomic regions. In other words, we take a gene as a unit of analysis and use functional data analysis techniques as dimensional reduction tools to develop a novel statistic to collectively test interaction between all possible pairs of SNPs within two genome regions. By intensive simulations, we demonstrate that the functional logistic regression for interaction analysis has the correct type 1 error rates and higher power to detect interaction than the currently used methods. The proposed method was applied to a coronary artery disease dataset from the Wellcome Trust Case Control Consortium (WTCCC) study and the Framingham Heart Study (FHS) dataset, and the early-onset myocardial infarction (EOMI) exome sequence datasets with European origin from the NHLBI's Exome Sequencing Project. We discovered that 6 of 27 pairs of significantly interacted genes in the FHS were replicated in the independent WTCCC study and 24 pairs of significantly interacted genes after applying Bonferroni correction in the EOMI study. PMID:26173972

Studying Axon-Astrocyte Functional Interactions by 3D Two-Photon Ca2+ Imaging: A Practical Guide to Experiments and "Big Data" Analysis.

PubMed

Savtchouk, Iaroslav; Carriero, Giovanni; Volterra, Andrea

2018-01-01

Recent advances in fast volumetric imaging have enabled rapid generation of large amounts of multi-dimensional functional data. While many computer frameworks exist for data storage and analysis of the multi-gigabyte Ca 2+ imaging experiments in neurons, they are less useful for analyzing Ca 2+ dynamics in astrocytes, where transients do not follow a predictable spatio-temporal distribution pattern. In this manuscript, we provide a detailed protocol and commentary for recording and analyzing three-dimensional (3D) Ca 2+ transients through time in GCaMP6f-expressing astrocytes of adult brain slices in response to axonal stimulation, using our recently developed tools to perform interactive exploration, filtering, and time-correlation analysis of the transients. In addition to the protocol, we release our in-house software tools and discuss parameters pertinent to conducting axonal stimulation/response experiments across various brain regions and conditions. Our software tools are available from the Volterra Lab webpage at https://wwwfbm.unil.ch/dnf/group/glia-an-active-synaptic-partner/member/volterra-andrea-volterra in the form of software plugins for Image J (NIH)-a de facto standard in scientific image analysis. Three programs are available: MultiROI_TZ_profiler for interactive graphing of several movable ROIs simultaneously, Gaussian_Filter5D for Gaussian filtering in several dimensions, and Correlation_Calculator for computing various cross-correlation parameters on voxel collections through time.

Integrated web visualizations for protein-protein interaction databases.

PubMed

Jeanquartier, Fleur; Jean-Quartier, Claire; Holzinger, Andreas

2015-06-16

Understanding living systems is crucial for curing diseases. To achieve this task we have to understand biological networks based on protein-protein interactions. Bioinformatics has come up with a great amount of databases and tools that support analysts in exploring protein-protein interactions on an integrated level for knowledge discovery. They provide predictions and correlations, indicate possibilities for future experimental research and fill the gaps to complete the picture of biochemical processes. There are numerous and huge databases of protein-protein interactions used to gain insights into answering some of the many questions of systems biology. Many computational resources integrate interaction data with additional information on molecular background. However, the vast number of diverse Bioinformatics resources poses an obstacle to the goal of understanding. We present a survey of databases that enable the visual analysis of protein networks. We selected M=10 out of N=53 resources supporting visualization, and we tested against the following set of criteria: interoperability, data integration, quantity of possible interactions, data visualization quality and data coverage. The study reveals differences in usability, visualization features and quality as well as the quantity of interactions. StringDB is the recommended first choice. CPDB presents a comprehensive dataset and IntAct lets the user change the network layout. A comprehensive comparison table is available via web. The supplementary table can be accessed on http://tinyurl.com/PPI-DB-Comparison-2015. Only some web resources featuring graph visualization can be successfully applied to interactive visual analysis of protein-protein interaction. Study results underline the necessity for further enhancements of visualization integration in biochemical analysis tools. Identified challenges are data comprehensiveness, confidence, interactive feature and visualization maturing.

The Biomolecular Interaction Network Database and related tools 2005 update

PubMed Central

Alfarano, C.; Andrade, C. E.; Anthony, K.; Bahroos, N.; Bajec, M.; Bantoft, K.; Betel, D.; Bobechko, B.; Boutilier, K.; Burgess, E.; Buzadzija, K.; Cavero, R.; D'Abreo, C.; Donaldson, I.; Dorairajoo, D.; Dumontier, M. J.; Dumontier, M. R.; Earles, V.; Farrall, R.; Feldman, H.; Garderman, E.; Gong, Y.; Gonzaga, R.; Grytsan, V.; Gryz, E.; Gu, V.; Haldorsen, E.; Halupa, A.; Haw, R.; Hrvojic, A.; Hurrell, L.; Isserlin, R.; Jack, F.; Juma, F.; Khan, A.; Kon, T.; Konopinsky, S.; Le, V.; Lee, E.; Ling, S.; Magidin, M.; Moniakis, J.; Montojo, J.; Moore, S.; Muskat, B.; Ng, I.; Paraiso, J. P.; Parker, B.; Pintilie, G.; Pirone, R.; Salama, J. J.; Sgro, S.; Shan, T.; Shu, Y.; Siew, J.; Skinner, D.; Snyder, K.; Stasiuk, R.; Strumpf, D.; Tuekam, B.; Tao, S.; Wang, Z.; White, M.; Willis, R.; Wolting, C.; Wong, S.; Wrong, A.; Xin, C.; Yao, R.; Yates, B.; Zhang, S.; Zheng, K.; Pawson, T.; Ouellette, B. F. F.; Hogue, C. W. V.

2005-01-01

The Biomolecular Interaction Network Database (BIND) (http://bind.ca) archives biomolecular interaction, reaction, complex and pathway information. Our aim is to curate the details about molecular interactions that arise from published experimental research and to provide this information, as well as tools to enable data analysis, freely to researchers worldwide. BIND data are curated into a comprehensive machine-readable archive of computable information and provides users with methods to discover interactions and molecular mechanisms. BIND has worked to develop new methods for visualization that amplify the underlying annotation of genes and proteins to facilitate the study of molecular interaction networks. BIND has maintained an open database policy since its inception in 1999. Data growth has proceeded at a tremendous rate, approaching over 100 000 records. New services provided include a new BIND Query and Submission interface, a Standard Object Access Protocol service and the Small Molecule Interaction Database (http://smid.blueprint.org) that allows users to determine probable small molecule binding sites of new sequences and examine conserved binding residues. PMID:15608229

POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations

PubMed Central

Porollo, Aleksey; Meller, Jaroslaw

2010-01-01

Molecular simulations offer important mechanistic and functional clues in studies of proteins and other macromolecules. However, interpreting the results of such simulations increasingly requires tools that can combine information from multiple structural databases and other web resources, and provide highly integrated and versatile analysis tools. Here, we present a new web server that integrates high-quality animation of molecular motion (MM) with structural and functional analysis of macromolecules. The new tool, dubbed POLYVIEW-MM, enables animation of trajectories generated by molecular dynamics and related simulation techniques, as well as visualization of alternative conformers, e.g. obtained as a result of protein structure prediction methods or small molecule docking. To facilitate structural analysis, POLYVIEW-MM combines interactive view and analysis of conformational changes using Jmol and its tailored extensions, publication quality animation using PyMol, and customizable 2D summary plots that provide an overview of MM, e.g. in terms of changes in secondary structure states and relative solvent accessibility of individual residues in proteins. Furthermore, POLYVIEW-MM integrates visualization with various structural annotations, including automated mapping of known inter-action sites from structural homologs, mapping of cavities and ligand binding sites, transmembrane regions and protein domains. URL: http://polyview.cchmc.org/conform.html. PMID:20504857

Visualization and Interaction in Research, Teaching, and Scientific Communication

NASA Astrophysics Data System (ADS)

Ammon, C. J.

2017-12-01

Modern computing provides many tools for exploring observations, numerical calculations, and theoretical relationships. The number of options is, in fact, almost overwhelming. But the choices provide those with modest programming skills opportunities to create unique views of scientific information and to develop deeper insights into their data, their computations, and the underlying theoretical data-model relationships. I present simple examples of using animation and human-computer interaction to explore scientific data and scientific-analysis approaches. I illustrate how valuable a little programming ability can free scientists from the constraints of existing tools and can facilitate the development of deeper appreciation data and models. I present examples from a suite of programming languages ranging from C to JavaScript including the Wolfram Language. JavaScript is valuable for sharing tools and insight (hopefully) with others because it is integrated into one of the most powerful communication tools in human history, the web browser. Although too much of that power is often spent on distracting advertisements, the underlying computation and graphics engines are efficient, flexible, and almost universally available in desktop and mobile computing platforms. Many are working to fulfill the browser's potential to become the most effective tool for interactive study. Open-source frameworks for visualizing everything from algorithms to data are available, but advance rapidly. One strategy for dealing with swiftly changing tools is to adopt common, open data formats that are easily adapted (often by framework or tool developers). I illustrate the use of animation and interaction in research and teaching with examples from earthquake seismology.

Open | SpeedShop: An Open Source Infrastructure for Parallel Performance Analysis

DOE PAGES

Schulz, Martin; Galarowicz, Jim; Maghrak, Don; ...

2008-01-01

Over the last decades a large number of performance tools has been developed to analyze and optimize high performance applications. Their acceptance by end users, however, has been slow: each tool alone is often limited in scope and comes with widely varying interfaces and workflow constraints, requiring different changes in the often complex build and execution infrastructure of the target application. We started the Open | SpeedShop project about 3 years ago to overcome these limitations and provide efficient, easy to apply, and integrated performance analysis for parallel systems. Open | SpeedShop has two different faces: it provides an interoperable tool set covering themore » most common analysis steps as well as a comprehensive plugin infrastructure for building new tools. In both cases, the tools can be deployed to large scale parallel applications using DPCL/Dyninst for distributed binary instrumentation. Further, all tools developed within or on top of Open | SpeedShop are accessible through multiple fully equivalent interfaces including an easy-to-use GUI as well as an interactive command line interface reducing the usage threshold for those tools.« less

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

Zhu, Yitan; Xu, Yanxun; Helseth, Donald L.

Background: Genetic interactions play a critical role in cancer development. Existing knowledge about cancer genetic interactions is incomplete, especially lacking evidences derived from large-scale cancer genomics data. The Cancer Genome Atlas (TCGA) produces multimodal measurements across genomics and features of thousands of tumors, which provide an unprecedented opportunity to investigate the interplays of genes in cancer. Methods: We introduce Zodiac, a computational tool and resource to integrate existing knowledge about cancer genetic interactions with new information contained in TCGA data. It is an evolution of existing knowledge by treating it as a prior graph, integrating it with a likelihood modelmore » derived by Bayesian graphical model based on TCGA data, and producing a posterior graph as updated and data-enhanced knowledge. In short, Zodiac realizes “Prior interaction map + TCGA data → Posterior interaction map.” Results: Zodiac provides molecular interactions for about 200 million pairs of genes. All the results are generated from a big-data analysis and organized into a comprehensive database allowing customized search. In addition, Zodiac provides data processing and analysis tools that allow users to customize the prior networks and update the genetic pathways of their interest. Zodiac is publicly available at www.compgenome.org/ZODIAC. Conclusions: Zodiac recapitulates and extends existing knowledge of molecular interactions in cancer. It can be used to explore novel gene-gene interactions, transcriptional regulation, and other types of molecular interplays in cancer.« less

Making Sense of Conceptual Tools in Student-Generated Cases: Student Teachers' Problem-Solving Processes

ERIC Educational Resources Information Center

Jahreie, Cecilie Flo

2010-01-01

This article examines the way student teachers make sense of conceptual tools when writing cases. In order to understand the problem-solving process, an analysis of the interactions is conducted. The findings show that transforming practical experiences into theoretical reflection is not a straightforward matter. To be able to elaborate on the…

Interaction between Tool and Talk: How Instruction and Tools Support Consensus Building in Collaborative Inquiry-Learning Environments

ERIC Educational Resources Information Center

Gijlers, H.; Saab, N.; Van Joolingen, W. R.; De Jong, T.; Van Hout-Wolters, B. H. A. M.

2009-01-01

The process of collaborative inquiry learning requires maintaining a mutual understanding of the task, along with reaching consensus on strategies, plans and domain knowledge. In this study, we explore how different supportive measures affect students' consensus-building process, based on a re-analysis of data from four studies. We distinguish…

d-Omix: a mixer of generic protein domain analysis tools.

PubMed

Wichadakul, Duangdao; Numnark, Somrak; Ingsriswang, Supawadee

2009-07-01

Domain combination provides important clues to the roles of protein domains in protein function, interaction and evolution. We have developed a web server d-Omix (a Mixer of Protein Domain Analysis Tools) aiming as a unified platform to analyze, compare and visualize protein data sets in various aspects of protein domain combinations. With InterProScan files for protein sets of interest provided by users, the server incorporates four services for domain analyses. First, it constructs protein phylogenetic tree based on a distance matrix calculated from protein domain architectures (DAs), allowing the comparison with a sequence-based tree. Second, it calculates and visualizes the versatility, abundance and co-presence of protein domains via a domain graph. Third, it compares the similarity of proteins based on DA alignment. Fourth, it builds a putative protein network derived from domain-domain interactions from DOMINE. Users may select a variety of input data files and flexibly choose domain search tools (e.g. hmmpfam, superfamily) for a specific analysis. Results from the d-Omix could be interactively explored and exported into various formats such as SVG, JPG, BMP and CSV. Users with only protein sequences could prepare an InterProScan file using a service provided by the server as well. The d-Omix web server is freely available at http://www.biotec.or.th/isl/Domix.

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

PubMed

Grapov, Dmitry; Newman, John W

2012-09-01

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

ArrayNinja: An Open Source Platform for Unified Planning and Analysis of Microarray Experiments.

PubMed

Dickson, B M; Cornett, E M; Ramjan, Z; Rothbart, S B

2016-01-01

Microarray-based proteomic platforms have emerged as valuable tools for studying various aspects of protein function, particularly in the field of chromatin biochemistry. Microarray technology itself is largely unrestricted in regard to printable material and platform design, and efficient multidimensional optimization of assay parameters requires fluidity in the design and analysis of custom print layouts. This motivates the need for streamlined software infrastructure that facilitates the combined planning and analysis of custom microarray experiments. To this end, we have developed ArrayNinja as a portable, open source, and interactive application that unifies the planning and visualization of microarray experiments and provides maximum flexibility to end users. Array experiments can be planned, stored to a private database, and merged with the imaged results for a level of data interaction and centralization that is not currently attainable with available microarray informatics tools. © 2016 Elsevier Inc. All rights reserved.

FluoRender: joint freehand segmentation and visualization for many-channel fluorescence data analysis.

PubMed

Wan, Yong; Otsuna, Hideo; Holman, Holly A; Bagley, Brig; Ito, Masayoshi; Lewis, A Kelsey; Colasanto, Mary; Kardon, Gabrielle; Ito, Kei; Hansen, Charles

2017-05-26

Image segmentation and registration techniques have enabled biologists to place large amounts of volume data from fluorescence microscopy, morphed three-dimensionally, onto a common spatial frame. Existing tools built on volume visualization pipelines for single channel or red-green-blue (RGB) channels have become inadequate for the new challenges of fluorescence microscopy. For a three-dimensional atlas of the insect nervous system, hundreds of volume channels are rendered simultaneously, whereas fluorescence intensity values from each channel need to be preserved for versatile adjustment and analysis. Although several existing tools have incorporated support of multichannel data using various strategies, the lack of a flexible design has made true many-channel visualization and analysis unavailable. The most common practice for many-channel volume data presentation is still converting and rendering pseudosurfaces, which are inaccurate for both qualitative and quantitative evaluations. Here, we present an alternative design strategy that accommodates the visualization and analysis of about 100 volume channels, each of which can be interactively adjusted, selected, and segmented using freehand tools. Our multichannel visualization includes a multilevel streaming pipeline plus a triple-buffer compositing technique. Our method also preserves original fluorescence intensity values on graphics hardware, a crucial feature that allows graphics-processing-unit (GPU)-based processing for interactive data analysis, such as freehand segmentation. We have implemented the design strategies as a thorough restructuring of our original tool, FluoRender. The redesign of FluoRender not only maintains the existing multichannel capabilities for a greatly extended number of volume channels, but also enables new analysis functions for many-channel data from emerging biomedical-imaging techniques.

Data Interactive Publications

NASA Astrophysics Data System (ADS)

Domenico, B.; Weber, J.

2012-04-01

For some years now, the authors have developed examples of online documents that allowed the reader to interact directly with datasets, but there were limitations that restricted the interaction to specific desktop analysis and display tools that were not generally available to all readers of the documents. Recent advances in web service technology and related standards are making it possible to develop systems for publishing online documents that enable readers to access, analyze, and display the data discussed in the publication from the perspective and in the manner from which the author wants it to be represented. By clicking on embedded links, the reader accesses not only the usual textual information in a publication, but also data residing on a local or remote web server as well as a set of processing tools for analyzing and displaying the data. With the option of having the analysis and display processing provided on the server (or in the cloud), there are now a broader set of possibilities on the client side where the reader can interact with the data via a thin web client, a rich desktop application, or a mobile platform "app." The presentation will outline the architecture of data interactive publications along with illustrative examples.

Data Interactive Publications Revisited

NASA Astrophysics Data System (ADS)

Domenico, B.; Weber, W. J.

2011-12-01

A few years back, the authors presented examples of online documents that allowed the reader to interact directly with datasets, but there were limitations that restricted the interaction to specific desktop analysis and display tools that were not generally available to all readers of the documents. Recent advances in web service technology and related standards are making it possible to develop systems for publishing online documents that enable readers to access, analyze, and display the data discussed in the publication from the perspective and in the manner from which the author wants it to be represented. By clicking on embedded links, the reader accesses not only the usual textual information in a publication, but also data residing on a local or remote web server as well as a set of processing tools for analyzing and displaying the data. With the option of having the analysis and display processing provided on the server, there are now a broader set of possibilities on the client side where the reader can interact with the data via a thin web client, a rich desktop application, or a mobile platform "app." The presentation will outline the architecture of data interactive publications along with illustrative examples.

Understanding How Families Use Magnifiers during Nature Center Walks

ERIC Educational Resources Information Center

Zimmerman, Heather Toomey; McClain, Lucy Richardson; Crowl, Michele

2013-01-01

This analysis uses a sociocultural learning theory and parent-child interaction framework to understand families' interactions with one type of scientific tool, the magnifier, during nature walks offered by a nature center. Families were video recorded to observe how they organized their activities where they used magnifiers to explore in the…

Let's Dance the "Robot Hokey-Pokey!": Children's Programming Approaches and Achievement throughout Early Cognitive Development

ERIC Educational Resources Information Center

Flannery, Louise P.; Bers, Marina Umaschi

2013-01-01

Young learners today generate, express, and interact with sophisticated ideas using a range of digital tools to explore interactive stories, animations, computer games, and robotics. In recent years, new developmentally appropriate robotics kits have been entering early childhood classrooms. This paper presents a retrospective analysis of one…

SysBioCube: A Data Warehouse and Integrative Data Analysis Platform Facilitating Systems Biology Studies of Disorders of Military Relevance

DTIC Science & Technology

2013-12-18

include interactive gene and methylation profiles, interactive heatmaps, cytoscape network views, integrative genomics viewer ( IGV ), and protein-protein...single chart. The website also provides an option to include multiple genes. Integrative Genomics Viewer ( IGV )1, is a high-performance desktop tool for

You Know Arnold Schwarzenegger? On Doing Questioning in Second Language Dyadic Tutorials

ERIC Educational Resources Information Center

Belhiah, Hassan

2012-01-01

This study analyses question-answer (QA) sequences in second language tutorial interaction. Using conversation analysis methodology as an analytical tool, the study demonstrates how the act of questioning is a dominant form of interaction in tutoring discourse. The doing of questioning is accomplished through a myriad of forms other than…

Visualization of metabolic interaction networks in microbial communities using VisANT 5.0

DOE PAGES

Granger, Brian R.; Chang, Yi -Chien; Wang, Yan; ...

2016-04-15

Here, the complexity of metabolic networks in microbial communities poses an unresolved visualization and interpretation challenge. We address this challenge in the newly expanded version of a software tool for the analysis of biological networks, VisANT 5.0. We focus in particular on facilitating the visual exploration of metabolic interaction between microbes in a community, e.g. as predicted by COMETS (Computation of Microbial Ecosystems in Time and Space), a dynamic stoichiometric modeling framework. Using VisANT's unique meta-graph implementation, we show how one can use VisANT 5.0 to explore different time-dependent ecosystem-level metabolic networks. In particular, we analyze the metabolic interaction networkmore » between two bacteria previously shown to display an obligate cross-feeding interdependency. In addition, we illustrate how a putative minimal gut microbiome community could be represented in our framework, making it possible to highlight interactions across multiple coexisting species. We envisage that the "symbiotic layout" of VisANT can be employed as a general tool for the analysis of metabolism in complex microbial communities as well as heterogeneous human tissues.« less

Analysis of In Vivo Chromatin and Protein Interactions of Arabidopsis Transcript Elongation Factors.

PubMed

Pfab, Alexander; Antosz, Wojciech; Holzinger, Philipp; Bruckmann, Astrid; Griesenbeck, Joachim; Grasser, Klaus D

2017-01-01

A central step to elucidate the function of proteins commonly comprises the analysis of their molecular interactions in vivo. For nuclear regulatory proteins this involves determining protein-protein interactions as well as mapping of chromatin binding sites. Here, we present two protocols to identify protein-protein and chromatin interactions of transcript elongation factors (TEFs) in Arabidopsis. The first protocol (Subheading 3.1) describes protein affinity-purification coupled to mass spectrometry (AP-MS) that utilizes suspension cultured cells as experimental system. This approach provides an unbiased view of proteins interacting with epitope-tagged TEFs. The second protocol (Subheading 3.2) depicts details about a chromatin immunoprecipitation (ChIP) procedure to characterize genomic binding sites of TEFs. These methods should be valuable tools for the analysis of a broad variety of nuclear proteins.

MODIS Interactive Subsetting Tool (MIST)

NASA Astrophysics Data System (ADS)

McAllister, M.; Duerr, R.; Haran, T.; Khalsa, S. S.; Miller, D.

2008-12-01

In response to requests from the user community, NSIDC has teamed with the Oak Ridge National Laboratory Distributive Active Archive Center (ORNL DAAC) and the Moderate Resolution Data Center (MrDC) to provide time series subsets of satellite data covering stations in the Greenland Climate Network (GC-NET) and the International Arctic Systems for Observing the Atmosphere (IASOA) network. To serve these data NSIDC created the MODIS Interactive Subsetting Tool (MIST). MIST works with 7 km by 7 km subset time series of certain Version 5 (V005) MODIS products over GC-Net and IASOA stations. User- selected data are delivered in a text Comma Separated Value (CSV) file format. MIST also provides online analysis capabilities that include generating time series and scatter plots. Currently, MIST is a Beta prototype and NSIDC intends that user requests will drive future development of the tool. The intent of this poster is to introduce MIST to the MODIS data user audience and illustrate some of the online analysis capabilities.

The Cerefy Neuroradiology Atlas: a Talairach-Tournoux atlas-based tool for analysis of neuroimages available over the internet.

PubMed

Nowinski, Wieslaw L; Belov, Dmitry

2003-09-01

The article introduces an atlas-assisted method and a tool called the Cerefy Neuroradiology Atlas (CNA), available over the Internet for neuroradiology and human brain mapping. The CNA contains an enhanced, extended, and fully segmented and labeled electronic version of the Talairach-Tournoux brain atlas, including parcelated gyri and Brodmann's areas. To our best knowledge, this is the first online, publicly available application with the Talairach-Tournoux atlas. The process of atlas-assisted neuroimage analysis is done in five steps: image data loading, Talairach landmark setting, atlas normalization, image data exploration and analysis, and result saving. Neuroimage analysis is supported by a near-real-time, atlas-to-data warping based on the Talairach transformation. The CNA runs on multiple platforms; is able to process simultaneously multiple anatomical and functional data sets; and provides functions for a rapid atlas-to-data registration, interactive structure labeling and annotating, and mensuration. It is also empowered with several unique features, including interactive atlas warping facilitating fine tuning of atlas-to-data fit, navigation on the triplanar formed by the image data and the atlas, multiple-images-in-one display with interactive atlas-anatomy-function blending, multiple label display, and saving of labeled and annotated image data. The CNA is useful for fast atlas-assisted analysis of neuroimage data sets. It increases accuracy and reduces time in localization analysis of activation regions; facilitates to communicate the information on the interpreted scans from the neuroradiologist to other clinicians and medical students; increases the neuroradiologist's confidence in terms of anatomy and spatial relationships; and serves as a user-friendly, public domain tool for neuroeducation. At present, more than 700 users from five continents have subscribed to the CNA.

MONGKIE: an integrated tool for network analysis and visualization for multi-omics data.

PubMed

Jang, Yeongjun; Yu, Namhee; Seo, Jihae; Kim, Sun; Lee, Sanghyuk

2016-03-18

Network-based integrative analysis is a powerful technique for extracting biological insights from multilayered omics data such as somatic mutations, copy number variations, and gene expression data. However, integrated analysis of multi-omics data is quite complicated and can hardly be done in an automated way. Thus, a powerful interactive visual mining tool supporting diverse analysis algorithms for identification of driver genes and regulatory modules is much needed. Here, we present a software platform that integrates network visualization with omics data analysis tools seamlessly. The visualization unit supports various options for displaying multi-omics data as well as unique network models for describing sophisticated biological networks such as complex biomolecular reactions. In addition, we implemented diverse in-house algorithms for network analysis including network clustering and over-representation analysis. Novel functions include facile definition and optimized visualization of subgroups, comparison of a series of data sets in an identical network by data-to-visual mapping and subsequent overlaying function, and management of custom interaction networks. Utility of MONGKIE for network-based visual data mining of multi-omics data was demonstrated by analysis of the TCGA glioblastoma data. MONGKIE was developed in Java based on the NetBeans plugin architecture, thus being OS-independent with intrinsic support of module extension by third-party developers. We believe that MONGKIE would be a valuable addition to network analysis software by supporting many unique features and visualization options, especially for analysing multi-omics data sets in cancer and other diseases. .

SOCR Motion Charts: An Efficient, Open-Source, Interactive and Dynamic Applet for Visualizing Longitudinal Multivariate Data

PubMed Central

Al-Aziz, Jameel; Christou, Nicolas; Dinov, Ivo D.

2011-01-01

The amount, complexity and provenance of data have dramatically increased in the past five years. Visualization of observed and simulated data is a critical component of any social, environmental, biomedical or scientific quest. Dynamic, exploratory and interactive visualization of multivariate data, without preprocessing by dimensionality reduction, remains a nearly insurmountable challenge. The Statistics Online Computational Resource (www.SOCR.ucla.edu) provides portable online aids for probability and statistics education, technology-based instruction and statistical computing. We have developed a new Java-based infrastructure, SOCR Motion Charts, for discovery-based exploratory analysis of multivariate data. This interactive data visualization tool enables the visualization of high-dimensional longitudinal data. SOCR Motion Charts allows mapping of ordinal, nominal and quantitative variables onto time, 2D axes, size, colors, glyphs and appearance characteristics, which facilitates the interactive display of multidimensional data. We validated this new visualization paradigm using several publicly available multivariate datasets including Ice-Thickness, Housing Prices, Consumer Price Index, and California Ozone Data. SOCR Motion Charts is designed using object-oriented programming, implemented as a Java Web-applet and is available to the entire community on the web at www.socr.ucla.edu/SOCR_MotionCharts. It can be used as an instructional tool for rendering and interrogating high-dimensional data in the classroom, as well as a research tool for exploratory data analysis. PMID:21479108

Automated Video Analysis of Non-verbal Communication in a Medical Setting.

PubMed

Hart, Yuval; Czerniak, Efrat; Karnieli-Miller, Orit; Mayo, Avraham E; Ziv, Amitai; Biegon, Anat; Citron, Atay; Alon, Uri

2016-01-01

Non-verbal communication plays a significant role in establishing good rapport between physicians and patients and may influence aspects of patient health outcomes. It is therefore important to analyze non-verbal communication in medical settings. Current approaches to measure non-verbal interactions in medicine employ coding by human raters. Such tools are labor intensive and hence limit the scale of possible studies. Here, we present an automated video analysis tool for non-verbal interactions in a medical setting. We test the tool using videos of subjects that interact with an actor portraying a doctor. The actor interviews the subjects performing one of two scripted scenarios of interviewing the subjects: in one scenario the actor showed minimal engagement with the subject. The second scenario included active listening by the doctor and attentiveness to the subject. We analyze the cross correlation in total kinetic energy of the two people in the dyad, and also characterize the frequency spectrum of their motion. We find large differences in interpersonal motion synchrony and entrainment between the two performance scenarios. The active listening scenario shows more synchrony and more symmetric followership than the other scenario. Moreover, the active listening scenario shows more high-frequency motion termed jitter that has been recently suggested to be a marker of followership. The present approach may be useful for analyzing physician-patient interactions in terms of synchrony and dominance in a range of medical settings.

MONA – Interactive manipulation of molecule collections

PubMed Central

2013-01-01

Working with small‐molecule datasets is a routine task for cheminformaticians and chemists. The analysis and comparison of vendor catalogues and the compilation of promising candidates as starting points for screening campaigns are but a few very common applications. The workflows applied for this purpose usually consist of multiple basic cheminformatics tasks such as checking for duplicates or filtering by physico‐chemical properties. Pipelining tools allow to create and change such workflows without much effort, but usually do not support interventions once the pipeline has been started. In many contexts, however, the best suited workflow is not known in advance, thus making it necessary to take the results of the previous steps into consideration before proceeding. To support intuition‐driven processing of compound collections, we developed MONA, an interactive tool that has been designed to prepare and visualize large small‐molecule datasets. Using an SQL database common cheminformatics tasks such as analysis and filtering can be performed interactively with various methods for visual support. Great care was taken in creating a simple, intuitive user interface which can be instantly used without any setup steps. MONA combines the interactivity of molecule database systems with the simplicity of pipelining tools, thus enabling the case‐to‐case application of chemistry expert knowledge. The current version is available free of charge for academic use and can be downloaded at http://www.zbh.uni‐hamburg.de/mona. PMID:23985157

User Guide for the Plotting Software for the Los Alamos National Laboratory Nuclear Weapons Analysis Tools Version 2.0

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

Cleland, Timothy James

The Los Alamos National Laboratory Plotting Software for the Nuclear Weapons Analysis Tools is a Java™ application based upon the open source library JFreeChart. The software provides a capability for plotting data on graphs with a rich variety of display options while allowing the viewer interaction via graph manipulation and scaling to best view the data. The graph types include XY plots, Date XY plots, Bar plots and Histogram plots.

Tools for the Conceptual Design and Engineering Analysis of Micro Air Vehicles

DTIC Science & Technology

2009-03-01

problem with two DC motors with propellers, mounted on each wing tip and oriented such that the thrust vectors had an angular separation of 180...ElectriCalc or MotoCalc Database • Script Program (MC) In determination of the components to be integrated into MC, the R/C world was explored since the tools...Excel, ProE, QuickWrap and Script . Importing outside applications can be achieved by direct interaction with MC or through analysis server connections [11

EPSAT - A workbench for designing high-power systems for the space environment

NASA Technical Reports Server (NTRS)

Kuharski, R. A.; Jongeward, G. A.; Wilcox, K. G.; Kennedy, E. M.; Stevens, N. J.; Putnam, R. M.; Roche, J. C.

1990-01-01

The Environment Power System Analysis Tool (EPSAT) is being developed to provide space power system design engineers with an analysis tool for determining the performance of power systems in both naturally occurring and self-induced environments. This paper presents the results of the project after two years of a three-year development program. The relevance of the project result for SDI are pointed out, and models of the interaction of the environment and power systems are discussed.

Performance Refactoring of Instrumentation, Measurement, and Analysis Technologies for Petascale Computing. The PRIMA Project

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

Malony, Allen D.; Wolf, Felix G.

2014-01-31

The growing number of cores provided by today’s high-­end computing systems present substantial challenges to application developers in their pursuit of parallel efficiency. To find the most effective optimization strategy, application developers need insight into the runtime behavior of their code. The University of Oregon (UO) and the Juelich Supercomputing Centre of Forschungszentrum Juelich (FZJ) develop the performance analysis tools TAU and Scalasca, respectively, which allow high-­performance computing (HPC) users to collect and analyze relevant performance data – even at very large scales. TAU and Scalasca are considered among the most advanced parallel performance systems available, and are used extensivelymore » across HPC centers in the U.S., Germany, and around the world. The TAU and Scalasca groups share a heritage of parallel performance tool research and partnership throughout the past fifteen years. Indeed, the close interactions of the two groups resulted in a cross-­fertilization of tool ideas and technologies that pushed TAU and Scalasca to what they are today. It also produced two performance systems with an increasing degree of functional overlap. While each tool has its specific analysis focus, the tools were implementing measurement infrastructures that were substantially similar. Because each tool provides complementary performance analysis, sharing of measurement results is valuable to provide the user with more facets to understand performance behavior. However, each measurement system was producing performance data in different formats, requiring data interoperability tools to be created. A common measurement and instrumentation system was needed to more closely integrate TAU and Scalasca and to avoid the duplication of development and maintenance effort. The PRIMA (Performance Refactoring of Instrumentation, Measurement, and Analysis) project was proposed over three years ago as a joint international effort between UO and FZJ to accomplish these objectives: (1) refactor TAU and Scalasca performance system components for core code sharing and (2) integrate TAU and Scalasca functionality through data interfaces, formats, and utilities. As presented in this report, the project has completed these goals. In addition to shared technical advances, the groups have worked to engage with users through application performance engineering and tools training. In this regard, the project benefits from the close interactions the teams have with national laboratories in the United States and Germany. We have also sought to enhance our interactions through joint tutorials and outreach. UO has become a member of the Virtual Institute of High-­Productivity Supercomputing (VI-­HPS) established by the Helmholtz Association of German Research Centres as a center of excellence, focusing on HPC tools for diagnosing programming errors and optimizing performance. UO and FZJ have conducted several VI-­HPS training activities together within the past three years.« less

Performance Refactoring of Instrumentation, Measurement, and Analysis Technologies for Petascale Computing: the PRIMA Project

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

Malony, Allen D.; Wolf, Felix G.

2014-01-31

The growing number of cores provided by today’s high-end computing systems present substantial challenges to application developers in their pursuit of parallel efficiency. To find the most effective optimization strategy, application developers need insight into the runtime behavior of their code. The University of Oregon (UO) and the Juelich Supercomputing Centre of Forschungszentrum Juelich (FZJ) develop the performance analysis tools TAU and Scalasca, respectively, which allow high-performance computing (HPC) users to collect and analyze relevant performance data – even at very large scales. TAU and Scalasca are considered among the most advanced parallel performance systems available, and are used extensivelymore » across HPC centers in the U.S., Germany, and around the world. The TAU and Scalasca groups share a heritage of parallel performance tool research and partnership throughout the past fifteen years. Indeed, the close interactions of the two groups resulted in a cross-fertilization of tool ideas and technologies that pushed TAU and Scalasca to what they are today. It also produced two performance systems with an increasing degree of functional overlap. While each tool has its specific analysis focus, the tools were implementing measurement infrastructures that were substantially similar. Because each tool provides complementary performance analysis, sharing of measurement results is valuable to provide the user with more facets to understand performance behavior. However, each measurement system was producing performance data in different formats, requiring data interoperability tools to be created. A common measurement and instrumentation system was needed to more closely integrate TAU and Scalasca and to avoid the duplication of development and maintenance effort. The PRIMA (Performance Refactoring of Instrumentation, Measurement, and Analysis) project was proposed over three years ago as a joint international effort between UO and FZJ to accomplish these objectives: (1) refactor TAU and Scalasca performance system components for core code sharing and (2) integrate TAU and Scalasca functionality through data interfaces, formats, and utilities. As presented in this report, the project has completed these goals. In addition to shared technical advances, the groups have worked to engage with users through application performance engineering and tools training. In this regard, the project benefits from the close interactions the teams have with national laboratories in the United States and Germany. We have also sought to enhance our interactions through joint tutorials and outreach. UO has become a member of the Virtual Institute of High-Productivity Supercomputing (VI-HPS) established by the Helmholtz Association of German Research Centres as a center of excellence, focusing on HPC tools for diagnosing programming errors and optimizing performance. UO and FZJ have conducted several VI-HPS training activities together within the past three years.« less

OCSEGen: Open Components and Systems Environment Generator

NASA Technical Reports Server (NTRS)

Tkachuk, Oksana

2014-01-01

To analyze a large system, one often needs to break it into smaller components.To analyze a component or unit under analysis, one needs to model its context of execution, called environment, which represents the components with which the unit interacts. Environment generation is a challenging problem, because the environment needs to be general enough to uncover unit errors, yet precise enough to make the analysis tractable. In this paper, we present a tool for automated environment generation for open components and systems. The tool, called OCSEGen, is implemented on top of the Soot framework. We present the tool's current support and discuss its possible future extensions.

Hospital-based nurses' perceptions of the adoption of Web 2.0 tools for knowledge sharing, learning, social interaction and the production of collective intelligence.

PubMed

Lau, Adela S M

2011-11-11

Web 2.0 provides a platform or a set of tools such as blogs, wikis, really simple syndication (RSS), podcasts, tags, social bookmarks, and social networking software for knowledge sharing, learning, social interaction, and the production of collective intelligence in a virtual environment. Web 2.0 is also becoming increasingly popular in e-learning and e-social communities. The objectives were to investigate how Web 2.0 tools can be applied for knowledge sharing, learning, social interaction, and the production of collective intelligence in the nursing domain and to investigate what behavioral perceptions are involved in the adoption of Web 2.0 tools by nurses. The decomposed technology acceptance model was applied to construct the research model on which the hypotheses were based. A questionnaire was developed based on the model and data from nurses (n = 388) were collected from late January 2009 until April 30, 2009. Pearson's correlation analysis and t tests were used for data analysis. Intention toward using Web 2.0 tools was positively correlated with usage behavior (r = .60, P < .05). Behavioral intention was positively correlated with attitude (r = .72, P < .05), perceived behavioral control (r = .58, P < .05), and subjective norm (r = .45, P < .05). In their decomposed constructs, perceived usefulness (r = .7, P < .05), relative advantage (r = .64, P < .05), and compatibility (r = .60,P < .05) were positively correlated with attitude, but perceived ease of use was not significantly correlated (r = .004, P < .05) with it. Peer (r = .47, P < .05), senior management (r = .24,P < .05), and hospital (r = .45, P < .05) influences had positive correlations with subjective norm. Resource (r = .41,P < .05) and technological (r = .69,P < .05) conditions were positively correlated with perceived behavioral control. The identified behavioral perceptions may further health policy makers' understanding of nurses' concerns regarding and barriers to the adoption of Web 2.0 tools and enable them to better plan the strategy of implementation of Web 2.0 tools for knowledge sharing, learning, social interaction, and the production of collective intelligence.

Hospital-Based Nurses’ Perceptions of the Adoption of Web 2.0 Tools for Knowledge Sharing, Learning, Social Interaction and the Production of Collective Intelligence

PubMed Central

2011-01-01

Background Web 2.0 provides a platform or a set of tools such as blogs, wikis, really simple syndication (RSS), podcasts, tags, social bookmarks, and social networking software for knowledge sharing, learning, social interaction, and the production of collective intelligence in a virtual environment. Web 2.0 is also becoming increasingly popular in e-learning and e-social communities. Objectives The objectives were to investigate how Web 2.0 tools can be applied for knowledge sharing, learning, social interaction, and the production of collective intelligence in the nursing domain and to investigate what behavioral perceptions are involved in the adoption of Web 2.0 tools by nurses. Methods The decomposed technology acceptance model was applied to construct the research model on which the hypotheses were based. A questionnaire was developed based on the model and data from nurses (n = 388) were collected from late January 2009 until April 30, 2009. Pearson’s correlation analysis and t tests were used for data analysis. Results Intention toward using Web 2.0 tools was positively correlated with usage behavior (r = .60, P < .05). Behavioral intention was positively correlated with attitude (r = .72, P < .05), perceived behavioral control (r = .58, P < .05), and subjective norm (r = .45, P < .05). In their decomposed constructs, perceived usefulness (r = .7, P < .05), relative advantage (r = .64, P < .05), and compatibility (r = .60, P < .05) were positively correlated with attitude, but perceived ease of use was not significantly correlated (r = .004, P < .05) with it. Peer (r = .47, P < .05), senior management (r = .24, P < .05), and hospital (r = .45, P < .05) influences had positive correlations with subjective norm. Resource (r = .41, P < .05) and technological (r = .69, P < .05) conditions were positively correlated with perceived behavioral control. Conclusions The identified behavioral perceptions may further health policy makers’ understanding of nurses’ concerns regarding and barriers to the adoption of Web 2.0 tools and enable them to better plan the strategy of implementation of Web 2.0 tools for knowledge sharing, learning, social interaction, and the production of collective intelligence. PMID:22079851

iReport: a generalised Galaxy solution for integrated experimental reporting.

PubMed

Hiltemann, Saskia; Hoogstrate, Youri; der Spek, Peter van; Jenster, Guido; Stubbs, Andrew

2014-01-01

Galaxy offers a number of visualisation options with components, such as Trackster, Circster and Galaxy Charts, but currently lacks the ability to easily combine outputs from different tools into a single view or report. A number of tools produce HTML reports as output in order to combine the various output files from a single tool; however, this requires programming and knowledge of HTML, and the reports must be custom-made for each new tool. We have developed a generic and flexible reporting tool for Galaxy, iReport, that allows users to create interactive HTML reports directly from the Galaxy UI, with the ability to combine an arbitrary number of outputs from any number of different tools. Content can be organised into different tabs, and interactivity can be added to components. To demonstrate the capability of iReport we provide two publically available examples, the first is an iReport explaining about iReports, created for, and using content from the recent Galaxy Community Conference 2014. The second is a genetic report based on a trio analysis to determine candidate pathogenic variants which uses our previously developed Galaxy toolset for whole-genome NGS analysis, CGtag. These reports may be adapted for outputs from any sequencing platform and any results, such as omics data, non-high throughput results and clinical variables. iReport provides a secure, collaborative, and flexible web-based reporting system that is compatible with Galaxy (and non-Galaxy) generated content. We demonstrate its value with a real-life example of reporting genetic trio-analysis.

An interactive multi-block grid generation system

NASA Technical Reports Server (NTRS)

Kao, T. J.; Su, T. Y.; Appleby, Ruth

1992-01-01

A grid generation procedure combining interactive and batch grid generation programs was put together to generate multi-block grids for complex aircraft configurations. The interactive section provides the tools for 3D geometry manipulation, surface grid extraction, boundary domain construction for 3D volume grid generation, and block-block relationships and boundary conditions for flow solvers. The procedure improves the flexibility and quality of grid generation to meet the design/analysis requirements.

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

ERIC Educational Resources Information Center

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

2007-01-01

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

A topological multilayer model of the human body.

PubMed

Barbeito, Antonio; Painho, Marco; Cabral, Pedro; O'Neill, João

2015-11-04

Geographical information systems deal with spatial databases in which topological models are described with alphanumeric information. Its graphical interfaces implement the multilayer concept and provide powerful interaction tools. In this study, we apply these concepts to the human body creating a representation that would allow an interactive, precise, and detailed anatomical study. A vector surface component of the human body is built using a three-dimensional (3-D) reconstruction methodology. This multilayer concept is implemented by associating raster components with the corresponding vector surfaces, which include neighbourhood topology enabling spatial analysis. A root mean square error of 0.18 mm validated the three-dimensional reconstruction technique of internal anatomical structures. The expansion of the identification and the development of a neighbourhood analysis function are the new tools provided in this model.

Functional interaction analysis of GM1-related carbohydrates and Vibrio cholerae toxins using carbohydrate microarray.

PubMed

Kim, Chang Sup; Seo, Jeong Hyun; Cha, Hyung Joon

2012-08-07

The development of analytical tools is important for understanding the infection mechanisms of pathogenic bacteria or viruses. In the present work, a functional carbohydrate microarray combined with a fluorescence immunoassay was developed to analyze the interactions of Vibrio cholerae toxin (ctx) proteins and GM1-related carbohydrates. Ctx proteins were loaded onto the surface-immobilized GM1 pentasaccharide and six related carbohydrates, and their binding affinities were detected immunologically. The analysis of the ctx-carbohydrate interactions revealed that the intrinsic selectivity of ctx was GM1 pentasaccharide ≫ GM2 tetrasaccharide > asialo GM1 tetrasaccharide ≥ GM3trisaccharide, indicating that a two-finger grip formation and the terminal monosaccharides play important roles in the ctx-GM1 interaction. In addition, whole cholera toxin (ctxAB(5)) had a stricter substrate specificity and a stronger binding affinity than only the cholera toxin B subunit (ctxB). On the basis of the quantitative analysis, the carbohydrate microarray showed the sensitivity of detection of the ctxAB(5)-GM1 interaction with a limit-of-detection (LOD) of 2 ng mL(-1) (23 pM), which is comparable to other reported high sensitivity assay tools. In addition, the carbohydrate microarray successfully detected the actual toxin directly secreted from V. cholerae, without showing cross-reactivity to other bacteria. Collectively, these results demonstrate that the functional carbohydrate microarray is suitable for analyzing toxin protein-carbohydrate interactions and can be applied as a biosensor for toxin detection.

Fully automated analysis of multi-resolution four-channel micro-array genotyping data

NASA Astrophysics Data System (ADS)

Abbaspour, Mohsen; Abugharbieh, Rafeef; Podder, Mohua; Tebbutt, Scott J.

2006-03-01

We present a fully-automated and robust microarray image analysis system for handling multi-resolution images (down to 3-micron with sizes up to 80 MBs per channel). The system is developed to provide rapid and accurate data extraction for our recently developed microarray analysis and quality control tool (SNP Chart). Currently available commercial microarray image analysis applications are inefficient, due to the considerable user interaction typically required. Four-channel DNA microarray technology is a robust and accurate tool for determining genotypes of multiple genetic markers in individuals. It plays an important role in the state of the art trend where traditional medical treatments are to be replaced by personalized genetic medicine, i.e. individualized therapy based on the patient's genetic heritage. However, fast, robust, and precise image processing tools are required for the prospective practical use of microarray-based genetic testing for predicting disease susceptibilities and drug effects in clinical practice, which require a turn-around timeline compatible with clinical decision-making. In this paper we have developed a fully-automated image analysis platform for the rapid investigation of hundreds of genetic variations across multiple genes. Validation tests indicate very high accuracy levels for genotyping results. Our method achieves a significant reduction in analysis time, from several hours to just a few minutes, and is completely automated requiring no manual interaction or guidance.

MI-Sim: A MATLAB package for the numerical analysis of microbial ecological interactions.

PubMed

Wade, Matthew J; Oakley, Jordan; Harbisher, Sophie; Parker, Nicholas G; Dolfing, Jan

2017-01-01

Food-webs and other classes of ecological network motifs, are a means of describing feeding relationships between consumers and producers in an ecosystem. They have application across scales where they differ only in the underlying characteristics of the organisms and substrates describing the system. Mathematical modelling, using mechanistic approaches to describe the dynamic behaviour and properties of the system through sets of ordinary differential equations, has been used extensively in ecology. Models allow simulation of the dynamics of the various motifs and their numerical analysis provides a greater understanding of the interplay between the system components and their intrinsic properties. We have developed the MI-Sim software for use with MATLAB to allow a rigorous and rapid numerical analysis of several common ecological motifs. MI-Sim contains a series of the most commonly used motifs such as cooperation, competition and predation. It does not require detailed knowledge of mathematical analytical techniques and is offered as a single graphical user interface containing all input and output options. The tools available in the current version of MI-Sim include model simulation, steady-state existence and stability analysis, and basin of attraction analysis. The software includes seven ecological interaction motifs and seven growth function models. Unlike other system analysis tools, MI-Sim is designed as a simple and user-friendly tool specific to ecological population type models, allowing for rapid assessment of their dynamical and behavioural properties.

Brain Modulyzer: Interactive Visual Analysis of Functional Brain Connectivity

DOE PAGES

Murugesan, Sugeerth; Bouchard, Kristopher; Brown, Jesse A.; ...

2016-05-09

Here, we present Brain Modulyzer, an interactive visual exploration tool for functional magnetic resonance imaging (fMRI) brain scans, aimed at analyzing the correlation between different brain regions when resting or when performing mental tasks. Brain Modulyzer combines multiple coordinated views—such as heat maps, node link diagrams, and anatomical views—using brushing and linking to provide an anatomical context for brain connectivity data. Integrating methods from graph theory and analysis, e.g., community detection and derived graph measures, makes it possible to explore the modular and hierarchical organization of functional brain networks. Providing immediate feedback by displaying analysis results instantaneously while changing parametersmore » gives neuroscientists a powerful means to comprehend complex brain structure more effectively and efficiently and supports forming hypotheses that can then be validated via statistical analysis. In order to demonstrate the utility of our tool, we also present two case studies—exploring progressive supranuclear palsy, as well as memory encoding and retrieval« less

Brain Modulyzer: Interactive Visual Analysis of Functional Brain Connectivity

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

Murugesan, Sugeerth; Bouchard, Kristopher; Brown, Jesse A.

Here, we present Brain Modulyzer, an interactive visual exploration tool for functional magnetic resonance imaging (fMRI) brain scans, aimed at analyzing the correlation between different brain regions when resting or when performing mental tasks. Brain Modulyzer combines multiple coordinated views—such as heat maps, node link diagrams, and anatomical views—using brushing and linking to provide an anatomical context for brain connectivity data. Integrating methods from graph theory and analysis, e.g., community detection and derived graph measures, makes it possible to explore the modular and hierarchical organization of functional brain networks. Providing immediate feedback by displaying analysis results instantaneously while changing parametersmore » gives neuroscientists a powerful means to comprehend complex brain structure more effectively and efficiently and supports forming hypotheses that can then be validated via statistical analysis. In order to demonstrate the utility of our tool, we also present two case studies—exploring progressive supranuclear palsy, as well as memory encoding and retrieval« less

Use of LEED, Auger emission spectroscopy and field ion microscopy in microstructural studies

NASA Technical Reports Server (NTRS)

Ferrante, J.; Buckley, D. H.; Pepper, S. V.; Brainard, W. A.

1972-01-01

Surface research tools such as LEED, Auger emission spectroscopy analysis, and field ion microscopy are discussed. Examples of their use in studying adhesion, friction, wear, and lubrication presented. These tools have provided considerable insight into the basic nature of solid surface interactions. The transfer of metals from one surface to another at the atomic level has been observed and studied with each of these devices. The field ion microscope has been used to study polymer-metal interactions and Auger analysis to study the mechanism of polymer adhesion to metals. LEED and Auger analysis have identified surface segregation of alloying elements and indicated the influence of these elements in metallic adhesion. LEED and Auger analysis have assisted in adsorption studies in determining the structural arrangement and quantity of adsorbed species present in making an understanding of the influence of these species on adhesion possible. These devices are assisting in the furtherance of understanding of the fundamental mechanism involved in the adhesion, friction, wear, and lubrication processes.

SpecTracer: A Python-Based Interactive Solution for Echelle Spectra Reduction

NASA Astrophysics Data System (ADS)

Romero Matamala, Oscar Fernando; Petit, Véronique; Caballero-Nieves, Saida Maria

2018-01-01

SpecTracer is a newly developed interactive solution to reduce cross dispersed echelle spectra. The use of widgets saves the user the steep learning curves of currently available reduction software. SpecTracer uses well established image processing techniques based on IRAF to succesfully extract the stellar spectra. Comparisons with other reduction software, like IRAF, show comparable results, with the added advantages of ease of use, platform independence and portability. This tool can obtain meaningful scientific data and serve also as a training tool, especially for undergraduates doing research, in the procedure for spectroscopic analysis.

An Interactive Virtual 3D Tool for Scientific Exploration of Planetary Surfaces

NASA Astrophysics Data System (ADS)

Traxler, Christoph; Hesina, Gerd; Gupta, Sanjeev; Paar, Gerhard

2014-05-01

In this paper we present an interactive 3D visualization tool for scientific analysis and planning of planetary missions. At the moment scientists have to look at individual camera images separately. There is no tool to combine them in three dimensions and look at them seamlessly as a geologist would do (by walking backwards and forwards resulting in different scales). For this reason a virtual 3D reconstruction of the terrain that can be interactively explored is necessary. Such a reconstruction has to consider multiple scales ranging from orbital image data to close-up surface image data from rover cameras. The 3D viewer allows seamless zooming between these various scales, giving scientists the possibility to relate small surface features (e.g. rock outcrops) to larger geological contexts. For a reliable geologic assessment a realistic surface rendering is important. Therefore the material properties of the rock surfaces will be considered for real-time rendering. This is achieved by an appropriate Bidirectional Reflectance Distribution Function (BRDF) estimated from the image data. The BRDF is implemented to run on the Graphical Processing Unit (GPU) to enable realistic real-time rendering, which allows a naturalistic perception for scientific analysis. Another important aspect for realism is the consideration of natural lighting conditions, which means skylight to illuminate the reconstructed scene. In our case we provide skylights from Mars and Earth, which allows switching between these two modes of illumination. This gives geologists the opportunity to perceive rock outcrops from Mars as they would appear on Earth facilitating scientific assessment. Besides viewing the virtual reconstruction on multiple scales, scientists can also perform various measurements, i.e. geo-coordinates of a selected point or distance between two surface points. Rover or other models can be placed into the scene and snapped onto certain location of the terrain. These are important features to support the planning of rover paths. In addition annotations can be placed directly into the 3D scene, which also serve as landmarks to aid navigation. The presented visualization and planning tool is a valuable asset for scientific analysis of planetary mission data. It complements traditional methods by giving access to an interactive virtual 3D reconstruction, which is realistically rendered. Representative examples and further information about the interactive 3D visualization tool can be found on the FP7-SPACE Project PRoViDE web page http://www.provide-space.eu/interactive-virtual-3d-tool/. The research leading to these results has received funding from the European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreement n° 312377 'PRoViDE'.

An attempt to understand glioma stem cell biology through centrality analysis of a protein interaction network.

PubMed

Mallik, Mrinmay Kumar

2018-02-07

Biological networks can be analyzed using "Centrality Analysis" to identify the more influential nodes and interactions in the network. This study was undertaken to create and visualize a biological network comprising of protein-protein interactions (PPIs) amongst proteins which are preferentially over-expressed in glioma cancer stem cell component (GCSC) of glioblastomas as compared to the glioma non-stem cancer cell (GNSC) component and then to analyze this network through centrality analyses (CA) in order to identify the essential proteins in this network and their interactions. In addition, this study proposes a new centrality analysis method pertaining exclusively to transcription factors (TFs) and interactions amongst them. Moreover the relevant molecular functions, biological processes and biochemical pathways amongst these proteins were sought through enrichment analysis. A protein interaction network was created using a list of proteins which have been shown to be preferentially expressed or over-expressed in GCSCs isolated from glioblastomas as compared to the GNSCs. This list comprising of 38 proteins, created using manual literature mining, was submitted to the Reactome FIViz tool, a web based application integrated into Cytoscape, an open source software platform for visualizing and analyzing molecular interaction networks and biological pathways to produce the network. This network was subjected to centrality analyses utilizing ranked lists of six centrality measures using the FIViz application and (for the first time) a dedicated centrality analysis plug-in ; CytoNCA. The interactions exclusively amongst the transcription factors were nalyzed through a newly proposed centrality analysis method called "Gene Expression Associated Degree Centrality Analysis (GEADCA)". Enrichment analysis was performed using the "network function analysis" tool on Reactome. The CA was able to identify a small set of proteins with consistently high centrality ranks that is indicative of their strong influence in the protein protein interaction network. Similarly the newly proposed GEADCA helped identify the transcription factors with high centrality values indicative of their key roles in transcriptional regulation. The enrichment studies provided a list of molecular functions, biological processes and biochemical pathways associated with the constructed network. The study shows how pathway based databases may be used to create and analyze a relevant protein interaction network in glioma cancer stem cells and identify the essential elements within it to gather insights into the molecular interactions that regulate the properties of glioma stem cells. How these insights may be utilized to help the development of future research towards formulation of new management strategies have been discussed from a theoretical standpoint. Copyright © 2017 Elsevier Ltd. All rights reserved.

SamuROI, a Python-Based Software Tool for Visualization and Analysis of Dynamic Time Series Imaging at Multiple Spatial Scales.

PubMed

Rueckl, Martin; Lenzi, Stephen C; Moreno-Velasquez, Laura; Parthier, Daniel; Schmitz, Dietmar; Ruediger, Sten; Johenning, Friedrich W

2017-01-01

The measurement of activity in vivo and in vitro has shifted from electrical to optical methods. While the indicators for imaging activity have improved significantly over the last decade, tools for analysing optical data have not kept pace. Most available analysis tools are limited in their flexibility and applicability to datasets obtained at different spatial scales. Here, we present SamuROI (Structured analysis of multiple user-defined ROIs), an open source Python-based analysis environment for imaging data. SamuROI simplifies exploratory analysis and visualization of image series of fluorescence changes in complex structures over time and is readily applicable at different spatial scales. In this paper, we show the utility of SamuROI in Ca 2+ -imaging based applications at three spatial scales: the micro-scale (i.e., sub-cellular compartments including cell bodies, dendrites and spines); the meso-scale, (i.e., whole cell and population imaging with single-cell resolution); and the macro-scale (i.e., imaging of changes in bulk fluorescence in large brain areas, without cellular resolution). The software described here provides a graphical user interface for intuitive data exploration and region of interest (ROI) management that can be used interactively within Jupyter Notebook: a publicly available interactive Python platform that allows simple integration of our software with existing tools for automated ROI generation and post-processing, as well as custom analysis pipelines. SamuROI software, source code and installation instructions are publicly available on GitHub and documentation is available online. SamuROI reduces the energy barrier for manual exploration and semi-automated analysis of spatially complex Ca 2+ imaging datasets, particularly when these have been acquired at different spatial scales.

SamuROI, a Python-Based Software Tool for Visualization and Analysis of Dynamic Time Series Imaging at Multiple Spatial Scales

PubMed Central

Rueckl, Martin; Lenzi, Stephen C.; Moreno-Velasquez, Laura; Parthier, Daniel; Schmitz, Dietmar; Ruediger, Sten; Johenning, Friedrich W.

2017-01-01

The measurement of activity in vivo and in vitro has shifted from electrical to optical methods. While the indicators for imaging activity have improved significantly over the last decade, tools for analysing optical data have not kept pace. Most available analysis tools are limited in their flexibility and applicability to datasets obtained at different spatial scales. Here, we present SamuROI (Structured analysis of multiple user-defined ROIs), an open source Python-based analysis environment for imaging data. SamuROI simplifies exploratory analysis and visualization of image series of fluorescence changes in complex structures over time and is readily applicable at different spatial scales. In this paper, we show the utility of SamuROI in Ca2+-imaging based applications at three spatial scales: the micro-scale (i.e., sub-cellular compartments including cell bodies, dendrites and spines); the meso-scale, (i.e., whole cell and population imaging with single-cell resolution); and the macro-scale (i.e., imaging of changes in bulk fluorescence in large brain areas, without cellular resolution). The software described here provides a graphical user interface for intuitive data exploration and region of interest (ROI) management that can be used interactively within Jupyter Notebook: a publicly available interactive Python platform that allows simple integration of our software with existing tools for automated ROI generation and post-processing, as well as custom analysis pipelines. SamuROI software, source code and installation instructions are publicly available on GitHub and documentation is available online. SamuROI reduces the energy barrier for manual exploration and semi-automated analysis of spatially complex Ca2+ imaging datasets, particularly when these have been acquired at different spatial scales. PMID:28706482

An integrated workflow for analysis of ChIP-chip data.

PubMed

Weigelt, Karin; Moehle, Christoph; Stempfl, Thomas; Weber, Bernhard; Langmann, Thomas

2008-08-01

Although ChIP-chip is a powerful tool for genome-wide discovery of transcription factor target genes, the steps involving raw data analysis, identification of promoters, and correlation with binding sites are still laborious processes. Therefore, we report an integrated workflow for the analysis of promoter tiling arrays with the Genomatix ChipInspector system. We compare this tool with open-source software packages to identify PU.1 regulated genes in mouse macrophages. Our results suggest that ChipInspector data analysis, comparative genomics for binding site prediction, and pathway/network modeling significantly facilitate and enhance whole-genome promoter profiling to reveal in vivo sites of transcription factor-DNA interactions.

Avanti lipid tools: connecting lipids, technology, and cell biology.

PubMed

Sims, Kacee H; Tytler, Ewan M; Tipton, John; Hill, Kasey L; Burgess, Stephen W; Shaw, Walter A

2014-08-01

Lipid research is challenging owing to the complexity and diversity of the lipidome. Here we review a set of experimental tools developed for the seasoned lipid researcher, as well as, those who are new to the field of lipid research. Novel tools for probing protein-lipid interactions, applications for lipid binding antibodies, enhanced systems for the cellular delivery of lipids, improved visualization of lipid membranes using gold-labeled lipids, and advances in mass spectrometric analysis techniques will be discussed. Because lipid mediators are known to participate in a host of signal transduction and trafficking pathways within the cell, a comprehensive lipid toolbox that aids the science of lipidomics research is essential to better understand the molecular mechanisms of interactions between cellular components. This article is part of a Special Issue entitled Tools to study lipid functions. Copyright © 2014. Published by Elsevier B.V.

The boundary structure in the analysis of reversibly interacting systems by sedimentation velocity.

PubMed

Zhao, Huaying; Balbo, Andrea; Brown, Patrick H; Schuck, Peter

2011-05-01

Sedimentation velocity (SV) experiments of heterogeneous interacting systems exhibit characteristic boundary structures that can usually be very easily recognized and quantified. For slowly interacting systems, the boundaries represent concentrations of macromolecular species sedimenting at different rates, and they can be interpreted directly with population models based solely on the mass action law. For fast reactions, migration and chemical reactions are coupled, and different, but equally easily discernable boundary structures appear. However, these features have not been commonly utilized for data analysis, for the lack of an intuitive and computationally simple model. The recently introduced effective particle theory (EPT) provides a suitable framework. Here, we review the motivation and theoretical basis of EPT, and explore practical aspects for its application. We introduce an EPT-based design tool for SV experiments of heterogeneous interactions in the software SEDPHAT. As a practical tool for the first step of data analysis, we describe how the boundary resolution of the sedimentation coefficient distribution c(s) can be further improved with a Bayesian adjustment of maximum entropy regularization to the case of heterogeneous interactions between molecules that have been previously studied separately. This can facilitate extracting the characteristic boundary features by integration of c(s). In a second step, these are assembled into isotherms as a function of total loading concentrations and fitted with EPT. Methods for addressing concentration errors in isotherms are discussed. Finally, in an experimental model system of alpha-chymotrypsin interacting with soybean trypsin inhibitor, we show that EPT provides an excellent description of the experimental sedimentation boundary structure of fast interacting systems. Published by Elsevier Inc.

[Infobarris: an interactive tool to monitor and disseminate information on health and its determinants in the neighbourhoods of Barcelona (Spain)].

PubMed

Llimona, Pere; Pérez, Glòria; Rodríguez-Sanz, Maica; Novoa, Ana M; Espelt, Albert; García de Olalla, Patricia; Borrell, Carme

In order to know about the health of the population, it is necessary to perform a systematic and continuous analysis of their health status and social and economic health determinants. The objective of this paper is to describe the development and implementation of the Infobarris tool, which allows to visualize a wide battery of indicators and social determinants of health by neighbourhoods in the city of Barcelona (Spain). For the development of the Infobarris tool, we used an agile methodology that allows the development of a project in iterative and incremental stages, which are the following: selection of indicators, design of the prototype, development of the tool, data loading, and tool review and improvements. Infobarris displays 64 indicators of health and its determinants through graphics, maps and tables, in a friendly, interactive and attractive way, which facilitates health surveillance in the neighbourhoods of Barcelona. Copyright © 2017 SESPAS. Publicado por Elsevier España, S.L.U. All rights reserved.

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

Pachuilo, Andrew R; Ragan, Eric; Goodall, John R

Visualization tools can take advantage of multiple coordinated views to support analysis of large, multidimensional data sets. Effective design of such views and layouts can be challenging, but understanding users analysis strategies can inform design improvements. We outline an approach for intelligent design configuration of visualization tools with multiple coordinated views, and we discuss a proposed software framework to support the approach. The proposed software framework could capture and learn from user interaction data to automate new compositions of views and widgets. Such a framework could reduce the time needed for meta analysis of the visualization use and lead tomore » more effective visualization design.« less

Objective laparoscopic skills assessments of surgical residents using Hidden Markov Models based on haptic information and tool/tissue interactions.

PubMed

Rosen, J; Solazzo, M; Hannaford, B; Sinanan, M

2001-01-01

Laparoscopic surgical skills evaluation of surgery residents is usually a subjective process, carried out in the operating room by senior surgeons. By its nature, this process is performed using fuzzy criteria. The objective of the current study was to develop and assess an objective laparoscopic surgical skill scale using Hidden Markov Models (HMM) based on haptic information, tool/tissue interactions and visual task decomposition. Eight subjects (six surgical trainees: first year surgical residents 2 x R1, third year surgical residents 2 x R3 fifth year surgical residents 2 x R5; and two expert laparoscopic surgeons: 2 x ES) performed laparoscopic cholecystectomy following a specific 7 steps protocol on a pig. An instrumented laparoscopic grasper equipped with a three-axis force/torque sensor located at the proximal end with an additional force sensor located on the handle, was used to measure the forces and torques. The hand/tool interface force/torque data was synchronized with a video of the tool operative maneuvers. A synthesis of frame-by-frame video analysis was used to define 14 different types of tool/tissue interactions, each one associated with unique force/torque (F/T) signatures. HMMs were developed for each subject representing the surgical skills by defining the various tool/tissue interactions as states and the associated F/T signatures as observations. The statistical distance between the HMMs representing residents at different levels of their training and the HMMs of expert surgeons were calculated in order to generate a learning curve of selected steps during laparoscopic cholecystectomy. Comparison of HMM's between groups showed significant differences between all skill levels, supporting the objective definition of a learning curve. The major differences between skill levels were: (i) magnitudes of F/T applied (ii) types of tool/tissue interactions used and the transition between them and (iii) time intervals spent in each tool/tissue interaction and the overall completion time. The objective HMM analysis showed that the greatest difference in performance was between R1 and R3 groups and then decreased as the level of expertise increased, suggesting that significant laparoscopic surgical capability develops between the first and the third years of their residency training. The power of the methodology using HMM for objective surgical skill assessment arises from the fact that it compiles enormous amount of data regarding different aspects of surgical skill into a very compact model that can be translated into a single number representing the distance from expert performance. Moreover, the methodology is not limited to in-vivo condition as demonstrated in the current study. It can be extended to other modalities such as measuring performance in surgical simulators and robotic systems.

Manipulator interactive design with interconnected flexible elements

NASA Technical Reports Server (NTRS)

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

1983-01-01

This paper describes the development of an analysis tool for the interactive design of control systems for manipulators and similar electro-mechanical systems amenable to representation as structures in a topological chain. The chain consists of a series of elastic bodies subject to small deformations and arbitrary displacements. The bodies are connected by hinges which permit kinematic constraints, control, or relative motion with six degrees of freedom. The equations of motion for the chain configuration are derived via Kane's method, extended for application to interconnected flexible bodies with time-varying boundary conditions. A corresponding set of modal coordinates has been selected. The motion equations are imbedded within a simulation that transforms the vector-dyadic equations into scalar form for numerical integration. The simulation also includes a linear, time-invariant controler specified in transfer function format and a set of sensors and actuators that interface between the structure and controller. The simulation is driven by an interactive set-up program resulting in an easy-to-use analysis tool.

Visual analytics for aviation safety: A collaborative approach to sensemaking

NASA Astrophysics Data System (ADS)

Wade, Andrew

Visual analytics, the "science of analytical reasoning facilitated by interactive visual interfaces", is more than just visualization. Understanding the human reasoning process is essential for designing effective visualization tools and providing correct analyses. This thesis describes the evolution, application and evaluation of a new method for studying analytical reasoning that we have labeled paired analysis. Paired analysis combines subject matter experts (SMEs) and tool experts (TE) in an analytic dyad, here used to investigate aircraft maintenance and safety data. The method was developed and evaluated using interviews, pilot studies and analytic sessions during an internship at the Boeing Company. By enabling a collaborative approach to sensemaking that can be captured by researchers, paired analysis yielded rich data on human analytical reasoning that can be used to support analytic tool development and analyst training. Keywords: visual analytics, paired analysis, sensemaking, boeing, collaborative analysis.

Exploratory Climate Data Visualization and Analysis Using DV3D and UVCDAT

NASA Technical Reports Server (NTRS)

Maxwell, Thomas

2012-01-01

Earth system scientists are being inundated by an explosion of data generated by ever-increasing resolution in both global models and remote sensors. Advanced tools for accessing, analyzing, and visualizing very large and complex climate data are required to maintain rapid progress in Earth system research. To meet this need, NASA, in collaboration with the Ultra-scale Visualization Climate Data Analysis Tools (UVCOAT) consortium, is developing exploratory climate data analysis and visualization tools which provide data analysis capabilities for the Earth System Grid (ESG). This paper describes DV3D, a UV-COAT package that enables exploratory analysis of climate simulation and observation datasets. OV3D provides user-friendly interfaces for visualization and analysis of climate data at a level appropriate for scientists. It features workflow inte rfaces, interactive 40 data exploration, hyperwall and stereo visualization, automated provenance generation, and parallel task execution. DV30's integration with CDAT's climate data management system (COMS) and other climate data analysis tools provides a wide range of high performance climate data analysis operations. DV3D expands the scientists' toolbox by incorporating a suite of rich new exploratory visualization and analysis methods for addressing the complexity of climate datasets.

Multimodal Redesign in Filmmaking Practices: An Inquiry of Young Filmmakers' Deployment of Semiotic Tools in Their Filmmaking Practice

ERIC Educational Resources Information Center

Gilje, Oystein

2010-01-01

This article traces the trajectory of one particular scene in the work of three media students writing and filmmaking. The analysis scrutinizes the role of semiotic tools, such as synopsis and storyboard, in students' filmmaking practice. Moreover, the use of interactional data combined with textual data allows for a rich recording of the…

Analyzing Collaborative Learning Processes Automatically: Exploiting the Advances of Computational Linguistics in Computer-Supported Collaborative Learning

ERIC Educational Resources Information Center

Rose, Carolyn; Wang, Yi-Chia; Cui, Yue; Arguello, Jaime; Stegmann, Karsten; Weinberger, Armin; Fischer, Frank

2008-01-01

In this article we describe the emerging area of text classification research focused on the problem of collaborative learning process analysis both from a broad perspective and more specifically in terms of a publicly available tool set called TagHelper tools. Analyzing the variety of pedagogically valuable facets of learners' interactions is a…

Social Information Processing Analysis (SIPA): Coding Ongoing Human Communication.

ERIC Educational Resources Information Center

Fisher, B. Aubrey; And Others

1979-01-01

The purpose of this paper is to present a new analytical system to be used in communication research. Unlike many existing systems devised ad hoc, this research tool, a system for interaction analysis, is embedded in a conceptual rationale based on modern systems theory. (Author)

Making Accounting Tutorials Enjoyable

ERIC Educational Resources Information Center

Bargate, Karen

2018-01-01

This paper emanates from a case study which focussed on 15 Managerial Accounting and Financial Management (MAFM) students' "enjoyment" of learning MAFM in an 18-week Writing Intensive Tutorial (WIT) programme. Interactive Qualitative Analysis (IQA) was used for the research design and as a data analysis tool. Following IQA protocols…

Common features of microRNA target prediction tools

PubMed Central

Peterson, Sarah M.; Thompson, Jeffrey A.; Ufkin, Melanie L.; Sathyanarayana, Pradeep; Liaw, Lucy; Congdon, Clare Bates

2014-01-01

The human genome encodes for over 1800 microRNAs (miRNAs), which are short non-coding RNA molecules that function to regulate gene expression post-transcriptionally. Due to the potential for one miRNA to target multiple gene transcripts, miRNAs are recognized as a major mechanism to regulate gene expression and mRNA translation. Computational prediction of miRNA targets is a critical initial step in identifying miRNA:mRNA target interactions for experimental validation. The available tools for miRNA target prediction encompass a range of different computational approaches, from the modeling of physical interactions to the incorporation of machine learning. This review provides an overview of the major computational approaches to miRNA target prediction. Our discussion highlights three tools for their ease of use, reliance on relatively updated versions of miRBase, and range of capabilities, and these are DIANA-microT-CDS, miRanda-mirSVR, and TargetScan. In comparison across all miRNA target prediction tools, four main aspects of the miRNA:mRNA target interaction emerge as common features on which most target prediction is based: seed match, conservation, free energy, and site accessibility. This review explains these features and identifies how they are incorporated into currently available target prediction tools. MiRNA target prediction is a dynamic field with increasing attention on development of new analysis tools. This review attempts to provide a comprehensive assessment of these tools in a manner that is accessible across disciplines. Understanding the basis of these prediction methodologies will aid in user selection of the appropriate tools and interpretation of the tool output. PMID:24600468

Common features of microRNA target prediction tools.

PubMed

Peterson, Sarah M; Thompson, Jeffrey A; Ufkin, Melanie L; Sathyanarayana, Pradeep; Liaw, Lucy; Congdon, Clare Bates

2014-01-01

The human genome encodes for over 1800 microRNAs (miRNAs), which are short non-coding RNA molecules that function to regulate gene expression post-transcriptionally. Due to the potential for one miRNA to target multiple gene transcripts, miRNAs are recognized as a major mechanism to regulate gene expression and mRNA translation. Computational prediction of miRNA targets is a critical initial step in identifying miRNA:mRNA target interactions for experimental validation. The available tools for miRNA target prediction encompass a range of different computational approaches, from the modeling of physical interactions to the incorporation of machine learning. This review provides an overview of the major computational approaches to miRNA target prediction. Our discussion highlights three tools for their ease of use, reliance on relatively updated versions of miRBase, and range of capabilities, and these are DIANA-microT-CDS, miRanda-mirSVR, and TargetScan. In comparison across all miRNA target prediction tools, four main aspects of the miRNA:mRNA target interaction emerge as common features on which most target prediction is based: seed match, conservation, free energy, and site accessibility. This review explains these features and identifies how they are incorporated into currently available target prediction tools. MiRNA target prediction is a dynamic field with increasing attention on development of new analysis tools. This review attempts to provide a comprehensive assessment of these tools in a manner that is accessible across disciplines. Understanding the basis of these prediction methodologies will aid in user selection of the appropriate tools and interpretation of the tool output.

On the Use of Interactive Texts in Undergraduate Chemical Reaction Engineering Courses: A Pedagogical Experience

ERIC Educational Resources Information Center

Asensio, Daniela A.; Barassi, Francisca J.; Zambon, Mariana T.; Mazza, Germán D.

2010-01-01

This paper describes the results of a pedagogical experience carried out at the University of Comahue, Argentina, with an interactive text (IT) concerning Homogeneous Chemical Reactors Analysis. The IT was built on the frame of the "Mathematica" software with the aim of providing students with a robust computational tool. Students'…

Interactive Book Reading in Early Education: A Tool to Stimulate Print Knowledge as Well as Oral Language

ERIC Educational Resources Information Center

Mol, Suzanne E.; Bus, Adriana G.; de Jong, Maria T.

2009-01-01

This meta-analysis examines to what extent interactive storybook reading stimulates two pillars of learning to read: vocabulary and print knowledge. The authors quantitatively reviewed 31 (quasi) experiments (n = 2,049 children) in which educators were trained to encourage children to be actively involved before, during, and after joint book…

TACIT: An open-source text analysis, crawling, and interpretation tool.

PubMed

Dehghani, Morteza; Johnson, Kate M; Garten, Justin; Boghrati, Reihane; Hoover, Joe; Balasubramanian, Vijayan; Singh, Anurag; Shankar, Yuvarani; Pulickal, Linda; Rajkumar, Aswin; Parmar, Niki Jitendra

2017-04-01

As human activity and interaction increasingly take place online, the digital residues of these activities provide a valuable window into a range of psychological and social processes. A great deal of progress has been made toward utilizing these opportunities; however, the complexity of managing and analyzing the quantities of data currently available has limited both the types of analysis used and the number of researchers able to make use of these data. Although fields such as computer science have developed a range of techniques and methods for handling these difficulties, making use of those tools has often required specialized knowledge and programming experience. The Text Analysis, Crawling, and Interpretation Tool (TACIT) is designed to bridge this gap by providing an intuitive tool and interface for making use of state-of-the-art methods in text analysis and large-scale data management. Furthermore, TACIT is implemented as an open, extensible, plugin-driven architecture, which will allow other researchers to extend and expand these capabilities as new methods become available.

Using Galaxy to Perform Large-Scale Interactive Data Analyses

PubMed Central

Hillman-Jackson, Jennifer; Clements, Dave; Blankenberg, Daniel; Taylor, James; Nekrutenko, Anton

2014-01-01

Innovations in biomedical research technologies continue to provide experimental biologists with novel and increasingly large genomic and high-throughput data resources to be analyzed. As creating and obtaining data has become easier, the key decision faced by many researchers is a practical one: where and how should an analysis be performed? Datasets are large and analysis tool set-up and use is riddled with complexities outside of the scope of core research activities. The authors believe that Galaxy provides a powerful solution that simplifies data acquisition and analysis in an intuitive Web application, granting all researchers access to key informatics tools previously only available to computational specialists working in Unix-based environments. We will demonstrate through a series of biomedically relevant protocols how Galaxy specifically brings together (1) data retrieval from public and private sources, for example, UCSC's Eukaryote and Microbial Genome Browsers, (2) custom tools (wrapped Unix functions, format standardization/conversions, interval operations), and 3rd-party analysis tools. PMID:22700312

Expression of masculine identity in individuals with a traumatic brain injury.

PubMed

Keegan, Louise C; Togher, Leanne; Murdock, Macy; Hendry, Emma

2017-01-01

This research seeks to examine and describe how four males with a traumatic brain injury (TBI) use language to negotiate their masculine identities. Qualitative research methods were employed with a 'case study' design that allows for a detailed description of the cases, and the interactions examined. The tools of inquiry applied included a topic analysis, as well as linguistic analysis methods that incorporated the theory of Systemic Functional Linguistics. Such tools were employed in the analysis of 12, two-hour group treatment sessions in order to describe how linguistic choices contributed to the construction of a masculine identity in communicative interactions. Although all participants had significant difficulties with cognitive communication, they all demonstrated an ability to use language to assert their masculine identities. Results revealed that prominent topics used to assert masculinity included confidence, women, risk-taking behaviour and interests and that expressions of masculinity often occurred in giving information roles and involved appraisal and modality. The results have implications for the development of rehabilitation interventions for social communication that provide individuals with TBI with the linguistic tools and communication opportunities necessary in order to successfully express identity and reveal masculinity.

TableViewer for Herschel Data Processing

NASA Astrophysics Data System (ADS)

Zhang, L.; Schulz, B.

2006-07-01

The TableViewer utility is a GUI tool written in Java to support interactive data processing and analysis for the Herschel Space Observatory (Pilbratt et al. 2001). The idea was inherited from a prototype written in IDL (Schulz et al. 2005). It allows to graphically view and analyze tabular data organized in columns with equal numbers of rows. It can be run either as a standalone application, where data access is restricted to FITS (FITS 1999) files only, or it can be run from the Quick Look Analysis(QLA) or Interactive Analysis(IA) command line, from where also objects are accessible. The graphic display is very versatile, allowing plots in either linear or log scales. Zooming, panning, and changing data columns is performed rapidly using a group of navigation buttons. Selecting and de-selecting of fields of data points controls the input to simple analysis tasks like building a statistics table, or generating power spectra. The binary data stored in a TableDataset^1, a Product or in FITS files can also be displayed as tabular data, where values in individual cells can be modified. TableViewer provides several processing utilities which, besides calculation of statistics either for all channels or for selected channels, and calculation of power spectra, allows to convert/repair datasets by changing the unit name of data columns, and by modifying data values in columns with a simple calculator tool. Interactively selected data can be separated out, and modified data sets can be saved to FITS files. The tool will be very helpful especially in the early phases of Herschel data analysis when a quick access to contents of data products is important. TableDataset and Product are Java classes defined in herschel.ia.dataset.

Sedimentation equilibrium analysis of protein interactions with global implicit mass conservation constraints and systematic noise decomposition.

PubMed

Vistica, Jennifer; Dam, Julie; Balbo, Andrea; Yikilmaz, Emine; Mariuzza, Roy A; Rouault, Tracey A; Schuck, Peter

2004-03-15

Sedimentation equilibrium is a powerful tool for the characterization of protein self-association and heterogeneous protein interactions. Frequently, it is applied in a configuration with relatively long solution columns and with equilibrium profiles being acquired sequentially at several rotor speeds. The present study proposes computational tools, implemented in the software SEDPHAT, for the global analysis of equilibrium data at multiple rotor speeds with multiple concentrations and multiple optical detection methods. The detailed global modeling of such equilibrium data can be a nontrivial computational problem. It was shown previously that mass conservation constraints can significantly improve and extend the analysis of heterogeneous protein interactions. Here, a method for using conservation of mass constraints for the macromolecular redistribution is proposed in which the effective loading concentrations are calculated from the sedimentation equilibrium profiles. The approach is similar to that described by Roark (Biophys. Chem. 5 (1976) 185-196), but its utility is extended by determining the bottom position of the solution columns from the macromolecular redistribution. For analyzing heterogeneous associations at multiple protein concentrations, additional constraints that relate the effective loading concentrations of the different components or their molar ratio in the global analysis are introduced. Equilibrium profiles at multiple rotor speeds also permit the algebraic determination of radial-dependent baseline profiles, which can govern interference optical ultracentrifugation data, but usually also occur, to a smaller extent, in absorbance optical data. Finally, the global analysis of equilibrium profiles at multiple rotor speeds with implicit mass conservation and computation of the bottom of the solution column provides an unbiased scale for determining molar mass distributions of noninteracting species. The properties of these tools are studied with theoretical and experimental data sets.

Listeriomics: an Interactive Web Platform for Systems Biology of Listeria

PubMed Central

Koutero, Mikael; Tchitchek, Nicolas; Cerutti, Franck; Lechat, Pierre; Maillet, Nicolas; Hoede, Claire; Chiapello, Hélène; Gaspin, Christine

2017-01-01

ABSTRACT As for many model organisms, the amount of Listeria omics data produced has recently increased exponentially. There are now >80 published complete Listeria genomes, around 350 different transcriptomic data sets, and 25 proteomic data sets available. The analysis of these data sets through a systems biology approach and the generation of tools for biologists to browse these various data are a challenge for bioinformaticians. We have developed a web-based platform, named Listeriomics, that integrates different tools for omics data analyses, i.e., (i) an interactive genome viewer to display gene expression arrays, tiling arrays, and sequencing data sets along with proteomics and genomics data sets; (ii) an expression and protein atlas that connects every gene, small RNA, antisense RNA, or protein with the most relevant omics data; (iii) a specific tool for exploring protein conservation through the Listeria phylogenomic tree; and (iv) a coexpression network tool for the discovery of potential new regulations. Our platform integrates all the complete Listeria species genomes, transcriptomes, and proteomes published to date. This website allows navigation among all these data sets with enriched metadata in a user-friendly format and can be used as a central database for systems biology analysis. IMPORTANCE In the last decades, Listeria has become a key model organism for the study of host-pathogen interactions, noncoding RNA regulation, and bacterial adaptation to stress. To study these mechanisms, several genomics, transcriptomics, and proteomics data sets have been produced. We have developed Listeriomics, an interactive web platform to browse and correlate these heterogeneous sources of information. Our website will allow listeriologists and microbiologists to decipher key regulation mechanism by using a systems biology approach. PMID:28317029

A CAD approach to magnetic bearing design

NASA Technical Reports Server (NTRS)

Jeyaseelan, M.; Anand, D. K.; Kirk, J. A.

1988-01-01

A design methodology has been developed at the Magnetic Bearing Research Laboratory for designing magnetic bearings using a CAD approach. This is used in the algorithm of an interactive design software package. The package is a design tool developed to enable the designer to simulate the entire process of design and analysis of the system. Its capabilities include interactive input/modification of geometry, finding any possible saturation at critical sections of the system, and the design and analysis of a control system that stabilizes and maintains magnetic suspension.

Docking and free energy simulations to predict conformational domains involved in hCG-LH receptor interactions using recombinant antibodies.

PubMed

Majumdar, Ritankar; Railkar, Reema; Dighe, Rajan R

2011-11-01

Single chain fragment variables (ScFvs) have been extensively employed in studying the protein-protein interactions. ScFvs derived from phage display libraries have an additional advantage of being generated against a native antigen, circumventing loss of information on conformational epitopes. In the present study, an attempt has been made to elucidate human chorionic gonadotropin (hCG)-luteinizing hormone (LH) receptor interactions by using a neutral and two inhibitory ScFvs against hCG. The objective was to dock a computationally derived model of these ScFvs onto the crystal structure of hCG and understand the differential roles of the mapped epitopes in hCG-LH receptor interactions. An anti-hCG ScFv, whose epitope was mapped previously using biochemical tools, served as the positive control for assessing the quality of docking analysis. To evaluate the role of specific side chains at the hCG-ScFv interface, binding free energy as well as residue interaction energies of complexes in solution were calculated using molecular mechanics Poisson-Boltzmann/surface area method after performing the molecular dynamic simulations on the selected hCG-ScFv models and validated using biochemical and SPR analysis. The robustness of these calculations was demonstrated by comparing the theoretically determined binding energies with the experimentally obtained kinetic parameters for hCG-ScFv complexes. Superimposition of hCG-ScFv model onto a model of hCG complexed with the 51-266 residues of LH receptor revealed importance of the residues previously thought to be unimportant for hormone binding and response. This analysis provides an alternate tool for understanding the structure-function analysis of ligand-receptor interactions. Copyright © 2011 Wiley-Liss, Inc.

Developing Healthcare Data Analytics APPs with Open Data Science Tools.

PubMed

Hao, Bibo; Sun, Wen; Yu, Yiqin; Xie, Guotong

2017-01-01

Recent advances in big data analytics provide more flexible, efficient, and open tools for researchers to gain insight from healthcare data. Whilst many tools require researchers to develop programs with programming languages like Python, R and so on, which is not a skill set grasped by many researchers in the healthcare data analytics area. To make data science more approachable, we explored existing tools and developed a practice that can help data scientists convert existing analytics pipelines to user-friendly analytics APPs with rich interactions and features of real-time analysis. With this practice, data scientists can develop customized analytics pipelines as APPs in Jupyter Notebook and disseminate them to other researchers easily, and researchers can benefit from the shared notebook to perform analysis tasks or reproduce research results much more easily.

PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data.

PubMed

Hernández-de-Diego, Rafael; Tarazona, Sonia; Martínez-Mira, Carlos; Balzano-Nogueira, Leandro; Furió-Tarí, Pedro; Pappas, Georgios J; Conesa, Ana

2018-05-25

The increasing availability of multi-omic platforms poses new challenges to data analysis. Joint visualization of multi-omics data is instrumental in better understanding interconnections across molecular layers and in fully utilizing the multi-omic resources available to make biological discoveries. We present here PaintOmics 3, a web-based resource for the integrated visualization of multiple omic data types onto KEGG pathway diagrams. PaintOmics 3 combines server-end capabilities for data analysis with the potential of modern web resources for data visualization, providing researchers with a powerful framework for interactive exploration of their multi-omics information. Unlike other visualization tools, PaintOmics 3 covers a comprehensive pathway analysis workflow, including automatic feature name/identifier conversion, multi-layered feature matching, pathway enrichment, network analysis, interactive heatmaps, trend charts, and more. It accepts a wide variety of omic types, including transcriptomics, proteomics and metabolomics, as well as region-based approaches such as ATAC-seq or ChIP-seq data. The tool is freely available at www.paintomics.org.

PodNet, a protein-protein interaction network of the podocyte.

PubMed

Warsow, Gregor; Endlich, Nicole; Schordan, Eric; Schordan, Sandra; Chilukoti, Ravi K; Homuth, Georg; Moeller, Marcus J; Fuellen, Georg; Endlich, Karlhans

2013-07-01

Interactions between proteins crucially determine cellular structure and function. Differential analysis of the interactome may help elucidate molecular mechanisms during disease development; however, this analysis necessitates mapping of expression data on protein-protein interaction networks. These networks do not exist for the podocyte; therefore, we built PodNet, a literature-based mouse podocyte network in Cytoscape format. Using database protein-protein interactions, we expanded PodNet to XPodNet with enhanced connectivity. In order to test the performance of XPodNet in differential interactome analysis, we examined podocyte developmental differentiation and the effect of cell culture. Transcriptomes of podocytes in 10 different states were mapped on XPodNet and analyzed with the Cytoscape plugin ExprEssence, based on the law of mass action. Interactions between slit diaphragm proteins are most significantly upregulated during podocyte development and most significantly downregulated in culture. On the other hand, our analysis revealed that interactions lost during podocyte differentiation are not regained in culture, suggesting a loss rather than a reversal of differentiation for podocytes in culture. Thus, we have developed PodNet as a valuable tool for differential interactome analysis in podocytes, and we have identified established and unexplored regulated interactions in developing and cultured podocytes.

Music and Cultural Analysis in the Classroom: Introducing Sociology through Heavy Metal.

ERIC Educational Resources Information Center

Ahlkvist, Jarl A.

1999-01-01

Demonstrates that popular music's potential as a tool for teaching interactive introductory sociology courses is enhanced when a cultural analysis of a specific music genre is incorporated into the classroom. Presents a two-part model for integrating a cultural analysis of heavy metal music and its subculture into the introductory course. Includes…

High Accuracy Liquid Propellant Slosh Predictions Using an Integrated CFD and Controls Analysis Interface

NASA Technical Reports Server (NTRS)

Marsell, Brandon; Griffin, David; Schallhorn, Dr. Paul; Roth, Jacob

2012-01-01

Coupling computational fluid dynamics (CFD) with a controls analysis tool elegantly allows for high accuracy predictions of the interaction between sloshing liquid propellants and th e control system of a launch vehicle. Instead of relying on mechanical analogs which are not valid during aU stages of flight, this method allows for a direct link between the vehicle dynamic environments calculated by the solver in the controls analysis tool to the fluid flow equations solved by the CFD code. This paper describes such a coupling methodology, presents the results of a series of test cases, and compares said results against equivalent results from extensively validated tools. The coupling methodology, described herein, has proven to be highly accurate in a variety of different cases.

Integrated CFD and Controls Analysis Interface for High Accuracy Liquid Propellant Slosh Predictions

NASA Technical Reports Server (NTRS)

Marsell, Brandon; Griffin, David; Schallhorn, Paul; Roth, Jacob

2012-01-01

Coupling computational fluid dynamics (CFD) with a controls analysis tool elegantly allows for high accuracy predictions of the interaction between sloshing liquid propellants and the control system of a launch vehicle. Instead of relying on mechanical analogs which are n0t va lid during all stages of flight, this method allows for a direct link between the vehicle dynamic environments calculated by the solver in the controls analysis tool to the fluid now equations solved by the CFD code. This paper describes such a coupling methodology, presents the results of a series of test cases, and compares said results against equivalent results from extensively validated tools. The coupling methodology, described herein, has proven to be highly accurate in a variety of different cases.

Unified Approach to Modeling and Simulation of Space Communication Networks and Systems

NASA Technical Reports Server (NTRS)

Barritt, Brian; Bhasin, Kul; Eddy, Wesley; Matthews, Seth

2010-01-01

Network simulator software tools are often used to model the behaviors and interactions of applications, protocols, packets, and data links in terrestrial communication networks. Other software tools that model the physics, orbital dynamics, and RF characteristics of space systems have matured to allow for rapid, detailed analysis of space communication links. However, the absence of a unified toolset that integrates the two modeling approaches has encumbered the systems engineers tasked with the design, architecture, and analysis of complex space communication networks and systems. This paper presents the unified approach and describes the motivation, challenges, and our solution - the customization of the network simulator to integrate with astronautical analysis software tools for high-fidelity end-to-end simulation. Keywords space; communication; systems; networking; simulation; modeling; QualNet; STK; integration; space networks

Verbal and Nonverbal Classroom Communication: The Development of an Observational Instrument.

ERIC Educational Resources Information Center

Heger, Herbert K.

This paper reports the development of a classroom observation instrument designed to broaden and extend the power of existing tools to provide a balanced, reciprocal perspective of both verbal and nonverbal communication. An introductory section discusses developments in communication analysis. The Miniaturized Total Interaction Analysis System…

Relevance Rank Platform (RRP) for Functional Filtering of High Content Protein-Protein Interaction Data.

PubMed

Pokharel, Yuba Raj; Saarela, Jani; Szwajda, Agnieszka; Rupp, Christian; Rokka, Anne; Lal Kumar Karna, Shibendra; Teittinen, Kaisa; Corthals, Garry; Kallioniemi, Olli; Wennerberg, Krister; Aittokallio, Tero; Westermarck, Jukka

2015-12-01

High content protein interaction screens have revolutionized our understanding of protein complex assembly. However, one of the major challenges in translation of high content protein interaction data is identification of those interactions that are functionally relevant for a particular biological question. To address this challenge, we developed a relevance ranking platform (RRP), which consist of modular functional and bioinformatic filters to provide relevance rank among the interactome proteins. We demonstrate the versatility of RRP to enable a systematic prioritization of the most relevant interaction partners from high content data, highlighted by the analysis of cancer relevant protein interactions for oncoproteins Pin1 and PME-1. We validated the importance of selected interactions by demonstration of PTOV1 and CSKN2B as novel regulators of Pin1 target c-Jun phosphorylation and reveal previously unknown interacting proteins that may mediate PME-1 effects via PP2A-inhibition. The RRP framework is modular and can be modified to answer versatile research problems depending on the nature of the biological question under study. Based on comparison of RRP to other existing filtering tools, the presented data indicate that RRP offers added value especially for the analysis of interacting proteins for which there is no sufficient prior knowledge available. Finally, we encourage the use of RRP in combination with either SAINT or CRAPome computational tools for selecting the candidate interactors that fulfill the both important requirements, functional relevance, and high confidence interaction detection. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Silicon photonics cloud (SiCloud)

NASA Astrophysics Data System (ADS)

DeVore, Peter T. S.; Jiang, Yunshan; Lynch, Michael; Miyatake, Taira; Carmona, Christopher; Chan, Andrew C.; Muniam, Kuhan; Jalali, Bahram

2015-02-01

We present SiCloud (Silicon Photonics Cloud), the first free, instructional web-based research and education tool for silicon photonics. SiCloud's vision is to provide a host of instructional and research web-based tools. Such interactive learning tools enhance traditional teaching methods by extending access to a very large audience, resulting in very high impact. Interactive tools engage the brain in a way different from merely reading, and so enhance and reinforce the learning experience. Understanding silicon photonics is challenging as the topic involves a wide range of disciplines, including material science, semiconductor physics, electronics and waveguide optics. This web-based calculator is an interactive analysis tool for optical properties of silicon and related material (SiO2, Si3N4, Al2O3, etc.). It is designed to be a one stop resource for students, researchers and design engineers. The first and most basic aspect of Silicon Photonics is the Material Parameters, which provides the foundation for the Device, Sub-System and System levels. SiCloud includes the common dielectrics and semiconductors for waveguide core, cladding, and photodetection, as well as metals for electrical contacts. SiCloud is a work in progress and its capability is being expanded. SiCloud is being developed at UCLA with funding from the National Science Foundation's Center for Integrated Access Networks (CIAN) Engineering Research Center.

Screening large-scale association study data: exploiting interactions using random forests.

PubMed

Lunetta, Kathryn L; Hayward, L Brooke; Segal, Jonathan; Van Eerdewegh, Paul

2004-12-10

Genome-wide association studies for complex diseases will produce genotypes on hundreds of thousands of single nucleotide polymorphisms (SNPs). A logical first approach to dealing with massive numbers of SNPs is to use some test to screen the SNPs, retaining only those that meet some criterion for further study. For example, SNPs can be ranked by p-value, and those with the lowest p-values retained. When SNPs have large interaction effects but small marginal effects in a population, they are unlikely to be retained when univariate tests are used for screening. However, model-based screens that pre-specify interactions are impractical for data sets with thousands of SNPs. Random forest analysis is an alternative method that produces a single measure of importance for each predictor variable that takes into account interactions among variables without requiring model specification. Interactions increase the importance for the individual interacting variables, making them more likely to be given high importance relative to other variables. We test the performance of random forests as a screening procedure to identify small numbers of risk-associated SNPs from among large numbers of unassociated SNPs using complex disease models with up to 32 loci, incorporating both genetic heterogeneity and multi-locus interaction. Keeping other factors constant, if risk SNPs interact, the random forest importance measure significantly outperforms the Fisher Exact test as a screening tool. As the number of interacting SNPs increases, the improvement in performance of random forest analysis relative to Fisher Exact test for screening also increases. Random forests perform similarly to the univariate Fisher Exact test as a screening tool when SNPs in the analysis do not interact. In the context of large-scale genetic association studies where unknown interactions exist among true risk-associated SNPs or SNPs and environmental covariates, screening SNPs using random forest analyses can significantly reduce the number of SNPs that need to be retained for further study compared to standard univariate screening methods.

Geometric modeling for computer aided design

NASA Technical Reports Server (NTRS)

Schwing, James L.

1992-01-01

The goal was the design and implementation of software to be used in the conceptual design of aerospace vehicles. Several packages and design studies were completed, including two software tools currently used in the conceptual level design of aerospace vehicles. These tools are the Solid Modeling Aerospace Research Tool (SMART) and the Environment for Software Integration and Execution (EASIE). SMART provides conceptual designers with a rapid prototyping capability and additionally provides initial mass property analysis. EASIE provides a set of interactive utilities that simplify the task of building and executing computer aided design systems consisting of diverse, stand alone analysis codes that result in the streamlining of the exchange of data between programs, reducing errors and improving efficiency.

Computer-aided system design

NASA Technical Reports Server (NTRS)

Walker, Carrie K.

1991-01-01

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

SLIDE - a web-based tool for interactive visualization of large-scale -omics data.

PubMed

Ghosh, Soumita; Datta, Abhik; Tan, Kaisen; Choi, Hyungwon

2018-06-28

Data visualization is often regarded as a post hoc step for verifying statistically significant results in the analysis of high-throughput data sets. This common practice leaves a large amount of raw data behind, from which more information can be extracted. However, existing solutions do not provide capabilities to explore large-scale raw datasets using biologically sensible queries, nor do they allow user interaction based real-time customization of graphics. To address these drawbacks, we have designed an open-source, web-based tool called Systems-Level Interactive Data Exploration, or SLIDE to visualize large-scale -omics data interactively. SLIDE's interface makes it easier for scientists to explore quantitative expression data in multiple resolutions in a single screen. SLIDE is publicly available under BSD license both as an online version as well as a stand-alone version at https://github.com/soumitag/SLIDE. Supplementary Information are available at Bioinformatics online.

Running SINDA '85/FLUINT interactive on the VAX

NASA Technical Reports Server (NTRS)

Simmonds, Boris

1992-01-01

Computer software as engineering tools are typically run in three modes: Batch, Demand, and Interactive. The first two are the most popular in the SINDA world. The third one is not so popular, due probably to the users inaccessibility to the command procedure files for running SINDA '85, or lack of familiarity with the SINDA '85 execution processes (pre-processor, processor, compilation, linking, execution and all of the file assignment, creation, deletions and de-assignments). Interactive is the mode that makes thermal analysis with SINDA '85 a real-time design tool. This paper explains a command procedure sufficient (the minimum modifications required in an existing demand command procedure) to run SINDA '85 on the VAX in an interactive mode. To exercise the procedure a sample problem is presented exemplifying the mode, plus additional programming capabilities available in SINDA '85. Following the same guidelines the process can be extended to other SINDA '85 residence computer platforms.

TRI National Analysis

EPA Pesticide Factsheets

Interpretation of annual TRI data reported by industrial facilities. Interactive maps and other tools give a close look at how industries, parent companies, and individual facilities manage toxic chemical waste and how they prevent and reduce pollution.

Planetary Surface Visualization and Analytics

NASA Astrophysics Data System (ADS)

Law, E. S.; Solar System Treks Team

2018-04-01

An introduction and update of the Solar System Treks Project which provides a suite of interactive visualization and analysis tools to enable users (engineers, scientists, public) to access large amounts of mapped planetary data products.

PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system

PubMed Central

Droit, Arnaud; Hunter, Joanna M; Rouleau, Michèle; Ethier, Chantal; Picard-Cloutier, Aude; Bourgais, David; Poirier, Guy G

2007-01-01

Background In the "post-genome" era, mass spectrometry (MS) has become an important method for the analysis of proteins and the rapid advancement of this technique, in combination with other proteomics methods, results in an increasing amount of proteome data. This data must be archived and analysed using specialized bioinformatics tools. Description We herein describe "PARPs database," a data analysis and management pipeline for liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics. PARPs database is a web-based tool whose features include experiment annotation, protein database searching, protein sequence management, as well as data-mining of the peptides and proteins identified. Conclusion Using this pipeline, we have successfully identified several interactions of biological significance between PARP-1 and other proteins, namely RFC-1, 2, 3, 4 and 5. PMID:18093328

Preparation of Gap Junctions in Membrane Microdomains for Immunoprecipitation and Mass Spectrometry Interactome Analysis.

PubMed

Fowler, Stephanie; Akins, Mark; Bennett, Steffany A L

2016-01-01

Protein interaction networks at gap junction plaques are increasingly implicated in a variety of intracellular signaling cascades. Identifying protein interactions of integral membrane proteins is a valuable tool for determining channel function. However, several technical challenges exist. Subcellular fractionation of the bait protein matrix is usually required to identify less abundant proteins in complex homogenates. Sufficient solvation of the lipid environment without perturbation of the protein interactome must also be achieved. The present chapter describes the flotation of light and heavy liver tissue membrane microdomains to facilitate the identification and analysis of endogenous gap junction proteins and includes technical notes for translation to other integral membrane proteins, tissues, or cell culture models. These procedures are valuable tools for the enrichment of gap junction membrane compartments and for the identification of gap junction signaling interactomes.

Post hoc support vector machine learning for impedimetric biosensors based on weak protein-ligand interactions.

PubMed

Rong, Y; Padron, A V; Hagerty, K J; Nelson, N; Chi, S; Keyhani, N O; Katz, J; Datta, S P A; Gomes, C; McLamore, E S

2018-04-30

Impedimetric biosensors for measuring small molecules based on weak/transient interactions between bioreceptors and target analytes are a challenge for detection electronics, particularly in field studies or in the analysis of complex matrices. Protein-ligand binding sensors have enormous potential for biosensing, but achieving accuracy in complex solutions is a major challenge. There is a need for simple post hoc analytical tools that are not computationally expensive, yet provide near real time feedback on data derived from impedance spectra. Here, we show the use of a simple, open source support vector machine learning algorithm for analyzing impedimetric data in lieu of using equivalent circuit analysis. We demonstrate two different protein-based biosensors to show that the tool can be used for various applications. We conclude with a mobile phone-based demonstration focused on the measurement of acetone, an important biomarker related to the onset of diabetic ketoacidosis. In all conditions tested, the open source classifier was capable of performing as well as, or better, than the equivalent circuit analysis for characterizing weak/transient interactions between a model ligand (acetone) and a small chemosensory protein derived from the tsetse fly. In addition, the tool has a low computational requirement, facilitating use for mobile acquisition systems such as mobile phones. The protocol is deployed through Jupyter notebook (an open source computing environment available for mobile phone, tablet or computer use) and the code was written in Python. For each of the applications, we provide step-by-step instructions in English, Spanish, Mandarin and Portuguese to facilitate widespread use. All codes were based on scikit-learn, an open source software machine learning library in the Python language, and were processed in Jupyter notebook, an open-source web application for Python. The tool can easily be integrated with the mobile biosensor equipment for rapid detection, facilitating use by a broad range of impedimetric biosensor users. This post hoc analysis tool can serve as a launchpad for the convergence of nanobiosensors in planetary health monitoring applications based on mobile phone hardware.

Applied Meteorology Unit (AMU)

NASA Technical Reports Server (NTRS)

Bauman, William; Crawford, Winifred; Barrett, Joe; Watson, Leela; Wheeler, Mark

2010-01-01

This report summarizes the Applied Meteorology Unit (AMU) activities for the first quarter of Fiscal Year 2010 (October - December 2009). A detailed project schedule is included in the Appendix. Included tasks are: (1) Peak Wind Tool for User Launch Commit Criteria (LCC), (2) Objective Lightning Probability Tool, Phase III, (3) Peak Wind Tool for General Forecasting, Phase II, (4) Upgrade Summer Severe Weather Tool in Meteorological Interactive Data Display System (MIDDS), (5) Advanced Regional Prediction System (ARPS) Data Analysis System (ADAS) Update and Maintainability, (5) Verify 12-km resolution North American Model (MesoNAM) Performance, and (5) Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) Graphical User Interface.

Analysis of complex neural circuits with nonlinear multidimensional hidden state models

PubMed Central

Friedman, Alexander; Slocum, Joshua F.; Tyulmankov, Danil; Gibb, Leif G.; Altshuler, Alex; Ruangwises, Suthee; Shi, Qinru; Toro Arana, Sebastian E.; Beck, Dirk W.; Sholes, Jacquelyn E. C.; Graybiel, Ann M.

2016-01-01

A universal need in understanding complex networks is the identification of individual information channels and their mutual interactions under different conditions. In neuroscience, our premier example, networks made up of billions of nodes dynamically interact to bring about thought and action. Granger causality is a powerful tool for identifying linear interactions, but handling nonlinear interactions remains an unmet challenge. We present a nonlinear multidimensional hidden state (NMHS) approach that achieves interaction strength analysis and decoding of networks with nonlinear interactions by including latent state variables for each node in the network. We compare NMHS to Granger causality in analyzing neural circuit recordings and simulations, improvised music, and sociodemographic data. We conclude that NMHS significantly extends the scope of analyses of multidimensional, nonlinear networks, notably in coping with the complexity of the brain. PMID:27222584

Recent Advances in Nanobiotechnology and High-Throughput Molecular Techniques for Systems Biomedicine

PubMed Central

Kim, Eung-Sam; Ahn, Eun Hyun; Chung, Euiheon; Kim, Deok-Ho

2013-01-01

Nanotechnology-based tools are beginning to emerge as promising platforms for quantitative high-throughput analysis of live cells and tissues. Despite unprecedented progress made over the last decade, a challenge still lies in integrating emerging nanotechnology-based tools into macroscopic biomedical apparatuses for practical purposes in biomedical sciences. In this review, we discuss the recent advances and limitations in the analysis and control of mechanical, biochemical, fluidic, and optical interactions in the interface areas of nanotechnology-based materials and living cells in both in vitro and in vivo settings. PMID:24258011

iGlobe Interactive Visualization and Analysis of Spatial Data

NASA Technical Reports Server (NTRS)

Hogan, Patrick

2012-01-01

iGlobe is open-source software built on NASA World Wind virtual globe technology. iGlobe provides a growing set of tools for weather science, climate research, and agricultural analysis. Up until now, these types of sophisticated tools have been developed in isolation by national agencies, academic institutions, and research organizations. By providing an open-source solution to analyze and visualize weather, climate, and agricultural data, the scientific and research communities can more readily advance solutions needed to understand better the dynamics of our home planet, Earth

Recent advances in nanobiotechnology and high-throughput molecular techniques for systems biomedicine.

PubMed

Kim, Eung-Sam; Ahn, Eun Hyun; Chung, Euiheon; Kim, Deok-Ho

2013-12-01

Nanotechnology-based tools are beginning to emerge as promising platforms for quantitative high-throughput analysis of live cells and tissues. Despite unprecedented progress made over the last decade, a challenge still lies in integrating emerging nanotechnology-based tools into macroscopic biomedical apparatuses for practical purposes in biomedical sciences. In this review, we discuss the recent advances and limitations in the analysis and control of mechanical, biochemical, fluidic, and optical interactions in the interface areas of nanotechnologybased materials and living cells in both in vitro and in vivo settings.

Using Discursis to enhance the qualitative analysis of hospital pharmacist-patient interactions.

PubMed

Chevalier, Bernadette A M; Watson, Bernadette M; Barras, Michael A; Cottrell, William N; Angus, Daniel J

2018-01-01

Pharmacist-patient communication during medication counselling has been successfully investigated using Communication Accommodation Theory (CAT). Communication researchers in other healthcare professions have utilised Discursis software as an adjunct to their manual qualitative analysis processes. Discursis provides a visual, chronological representation of communication exchanges and identifies patterns of interactant engagement. The aim of this study was to describe how Discursis software was used to enhance previously conducted qualitative analysis of pharmacist-patient interactions (by visualising pharmacist-patient speech patterns, episodes of engagement, and identifying CAT strategies employed by pharmacists within these episodes). Visual plots from 48 transcribed audio recordings of pharmacist-patient exchanges were generated by Discursis. Representative plots were selected to show moderate-high and low- level speaker engagement. Details of engagement were investigated for pharmacist application of CAT strategies (approximation, interpretability, discourse management, emotional expression, and interpersonal control). Discursis plots allowed for identification of distinct patterns occurring within pharmacist-patient exchanges. Moderate-high pharmacist-patient engagement was characterised by multiple off-diagonal squares while alternating single coloured squares depicted low engagement. Engagement episodes were associated with multiple CAT strategies such as discourse management (open-ended questions). Patterns reflecting pharmacist or patient speaker dominance were dependant on clinical setting. Discursis analysis of pharmacist-patient interactions, a novel application of the technology in health communication, was found to be an effective visualisation tool to pin-point episodes for CAT analysis. Discursis has numerous practical and theoretical applications for future health communication research and training. Researchers can use the software to support qualitative analysis where large data sets can be quickly reviewed to identify key areas for concentrated analysis. Because Discursis plots are easily generated from audio recorded transcripts, they are conducive as teaching tools for both students and practitioners to assess and develop their communication skills.

Automated Video Analysis of Non-verbal Communication in a Medical Setting

PubMed Central

Hart, Yuval; Czerniak, Efrat; Karnieli-Miller, Orit; Mayo, Avraham E.; Ziv, Amitai; Biegon, Anat; Citron, Atay; Alon, Uri

2016-01-01

Non-verbal communication plays a significant role in establishing good rapport between physicians and patients and may influence aspects of patient health outcomes. It is therefore important to analyze non-verbal communication in medical settings. Current approaches to measure non-verbal interactions in medicine employ coding by human raters. Such tools are labor intensive and hence limit the scale of possible studies. Here, we present an automated video analysis tool for non-verbal interactions in a medical setting. We test the tool using videos of subjects that interact with an actor portraying a doctor. The actor interviews the subjects performing one of two scripted scenarios of interviewing the subjects: in one scenario the actor showed minimal engagement with the subject. The second scenario included active listening by the doctor and attentiveness to the subject. We analyze the cross correlation in total kinetic energy of the two people in the dyad, and also characterize the frequency spectrum of their motion. We find large differences in interpersonal motion synchrony and entrainment between the two performance scenarios. The active listening scenario shows more synchrony and more symmetric followership than the other scenario. Moreover, the active listening scenario shows more high-frequency motion termed jitter that has been recently suggested to be a marker of followership. The present approach may be useful for analyzing physician-patient interactions in terms of synchrony and dominance in a range of medical settings. PMID:27602002

Fast 3D Net Expeditions: Tools for Effective Scientific Collaboration on the World Wide Web

NASA Technical Reports Server (NTRS)

Watson, Val; Chancellor, Marisa K. (Technical Monitor)

1996-01-01

Two new technologies, the FASTexpedition and Remote FAST, have been developed that provide remote, 3D (three dimensional), high resolution, dynamic, interactive viewing of scientific data. The FASTexpedition permits one to access scientific data from the World Wide Web, take guided expeditions through the data, and continue with self controlled expeditions through the data. Remote FAST permits collaborators at remote sites to simultaneously view an analysis of scientific data being controlled by one of the collaborators. Control can be transferred between sites. These technologies are now being used for remote collaboration in joint university, industry, and NASA projects. Also, NASA Ames Research Center has initiated a project to make scientific data and guided expeditions through the data available as FASTexpeditions on the World Wide Web for educational purposes. Previously, remote visualization of dynamic data was done using video format (transmitting pixel information) such as video conferencing or MPEG (Motion Picture Expert Group) movies on the Internet. The concept for this new technology is to send the raw data (e.g., grids, vectors, and scalars) along with viewing scripts over the Internet and have the pixels generated by a visualization tool running on the viewers local workstation. The visualization tool that is currently used is FAST (Flow Analysis Software Toolkit). The advantages of this new technology over using video format are: (1) The visual is much higher in resolution (1280x1024 pixels with 24 bits of color) than typical video format transmitted over the network. (2) The form of the visualization can be controlled interactively (because the viewer is interactively controlling the visualization tool running on his workstation). (3) A rich variety of guided expeditions through the data can be included easily. (4) A capability is provided for other sites to see a visual analysis of one site as the analysis is interactively performed. Control of the analysis can be passed from site to site. (5) The scenes can be viewed in 3D using stereo vision. (6) The network bandwidth for the visualization using this new technology is much smaller than when using video format. (The measured peak bandwidth used was 1 Kbit/sec whereas the measured bandwidth for a small video picture was 500 Kbits/sec.) This talk will illustrate the use of these new technologies and present a proposal for using these technologies to improve science education.

Demonstration of Data Interactive Publications

NASA Astrophysics Data System (ADS)

Domenico, B.; Weber, J.

2012-04-01

This is a demonstration version of the talk given in session ESSI2.4 "Full lifecycle of data." For some years now, the authors have developed examples of online documents that allowed the reader to interact directly with datasets, but there were limitations that restricted the interaction to specific desktop analysis and display tools that were not generally available to all readers of the documents. Recent advances in web service technology and related standards are making it possible to develop systems for publishing online documents that enable readers to access, analyze, and display the data discussed in the publication from the perspective and in the manner from which the author wants it to be represented. By clicking on embedded links, the reader accesses not only the usual textual information in a publication, but also data residing on a local or remote web server as well as a set of processing tools for analyzing and displaying the data. With the option of having the analysis and display processing provided on the server (or in the cloud), there are now a broader set of possibilities on the client side where the reader can interact with the data via a thin web client, a rich desktop application, or a mobile platform "app." The presentation will outline the architecture of data interactive publications along with illustrative examples.

Knowledge as an interactional tool in the management of client empowerment.

PubMed

Moore, John

2016-06-01

To examine the way speaker and recipient knowledge is managed in interaction by a call taker at a mental-health information line, to achieve the institutional goals of information provision and client empowerment. This study utilizes conversation analysis in the analysis of a single call to the line. Analysis demonstrates the ways in which a call taker produces turns-at-talk that construct a caller as knowing what help they wanted prior to that moment in the interaction, and that invoke 'common' knowledge of sources of such help. Talk that orients to knowledge is used as an interactional resource that allows the call taker to avoid talk that may be considered advice, and to be heard to achieve the goal of client empowerment. The asymmetric identities of help-seeker and help-provider are managed in this process. Client empowerment can be seen as something interactionally achieved and managed in talk-in-interaction, while not necessarily objectively experienced by the client. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Comparative analysis and visualization of multiple collinear genomes

PubMed Central

2012-01-01

Background Genome browsers are a common tool used by biologists to visualize genomic features including genes, polymorphisms, and many others. However, existing genome browsers and visualization tools are not well-suited to perform meaningful comparative analysis among a large number of genomes. With the increasing quantity and availability of genomic data, there is an increased burden to provide useful visualization and analysis tools for comparison of multiple collinear genomes such as the large panels of model organisms which are the basis for much of the current genetic research. Results We have developed a novel web-based tool for visualizing and analyzing multiple collinear genomes. Our tool illustrates genome-sequence similarity through a mosaic of intervals representing local phylogeny, subspecific origin, and haplotype identity. Comparative analysis is facilitated through reordering and clustering of tracks, which can vary throughout the genome. In addition, we provide local phylogenetic trees as an alternate visualization to assess local variations. Conclusions Unlike previous genome browsers and viewers, ours allows for simultaneous and comparative analysis. Our browser provides intuitive selection and interactive navigation about features of interest. Dynamic visualizations adjust to scale and data content making analysis at variable resolutions and of multiple data sets more informative. We demonstrate our genome browser for an extensive set of genomic data sets composed of almost 200 distinct mouse laboratory strains. PMID:22536897

Network pharmacology: reigning in drug attrition?

PubMed

Alian, Osama M; Shah, Minjel; Mohammad, Momin; Mohammad, Ramzi M

2013-06-01

In the process of drug development, there has been an exceptionally high attrition rate in oncological compounds entering late phases of testing. This has seen a concurrent reduction in approved NCEs (new chemical entities) reaching patients. Network pharmacology has become a valuable tool in understanding the fine details of drug-target interactions as well as painting a more practical picture of phenotype relationships to patients and drugs. By utilizing all the tools achieved through molecular medicine and combining it with high throughput data analysis, interactions and mechanisms can be elucidated and treatments reasonably tailored to patients expressing specific phenotypes (or genotypes) of disease, essentially reigning in the phenomenon of drug attrition.

ASTEC: Controls analysis for personal computers

NASA Technical Reports Server (NTRS)

Downing, John P.; Bauer, Frank H.; Thorpe, Christopher J.

1989-01-01

The ASTEC (Analysis and Simulation Tools for Engineering Controls) software is under development at Goddard Space Flight Center (GSFC). The design goal is to provide a wide selection of controls analysis tools at the personal computer level, as well as the capability to upload compute-intensive jobs to a mainframe or supercomputer. The project is a follow-on to the INCA (INteractive Controls Analysis) program that has been developed at GSFC over the past five years. While ASTEC makes use of the algorithms and expertise developed for the INCA program, the user interface was redesigned to take advantage of the capabilities of the personal computer. The design philosophy and the current capabilities of the ASTEC software are described.

Exploring JavaScript and ROOT technologies to create Web-based ATLAS analysis and monitoring tools

NASA Astrophysics Data System (ADS)

Sánchez Pineda, A.

2015-12-01

We explore the potential of current web applications to create online interfaces that allow the visualization, interaction and real cut-based physics analysis and monitoring of processes through a web browser. The project consists in the initial development of web- based and cloud computing services to allow students and researchers to perform fast and very useful cut-based analysis on a browser, reading and using real data and official Monte- Carlo simulations stored in ATLAS computing facilities. Several tools are considered: ROOT, JavaScript and HTML. Our study case is the current cut-based H → ZZ → llqq analysis of the ATLAS experiment. Preliminary but satisfactory results have been obtained online.

Utilizing Semantic Big Data for realizing a National-scale Infrastructure Vulnerability Analysis System

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

Chinthavali, Supriya; Shankar, Mallikarjun

Critical Infrastructure systems(CIs) such as energy, water, transportation and communication are highly interconnected and mutually dependent in complex ways. Robust modeling of CIs interconnections is crucial to identify vulnerabilities in the CIs. We present here a national-scale Infrastructure Vulnerability Analysis System (IVAS) vision leveraging Se- mantic Big Data (SBD) tools, Big Data, and Geographical Information Systems (GIS) tools. We survey existing ap- proaches on vulnerability analysis of critical infrastructures and discuss relevant systems and tools aligned with our vi- sion. Next, we present a generic system architecture and discuss challenges including: (1) Constructing and manag- ing a CI network-of-networks graph,more » (2) Performing analytic operations at scale, and (3) Interactive visualization of ana- lytic output to generate meaningful insights. We argue that this architecture acts as a baseline to realize a national-scale network based vulnerability analysis system.« less

Information Extraction for System-Software Safety Analysis: Calendar Year 2007 Year-End Report

NASA Technical Reports Server (NTRS)

Malin, Jane T.

2008-01-01

This annual report describes work to integrate a set of tools to support early model-based analysis of failures and hazards due to system-software interactions. The tools perform and assist analysts in the following tasks: 1) extract model parts from text for architecture and safety/hazard models; 2) combine the parts with library information to develop the models for visualization and analysis; 3) perform graph analysis on the models to identify possible paths from hazard sources to vulnerable entities and functions, in nominal and anomalous system-software configurations; 4) perform discrete-time-based simulation on the models to investigate scenarios where these paths may play a role in failures and mishaps; and 5) identify resulting candidate scenarios for software integration testing. This paper describes new challenges in a NASA abort system case, and enhancements made to develop the integrated tool set.

Analysis tools for discovering strong parity violation at hadron colliders

NASA Astrophysics Data System (ADS)

Backović, Mihailo; Ralston, John P.

2011-07-01

Several arguments suggest parity violation may be observable in high energy strong interactions. We introduce new analysis tools to describe the azimuthal dependence of multiparticle distributions, or “azimuthal flow.” Analysis uses the representations of the orthogonal group O(2) and dihedral groups DN necessary to define parity completely in two dimensions. Classification finds that collective angles used in event-by-event statistics represent inequivalent tensor observables that cannot generally be represented by a single “reaction plane.” Many new parity-violating observables exist that have never been measured, while many parity-conserving observables formerly lumped together are now distinguished. We use the concept of “event-shape sorting” to suggest separating right- and left-handed events, and we discuss the effects of transverse and longitudinal spin. The analysis tools are statistically robust, and can be applied equally to low or high multiplicity events at the Tevatron, RHIC or RHIC Spin, and the LHC.

Promoting Argumentation in Primary Science Contexts: An Analysis of Students' Interactions in Formal and Informal Learning Environments

ERIC Educational Resources Information Center

Simon, S.; Johnson, S; Cavell, S.; Parsons, T.

2012-01-01

The paper reports on the outcomes of a study that utilized a graphical tool, Digalo, to stimulate argumentative interactions in both school and informal learning settings. Digalo was developed in a European study to explore argumentation in a range of learning environments. The focus here is on the potential for using Digalo in promoting…

A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maize

PubMed Central

Musungu, Bryan; Bhatnagar, Deepak; Brown, Robert L.; Fakhoury, Ahmad M.; Geisler, Matt

2015-01-01

Interactomes are genome-wide roadmaps of protein-protein interactions. They have been produced for humans, yeast, the fruit fly, and Arabidopsis thaliana and have become invaluable tools for generating and testing hypotheses. A predicted interactome for Zea mays (PiZeaM) is presented here as an aid to the research community for this valuable crop species. PiZeaM was built using a proven method of interologs (interacting orthologs) that were identified using both one-to-one and many-to-many orthology between genomes of maize and reference species. Where both maize orthologs occurred for an experimentally determined interaction in the reference species, we predicted a likely interaction in maize. A total of 49,026 unique interactions for 6004 maize proteins were predicted. These interactions are enriched for processes that are evolutionarily conserved, but include many otherwise poorly annotated proteins in maize. The predicted maize interactions were further analyzed by comparing annotation of interacting proteins, including different layers of ontology. A map of pairwise gene co-expression was also generated and compared to predicted interactions. Two global subnetworks were constructed for highly conserved interactions. These subnetworks showed clear clustering of proteins by function. Another subnetwork was created for disease response using a bait and prey strategy to capture interacting partners for proteins that respond to other organisms. Closer examination of this subnetwork revealed the connectivity between biotic and abiotic hormone stress pathways. We believe PiZeaM will provide a useful tool for the prediction of protein function and analysis of pathways for Z. mays researchers and is presented in this paper as a reference tool for the exploration of protein interactions in maize. PMID:26089837

Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0

PubMed Central

Wang, Yan; DeLisi, Charles; Segrè, Daniel; Hu, Zhenjun

2016-01-01

The complexity of metabolic networks in microbial communities poses an unresolved visualization and interpretation challenge. We address this challenge in the newly expanded version of a software tool for the analysis of biological networks, VisANT 5.0. We focus in particular on facilitating the visual exploration of metabolic interaction between microbes in a community, e.g. as predicted by COMETS (Computation of Microbial Ecosystems in Time and Space), a dynamic stoichiometric modeling framework. Using VisANT’s unique metagraph implementation, we show how one can use VisANT 5.0 to explore different time-dependent ecosystem-level metabolic networks. In particular, we analyze the metabolic interaction network between two bacteria previously shown to display an obligate cross-feeding interdependency. In addition, we illustrate how a putative minimal gut microbiome community could be represented in our framework, making it possible to highlight interactions across multiple coexisting species. We envisage that the “symbiotic layout” of VisANT can be employed as a general tool for the analysis of metabolism in complex microbial communities as well as heterogeneous human tissues. VisANT is freely available at: http://visant.bu.edu and COMETS at http://comets.bu.edu. PMID:27081850

Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.

PubMed

Granger, Brian R; Chang, Yi-Chien; Wang, Yan; DeLisi, Charles; Segrè, Daniel; Hu, Zhenjun

2016-04-01

The complexity of metabolic networks in microbial communities poses an unresolved visualization and interpretation challenge. We address this challenge in the newly expanded version of a software tool for the analysis of biological networks, VisANT 5.0. We focus in particular on facilitating the visual exploration of metabolic interaction between microbes in a community, e.g. as predicted by COMETS (Computation of Microbial Ecosystems in Time and Space), a dynamic stoichiometric modeling framework. Using VisANT's unique metagraph implementation, we show how one can use VisANT 5.0 to explore different time-dependent ecosystem-level metabolic networks. In particular, we analyze the metabolic interaction network between two bacteria previously shown to display an obligate cross-feeding interdependency. In addition, we illustrate how a putative minimal gut microbiome community could be represented in our framework, making it possible to highlight interactions across multiple coexisting species. We envisage that the "symbiotic layout" of VisANT can be employed as a general tool for the analysis of metabolism in complex microbial communities as well as heterogeneous human tissues. VisANT is freely available at: http://visant.bu.edu and COMETS at http://comets.bu.edu.

BURRITO: An Interactive Multi-Omic Tool for Visualizing Taxa–Function Relationships in Microbiome Data

PubMed Central

McNally, Colin P.; Eng, Alexander; Noecker, Cecilia; Gagne-Maynard, William C.; Borenstein, Elhanan

2018-01-01

The abundance of both taxonomic groups and gene categories in microbiome samples can now be easily assayed via various sequencing technologies, and visualized using a variety of software tools. However, the assemblage of taxa in the microbiome and its gene content are clearly linked, and tools for visualizing the relationship between these two facets of microbiome composition and for facilitating exploratory analysis of their co-variation are lacking. Here we introduce BURRITO, a web tool for interactive visualization of microbiome multi-omic data with paired taxonomic and functional information. BURRITO simultaneously visualizes the taxonomic and functional compositions of multiple samples and dynamically highlights relationships between taxa and functions to capture the underlying structure of these data. Users can browse for taxa and functions of interest and interactively explore the share of each function attributed to each taxon across samples. BURRITO supports multiple input formats for taxonomic and metagenomic data, allows adjustment of data granularity, and can export generated visualizations as static publication-ready formatted figures. In this paper, we describe the functionality of BURRITO, and provide illustrative examples of its utility for visualizing various trends in the relationship between the composition of taxa and functions in complex microbiomes. PMID:29545787

ISAC: A tool for aeroservoelastic modeling and analysis

NASA Technical Reports Server (NTRS)

Adams, William M., Jr.; Hoadley, Sherwood Tiffany

1993-01-01

The capabilities of the Interaction of Structures, Aerodynamics, and Controls (ISAC) system of program modules is discussed. The major modeling, analysis, and data management components of ISAC are identified. Equations of motion are displayed for a Laplace-domain representation of the unsteady aerodynamic forces. Options for approximating a frequency-domain representation of unsteady aerodynamic forces with rational functions of the Laplace variable are shown. Linear time invariant state-space equations of motion that result are discussed. Model generation and analyses of stability and dynamic response characteristics are shown for an aeroelastic vehicle which illustrates some of the capabilities of ISAC as a modeling and analysis tool for aeroelastic applications.

Interactive 3D visualization for theoretical virtual observatories

NASA Astrophysics Data System (ADS)

Dykes, T.; Hassan, A.; Gheller, C.; Croton, D.; Krokos, M.

2018-06-01

Virtual observatories (VOs) are online hubs of scientific knowledge. They encompass a collection of platforms dedicated to the storage and dissemination of astronomical data, from simple data archives to e-research platforms offering advanced tools for data exploration and analysis. Whilst the more mature platforms within VOs primarily serve the observational community, there are also services fulfilling a similar role for theoretical data. Scientific visualization can be an effective tool for analysis and exploration of data sets made accessible through web platforms for theoretical data, which often contain spatial dimensions and properties inherently suitable for visualization via e.g. mock imaging in 2D or volume rendering in 3D. We analyse the current state of 3D visualization for big theoretical astronomical data sets through scientific web portals and virtual observatory services. We discuss some of the challenges for interactive 3D visualization and how it can augment the workflow of users in a virtual observatory context. Finally we showcase a lightweight client-server visualization tool for particle-based data sets, allowing quantitative visualization via data filtering, highlighting two example use cases within the Theoretical Astrophysical Observatory.

Young macaques (Macaca fascicularis) preferentially bias attention towards closer, older, and better tool users.

PubMed

Tan, Amanda W Y; Hemelrijk, Charlotte K; Malaivijitnond, Suchinda; Gumert, Michael D

2018-05-12

Examining how animals direct social learning during skill acquisition under natural conditions, generates data for examining hypotheses regarding how transmission biases influence cultural change in animal populations. We studied a population of macaques on Koram Island, Thailand, and examined model-based biases during interactions by unskilled individuals with tool-using group members. We first compared the prevalence of interactions (watching, obtaining food, object exploration) and proximity to tool users during interactions, in developing individuals (infants, juveniles) versus mature non-learners (adolescents, adults), to provide evidence that developing individuals are actively seeking information about tool use from social partners. All infants and juveniles, but only 49% of mature individuals carried out interacted with tool users. Macaques predominantly obtained food by scrounging or stealing, suggesting maximizing scrounging opportunities motivates interactions with tool users. However, while interactions by adults was limited to obtaining food, young macaques and particularly infants also watched tool users and explored objects, indicating additional interest in tool use itself. We then ran matrix correlations to identify interaction biases, and what attributes of tool users influenced these. Biases correlated with social affiliation, but macaques also preferentially targeted tool users that potentially increase scrounging and learning opportunities. Results suggest that social structure may constrain social learning, but the motivation to bias interactions towards tool users to maximize feeding opportunities may also socially modulate learning by facilitating close proximity to better tool users, and further interest in tool-use actions and materials, especially during development.

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

PubMed Central

Grapov, Dmitry; Newman, John W.

2012-01-01

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

DNAproDB: an interactive tool for structural analysis of DNA–protein complexes

PubMed Central

Sagendorf, Jared M.

2017-01-01

Abstract Many biological processes are mediated by complex interactions between DNA and proteins. Transcription factors, various polymerases, nucleases and histones recognize and bind DNA with different levels of binding specificity. To understand the physical mechanisms that allow proteins to recognize DNA and achieve their biological functions, it is important to analyze structures of DNA–protein complexes in detail. DNAproDB is a web-based interactive tool designed to help researchers study these complexes. DNAproDB provides an automated structure-processing pipeline that extracts structural features from DNA–protein complexes. The extracted features are organized in structured data files, which are easily parsed with any programming language or viewed in a browser. We processed a large number of DNA–protein complexes retrieved from the Protein Data Bank and created the DNAproDB database to store this data. Users can search the database by combining features of the DNA, protein or DNA–protein interactions at the interface. Additionally, users can upload their own structures for processing privately and securely. DNAproDB provides several interactive and customizable tools for creating visualizations of the DNA–protein interface at different levels of abstraction that can be exported as high quality figures. All functionality is documented and freely accessible at http://dnaprodb.usc.edu. PMID:28431131

SECIMTools: a suite of metabolomics data analysis tools.

PubMed

Kirpich, Alexander S; Ibarra, Miguel; Moskalenko, Oleksandr; Fear, Justin M; Gerken, Joseph; Mi, Xinlei; Ashrafi, Ali; Morse, Alison M; McIntyre, Lauren M

2018-04-20

Metabolomics has the promise to transform the area of personalized medicine with the rapid development of high throughput technology for untargeted analysis of metabolites. Open access, easy to use, analytic tools that are broadly accessible to the biological community need to be developed. While technology used in metabolomics varies, most metabolomics studies have a set of features identified. Galaxy is an open access platform that enables scientists at all levels to interact with big data. Galaxy promotes reproducibility by saving histories and enabling the sharing workflows among scientists. SECIMTools (SouthEast Center for Integrated Metabolomics) is a set of Python applications that are available both as standalone tools and wrapped for use in Galaxy. The suite includes a comprehensive set of quality control metrics (retention time window evaluation and various peak evaluation tools), visualization techniques (hierarchical cluster heatmap, principal component analysis, modular modularity clustering), basic statistical analysis methods (partial least squares - discriminant analysis, analysis of variance, t-test, Kruskal-Wallis non-parametric test), advanced classification methods (random forest, support vector machines), and advanced variable selection tools (least absolute shrinkage and selection operator LASSO and Elastic Net). SECIMTools leverages the Galaxy platform and enables integrated workflows for metabolomics data analysis made from building blocks designed for easy use and interpretability. Standard data formats and a set of utilities allow arbitrary linkages between tools to encourage novel workflow designs. The Galaxy framework enables future data integration for metabolomics studies with other omics data.

EEGLAB, SIFT, NFT, BCILAB, and ERICA: new tools for advanced EEG processing.

PubMed

Delorme, Arnaud; Mullen, Tim; Kothe, Christian; Akalin Acar, Zeynep; Bigdely-Shamlo, Nima; Vankov, Andrey; Makeig, Scott

2011-01-01

We describe a set of complementary EEG data collection and processing tools recently developed at the Swartz Center for Computational Neuroscience (SCCN) that connect to and extend the EEGLAB software environment, a freely available and readily extensible processing environment running under Matlab. The new tools include (1) a new and flexible EEGLAB STUDY design facility for framing and performing statistical analyses on data from multiple subjects; (2) a neuroelectromagnetic forward head modeling toolbox (NFT) for building realistic electrical head models from available data; (3) a source information flow toolbox (SIFT) for modeling ongoing or event-related effective connectivity between cortical areas; (4) a BCILAB toolbox for building online brain-computer interface (BCI) models from available data, and (5) an experimental real-time interactive control and analysis (ERICA) environment for real-time production and coordination of interactive, multimodal experiments.

Power-Production Diagnostic Tools for Low-Density Wind Farms with Applications to Wake Steering

NASA Astrophysics Data System (ADS)

Takle, E. S.; Herzmann, D.; Rajewski, D. A.; Lundquist, J. K.; Rhodes, M. E.

2016-12-01

Hansen (2011) provided guidelines for wind farm wake analysis with applications to "high density" wind farms (where average distance between turbines is less than ten times rotor diameter). For "low-density" (average distance greater than fifteen times rotor diameter) wind farms, or sections of wind farms we demonstrate simpler sorting and visualization tools that reveal wake interactions and opportunities for wind farm power prediction and wake steering. SCADA data from a segment of a large mid-continent wind farm, together with surface flux measurements and lidar data are subjected to analysis and visualization of wake interactions. A time-history animated visualization of a plan view of power level of individual turbines provides a quick analysis of wake interaction dynamics. Yaw-based sectoral histograms of enhancement/decline of wind speed and power from wind farm reference levels reveals angular width of wake interactions and identifies the turbine(s) responsible for the power reduction. Concurrent surface flux measurements within the wind farm allowed us to evaluate stability influence on wake loss. A one-season climatology is used to identify high-priority candidates for wake steering based on estimated power recovery. Typical clearing prices on the day-ahead market are used to estimate the added value of wake steering. Current research is exploring options for identifying candidate locations for wind farm "build-in" in existing low-density wind farms.

A femtoscopic correlation analysis tool using the Schrödinger equation (CATS)

NASA Astrophysics Data System (ADS)

Mihaylov, D. L.; Mantovani Sarti, V.; Arnold, O. W.; Fabbietti, L.; Hohlweger, B.; Mathis, A. M.

2018-05-01

We present a new analysis framework called "Correlation Analysis Tool using the Schrödinger equation" (CATS) which computes the two-particle femtoscopy correlation function C( k), with k being the relative momentum for the particle pair. Any local interaction potential and emission source function can be used as an input and the wave function is evaluated exactly. In this paper we present a study on the sensitivity of C( k) to the interaction potential for different particle pairs: p-p, p-Λ, K^-p, K^+-p, p-Ξ ^- and Λ- Λ. For the p-p Argonne v_{18} and Reid Soft-Core potentials have been tested. For the other pair systems we present results based on strong potentials obtained from effective Lagrangians such as χ EFT for p-Λ, Jülich models for K(\\bar{K})-N and Nijmegen models for Λ-Λ. For the p-Ξ^- pairs we employ the latest lattice results from the HAL QCD collaboration. Our detailed study of different interacting particle pairs as a function of the source size and different potentials shows that femtoscopic measurements can be exploited in order to constrain the final state interactions among hadrons. In particular, small collision systems of the order of 1 fm, as produced in pp collisions at the LHC, seem to provide a suitable environment for quantitative studies of this kind.

Robustness of meta-analyses in finding gene × environment interactions

PubMed Central

Shi, Gang; Nehorai, Arye

2017-01-01

Meta-analyses that synthesize statistical evidence across studies have become important analytical tools for genetic studies. Inspired by the success of genome-wide association studies of the genetic main effect, researchers are searching for gene × environment interactions. Confounders are routinely included in the genome-wide gene × environment interaction analysis as covariates; however, this does not control for any confounding effects on the results if covariate × environment interactions are present. We carried out simulation studies to evaluate the robustness to the covariate × environment confounder for meta-regression and joint meta-analysis, which are two commonly used meta-analysis methods for testing the gene × environment interaction or the genetic main effect and interaction jointly. Here we show that meta-regression is robust to the covariate × environment confounder while joint meta-analysis is subject to the confounding effect with inflated type I error rates. Given vast sample sizes employed in genome-wide gene × environment interaction studies, non-significant covariate × environment interactions at the study level could substantially elevate the type I error rate at the consortium level. When covariate × environment confounders are present, type I errors can be controlled in joint meta-analysis by including the covariate × environment terms in the analysis at the study level. Alternatively, meta-regression can be applied, which is robust to potential covariate × environment confounders. PMID:28362796

Experimenter's laboratory for visualized interactive science

NASA Technical Reports Server (NTRS)

Hansen, Elaine R.; Klemp, Marjorie K.; Lasater, Sally W.; Szczur, Marti R.; Klemp, Joseph B.

1992-01-01

The science activities of the 1990's will require the analysis of complex phenomena and large diverse sets of data. In order to meet these needs, we must take advantage of advanced user interaction techniques: modern user interface tools; visualization capabilities; affordable, high performance graphics workstations; and interoperable data standards and translator. To meet these needs, we propose to adopt and upgrade several existing tools and systems to create an experimenter's laboratory for visualized interactive science. Intuitive human-computer interaction techniques have already been developed and demonstrated at the University of Colorado. A Transportable Applications Executive (TAE+), developed at GSFC, is a powerful user interface tool for general purpose applications. A 3D visualization package developed by NCAR provides both color shaded surface displays and volumetric rendering in either index or true color. The Network Common Data Form (NetCDF) data access library developed by Unidata supports creation, access and sharing of scientific data in a form that is self-describing and network transparent. The combination and enhancement of these packages constitutes a powerful experimenter's laboratory capable of meeting key science needs of the 1990's. This proposal encompasses the work required to build and demonstrate this capability.

Experimenter's laboratory for visualized interactive science

NASA Technical Reports Server (NTRS)

Hansen, Elaine R.; Klemp, Marjorie K.; Lasater, Sally W.; Szczur, Marti R.; Klemp, Joseph B.

1993-01-01

The science activities of the 1990's will require the analysis of complex phenomena and large diverse sets of data. In order to meet these needs, we must take advantage of advanced user interaction techniques: modern user interface tools; visualization capabilities; affordable, high performance graphics workstations; and interoperatable data standards and translator. To meet these needs, we propose to adopt and upgrade several existing tools and systems to create an experimenter's laboratory for visualized interactive science. Intuitive human-computer interaction techniques have already been developed and demonstrated at the University of Colorado. A Transportable Applications Executive (TAE+), developed at GSFC, is a powerful user interface tool for general purpose applications. A 3D visualization package developed by NCAR provides both color-shaded surface displays and volumetric rendering in either index or true color. The Network Common Data Form (NetCDF) data access library developed by Unidata supports creation, access and sharing of scientific data in a form that is self-describing and network transparent. The combination and enhancement of these packages constitutes a powerful experimenter's laboratory capable of meeting key science needs of the 1990's. This proposal encompasses the work required to build and demonstrate this capability.

Research resource: Update and extension of a glycoprotein hormone receptors web application.

PubMed

Kreuchwig, Annika; Kleinau, Gunnar; Kreuchwig, Franziska; Worth, Catherine L; Krause, Gerd

2011-04-01

The SSFA-GPHR (Sequence-Structure-Function-Analysis of Glycoprotein Hormone Receptors) database provides a comprehensive set of mutation data for the glycoprotein hormone receptors (covering the lutropin, the FSH, and the TSH receptors). Moreover, it provides a platform for comparison and investigation of these homologous receptors and helps in understanding protein malfunctions associated with several diseases. Besides extending the data set (> 1100 mutations), the database has been completely redesigned and several novel features and analysis tools have been added to the web site. These tools allow the focused extraction of semiquantitative mutant data from the GPHR subtypes and different experimental approaches. Functional and structural data of the GPHRs are now linked interactively at the web interface, and new tools for data visualization (on three-dimensional protein structures) are provided. The interpretation of functional findings is supported by receptor morphings simulating intramolecular changes during the activation process, which thus help to trace the potential function of each amino acid and provide clues to the local structural environment, including potentially relocated spatial counterpart residues. Furthermore, double and triple mutations are newly included to allow the analysis of their functional effects related to their spatial interrelationship in structures or homology models. A new important feature is the search option and data visualization by interactive and user-defined snake-plots. These new tools allow fast and easy searches for specific functional data and thereby give deeper insights in the mechanisms of hormone binding, signal transduction, and signaling regulation. The web application "Sequence-Structure-Function-Analysis of GPHRs" is accessible on the internet at http://www.ssfa-gphr.de/.

[Designing a tool to describe drug interactions and adverse events for learning and clinical routine].

PubMed

Auzéric, M; Bellemère, J; Conort, O; Roubille, R; Allenet, B; Bedouch, P; Rose, F-X; Juste, M; Charpiat, B

2009-11-01

Pharmacists play an important role in prescription analysis. They are involved in therapeutic drug monitoring, particularly for drugs with a narrow therapeutic index, prevention and management of drug interactions, and may be called in to identify side effects and adverse events related to drug therapy. For the polymedicated patient, the medical file, the list of prescribed drugs and the history of their administration may be insufficient to adequately assign the responsibility of a given adverse effect to one or more drugs. Graphical representations can sometimes be useful to describe and clarify a sequence of events. In addition, as part of their academic course, students have many occasions to hear about "side effects" and "drug interactions". However, in the academic setting, there are few opportunities to observe the evolution and the consequences of these events. In the course of their hospital training, these students are required to perform patient follow-up for pharmacotherapeutic or educational purposes and to comment case reports to physicians. The aim of this paper is to present a tool facilitating the graphic display of drug interaction consequences and side effects. This tool can be a useful aid for causality assessment. It structures the students' training course and helps them better understand the commentaries pharmacists provide for physicians. Further development of this tool should contribute to the prevention of adverse drug events.

Understanding human uses and values in watershed analysis.

Treesearch

Roger D. Fight; Linda E. Kruger; Christopher Hansen-Murray; Arnold Holden; Dale Bays

2000-01-01

Watershed analysis is used as a tool to understand the functioning of aquatic and terrestrial ecosystem processes at the landscape scale and to assess opportunities to restore or improve those processes and associated watershed conditions. Assessing those opportunities correctly requires an understanding of how humans have interacted with the watershed in the past and...

Interactive visual analysis promotes exploration of long-term ecological data

Treesearch

T.N. Pham; J.A. Jones; R. Metoyer; F.J. Swanson; R.J. Pabst

2013-01-01

Long-term ecological data are crucial in helping ecologists understand ecosystem function and environmental change. Nevertheless, these kinds of data sets are difficult to analyze because they are usually large, multivariate, and spatiotemporal. Although existing analysis tools such as statistical methods and spreadsheet software permit rigorous tests of pre-conceived...

Blogging as a Tool for Intercultural Learning in a Telecollaborative Study

ERIC Educational Resources Information Center

Yang, Se Jeong

2016-01-01

This paper is based on an analysis of blog writings from an English-Korean telecollaborative project. This research found that rich intercultural interactions occur between Korean learners and English learners. Through a discursive analysis of the blog writings in which participants compared Korean and American cultures, this paper elucidates…

OpenMSI Arrayed Analysis Tools v2.0

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

BOWEN, BENJAMIN; RUEBEL, OLIVER; DE ROND, TRISTAN

2017-02-07

Mass spectrometry imaging (MSI) enables high-resolution spatial mapping of biomolecules in samples and is a valuable tool for the analysis of tissues from plants and animals, microbial interactions, high-throughput screening, drug metabolism, and a host of other applications. This is accomplished by desorbing molecules from the surface on spatially defined locations, using a laser or ion beam. These ions are analyzed by a mass spectrometry and collected into a MSI 'image', a dataset containing unique mass spectra from the sampled spatial locations. MSI is used in a diverse and increasing number of biological applications. The OpenMSI Arrayed Analysis Tool (OMAAT)more » is a new software method that addresses the challenges of analyzing spatially defined samples in large MSI datasets, by providing support for automatic sample position optimization and ion selection.« less

iCanPlot: Visual Exploration of High-Throughput Omics Data Using Interactive Canvas Plotting

PubMed Central

Sinha, Amit U.; Armstrong, Scott A.

2012-01-01

Increasing use of high throughput genomic scale assays requires effective visualization and analysis techniques to facilitate data interpretation. Moreover, existing tools often require programming skills, which discourages bench scientists from examining their own data. We have created iCanPlot, a compelling platform for visual data exploration based on the latest technologies. Using the recently adopted HTML5 Canvas element, we have developed a highly interactive tool to visualize tabular data and identify interesting patterns in an intuitive fashion without the need of any specialized computing skills. A module for geneset overlap analysis has been implemented on the Google App Engine platform: when the user selects a region of interest in the plot, the genes in the region are analyzed on the fly. The visualization and analysis are amalgamated for a seamless experience. Further, users can easily upload their data for analysis—which also makes it simple to share the analysis with collaborators. We illustrate the power of iCanPlot by showing an example of how it can be used to interpret histone modifications in the context of gene expression. PMID:22393367

VisRseq: R-based visual framework for analysis of sequencing data

PubMed Central

2015-01-01

Background Several tools have been developed to enable biologists to perform initial browsing and exploration of sequencing data. However the computational tool set for further analyses often requires significant computational expertise to use and many of the biologists with the knowledge needed to interpret these data must rely on programming experts. Results We present VisRseq, a framework for analysis of sequencing datasets that provides a computationally rich and accessible framework for integrative and interactive analyses without requiring programming expertise. We achieve this aim by providing R apps, which offer a semi-auto generated and unified graphical user interface for computational packages in R and repositories such as Bioconductor. To address the interactivity limitation inherent in R libraries, our framework includes several native apps that provide exploration and brushing operations as well as an integrated genome browser. The apps can be chained together to create more powerful analysis workflows. Conclusions To validate the usability of VisRseq for analysis of sequencing data, we present two case studies performed by our collaborators and report their workflow and insights. PMID:26328469

VisRseq: R-based visual framework for analysis of sequencing data.

PubMed

Younesy, Hamid; Möller, Torsten; Lorincz, Matthew C; Karimi, Mohammad M; Jones, Steven J M

2015-01-01

Several tools have been developed to enable biologists to perform initial browsing and exploration of sequencing data. However the computational tool set for further analyses often requires significant computational expertise to use and many of the biologists with the knowledge needed to interpret these data must rely on programming experts. We present VisRseq, a framework for analysis of sequencing datasets that provides a computationally rich and accessible framework for integrative and interactive analyses without requiring programming expertise. We achieve this aim by providing R apps, which offer a semi-auto generated and unified graphical user interface for computational packages in R and repositories such as Bioconductor. To address the interactivity limitation inherent in R libraries, our framework includes several native apps that provide exploration and brushing operations as well as an integrated genome browser. The apps can be chained together to create more powerful analysis workflows. To validate the usability of VisRseq for analysis of sequencing data, we present two case studies performed by our collaborators and report their workflow and insights.

Visualization techniques for computer network defense

NASA Astrophysics Data System (ADS)

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

2011-06-01

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

Development of a User Interface for a Regression Analysis Software Tool

NASA Technical Reports Server (NTRS)

Ulbrich, Norbert Manfred; Volden, Thomas R.

2010-01-01

An easy-to -use user interface was implemented in a highly automated regression analysis tool. The user interface was developed from the start to run on computers that use the Windows, Macintosh, Linux, or UNIX operating system. Many user interface features were specifically designed such that a novice or inexperienced user can apply the regression analysis tool with confidence. Therefore, the user interface s design minimizes interactive input from the user. In addition, reasonable default combinations are assigned to those analysis settings that influence the outcome of the regression analysis. These default combinations will lead to a successful regression analysis result for most experimental data sets. The user interface comes in two versions. The text user interface version is used for the ongoing development of the regression analysis tool. The official release of the regression analysis tool, on the other hand, has a graphical user interface that is more efficient to use. This graphical user interface displays all input file names, output file names, and analysis settings for a specific software application mode on a single screen which makes it easier to generate reliable analysis results and to perform input parameter studies. An object-oriented approach was used for the development of the graphical user interface. This choice keeps future software maintenance costs to a reasonable limit. Examples of both the text user interface and graphical user interface are discussed in order to illustrate the user interface s overall design approach.

NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks.

PubMed

Theodosiou, Theodosios; Efstathiou, Georgios; Papanikolaou, Nikolas; Kyrpides, Nikos C; Bagos, Pantelis G; Iliopoulos, Ioannis; Pavlopoulos, Georgios A

2017-07-14

Nowadays, due to the technological advances of high-throughput techniques, Systems Biology has seen a tremendous growth of data generation. With network analysis, looking at biological systems at a higher level in order to better understand a system, its topology and the relationships between its components is of a great importance. Gene expression, signal transduction, protein/chemical interactions, biomedical literature co-occurrences, are few of the examples captured in biological network representations where nodes represent certain bioentities and edges represent the connections between them. Today, many tools for network visualization and analysis are available. Nevertheless, most of them are standalone applications that often (i) burden users with computing and calculation time depending on the network's size and (ii) focus on handling, editing and exploring a network interactively. While such functionality is of great importance, limited efforts have been made towards the comparison of the topological analysis of multiple networks. Network Analysis Provider (NAP) is a comprehensive web tool to automate network profiling and intra/inter-network topology comparison. It is designed to bridge the gap between network analysis, statistics, graph theory and partially visualization in a user-friendly way. It is freely available and aims to become a very appealing tool for the broader community. It hosts a great plethora of topological analysis methods such as node and edge rankings. Few of its powerful characteristics are: its ability to enable easy profile comparisons across multiple networks, find their intersection and provide users with simplified, high quality plots of any of the offered topological characteristics against any other within the same network. It is written in R and Shiny, it is based on the igraph library and it is able to handle medium-scale weighted/unweighted, directed/undirected and bipartite graphs. NAP is available at http://bioinformatics.med.uoc.gr/NAP .

Advanced composites structural concepts and materials technologies for primary aircraft structures. Structural response and failure analysis: ISPAN modules users manual

NASA Technical Reports Server (NTRS)

Hairr, John W.; Huang, Jui-Ten; Ingram, J. Edward; Shah, Bharat M.

1992-01-01

The ISPAN Program (Interactive Stiffened Panel Analysis) is an interactive design tool that is intended to provide a means of performing simple and self contained preliminary analysis of aircraft primary structures made of composite materials. The program combines a series of modules with the finite element code DIAL as its backbone. Four ISPAN Modules were developed and are documented. These include: (1) flat stiffened panel; (2) curved stiffened panel; (3) flat tubular panel; and (4) curved geodesic panel. Users are instructed to input geometric and material properties, load information and types of analysis (linear, bifurcation buckling, or post-buckling) interactively. The program utilizing this information will generate finite element mesh and perform analysis. The output in the form of summary tables of stress or margins of safety, contour plots of loads or stress, and deflected shape plots may be generalized and used to evaluate specific design.

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

PubMed Central

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

2010-01-01

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

Causal inference in nonlinear systems: Granger causality versus time-delayed mutual information

NASA Astrophysics Data System (ADS)

Li, Songting; Xiao, Yanyang; Zhou, Douglas; Cai, David

2018-05-01

The Granger causality (GC) analysis has been extensively applied to infer causal interactions in dynamical systems arising from economy and finance, physics, bioinformatics, neuroscience, social science, and many other fields. In the presence of potential nonlinearity in these systems, the validity of the GC analysis in general is questionable. To illustrate this, here we first construct minimal nonlinear systems and show that the GC analysis fails to infer causal relations in these systems—it gives rise to all types of incorrect causal directions. In contrast, we show that the time-delayed mutual information (TDMI) analysis is able to successfully identify the direction of interactions underlying these nonlinear systems. We then apply both methods to neuroscience data collected from experiments and demonstrate that the TDMI analysis but not the GC analysis can identify the direction of interactions among neuronal signals. Our work exemplifies inference hazards in the GC analysis in nonlinear systems and suggests that the TDMI analysis can be an appropriate tool in such a case.

The Configuration Process of a Community of Practice in the Collective Text Editor

ERIC Educational Resources Information Center

Zank, Cláudia; Behar, Patricia Alejandra

2013-01-01

The various tools available on Web 2.0 enable the interactions in a Community of Practice (CoP) to be optimized and may discourage the participation of members. Thus, the choice of the tools is fundamental for the growth and maintenance of a CoP. With a focus on this and, from the analysis of the characteristics of the group and the activities…

The Multimedia Case as a Tool for Professional Development: An Analysis of Online and Face-to-Face Interaction among Mathematics Pre-Service Teachers, In-Service Teachers, Mathematicians, and Mathematics Teacher Educators

ERIC Educational Resources Information Center

McGraw, Rebecca; Lynch, Kathleen; Koc, Yusuf; Budak, Ayfer; Brown, Catherine A.

2007-01-01

In this study, we consider the potential of multimedia cases as tools for teacher professional development. Specifically, we examined online and face-to-face discussions that occurred within groups composed of pre-service mathematics teachers, in-service mathematics teachers, mathematicians, and mathematics teacher educators. Discussions within…

Graphical Acoustic Liner Design and Analysis Tool

NASA Technical Reports Server (NTRS)

Howerton, Brian M. (Inventor); Jones, Michael G. (Inventor)

2016-01-01

An interactive liner design and impedance modeling tool comprises software utilized to design acoustic liners for use in constrained spaces, both regularly and irregularly shaped. A graphical user interface allows the acoustic channel geometry to be drawn in a liner volume while the surface impedance calculations are updated and displayed in real-time. A one-dimensional transmission line model may be used as the basis for the impedance calculations.

Application priority of GSHP systems in the climate conditions of the United States

DOE PAGES

Cho, Soolyeon; Ray, Saurabh; Im, Piljae; ...

2017-05-15

Building energy-performance simulation programs are powerful tools for many aspects of feasibility studies regarding ground source heat pump (GSHP). However, the understanding of the limitations of the energy modelling programs, their capability of predicting energy performance early in the design process, and the complicated functionality of these programs makes the software programs harder to use and less practical. The interactive tool developed in this study seeks to provide analysis information in a straightforward manner that is inexpensive, convenient, and sophisticated. This tool uses an inclusive approach to assess the feasibility of GSHPs by prescreening critical factors such as climate conditions,more » ground temperatures, energy use, and cost savings. It is interactive and enables the user to do a feasibility analysis with a weighting factor for each feasibility criterion based on the user’s preference and interests. The application of the tool explains feasibility scores of 15 representative cities in various climatic conditions across the US. Results for commercial buildings show that the GSHP systems are more feasible in cold and dry, cool and humid, and very cold areas than warm and dry, very hot and humid, and mixed marine areas, and that most feasibility levels are located on good and moderate.« less

Quantitative analysis of small molecule-nucleic acid interactions with a biosensor surface and surface plasmon resonance detection.

PubMed

Liu, Yang; Wilson, W David

2010-01-01

Surface plasmon resonance (SPR) technology with biosensor surfaces has become a widely-used tool for the study of nucleic acid interactions without any labeling requirements. The method provides simultaneous kinetic and equilibrium characterization of the interactions of biomolecules as well as small molecule-biopolymer binding. SPR monitors molecular interactions in real time and provides significant advantages over optical or calorimetic methods for systems with strong binding coupled to small spectroscopic signals and/or reaction heats. A detailed and practical guide for nucleic acid interaction analysis using SPR-biosensor methods is presented. Details of the SPR technology and basic fundamentals are described with recommendations on the preparation of the SPR instrument, sensor chips, and samples, as well as extensive information on experimental design, quantitative and qualitative data analysis and presentation. A specific example of the interaction of a minor-groove-binding agent with DNA is evaluated by both kinetic and steady-state SPR methods to illustrate the technique. Since the molecules that bind cooperatively to specific DNA sequences are attractive for many applications, a cooperative small molecule-DNA interaction is also presented.

Toyz: A framework for scientific analysis of large datasets and astronomical images

NASA Astrophysics Data System (ADS)

Moolekamp, F.; Mamajek, E.

2015-11-01

As the size of images and data products derived from astronomical data continues to increase, new tools are needed to visualize and interact with that data in a meaningful way. Motivated by our own astronomical images taken with the Dark Energy Camera (DECam) we present Toyz, an open source Python package for viewing and analyzing images and data stored on a remote server or cluster. Users connect to the Toyz web application via a web browser, making it ​a convenient tool for students to visualize and interact with astronomical data without having to install any software on their local machines. In addition it provides researchers with an easy-to-use tool that allows them to browse the files on a server and quickly view very large images (>2 Gb) taken with DECam and other cameras with a large FOV and create their own visualization tools that can be added on as extensions to the default Toyz framework.

A CFD/CSD Interaction Methodology for Aircraft Wings

NASA Technical Reports Server (NTRS)

Bhardwaj, Manoj K.

1997-01-01

With advanced subsonic transports and military aircraft operating in the transonic regime, it is becoming important to determine the effects of the coupling between aerodynamic loads and elastic forces. Since aeroelastic effects can contribute significantly to the design of these aircraft, there is a strong need in the aerospace industry to predict these aero-structure interactions computationally. To perform static aeroelastic analysis in the transonic regime, high fidelity computational fluid dynamics (CFD) analysis tools must be used in conjunction with high fidelity computational structural fluid dynamics (CSD) analysis tools due to the nonlinear behavior of the aerodynamics in the transonic regime. There is also a need to be able to use a wide variety of CFD and CSD tools to predict these aeroelastic effects in the transonic regime. Because source codes are not always available, it is necessary to couple the CFD and CSD codes without alteration of the source codes. In this study, an aeroelastic coupling procedure is developed which will perform static aeroelastic analysis using any CFD and CSD code with little code integration. The aeroelastic coupling procedure is demonstrated on an F/A-18 Stabilator using NASTD (an in-house McDonnell Douglas CFD code) and NASTRAN. In addition, the Aeroelastic Research Wing (ARW-2) is used for demonstration of the aeroelastic coupling procedure by using ENSAERO (NASA Ames Research Center CFD code) and a finite element wing-box code (developed as part of this research).

The Habitable Zone Gallery 2.0: The Online Exoplanet System Visualization Suite

NASA Astrophysics Data System (ADS)

Chandler, C. O.; Kane, S. R.; Gelino, D. M.

2017-11-01

The Habitable Zone Gallery 2.0 provides new and improved visualization and data analysis tools to the exoplanet habitability community and beyond. Modules include interactive habitable zone plotting and downloadable 3D animations.

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

Granger, Brian R.; Chang, Yi -Chien; Wang, Yan

Here, the complexity of metabolic networks in microbial communities poses an unresolved visualization and interpretation challenge. We address this challenge in the newly expanded version of a software tool for the analysis of biological networks, VisANT 5.0. We focus in particular on facilitating the visual exploration of metabolic interaction between microbes in a community, e.g. as predicted by COMETS (Computation of Microbial Ecosystems in Time and Space), a dynamic stoichiometric modeling framework. Using VisANT's unique meta-graph implementation, we show how one can use VisANT 5.0 to explore different time-dependent ecosystem-level metabolic networks. In particular, we analyze the metabolic interaction networkmore » between two bacteria previously shown to display an obligate cross-feeding interdependency. In addition, we illustrate how a putative minimal gut microbiome community could be represented in our framework, making it possible to highlight interactions across multiple coexisting species. We envisage that the "symbiotic layout" of VisANT can be employed as a general tool for the analysis of metabolism in complex microbial communities as well as heterogeneous human tissues.« less

CollaborationViz: Interactive Visual Exploration of Biomedical Research Collaboration Networks

PubMed Central

Bian, Jiang; Xie, Mengjun; Hudson, Teresa J.; Eswaran, Hari; Brochhausen, Mathias; Hanna, Josh; Hogan, William R.

2014-01-01

Social network analysis (SNA) helps us understand patterns of interaction between social entities. A number of SNA studies have shed light on the characteristics of research collaboration networks (RCNs). Especially, in the Clinical Translational Science Award (CTSA) community, SNA provides us a set of effective tools to quantitatively assess research collaborations and the impact of CTSA. However, descriptive network statistics are difficult for non-experts to understand. In this article, we present our experiences of building meaningful network visualizations to facilitate a series of visual analysis tasks. The basis of our design is multidimensional, visual aggregation of network dynamics. The resulting visualizations can help uncover hidden structures in the networks, elicit new observations of the network dynamics, compare different investigators and investigator groups, determine critical factors to the network evolution, and help direct further analyses. We applied our visualization techniques to explore the biomedical RCNs at the University of Arkansas for Medical Sciences – a CTSA institution. And, we created CollaborationViz, an open-source visual analytical tool to help network researchers and administration apprehend the network dynamics of research collaborations through interactive visualization. PMID:25405477

Using Interactive Data Visualizations for Exploratory Analysis in Undergraduate Genomics Coursework: Field Study Findings and Guidelines

NASA Astrophysics Data System (ADS)

Mirel, Barbara; Kumar, Anuj; Nong, Paige; Su, Gang; Meng, Fan

2016-02-01

Life scientists increasingly use visual analytics to explore large data sets and generate hypotheses. Undergraduate biology majors should be learning these same methods. Yet visual analytics is one of the most underdeveloped areas of undergraduate biology education. This study sought to determine the feasibility of undergraduate biology majors conducting exploratory analysis using the same interactive data visualizations as practicing scientists. We examined 22 upper level undergraduates in a genomics course as they engaged in a case-based inquiry with an interactive heat map. We qualitatively and quantitatively analyzed students' visual analytic behaviors, reasoning and outcomes to identify student performance patterns, commonly shared efficiencies and task completion. We analyzed students' successes and difficulties in applying knowledge and skills relevant to the visual analytics case and related gaps in knowledge and skill to associated tool designs. Findings show that undergraduate engagement in visual analytics is feasible and could be further strengthened through tool usability improvements. We identify these improvements. We speculate, as well, on instructional considerations that our findings suggested may also enhance visual analytics in case-based modules.

Using Interactive Data Visualizations for Exploratory Analysis in Undergraduate Genomics Coursework: Field Study Findings and Guidelines

PubMed Central

Kumar, Anuj; Nong, Paige; Su, Gang; Meng, Fan

2016-01-01

Life scientists increasingly use visual analytics to explore large data sets and generate hypotheses. Undergraduate biology majors should be learning these same methods. Yet visual analytics is one of the most underdeveloped areas of undergraduate biology education. This study sought to determine the feasibility of undergraduate biology majors conducting exploratory analysis using the same interactive data visualizations as practicing scientists. We examined 22 upper level undergraduates in a genomics course as they engaged in a case-based inquiry with an interactive heat map. We qualitatively and quantitatively analyzed students’ visual analytic behaviors, reasoning and outcomes to identify student performance patterns, commonly shared efficiencies and task completion. We analyzed students’ successes and difficulties in applying knowledge and skills relevant to the visual analytics case and related gaps in knowledge and skill to associated tool designs. Findings show that undergraduate engagement in visual analytics is feasible and could be further strengthened through tool usability improvements. We identify these improvements. We speculate, as well, on instructional considerations that our findings suggested may also enhance visual analytics in case-based modules. PMID:26877625

Interactive Visualization of Computational Fluid Dynamics using Mosaic

NASA Technical Reports Server (NTRS)

Clucas, Jean; Watson, Velvin; Chancellor, Marisa K. (Technical Monitor)

1994-01-01

The Web provides new Methods for accessing Information world-wide, but the current text-and-pictures approach neither utilizes all the Web's possibilities not provides for its limitations. While the inclusion of pictures and animations in a paper communicates more effectively than text alone, It Is essentially an extension of the concept of "publication." Also, as use of the Web increases putting images and animations online will quickly load even the "Information Superhighway." We need to find forms of communication that take advantage of the special nature of the Web. This paper presents one approach: the use of the Internet and the Mosaic interface for data sharing and collaborative analysis. We will describe (and In the presentation, demonstrate) our approach: using FAST (Flow Analysis Software Toolkit), a scientific visualization package, as a data viewer and interactive tool called from MOSAIC. Our intent is to stimulate the development of other tools that utilize the unique nature of electronic communication.

Investigation into the computerized data bases of the Employment and Training Administration. Regional Management Information System Project (RMIS) report on second-year activities, 1975--1976

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

Postle, W.; Heckman, B.

1977-01-01

The research and development project discussed was aimed at creating the necessary computer system for the rapid retrieval, analysis, and display of information to meet the individual and nonroutine needs of the Department of Labor's Employment and Training Administration and the general public. The major objective was to demonstrate that it was both feasible and practical to organize data that are currently available and to provide planning and management information in a much more usable and timely fashion than previously possible. Fast access to data with a system which is easy to use was an important project goal. Programs weremore » written to analyze and display data by means of bar, pie, and line charts, etc. Although prototypical interactive retrieval, analysis, and report formation tools have been developed, further research and development of interactive tools is required. (RWR)« less

VESPA: Software to Facilitate Genomic Annotation of Prokaryotic Organisms Through Integration of Proteomic and Transcriptomic Data

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

Peterson, Elena S.; McCue, Lee Ann; Rutledge, Alexandra C.

2012-04-25

Visual Exploration and Statistics to Promote Annotation (VESPA) is an interactive visual analysis software tool that facilitates the discovery of structural mis-annotations in prokaryotic genomes. VESPA integrates high-throughput peptide-centric proteomics data and oligo-centric or RNA-Seq transcriptomics data into a genomic context. The data may be interrogated via visual analysis across multiple levels of genomic resolution, linked searches, exports and interaction with BLAST to rapidly identify location of interest within the genome and evaluate potential mis-annotations.

Applied Graph-Mining Algorithms to Study Biomolecular Interaction Networks

PubMed Central

2014-01-01

Protein-protein interaction (PPI) networks carry vital information on the organization of molecular interactions in cellular systems. The identification of functionally relevant modules in PPI networks is one of the most important applications of biological network analysis. Computational analysis is becoming an indispensable tool to understand large-scale biomolecular interaction networks. Several types of computational methods have been developed and employed for the analysis of PPI networks. Of these computational methods, graph comparison and module detection are the two most commonly used strategies. This review summarizes current literature on graph kernel and graph alignment methods for graph comparison strategies, as well as module detection approaches including seed-and-extend, hierarchical clustering, optimization-based, probabilistic, and frequent subgraph methods. Herein, we provide a comprehensive review of the major algorithms employed under each theme, including our recently published frequent subgraph method, for detecting functional modules commonly shared across multiple cancer PPI networks. PMID:24800226

A unified approach to computer analysis and modeling of spacecraft environmental interactions

NASA Technical Reports Server (NTRS)

Katz, I.; Mandell, M. J.; Cassidy, J. J.

1986-01-01

A new, coordinated, unified approach to the development of spacecraft plasma interaction models is proposed. The objective is to eliminate the unnecessary duplicative work in order to allow researchers to concentrate on the scientific aspects. By streamlining the developmental process, the interchange between theories and experimentalists is enhanced, and the transfer of technology to the spacecraft engineering community is faster. This approach is called the UNIfied Spacecraft Interaction Model (UNISIM). UNISIM is a coordinated system of software, hardware, and specifications. It is a tool for modeling and analyzing spacecraft interactions. It will be used to design experiments, to interpret results of experiments, and to aid in future spacecraft design. It breaks a Spacecraft Ineraction analysis into several modules. Each module will perform an analysis for some physical process, using phenomenology and algorithms which are well documented and have been subject to review. This system and its characteristics are discussed.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.

PubMed

McGibbon, Robert T; Beauchamp, Kyle A; Harrigan, Matthew P; Klein, Christoph; Swails, Jason M; Hernández, Carlos X; Schwantes, Christian R; Wang, Lee-Ping; Lane, Thomas J; Pande, Vijay S

2015-10-20

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

PubMed Central

McGibbon, Robert T.; Beauchamp, Kyle A.; Harrigan, Matthew P.; Klein, Christoph; Swails, Jason M.; Hernández, Carlos X.; Schwantes, Christian R.; Wang, Lee-Ping; Lane, Thomas J.; Pande, Vijay S.

2015-01-01

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. PMID:26488642

Chronodes: Interactive Multifocus Exploration of Event Sequences

PubMed Central

POLACK, PETER J.; CHEN, SHANG-TSE; KAHNG, MINSUK; DE BARBARO, KAYA; BASOLE, RAHUL; SHARMIN, MOUSHUMI; CHAU, DUEN HORNG

2018-01-01

The advent of mobile health (mHealth) technologies challenges the capabilities of current visualizations, interactive tools, and algorithms. We present Chronodes, an interactive system that unifies data mining and human-centric visualization techniques to support explorative analysis of longitudinal mHealth data. Chronodes extracts and visualizes frequent event sequences that reveal chronological patterns across multiple participant timelines of mHealth data. It then combines novel interaction and visualization techniques to enable multifocus event sequence analysis, which allows health researchers to interactively define, explore, and compare groups of participant behaviors using event sequence combinations. Through summarizing insights gained from a pilot study with 20 behavioral and biomedical health experts, we discuss Chronodes’s efficacy and potential impact in the mHealth domain. Ultimately, we outline important open challenges in mHealth, and offer recommendations and design guidelines for future research. PMID:29515937

Irena : tool suite for modeling and analysis of small-angle scattering.

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

Ilavsky, J.; Jemian, P.

2009-04-01

Irena, a tool suite for analysis of both X-ray and neutron small-angle scattering (SAS) data within the commercial Igor Pro application, brings together a comprehensive suite of tools useful for investigations in materials science, physics, chemistry, polymer science and other fields. In addition to Guinier and Porod fits, the suite combines a variety of advanced SAS data evaluation tools for the modeling of size distribution in the dilute limit using maximum entropy and other methods, dilute limit small-angle scattering from multiple non-interacting populations of scatterers, the pair-distance distribution function, a unified fit, the Debye-Bueche model, the reflectivity (X-ray and neutron)more » using Parratt's formalism, and small-angle diffraction. There are also a number of support tools, such as a data import/export tool supporting a broad sampling of common data formats, a data modification tool, a presentation-quality graphics tool optimized for small-angle scattering data, and a neutron and X-ray scattering contrast calculator. These tools are brought together into one suite with consistent interfaces and functionality. The suite allows robust automated note recording and saving of parameters during export.« less

What's Next in Complex Networks? Capturing the Concept of Attacking Play in Invasive Team Sports.

PubMed

Ramos, João; Lopes, Rui J; Araújo, Duarte

2018-01-01

The evolution of performance analysis within sports sciences is tied to technology development and practitioner demands. However, how individual and collective patterns self-organize and interact in invasive team sports remains elusive. Social network analysis has been recently proposed to resolve some aspects of this problem, and has proven successful in capturing collective features resulting from the interactions between team members as well as a powerful communication tool. Despite these advances, some fundamental team sports concepts such as an attacking play have not been properly captured by the more common applications of social network analysis to team sports performance. In this article, we propose a novel approach to team sports performance centered on sport concepts, namely that of an attacking play. Network theory and tools including temporal and bipartite or multilayered networks were used to capture this concept. We put forward eight questions directly related to team performance to discuss how common pitfalls in the use of network tools for capturing sports concepts can be avoided. Some answers are advanced in an attempt to be more precise in the description of team dynamics and to uncover other metrics directly applied to sport concepts, such as the structure and dynamics of attacking plays. Finally, we propose that, at this stage of knowledge, it may be advantageous to build up from fundamental sport concepts toward complex network theory and tools, and not the other way around.

CoryneBase: Corynebacterium Genomic Resources and Analysis Tools at Your Fingertips

PubMed Central

Tan, Mui Fern; Jakubovics, Nick S.; Wee, Wei Yee; Mutha, Naresh V. R.; Wong, Guat Jah; Ang, Mia Yang; Yazdi, Amir Hessam; Choo, Siew Woh

2014-01-01

Corynebacteria are used for a wide variety of industrial purposes but some species are associated with human diseases. With increasing number of corynebacterial genomes having been sequenced, comparative analysis of these strains may provide better understanding of their biology, phylogeny, virulence and taxonomy that may lead to the discoveries of beneficial industrial strains or contribute to better management of diseases. To facilitate the ongoing research of corynebacteria, a specialized central repository and analysis platform for the corynebacterial research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. Here we present CoryneBase, a genomic database for Corynebacterium with diverse functionality for the analysis of genomes aimed to provide: (1) annotated genome sequences of Corynebacterium where 165,918 coding sequences and 4,180 RNAs can be found in 27 species; (2) access to comprehensive Corynebacterium data through the use of advanced web technologies for interactive web interfaces; and (3) advanced bioinformatic analysis tools consisting of standard BLAST for homology search, VFDB BLAST for sequence homology search against the Virulence Factor Database (VFDB), Pairwise Genome Comparison (PGC) tool for comparative genomic analysis, and a newly designed Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomic analysis. CoryneBase offers the access of a range of Corynebacterium genomic resources as well as analysis tools for comparative genomics and pathogenomics. It is publicly available at http://corynebacterium.um.edu.my/. PMID:24466021

TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes

PubMed Central

Lerat, Emmanuelle; Fablet, Marie; Modolo, Laurent; Lopez-Maestre, Hélène

2017-01-01

Abstract Over recent decades, substantial efforts have been made to understand the interactions between host genomes and transposable elements (TEs). The impact of TEs on the regulation of host genes is well known, with TEs acting as platforms of regulatory sequences. Nevertheless, due to their repetitive nature it is considerably hard to integrate TE analysis into genome-wide studies. Here, we developed a specific tool for the analysis of TE expression: TEtools. This tool takes into account the TE sequence diversity of the genome, it can be applied to unannotated or unassembled genomes and is freely available under the GPL3 (https://github.com/l-modolo/TEtools). TEtools performs the mapping of RNA-seq data obtained from classical mRNAs or small RNAs onto a list of TE sequences and performs differential expression analyses with statistical relevance. Using this tool, we analyzed TE expression from five Drosophila wild-type strains. Our data show for the first time that the activity of TEs is strictly linked to the activity of the genes implicated in the piwi-interacting RNA biogenesis and therefore fits an arms race scenario between TE sequences and host control genes. PMID:28204592

A descriptive framework for country-level analysis of health care financing arrangements.

PubMed

Kutzin, J

2001-06-01

Health financing policies are marked by confusion between policy tools and policy objectives, especially in low and middle income countries. This paper attempts to address this problem by providing a conceptual framework that is driven by the normative objective of enhancing the 'insurance function' (access to needed care without financial impoverishment) of health care systems. The framework is proposed as a tool for descriptive analysis of the key functions, policies, and interactions within an existing health care system, and equally as a tool to assist the identification and preliminary assessment of policy options. The aim is to help to clarify the policy levers that are available to enhance the insurance function for the population as efficiently as possible, given the 'starting point' of a country's existing institutional and organizational arrangements. Analysis of health care financing systems using this framework highlights the interactions of various policies and the need for a coherent package of coordinated reforms, rather than a focus on particular organizational forms of 'health insurance'. The content of each main health care system function (revenue collection, pooling of funds, purchasing of services, provision of services) and the market structure with which the implementation of each is organized are found to be particularly important, as are policies with respect to the benefit package and user fees.

Spark and HPC for High Energy Physics Data Analyses

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

Sehrish, Saba; Kowalkowski, Jim; Paterno, Marc

A full High Energy Physics (HEP) data analysis is divided into multiple data reduction phases. Processing within these phases is extremely time consuming, therefore intermediate results are stored in files held in mass storage systems and referenced as part of large datasets. This processing model limits what can be done with interactive data analytics. Growth in size and complexity of experimental datasets, along with emerging big data tools are beginning to cause changes to the traditional ways of doing data analyses. Use of big data tools for HEP analysis looks promising, mainly because extremely large HEP datasets can be representedmore » and held in memory across a system, and accessed interactively by encoding an analysis using highlevel programming abstractions. The mainstream tools, however, are not designed for scientific computing or for exploiting the available HPC platform features. We use an example from the Compact Muon Solenoid (CMS) experiment at the Large Hadron Collider (LHC) in Geneva, Switzerland. The LHC is the highest energy particle collider in the world. Our use case focuses on searching for new types of elementary particles explaining Dark Matter in the universe. We use HDF5 as our input data format, and Spark to implement the use case. We show the benefits and limitations of using Spark with HDF5 on Edison at NERSC.« less

Taylor Dispersion Analysis as a promising tool for assessment of peptide-peptide interactions.

PubMed

Høgstedt, Ulrich B; Schwach, Grégoire; van de Weert, Marco; Østergaard, Jesper

2016-10-10

Protein-protein and peptide-peptide (self-)interactions are of key importance in understanding the physiochemical behavior of proteins and peptides in solution. However, due to the small size of peptide molecules, characterization of these interactions is more challenging than for proteins. In this work, we show that protein-protein and peptide-peptide interactions can advantageously be investigated by measurement of the diffusion coefficient using Taylor Dispersion Analysis. Through comparison to Dynamic Light Scattering it was shown that Taylor Dispersion Analysis is well suited for the characterization of protein-protein interactions of solutions of α-lactalbumin and human serum albumin. The peptide-peptide interactions of three selected peptides were then investigated in a concentration range spanning from 0.5mg/ml up to 80mg/ml using Taylor Dispersion Analysis. The peptide-peptide interactions determination indicated that multibody interactions significantly affect the PPIs at concentration levels above 25mg/ml for the two charged peptides. Relative viscosity measurements, performed using the capillary based setup applied for Taylor Dispersion Analysis, showed that the viscosity of the peptide solutions increased with concentration. Our results indicate that a viscosity difference between run buffer and sample in Taylor Dispersion Analysis may result in overestimation of the measured diffusion coefficient. Thus, Taylor Dispersion Analysis provides a practical, but as yet primarily qualitative, approach to assessment of the colloidal stability of both peptide and protein formulations. Copyright © 2016 Elsevier B.V. All rights reserved.

Interactive graphic editing tools in bioluminescent imaging simulation

NASA Astrophysics Data System (ADS)

Li, Hui; Tian, Jie; Luo, Jie; Wang, Ge; Cong, Wenxiang

2005-04-01

It is a challenging task to accurately describe complicated biological tissues and bioluminescent sources in bioluminescent imaging simulation. Several graphic editing tools have been developed to efficiently model each part of the bioluminescent simulation environment and to interactively correct or improve the initial models of anatomical structures or bioluminescent sources. There are two major types of graphic editing tools: non-interactive tools and interactive tools. Geometric building blocks (i.e. regular geometric graphics and superquadrics) are applied as non-interactive tools. To a certain extent, complicated anatomical structures and bioluminescent sources can be approximately modeled by combining a sufficient large number of geometric building blocks with Boolean operators. However, those models are too simple to describe the local features and fine changes in 2D/3D irregular contours. Therefore, interactive graphic editing tools have been developed to facilitate the local modifications of any initial surface model. With initial models composed of geometric building blocks, interactive spline mode is applied to conveniently perform dragging and compressing operations on 2D/3D local surface of biological tissues and bioluminescent sources inside the region/volume of interest. Several applications of the interactive graphic editing tools will be presented in this article.

An interactive environment for the analysis of large Earth observation and model data sets

NASA Technical Reports Server (NTRS)

Bowman, Kenneth P.; Walsh, John E.; Wilhelmson, Robert B.

1993-01-01

We propose to develop an interactive environment for the analysis of large Earth science observation and model data sets. We will use a standard scientific data storage format and a large capacity (greater than 20 GB) optical disk system for data management; develop libraries for coordinate transformation and regridding of data sets; modify the NCSA X Image and X DataSlice software for typical Earth observation data sets by including map transformations and missing data handling; develop analysis tools for common mathematical and statistical operations; integrate the components described above into a system for the analysis and comparison of observations and model results; and distribute software and documentation to the scientific community.

An interactive environment for the analysis of large Earth observation and model data sets

NASA Technical Reports Server (NTRS)

Bowman, Kenneth P.; Walsh, John E.; Wilhelmson, Robert B.

1992-01-01

We propose to develop an interactive environment for the analysis of large Earth science observation and model data sets. We will use a standard scientific data storage format and a large capacity (greater than 20 GB) optical disk system for data management; develop libraries for coordinate transformation and regridding of data sets; modify the NCSA X Image and X Data Slice software for typical Earth observation data sets by including map transformations and missing data handling; develop analysis tools for common mathematical and statistical operations; integrate the components described above into a system for the analysis and comparison of observations and model results; and distribute software and documentation to the scientific community.

High-Performance Data Analysis Tools for Sun-Earth Connection Missions

NASA Technical Reports Server (NTRS)

Messmer, Peter

2011-01-01

The data analysis tool of choice for many Sun-Earth Connection missions is the Interactive Data Language (IDL) by ITT VIS. The increasing amount of data produced by these missions and the increasing complexity of image processing algorithms requires access to higher computing power. Parallel computing is a cost-effective way to increase the speed of computation, but algorithms oftentimes have to be modified to take advantage of parallel systems. Enhancing IDL to work on clusters gives scientists access to increased performance in a familiar programming environment. The goal of this project was to enable IDL applications to benefit from both computing clusters as well as graphics processing units (GPUs) for accelerating data analysis tasks. The tool suite developed in this project enables scientists now to solve demanding data analysis problems in IDL that previously required specialized software, and it allows them to be solved orders of magnitude faster than on conventional PCs. The tool suite consists of three components: (1) TaskDL, a software tool that simplifies the creation and management of task farms, collections of tasks that can be processed independently and require only small amounts of data communication; (2) mpiDL, a tool that allows IDL developers to use the Message Passing Interface (MPI) inside IDL for problems that require large amounts of data to be exchanged among multiple processors; and (3) GPULib, a tool that simplifies the use of GPUs as mathematical coprocessors from within IDL. mpiDL is unique in its support for the full MPI standard and its support of a broad range of MPI implementations. GPULib is unique in enabling users to take advantage of an inexpensive piece of hardware, possibly already installed in their computer, and achieve orders of magnitude faster execution time for numerically complex algorithms. TaskDL enables the simple setup and management of task farms on compute clusters. The products developed in this project have the potential to interact, so one can build a cluster of PCs, each equipped with a GPU, and use mpiDL to communicate between the nodes and GPULib to accelerate the computations on each node.

Creating a cultural analysis tool for the implementation of Ontario's civil mental health laws.

PubMed

Dhand, Ruby

2016-01-01

Ethno-racial people with mental health disabilities experience multiple inequities and differential outcomes when interacting with Ontario's civil mental health laws. Given the increasing multi-racial population in Ontario, there is a need to develop mechanisms to address these intersecting issues. Other countries that have created evaluative tools for mental health legislation include the United Kingdom and Australia. Australia's Rights Analysis Tool, the United Kingdom's Race Equality Impact Assessment, the Scottish Recovery Tool, and the World Health Organization's Mental Health and Human Rights checklist are examples of evaluative tools developed for mental health legislation. Such a tool does not exist in Canada, let alone in Ontario specifically. Thus, this study developed a Cultural Analysis Tool (CAT) consisting of specific and meaningful thematic questions that can be used by practitioners when addressing issues of culture and equity for ethno-racial people with mental health disabilities interacting with Ontario's civil mental health laws. It is hoped that the CAT, and the research underlying its development, will enable practitioners to critically question whether cultural and intersecting concerns are being appropriately addressed within an ethno-racial client's case and, furthermore, how equitable outcomes can be achieved. This article describes and analyzes the methodology, research and qualitative data used to develop the CAT. It then presents and examines the CAT itself. The qualitative data was drawn from thirty-five semi-structured interviews with seven members of each of the following groups: (1) ethno-racial people with mental health disabilities including in-patients and ex-patients, (2) lawyers who practice in the area of mental health law, (3) health care professionals including psychiatrists, nurses and social workers, (4) service providers such as front-line case workers at mental health agencies and (5) adjudicators, government advisors and academics. After an analysis of these data, the CAT's questions were refined through an expert review (involving the qualitative technique of member-checking) using three focus groups comprised of ethno-racial people with mental health disabilities, mental health lawyers and service providers and health care professionals. Copyright © 2016 Elsevier Ltd. All rights reserved.

Bayesian inference of interaction properties of noisy dynamical systems with time-varying coupling: capabilities and limitations

NASA Astrophysics Data System (ADS)

Wilting, Jens; Lehnertz, Klaus

2015-08-01

We investigate a recently published analysis framework based on Bayesian inference for the time-resolved characterization of interaction properties of noisy, coupled dynamical systems. It promises wide applicability and a better time resolution than well-established methods. At the example of representative model systems, we show that the analysis framework has the same weaknesses as previous methods, particularly when investigating interacting, structurally different non-linear oscillators. We also inspect the tracking of time-varying interaction properties and propose a further modification of the algorithm, which improves the reliability of obtained results. We exemplarily investigate the suitability of this algorithm to infer strength and direction of interactions between various regions of the human brain during an epileptic seizure. Within the limitations of the applicability of this analysis tool, we show that the modified algorithm indeed allows a better time resolution through Bayesian inference when compared to previous methods based on least square fits.

Anvil Forecast Tool in the Advanced Weather Interactive Processing System (AWIPS)

NASA Technical Reports Server (NTRS)

Barrett, Joe H., III; Hood, Doris

2009-01-01

Launch Weather Officers (LWOs) from the 45th Weather Squadron (45 WS) and forecasters from the National Weather Service (NWS) Spaceflight Meteorology Group (SMG) have identified anvil forecasting as one of their most challenging tasks when predicting the probability of violating the Lightning Launch Commit Criteria (LLCC) (Krider et al. 2006; Space Shuttle Flight Rules (FR), NASA/JSC 2004)). As a result, the Applied Meteorology Unit (AMU) developed a tool that creates an anvil threat corridor graphic that can be overlaid on satellite imagery using the Meteorological Interactive Data Display System (MIDDS, Short and Wheeler, 2002). The tool helps forecasters estimate the locations of thunderstorm anvils at one, two, and three hours into the future. It has been used extensively in launch and landing operations by both the 45 WS and SMG. The Advanced Weather Interactive Processing System (AWIPS) is now used along with MIDDS for weather analysis and display at SMG. In Phase I of this task, SMG tasked the AMU to transition the tool from MIDDS to AWIPS (Barrett et aI., 2007). For Phase II, SMG requested the AMU make the Anvil Forecast Tool in AWIPS more configurable by creating the capability to read model gridded data from user-defined model files instead of hard-coded files. An NWS local AWIPS application called AGRID was used to accomplish this. In addition, SMG needed to be able to define the pressure levels for the model data, instead of hard-coding the bottom level as 300 mb and the top level as 150 mb. This paper describes the initial development of the Anvil Forecast Tool for MIDDS, followed by the migration of the tool to AWIPS in Phase I. It then gives a detailed presentation of the Phase II improvements to the AWIPS tool.

Engaging stakeholders: lessons from the use of participatory tools for improving maternal and child care health services.

PubMed

Ekirapa-Kiracho, Elizabeth; Ghosh, Upasona; Brahmachari, Rittika; Paina, Ligia

2017-12-28

Effective stakeholder engagement in research and implementation is important for improving the development and implementation of policies and programmes. A varied number of tools have been employed for stakeholder engagement. In this paper, we discuss two participatory methods for engaging with stakeholders - participatory social network analysis (PSNA) and participatory impact pathways analysis (PIPA). Based on our experience, we derive lessons about when and how to apply these tools. This paper was informed by a review of project reports and documents in addition to reflection meetings with the researchers who applied the tools. These reports were synthesised and used to make thick descriptions of the applications of the methods while highlighting key lessons. PSNA and PIPA both allowed a deep understanding of how the system actors are interconnected and how they influence maternal health and maternal healthcare services. The findings from the PSNA provided guidance on how stakeholders of a health system are interconnected and how they can stimulate more positive interaction between the stakeholders by exposing existing gaps. The PIPA meeting enabled the participants to envision how they could expand their networks and resources by mentally thinking about the contributions that they could make to the project. The processes that were considered critical for successful application of the tools and achievement of outcomes included training of facilitators, language used during the facilitation, the number of times the tool is applied, length of the tools, pretesting of the tools, and use of quantitative and qualitative methods. Whereas both tools allowed the identification of stakeholders and provided a deeper understanding of the type of networks and dynamics within the network, PIPA had a higher potential for promoting collaboration between stakeholders, likely due to allowing interaction between them. Additionally, it was implemented within a participatory action research project. PIPA also allowed participatory evaluation of the project from the perspective of the community. This paper provides lessons about the use of these participatory tools.

Multicriteria decision analysis: Overview and implications for environmental decision making

USGS Publications Warehouse

Hermans, Caroline M.; Erickson, Jon D.; Erickson, Jon D.; Messner, Frank; Ring, Irene

2007-01-01

Environmental decision making involving multiple stakeholders can benefit from the use of a formal process to structure stakeholder interactions, leading to more successful outcomes than traditional discursive decision processes. There are many tools available to handle complex decision making. Here we illustrate the use of a multicriteria decision analysis (MCDA) outranking tool (PROMETHEE) to facilitate decision making at the watershed scale, involving multiple stakeholders, multiple criteria, and multiple objectives. We compare various MCDA methods and their theoretical underpinnings, examining methods that most realistically model complex decision problems in ways that are understandable and transparent to stakeholders.

Tracing social interactions in Pleistocene North America via 3D model analysis of stone tool asymmetry

PubMed Central

Sholts, Sabrina B.; Gingerich, Joseph A. M.; Schlager, Stefan; Stanford, Dennis J.

2017-01-01

Stone tools, often the sole remnant of prehistoric hunter-gatherer behavior, are frequently used as evidence of ancient human mobility, resource use, and environmental adaptation. In North America, studies of morphological variation in projectile points have provided important insights into migration and interactions of human groups as early as 12–13 kya. Using new approaches to 3D imaging and morphometric analysis, we here quantify bifacial asymmetry among early North American projectile point styles to better understand changes in knapping technique and cultural transmission. Using a sample of 100 fluted bifaces of Clovis and post-Clovis styles in the eastern United States ca. 13,100–9,000 cal BP (i.e., Clovis, Debert-Vail, Bull Brook, Michaud-Neponset/Barnes, and Crowfield), we employed two different approaches for statistical shape analysis: our previously presented method for analysis of 2D flake scar contours, and a new approach for 3D surface analysis using spherical harmonics (SPHARM). Whereas bifacial asymmetry in point shape does not vary significantly across this stylistic sequence, our measure of asymmetric flake scar patterning shows temporal variation that may signify the beginning of regionalization among early New World colonists. PMID:28700598

An activity theory perspective of how scenario-based simulations support learning: a descriptive analysis.

PubMed

Battista, Alexis

2017-01-01

The dominant frameworks for describing how simulations support learning emphasize increasing access to structured practice and the provision of feedback which are commonly associated with skills-based simulations. By contrast, studies examining student participants' experiences during scenario-based simulations suggest that learning may also occur through participation. However, studies directly examining student participation during scenario-based simulations are limited. This study examined the types of activities student participants engaged in during scenario-based simulations and then analyzed their patterns of activity to consider how participation may support learning. Drawing from Engeström's first-, second-, and third-generation activity systems analysis, an in-depth descriptive analysis was conducted. The study drew from multiple qualitative methods, namely narrative, video, and activity systems analysis, to examine student participants' activities and interaction patterns across four video-recorded simulations depicting common motivations for using scenario-based simulations (e.g., communication, critical patient management). The activity systems analysis revealed that student participants' activities encompassed three clinically relevant categories, including (a) use of physical clinical tools and artifacts, (b) social interactions, and (c) performance of structured interventions. Role assignment influenced participants' activities and the complexity of their engagement. Importantly, participants made sense of the clinical situation presented in the scenario by reflexively linking these three activities together. Specifically, student participants performed structured interventions, relying upon the use of physical tools, clinical artifacts, and social interactions together with interactions between students, standardized patients, and other simulated participants to achieve their goals. When multiple student participants were present, such as in a team-based scenario, they distributed the workload to achieve their goals. The findings suggest that student participants learned as they engaged in these scenario-based simulations when they worked to make sense of the patient's clinical presentation. The findings may provide insight into how student participants' meaning-making efforts are mediated by the cultural artifacts (e.g., physical clinical tools) they access, the social interactions they engage in, the structured interventions they perform, and the roles they are assigned. The findings also highlight the complex and emergent properties of scenario-based simulations as well as how activities are nested. Implications for learning, instructional design, and assessment are discussed.

Safety Analysis of FMS/CTAS Interactions During Aircraft Arrivals

NASA Technical Reports Server (NTRS)

Leveson, Nancy G.

1998-01-01

This grant funded research on human-computer interaction design and analysis techniques, using future ATC environments as a testbed. The basic approach was to model the nominal behavior of both the automated and human procedures and then to apply safety analysis techniques to these models. Our previous modeling language, RSML, had been used to specify the system requirements for TCAS II for the FAA. Using the lessons learned from this experience, we designed a new modeling language that (among other things) incorporates features to assist in designing less error-prone human-computer interactions and interfaces and in detecting potential HCI problems, such as mode confusion. The new language, SpecTRM-RL, uses "intent" abstractions, based on Rasmussen's abstraction hierarchy, and includes both informal (English and graphical) specifications and formal, executable models for specifying various aspects of the system. One of the goals for our language was to highlight the system modes and mode changes to assist in identifying the potential for mode confusion. Three published papers resulted from this research. The first builds on the work of Degani on mode confusion to identify aspects of the system design that could lead to potential hazards. We defined and modeled modes differently than Degani and also defined design criteria for SpecTRM-RL models. Our design criteria include the Degani criteria but extend them to include more potential problems. In a second paper, Leveson and Palmer showed how the criteria for indirect mode transitions could be applied to a mode confusion problem found in several ASRS reports for the MD-88. In addition, we defined a visual task modeling language that can be used by system designers to model human-computer interaction. The visual models can be translated into SpecTRM-RL models, and then the SpecTRM-RL suite of analysis tools can be used to perform formal and informal safety analyses on the task model in isolation or integrated with the rest of the modeled system. We had hoped to be able to apply these modeling languages and analysis tools to a TAP air/ground trajectory negotiation scenario, but the development of the tools took more time than we anticipated.

gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations.

PubMed

Serçinoglu, Onur; Ozbek, Pemra

2018-05-25

Atomistic molecular dynamics (MD) simulations generate a wealth of information related to the dynamics of proteins. If properly analyzed, this information can lead to new insights regarding protein function and assist wet-lab experiments. Aiming to identify interactions between individual amino acid residues and the role played by each in the context of MD simulations, we present a stand-alone software called gRINN (get Residue Interaction eNergies and Networks). gRINN features graphical user interfaces (GUIs) and a command-line interface for generating and analyzing pairwise residue interaction energies and energy correlations from protein MD simulation trajectories. gRINN utilizes the features of NAMD or GROMACS MD simulation packages and automatizes the steps necessary to extract residue-residue interaction energies from user-supplied simulation trajectories, greatly simplifying the analysis for the end-user. A GUI, including an embedded molecular viewer, is provided for visualization of interaction energy time-series, distributions, an interaction energy matrix, interaction energy correlations and a residue correlation matrix. gRINN additionally offers construction and analysis of Protein Energy Networks, providing residue-based metrics such as degrees, betweenness-centralities, closeness centralities as well as shortest path analysis. gRINN is free and open to all users without login requirement at http://grinn.readthedocs.io.

Lunar and Vesta Web Portals

NASA Astrophysics Data System (ADS)

Law, E.; JPL Luna Mapping; Modeling Project Team

2015-06-01

The Lunar Mapping and Modeling Project offers Lunar Mapping and Modeling Portal (http://lmmp.nasa.gov) and Vesta Trek Portal (http://vestatrek.jpl.nasa.gov) providing interactive visualization and analysis tools to enable users to access mapped Lunar and Vesta data products.

miRNet - dissecting miRNA-target interactions and functional associations through network-based visual analysis

PubMed Central

Fan, Yannan; Siklenka, Keith; Arora, Simran K.; Ribeiro, Paula; Kimmins, Sarah; Xia, Jianguo

2016-01-01

MicroRNAs (miRNAs) can regulate nearly all biological processes and their dysregulation is implicated in various complex diseases and pathological conditions. Recent years have seen a growing number of functional studies of miRNAs using high-throughput experimental technologies, which have produced a large amount of high-quality data regarding miRNA target genes and their interactions with small molecules, long non-coding RNAs, epigenetic modifiers, disease associations, etc. These rich sets of information have enabled the creation of comprehensive networks linking miRNAs with various biologically important entities to shed light on their collective functions and regulatory mechanisms. Here, we introduce miRNet, an easy-to-use web-based tool that offers statistical, visual and network-based approaches to help researchers understand miRNAs functions and regulatory mechanisms. The key features of miRNet include: (i) a comprehensive knowledge base integrating high-quality miRNA-target interaction data from 11 databases; (ii) support for differential expression analysis of data from microarray, RNA-seq and quantitative PCR; (iii) implementation of a flexible interface for data filtering, refinement and customization during network creation; (iv) a powerful fully featured network visualization system coupled with enrichment analysis. miRNet offers a comprehensive tool suite to enable statistical analysis and functional interpretation of various data generated from current miRNA studies. miRNet is freely available at http://www.mirnet.ca. PMID:27105848

Efficient simulation of press hardening process through integrated structural and CFD analyses

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

Palaniswamy, Hariharasudhan; Mondalek, Pamela; Wronski, Maciek

Press hardened steel parts are being increasingly used in automotive structures for their higher strength to meet safety standards while reducing vehicle weight to improve fuel consumption. However, manufacturing of sheet metal parts by press hardening process to achieve desired properties is extremely challenging as it involves complex interaction of plastic deformation, metallurgical change, thermal distribution, and fluid flow. Numerical simulation is critical for successful design of the process and to understand the interaction among the numerous process parameters to control the press hardening process in order to consistently achieve desired part properties. Until now there has been no integratedmore » commercial software solution that can efficiently model the complete process from forming of the blank, heat transfer between the blank and tool, microstructure evolution in the blank, heat loss from tool to the fluid that flows through water channels in the tools. In this study, a numerical solution based on Altair HyperWorks® product suite involving RADIOSS®, a non-linear finite element based structural analysis solver and AcuSolve®, an incompressible fluid flow solver based on Galerkin Least Square Finite Element Method have been utilized to develop an efficient solution for complete press hardening process design and analysis. RADIOSS is used to handle the plastic deformation, heat transfer between the blank and tool, and microstructure evolution in the blank during cooling. While AcuSolve is used to efficiently model heat loss from tool to the fluid that flows through water channels in the tools. The approach is demonstrated through some case studies.« less

Beyond Logging of Fingertip Actions: Analysis of Collaborative Learning Using Multiple Sources of Data

ERIC Educational Resources Information Center

Avouris, N.; Fiotakis, G.; Kahrimanis, G.; Margaritis, M.; Komis, V.

2007-01-01

In this article, we discuss key requirements for collecting behavioural data concerning technology-supported collaborative learning activities. It is argued that the common practice of analysis of computer generated log files of user interactions with software tools is not enough for building a thorough view of the activity. Instead, more…

A Graphics System for Pole-Zero Map Analysis.

ERIC Educational Resources Information Center

Beyer, William Fred, III

Computer scientists have developed an interactive, graphical display system for pole-zero map analysis. They designed it for use as an educational tool in teaching introductory courses in automatic control systems. The facilities allow the user to specify a control system and an input function in the form of a pole-zero map and then examine the…

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

T.Rex is used to explore tabular data sets containing up to ten million records to help rapidly understand a previously unknown data set. Analysis can quickly identify patterns of interest and the records and fields that capture those patterns. T.Rex contains a growing set of deep analytical tools and supports robust export capabilities that selected data can be incorporated into to other specialized tools for further analysis. T.Rex is flexible in ingesting different types and formats of data, allowing the user to interactively experiment and perform trial and error guesses on the structure of the data; and also has amore » variety of linked visual analytic tools that enable exploration of the data to find relevant content, relationships among content, trends within the content, and capture knowledge about the content. Finally, T.Rex has a rich export capability, to extract relevant subsets of a larger data source, to further analyze their data in other analytic tools.« less

T.Rex

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

2016-06-08

T.Rex is used to explore tabular data sets containing up to ten million records to help rapidly understand a previously unknown data set. Analysis can quickly identify patterns of interest and the records and fields that capture those patterns. T.Rex contains a growing set of deep analytical tools and supports robust export capabilities that selected data can be incorporated into to other specialized tools for further analysis. T.Rex is flexible in ingesting different types and formats of data, allowing the user to interactively experiment and perform trial and error guesses on the structure of the data; and also has amore » variety of linked visual analytic tools that enable exploration of the data to find relevant content, relationships among content, trends within the content, and capture knowledge about the content. Finally, T.Rex has a rich export capability, to extract relevant subsets of a larger data source, to further analyze their data in other analytic tools.« less

Large High Resolution Displays for Co-Located Collaborative Sensemaking: Display Usage and Territoriality

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

Bradel, Lauren; Endert, Alexander; Koch, Kristen

2013-08-01

Large, high-resolution vertical displays carry the potential to increase the accuracy of collaborative sensemaking, given correctly designed visual analytics tools. From an exploratory user study using a fictional textual intelligence analysis task, we investigated how users interact with the display to construct spatial schemas and externalize information, as well as how they establish shared and private territories. We investigated the space management strategies of users partitioned by type of tool philosophy followed (visualization- or text-centric). We classified the types of territorial behavior exhibited in terms of how the users interacted with information on the display (integrated or independent workspaces). Next,more » we examined how territorial behavior impacted the common ground between the pairs of users. Finally, we offer design suggestions for building future co-located collaborative visual analytics tools specifically for use on large, high-resolution vertical displays.« less

EEGLAB, SIFT, NFT, BCILAB, and ERICA: New Tools for Advanced EEG Processing

PubMed Central

Delorme, Arnaud; Mullen, Tim; Kothe, Christian; Akalin Acar, Zeynep; Bigdely-Shamlo, Nima; Vankov, Andrey; Makeig, Scott

2011-01-01

We describe a set of complementary EEG data collection and processing tools recently developed at the Swartz Center for Computational Neuroscience (SCCN) that connect to and extend the EEGLAB software environment, a freely available and readily extensible processing environment running under Matlab. The new tools include (1) a new and flexible EEGLAB STUDY design facility for framing and performing statistical analyses on data from multiple subjects; (2) a neuroelectromagnetic forward head modeling toolbox (NFT) for building realistic electrical head models from available data; (3) a source information flow toolbox (SIFT) for modeling ongoing or event-related effective connectivity between cortical areas; (4) a BCILAB toolbox for building online brain-computer interface (BCI) models from available data, and (5) an experimental real-time interactive control and analysis (ERICA) environment for real-time production and coordination of interactive, multimodal experiments. PMID:21687590

Combining biophysical methods for the analysis of protein complex stoichiometry and affinity in SEDPHAT

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

Zhao, Huaying, E-mail: zhaoh3@mail.nih.gov; Schuck, Peter, E-mail: zhaoh3@mail.nih.gov

2015-01-01

Global multi-method analysis for protein interactions (GMMA) can increase the precision and complexity of binding studies for the determination of the stoichiometry, affinity and cooperativity of multi-site interactions. The principles and recent developments of biophysical solution methods implemented for GMMA in the software SEDPHAT are reviewed, their complementarity in GMMA is described and a new GMMA simulation tool set in SEDPHAT is presented. Reversible macromolecular interactions are ubiquitous in signal transduction pathways, often forming dynamic multi-protein complexes with three or more components. Multivalent binding and cooperativity in these complexes are often key motifs of their biological mechanisms. Traditional solution biophysicalmore » techniques for characterizing the binding and cooperativity are very limited in the number of states that can be resolved. A global multi-method analysis (GMMA) approach has recently been introduced that can leverage the strengths and the different observables of different techniques to improve the accuracy of the resulting binding parameters and to facilitate the study of multi-component systems and multi-site interactions. Here, GMMA is described in the software SEDPHAT for the analysis of data from isothermal titration calorimetry, surface plasmon resonance or other biosensing, analytical ultracentrifugation, fluorescence anisotropy and various other spectroscopic and thermodynamic techniques. The basic principles of these techniques are reviewed and recent advances in view of their particular strengths in the context of GMMA are described. Furthermore, a new feature in SEDPHAT is introduced for the simulation of multi-method data. In combination with specific statistical tools for GMMA in SEDPHAT, simulations can be a valuable step in the experimental design.« less

Advanced space system analysis software. Technical, user, and programmer guide

NASA Technical Reports Server (NTRS)

Farrell, C. E.; Zimbelman, H. F.

1981-01-01

The LASS computer program provides a tool for interactive preliminary and conceptual design of LSS. Eight program modules were developed, including four automated model geometry generators, an associated mass properties module, an appendage synthesizer module, an rf analysis module, and an orbital transfer analysis module. The existing rigid body controls analysis module was modified to permit analysis of effects of solar pressure on orbital performance. A description of each module, user instructions, and programmer information are included.

NMR studies of protein-nucleic acid interactions.

PubMed

Varani, Gabriele; Chen, Yu; Leeper, Thomas C

2004-01-01

Protein-DNA and protein-RNA complexes play key functional roles in every living organism. Therefore, the elucidation of their structure and dynamics is an important goal of structural and molecular biology. Nuclear magnetic resonance (NMR) studies of protein and nucleic acid complexes have common features with studies of protein-protein complexes: the interaction surfaces between the molecules must be carefully delineated, the relative orientation of the two species needs to be accurately and precisely determined, and close intermolecular contacts defined by nuclear Overhauser effects (NOEs) must be obtained. However, differences in NMR properties (e.g., chemical shifts) and biosynthetic pathways for sample productions generate important differences. Chemical shift differences between the protein and nucleic acid resonances can aid the NMR structure determination process; however, the relatively limited dispersion of the RNA ribose resonances makes the process of assigning intermolecular NOEs more difficult. The analysis of the resulting structures requires computational tools unique to nucleic acid interactions. This chapter summarizes the most important elements of the structure determination by NMR of protein-nucleic acid complexes and their analysis. The main emphasis is on recent developments (e.g., residual dipolar couplings and new Web-based analysis tools) that have facilitated NMR studies of these complexes and expanded the type of biological problems to which NMR techniques of structural elucidation can now be applied.

3Drefine: an interactive web server for efficient protein structure refinement

PubMed Central

Bhattacharya, Debswapna; Nowotny, Jackson; Cao, Renzhi; Cheng, Jianlin

2016-01-01

3Drefine is an interactive web server for consistent and computationally efficient protein structure refinement with the capability to perform web-based statistical and visual analysis. The 3Drefine refinement protocol utilizes iterative optimization of hydrogen bonding network combined with atomic-level energy minimization on the optimized model using a composite physics and knowledge-based force fields for efficient protein structure refinement. The method has been extensively evaluated on blind CASP experiments as well as on large-scale and diverse benchmark datasets and exhibits consistent improvement over the initial structure in both global and local structural quality measures. The 3Drefine web server allows for convenient protein structure refinement through a text or file input submission, email notification, provided example submission and is freely available without any registration requirement. The server also provides comprehensive analysis of submissions through various energy and statistical feedback and interactive visualization of multiple refined models through the JSmol applet that is equipped with numerous protein model analysis tools. The web server has been extensively tested and used by many users. As a result, the 3Drefine web server conveniently provides a useful tool easily accessible to the community. The 3Drefine web server has been made publicly available at the URL: http://sysbio.rnet.missouri.edu/3Drefine/. PMID:27131371

A gene network bioinformatics analysis for pemphigoid autoimmune blistering diseases.

PubMed

Barone, Antonio; Toti, Paolo; Giuca, Maria Rita; Derchi, Giacomo; Covani, Ugo

2015-07-01

In this theoretical study, a text mining search and clustering analysis of data related to genes potentially involved in human pemphigoid autoimmune blistering diseases (PAIBD) was performed using web tools to create a gene/protein interaction network. The Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database was employed to identify a final set of PAIBD-involved genes and to calculate the overall significant interactions among genes: for each gene, the weighted number of links, or WNL, was registered and a clustering procedure was performed using the WNL analysis. Genes were ranked in class (leader, B, C, D and so on, up to orphans). An ontological analysis was performed for the set of 'leader' genes. Using the above-mentioned data network, 115 genes represented the final set; leader genes numbered 7 (intercellular adhesion molecule 1 (ICAM-1), interferon gamma (IFNG), interleukin (IL)-2, IL-4, IL-6, IL-8 and tumour necrosis factor (TNF)), class B genes were 13, whereas the orphans were 24. The ontological analysis attested that the molecular action was focused on extracellular space and cell surface, whereas the activation and regulation of the immunity system was widely involved. Despite the limited knowledge of the present pathologic phenomenon, attested by the presence of 24 genes revealing no protein-protein direct or indirect interactions, the network showed significant pathways gathered in several subgroups: cellular components, molecular functions, biological processes and the pathologic phenomenon obtained from the Kyoto Encyclopaedia of Genes and Genomes (KEGG) database. The molecular basis for PAIBD was summarised and expanded, which will perhaps give researchers promising directions for the identification of new therapeutic targets.

PyHLA: tests for the association between HLA alleles and diseases.

PubMed

Fan, Yanhui; Song, You-Qiang

2017-02-06

Recently, several tools have been designed for human leukocyte antigen (HLA) typing using single nucleotide polymorphism (SNP) array and next-generation sequencing (NGS) data. These tools provide high-throughput and cost-effective approaches for identifying HLA types. Therefore, tools for downstream association analysis are highly desirable. Although several tools have been designed for multi-allelic marker association analysis, they were designed only for microsatellite markers and do not scale well with increasing data volumes, or they were designed for large-scale data but provided a limited number of tests. We have developed a Python package called PyHLA, which implements several methods for HLA association analysis, to fill the gap. PyHLA is a tailor-made, easy to use, and flexible tool designed specifically for the association analysis of the HLA types imputed from genome-wide genotyping and NGS data. PyHLA provides functions for association analysis, zygosity tests, and interaction tests between HLA alleles and diseases. Monte Carlo permutation and several methods for multiple testing corrections have also been implemented. PyHLA provides a convenient and powerful tool for HLA analysis. Existing methods have been integrated and desired methods have been added in PyHLA. Furthermore, PyHLA is applicable to small and large sample sizes and can finish the analysis in a timely manner on a personal computer with different platforms. PyHLA is implemented in Python. PyHLA is a free, open source software distributed under the GPLv2 license. The source code, tutorial, and examples are available at https://github.com/felixfan/PyHLA.

The visible touch: in planta visualization of protein-protein interactions by fluorophore-based methods

PubMed Central

Bhat, Riyaz A; Lahaye, Thomas; Panstruga, Ralph

2006-01-01

Non-invasive fluorophore-based protein interaction assays like fluorescence resonance energy transfer (FRET) and bimolecular fluorescence complementation (BiFC, also referred to as "split YFP") have been proven invaluable tools to study protein-protein interactions in living cells. Both methods are now frequently used in the plant sciences and are likely to develop into standard techniques for the identification, verification and in-depth analysis of polypeptide interactions. In this review, we address the individual strengths and weaknesses of both approaches and provide an outlook about new directions and possible future developments for both techniques. PMID:16800872

DiscoverySpace: an interactive data analysis application

PubMed Central

Robertson, Neil; Oveisi-Fordorei, Mehrdad; Zuyderduyn, Scott D; Varhol, Richard J; Fjell, Christopher; Marra, Marco; Jones, Steven; Siddiqui, Asim

2007-01-01

DiscoverySpace is a graphical application for bioinformatics data analysis. Users can seamlessly traverse references between biological databases and draw together annotations in an intuitive tabular interface. Datasets can be compared using a suite of novel tools to aid in the identification of significant patterns. DiscoverySpace is of broad utility and its particular strength is in the analysis of serial analysis of gene expression (SAGE) data. The application is freely available online. PMID:17210078

Incorporating INTERACT II Clinical Decision Support Tools into Nursing Home Health Information Technology

PubMed Central

Handler, Steven M.; Sharkey, Siobhan S.; Hudak, Sandra; Ouslander, Joseph G.

2012-01-01

A substantial reduction in hospitalization rates has been associated with the implementation of the Interventions to Reduce Acute Care Transfers (INTERACT) quality improvement intervention using the accompanying paper-based clinical practice tools (INTERACT II). There is significant potential to further increase the impact of INTERACT by integrating INTERACT II tools into nursing home (NH) health information technology (HIT) via standalone or integrated clinical decision support (CDS) systems. This article highlights the process of translating INTERACT II tools from paper to NH HIT. The authors believe that widespread dissemination and integration of INTERACT II CDS tools into various NH HIT products could lead to sustainable improvement in resident and clinician process and outcome measures, including enhanced interclinician communication and a reduction in potentially avoidable hospitalizations. PMID:22267955

Virtual Interactomics of Proteins from Biochemical Standpoint

PubMed Central

Kubrycht, Jaroslav; Sigler, Karel; Souček, Pavel

2012-01-01

Virtual interactomics represents a rapidly developing scientific area on the boundary line of bioinformatics and interactomics. Protein-related virtual interactomics then comprises instrumental tools for prediction, simulation, and networking of the majority of interactions important for structural and individual reproduction, differentiation, recognition, signaling, regulation, and metabolic pathways of cells and organisms. Here, we describe the main areas of virtual protein interactomics, that is, structurally based comparative analysis and prediction of functionally important interacting sites, mimotope-assisted and combined epitope prediction, molecular (protein) docking studies, and investigation of protein interaction networks. Detailed information about some interesting methodological approaches and online accessible programs or databases is displayed in our tables. Considerable part of the text deals with the searches for common conserved or functionally convergent protein regions and subgraphs of conserved interaction networks, new outstanding trends and clinically interesting results. In agreement with the presented data and relationships, virtual interactomic tools improve our scientific knowledge, help us to formulate working hypotheses, and they frequently also mediate variously important in silico simulations. PMID:22928109

Effectiveness of interactive, online games in learning neuroscience and students' perception of the games as learning tools. A pre-experimental study.

PubMed

Thompson, Marilyn E; Ford, Ruth; Webster, Andrew

2011-01-01

Neurological concepts applicable to a doctorate in occupational therapy are often challenging to comprehend, and students are required to demonstrate critical reasoning skills beyond simply recalling the information. To achieve this, various learning and teaching strategies are used, including the use of technology in the classroom. The availability of technology in academic settings has allowed for diverse and active teaching approaches. This includes videos, web-based instruction, and interactive online games. In this quantitative pre-experimental analysis, the learning and retention of neuroscience concepts by 30 occupational therapy doctoral students, who participated in an interactive online learning experience, were assessed. The results suggest that student use of these tools may enhance their learning of neuroscience. Furthermore, the students felt that the sites were appropriate, beneficial to them, and easy to use. Thus, the use of online, interactive neuroscience games may be effective in reinforcing lecture materials. This needs to be further assessed in a larger sample size.

Interactive visualization of numerical simulation results: A tool for mission planning and data analysis

NASA Technical Reports Server (NTRS)

Berchem, J.; Raeder, J.; Walker, R. J.; Ashour-Abdalla, M.

1995-01-01

We report on the development of an interactive system for visualizing and analyzing numerical simulation results. This system is based on visualization modules which use the Application Visualization System (AVS) and the NCAR graphics packages. Examples from recent simulations are presented to illustrate how these modules can be used for displaying and manipulating simulation results to facilitate their comparison with phenomenological model results and observations.

NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology.

PubMed

Wei, Qing; Khan, Ishita K; Ding, Ziyun; Yerneni, Satwica; Kihara, Daisuke

2017-03-20

The number of genomics and proteomics experiments is growing rapidly, producing an ever-increasing amount of data that are awaiting functional interpretation. A number of function prediction algorithms were developed and improved to enable fast and automatic function annotation. With the well-defined structure and manual curation, Gene Ontology (GO) is the most frequently used vocabulary for representing gene functions. To understand relationship and similarity between GO annotations of genes, it is important to have a convenient pipeline that quantifies and visualizes the GO function analyses in a systematic fashion. NaviGO is a web-based tool for interactive visualization, retrieval, and computation of functional similarity and associations of GO terms and genes. Similarity of GO terms and gene functions is quantified with six different scores including protein-protein interaction and context based association scores we have developed in our previous works. Interactive navigation of the GO function space provides intuitive and effective real-time visualization of functional groupings of GO terms and genes as well as statistical analysis of enriched functions. We developed NaviGO, which visualizes and analyses functional similarity and associations of GO terms and genes. The NaviGO webserver is freely available at: http://kiharalab.org/web/navigo .

User-Driven Sampling Strategies in Image Exploitation

DOE PAGES

Harvey, Neal R.; Porter, Reid B.

2013-12-23

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

User-driven sampling strategies in image exploitation

NASA Astrophysics Data System (ADS)

Harvey, Neal; Porter, Reid

2013-12-01

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

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.

PubMed

Peterson, Elena S; McCue, Lee Ann; Schrimpe-Rutledge, Alexandra C; Jensen, Jeffrey L; Walker, Hyunjoo; Kobold, Markus A; Webb, Samantha R; Payne, Samuel H; Ansong, Charles; Adkins, Joshua N; Cannon, William R; Webb-Robertson, Bobbie-Jo M

2012-04-05

The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq), global microarrays, and tandem mass spectrometry (MS/MS)-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates. VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002) to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data. VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis-annotations in prokaryotic genomes. Data is evaluated via visual analysis across multiple levels of genomic resolution, linked searches and interaction with existing bioinformatics tools. We highlight the novel functionality of VESPA and core programming requirements for visualization of these large heterogeneous datasets for a client-side application. The software is freely available at https://www.biopilot.org/docs/Software/Vespa.php.

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data

PubMed Central

2012-01-01

Background The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq), global microarrays, and tandem mass spectrometry (MS/MS)-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates. Results VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002) to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data. Conclusions VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis-annotations in prokaryotic genomes. Data is evaluated via visual analysis across multiple levels of genomic resolution, linked searches and interaction with existing bioinformatics tools. We highlight the novel functionality of VESPA and core programming requirements for visualization of these large heterogeneous datasets for a client-side application. The software is freely available at https://www.biopilot.org/docs/Software/Vespa.php. PMID:22480257

InCHlib - interactive cluster heatmap for web applications.

PubMed

Skuta, Ctibor; Bartůněk, Petr; Svozil, Daniel

2014-12-01

Hierarchical clustering is an exploratory data analysis method that reveals the groups (clusters) of similar objects. The result of the hierarchical clustering is a tree structure called dendrogram that shows the arrangement of individual clusters. To investigate the row/column hierarchical cluster structure of a data matrix, a visualization tool called 'cluster heatmap' is commonly employed. In the cluster heatmap, the data matrix is displayed as a heatmap, a 2-dimensional array in which the colour of each element corresponds to its value. The rows/columns of the matrix are ordered such that similar rows/columns are near each other. The ordering is given by the dendrogram which is displayed on the side of the heatmap. We developed InCHlib (Interactive Cluster Heatmap Library), a highly interactive and lightweight JavaScript library for cluster heatmap visualization and exploration. InCHlib enables the user to select individual or clustered heatmap rows, to zoom in and out of clusters or to flexibly modify heatmap appearance. The cluster heatmap can be augmented with additional metadata displayed in a different colour scale. In addition, to further enhance the visualization, the cluster heatmap can be interconnected with external data sources or analysis tools. Data clustering and the preparation of the input file for InCHlib is facilitated by the Python utility script inchlib_clust . The cluster heatmap is one of the most popular visualizations of large chemical and biomedical data sets originating, e.g., in high-throughput screening, genomics or transcriptomics experiments. The presented JavaScript library InCHlib is a client-side solution for cluster heatmap exploration. InCHlib can be easily deployed into any modern web application and configured to cooperate with external tools and data sources. Though InCHlib is primarily intended for the analysis of chemical or biological data, it is a versatile tool which application domain is not limited to the life sciences only.

An Agro-Climatological Early Warning Tool Based on the Google Earth Engine to Support Regional Food Security Analysis

NASA Astrophysics Data System (ADS)

Landsfeld, M. F.; Daudert, B.; Friedrichs, M.; Morton, C.; Hegewisch, K.; Husak, G. J.; Funk, C. C.; Peterson, P.; Huntington, J. L.; Abatzoglou, J. T.; Verdin, J. P.; Williams, E. L.

2015-12-01

The Famine Early Warning Systems Network (FEWS NET) focuses on food insecurity in developing nations and provides objective, evidence based analysis to help government decision-makers and relief agencies plan for and respond to humanitarian emergencies. The Google Earth Engine (GEE) is a platform provided by Google Inc. to support scientific research and analysis of environmental data in their cloud environment. The intent is to allow scientists and independent researchers to mine massive collections of environmental data and leverage Google's vast computational resources to detect changes and monitor the Earth's surface and climate. GEE hosts an enormous amount of satellite imagery and climate archives, one of which is the Climate Hazards Group Infrared Precipitation with Stations dataset (CHIRPS). The CHIRPS dataset is land based, quasi-global (latitude 50N-50S), 0.05 degree resolution, and has a relatively long term period of record (1981-present). CHIRPS is on a continuous monthly feed into the GEE as new data fields are generated each month. This precipitation dataset is a key input for FEWS NET monitoring and forecasting efforts. FEWS NET intends to leverage the GEE in order to provide analysts and scientists with flexible, interactive tools to aid in their monitoring and research efforts. These scientists often work in bandwidth limited regions, so lightweight Internet tools and services that bypass the need for downloading massive datasets to analyze them, are preferred for their work. The GEE provides just this type of service. We present a tool designed specifically for FEWS NET scientists to be utilized interactively for investigating and monitoring for agro-climatological issues. We are able to utilize the enormous GEE computing power to generate on-the-fly statistics to calculate precipitation anomalies, z-scores, percentiles and band ratios, and allow the user to interactively select custom areas for statistical time series comparisons and predictions.

Learning Photogrammetry with Interactive Software Tool PhoX

NASA Astrophysics Data System (ADS)

Luhmann, T.

2016-06-01

Photogrammetry is a complex topic in high-level university teaching, especially in the fields of geodesy, geoinformatics and metrology where high quality results are demanded. In addition, more and more black-box solutions for 3D image processing and point cloud generation are available that generate nice results easily, e.g. by structure-from-motion approaches. Within this context, the classical approach of teaching photogrammetry (e.g. focusing on aerial stereophotogrammetry) has to be reformed in order to educate students and professionals with new topics and provide them with more information behind the scene. Since around 20 years photogrammetry courses at the Jade University of Applied Sciences in Oldenburg, Germany, include the use of digital photogrammetry software that provide individual exercises, deep analysis of calculation results and a wide range of visualization tools for almost all standard tasks in photogrammetry. During the last years the software package PhoX has been developed that is part of a new didactic concept in photogrammetry and related subjects. It also serves as analysis tool in recent research projects. PhoX consists of a project-oriented data structure for images, image data, measured points and features and 3D objects. It allows for almost all basic photogrammetric measurement tools, image processing, calculation methods, graphical analysis functions, simulations and much more. Students use the program in order to conduct predefined exercises where they have the opportunity to analyse results in a high level of detail. This includes the analysis of statistical quality parameters but also the meaning of transformation parameters, rotation matrices, calibration and orientation data. As one specific advantage, PhoX allows for the interactive modification of single parameters and the direct view of the resulting effect in image or object space.

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

PubMed Central

2013-01-01

Background System-wide profiling of genes and proteins in mammalian cells produce lists of differentially expressed genes/proteins that need to be further analyzed for their collective functions in order to extract new knowledge. Once unbiased lists of genes or proteins are generated from such experiments, these lists are used as input for computing enrichment with existing lists created from prior knowledge organized into gene-set libraries. While many enrichment analysis tools and gene-set libraries databases have been developed, there is still room for improvement. Results Here, we present Enrichr, an integrative web-based and mobile software application that includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library, Data Driven Documents (D3). The software can also be embedded into any tool that performs gene list analysis. We applied Enrichr to analyze nine cancer cell lines by comparing their enrichment signatures to the enrichment signatures of matched normal tissues. We observed a common pattern of up regulation of the polycomb group PRC2 and enrichment for the histone mark H3K27me3 in many cancer cell lines, as well as alterations in Toll-like receptor and interlukin signaling in K562 cells when compared with normal myeloid CD33+ cells. Such analyses provide global visualization of critical differences between normal tissues and cancer cell lines but can be applied to many other scenarios. Conclusions Enrichr is an easy to use intuitive enrichment analysis web-based tool providing various types of visualization summaries of collective functions of gene lists. Enrichr is open source and freely available online at: http://amp.pharm.mssm.edu/Enrichr. PMID:23586463

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool.

PubMed

Chen, Edward Y; Tan, Christopher M; Kou, Yan; Duan, Qiaonan; Wang, Zichen; Meirelles, Gabriela Vaz; Clark, Neil R; Ma'ayan, Avi

2013-04-15

System-wide profiling of genes and proteins in mammalian cells produce lists of differentially expressed genes/proteins that need to be further analyzed for their collective functions in order to extract new knowledge. Once unbiased lists of genes or proteins are generated from such experiments, these lists are used as input for computing enrichment with existing lists created from prior knowledge organized into gene-set libraries. While many enrichment analysis tools and gene-set libraries databases have been developed, there is still room for improvement. Here, we present Enrichr, an integrative web-based and mobile software application that includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library, Data Driven Documents (D3). The software can also be embedded into any tool that performs gene list analysis. We applied Enrichr to analyze nine cancer cell lines by comparing their enrichment signatures to the enrichment signatures of matched normal tissues. We observed a common pattern of up regulation of the polycomb group PRC2 and enrichment for the histone mark H3K27me3 in many cancer cell lines, as well as alterations in Toll-like receptor and interlukin signaling in K562 cells when compared with normal myeloid CD33+ cells. Such analyses provide global visualization of critical differences between normal tissues and cancer cell lines but can be applied to many other scenarios. Enrichr is an easy to use intuitive enrichment analysis web-based tool providing various types of visualization summaries of collective functions of gene lists. Enrichr is open source and freely available online at: http://amp.pharm.mssm.edu/Enrichr.

Interactive visualization of multi-data-set Rietveld analyses using Cinema:Debye-Scherrer.

PubMed

Vogel, Sven C; Biwer, Chris M; Rogers, David H; Ahrens, James P; Hackenberg, Robert E; Onken, Drew; Zhang, Jianzhong

2018-06-01

A tool named Cinema:Debye-Scherrer to visualize the results of a series of Rietveld analyses is presented. The multi-axis visualization of the high-dimensional data sets resulting from powder diffraction analyses allows identification of analysis problems, prediction of suitable starting values, identification of gaps in the experimental parameter space and acceleration of scientific insight from the experimental data. The tool is demonstrated with analysis results from 59 U-Nb alloy samples with different compositions, annealing times and annealing temperatures as well as with a high-temperature study of the crystal structure of CsPbBr 3 . A script to extract parameters from a series of Rietveld analyses employing the widely used GSAS Rietveld software is also described. Both software tools are available for download.

Interactive visualization of multi-data-set Rietveld analyses using Cinema:Debye-Scherrer

PubMed Central

Biwer, Chris M.; Rogers, David H.; Ahrens, James P.; Hackenberg, Robert E.; Onken, Drew; Zhang, Jianzhong

2018-01-01

A tool named Cinema:Debye-Scherrer to visualize the results of a series of Rietveld analyses is presented. The multi-axis visualization of the high-dimensional data sets resulting from powder diffraction analyses allows identification of analysis problems, prediction of suitable starting values, identification of gaps in the experimental parameter space and acceleration of scientific insight from the experimental data. The tool is demonstrated with analysis results from 59 U–Nb alloy samples with different compositions, annealing times and annealing temperatures as well as with a high-temperature study of the crystal structure of CsPbBr3. A script to extract parameters from a series of Rietveld analyses employing the widely used GSAS Rietveld software is also described. Both software tools are available for download. PMID:29896062

GARNET--gene set analysis with exploration of annotation relations.

PubMed

Rho, Kyoohyoung; Kim, Bumjin; Jang, Youngjun; Lee, Sanghyun; Bae, Taejeong; Seo, Jihae; Seo, Chaehwa; Lee, Jihyun; Kang, Hyunjung; Yu, Ungsik; Kim, Sunghoon; Lee, Sanghyuk; Kim, Wan Kyu

2011-02-15

Gene set analysis is a powerful method of deducing biological meaning for an a priori defined set of genes. Numerous tools have been developed to test statistical enrichment or depletion in specific pathways or gene ontology (GO) terms. Major difficulties towards biological interpretation are integrating diverse types of annotation categories and exploring the relationships between annotation terms of similar information. GARNET (Gene Annotation Relationship NEtwork Tools) is an integrative platform for gene set analysis with many novel features. It includes tools for retrieval of genes from annotation database, statistical analysis & visualization of annotation relationships, and managing gene sets. In an effort to allow access to a full spectrum of amassed biological knowledge, we have integrated a variety of annotation data that include the GO, domain, disease, drug, chromosomal location, and custom-defined annotations. Diverse types of molecular networks (pathways, transcription and microRNA regulations, protein-protein interaction) are also included. The pair-wise relationship between annotation gene sets was calculated using kappa statistics. GARNET consists of three modules--gene set manager, gene set analysis and gene set retrieval, which are tightly integrated to provide virtually automatic analysis for gene sets. A dedicated viewer for annotation network has been developed to facilitate exploration of the related annotations. GARNET (gene annotation relationship network tools) is an integrative platform for diverse types of gene set analysis, where complex relationships among gene annotations can be easily explored with an intuitive network visualization tool (http://garnet.isysbio.org/ or http://ercsb.ewha.ac.kr/garnet/).

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update).

PubMed

Pravda, Lukáš; Sehnal, David; Toušek, Dominik; Navrátilová, Veronika; Bazgier, Václav; Berka, Karel; Svobodová Vareková, Radka; Koca, Jaroslav; Otyepka, Michal

2018-04-30

MOLEonline is an interactive, web-based application for the detection and characterization of channels (pores and tunnels) within biomacromolecular structures. The updated version of MOLEonline overcomes limitations of the previous version by incorporating the recently developed LiteMol Viewer visualization engine and providing a simple, fully interactive user experience. The application enables two modes of calculation: one is dedicated to the analysis of channels while the other was specifically designed for transmembrane pores. As the application can use both PDB and mmCIF formats, it can be leveraged to analyze a wide spectrum of biomacromolecular structures, e.g. stemming from NMR, X-ray and cryo-EM techniques. The tool is interconnected with other bioinformatics tools (e.g., PDBe, CSA, ChannelsDB, OPM, UniProt) to help both setup and the analysis of acquired results. MOLEonline provides unprecedented analytics for the detection and structural characterization of channels, as well as information about their numerous physicochemical features. Here we present the application of MOLEonline for structural analyses of α-hemolysin and transient receptor potential mucolipin 1 (TRMP1) pores. The MOLEonline application is freely available via the Internet at https://mole.upol.cz.

Tool Support for Parametric Analysis of Large Software Simulation Systems

NASA Technical Reports Server (NTRS)

Schumann, Johann; Gundy-Burlet, Karen; Pasareanu, Corina; Menzies, Tim; Barrett, Tony

2008-01-01

The analysis of large and complex parameterized software systems, e.g., systems simulation in aerospace, is very complicated and time-consuming due to the large parameter space, and the complex, highly coupled nonlinear nature of the different system components. Thus, such systems are generally validated only in regions local to anticipated operating points rather than through characterization of the entire feasible operational envelope of the system. We have addressed the factors deterring such an analysis with a tool to support envelope assessment: we utilize a combination of advanced Monte Carlo generation with n-factor combinatorial parameter variations to limit the number of cases, but still explore important interactions in the parameter space in a systematic fashion. Additional test-cases, automatically generated from models (e.g., UML, Simulink, Stateflow) improve the coverage. The distributed test runs of the software system produce vast amounts of data, making manual analysis impossible. Our tool automatically analyzes the generated data through a combination of unsupervised Bayesian clustering techniques (AutoBayes) and supervised learning of critical parameter ranges using the treatment learner TAR3. The tool has been developed around the Trick simulation environment, which is widely used within NASA. We will present this tool with a GN&C (Guidance, Navigation and Control) simulation of a small satellite system.

Earth Observation from the International Space Station -Remote Sensing in Schools-

NASA Astrophysics Data System (ADS)

Schultz, Johannes; Rienow, Andreas; Graw, Valerie; Heinemann, Sascha; Selg, Fabian; Menz, Gunter

2016-04-01

Since spring 2014, the NASA High Definition Earth Viewing (HDEV) mission at the International Space Station (ISS) is online. HDEV consists of four cameras mounted at ESA's Columbus laboratory and is recording the earth 24/7. The educational project 'Columbus Eye - Live-Imagery from the ISS in Schools' has published a learning portal for earth observation from the ISS (www.columbuseye.uni-bonn.de). Besides a video live stream, the portal contains an archive providing spectacular footage, web-GIS and an observatory with interactive materials for school lessons. Columbus Eye is carried out by the University of Bonn and funded by the German Aerospace Center (DLR) Space Administration. Pupils should be motivated to work with the footage in order to learn about patterns and processes of the coupled human-environment system like volcano eruptions or deforestation. The material is developed on the experiences of the FIS (German abbreviation for "Remote Sensing in Schools") project and its learning portal (http://www.fis.uni-bonn.de). Based on the ISS videos three different teaching material types are developed. The simplest teaching type are provided by worksheets, which have a low degree of interactivity. Alongside a short didactical commentary for teachers is included. Additionally, videos, ancillary information, maps, and instructions for interactive school experiments are provided. The observatory contains the second type of the Columbus Eye teaching materials. It requires a high degree of self-organisation and responsibility of the pupils. Thus, the observatory provides the opportunity for pupils to freely construct their own hypotheses based on a spatial analysis tool similar to those provided by commercial software. The third type are comprehensive learning and teaching modules with a high degree of interactivity, including background information, interactive animations, quizzes and different analysis tools (e.g. change detection, classification, polygon or NDVI tool). All materials and modules are developed based on the school curricular and can be used in lessons that are mainly based on self-reliant learning and require only minimal lead and instruction by the teacher. The poster presents new tools and strategies to educate pupils and to enhance their fascination of earth observation imagery in the light of problem-based learning in everyday school lessons.

Epiviz: a view inside the design of an integrated visual analysis software for genomics

PubMed Central

2015-01-01

Background Computational and visual data analysis for genomics has traditionally involved a combination of tools and resources, of which the most ubiquitous consist of genome browsers, focused mainly on integrative visualization of large numbers of big datasets, and computational environments, focused on data modeling of a small number of moderately sized datasets. Workflows that involve the integration and exploration of multiple heterogeneous data sources, small and large, public and user specific have been poorly addressed by these tools. In our previous work, we introduced Epiviz, which bridges the gap between the two types of tools, simplifying these workflows. Results In this paper we expand on the design decisions behind Epiviz, and introduce a series of new advanced features that further support the type of interactive exploratory workflow we have targeted. We discuss three ways in which Epiviz advances the field of genomic data analysis: 1) it brings code to interactive visualizations at various different levels; 2) takes the first steps in the direction of collaborative data analysis by incorporating user plugins from source control providers, as well as by allowing analysis states to be shared among the scientific community; 3) combines established analysis features that have never before been available simultaneously in a genome browser. In our discussion section, we present security implications of the current design, as well as a series of limitations and future research steps. Conclusions Since many of the design choices of Epiviz are novel in genomics data analysis, this paper serves both as a document of our own approaches with lessons learned, as well as a start point for future efforts in the same direction for the genomics community. PMID:26328750

Innovative Tools and Technology for Analysis of Single Cells and Cell-Cell Interaction.

PubMed

Konry, Tania; Sarkar, Saheli; Sabhachandani, Pooja; Cohen, Noa

2016-07-11

Heterogeneity in single-cell responses and intercellular interactions results from complex regulation of cell-intrinsic and environmental factors. Single-cell analysis allows not only detection of individual cellular characteristics but also correlation of genetic content with phenotypic traits in the same cell. Technological advances in micro- and nanofabrication have benefited single-cell analysis by allowing precise control of the localized microenvironment, cell manipulation, and sensitive detection capabilities. Additionally, microscale techniques permit rapid, high-throughput, multiparametric screening that has become essential for -omics research. This review highlights innovative applications of microscale platforms in genetic, proteomic, and metabolic detection in single cells; cell sorting strategies; and heterotypic cell-cell interaction. We discuss key design aspects of single-cell localization and isolation in microfluidic systems, dynamic and endpoint analyses, and approaches that integrate highly multiplexed detection of various intracellular species.

Rapid State Space Modeling Tool for Rectangular Wing Aeroservoelastic Studies

NASA Technical Reports Server (NTRS)

Suh, Peter M.; Conyers, Howard J.; Mavris, Dimitri N.

2014-01-01

This paper introduces a modeling and simulation tool for aeroservoelastic analysis of rectangular wings with trailing edge control surfaces. The inputs to the code are planform design parameters such as wing span, aspect ratio and number of control surfaces. A doublet lattice approach is taken to compute generalized forces. A rational function approximation is computed. The output, computed in a few seconds, is a state space aeroservoelastic model which can be used for analysis and control design. The tool is fully parameterized with default information so there is little required interaction with the model developer. Although, all parameters can be easily modified if desired.The focus of this paper is on tool presentation, verification and validation. This process is carried out in stages throughout the paper. The rational function approximation is verified against computed generalized forces for a plate model. A model composed of finite element plates is compared to a modal analysis from commercial software and an independently conducted experimental ground vibration test analysis. Aeroservoelastic analysis is the ultimate goal of this tool. Therefore the flutter speed and frequency for a clamped plate are computed using V-g and V-f analysis. The computational results are compared to a previously published computational analysis and wind tunnel results for the same structure. Finally a case study of a generic wing model with a single control surface is presented. Verification of the state space model is presented in comparison to V-g and V-f analysis. This also includes the analysis of the model in response to a 1-cos gust.

Rapid State Space Modeling Tool for Rectangular Wing Aeroservoelastic Studies

NASA Technical Reports Server (NTRS)

Suh, Peter M.; Conyers, Howard J.; Mavris, Dimitri N.

2015-01-01

This paper introduces a modeling and simulation tool for aeroservoelastic analysis of rectangular wings with trailing-edge control surfaces. The inputs to the code are planform design parameters such as wing span, aspect ratio, and number of control surfaces. Using this information, the generalized forces are computed using the doublet-lattice method. Using Roger's approximation, a rational function approximation is computed. The output, computed in a few seconds, is a state space aeroservoelastic model which can be used for analysis and control design. The tool is fully parameterized with default information so there is little required interaction with the model developer. All parameters can be easily modified if desired. The focus of this paper is on tool presentation, verification, and validation. These processes are carried out in stages throughout the paper. The rational function approximation is verified against computed generalized forces for a plate model. A model composed of finite element plates is compared to a modal analysis from commercial software and an independently conducted experimental ground vibration test analysis. Aeroservoelastic analysis is the ultimate goal of this tool, therefore, the flutter speed and frequency for a clamped plate are computed using damping-versus-velocity and frequency-versus-velocity analysis. The computational results are compared to a previously published computational analysis and wind-tunnel results for the same structure. A case study of a generic wing model with a single control surface is presented. Verification of the state space model is presented in comparison to damping-versus-velocity and frequency-versus-velocity analysis, including the analysis of the model in response to a 1-cos gust.

Rapid State Space Modeling Tool for Rectangular Wing Aeroservoelastic Studies

NASA Technical Reports Server (NTRS)

Suh, Peter M.; Conyers, Howard Jason; Mavris, Dimitri N.

2015-01-01

This report introduces a modeling and simulation tool for aeroservoelastic analysis of rectangular wings with trailing-edge control surfaces. The inputs to the code are planform design parameters such as wing span, aspect ratio, and number of control surfaces. Using this information, the generalized forces are computed using the doublet-lattice method. Using Roger's approximation, a rational function approximation is computed. The output, computed in a few seconds, is a state space aeroservoelastic model which can be used for analysis and control design. The tool is fully parameterized with default information so there is little required interaction with the model developer. All parameters can be easily modified if desired. The focus of this report is on tool presentation, verification, and validation. These processes are carried out in stages throughout the report. The rational function approximation is verified against computed generalized forces for a plate model. A model composed of finite element plates is compared to a modal analysis from commercial software and an independently conducted experimental ground vibration test analysis. Aeroservoelastic analysis is the ultimate goal of this tool, therefore, the flutter speed and frequency for a clamped plate are computed using damping-versus-velocity and frequency-versus-velocity analysis. The computational results are compared to a previously published computational analysis and wind-tunnel results for the same structure. A case study of a generic wing model with a single control surface is presented. Verification of the state space model is presented in comparison to damping-versus-velocity and frequency-versus-velocity analysis, including the analysis of the model in response to a 1-cos gust.

Interactive and coordinated visualization approaches for biological data analysis.

PubMed

Cruz, António; Arrais, Joel P; Machado, Penousal

2018-03-26

The field of computational biology has become largely dependent on data visualization tools to analyze the increasing quantities of data gathered through the use of new and growing technologies. Aside from the volume, which often results in large amounts of noise and complex relationships with no clear structure, the visualization of biological data sets is hindered by their heterogeneity, as data are obtained from different sources and contain a wide variety of attributes, including spatial and temporal information. This requires visualization approaches that are able to not only represent various data structures simultaneously but also provide exploratory methods that allow the identification of meaningful relationships that would not be perceptible through data analysis algorithms alone. In this article, we present a survey of visualization approaches applied to the analysis of biological data. We focus on graph-based visualizations and tools that use coordinated multiple views to represent high-dimensional multivariate data, in particular time series gene expression, protein-protein interaction networks and biological pathways. We then discuss how these methods can be used to help solve the current challenges surrounding the visualization of complex biological data sets.

Spectacle and SpecViz: New Spectral Analysis and Visualization Tools

NASA Astrophysics Data System (ADS)

Earl, Nicholas; Peeples, Molly; JDADF Developers

2018-01-01

A new era of spectroscopic exploration of our universe is being ushered in with advances in instrumentation and next-generation space telescopes. The advent of new spectroscopic instruments has highlighted a pressing need for tools scientists can use to analyze and explore these new data. We have developed Spectacle, a software package for analyzing both synthetic spectra from hydrodynamic simulations as well as real COS data with an aim of characterizing the behavior of the circumgalactic medium. It allows easy reduction of spectral data and analytic line generation capabilities. Currently, the package is focused on automatic determination of absorption regions and line identification with custom line list support, simultaneous line fitting using Voigt profiles via least-squares or MCMC methods, and multi-component modeling of blended features. Non-parametric measurements, such as equivalent widths, delta v90, and full-width half-max are available. Spectacle also provides the ability to compose compound models used to generate synthetic spectra allowing the user to define various LSF kernels, uncertainties, and to specify sampling.We also present updates to the visualization tool SpecViz, developed in conjunction with the JWST data analysis tools development team, to aid in the exploration of spectral data. SpecViz is an open source, Python-based spectral 1-D interactive visualization and analysis application built around high-performance interactive plotting. It supports handling general and instrument-specific data and includes advanced tool-sets for filtering and detrending one-dimensional data, along with the ability to isolate absorption regions using slicing and manipulate spectral features via spectral arithmetic. Multi-component modeling is also possible using a flexible model fitting tool-set that supports custom models to be used with various fitting routines. It also features robust user extensions such as custom data loaders and support for user-created plugins that add new functionality.This work was supported in part by HST AR #13919, HST GO #14268, and HST AR #14560.

Rewiring of the inferred protein interactome during blood development studied with the tool PPICompare.

PubMed

Will, Thorsten; Helms, Volkhard

2017-04-04

Differential analysis of cellular conditions is a key approach towards understanding the consequences and driving causes behind biological processes such as developmental transitions or diseases. The progress of whole-genome expression profiling enabled to conveniently capture the state of a cell's transcriptome and to detect the characteristic features that distinguish cells in specific conditions. In contrast, mapping the physical protein interactome for many samples is experimentally infeasible at the moment. For the understanding of the whole system, however, it is equally important how the interactions of proteins are rewired between cellular states. To overcome this deficiency, we recently showed how condition-specific protein interaction networks that even consider alternative splicing can be inferred from transcript expression data. Here, we present the differential network analysis tool PPICompare that was specifically designed for isoform-sensitive protein interaction networks. Besides detecting significant rewiring events between the interactomes of grouped samples, PPICompare infers which alterations to the transcriptome caused each rewiring event and what is the minimal set of alterations necessary to explain all between-group changes. When applied to the development of blood cells, we verified that a reasonable amount of rewiring events were reported by the tool and found that differential gene expression was the major determinant of cellular adjustments to the interactome. Alternative splicing events were consistently necessary in each developmental step to explain all significant alterations and were especially important for rewiring in the context of transcriptional control. Applying PPICompare enabled us to investigate the dynamics of the human protein interactome during developmental transitions. A platform-independent implementation of the tool PPICompare is available at https://sourceforge.net/projects/ppicompare/ .

SATRAT: Staphylococcus aureus transcript regulatory network analysis tool.

PubMed

Gopal, Tamilselvi; Nagarajan, Vijayaraj; Elasri, Mohamed O

2015-01-01

Staphylococcus aureus is a commensal organism that primarily colonizes the nose of healthy individuals. S. aureus causes a spectrum of infections that range from skin and soft-tissue infections to fatal invasive diseases. S. aureus uses a large number of virulence factors that are regulated in a coordinated fashion. The complex regulatory mechanisms have been investigated in numerous high-throughput experiments. Access to this data is critical to studying this pathogen. Previously, we developed a compilation of microarray experimental data to enable researchers to search, browse, compare, and contrast transcript profiles. We have substantially updated this database and have built a novel exploratory tool-SATRAT-the S. aureus transcript regulatory network analysis tool, based on the updated database. This tool is capable of performing deep searches using a query and generating an interactive regulatory network based on associations among the regulators of any query gene. We believe this integrated regulatory network analysis tool would help researchers explore the missing links and identify novel pathways that regulate virulence in S. aureus. Also, the data model and the network generation code used to build this resource is open sourced, enabling researchers to build similar resources for other bacterial systems.

Molecular ecological network analyses.

PubMed

Deng, Ye; Jiang, Yi-Huei; Yang, Yunfeng; He, Zhili; Luo, Feng; Zhou, Jizhong

2012-05-30

Understanding the interaction among different species within a community and their responses to environmental changes is a central goal in ecology. However, defining the network structure in a microbial community is very challenging due to their extremely high diversity and as-yet uncultivated status. Although recent advance of metagenomic technologies, such as high throughout sequencing and functional gene arrays, provide revolutionary tools for analyzing microbial community structure, it is still difficult to examine network interactions in a microbial community based on high-throughput metagenomics data. Here, we describe a novel mathematical and bioinformatics framework to construct ecological association networks named molecular ecological networks (MENs) through Random Matrix Theory (RMT)-based methods. Compared to other network construction methods, this approach is remarkable in that the network is automatically defined and robust to noise, thus providing excellent solutions to several common issues associated with high-throughput metagenomics data. We applied it to determine the network structure of microbial communities subjected to long-term experimental warming based on pyrosequencing data of 16 S rRNA genes. We showed that the constructed MENs under both warming and unwarming conditions exhibited topological features of scale free, small world and modularity, which were consistent with previously described molecular ecological networks. Eigengene analysis indicated that the eigengenes represented the module profiles relatively well. In consistency with many other studies, several major environmental traits including temperature and soil pH were found to be important in determining network interactions in the microbial communities examined. To facilitate its application by the scientific community, all these methods and statistical tools have been integrated into a comprehensive Molecular Ecological Network Analysis Pipeline (MENAP), which is open-accessible now (http://ieg2.ou.edu/MENA). The RMT-based molecular ecological network analysis provides powerful tools to elucidate network interactions in microbial communities and their responses to environmental changes, which are fundamentally important for research in microbial ecology and environmental microbiology.

Small Talk: Children's Everyday `Molecule' Ideas

NASA Astrophysics Data System (ADS)

Jakab, Cheryl

2013-08-01

This paper reports on 6-11-year-old children's `sayings and doings' (Harré 2002) as they explore molecule artefacts in dialectical-interactive teaching interviews (Fleer, Cultural Studies of Science Education 3:781-786, 2008; Hedegaard et al. 2008). This sociocultural study was designed to explore children's everyday awareness of and meaning-making with cultural molecular artefacts. Our everyday world is populated with an ever increasing range of molecular or nanoworld words, symbols, images, and games. What do children today say about these artefacts that are used to represent molecular world entities? What are the material and social resources that can influence a child's everyday and developing scientific ideas about `molecules'? How do children interact with these cognitive tools when given expert assistance? What meaning-making is afforded when children are socially and materially assisted in using molecular tools in early chemical and nanoworld thinking? Tool-dependent discursive studies show that provision of cultural artefacts can assist and direct developmental thinking across many domains of science (Schoultz et al., Human Development 44:103-118, 2001; Siegal 2008). Young children's use of molecular artefacts as cognitive tools has not received much attention to date (Jakab 2009a, b). This study shows 6-11-year-old children expressing everyday ideas of molecular artefacts and raising their own questions about the artefacts. They are seen beginning to domesticate (Erneling 2010) the words, symbols, and images to their own purposes when given the opportunity to interact with such artefacts in supported activity. Discursive analysis supports the notion that using `molecules' as cultural tools can help young children to begin `putting on molecular spectacles' (Kind 2004). Playing with an interactive game (ICT) is shown to be particularly helpful in assisting children's early meaning-making with representations of molecules, atoms, and their chemical symbols.

Using Discursis to enhance the qualitative analysis of hospital pharmacist-patient interactions

PubMed Central

Barras, Michael A.; Angus, Daniel J.

2018-01-01

Introduction Pharmacist-patient communication during medication counselling has been successfully investigated using Communication Accommodation Theory (CAT). Communication researchers in other healthcare professions have utilised Discursis software as an adjunct to their manual qualitative analysis processes. Discursis provides a visual, chronological representation of communication exchanges and identifies patterns of interactant engagement. Aim The aim of this study was to describe how Discursis software was used to enhance previously conducted qualitative analysis of pharmacist-patient interactions (by visualising pharmacist-patient speech patterns, episodes of engagement, and identifying CAT strategies employed by pharmacists within these episodes). Methods Visual plots from 48 transcribed audio recordings of pharmacist-patient exchanges were generated by Discursis. Representative plots were selected to show moderate-high and low- level speaker engagement. Details of engagement were investigated for pharmacist application of CAT strategies (approximation, interpretability, discourse management, emotional expression, and interpersonal control). Results Discursis plots allowed for identification of distinct patterns occurring within pharmacist-patient exchanges. Moderate-high pharmacist-patient engagement was characterised by multiple off-diagonal squares while alternating single coloured squares depicted low engagement. Engagement episodes were associated with multiple CAT strategies such as discourse management (open-ended questions). Patterns reflecting pharmacist or patient speaker dominance were dependant on clinical setting. Discussion and conclusions Discursis analysis of pharmacist-patient interactions, a novel application of the technology in health communication, was found to be an effective visualisation tool to pin-point episodes for CAT analysis. Discursis has numerous practical and theoretical applications for future health communication research and training. Researchers can use the software to support qualitative analysis where large data sets can be quickly reviewed to identify key areas for concentrated analysis. Because Discursis plots are easily generated from audio recorded transcripts, they are conducive as teaching tools for both students and practitioners to assess and develop their communication skills. PMID:29787568

WONKA: objective novel complex analysis for ensembles of protein-ligand structures.

PubMed

Bradley, A R; Wall, I D; von Delft, F; Green, D V S; Deane, C M; Marsden, B D

2015-10-01

WONKA is a tool for the systematic analysis of an ensemble of protein-ligand structures. It makes the identification of conserved and unusual features within such an ensemble straightforward. WONKA uses an intuitive workflow to process structural co-ordinates. Ligand and protein features are summarised and then presented within an interactive web application. WONKA's power in consolidating and summarising large amounts of data is described through the analysis of three bromodomain datasets. Furthermore, and in contrast to many current methods, WONKA relates analysis to individual ligands, from which we find unusual and erroneous binding modes. Finally the use of WONKA as an annotation tool to share observations about structures is demonstrated. WONKA is freely available to download and install locally or can be used online at http://wonka.sgc.ox.ac.uk.

The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis

PubMed Central

Rampp, Markus; Soddemann, Thomas; Lederer, Hermann

2006-01-01

We describe a versatile and extensible integrated bioinformatics toolkit for the analysis of biological sequences over the Internet. The web portal offers convenient interactive access to a growing pool of chainable bioinformatics software tools and databases that are centrally installed and maintained by the RZG. Currently, supported tasks comprise sequence similarity searches in public or user-supplied databases, computation and validation of multiple sequence alignments, phylogenetic analysis and protein–structure prediction. Individual tools can be seamlessly chained into pipelines allowing the user to conveniently process complex workflows without the necessity to take care of any format conversions or tedious parsing of intermediate results. The toolkit is part of the Max-Planck Integrated Gene Analysis System (MIGenAS) of the Max Planck Society available at (click ‘Start Toolkit’). PMID:16844980

Direct Duplex Detection: An Emerging Tool in the RNA Structure Analysis Toolbox.

PubMed

Weidmann, Chase A; Mustoe, Anthony M; Weeks, Kevin M

2016-09-01

While a variety of powerful tools exists for analyzing RNA structure, identifying long-range and intermolecular base-pairing interactions has remained challenging. Recently, three groups introduced a high-throughput strategy that uses psoralen-mediated crosslinking to directly identify RNA-RNA duplexes in cells. Initial application of these methods highlights the preponderance of long-range structures within and between RNA molecules and their widespread structural dynamics. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

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

Calderer, Antoni; Yang, Xiaolei; Angelidis, Dionysios

2015-10-30

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

MsViz: A Graphical Software Tool for In-Depth Manual Validation and Quantitation of Post-translational Modifications.

PubMed

Martín-Campos, Trinidad; Mylonas, Roman; Masselot, Alexandre; Waridel, Patrice; Petricevic, Tanja; Xenarios, Ioannis; Quadroni, Manfredo

2017-08-04

Mass spectrometry (MS) has become the tool of choice for the large scale identification and quantitation of proteins and their post-translational modifications (PTMs). This development has been enabled by powerful software packages for the automated analysis of MS data. While data on PTMs of thousands of proteins can nowadays be readily obtained, fully deciphering the complexity and combinatorics of modification patterns even on a single protein often remains challenging. Moreover, functional investigation of PTMs on a protein of interest requires validation of the localization and the accurate quantitation of its changes across several conditions, tasks that often still require human evaluation. Software tools for large scale analyses are highly efficient but are rarely conceived for interactive, in-depth exploration of data on individual proteins. We here describe MsViz, a web-based and interactive software tool that supports manual validation of PTMs and their relative quantitation in small- and medium-size experiments. The tool displays sequence coverage information, peptide-spectrum matches, tandem MS spectra and extracted ion chromatograms through a single, highly intuitive interface. We found that MsViz greatly facilitates manual data inspection to validate PTM location and quantitate modified species across multiple samples.

Study of the Effect of Lubricant Emulsion Percentage and Tool Material on Surface Roughness in Machining of EN-AC 48000 Alloy

NASA Astrophysics Data System (ADS)

Soltani, E.; Shahali, H.; Zarepour, H.

2011-01-01

In this paper, the effect of machining parameters, namely, lubricant emulsion percentage and tool material on surface roughness has been studied in machining process of EN-AC 48000 aluminum alloy. EN-AC 48000 aluminum alloy is an important alloy in industries. Machining of this alloy is of vital importance due to built-up edge and tool wear. A L9 Taguchi standard orthogonal array has been applied as experimental design to investigate the effect of the factors and their interaction. Nine machining tests have been carried out with three random replications resulting in 27 experiments. Three type of cutting tools including coated carbide (CD1810), uncoated carbide (H10), and polycrystalline diamond (CD10) have been used in this research. Emulsion percentage of lubricant is selected at three levels including 3%, 5% and 10%. Statistical analysis has been employed to study the effect of factors and their interactions using ANOVA method. Moreover, the optimal factors level has been achieved through signal to noise ratio (S/N) analysis. Also, a regression model has been provided to predict the surface roughness. Finally, the results of the confirmation tests have been presented to verify the adequacy of the predictive model. In this research, surface quality was improved by 9% using lubricant and statistical optimization method.

Visualization Techniques for Computer Network Defense

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

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

2011-01-01

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

Chembank | Office of Cancer Genomics

Cancer.gov

Funded in large part by the Initiative for Chemical Genetics (ICG), Chembank is an interactive database for small molecules. It contains data from hundreds of biomedically relevant small molecule screens that involved hundreds-of-thousands of compounds. Chembank also provides analysis tools to facilitate data mining.

Internet-Based Approaches to Building Stakeholder Networks for Conservation and Natural Resource Management

EPA Science Inventory

Social network analysis (SNA) is based on a conceptual network representation of social interactions and is an invaluable tool for conservation professionals to increase collaboration, improve information flow, and increase efficiency. We present two approaches to constructing i...

Internet-Based Approaches to Building Stakeholder Networks for Conservation and Natural Resource Management.

EPA Science Inventory

Social network analysis (SNA) is based on a conceptual network representation of social interactions and is an invaluable tool for conservation professionals to increase collaboration, improve information flow, and increase efficiency. We present two approaches to constructing in...

Development of an expert analysis tool based on an interactive subsidence hazard map for urban land use in the city of Celaya, Mexico

NASA Astrophysics Data System (ADS)

Alloy, A.; Gonzalez Dominguez, F.; Nila Fonseca, A. L.; Ruangsirikulchai, A.; Gentle, J. N., Jr.; Cabral, E.; Pierce, S. A.

2016-12-01

Land Subsidence as a result of groundwater extraction in central Mexico's larger urban centers initiated in the 80's as a result of population and economic growth. The city of Celaya has undergone subsidence for a few decades and a consequence is the development of an active normal fault system that affects its urban infrastructure and residential areas. To facilitate its analysis and a land use decision-making process we created an online interactive map enabling users to easily obtain information associated with land subsidence. Geological and socioeconomic data of the city was collected, including fault location, population data, and other important infrastructure and structural data has been obtained from fieldwork as part of a study abroad interchange undergraduate course. The subsidence and associated faulting hazard map was created using an InSAR derived subsidence velocity map and population data from INEGI to identify hazard zones using a subsidence gradient spatial analysis approach based on a subsidence gradient and population risk matrix. This interactive map provides a simple perspective of different vulnerable urban elements. As an accessible visualization tool, it will enhance communication between scientific and socio-economic disciplines. Our project also lays the groundwork for a future expert analysis system with an open source and easily accessible Python coded, SQLite database driven website which archives fault and subsidence data along with visual damage documentation to civil structures. This database takes field notes and provides an entry form for uniform datasets, which are used to generate a JSON. Such a database is useful because it allows geoscientists to have a centralized repository and access to their observations over time. Because of the widespread presence of the subsidence phenomena throughout cities in central Mexico, the spatial analysis has been automated using the open source software R. Raster, rgeos, shapefiles, and rgdal libraries have been used to develop the script which permits to obtain the raster maps of horizontal gradient and population density. An advantage is that this analysis can be automated for periodic updates or repurposed for similar analysis in other cities, providing an easily accessible tool for land subsidence hazard assessments.

Analysis of DNA interactions using single-molecule force spectroscopy.

PubMed

Ritzefeld, Markus; Walhorn, Volker; Anselmetti, Dario; Sewald, Norbert

2013-06-01

Protein-DNA interactions are involved in many biochemical pathways and determine the fate of the corresponding cell. Qualitative and quantitative investigations on these recognition and binding processes are of key importance for an improved understanding of biochemical processes and also for systems biology. This review article focusses on atomic force microscopy (AFM)-based single-molecule force spectroscopy and its application to the quantification of forces and binding mechanisms that lead to the formation of protein-DNA complexes. AFM and dynamic force spectroscopy are exciting tools that allow for quantitative analysis of biomolecular interactions. Besides an overview on the method and the most important immobilization approaches, the physical basics of the data evaluation is described. Recent applications of AFM-based force spectroscopy to investigate DNA intercalation, complexes involving DNA aptamers and peptide- and protein-DNA interactions are given.

Applicability of computer-aided comprehensive tool (LINDA: LINeament Detection and Analysis) and shaded digital elevation model for characterizing and interpreting morphotectonic features from lineaments

NASA Astrophysics Data System (ADS)

Masoud, Alaa; Koike, Katsuaki

2017-09-01

Detection and analysis of linear features related to surface and subsurface structures have been deemed necessary in natural resource exploration and earth surface instability assessment. Subjectivity in choosing control parameters required in conventional methods of lineament detection may cause unreliable results. To reduce this ambiguity, we developed LINDA (LINeament Detection and Analysis), an integrated tool with graphical user interface in Visual Basic. This tool automates processes of detection and analysis of linear features from grid data of topography (digital elevation model; DEM), gravity and magnetic surfaces, as well as data from remote sensing imagery. A simple interface with five display windows forms a user-friendly interactive environment. The interface facilitates grid data shading, detection and grouping of segments, lineament analyses for calculating strike and dip and estimating fault type, and interactive viewing of lineament geometry. Density maps of the center and intersection points of linear features (segments and lineaments) are also included. A systematic analysis of test DEMs and Landsat 7 ETM+ imagery datasets in the North and South Eastern Deserts of Egypt is implemented to demonstrate the capability of LINDA and correct use of its functions. Linear features from the DEM are superior to those from the imagery in terms of frequency, but both linear features agree with location and direction of V-shaped valleys and dykes and reference fault data. Through the case studies, LINDA applicability is demonstrated to highlight dominant structural trends, which can aid understanding of geodynamic frameworks in any region.

New Techniques for the Generation and Analysis of Tailored Microbial Systems on Surfaces.

PubMed

Furst, Ariel L; Smith, Matthew J; Francis, Matthew B

2018-05-17

The interactions between microbes and surfaces provide critically important cues that control the behavior and growth of the cells. As our understanding of complex microbial communities improves, there is a growing need for experimental tools that can establish and control the spatial arrangements of these cells in a range of contexts. Recent improvements in methods to attach bacteria and yeast to nonbiological substrates, combined with an expanding set of techniques available to study these cells, position this field for many new discoveries. Improving methods for controlling the immobilization of bacteria provides powerful experimental tools for testing hypotheses regarding microbiome interactions, studying the transfer of nutrients between bacterial species, and developing microbial communities for green energy production and pollution remediation.

Engineering computer graphics in gas turbine engine design, analysis and manufacture

NASA Technical Reports Server (NTRS)

Lopatka, R. S.

1975-01-01

A time-sharing and computer graphics facility designed to provide effective interactive tools to a large number of engineering users with varied requirements was described. The application of computer graphics displays at several levels of hardware complexity and capability is discussed, with examples of graphics systems tracing gas turbine product development, beginning with preliminary design through manufacture. Highlights of an operating system stylized for interactive engineering graphics is described.

An Arctic Ice/Ocean Coupled Model with Wave Interactions

DTIC Science & Technology

2015-09-30

seas within and in the waters adjoining MIZs, using a conservative, multiple wave scattering approach in a medium with random geometrical properties...relating to wave-ice interactions have been collected since the MIZEX campaign of the 1980s, aside from a small number of ad hoc field experiments. This...from the better technology and analysis tools now available, including those related to the field experiments supported by an intensive remote sensing

Investigation of type-I interferon dysregulation by arenaviruses : a multidisciplinary approach.

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

Kozina, Carol L.; Moorman, Matthew Wallace; Branda, Catherine

2011-09-01

This report provides a detailed overview of the work performed for project number 130781, 'A Systems Biology Approach to Understanding Viral Hemorrhagic Fever Pathogenesis.' We report progress in five key areas: single cell isolation devices and control systems, fluorescent cytokine and transcription factor reporters, on-chip viral infection assays, molecular virology analysis of Arenavirus nucleoprotein structure-function, and development of computational tools to predict virus-host protein interactions. Although a great deal of work remains from that begun here, we have developed several novel single cell analysis tools and knowledge of Arenavirus biology that will facilitate and inform future publications and funding proposals.

A computer-aided approach to nonlinear control systhesis

NASA Technical Reports Server (NTRS)

Wie, Bong; Anthony, Tobin

1988-01-01

The major objective of this project is to develop a computer-aided approach to nonlinear stability analysis and nonlinear control system design. This goal is to be obtained by refining the describing function method as a synthesis tool for nonlinear control design. The interim report outlines the approach by this study to meet these goals including an introduction to the INteractive Controls Analysis (INCA) program which was instrumental in meeting these study objectives. A single-input describing function (SIDF) design methodology was developed in this study; coupled with the software constructed in this study, the results of this project provide a comprehensive tool for design and integration of nonlinear control systems.

3-D interactive visualisation tools for Hi spectral line imaging

NASA Astrophysics Data System (ADS)

van der Hulst, J. M.; Punzo, D.; Roerdink, J. B. T. M.

2017-06-01

Upcoming HI surveys will deliver such large datasets that automated processing using the full 3-D information to find and characterize HI objects is unavoidable. Full 3-D visualization is an essential tool for enabling qualitative and quantitative inspection and analysis of the 3-D data, which is often complex in nature. Here we present SlicerAstro, an open-source extension of 3DSlicer, a multi-platform open source software package for visualization and medical image processing, which we developed for the inspection and analysis of HI spectral line data. We describe its initial capabilities, including 3-D filtering, 3-D selection and comparative modelling.

Solar Tutorial and Annotation Resource (STAR)

NASA Astrophysics Data System (ADS)

Showalter, C.; Rex, R.; Hurlburt, N. E.; Zita, E. J.

2009-12-01

We have written a software suite designed to facilitate solar data analysis by scientists, students, and the public, anticipating enormous datasets from future instruments. Our “STAR" suite includes an interactive learning section explaining 15 classes of solar events. Users learn software tools that exploit humans’ superior ability (over computers) to identify many events. Annotation tools include time slice generation to quantify loop oscillations, the interpolation of event shapes using natural cubic splines (for loops, sigmoids, and filaments) and closed cubic splines (for coronal holes). Learning these tools in an environment where examples are provided prepares new users to comfortably utilize annotation software with new data. Upon completion of our tutorial, users are presented with media of various solar events and asked to identify and annotate the images, to test their mastery of the system. Goals of the project include public input into the data analysis of very large datasets from future solar satellites, and increased public interest and knowledge about the Sun. In 2010, the Solar Dynamics Observatory (SDO) will be launched into orbit. SDO’s advancements in solar telescope technology will generate a terabyte per day of high-quality data, requiring innovation in data management. While major projects develop automated feature recognition software, so that computers can complete much of the initial event tagging and analysis, still, that software cannot annotate features such as sigmoids, coronal magnetic loops, coronal dimming, etc., due to large amounts of data concentrated in relatively small areas. Previously, solar physicists manually annotated these features, but with the imminent influx of data it is unrealistic to expect specialized researchers to examine every image that computers cannot fully process. A new approach is needed to efficiently process these data. Providing analysis tools and data access to students and the public have proven efficient in similar astrophysical projects (e.g. the “Galaxy Zoo.”) For “crowdsourcing” to be effective for solar research, the public needs knowledge and skills to recognize and annotate key events on the Sun. Our tutorial can provide this training, with over 200 images and 18 movies showing examples of active regions, coronal dimmings, coronal holes, coronal jets, coronal waves, emerging flux, sigmoids, coronal magnetic loops, filaments, filament eruption, flares, loop oscillation, plage, surges, and sunspots. Annotation tools are provided for many of these events. Many features of the tutorial, such as mouse-over definitions and interactive annotation examples, are designed to assist people without previous experience in solar physics. After completing the tutorial, the user is presented with an interactive quiz: a series of movies and images to identify and annotate. The tutorial teaches the user, with feedback on correct and incorrect answers, until the user develops appropriate confidence and skill. This prepares users to annotate new data, based on their experience with event recognition and annotation tools. Trained users can contribute significantly to our data analysis tasks, even as our training tool contributes to public science literacy and interest in solar physics.

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

PubMed

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

2016-08-01

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

Discovering new methods of data fusion, visualization, and analysis in 3D immersive environments for hyperspectral and laser altimetry data

NASA Astrophysics Data System (ADS)

Moore, C. A.; Gertman, V.; Olsoy, P.; Mitchell, J.; Glenn, N. F.; Joshi, A.; Norpchen, D.; Shrestha, R.; Pernice, M.; Spaete, L.; Grover, S.; Whiting, E.; Lee, R.

2011-12-01

Immersive virtual reality environments such as the IQ-Station or CAVE° (Cave Automated Virtual Environment) offer new and exciting ways to visualize and explore scientific data and are powerful research and educational tools. Combining remote sensing data from a range of sensor platforms in immersive 3D environments can enhance the spectral, textural, spatial, and temporal attributes of the data, which enables scientists to interact and analyze the data in ways never before possible. Visualization and analysis of large remote sensing datasets in immersive environments requires software customization for integrating LiDAR point cloud data with hyperspectral raster imagery, the generation of quantitative tools for multidimensional analysis, and the development of methods to capture 3D visualizations for stereographic playback. This study uses hyperspectral and LiDAR data acquired over the China Hat geologic study area near Soda Springs, Idaho, USA. The data are fused into a 3D image cube for interactive data exploration and several methods of recording and playback are investigated that include: 1) creating and implementing a Virtual Reality User Interface (VRUI) patch configuration file to enable recording and playback of VRUI interactive sessions within the CAVE and 2) using the LiDAR and hyperspectral remote sensing data and GIS data to create an ArcScene 3D animated flyover, where left- and right-eye visuals are captured from two independent monitors for playback in a stereoscopic player. These visualizations can be used as outreach tools to demonstrate how integrated data and geotechnology techniques can help scientists see, explore, and more adequately comprehend scientific phenomena, both real and abstract.

Integrated Tools for Future Distributed Engine Control Technologies

NASA Technical Reports Server (NTRS)

Culley, Dennis; Thomas, Randy; Saus, Joseph

2013-01-01

Turbine engines are highly complex mechanical systems that are becoming increasingly dependent on control technologies to achieve system performance and safety metrics. However, the contribution of controls to these measurable system objectives is difficult to quantify due to a lack of tools capable of informing the decision makers. This shortcoming hinders technology insertion in the engine design process. NASA Glenn Research Center is developing a Hardware-inthe- Loop (HIL) platform and analysis tool set that will serve as a focal point for new control technologies, especially those related to the hardware development and integration of distributed engine control. The HIL platform is intended to enable rapid and detailed evaluation of new engine control applications, from conceptual design through hardware development, in order to quantify their impact on engine systems. This paper discusses the complex interactions of the control system, within the context of the larger engine system, and how new control technologies are changing that paradigm. The conceptual design of the new HIL platform is then described as a primary tool to address those interactions and how it will help feed the insertion of new technologies into future engine systems.

A sophisticated cad tool for the creation of complex models for electromagnetic interaction analysis

NASA Astrophysics Data System (ADS)

Dion, Marc; Kashyap, Satish; Louie, Aloisius

1991-06-01

This report describes the essential features of the MS-DOS version of DIDEC-DREO, an interactive program for creating wire grid, surface patch, and cell models of complex structures for electromagnetic interaction analysis. It uses the device-independent graphics library DIGRAF and the graphics kernel system HALO, and can be executed on systems with various graphics devices. Complicated structures can be created by direct alphanumeric keyboard entry, digitization of blueprints, conversion form existing geometric structure files, and merging of simple geometric shapes. A completed DIDEC geometric file may then be converted to the format required for input to a variety of time domain and frequency domain electromagnetic interaction codes. This report gives a detailed description of the program DIDEC-DREO, its installation, and its theoretical background. Each available interactive command is described. The associated program HEDRON which generates simple geometric shapes, and other programs that extract the current amplitude data from electromagnetic interaction code outputs, are also discussed.

Finite-element analysis of NiTi wire deflection during orthodontic levelling treatment

NASA Astrophysics Data System (ADS)

Razali, M. F.; Mahmud, A. S.; Mokhtar, N.; Abdullah, J.

2016-02-01

Finite-element analysis is an important product development tool in medical devices industry for design and failure analysis of devices. This tool helps device designers to quickly explore various design options, optimizing specific designs and providing a deeper insight how a device is actually performing. In this study, three-dimensional finite-element models of superelastic nickel-titanium arch wire engaged in a three brackets system were developed. The aim was to measure the effect of binding friction developed on wire-bracket interaction towards the remaining recovery force available for tooth movement. Uniaxial and three brackets bending test were modelled and validated against experimental works. The prediction made by the three brackets bending models shows good agreement with the experimental results.

ANDSystem: an Associative Network Discovery System for automated literature mining in the field of biology

PubMed Central

2015-01-01

Background Sufficient knowledge of molecular and genetic interactions, which comprise the entire basis of the functioning of living systems, is one of the necessary requirements for successfully answering almost any research question in the field of biology and medicine. To date, more than 24 million scientific papers can be found in PubMed, with many of them containing descriptions of a wide range of biological processes. The analysis of such tremendous amounts of data requires the use of automated text-mining approaches. Although a handful of tools have recently been developed to meet this need, none of them provide error-free extraction of highly detailed information. Results The ANDSystem package was developed for the reconstruction and analysis of molecular genetic networks based on an automated text-mining technique. It provides a detailed description of the various types of interactions between genes, proteins, microRNA's, metabolites, cellular components, pathways and diseases, taking into account the specificity of cell lines and organisms. Although the accuracy of ANDSystem is comparable to other well known text-mining tools, such as Pathway Studio and STRING, it outperforms them in having the ability to identify an increased number of interaction types. Conclusion The use of ANDSystem, in combination with Pathway Studio and STRING, can improve the quality of the automated reconstruction of molecular and genetic networks. ANDSystem should provide a useful tool for researchers working in a number of different fields, including biology, biotechnology, pharmacology and medicine. PMID:25881313

Integrated tools for control-system analysis

NASA Technical Reports Server (NTRS)

Ostroff, Aaron J.; Proffitt, Melissa S.; Clark, David R.

1989-01-01

The basic functions embedded within a user friendly software package (MATRIXx) are used to provide a high level systems approach to the analysis of linear control systems. Various control system analysis configurations are assembled automatically to minimize the amount of work by the user. Interactive decision making is incorporated via menu options and at selected points, such as in the plotting section, by inputting data. There are five evaluations such as the singular value robustness test, singular value loop transfer frequency response, Bode frequency response, steady-state covariance analysis, and closed-loop eigenvalues. Another section describes time response simulations. A time response for random white noise disturbance is available. The configurations and key equations used for each type of analysis, the restrictions that apply, the type of data required, and an example problem are described. One approach for integrating the design and analysis tools is also presented.

Software Tools to Support Research on Airport Departure Planning

NASA Technical Reports Server (NTRS)

Carr, Francis; Evans, Antony; Feron, Eric; Clarke, John-Paul

2003-01-01

A simple, portable and useful collection of software tools has been developed for the analysis of airport surface traffic. The tools are based on a flexible and robust traffic-flow model, and include calibration, validation and simulation functionality for this model. Several different interfaces have been developed to help promote usage of these tools, including a portable Matlab(TM) implementation of the basic algorithms; a web-based interface which provides online access to automated analyses of airport traffic based on a database of real-world operations data which covers over 250 U.S. airports over a 5-year period; and an interactive simulation-based tool currently in use as part of a college-level educational module. More advanced applications for airport departure traffic include taxi-time prediction and evaluation of "windowing" congestion control.

LES Investigation of Wake Development in a Transonic Fan Stage for Aeroacoustic Analysis

NASA Technical Reports Server (NTRS)

Hah, Chunill; Romeo, Michael

2017-01-01

Detailed development of the rotor wake and its interaction with the stator are investigated with a large eddy simulation (LES). Typical steady and unsteady Navier-Stokes approaches (RANS and URANS) do not calculate wake development accurately and do not provide all the necessary information for an aeroacoustic analysis. It is generally believed that higher fidelity analysis tools are required for an aeroacoustic investigation of transonic fan stages.

Learning to merge: a new tool for interactive mapping

NASA Astrophysics Data System (ADS)

Porter, Reid B.; Lundquist, Sheng; Ruggiero, Christy

2013-05-01

The task of turning raw imagery into semantically meaningful maps and overlays is a key area of remote sensing activity. Image analysts, in applications ranging from environmental monitoring to intelligence, use imagery to generate and update maps of terrain, vegetation, road networks, buildings and other relevant features. Often these tasks can be cast as a pixel labeling problem, and several interactive pixel labeling tools have been developed. These tools exploit training data, which is generated by analysts using simple and intuitive paint-program annotation tools, in order to tailor the labeling algorithm for the particular dataset and task. In other cases, the task is best cast as a pixel segmentation problem. Interactive pixel segmentation tools have also been developed, but these tools typically do not learn from training data like the pixel labeling tools do. In this paper we investigate tools for interactive pixel segmentation that also learn from user input. The input has the form of segment merging (or grouping). Merging examples are 1) easily obtained from analysts using vector annotation tools, and 2) more challenging to exploit than traditional labels. We outline the key issues in developing these interactive merging tools, and describe their application to remote sensing.

Detecting treatment-subgroup interactions in clustered data with generalized linear mixed-effects model trees.

PubMed

Fokkema, M; Smits, N; Zeileis, A; Hothorn, T; Kelderman, H

2017-10-25

Identification of subgroups of patients for whom treatment A is more effective than treatment B, and vice versa, is of key importance to the development of personalized medicine. Tree-based algorithms are helpful tools for the detection of such interactions, but none of the available algorithms allow for taking into account clustered or nested dataset structures, which are particularly common in psychological research. Therefore, we propose the generalized linear mixed-effects model tree (GLMM tree) algorithm, which allows for the detection of treatment-subgroup interactions, while accounting for the clustered structure of a dataset. The algorithm uses model-based recursive partitioning to detect treatment-subgroup interactions, and a GLMM to estimate the random-effects parameters. In a simulation study, GLMM trees show higher accuracy in recovering treatment-subgroup interactions, higher predictive accuracy, and lower type II error rates than linear-model-based recursive partitioning and mixed-effects regression trees. Also, GLMM trees show somewhat higher predictive accuracy than linear mixed-effects models with pre-specified interaction effects, on average. We illustrate the application of GLMM trees on an individual patient-level data meta-analysis on treatments for depression. We conclude that GLMM trees are a promising exploratory tool for the detection of treatment-subgroup interactions in clustered datasets.

Web-based interactive visualization in a Grid-enabled neuroimaging application using HTML5.

PubMed

Siewert, René; Specovius, Svenja; Wu, Jie; Krefting, Dagmar

2012-01-01

Interactive visualization and correction of intermediate results are required in many medical image analysis pipelines. To allow certain interaction in the remote execution of compute- and data-intensive applications, new features of HTML5 are used. They allow for transparent integration of user interaction into Grid- or Cloud-enabled scientific workflows. Both 2D and 3D visualization and data manipulation can be performed through a scientific gateway without the need to install specific software or web browser plugins. The possibilities of web-based visualization are presented along the FreeSurfer-pipeline, a popular compute- and data-intensive software tool for quantitative neuroimaging.

Analysis of gene expression profile microarray data in complex regional pain syndrome.

PubMed

Tan, Wulin; Song, Yiyan; Mo, Chengqiang; Jiang, Shuangjian; Wang, Zhongxing

2017-09-01

The aim of the present study was to predict key genes and proteins associated with complex regional pain syndrome (CRPS) using bioinformatics analysis. The gene expression profiling microarray data, GSE47603, which included peripheral blood samples from 4 patients with CRPS and 5 healthy controls, was obtained from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) in CRPS patients compared with healthy controls were identified using the GEO2R online tool. Functional enrichment analysis was then performed using The Database for Annotation Visualization and Integrated Discovery online tool. Protein‑protein interaction (PPI) network analysis was subsequently performed using Search Tool for the Retrieval of Interaction Genes database and analyzed with Cytoscape software. A total of 257 DEGs were identified, including 243 upregulated genes and 14 downregulated ones. Genes in the human leukocyte antigen (HLA) family were most significantly differentially expressed. Enrichment analysis demonstrated that signaling pathways, including immune response, cell motion, adhesion and angiogenesis were associated with CRPS. PPI network analysis revealed that key genes, including early region 1A binding protein p300 (EP300), CREB‑binding protein (CREBBP), signal transducer and activator of transcription (STAT)3, STAT5A and integrin α M were associated with CRPS. The results suggest that the immune response may therefore serve an important role in CRPS development. In addition, genes in the HLA family, such as HLA‑DQB1 and HLA‑DRB1, may present potential biomarkers for the diagnosis of CRPS. Furthermore, EP300, its paralog CREBBP, and the STAT family genes, STAT3 and STAT5 may be important in the development of CRPS.

Development and validation of automatic tools for interactive recurrence analysis in radiation therapy: optimization of treatment algorithms for locally advanced pancreatic cancer.

PubMed

Kessel, Kerstin A; Habermehl, Daniel; Jäger, Andreas; Floca, Ralf O; Zhang, Lanlan; Bendl, Rolf; Debus, Jürgen; Combs, Stephanie E

2013-06-07

In radiation oncology recurrence analysis is an important part in the evaluation process and clinical quality assurance of treatment concepts. With the example of 9 patients with locally advanced pancreatic cancer we developed and validated interactive analysis tools to support the evaluation workflow. After an automatic registration of the radiation planning CTs with the follow-up images, the recurrence volumes are segmented manually. Based on these volumes the DVH (dose volume histogram) statistic is calculated, followed by the determination of the dose applied to the region of recurrence and the distance between the boost and recurrence volume. We calculated the percentage of the recurrence volume within the 80%-isodose volume and compared it to the location of the recurrence within the boost volume, boost + 1 cm, boost + 1.5 cm and boost + 2 cm volumes. Recurrence analysis of 9 patients demonstrated that all recurrences except one occurred within the defined GTV/boost volume; one recurrence developed beyond the field border/outfield. With the defined distance volumes in relation to the recurrences, we could show that 7 recurrent lesions were within the 2 cm radius of the primary tumor. Two large recurrences extended beyond the 2 cm, however, this might be due to very rapid growth and/or late detection of the tumor progression. The main goal of using automatic analysis tools is to reduce time and effort conducting clinical analyses. We showed a first approach and use of a semi-automated workflow for recurrence analysis, which will be continuously optimized. In conclusion, despite the limitations of the automatic calculations we contributed to in-house optimization of subsequent study concepts based on an improved and validated target volume definition.

IDEAS: A multidisciplinary computer-aided conceptual design system for spacecraft

NASA Technical Reports Server (NTRS)

Ferebee, M. J., Jr.

1984-01-01

During the conceptual development of advanced aerospace vehicles, many compromises must be considered to balance economy and performance of the total system. Subsystem tradeoffs may need to be made in order to satisfy system-sensitive attributes. Due to the increasingly complex nature of aerospace systems, these trade studies have become more difficult and time-consuming to complete and involve interactions of ever-larger numbers of subsystems, components, and performance parameters. The current advances of computer-aided synthesis, modeling and analysis techniques have greatly helped in the evaluation of competing design concepts. Langley Research Center's Space Systems Division is currently engaged in trade studies for a variety of systems which include advanced ground-launched space transportation systems, space-based orbital transfer vehicles, large space antenna concepts and space stations. The need for engineering analysis tools to aid in the rapid synthesis and evaluation of spacecraft has led to the development of the Interactive Design and Evaluation of Advanced Spacecraft (IDEAS) computer-aided design system. The ADEAS system has been used to perform trade studies of competing technologies and requirements in order to pinpoint possible beneficial areas for research and development. IDEAS is presented as a multidisciplinary tool for the analysis of advanced space systems. Capabilities range from model generation and structural and thermal analysis to subsystem synthesis and performance analysis.

The Joint Accomplishment of Identity

ERIC Educational Resources Information Center

Hand, Victoria; Gresalfi, Melissa

2015-01-01

Identity has become a central concept in the analysis of learning from social perspectives. In this article, we draw on a situative perspective to conceptualize identity as a "joint accomplishment" between individuals and their interactions with norms, practices, cultural tools, relationships, and institutional and cultural contexts.…

Time-gated detection of protein-protein interactions with transcriptional readout

PubMed Central

Sanchez, Mateo I; Coukos, Robert; von Zastrow, Mark

2017-01-01

Transcriptional assays, such as yeast two-hybrid and TANGO, that convert transient protein-protein interactions (PPIs) into stable expression of transgenes are powerful tools for PPI discovery, screens, and analysis of cell populations. However, such assays often have high background and lose information about PPI dynamics. We have developed SPARK (Specific Protein Association tool giving transcriptional Readout with rapid Kinetics), in which proteolytic release of a membrane-tethered transcription factor (TF) requires both a PPI to deliver a protease proximal to its cleavage peptide and blue light to uncage the cleavage site. SPARK was used to detect 12 different PPIs in mammalian cells, with 5 min temporal resolution and signal ratios up to 37. By shifting the light window, we could reconstruct PPI time-courses. Combined with FACS, SPARK enabled 51 fold enrichment of PPI-positive over PPI-negative cells. Due to its high specificity and sensitivity, SPARK has the potential to advance PPI analysis and discovery. PMID:29189201

Elucidating distinct ion channel populations on the surface of hippocampal neurons via single-particle tracking recurrence analysis

NASA Astrophysics Data System (ADS)

Sikora, Grzegorz; Wyłomańska, Agnieszka; Gajda, Janusz; Solé, Laura; Akin, Elizabeth J.; Tamkun, Michael M.; Krapf, Diego

2017-12-01

Protein and lipid nanodomains are prevalent on the surface of mammalian cells. In particular, it has been recently recognized that ion channels assemble into surface nanoclusters in the soma of cultured neurons. However, the interactions of these molecules with surface nanodomains display a considerable degree of heterogeneity. Here, we investigate this heterogeneity and develop statistical tools based on the recurrence of individual trajectories to identify subpopulations within ion channels in the neuronal surface. We specifically study the dynamics of the K+ channel Kv1.4 and the Na+ channel Nav1.6 on the surface of cultured hippocampal neurons at the single-molecule level. We find that both these molecules are expressed in two different forms with distinct kinetics with regards to surface interactions, emphasizing the complex proteomic landscape of the neuronal surface. Further, the tools presented in this work provide new methods for the analysis of membrane nanodomains, transient confinement, and identification of populations within single-particle trajectories.

Open-source framework for power system transmission and distribution dynamics co-simulation

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

Huang, Renke; Fan, Rui; Daily, Jeff

The promise of the smart grid entails more interactions between the transmission and distribution networks, and there is an immediate need for tools to provide the comprehensive modelling and simulation required to integrate operations at both transmission and distribution levels. Existing electromagnetic transient simulators can perform simulations with integration of transmission and distribution systems, but the computational burden is high for large-scale system analysis. For transient stability analysis, currently there are only separate tools for simulating transient dynamics of the transmission and distribution systems. In this paper, we introduce an open source co-simulation framework “Framework for Network Co-Simulation” (FNCS), togethermore » with the decoupled simulation approach that links existing transmission and distribution dynamic simulators through FNCS. FNCS is a middleware interface and framework that manages the interaction and synchronization of the transmission and distribution simulators. Preliminary testing results show the validity and capability of the proposed open-source co-simulation framework and the decoupled co-simulation methodology.« less

NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways.

PubMed

Brohée, Sylvain; Faust, Karoline; Lima-Mendez, Gipsi; Sand, Olivier; Janky, Rekin's; Vanderstocken, Gilles; Deville, Yves; van Helden, Jacques

2008-07-01

The network analysis tools (NeAT) (http://rsat.ulb.ac.be/neat/) provide a user-friendly web access to a collection of modular tools for the analysis of networks (graphs) and clusters (e.g. microarray clusters, functional classes, etc.). A first set of tools supports basic operations on graphs (comparison between two graphs, neighborhood of a set of input nodes, path finding and graph randomization). Another set of programs makes the connection between networks and clusters (graph-based clustering, cliques discovery and mapping of clusters onto a network). The toolbox also includes programs for detecting significant intersections between clusters/classes (e.g. clusters of co-expression versus functional classes of genes). NeAT are designed to cope with large datasets and provide a flexible toolbox for analyzing biological networks stored in various databases (protein interactions, regulation and metabolism) or obtained from high-throughput experiments (two-hybrid, mass-spectrometry and microarrays). The web interface interconnects the programs in predefined analysis flows, enabling to address a series of questions about networks of interest. Each tool can also be used separately by entering custom data for a specific analysis. NeAT can also be used as web services (SOAP/WSDL interface), in order to design programmatic workflows and integrate them with other available resources.

GBOOST: a GPU-based tool for detecting gene-gene interactions in genome-wide case control studies.

PubMed

Yung, Ling Sing; Yang, Can; Wan, Xiang; Yu, Weichuan

2011-05-01

Collecting millions of genetic variations is feasible with the advanced genotyping technology. With a huge amount of genetic variations data in hand, developing efficient algorithms to carry out the gene-gene interaction analysis in a timely manner has become one of the key problems in genome-wide association studies (GWAS). Boolean operation-based screening and testing (BOOST), a recent work in GWAS, completes gene-gene interaction analysis in 2.5 days on a desktop computer. Compared with central processing units (CPUs), graphic processing units (GPUs) are highly parallel hardware and provide massive computing resources. We are, therefore, motivated to use GPUs to further speed up the analysis of gene-gene interactions. We implement the BOOST method based on a GPU framework and name it GBOOST. GBOOST achieves a 40-fold speedup compared with BOOST. It completes the analysis of Wellcome Trust Case Control Consortium Type 2 Diabetes (WTCCC T2D) genome data within 1.34 h on a desktop computer equipped with Nvidia GeForce GTX 285 display card. GBOOST code is available at http://bioinformatics.ust.hk/BOOST.html#GBOOST.

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

PubMed

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

2011-10-14

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

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

PubMed Central

2011-01-01

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

Development of Waypoint Planning Tool in Response to NASA Field Campaign Challenges

NASA Technical Reports Server (NTRS)

He, Matt; Hardin, Danny; Conover, Helen; Graves, Sara; Meyer, Paul; Blakeslee, Richard; Goodman, Michael

2012-01-01

Airborne real time observations are a major component of NASA's Earth Science research and satellite ground validation studies. For mission scientists, planning a research aircraft mission within the context of meeting the science objectives is a complex task because it requires real time situational awareness of the weather conditions that affect the aircraft track. Multiple aircrafts are often involved in NASA field campaigns. The coordination of the aircrafts with satellite overpasses, other airplanes and the constantly evolving, dynamic weather conditions often determines the success of the campaign. A flight planning tool is needed to provide situational awareness information to the mission scientists, and help them plan and modify the flight tracks. Scientists at the University of Alabama-Huntsville and the NASA Marshall Space Flight Center developed the Waypoint Planning Tool, an interactive software tool that enables scientists to develop their own flight plans (also known as waypoints) with point -and-click mouse capabilities on a digital map filled with real time raster and vector data. The development of this Waypoint Planning Tool demonstrates the significance of mission support in responding to the challenges presented during NASA field campaigns. Analysis during and after each campaign helped identify both issues and new requirements, and initiated the next wave of development. Currently the Waypoint Planning Tool has gone through three rounds of development and analysis processes. The development of this waypoint tool is directly affected by the technology advances on GIS/Mapping technologies. From the standalone Google Earth application and simple KML functionalities, to Google Earth Plugin and Java Web Start/Applet on web platform, and to the rising open source GIS tools with new JavaScript frameworks, the Waypoint Planning Tool has entered its third phase of technology advancement. The newly innovated, cross ]platform, modular designed JavaScript ]controlled Way Point Tool is planned to be integrated with NASA Airborne Science Mission Tool Suite. Adapting new technologies for the Waypoint Planning Tool ensures its success in helping scientists reach their mission objectives. This presentation will discuss the development processes of the Waypoint Planning Tool in responding to field campaign challenges, identify new information technologies, and describe the capabilities and features of the Waypoint Planning Tool with the real time aspect, interactive nature, and the resultant benefits to the airborne science community.

Development of Way Point Planning Tool in Response to NASA Field Campaign Challenges

NASA Astrophysics Data System (ADS)

He, M.; Hardin, D. M.; Conover, H.; Graves, S. J.; Meyer, P.; Blakeslee, R. J.; Goodman, M. L.

2012-12-01

Airborne real time observations are a major component of NASA's Earth Science research and satellite ground validation studies. For mission scientists, planning a research aircraft mission within the context of meeting the science objectives is a complex task because it requires real time situational awareness of the weather conditions that affect the aircraft track. Multiple aircrafts are often involved in NASA field campaigns. The coordination of the aircrafts with satellite overpasses, other airplanes and the constantly evolving, dynamic weather conditions often determines the success of the campaign. A flight planning tool is needed to provide situational awareness information to the mission scientists, and help them plan and modify the flight tracks. Scientists at the University of Alabama-Huntsville and the NASA Marshall Space Flight Center developed the Waypoint Planning Tool, an interactive software tool that enables scientists to develop their own flight plans (also known as waypoints) with point-and-click mouse capabilities on a digital map filled with real time raster and vector data. The development of this Waypoint Planning Tool demonstrates the significance of mission support in responding to the challenges presented during NASA field campaigns. Analysis during and after each campaign helped identify both issues and new requirements, and initiated the next wave of development. Currently the Waypoint Planning Tool has gone through three rounds of development and analysis processes. The development of this waypoint tool is directly affected by the technology advances on GIS/Mapping technologies. From the standalone Google Earth application and simple KML functionalities, to Google Earth Plugin and Java Web Start/Applet on web platform, and to the rising open source GIS tools with new JavaScript frameworks, the Waypoint Planning Tool has entered its third phase of technology advancement. The newly innovated, cross-platform, modular designed JavaScript-controlled Way Point Tool is planned to be integrated with NASA Airborne Science Mission Tool Suite. Adapting new technologies for the Waypoint Planning Tool ensures its success in helping scientists reach their mission objectives. This presentation will discuss the development processes of the Waypoint Planning Tool in responding to field campaign challenges, identify new information technologies, and describe the capabilities and features of the Waypoint Planning Tool with the real time aspect, interactive nature, and the resultant benefits to the airborne science community.

Ion mobility-mass spectrometry as a tool to investigate protein-ligand interactions.

PubMed

Göth, Melanie; Pagel, Kevin

2017-07-01

Ion mobility-mass spectrometry (IM-MS) is a powerful tool for the simultaneous analysis of mass, charge, size, and shape of ionic species. It allows the characterization of even low-abundant species in complex samples and is therefore particularly suitable for the analysis of proteins and their assemblies. In the last few years even complex and intractable species have been investigated successfully with IM-MS and the number of publications in this field is steadily growing. This trend article highlights recent advances in which IM-MS was used to study protein-ligand complexes and in particular focuses on the catch and release (CaR) strategy and collision-induced unfolding (CIU). Graphical Abstract Native mass spectrometry and ion mobility-mass spectrometry are versatile tools to follow the stoichiometry, energetics, and structural impact of protein-ligand binding.

Solid Modeling Aerospace Research Tool (SMART) user's guide, version 2.0

NASA Technical Reports Server (NTRS)

Mcmillin, Mark L.; Spangler, Jan L.; Dahmen, Stephen M.; Rehder, John J.

1993-01-01

The Solid Modeling Aerospace Research Tool (SMART) software package is used in the conceptual design of aerospace vehicles. It provides a highly interactive and dynamic capability for generating geometries with Bezier cubic patches. Features include automatic generation of commonly used aerospace constructs (e.g., wings and multilobed tanks); cross-section skinning; wireframe and shaded presentation; area, volume, inertia, and center-of-gravity calculations; and interfaces to various aerodynamic and structural analysis programs. A comprehensive description of SMART and how to use it is provided.

Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns

DOE PAGES

Tian, Wenhong; Samatova, Nagiza F.

2013-01-01

A number of tools for the alignment of protein-protein interaction (PPI) networks have laid the foundation for PPI network analysis. Most of alignment tools focus on finding conserved interaction regions across the PPI networks through either local or global mapping of similar sequences. Researchers are still trying to improve the speed, scalability, and accuracy of network alignment. In view of this, we introduce a connected-components based fast algorithm, HopeMap, for network alignment. Observing that the size of true orthologs across species is small comparing to the total number of proteins in all species, we take a different approach based onmore » a precompiled list of homologs identified by KO terms. Applying this approach to S. cerevisiae (yeast) and D. melanogaster (fly), E. coli K12 and S. typhimurium , E. coli K12 and C. crescenttus , we analyze all clusters identified in the alignment. The results are evaluated through up-to-date known gene annotations, gene ontology (GO), and KEGG ortholog groups (KO). Comparing to existing tools, our approach is fast with linear computational cost, highly accurate in terms of KO and GO terms specificity and sensitivity, and can be extended to multiple alignments easily.« less

The Tracking Meteogram, an AWIPS II Tool for Time-Series Analysis

NASA Technical Reports Server (NTRS)

Burks, Jason Eric; Sperow, Ken

2015-01-01

A new tool has been developed for the National Weather Service (NWS) Advanced Weather Interactive Processing System (AWIPS) II through collaboration between NASA's Short-term Prediction Research and Transition (SPoRT) and the NWS Meteorological Development Laboratory (MDL). Referred to as the "Tracking Meteogram", the tool aids NWS forecasters in assessing meteorological parameters associated with moving phenomena. The tool aids forecasters in severe weather situations by providing valuable satellite and radar derived trends such as cloud top cooling rates, radial velocity couplets, reflectivity, and information from ground-based lightning networks. The Tracking Meteogram tool also aids in synoptic and mesoscale analysis by tracking parameters such as the deepening of surface low pressure systems, changes in surface or upper air temperature, and other properties. The tool provides a valuable new functionality and demonstrates the flexibility and extensibility of the NWS AWIPS II architecture. In 2014, the operational impact of the tool was formally evaluated through participation in the NOAA/NWS Operations Proving Ground (OPG), a risk reduction activity to assess performance and operational impact of new forecasting concepts, tools, and applications. Performance of the Tracking Meteogram Tool during the OPG assessment confirmed that it will be a valuable asset to the operational forecasters. This presentation reviews development of the Tracking Meteogram tool, performance and feedback acquired during the OPG activity, and future goals for continued support and extension to other application areas.

Methodological tools for the collection and analysis of participant observation data using grounded theory.

PubMed

Laitinen, Heleena; Kaunonen, Marja; Astedt-Kurki, Päivi

2014-11-01

To give clarity to the analysis of participant observation in nursing when implementing the grounded theory method. Participant observation (PO) is a method of collecting data that reveals the reality of daily life in a specific context. In grounded theory, interviews are the primary method of collecting data but PO gives a distinctive insight, revealing what people are really doing, instead of what they say they are doing. However, more focus is needed on the analysis of PO. An observational study carried out to gain awareness of nursing care and its electronic documentation in four acute care wards in hospitals in Finland. Discussion of using the grounded theory method and PO as a data collection tool. The following methodological tools are discussed: an observational protocol, jotting of notes, microanalysis, the use of questioning, constant comparison, and writing and illustrating. Each tool has specific significance in collecting and analysing data, working in constant interaction. Grounded theory and participant observation supplied rich data and revealed the complexity of the daily reality of acute care. In this study, the methodological tools provided a base for the study at the research sites and outside. The process as a whole was challenging. It was time-consuming and it required rigorous and simultaneous data collection and analysis, including reflective writing. Using these methodological tools helped the researcher stay focused from data collection and analysis to building theory. Using PO as a data collection method in qualitative nursing research provides insights. It is not commonly discussed in nursing research and therefore this study can provide insight, which cannot be seen or revealed by using other data collection methods. Therefore, this paper can produce a useful tool for those who intend to use PO and grounded theory in their nursing research.

Seismic Canvas: Evolution as a Data Exploration and Analysis Tool

NASA Astrophysics Data System (ADS)

Kroeger, G. C.

2015-12-01

SeismicCanvas, originally developed as a prototype interactive waveform display and printing application for educational use has evolved to include significant data exploration and analysis functionality. The most recent version supports data import from a variety of standard file formats including SAC and mini-SEED, as well as search and download capabilities via IRIS/FDSN Web Services. Data processing tools now include removal of means and trends, interactive windowing, filtering, smoothing, tapering, resampling. Waveforms can be displayed in a free-form canvas or as a record section based on angular or great circle distance, azimuth or back azimuth. Integrated tau-p code allows the calculation and display of theoretical phase arrivals from a variety of radial Earth models. Waveforms can be aligned by absolute time, event time, picked or theoretical arrival times and can be stacked after alignment. Interactive measurements include means, amplitudes, time delays, ray parameters and apparent velocities. Interactive picking of an arbitrary list of seismic phases is supported. Bode plots of amplitude and phase spectra and spectrograms can be created from multiple seismograms or selected windows of seismograms. Direct printing is implemented on all supported platforms along with output of high-resolution pdf files. With these added capabilities, the application is now being used as a data exploration tool for research. Coded in C++ and using the cross-platform Qt framework, the most recent version is available as a 64-bit application for Windows 7-10, Mac OS X 10.6-10.11, and most distributions of Linux, and a 32-bit version for Windows XP and 7. With the latest improvements and refactoring of trace display classes, the 64-bit versions have been tested with over 250 million samples and remain responsive in interactive operations. The source code is available under a LPGLv3 license and both source and executables are available through the IRIS SeisCode repository.

3Drefine: an interactive web server for efficient protein structure refinement.

PubMed

Bhattacharya, Debswapna; Nowotny, Jackson; Cao, Renzhi; Cheng, Jianlin

2016-07-08

3Drefine is an interactive web server for consistent and computationally efficient protein structure refinement with the capability to perform web-based statistical and visual analysis. The 3Drefine refinement protocol utilizes iterative optimization of hydrogen bonding network combined with atomic-level energy minimization on the optimized model using a composite physics and knowledge-based force fields for efficient protein structure refinement. The method has been extensively evaluated on blind CASP experiments as well as on large-scale and diverse benchmark datasets and exhibits consistent improvement over the initial structure in both global and local structural quality measures. The 3Drefine web server allows for convenient protein structure refinement through a text or file input submission, email notification, provided example submission and is freely available without any registration requirement. The server also provides comprehensive analysis of submissions through various energy and statistical feedback and interactive visualization of multiple refined models through the JSmol applet that is equipped with numerous protein model analysis tools. The web server has been extensively tested and used by many users. As a result, the 3Drefine web server conveniently provides a useful tool easily accessible to the community. The 3Drefine web server has been made publicly available at the URL: http://sysbio.rnet.missouri.edu/3Drefine/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Development of students' conceptual thinking by means of video analysis and interactive simulations at technical universities

NASA Astrophysics Data System (ADS)

Hockicko, Peter; Krišt‧ák, L.‧uboš; Němec, Miroslav

2015-03-01

Video analysis, using the program Tracker (Open Source Physics), in the educational process introduces a new creative method of teaching physics and makes natural sciences more interesting for students. This way of exploring the laws of nature can amaze students because this illustrative and interactive educational software inspires them to think creatively, improves their performance and helps them in studying physics. This paper deals with increasing the key competencies in engineering by analysing real-life situation videos - physical problems - by means of video analysis and the modelling tools using the program Tracker and simulations of physical phenomena from The Physics Education Technology (PhET™) Project (VAS method of problem tasks). The statistical testing using the t-test confirmed the significance of the differences in the knowledge of the experimental and control groups, which were the result of interactive method application.

Research in interactive scene analysis

NASA Technical Reports Server (NTRS)

Tenenbaum, J. M.; Garvey, T. D.; Weyl, S. A.; Wolf, H. C.

1975-01-01

An interactive scene interpretation system (ISIS) was developed as a tool for constructing and experimenting with man-machine and automatic scene analysis methods tailored for particular image domains. A recently developed region analysis subsystem based on the paradigm of Brice and Fennema is described. Using this subsystem a series of experiments was conducted to determine good criteria for initially partitioning a scene into atomic regions and for merging these regions into a final partition of the scene along object boundaries. Semantic (problem-dependent) knowledge is essential for complete, correct partitions of complex real-world scenes. An interactive approach to semantic scene segmentation was developed and demonstrated on both landscape and indoor scenes. This approach provides a reasonable methodology for segmenting scenes that cannot be processed completely automatically, and is a promising basis for a future automatic system. A program is described that can automatically generate strategies for finding specific objects in a scene based on manually designated pictorial examples.

Assessment of pharmacy students' communication competence using the Roter Interaction Analysis System during objective structured clinical examinations.

PubMed

Kubota, Yoshie; Yano, Yoshitaka; Seki, Susumu; Takada, Kaori; Sakuma, Mio; Morimoto, Takeshi; Akaike, Akinori; Hiraide, Atsushi

2011-04-11

To determine the value of using the Roter Interaction Analysis System during objective structured clinical examinations (OSCEs) to assess pharmacy students' communication competence. As pharmacy students completed a clinical OSCE involving an interview with a simulated patient, 3 experts used a global rating scale to assess students' overall performance in the interview, and both the student's and patient's languages were coded using the Roter Interaction Analysis System (RIAS). The coders recorded the number of utterances (ie, units of spoken language) in each RIAS category. Correlations between the raters' scores and the number and types of utterances were examined. There was a significant correlation between students' global rating scores on the OSCE and the number of utterances in the RIAS socio-emotional category but not the RIAS business category. The RIAS proved to be a useful tool for assessing the socio-emotional aspect of students' interview skills.

PSSMSearch: a server for modeling, visualization, proteome-wide discovery and annotation of protein motif specificity determinants.

PubMed

Krystkowiak, Izabella; Manguy, Jean; Davey, Norman E

2018-06-05

There is a pressing need for in silico tools that can aid in the identification of the complete repertoire of protein binding (SLiMs, MoRFs, miniMotifs) and modification (moiety attachment/removal, isomerization, cleavage) motifs. We have created PSSMSearch, an interactive web-based tool for rapid statistical modeling, visualization, discovery and annotation of protein motif specificity determinants to discover novel motifs in a proteome-wide manner. PSSMSearch analyses proteomes for regions with significant similarity to a motif specificity determinant model built from a set of aligned motif-containing peptides. Multiple scoring methods are available to build a position-specific scoring matrix (PSSM) describing the motif specificity determinant model. This model can then be modified by a user to add prior knowledge of specificity determinants through an interactive PSSM heatmap. PSSMSearch includes a statistical framework to calculate the significance of specificity determinant model matches against a proteome of interest. PSSMSearch also includes the SLiMSearch framework's annotation, motif functional analysis and filtering tools to highlight relevant discriminatory information. Additional tools to annotate statistically significant shared keywords and GO terms, or experimental evidence of interaction with a motif-recognizing protein have been added. Finally, PSSM-based conservation metrics have been created for taxonomic range analyses. The PSSMSearch web server is available at http://slim.ucd.ie/pssmsearch/.

THE SMALL BODY GEOPHYSICAL ANALYSIS TOOL

NASA Astrophysics Data System (ADS)

Bercovici, Benjamin; McMahon, Jay

2017-10-01

The Small Body Geophysical Analysis Tool (SBGAT) that we are developing aims at providing scientists and mission designers with a comprehensive, easy to use, open-source analysis tool. SBGAT is meant for seamless generation of valuable simulated data originating from small bodies shape models, combined with advanced shape-modification properties.The current status of SBGAT is as follows:The modular software architecture that was specified in the original SBGAT proposal was implemented in the form of two distinct packages: a dynamic library SBGAT Core containing the data structure and algorithm backbone of SBGAT, and SBGAT Gui which wraps the former inside a VTK, Qt user interface to facilitate user/data interaction. This modular development facilitates maintenance and addi- tion of new features. Note that SBGAT Core can be utilized independently from SBGAT Gui.SBGAT is presently being hosted on a GitHub repository owned by SBGAT’s main developer. This repository is public and can be accessed at https://github.com/bbercovici/SBGAT. Along with the commented code, one can find the code documentation at https://bbercovici.github.io/sbgat-doc/index.html. This code documentation is constently updated in order to reflect new functionalities.SBGAT’s user’s manual is available at https://github.com/bbercovici/SBGAT/wiki. This document contains a comprehensive tutorial indicating how to retrieve, compile and run SBGAT from scratch.Some of the upcoming development goals are listed hereafter. First, SBGAT's dynamics module will be extented: the PGM algorithm is the only type of analysis method currently implemented. Future work will therefore consists in broadening SBGAT’s capabilities with the Spherical Harmonics Expansion of the gravity field and the calculation of YORP coefficients. Second, synthetic measurements will soon be available within SBGAT. The software should be able to generate synthetic observations of different type (radar, lightcurve, point clouds,...) from the shape model currently manipulated. Finally, shape interaction capabilities will be added to SBGAT GUI, as it will be augmented with these functionalities using built-in VTK interaction methods.

Quantum chemical exploration of the intramolecular hydrogen bond interaction in 2-thiazol-2-yl-phenol and 2-benzothiazol-2-yl-phenol in the context of excited-state intramolecular proton transfer: A focus on the covalency in hydrogen bond

NASA Astrophysics Data System (ADS)

Paul, Bijan Kumar; Ganguly, Aniruddha; Guchhait, Nikhil

2014-10-01

The present work demonstrates a computational exploration of the intramolecular H-bond (IMHB) interaction in two model heterocyclic compounds - 2-thiazol-2-yl-phenol (2T2YP) and 2-benzothiazol-2-yl-phenol (2B2YP) by meticulous application of various quantum chemical tools. Major emphasis is rendered on the analysis of IMHB interaction by calculation of electron density ρ(r) and Laplacian ∇2ρ(r) at the bond critical point using the Atoms-In-Molecule methodology. Topological features based on ρ(r) suggest that at equilibrium geometry the IMHB interaction develops certain characteristics typical of a covalent interaction. The interplay between aromaticity and Resonance-Assisted H-Bond (RAHB) has also been discussed using both geometrical and magnetic criteria. The occurrence of IMHB interaction in 2T2YP and 2B2YP has also been criticized under the provision of the Natural Bond Orbital (NBO) analysis. The ESIPT phenomenon in the molecular systems is also critically addressed on the lexicon of potential energy surface (PES) analysis.

LENS: web-based lens for enrichment and network studies of human proteins

PubMed Central

2015-01-01

Background Network analysis is a common approach for the study of genetic view of diseases and biological pathways. Typically, when a set of genes are identified to be of interest in relation to a disease, say through a genome wide association study (GWAS) or a different gene expression study, these genes are typically analyzed in the context of their protein-protein interaction (PPI) networks. Further analysis is carried out to compute the enrichment of known pathways and disease-associations in the network. Having tools for such analysis at the fingertips of biologists without the requirement for computer programming or curation of data would accelerate the characterization of genes of interest. Currently available tools do not integrate network and enrichment analysis and their visualizations, and most of them present results in formats not most conducive to human cognition. Results We developed the tool Lens for Enrichment and Network Studies of human proteins (LENS) that performs network and pathway and diseases enrichment analyses on genes of interest to users. The tool creates a visualization of the network, provides easy to read statistics on network connectivity, and displays Venn diagrams with statistical significance values of the network's association with drugs, diseases, pathways, and GWASs. We used the tool to analyze gene sets related to craniofacial development, autism, and schizophrenia. Conclusion LENS is a web-based tool that does not require and download or plugins to use. The tool is free and does not require login for use, and is available at http://severus.dbmi.pitt.edu/LENS. PMID:26680011

Segmentation and learning in the quantitative analysis of microscopy images

NASA Astrophysics Data System (ADS)

Ruggiero, Christy; Ross, Amy; Porter, Reid

2015-02-01

In material science and bio-medical domains the quantity and quality of microscopy images is rapidly increasing and there is a great need to automatically detect, delineate and quantify particles, grains, cells, neurons and other functional "objects" within these images. These are challenging problems for image processing because of the variability in object appearance that inevitably arises in real world image acquisition and analysis. One of the most promising (and practical) ways to address these challenges is interactive image segmentation. These algorithms are designed to incorporate input from a human operator to tailor the segmentation method to the image at hand. Interactive image segmentation is now a key tool in a wide range of applications in microscopy and elsewhere. Historically, interactive image segmentation algorithms have tailored segmentation on an image-by-image basis, and information derived from operator input is not transferred between images. But recently there has been increasing interest to use machine learning in segmentation to provide interactive tools that accumulate and learn from the operator input over longer periods of time. These new learning algorithms reduce the need for operator input over time, and can potentially provide a more dynamic balance between customization and automation for different applications. This paper reviews the state of the art in this area, provides a unified view of these algorithms, and compares the segmentation performance of various design choices.

Interactive simulations as teaching tools for engineering mechanics courses

NASA Astrophysics Data System (ADS)

Carbonell, Victoria; Romero, Carlos; Martínez, Elvira; Flórez, Mercedes

2013-07-01

This study aimed to gauge the effect of interactive simulations in class as an active teaching strategy for a mechanics course. Engineering analysis and design often use the properties of planar sections in calculations. In the stress analysis of a beam under bending and torsional loads, cross-sectional properties are used to determine stress and displacement distributions in the beam cross section. The centroid, moments and products of inertia of an area made up of several common shapes (rectangles usually) may thus be obtained by adding the moments of inertia of the component areas (U-shape, L-shape, C-shape, etc). This procedure is used to calculate the second moments of structural shapes in engineering practice because the determination of their moments of inertia is necessary for the design of structural components. This paper presents examples of interactive simulations developed for teaching the ‘Mechanics and mechanisms’ course at the Universidad Politecnica de Madrid, Spain. The simulations focus on fundamental topics such as centroids, the properties of the moment of inertia, second moments of inertia with respect to two axes, principal moments of inertia and Mohr's Circle for plane stress, and were composed using Geogebra software. These learning tools feature animations, graphics and interactivity and were designed to encourage student participation and engagement in active learning activities, to effectively explain and illustrate course topics, and to build student problem-solving skills.

The MetabolomeExpress Project: enabling web-based processing, analysis and transparent dissemination of GC/MS metabolomics datasets.

PubMed

Carroll, Adam J; Badger, Murray R; Harvey Millar, A

2010-07-14

Standardization of analytical approaches and reporting methods via community-wide collaboration can work synergistically with web-tool development to result in rapid community-driven expansion of online data repositories suitable for data mining and meta-analysis. In metabolomics, the inter-laboratory reproducibility of gas-chromatography/mass-spectrometry (GC/MS) makes it an obvious target for such development. While a number of web-tools offer access to datasets and/or tools for raw data processing and statistical analysis, none of these systems are currently set up to act as a public repository by easily accepting, processing and presenting publicly submitted GC/MS metabolomics datasets for public re-analysis. Here, we present MetabolomeExpress, a new File Transfer Protocol (FTP) server and web-tool for the online storage, processing, visualisation and statistical re-analysis of publicly submitted GC/MS metabolomics datasets. Users may search a quality-controlled database of metabolite response statistics from publicly submitted datasets by a number of parameters (eg. metabolite, species, organ/biofluid etc.). Users may also perform meta-analysis comparisons of multiple independent experiments or re-analyse public primary datasets via user-friendly tools for t-test, principal components analysis, hierarchical cluster analysis and correlation analysis. They may interact with chromatograms, mass spectra and peak detection results via an integrated raw data viewer. Researchers who register for a free account may upload (via FTP) their own data to the server for online processing via a novel raw data processing pipeline. MetabolomeExpress https://www.metabolome-express.org provides a new opportunity for the general metabolomics community to transparently present online the raw and processed GC/MS data underlying their metabolomics publications. Transparent sharing of these data will allow researchers to assess data quality and draw their own insights from published metabolomics datasets.

Coupled rotor/airframe vibration analysis

NASA Technical Reports Server (NTRS)

Sopher, R.; Studwell, R. E.; Cassarino, S.; Kottapalli, S. B. R.

1982-01-01

A coupled rotor/airframe vibration analysis developed as a design tool for predicting helicopter vibrations and a research tool to quantify the effects of structural properties, aerodynamic interactions, and vibration reduction devices on vehicle vibration levels is described. The analysis consists of a base program utilizing an impedance matching technique to represent the coupled rotor/airframe dynamics of the system supported by inputs from several external programs supplying sophisticated rotor and airframe aerodynamic and structural dynamic representation. The theoretical background, computer program capabilities and limited correlation results are presented in this report. Correlation results using scale model wind tunnel results show that the analysis can adequately predict trends of vibration variations with airspeed and higher harmonic control effects. Predictions of absolute values of vibration levels were found to be very sensitive to modal characteristics and results were not representative of measured values.

HIDRA-MAT: A Material Analysis Tool for Fusion Devices

NASA Astrophysics Data System (ADS)

Andruczyk, Daniel; Rizkallah, Rabel; Bedoya, Felipe; Kapat, Aveek; Schamis, Hanna; Allain, Jean Paul

2017-10-01

The former WEGA stellarator which is now operating as HIDRA at the University of Illinois will be almost exclusively used to study the intimate relationship between the plasma interacting with surfaces of different materials. A Material Analysis Tool (HIDRA-MAT) is being designed and will be built based on the successful Material Analysis and Particle Probe (MAPP) which is currently used on NSTX-U at PPPL. This will be an in-situ material diagnostic probe, meaning that all analysis can be done without breaking vacuum. This allows surface changes to be studied in real-time. HIDRA-MAT will consist of several in-situ diagnostics including Langmuir probes (LP), Thermal Desorption Spectroscopy (TDS), X-ray Photo Spectroscopy (XPS) and Ion Scattering Spectroscopy (ISS). This presentation will outline the HIDRA-MAT diagnostic and initial design, as well as its integration into the HIDRA system.

Functionalized C-Glycoside Ketohydrazones: Carbohydrate Derivatization that Retains the Ring Integrity of the Terminal Reducing Sugar

USDA-ARS?s Scientific Manuscript database

Glycosylation often mediates important biological processes through the interaction of carbohydrates with complementary proteins. Most chemical tools for the functional analysis of glycans are highly dependent upon various linkage chemistries that involve the reducing-terminus of carbohydrates. Ho...

Designing Effective Curricula with an Interactive Collaborative Curriculum Design Tool (CCDT)

ERIC Educational Resources Information Center

Khadimally, Seda

2015-01-01

Guided by the principles of the Analysis, Design, Development, Implementation, and Evaluation (ADDIE) instructional design (ID) model, this creative instructional product presents a learning/teaching approach that is fundamentally constructivist. For the purposes of designing effective instruction in an academic preparation course, a…

The Integrated Farm System Model: A Tool for Whole Farm Nutrient Management Analysis

USDA-ARS?s Scientific Manuscript database

With tighter profit margins and increasing environmental constraints, strategic planning of farm production systems is becoming both more important and more difficult. This is especially true for integrated crop and animal production systems. Animal production is complex with a number of interacting...

Undergraduates, Technology, and Social Connections

ERIC Educational Resources Information Center

Palmer, Betsy; Boniek, Susan; Turner, Elena; Lovell, Elyse D'nn

2014-01-01

The purpose of this study was to examine the spectrum of undergraduate students' social interactions and related technological tools. Qualitative methods were used for this phenomenological study exploring 35 in-person interviews, with horizonalization in an open coding system secured by in-depth analysis which revealed nuanced themes and…

Simulation Tools for Power Electronics Courses Based on Java Technologies

ERIC Educational Resources Information Center

Canesin, Carlos A.; Goncalves, Flavio A. S.; Sampaio, Leonardo P.

2010-01-01

This paper presents interactive power electronics educational tools. These interactive tools make use of the benefits of Java language to provide a dynamic and interactive approach to simulating steady-state ideal rectifiers (uncontrolled and controlled; single-phase and three-phase). Additionally, this paper discusses the development and use of…

Learning SQL Programming with Interactive Tools: From Integration to Personalization

ERIC Educational Resources Information Center

Brusilovsky, Pete; Sosnovsky, Sergey; Yudelson, Michael V.; Lee, Danielle H.; Zadorozhny, Vladimir; Zhou, Xin

2010-01-01

Rich, interactive eLearning tools receive a lot of attention nowadays from both practitioners and researchers. However, broader dissemination of these tools is hindered by the technical difficulties of their integration into existing platforms. This article explores the technical and conceptual problems of using several interactive educational…

Bringing "Scientific Expeditions" Into the Schools

NASA Technical Reports Server (NTRS)

Watson, Val; Lasinski, T. A. (Technical Monitor)

1995-01-01

Two new technologies, the FASTexpedition and Remote FAST, have been developed that provide remote, 3D, high resolution, dynamic, interactive viewing of scientific data (such as simulations or measurements of fluid dynamics). The FASTexpedition permits one to access scientific data from the World Wide Web, take guided expeditions through the data, and continue with self controlled expeditions through the data. Remote FAST permits collaborators at remote sites to simultaneously view an analysis of scientific data being controlled by one of the collaborators. Control can be transferred between sites. These technologies are now being used for remote collaboration in joint university, industry, and NASA projects in computational fluid dynamics (CFD) and wind tunnel testing. Also, NASA Ames Research Center has initiated a project to make scientific data and guided expeditions through the data available as FASTexpeditions on the World Wide Web for educational purposes. Previously, remote visualiZation of dynamic data was done using video format (transmitting pixel information) such as video conferencing or MPEG movies on the Internet. The concept for this new technology is to send the raw data (e.g., grids, vectors, and scalars) along with viewing scripts over the Internet and have the pixels generated by a visualization tool running on the viewer's local workstation. The visualization tool that is currently used is FAST (Flow Analysis Software Toolkit). The advantages of this new technology over using video format are: 1. The visual is much higher in resolution (1280xl024 pixels with 24 bits of color) than typical video format transmitted over the network. 2. The form of the visualization can be controlled interactively (because the viewer is interactively controlling the visualization tool running on his workstation). 3. A rich variety of guided expeditions through the data can be included easily. 4. A capability is provided for other sites to see a visual analysis of one site as the analysis is interactively performed. Control of the analysis can be passed from site to site. 5. The scenes can be viewed in 3D using stereo vision. 6. The network bandwidth used for the visualization using this new technology is much smaller than when using video format. (The measured peak bandwidth used was 1 Kbit/sec whereas the measured bandwidth for a small video picture was 500 Kbits/sec.)

An Interactive, Integrated, Instructional Pathway to the LEAD Science Gateway

NASA Astrophysics Data System (ADS)

Yalda, S.; Clark, R.; Davis, L.; Wiziecki, E. N.

2008-12-01

Linked Environments for Atmospheric Discovery (LEAD) is a bold and revolutionary paradigm that through a Web-based Service Oriented Architecture (SOA) exposes the user to a rich environment of data, models, data mining and visualization and analysis tools, enabling the user to ask science questions of applications while the complexity of the software and middleware managing these applications is hidden from the user. From its inception in 2003, LEAD has championed goals that have context for the future of weather and related research and education. LEAD espouses to lowering the barrier for using complex end-to-end weather technologies by a) democratizing the availability of advanced weather technologies, b) empowering the user of these technologies to tackle a variety of problems, and c) facilitating learning and understanding. LEAD, as it exists today, is poised to enable a diverse community of scientists, educators, students, and operational practitioners. The project has been informed by atmospheric and computer scientists, educators, and educational consultants who, in search of new knowledge, understanding, ideas, and learning methodologies, seek easy access to new capabilities that allow for user-directed and interactive query and acquisition, simulation, assimilation, data mining, computational modeling, and visualization. As one component of the total LEAD effort, the LEAD education team has designed interactive, integrated, instructional pathways within a set of learning modules (LEAD-to-Learn) to facilitate, enhance, and enable the use of the LEAD gateway in the classroom. The LEAD education initiative focuses on the means to integrate data, tools, and services used by researchers into undergraduate meteorology education in order to provide an authentic and contextualized environment for teaching and learning. Educators, educational specialists, and students from meteorology and computer science backgrounds have collaborated on the design and development of learning materials, as well as new tools and features, to enhance the appearance and use of the LEAD portal gateway and its underlying cyberinfrastructure in an educational setting. The development of educational materials has centered on promoting the accessibility and use of meteorological data and analysis tools through the LEAD portal by providing instructional materials, additional custom designed tools that build off of Unidata's Integrated Data Viewer (IDV) (e.g. IDV Basic and NCDestroyer), and an interactive component that takes the user through specific tasks utilizing multiple tools. In fact, select improvements to parameter lists and domain subsetting have inspired IDV developers to incorporate changes in IDV revisions that are now available to the entire community. This collection of materials, demonstrations, interactive guides, student exercises, and customized tools, which are now available to the educator and student through the LEAD portal gateway, can serve as an instructional pathway for a set of guided, phenomenon-based exercises (e.g. fronts, lake-effect snows, etc.). This paper will provide an overview of the LEAD education and outreach efforts with a focus on the design of Web-based educational materials and instructional approaches for user interaction with the LEAD portal gateway and the underlying cyberinfrastructure, and will encourage educators, especially those involved in undergraduate meteorology education, to begin incorporating these capabilities into their course materials.

Scientists' sense making when hypothesizing about disease mechanisms from expression data and their needs for visualization support.

PubMed

Mirel, Barbara; Görg, Carsten

2014-04-26

A common class of biomedical analysis is to explore expression data from high throughput experiments for the purpose of uncovering functional relationships that can lead to a hypothesis about mechanisms of a disease. We call this analysis expression driven, -omics hypothesizing. In it, scientists use interactive data visualizations and read deeply in the research literature. Little is known, however, about the actual flow of reasoning and behaviors (sense making) that scientists enact in this analysis, end-to-end. Understanding this flow is important because if bioinformatics tools are to be truly useful they must support it. Sense making models of visual analytics in other domains have been developed and used to inform the design of useful and usable tools. We believe they would be helpful in bioinformatics. To characterize the sense making involved in expression-driven, -omics hypothesizing, we conducted an in-depth observational study of one scientist as she engaged in this analysis over six months. From findings, we abstracted a preliminary sense making model. Here we describe its stages and suggest guidelines for developing visualization tools that we derived from this case. A single case cannot be generalized. But we offer our findings, sense making model and case-based tool guidelines as a first step toward increasing interest and further research in the bioinformatics field on scientists' analytical workflows and their implications for tool design.

Scientists’ sense making when hypothesizing about disease mechanisms from expression data and their needs for visualization support

PubMed Central

2014-01-01

A common class of biomedical analysis is to explore expression data from high throughput experiments for the purpose of uncovering functional relationships that can lead to a hypothesis about mechanisms of a disease. We call this analysis expression driven, -omics hypothesizing. In it, scientists use interactive data visualizations and read deeply in the research literature. Little is known, however, about the actual flow of reasoning and behaviors (sense making) that scientists enact in this analysis, end-to-end. Understanding this flow is important because if bioinformatics tools are to be truly useful they must support it. Sense making models of visual analytics in other domains have been developed and used to inform the design of useful and usable tools. We believe they would be helpful in bioinformatics. To characterize the sense making involved in expression-driven, -omics hypothesizing, we conducted an in-depth observational study of one scientist as she engaged in this analysis over six months. From findings, we abstracted a preliminary sense making model. Here we describe its stages and suggest guidelines for developing visualization tools that we derived from this case. A single case cannot be generalized. But we offer our findings, sense making model and case-based tool guidelines as a first step toward increasing interest and further research in the bioinformatics field on scientists’ analytical workflows and their implications for tool design. PMID:24766796