Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “interactive visual analysis tool”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 55 records · Page 3

Online Interactive Platform for COVID-19 Literature Visual Analytics: Platform Development Study

Background Papers on COVID-19 are being published at a high rate and concern many different topics. Innovative tools are needed to aid researchers to find patterns in this vast amount of literature to identify subsets of interest in an automated fashion. Objective We present a new online software resource with a friendly user interface that allows users to query and interact with visual representations of relationships between publications. Methods We publicly released an application called PLATIPUS (Publication Literature Analysis and Text Interaction Platform for User Studies) that allows researchers to interact with literature supplied by COVIDScholar via a visual analytics platform. This tool contains standard filtering capabilities based on authors, journals, high-level categories, and various research-specific details via natural language processing and dozens of customizable visualizations that dynamically update from a researcher’s query. Results PLATIPUS is available online and currently links to over 100,000 publications and is still growing. This application has the potential to transform how COVID-19 researchers use public literature to enable their research. Conclusions The PLATIPUS application provides the end user with a variety of ways to search, filter, and visualize over 100,00 COVID-19 publications.</:p>

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

A browser-based tool for visualization and analysis of diffusion MRI data

Human neuroscience research faces several challenges with regards to reproducibility. While scientists are generally aware that data sharing is important, it is not always clear how to share data in a manner that allows other labs to understand and reproduce published findings. Here we report a new open source tool, AFQ-Browser, that builds an interactive website as a companion to a diffusion MRI study. Because AFQ-Browser is portable—it runs in any web-browser—it can facilitate transparency and data sharing. Moreover, by leveraging new web-visualization technologies to create linked views between different dimensions of the dataset (anatomy, diffusion metrics, subject metadata), AFQ-Browser facilitates exploratory data analysis, fueling new discoveries based on previously published datasets. In an era where Big Data is playing an increasingly prominent role in scientific discovery, so will browser-based tools for exploring high-dimensional datasets, communicating scientific discoveries, aggregating data across labs, and publishing data alongside manuscripts.

60 APPLIED LIFE SCIENCES↗

Hardening DOE R&D Software Tools for Web-based Visualization SBIR Phase I Final Report

Ubiquitous web-based visualization is essential to delivering large-scale data visualization to various stakeholders, from the scientist to the board member. These stakeholders will not tolerate a stalled application or a pop-up window asking them to wait for the processing to complete. They require a responsive and interactive visualization environment with high-quality imagery suitable for detailed analysis and boardroom presentations. At Kitware, Inc., we have accomplished web visualization to this point, leveraging state-of-the-art tools like HTML5, CSS3, SVG, Canvas, and WebGL. Solutions that leverage a combination of these technologies are necessary to handle workloads that vary significantly in data size efficiently. However, it is not always practical to move large data to the web client for visualization. Kitware's ParaView as a Service combines client-side visualization using both distributed processing and remote rendering on big data impractical to move. Existing distributed processing and remote rendering solution's interactivity is below the expectations of web-based applications. Our project examined proposed solutions to the areas outlined above in ParaView as a Service. We have investigated concurrent pipelines, streaming images, progressive rendering, and optimization of algorithms and data movement to address these concerns. For the Phase I project, we completed the proposed work plan. As a result, the project produced three prototypes of essential importance for web visualization and the ParaView as a Service community. We created a simple desktop application for an interactive streamline placement prototype, a web-based interactive streamline placement prototype, and a web-based progressive rendering utilizing raytracing prototype. These prototypes relied on the hardening of emerging software toolkits funded by the Department of Energy (DOE) Advanced Scientific Computing Research (ASCR) program (such as ParaView, VTK-m, and Mochi). We blended these components into web-based visualization prototypes that meet the industry's expectations for interactivity and responsiveness. The Phase I project had four essential focus areas: 1. Develop prototype ParaView as a Service backend server using asynchronous, non-blocking design principles. 2. Develop a prototype web application that uses the ParaView as a Service backend server for remote data visualization. 3. Implement image streaming with encoding/compression and progressive rendering capabilities in the proposed platform. 4. Evaluate the prototype developed and summarize observations, including the challenges and pitfalls of our approach. After our successful completion of Phase I, we are strongly positioned to propose a successful Phase II project.

Geveci, Berk↗

Visual‐Analytics Bridge Complexity and Accessibility for Robust Urban Water Planning

Urban water resources planning is complicated by unprecedented uncertainty in supply and demand. Real‐world planning often simplifies the full range of uncertainty faced by a system into a limited set of deterministic scenarios to enhance accessibility for decision‐makers and the public. However, overlooking uncertainty can expose the system to failures. On the other end of the spectrum, academically developed tools for scenario analysis rigorously quantify the combined effects of multiple sources of uncertainty, but the practical application of these models is limited by the challenges of information visualization and communication of results. In short, municipal water supply planners lack access to planning frameworks that effectively integrate a rigorous treatment of uncertainty with accessible, user‐friendly visual and interactive tools to enhance user accessibility. In this work, we fill this gap by proposing Visual‐Robust Decision Making, and demonstrate an application for the city of Santa Barbara (SB), CA. Santa Barbara faces multiple uncertainties from pending state and federal regulations to changing hydrology and water demand. The city seeks to increase its water portfolio robustness by expanding its seawater desalination plant, but must decide how much capacity to add. We introduce computational tools that assess uncertainty across nine uncertain drivers identified with the help of water planners in SB. To allow public participation in the desalination expansion decision, we develop interactive visual‐analytics to aid decision‐makers and stakeholders in navigating complex scenario analysis outcomes. Our results quantify the tradeoffs between increased capacity and system robustness and aim to enhance participation and uncertainty characterization of urban water planning efforts.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Determining Patterns from Radiation Portal Monitor Data: Enabling Data Insight with Visual and Interactive Exploratory Data Analysis

Smuggling of nuclear and radiological material is a complex problem that will need to be analyzed from a variety of angles in order to effectively combat something so rare, yet so hazardous. One crucial tool in the effort to detect and deter smuggling of rad/nuc materials is the radiation portal monitor (RPM)—machines that scan passengers at airports, vehicles and trains at border crossings, and shipping containers at ports throughout the world. While data from RPMs are regularly analyzed at the individual lane level to ensure monitor health and good operation, aggregate analysis of the data has not gone far beyond summary statistics such as number of occupancies and alarm rates. In particular, there are opportunities to carry out interactive exploratory data analysis with the help of tools like the R package Shiny and methods that lend themselves to the visual display of spatiotemporal correlations such as spatial PCA and detrended cross-correlation analysis. By doing so, we discover interesting spatiotemporal patterns in the data that point to specific events or anomalous moments in time that warrant further analysis.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

A Visual Analytics Approach to Structured Data Analysis to Enhance Nonproliferation and Arms Control Verification Activities

Analysis activities for Nonproliferation and Arms Control verification require the use of many types of data. Tabular structured data, such as Excel spreadsheets and relational databases, have traditionally been used for data mining activities, where specific queries are issued against data to look for matching results. The application of visual analytics tools to structured data enables further exploration of datasets to promote discovery of previously unknown results. This paper discusses the application of a specific visual analytics tool to datasets related to the field of Arms Control and Nonproliferation to promote the use of visual analytics more broadly in this domain. Visual analytics focuses on analytical reasoning facilitated by interactive visual interfaces (Wong and Thomas 2004). It promotes exploratory analysis of data, and complements data mining technologies where known patterns can be mined for. Also with a human in the loop, they can bring in domain knowledge and subject matter expertise. Visual analytics has not widely been applied to this domain. In this paper, we will focus on one type of data: structured data, and show the results of applying a specific visual analytics tool to answer questions in the Arms Control and Nonproliferation domain. We chose to use the T.Rex tool, a visual analytics tool developed at PNNL, which uses a variety of visual exploration patterns to discover relationships in structured datasets, including a facet view, graph view, matrix view, and timeline view. The facet view enables discovery of relationships between categorical information, such as countries and locations. The graph tool visualizes node-link relationship patterns, such as the flow of materials being shipped between parties. The matrix visualization shows highly correlated categories of information. The timeline view shows temporal patterns in data. In this paper, we will use T.Rex with two different datasets to demonstrate how interactive exploration of the data can aid an analyst with arms control and nonproliferation verification activities. Using a dataset from PIERS (PIERS 2014), we will show how container shipment imports and exports can aid an analyst in understanding the shipping patterns between two countries. We will also use T.Rex to examine a collection of research publications from the IAEA International Nuclear Information System (IAEA 2014) to discover collaborations of concern. We hope this paper will encourage the use of visual analytics structured data analytics in the field of nonproliferation and arms control verification. Our paper outlines some of the challenges that exist before broad adoption of these kinds of tools can occur and offers next steps to overcome these challenges.

arms control↗

ParaView Catalyst: Enabling In Situ Data Analysis and Visualization

Computer simulations are growing in sophistication and producing results of ever greater fidelity. This trend has been enabled by advances in numerical methods and increasing computing power. However these advances come with several costs including massive increases in data size, difficulties examining output data, challenges in configuring simulation runs, and difficulty debugging running codes. Interactive visualization tools, like ParaView, have been used for post-processing of simulation results. However, the increasing data sizes, and limited storage and bandwidth make high fidelity post-processing impractical. In situ analysis is recognized as one of the ways to address these challenges. In situ analysis moves some of the post-processing tasks in line with the simulation code thus short circuiting the need to communicate the data between the simulation and analysis via storage. ParaView Catalyst is a data processing and visualization library that enables in situ analysis and visualization. Built on and designed to interoperate with the standard visualization toolkit VTK and the ParaView application, Catalyst enables simulations to intelligently perform analysis, generate relevant output data, and visualize results concurrent with a running simulation. Here, we provide an overview of the Catalyst framework and some of the success stories.

97 MATHEMATICS AND COMPUTING↗

Scoreboard

Emerging HPC machines have given rise to enhanced compute power that far outstrips the machine's ability to save large scale results for post-processing. To combat this, in situ data analysis techniques are slowly being adopted. With in situ data management favoring workflows composed of multiple simulations and analyses connected in transit on heterogeneous machines, scientists and engineers need a tool that enables them to create data extracts, visualizations, and interactively monitor and steer their simulations. Scoreboard Phase II is a next generation analysis software that supports composite in transit workflows on heterogeneous architectures and restores interactivity to in situ data analysis through simulation monitoring and computational steering. Scoreboard provides a simulation dashboard with graphs of metrics over time, controls for setting custom simulation steering parameters, controls for managing the set of data extracts being produced in the simulation, as well as the ability to explore data extracts, all from a web browser. Realizing the vision outlined in this project required research into making a system that integrates end to end from simulations all the way to the user. In situ tools generally suffer from complexity and excessive software dependencies. Scoreboard, by contrast, is easy to build and integrate into simulation codes and it provides first class FORTRAN support. The Scoreboard library is capable of in situ and in transit data analysis that can produce data extracts commonly needed for Computational Fluid Dynamics (CFD) analysis. Simulations can transparently stage data in transit to a Scoreboard Endpoint program, which can accept their data and produce the requested data extracts. This lets simulations return to their work while the Endpoint works on the analysis. Efficiently staging the data at scale was a topic of this research. Scoreboard provides the means to let the user manage data extracts and monitor/steer many simulations from a web browser. This area of the research focused on discovery of in transit network components to expose and control their steering parameters within an interactive browser-based user interface that includes: system topology, gathered metrics, notifications, dynamically-generated steering controls, and exploration of visualization data products.

Whitlock, BradJoseph [Intelligent Light] (00000001↗

T.Rex

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 a 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.

Source record↗

Modeling and evaluating user behavior in exploratory visual analysis

Empirical evaluation methods for visualizations have traditionally focused on assessing the outcome of the visual analytic process as opposed to characterizing how that process unfolds. There are only a handful of methods that can be used to systematically study how people use visualizations, making it difficult for researchers to capture and characterize the subtlety of cognitive and interaction behaviors users exhibit during visual analysis. To validate and improve visualization design, however, it is important for researchers to be able to assess and understand how users interact with visualization systems under realistic scenarios. This paper presents a methodology for modeling and evaluating the behavior of users in exploratory visual analysis. We model visual exploration using a Markov chain process comprising transitions between mental, interaction, and computational states. These states and the transitions between them can be deduced from a variety of sources, including verbal transcripts, videos and audio recordings, and log files. This model enables the evaluator to characterize the cognitive and computational processes that are essential to insight acquisition in exploratory visual analysis, and reconstruct the dynamics of interaction between the user and the visualization system. We illustrate this model with two exemplar user studies, and demonstrate the qualitative and quantitative analytical tools it affords.

97 MATHEMATICS AND COMPUTING↗

User-Driven Sampling Strategies in Image Exploitation

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. 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.

97 MATHEMATICS AND COMPUTING↗

Interactive Corpus Analysis Tool

The Interactive Corpus Analysis Tool (ICAT) is an interactive machine learning dashboard for unlabeled text/natural language processing datasets that allows a user to iteratively and visually define features, explore and label instances of their dataset, and simultaneously train a logistic regression model. ICAT was created to allow subject matter experts in a specific domain to directly train their own models for unlabeled datasets visually, without needing to be a machine learning expert or needing to know how to code the models themselves. This approach allows users to directly leverage the power of machine learning, but critically, also involves the user in the development of the machine learning model.

Martindale, Nathan [Oak Ridge National Lab. (ORNL)↗

Measurement of a Neutrino-Induced Charged Current Single Neutral Pion Cross Section at MicroBooNE

Micro Booster Neutrino Experiment (MicroBooNE) is a Liquid Argon Time Projection Chamber (LArTPC) operating in the Booster Neutrino Beamline at Fermi National Accelerator Laboratory. MicroBooNE's physics goals include studying short basline $\nu$ oscillation and performing a suite of low energy $\nu$ cross section measurements. Of particular interest to MicroBooNE, and the broader LArTPC community, are electromagnetic showers; these showers are at the heart of searches for charged current $\nu_e$ interactions, including MicroBooNE's flagship search for a MiniBooNE-like low energy excess (LEE). Neutral current $\pi^0$'s, which decay into 2 electromagnetic showers ($\gamma$'s), are the dominant source of non-$\nu_e$ backgrounds in searches for $\nu_{\mu}\rightarrow\nu_e$ oscillations in LArTPCs, such as the LEE. While precise measurements of this neutral current channel will provide a tight constraint on our modeling uncertainties, such events are particularly difficult to iden tify in data with our current tools, as there is often little or no activity at the neutrino interaction point. Charged current interactions, on the other hand, have simpler topologies with a long $\mu$ track that anchors to the interaction vertex. With a vertex in hand, we can develop automated reconstruction tools for neutrino-induced shower topologies (like the $\gamma$'s from $\pi^0$ decay). Thus, in studying charged current $\pi^0$ interactions, we are developing tools that can potentially be used to reconstruct an important LEE background, while also studying the physics of neutrino interactions, of which data is sparse for argon. This thesis reports the world's first measurement of the absolute, flux-averaged cross section of $\nu_{\mu}$-charged current single $\pi^0$ production on argon. The analysis chain begins with the selection of inclusive $\nu_\mu$ charged current events, where a candidate $\mu$ and neutrino interaction vertex are identified. These events are t hen passed to a reconstruction framework where electromagnet! ic shower candidates are reconstructed using computer visualization tools. Finally, the cross section is calculated on two reconstructed topologies: those with at least two reconstructed showers and those with at least one. Additionally, this work describes the first fully-automated electromagnetic shower reconstruction process employed by a LArTPC to perform a cross section analysis. We measure the flux averaged cross section on argon at 824 MeV via the two and one shower selections respectively to be \par \noindent $\sigma_{\geq2 Shower}$ = (2.56 $\pm$ $0.50_{stat}$ $\pm$ $0.31_{genie}$ $\pm$ $0.37_{flux}$ $\pm$ $0.31_{det}$) $\times$ $10^{-38}$ $\frac{cm^2}{Ar}$, \par \noindent $\sigma_{\geq 1 Shower}$ = (2.64 $\pm$ $0.33_{stat}$ $\pm$ $0.36_{genie}$ $\pm$ $0.38_{flux}$ $\pm$ $0.35_{det}$) $\times$ $10^{-38}$ $\frac{cm^2}{Ar}$.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Enabling a systems biology knowledgebase with gaggle and firegoose

The overall goal of this project was to extend the existing Gaggle and Firegoose systems to develop an open-source technology that runs over the web and links desktop applications with many databases and software applications. This technology would enable researchers to incorporate workflows for data analysis that can be executed from this interface to other online applications. The four specific aims were to (1) provide one-click mapping of genes, proteins, and complexes across databases and species; (2) enable multiple simultaneous workflows; (3) expand sophisticated data analysis for online resources; and enhance open-source development of the Gaggle-Firegoose infrastructure. Gaggle is an open-source Java software system that integrates existing bioinformatics programs and data sources into a user-friendly, extensible environment to allow interactive exploration, visualization, and analysis of systems biology data. Firegoose is an extension to the Mozilla Firefox web browser that enables data transfer between websites and desktop tools including Gaggle. In the last phase of this funding period, we have made substantial progress on development and application of the Gaggle integration framework. We implemented the workspace to the Network Portal. Users can capture data from Firegoose and save them to the workspace. Users can create workflows to start multiple software components programmatically and pass data between them. Results of analysis can be saved to the cloud so that they can be easily restored on any machine. We also developed the Gaggle Chrome Goose, a plugin for the Google Chrome browser in tandem with an opencpu server in the Amazon EC2 cloud. This allows users to interactively perform data analysis on a single web page using the R packages deployed on the opencpu server. The cloud-based framework facilitates collaboration between researchers from multiple organizations. We have made a number of enhancements to the cmonkey2 application to enable and improve the integration within different environments, and we have created a new tools pipeline for generating EGRIN2 models in a largely automated way.

97 MATHEMATICS AND COMPUTING↗

Quantifying element incorporation in multispecies biofilms using nanoscale secondary ion mass spectrometry image analysis

Elucidating nutrient exchange in microbial communities is an important step in understanding the relationships between microbial systems and global biogeochemical cycles, but these communities are complex and the interspecies interactions that occur within them are not well understood. Phototrophic consortia are useful and relevant experimental systems to investigate such interactions as they are not only prevalent in the environment, but some are cultivable in vitro and amenable to controlled scientific experimentation. Nanoscale secondary ion mass spectrometry (NanoSIMS) is a powerful, high spatial resolution tool capable of visualizing the metabolic activities of single cells within a biofilm, but quantitative analysis of the resulting data has typically been a manual process, resulting in a task that is both laborious and susceptible to human error. In this work, the authors describe the creation and application of a semiautomated image-processing pipeline that can analyze NanoSIMS-generated data, applied to phototrophic biofilms as an example. The tool employs an image analysis process, which includes both elemental and morphological segmentation, producing a final segmented image that allows for discrimination between autotrophic and heterotrophic biomass, the detection of individual cyanobacterial filaments and heterotrophic cells, the quantification of isotopic incorporation of individual heterotrophic cells, and calculation of relevant population statistics. The authors demonstrate the functionality of the tool by using it to analyze the uptake of 15 N provided as either nitrate or ammonium through the unicyanobacterial consortium UCC-O and imaged via NanoSIMS. The authors found that the degree of 15N incorporation by individual cells was highly variable when labeled with 15 NH 4 + , but much more even when biofilms were labeled with 15 NO 3 – . In the 15 NH 4 + -amended biofilms, the heterotrophic distribution of 15 N incorporation was highly skewed, with a large population showing moderate 15 N incorporation and a small number of organisms displaying very high 15 N uptake. The results showed that analysis of NanoSIMS data can be performed in a way that allows for quantitation of the elemental uptake of individual cells, a technique necessary for advancing research into the metabolic networks that exist within biofilms with statistical analyses that are supported by automated, user-friendly processes.

59 BASIC BIOLOGICAL SCIENCES↗

EnergyPlus Model Context Protocol Server (EnergyPlus-MCP) v0.1

EnergyPlus-MCP is the first open-source Model Context Protocol server specifically designed for EnergyPlus building energy simulation. This innovative software enables AI assistants and other applications to interact programmatically with EnergyPlus through a standardized, secure interface, eliminating traditional technical barriers in building energy modeling. The software provides specialized tools across five functional domains: server management, model configuration and loading, comprehensive building component inspection, systematic model modification, and simulation execution with results visualization. Key features include automated HVAC system discovery and topology mapping, advanced schedule analysis, intelligent model validation, and interactive visualization capabilities. EnergyPlus-MCP's layered architecture ensures robust separation between protocol communication and domain expertise, enabling scalable deployment across organizations, educational institutions, and research teams. Unlike direct LLM approaches that suffer from inconsistent results and security gaps, EnergyPlus-MCP provides validated, reliable interactions while maintaining scientific rigor. This democratizes sophisticated building energy analysis, making EnergyPlus accessible to broader audiences through conversational interfaces and streamlined workflows.

Li, Han [Lawrence Berkeley National Laboratory (LB↗

Evaluation system and web infrastructure for the second cryo-EM model challenge

An evaluation system and a web infrastructure were developed for the second cryo-EM model challenge. The evaluation system includes tools to validate stereo-chemical plausibility of submitted models, check their fit to the corresponding density maps, estimate their overall and per-residue accuracy, and assess their similarity to reference cryo-EM or X-ray structures as well as other models submitted in this challenge. The web infrastructure provides a convenient interface for analyzing models at different levels of detail. As a result, it includes interactively sortable tables of evaluation scores for different subsets of models and different sublevels of structure organization, and a suite of visualization tools facilitating model analysis.

59 BASIC BIOLOGICAL SCIENCES↗

ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data

The high-resolution and mass accuracy of Fourier transform mass spectrometry (FT-MS) has made it an increasingly popular technique for discerning the composition of soil, plant and aquatic samples containing complex mixtures of proteins, carbohydrates, lipids, lignins, hydrocarbons, phytochemicals and other compounds. Thus, there is a growing demand for informatics tools to analyze FT-MS data that will aid investigators seeking to understand the availability of carbon compounds to biotic and abiotic oxidation and to compare fundamental chemical properties of complex samples across groups. We present ftmsRanalysis, an R package which provides an extensive collection of data formatting and processing, filtering, visualization, and sample and group comparison functionalities. The package provides a suite of plotting methods and enables expedient, flexible and interactive visualization of complex datasets through functions which link to a powerful and interactive visualization user interface, Trelliscope. Example analysis using FT-MS data from a soil microbiology study demonstrates the core functionality of the package and highlights the capabilities for producing interactive visualizations.

97 MATHEMATICS AND COMPUTING↗