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At least 19 records

Leveraging Application Data Constraints to Optimize Database-Backed Web Applications

Exploiting the relationships among data is a classical query optimization technique. As persistent data is increasingly being created and maintained programmatically, prior work that infers data relationships from data statistics misses an important opportunity. We present Coco, the first tool that identifies data relationships by analyzing database-backed applications. Once identified, Coco leverages the constraints to optimize the application's physical design and query execution. Instead of developing a fixed set of predefined rewriting rules, Coco employs an enumerate-test-verify technique to automatically exploit the discovered data constraints to improve query execution. Each resulting rewrite is provably equivalent to the original query. Using 14 real-world web applications, our experiments show that Coco can discover numerous data constraints from code analysis and improve real-world application performance significantly.

Computer Science↗

Offshore Geologic Carbon Storage (GCS) Data Collection Web Application

The Offshore Geologic Carbon Storage Data Collection Web Application is an interactive data collection which aggregates and disseminates publicly available data to support offshore geologic carbon storage (GCS) in the United States. This data collection can be leveraged by stakeholders to understand where GCS may be viable offshore, create GCS project analogs, and address challenges to GCS in offshore environments. Use of this tool is solely at the discretion of the user. See full Federal Disclaimer for further information (https://netl.doe.gov/home/disclaimer).

Carbon Sequestration↗

FREDA: A Web Application for the Processing, Analysis, and Visualization of Fourier‐Transform Mass Spectrometry Data

The high-resolution measurement capability of Fourier-transform mass spectrometry (FT-MS) has made it a necessity for exploring the molecular composition of complex organic mixtures, like soil, plant, aquatic, and petroleum samples. This demand has driven a need for informatics tools to explore and analyze FT-MS data in a robust and reproducible manner. FREDA is an interactive web application developed to enable spectrometrists to format, process, and explore their FT-MS data without the need for statistical programming expertise. FREDA was built to explore outputs from a molecular identification tool, like CoreMS, and provide a suite of methods to filter data, compute chemical properties of peaks, statistically compare samples and groups of samples, conduct exploratory data analysis, and download the results with a report detailing all steps conducted. To demonstrate the utility of FREDA, an example analysis was conducted using FT-MS data from a soil microbiology study of samples collected in two different soil depths at the Sphagnum bog forest north of Grand Rapids, Minnesota. Differences between the two depths are observed using Kendrick, Gibbs free energy, and van Krevelen plots. G-tests are used to quantify a significant difference between the groups. All analyses and plotting are conducted using only the FREDA application. FREDA is an open-source and readily available web application that allows users to explore and make statistically valid conclusions about their FT-MS data. The application is available online (https://map.emsl.pnnl.gov/app/freda) with a tutorial web series (https://youtu.be/k5HLE2kNSBY?si=yB6sGoyvzxrFf5MP) and freely accessible code on Github (https://github.com/EMSL-Computing/FREDA).

47 OTHER INSTRUMENTATION↗

Asc-Seurat: analytical single-cell Seurat-based web application

Abstract Background Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of transcriptomes, arising as a powerful tool for discovering and characterizing cell types and their developmental trajectories. However, scRNA-seq analysis is complex, requiring a continuous, iterative process to refine the data and uncover relevant biological information. A diversity of tools has been developed to address the multiple aspects of scRNA-seq data analysis. However, an easy-to-use web application capable of conducting all critical steps of scRNA-seq data analysis is still lacking. Summary We present Asc-Seurat, a feature-rich workbench, providing an user-friendly and easy-to-install web application encapsulating tools for an all-encompassing and fluid scRNA-seq data analysis. Asc-Seurat implements functions from the Seurat package for quality control, clustering, and genes differential expression. In addition, Asc-Seurat provides a pseudotime module containing dozens of models for the trajectory inference and a functional annotation module that allows recovering gene annotation and detecting gene ontology enriched terms. We showcase Asc-Seurat’s capabilities by analyzing a peripheral blood mononuclear cell dataset. Conclusions Asc-Seurat is a comprehensive workbench providing an accessible graphical interface for scRNA-seq analysis by biologists. Asc-Seurat significantly reduces the time and effort required to analyze and interpret the information in scRNA-seq datasets.

60 APPLIED LIFE SCIENCES↗

Web application for machining parameter recommendation using visual analytics

The computer codes create a web application including multiple user interfaces, visualizations, interaction modules between the user, and visualizations. The visualizations will be interactive, allowing users to query the data directly, and they will be arranged in a dashboard. When selections are made in one visualization, filters will be applied to all other visualizations providing a coordinated system for asking questions about the data. The visualization can be utilized for manufacturing data management, analysis, and recommendation.

Chae, Junghoon↗

Dynamic CCS-EJ-SJ Database and Web Application - What's New

At the 2024 FECM/NETL Carbon Management Research Project Review Meeting, within the Carbon Transport and Storage Breakout Session 3, the presentation "Dynamic CCS-EJ-SJ Database and Web Application - What's New" highlights the critical tool designed to integrate environmental and social justice considerations into Carbon Capture and Storage (CCS) projects. Key features include an interactive dashboard for data access and visualization, which supports stakeholders in making informed decisions regarding CCS implementation, and updated data layers. The latest version enhances data integration and usability, providing a comprehensive resource for assessing the social and environmental impacts of CCS projects. There are 7 categories in the CCS EJSJ v2 database (released 03/31/2024): environmental justice, energy justice, economic justice, social justice, ecosystem assets, clean energy, and infrastructure. Most of the layers within each category have been updated in this version. As compared to the old database, there are 3 new categories in the v2 database: ecosystem assets, clean energy, and infrastructure.

Sharma, Maneesh↗

OmicsMLMentor: A Web Application for Guided Machine Learning Analysis of Omics Data

Expression-based omics technologies (e.g. proteomics, metabolomics, transcriptomics, etc.) increasingly rely on supervised and unsupervised machine learning (ML) models to find key biomolecules distinguishing conditions, identify natural groupings in biological data, or generate predictions for outcomes of interest. Fitting ML models to omics data presents several challenges, including handling missing data, selecting a normalization method, choosing a valid model, and optimizing hyperparameters, all requiring statistical programming skills to address these challenges. Thus, the open-source web application SLOPE was designed to lower the barrier to ML modeling for omics data. SLOPE supports the fitting of 15 ML models (10 supervised and 5 unsupervised) tailored to omics datasets, such as proteomics, metabolomics, lipidomics, and transcriptomics. SLOPE offers several omics-specific features, including methods for handling missingness (imputation, conversion, removal), normalization tests, ranking of models based on the structure of a user’s data and user input, and optimal hyperparameter selections using cross-validation splits. By streamlining ML workflows for omics analysis, SLOPE address critical gaps in existing online web tools, facilitating a broader adoption of these models for omics research. Here, SLOPE is applied to data from a lignin exposure study to highlight the workflow for fitting both supervised and unsupervised models to data.

lipidomics↗

Visualizing the NIOSH Pocket Guide: Open-source web application for accessing and exploring the NIOSH Pocket Guide to Chemical Hazards

The NIOSH Pocket Guide to Chemical Hazards is a trusted resource that displays key information for a collection of chemicals commonly encountered in the workplace. Entries contain chemical structures—occupational exposure limit information ranging from limits based on full-shift time-weighted averages to acute limits such as short-term exposure limits and immediately dangerous to life or health values, as well as a variety of other data such as chemical-physical properties and symptoms of exposure. The NIOSH Pocket Guide (NPG) is available as a printed, hardcopy book, a PDF version, an electronic database, and a downloadable application for mobile phones. All formats of the NIOSH Pocket Guide allow users to access the data for each chemical separately, however, the guide does not support data analytics or visualization across chemicals. This project reformatted existing data in the NPG to make it searchable and compatible with exploration and analysis using a web application. The resulting application allows users to investigate the relationships between occupational exposure limits, the range and distribution of occupational exposure limits, and the specialized sorting of chemicals by health endpoint or to summarize information of particular interest. These tasks would have previously required manual extraction of the data and analysis. The usability of this application was evaluated among industrial hygienists and researchers and while the existing application seems most relevant to researchers, the open-source code and data are amenable to modification by users to increase customization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

nmRanalysis: An Open-Source Web Application for Semi-automated NMR Metabolite Profiling

Though data acquisition and initial signal pre-processing of nuclear magnetic resonance (NMR) spectra have achieved high degrees of automation, downstream processing - specifically the profiling of spectra - has bottlenecked the overall NMR analysis workflow. Several efforts have been made to mitigate this bottleneck, but these solutions often trade an increase in automation for limitations elsewhere. Here, in this technical note, we introduce nmRanalysis, a user-friendly web-application that integrates the strengths of existing profiling tools for a more automated profiling workflow. nmRa-nalysis additionally incorporates novel features, including a machine-learning-driven recommender system for me-tabolite identification, further increasing the utility of nmRanalysis over the individual tools that it incorporates.

Flores, Javier E. [Pacific Northwest National Labo↗

Building Toward the Future in Chemical and Materials Simulation with Accessible and Intelligently Designed Web Applications

Over the last few decades, significant progress has been made in the development and use of electronic structure and other molecular simulation methods. As these methods become more mature and are able to simulate larger and more complex chemical simulations, the need for improvement in scientific visualization, molecular builders, simplified input to simulation methods, and the development of new approaches and languages to describe simulations, along with workflows to carry them out, becomes more apparent. In this chapter, we describe our recent efforts in developing a prototype open-source computational tool called Arrows that combines NWChem, SQL and NoSQL databases, email, web APIs, and web applications in a way that make molecular and materials modeling accessible to all scientists and engineers. At the same time, because of its simplified input, it provides a framework for expert users to carry out large numbers of calculations and run complex workflows.

MODE: A Web Application for Interactive Visualization and Exploration of Omics Data

Studies generating transcriptomics, proteomics, lipidomics, and metabolomics (colloquially referred to as “omics”) data allow researchers to find biomarkers or molecular targets, or understand complex biological structures and functions by identifying changes in biomolecule abundance and expression between experimental conditions. Omics data is multi-dimensional and oftentimes summarization techniques such as principal component analysis (PCA) are used to identify high-level patterns in data. Though useful, these summaries don’t allow exploration of detailed patterns in omics data that may have biological relevance. The use of interactive HTML displays with plots allows researchers to interact with omics data at a detailed level, but building these displays requires significant coding expertise. To overcome this barrier, the software MODE was built to empower users to build their own interactive HTML displays to support scientific discovery. These displays are easily shareable, do not depend on a specific operating system, and allow users to effortlessly sort and filter plots by categorical or numerical variables. MODE allows users to build and share these displays with several options for plot design and meta selection. In conclusion, the MODE web application and its capabilities are presented and then demonstrated on lipidomics data from a leaf wounding study.

lipidomics↗

Foldy: An open-source web application for interactive protein structure analysis

Foldy is a cloud-based application that allows non-computational biologists to easily utilize advanced AI-based structural biology tools, including AlphaFold and DiffDock. With many deployment options, it can be employed by individuals, labs, universities, and companies in the cloud without requiring hardware resources, but it can also be configured to utilize locally available computers. Foldy enables scientists to predict the structure of proteins and complexes up to 6000 amino acids with AlphaFold, visualize Pfam annotations, and dock ligands with AutoDock Vina and DiffDock. In our manuscript, we detail Foldy’s interface design, deployment strategies, and optimization for various user scenarios. We demonstrate its application through case studies including rational enzyme design and analyzing proteins with domains of unknown function. Furthermore, we compare Foldy’s interface and management capabilities with other open and closed source tools in the field, illustrating its practicality in managing complex data and computation tasks. Our manuscript underlines the benefits of Foldy as a day-to-day tool for life science researchers, and shows how Foldy can make modern tools more accessible and efficient.

59 BASIC BIOLOGICAL SCIENCES↗

A VOI Web Application for Distinct Geothermal Domains: Statistical Evaluation of Different Data Types within the Great Basin

The Great Basin region contains different domains that have different structural and hydrothermal flow patterns. Depending on the characteristics of these patterns, certain data types may be more successful at detecting hidden geothermal resources. In this paper, we quantitatively evaluate if certain data types are more successful in certain domains. Given different aquifer, strain and structural conditions, we explore which data types statistically reveal positively labeled geothermal sites. We utilize value of information (VOI) metrics to help quantify the reliability of data types to discriminate against "positive" and "negative" labeled geothermal sites. We also evaluate how kernel density estimation can help generalize the statistics that inform VOI, which is necessary given the limited data in geothermal exploration. Except for the Carbonate Aquifer, the highest ranking of the Vimperfect is the Local Structural Setting. Next, the slip and dilation tendency is first for Carbonate Aquifer and second for Central Nevada Seismic Belt and Western Great Basin. For the Carbonate Aquifer, heat flow is has the lowest Vimperfect value compared to the other three domains, which is consistent with the understanding of how heat flow measurements are masked by regional groundwater flow.

Bayesian analysis↗

Scribe Network API v.1.0.0

SAND2023-07864O Scribe Network API is an add-on tool for Scribe3D software. Scribe Network API documents tabletop exercises in trainings and plays back simulated videos of the scenarios and responses. Users can apply the software to compiled projects, or to a simple visual studio project solution package. The software runs a web application that relays information between computers using Scribe3D through a web application, or web app. The web app involves a representational state transfer (REST) application programming interface that handles sending and receiving Scribe save files and an SQL server that stores the save files. This follow-on package allows users to facilitate a networked tabletop exercise. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Noel, Todd↗

Energy Assets Transformation Web Mapping Application

This submission contains the link and geospatial materials used in the Energy Assets Transformation Web Mapping Application. The zip file contains 19 geospatial layers in a file geodatabase called EAT.gdb to be grouped in the following categories. 1. Industrial Assets: Coal Generation Units Retirements 2012-2040 (EIA); Examples of Repurposing Projects (32 projects in total); Abandoned Coal Mines (CORD, SkyTruth); Abandoned or Orphaned Wells (for ten states only). 2. Energy Transition Communities: 48C (e) Tax Credits - Designated Energy Communities (IRA); Index of Deep Disadvantage; Local Energy Action Program (LEAP); EJ Index for Proximity to Hazardous Waste (EPA). 3. Regional Landscape: State-Level Funding Programs (relevant to repurposing projects, for 2022 and 2023 only); Coal Flows from Mine to Plant 2021 (EIA), Variable Renewable Energy Shares (Wind and Solar, 2021, EIA). 4. Supporting Infrastructure: Railroads (HIFLD), Electric Power Transmission Lines (HIFLD), Major Highways (NHPN, DOT), Major Ports (National Atlas of the U.S.); Independent System Operators (HIFLD), NERC Regions and Subregions (HIFLD).

abandoned coal mines↗

Offshore Geologic Carbon Storage Data Collection and International Project Inventory

We present an interactive data collection to aggregate, understand, and disseminate the data that are publicly available to support offshore GCS which can be leveraged by stakeholders to understand where GCS may be viable offshore, create GCS project analogs, and address challenges to GCS in offshore environments. The Offshore Geologic Carbon Storage Data Collection is an Experience Builder web application of multiple web mapping applications, aggregated into a single tool for each data type for access, visualization, and exploration. We also present a spatial inventory of global offshore GCS efforts to visualize the scale and locations of actualized and potential offshore GCS. It includes project location, project type and stage, CO2 storage resource potential, injection rate, reservoir and seal geology, and key literature references. Quantitative and qualitative comparisons of the distribution and magnitude of projects by their attributes lends spatial insight into the status of global GCS operations and storage resource potential, thereby enabling comparative assessments and cross-cutting knowledge transfer for projects in development. These datasets illuminate trends in ongoing offshore projects and can be leveraged by stakeholders to estimate storage resources, identify subsurface analogs, review regulations, and address challenges to offshore GCS. Additionally, opportunities for concurrent decarbonization strategies can be identified.

Mulhern, Julia↗

International Offshore Geologic Carbon Storage Project Inventory and Data Collection

We present an interactive data collection to aggregate, understand, and disseminate the data that are publicly available to support offshore GCS which can be leveraged by stakeholders to understand where GCS may be viable offshore, create GCS project analogs, and address challenges to GCS in offshore environments. The Offshore Geologic Carbon Storage Data Collection is an Experience Builder web application of multiple web mapping applications, aggregated into a single tool for each data type for access, visualization, and exploration. We also present a spatial inventory of global offshore GCS efforts to visualize the scale and locations of actualized and potential offshore GCS. It includes project location, project type and stage, CO2 storage resource potential, injection rate, reservoir and seal geology, and key literature references. Quantitative and qualitative comparisons of the distribution and magnitude of projects by their attributes lends spatial insight into the status of global GCS operations and storage resource potential, thereby enabling comparative assessments and cross-cutting knowledge transfer for projects in development. These datasets illuminate trends in ongoing offshore projects and can be leveraged by stakeholders to estimate storage resources, identify subsurface analogs, review regulations, and address challenges to offshore GCS. Additionally, opportunities for concurrent decarbonization strategies can be identified.

Mulhern, Julia↗