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93 records · Page 6

VizBrick: A GUI-based Interactive Tool for Authoring Semantic Metadata for Building Datasets

Brick ontology is a unified semantic metadata schema to address the stand-ardization problem of buildings' physical, logical, and virtual assets and the relationships between them. Creating a Brick model for a building dataset means that the dataset's contents are semantically described using the standard terms defined in the Brick ontology. It will enable the benefits of data standardization, without having to recollect or reorganize the data and opens the possibility of automation leveraging the machine readability of the semantic metadata. The problem is that authoring Brick models for building datasets often requires knowledge of semantic technology (e.g., on-tology declarations and RDF syntax) and leads to repeated manual trial and error processes, which can be time-consuming and challenging to do with-out an interactive visual representation of the data. We developed VizBrick, a tool with a graphical user interface that can assist users in creating Brick models visually and interactively without having to understand the Re-source Description Framework (RDF) syntax. VizBrick provides handy ca-pabilities such as keyword search for easy find of relevant brick concepts and relations to their data columns and automatic suggestions of concept mapping. In this demonstration, we present a use-case of VizBrick to show-case how a Brick model can be created for a real-world building dataset.

Lee, Sangkeun (Matt)↗

pyXPCSviewer : an open-source interactive tool for X-ray photon correlation spectroscopy visualization and analysis

pyXPCSviewer , a Python-based graphical user interface that is deployed at beamline 8-ID-I of the Advanced Photon Source for interactive visualization of XPCS results, is introduced. pyXPCSviewer parses rich X-ray photon correlation spectroscopy (XPCS) results into independent PyQt widgets that are both interactive and easy to maintain. pyXPCSviewer is open-source and is open to customization by the XPCS community for ingestion of diversified data structures and inclusion of novel XPCS techniques, both of which are growing demands particularly with the dawn of near-diffraction-limited synchrotron sources and their dedicated XPCS beamlines.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom

Abstract Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.

59 BASIC BIOLOGICAL SCIENCES↗