PNNL OMICS
The PNNL Omics Library (PNNLOmics.dll) is a collection of data analysis, file I/O, and visualization routines used by several of the omics-related software developed at PNNL.
Degan, Michael↗
SEARCH · Search NASA
Results for “visualization software”
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.
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via-wind (A Visual Impact Assessment Tool for Wind Turbines) [SWR-24-87]
Via-wind is an open-source tool for conducting visual impact assessments for wind turbines. It combines geographic information system (GIS) and 3D simulation methods to account for the key factors driving the visual impact of installed wind turbines, including distance, viewing angle, turbine orientation, visual exposure, and the cumulative effects of multiple turbines. This software is optimized for use in high-performance computing environments to enable large scale (e.g., country-wide) analysis, but can also be run on a single server or personal computer. For more information, please see the related journal article: https://www.sciencedirect.com/science/article/pii/S0306261924021846
Lopez, Anthony↗
MAMA Software Features: Quantified Attributes
This document reviews the size and shape attributes that are quantified by the MAMA software, shows how they are calculated, and then gives some visual example shapes.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
GrayQb TM Single-Faced Version 2 (SF2) Open Environment Test Report (Rev. 1)
This report details the design upgrades incorporated into the new version of the GrayQb TM SF2 device and the characterization testing of this upgraded device. Results from controlled characterization testing in the Savannah River National Laboratory (SRNL) R&D Engineering Imaging and Radiation Lab (IRL) and the Savannah River Site (SRS) Health Physics Instrument Calibration Laboratory (HPICL) is presented, as well as results from the open environment field testing performed in the E-Area Low Level Waste Storage Area. Resultant images presented in this report were generated using the SRNL developed Radiation Analyzer (RAzer TM ) software program which overlays the radiation contour images onto the visual image of the location being surveyed.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Extracting Metrics for Three-dimensional Root Systems: Volume and Surface Analysis from In-soil X-ray Computed Tomography Data
Plant roots play a critical role in plant-soil-microbe interactions that occur in the rhizosphere, as well as processes with important implications to climate change and forest management. Quantitative size information on roots in their native environment is invaluable for studying root growth and environmental processes involving the plant. X ray computed tomography (XCT) has been demonstrated to be an effective tool for in situ root scanning and analysis. Our group at the Environmental Molecular Sciences Laboratory (EMSL) has developed an XCT-based tool to image and quantitatively analyze plant root structures in their native soil environment. XCT data collected on a Prairie dropseed (Sporobolus heterolepis) specimen was used to visualize its root structure. A combination of open-source software RooTrak and DDV were employed to segment the root from the soil, and calculate its isosurface, respectively. Our own computer script named 3DRoot-SV was developed and used to calculate root volume and surface area from a triangular mesh. The process utilizing a unique combination of tools, from imaging to quantitative root analysis, including the 3DRoot-SV computer script, is described.
58 GEOSCIENCES↗
Mechanical Serial-Sectioning Data Assistant
Mechanical Serial-Sectioning Data Assistant (MECH-SSDA) is a real-time data analytics software with graphical user-interface that; 1) tracks and visualizes material removal rates for mechanical serial-sectioning experiments using at least two height measurement methods; 2) tracks process time for specific segments of the serial-sectioning experiment; and 3) alerts the user to anomalies in expected removal rate, process time or unanticipated operational pauses
Poulter, Gregory A.↗
Quantitative Analysis Of Three-dimensional Branching Systems From X-ray Computed Microtomography Data
Branching structures such as lungs, blood vessels and plant roots play a critical role in life. Growth, structure, and function of these branching structures have an immense effect on our lives. Therefore, quantitative size information on such structures in their native environment is invaluable for studying their growth and the effect of the environment on them. X-ray computed tomography (XCT) has been an effective tool for in situ imaging and analysis of branching structures. We developed a costless tool that approximates the surface and volume of branching structures. Our methodology of noninvasive imaging, segmentation and extraction of quantitative information is demonstrated through the analysis of a plant root in its soil medium from 3D tomography data. XCT data collected on a grass specimen was used to visualize its root structure. A suite of open-source software was employed to segment the root from the soil and determine its isosurface, which was used to calculate its volume and surface. This methodology of processing 3D data is applicable to other branching structures even when the structure of interest is of similar x-ray attenuation to its environment and difficulties arise with sample segmentation.
Environmental Molecular Sciences Laboratory↗
Snorri Version 1.0
The software decomposes n-component time-series data into persistence vectors and provide visualizations of various summaries of this information. Persistence vectors are a type of vector, based on multidimensional persistent homology theory, which have magnitudes and directions that reflect dominant trends in the multi-component data. The software is a collection of MATLAB scripts, and thus MATLAB runs the scripts. The master script that calls other scripts is called Snorri. The purpose is thus analysis of time-series data to extract dominant trends or events and to classify the type of event. The software produces characteristic vectors (an average of the persistence vectors), which can have directions that reflect the overall dominant trend in a time-series data set. The MATLAB scripts have been partially converted to the PYTHON language and no do not have the full functionality of the MATLAB and are not fully tested; the python scripts are to be covered under this copyright assertion. Two versions of the PYTHON scripts are included, called: mph25.py and mph38.py, each with their own main.py file.
Callor, Nickolas↗
Quantum Computing and Visualization Research Challenges and Opportunities
Here, quantum computing (QC) has experienced rapid growth in recent years with the advent of robust programming environments, readily accessible software simulators and cloud-based QC hardware platforms, and growing interest in learning how to design useful methods that leverage this emerging technology for practical applications. From the perspective of the field of visualization, this article examines research challenges and opportunities along the path from initial feasibility to practical use of QC platforms applied to meaningful problems.
Data visualization↗
ORBiT - The Oak Ridge Biosurveillance Toolkit
We describe ORBiT, the Oak Ridge Biosurveillance Toolkit, the objective of which is to provide 1) forecasting and early warning, and 2) an extensible data analytics platform for biosurveillance by enabling the use of traditional and non-traditional datasets, consisting of heterogeneous data types and modalities. ORBiT includes a data collection interface, analytic components, higher-order statistical tools, and a visual front-end with visual analytics. ORBiT is implemented as a distributed analytic platform consisting of a software stack atop of Hadoop and uses Titan, a distributed graph database as a backend for data storage.
59 BASIC BIOLOGICAL SCIENCES↗
SBOL Visual: A Graphical Language for Genetic Designs
Synthetic Biology Open Language (SBOL) Visual is a graphical standard for genetic engineering. We report that it consists of symbols representing DNA subsequences, including regulatory elements and DNA assembly features. These symbols can be used to draw illustrations for communication and instruction, and as image assets for computer-aided design. SBOL Visual is a community standard, freely available for personal, academic, and commercial use (Creative Commons CC0 license). We provide prototypical symbol images that have been used in scientific publications and software tools. We encourage users to use and modify them freely, and to join the SBOL Visual community: http://www.sbolstandard.org/visual.
59 BASIC BIOLOGICAL SCIENCES↗
A 15-Year Retrospective on Immersive Visualization Lessons from the Applied Visualization Laboratory
This article shares the experiences of operating an immersive visualization laboratory over a 15-year period. The paper discusses valuable insights into the lessons learned from various projects, including the challenges they faced, such as technical difficulties, user adoption, and opportunities, and practical solutions for overcoming them. One crucial element for successful immersive visualization projects is interdisciplinary collaboration. The paper presents the advantages of immersive visualization technology, such as improved data comprehension, enhanced communication, and increased engagement in complex scenarios. We present the dynamic realm of virtual and augmented truth (VR/AR) technology in the context of a immersive laboratory system. We spotlight rising trends inside the integration of VR/AR tools for visualization. We also present our experience in dealing with the hardware and software additives in an immersive VR/AR labs, dropping light on the demanding situations and successes encountered throughout everyday operations. Furthermore, it offers practical knowledge and guidance based on years of experience in the field, which can help you overcome challenges and achieve success in your project.
99 GENERAL AND MISCELLANEOUS↗
Visual Sample Plan Version 7.0 User's Guide
User's guide for VSP 7.0 This user's guide describes Visual Sample Plan (VSP) Version 7.0 and provides instructions for using the software. VSP selects the appropriate number and location of environmental samples to ensure that the results of statistical tests performed to provide input to risk decisions have the required confidence and performance. VSP Version 7.0 provides sample-size equations or algorithms needed by specific statistical tests appropriate for specific environmental sampling objectives. It also provides data quality assessment and statistical analysis functions to support evaluation of the data and determine whether the data support decisions regarding sites suspected of contamination. The easy-to-use program is highly visual and graphic. VSP runs on personal computers with Microsoft Windows operating systems (XP, Vista, Windows 7, and Windows 8). Designed primarily for project managers and users without expertise in statistics, VSP is applicable to two- and three-dimensional populations to be sampled (e.g., rooms and buildings, surface soil, a defined layer of subsurface soil, water bodies, and other similar applications) for studies of environmental quality. VSP is also applicable for designing sampling plans for assessing chem/rad/bio threat and hazard identification within rooms and buildings, and for designing geophysical surveys for unexploded ordnance (UXO) identification.
97 MATHEMATICS AND COMPUTING↗
CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites
High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Here, data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. Cis SERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated to enhance the usefulness of the software. Cis SERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, Cis SERS utilizes the REBASE enzyme database. Results from Cis SERSenable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3’UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. Cis SERS is a java based graphical user interface built around a perl backbone. Several of the applications of Cis SERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool Cis SERSand results from in-silico and corresponding wet-lab analyses demonstrating that Cis SERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies.
59 BASIC BIOLOGICAL SCIENCES↗
Data Processor 3 QASPR Project
The following discussion contains a high-level description of methods used to implement software for data processing. It describes the required directory structures and file handling required to use Excel's Visual Basic for Applications programming language and how to identify shot, test and capture types to appropriately process data. It also describes how to interface with the software.
97 MATHEMATICS AND COMPUTING↗
P-Mart: Interactive Analysis of Ion Abundance Global Proteomics Data
The use of mass-spectrometry-based techniques for global protein profiling of biomedical or environmental experiments has become a major focus in research centered on biomarker discovery; however, one of the most important issues recently highlighted in the new era of omics data generation is the ability to perform analyses in a robust and reproducible manner. This has been hypothesized to be one of the issues hindering the ability of clinical proteomics to successfully identify clinical diagnostic and prognostic biomarkers of disease. P-Mart (https://pmart.labworks.org) is an interactive web-based software environment that enables domain scientists to perform quality-control processing, statistics, and exploration of large-complex proteomics data sets without requiring statistical programming. P-Mart is developed in a manner that allows researchers to perform analyses via a series of modules, explore the results using interactive visualization, and finalize the analyses with a collection of output files documenting all stages of the analysis and a report to allow reproduction of the analysis.
59 BASIC BIOLOGICAL SCIENCES↗
MSiReader v1.0: Evolving Open-Source Mass Spectrometry Imaging Software for Targeted and Untargeted Analyses
A major update to the mass spectrometry imaging (MSI) software MSiReader is presented, offering a multitude of newly added features critical to MSI analyses. MSiReader is a free, open-source, and vendor-neutral software written in the MATLAB platform and is capable of analyzing most common MSI data formats. A standalone version of the software, which does not require a MATLAB license, is also distributed. The newly incorporated data analysis features expand the utility of MSiReader beyond simple visualization of molecular distributions. The MSiQuantification tool allows researchers to calculate absolute concentrations from quantification MSI experiments exclusively through MSiReader software, significantly reducing data analysis time. An image overlay feature allows the incorporation of complementary imaging modalities to be displayed with the MSI data. A polarity filter has also been incorporated into the data loading step, allowing the facile analysis of polarity switching experiments without the need for data parsing prior to loading the data file into MSiReader. A quality assurance feature to generate a mass measurement accuracy (MMA) heatmap for an analyte of interest has also been added to allow for the investigation of MMA across the imaging experiment. Most importantly, as new features have been added performance has not degraded, in fact it has been dramatically improved. These new tools and the improvements to the performance in MSiReader v1.0 enable the MSI community to evaluate their data in greater depth and in less time. .
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
State of the Art of Molecular Visualization in Immersive Virtual Environments
Abstract Visualization plays a crucial role in molecular and structural biology. It has been successfully applied to a variety of tasks, including structural analysis and interactive drug design. While some of the challenges in this area can be overcome with more advanced visualization and interaction techniques, others are challenging primarily due to the limitations of the hardware devices used to interact with the visualized content. Consequently, visualization researchers are increasingly trying to take advantage of new technologies to facilitate the work of domain scientists. Some typical problems associated with classic 2D interfaces, such as regular desktop computers, are a lack of natural spatial understanding and interaction, and a limited field of view. These problems could be solved by immersive virtual environments and corresponding hardware, such as virtual reality head‐mounted displays. Thus, researchers are investigating the potential of immersive virtual environments in the field of molecular visualization. There is already a body of work ranging from educational approaches to protein visualization to applications for collaborative drug design. This review focuses on molecular visualization in immersive virtual environments as a whole, aiming to cover this area comprehensively. We divide the existing papers into different groups based on their application areas, and types of tasks performed. Furthermore, we also include a list of available software tools. We conclude the report with a discussion of potential future research on molecular visualization in immersive environments.
97 MATHEMATICS AND COMPUTING↗