Curiosity: a tool for exploring density features in crystallographic and cryoEM maps
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Young, Iris D↗
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RCSB Protein Data Bank 1D tools and services
Abstract Motivation Interoperability between polymer sequences and structural data is essential for providing a complete picture of protein and gene features and helping to understand biomolecular function. Results Herein, we present two resources designed to improve interoperability between the RCSB Protein Data Bank, the NCBI and the UniProtKB data resources and visualize integrated data therefrom. The underlying tools provide a flexible means of mapping between the different coordinate spaces and an interactive tool allows convenient visualization of the 1-dimensional data over the web. Availabilityand implementation https://1d-coordinates.rcsb.org and https://rcsb.github.io/rcsb-saguaro. Supplementary information Supplementary data are available at Bioinformatics online.
59 BASIC BIOLOGICAL SCIENCES↗
SatCORPS Hybridized Cloud Product Web Mapping Application: Leveraging the Strengths of Satellite Imagers, AWS Tools, and Cloud Parameters
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Douglas F Chope↗
Neural lumped parameter differential equations with application in friction-stir processing
Lumped parameter methods aim to simplify the evolution of spatially-extended or continuous physical systems to that of a “lumped” element representative of the physical scales of the modeled system. For systems where the definition of a lumped element or its associated physics may be unknown, modeling tasks may be restricted to full-fidelity physics simulations. Here, in this work, we consider data-driven modeling tasks with limited point-wise measurements of otherwise continuous systems. We build upon the notion of the Universal Differential Equation (UDE) to construct data-driven models for reducing dynamics to that of a lumped parameter and inferring its properties. The flexibility of UDEs allow for composing various known physical priors suitable for application-specific modeling tasks, including lumped parameter methods. The motivating example for this work is the plunge and dwell stages for friction-stir welding; specifically, (i) mapping power input into the tool to a point-measurement of temperature and (ii) using this learned mapping for process control.
97 MATHEMATICS AND COMPUTING↗
Selection and Simulation-Based Validation of a Radiation Mapping Device for Field Emission Characterization during SRF Cold Testing
Building a simulation tool to select a suitable radiation mapping device for FE detection during Cold Testing. Evaluating asymmetries in photons angular distribution to get information about the FE site position. The final goal is to focus cleaning efforts in that point to reduce employed resources, iterations and costs.
Martella, Giuseppe↗
The Maneuver Planning Process for the Microwave Anisotropy Probe (MAP) Mission
The Microwave Anisotropy Probe (MAP) was successfully launched from Kennedy Space Center's Eastern Range on June 30, 2001. MAP will measure the cosmic microwave background as a follow up to NASA's Cosmic Background Explorer (COBE) mission from the early 1990's. MAP will take advantage of its mission orbit about the Sun-Earth/Moon L2 Lagrangian point to produce results with higher resolution, sensitivity, and accuracy than COBE. A strategy comprising highly eccentric phasing loops with a lunar gravity assist was utilized to provide a zero-cost insertion into a lissajous orbit about L2. Maneuvers were executed at the phasing loop perigees to correct for launch vehicle errors and to target the lunar gravity assist so that a suitable orbit at L2 was achieved. This paper will discuss the maneuver planning process for designing, verifying, and executing MAP's maneuvers. A discussion of the tools and how they interacted will also be included. The maneuver planning process was iterative and crossed several disciplines, including trajectory design, attitude control, propulsion, power, thermal, communications, and ground planning. Several commercial, off-the-shelf (COTS) packages were used to design the maneuvers. STK/Astrogator was used as the trajectory design tool. All maneuvers were designed in Astrogator to ensure that the Moon was met at the correct time and orientation to provide the energy needed to achieve an orbit about L2. The Mathworks Matlab product was used to develop a tool for generating command quaternions. The command quaternion table (CQT) was used to drive the attitude during the perigee maneuvers. The MatrixX toolset, originally written by Integrated Systems, Inc., now distributed by Mathworks, was used to create HiFi, a high fidelity simulator of the MAP attitude control system. HiFi was used to test the CQT and to make sure that all attitude requirements were met during the maneuver. In addition, all ACS data plotting and output were generated in MatrixX. A final test used FlatSat, a real-time hardware-in-the-loop simulator, which used identical MAP flight code to simulate operations on the spacecraft. Simulations in FlatSat allowed the MAP team to verify maneuver commands, timing, and spacecraft configuration before the commands were sent up to the spacecraft for execution. The MAP maneuver team successfully pieced together all of these COTS tools for designing MAP's maneuvers and MAP is now collecting data at L2.
Mesarch, Michael A.↗
Statistical Tool Size Study for Computer-Controlled Optical Surfacing
Over the past few decades, computer-controlled optical surfacing (CCOS) systems have become more deterministic. A target surface profile can be predictably achieved with a combination of tools of different sizes. However, deciding the optimal set of tool sizes that will achieve the target residual error in the shortest run time is difficult, and no general guidance has been proposed in the literature. In this paper, we present a computer-assisted study on choosing the proper tool size for a given surface error map. First, we propose that the characteristic frequency ratio (CFR) can be used as a general measure of the correction capability of a tool over a surface map. Second, the performance of different CFRs is quantitatively studied with a computer simulation by applying them to guide the tool size selection for polishing a large number of randomly generated surface maps with similar initial spatial frequencies and root mean square errors. Finally, we find that CFR = 0.75 achieves the most stable trade-off between the total run time and the number of iterations and thus can be used as a general criterion in tool size selection for CCOS processes. To the best of our knowledge, the CFR is the first criterion that ties tool size selection to overall efficiency.
36 MATERIALS SCIENCE↗
Guiding the choice of informatics software and tools for lipidomics research applications
Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.
59 BASIC BIOLOGICAL SCIENCES↗
The derivation of sub-canopy surface terrain models of coastal forests using synthetic aperture radar
Radar data acquired by the Shuttle Imaging Radar-B mission covering a portion of the Mouths of the Ganges forests were used to create a terrain model for use in determining tidal flow and eventual nutrient transport from the forest to the marine habitat. Results show that good digital topographic terrain models of wet coastal forests can be generated using multiple sets of L-band SAR and ancillary tide elevation data. The dominance of the interaction phenomenon in the radar backscatter of flooded forests can be used to create sub-canopy inundation maps which when merged with tide surface data can be used to generate reasonable topographic models. Ideally models could be improved by using multiple sets of data at a constant incidence angle over the total tide range. The optimal angle for the SAR depends upon the characteristics of the forest. The range of 46 to 57 deg seems applicable to the 12.5 m tall closed canopy in this example. Such models can be an extremely valuable tool for studying and mapping the mangal ecosystem.
Imhoff, M. L.↗
Using Earth Observations to Map Bull Kelp in the Puget Sound, Washington, to Support Conservation and Restoration
Bull kelp (Nereocystis luetkeana) is a critical component of nearshore ecosystems in the Puget Sound region of the Salish Sea. The Port of Seattle and Washington State Department of Natural Resources (DNR) have identified possible declines in bull kelp extent and changes in its distribution throughout the Central Puget Sound near Seattle, Washington. Bull kelp losses threaten critical ecological services and marine habitat, as well as important cultural resources. However, these changes are not well tracked or understood due to the expensive and time-intensive nature of traditional kelp canopy monitoring methods. The Port of Seattle and Washington DNR partnered with the NASA DEVELOP team to explore the feasibility of using Earth observations between 2016 and 2021 obtained from Landsat 8 Operational Land Imager (OLI) and Sentinel-2 MultiSpectral Instrument (MSI) as a potential tool to monitor and map bull kelp. Our team identified a variety of challenges that need to be addressed before this approach can be utilized as an effective means for identifying or mapping nearshore urban kelp beds. We found that neither Sentinel-2 nor Landsat 8 significantly differentiates between kelp and no-known kelp using the Normalized Difference Vegetation Index (NDVI) or Normalized Difference Red-Edge Blue (NDREB). While the tidal and current filtering methods discussed here may be beneficial for identifying promising single image dates for kelp classification, the filters we used reduced the number of images each year to the point that modeling or mapping yearly kelp extent or creating time series of kelp did not appear to be feasible.
Mike Hitchner↗
Puget Sound Water Resources: Using Earth Observations to Map Bull Kelp in the Puget Sound, Washington, to Support Conservation and Restoration
Bull kelp (Nereocystis luetkeana) is a critical component of nearshore ecosystems in the Puget Sound region of the Salish Sea. The Port of Seattle and Washington State Department of Natural Resources (DNR) have identified possible declines in bull kelp extent and changes in its distribution throughout the Central Puget Sound near Seattle, Washington. Bull kelp losses threaten critical ecological services and marine habitat, as well as important cultural resources. However, these changes are not well tracked or understood due to the expensive and time-intensive nature of traditional kelp canopy monitoring methods. The Port of Seattle and Washington DNR partnered with the NASA DEVELOP team to explore the feasibility of using Earth observations between 2016 and 2021 obtained from Landsat 8 Operational Land Imager (OLI) and Sentinel-2 MultiSpectral Instrument (MSI) as a potential tool to monitor and map bull kelp. Our team identified a variety of challenges that need to be addressed before this approach can be utilized as an effective means for identifying or mapping nearshore urban kelp beds. We found that neither Sentinel-2 nor Landsat 8 significantly differentiates between kelp and no-known kelp using the Normalized Difference Vegetation Index (NDVI) or Normalized Difference Red-Edge Blue (NDREB). While the tidal and current filtering methods discussed here may be beneficial for identifying promising single image dates for kelp classification, the filters we used reduced the number of images each year to the point that modeling or mapping yearly kelp extent or creating time series of kelp did not appear to be feasible.
Mike Hitchner↗
Visualizing Geospatial Data through ESRI Story Maps for Earth Science Education: Lessons Learned from My NASA Data
For 20 years My NASA Data (MND) has curated NASA Earth science data and provided the data to educators in engaging learner-centered resources. MND has recently featured story maps as an innovative way to engage students in NASA Earth data. A story map is a cloud-based lesson that engages the learner in interactive geospatial maps using NASA data, and other multimedia content, text, and tasks that can be seamlessly incorporated in classroom instruction. This immersive technology eliminates the need for the user to move among tricky interfaces to access and visualize Earth science data, and no special software is required to be downloaded. Each story map integrates data from different NASA satellite missions, retrieved from Distributed Active Archive Centers (DAACs). Story maps also employ data analysis tools, such as time series options and swipe tools that allow learners to view and analyze relationships between scientific variables. MND has produced 25 story map lesson plans on the topics of air quality, the urban heat island effect, Earth’s energy budget, phytoplankton distribution, hurricane formation, solar eclipses, ocean circulation patterns, sea ice extent, and volcanic eruptions. Nine of them are extended story maps and written in the 5E format, which is internationally recognized as best practice based on how children learn science. Each story map resource is developed by the MND team featuring a GIS programming specialist, a lead scientist, and educational specialist/s to ensure the context, content, and methods are scientifically and educationally sound. The MND story maps are written for middle and high school science teachers and students as they connect with the Earth Systems Science phenomena featured in the Next Generation Science Standards. Each story map includes supporting resources for smooth integration in the classroom. During Fiscal Year 2023, The My NASA Data website received over 100,000 story map engagements during. These metrics highlight the interest in story maps as an Earth Science educational resource.
Desiray Wilson↗
ENERGY STAR for Tenants: An Online Energy Estimation Tool for Commercial Office Building Tenants
The commercial building sector consumes over 18% of the total energy in the United States. According to the 2012 Commercial Building Energy Consumption Survey (CBECS), office buildings comprise nearly 16 billion square feet of floor space and consume 253 billion kWh of energy annually. Office buildings represent nearly one-fifth of the energy consumed by commercial buildings, more than any other building type. Therefore, monitoring and reducing energy consumption in office buildings has become an increasingly important focus across the United States. The goal of the ENERGY STAR for Tenants program is to recognize office building tenants who demonstrate commitment to energy efficiency and environmental stewardship. Tenants seeking recognition must complete five major steps: estimate energy use, meter energy use, use efficient lighting, use efficient equipment, and share data. NREL is responsible for the underlying analysis performed for step one, estimating energy use. An online survey was developed for tenants to input information about their office space and its internal loads. NREL performed a parametric analysis across a large parameter space of office buildings. The analysis results were processed to map the user inputs to output energy ranges. The mappings enable the web tool to provide users with instant energy usage estimates based on a limited number of inputs.
32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
Using commercial high-resolution satellite imagery to monitor a nuisance macroalga in the largest marine protected area in the U.S.A.
Satellite imagery is a useful tool for monitoring and mapping the distribution of invasive or nuisance algal species on coral reefs over the temporal and spatial scales needed for ecosystem management. Visual inspections of high-resolution satellite imagery were used to detect the newly discovered nuisance alga, Chondria tumulosa , at Manawai (Pearl and Hermes Atoll) in combination with ground-truthing surveys. Low-albedo (“dark”) survey sites on spur habitats were associated with mean C. tumulosa cover seven times higher than adjacent high-albedo (“light”) sites. There was an inverse relationship between C. tumulosa percent cover at ground-truthing sites and mean reflectance values. Archival satellite imagery showed that areas of high C. tumulosa cover (i.e., dark patches) were not evident on or before 2015 on the northeast backreef. This case study is the first to apply satellite imagery to target a nuisance red macroalgal bloom on a coral reef. The ability to use satellites for the detection of nuisance or invasive benthic species, such as expansive mats of C. tumulosa , provides managers with a valuable tool, especially in remote regions.
Invasive↗
Scheduling Results for the THEMIS Observation Scheduling Tool
We describe a scheduling system intended to assist in the development of instrument data acquisitions for the THEMIS instrument, onboard the Mars Odyssey spacecraft, and compare results from multiple scheduling algorithms. This tool creates observations of both (a) targeted geographical regions of interest and (b) general mapping observations, while respecting spacecraft constraints such as data volume, observation timing, visibility, lighting, season, and science priorities. This tool therefore must address both geometric and state/timing/resource constraints. We describe a tool that maps geometric polygon overlap constraints to set covering constraints using a grid-based approach. These set covering constraints are then incorporated into a greedy optimization scheduling algorithm incorporating operations constraints to generate feasible schedules. The resultant tool generates schedules of hundreds of observations per week out of potential thousands of observations. This tool is currently under evaluation by the THEMIS observation planning team at Arizona State University.
Thermal Emission Imaging System (THEMIS)↗
Raptor
Raptor is an efficient Python-based tool for predicting the formation and morphology of stochastic lack of fusion defects in metal AM processes. A major obstacle for the qualification and certification of additively manufactured parts in critical applications continues to be performance variability caused in part by porosity-related defects. High-fidelity process models that could predict these defect features are currently too computationally expensive for component-level analysis. To address this, Raptor employs a high-performance geometric method to model the dynamic melt pool rather than relying on computationally intensive thermal fluid dynamics. This allows Raptor to rapidly identify regions of unmelted material that correspond to lack of fusion pores. The efficiency of this approach significantly reduces the time and resources needed for generating 3D defect predictions, which enables users to conduct large-scale parameter studies and evaluate how process variations affect part quality. The framework offers operational flexibility; users can execute simulations through a simple command line interface or integrate core functions as a library within larger computational workflows. Simulation outputs include 3D porosity maps for visualization and tools for quantitative morphological analysis. These results are suitable for direct comparison with experimental characterization data from methods such as X-ray computed tomography and can be used for statistical process optimization.
Subraveti, Vamsi [Vanderbilt Univ., Nashville, TN ↗
Damage modeling of power tower receiver tubes using the SRLIFE tool
Concentrating Solar Power (CSP) molten-salt central receivers are subject to high, transient incident flux during daily operation. The resulting creep-fatigue damage impacts the receiver’s reliability and restricts the permissible incident flux distribution for a given receiver. This paper aims to reduce CSP plants’ levelized cost of electricity by developing a methodology to predict lifetime and identifies the primary damage mechanism (creep vs fatigue) for any given fluid temperature and temperature gradient. Results are presented in the form of a damage map that serves as a valuable operation guide and design tool. Damage maps can be used to reduce maintenance costs by improving reliability and reduce receiver capital costs by better utilizing the receiver area. FEA simulation and damage modeling of tubes subject to asymmetrical flux conditions is performed in the open-source receiver design tool srlife. Parametric studies are performed over a range of inner tube temperatures and thermal gradients for A230, 316H, 740H, A282, A617, and 800H high temperature alloys. Damage maps are presented for each alloy. A parametric, FEA-based methodology is presented for comparison of fatigue-creep ratios and prediction of tube lifetime based on the critical thermal operating conditions. Fatigue is found to be negligible compared to creep for almost every case. Here, this finding suggests that fatigue effects associated with cloud events are insignificant compared to creep at these high temperature operating conditions. Additionally, lifetime predictions identify thermal conditions where small changes in operating conditions can result in large changes in predicted lifetime.
14 SOLAR ENERGY↗
Application of transport-based metric for continuous interpolation between cryo-EM density maps
Cryogenic electron microscopy (cryo-EM) has become widely used for the past few years in structural biology, to collect single images of macromolecules "frozen in time". As this technique facilitates the identification of multiple conformational states adopted by the same molecule, a direct product of it is a set of 3D volumes, also called EM maps. To gain more insights on the possible mechanisms that govern transitions between different states, and hence the mode of action of a molecule, we recently introduced a bioinformatic tool that interpolates and generates morphing trajectories joining two given EM maps. This tool is based on recent advances made in optimal transport, that allow efficient evaluation of Wasserstein barycenters of 3D shapes. As the overall performance of the method depends on various key parameters, including the sensitivity of the regularization parameter, we performed various numerical experiments to demonstrate how MorphOT can be applied in different contexts and settings. Finally, we discuss current limitations and further potential connections between other optimal transport theories and the conformational heterogeneity problem inherent with cryo-EM data.
3D shapes↗