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DOE OSTI2020

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

Background: Metagenomics and metatranscriptomics studies provide valuable insight into the composition and function of microbial populations from diverse environments, however the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers. Results: Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome and metatranscriptome data. Genome-centric resolution and abundance estimates are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license. Conclusions: ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome and metatranscriptome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2003

Inflatably Deployed Membrane Waveguide Array Antenna for Space

As an alternative to parabolic antennas and Synthetic Aperture Radar (SAR) systems, waveguide arrays offer another method of providing RF transmit/receive communication apertures for spacecraft. The advantage of the membrane waveguide array concept, in addition to its lightweight and low packaged volume, is its inherent shape. Relative to parabolic antennas, the requirement to make an accurate doubly curved surface is removed. L'Garde and Langley Research Center (LaRC), are currently working in this area to develop lightweight waveguide array technologies utilizing thin film membrane structures. Coupled with an ultra-lightweight inflatably deployed rigidizable planar support structure, the system offers a very compelling technology in the fields of space-based radar, communications, and earth resource mapping.

Lichodziejewski, David↗

NASA NTRS2015

The I4 Online Query Tool for Earth Observations Data

The NASA Earth Observation System Data and Information System (EOSDIS) delivers an average of 22 terabytes per day of data collected by orbital and airborne sensor systems to end users through an integrated online search environment (the Reverb/ECHO system). Earth observations data collected by sensors on the International Space Station (ISS) are not currently included in the EOSDIS system, and are only accessible through various individual online locations. This increases the effort required by end users to query multiple datasets, and limits the opportunity for data discovery and innovations in analysis. The Earth Science and Remote Sensing Unit of the Exploration Integration and Science Directorate at NASA Johnson Space Center has collaborated with the School of Earth and Space Exploration at Arizona State University (ASU) to develop the ISS Instrument Integration Implementation (I4) data query tool to provide end users a clean, simple online interface for querying both current and historical ISS Earth Observations data. The I4 interface is based on the Lunaserv and Lunaserv Global Explorer (LGE) open-source software packages developed at ASU for query of lunar datasets. In order to avoid mirroring existing databases - and the need to continually sync/update those mirrors - our design philosophy is for the I4 tool to be a pure query engine only. Once an end user identifies a specific scene or scenes of interest, I4 transparently takes the user to the appropriate online location to download the data. The tool consists of two public-facing web interfaces. The Map Tool provides a graphic geobrowser environment where the end user can navigate to an area of interest and select single or multiple datasets to query. The Map Tool displays active image footprints for the selected datasets (Figure 1). Selecting a footprint will open a pop-up window that includes a browse image and a link to available image metadata, along with a link to the online location to order or download the actual data. Search results are either delivered in the form of browse images linked to the appropriate online database, similar to the Map Tool, or they may be transferred within the I4 environment for display as footprints in the Map Tool. Datasets searchable through I4 (http://eol.jsc.nasa.gov/I4_tool) currently include: Crew Earth Observations (CEO) cataloged and uncataloged handheld astronaut photography; Sally Ride EarthKAM; Hyperspectral Imager for the Coastal Ocean (HICO); and the ISS SERVIR Environmental Research and Visualization System (ISERV). The ISS is a unique platform in that it will have multiple users over its lifetime, and that no single remote sensing system has a permanent internal or external berth. The open source I4 tool is designed to enable straightforward addition of new datasets as they become available such as ISS-RapidSCAT, Cloud Aerosol Transport System (CATS), and the High Definition Earth Viewing (HDEV) system. Data from other sensor systems, such as those operated by the ISS International Partners or under the auspices of the US National Laboratory program, can also be added to I4 provided sufficient access to enable searching of data or metadata is available. Commercial providers of remotely sensed data from the ISS may be particularly interested in I4 as an additional means of directing potential customers and clients to their products.

Stefanov, William L.↗

NASA NTRS2015

Phase 1 Final Report: Titan Submarine

The conceptual design of a submarine for Saturn's moon Titan was a funded NASA Innovative Advanced Concepts (NIAC) Phase 1 for 2014. The proposal stated the desire to investigate what science a submarine for Titan's liquid hydrocarbon seas might accomplish and what that submarine might look like. Focusing on a flagship class science system (100 kg), it was found that a submersible platform can accomplish extensive science both above and below the surface of the Kraken Mare. Submerged science includes mapping using side-looking sonar, imaging and spectroscopy of the lake, as well as sampling of the lake's bottom and shallow shoreline. While surfaced, the submarine will not only sense weather conditions (including the interaction between the liquid and atmosphere) but also image the shoreline, as much as 2 km inland. This imaging requirement pushed the landing date to Titan's next summer period (2047) to allow for lighted conditions, as well as direct-to-Earth communication, avoiding the need for a separate relay orbiter spacecraft. Submerged and surfaced investigation are key to understanding both the hydrological cycle of Titan as well as gather hints to how life may have begun on Earth using liquid, sediment, and chemical interactions. An estimated 25 Mb of data per day would be generated by the various science packages. Most of the science packages (electronics at least) can be safely kept inside the submarine pressure vessel and warmed by the isotope power system.The baseline 90-day mission would be to sail submerged and surfaced around and through Kraken Mare investigating the shoreline and inlets to evaluate the sedimentary interaction both on the surface and then below. Depths of Kraken have yet to be sensed (Ligeia to the north is thought to be 200 m (656 ft) deep), but a maximum depth of 1,000 m (3,281 ft) for Kraken Mare was assumed for the design). The sub would spend 20 d at the interface between Kraken Mare and Ligeia Mare for clues to the drainage of liquid methane into the currently predicted predominantly ethane Kraken Mare. During an extended ninety-day mission, it would transit the throat of Kraken (now Seldon Fretum) and perform similar explorations in other areas of Kraken Mare. Once this half year of exploration is completed the submarine could be tasked to revisit points of interest and perhaps do a complete sonar mapping of the seas. All in all, the submarine could explore over 3,000 km (1,864 mi) in its primary mission at an average speed of 0.3 meters per second.

Titan↗

DOE OSTI2021

Designing Energy-Efficient Quantum Computers Through Prediction and Reduction of Cooling Requirements for Cryogenic Electronics

Quantum computing has been identified as a “wild card” by the International Energy Agency in predicting future global data center energy usage. This is primarily because both uncertainty in the extent to which quantum computing will be adopted, and uncertainty in the power consumption of individual quantum data centers. Unlike the classical counterparts, quantum computers need to be maintained at near absolute zero, requiring energy-intensive cryogenic cooling systems. Therefore, as quantum computers scale up from existing 50 qubit technology demonstrations to the 10,000 to 100,000 qubit systems that will be able to solve complex problems, the energy consumption of both the electronics and the required cooling systems will also increase. To predict this scaling, this work analyzes the energy requirements for both computation and cooling of quantum hardware. We show that the energy requirements for cooling of quantum computers is determined by several computing system parameters, including the number and type of physical qubits, the operating temperature, the packaging efficiency of the system, and the split between circuits operating at cryogenic temperatures and those operating at room temperature. The energy requirements can then be found based on thermal system parameters such as cooling efficiency and cryostat heat transfer. Analysis of these parameters shows that the energy required for cooling is significantly larger than that required for computation, a reversal from energy usage patterns seen in conventional computing. The results and discussions provide a road-map for creating energy efficient quantum computers through the selection of computer architectures and cryogenic system configurations that minimize cooling requirements.

energy efficiency↗

NASA NTRS1997

Development of Software to Model AXAF-I Image Quality

This report describes work conducted on Delivery Order 181 between October 1996 through June 1997. During this period software was written to: compute axial PSD's from RDOS AXAF-I mirror surface maps; plot axial surface errors and compute PSD's from HDOS "Big 8" axial scans; plot PSD's from FITS format PSD files; plot band-limited RMS vs axial and azimuthal position for multiple PSD files; combine and organize PSD's from multiple mirror surface measurements formatted as input to GRAZTRACE; modify GRAZTRACE to read FITS formatted PSD files; evaluate AXAF-I test results; improve and expand the capabilities of the GT x-ray mirror analysis package. During this period work began on a more user-friendly manual for the GT program, and improvements were made to the on-line help manual.

Geary, Joseph↗

DOE OSTI2019

Automated Computational Thermochemistry for Butane Oxidation: A Prelude to Predictive Automated Combustion Kinetics

arge-scale implementation of high level computational theoretical chemical kinetics offers the prospect for dramatically improving the fidelity of combustion chemical modeling. As a first step toward this goal, we developed a procedure for automatically generating the thermochemical data for combustion of an arbitrary fuel. The procedure begins by producing a list of combustion relevant species from a specification of the fuel and combustion conditions of interest. Then, for each element in the list of species, the procedure determines an internal coordinate z-matrix description of its structure, the optimal torsional configuration via Monte Carlo sampling, key rovibrational properties for that optimal geometry (including anharmonic corrections from torsional mappings and/or vibrational perturbation theory), and high level estimates of the electronic and zero-point energies via arbitrarily defined composite methods. This dataset is then converted first to partition functions, then to thermodynamic properties, and finally to NASA polynomial representations of the data. The end product is an automatically generated database of electronic structure results and thermochemical data including representations in a format appropriate for combustion simulations. The utility and functioning of this predictive automated computational thermochemistry (PACT) software package is illustrated through application to the automated generation of thermochemical data for the combustion of n-butane. Butane is chosen for this demonstration as its species list is of reasonably manageable size for debugging level computations, while still presenting most of the key challenges that need to be surmounted in the consideration of larger fuels. Furthermore, its low temperature chemistry is representative of that oc-curring with larger alkanes.

Keceli, Murat↗

NASA NTRS2016

Space Suit Portable Life Support System (PLSS) 2.0 Unmanned Vacuum Environment Testing

For the first time in more than 30 years, an advanced space suit Portable Life Support System (PLSS) design was operated inside a vacuum chamber representative of the flight operating environment. The test article, PLSS 2.0, was the second system-level integrated prototype of the advanced PLSS design, following the PLSS 1.0 Breadboard that was developed and tested throughout 2011. Whereas PLSS 1.0 included five technology development components with the balance the system simulated using commercial-off-the-shelf items, PLSS 2.0 featured first generation or later prototypes for all components less instrumentation, tubing and fittings. Developed throughout 2012, PLSS 2.0 was the first attempt to package the system into a flight-like representative volume. PLSS 2.0 testing included an extensive functional evaluation known as Pre-Installation Acceptance (PIA) testing, Human-in-the-Loop testing in which the PLSS 2.0 prototype was integrated via umbilicals to a manned prototype space suit for 19 two-hour simulated EVAs, and unmanned vacuum environment testing. Unmanned vacuum environment testing took place from 1/9/15-7/9/15 with PLSS 2.0 located inside a vacuum chamber. Test sequences included performance mapping of several components, carbon dioxide removal evaluations at simulated intravehicular activity (IVA) conditions, a regulator pressure schedule assessment, and culminated with 25 simulated extravehicular activities (EVAs). During the unmanned vacuum environment test series, PLSS 2.0 accumulated 378 hours of integrated testing including 291 hours of operation in a vacuum environment and 199 hours of simulated EVA time. The PLSS prototype performed nominally throughout the test series, with two notable exceptions including a pump failure and a Spacesuit Water Membrane Evaporator (SWME) leak, for which post-test failure investigations were performed. In addition to generating an extensive database of PLSS 2.0 performance data, achievements included requirements and operational concepts verification, as well as demonstration of vehicular interfaces, consumables sizing and recharge, and water quality control.

Watts, Carly↗

DOE OSTI2026

WHONDRS Surface Water Geochemistry and Organic Matter Characterization Data from Streams Distributed across Latin America

This dataset supports a broader study examining global transferability of stream biogeochemistry and was generated in collaboration with the MicroSudAqua (µSudAqua) network (https://microsudaqua.netlify.app/en/). The dataset provides surface water geochemistry (dissolved organic carbon, total dissolved nitrogen, cations) and organic matter characterization (FTICR-MS) from streams in Argentina, Brazil, Chile, and Colombia. Samples were collected across stream orders (1st to 6th order) within five basins. Related data were collected and will be published separately in collaboration with the µSudAqua network. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. In addition to this readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. This dataset is comprised of (1) a folder of field photos; (2) a folder of surface water sample data, (3) a folder of raw Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) data; (4) file-level metadata; (5) data dictionary; (6) field metadata; (7) readme; (8) international generic sample number (IGSN) mapping file; and (9) field protocol. The sample data subfolder contains (1) dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC) data and averages; (2) total dissolved nitrogen data and averages; (3) anions and averages; (4) methods codes; (5) FTICR-MS methods; and (15) a subfolder of 9.4 Tesla (9.4T) FTICR-MS data. This folder contains the processed data and three subfolders, one containing the .xml files, one containing the water CoreMS output files, and the other containing instructions and scripts for processing the files in CoreMS (https://github.com/EMSL-Computing/CoreMS). All files are .csv, .pdf, .R, .xml, .d, .html, .Rmd, .py, .cal, .json, .jpg, .jpeg, .png, .mov, or .mp4.

Anions↗

DOE OSTI2026

Model Data Archive for Manuscript Titled "Evaluation of a Coupled Surface–Subsurface Hydrologic Model Using Dense Water‑Level Sensors in a Mixed Urban–Rural Watershed"

This archive provides scripts, input files, and datasets used for the implementation and evaluation of a fully coupled surface–subsurface hydrologic model in the Neches River Basin, southeast Texas. The study uses the Advanced Terrestrial Simulator (ATS) to simulate coupled surface–subsurface hydrologic processes over a mixed urban–rural watershed and evaluates model performance using a dense network of 136 in situ water-level sensors, nine U.S. Geological Survey (USGS) stream gauges, and SSEBop-derived evapotranspiration estimates during the period October 2014–June 2024. The workflow is implemented primarily in Python 3 using the Watershed Workflow package. The Jupyter notebooks can be executed using open-source software such as Anaconda JupyterLab or Visual Studio Code. Other data files include TXT, CSV, XML, SHP, TIF, NetCDF, HDF5, and ExodusII files, which can be processed using the provided Python scripts. ATS input files are provided in XML format and can be edited using any commonly used text editor. This archive contains: *Scripts and input files used to generate the ATS model setup, including watershed discretization, mesh generation, parameter mapping, and model configuration. *Jupyter notebooks used for preprocessing observational data, evaluating streamflow, water levels, and evapotranspiration, computing performance metrics, and generating the figures presented in the manuscript. *ATS simulation outputs and processed observational datasets, including OneRain and DD6 water-level sensors, USGS streamflow observations, GIS data, and supporting spatial datasets used throughout the study.

Dense water-level sensor network↗

DOE OSTI2024

Interim report for the International Muon Collider Collaboration (IMCC)

The International Muon Collider Collaboration (IMCC) [1] was established in 2020 following the recommendations of the European Strategy for Particle Physics (ESPP) and the implementation of the European Strategy for Particle Physics-Accelerator R&D Roadmap by the Laboratory Directors Group [2], hereinafter referred to as the the European LDG roadmap. The Muon Collider Study (MuC) covers the accelerator complex, detectors and physics for a future muon collider. In 2023, European Commission support was obtained for a design study of a muon collider (MuCol) [3]. This project started on 1st March 2023, with work-packages aligned with the overall muon collider studies. In preparation of and during the 2021-22 U.S. Snowmass process, the muon collider project parameters, technical studies and physics performance studies were performed and presented in great detail. Recently, the P5 panel [4] in the U.S. recommended a muon collider R&D, proposed to join the IMCC and envisages that the U.S. should prepare to host a muon collider, calling this their "muon shot". In the past, the U.S. Muon Accelerator Programme (MAP) [5] has been instrumental in studies of concepts and technologies for a muon collider.

43 PARTICLE ACCELERATORS↗

DOE OSTI2024

Interim report for the International Muon Collider Collaboration (IMCC)

Accelerator Physics (physics.acc-ph)↗

DOE OSTI2022

ESS-DIVE Reporting Format for Dataset Package Metadata

ESS-DIVE’s (Environmental Systems Science Data Infrastructure for a Virtual Ecosystem) dataset metadata reporting format is intended to compile information about a dataset (e.g., title, description, funding sources) that can enable reuse of data submitted to the ESS-DIVE data repository. The files contained in this dataset include instructions (dataset_metadata_guide.md and README.md) that can be used to understand the types of metadata ESS-DIVE collects. The data dictionary (dd.csv) follows ESS-DIVE’s file-level metadata reporting format and includes brief descriptions about each element of the dataset metadata reporting format. This dataset also includes a terminology crosswalk (dataset_metadata_crosswalk.csv) that shows how ESS-DIVE’s metadata reporting format maps onto other existing metadata standards and reporting formats.Data contributors to ESS-DIVE can provide this metadata by manual entry using a web form or programmatically via ESS-DIVE’s API (Application Programming Interface). A metadata template (dataset_metadata_template.docx or dataset_metadata_template.pdf) can be used to collaboratively compile metadata before providing it to ESS-DIVE.Since being incorporated into ESS-DIVE’s data submission user interface, ESS-DIVE’s dataset metadata reporting format, has enabled features like automated metadata quality checks, and dissemination of ESS-DIVE datasets onto other data platforms including Google Dataset Search and DataCite.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Temporal Study 2021-2022: Sample-Based Surface Water Chemistry and Organic Matter Characterization across Watersheds in the Yakima River Basin, Washington, USA (v3)

This dataset supports a broader study examining the drivers of temporal variability in sediment respiration rates in the Yakima River Basin. The dataset provides geochemistry and organic matter characterization data generated from samples collected at weekly or bi-weekly intervals at six sites across the Yakima River Basin in Washington, USA. Related sensor data will be published separately and can be used to link sediment respiration rates to biogeochemical processing rates. The data package was originally published in November 2022. It was updated in November 2023 (v2; modified files) and April 2025 (new and modified files). See the change history section in readme for more details. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) dissolved inorganic carbon (DIC), dissolved organic carbon (DOC; reported as non-purgeable organic carbon; NPOC), total nitrogen (TN), total suspended solids (TSS), and ions; (5) averaged values from water chemistry data; (6) surface water sampling protocol; (7) sensor protocol; (8) readme; (9) methods codes; (10) international generic sample number (IGSN) mapping file; and (11) folder of high resolution characterization of organic via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory). This folder contains two subfolders, one containing the .xml data files and the other containing instructions for using Formularity (https://omics.pnl.gov/software/formularity) and an R script to process the data based on the user's specific needs. All files are .csv, .pdf, .R, .ref, or .xml. We acknowledge the Yakama Nation as owners and caretakers of the lands where we collected our data. We thank the Confederated Tribes and Bands of the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1986

Application of NCOREL to aircraft configurations

The NCOREL computer program and methodology (Grossman, 1979) modified for computation of flows over complex geometries is described. The newly introduced features include a more flexible grid-generation package, capable of generating grids for realistic wing-body cross sections, and a more general numerical method, developed for the capture of highly three-dimensional embedded, oblique shocks. In addition, an inlet capability is included, by means of which the cross section is allowed to change discontinuously with the addition of the inlet geometry. The new cross section is regridded and the potentials and their derivatives are interpolated for the marching to continue. Hence, a discontinuity in the grid or mappings is taken into account at the inlet station. The results of the flow-field computation for a realistic fighter configuration are discussed.

Siclari, M. J.↗

NASA NTRS2019

Leveraging STARE for Co-aligned Data Locality with netCDF and Python MPI

We have leveraged STARE indexing to package partitioned data chunks from diverse datasets into netCDF files, distributed them on a cluster of 16 lightweight nodes with their placements spatiotemporally co-aligned, and demonstrated a few integrative analyses using netCDF parallel I/O and Python MPI, with single-user performance and scalability comparable to, or even better than, that of a parallel array database management system (ADBMS) such as SciDB. However, records of the node location and STARE index ranges for each data chunk, similar to the chunk maps of SciDB, must be maintained and consulted by the I/O and analysis code for coordinating the analytic operations in parallel, in order to achieve the good performance and scalability.

Kwo-Sen Kuo↗

DOE OSTI2021

radkit v1.2

The radkit software suite (python) consists of three primary libraries: stark, trajan, and curie. The trajan library provides the tools to analyze and manipulate data from lidar and inertial measurement unit (IMU) devices as well as trajectories from algorithms such as simultaneous localization and mapping (SLAM). These components allow reading and writing standard data formats, performing rigid affine transformations, discretizing three-dimensional space, and visualizing data products. The curie library comprises a standard set of object-oriented tools for radiation data and analysis in the following modules: (1) listmode and binmode data classes with methods for manipulation, plotting, slicing and file IO; (2) radiological/nuclear source detection/identification analysis results; (3) source encounters of correlated analyses and (4) energy-dependent angular detector response functions. The stark package provides low-level tools that are leveraged by both curie and trajan. The tools are flexible for offline analysis as well as performant for real-time integrations. The radkit libraries have associated Robot Operating System packages for use in real-time and robotic systems.

Joshi, Tenzing↗

DOE OSTI2026

radkit base v1.6

The radkit (base) software suite (python) consists of three primary libraries: stark, trajan, and curie. The trajan library provides the tools to analyze and manipulate data from lidar and inertial measurement unit (IMU) devices, cameras, as well as trajectories from algorithms such as simultaneous localization and mapping (SLAM). These components allow reading and writing standard data formats, performing rigid affine transformations, discretizing three-dimensional space, and visualizing data products. The curie library comprises a standard set of object-oriented tools for radiation data and analysis in the following modules: (1) listmode and binmode data classes with methods for manipulation, plotting, slicing and file IO; (2) radiological/nuclear source detection/identification analysis results; (3) source encounters of correlated analyses and (4) energy-dependent angular detector response functions. The stark package provides low-level tools that are leveraged by both curie and trajan. The tools are flexible for offline analysis as well as performant for real-time integrations.

Salathe, Marco [Lawrence Berkeley National Laborat↗