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DOE OSTI2022

Metagenome-assembled genome extraction and analysis from microbiomes using KBase

Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only become possible recently. In order to realize the hope of capturing Earth’s microbial genetic complement and to facilitate the investigation of the functional roles of specific lineages in a given ecosystem, technologies that accelerate the recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high-quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). Overall, these steps take about a day to obtain extracted genomes when starting from smaller environmental shotgun read libraries, or up to about a week from larger libraries. In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAGs, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq and others. While portions of such capabilities are available individually from other resources, the combination of the intuitive usability, data interoperability and integration of tools in a freely available computational resource makes KBase a powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended with additional MAG recovery and analysis tools, via the KBase software development kit (SDK).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

diffpy.mpdf : open-source software for magnetic pair distribution function analysis

The open-source Python package diffpy.mpdf , part of the DiffPy suite for diffraction and pair distribution function analysis, provides a user-friendly approach for performing magnetic pair distribution function (mPDF) analysis. The package builds on existing libraries in the DiffPy suite to allow users to create models of magnetic structures and calculate corresponding one- and three-dimensional mPDF patterns. diffpy.mpdf can be used to perform fits to mPDF data either in isolation or in combination with atomic pair distribution function data for joint refinement of the atomic and magnetic structure. Examples are given using MnO and MnTe as representative antiferromagnetic compounds and MnSb as a representative ferromagnet.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Analysis and Recommendation of Alpha-Beta Continuous Air Monitor Alarm Setpoints for the RPL Stack Exhaust

The Radiochemical Processing Laboratory (RPL) alpha-beta continuous air monitor (CAM) is used for real-time detection of “artificial” alpha-beta particulates from the stack exhaust. The CAM interfaces with software developed by the Pacific Northwest National Laboratory—called the “PNNL OS3300 Alpha-Beta Monitoring Software”—that provides real-time estimates of alpha-beta air concentrations and integrated activities that are calculated from measured CAM counts. The OS3300 software has alarm setpoints that can be used to provide an early indication of larger releases, that if allowed to persist, could approach defined dose limits. This report performs a detailed review of historical and current alarm setpoints used at RPL, including discussion of the technical basis used in their development, analysis of alarm frequencies using measured historical data, and performs a detailed dose assessment using more realistic release scenarios, meteorology, and adjustment factors used in estimating released stack activity. Based on the results, the alpha and beta air concentration alarm setpoints will remain 1.77 × 10 -8 µCi/ml and 3.47 × 10 -8 µCi/ml, respectively; and the alpha and beta integrated activity alarm setpoints will remain 70.22 µCi and 137.63 µCi, respectively. These setpoints achieve the right operational balance in identifying larger releases from planned radiological work at RPL, without being overly conservative so as to cause nuisance alarming. Furthermore, implied doses associated with these setpoints are below defined and regulatory limits.

325RPL↗

DOE OSTI2024

DEEPEN: Final 3D PFA Favorability Models and 2D Favorability Maps at Newberry Volcano

Part of the DEEPEN (DE-risking Exploration of geothermal Plays in magmatic ENvironments) project involved developing and testing a methodology for a 3D play fairway analysis (PFA) for multiple play types (conventional hydrothermal, superhot EGS, and supercritical). This was tested using new and existing geoscientific exploration datasets at Newberry Volcano. This GDR submission includes images, data, and models related to the 3D favorability and uncertainty models and the 2D favorability and uncertainty maps. The DEEPEN PFA Methodology, detailed in the journal article below, is based on the method proposed by Poux & O'brien (2020), which uses the Leapfrog Geothermal software with the Edge extension to conduct PFA in 3D. This method uses all available data to build a 3D geodata model which can be broken down into smaller blocks and analyzed with advanced geostatistical methods. Each data set is imported into a 3D model in Leapfrog and divided into smaller blocks. Conditional queries can then be used to assign each block an index value which conditionally ranks each block's favorability, from 0-5 with 5 being most favorable, for each model (e.g., lithologic, seismic, magnetic, structural). The values between 0-5 assigned to each block are referred to as index values. The final step of the process is to combine all the index models to create a favorability index. This involves multiplying each index model by a given weight and then summing the resulting values. The DEEPEN PFA Methodology follows this approach, but split up by the specific geologic components of each play type. These components are defined as follows for each magmatic play type: 1. Conventional hydrothermal plays in magmatic environments: Heat, fluid, and permeability 2. Superhot EGS plays: Heat, thermal insulation, and producibility (the ability to create and sustain fractures suitable for and EGS reservoir) 3. Supercritical plays: Heat, supercritical fluid, pressure seal, and producibility (the proper permeability and pressure conditions to allow production of supercritical fluid) More information on these components and their development can be found in Kolker et al., (2022). For the purposes of subsurface imaging, it is easier to detect a permeable fluid-filled reservoir than it is to detect separate fluid and permeability components. Therefore, in this analysis, we combine fluid and permeability for conventional hydrothermal plays, and supercritical fluid and producibility for supercritical plays. We also project the 3D favorability volumes onto 2D surfaces for simplified joint interpretation, and we incorporate an uncertainty component. Uncertainty was modeled using the best approach for the dataset in question, for the datasets where we had enough information to do so. Identifying which subsurface parameters are the least resolved can help qualify current PFA results and focus future efforts in data collection. Where possible, the resulting uncertainty models/indices were weighted using the same weights applied to the respective datasets, and summed, following the PFA methodology above, but for uncertainty.

15 GEOTHERMAL ENERGY↗

DOE OSTI2021

Validation and Verification for INL Modelica-based TEDS models Via Experimental Results

This report provides an overview on the verification and validation (V&V) of the Thermal Energy Distribution System (TEDS) model developed in the Modelica process modeling ecosystem using experimental data. Model development has led to the creation of a dynamic process model of the experimental TEDS facility housed within the Energy Systems Laboratory (ESL) at Idaho National Laboratory (INL). The model was then used during the preconstruction phase of the experimental effort to inform experimental design (e.g., insulation requirements, bypass line placement, expected performance of components) and to test innovative control schemes prior to the initial operation. The TEDS model developed in Modelica includes the primary components of the TEDS experimental unit: a 200kW Chromalox heater; a single-tank packed-bed thermal energy storage system filled with 0.125-inch alumina (Al2O3) beads; an ethylene-glycol-to-Therminol-66 heat exchanger; system piping; five control valves; and all associated temperature, pressure, and volumetric flow sensors. Using the Institute of Electrical and Electronics Engineers (IEEE) V&V methodologies, considered the gold standard in the engineering field, the model was verified using a combination of static analysis, spatial convergence, and regression tests. Then using dynamic time warping (DTW) initial runs to validate and tune the TEDS model versus the experiment were conducted. This tuning method was accomplished using the INL Risk Analysis Virtual ENvironment (RAVEN) software package. Tuning is required to account for physical phenomena that are less understood within the empirical heat transfer correlations. Through the commencement of this work, a systems-level model of TEDS with associated control systems, sensors, piping diameters, and component capabilities has been created. This model was utilized in the pre-experimental phase to inform system design, insulation thicknesses, and potential control schemes to operate the system effectively and safely. Then, initial experimental startup and operational data were used to demonstrate the validation and tuning methodology. This process demonstrates the classical two-step approach of a model informing experimental design followed by the experiment validation and tuning the model.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

Toward designing effective exascale scientific computing workflows: experiences and best practices

Many fields within scientific computing have embraced advances in big-data analysis and machine learning, which often requires the deployment of large, distributed and complicated workflows that may combine training neural networks, performing simulations, running inference, and performing database queries and data analysis in asynchronous, parallel and pipelined execution frameworks. Such a shift has brought into focus the need for scalable, efficient workflow management solutions with reproducibility, error and provenance handling, traceability, and checkpoint-restart capabilities, among other needs. Here, we discuss challenges and best-practices for deploying exascale-generation computational science workflows on resources at the Oak Ridge Leadership Computing Facility (OLCF). We present our experiences with large-scale deployment of distributed workflows on the Summit supercomputer, including for bioinformatics and computational biophysics, materials science, and deep learning model optimization. We also present problems and solutions created by working within a Python-centric software base on traditional HPC systems, and discuss steps that will be required before the convergence of HPC, AI, and data science can be fully realized. Our results point to a wealth of exciting new possibilities for harnessing this convergence to tackle new scientific challenges.

Coletti, Mark↗

DOE OSTI2020

Charged particle track reconstruction with SπRIT Time Projection Chamber

In this work, we present a software framework, SπRITROOT, which is capable of track reconstruction and analysis of heavy-ion collision events recorded with the SRIT time projection chamber. The track-fitting toolkit GENFIT and the vertex reconstruction toolkit RAVE are applied to a box-type detector system. A pattern recognition algorithm which performs helix track finding and handles overlapping pulses is described. The performance of the software is investigated using experimental data obtained at the Radioactive Isotope Beam Facility (RIBF) at RIKEN. This work focuses on data from 132 Sn + 124 Sn collision events with beam energy of 270 AMeV. Particle identification is established using < dE/dx >and magnetic rigidity, with pions, hydrogen isotopes, and helium isotopes.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

River bank erosion and accretion rates, and planform metrics of the East River, downstream of Gothic Colorado over intervals between 1955 and 2015

This dataset provides the tabular summary of analysis of an alluvial floodplain reach of the East River, downstream of Gothic, CO near Crested Butte. The measurements include bank erosion and accretion rates, channel width, bank curvature, and the aspect/orientation of the river banks. The measurements were derived from binary masks of the location of the river channel from aerial and satellite imagery collected on seven dates over a sixty-year timespan: 1955, 1973, 1983, 1990, 2001, 2011, and 2015. The masks were analyzed using the Spatially Continuous Riverbank Erosion and Accretion Measurements (SCREAM) software detailed in Rowland et al. 2016. The masks used in this analysis can be found an accompanying dataset (DOI: ). Rates of change along the East River were measured over a total of 8-time intervals: 1955-1973; 1955-2015; 1973-1983; 1983-1990; 1990-2001; 2001-2011; 2001-2015; and 2011-2015.In files with “summary” in the name, the data is provided at a pixel level, where each mapped bank pixel has an associated erosion or accretion value, a channel width, a curvature value, and an aspect each river and time period will have an individual file. Files with “Segments” in name provide data that is averaged along segments of the rivers. These segments are approximately 10 channel widths in length. In addition to erosion and accretion rates, the segment-based results include area measurements of erosion and accretion, islands, and channels. The number of islands is also included.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Designing a Magnetic Measurement Data Acquisition and Control System With Reuse in Mind: A Rotating Coil System Example

Accelerator magnet test facilities frequently need to measure different magnets on differently equipped test stands and with different instrumentation. Designing a modular and highly reusable system that combines flexibility built-in at the architectural level as well as on the component level addresses this need. Specification of the backbone of the system, with the interfaces and dataflow for software components and core hardware modules, serves as a basis for building such a system. The design process and implementation of an extensible magnetic measurement data acquisition and control system are described, including techniques for maximizing the reuse of software. The discussion is supported by showing the application of this methodology to constructing two dissimilar systems for rotating coil measurements, both based on the same architecture and sharing core hardware modules and many software components. The first system is for production testing 10 m long cryo-assemblies containing two MQXFA quadrupole magnets for the high-luminosity upgrade of the Large Hadron Collider and the second for testing IQC conventional quadrupole magnets in support of the accelerator system at Fermilab.

43 PARTICLE ACCELERATORS↗

DOE OSTI2023

Demonstration of sub-micron UCN position resolution using room-temperature CMOS sensor

High spatial resolution of ultracold neutron (UCN) measurement is of growing interest to UCN experiments such as UCN spectrometers, UCN polarimeters, quantum physics of UCNs, and quantum gravity. Here we utilize physics informed deep learning to enhance the experimental position resolution and to demonstrate sub-micron spatial resolutions for UCN position measurements obtained using a room-temperature CMOS sensor, extending our previous work that demonstrated a position uncertainty of 1.5 microns. We explore the use of the open-source software Allpix Squared to generate experiment-like synthetic hit images with ground-truth position labels. We use physics-informed deep learning by training a fully connected neural network (FCNN) to learn a mapping from input hit images to output hit position. The automated analysis for sub-micron position resolution in UCN detection combined with the fast data rates of current and next generation UCN sources will enable improved precision for future UCN research and applications.

10B nanometer thin film↗

DOE OSTI2024

Accelerating science: The usage of commercial clouds in ATLAS Distributed Computing

The ATLAS experiment at CERN is one of the largest scientific machines built to date and will have ever growing computing needs as the Large Hadron Collider collects an increasingly larger volume of data over the next 20 years. ATLAS is conducting R&D projects on Amazon Web Services and Google Cloud as complementary resources for distributed computing, focusing on some of the key features of commercial clouds: lightweight operation, elasticity and availability of multiple chip architectures. The proof of concept phases have concluded with the cloud-native, vendoragnostic integration with the experiment’s data and workload management frameworks. Google Cloud has been used to evaluate elastic batch computing, ramping up ephemeral clusters of up to O(100k) cores to process tasks requiring quick turnaround. Amazon Web Services has been exploited for the successful physics validation of the Athena simulation software on ARM processors. We have also set up an interactive facility for physics analysis allowing endusers to spin up private, on-demand clusters for parallel computing with up to 4 000 cores, or run GPU enabled notebooks and jobs for machine learning applications. The success of the proof of concept phases has led to the extension of the Google Cloud project, where ATLAS will study the total cost of ownership of a production cloud site during 15 months with 10k cores on average, fully integrated with distributed grid computing resources and continue the R&D projects.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture

Background Characterizing the physical organization of the genome is essential for understanding long-range gene regulation, chromatin compartmentalization, and epigenetic accessibility. Hi-C experiments generate two-dimensional (2D) genome-wide contact maps of chromatin interactions by capturing the spatial proximity between genomic loci, which reveal interaction frequencies but lack the spatial resolution needed to interpret the three-dimensional (3D) genome structure(s). Emerging evidence suggests that epigenetic regulation is closely linked to 3D genome architecture, and that structural changes over time (4D) drive key biological processes in development, disease, and environmental response. Thus, integrating 3D structure with functional data is critical for a more complete understanding of genome regulation. Previous work, most notably the 4DHiC chromosome modeling framework, has shown that physical multi-dimensional modeling approaches rooted in polymer physics and molecular dynamics can resolve these structures at biologically meaningful resolutions by integrating temporal Hi-C data with physical constraints to uncover dynamic chromosome reorganization. Thus, molecular dynamics simulations, constrained by Hi-C contact matrices, can resolve fine-scale structural changes and reveal functionally significant transitions in chromatin conformation. Results Herein, we present the 4D Genome Browser Workflow (4DGBWorkflow) and the 4D Genome Browser (4DGB). The algorithm is based on the 4DHiC method, and the containerized tool is an end-to-end workflow that can transform, filter, and view 4D epigenomics and chromatin datasets, allowing non-specialists to apply three-dimensional modeling principles to diverse datasets and experimental conditions. The software executes on a laptop running macOS, Linux or Windows. From input Hi-C files (.hic), the 4DGBWorkflow produces 3D reconstructions of chromosomes, integrates the reconstruction with track data (e.g., epigenetic marks, transcriptome profiles), and provides comparative visualization of the results in a single workflow. Conclusions The 4DGBWorkflow and 4D Genome Browser are open-source tools for comparative analysis and visualization of 4D chromosome datasets, including chromatin architecture and epigenomic signals. Automatic integration of Hi-C data with molecular dynamics democratizes the construction of time resolved 3D genome structures, simplifying complex simulations and data integration schemes.

3D Genome Browser↗

DOE OSTI2020

A Parallel Computing Infrastructure for Building Energy Simulation

In order to study grid-interactive efficient buildings, Pacific Northwest National Laboratories (PNNL) needs an infrastructure for urban-scale building energy modeling. Such an infrastructure should be fast, scalable, and easy-to-use. Given a set of data from the Energy Information Administration’s Commercial Building Energy Consumption Survey (CBECS) and tool to translate survey data into simulation inputs, this project aimed to conduct the simulation of the entire dataset in parallel. Before running the simulations, the necessary software was bundled into a container for use on the PNNL supercomputing network. Then, the parallel simulation workflow was designed using GNU Make, a file creation software, and submitted to a supercomputing partition which could run hundreds of simulations simultaneously. The EnergyPlus simulations output hourly electric meter data for each CBECS sample, which represents the electricity consumption of similar commercial buildings across the United States. Analyzing and visualizing the meter data is important to the future of the work, and this project wrote code to make common analysis methods simple, fast, and accessible. Moving forwards, the model will need to be expanded to include data from other sources and its accuracy will need to be improved and eventually validated.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2021

Nanosecond Gated CMOS Camera (NSGCC) ICD (Rev. 2.1)

The Ultra-Fast X-ray Imager (UXI) program is an ongoing effort at Sandia National Laboratories to create high speed, multi-frame, time-gated Read Out Integrated Circuits (ROICs), and a corresponding suite of photodetectors to image a wide variety of High Energy Density (HED) physics experiments on both Sandia’s Z-Machine and LLNL’s National Ignition Facility (NIF). Several cameras have been designed over the length of the program; one of the most recent is the Icarus, which is an improvement on past imagers (Furi and Hippogriff). A second sensor that can be connected is the Daedalus sensor. The Icarus is a 1024 × 512-pixel array with either 25 μm or 8 µm spatial resolution containing four frames of storage per pixel and has improved timing generation and distribution components while achieved 2 ns time gating. The Daedalus sensor is also a 1024 x 512-pixel array with 25 µm special resolution containing three frames of storage per pixel and has an increased set of features for a wider variety of applications from interlacing of rows in each frame to configurability of all shutters. See Section 14 for details regarding the Icarus implementation of the firmware and Section 15 for details regarding the Daedalus implementation. Due to the unique test environments UXI sensors are targeted for, full custom hardware was required to physically mount an Icarus or Daedalus sensor, manage its various functions, and read out pixel data for transfer to a host computer. Beyond experimental functionality, the hardware also needed to accommodate sensor characterization requirements. Lawrence Livermore National Laboratory’s ‘Version 4.0 Board’ was the result of these efforts. It mounts all the components required to fully utilize the Icarus and Daedalus sensors including analog to digital converters to convert pixel data and various system voltages to digital form for readout and analysis, DAC channels for remote configuration of critical bias voltages, static random-access memories to buffer pixel data, RS422 and Gigabit Ethernet communications for remote access, and an FPGA to tie these components together. This document describes the FPGA electrical interfaces in detail to allow the reader a greater understanding of the device, and to facilitate implementation of custom software to control and manage it. The Version 4.0 Board is a continuation of the Nano-second Gated CMOS hardware design that retains much of the functionality of the Version 1.0 Board while adding features including a DAC instead of digital potentiometers, as well as sensors for pressure and radiation. The Version 4.0 board is intended for applications requiring tight form-factor enclosures. It is composed of two stacking boards; one holds the FPGA and regulators to power the various components of the board while the other contains the mating connector to the sensor, image-readoff ADCs, the DAC, and other components.

42 ENGINEERING↗

DOE OSTI2021

Genome Extraction from Shotgun Metagenome Sequence Data

Uncultivated Bacteria and Archaea comprise the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only recently become possible. To realize the hope of capturing Earth’s microbial genetic complement, technologies that accelerate recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAG genomes, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq, and others. While portions of such capabilities are individually available from other resources, the combination of the intuitive usability, data interoperability, and integration of tools in a freely available compute resource makes KBase a uniquely powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended, with additional MAG recovery and analysis tools, via the KBase SDK (Software Development Kit).

Chivian, Dylan↗

DOE OSTI2021

Moab Desert Crust - Sample 4E

Chivian, Dylan↗

DOE OSTI2022

NRAP-Open-IAM: NRAP Open Source Integrated Assessment Model

Note: This is the last version (a2.6.1) of NRAP-Open-IAM released during NRAP Phase II in 2022. The latest version of NRAP-Open-IAM is available here: https://edx.netl.doe.gov/dataset/phase-iii-nrap-open-iam NRAP-Open-IAM is an open-source software product that enables quantification of containment effectiveness and leakage risk at storage sites in the context of system uncertainties and variability. NRAP-Open-IAM represents the next-generation in a line of systems-based computational models developed for quantitative geological carbon storage (GCS) risk assessment. The model comprises a set of reduced-order and analytical models of various components of the GCS system, potential leakage pathways, receptors of concern including impact to groundwater resources and the atmosphere, a framework to support stochastic simulation, time stepping, uncertainty quantification, other analytical functionality for scenario and risk-performance evaluation, and a basic graphical user interface to support scenario development, data input simulation definition, and basic post-processing and results display. As the NRAP Open-IAM functionality continues to evolve, we continue to add to its capability to develop quantitative, probabilistic, and time-dependent profiles of the evolution of risk at a GCS site and evaluate the influence of uncertain parameters on uncertainty in predicted risk. It can be used to quantify the dynamics of reservoir saturation plume and pressure-affected area, for evaluation of the area of potential groundwater impact (i.e., Area of Review) and monitoring requirements to support cost and regulatory analysis, and for consideration of different post-injection site care and closure scenarios. This submission contains the current version of NRAP-Open-IAM available for evaluation and testing. To use the NRAP-Open-IAM, download the source code (https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/4c24a3da-3b40-4ffe-9892-c807ae9f8760) then open the NRAP-Open-IAM user's guide (https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/8b27335a-343c-4836-b8a3-3ad0bdc9e669) to read more about the tool. Installation instructions for Windows, Mac, and Linux can be found in the "installers" folder of the extracted NRAP-Open-IAM folder and describe setup of environment (e.g., Python libraries) needed for proper work of the tool. Test of installation can be done by running "python openiam_setup_tests.py" in the "setup" folder. The installation test also runs a test suite to see if the NRAP-Open-IAM has been installed correctly. To run the test suite separately, run "python iam_test.py" in the "test" folder. User's guide: https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/8b27335a-343c-4836-b8a3-3ad0bdc9e669 Developer's guide: https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/3bc6ee7d-609d-4eb6-80ba-fa6130ee0313 Reservoir simulation data used in some examples distributed with NRAP-Open-IAM: - Kimberlina: https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/eb62cece-61b2-4037-9b6d-32407dde2ab8 - Kimberlina (compartmentalized): https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/366f9530-3b32-4b84-affe-ab2df1d9a8b5 - FutureGen 2.0: https://edx.netl.doe.gov/dataset/futuregen-2-0-1008-simulation-reservoir-lookup-table NRAP-Open-IAM GitLab repository: https://gitlab.com/NRAP/OpenIAM Related publications: - Bacon, D., Yonkofski, C., Brown, C., Demirkanli, D. and Whiting, J., 2019. Risk-based post injection site care and monitoring for commercial-scale carbon storage: Reevaluation of the FutureGen 2.0 site using NRAP-Open-IAM and DREAM. International Journal of Greenhouse Gas Control 90: 102784. - Bacon, D. Demirkanli, D., and White, S., 2020. Probabilistic risk-based Area of Review (AoR) determination for a deep-saline carbon storage site. International Journal of Greenhouse Gas Control 102: 103153. - Harp, D., Oldenburg, C., and Pawar, R., 2019. A metric for evaluating conformance robustness during geologic CO2 sequestration operations. International Journal of Greenhouse Gas Control 85: 100-108. - Lackey, G., Vasylkivska, V., Huerta, N., King, S., and Dilmore, R., 2019. Managing well leakage risks at a geologic carbon storage site with many wells, International Journal of Greenhouse Gas Control, 88 :182-194. - Vasylkivska, V., Dilmore, R., Lackey, G., Zhang, Y., King, S., Bacon, D., Chen, B., Mansoor, K., and Harp, D., 2021. NRAP-Open-IAM: A flexible open-source integrated assessment model for geologic carbon storage risk assessment and management, Environmental Modelling & Software, 143: 105114. Presentations: - Chen, B., Harp, D., and Pawar, R., A data assimilation approach (ES-MDA) coupling with NRAP-Open-IAM for quantifying uncertainty reduction in geological CO2 sequestration. AGUFM 2019: T44A-02. - Chen, B., and Harp, D., Improving risk analysis precision for geologic CO2 sequestration by quantifying the uncertainty reduction before and after acquiring monitoring data. 14th Greenhouse Gas Control Technologies Conference, Melbourne, Australia, 2018, pp. 21-26. - Harp, D., National Risk Assessment Partnership Task 2: Containment Assurance. No. LA-UR-19-28654, Los Alamos National Laboratory (LANL), Los Alamos, NM (United States), 2019. - Vasylkivska, V., King, S., Bacon, D., Harp, D., Chen, B., Mansoor, K., Onishi, T., Yang, Y., Zhang, Y., and Keating, E., NRAP-Open-IAM: An open-source integrated assessment model, poster, Mastering the Subsurface Through Technology Innovation, Partnerships and Collaboration: Carbon Storage and Oil and Natural Gas Technologies Review Meeting, Pittsburgh, PA, August 13-16, 2018. - Vasylkivska, V., Lackey, G., King, S., Wentworth, A., Huerta, N., Creason, C., DiGiulio, J., Yang, Y., and Dilmore, R., Long-term risk analysis of a geologic CO2 storage project during the post-injection period, SIAM Conference on Computational Science and Engineering, Spokane, WA, February 25-March 1, 2019. - Vasylkivska, V., Overview of the NRAP-Open-IAM tool for carbon storage (beta release), 2019 Annual NRAP Tool Users Meeting, Pittsburgh, PA, August 27, 2019. - Vasylkivska, V., Bacon, D., Chen, B., Dilmore, R., Harp, D., King, S., Lackey, G., Lindner, E., Liu, G., Mansoor, K. and Zhang, Y., NRAP-Open-IAM: A new, open-source code for integrated assessment of geologic carbon storage containment effectiveness and leakage risk, poster, American Geophysical Union Fall Meeting 2020 (virtual meeting), December 2020. - Vasylkivska, V., NRAP open-source integrated assessment model and relevant application, oral presentation, NRAP workshop "NRAP Tools for Geologic Carbon Storage Risk-Based Decision Making" held in conjunction with Groundwater Protection Council (GWPC) 2021 Annual Forum (virtual meeting), Salt Lake City, UT, September 2021. - Vasylkivska, V., NRAP-Open-IAM: open-source integrated assessment model, digital poster/demonstration, software demonstration session, 2022 Carbon Management Project Review Meeting, August 16, 2022

AoR↗

DOE OSTI2025

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↗