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COVIDScholar: An automated COVID-19 research aggregation and analysis platform

The ongoing COVID-19 pandemic produced far-reaching effects throughout society, and science is no exception. The scale, speed, and breadth of the scientific community’s COVID-19 response lead to the emergence of new research at the remarkable rate of more than 250 papers published per day. This posed a challenge for the scientific community as traditional methods of engagement with the literature were strained by the volume of new research being produced. Meanwhile, the urgency of response lead to an increasingly prominent role for preprint servers and a diffusion of relevant research through many channels simultaneously. These factors created a need for new tools to change the way scientific literature is organized and found by researchers. With this challenge in mind, we present an overview of COVIDScholar https://covidscholar.org/, an automated knowledge portal which utilizes natural language processing (NLP) that was built to meet these urgent needs. The search interface for this corpus of more than 260,000 research articles, patents, and clinical trials served more than 33,000 users at an average of 2,000 monthly active users and a peak of more than 8,600 weekly active users in the summer of 2020. Additionally, we include an analysis of trends in COVID-19 research over the course of the pandemic with a particular focus on the first 10 months, which represents a unique period of rapid worldwide shift in scientific attention.

60 APPLIED LIFE SCIENCES↗

Coreii - Scout

COREII Scout employs React, Vite, TypeScript, Tailwind, and Daisy UI for its graphical user interface (GUI), offering both dark and light modes. The code is modular, with components and reusable wrappers to enhance efficiency. The primary goal of COREII Scout is to aid analysts in collecting and analyzing various sources related to cyber attacks, utilizing models to automate the report writing process. It uses Named Entity Recognition (NER), a type of Natural Language Processing (NLP), to extract key entities from each source. Analysts review and classify these entities using the COREII Attack Chain Estimator (ACE), adding their comments. Ultimately, a Large Language Model (LLM) generates a detailed report with user guidance. This setup ensures a streamlined and effective approach to cyber attack analysis and reporting.

Pluth, Adam [Idaho National Laboratory (INL), Idah↗

cclib 2.0: An updated architecture for interoperable computational chemistry

Interoperability in computational chemistry is elusive, impeded by the independent development of software packages and idiosyncratic nature of their output files. The cclib library was introduced in 2006 as an attempt to improve this situation by providing a consistent interface to the results of various quantum chemistry programs. The shared API across programs enabled by cclib has allowed users to focus on results as opposed to output and to combine data from multiple programs or develop generic downstream tools. Initial development, however, did not anticipate the rapid progress of computational capabilities, novel methods, and new programs; nor did it foresee the growing need for customizability. Here, we recount this history and present cclib 2, focused on extensibility and modularity. We also introduce recent design pivots—the formalization of cclib’s intermediate data representation as a tree-based structure, a new combinator-based parser organization, and parsed chemical properties as extensible objects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Taking the MPI standard and the open MPI library to exascale

The Open MPI for Exascale (OMPI-X) project was one of two in the Exascale Computing Project (ECP) focused on advancing the MPI ecosystem. The OMPI-X team worked with other MPI Forum members to champion several important features for inclusion in the MPI 4.0, 4.1, and upcoming 5.0 MPI standard versions, in support of the needs of exascale applications and systems. The team also worked with the larger Open MPI community to bring implementations of these new features and other enhancements into Open MPI, one of the leading open-source implementations of the MPI interface. Here, this paper describes the motivation for the work of the OMPI-X project in the context of exascale computing needs, the nature of the resulting new capabilities in the MPI standard, and how they were implemented in the Open MPI library. Features include improved support for “MPI + X” programming models through partitioned communications and support for user-level threading, sessions, fault tolerance through the user-level fault mitigation (ULFM) and Reinit models, and other features. We also discuss enhancements to Open MPI providing improved performance and scalability for existing features, such as collective operations, one-sided operations, support for the Slingshot-11 interconnect of the initial exascale systems, and how the OMPI-X team worked to improve quality assurance for the Open MPI library, particularly on platforms of interest to the Department of Energy community.

97 MATHEMATICS AND COMPUTING↗

Machine-Learning-Based Mapping and Modeling of Solar Energy with Ultra-High Spatiotemporal Granularity

Despite the rapid growth of solar energy, we still lack a dynamic, high-fidelity database that tracks the spatiotemporal variations of solar PVs and their associated infrastructures across different places at a spatially resolved scale. The absence of such data presents a barrier to various applications such as solar PV growth projection, solar energy integration, solar incentive design, and climate risk assessment. In this project, we aim to bridge this gap by developing AI-based algorithms to extract granular information about solar PV installations and their associated infrastructures (i.e., distribution grids) from widely available unstructured data like remote sensing images and street views. As a result, we have built the Solar Energy Atlas, a fine-grained, large-scale geospatial overlay of distributed solar PVs and distribution grids. On top of it, we have advanced the understanding of solar adoption and distribution grid vulnerability to climate-induced extremes. Our major contributions can be summarized as follow: (1) By developing new AI algorithms, we have built the most comprehensive solar PV spatiotemporal database covering the entire US. This is the first time we obtained the exact GPS locations, size, subtype, and installation year information for rooftop solar PVs across the US. This database can be used for solar PV growth projection, solar energy integration, solar energy policy analysis and design, and spatially-resolved climate risk assessment. (2) Leveraging this database, we have uncovered the socioeconomic driving factors that are correlated with earlier onset of solar adoption and higher saturated adoption levels. We have identified the heterogeneity in the effects of different types of financial incentives on solar adoption and provided implications for tailoring incentive design based on local income levels to promote equitable solar adoption. (3) We have developed a distribution grid GIS mapping algorithm which can obtain granular geospatial and topology information about distribution grids using multi-modal open data, reducing the dependency on hard-to-obtain smart meter data of conventional approaches. It shows effectiveness in both the U.S. and Sub-Saharan Africa. Using this algorithm, we have uncovered the non-uniform vulnerability of distribution grids to wildfires in California in the aspects of undergrounding protection and Distributed Energy Resources (DER) preparedness. This has provided important implications for improving the affordability and equity of grid adaptation approaches. (3) We have made our produced database publicly available and provided user-friendly interface to enable various stakeholders and the general public to interact with the data. We have also integrated the produced data into the Data Commons platform to enable the public to access the data and correlate it with other location-specific characteristics simply using natural language as queries. The impact of our project is three-fold: (1) New algorithms for mapping solar PVs and distribution grids across space and time, which are open source to facilitate researchers and industry; (2) New databases of solar PVs and distribution grids that have been made publicly available for engineering, social, and policy applications; (3) New understandings and actionable insights on the potential approaches to promoting solar adoption and reducing energy infrastructure vulnerabilities. In this report, we start by discussing the project background and motivation (section 5), followed by the overview of project objectives (section 6). Results and discussion for each task are presented in section 7. Significant accomplishments are summarized in section 8. This report will be concluded by discussing the paths forwards (section 9), products (section 10), and team roles (section 11).

14 SOLAR ENERGY↗

Procedure Parsing: A Method for Parsing Handwritten Documents into Computer-Based Procedures

The nuclear industry is heavily procedure driven, where almost everything has a step-by-step instruction that is expected to be followed in detail. Historically, these procedures were printed on paper copies. Recently, the industry transitioned towards electronic copies (i.e., PDFs on tablets). One major drive for this transition is the introduction of human error and loss of situation awareness when using paper copies. However, electronic copies of documents inherently have the same error traps as their paper cousins. Therefore, there is an increased interest in a way to utilize the information in the step-by-step guidance, but to present it in a dynamic manner that guides the user and adapts to any encountered conditions. Researchers at Idaho National Laboratory propose a flexible, automated method based on document parsing and augmented by natural language processing (NLP) techniques, to address these shortcomings and capitalize on these recent advancements in machine learning. The proposed method provides a cost-effective solution for computer-assisted procedure parsing of hand-written control room procedures, originally authored in Word or PDF formats, into instructions that can be displayed as computer-based procedures (CBP) in a modern graphical user interface. The researchers devised, implemented and demonstrated the Operating Procedure Extender for Novel Systems (OPENS) method in 2020. The key to OPENS is to map the original procedure text into a context-free grammar, tying content to equipment, locations, and other steps, actions, etc. This formal grammar is then used to isolate and define keywords and actions verbs, such as “measure” or “evaluate” and tie them to specific equipment referenced within that step or located in other steps, substeps, actions, subactions and tables throughout the procedure. OPENS generates an abstract syntax tree from the document which it uses to store a copy of this information in the open-standard, machine-readable and human-readable file formats XML and JSON. The XML is useful to preserve the relational aspects of the procedure for referencing tables and branching information so the user can be directed to the next appropriate active step based on the values entered for that step and previous steps. The JSON is useful for storing and exchanging data objects used to track responses to previous steps and state changes in simulated environments. In future iterations, these formats can also be used for storing more detailed information about input during plant operation or simulation. The techniques the researcher developed could further be improved by integration of recent advancements in machine learning. NLP methods could standardize documents, correct for grammatical error, and provide automated semantic validation. The researcher expects that self-supervised techniques applied to collections of natural language instructions could strengthen the model with broader context. All these methods together give us a practical way to automatically extract protocols from documents and user interactions, empowering researchers, procedure writers and nuclear operators while moving the industry forward.

99 GENERAL AND MISCELLANEOUS↗

TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations

TURBOMOLE is a collaborative, multi-national software development project aiming to provide highly efficient and stable computational tools for quantum chemical simulations of molecules, clusters, periodic systems, and solutions. The TURBOMOLE software suite is optimized for widely available, inexpensive, and resource-efficient hardware such as multi-core workstations and small computer clusters. TURBOMOLE specializes in electronic structure methods with outstanding accuracy–cost ratio, such as density functional theory including local hybrids and the random phase approximation (RPA), GW-Bethe–Salpeter methods, second-order Møller–Plesset theory, and explicitly correlated coupled-cluster methods. TURBOMOLE is based on Gaussian basis sets and has been pivotal for the development of many fast and low-scaling algorithms in the past three decades, such as integral-direct methods, fast multipole methods, the resolution-of-the-identity approximation, imaginary frequency integration, Laplace transform, and pair natural orbital methods. This review focuses on recent additions to TURBOMOLE’s functionality, including excited-state methods, RPA and Green’s function methods, relativistic approaches, high-order molecular properties, solvation effects, and periodic systems. A variety of illustrative applications along with accuracy and timing data are discussed. Moreover, available interfaces to users as well as other software are summarized. TURBOMOLE’s current licensing, distribution, and support model are discussed, and an overview of TURBOMOLE’s development workflow is provided. Challenges such as communication and outreach, software infrastructure, and funding are highlighted.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

GANpiler

Focal Area(s): Rather than augment or replace physical models with machine learning, we instead preserve the existing models and augment the underlying code with faster surrogate models created by generative adversarial networks (GAN). To leverage the performance optimization, we also propose a runtime system and user interfaces that allow prediction and tracking of accumulated error as well as dynamic, per-process decision making as to which model (if any) to use for each iteration. Science Challenge: This proposal sits at the nexus of two hard problems. First, climate models based on machine learning will be, by their nature, difficult to trust once their predictions begin diverging from the consensus. Second, compilers and hardware have been making only incremental performance gains for decades. GPGPUs have provided a welcome performance boost for codes that can take advantage of them, but there is no similar technology on the horizon to provide the next performance leap.

54 ENVIRONMENTAL SCIENCES↗

Phase Segmentation in Atom-Probe Tomography Using Deep Learning-Based Edge Detection

Abstract Atom-probe tomography (APT) facilitates nano- and atomic-scale characterization and analysis of microstructural features. Specifically, APT is well suited to study the interfacial properties of granular or heterophase systems. Traditionally, the identification of the interface between, for precipitate and matrix phases, in APT data has been obtained either by extracting iso-concentration surfaces based on a user-supplied concentration value or by manually perturbing the concentration value until the iso-concentration surface qualitatively matches the interface. These approaches are subjective, not scalable, and may lead to inconsistencies due to local composition inhomogeneities. We introduce a digital image segmentation approach based on deep neural networks that transfer learned knowledge from natural images to automatically segment the data obtained from APT into different phases. This approach not only provides an efficient way to segment the data and extract interfacial properties but does so without the need for expensive interface labeling for training the segmentation model. We consider here a system with a precipitate phase in a matrix and with three different interface modalities—layered, isolated, and interconnected—that are obtained for different relative geometries of the precipitate phase. We demonstrate the accuracy of our segmentation approach through qualitative visualization of the interfaces, as well as through quantitative comparisons with proximity histograms obtained by using more traditional approaches.

47 OTHER INSTRUMENTATION↗

Single Bimodular Sensor for Differentiated Detection of Multiple Oxidative Gases

Semiconductive metal-oxide sensors suffer from cross-sensitivities under mixed chemical condition, specifically upon mixture of multiple oxidative or reductive gases. Herein, a single bimodular sensor is demonstrated for smart differentiation of multiple oxidative analytes by relating the resistance-metric mode to impedance-metric mode. The sensor construct based on ZnO nanorods readily outputs three response datasets upon exposure of oxidative-gas mixture including O 2 , SO 2 , and NO 2 , the resistance, real part impedance, and imaginary part impedance. The differentiative and correlated nature between these response signals allows such a single sensor platform to differentiate these oxidative gases accurately and robustly. Linear and non-linear decision boundaries are established over a large gas-concentration range from 2 ppm to 3% through a combination of principal component analysis and artificial neural network training. A facile user interface is demonstrated for recognition and measurement of unknown gas analytes, with the error of the predicted analyte-concentration as low as 2%.

36 MATERIALS SCIENCE↗

OpenPATH and Itinerum Integration: A Case Study of Merging Open-Source Projects: Preprint

Throughout the transportation sector, multiple mobility tracking platforms have been developed independently, in parallel, with similar use cases and infrastructure. Maintaining such platforms on an individual level can result in duplicated effort. Innovation within the field could be slowed by the limited resource of people working on extremely similar projects. We provide a case study in how such platforms can be combined with low effort and provide an example in the mobility domain of what the resulting integration points, modules and ownership may look like. OpenPATH (formerly e-mission) and Itinerum are two examples of similar independently developed human mobility tracking platforms that extend beyond standard traffic data collection. Due to the open source nature of the projects, members from both teams decided to merge the functionality, thereby only hosting a single data collection process and limiting maintenance of separate intake platforms. On the front-end, specific questionnaire functionality from Itinerum, mainly the ability to display and return questions and results focused on sociodemographic attributes, was integrated into the OpenPATH user interface. On the back-end, an export pipeline stage was created to transport collected data back to the Itinerum database. Upon completion, the OpenPATH application retained its original functionality while adding the ability to export data for future data sharing and creating an avenue to incorporate Itinerum hosted questions and answers. Itinerum benefits from the rich feature set and infrastructure of OpenPATH without losing needed elements such as the questionnaire component. This case study, within the transportation sector, illustrates the various configurations in which open source software can be developed, maintained and deployed.

ADVANCED PROPULSION SYSTEMS↗

ReVise: A Human-AI Interface for Incremental Algorithmic Recourse

The recent adoption of artificial intelligence in socio-technical systems raises concerns about the black-box nature of the resulting decisions in fields such as hiring, finance, admissions, etc. If data subjects—such as job applicants, loan applicants, and students—receive an unfavorable outcome, they may be interested in algorithmic recourse, which involves updating certain features to yield a more favorable result when re-evaluated by algorithmic decision-making. Unfortunately, when individuals do not fully understand the incremental steps needed to change their circumstances, they risk following misguided paths that can lead to significant, long-term adverse consequences. Existing recourse approaches focus exclusively on the final recourse goal but neglect the possible incremental steps to reach the goal with real-life constraints, user preferences, and model artifacts. To address this gap, we formulate a visual analytic workflow for incremental recourse planning in collaboration with AI/ML experts and contribute an interactive visualization interface that helps data subjects efficiently navigate the recourse alternatives and make an informed decision. We also present one of the many usage scenarios, developed during exploratory feedback sessions with twelve graduate students using a real-world dataset, which demonstrates that our approach can be instrumental for data subjects in choosing a suitable recourse path.

algorithmic recourse↗

Tracking Radioactive Isotopes in HVAC and Application for Hot Cell Analyses - 20155

In recent years, the surge in the number of isotope production facilities under design has increased the need to analyze isotope migration in facility Heating, Ventilation, and Air Conditioning (HVAC) during normal operations and accident scenarios. These facilities are used to produce isotopes for medical, security, and industrial applications and as such are subject to license and regulatory requirements 10CFR20, 10CFR30, 10CFR50, and 10CFR70. GOTHIC, a general-purpose thermal-hydraulics software package, includes the ability to model isotopic tracers, radioactive decay and isotope migration as well as HEPA and charcoal filters for isotope retention. A GOTHIC model was developed by Zachry Nuclear Engineering (ZNE) to examine the effect of negative room pressure, HEPA filtration, and HVAC fluctuations on radiation areas, hot cells and gloveboxes. Radioactive tracers were used to simulate the concentration of spills within contaminated areas, track the migration of isotopes of interest, and determine the isotopic retention and buildup on facility HEPA filters. A variety of isotopes with concern to dose (e.g., Kr-85, Sr-90, I-131, etc.), including their decay and progeny, are included in the analysis. Negative pressures are maintained in the regions of interest by a representative central HVAC system equipped with a volumetric fan that exhausts to the environment after a series of isolation valves and HEPA filters. GOTHIC is an industry trusted tool for providing engineering solutions for a variety of applications, including fission product tracking, aerosol and particulate transport and ventilation assessments. The software provides an integrated analysis environment that includes a graphical user interface (GUI) for constructing analysis models, a numerical solver that includes parallel processing capabilities and a post-processor for evaluating simulation results. It solves the conservation equations for mass, momentum and energy for multicomponent, multi-phase flow in lumped parameter and multi-dimensional geometries (1, 2, or full 3D), including the effects of turbulence, diffusion and buoyancy. It has been developed and maintained under a Quality Assurance program in compliance with the requirements of 10CFR50 Appendix B and applicable portions of ASME NQA-1 since 1995. GOTHIC has been used for assessing both forced and natural convection conditions for a wide range of applications, including: - Tracking concentration of hazardous gases and chemicals for habitability and safety assessments - Determining ventilation and filtration requirements and optimizing location and arrangement of these systems - Room heat-up, including diverse and Flexible coping strategies for Extended Loss of AC Power (FLEX/ELAP) - Equipment Qualification (EQ) A distinctive feature of GOTHIC is the ability to track many different fields/substances in a simulation, including user defined tracer elements, in the liquid, vapor and droplet fields as well as surfaces and filters. This capability allows GOTHIC to model fission product transport and release or the removal of particulates or harmful toxins from exhaust gases using a spray scrubber or other types of filtration systems. GOTHIC also includes models for engineered equipment, such as fans, filters, charcoal filters, dryers/demisters, dampers, etc. The aerosols and other filtered material are removed or accumulated in these components. The range of aerosol and radiological applications that GOTHIC has been used for includes: - Source Term: Primary Coolant (Equilibrium) Activity; Non-Water Coolant Source/Leakage. - Conditions for Iodine Re-evolution: Sump/Suppression Pool Conditions and pH; - RWST Conditions and pH. - Isotope Removal Mechanisms: Containment Sprayed and Unsprayed Region Mixing; Charcoal Filter Heating due to Iodine decay. - Radionuclide Transport and Decay: Post-LOCA Release in containment; Transport between connected Compartments and vent systems; Groundwater transport of radionuclides. - Non-Newtonian Fluid modeling for sludge, waste tanks, etc. ADAMS ML071581053 (titled 'Best Practice Guidelines for the use of CFD in Nuclear Reactor Safety Applications') poses guidelines for applying single phase CFD codes in nuclear reactor safety problems and GOTHIC is listed as a 'tool for 3D flows' and 'dispersal and deposition of radionuclides.' The Nuclear Quality Assurance (NQA) pedigree of GOTHIC is an important aspect for applications in the nuclear industry. The fundamental tracer models (convective transport, molecular and turbulent diffusion, removal mechanisms, etc.) have been verified using analytical solutions and validated against applicable separate effects tests. Also, GOTHIC has been benchmarked to many integrated effects tests, including Phebus FP (Fission Product). GOTHIC gives good agreement for the buildup and decay of fission products in Phebus Test 3. The model developed by ZNE demonstrates GOTHIC's applicability and acceptability for use in analyzing the migration and retention of radioactive isotopes and their progeny in normal operation and accident scenario analyses for isotope production facilities, hot cells, and gloveboxes. The tracer activities calculated by GOTHIC can then be used in downstream radiation transport and shielding codes like RADTRAD-NAI{sup C}, MCNP{sup R}, and MicroShield{sup R} to determine on-site and of-site doses. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

AFUE Analysis Software Tool

The Annual Fuel Utilization Efficiency (AFUE) analysis of residential and light commercial furnaces follows ANSI/ASHRAE Standard 103-2017 (i.e., Method of Testing for Annual Fuel Utilization Efficiency of Residential Central Furnaces and Boilers) . The analysis is a complex, comprehensive method based on furnace configuration and specific components equipped, requiring detailed furnace testing and measurement data. For this reason, an AFUE Analysis Tool using Microsoft Excel enabled with Visual Basic for Applications (VBA) was developed with a user-friendly interface and comprehensive coverage. The tool consists of three worksheets: unit and configuration selection, geometry and measurement data input, and AFUE plus key results. This tool can be used to estimate the AFUE of both condensing and noncondensing furnaces with single-stage, two-stage, and step-modulating functions. The tool was validated with experimental data from Oak Ridge National Laboratory’s natural gas furnace projects that are commercially available. The results indicate the tool is reasonably accurate in the evaluation of a new R&D modified furnace unit.

Gao, Zhiming [Oak Ridge National Laboratory (ORNL)↗

Multi-Scale Integrated Monitoring System for Enhancing Methane Emission Detection, Quantification & Prediction

This report details the progress and findings of a comprehensive study on reviewing existing solutions, identifying technology gaps, and formulating an “all-in-one” integrated strategy for developing the next-generation multiscale methane monitoring and modeling platform, conducted under grant number DE-FE0032292. Co-led by Dr. David Ebert, Dr. Binbin Weng, and Dr. Chenghao Wang at the University of Oklahoma, the project’s goal was to develop an integrated approach for building this engineering platform to detect, quantify, and mitigate methane emissions across various temporal scale, spatial scales, and sectors. The planning grant study began with an extensive review of various methane sensing and monitoring technologies and systems, surveying over 100 technology providers globally. This review revealed the prevalence of optical methods over chemical methods in commercially available sensors, with Non-Dispersive Infrared (NDIR), Tunable Diode Laser Absorption Spectroscopy (TDLAS), and Optical Gas Imaging (OGI) cameras being the most prevalent options. A trend towards more advanced optical techniques was observed, driven by increased regulatory focus and technological advancements. The technical evaluation of these sensing technologies provided crucial insights into their capabilities and limitations. The study examined emerging technologies such as Differential Absorption LiDAR (DIAL), which show promise for high-precision and long-range detection. The team then investigated the features and application bandwidth of various sensing platforms, including handheld, fixed/stationary, mobile, aerials, and spaceborne monitors. Pilot field studies were conducted to assess the capabilities of solutions for different emission scenarios. Field work with sensor deployments was conducted at three distinct site types: an oil & gas industry site, a cattle ranching operation, and a waste processing facility. The team also conducted a thorough review of methane flux inverse modeling approaches, focused on physically based methods. These approaches were categorized into simple, intermediate, and advanced methods. A realtime WRF-GHG (Weather Research and Forecasting-Greenhouse Gas) modeling system was developed and applied, incorporating multiple data sources to guide field experiments and inform methane plume detection. The project identified and analyzed numerous categories of methane data sources, including satellite measurements, ground-based sensors, and inventory databases. Key platforms examined include EDGAR, EPA GHGI, NASA TROPOMI, Carbon Mapper, and Climate TRACE, among others. The team proposed an architecture for a comprehensive methane monitoring platform. This system incorporates multi-source data acquisition, advanced data processing and assimilation, interactive visualization tools, and analytical capabilities for emissions forecasting and scenario analysis. The proposed platform aims to provide a user-friendly interface catering to various stakeholders, from researchers to policymakers. The architecture includes sophisticated data ingestion methods, a centralized data warehouse, and advanced analytical tools for data fusion and interpretation. To ensure the relevance and effectiveness of the proposed system, a comprehensive survey was conducted to gather stakeholder input on system requirements. Key findings include a strong need for integrating various data types and formats, a preference for real-time data updates and advanced visualization tools, and a demand for user-friendly interfaces catering to different expertise levels.

03 NATURAL GAS↗

Online Interactive Platform for COVID-19 Literature Visual Analytics: Platform Development Study

Background Papers on COVID-19 are being published at a high rate and concern many different topics. Innovative tools are needed to aid researchers to find patterns in this vast amount of literature to identify subsets of interest in an automated fashion. Objective We present a new online software resource with a friendly user interface that allows users to query and interact with visual representations of relationships between publications. Methods We publicly released an application called PLATIPUS (Publication Literature Analysis and Text Interaction Platform for User Studies) that allows researchers to interact with literature supplied by COVIDScholar via a visual analytics platform. This tool contains standard filtering capabilities based on authors, journals, high-level categories, and various research-specific details via natural language processing and dozens of customizable visualizations that dynamically update from a researcher’s query. Results PLATIPUS is available online and currently links to over 100,000 publications and is still growing. This application has the potential to transform how COVID-19 researchers use public literature to enable their research. Conclusions The PLATIPUS application provides the end user with a variety of ways to search, filter, and visualize over 100,00 COVID-19 publications.</:p>

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

EXSCLAIM!

Due to recent improvements in image resolution and acquisition speed, materials microscopy is experiencing an explosion of published imaging data. The standard publication format, while sufficient for traditional data ingestion scenarios where a select number of images can be critically examined and curated manually, is not conducive tolarge-scale data aggregation or analysis, hindering data sharing and reuse. Most images in publications are presented as components of a larger figure with their explicit context buried in the main body or caption text, so even if aggregated, collections of images with weak or no digitized contextual labels have limited value. To solve the problem of curating labeled microscopy data from literature, we introduce the EXSCLAIM! Python toolkit for the automatic EXtraction, Separation, and Caption-based natural Language Annotation of IMages from scientific literature. The software is implemented through a three part pipeline: the JournalScraper, which searches the web and downloads figures and captions based on a user provided query, the CaptionDistributor, which separates caption text based on the subfigure each portion of the caption refers to, and the FigueSeparator, which separates figures into component subfigures and extracts other visual information. Also included is a Django user interface for exploring the resulting dataset.

CHAN, MARIA↗

Aquifer Injection Modeling (AIM) Toolbox User Guide

The Aquifer Injection Modeling Toolbox (“AIM Toolbox”) software was developed by the Pacific Northwest National Laboratory (PNNL) for the U.S. Environmental Protection Agency’s (EPA) to provide a collection of analytical solutions suitable for evaluating the potential extent of the area impacted by subsurface injection operations. Subsurface injection operations are regulated under the EPA’s Underground Injection Control (UIC) program and are typically related to oil/gas development, waste disposal, or subsurface mining or storage. The analytical algorithms provided in the AIM Toolbox each have different approaches/assumptions/focus with respect to the nature and processes in subsurface and the nature of the injection operations. Collectively the set of analysis algorithms provides a broader evaluation of the area that can potentially be impacted by an injection operation. By providing estimates for the injectate plume extent, the software supports technical aspects of planning, evaluation, and overseeing injection activities. That is, the results help assess when further regulatory controls (e.g., monitoring, reporting) may be required and, in the case of disposal into an underground source of drinking water, the extent of the impacted area would require exemption from protection under the Safe Drinking Water Act. The AIM Toolbox software is available as a single-page web application, providing an interface to provide the necessary inputs, and both chart and map panes for visualizing the results. This User Guide describes the AIM Toolbox software, information required, user interactions, and the underlying basis of the calculations.

54 ENVIRONMENTAL SCIENCES↗