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At least 379 records · Page 21

Conquering Data Chaos: Research Data Management with Kubernetes

Managing massive volumes of data and effectively making it accessible to researchers poses significant challenges and is a barrier to scientific discovery. In many cases, critical data is locked up in unwieldy file formats or one-off databases and is too large to effectively process on a single machine. This talk explores the role of Kubernetes, an open-source container orchestration platform, in addressing research data management challenges. I will discuss how we are using a set of publicly available open-source and home-grown tools in the National Renewable Energy Lab (NREL) Data, Analysis, and Visualization (DAV) group to help researchers overcome data-related bottlenecks. The talk will begin by providing an overview of the data challenges faced in research data management, including data storage, processing, and analysis. I will highlight Kubernetes' ability to handle large-scale data by leveraging containerization and distributed computing, including distributed storage. Kubernetes allows researchers to encapsulate data processing infrastructure and workflows into portable containers, enabling reproducibility and ease of deployment. Kubernetes can then schedule and manage the resource allocation of these containers to enable efficient utilization of limited computing resources, leading to more efficient data processing and analysis. I will discuss some limitations of traditional, siloed approaches to dealing with data and emphasize the need for solutions which foster collaboration. I will highlight how we are using Kubernetes at NREL to facilitate data sharing and cooperation among research teams. Kubernetes' flexible architecture enables the deployment of shared computing environments, such as Apache Superset, where researchers can seamlessly access and analyze shared datasets. Providing the ability to have one research team easily consume data generated by another, utilizing Kubernetes' as a central data platform, is one of the major wins we've encountered by adopting the platform. Finally, I will showcase real-world use cases from NREL where we have used Kubernetes to solve some persistent data challenges involving large volumes of sensor and monitoring data. I will discuss the challenges we encountered when creating our cluster and making it available as a production-ready resource. I will also discuss the specific suite of tools, including Postgres and Apache Druid for columnar and timeseries data, and Redpanda Kafka for streaming data we have deployed in our infrastructure, and the process that went into the selection of these tools.

collaborative environment↗

Flight Test Evaluation of an Unmanned Aircraft System Traffic Management (UTM) Concept for Multiple Beyond-Visual-Line-of-Sight (BVLOS) Operations

Many applications of small Unmanned Aircraft System (UAS) have been envisioned. These include surveillance of key assets such as pipelines, rail, or electric wires, deliveries, search and rescue, traffic monitoring, videography, and precision agriculture. These operations are likely to occur in the same airspace in the presence of many static and dynamic constraints such as airports, and high wind areas. Therefore, operations of small UAS need to be managed to ensure safety and operation efficiency is maintained. NASA has advanced a concept for UAS Traffic Management (UTM) and has initiated a research effort to refine that concept and develop operational and system requirements. A UTM research platform is in development and flight test activities to evaluate core functions and key assumptions focusing exclusively on UAS operations in different environments are underway. This seminar will present lessons learned from a recent flight test focused on enabling operations of multiple UAS in lower-risk environments within and beyond visual line of sight (BVLOS).

UTM↗

Five-second STEM dislocation tomography for 300 nm thick specimen assisted by deep-learning-based noise filtering

Scanning transmission electron microscopy (STEM) is suitable for visualizing the inside of a relatively thick specimen than the conventional transmission electron microscopy, whose resolution is limited by the chromatic aberration of image forming lenses, and thus, the STEM mode has been employed frequently for computed electron tomography based three-dimensional (3D) structural characterization and combined with analytical methods such as annular dark field imaging or spectroscopies. However, the image quality of STEM is severely suffered by noise or artifacts especially when rapid imaging, in the order of millisecond per frame or faster, is pursued. Here we demonstrate a deep-learning-assisted rapid STEM tomography, which visualizes 3D dislocation arrangement only within five-second acquisition of all the tilt-series images even in a 300 nm thick steel specimen. The developed method offers a new platform for various in situ or operando 3D microanalyses in which dealing with relatively thick specimens or covering media like liquid cells are required.

47 OTHER INSTRUMENTATION↗

Inventory of Composable Elements (ICE) v6.0.0

The Inventory of Composable Elements (ICE) is an open source registry software platform for managing information about biological parts. It is capable of recording information about plasmids, microbial host strains and seeds, as well as DNA parts. Includes features such as DNA sequence visualization, editing and annotation, auto-aligning sequencing trace files against reference templates, SBOL XML/RDF support, and web-of-registries functionality. The web of registries functionality provides strong support for distributed interconnected use and enables sharing and transfer of biological parts across various independent ICE instances. ICE adopts modern software development principles, leveraging component-base frameworks, offering a REST API for convenient third-party integration and emphasizing scalability, security, and service integrations for dynamic content availability. The source code is hosted at https://github.com/JBEI/ice. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects.

Plahar, Hector↗

The SONATA data format for efficient description of large-scale network models

Increasing availability of comprehensive experimental datasets and of high-performance computing resources are driving rapid growth in scale, complexity, and biological realism of computational models in neuroscience. To support construction and simulation, as well as sharing of such large-scale models, a broadly applicable, flexible, and high-performance data format is necessary. To address this need, we have developed the Scalable Open Network Architecture TemplAte (SONATA) data format. It is designed for memory and computational efficiency and works across multiple platforms. The format represents neuronal circuits and simulation inputs and outputs via standardized files and provides much flexibility for adding new conventions or extensions. SONATA is used in multiple modeling and visualization tools, and we also provide reference Application Programming Interfaces and model examples to catalyze further adoption. SONATA format is free and open for the community to use and build upon with the goal of enabling efficient model building, sharing, and reproducibility.

59 BASIC BIOLOGICAL SCIENCES↗

Towards Streamlining Auditing for Compliance With Requirements in Open-Source Software at NASA

Context: NASA requires all software to meet several requirements (NPR 7150.2) depending on software criticality. The instantiation of these requirements may vary per project; however, once decided upon, projects must undergo audits to evaluate compliance with these requirements. Aim: We propose that audit effort can be reduced when requirements are realized by leveraging commonly used open-source infrastructure for version control, issue tracking and continuous integration, and the generated records are analyzed using a repository mining software tool to quantify process compliance. Method: We perform a case study in the NASA-funded Copilot project, utilizing Kaiaulu, a repository mining software tool. We define four software compliance metrics based on the Copilot’s requirements, and analyze their impact on source code quality. Results: Our work demonstrates how it is possible to leverage existing open source tools and platforms to facilitate software certification and qualification, and to streamline the auditing process required even when stringent requirements must be enforced. Conclusion: Together, both project and tool can be utilized to visualize project compliance, and metrics can be defined to more easily identify process irregularities to minimize auditing efforts. Project Repository: github.com/Copilot-Language/copilot Tool Repository: github.com/sailuh/kaiaulu

code-quality↗

Lightfall v0.0.1

Lightfall is a desktop application for synchrotron beamline instrument control, data acquisition, and live analysis at the Advanced Light Source (ALS). Built on Python and Qt, it provides a native graphical interface for operating beamline hardware, configuring and executing experimental scans, and visualizing results in real time. Key features include direct integration with EPICS control systems, a built-in electronic logbook, remote beamline access over secure tunnels, and an interprocess communication (IPC) architecture that coordinates with external analysis applications via ZMQ and EPICS process variables. This IPC approach allows Lightfall to orchestrate specialized analysis tools—including GPU-accelerated streaming correlators—without embedding them, avoiding the dependency conflicts common in monolithic scientific software platforms. Compared to prior approaches such as Xi-CAM's plugin-based architecture, Lightfall's design cleanly separates instrument control from domain-specific analysis, enabling feedback-driven acquisition where live analysis results can adjust scan parameters during an experiment. Its native Qt interface provides responsive performance for real-time data visualization that web-based alternatives struggle to match. Lightfall is designed for use by beamline scientists and staff operating synchrotron instruments at national user facilities.

Pandolfi, Ronald [Lawrence Berkeley National Labor↗

RAVIS: Resource Forecast and Ramp Visualization for Situational Awareness - An Introduction to the Open-Source Tool and Use Cases

The Resource Forecast and Ramp Visualization for Situational Awareness (RAVIS) is an open-source tool for visualizing variable renewable resource forecasts and ramp alerts for significant up/down ramps in renewable resource and the consequent net-load. The modular dashboard of RAVIS contains configurable panes for viewing- probabilistic time series forecasts, ramp event alerts on the look-ahead timeline, spatially resolved resource sites and forecasts, and system simulation and market clearing data such as transmission lines utilization, nodal prices and available generation flexibility. RAVIS uses a technology suite that is assembled to provide optimum visualization facility while maintaining a wide pool of potential deployment and client environments. The tool is designed to take advantage of web application technologies, open source visualization libraries and tooling. Utilizing this technology will enable deployment in any environment, using any operating system, and is scalable to much higher spatial and temporal scales of visualization. As a prototype of the tool and demonstrating a use case of variable renewable integration, RAVIS currently integrates site-specific solar power forecasts in the California Independent System Operator (CAISO) and Mid-continent ISO (MISO) footprint from the IBM WattSun forecasting platform, and also superimposes market simulation data for CAISO footprint from as in-house NREL market clearing tool. The tool has the ability to alert the viewer for excessive up or down ramps for both individual solar sites as well as regionally aggregated net-load ramps, and alerts can also be qualified with respect to available flexible generation. This report will provide an introduction to the RAVIS tool, and summarize the above mentioned capabilities, typical use cases and possible extensions of the tool. The RAVIS development team believes there are likely to be high economic and reliability benefits of integrating probabilistic forecasts of variable renewables into control center visualizations and improved ramp events situational awareness for system operators and forecasting teams in the ISOs and electric utilities in comparison with their business as usual practices.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

ROBIN (RuciO/BIgData Express/SENSE) A Next-Generation High-Performance Data Service Platform

Increasingly, scientific research discoverydepends on the analysis of extremely large amounts of data. Thisdata is gathered through very large scientific instruments, verylarge numbers of small devices, and mid-scale instruments.These devices generate exponentially increasing volumes of data.Such data is often obtained, analyzed, stored, visualized, andtransferred at and among sites world-wide by largecollaborations of science communities. Managing and movingextremely large volumes of data across today’s networks is aspecial multidimensional challenge. Also, existing datamanagement and movement services and tools often areinadequate to address all specific requirements. This paperdescribes the various components of this challenge and howthose issues can be addressed by ROBIN, a uniquecomprehensive set of integrated services designed specificallyfor managing and moving extremely large amounts of data overlong distances, e.g., thousands of miles around the globe. Thispaper also describes the results of initial experiments using thatset of integrated services.

Wu, Wenji↗

Nonmonotonic Band Flattening near the Magic Angle of Twisted Bilayer MoTe 2

Twisted bilayer MoTe 2 (tMoTe 2 ) is an emergent platform for exploring exotic quantum phases driven by the interplay between nontrivial band topology and strong electron correlations. Direct experimental access to its momentum-resolved electronic structure is essential for uncovering the microscopic origins of the correlated topological phases therein. Here, we report angle-resolved photoemission spectroscopy measurements of tMoTe 2 , revealing pronounced twist-angle-dependent band reconstruction shaped by orbital character, interlayer coupling, and moiré potential modulation. Density functional theory captures the qualitative evolution, yet underestimates key energy scales across twist angles, highlighting the importance of electronic correlations. Notably, the hole effective mass at the 𝐾 point exhibits a nonmonotonic dependence on twist angle, peaking near 2°, consistent with band flattening at the magic angle predicted by continuum models. Via electrostatic gating and surface dosing, we further visualize the evolution of electronic structure versus doping, enabling direct observation of the conduction band minimum and confirm tMoTe 2 as a direct band gap semiconductor. These results establish a spectroscopic foundation for modeling and engineering emergent quantum phases in this moiré platform.

2D materials↗

First Plant Cell Atlas symposium report

The Plant Cell Atlas (PCA) community hosted a virtual symposium on December 9 and 10, 2021 on single cell and spatial omics technologies. The conference gathered almost 500 academic, industry, and government leaders to identify the needs and directions of the PCA community and to explore how establishing a data synthesis center would address these needs and accelerate progress. This report details the presentations and discussions focused on the possibility of a data synthesis center for a PCA and the expected impacts of such a center on advancing science and technology globally. Community discussions focused on topics such as data analysis tools and annotation standards; computational expertise and cyber-infrastructure; modes of community organization and engagement; methods for ensuring a broad reach in the PCA community; recruitment, training, and nurturing of new talent; and the overall impact of the PCA initiative. These targeted discussions facilitated dialogue among the participants to gauge whether PCA might be a vehicle for formulating a data synthesis center. The conversations also explored how online tools can be leveraged to help broaden the reach of the PCA (i.e., online contests, virtual networking, and social media stakeholder engagement) and decrease costs of conducting research (e.g., virtual REU opportunities). Major recommendations for the future of the PCA included establishing standards, creating dashboards for easy and intuitive access to data, and engaging with a broad community of stakeholders. The discussions also identified the following as being essential to the PCA's success: identifying homologous cell-type markers and their biocuration, publishing datasets and computational pipelines, utilizing online tools for communication (such as Slack), and user-friendly data visualization and data sharing. In conclusion, the development of a data synthesis center will help the PCA community achieve these goals by providing a centralized repository for existing and new data, a platform for sharing tools, and new analytical approaches through collaborative, multidisciplinary efforts. A data synthesis center will help the PCA reach milestones, such as community-supported data evaluation metrics, accelerating plant research necessary for human and environmental health.

59 BASIC BIOLOGICAL SCIENCES↗

Science Activity Planner for the MER Mission

The Maestro Science Activity Planner is a computer program that assists human users in planning operations of the Mars Explorer Rover (MER) mission and visualizing scientific data returned from the MER rovers. Relative to its predecessors, this program is more powerful and easier to use. This program is built on the Java Eclipse open-source platform around a Web-browser-based user-interface paradigm to provide an intuitive user interface to Mars rovers and landers. This program affords a combination of advanced display and simulation capabilities. For example, a map view of terrain can be generated from images acquired by the High Resolution Imaging Science Explorer instrument aboard the Mars Reconnaissance Orbiter spacecraft and overlaid with images from a navigation camera (more precisely, a stereoscopic pair of cameras) aboard a rover, and an interactive, annotated rover traverse path can be incorporated into the overlay. It is also possible to construct an overhead perspective mosaic image of terrain from navigation-camera images. This program can be adapted to similar use on other outer-space missions and is potentially adaptable to numerous terrestrial applications involving analysis of data, operations of robots, and planning of such operations for acquisition of scientific data.

Norris, Jeffrey S.↗

The Pheno-Evo Model: Evolution of Microbial Phenotypic Diversity in 2D Space

Biologists appreciate microbes for their simplicity and predictability: we assume that a population of genetically identical cells in a uniform environment will all behave the same way. While this assumption is often useful, it is also often wrong. Not only might microbes in a clonal population act differently from one another, the differences may be categorical (growing v. non-growing; toxin-sensitive v. tolerant), and this diversity might be an evolved trait conferring increased fitness on the population. How does such phenotypic heterogeneity evolve? And how does a population find the optimal distribution of phenotypes for a given environment? Efforts at modeling microbial phenotypic heterogeneity often focus on populations with two discrete phenotypic types; phenotypes in continuous distributions remain poorly explored. To address this gap and to explore the role of spatial relationships, we use agent-based modeling to simulate a phenotypically diverse population of microbial cells evolving in the presence of periodic toxic stress. Cells on patches in a 2D grid may degrade toxin, suffer damage from toxin, switch phenotype, and reproduce. An individual's phenotype its toxin degradation rate-- for which there is a tradeoff with reproduction-- and the genotype encodes the distribution of phenotypic values in the population. The rate of toxin diffusion determines how individuals influence their neighbors' environments. We examine the effects of toxin concentration, diffusion rate, and environmental predictability on the survival success of populations with different phenotype distributions, and populations' evolutionary trajectories when phenotype distribution is allowed to evolve. We conduct all simulations on the platform NetLogo, which provides a friendly interface allowing users of any experience level to tweak parameters and run their own simulations. We have also created custom tools in R for analyzing and visualizing the results of multiple runs.

microbial evolution↗

UrbanScaping: Community Spatial Data Visualization & Analytics

Evaluating the electrification potential of buildings through retrofitting is crucial for reducing carbon emissions and the carbon footprint of built environments. This study leverages the Automatic Building Energy Modeling (AutoBEM) software, integrating the Model America database to create an urban context-based spatial analysis platform for community engagement and development. We selected Camp Hill Borough, PA, as a case study to analyze building-specific energy performance and evaluate the electrification potential of each building by switching to different Heating, Ventilation, and Air Conditioning (HVAC) systems and measurement components. The simulation results generated by the workflow provide retrofitting suggestions to help mitigate the carbon footprint as well as energy saving statistics of buildings. Additionally, the developed web-based interface serves as a community engagement platform, allowing residents to provide feedback and further develop interactive communication protocols. The outcomes of this project offer a baseline for community electrification planning and contribute to the design of low-carbon communities.

Chowdhury, Shovan [ORNL]↗

Volcanic Gas Emissions Mapping Using a Mass Spectrometer System

The visualization of hazardous gaseous emissions at volcanoes using in-situ mass spectrometry (MS) is a key step towards a better comprehension of the geophysical phenomena surrounding eruptive activity. In-Situ gas data consisting of helium, carbon dioxide, sulfur dioxide, and other gas species, were acquired with an MS system. MS and global position system (GPS) data were plotted on ground imagery, topography, and remote sensing data collected by a host of instruments during the second Costa Rica Airborne Research and Technology Applications (CARTA) mission This combination of gas and imaging data allowed 3-dimensional (3-D) visualization of the volcanic plume end the mapping of gas concentration at several volcanic structures and urban areas This combined set of data has demonstrated a better tool to assess hazardous conditions by visualizing and modeling of possible scenarios of volcanic activity. The MS system is used for in-situ measurement of three-dimensional gas concentrations at different volcanic locations with three different transportation platforms, aircraft, auto, and hand carried. The demonstration for urban contamination mapping is also presented as another possible use for the MS system.

Griffin, Timothy P.↗

Upcoming Lunar Mission Landing Sites: Viewing and Analysis with Celestial Mapping System

The Celestial Mapping System (CMS) is a powerful software platform designed to create virtual 3D globes for celestial bodies within our solar system, with a specific focus on lunar mapping. CMS offers a rich array of functionalities, including high-resolution imagery visualization, precise measurement tools, and analytical capabilities that cater to the needs of planetary scientists and mission planners. This abstract explores how CMS has been leveraged to conduct in-depth analyses of 12 lunar missions to the South Pole, including missions like Chandraayan 3, Russian Space Agency's Luna 25, Xelene 1, and Intuitive Machines Nova-C lander I. Moreover, the integration of HORUS (Hyper-effective nOise Removal Unit Software) into CMS enhances its capabilities, allowing for the rendering of images in a 3D globe format and providing visibility into permanently shadowed regions. CMS represents a cutting-edge tool for lunar surface awareness, equipment placement planning, and traverse path optimization

Moon↗

MSTAR2019 Code Description and User's Manual

This report describes an ideal cascade model of uranium enrichment that includes side feed and side product streams and flexible input options. It is based on the original MSTAR model developed by Ed Von Halle and implemented in a Visual Basic code. The current version allows the user to specify integer numbers of stages or the stage numbers of external flows instead of assays in those flows. The computational engine is written in FORTRAN-90 and is invoked by a user-friendly GUI written in C++. This version of MSTAR has been demonstrated to operate on Linux, Mac, and Windows platforms, and has undergone significant testing and quality analysis. A number of examples are presented to illustrate the operation of the code and guide the user. The code is extremely fast, and results are returned immediately. The input and output have been specially configured for analysis by the environmental sampling team of the International Atomic Energy Agency (IAEA). A number of additional output features are included to assist the user in visualizing computational results and downloading data to files for use in other analysis software.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Visualizing electron localization of WS 2 /WSe 2 moiré superlattices in momentum space

The search for materials with flat electronic bands continues due to their potential to drive strong correlation and symmetry breaking orders. Electronic moirés formed in van der Waals heterostructures have proved to be an ideal platform. However, there is no holistic experimental picture for how superlattices modify electronic structure. By combining spatially resolved angle-resolved photoemission spectroscopy with optical spectroscopy, we report the first direct evidence of how strongly correlated phases evolve from a weakly interacting regime in a transition metal dichalcogenide superlattice. By comparing short and long wave vector moirés, we find that the electronic structure evolves into a highly localized regime with increasingly flat bands and renormalized effective mass. The flattening is accompanied by the opening of a large gap in the spectral function and splitting of the exciton peaks. These results advance our understanding of emerging phases in moiré superlattices and point to the importance of interlayer physics.

36 MATERIALS SCIENCE↗