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A New Architecture for Visualization: Open Mission Control Technologies

Open Mission Control Technologies (MCT) is a new architecture for visualisation of mission data. Driven by requirements for new mission capabilities, including distributed mission operations, access to data anywhere, customization by users, synthesis of multiple data sources, and flexibility for multi-mission adaptation, Open MCT provides users with an integrated customizable environment. Developed at NASAs Ames Research Center (ARC), in collaboration with NASAs Advanced Multimission Operations System (AMMOS) and NASAs Jet Propulsion Laboratory (JPL), Open MCT is getting its first mission use on the Jason 3 Mission, and is also available in the testbed for the Mars 2020 Rover and for development use for NASAs Resource Prospector Lunar Rover. The open source nature of the project provides for use outside of space missions, including open source contributions from a community of users. The defining features of Open MCT for mission users are data integration, end user composition and multiple views. Data integration provides access to mission data across domains in one place, making data such as activities, timelines, telemetry, imagery, event timers and procedures available in one place, without application switching. End user composition provides users with layouts, which act as a canvas to assemble visualisations. Multiple views provide the capability to view the same data in different ways, with live switching of data views in place. Open MCT is browser based, and works on the desktop as well as tablets and phones, providing access to data anywhere. An early use case for mobile data access took place on the Resource Prospector (RP) Mission Distributed Operations Test, in which rover engineers in the field were able to view telemetry on their phones. We envision this capability providing decision support to on console operators from off duty personnel. The plug-in architecture also allows for adaptation for different mission capabilities. Different data types and capabilities may be added or removed using plugins. An API provides a means to write new capabilities and to create data adaptors. Data plugins exist for mission data sources for NASA missions. Adaptors have been written by international and commercial users. Open MCT is open source. Open source enables collaborative development across organizations and also makes the product available outside of the space community, providing a potential source of usage and ideas to drive product design and development. The combination of open source with an Apache 2 license, and distribution on GitHub, has enabled an active community of users and contributors. The spectrum of users for Open MCT is, to our knowledge, unprecedented for mission software. In addition to our NASA users, we have, through open source, had users and inquires on projects ranging from Internet of Things, to radio hobbyists, to farming projects. We have an active community of contributors, enabling a flow of ideas inside and outside of the space community.

Trimble, Jay↗

LevSeq: Rapid Generation of Sequence-Function Data for Directed Evolution and Machine Learning

Sequence-function data provides valuable information about the protein functional landscape but is rarely obtained during directed evolution campaigns. Here, we present Long-read every variant Sequencing (LevSeq), a pipeline that combines a dual barcoding strategy with nanopore sequencing to rapidly generate sequence-function data for entire protein-coding genes. LevSeq integrates into existing protein engineering workflows and comes with open-source software for data analysis and visualization. The pipeline facilitates data-driven protein engineering by consolidating sequence-function data to inform directed evolution and provide the requisite data for machine learning-guided protein engineering (MLPE). LevSeq enables quality control of mutagenesis libraries prior to screening, which reduces time and resource costs. Simulation studies demonstrate LevSeq’s ability to accurately detect variants under various experimental conditions. Lastly, we show LevSeq’s utility in engineering protoglobins for new-to-nature chemistry. Widespread adoption of LevSeq and sharing of the data will enhance our understanding of protein sequence-function landscapes and empower data-driven directed evolution.

59 BASIC BIOLOGICAL SCIENCES↗

Livewire User Guide

The Livewire Data Platform houses a catalog of transportation- and mobility-related project data, as well as a publications database, making it easy to search and share data. It allows transportation researchers, industry, and academic partners to increase the visibility of their projects within the research community, securely share and preserve data, and leverage datasets from other projects. Public data on Livewire are open to anyone with a Livewire account. This guide will help Livewire users understand how to store project data as a data steward, as well as access data as a data consumer.

33 ADVANCED PROPULSION SYSTEMS↗

GL4U: Bioinformatics training for students and educators using space omics data

NASA’s GeneLab project provides researchers open access to space-relevant experiment multi-omics data that can be mined to understand the effects of spaceflight on biological systems. To maximize the number of scientists who understand and utilize GeneLab data and data processing pipelines, GeneLab has created GeneLab for Colleges and Universities (GL4U). GL4U provides space biology-relevant training in bioinformatics to the next generation of scientists through direct and indirect approaches. The GeneLab team plans to host two annual data processing bootcamps, one for college-level students (direct) and one for college educators (indirect – training of trainers), in which participants learn to analyze GeneLab’s space-relevant omics data. The GL4U direct training pilot program was conducted in June 2021. During the pilot, students participated in a week-long bootcamp consisting of space biology-specific lectures and hands-on instruction using Jupyter Notebooks to analyze RNA sequence data. This pilot demonstrated the capacity of GL4U for training young scientists and encouraging data re-use. During the educator pilot, scheduled for June 2022, educators will receive materials and training to enable them to run the bootcamp at their home institutions or alternatively to adapt the content to implement within existing courses, thereby extending the reach of this initiative.

Amanda Marie Saravia-butler↗

GL4U: Bioinformatics Training for Students and Educators Using Space Omics Data

NASA’s GeneLab project provides researchers open access to space-relevant experiment multi-omics data that can be mined to understand the effects of spaceflight on biological systems. To maximize the number of scientists who understand and utilize GeneLab data and data processing pipelines, GeneLab has created GeneLab for Colleges and Universities (GL4U). GL4U provides space biology-relevant training in bioinformatics to the next generation of scientists through direct and indirect approaches. The GeneLab team plans to host two annual data processing bootcamps, one for college-level students (direct) and one for college educators (indirect – training of trainers), in which participants learn to analyze GeneLab’s space-relevant omics data. The GL4U direct training pilot program was conducted in June 2021. During the pilot, students participated in a week-long bootcamp consisting of space biology-specific lectures and hands-on instruction using Jupyter Notebooks to analyze RNA sequence data. This pilot demonstrated the capacity of GL4U for training young scientists and encouraging data re-use. During the educator pilot, scheduled for June 2022, educators will receive materials and training to enable them to run the bootcamp at their home institutions or alternatively to adapt the content to implement within existing courses, thereby extending the reach of this initiative.

Amanda Marie Saravia-butler↗

Connecting Users and Applications with Po.daac Hosted GHRSST Data

The 80+ GHRSST public datasets represent a rich resource for sea surface temperature research and applications given their time series length, resolution, spatial coverage, varying measurement types and processing levels, and availability in the full spectrum of PO.DAAC tools and services ecosystem. The PO.DAAC has created a publicly accessible recipe suite for the user community to perform straightforward yet powerful computations on GHRSST data using python recipes, Jupyter notebooks, R, Matlab, and the NCO programming language. These recipes include numerical computations for regional and global SST trends, anomaly derivations, EOF analysis, climate signal reproduction, and ocean phenology. For example, one recipe reproduces a famous SST based warming figure from the Fourth National Climate Assessment (USA) while another focuses on quantifying the regional changes in ocean SST phenology. Most are python-based while some contain hybrid calls and leverage the NCO programming interface too. All are available on the PO.DAAC user forum (https://podaac.jpl.nasa.gov/forum/) and/or via the open source NASA GitHub repository (https://github.com/nasa/podaac_tools_and_services). Several are available in the Jupyter notebook framework including podaacypy (https://github.com/nasa/podaacpy), a recipe for GHRSST granule metadata discovery and application, and more recently a Jupyter notebook developed to support data analysis and visualization of a cloud-based Zarr formatted Level 4 MUR dataset in the AWS Open Data Registry. Throughout the summer of 2020, the PO.DAAC intends to add and migrate more of its numerical recipes to the Jupyter notebook framework and publish them on its open source GitHub repository.

Gentemann, Chelle↗

Development INTERDATA 8/32 computer system

The capabilities of the Interdata 8/32 minicomputer were examined regarding data and word processing, editing, retrieval, and budgeting as well as data management demands of the user groups in the network. Based on four projected needs: (1) a hands on (open shop) computer for data analysis with large core and disc capability; (2) the expected requirements of the NASA data networks; (3) the need for intermittent large core capacity for theoretical modeling; (4) the ability to access data rapidly either directly from tape or from core onto hard copy, the system proved useful and adequate for the planned requirements.

Sonett, C. P.↗

Tropical Rainfall Measuring Mission (TRMM) Precipitation Data and Services for Research and Applications

Precipitation is a critical component of the Earth's hydrological cycle. Launched on 27 November 1997, TRMM is a joint U.S.-Japan satellite mission to provide the first detailed and comprehensive data set of the four-dimensional distribution of rainfall and latent heating over vastly under-sampled tropical and subtropical oceans and continents (40 S - 40 N). Over the past 14 years, TRMM has been a major data source for meteorological, hydrological and other research and application activities around the world. The purpose of this short article is to inform that the NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) provides TRMM archive and near-real-time precipitation data sets and services for research and applications. TRMM data consist of orbital data from TRMM instruments at the sensor s resolution, gridded data at a range of spatial and temporal resolutions, subsets, ground-based instrument data, and ancillary data. Data analysis, display, and delivery are facilitated by the following services: (1) Mirador (data search and access); (2) TOVAS (TRMM Online Visualization and Analysis System); (3) OPeNDAP (Open-source Project for a Network Data Access Protocol); (4) GrADS Data Server (GDS); and (5) Open Geospatial Consortium (OGC) Web Map Service (WMS) for the GIS community. Precipitation data application services are available to support a wide variety of applications around the world. Future plans include enhanced and new services to address data related issues from the user community. Meanwhile, the GES DISC is preparing for the Global Precipitation Measurement (GPM) mission which is scheduled for launch in 2014.

Liu, Zhong↗

A Curated Dataset of Regional Meteor Events with Simultaneous Optical and Infrasound Observations (2006–2011)

We present a curated, openly accessible dataset of 71 regional meteor events simultaneously recorded by optical and infrasound instrumentation between 2006 and 2011. These events were captured during an observational campaign using the all-sky cameras of the Southern Ontario Meteor Network and the co-located Elginfield Infrasound Array. Each entry provides optical trajectory measurements, infrasound waveforms, and atmospheric specification profiles. The integration of optical and acoustic data enables robust linkage between observed acoustic signals and specific points along meteor trajectories, offering new opportunities to examine shock wave generation, propagation, and energy deposition processes. This release fills a critical observational gap by providing the first validated, openly accessible archive of simultaneous optical–infrasound meteor observations that supports trajectory reconstruction, acoustic propagation modeling, and energy deposition analyses. By making these data openly available in a structured format, this work establishes a durable reference resource that advances reproducibility, fosters cross-disciplinary research, and underpins future developments in meteor physics, atmospheric acoustics, and planetary defense.

astrometry↗

Structural basis for ring-opening fluorescence by the RhoBAST RNA aptamer

Abstract Tagging RNAs with fluorogenic aptamers has enabled imaging of transcripts in living cells, revealing novel aspects of RNA metabolism and dynamics. While a diverse set of fluorogenic aptamers has been developed, a new generation of aptamers uses the ring-opening of spirocyclic rhodamine dyes to achieve robust performance in live mammalian cells. These fluorophores have two chemical states: a cell-permeable spirocyclic state and a fluorescent zwitterionic state. The SpyRho555 dye is mostly non-fluorescent in solution and becomes fluorescent in complex with the RhoBAST aptamer. To understand the basis for RhoBAST-SpyRho555 fluorogenicity, we have determined crystal structures of RhoBAST in complex with 5-carboxytetramethylrhodamine and a SpyRho555 analogue, MaP555. RhoBAST is organized by a perfect four-way junction that positions two loops to form the dye-binding pocket. The core of the ligand resides between a tri-adenine floor and a single guanine base, largely driven by π-stacking interactions. Importantly, the unpaired guanine interacts with the 3-position group of MaP555 to stabilize the open conformation, supported by mutagenesis data, and may play an active role in promoting the open conformation of the dye. This work has implications for the development of new fluorogenic aptamers with improved properties using structure-guided design approaches.

Biochemistry & Molecular Biology↗

Learning thermodynamic master equations for open quantum systems

The characterization of Hamiltonians and other components of open quantum dynamical systems plays a crucial role in quantum computing and other applications. Scientific machine learning techniques have been applied to this problem in a variety of ways, including by modeling with deep neural networks. However, the majority of mathematical models describing open quantum systems are linear, and the natural nonlinearities in learnable models have not been incorporated using physical principles. We present a data-driven model for open quantum systems that includes learnable, thermodynamically consistent terms. The trained model is interpretable, as it directly estimates the system Hamiltonian and linear components of coupling to the environment. We validate the model on synthetic two and three-level data, as well as experimental two-level data collected from a quantum device at Lawrence Livermore National Laboratory.

Mathematics and Computing↗

Biomass Harmonization and SAR Analysis with the Multi-mission Algorithm and Analysis Platform (MAAP)

The Multi‐mission Algorithm and Analysis Platform (MAAP) is a collaborative effort between NASA and the European Space Agency (ESA) to support above ground biomass (AGB) research in an open science framework. MAAP brings together relevant data, algorithms, and computing capabilities in a common cloud environment to address the challenges of sharing and processing data from field, airborne and satellite measurements. MAAP was publicly released in October 2021, providing computing capabilities co-located with the data, a collaborative coding and analysis environment, and a set of interoperable tools and algorithms developed to support the estimation and visualization of data. MAAP has allowed scientists from both North America and Europe to collaborate on the generation and analysis/visualization of data derived from multiple, discipline-adjacent missions in an open, collaborative environment that has reached beyond traditional scientific investigation. MAAP has been used to support multiple scientific activities. To date, existing LiDAR data from multiple platforms has been calibrated with field measurements and combined for more comprehensive and accurate estimates of above ground biomass AGB; these LiDAR platforms include airborne (e.g. LVIS), the International Space Station (NASA’s Global Ecosystem Dynamics Investigation (GEDI), and satellites (e.g. ICESat-2). The current challenge is to effectively and seamlessly combine the aforementioned LiDAR-based data with new data sources such as P-band RADAR from ESA’s upcoming BIOMASS mission, existing ESA Sentinel-1 C-band SAR, and the 30 PB/yr of high cadence global coverage L-band SAR data from the upcoming NASA-ISRO SAR (NISAR) mission. Recent analysis using MAAP merged ICESat-2 and optical data (Harmonized Landsat Sentinel) produced the most comprehensively precise estimate of boreal-wide AGB to date. Another effort using MAAP is the production and open distribution of global comparisons of AGB map estimates, including from ICESat-2 and GEDI, to bolster stakeholder uptake for policy applications. These map estimates will feed into the Intergovernmental Panel on Climate Change (IPCC) database, likely aiding the next Global Carbon Stocktake of the UNFCCC. Furthermore, the biomass retrieval intercomparison exercise BRIX-2 could benefit from the MAAP providing standardized test cases (based on airborne campaign and spaceborne data) allowing the community to develop and apply retrieval algorithms based on these test cases, while forthcoming SAR data training curricula could also use the MAAP as a teaching and learning platform. The MAAP is meeting the challenges inherent in international, open science collaboration and large scale computing with a platform that is entirely open source and cloud native, using open standards for data access, manipulation, protocols, and formats. The MAAP data system consists of a dedicated data store whose data is indexed in an online catalog conforming to established metadata, application programmatic interfaces (APIs), and service interface standards, using an implementation of the open sourced NASA Common Metadata Repository. Federation of user identities allows users from either NASA or ESA to access and consume services from the other using a unified metadata catalog for the data utilized across the ESA and NASA MAAP platforms. Similarly, we are exploring how to increase interoperability to achieve a common approach to packaging, orchestrating and executing algorithms, with interoperable access to data for subsetting, fast browse, and cloud-optimized access, all using interoperable standards such as those from the Open Geospatial Consortium (OGC). Designed for interoperability, ESA and NASA utilize a common architecture for the software platform. It provides a cloud-based algorithm development environment (ADE) that enables scientists to develop algorithms collaboratively with access to the MAAP data catalog as well as other data archives. MAAP provides an Eclipse Che-based ADE supporting both Python and R languages, popular in this biomass community. Algorithms developed and containerized within the ADE can be deployed to run to thousands of computational nodes in the MAAP’s data processing system (DPS), dramatically speeding up processing and giving scientists a rapid, iterative turnaround of results. NASA’s implementation of the DPS is based on the Hybrid Science Data System (HySDS) framework, used by NASA flight projects to produce Earth science standard products.

cloud computing↗

Open Science Approach to Analyze Climate-Crop Relationships in the US Leveraging GES DISC and Galaxy Workflows

Understanding the intricate relationship between climate variability and agricultural production is crucial for ensuring food security. This study investigates the impact of climate parameters, such as temperature, precipitation, and soil moisture, on major US crop yields. Adopting an open science approach, the study analyzes the impact of climate on agricultural production in the United States. The Galaxy workflow engine serves as the primary tool for integrating climate data from the Goddard Earth Sciences Data and Information Services Center (GES DISC), retrieved via the Giovanni system, with yield statistics from the United States Department of Agriculture’s National Agricultural Statistics Service (USDA NASS). Extensions for reading, preprocessing, and analyzing external data have been developed, enabling the creation of workflows within the Galaxy platform. The development of a reproducible workflow allows for the calculation of seasonal climate averages, which are then assessed for their correlation with crop yields. This methodology ensures the replicability of the research, promoting transparency and collaboration in the scientific community. Correlational and regression analyses have been applied to different sub-zones and crops. The findings from this research offer valuable insights into the relationship between climate parameters and crop yields. These insights contribute to a deeper understanding of climate-crop relationships, providing a solid foundation for informed decision-making in the agricultural sector. The high correlation values indicate a significant relationship between climate parameters and crop yields, underscoring the importance of considering climate factors in agricultural planning and policymaking. This research also exemplifies the power of open science in advancing our understanding of complex environmental and agricultural phenomena. By leveraging open data and services, it provides a robust and replicable framework for future studies in this critical field.

Open science↗

Open-Source Science-led Development of the Atmosphere Observing System (AOS) Mission Science Data System (SDS)

The Earth System Observatory (ESO) Atmosphere Observing System (AOS) mission will provide space-based and suborbital observations of collocated cloud, dynamic, precipitation and aerosol processing leading to improved weather, air quality, and climate predictions. The AOS Science Data System (SDS) will be a system of systems developed within the Cloud to manage the research and operational processing of AOS mission orbital and suborbital sensors and curate these data for reprocessing (e.g., in near real-time or by collection) and transfer them to a NASA Distributed Active Archive Center (DAAC) for long-term storage. Further, AOS SDS will follow guidelines provided by NASA Earth Science Data Systems (ESDS) program including standard conventions for data file formats, naming, and metadata to improve data interoperability, interpretability, usability, discovery, provenance, and spatiotemporal representativeness. The AOS mission follows NASA’s lead in making a commitment to Open-Source Science (OSS) including the sharing of data, software, and knowledge in an open and timely manner. Each of the AOS SDS system components will be developed with open-source concepts including components of SDS itself as well as AOS mission algorithms. Further, the AOS SDS assumes the role to lead and facilitate OSS activities for the AOS mission. This presentation describes the framework of the AOS SDS and its integral part in facilitating OSS within the AOS mission.

David Giles↗

Recovery, Restoration and Archiving of Previously Lost Data and Metadata from the Apollo Lunar Surface Experiments Package (ALSEP)

The Apollo Lunar Surface Experiments Package (ALSEP) is the name used to collectively represent the geophysical instruments deployed on the lunar surface by the astronauts on Apollo 12, 14, 15, 16, and 17. These instruments were active from the times of their deployment (November 1969 – December 1972) to September 1977. During that time, fourteen types of experiments were conducted, and their data were transmitted to Earth. The experiment PIs processed them. At the conclusion of the experiments, some of these data were submitted to the NASA Space Science Data Coordinated Archive (NSSDCA) for archiving, while others were not. The raw instrument data received from the Moon prior to March 1976 were not archived, either. The unarchived data, resided on open-reel magnetic tapes, became lost in the decades since, along with much of the metadata (the information necessary/useful in properly processing/analyzing the data). This article retraces the history of the ALSEP data archiving efforts in the 1970s, the subsequent loss of the data tapes, and the search, recovery, and restoration of the lost data by contemporary researchers in the 21st century. In 2006, NSSDCA began reformatting some of the ALSEP data archived in the 1970s to conform with the current Planetary Data System (PDS). In 2010, 440 of the previously lost magnetic tapes containing the raw ALSEP data were recovered. From these tapes, the data were extracted, re-packaged for individual experiments, and, for those with sufficient metadata, processed into higher order data readily usable by researchers. All of these data products have been recently archived with either PDS or NSSDCA. These newly restored data fill a number of gaps in the previously existing archive of the ALSEP data. In addition, tens of thousands of pages of Apollo era documents have been optically scanned and compiled into an online searchable catalog. This article also describes the content, organization, and usage of the restored raw ALSEP data and metadata.

S Nagihara↗

ENDFtk: A robust tool for reading and writing ENDF-formatted nuclear data

ENDFtk is a recently developed C++ and Python interface to interact with ENDF-6 formatted nuclear data files. It provides a robust and complete interface, allowing the reading and writing of all formats currently part of the ENDF-6 formats manual, as well as some non-ENDF formats used by the NJOY processing code. It provides an interface that mimics the names in the ENDF-6 formats manual as well as an equivalent interface using human-readable attribute names. It is robust and powerful enogh for nuclear data experts to develop complex applications, while also simple enough to be used non-experts to retrieve and manipulate evaluated nuclear data. ENDFtk offers the ability to easily interrogate and manipulate data either in large-scale code projects or in simple Python scripts. Here, in this paper, a brief overview of the interface is given, as well as more substantial examples demonstrating plotting simple data, interacting with more complex data, and writing new data to files. ENDFtk is open source and available for download via GitHub (https://github.com/njoy/ENDFtk).

97 MATHEMATICS AND COMPUTING↗

Improvements in lake volume predictions using Landsat data

A cumulative error in the water balance budget for Lake Okeechobee produces a one million acre-foot discrepancy in the predicted water volume over a 4-year period. The major source of error appears to be complex shoreline marshes that comprise 20 percent of the lake surface. The water balance budget model presently treats these marshes as open water. Using Landsat data, the vegetation in the lake's littoral zone was classified multispectrally to provide a data base for determining water budget information. First, the acreage of a given plant species in the littoral zone was obtained with satellite data. Second, the surface area occupied by plants (which therefore could not be considered open water) was used to adjust the vegetation acreage giving an effective water surface. Based on this information, more detailed representations of evapotranspiration and total water surface (and hence total lake volume) could be provided to the water balance budget computation.

Gervin, J. C.↗

Pretraining Billion-Scale Geospatial Foundational Models on Frontier

As AI workloads increase in scope, generalization capability becomes challenging for small task-specific models and their demand for large amounts of labeled training samples increases. On the contrary, Foundation Models (FMs) are trained with internet-scale unlabeled data via self-supervised learning and have been shown to adapt to various tasks with minimal fine-tuning. Although large FMs have demonstrated significant impact in natural language processing and computer vision, efforts toward FMs for geospatial applications have been restricted to smaller size models, as pretraining larger models requires very large computing resources equipped with state-of-the-art hardware accelerators. Current satellite constellations collect 100+TBs of data a day, resulting in images that are billions of pixels and multimodal in nature. Such geospatial data poses unique challenges opening up new opportunities to develop FMs. We investigate billion scale FMs and HPC training profiles for geospatial applications by pretraining on publicly available data. We studied from end-to-end the performance and impact in the solution by scaling the model size. Our larger 3B parameter size model achieves up to 30% improvement in top1 scene classification accuracy when comparing a 100M parameter model. Moreover, we detail performance experiments on the Frontier supercomputer, America's first exascale system, where we study different model and data parallel approaches using PyTorch's Fully Sharded Data Parallel library. Specifically, we study variants of the Vision Transformer architecture (ViT), conducting performance analysis for ViT models with size up to 15B parameters. By discussing throughput and performance bottlenecks under different parallelism configurations, we offer insights on how to leverage such leadership-class HPC resources when developing large models for geospatial imagery applications.

Tsaris, Aristeidis (aris)↗