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DOE OSTI2025

A Performant, Scalable Processing Pipeline for High‐Quality and FAIR Environmental Sensor Data

High-resolution environmental monitoring is necessary to record, understand, and predict biogeochemical and ecological changes particularly in coastal systems but brings significant challenges in processing and making rapidly available the resulting data. The COMPASS-FME project established a network of coastal observational sites across the Chesapeake Bay and western Lake Erie regions extensively instrumented with soil, vegetation, and weather sensors logging data every 15 min. Our data processing framework, written in R and completely open source, prioritizes rapid model-experiment iteration and makes biogeochemical data rapidly available for quality assurance/quality control, analysis, and model ingestion. This pipeline is distinguished by a standardized and modular approach to data curation, extensive metadata and documentation, and its high performance. These attributes combine to make biogeochemical data rapidly accessible across COMPASS-FME and the broader community. Flexible, powerful, and reproducible approaches to handling high-volume environmental data are crucial for accelerating biogeosciences research.

Pennington, Stephanie C. [Pacific Northwest Nation↗

DOE OSTI2025

Machine learning model inputs, outputs, and scripts associated with “Artificial intelligence-guided iterations between observations and modeling significantly improve environmental predictions”

NOTE: The manuscript associated with this data package is currently in review. The data may be revised based on reviewer feedback. Upon manuscript acceptance, this data package will be updated with the final dataset and additional metadata. This data package is associated with the manuscript “Artificial intelligence-guided iterations between observations and modeling significantly improve environmental predictions” (Malhotra et al., in prep). This effort was designed following ICON (integrated, coordinated, open, and networked) principles to facilitate a model-experiment (ModEx) iteration approach, leveraging crowdsourced sampling across the contiguous United States (CONUS). New machine learning models were created every month to guide sampling locations. Data from the resulting samples were used to test and rebuild the machine learning models for the next round of sampling guidance. Associated sediment and water geochemistry and in situ sensor data can be found at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1923689, https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1729719, and https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1603775. This data package is associated with two GitHub repositories found at https://github.com/parallelworks/dynamic-learning-rivers and https://github.com/WHONDRS-Hub/ICON-ModEx_Open_Manuscript. In addition to this readme, this data package also includes two file-level metadata (FLMD) files that describes each file and two data dictionaries (DD) that describe all column/row headers and variable definitions. This data package consists of two main folders (1) dynamic-learning-rivers and (2) ICON-ModEx_Open_Manuscript which contain snapshots of the associated GitHub repositories. The input data, output data, and machine learning models used to guide sampling locations are within dynamic-learning-rivers. The folder is organized into five top-level directories: (1) “input_data” holds the training data for the ML models; (2) “ml_models” holds machine learning (ML) models trained on the data in “input_data”; (3) “examples” contains files for direct experimentation with the machine learning model, including scripts for setting up “hindcast” run; (4) “scripts” contains data preprocessing and postprocessing scripts and intermediate results specific to this data set that bookend the ML workflow; and (5) “output_data” holds the overall results of the ML model on that branch. Each trained ML model resides on its own branch in the repository; this means that inputs and outputs can be different branch-to-branch. There is also one hidden directory “.github/workflows”. This hidden directory contains information for how to run the ML workflow as an end-to-end automated GitHub Action but it is not needed for reusing the ML models archived here. Please see the top-level README.md in the GitHub repository for more details on the automation. The scripts and data used to create figures in the manuscript are within ICON-ModEx_Open_Manuscript. The folder is organized into four folders which contain the scripts, data, and pdf for each figure. Within the “fig-model-score-evolution” folder, there is a folder called “intermediate_branch_data” which contains some intermediate files pulled from dynamic-learning-rivers and reorganized to easily integrate into the workflows. NOTE: THIS FOLDER INCLUDES THE FILES AT THE POINT OF PAPER SUBMISSION. IT WILL BE UPDATED ONCE THE PAPER IS ACCEPTED WITH ANY REVISIONS AND WILL INCLUDE A DD/FLMD AT THAT POINT. We thank the United States Forest Service, Washington Department of Fish and Wildlife, Washington Department of Natural Resources, Cowiche Canyon Conservatory, Washington State Parks and Recreation Commission (Scientific Research Permit #210901), and the Confederated Tribes and Bands of the Yakama Nation for access to field locations where the samples labeled “SSS” were collected. We also thank the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview. WHONDRS consortium members were asked to provide any acknowledgments for the collection of samples labeled “CM” and the following is a list of acknowledgments that were submitted with their corresponding Site IDs: (MART) Research activities were conducted in part on the Wind River Experimental Forest within the Gifford Pinchot National Forest; (MP- 100379) Philadelphia is part of Lenapehoking, the ancestral homelands of the Lenape peoples; (MP-102398) Land surveyed is the ancestral homelands of the Nookhose'iinenno (Arapaho), Tsis tsis'tas (Cheyenne), and Nuuchu (Ute); (MP-100749 and MP- 100747) Georgia Coastal Ecosystem LTER, OCE-1832178; (SP-70 and SP-72) Eastern Shoshone, Shoshone-Bannock; (MP- 102944) Funded by Oregon Watershed Enhancement Board. On the traditional lands of the Confederated Tribes of the Siletz, Confederated Tribes of the Grand Rhonde, and the Clatsop-Nehalem Confederated Tribe; (MP- 100607) Holiday Creek is located on the traditional territory of the Monacan Indian Nation; (SP-45) Lafayette Blue Springs State Park; (MP-102420) NSF DEB-2016749; (MP-100019) New Hampshire Agriculture Experiment Station; (SP-35) Rayonier (land owner; https://www.rayonier.com/); (MP- 101276) US Department of Energy, Office of Science, Biological and Environmental Research, Subsurface Biogeochemical Research, Watershed Dynamics and Evolution SFA at ORNL; (MP- 103224) Watershed Dynamics and Evolution SFA at ORNL; (MP- 101584) Traditional lands of the Oceti Sakowin (Dakota, Lakota, Nakoda) and Anishinaabe Peoples.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Laboratory time series moisture manipulative experiment from sediment across the contiguous US: time series aerobic respiration and geochemistry (v2)

This dataset supports a broader study examining the effects of wetting and drying on hyporheic zone respiration across the contiguous United States (CONUS). The dataset provides data generated from a laboratory moisture manipulation experiment. The contents include time series aerobic respiration and moisture; dissolved oxygen; sediment geochemistry data; and field metadata (including qualitative information on instream and river corridor characteristics). Samples were collected as part of the WHONDRS CONUS-Scale Model-Sample Study (CM). This study was designed following ICON (integrated, coordinated, open, and networked) principles to facilitate a model-experiment (ModEx) iteration approach, leveraging crowdsourced sampling across the CONUS. The data package associated with the CM study is available at https://data.ess-dive.lbl.gov/view/doi:10.15485/1923689. CM sampling began in April 2022 and ended in October 2023. This study uses subsamples from a subset of CM samples collected between June 2022 and June 2023. The original field samples were labeled as CM_###. Subsequent subsamples for this study were labeled as EC_###. The labels from the field samples and the EC subsamples can be mapped directly based on the digits following the prefix and underscore (i.e., EC_001 is a subsample from CM_001). See the critical details section below for more details on sample naming. This data package was originally published in August 2024. It was updated in February 2026 (v2; new and modified files). See the change history section in the readme for more details. For details on how to navigate this data package, see this infographic from the River Corridor SFA https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. This dataset is comprised of one folder of raw Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) data and one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) readme; (5) field protocol; and a (6) a subfolder with sediment sample data from the incubation experiment. The sample data subfolder contains (1) dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC); (2) total nitrogen (TN); (3) adenosine triphosphate (ATP); (4) percent carbon and nitrogen; (5) effect size; (6) iron (II); (7) gravimetric moisture; (8) respiration rates and raw dissolved oxygen values; (9) specific conductance; (10) pH; (11) temperature; (12) a summary containing median values of each data type for each treatment (wet and dry); (13) methods codes; (14) FTICR-MS methods; and (15) a subfolder of 9.4 Tesla FTICR-MS data. This folder contains three subfolders, one containing the sediment .xml data files, one containing the sediment CoreMS output files, the other containing instructions and scripts for processing the files in CoreMS (https://github.com/EMSL-Computing/CoreMS). All files are .csv, .pdf, .R, .ref, or .xml.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Post-fire time series of sensor and geochemistry sample data from surface water, groundwater, precipitation, soil, and vegetation across Oak Creek watershed, Washington

This dataset supports a broader study examining wildfire impacts on hydrologic connectivity across 5 sites within the Oak Creek watershed and the resulting biogeochemical impacts. Stream sites were selected using the Advanced Terrestrial Simulator (ATS) hydrologic model to identify locations with varying groundwater contributions and hydrologic responses across different burn severity scenarios. The Retreat Fire burned from July 23 to August 2 in 2024, affecting the five study sites at varying burn severities. Each site is equipped with YSI EXO2 sondes logging sub-hourly throughout the year, and grab samples are collected approximately every six weeks. YSI sondes are used to measure temporally resolved proxies for groundwater inputs (specific conductivity) and organic matter (fluorescent dissolved organic matter; fDOM) along with basic water quality and depth. Grab samples of surface water, groundwater, and precipitation are analyzed for water stable isotopes and conductivity to understand endmembers for hydrologic mixing Grab samples of surface water, groundwater, soil water, and litter/vegetation/soil leachates are analyzed for organic matter composition measured by Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS) to understand organic matter dynamics. Game camera photos are provided in a separate data package available at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/3018598. Future versions of this dataset will include time series data from YSI EXO2 sondes (fDOM, dissolved oxygen, temperature, depth, specific conductance, turbidity, pH), BaroTROLL sensors (air temperature and barometric pressure), rain gauges (precipitation), and data from the soil and vegetation samples. Because this study is ongoing, this data package will be updated regularly to include newly collected data and the additional data types. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. In addition to a readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. This dataset is comprised of (1) a folder of field photos; (2) a folder of surface water sample data; (3) a folder of raw Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) data; (4) a data checks report; (5) file-level metadata; (6) data dictionary; (7) field metadata; (8) readme; (9) international generic sample number (IGSN) mapping file; and (10) field protocols. The sample data subfolder contains (1) dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC) data and averages; (2) total dissolved nitrogen data and averages; (3) stable water isotopes and averages; (4) methods codes; (5) FTICR-MS methods; and (15) a subfolder of 9.4 Tesla (9.4T) FTICR-MS data. This folder contains the processed data and three subfolders, one containing the .xml files, one containing the water CoreMS output files, and the other containing instructions and scripts for processing the files in CoreMS (https://github.com/EMSL-Computing/CoreMS). All files are .csv, .pdf, .R, .xml, .d, .html, .Rmd, .py, .cal, .json, .jpg, .jpeg, .png, .mov, or .mp4.

Biogeochemistry↗

DOE OSTI2026

Post-fire time series photos from five sites across the Oak Creek watershed, Washington

Burn severity↗