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At least 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Modularization of EDGE Workflows Using Nextflow: Improving the Efficiency and Maintainability of Bioinformatics Software

EDGE is a bioinformatics platform developed in 2016 by researchers at Los Alamos National Laboratory (LANL) to facilitate the analysis of next-generation sequencing data by researchers with varying levels of experience in bioinformatics (Li et al., 2017). Users with single-end, paired-end or long-read sequencing data can provide their reads as input to EDGE and select the combination of workflows to run that are most useful for their research (e.g., quality control of reads, genome assembly, or the taxonomic classification of input reads). Table 1 summarizes the modules available in EDGE. EDGE is available as a web platform at https://edgebioinformatics.org, as installable source code maintained on GitHub under a GPLv3 license, and as a publicly hosted Docker image.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Shotgun Immunoproteomic Approach for the Discovery of Linear B-Cell Epitopes in Biothreat Agents Francisella tularensis and Burkholderia pseudomallei

Peptide-based subunit vaccines are coming to the forefront of current vaccine approaches, with safety and cost-effective production among their top advantages. Peptide vaccine formulations consist of multiple synthetic linear epitopes that together trigger desired immune responses that can result in robust immune memory. The advantages of linear compared to conformational epitopes are their simple structure, ease of synthesis, and ability to stimulate immune responses by means that do not require complex 3D conformation. Prediction of linear epitopes through use of computational tools is fast and cost-effective, but typically of low accuracy, necessitating extensive experimentation to verify results. On the other hand, identification of linear epitopes through experimental screening has been an inefficient process that requires thorough characterization of previously identified full-length protein antigens, or laborious techniques involving genetic manipulation of organisms. In this study, we apply a newly developed generalizable screening method that enables efficient identification of B-cell epitopes in the proteomes of pathogenic bacteria. As a test case, we used this method to identify epitopes in the proteome of Francisella tularensis (Ft), a Select Agent with a well-characterized immunoproteome. Our screen identified many peptides that map to known antigens, including verified and predicted outer membrane proteins and extracellular proteins, validating the utility of this approach. We then used the method to identify seroreactive peptides in the less characterized immunoproteome of Select Agent Burkholderia pseudomallei (Bp). This screen revealed known Bp antigens as well as proteins that have not been previously identified as antigens. Although B-cell epitope prediction tools Bepipred 2.0 and iBCE-EL classified many of our seroreactive peptides as epitopes, they did not score them significantly higher than the non-reactive tryptic peptides in our study, nor did they assign higher scores to seroreactive peptides from known Ft or Bp antigens, highlighting the need for experimental data instead of relying on computational epitope predictions alone. The present workflow is easily adaptable to detecting peptide targets relevant to the immune systems of other mammalian species, including humans (depending upon the availability of convalescent sera from patients), and could aid in accelerating the discovery of B-cell epitopes and development of vaccines to counter emerging biological threats.

60 APPLIED LIFE SCIENCES↗
NASA NTRSDate not supplied

Kamodo’s Satellite Constellation Mission Planning Tool

Kamodo provides a functional model-agnostic interface to a growing collection of Heliophysics model outputs. The CCMC, in collaboration with the Geospace Dynamics Constellation Science Team, has recently developed Kamodo’s satellite constellation mission planning tool to perform reconstructions in any pair of dimensions, including time. The ‘reconstruction’ tool enables users to fly any 4-dimensional grid of satellites through a given model data set, reconstructing what the given constellation would observe during the mission. This capability facilitates determination of what satellite configuration is best for a given science question, even allowing comparison across multiple models. This tool, written in Python, is built upon Kamodo’s flythrough tool, which in turn depends on a growing network of model-specific interfaces. Since each model interface is designed with model-agnostic syntax, the flythrough tool and the satellite constellation mission planning tool also feature model-agnostic syntax. In this work, we will describe the basic analysis choices available in the tool and provide a variety of sample workflows. The tool is freely available at https://github.com/nasa/Kamodo for the public. We invite the community to use the reconstruction tool and adapt the provided workflows for their mission planning, and to contribute their own workflows to share with others.

software↗
NASA NTRSDate not supplied

SM25C-2002: Kamodo’s Satellite Constellation Mission Planning Tool

Kamodo provides a functional model-agnostic interface to a growing collection of Heliophysics model outputs. The CCMC, in collaboration with the Geospace Dynamics Constellation Science Team, has recently developed Kamodo’s satellite constellation mission planning tool to perform reconstructions in any pair of dimensions, including time. The ‘reconstruction’ tool enables users to fly any 4-dimensional grid of satellites through a given model data set, reconstructing what the given constellation would observe during the mission. This capability facilitates determination of what satellite configuration is best for a given science question, even allowing comparison across multiple models. This tool, written in Python, is built upon Kamodo’s flythrough tool, which in turn depends on a growing network of model-specific interfaces. Since each model interface is designed with model-agnostic syntax, the flythrough tool and the satellite constellation mission planning tool also feature model-agnostic syntax. In this work, we will describe the basic analysis choices available in the tool and provide a variety of sample workflows. The tool is freely available at https://github.com/nasa/Kamodo for the public. We invite the community to use the reconstruction tool and adapt the provided workflows for their mission planning, and to contribute their own workflows to share with others.

python↗
DOE OSTI2024

Regional-scale fault-to-structure earthquake simulations with the EQSIM framework: Workflow maturation and computational performance on GPU-accelerated exascale platforms

Continuous advancements in scientific and engineering understanding of earthquake phenomena, combined with the associated development of representative physics-based models, is providing a foundation for high-performance, fault-to-structure earthquake simulations. However, regional-scale applications of high-performance models have been challenged by the computational requirements at the resolutions required for engineering risk assessments. The EarthQuake SIMulation (EQSIM) framework, a software application development under the US Department of Energy (DOE) Exascale Computing Project, is focused on overcoming the existing computational barriers and enabling routine regional-scale simulations at resolutions relevant to a breadth of engineered systems. This multidisciplinary software development—drawing upon expertise in geophysics, engineering, applied math and computer science—is preparing the advanced computational workflow necessary to fully exploit the DOE’s exaflop computer platforms coming online in the 2023 to 2024 timeframe. Achievement of the computational performance required for high-resolution regional models containing upward of hundreds of billions to trillions of model grid points requires numerical efficiency in every phase of a regional simulation. This includes run time start-up and regional model generation, effective distribution of the computational workload across thousands of computer nodes, efficient coupling of regional geophysics and local engineering models, and application-tailored highly efficient transfer, storage, and interrogation of very large volumes of simulation data. This article summarizes the most recent advancements and refinements incorporated in the workflow design for the EQSIM integrated fault-to-structure framework, which are based on extensive numerical testing across multiple graphics processing unit (GPU)-accelerated platforms, and demonstrates the computational performance achieved on the world’s first exaflop computer platform through representative regional-scale earthquake simulations for the San Francisco Bay Area in California, USA.

58 GEOSCIENCES↗
DOE OSTI2023

Deep learning workflow for the inverse design of molecules with specific optoelectronic properties

The inverse design of novel molecules with a desirable optoelectronic property requires consideration of the vast chemical spaces associated with varying chemical composition and molecular size. First principles-based property predictions have become increasingly helpful for assisting the selection of promising candidate chemical species for subsequent experimental validation. However, a brute-force computational screening of the entire chemical space is decidedly impossible. To alleviate the computational burden and accelerate rational molecular design, we here present an iterative deep learning workflow that combines (i) the density-functional tight-binding method for dynamic generation of property training data, (ii) a graph convolutional neural network surrogate model for rapid and reliable predictions of chemical and physical properties, and (iii) a masked language model. As proof of principle, we employ our workflow in the iterative generation of novel molecules with a target energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Enabling AI in synthetic biology through Construction File specification

The Construction File (CF) specification establishes a standardized interface for molecular biology operations, laying a foundation for automation and enhanced efficiency in experiment design. It is implemented across three distinct software projects: PyDNA_CF_Simulator, a Python project featuring a ChatGPT plugin for interactive parsing and simulating experiments; ConstructionFileSimulator, a field-tested Java project that showcases 'Experiment' objects expressed as flat files; and C6-Tools, a JavaScript project integrated with Google Sheets via Apps Script, providing a user-friendly interface for authoring and simulation of CF. The CF specification not only standardizes and modularizes molecular biology operations but also promotes collaboration, automation, and reuse, significantly reducing potential errors. The potential integration of CF with artificial intelligence, particularly GPT-4, suggests innovative automation strategies for synthetic biology. While challenges such as token limits, data storage, and biosecurity remain, proposed solutions promise a way forward in harnessing AI for experiment design. This shift from human-driven design to AI-assisted workflows, steered by high-level objectives, charts a potential future path in synthetic biology, envisioning an environment where complexities are managed more effectively.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Charged Wellbore Casing Controlled Source Electromagnetics (CWC-CSEM) for Reservoir Imaging and Monitoring (Final report)

This project addresses the needs of the U.S. Department of Energy (DOE) to develop advanced monitoring technologies and protocols to track the fate of subsurface carbon dioxide (CO2) plumes for carbon storage. Specifically, the project seeks to develop and test a unique and novel system of technologies consisting of electromagnetic data acquisition, coupled multiphysics imaging, and reservoir model enhancement to understand the migration and long-term distribution of CO2 in the subsurface. The overarching objective is to develop an integrated approach for long term monitoring of carbon storage. The two main components of the project include the methodology development and the test of the method at a field site. The methodology component consists of 1) developing the field procedure and protocol for collecting time-lapse controlled-source electromagnetic (CSEM) data with source electric current injected into the subsurface through wellbore casings; 2) building of background 3D electrical conductivity utilizing multiple sources of data such as supplemental surface transient EM (TEM) surveys, well-logs, and seismic structural information, for enhancing CSEM signal from reservoir depths; and 3) coupled multiphysics simulations and inversion of CSEM data constrained by production data and by structural information from seismic imaging of the reservoir and overlying formations. The testing component used the field site of Bell Creek Oil Field, which served both as a field laboratory for the method development as well as a test site to evaluate the CSEM signal strengths and the methodology developed in this research project. We have accomplished all the proposed tasks and developed the methodology as planned. These include the procedure for time-lapse CSEM data acquisition, data processing techniques, integration with 3D conductivity model building, fast reservoir simulation for history matching using machine learning, and interpreting CSEM data with coupling to the reservoir modeling. Collectively, the outcome of these tasks form a coherent workflow that can be applied to monitor dedicated carbon storage in saline reservoirs. The testing component evaluated the applicability and limitations of the method, and concluded that the method would be ideal for monitoring dedicated carbon storage sites utilizing saline reservoirs.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2019

Collecting and Processing Earth Science Data Metrics at NASA ESDIS

Since the launch of Terra satellite in 1999, the number of Earth Science remote sensing data products created and distributed by NASA's Earth Observing System (EOS) Data and Information System (EOSDIS) has increased from a few hundred to nearly ten thousand. NASA's Earth Science Data and Information System (ESDIS) Metrics System (EMS) collects metrics on data ingest, archive, and distribution by its Distributed Active Archive Centers (DAACs) and the Science Investigator-led Systems (SIPS), known as Data Providers. These metrics are critical in helping NASA management as well as data producers in resource planning and gaining a wide range of knowledge of data users and data usage.EMS receives flat files, or log files of data archive, ingest, and distribution either in their raw format, such as Apache web logs, or text files of log records formatted by the Data Providers. Tens of millions of records are processed each day to extract metrics on data products, user information, distribution protocols and services, and so on. The metrics are then made available to designated parties.This presentation provides an overview of the EMS processing workflow and improvement efforts made in recent years to handle ever-increasing number of data records and new metrics requirements, discusses several key steps including mapping log records to data products and identifying user communities along with geo-distribution, and demonstrates typical metrics capabilities produced by the EMS system. Challenges and potential approaches to improve the system are also discussed.

Pan, Jianfu↗
DOE OSTI2020

Development of Lipid-Coated Semiconductor Nanosensors for Recording of Membrane Potential in Neurons

In the past decade, optical imaging methods have significantly improved our understanding of the information processing principles in the brain. Although many promising tools have been designed, sensors of membrane potential are lagging behind the rest. Semiconductor nanoparticles are an attractive alternative to classical voltage indicators, such as voltage-sensitive dyes and proteins. Such nanoparticles exhibit high sensitivity to external electric fields via the quantum-confine Stark effect. Here we report the development of semiconductor voltage-sensitive nanorods (vsNRs) that self-insert into the neuronal membrane. To facilitate interaction of the nanorods with the membrane, we functionalized their surface with the lipid mixture derived from brain extract. We describe a workflow to detect and process the photoluminescent signal of vsNRs after widefield time-lapse recordings. We also present data indicating that vsNRs are feasible for sensing membrane potential in neurons at a single-particle level. This shows the potential of vsNRs for the detection of neuronal activity with unprecedentedly high spatial and temporal resolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Multi-fidelity information fusion with concatenated neural networks

Recently, computational modeling has shifted towards the use of statistical inference, deep learning, and other data-driven modeling frameworks. Although this shift in modeling holds promise in many applications like design optimization and real-time control by lowering the computational burden, training deep learning models needs a huge amount of data. This big data is not always available for scientific problems and leads to poorly generalizable data-driven models. This gap can be furnished by leveraging information from physics-based models. Exploiting prior knowledge about the problem at hand, this study puts forth a physics-guided machine learning (PGML) approach to build more tailored, effective, and efficient surrogate models. For our analysis, without losing its generalizability and modularity, we focus on the development of predictive models for laminar and turbulent boundary layer flows. In particular, we combine the self-similarity solution and power-law velocity profile (low-fidelity models) with the noisy data obtained either from experiments or computational fluid dynamics simulations (high-fidelity models) through a concatenated neural network. We illustrate how the knowledge from these simplified models results in reducing uncertainties associated with deep learning models applied to boundary layer flow prediction problems. The proposed multi-fidelity information fusion framework produces physically consistent models that attempt to achieve better generalization than data-driven models obtained purely based on data. While we demonstrate our framework for a problem relevant to fluid mechanics, its workflow and principles can be adopted for many scientific problems where empirical, analytical, or simplified models are prevalent. In line with grand demands in novel PGML principles, this work builds a bridge between extensive physics-based theories and data-driven modeling paradigms and paves the way for using hybrid physics and machine learning modeling approaches for next-generation digital twin technologies.

42 ENGINEERING↗
DOE OSTI2023

Model Data for the Mesh Convergence Study Demonstrating Benefits of Mixed-polyhedral Mesh in Integrated Hydrology Simulations

This archived model data is related to a study introducing a unique method that employs a stream-aligned mixed-polyhedral mesh to effectively and accurately represent river valleys, stream corridors, and narrow engineered channels in integrated hydrology simulations. The study finds that utilizing stream-aligned mixed-polyhedral meshes in integrated hydrology simulations achieves accuracy on par with a finely refined TIN-based mesh while markedly diminishing computational costs. This archive contains scripts and data files needed to generate the ATS model input, including mesh and ATS input files, for all mesh scenarios using the Watershed Workflow package. Additionally, this archive also provides key outputs from the model simulations that are used in the analysis and post-processing scripts to reproduce figures in the manuscript. The Watershed Workflow package is implemented in Python3. The Jupyter notebooks can be executed through multiple open-source tools, for example, Anaconda Jupyter Lab, VS Studio Code, etc. Other data files include CSV and HDF5 files, which can be read through Python scripts. The input files for the ATS model, open-source integrated hydrology, and transport model are in XML format and can be edited in any commonly used text editors.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Rapid Evaluation Framework for the CMIP7 Assessment Fast Track

As Earth system models (ESMs) grow in complexity and in volume of output data, there is an increasing need for rapid, comprehensive evaluation of their scientific performance. The upcoming Assessment Fast Track for the Seventh Phase of the Coupled Model Intercomparison Project (CMIP7) will require expeditious response for model analyses designed to inform and drive integrated Earth system assessments. To meet this challenge, the Rapid Evaluation Framework (REF), a community-driven platform for benchmarking and performance assessment of ESMs, was designed and developed. The initial implementation of the REF, constructed to meet the near-term needs of the CMIP7 Assessment Fast Track, builds upon four disparate community evaluation and benchmarking tools that are coupled together using the Coordinated Model Evaluation Capabilities (CMEC) framework. The REF runs within a containerized workflow for portability and reproducibility and is aimed at generating and organizing diagnostics covering a variety of model variables. The REF leverages well documented observational datasets to provide assessments of model fidelity across a collection of diagnostics. All diagnostics were identified and selected with community involvement and consultation. Operational integration with the Earth System Grid Federation (ESGF) will permit automated execution of the REF for selected diagnostics as soon as model output data are published on ESGF by the originating modeling centers. The REF is designed to be portable across a range of current computational platforms to facilitate use by modeling centers for assessing the evolution of model versions or gauging the relative performance of CMIP simulations before being published on ESGF. When integrated into production simulation workflows, results from the REF provide immediate quantitative feedback that allows model developers and scientists to quickly identify model biases and performance issues. After the REF is released to the community, its subsequent development and support will be prioritized by an international consortium of scientists and engineers, enabling a broader impact across Earth science disciplines. For instance, the REF will facilitate improvements to models and will enhance confidence in model projections through process-based selection of models based on their performance with respect to observations. Production of reproducible diagnostics and community-based assessments are key features of the REF. Furthermore, providing interoperability with existing evaluation packages assures that contributions from previous community efforts will be available for use in future model intercomparison projects.

Hoffman, Forrest [ORNL] (ORCID:0000000158024134)↗
NASA NTRS2019

Implementing Polar Projections with OGC Services for the Enhancement of AIRS NRT Visualization in LANCE

The Atmospheric Infrared Sounder (AIRS) NRT product is one important element in the Land, Atmosphere Near real-time Capability for EOS (LANCE). The LANCE processing of AIRS NRT products and the image generation are performed at the NASA Goddard Earth Sciences Data and Information Services Center (GES DISC). The Open Geospatial Consortium (OGC) services are being utilized to access AIRS NRT images. The ongoing AIRS NRT imagery enhancement work includes adding a new set of the images in polar projections. Polar projections are commonly used for mapping Antarctica and Arctic regions. We have implemented more precise south polar (EPSG:3031) projection and north polar (EPSG:3413) projection making our OGC service instances more useful and interoperable. Thus, AIRS NRT data can be easily accessed and integrated with other applications. It greatly increases the impact of our data on researches in polar regions.In this presentation, we will introduce the optimized processing workflow for OGC services from data access with spatial-temporal index to data visualization with different SLD, and demonstrate how to use open source software to provide more precise map images in polar projections.

Zhao, Peisheng↗
DOE OSTI2022

MZA: A Data Conversion Tool to Facilitate Software Development and Artificial Intelligence Research in Multidimensional Mass Spectrometry

Modern mass spectrometry-based workflows employing hybrid instrumentation and orthogonal separations collect multidimensional data, potentially allowing deeper understanding in omics studies through adoption of artificial intelligence methods. However, the large volume of these rich data challenges existing data storage and access technologies, therefore precluding informatics advancements. Here we present MZA™ (pronounced m-za), the mass-to-charge (m/z) generic data storage and access tool designed to facilitate software development and artificial intelligence research in multidimensional mass spectrometry measurements. Composed by a data conversion tool and a simple file structure based on the HDF5 format, MZA provides easy, cross-platform and efficient programmatic access to raw MS-data, enabling fast development of new tools in data science programming languages such as Python and R. The software executable and example Python and R scripts are freely available at https://github.com/PNNL-m-q/mza.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format

Advances in mass spectrometry (MS) instrumentation, such as higher resolution, faster scan speeds, and improved sensitivity, have significantly increased the volume and complexity of data. The growing adoption of imaging and ion mobility further amplifies these challenges across MS-based omics fields, including proteomics, metabolomics, and lipidomics. While these technologies unlock new possibilities, they also present significant challenges in data management, storage, and accessibility. Existing open formats, such as the XML-based community standards mzML and imzML, struggle to meet the demands of modern MS workflows due to their large file sizes, slow data access, and limited metadata support. Vendor-specific formats, while optimized for proprietary instruments, lack interoperability, comprehensive metadata support and long-term archival reliability. This white paper lays the groundwork for mzPeak, a next-generation community data format designed to address these challenges and support high-throughput, multi-dimensional MS workflows. By adopting a hybrid model that combines efficient binary storage for numerical data and both human and machine-readable metadata storage, mzPeak will reduce file sizes, accelerate data access, and offer a scalable, adaptable solution for evolving MS technologies. For researchers, mzPeak will enable enhanced interoperability across platforms, seamless support for complex workflows including ion mobility and MS imaging, and faster data access compared to existing community formats such as mzML. Its design will ensure data is managed in compliance with regulatory standards, essential for applications such as precision medicine and chemical safety, where long-term data integrity and accessibility are critical. For vendors, mzPeak provides a streamlined, open alternative to proprietary formats, reducing the burden of regulatory compliance while aligning with the industry's push for transparency and standardization. By offering a high-performance, interoperable solution, mzPeak positions vendors to meet customer demands for sustainable data management tools which will be able to handle emerging and future data types and workflows. mzPeak aspires to become the cornerstone of MS data management, empowering researchers, vendors, and developers to innovate and collaborate more effectively.

data formats↗
DOE OSTI2022

SBbadger: biochemical reaction networks with definable degree distributions

Abstract Motivation An essential step in developing computational tools for the inference, optimization and simulation of biochemical reaction networks is gauging tool performance against earlier efforts using an appropriate set of benchmarks. General strategies for the assembly of benchmark models include collection from the literature, creation via subnetwork extraction and de novo generation. However, with respect to biochemical reaction networks, these approaches and their associated tools are either poorly suited to generate models that reflect the wide range of properties found in natural biochemical networks or to do so in numbers that enable rigorous statistical analysis. Results In this work, we present SBbadger, a python-based software tool for the generation of synthetic biochemical reaction or metabolic networks with user-defined degree distributions, multiple available kinetic formalisms and a host of other definable properties. SBbadger thus enables the creation of benchmark model sets that reflect properties of biological systems and generate the kinetics and model structures typically targeted by computational analysis and inference software. Here, we detail the computational and algorithmic workflow of SBbadger, demonstrate its performance under various settings, provide sample outputs and compare it to currently available biochemical reaction network generation software. Availability and implementation SBbadger is implemented in Python and is freely available at https://github.com/sys-bio/SBbadger and via PyPI at https://pypi.org/project/SBbadger/. Documentation can be found at https://SBbadger.readthedocs.io. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Depth-resolved sagebrush root metabolomics, rhizosphere microbial communities, and geochemistry at the East River Watershed

This data set consists of results from soil nutrient profile, untargeted metabolomics, mass spec imaging, and amplicon sequencing. Data for soil nutrient profile includes common cations (Ca, Mg, Na, and K etc.) extracted from 3 digesting steps – ammonia acetate (for exchangeable cations), nitric acid (for acid dissolved fraction), and hydrofluoric acid/perchloric acid (HF/HClO4) for whole soil digestion. It also includes concentration of organic carbon, inorganic nitrogen (ammonia and nitrate) and phosphorus (Bray-1 P and nitric acid extract), and total nitrogen and phosphorus. Data for untargeted metabolomics includes metabolomic profile for root exudate/tissues and soil extracts from depths at surface soil to saprolite, that were measured using gas chromatography – mass spectrometry (GC-MS), and liquid chromatography – tandem mass spectrometry (LC-MS/MS). Data for mass spec imaging includes spatial distribution of metabolites that were detected and annotated with Fourier transformation ion cyclotron resonance mass spectrometer (FTICR-MS). Data for amplicon sequencing includes the base paired 16S and ITS ribosomal RNA sequences from Miseq Illumina sequencing. All samples were collected from 2 sampling campaign October 2022 and June 2023. Collectively, these datasets enable a mechanistic evaluation of how nutrient acquisition, especially nitrogen and phosphorus, differs between shallow roots operating in soil and deep roots functioning within the fractured bedrock zone. All files are provided as comma-separated values (CSV) fies (.csv) and (GZIP) file (.gz). The compressed .gz FASTQ files can be read directly in R using the dada2 package as part of the amplicon sequence analysis workflow. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. This research was performed on a project award 60563 (https://dx.doi.org/10.46936/expl.proj.2022.60563/60008727) from the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility sponsored by the Biological and Environmental Research program under Contract No. DE-AC05-76RL01830.

EARTH SCIENCE > AGRICULTURE > SOILS > CARBON↗