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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Exascale workflow applications and middleware: An ExaWorks retrospective

Exascale computers offer transformative capabilities to combine data-driven and learning-based approaches with traditional simulation applications to accelerate scientific discovery and insight. However, these software combinations and integrations are difficult to achieve due to the challenges of coordinating and deploying heterogeneous software components on diverse and massive platforms. Here, we present the ExaWorks project, which addresses many of these challenges. We developed a workflow Software Development Toolkit (SDK), a curated collection of workflow technologies that can be composed and interoperated through a common interface, engineered following current best practices, and specifically designed to work on HPC platforms. ExaWorks also developed PSI/J, a job management abstraction API, to simplify the construction of portable software components and applications that can be used over various HPC schedulers. The PSI/J API is a minimal interface for submitting and monitoring jobs and their execution state across multiple and commonly used HPC schedulers. We also describe several leading and innovative workflow examples of ExaWorks tools used on DOE leadership platforms. Furthermore, we discuss how our project is working with the workflow community, large computing facilities, and HPC platform vendors to address the requirements of workflows sustainably at the exascale.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Enabling kilometer-scale E3SM land model simulation over North America: A new integrated framework solution

This study introduces a novel framework designed to enhance the performance, scalability, and portability of the kilometer-scale E3SM Land Model (km-ELM) within the E3SM modeling infrastructure. By seamlessly integrating cutting-edge data tools, we address existing challenges such as slow performance, limited scalability, and difficulties in software integration in current data-driven ELM simulation over large geographic areas. Our innovative approach leverages the KiloCraft data toolkit to generate unified inputs for simulations ranging from a single-cite case, to a 72,083-cell regional case to a continental configuration encompassing 21.6 million land grid cells at a 1 km × 1 km resolution. We conduct extensive strong- and weak-scaling experiments on three state-of-the-art supercomputers, utilizing up to 100,800 CPU cores across 2400 compute nodes to evaluate end-to-end metrics including wall-clock time, simulation-years-per-day (SYPD), initialization costs, and I/O throughput. Our results reveal the land (LND) component’s efficient scaling, demonstrating near-ideal weak scaling and strong-scaling parallel efficiencies reaching up to 87% at 50,400 cores. We confirm portability and reproducibility through bitwise-equivalent outputs across different machines using identical inputs over supported machines. Notably, at extreme scales, we identify I/O as a critical bottleneck and that leads to effective solution with the SCORPIO/ADIOS stack. Collectively, these findings validate the deployment of km-ELM at a continental scale with high parallel efficiency and provide essential guidance on configuration, decomposition, and I/O settings for optimized kilometer-scale land simulations in E3SM. This work emphasizes the innovative design and practical solutions that enhance the operational capabilities of km-ELM, focusing on software performance and scalability while leaving detailed scientific evaluations of simulated land processes for future investigations.

E3SM land model (ELM), km-ELM, scalability, perfor↗
DOE OSTI2016

acdc – Automated Contamination Detection and Confidence estimation for single-cell genome data

Abstract Background A major obstacle in single-cell sequencing is sample contamination with foreign DNA. To guarantee clean genome assemblies and to prevent the introduction of contamination into public databases, considerable quality control efforts are put into post-sequencing analysis. Contamination screening generally relies on reference-based methods such as database alignment or marker gene search, which limits the set of detectable contaminants to organisms with closely related reference species. As genomic coverage in the tree of life is highly fragmented, there is an urgent need for a reference-free methodology for contaminant identification in sequence data. Results We present acdc, a tool specifically developed to aid the quality control process of genomic sequence data. By combining supervised and unsupervised methods, it reliably detects both known and de novo contaminants. First, 16S rRNA gene prediction and the inclusion of ultrafast exact alignment techniques allow sequence classification using existing knowledge from databases. Second, reference-free inspection is enabled by the use of state-of-the-art machine learning techniques that include fast, non-linear dimensionality reduction of oligonucleotide signatures and subsequent clustering algorithms that automatically estimate the number of clusters. The latter also enables the removal of any contaminant, yielding a clean sample. Furthermore, given the data complexity and the ill-posedness of clustering, acdc employs bootstrapping techniques to provide statistically profound confidence values. Tested on a large number of samples from diverse sequencing projects, our software is able to quickly and accurately identify contamination. Results are displayed in an interactive user interface. Acdc can be run from the web as well as a dedicated command line application, which allows easy integration into large sequencing project analysis workflows. Conclusions Acdc can reliably detect contamination in single-cell genome data. In addition to database-driven detection, it complements existing tools by its unsupervised techniques, which allow for the detection of de novo contaminants. Our contribution has the potential to drastically reduce the amount of resources put into these processes, particularly in the context of limited availability of reference species. As single-cell genome data continues to grow rapidly, acdc adds to the toolkit of crucial quality assurance tools.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Simulating metagenomic stable isotope probing datasets with MetaSIPSim

DNA-stable isotope probing (DNA-SIP) links microorganisms to their in-situ function in diverse environmental samples. Combining DNA-SIP and metagenomics (metagenomic-SIP) allows us to link genomes from complex communities to their specific functions and improves the assembly and binning of these targeted genomes. However, empirical development of metagenomic-SIP methods is hindered by the complexity and cost of these studies. We developed a toolkit, ‘MetaSIPSim,’ to simulate sequencing read libraries for metagenomic-SIP experiments. MetaSIPSim is intended to generate datasets for method development and testing. To this end, we used MetaSIPSim generated data to demonstrate the advantages of metagenomic-SIP over a conventional shotgun metagenomic sequencing experiment. Through simulation we show that metagenomic-SIP improves the assembly and binning of isotopically labeled genomes relative to a conventional metagenomic approach. Improvements were dependent on experimental parameters and on sequencing depth. Community level G + C content impacted the assembly of labeled genomes and subsequent binning, where high community G + C generally reduced the benefits of metagenomic-SIP. Furthermore, when a high proportion of the community is isotopically labeled, the benefits of metagenomic-SIP decline. Finally, the choice of gradient fractions to sequence greatly influences method performance. Metagenomic-SIP is a valuable method for recovering isotopically labeled genomes from complex communities. We show that metagenomic-SIP performance depends on optimization of experimental parameters. MetaSIPSim allows for simulation of metagenomic-SIP datasets which facilitates the optimization and development of metagenomic-SIP experiments and analytical approaches for dealing with these data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Fluorescent amplification for next generation sequencing (FA-NGS) library preparation

BACKGROUND: Next generation sequencing (NGS) has become a universal practice in modern molecular biology. As the throughput of sequencing experiments increases, the preparation of conventional multiplexed libraries becomes more labor intensive. Conventional library preparation typically requires quality control (QC) testing for individual libraries such as amplification success evaluation and quantification, none of which occur until the end of the library preparation process. RESULTS: In this study, we address the need for a more streamlined high-throughput NGS workflow by tethering real-time quantitative PCR (qPCR) to conventional workflows to save time and implement single tube and single reagent QC. We modified two distinct library preparation workflows by replacing PCR and quantification with qPCR using SYBR Green I. qPCR enabled individual library quantification for pooling in a single tube without the need for additional reagents. Additionally, a melting curve analysis was implemented as an intermediate QC test to confirm successful amplification. Sequencing analysis showed comparable percent reads for each indexed library, demonstrating that pooling calculations based on qPCR allow for an even representation of sequencing reads. To aid the modified workflow, a software toolkit was developed and used to generate pooling instructions and analyze qPCR and melting curve data. CONCLUSIONS: We successfully applied fluorescent amplification for next generation sequencing (FA-NGS) library preparation to both plasmids and bacterial genomes. As a result of using qPCR for quantification and proceeding directly to library pooling, the modified library preparation workflow has fewer overall steps. Therefore, we speculate that the FA-NGS workflow has less risk of user error. The melting curve analysis provides the necessary QC test to identify and troubleshoot library failures prior to sequencing. While this study demonstrates the value of FA-NGS for plasmid or gDNA libraries, we speculate that its versatility could lead to successful application across other library types.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Genetic tools for engineering Zymomonas mobilis , Cereibacter sphaeroides and Novosphingobium aromaticivorans to improve production of bioenergy compounds

Limited genetic tools for non-model bacteria are one of the limiting factors for genetic studies. This review compiles genetic tools used for three non-model alpha-proteobacteria, such as Zymomonas mobilis, Cereibacter (Rhodobacter) sphaeroides, and Novosphingobium aromaticivorans, which hold significant potential to produce industrially essential bioenergy compounds due to their distinctive metabolic pathways and resilience in extreme environments. Each of these strains has a unique genetic profile that enables them to efficiently carry out key reactions relevant to producing bioenergy compounds, such as converting sugars into bioenergy compounds and breaking down lignotoxins. Genetic tools can further optimize these strains for enhanced bioenergy compound production. This review explores the metabolic advantages of these organisms. It highlights the available array of genetic toolkits that can be shared among them to unlock their full potential for sustainable biofuel production.

Biofuel↗
DOE OSTI2018

NovoGraph: Human genome graph construction from multiple long-read de novo assemblies

Genome graphs are emerging as an important novel approach to the analysis of high-throughput human sequencing data. By explicitly representing genetic variants and alternative haplotypes in a mappable data structure, they can enable the improved analysis of structurally variable and hyperpolymorphic regions of the genome. In most existing approaches, graphs are constructed from variant call sets derived from short-read sequencing. As long-read sequencing becomes more cost-effective and enables de novo assembly for increasing numbers of whole genomes, a method for the direct construction of a genome graph from sets of assembled human genomes would be desirable. Such assembly-based genome graphs would encompass the wide spectrum of genetic variation accessible to long-read-based de novo assembly, including large structural variants and divergent haplotypes. We present NovoGraph, a method for the construction of a human genome graph directly from a set of de novo assemblies. NovoGraph constructs a genome-wide multiple sequence alignment of all input contigs and creates a graph by merging the input sequences at positions that are both homologous and sequence-identical. NovoGraph outputs resulting graphs in VCF format that can be loaded into third-party genome graph toolkits. To demonstrate NovoGraph, we construct a genome graph with 23,478,835 variant sites and 30,582,795 variant alleles from de novo assemblies of seven ethnically diverse human genomes (AK1, CHM1, CHM13, HG003, HG004, HX1, NA19240). Initial evaluations show that mapping against the constructed graph reduces the average mismatch rate of reads from sample NA12878 by approximately 0.2%, albeit at a slightly increased rate of reads that remain unmapped.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Data for Development, Optimization, and Application of an Episomal Plasmid System for Rhodotorula toruloides

Rhodotorula toruloides is an emerging oleaginous yeast with strong potential as a microbial cell factory for the production of acetyl-CoA-derived bioproducts. However, engineering of this organism has been limited by the absence of a functional episomal plasmid system, a foundational genetic tool for rapid gene expression, pathway testing, and CRISPR-based genome engineering. Here, we report the first episomal plasmid system for R. toruloides . Through systematic screening of candidate autonomously replicating sequences (ARSs) from diverse sources, we identified multiple functional ARS elements and selected C63F4, a fragment derived from Contig 63 of R. toruloides CBS14, because of its stable performance. The resulting pC63F4 plasmid was maintained episomally, supported GFP reporter expression, exhibited a copy number of 2.39 ± 0.13, and showed good stability during long term cultivation. To overcome poor transformation efficiency, we developed a Cre-loxP-mediated in vivo re-circularization strategy that enabled reliable delivery of the episomal plasmid. Using this improved system, we demonstrated functional episomal expression of metabolic engineering genes and multi-gene pathways for the production of triacetic acid lactone, fatty alcohols, and limonene. Finally, we leveraged this platform to establish a redesigned CRISPR system that enables seamless genome editing in R. toruloides for the first time, while also simplifying marker recycling. Together, this work establishes a long-needed episomal plasmid platform and associated CRISPR toolkit that will accelerate metabolic engineering, synthetic biology, and fundamental studies in R. toruloides .

Gene Editing↗
DOE OSTI2025

Dataset for Leveraging CryoEM and AI-Driven Morphological Feature Analysis for Insights on Bacterial Structures

This repository hosts an AI-assisted image segmentation and analysis pipeline for Pantoea sp. YR343 cryo-electron microscopy (cryoEM) datasets. The workflow automates membrane thickness measurements, flagella detection, and field-of-view (FOV) screening from low-dose, high-resolution cryoEM micrographs eliminating the need for slow manual annotation. By integrating deep-learning based segmentation (YOLOv11) with quantitative post-processing, this toolkit provides a scalable and reproducible way to study bacterial morphology under hydrated, near-native conditions. The GitHub repository for AI-based tools for cryoEM bacteria ultrastructures can be found here: https://github.com/Sireesiru/Cryo-EM-Ultrastructures/tree/main

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Characterization and simulation of soft gamma-ray mirrors for their use with spent fuel rods at reprocessing facilities

The use of a grazing incidence optic to selectively reflect K-shell fluorescence emission and isotope-specific lines from special nuclear materials is a highly desirable nondestructive analysis method for use in reprocessing fuel environments. Preliminary measurements have been performed, and a simulation suite has been developed to give insight into the design of the x ray optics system as a function of the source emission, multilayer coating characteristics, and general experimental configurations. As a result, the experimental results are compared to the predictions from our simulation toolkit to illustrate the ray-tracing capability and explore the effect of modified optics in future measurement campaigns.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2021

Mathematical model of a personalized neoantigen cancer vaccine and the human immune system

Cancer vaccines are an important component of the cancer immunotherapy toolkit enhancing immune response to malignant cells by activating CD4 + and CD8 + T cells. Multiple successful clinical applications of cancer vaccines have shown good safety and efficacy. Despite the notable progress, significant challenges remain in obtaining consistent immune responses across heterogeneous patient populations, as well as various cancers. We present a mechanistic mathematical model describing key interactions of a personalized neoantigen cancer vaccine with an individual patient’s immune system. Specifically, the model considers the vaccine concentration of tumor-specific antigen peptides and adjuvant, the patient’s major histocompatibility complexes I and II copy numbers, tumor size, T cells, and antigen presenting cells. We parametrized the model using patient-specific data from a clinical study in which individualized cancer vaccines were used to treat six melanoma patients. Model simulations predicted both immune responses, represented by T cell counts, to the vaccine as well as clinical outcome (determined as change of tumor size). This model, although complex, can be used to describe, simulate, and predict the behavior of the human immune system to a personalized cancer vaccine.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Using social media for actionable disease surveillance and outbreak management. A systematic literature review

Here, research studies show that social media may be valuable tools in the disease surveillance toolkit used for improving public health professionals’ ability to detect disease outbreaks faster than traditional methods and to enhance outbreak response. A social media work group, consisting of surveillance practitioners, academic researchers, and other subject matter experts convened by the International Society for Disease Surveillance, conducted a systematic primary literature review using the PRISMA framework to identify research, published through February 2013, answering either of the following questions: 1) Can social media be integrated into disease surveillance practice and outbreak management to support and improve public health? 2) Can social media be used to effectively target populations, specifically vulnerable populations, to test an intervention and interact with a community to improve health outcomes? Examples of social media included are Facebook, MySpace, microblogs (e.g., Twitter), blogs, and discussion forums. For Question 1, 33 manuscripts were identified, starting in 2009 with topics on Influenza-like Illnesses (n=15), Infectious Diseases (n = 6), Non-infectious Diseases (n=4), Medication and Vaccines (n=3), and Other (n=5). For Question 2, 32 manuscripts were identified, the first in 2000 with topics on Health Risk Behaviors (n=10), Infectious Diseases (n = 3), Non-infectious Diseases (n=9), and Other (n=10). The literature on the use of social media to support public health practice has identified many gaps and biases in current knowledge. Despite the potential for success identified in exploratory studies, there are limited studies on interventions and little use of social media in practice. However, information gleaned from the articles demonstrates the effectiveness of social media in supporting and improving public health and in identifying target populations for intervention. A primary recommendation resulting from the review is to identify opportunities that enable public health professionals to integrate social media analytics into disease surveillance and outbreak management practice.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Crewmember microbiome may influence microbial composition of ISS habitable surfaces

The International Space Station (ISS) is a complex built environment physically isolated from Earth. Assessing the interplay between the microbial community of the ISS and its crew is important for preventing biomedical and structural complications for long term human spaceflight missions. In this study, we describe one crewmember’s microbial profile from body swabs of mouth, nose, ear, skin and saliva that were collected at eight different time points pre-, during and post-flight. Additionally, environmental surface samples from eight different habitable locations in the ISS were collected from two flights. Environmental samples from one flight were collected by the crewmember and samples from the next flight were collected after the crewmember departed. The microbial composition in both environment and crewmember samples was measured using shotgun metagenomic sequencing and processed using the Livermore Metagenomics Analysis Toolkit. Ordination of sample to sample distances showed that of the eight crew body sites analyzed, skin, nostril, and ear samples are more similar in microbial composition to the ISS surfaces than mouth and saliva samples; and that the microbial composition of the crewmember’s skin samples are more closely related to the ISS surface samples collected by the crewmember on the same flight than ISS surface samples collected by other crewmembers on different flights. In these collections, species alpha diversity in saliva samples appears to decrease during flight and rebound after returning to Earth. This is the first study to compare the ISS microbiome to a crewmember’s microbiome via shotgun metagenomic sequencing. We observed that the microbiome of the surfaces inside the ISS resemble those of the crew’s skin. These data support future crew and ISS microbial surveillance efforts and the design of preventive measures to maintain crew habitat onboard spacecraft destined for long term space travel.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Cherenkov and Transition Radiation as Low-Energy Background Sources in SuperCDMS Detectors

The Weakly Interacting Massive Particle (WIMP) has historically been a prime candidate for dark matter due to its elegant compatibility with the Minimally Supersymmetric Standard Model (MSSM). Recent dark matter experiments have ruled out much of the GeV-TeV mass range predicted by the MSSM, however, and the newest generation of direct detection experiments, such as SuperCDMS SNOLAB, have begunto explore sub-GeV dark matter. As experiments push towards lower masses, sensitivity to eV-scale electron recoil events has become increasingly important. A variety of unexplained excesses at energy deposits of 1-100 eV have been found inmany such low-mass experiments, across different detection techniques and at different excess rates. These low-energy events are not thought to be dark matter, and they must be understood and effectively removed to further improve detector energy resolution. This thesis will outline the simulation of one possible source of low-energy excess at SuperCDMS: optical photons produced from charges in uniform motion, specifically from Cherenkov radiation (CR), transition radiation (TR), and the intermediate hybrid transition-Cherenkov radiation (HR). In the latter case, the standard formulae for HR contain divergences at certain angles in transparent media, which are an artifact of their derivation and become problematic to simulate. To rsolve this, we present a novel approach to normalize the divergent HR peaks, which allows HR to transition smoothly between TR and CR in a numerical simulation. We also add TR and CR as a physics process to the SuperCDMS Monte Carlo simulation package SuperSim, based on the Geant4 simulation toolkit. To verify the physics of our addition, we show some test simulations in comparison to theoretical predictions of optical radiation intensity. We also use the simulation to make some preliminary predictions on the contribution of TR and CR to the low energy background, with the expectation that more thorough analyses will be conducted in the future.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Conservation and conviviality in the American West

The emerging field of convivial conservation (CC) draws on the tradition of political ecology (PE) to present a “radical” alternative to contemporary environmentalisms, speaking to the challenges of conservation in the Anthropocene as well as the global ascent of reactionary populism. Building on previous work arguing for the ongoing value of dialogue between PE and the American West, I here develop a conversation between CC and another radical intervention, the collaborative conservation of the West’s so-called “radical center” (RC). Using the nexus of wolf–livestock conflict and public lands grazing, I first trace a genealogical history of western environmental politics before turning to CC as critical corrective to the shortcomings of the RC. Scholarship on the commons and commoning provides an analytical bridge and political toolkit for linking the empirics of place with the aspirational aims of conviviality, and naming and navigating on-the-ground obstacles to collaborative conservation efforts in the region. This dialogue in turn highlights deeply rooted tensions of capitalist political economy and questions of non/belonging rooted in settler colonialism—necessary regional engagements for building from polarized antagonism toward an alternative environmental politics of coexistence and conviviality.

Environmental Sciences & Ecology↗
DOE OSTI2019

Developing a High-Quality Linkage Map for the Atlantic Killifish Fundulus heteroclitus

Killifish (Fundulus heteroclitus) are widely distributed among different aquatic environments where they demonstrate an impressive range of highly-plastic and locally adaptive phenotypes. High-throughput sequencing has begun to unravel the mechanisms and evolutionary history of these interesting features by establishing relationships in the genotype-phenotype map. However, some genotype-phenotype analyses require a higher order of contiguity than what initial scaffolded (fragmented genome assembly where contigs have been assemble into scaffolds) genome assemblies can provide. Here, we used 5,685 high-quality RAD-Seq markers from a single mapping family to order 84% of the scaffolded genome assembly to 24 chromosomes. This serves to: 1) expand the killifish genomic toolkit, 2) estimate genome-wide recombination rates, and 3) compare genome synteny to humans and other fishes. After initially building our map, we found that the selection of thresholds for sequence data filtration highly impacted scaffold placement in the map. We outline each step of the approach that dramatically improved our map to help guide others toward more effective linkage mapping for genome assembly. Our final map supports strong conservation of genomic synteny among closely related fish species and reveals previously described chromosomal rearrangements between more distantly related clades. However, we also commonly found minor scaffold misorientations in F. heteroclitus and in other assemblies, suggesting that further mapping (such as optical mapping) is necessary for finer scale resolution of genome structure. Lastly, we discuss the problems that would be expected from misoriented/unplaced scaffolds and stress the importance of a quality mapped genome as a key feature for further investigating population and comparative genomic questions with F. heteroclitus and other taxa.

Genetics & Heredity↗
DOE OSTI2024

CROCUS Air Quality Data at Northeastern Illinois University Rooftop

This dataset is from the Department of Energy Office of Science funded project, Community Research on Urban and Climate Science (CROCUS) (https://crocus-urban.org/). The AQT (Vaisala AQT530) instrument provides observations on meteorological conditions, including particulate matter (PM2.5, PM10), gas species concentrations (NO, NO2, O3, CO), and environment temperature and moisture. These measurements are critical for understanding air quality. These measurements are useful for understanding changes in aerosol properties, air quality research, and comparing to model experiments especially in urban environments.Datasets are stored in the netCDF data format, and we we encourage users to make use the associated toolkits available from Unidata (https://www.unidata.ucar.edu/software/netcdf/), Project Pythia (https://foundations.projectpythia.org/core/data-formats/netcdf-cf.html), and our “Instrument Cookbooks” (https://crocus-urban.github.io/instrument-cookbooks) for more information on how to process the metadata-rich datasets.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

CROCUS Weather Data at Northeastern Illinois University Rooftop

This dataset is from the Department of Energy Office of Science funded project, Community Research on Urban and Climate Science (CROCUS) (https://crocus-urban.org/). Vaisala WXT sensor is an all-in-one weather instrument that provides 6 of the most important weather parameters: barometric pressure, temperature, relative humidity, rainfall, wind speed and direction. Temperature, pressure, relative humidity, and rainfall are sampled at 1 second frequency, while wind speed/direction is measured at ten per second (10Hz) frequency. These measurements are useful for looking at characterizing local weather, identifying unique weather events, and studying local turbulence, especially given the high temporal resolution of the wind measurements.Datasets are stored in the netCDF data format, and we we encourage users to make use the associated toolkits available from Unidata (https://www.unidata.ucar.edu/software/netcdf/), Project Pythia (https://foundations.projectpythia.org/core/data-formats/netcdf-cf.html), and our “Instrument Cookbooks” (https://crocus-urban.github.io/instrument-cookbooks) for more information on how to process the metadata-rich datasets.

54 ENVIRONMENTAL SCIENCES↗