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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

A Short-Term Solar Forecasting Platform Using a Physics-Based Smart Persistence Model and Data Imputation Method

Electrical energy plays vital role in our socio-economic activity and therefore ensuring the reliability of the electric grid, from the generation, transmission and distribution level is critical. In order to maintain the power system parameter viz., frequency, voltage, etc., optimally, balancing of generation and consumption is very much essential. However, solar energy is infirm power by nature this is due to cloud cover / other local phenomena. Hence, Photovoltaic (PV) power generation brings a significant challenge to the grid operator due to the variability of the solar energy. The complexity of this challenge in terms of planning and dispatch ability of PV resources, aggravates with the high penetration of solar energy into the electric grid. In this setting, reliable solar radiation forecasting models based on accurate and quality input data become essential. In order to develop a suitable model for predicting solar radiation, quality historical / real time measurement is also needed. Under this study NIWE and NREL jointly developed / tested short-term solar forecasting frameworks using a smart persistence and physics-based smart persistence models for intra-hour forecasting of solar radiation (PSPI) and benchmarked 9 different data imputation techniques in 15 Solar Radiation Resource Assessment (SRRA) stations, located at different parts of India. During any measurement campaign, due to various technical reasons, we may miss few observations. However, the missing observation often reduce the performance of any forecasting model. Therefore, suitable data imputation method would assist us to obtain continuous observation of solar radiation. A station-by-station and method-by-method analysis was carried out to understand the performance of each model. Based on our analysis, among all the data imputation methods, the Kalman data imputation method is better for Indian Weather condition. In addition, Kalman StructTS, Linear, Stine and Arima methods yield slightly inferior accuracy compared to Kalman, but outperform the other methods. The extended solar radiation data are used by solar forecasting models to provide the prediction of solar radiation at 15 SRRA stations. As far as short term forecasting model is concerned, the PSPI model outperforms the Smart Persistence model. However, the forecast error is increases with the forecasting horizon.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2024

Modeling Grid Data Flows for Transmission and Distribution Operations: Review, Design, Next Steps

Operational scenarios of the power grids grow multifold to accommodate the diverse needs of both the utilities and end consumers, and the various other stakeholders in-between. To comprehensively model and apply analytics to support objectives and business functions of grid sectors, a reliable approach to characterize and design data flows is crucial. The flows bridge business functions with communications protocols, stakeholders such as the grid actors, and data interfaces comprising different data objects. Additionally, constraints applied to the flow such as cybersecurity, trust, privacy, and ownership among others intersect these entities, requiring the delineation of their interactions under different scenarios. This paper aims to not only highlight relevant research in the space of grid data flows, but also proposes, for the transmission-distribution sector, a novel modeling approach that marries the aforementioned entities: objectives, business functions, data interfaces, communication protocols, data stakeholders, and flow constraints. It elaborates on the design philosophy and the significance of each entity within the model and applies it to an example function of fault location, isolation and service restoration (FLISR). Finally, the next steps to extend the application of this data flow model for other practical operational scenarios are discussed.

Sundararajan, Aditya [ORNL] (ORCID:000000033577854↗
DOE OSTI2025

Data-driven modeling of dynamic occupant thermostat override behavior for demand response applications

Buildings consume nearly 40% of global energy and produce similar emissions. Whiletechnological advances address efficiency, occupant behavior causes energy use variations up to 300% between identical buildings. This gap between predicted and actual building performance impacts building design, operations, and grid demand management programs. Through analyses of smart thermostat data from 1,400 single-occupant homes, the researchdemonstrates that occupants respond to 8°F thermostat setpoint changes within a median of 15 minutes, while 2°F changes trigger responses within a median of 30 minutes. This highlights an understudied temporal relationship between thermostat setbacks and response time of occupant behaviors. Models of such behavior dynamics are required to incorporate occupant impacts into building performance simulation. A key contribution of this dissertation is the Thermal Frustration Theory (TFT), which positsthat thermal discomfort driven behaviors are caused by the time-accumulation of discomfort, not simply a temperature deviation threshold or a delay from an initiating event. Using a dataset of 634 thermostats, each with 25+ manual setpoint changes, a comparative analysis of TFT and comfort zone and a delayed response theories demonstrated that personalized TFT models better predict when manual setpoint change occur. This was measured by the area under the curve statistical measure (AUC); all three models perform similarly by a Matthews Correlation Coefficient measure. Higher AUC performance is especially important for modeling occupant behavior in demand response programs where false negatives of rare occupant interactions could adversely affect grid stability. EnergyPlus based simulations were conducted with TFT-derived occupant models, demonstrating the ability to identify parameters of known TFT models from only data observable with smart thermostats, even under the presence of noise from routine overrides. Overall, the dissertation highlights that thermostat interactions are neither static,instantaneous, nor driven solely by the environment. Instead, temporal accumulation of discomfort and routine-based behavior play important roles. The methodology and results offer a pathway towards more accurate modeling of human-building interactions for policy assessment, building design, and demand response programs.

Sharma, Kunind [Northeastern University] (ORCID:00↗
DOE OSTI2021

Assimilation of citizen science data in snowpack modeling using a new snow data set: Community Snow Observations

A physically based snowpack evolution and redistribution model was used to test the effectiveness of assimilating crowd-sourced snow depth measurements collected by citizen scientists. The Community Snow Observations project gathers, stores, and distributes measurements of snow depth recorded by recreational users and snow professionals in high mountain environments. These citizen science measurements are valuable since they come from terrain that is relatively undersampled and can offer in situ snow information in locations where snow information is sparse or nonexistent. The present study investigates (1) the improvements to model performance when citizen science measurements are assimilated, and (2) the number of measurements necessary to obtain those improvements. Model performance is assessed by comparing time series of observed (snow pillow) and modeled snow water equivalent values, by comparing spatially distributed maps of observed (remotely sensed) and modeled snow depth, and by comparing fieldwork results from within the study area. The results demonstrate that few citizen science measurements are needed to obtain improvements in model performance, and these improvements are found in 62 % to 78 % of the ensemble simulations, depending on the model year. Model estimations of total water volume from a subregion of the study area also demonstrate improvements in accuracy after CSO measurements have been assimilated. These results suggest that even modest measurement efforts by citizen scientists have the potential to improve efforts to model snowpack processes in high mountain environments, with implications for water resource management and process-based snow modeling.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Efficient data-driven models for prediction and optimization of geothermal power plant operations

Increasing the capacity of geothermal energy as a renewable resource calls for development and deployment of efficient control and optimization technologies for geothermal power plants. A data-driven prediction and optimization model is presented as a cost-effective and efficient alternative to physics-based approach. The model predicts power output and operational cost by propagating the influence of control and disturbance variables within an artificial neural network (ANN). Numerical experiments with simulated and field data from a real geothermal power plant are first used to demonstrate the prediction performance of the ANN model. The model is then adopted to maximize the net predicted power production by automatically adjusting the working fluid circulation rate. The optimization performance of the model in evaluated using a thermodynamic flowsheet simulation model. The workflow is applied to model and control the effect of ambient temperature on an air-cooled binary cycle power plant, which is complex and costly to perform using a physics-based predictive model. As a result, the performance of the method is demonstrated by applying it to both simulated and field datasets from a binary cycle geothermal power plant.

15 GEOTHERMAL ENERGY↗
DOE OSTI2022

The Dark Machines Anomaly Score Challenge: Benchmark Data and Model Independent Event Classification for the Large Hadron Collider

We describe the outcome of a data challenge conducted as part of the Dark Machines (https://www.darkmachines.org) initiative and the Les Houches 2019 workshop on Physics at TeV colliders. The challenged aims to detect signals of new physics at the Large Hadron Collider (LHC) using unsupervised machine learning algorithms. First, we propose how an anomaly score could be implemented to define model-independent signal regions in LHC searches. We define and describe a large benchmark dataset, consisting of >1 billion simulated LHC events corresponding to 10\, fb^{-1} 10 f b − 1 of proton-proton collisions at a center-of-mass energy of 13 TeV. We then review a wide range of anomaly detection and density estimation algorithms, developed in the context of the data challenge, and we measure their performance in a set of realistic analysis environments. We draw a number of useful conclusions that will aid the development of unsupervised new physics searches during the third run of the LHC, and provide our benchmark dataset for future studies at https://www.phenoMLdata.org. Code to reproduce the analysis is provided at https://github.com/bostdiek/DarkMachines-UnsupervisedChallenge.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Equation-based and data-driven modeling: Open-source software current state and future directions

Here, a review of current trends in scientific computing reveals a broad shift to open-source and higher-level programming languages such as Python and growing career opportunities over the next decade. Open-source modeling tools accelerate innovation in equation-based and data-driven applications. Significant resources have been deployed to develop data-driven tools (PyTorch, TensorFlow, Scikit-learn) from tech companies that rely on machine learning services to meet business needs while keeping the foundational tools open. Open-source equation-based tools such as Pyomo, CasADi, Gekko, and JuMP are also gaining momentum according to user community and development pace metrics. Integration of data-driven and principles-based tools is emerging. New compute hardware, productivity software, and training resources have the potential to radically accelerate progress. However, long-term support mechanisms are still necessary to sustain the momentum and maintenance of critical foundational packages.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Hysteretic temperature sensitivity of wetland CH4 fluxes explained by substrate availability and microbial activity: Model Archive

This Modeling Archive is in support of an NGEE Arctic publication "Hysteretic temperature sensitivity of wetland CH4 fluxes explained by substrate availability and microbial activity" in the Journal Biogeosciences (https://doi.org/10.5194/bg-17-5849-2020), which includes the model data used in the publication. CH4 emissions from terrestrial systems are posited to increase, which can offset mitigation efforts and accelerate climate change. Yet, the accuracy of modeled CH4 emissions is sensitive to the prescribed CH4 production (or emission) temperature dependencies that are currently uncertain. Here, we use a comprehensive biogeochemistry model (ecosys) to investigate factors modulating CH4 production and emission rates across a permafrost thaw gradient encompassing a partly thawed bog and a fully thawed fen. We find that seasonally varying substrate availability drives lower and higher modeled methanogen biomass and activity, and thereby CH4 production, during the earlier and later periods of the thawed season, respectively. Package follows the Model data archiving guidelines with data in a *.zip file with three subfolders containing *.csv files and raw model output files; a data dictionary table (data_dictionary.csv) and two model output description tables (ecosys_plantspecies_output_notes.csv and ecosys_soil_ouput_notes.csv) to explain the format and meaning of individual output variables; and a user guide as a *.pdf. A detailed model description can be found in the supplement of (Grant, 2013). The ecosys source code is available at https://doi:10.5281/zenodo.3906642. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Large-Scale Visualization of 3D Unstructured Groundwater Model Using Cave Automated Virtual Environment

The immersive three-dimensional (3D) virtual reality (VR) visualization of groundwater models allows us to deepen our understanding of aquifer systems and provide better solutions to present groundwater-related problems, such as groundwater recharge, water quality, and sustainability. Visualization assists in accurately developing groundwater models and revealing important subsurface features, including faulting, folding, and unconformity. However, assessing model accuracy poses challenges due to the complexity of geology and groundwater systems. This research demonstrates a workflow to visualize and analyze raw 3D unstructured groundwater model data using an immersive Cave Automated Virtual Environment (CAVE). To visualize the unstructured groundwater model data, the raw dataset is converted into interactive CAVE-compatible formats utilizing a set of tools: ParaView, Blender, and Unity. This enables researchers to immerse themselves in the data, identifying influential patterns and relationships. e resulting insights can inform the development of sophisticated machine-learning models for groundwater level prediction. The CAVE’s immersive capabilities allow intuitive exploration from various perspectives, providing a more holistic understanding of the factors affecting groundwater levels. These insights are crucial to improve predictive models. The CAVE results also facilitate collaborative analysis and have potential applications in training and education. is research demonstrates the value of immersive VR tools such as the CAVE for unraveling intricacies within high-dimensional scientific data to drive real-world forecasting and modeling applications.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Spin-Controllable Dynamics in Defect-Engineered Carbon Nanotubes as Single Photon Emitters: Data-Driven Modeling and Computations

Quantum technologies, such as quantum computing and sensing, require efficient single-photon emission (SPE) sources that operate at room temperature in telecom wavelengths. While several materials can serve as SPE sources, no single platform meets all the criteria for efficiency, ambient operation, and scalability. Single-walled carbon nanotubes (SWCNTs) with covalently attached molecules offer a promising solution. Their SPE can be easily tuned via modifications of the SWCNT's diameter, chirality, and bonded molecules, enabling emission across near-IR to telecom wavelengths at ambient conditions. However, to fully realize the potential of SWCNTs and unlock their quantum capabilities, a deeper understanding of how structural defects from molecular adducts affect their emission and competing photoexcited processes is essential. To address this gap in our knowledge, this project combined quantum chemistry calculations with data-driven methods of cheminformatics (QSAR) and machine learning (ML). The developed computational approaches have provided several design strategies for covalent functionalization of SWCNTs to improve their optical response. The collaboration with Los Alamos National Lab (LANL) enabled direct comparison of computational and experimental data, facilitating method validation. This partnership was enhanced through access to LANL's Center for Integrated Nanotechnologies (CINT) utilizing User Facility Program and summer internships, which provided three NDSU graduate students with hands-on experience at LANL. The outcomes of this project included (1) Advancing the current stage of computational methods in accurate modeling of non-adiabatic spin-dependent photoexcited dynamics and its applicability to nanosystems consisting of thousands of atoms, realized as open-access codes linked to existing DFT-based software; (2) Establishing the relationship between the structure of adducts and SWCNTs and intrinsic excitonic and spin properties of defect states for guiding novel synthetic strategies and experimental probes of chemically functionalized SWCNTs as near-IR emitting materials; (3) Generating virtual libraries of hypothetical functionalized SWCNTs for virtual screening of their chemical structures and optical properties, leveraging new functionalities of SWCNTs; (4) Offering a unique experience for NDSU graduate students that prepared them for future scientific careers related to materials modeling and big data processing. These results were summarized in 12 published journal papers and 3 recently submitted papers. One of a key finding is that the position of defect sites on the SWCNT surface primarily drives the emission redshift (up to 100 meV), while the polarity of the defect-inducing molecules has a much smaller effect (~10 meV). However, the electron-donating or withdrawing properties of a molecule influence selecting reactivity of defect sites. These insights important for optimizing synthetic protocols for desired emissions in SWCNTs. We also revealed that the interaction between two defects at various positions on the SWCNT enhances the redshift and optical activity of states, favoring strong near-IR emission. This suggests that manipulations in defect concentrations is a promising strategy for controlling efficient emission. Mostly important, the defect position was found controllable by the spin states of photoexcited intermediates: Excited aromatic molecules form ortho defects with SWCNTs at their singlet states in the presence of oxygen, while oxygen-free conditions favor para defects via the triplet-state mechanism. Additionally, a heat-activated [2+2] cycloaddition reaction facilitates divalent defect formation with fewer bonding positions that narrows emission bands. These groundbreaking findings have been experimentally validated and significantly advance our understanding of defect chemistry in SWCNTs. Using a novel encoding technique and 3D-MoRSE descriptors, we developed highly accurate ML/QSAR models to predict both the 3D structure and optical properties of SWCNTs with chemical defects. This model enabled the creation of a virtual library of 125,556 structures, providing new insights into the relationship between SWCNT-defect structure and emission.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2026

ZENN: A thermodynamics-inspired computational framework for heterogeneous data–driven modeling

Traditional entropy-based methods—such as cross-entropy loss in classification problems—have long been essential tools for representing the information uncertainty and physical disorder in data and for developing artificial intelligence algorithms. However, the rapid growth of data across various domains has introduced new challenges, particularly the integration of heterogeneous datasets with intrinsic disparities. To address this, we introduce a zentropy-enhanced neural network (ZENN), extending zentropy theory into the data science domain via intrinsic entropy, enabling more effective learning from heterogeneous data sources. ZENN simultaneously learns both energy and intrinsic entropy components, capturing the underlying structure of multisource data. To support this, we redesign the neural network architecture to better reflect the intrinsic properties and variability inherent in diverse datasets. We demonstrate the effectiveness of ZENN on classification tasks and energy landscape reconstructions, showing its superior generalization capabilities and robustness-particularly in predicting high-order derivatives. In image and text classification tasks, ZENN demonstrates superior generalization by introducing a learnable temperature variable that models latent multisource heterogeneity, allowing it to surpass state-of-the-art models on CIFAR-10/100, BBC News, and AG News. As a practical application in materials science, we employ ZENN to reconstruct the Helmholtz energy landscape of Fe3Pt using data generated from density functional theory and capture key material behaviors, including negative thermal expansion and the critical point in the temperature–pressure space. Overall, this work presents a zentropy-grounded framework for data-driven machine learning, positioning ZENN as a versatile and robust approach for scientific problems involving complex, heterogeneous datasets.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Data-driven models of nonautonomous systems

Nonautonomous dynamical systems are characterized by time-dependent inputs, which complicates the discovery of predictive models describing the spatiotemporal evolution of the state variables of quantities of interest from their temporal snapshots. When dynamic mode decomposition (DMD) is used to infer a linear model, this difficulty manifests itself in the need to approximate the time-dependent Koopman operators. Our approach is to approximate the original nonautonomous system with a modified system derived via a local parameterization of the time-dependent inputs. The modified system comprises a sequence of local parametric systems, which are subsequently approximated by a parametric surrogate model using the DRIPS (dimension reduction and interpolation in parameter space) framework. The offline step of DRIPS relies on DMD to build a linear surrogate model, endowed with reduced-order bases for the observables mapped from training data. The online step interpolates on suitable manifolds to construct a sequence of iterative parametric surrogate models; the target/test parameter points on these manifolds are specified by a local parameterization of the test time-dependent inputs. Here, we use numerical experimentation to demonstrate the robustness of our method and compare its performance with that of deep neural networks.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Development of a New Chelation Model: Bioassay Data Interpretation and Dose Assessment after Plutonium Intake via Wound and Treatment with DTPA

The administration of chelation therapy to treat significant intakes of actinides, such as plutonium, affects the actinide’s normal biokinetics. In particular, it enhances the actinide’s rate of excretion, such that the standard biokinetic models cannot be applied directly to the chelation-affected bioassay data in order to estimate the intake and assess the radiation dose. Here we propose a new chelation model that can be applied to the chelation-affected bioassay data after plutonium intake via wound and treatment with DTPA. In the proposed model, chelation is assumed to occur in the blood, liver, and parts of the skeleton. Ten datasets, consisting of measurements of 14 C-DTPA, 238 Pu, and 239 Pu involving humans given radiolabeled DTPA and humans occupationally exposed to plutonium via wound and treated with chelation therapy, were used for model development. The combined dataset consisted of daily and cumulative excretion (urine and feces), wound counts, measurements of excised tissue, blood, and post-mortem tissue analyses of liver and skeleton. The combined data were simultaneously fit using the chelation model linked with a plutonium systemic model, which was linked to an ad hoc wound model. The proposed chelation model was used for dose assessment of the wound cases used in this study.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Reliable Integration of AI Data Centers at Scale – Analysis, Modeling and Synthetic Data Generation

This report analyzes the power consumption of large dynamic digital loads using the open-source MIT supercloud and SURF datasets. With an emphasis on the MIT data, we calculate important power consumption characteristics to help system operators improve generation planning and resource allocation. We also introduce a rudimentary model for generating synthetic load profiles.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Alaskan carbon-climate feedbacks will be weaker than inferred from short-term manipulations: Alaskan Benchmark Data and Model runs

This submission aimed to assess differences in short-term step warming manipulations and long-term chronic response to climate change in Alaskan ecosystems. Briefly, climate warming is occurring fastest at high latitudes. Based on short-term field experiments, this warming is projected to stimulate soil organic matter decomposition, and promote a positive feedback to climate change. We show here that the tightly coupled, nonlinear nature of high-latitude ecosystems implies that short-term (< 10 year) warming experiments produce emergent ecosystem carbon stock temperature sensitivities inconsistent with emergent multi-decadal responses. We first demonstrate that a well-tested mechanistic ecosystem model accurately represents observed carbon cycle and active layer depth responses to short-term summer warming in four diverse Alaskan sites. We then show that short-term warming manipulations do not capture the non-linear, long-term dynamics of vegetation, and thereby soil organic matter, that occur in response to thermal, hydrological, and nutrient transformations belowground. Our results demonstrate significant spatial heterogeneity in multi-decadal Arctic carbon cycle trajectories and argue for more mechanistic models to improve predictive capabilities.The model used in the current study is available publicly (https://github.com/jinyun1tang/ECOSYS), and the current submission contains the python/ matlab codes for analyzing output from the model (includng a readme file to explain the codes). The benchmark data, also enclosed, was collected from a range of published and publicly available sources (extracted using GRABIT: https://www.mathworks.com/matlabcentral/fileexchange/7173-grabit). These sources describe warming induced changes in tundra/ boreal ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Data-driven modeling of power generation for a coal power plant under cycling

Increased penetration of renewables for power generation has negatively impacted the dynamics of conventional fossil fuel-based power plants. The power plants operating on the base load are forced to cycle, to adjust to the fluctuating power demands. This results in an inefficient operation of the coal power plants, which leads up to higher operating losses. To overcome such operational challenge associated with cycling and to develop an optimal process control, this work analyzes a set of models for predicting power generation. Moreover, the power generation is intrinsically affected by the state of the power plant components, and therefore our model development also incorporates additional power plant process variables while forecasting the power generation. We present and compare multiple state-of-the-art forecasting data-driven methods for power generation to determine the most adequate and accurate model. We also develop an interpretable attention-based transformer model to explain the importance of process variables during training and forecasting. The trained deep neural network (DNN) LSTM model has good accuracy in predicting gross power generation under various prediction horizons with/without cycling events and outperforms the other models for long-term forecasting. The DNN memory-based models show significant superiority over other state-of-the-art machine learning models for short, medium and long range predictions. The transformer-based model with attention enhances the selection of historical data for multi-horizon forecasting, and also allows to interpret the significance of internal power plant components on the power generation. This newly gained insights can be used by operation engineers to anticipate and monitor the health of power plant equipment during high cycling periods.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2026

Finding the missing pieces: filling gaps that impede the translation of omics data into models

High-throughput omics technologies such as DNA sequencing have made the sequencing and computational assembly of microbial genomes recovered from the environment relatively routine. Computational inference of the protein products encoded by these genomes, and the associated biochemical functions, should enable the accurate prediction and modeling of microbial metabolism, organismal interactions, and ecosystem processes. However, a lack of scalable, probabilistic protein annotation tools limits the full potential of modeling for understanding the metabolism and biogeochemical cycles of microbial communities. Our approach to improve inference of protein annotations and metabolic models relied on learning from and emulating expert manual curation, leveraging software engineering and data science best practices to scale up the throughput and accuracy of annotations and metabolic model construction, building software to objectively evaluate different annotation strategies, and more closely linking the protein annotation and metabolic model inference process. Outcomes of this research include several improved or new computational tools, including DRAM (Distilled and Refined Annotation of Metabolism) for annotating microbial genomes with protein function and metabolic traits, CAMPER (Curated Annotations for Microbial Polyphenol Enzymes and Reactions) for annotating key polyphenol metabolisms, EC-Bench for comprehensive and unbiased benchmarking of annotation tools, and several apps available via the DOE Systems Biology Knowledgebase (KBase) for building genome-scale metabolic models. We demonstrate that these tools allow us to scalably annotate and understand thousands of genomes for microbial communities from a variety of systems and test cases, including rivers, thawing permafrost, and gut microbiomes. All of these computational tools are available as open-source software, with most broadly and easily accessible to the scientific community via KBase apps.

59 BASIC BIOLOGICAL SCIENCES↗