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merlin , an improved framework for the reconstruction of high-quality genome-scale metabolic models

Abstract Genome-scale metabolic models have been recognised as useful tools for better understanding living organisms’ metabolism. merlin (https://www.merlin-sysbio.org/) is an open-source and user-friendly resource that hastens the models’ reconstruction process, conjugating manual and automatic procedures, while leveraging the user's expertise with a curation-oriented graphical interface. An updated and redesigned version of merlin is herein presented. Since 2015, several features have been implemented in merlin, along with deep changes in the software architecture, operational flow, and graphical interface. The current version (4.0) includes the implementation of novel algorithms and third-party tools for genome functional annotation, draft assembly, model refinement, and curation. Such updates increased the user base, resulting in multiple published works, including genome metabolic (re-)annotations and model reconstructions of multiple (lower and higher) eukaryotes and prokaryotes. merlin version 4.0 is the only tool able to perform template based and de novo draft reconstructions, while achieving competitive performance compared to state-of-the art tools both for well and less-studied organisms.

Capela, João (ORCID:0000000212352922)↗

LSKnowledge: Nexus for Transformative Scientific Discoveries and Enhanced Information Retrieval in NASA Life Sciences Portal

We stand at the brink of an extraordinary transformation in the field of AI, driven by the convergence of generative AI and semantic technologies (e.g., knowledge graphs). This fusion holds immense potential and could redefine the future of scientific exploration, particularly in the realm of life sciences research. In this context, we shed light on the pivotal roles that Large Language Models (LLMs) and semantic technologies will play in advancing research, unearthing and comprehending life sciences information through innovative approaches, and empowering researchers to extract insights from NASA's extensive Life Sciences Data Archive. Within the NASA Life Sciences Portal (NLSP), the integration of LLMs and semantic technologies unlocks several advanced capabilities. First and foremost, it equips scientists with sophisticated tools to manage the ever-expanding wealth of scientific literature and data. Furthermore, it facilitates the creation of knowledge graphs that visually represent intricate relationships among biological entities, enabling comprehensive systems-level analysis. Additionally, the fusion of generative AI (including LLMs) and semantic technology can significantly benefit NASA's life sciences research by enhancing information retrieval and hypothesis generation. These tools enhance natural language understanding, facilitating knowledge discovery within NLSP. The overarching vision is to establish a cohesive knowledge ecosystem within NLSP, harnessing the power of LLMs and semantic technologies to synthesize and cross-reference data from diverse missions, disciplines, and research domains. This holistic approach ultimately deepens our understanding of how space environments impact life sciences data. To advance this initiative, we have launched LSKnowledge, aimed at enhancing the information retrieval capabilities of NLSP. In the short term, our primary goal is to develop a robust semantic search system. This system will empower HRP (Human Research Program) researchers to navigate NLSP data repositories more efficiently and precisely, catalyzing the process of hypothesis formation and scientific breakthroughs. To achieve this, we have employed pre-trained LLMs as part of a semantic search tool that can rank and highlight the most relevant records for user queries. To assess the tool's performance, we have curated a set of approximately 200 queries from subject matter experts (SMEs) and manually ranked the top records retrieved by both the current search system and the new semantic search, using SME judgments as the gold standard for relevancy. Herein, we present the results of our comparative analysis and illustrate how these findings have informed the fine-tuning of the system for enhanced performance. In the long term, our objectives include 1) retrieving publicly available information and integrating it with NLSP data to provide more precise answers to user queries, and 2) incorporating non-textual information from the NLSP database into our approach. In conclusion, the fusion of LLMs and semantic technologies within NLSP represents a pioneering stride towards reshaping the landscape of scientific discovery. This synergy not only equips researchers with powerful tools to navigate the burgeoning sea of information but also facilitates a deeper understanding of complex biological relationships, all while accelerating hypothesis generation and knowledge discovery. Through our initiative, LSKnowledge, we are committed to continually refining and expanding these capabilities, with the aim of not only enhancing information retrieval but also integrating diverse data sources to provide more precise insights. In the grand vision, NLSP strives to become the cornerstone of a comprehensive knowledge ecosystem, unraveling the enigmatic intricacies of life sciences phenomena in the context of space environments.

Life Sciences↗

Meca500 Robotic Arm Developments Towards Astromaterials Curation Applications

As a part of the ongoing efforts to develop new curation tools and techniques for astromaterials within the Astromaterials Acquisition and Curation office at NASA’s Johnson Space Center, we are developing a variety of manually and electrically controlled micromanipulation systems. Most current techniques require manual manipulation, and in some cases the manipulation task is being done entirely freehand. The motorized systems avail-able are restricted to three degrees of freedom and use proprietary control systems. For example, the MicroSupport AxisPro manipulation system currently used in microscale particle experiments is limited in its range of motion, as it can only move the manipulators in a three axis Cartesian range over a predetermined area above microscope slides. While having an efficient user interface, the control system is proprietary and prevents custom development and optimization to extend the viable applications of the system. In order to address some of these limitations, we have been testing robotic designs with multiple degrees of freedom and of a variety of designs. We are currently investigating the Meca500 robotic arm by Mecademic as a potential manipulation system to overcome some of these obstacles.

Cowden, T. R.↗

Data Albums: An Event Driven Search, Aggregation and Curation Tool for Earth Science

Approaches used in Earth science research such as case study analysis and climatology studies involve discovering and gathering diverse data sets and information to support the research goals. To gather relevant data and information for case studies and climatology analysis is both tedious and time consuming. Current Earth science data systems are designed with the assumption that researchers access data primarily by instrument or geophysical parameter. In cases where researchers are interested in studying a significant event, they have to manually assemble a variety of datasets relevant to it by searching the different distributed data systems. This paper presents a specialized search, aggregation and curation tool for Earth science to address these challenges. The search rool automatically creates curated 'Data Albums', aggregated collections of information related to a specific event, containing links to relevant data files [granules] from different instruments, tools and services for visualization and analysis, and information about the event contained in news reports, images or videos to supplement research analysis. Curation in the tool is driven via an ontology based relevancy ranking algorithm to filter out non relevant information and data.

Ramachandran, Rahul↗

ES2Vec: Earth Science Metadata Suggestions and Analogical Reasoning

As the volume of text-based Earth science research grows, it is increasingly possible to discover latent relationships in the literature. However, traditional methodologies are restricted by limited computational capabilities and intractable problem spaces. Advancements in natural language processing (NLP) have allowed us to use an extensive Earth science corpus to create a domain-specific word vector model, Es2Vec, which we have used to surface latent relationships between Earth science concepts and generate improved keyword tags. Earth science metadata keyword assignment is a challenging problem. Dataset curators select appropriate keywords from the Global Change Master Directory (GCMD) set of keywords. The keywords an are integral part of the search and discovery of these datasets. Hence, the selection of keywords is crucial to increasing the discoverability of datasets. Utilizing machine learning techniques, we provide users with automated keyword suggestions to complement manual selection. We trained a machine learning model that leverages the semantic embedding ability of Word2Vec models to process abstracts and suggest relevant keywords. A user interface tool we built to assist data curators in the assignment of such keywords is also described.

word vectors↗

Event Log / Raw Data

The WFIP3 event log is a curated record spanning 578 days of meteorological phenomena and field observations that complements the campaign’s high-frequency measurements. The log combines manually documented daily weather discussions with automatically derived indicators of key atmospheric processes, providing standardized, publicly available context to support model evaluation, forecast verification, and case-study selection for offshore boundary-layer research.

17 WIND ENERGY↗

Populating a Graph Database to Run a Usage-Based Discovery Tool

Most dataset discovery tools for Earth Observation data rely on descriptions and other metadata of the datasets, using keyword searches or attribute filtering to determine relevance. However, these descriptions often do not include the potential uses of the data. Thus, a user working on floods will rarely see few if any rainfall datasets show up in such a search. The Usage Based Discovery tool, on the other hand, offers usage instances to the user, either research articles or applications, along with the datasets that those usage instances used. This allows a user, particularly one new to the world of Earth Observation data, to investigate which datasets are used in similar cases. The information that powers Usage-Based Discovery is a graph database of relationships of usage to dataset and usage to topic, allowing the user to narrow their search for similar cases. In order to scale out to a graph database rich enough to provide a satisfactory user experience, we combine manual and automated processes to populate the graph. The initial content of the graph has been seeded primarily via human-aided data curation methods, using sites like Google Scholar. To scale up this effort, we’ve employed crowdsourcing. It is easy for anyone to contribute to our graph using their Open Researcher and Contributor Identifier for authorization. We’re now experimenting with Machine Learning and Natural Language Processing to help automate population of the graph, starting with the classification of research articles by topic. Finding adequate training data in the absence of a comprehensive and open research article API continues to be a significant challenge.

Vincent Inverso↗

BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. Furthermore, we observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

97 MATHEMATICS AND COMPUTING↗

Large language model-driven database for thermoelectric materials

Thermoelectric materials have the ability to convert waste heat into electricity, offering a valuable solution for energy harvesting. However, their widespread use is hindered by low conversion efficiency, the reliance on expensive rare earth elements, and the environmental and regulatory concerns associated with lead-based materials. A fast and cost-effective way to identify highly efficient thermoelectric materials is through data-driven methods. These approaches rely on robust and comprehensive datasets to train models. Although there are several databases on thermoelectric materials, there is still a need to collect and integrate experimental data from peer-reviewed research articles to capture diverse compositions and properties of materials. Here, in this work, we developed a comprehensive database of 7,123 thermoelectric compounds, containing key information such as chemical composition, structural detail, seebeck coefficient, electrical and thermal conductivity, power factor, and figure of merit (ZT). We used the GPTArticleExtractor workflow, powered by large language models (LLM), to extract and curate data automatically from the scientific literature published in Elsevier journals. This process enabled the creation of a structured database that addresses the challenges of manual data collection. The open access database could stimulate data-driven research and advance thermoelectric material analysis and discovery.

Database↗

A total of 19 months of daily weather logging on the US east coast: the WFIP3 event log

The Third Wind Forecast Improvement Project (WFIP3) is a multi-institutional field campaign designed to advance the understanding and prediction of the offshore atmospheric boundary layer along the US east coast. Extending from February 2024 through August 2025, WFIP3 combines long-term coastal and offshore measurements with targeted modeling and forecasting efforts. This data paper presents the WFIP3 event log, a curated record of 578 d of meteorological phenomena and field observations that complements the campaign's extensive high-frequency datasets. The event log provides both manually documented daily weather discussions and automatically derived indicators of atmospheric processes – including low-level jets, wind ramps, extreme wind veer, and weak wind conditions – based on observations from scanning lidars deployed at three coastal and offshore sites. The dataset offers structured metadata, standardized time and site identifiers, and consistent terminology to facilitate its integration with WFIP3's observational and modeling data products. The log supports diverse applications, from model evaluation and forecast verification to the selection of case studies on offshore boundary-layer dynamics. The WFIP3 event log is publicly available through the US Department of Energy's Wind Data Hub, providing the research community with a transparent and enduring contextual reference for the interpretation and use of WFIP3 measurements.

17 WIND ENERGY↗

Automated annotation of scientific texts for ML-based keyphrase extraction and validation

Advanced omics technologies and facilities generate a wealth of valuable data daily; however, the data often lack the essential metadata required for researchers to find, curate, and search them effectively. The lack of metadata poses a significant challenge in the utilization of these data sets. Machine learning (ML)–based metadata extraction techniques have emerged as a potentially viable approach to automatically annotating scientific data sets with the metadata necessary for enabling effective search. Text labeling, usually performed manually, plays a crucial role in validating machine-extracted metadata. However, manual labeling is time-consuming and not always feasible; thus, there is a need to develop automated text labeling techniques in order to accelerate the process of scientific innovation. This need is particularly urgent in fields such as environmental genomics and microbiome science, which have historically received less attention in terms of metadata curation and creation of gold-standard text mining data sets. In this paper, we present two novel automated text labeling approaches for the validation of ML-generated metadata for unlabeled texts, with specific applications in environmental genomics. Our techniques show the potential of two new ways to leverage existing information that is only available for select documents within a corpus to validate ML models, which can then be used to describe the remaining documents in the corpus. The first technique exploits relationships between different types of data sources related to the same research study, such as publications and proposals. The second technique takes advantage of domain-specific controlled vocabularies or ontologies. In this paper, we detail applying these approaches in the context of environmental genomics research for ML-generated metadata validation. Our results show that the proposed label assignment approaches can generate both generic and highly specific text labels for the unlabeled texts, with up to 44% of the labels matching with those suggested by a ML keyword extraction algorithm.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

LLM Generation of Online Courses from a Curated Set of Documents in the Nuclear Safeguards Domain

A multidisciplinary team at Argonne National Laboratory explores the application of advanced technologies to enhance knowledge transfer and retention within the nuclear safeguards domain. Specifically, it examines the feasibility of leveraging secure large language models (LLMs) to streamline the creation of e-learning modules for the U.S. National Nuclear Security Administration (NNSA) Office of International Nuclear Safeguards (NA-241). The initiative addresses the critical need for preserving institutional memory and accelerating skill development amidst the imminent retirement of senior professionals in the field in addition to supporting good knowledge management practices. The project integrates instructional design theory with cutting-edge AI technologies to transform curated document sets from the Safeguards Knowledge Repository (SKR) into modular online courses. By automating the generation of learning objectives and instructional content, the effort aims to reduce manual effort while maintaining high-quality educational outcomes. A limited measure of human supervision, however, ensures accuracy, relevance, and alignment with NNSA’s strategic priorities. Key findings highlight the potential of AI-assisted course generation to support safeguards professionals by creating structured, interactive learning experiences. The report underscores the importance of SME validation to address limitations in AI-generated content, such as terminology errors and gaps in coverage. Recommendations include adopting a structured workflow combining LLM acceleration with expert oversight to ensure accuracy, usability, and alignment with learner needs. This work demonstrates Argonne’s commitment to advancing national security and scientific excellence through innovative knowledge management solutions.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Contrastive Machine Learning with Gamma Spectroscopy Data Augmentations for Detecting Shielded Radiological Material Transfers

Data analysis techniques can be powerful tools for rapidly analyzing data and extracting information that can be used in a latent space for categorizing observations between classes of data. Machine learning models that exploit learned data relationships can address a variety of nuclear nonproliferation challenges like the detection and tracking of shielded radiological material transfers. The high resource cost of manually labeling radiation spectra is a hindrance to the rapid analysis of data collected from persistent monitoring and to the adoption of supervised machine learning methods that require large volumes of curated training data. Instead, contrastive self-supervised learning on unlabeled spectra can enhance models that are built on limited labeled radiation datasets. This work demonstrates that contrastive machine learning is an effective technique for leveraging unlabeled data in detecting and characterizing nuclear material transfers demonstrated on radiation measurements collected at an Oak Ridge National Laboratory testbed, where sodium iodide detectors measure gamma radiation emitted by material transfers between the High Flux Isotope Reactor and the Radiochemical Engineering Development Center. Label-invariant data augmentations tailored for gamma radiation detection physics are used on unlabeled spectra to contrastively train an encoder, learning a complex, embedded state space with self-supervision. A linear classifier is then trained on a limited set of labeled data to distinguish transfer spectra between byproducts and tracked nuclear material using representations from the contrastively trained encoder. The optimized hyperparameter model achieves a balanced accuracy score of 80.30%. Any given model—that is, a trained encoder and classifier—shows preferential treatment for specific subclasses of transfer types. Regardless of the classifier complexity, a supervised classifier using contrastively trained representations achieves higher accuracy than using spectra when trained and tested on limited labeled data.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Use of Semantic Technology to Create Curated Data Albums

One of the continuing challenges in any Earth science investigation is the discovery and access of useful science content from the increasingly large volumes of Earth science data and related information available online. Current Earth science data systems are designed with the assumption that researchers access data primarily by instrument or geophysical parameter. Those who know exactly the data sets they need can obtain the specific files using these systems. However, in cases where researchers are interested in studying an event of research interest, they must manually assemble a variety of relevant data sets by searching the different distributed data systems. Consequently, there is a need to design and build specialized search and discover tools in Earth science that can filter through large volumes of distributed online data and information and only aggregate the relevant resources needed to support climatology and case studies. This paper presents a specialized search and discovery tool that automatically creates curated Data Albums. The tool was designed to enable key elements of the search process such as dynamic interaction and sense-making. The tool supports dynamic interaction via different modes of interactivity and visual presentation of information. The compilation of information and data into a Data Album is analogous to a shoebox within the sense-making framework. This tool automates most of the tedious information/data gathering tasks for researchers. Data curation by the tool is achieved via an ontology-based, relevancy ranking algorithm that filters out nonrelevant information and data. The curation enables better search results as compared to the simple keyword searches provided by existing data systems in Earth science.

Ramachandran, Rahul↗

Use of Semantic Technology to Create Curated Data Albums

One of the continuing challenges in any Earth science investigation is the discovery and access of useful science content from the increasingly large volumes of Earth science data and related information available online. Current Earth science data systems are designed with the assumption that researchers access data primarily by instrument or geophysical parameter. Those who know exactly the data sets they need can obtain the specific files using these systems. However, in cases where researchers are interested in studying an event of research interest, they must manually assemble a variety of relevant data sets by searching the different distributed data systems. Consequently, there is a need to design and build specialized search and discovery tools in Earth science that can filter through large volumes of distributed online data and information and only aggregate the relevant resources needed to support climatology and case studies. This paper presents a specialized search and discovery tool that automatically creates curated Data Albums. The tool was designed to enable key elements of the search process such as dynamic interaction and sense-making. The tool supports dynamic interaction via different modes of interactivity and visual presentation of information. The compilation of information and data into a Data Album is analogous to a shoebox within the sense-making framework. This tool automates most of the tedious information/data gathering tasks for researchers. Data curation by the tool is achieved via an ontology-based, relevancy ranking algorithm that filters out non-relevant information and data. The curation enables better search results as compared to the simple keyword searches provided by existing data systems in Earth science.

Ramachandran, Rahul↗

COVID-19 Data Curation Effort: An Initial Analysis of the Data

During the COVID-19 pandemic of 2020, major case reporting outlets quickly coalesced around two or three primary vendors. Johns Hopkins University and The New York Times were among the more prominent, and all were of great value to the nation, particularly during the uncertain early stages of the pandemic. They primarily focused on three major attributes: number of new cases, deaths, and recovery. Recognizing that many states were reporting very detailed data sets (e.g., hospital beds) at a county level or finer, the ORNL Pandemic Modeling team embarked on a major data curation effort from March to June 2020 for the purpose of capturing this wealth of detailed data. The challenge of curating this data was daunting. The number of attributes reported by the states grew on almost on a weekly basis. States were routinely shifting their web tool strategies away from easily parsable HTML-based formatting to new Tableau and ArcGIS content. This growth in the sheer number of attributes, combined with the unpredictable shifts in data format, meant an aggressive and agile combination of automated scripting and manual scraping was required to capture new daily streams. Further, the team had to scale up staff and widen its approach for capture and storage. As a result, the team collected more than 11 million data points. Following the close of this data collection effort on June 30 th , 2020, the team embarked on a major effort to appraise what had been collected, including an inventory list, spatial completeness, temporal completeness, scale and geographic characteristics, and a determination. A report on this matter was submitted on September 15 th , 2020, titled “DOE COVID-19 Data Curation Effort: Overview of Data Collection Coverage”. Over 2000 unique attributes had been netted over a wide range of spatial scales, including state, county, zip codes, health regions, and census blocks. Over 11 million individual data points were collected across these attributes, and spatial coverage (in total) included all 50 states and multiple territories. What became apparent in the process is that in the absence of any data standards, many states reported a wide variety of unique attributes that were not always compatible with attributes reported in other states. As time continued, states began adding new attributes and offering finer grain detail in some older attributes. This meant that not all data streams existed for the entire time period; in fact, the number tended to increase dramatically towards the end. Often, states would begin an attribute series and then stop altogether. These highly variable and uncertain conditions illuminated the need for harmonization approaches that would reconcile and conflate changing attribute names and detail over time. For example, grouping racial data reported as either Black or African American, depending on the state, into a single harmonized attribute. These choices would make a within-state analysis possible during the time period and lead to potential between-state analytics later on. This was almost entirely a manual decision process, requiring some subjective decision-making at times, to prevent a fragmented, short-lived collection of time series fragments that would offer few insights into trends, patterns, and correlates. This report imports harmonized data for state and county into the World Spatio-Temporal Analytics and Mapping Project (WSTAMP). WSTAMP is a major space-time analysis and visualization tool developed at ORNL for the National Geospatial-Intelligence Agency specifically for this kind of exploratory analysis. WSTAMP offers a rich analytical and graphical environment consisting of a wide range of analytics. These include time series plots, statistical summaries, data mining techniques, trend and pattern detection, and hypothesis generation.

59 BASIC BIOLOGICAL SCIENCES↗

Electricity and natural gas tariffs at United States wastewater treatment plants

Abstract Wastewater treatment plants (WWTPs) are large electricity and natural gas consumers with untapped potential to recover carbon-neutral biogas and provide energy services for the grid. Techno-economic analysis of emerging energy recovery and management technologies is critical to understanding their commercial viability, but quantifying their energy cost savings potential is stymied by a lack of well curated, nationally representative electricity and natural gas tariff data. We present a dataset of electricity tariffs for the 100 largest WWTPs in the Clean Watershed Needs Survey (CWNS) and natural gas tariffs for the 54 of 100 WWTPs with on-site cogeneration. We manually collected tariffs from each utility’s website and implemented data checks to ensure their validity. The dataset includes facility metadata, electricity tariffs, and natural gas tariffs (where cogeneration is present). Tariffs are current as of November 2021. We provide code for technical validation along with a sample simulation.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

A Comprehensive Calibration Framework for the Northwest River Forecast Center

We present a comprehensive framework developed by the Northwest River Forecast Center for calibrating hydrologically diverse basins. The framework includes models for snow, soil moisture, routing, channel loss, and consumptive use. Data inputs include a wide range of open-access datasets for meteorology, land use, topography, and land cover. The framework uses conceptual hydrologic models to handle basins with various hydrologic regimes including rain-driven and snowmelt-dominated basins. We also develop a flexible automatic calibration system that can handle numerous unobservable model parameters in a computationally efficient manner. A single-basin automatic calibration run can typically be completed on a modern laptop in under 10 min. We found that model performance metrics for this new approach match the quality of the NWRFC's previous labor-intensive manual calibrations. The model performance also rivals that of a state-of-the-art deep learning model at a fraction of the computational cost. This framework presents a new standard for the quality of calibrations possible with lumped conceptual hydrologic models, combining careful data curation, an objective calibration framework, and expert local knowledge. In addition, we have made software packages available for the entire suite of National Weather Service River Forecast System models, including SAC-SMA, SNOW-17, and Lag-K. These modern interfaces are intended to increase accessibility and facilitate future research.

Forecasting↗