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DOE OSTI2024

BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data

Abstract BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, training of artificial intelligence models and computational chemistry methods development. This update reports significant growth and enhancements since our last review in 2016. Of note, the database now contains 2.9 million binding measurements spanning 1.3 million compounds and thousands of protein targets. This growth is largely attributable to our unique focus on curating data from US patents, which has yielded a substantial influx of novel binding data. Recent improvements include a remake of the website following responsive web design principles, enhanced search and filtering capabilities, new data download options and webservices and establishment of a long-term data archive replicated across dispersed sites. We also discuss BindingDB’s positioning relative to related resources, its open data sharing policies, insights gleaned from the dataset and plans for future growth and development.

Liu, Tiqing↗

DOE OSTI2023

Status of genome function annotation in model organisms and crops

Abstract Since the entry into genome‐enabled biology several decades ago, much progress has been made in determining, describing, and disseminating the functions of genes and their products. Yet, this information is still difficult to access for many scientists and for most genomes. To provide easy access and a graphical summary of the status of genome function annotation for model organisms and bioenergy and food crop species, we created a web application ( https://genomeannotation.rheelab.org ) to visualize, search, and download genome annotation data for 28 species. The summary graphics and data tables will be updated semi‐annually, and snapshots will be archived to provide a historical record of the progress of genome function annotation efforts. Clear and simple visualization of up‐to‐date genome function annotation status, including the extent of what is unknown, will help address the grand challenge of elucidating the functions of all genes in organisms.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Ground Source Heat Pump Screening Tool and Related Resources

This archive contains both a link to Oak Ridge National Laboratory's Ground Source Heat Pump (GSHP) Screening Tool and related resources documenting its development, technical features, and applications. The web-based screening tool is a techno-economic analysis resource designed to evaluate the feasibility, costs, and benefits of implementing GSHP systems in buildings across various U.S. climate zones. It is intended for use by building owners, HVAC system designers, and installers to support decision-making in residential and commercial applications, incorporating advanced modeling capabilities such as ground heat exchanger design. The included resources detail the tool's creation and use, covering topics such as innovative ground heat exchanger design methodologies, the development of an open library of g-functions for borehole configurations, and studies on GSHP performance and economic viability in retrofitting single-family homes.

15 GEOTHERMAL ENERGY↗

DOE OSTI2020

GlideinMonitor

This document describes GlideinMonitor. GlideinMonitor is a Web application that allows viewing of GlideinWMS’s Glidein log files: it provides a user interface, tools to do quick searches and to decode the log content; it provides an efficient managed archive of the log files and a framework to add log processing, e.g. log sanitation.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB

Abstract Motivation Membrane proteins are encoded by approximately one fifth of human genes but account for more than half of all US FDA approved drug targets. Thanks to new technological advances, the number of membrane proteins archived in the PDB is growing rapidly. However, automatic identification of membrane proteins or inference of membrane location is not a trivial task. Results We present recent improvements to the RCSB Protein Data Bank web portal (RCSB PDB, rcsb.org) that provide a wealth of new membrane protein annotations integrated from four external resources: OPM, PDBTM, MemProtMD and mpstruc. We have substantially enhanced the presentation of data on membrane proteins. The number of membrane proteins with annotations available on rcsb.org was increased by ∼80%. Users can search for these annotations, explore corresponding tree hierarchies, display membrane segments at the 1D amino acid sequence level, and visualize the predicted location of the membrane layer in 3D. Availability and implementation Annotations, search, tree data and visualization are available at our rcsb.org web portal. Membrane visualization is supported by the open-source Mol* viewer (molstar.org and github.com/molstar/molstar). Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

rcsb-api : Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs

The Protein Data Bank (PDB) was founded in 1971 as the first open-access digital data resource in biology to serve as the single global archive for three-dimensional (3D) macromolecular structure data. Current PDB holdings exceed 230,000 experimentally determined structures of proteins, nucleic acids, viruses, and macromolecular machines. The RCSB Protein Data Bank RCSB.org research-focused web portal facilitates search, analyses, and visualization of every PDB structure along with more than one million Computed Structure Models from AlphaFold DB and the ModelArchive. It is powered by a set of publicly available Application Programming Interfaces (APIs) that both support RCSB.org users and provide programmatic access to PDB data. Given the breadth and levels of granularity encompassed in this rich data collection, efficiently accessing the information programmatically may be challenging for new users. RCSB PDB has developed a Python software package, rcsb-api , that facilitates easy and efficient use of RCSB PDB APIs within a Python environment. This software tool is designed to streamline access to the extensive corpus of data housed within the PDB, enabling researchers to search, retrieve, and analyze 3D biostructure data seamlessly. Its use will accelerate research in structural biology, molecular biology and biochemistry, drug discovery, and bioinformatics by providing more efficient tools for data integration and analysis. The new toolkit is available on GitHub (github.com/rcsb/py-rcsb-api) and published to the public Python package repository (PyPI) to foster wider usage and support basic and applied research in fundamental biology, biomedicine, and the energy sciences.

FAIR principles↗

DOE OSTI2022

RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning

Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a ‘living data resource.’ Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Slow control and data acquisition systems in the Mu2e experiment

The Mu2e experiment at the Fermilab Muon Campus will search for the coherent neutrinolessconversion of a muon into an electron in the field of an aluminum nucleus with a sensitivityimprovement by a factor of 10,000 over existing limits. The Mu2e Trigger and Data AcquisitionSystem (TDAQ) usesotsdaqas the online Data Acquisition System (DAQ) solution. Developed atFermilab,otsdaqintegrates both theartdaqDAQ and theartanalysis frameworks for event transfer,filtering, and processing.otsdaqis an online DAQ software suite with a focus on flexibility andscalability and provides a multi-user, web-based, interface accessible through a web browser. Thedata stream from the detector subsystems is read by a software filter algorithm that selects eventswhich are combined with the data flux coming from a Cosmic Ray Veto System. The DetectorControl System (DCS) has been developed using the Experimental Physics and Industrial ControlSystem (EPICS) open source platform for monitoring, controlling, alarming, and archiving. TheDCS System has been integrated intootsdaq. A prototype of the TDAQ and the DCS systems hasbeen built at Fermilab’s Feynman Computing Center. In this paper, we report on the progress ofthe integration of this prototype in the onlineotsdaqsoftware.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

Online DAQ and slow control interface for the Mu2e experiment

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

Mu2e DAQ and slow control systems

The Mu2e experiment at the Fermilab Muon Campus will search for the coherent neutrinoless conversion of a muon into an electron in the feld of an aluminum nucleus with a sensitivity improvement by a factor of 10,000 over existing limits. The Mu2e Trigger and Data Acquisition System (TDAQ) uses otsdaq as the online Data Acquisition System (DAQ) solution. Developed at Fermilab, otsdaq integrates both the artdaq DAQ and the art analysis frameworks for event transfer, fltering, and processing. otsdaq is an online DAQ software suite with a focus on fexibility and scalability and provides a multiuser, web-based, interface accessible through a web browser. The data stream from the detector subsystems is read by a software flter algorithm that selects events which are combined with the data fux coming from a Cosmic Ray Veto System. The Detector Control System (DCS) has been developed using the Experimental Physics and Industrial Control System (EPICS) open source platform for monitoring, controlling, alarming, and archiving. The DCS System has been integrated into otsdaq. A prototype of the TDAQ and the DCS systems has been built at Fermilab’s Feynman Computing Center. In this paper, we report on the progress of the integration of this prototype in the online otsdaq software.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Data acquisition and slow control interface for the Mu2e experiment

The Mu2e experiment at the Fermilab Muon Campus will search for the coherent neutrinoless conversion of a muon into an electron in the field of an aluminum nucleus with a sensitivity improvement by a factor of 10000 over existing limits. The Mu2e Trigger and Data Acquisition System (TDAQ) uses otsdaq as the online Data Acquisition System (DAQ) solution. Developed at Fermilab, otsdaq integrates both the artdaq DAQ and the art analysis frameworks for event transfer, filtering, and processing. otsdaq is an online DAQ software suite with a focus on flexibility and scalability and provides a multi-user, web-based, interface accessible through a web browser. The data stream from the detector subsystems is read by a software filter algorithm that selects events which are combined with the data flux coming from a cosmic ray veto system. The Detector Control System (DCS) has been developed using the Experimental Physics and Industrial Control System (EPICS) open source platform for monitoring, controlling, alarming, and archiving. The DCS system has been integrated into otsdaq. A prototype of the TDAQ and the DCS systems has been built at Fermilab's Feynman Computing Center. In this study, we report on the progress of the integration of this prototype in the online otsdaq software.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2023

Color Transformations of Photometric Measurements of Galaxies in Optical and Near-infrared Wide-field Imaging Surveys*

Abstract Over the past 2 decades, wide-field photometric surveys in optical and infrared domains reached a nearly all-sky coverage thanks to numerous observational facilities operating in both hemispheres. However, subtle differences among exact realizations of Johnson and SDSS photometric systems require one to convert photometric measurements into the same system prior to analysis of composite data sets originating from multiple surveys. It turns out that the published photometric transformations lead to substantial biases when applied to integrated photometry of galaxies from the corresponding catalogs. Here we present photometric transformations based on piece-wise linear approximations of integrated photometry of galaxies in the optical surveys SDSS, DECaLS, BASS, MzLS, DES, DELVE, KiDS, VST ATLAS, and the near-infrared surveys UKIDSS, UHS, VHS, and VIKING. We validate our transformations by constructing k -corrected color–magnitude diagrams of non-active galaxies and measuring the position and tightness of the “red sequence.” We also provide transformations for aperture magnitudes and show how they are affected by the image quality difference among the surveys. We present the implementation of the derived transformations in python and idl and also a web-based color transformation calculator for galaxies. By comparing DECaLS and DES, we identified systematic issues in DECaLS photometry for extended galaxies, which we attribute to the photometric software package used by DECaLS. As an application of our method, we compiled two multi-wavelength photometric catalogs for over 200,000 low- and intermediate-redshift galaxies originating from CfA FAST and Hectospec spectral archives.

Astronomy & Astrophysics↗

DOE OSTI2020

Status and Availability of OPTD, the Out-of-Pile Transient Database

The DOE Advanced Reactor Technology program has supported knowledge preservation efforts to recover and preserve fuel data from the US sodium cooled fast reactor (SFR) program. Databases have been established containing experimental data generated during the Integral Fast Reactor program (from in-pile experiments at EBR-II, FFTF, and TREAT) and during related outof-pile examinations of EBR-II-irradiated fuels. The information in these databases is essential to support further development and licensing activities for advanced fast reactor designs. OPTD, the Out-of-Pile Transient Database, is an organized, searchable archive of records describing out-ofpile furnace transient tests conducted on metallic fuels. It includes records of over 150 tests on irradiated fuel pins conducted in furnace apparatuses constructed in the Alpha-Gamma Hot Cell Facility at ANL. This report presents the content, functions, and accessibility of the Out-of-Pile Transient Database (OPTD). It describes the information presently available in the database, the web interface created to provide access to this information, the activities undertaken to build OPTD, and the enabling of online access to the database for DOE users. Plans for FY2021 and beyond are also included.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2020

Trigger-DAQ and Slow Controls Systems in the Mu2e Experiment

The muon campus program at Fermilab includes the Mu2e experiment that will search for a charged-lepton flavor violating processes where a negative muon converts into an electron in the field of an aluminum nucleus, improving by four orders of magnitude the search sensitivity reached so far. Mu2e's Trigger and Data Acquisition System (TDAQ) uses otsdaq as its solution. Developed at Fermilab, otsdaq uses the artdaq DAQ framework and art analysis framework, under the-hood, for event transfer, filtering, and processing. otsdaq is an online DAQ software suite with a focus on flexibility and scalability, while providing a multi-user, web-based, interface accessible through the Chrome or Firefox web browser. The detector Read Out Controller (ROC), from the tracker and calorimeter, stream out zero-suppressed data continuously to the Data Transfer Controller (DTC). Data is then read over the PCIe bus to a software filter algorithm that selects events which are finally combined with the data flux that comes froma Cosmic Ray Ve to System (CRV). A Detector Control System (DCS) for monitoring, controlling, alarming, and archiving has been developed using the Experimental Physics and Industrial Control System (EPICS) Open Source Platform. The DCS System has also been itegrated into otsdaq. The installation of the TDAQ and the DCS systems in the Mu2e building is planned for 2021-2022, and a prototype has been built at Fermilab's Feynman Computing Center. We report here on the developments and achievements of the integration of Mu2e's DCS system into the online otsdaq software.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

Bioenergy Feedstock Library Annual Summary Report

The Bioenergy Feedstock Library (BFL), part of the Biomass Feedstock National User Facility (BFNUF) located at INL, is a physical sample repository and a web-accessible electronic database. The BFL stores physical and chemical characteristics of biomass and waste carbon sources for energy use as well as samples generated from across U.S. Department of Energy (DOE) Bioenergy Technologies Office (BETO) funded projects. The objective of this Bioenergy Feedstock Library Annual Summary Report for 2022 is to focus on the (1) publicly available analytical data and equipment tracked through the BFNUF, (2) physical samples available for request, (3) sample and data archival progress from recent BETO-funded projects, and (4) publicly available data sets created upon request from BETO, INL projects, or outside entities. This report highlights key statistics from FY22 and available data and information important for INL, BFL users, academics, and industry.

09 BIOMASS FUELS↗

DOE OSTI2022

Status of the data acquisition, trigger, and slow control systems of the Mu2e experiment at Fermilab

The Mu2e experiment at the Fermilab will search for a coherent neutrinoless conversion of a muon into an electron in the field of an aluminum nucleus with a sensitivity improvement by a factor of 10,000 over existing limits. In this work, the Mu2e Trigger and Data Acquisition System (TDAQ) uses otsdaq framework as the online Data Acquisition System (DAQ) solution. Developed at Fermilab, otsdaq integrates several framework components — an artdaq-based DAQ, an art-based event processing, and an EPICS-based detector control system (DCS), and provides a uniform multi-user interface to its components through a web browser. Data streams from the Mu2e tracker and calorimeter are handled by the artdaq-based DAQ and processed by a one-level software trigger implemented within the art framework. Events accepted by the trigger have their data combined, post-trigger, with the separately read out data from the Mu2e Cosmic Ray Veto system. Foundation of the Mu2e DCS, EPICS – an Experimental Physics and Industrial Control System – is an open-source platform for monitoring, controlling, alarming, and archiving. A prototype of the TDAQ and the DCS systems has been built and tested over the last three years at Fermilab’s Feynman Computing Center, and now the production system installation is underway. This work presents their status and focus on the installation plans and procedures for racks, workstations, network switches, gateway computers, DAQ hardware, slow controls implementation, and testing.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2025

Automating Anomaly Detection for Target systems at Spallation Neutron Source

The Spallation Neutron Source (SNS) at Oak Ridge National Laboratory, produces the world’s most intense pulse neutrons beams. An accelerated proton beam is directed into a mercury target to generate neutrons via spallation. The target system accounted for over 40% of the overall downtime of the facility in 2022. Thus, early detection in anomalies in the target systems can enable taking corrective actions to avoid failures and reduce downtime. Fault prognostics and anomaly detection in accelerators, both at SNS and outside, has largely focused on the beam side. This paper presents one the first studies exploring leveraging machine learning to automate the detection of anomalies in the target system. The target system consists of over 30 different interconnected subsystems, and the present work focuses on the mercury process system as a use case. Analyzing data from 28 process variables from 2022 and 2023, tree-based and reconstruction-based algorithms are employed to detect anomalies in archived data. The algorithms detected previously unreported anomalies, several of which were deemed alert worthy by human experts, particularly those found by reconstruction-based algorithms. Using data from each production run in the accelerator increased the generalizability of the models in time. Efforts are now underway to implement a workflow for incorporating human feedback to update the models and evaluating performance on unseen data. The models will eventually be integrated into the existing System Tracking and Reliability system with a web interface for automated anomaly detection and reporting along with a pathway for incorporating human feedback for model updates.

Raj, Anant [ORNL] (ORCID:0000000306711244)↗

DOE OSTI2024

Enhancements and Deployment of the TDAQ System for the Mu2e Experiment

The Real Time Processing Systems Division at Fermilab has deployed new features to the Off-The-Shelf Data Acquisition framework (otsdaq) for the Mu2e experiment. The Mu2e experiment will search for the coherent neutrino-less conversion of a muon into an electron in the field of an aluminum nucleus with a sensitivity improvement of 10,000 times over existing limits. Such a charged lepton flavor-violating reaction probes new physics at a scale unavailable at present or planned high-energy colliders. The Mu2e Trigger and Data Acquisition (TDAQ) system uses otsdaq as its online Data Acquisition System (DAQ) framework. otsdaq integrates the artdaq and art frameworks for event transfer, filtering, and processing. otsdaq is a web-based DAQ software suite focusing on flexibility and scalability and provides a multi-user interface accessible through a web browser. artdaq handles the entire data stream, which is read over the peripheral component interconnect express (PCIe) bus to a software filter algorithm that selects events combined with the data flux coming from a cosmic-ray veto (CRV) system. Detector front-ends are configured through the PCIe bus by customized otsdaq plugins. The otsdaq slow controls infrastructure has been further developed using the experimental physics and industrial control system (EPICS) open-source platform for monitoring, controlling, alarming, and archiving. The detector control system (DCS) for Mu2e has been integrated into otsdaq. The production TDAQ and DCS system has been deployed at the experimental hall and is being debugged and optimized for experiment operations. We report on the feature enhancements and deployment of otsdaq for Mu2e.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗