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DOE OSTI2024

HERO WEC 2024 Hydraulic Configuration Deployment Data

The following submission includes raw and processed data from the in water deployment of NREL's Hydraulic and Electric Reverse Osmosis Wave Energy Converter (HERO WEC), in the form of parquet files, TDMS files, CSV files, bag files and MATLAB workspaces. This dataset was collected in March 2024 at the Jennette's pier test site in North Carolina. This submission includes the following: - Data description document (HERO WEC FY24 Hydraulic Deployment Data Descriptions.doc) - This document includes detailed descriptions of the type of data and how it was processed and/or calculated. - Processed MATLAB workspace - The processed data is provided in the form of a single MATLAB workspace containing data from the full deployment. This workspace contains data from all sensors down sampled to 10 Hz along with all array Value Added Products (VAPs). - MATLAB visualization scripts - The MATLAB workspaces can be visualized using the file "HERO_WEC_2024_Hydraulic_Config_Data_Viewer.m/mlx". The user simply needs to download the processed MATLAB workspaces, specify the desired start and end times and run this file. Both the .m and .mlx file format has been provided depending on the user's preference. - Summary Data - The fully processed data was used to create a summary data set with averages and important calculations performed on 30-minute intervals to align with the intervals of wave resource data reported from nearby CDIP ocean observing buoys located 20km East of Jennette's pier and 40km Northeast of Jennette's pier. The wave resource data provided in this data set is to be used for reference only due the difference in water depth and proximity to shore between the Jennette's pier test site and the locations of the ocean observing buoys. This data is provided in the Summary Data zip folder, which includes this data set in the form of a MATLAB workspace, parquet file, and excel spreadsheet. - Processed Parquet File - The processed data is provided in the form of a single parquet file containing data from all HERO WEC sensors collected during the full deployment. Data in these files has been down sampled to 10 Hz and all array VAPs are included. - Interim Filtered Data - Raw data from each sensor group partitioned into 30-minute parquet files. These files are outputs from an intermediate stage of data processing and contain the raw data with no Quality Control (QC) or calculations performed in a format that is easier to use than the raw data. - Raw Data - Raw, unprocessed data from this deployment can be found in the Raw Data zip folder. This data is provided in the form of TDMS, CSV, and bag files in the original format output by the MODAQ system. - Python Data Processing Script - This links to an NREL public github repository containing the python script used to go from raw data to fully processed parquet files. Additional documentation on how to use this script is included in the github repository. This data set has been developed by the National Renewable Energy Laboratory, operated by Alliance for Sustainable Energy, LLC, for the U.S. Department of Energy (DOE) under Contract No. DE-AC36-08GO28308. Funding provided by the U.S. Department of Energy Office of Energy Efficiency and Renewable Energy Water Power Technologies Office.

16 TIDAL AND WAVE POWER↗

DOE OSTI2020

ESS-DIVE reporting format for leaf-level gas exchange data and metadata

Here we present documentation of the ESS-DIVE reporting format for leaf-level gas exchange data and metadata. This reporting format provides guidance to data contributors on how to store data to maximize their discoverability, facilitate their efficient reuse, and add value to individual datasets. For data users, the reporting format will better allow data repositories to optimize data search and extraction, and more readily integrate similar data into harmonized synthesis products. The reporting format specifies data table variable naming and unit conventions, as well as metadata characterizing experimental conditions and protocols. For common data types that were the focus of this initial version of the reporting format, i.e., survey measurements, dark respiration, carbon dioxide and light response curves, and parameters derived from those measurements, we took a further step of defining required additional data that would maximize the potential reuse of those data types. To aid data contributors and the development of data ingest tools by data repositories we provided a translation table comparing the outputs of common gas exchange instruments. The reporting format presented here is intended to form a foundation for future development that will incorporate additional data types and variables as gas exchange systems and measurement approaches advance in the future. The reporting format documentation is maintained and updated on the ESS-DIVE Community Space GitHub. This data package is the first published version of this reporting format, and comprises a zip file of the complete content of https://github.com/ess-dive-community/essdive-leaf-gas-exchange v1.0. The zip contains the reporting format description, guidelines, variable tables and instructions in GitHub markdown language (*.md) and 2 metadata templates as spreadsheets with drop down options (*.xlsx files, also function in GoogleSheets).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

ESS-DIVE Unoccupied Aerial Systems (UAS) Reporting Format v1

Here we present documentation of the ESS-DIVE reporting format for Unoccupied Aerial System (UAS) data and metadata. This reporting format provides guidance to data contributors on how to store data to maximize their discoverability, facilitate their efficient reuse, and add value to individual datasets. For data users, the reporting format will better allow data repositories to optimize data search and extraction, and more readily integrate similar data into harmonized synthesis products. The reporting format provides templates and guidance for the reporting of metadata for UAS experimental campaigns, individual flights, platform and sensor description. To improve data access and discoverability, the reporting format proposes a data description scheme of Levels based on the degree of processing, where Level 0 includes raw data, through to Level 3 being derived data end products. A range of examples of data types for each Level are given, with suggested file naming schemes. The reporting format presented here is intended to form a foundation for future development that will accommodate new UAS technologies and approaches to data access and use in the future. The reporting format documentation is maintained and updated on the ESS-DIVE Community Space GitHub at https://github.com/ess-dive-community/essdive-uas. This data package is the first published version of this reporting format, and comprises a zip file of the complete content of https://github.com/ess-dive-community/essdive-uas v1.0. The zip contains the reporting format description, instructions and variable definitions in GitHub markdown language (*.md) and metadata templates in csv format. The reporting format is designed to be compatible with other ESS-DIVE formats, and it is specifically recommended that this reporting format be used in conjunction with the File-level metadata (FLMD) and comma separated values (csv) reporting formats for submission to the ESS-DIVE repository.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

useeio-infra-app

This GitHub repository hosts the source code to an RShiny web application that implements the U.S. Environmentally-Extended Input-Output (USEEIO) model in order to conduct a screening-level life cycle analysis. The USEEIO model is an open-source model developed and maintained by the Environmental Protection Agency (EPA), along with colleagues and contractors, and is available on GitHub (https://github.com/USEPA/USEEIO). The USEEIO model incorporates environmental data into pre-existing Economic Input-Output Models, which look at the interdependence of different economic industries. In this web application, the focus is on energy infrastructure applications; however, it can be used to implement USEEIO in any area for which this model is applicable.

AS↗

DOE OSTI2019

Performance tuning of CEED software and 1st and 2nd wave apps

The goal of this milestone was the performance tuning of the CEED software, as well as the use and tuning of CEED to accelerate the first and second wave of targeted ECP applications. In this milestone, the CEED team developed optimization techniques and tuned for performance the CEED software to accelerate the first and second wave target ECP applications. Specifically, the focus was on the following: (1) Efficient use of the memory sub-system for managing data motion and interactions among different physics packages and libraries; this included integration of the new developments in a libCEED 0.5 software release; (2) Enhancing the CEED libraries with GPU and AMD GPU support in close interaction with vendors; (3) Optimal data locality and motion, and enhanced scalability and parallelism; this included vendors interactions for improvements in data motion and making strong scaling easier and more efficient; and (4) Continue boosting performance for the first-wave and second-wave of ECP target applications, including ExaSMR, ExaWind, Urban, MARBL, E3SM, and ExaAM. A main part of this milestone was the performance tuning of the CEED first-wave and second-wave ECP applications. This included the ExaSMR application – Coupled Monte Carlo Neutronics and Fluid Flow Simulation of Small Modular Reactors (ORNL), the MARBL application – Next-Gen Multi-physics Simulation Code (LLNL), and the ExaAM ExaConstit – a miniapp for the Transforming Additive Manufacturing through Exascale Simulation applications project (ExaAM), as well as ExaWind, Urban, and E3SM. The artifacts delivered include performance improvements in CEED’s 1st and 2nd wave of applications, and tuned CEED software for various architectures through a number of backends, freely available in the CEED’s repository on GitHub. See the CEED website, http://ceed.exascaleproject.org and the CEED GitHub organization, http://github.com/ceed for more details. In addition to details and results from the above R&D efforts, in this document we are also reporting on other project-wide activities performed in Q4 of FY19 including: CEED’s third annual meeting, MFEM GPU kernels scaling improvements, libCEED 0.5 and NekRS releases, an overview paper covering latest results on a set of bake-off high-order finite element problems (BPs), and other outreach efforts.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Performance tuning of CEED software and first wave apps

The goal of this milestone was the performance tuning of the CEED software and first wave apps. In this milestone, the CEED team developed optimization techniques and tuned for performance the CEED software. Specifically, the focus was on the following: (1) Fast finite element operator storage and evaluation using partial assembly/matrix-free algorithms that take advantage of tensor-product element structure; (2) Architecture optimizations, including the development of performant discretization libraries targeting heterogeneous systems with multi-core CPUs, GPUs, and/or many-core CPUs in single node, cluster, or large-scale ECP supercomputer configurations; and (3) Global kernels for finite element operators, including the development of algorithms and libraries for fast gather-scatter exchanges for action assembly on unstructured graphs and for components needed for global linear solvers. A main part of this milestone was the performance tuning of the CEED first-wave ECP applications. This included the ExaSMR application – Coupled Monte Carlo Neutronics and Fluid Flow Simulation of Small Modular Reactors (ORNL), and the MARBL application – Next-Gen Multi-physics Simulation Code (LLNL). The artifacts delivered include performance improvements in CEED’s 1st wave of applications, and tuned CEED software for various architectures through a number of backends, freely available in the CEED’s repository on GitHub. See the CEED website, http://ceed.exascaleproject.org and the CEED GitHub organization, http://github.com/ceed for more details. In addition to details and results from the above R&D efforts, in this document we are also reporting on other project-wide activities performed in Q4 of FY18 including: CEED’s second annual meeting, a successful minisymposium at the premier international conference on high-order methods (ICOSAHOM), making the CEED milestone reports publicly available, new Laghos release, and other outreach efforts.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Development and Porting of Nuclear Reactor Computational Models for the NRIC Virtual Test Bed in FY23

The U.S. DOE’s National Reactor Innovation Center (NRIC) hosts an open-source website and associated GitHub repository called the Virtual Test Bed (VTB) on which computational models for advanced reactors are documented and shared with the reactor community. In FY23 under the NRIC program, computational models for nuclear reactor analysis were developed and contributed to the VTB Github repository during FY23 by contributors at Argonne National Laboratory. Other models developed outside of NRIC were also ported to the VTB as part of this work, serving a broader mission to make computational reactor analysis models more widely available to the reactor community. The model development activities focused on demonstration of gas-cooled microreactor models including computational fluid dynamics simulations of flow through an industry-inspired air jacket design, and simulation of multiphysics transients for a gas-cooled microreactor assembly. Additionally, development of a molten salt reactor (led at Idaho National Laboratory) was supported through Argonne’s expertise in multigroup cross sections generation. Models for these two reactor types were targeted due to their relevancy to NRIC’s Demonstration of Microreactor Experiments (DOME) and Laboratory for Operation and Testing in the U.S. (LOTUS) physical test beds, which are slated to host microreactor and molten salt reactor experiments. The model porting activities consisted of developing detailed documentation for several physics models which originate from the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. We include only contributions from Argonne National Laboratory in this report.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

Using Apptainer in a Pilot-based Distributed Workload

GlideinWMS is a pilot and pressure-based workload manager for distributed scientific computing. Many experiments like CMS and Fermilab’s Neutrino experiments use it to provision elastic clusters for their analysis and simulations, split into close to a million concurrent jobs. Most user jobs require containers, and the pilots use Apptainer to set up the desired platform. For the pilots that run as regular batch jobs, Apptainer is safer, lighter, and easier to use than other containerization solutions. Many images used by the pilots are expanded SIF images distributed via the CernVM-FS: this combination is very efficient. At Fermilab, for example, we store on GitHub Dockerfiles that mimic the platform in the worker nodes of local clusters. GitHub workflows build and push the images to Docker Hub, and a service periodically pulls and converts them to the expanded SIF images in the CernVM-FS, so the scientists can find a familiar environment everywhere. Apptainer has also been used to run services inside the pilot jobs, like benchmarks that characterize the worker node being used, or a Triton Inference Server that allows sharing a GPU with all the jobs that run in parallel on a node.

Mambelli, Marco [Fermilab] (ORCID:0000000294892681↗

DOE OSTI2020

Learning Spectral Templates for Photometric Redshift Estimation from Broadband Photometry

Estimating redshifts from broadband photometry is often limited by how accurately we can map the colors of galaxies to an underlying spectral template. Current techniques utilize spectrophotometric samples of galaxies or spectra derived from spectral synthesis models. Both of these approaches have their limitations: either the sample sizes are small and often not representative of the diversity of galaxy colors, or the model colors can be biased (often as a function of wavelength), which introduces systematics in the derived redshifts. In this paper, we learn the underlying spectral energy distributions from an ensemble of ∼100 K galaxies with measured redshifts and colors. We show that we are able to reconstruct emission and absorption lines at a significantly higher resolution than the broadband filters used to measure the photometry for a sample of 20 spectral templates. We find that our training algorithm reduces the fraction of outliers in the derived photometric redshifts by up to 28%, bias up to 91%, and scatter up to 25%, when compared to estimates using a standard set of spectral templates. We discuss the current limitations of this approach and its applicability for recovering the underlying properties of galaxies. Our derived templates and the code used to produce these results are publicly available in a dedicated Github repository: https://github.com/dirac-institute/photoz-template-learning.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

cnor_pub: R code and data for nitrous oxide synthesis by purified bacterial cNOR

This zipped archive of a GitHub repository includes the experimental data (csv files) collected for the reduction of NO to N2O by purified Paracoccus denitrificans cytochrome c nitric oxide reductase (cNOR) and the R code (qmd files) used to analyze these data. A link to the corresponding GitHub repository is also provided.

Hegg, Eric L. [GLBRC - Michigan State University]↗

DOE OSTI2024

MSD CoP Webinar: Using Meta-Repositories To Facilitate Open Science in MSD Research

Context: This webinar was hosted by the MultiSector Dynamics Community of Practice (MSD CoP; https://multisectordynamics.org). Abstract: In this webinar, we will describe the use of a GitHub meta-repository, for documenting and disseminating the tools and data supporting MSD publications. The goal is to make it easier for others to understand the flow of data and code through your experiment and to be able to reproduce your results and figures with only the information you have provided for them. The webinar will cover the role of open science in the MSD community, the origins and purpose of meta-repositories, and step-by-step instructions and best practices for building a meta-repository starting from the GitHub template (https://github.com/IMMM-SFA/metarepo). We will also discuss how to leverage MSD-LIVE (https://msdlive.org/) in your meta-repository, provide links to numerous examples you can learn from, and discuss the role of meta-repositories in the IM3 project's open science mandates. Presenters : Chris R. Vernon, Casey D. Burleyson, Jennie Rice, and Mengqi Zhao Moderator: Pat M. Reed (MSD CoP Facilitation Team) This webinar was held on: February 22nd, 2024 from 2-3 PM ET

Open Science↗

DOE OSTI2022

WaterTAP3 Model Input Data for NAWI's Eight Source Water Baseline Analyses

This folder contains the input data for the WaterTAP3 model that was used for the eight NAWI (National Alliance for Water Innovation) source water baselines studies published in the Environmental Science and Technology special issue: Technology Baselines and Innovation Priorities for Water Treatment and Supply. There are also eight other separate DAMS submissions, one per source water, that include the model results for the published studies. In this data submission, all model inputs across the eight baselines are included. The data structure and content are described in a README.txt file. For more details on how to use the data in WaterTAP3 please refer to the model documentation and GitHub site found at "WaterTAP3 Github" linked in the submission resources.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

NASA NTRSDate not supplied

INCREASING THE TRANSPARENCY AND REPRODUCIBILITY OF SPACE RADIATION SCIENCE: THE RADIATION BIOLOGY ONTOLOGY

Among the primary objectives of the Open/Open-Source Science paradigm are making scientific investigation data transparent and results reproducible [1], objectives shared by the FAIR principles [2]. To accomplish this, the conceptual framework that includes all the investigation objects needs to be accurately captured and communicated to all data consumers. A large part of this requires using metadata standards to annotate data collected. These standards should be readily accessible, informed by scientific community consensus and sufficiently specific to encompass all of the important aspects of the investigation. Starting in 2020 we have been co-leading an open consortium to develop a new metadata standard, the Radiation Biology Ontology (RBO), through the Open Biological and Biomedical Ontologies (OBO) Foundry [3]. We began by transforming many of the terms from the National Council on Radiation Protection and Measurement into concepts that can be formally related to existing OBO Foundry classes or attributes. We then identified and imported into the RBO existing OBO Foundry classes that have obvious relevance for radiation biomedicine (for example, concepts from the Environment Ontology that describe radiative processes, and concepts from the Gene Ontology dealing with molecular and cellular responses to radiation). Finally, we scrutinized datasets from investigations of radiation effects held in NASA GeneLab and LSDA repositories and added additional classes, instances, and attributes into the RBO that should be used to annotate these data. We developed the RBO using the open-source tools of GitHub and publish the RBO periodically through the NIH/NCBI BioPortal website, so systems worldwide can leverage the knowledge it contains [4]. This initial phase of concept modeling has yielded an RBO that at present has more than 300 declared concepts, with more than 3500 additional concepts imported from other OBO Foundry ontologies. While this first phase has focused on concepts for annotating samples, environments, exposures, and measurements, the next phase will center on supporting annotation of results and findings, such as concept models of molecular, cellular and tissue effects. The value of the RBO will be determined in part by our ability to engage the community in its development, and we have established a Radiobiology Informatics Consortium with unrestricted membership as the owner of the RBO in order to encourage investigators, system owners and other to join in this effort. Anyone can report issues or request new concept modeling or other features directly on GitHub. By using the BioPortal application programming interface, systems can pose dynamic queries to the latest version of the RBO for information on individual classes or entire hierarchies; this design eliminates the need for systems to be updated in order to use newer versions of the RBO. We hope to contribute to the advancement of open radiobiological science through the continued, open development of the RBO, that will provide more precise, machine-interpretable descriptions of investigations, as well as support data meta-analysis through machine learning or other artificial intelligence methods. REFERENCES [1] Open science in space. Nature Medicine, 2021. 27(9): p. 1485-1485. [2] Wilkinson, M.D., et al., The FAIR Guiding Principles for scientific data management and stewardship. Sci Data, 2016. 3: p. 160018. [3] Smith, B., et al., The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol, 2007. 25(11): p. 1251-5. [4] Whetzel, P.L., et al., BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res, 2011. 39(Web Server issue): p. W541-5.

informatics↗

NASA NTRSDate not supplied

INCREASING THE TRANSPARENCY AND REPRODUCIBILITY OF SPACE RADIATION SCIENCE: THE RADIATION BIOLOGY ONTOLOGY

knowledge↗

NASA NTRS2020

Connecting Users and Applications with Po.daac Hosted GHRSST Data

The 80+ GHRSST public datasets represent a rich resource for sea surface temperature research and applications given their time series length, resolution, spatial coverage, varying measurement types and processing levels, and availability in the full spectrum of PO.DAAC tools and services ecosystem. The PO.DAAC has created a publicly accessible recipe suite for the user community to perform straightforward yet powerful computations on GHRSST data using python recipes, Jupyter notebooks, R, Matlab, and the NCO programming language. These recipes include numerical computations for regional and global SST trends, anomaly derivations, EOF analysis, climate signal reproduction, and ocean phenology. For example, one recipe reproduces a famous SST based warming figure from the Fourth National Climate Assessment (USA) while another focuses on quantifying the regional changes in ocean SST phenology. Most are python-based while some contain hybrid calls and leverage the NCO programming interface too. All are available on the PO.DAAC user forum (https://podaac.jpl.nasa.gov/forum/) and/or via the open source NASA GitHub repository (https://github.com/nasa/podaac_tools_and_services). Several are available in the Jupyter notebook framework including podaacypy (https://github.com/nasa/podaacpy), a recipe for GHRSST granule metadata discovery and application, and more recently a Jupyter notebook developed to support data analysis and visualization of a cloud-based Zarr formatted Level 4 MUR dataset in the AWS Open Data Registry. Throughout the summer of 2020, the PO.DAAC intends to add and migrate more of its numerical recipes to the Jupyter notebook framework and publish them on its open source GitHub repository.

Gentemann, Chelle↗

NASA NTRSDate not supplied

Data Sharing in Radiobiology; Towards FAIR

The value of scientific data depends on their findability, accessibility, integrability and reusability according to the FAIR principles. Together with the sustainability of data preservation and access, these principles underpin the long term benefits of scientific research. Within the domain of radiobiology we have a huge array of data types, themes and complexities which make standardisation of metadata, data structure and data integration very challenging. Moreover, it is clear that, for example, in the area of disaster preparedness, the ready discovery and availability of multiple types of data, for example on biological effects of exposure, climatology, ecology, human behavioural and attitudinal studies, is important for an integrated scientific approach. Because these data are spread over many databases, journal supplementary information resources and even the computers of the investigators, their discovery and reuse can be challenging. Despite exhortations from funding agencies and scientific institutions over the past two decades there is still a serious deficit in the willingness and in some cases the ability of investigators to share data, and although much may not be formally „Public domain“, information about the existence of the data, their metadata, and how to obtain them should always be available. We report the progress of work on three databases, the STORE and the NASA GeneLab and LSDA repositories to leverage the Radiation Biology Ontology (RBO), a structured terminology for metadata that can be used by all radiation biology-relevant databases to unite federated and automated data searches across multiple databases, for example using web services, and through semantic web technologies supporting data discovery. The initial primary use-cases for RBO were archiving data in the STORE database (https://www.storedb.org/), the repository used for the RadoNorm and Pianoforte Projects among others, and in the NASA Open Science Data Repository (https://osdr.nasa.gov/bio). The scope of radiobiology research ranges from basic physics to radiation oncology to sociolegal studies; no existing ontology had the necessary breadth or depth to fulfill this need. In addition, a formal ontology has the advantage of being usable for machine learning and, importantly, for tasks like data integration, knowledge extraction from the scientific literature and for query extension and data classification. Standardisation of metadata is one of the primary objectives of the FAIR principles for open data; RBO is an important landmark for FAIR-compliant radiation biology data sharing. The RBO is developed using the open-source tools of GitHub and the OBO Foundry-led Ontology Development Kit, and published through GitHub and the NIH/NCBI BioPortal website. This initial phase of concept modeling has yielded an ontology that has more than 300 declared concepts, with more than 3500 additional concepts imported from other OBO Foundry ontologies with relevance to radiation biology (for example, concepts from the ISO standard Basic Formal Ontology, the Environment Ontology and the Gene Ontology). We welcome input into the development of RBO and encourage its adoption.

ontologies↗

NASA NTRS2023

Data Sharing in Radiation Biology: Towards FAIR

The value of scientific data depends on their findability, accessibility, integrability and reusability according to the FAIR principles. Together with the sustainability of data preservation and access, these principles underpin the long term benefits of scientific research. Within the domain of radiobiology we have a huge array of data types, themes and complexities which make standardisation of metadata, data structure and data integration very challenging. Moreover, it is clear that, for example, in the area of disaster preparedness, the ready discovery and availability of multiple types of data, for example on biological effects of exposure, climatology, ecology, human behavioural and attitudinal studies, is important for an integrated scientific approach. Because these data are spread over many databases, journal supplementary information resources and even the computers of the investigators, their discovery and reuse can be challenging. Despite exhortations from funding agencies and scientific institutions over the past two decades there is still a serious deficit in the willingness and in some cases the ability of investigators to share data, and although much may not be formally "Public domain“, information about the existence of the data, their metadata, and how to obtain them should always be available. We report the progress of work on three databases, the STORE and the NASA GeneLab and LSDA repositories to leverage the Radiation Biology Ontology (RBO), a structured terminology for metadata that can be used by all radiation biology-relevant databases to unite federated and automated data searches across multiple databases, for example using web services, and through semantic web technologies supporting data discovery. The initial primary use-cases for RBO were archiving data in the STORE database (https://www.storedb.org/), the repository used for the RadoNorm and Pianoforte Projects among others, and in the NASA Open Science Data Repository (https://osdr.nasa.gov/bio). The scope of radiobiology research ranges from basic physics to radiation oncology to sociolegal studies; no existing ontology had the necessary breadth or depth to fulfill this need. In addition, a formal ontology has the advantage of being usable for machine learning and, importantly, for tasks like data integration, knowledge extraction from the scientific literature and for query extension and data classification. Standardisation of metadata is one of the primary objectives of the FAIR principles for open data; RBO is an important landmark for FAIR-compliant radiation biology data sharing. The RBO is developed using the open-source tools of GitHub and the OBO Foundry-led Ontology Development Kit, and published through GitHub and the NIH/NCBI BioPortal website. This initial phase of concept modeling has yielded an ontology that has more than 300 declared concepts, with more than 3500 additional concepts imported from other OBO Foundry ontologies with relevance to radiation biology (for example, concepts from the ISO standard Basic Formal Ontology, the Environment Ontology and the Gene Ontology). We welcome input into the development of RBO and encourage its adoption.

ontologies↗

NASA NTRSDate not supplied

The Nasa SRA Process as It Relates to Open-Source Workflows Developed for GeneLab Data Processing

To release open, standards-compliant processed data sets in the Open Science Data Repository (OSDR), the GeneLab Data Processing team works with the scientific community through the OSDR Analysis Working Groups to design and build open-source data processing pipelines. Once baselined internally, these pipelines are wrapped into workflows and published on the NASA GeneLab Data Processing public GitHub repository along with detailed instructions for installation and use. Each workflow must be approved through NASA's Software Release Authorization (SRA) process prior to publishing. However, the SRA process lacks sufficient documentation and clarity regarding which forms are applicable for new open-source software that utilizes publicly available 3rd party tools, and the SRA process can take several months to complete, making sharing software outside of NASA cumbersome and in contradiction with the concept of Open Science. Furthermore, the SRA process was designed as a one-size fits all approach and thus many of the questions asked are not applicable to our open-source workflows. Here we describe the software provided on the NASA GeneLab Data Processing GitHub repository, summarize our experiences with the SRA process to release these software, and propose a more stream-lined approach for review of open-source projects.

Software Release Authorization↗