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At least 19 records
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DOE OSTI2014

A survey and taxonomy on energy efficient resource allocation techniques for cloud computing systems

In a cloud computing paradigm, energy efficient allocation of different virtualized ICT resources (servers, storage disks, and networks, and the like) is a complex problem due to the presence of heterogeneous application (e.g., content delivery networks, MapReduce, web applications, and the like) workloads having contentious allocation requirements in terms of ICT resource capacities (e.g., network bandwidth, processing speed, response time, etc.). Several recent papers have tried to address the issue of improving energy efficiency in allocating cloud resources to applications with varying degree of success. However, to the best of our knowledge there is no published literature on this subject that clearly articulates the research problem and provides research taxonomy for succinct classification of existing techniques. Hence, the main aim of this paper is to identify open challenges associated with energy efficient resource allocation. In this regard, the study, first, outlines the problem and existing hardware and software-based techniques available for this purpose. Furthermore, available techniques already presented in the literature are summarized based on the energy-efficient research dimension taxonomy. The advantages and disadvantages of the existing techniques are comprehensively analyzed against the proposed research dimension taxonomy namely: resource adaption policy, objective function, allocation method, allocation operation, and interoperability.

Cloud computing↗
DOE OSTI2025

Changes to virus taxonomy, the international code of virus classification and nomenclature, and the ICTV statutes ratified by the International Committee on Taxonomy of Viruses (2025)

Abstract The 56th meeting of the Executive Committee (EC) of the International Committee on Taxonomy of Viruses (ICTV) was held in Bari, Italy, in July/August, 2024, and 115 submitted taxonomy proposals were reviewed. A total of 112 were subsequently ratified by the ICTV membership. An additional 9 error correction proposals were also approved in August 2025. This article lists the taxonomy proposals that have now been incorporated into release 40 version v2 of the Master Species List ( https://ictv.global/msl ), the Virus Metadata Resource ( https://ictv.global/vmr ), and associated ICTV databases. In addition to the assignments of 1,563 new virus species, 243genera, 55 families, 11 orders, and 8 classes, there were substantial additions to higher taxonomic ranks. These include the creation of a new realm ( Singelaviria ), which is based on the recognition of a separate evolutionary origin for the hallmark capsid genes of members of the kingdom Helvetiavirae. These express capsid proteins forming a single jelly-roll fold that is structurally and evolutionarily distinct from those of members of the family Bamfordvirae , assigned to the realm Varidnaviria . Furthermore, the realm Varidnaviria underwent a major reorganization, including the addition of a new kingdom, Abadenavirae . Another notable change was the classification of the vertebrate-infecting single-stranded DNA anellovirids into a new phylum Commensaviricota (kingdom Shotokuvirae , realm Monodnaviria ). Archaeal viruses infecting the hyperthermophilic Archaeoglobi were assigned to a new phylum Calorviricota , in the kingdom Trapavirae (realm Monodnaviria ), whereas RNA viruses infecting hyperthermophilic bacteria were classified into a new phylum Artimaviricota (realm Riboviria ). In recognition of his extensive and valuable contributions to virus taxonomic developments in Study Groups and over the period of his EC membership, Stuart Siddell was honoured as a new life member of the ICTV. The ICTV has created a new strategy for disseminating information on taxonomy advances through annual open-access publication of citeable taxonomy proposal summaries from each ICTV Subcommittee. A collective total of 354 co-authors of the seven summaries were drawn from members of each Subcommittee, the EC, and a very large number of contributors from the wider virology community.

Simmonds, Peter (ORCID:0000000279644700)↗
DOE OSTI2011

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a ‘taxonomy to tree’ approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408 315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names (by prefixing rank designations) for better user orientation and classification consistency. The resulting merged taxonomy improved the classification of 75% of the sequences by one or more ranks relative to the original NCBI taxonomy with the most pronounced improvements occurring in under-classified environmental sequences. We also assessed candidate phyla (divisions) currently defined by NCBI and present recommendations for consolidation of 34 redundantly named groups. All intermediate results from the pipeline, which includes tree inference, jackknifing and transfer of a donor taxonomy to a recipient tree (tax2tree) are available for download. The improved Greengenes taxonomy should provide important infrastructure for a wide range of megasequencing projects studying ecosystems on scales ranging from our own bodies (the Human Microbiome Project) to the entire planet (the Earth Microbiome Project). The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2014

MO-G-BRE-08: Taxonomy of Corrective Actions in Radiotherapy

Purpose: Various causal taxonomies have been developed for healthcare incidents and for radiation therapy in particular. The causal analysis of incidents leads to corrective actions which can also be organized into a taxonomy. Such a corrective action classification system would provide information about the situational context, the action type, and the leverage of the action in order to detect patterns in the corrective actions frequently employed in radiation therapy. It would also provide practical guidance to the radiation therapy community for determining the appropriateness and potential effectiveness of proposed corrective actions. Materials: A review of causal analysis reports and corrective action plans was conducted using the following sources: US NRC medical event reports, IAEA reports, ROSIS submissions, US Veterans Health Administration reports, and singleincident report sources. The corrective actions presented in the published sources were then mapped onto four corrective action taxonomy prototypes: role-based, safety-context-based, responsibility-based, and hierarchy of hazard control. The resulting corrective action taxonomy was then validated through use of the published sources. Results: The responsibility-based taxonomy and hierarchy of hazard taxonomy provided more intuitive and sensible categories than the role-based taxonomy or the safety-context taxonomy. The most frequent corrective actions were added safety barriers, training, process standardization, and development of a quality improvement program where one was lacking. Conclusion: Published corrective action statements in radiation therapy emphasize what to do more so than whom the recipient is or which process step is affected. The hierarchy of hazard taxonomy provides a suitable framework for radiation therapy and has the advantage of providing insight into the likelihood that a particular corrective action will mitigate the recurrence of the error it was meant to correct. This information would be useful to medical center administration, safety personnel, and regulators who must assess the projected efficacy of corrective actions. Derek Brown is a director of TreatSafely, LLC.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2021

Development of a Unified Taxonomy for HVAC System Faults

Detecting and diagnosing HVAC faults is critical for maintaining building operation performance, reducing energy waste, and ensuring indoor comfort. An increasing deployment of commercial fault detection and diagnostics (FDD) software tools in commercial buildings in the past decade has significantly increased buildings’ operational reliability and reduced energy consumption. A massive amount of data has been generated by the FDD software tools. However, efficiently utilizing FDD data for ‘big data’ analytics, algorithm improvement, and other data-driven applications is challenging because the format and naming conventions of those data are very customized, unstructured, and hard to interpret. This paper presents the development of a unified taxonomy for HVAC faults. A taxonomy is an orderly classification of HVAC faults according to their characteristics and causal relations. The taxonomy includes fault categorization, physical hierarchy, fault library, relation model, and naming/tagging scheme. The taxonomy employs both a physical hierarchy of HVAC equipment and a cause-effect relationship model to reveal the root causes of faults in HVAC systems. A structured and standardized vocabulary library is developed to increase data representability and interpretability. The developed fault taxonomy can be used for HVAC system ‘big data’ analytics such as HVAC system fault prevalence analysis or the development of an HVAC FDD software standard. A common type of HVAC equipment-packaged rooftop unit (RTU) is used as an example to demonstrate the application of the developed fault taxonomy. Two RTU FDD software tools are used to show that after mapping FDD data according to the taxonomy, the meta-analysis of the multiple FDD reports is possible and efficient.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2021

A k-mer based approach for classifying viruses without taxonomy identifies viral associations in human autism and plant microbiomes

Viruses are an underrepresented taxa in the study and identification of microbiome constituents; however, they play an essential role in health, microbiome regulation, and transfer of genetic material. Only a few thousand viruses have been isolated, sequenced, and assigned a taxonomy, which limits the ability to identify and quantify viruses in the microbiome. Additionally, the vast diversity of viruses represents a challenge for classification, not only in constructing a viral taxonomy, but also in identifying similarities between a virus’ genotype and its phenotype. However, the diversity of viral sequences can be leveraged to classify their sequences in metagenomic and metatranscriptomic samples, even if they do not have a taxonomy. To identify and quantify viruses in transcriptomic and genomic samples, we developed a dynamic programming algorithm for creating a classification tree out of 715,672 metagenome viruses. To create the classification tree, we clustered proportional similarity scores generated from the k-mer profiles of each of the metagenome viruses to create a database of metagenomic viruses. The resulting Kraken2 database of the metagenomic viruses can be found here: https://www.osti.gov/biblio/1615774 and is compatible with Kraken2. We then integrated the viral classification database with databases created with genomes from NCBI for use with ParaKraken (a parallelized version of Kraken provided in Supplemental Zip 1), a metagenomic/transcriptomic classifier. To illustrate the breadth of our utility for classifying metagenome viruses, we analyzed data from a plant metagenome study identifying genotypic and compartment specific differences between two Populus genotypes in three different compartments. We also identified a significant increase in abundance of eight viral sequences in post mortem brains in a human metatranscriptome study comparing Autism Spectrum Disorder patients and controls. We also show the potential accuracy for classifying viruses by utilizing both the JGI and NCBI viral databases to identify the uniqueness of viral sequences. Finally, we validate the accuracy of viral classification with NCBI databases containing viruses with taxonomy to identify pathogenic viruses in known COVID-19 and cassava brown streak virus infection samples. Our method represents the compulsory first step in better understanding the role of viruses in the microbiome by allowing for a more complete identification of sequences without taxonomy. Better classification of viruses will improve identifying associations between viruses and their hosts as well as viruses and other microbiome members. Despite the lack of taxonomy, this database of metagenomic viruses can be used with any tool that utilizes a taxonomy, such as Kraken, for accurate classification of viruses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Four principles to establish a universal virus taxonomy

A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., “arboviruses”), infecting a certain type of host (e.g., “mycoviruses,” “bacteriophages”) or displaying specific pathogenicity (e.g., “human immunodeficiency viruses”), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

The Distributed Wind Cost Taxonomy

To date, there has been no standard method or tool to analyze the installed and operational costs for distributed wind turbine systems. This report describes the development of a classification system, or taxonomy, for distributed wind turbine project costs. The taxonomy establishes a framework to help collect, sort, and compare distributed wind cost data that mirrors how the industry categorizes information. The taxonomy organizes costs so they can be aggregated from installers, developers, vendors, and other sources without losing cost details. Developing a peer-reviewed taxonomy is valuable to industry stakeholders because a common understanding the details of distributed wind turbine costs and balance of station costs is a first step to identifying potential high-value cost reduction opportunities. Addressing cost reduction potential can help increase distributed wind's competitiveness and propel the U.S. distributed wind industry forward. The taxonomy can also be used to perform cost comparisons between technologies and track trends for distributed wind industry costs in the future. As an initial application and piloting of the taxonomy, preliminary cost data were collected for projects of different sizes and from different regions across the contiguous United States. Following the methods described in this report, these data are placed into the established cost categories.

17 WIND ENERGY↗
DOE OSTI2020

What's in a Name? Developing a Standardized Taxonomy for HVAC System Faults

Faults occurring in heating, ventilation and air-conditioning (HVAC) systems have significantly negative impacts on building energy consumption, occupant comfort, and indoor air quality. In the past thirty years, extensive research has been conducted on fault detection and diagnostics (FDD) methods, and there are now dozens of commercially available FDD software tools. Growing adoption of FDD tools has the potential to generate a massive and useful data set on fault characteristics. However, the lack of a unifying taxonomy is a significant barrier to efficient analysis and evaluation of FDD outputs. Therefore, there is a strong need to develop a robust taxonomy which can better represent and interpret FDD output data. This paper documents the development of a unifying taxonomy for HVAC system faults in commercial buildings, with initial focus on air handling units, variable air volume terminal units, and roof top unit systems. The developed fault taxonomy employs both a physical hierarchy of HVAC equipment and a cause-effect relationship model as tools to better understand and support root cause analysis for HVAC faults. A variable air volume terminal unit is used as an example to demonstrate the application of the developed fault taxonomy. The taxonomy has short-term application in a major U.S. study on fault prevalence, and promises longer term benefits to FDD software developers and building operators by creating a foundation for improved approaches to identifying and resolving HVAC faults.

Chen, Yimin↗
DOE OSTI2023

Function-based Taxonomy Implementation

Function-based taxonomies are relational mapping tools used to clearly illustrate how an organization delivers Critical Functions by using various people, processes, technologies, information, and infrastructure (PPTII). Critical Functions are the actions or activities that make up the organization’s primary purpose. Enabling Functions are the combination of PPTII used by the organization to deliver their Critical Functions. A function-based taxonomy provides a framework to categorize information and related artifacts that document an organization’s unique implementation of PPTII for Critical Function delivery. The ideal state of a function-based taxonomy is to organize the existing knowledge the organization already has throughout their numerous systems, policies, people, procedures, and configurations. A well-organized taxonomy helps organizations to effectively leverage their knowledge by clearly identifying dependencies and connections. This document is the result of combined engineering and analytical experience and describes a repeatable method for producing function-based taxonomies.

42 ENGINEERING↗
DOE OSTI2016

TH-C-204-02: Improving Manuscript Quality Via Structured Reviews, Enhanced Scientific Category Taxonomy, and Outreach

In this presentation, the Editors will outline our vision for the future of Medical Physics and review recent work-in-progress initiatives to implement this vision. Finally, we will close with guidance to authors on how to write a good Medical Physics paper. A major focus will be the transition to a new publisher in 2017 following a more than 40-year association with American Institute of Physics Publishing (AIPP). Vision for Medical Physics and status of current initiatives: Jeff Williamson, Editor-in-Chief The broad vision of Medical Physics is “to continue the Journal’s tradition of publishing the very best science that propels our discipline forward and improves our contribution to patient care.” More concretely, the Journal should be the preeminent forum for exchange of cutting edge medical physics science. We seek to identify the best contributions in (a) high impact clinical physics innovations; (b) clinical translation and validation of basic science innovations; and (c) cutting edge basic science developments with potential for patient care improvements. Among the challenges and opportunities, we face are: electronic-only and open access publishing; competition from new radiological science journals; trends towards more interactive, social-media based scientific communities; and diversification of the medical physics research, authorship, and readership domains, including clinical applications quite foreign to core ABR clinical competencies. Recently implemented and ongoing initiatives include: Revised Table of Contents (TOC) and more contemporary topical submission categories Structured review template in HTML format Comprehensive hierarchical taxonomy for identifying reviewer expertise Formal process for soliciting high quality and impact Review and Vision 20/20 Articles We have recruited four Review Article Co-editors: John Rowlands and Ingrid Reiser (imaging physics) and Joao Seco and Tim Zhu (therapy physics). The Co-Editors will identify timely topics and solicit high profile authors to submit review manuscripts. To submit an article, authors will need to work with an assigned Co-Editor to develop a mutually acceptable outline and abstract. 5) A new and exciting class of articles: Medical Physics Dataset Articles (MPDAs) MPDAs describe scientifically or clinically valuable open-access datasets with high potential for contributing to the research of medical physicists working on related problems. In contrast to Research Articles, MPDAs should not include hypothesis testing; or data analyses supporting generalizable conclusions. The publically accessible dataset must be permanently archived before the MPDA can be published. This initiative is being led by Joe Deasy. Update on new publisher transition: The transition of AAPM scientific publishing operations to a major publishing house is a major opportunity to expand Medical Physics readership and its scholarly impact. The advantages include: (a) common manuscript management and web hosting platforms for Medical Physics and its sister journal, JACMP; (b) greater than 4-fold expansion of subscribing institutions; and (c) resources to mount data-driven, highly targeted marketing campaigns to enhance citation and download rates. A transition update of this epochal development, which has only begun as of this writing (3/31/16), will be given. Improving manuscript quality via structured reviews, enhanced scientific category taxonomy, and outreach: Shiva Das, Therapy Physics Editor Medical Physics is committed to continuous improvement with the ultimate goal of improving the potential impact of accepted manuscripts. In order to do so, Medical Physics must be able to tap into important/emerging areas and be able to select high quality contributions consistently via discerning reviews. Improving the quality of reviews is crucial to selecting high quality manuscripts and also to improving manuscript impact via feedback in the review process. With this in mind, Medical Physics is in the process of: (a) fostering outreach to important areas that are currently underrepresented in Medical Physics; (b) implementing a structured template review form; and (c) implementing a comprehensive scientific category taxonomy to identify reviewers who are best suited to an article. Outreach efforts have begun to various scientific areas. Strategies to increase submissions from these areas will be discussed. As a consequence of this effort, a special issue on particle therapy is under development. A review template was implemented in late 2014 on a limited test basis. Based on reviewer feedback, the template was restructured and shortened to capture essential review elements. The restructured template is due to be released shortly. The new scientific category taxonomy is in the process of being deployed to reviewers and associate editors. Salient aspects of the structured review template and scientific category taxonomy will be discussed in this talk. Writing good scientific papers and responding to critiques: Mitch Goodsitt, Imaging Physics Editor The essential components of the abstract, introduction, methods, discussion and conclusion sections of manuscripts, as well as the desired writing style and style of the figures and tables will be reviewed. Publishable Medical Physics manuscripts must include clear and concise statements of the novelty and clinical and/or scientific importance of the authors’ work. Examples of novelty include: new technical solution to an important clinical problem; new generalizable knowledge; and first demonstration that an existing engineering solution solves a clinical problem. Please note that we encourage authors of recently published conference proceedings (e.g., SPIE, IEEE) papers on novel medical physics related work to submit more substantial versions of that work to our journal. All submissions must include: sufficient background information and rationale; enough detail for others to reproduce the authors’ work; sufficient statistical analysis to refute or validate the authors’ hypotheses; a description of how the present work compares to, is distinct from, and improves upon others’ work; and sections devoted to the limitations of the study and future directions. Writing should be polished. Poor wording, grammar and composition frustrate the review process. Our journal does not have copyeditors for revising manuscripts. When authors receive critiques from the referees and associate editor, the authors should provide a detailed point-by-point response to each comment. The authors’ rebuttal should include the text of the original criticism, the authors’ response, and a pasted copy of the modified text along with the line numbers in the revised article. The new text should be highlighted in a different font color in the revised submission. Following these recommendations will improve submissions and facilitate the review process.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Taxonomy for Common-Cause Failure Vulnerability and Mitigation

Applying current guidance and practices for common-cause failure (CCF) mitigation to digital instrumentation and control (I&C) systems has proven problematic, and the regulatory environment has been unpredictable. The potential for CCF vulnerability inhibits I&C modernization, thereby challenging the long-term sustainability of existing plants. For new plants and advanced reactor concepts, concern about CCF vulnerability in highly integrated digital I&C systems imposes a design burden that results in higher costs and increased complexity. The regulatory uncertainty in determining which mitigation strategies will be acceptable (e.g., what diversity is needed and how much is sufficient) drives designers to adopt complicated, costly solutions devised for existing plants. To address the conditions that constrain the transition to digital I&C technology by the US nuclear industry, crosscutting research is needed to resolve uncertainty, demonstrate necessary characteristics, and establish an objective basis for qualification of digital technology for nuclear power plant (NPP) I&C applications. To fulfill this research need, Oak Ridge National Laboratory is investigating mitigation of CCF vulnerability for nuclear-qualified applications. The outcome of this research is expected to contribute to a fundamentally sound, comprehensive basis to qualify digital technology for nuclear power applications. This report documents the development of a CCF taxonomy. The basis for the CCF taxonomy was generated by determining consistent terminology and establishing a classification approach. The terminology is based on definitions from standards, guides, and relevant nuclear power industry technical reports. The classification approach is derived from identified classification schemes focused on I&C systems and key characteristics, including failure modes. The CCF taxonomy provides the basis for a systematic organization of key systems aspects relevant to analyzing the potential for CCF vulnerability and the suitability of mitigation techniques. Development of an effective CCF taxonomy will help to provide a framework for establishing the objective analysis and assessment capabilities desired to facilitate rigorous identification of fault types and triggers that are the fundamental elements of CCF.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2014

Microbial taxonomy in the post-genomic era: Rebuilding from scratch?

Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. We re-evaluated the prokaryote species twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. We will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Gene sharing networks to automate genome-based prokaryotic viral taxonomy

Viruses of bacteria and archaea impact natural, engineered and human ecosystems, but their study is hampered by the lack of a universal or scalable taxonomic framework. Furthermore we introduce vConTACT v2.0, a network-based application to establish prokaryotic virus taxonomy that scales to thousands of uncultivated virus genomes, and integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions. Performance tests demonstrated significant improvements over the original tool and near-identical (96%) correspondence to current International Committee on Taxonomy of Viruses (ICTV) viral taxonomy where genus-level assignments are available. Beyond these “known viruses”, vConTACT v2.0 suggested automatic genus assignments for 1,364 previously unclassified reference viruses, with perfectly scoring assignments submitted as new taxonomic proposals to ICTV. Scaling experiments with 15,280 global ocean large viral genome fragments demonstrated that the reference network was rapidly scalable and robust to adding large-scale viral metagenomic datasets. Together these efforts provide a critically-needed, systematically classified reference network and an accurate, scalable, and automatable taxonomic analysis tool.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

A taxonomy of constraints in black-box simulation-based optimization

The types of constraints encountered in black-box simulation-based optimization problems differ significantly from those addressed in nonlinear programming. Here, we introduce a characterization of constraints to address this situation. We provide formal definitions for several constraint classes and present illustrative examples in the context of the resulting taxonomy. This taxonomy, denoted KARQ, is useful for modeling and problem formulation, as well as optimization software development and deployment. It can also be used as the basis for a dialog with practitioners in moving problems to increasingly solvable branches of optimization.

42 ENGINEERING↗
DOE OSTI2015

Taxonomy of USA east coast fishing communities in terms of social vulnerability and resilience

Increased concern with the impacts that changing coastal environments can have on coastal fishing communities led to a recent effort by NOAA Fisheries social scientists to develop a set of indicators of social vulnerability and resilience for the U.S. Southeast and Northeast coastal communities. A goal of the NOAA Fisheries social vulnerability and resilience indicator program is to support time and cost effective use of readily available data in furtherance of both social impact assessments of proposed changes to fishery management regulations and climate change adaptation planning. The use of the indicators to predict the response to change in coastal communities would be enhanced if community level analyses could be grouped effectively. This study examines the usefulness of combining 1130 communities into 35 relevant subgroups by comparing results of a numerical taxonomy with data collected by interview methods, a process herein referred to as “ground-truthing.” The validation of the taxonomic method by the method of ground-truthing indicates that the clusters are adequate to be used to select communities for in-depth research. - Highlights: • We develop a taxonomy of fishing communities based on vulnerability indicators. • We validate the community clusters through the use of surveys (“ground-truthing”). • Clusters differ along important aspects of fishing community vulnerability. • Clustering communities allows for accurate and timely social impact assessments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet?

Taxonomy is often criticized for being too conservative and too slow and having limited relevance because it has not taken into consideration the latest methods and findings. Yet the cumulative work product of its practitioners underpins contemporary microbiology and serves as a principal means of shaping and referencing knowledge. Here, using methods drawn from the field of exploratory data analysis, this minireview examines the current state of the field as it transitions from a taxonomy based on 16S rRNA gene sequences to one based on whole-genome sequences and tests the validity of some commonly held beliefs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

CPGminer: An Interactive Dashboard to Explore the Genomic Features and Taxonomy of Complete Prokaryotic Genomes

Prokaryotes, the earliest forms of life on Earth, play crucial roles in global biogeochemical processes in virtually all ecosystems. The ever-increasing amount of prokaryotic genome sequencing data provides a wealth of information to examine fundamental and applied questions through systematic genome comparison. Genomic features, such as genome size and GC content, and taxonomy-centric genomic features of complete prokaryotic genomes (CPGs) are crucial for various fields of microbial research and education, yet they are often overlooked. Additionally, creating systematically curated datasets that align with research concerns is an essential yet challenging task for wet-lab researchers. In this study, we introduce CPGminer, a user-friendly tool that allows researchers to quickly and easily examine the genomic features and taxonomy of CPGs and curate genome datasets. We also provide several examples to demonstrate its practical utility in addressing descriptive questions.

59 BASIC BIOLOGICAL SCIENCES↗