Copley Nancy J.

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Copley

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Nancy J.

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0000-0003-1473-8789

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Drawings and descriptions of some deep-sea copepods living above the Guaymas Basin hydrothermal vent field

(Woods Hole Oceanographic Institution, 1990-04) Copley, Nancy J. ; Wiebe, Peter H.

This report includes brief descriptions and illustrations of some of the copepods found in two bathypelagic MOCNESS samples. The MOCNESS was towed horizontally at an altitude of 100-200 m above the bottom in waters 1900 to 2000 m deep near hydrothermal vents in the southern trough of the Guaymas Basin, Gulf of California. Some copepods from one Alvin dive plankton tow collected three to four meters from the bottom in the vent field (2000 m depth) are also included.
What role should a domain-specific repository play in treating code as a first class research product? [poster]

( 2018-12-13) Biddle, Matt ; Ake, Hannah ; Copley, Nancy ; Kinkade, Danie ; Rauch, Shannon ; Saito, Mak A. ; Shepherd, Adam ; Wiebe, Peter ; York, Amber

The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is a publicly accessible earth science data repository created to curate, publicly serve (publish), and archive digital data and information from biological, chemical and biogeochemical research conducted in coastal, marine, great lakes and laboratory environments. The BCO-DMO repository works closely with investigators funded through the NSF OCE Division’s Biological and Chemical Sections and Antarctic Organisms & Ecosystems. The office provides services that span the full data life cycle, from data management planning support and DOI creation, to archiving with appropriate national facilities. Recently, more and more of the projects submitted to BCO-DMO represent modeling efforts which further increase our knowledge of the chemical and biological properties within the ocean ecosystem. But, as a repository traditionally focused on observational data as a primary research output, what roles should domain-specific data repositories play in this field? Recognizing code as a first class research product, how should repositories support the discovery, access and reuse of code and software used in hypothesis driven research? We feel the time is at hand for the community to begin a concerted and holistic approach to the curation of code and software. Such strategy development should begin with asking what is the appropriate output to curate? What is the minimum metadata required for re-use? How should code be stored and accessed? Should repositories support or facilitate peer reviewing code? The answers to these questions will better inform domain-specific repositories on how to better manage code as a first class research asset in order to support the scientific community. This presentation will explore these topics, inviting discussion from the audience to advance a collective strategy.
Share Your Thoughts [poster]

(Woods Hole Oceanographic Institution, 2020-02-21) Haskins, Christina ; Biddle, Matt ; Copley, Nancy J. ; Rauch, Shannon ; Soenen, Karen ; York, Amber ; Kinkade, Danie ; Saito, Mak A. ; Shepherd, Adam ; Wiebe, Peter

Oceanographic data, when well-documented and stewarded toward preservation, have the potential to accelerate new science and facilitate our understanding of complex natural systems. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is funded by the NSF to document and manage marine biological, chemical, physical, and biogeochemical data, ensuring their discovery and access, and facilitating their reuse. The task of curating and providing access to research data is a collaborative process, with associated actors and critical activities occurring throughout the data’s life cycle. BCO-DMO supports all phases of the data life cycle and works closely with investigators to ensure open access of well-documented project data and information. Supporting this curation process is a flexible cyberinfrastructure that provides the means for data submission, discovery, and access; ultimately enabling reuse. Based upon community feedback, this infrastructure is undergoing evaluation and improvement to better meet oceanographic research needs. This poster will introduce the repository and describe some of the strategic enhancements coming to BCO-DMO, and presents an opportunity for you to provide feedback on enhancements yet to come. We invite you to think about your own research workflow of searching and accessing new data for research, and to provide your feedback through the poster’s interactive sections. Your input can help BCO-DMO improve its service to the research community.
The Biological and Chemical Oceanography Data Management Office: Accelerating Scientific Discovery Through Responsive Management of Observational Oceanographic Data [poster]

(Woods Hole Oceanographic Institution, 2019-09-16) Kinkade, Danie ; Shepherd, Adam ; Biddle, Matt ; Copley, Nancy ; Haskins, Christina ; Soenen, Karen ; Rauch, Shannon ; York, Amber ; Saito, Mak A. ; Wiebe, Peter

Oceanographic data, when well-documented and stewarded toward preservation, have the potential to accelerate new science and facilitate our understanding of complex natural systems. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is funded by the NSF to document and manage marine biological, chemical, physical, and biogeochemical data, ensuring their discovery and access, and facilitating their reuse. The task of curating and providing access to research data is a collaborative process, with associated actors and critical activities occurring throughout the data’s life cycle. BCO-DMO supports all phases of the data life cycle and works closely with investigators to ensure open access of well-documented project data and information. Supporting this curation process is a flexible cyberinfrastructure that provides the means for data submission, discovery, and access; ultimately enabling reuse. This poster will introduce the repository and describe some of the strategic enhancements coming to BCO-DMO.
Capturing Provenance of Data Curation at BCO-DMO

(Woods Hole Oceanographic Institution, 2020-05-15) Shepherd, Adam ; York, Amber ; Schloer, Conrad ; Kinkade, Danie ; Rauch, Shannon ; Biddle, Matt ; Copley, Nancy ; Haskins, Christina ; Soenen, Karen ; Saito, Mak A. ; Wiebe, Peter

At domain-specific data repositories, curation that strives for FAIR principles often entails transforming data submissions to improve understanding and reuse. The Biological and Chemical Oceanography Data Management Office (BCO-DMO, https://www.bco-dmo.org) has been adopting the data containerization specification of the Frictionless Data project (https://frictionlessdata.io) in an effort to improve its data curation process efficiency. In doing so, BCO-DMO has been using the Frictionless Data Package Pipelines library (https://github.com/frictionlessdata/datapackage-pipelines) to define the processing steps that transform original submissions to final data products. Because these pipelines are defined using a declarative language they can be serialized into formal provenance data structures using the Provenance Ontology (PROV-O, https://www.w3.org/TR/prov-o/). While there may still be some curation steps that cannot be easily automated, this method is a step towards reproducible transforms that bridge the original data submission to its published state in machine-actionable ways that benefit the research community through transparency in the data curation process. BCO-DMO has built a user interface on top of these modular tools for making it easer for data managers to process submission, reuse existing workflows, and make transparent the added value of domain-specific data curation.
Capturing Provenance of Data Curation at BCO-DMO

(Woods Hole Oceanographic Institution, 2020-11-09) Shepherd, Adam ; York, Amber ; Schloer, Conrad ; Kinkade, Danie ; Rauch, Shannon ; Copley, Nancy ; Gerlach, Dana ; Haskins, Christina ; Soenen, Karen ; Saito, Mak A. ; Wiebe, Peter

At domain-specific data repositories, curation that strives for FAIR principles often entails transforming data submissions to improve understanding and reuse. The Biological and Chemical Oceanography Data Management Office (BCO-DMO, https://www.bco-dmo.org) has been adopting the data containerization specification of the Frictionless Data project (https://frictionlessdata.io) in an effort to improve its data curation process efficiency. In doing so, BCO-DMO has been using the Frictionless Data Package Pipelines library (https://github.com/frictionlessdata/datapackage-pipelines) to define the processing steps that transform original submissions to final data products. Because these pipelines are defined using a declarative language they can be serialized into formal provenance data structures using the Provenance Ontology (PROV-O, https://www.w3.org/TR/prov-o/). While there may still be some curation steps that cannot be easily automated, this method is a step towards reproducible transforms that bridge the original data submission to its published state in machine-actionable ways that benefit the research community through transparency in the data curation process. BCO-DMO has built a user interface on top of these modular tools for making it easier for data managers to process submission, reuse existing workflows, and make transparent the added value of domain-specific data curation.
Biological & Chemical Oceanography Data Management Office : a domain-specific repository for oceanographic data from around the world [poster]

( 2018-02-14) Ake, Hannah ; Biddle, Matt ; Copley, Nancy ; Kinkade, Danie ; Rauch, Shannon ; Saito, Mak A. ; Shepherd, Adam ; Switzer, Megan ; Wiebe, Peter ; York, Amber

The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is a domain-specific digital data repository that works with investigators funded under the National Science Foundation’s Division of Ocean Sciences and Office of Polar Programs to manage their data free of charge. Data managers work closely with investigators to satisfy their data sharing requirements and to develop comprehensive Data Management Plans, as well as to ensure that their data will be well described with extensive metadata creation. Additionally, BCO-DMO offers tools to find and reuse these high-quality data and metadata packages, and services such as DOI generation for publication and attribution. These resources are free for all to discover, access, and utilize. As a repository embedded in our research community, BCO-DMO is well positioned to offer knowledge and expertise from both domain trained data managers and the scientific community at large. BCO-DMO is currently home to more than 9000 datasets and 900 projects, all of which are or will be submitted for archive at the National Centers for Environmental Information (NCEI). Our data holdings continue to grow, and encompass a wide range of oceanographic research areas, including biological, chemical, physical, and ecological. These data represent cruises and experiments from around the world, and are managed using community best practices, standards, and technologies to ensure accuracy and promote re-use. BCO-DMO is a repository and tool for investigators, offering both ocean science data and resources for data dissemination and publication.
BCO-DMO Quick Guide

( 2018-09-19) Kinkade, Danie ; Shepherd, Adam ; Ake, Hannah ; Biddle, Matt ; Copley, Nancy ; Rauch, Shannon ; York, Amber

Curating and providing open access to research data is a collaborative process. This process may be thought of as a life cycle with data passing through various phases. Each phase has its own associated actors, roles, and critical activities. Good data management practices are necessary for all phases, from proposal to preservation.
Copepods from warm-core ring 82-H

(Woods Hole Oceanographic Institution, 1989-07) Copley, Nancy J. ; Wiebe, Peter H. ; Cowles, Timothy J.

Net tows were collected with a Multiple Opening/Closing Net Environmental Sampling System (MOCNESS) carrying twenty 1-m2 nets in October 1982 in and near warm-core ring 82-H in the North Atlantic (RV/Knorr cruise 98). This report includes the species list and abundance tables of the copepods found in five of the tows. There are four types of abundance tables: raw data, standardized to #/1000 m3 , integrated #/m2 to 1000 m depth, and cumulative percents over the depth of the tows.
Making OCB Data F.A.I.R [poster]

( 2019-06-24) Soenen, Karen ; Biddle, Matt ; Copley, Nancy ; Haskins, Christina ; Rauch, Shannon ; York, Amber ; Kinkade, Danie ; Saito, Mak A. ; Shepherd, Adam ; Wiebe, Peter

Oceanographic data, when well-documented and stewarded toward preservation, have the potential to accelerate new science and facilitate our understanding of complex natural systems. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is funded by the NSF to document and manage marine ecosystem data, ensuring their discovery and access, and facilitating their reuse. The task of curating and providing access to research data is a collaborative process, with associated actors and critical activities occurring throughout the data’s life cycle. BCO-DMO supports all phases of the data life cycle and works closely with investigators to ensure open access of well-documented project data and information. Supporting this curation process is a flexible cyberinfrastructure that provides the means for data submission, discovery, and access; ultimately enabling reuse. This poster describes some of the existing infrastructure and strategic enhancements at BCO-DMO in support of the F.A.I.R principles.
COI metabarcoding of zooplankton species diversity for time-series monitoring of the NW Atlantic continental shelf

(Frontiers Media, 2022-04-22) Bucklin, Ann ; Batta-Lona, Paola G. ; Questel, Jennifer M. ; Wiebe, Peter ; Richardson, David E. ; Copley, Nancy ; O'Brien, Todd D.

Marine zooplankton are rapid-responders and useful indicators of environmental variability and climate change impacts on pelagic ecosystems on time scales ranging from seasons to years to decades. The systematic complexity and taxonomic diversity of the zooplankton assemblage has presented significant challenges for routine morphological (microscopic) identification of species in samples collected during ecosystem monitoring and fisheries management surveys. Metabarcoding using the mitochondrial Cytochrome Oxidase I (COI) gene region has shown promise for detecting and identifying species of some – but not all – taxonomic groups in samples of marine zooplankton. This study examined species diversity of zooplankton on the Northwest Atlantic Continental Shelf using 27 samples collected in 2002-2012 from the Gulf of Maine, Georges Bank, and Mid-Atlantic Bight during Ecosystem Monitoring (EcoMon) Surveys by the NOAA NMFS Northeast Fisheries Science Center. COI metabarcodes were identified using the MetaZooGene Barcode Atlas and Database (https://metazoogene.org/MZGdb) specific to the North Atlantic Ocean. A total of 181 species across 23 taxonomic groups were detected, including a number of sibling and cryptic species that were not discriminated by morphological taxonomic analysis of EcoMon samples. In all, 67 species of 15 taxonomic groups had ≥ 50 COI sequences; 23 species had >1,000 COI sequences. Comparative analysis of molecular and morphological data showed significant correlations between COI sequence numbers and microscopic counts for 5 of 6 taxonomic groups and for 5 of 7 species with >1,000 COI sequences for which both types of data were available. Multivariate statistical analysis showed clustering of samples within each region based on both COI sequence numbers and EcoMon counts, although differences among the three regions were not statistically significant. The results demonstrate the power and potential of COI metabarcoding for identification of species of metazoan zooplankton in the context of ecosystem monitoring.
Seasonality and stable isotopes in planktonic foraminifera off Cape Cod, Massachusetts

(American Geophysical Union, 2005-07-18) Keigwin, Lloyd D. ; Bice, Marley ; Copley, Nancy J.

Monthly samples of stratified plankton tows taken from the slope waters off Cape Cod nearly 25 years ago are used to describe the seasonal succession of planktonic foraminifera and their oxygen isotope ratios. The 15°C seasonal cycle of sea surface temperature (SST) accounts for a diverse mixture of tropical to subpolar species. Summer samples include various Globigerinoides and Neogloboquadrina dutertrei, whereas winter and early spring species include Globigerina bulloides and Neogloboquadrina pachyderma (dextral). Globorotalia inflata lives all year but at varying water depths. Compared with the fauna in 1960–1961 (described by R. Cifelli), our samples seem warmer. Because sea surface salinity varies little during the year, δ18O is mostly a function of SST. Throughout the year, there are always species present with δ18O close to the calculated isotopic equilibrium of carbonate with surface seawater. This raises the possibility that seasonality can be estimated directly from the range of δ18O in a sediment sample provided that the δ18O-salinity relationship is the same as today.
WHOI silhouette DIGITIZER version 1.0 user’s guide

(Woods Hole Oceanographic Institution, 2003-07) Little, William S. ; Copley, Nancy J.

WHOI Silhouette DIGITIZER is a MATLAB-based computer program for measuring the lengths of marine organisms in the macrozooplankton size range. DIGITIZER displays a scanned photographic image of a seawater slurry containing large numbers of marine organisms, upon which is superimposed a reference grid. DIGITIZER then allows you to measure the organisms' lengths using the cursor on the computer screen. DIGITIZER automatically calculates each organism’s biomass and generates spreadsheet compatible output listings of basic statistics derived from the data. DIGITIZER also produces text files of lengths, weights, and size-frequency histograms.
Data Help Desk BCO-DMO Lightning Talk

(Woods Hole Oceanographic Institution, 2020-02-18) Biddle, Matt ; Shepherd, Adam ; Kinkade, Danie ; Haskins, Christina ; Soenen, Karen ; Rauch, Shannon ; Copley, Nancy ; York, Amber ; Schloer, Conrad ; Saito, Mak A. ; Wiebe, Peter

BCO-DMO is the Biological and Chemical Oceanography Data Management Office. We help oceanography researchers who are funded by the National Science Foundation’s (NSF's) Division of Ocean Sciences' (OCE) Biological or Chemical Oceanography Sections or the Division of Polar Programs' Antarctic Organisms & Ecosystems Program manage their data, making them accessible over the internet. This lightning talk gives a brief overview of who we are, who we work with, and the types of data we manage.
Share Your Thoughts [poster]

(Woods Hole Oceanographic Institution, 2019-06-24) Soenen, Karen ; Biddle, Matt ; Copley, Nancy ; Haskins, Christina ; Rauch, Shannon ; York, Amber ; Kinkade, Danie ; Saito, Mak A. ; Shepherd, Adam ; Wiebe, Peter

Oceanographic data, when well-documented and stewarded toward preservation, have the potential to accelerate new science and facilitate our understanding of complex natural systems. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is funded by the NSF to document and manage marine ecosystem data, ensuring their discovery and access, and facilitating their reuse. The task of curating and providing access to research data is a collaborative process, with associated actors and critical activities occurring throughout the data’s life cycle. BCO-DMO supports all phases of the data life cycle and works closely with investigators to ensure open access of well-documented project data and information. Supporting this curation process is a flexible cyberinfrastructure that provides the means for data submission, discovery, and access; ultimately enabling reuse. Based upon community feedback, this infrastructure is undergoing evaluation and improvement to better meet oceanographic research needs. This poster presents an opportunity for you to provide feedback on enhancements yet to come. We invite you to think about your own research workflow of searching and accessing new data for research, and to provide your feedback through the poster’s interactive sections. Your input will help BCO-DMO improve its service to the research community.
Determining dominant scatterers of sound in mixed zooplankton populations

(Acoustical Society of America, 2007-12) Lavery, Andone C. ; Wiebe, Peter H. ; Stanton, Timothy K. ; Lawson, Gareth L. ; Benfield, Mark C. ; Copley, Nancy J.

High-frequency acoustic scattering techniques have been used to investigate dominant scatterers in mixed zooplankton populations. Volume backscattering was measured in the Gulf of Maine at 43, 120, 200, and 420 kHz. Zooplankton composition and size were determined using net and video sampling techniques, and water properties were determined using conductivity, temperature, and depth sensors. Dominant scatterers have been identified using recently developed scattering models for zooplankton and microstructure. Microstructure generally did not contribute to the scattering. At certain locations, gas-bearing zooplankton, that account for a small fraction of the total abundance and biomass, dominated the scattering at all frequencies. At these locations, acoustically inferred size agreed well with size determined from the net samples. Significant differences between the acoustic, net, and video estimates of abundance for these zooplankton are most likely due to limitations of the net and video techniques. No other type of biological scatterer ever dominated the scattering at all frequencies. Copepods, fluid-like zooplankton that account for most of the abundance and biomass, dominated at select locations only at the highest frequencies. At these locations, acoustically inferred abundance agreed well with net and video estimates. A general approach for the difficult problem of interpreting high-frequency acoustic scattering in mixed zooplankton populations is described.
Towards Capturing Provenance of the Data Curation Process at Domain-specific Repositories

( 2018-12-14) Shepherd, Adam ; Rauch, Shannon ; Schloer, Conrad ; Kinkade, Danie ; Biddle, Matt ; Copley, Nancy ; Saito, Mak A. ; Wiebe, Peter ; York, Amber

Data repositories often transform submissions to improve understanding and reuse of data by researchers other than the original submitter. However, scientific workflows built by the data submitters often depend on the original data format. In some cases, this makes the repository’s final data product less useful to the submitter. As a result, these two workable but different versions of the data provide value to two disparate, non-interoperable research communities around what should be a single dataset. Data repositories could bridge these two communities by exposing provenance explaining the transform from original submission to final product. A subsequent benefit of this provenance would be the transparent value-add of domain repository data curation. To improve its data management process efficiency, the Biological and Chemical Oceanography Data Management Office (BCO-DMO, https://www.bco-dmo.org) has been adopting the data containerization specification defined by the Frictionless Data project (https://frictionlessdata.io). Recently, BCO-DMO has been using the Frictionless Data Package Pipelines Python library (https://github.com/frictionlessdata/datapackage-pipelines) to capture the data curation processing steps that transform original submissions to final data products. Because these processing steps are stored using a declarative language they can be converted to a structured provenance record using the Provenance Ontology (PROV-O, https://www.w3.org/TR/prov-o/). PROV-O abstracts the Frictionless Data elements of BCO-DMO’s workflow for capturing necessary curation provenance and enables interoperability with other external provenance sources and tools. Users who are familiar with PROV-O or the Frictionless Data Pipelines can use either record to reproduce the final data product in a machine-actionable way. While there may still be some curation steps that cannot be easily automated, this process is a step towards end-to-end reproducible transforms throughout the data curation process. In this presentation, BCO-DMO will demonstrate how Frictionless Data Package Pipelines can be used to capture data curation provenance from original submission to final data product exposing the concrete value-add of domain-specific repositories.
Data Management and Reporting: BCO-DMO Data Management Services and Best Practices

(Woods Hole Oceanographic Institution, 2019-06-14) Rauch, Shannon ; Kinkade, Danie ; Biddle, Matt ; Copley, Nancy ; York, Amber ; Soenen, Karen ; Shepherd, Adam

The University-National Oceanographic Laboratory System (UNOLS) hosted an Early Career Chief Scientist Training Workshop in June 2019. The goal of this workshop was to help early-career marine scientists plan and write effective cruise proposals, develop collaborative sampling strategies and plans, become familiar with shipboard equipment and sampling at sea, and communicate major findings through writing of manuscripts and cruise reports. This presentation provides information on data management and reporting best practices for chief scientists. It includes information on: National Science Foundation (NSF) data policy requirements, writing a Data Management Plan (DMP), the data lifecycle, data publication, and shipboard data management recommendations.
Code and Software: How would you share yours? [poster]

(Woods Hole Oceanographic Institution, 2020-02-21) Biddle, Matt ; Copley, Nancy ; Haskins, Christina ; Rauch, Shannon ; Soenen, Karen ; York, Amber ; Kinkade, Danie ; Saito, Mak A. ; Shepherd, Adam ; Wiebe, Peter

BCO-DMO curates earth science data where models become increasingly important. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is a publicly accessible earth science data repository created to curate, publicly serve (publish), and archive digital data and information from biological, chemical and biogeochemical research conducted in coastal, marine, great lakes and laboratory environments. Recently, more and more of the projects submitted to BCO-DMO represent modeling efforts which further increase our knowledge of chemical and biological properties within the ocean ecosystem. We feel the time is at hand for the scientific community to begin a concerted and holistic approach to the curation of code and software.
Share Your Thoughts [poster]

(Woods Hole Oceanographic Institution, 2019-09-16) Kinkade, Danie ; Shepherd, Adam ; Biddle, Matt ; Copley, Nancy ; Haskins, Christina ; Schloer, Conrad ; Soenen, Karen ; Rauch, Shannon ; York, Amber ; Saito, Mak A. ; Wiebe, Peter

Oceanographic data, when well-documented and stewarded toward preservation, have the potential to accelerate new science and facilitate our understanding of complex natural systems. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is funded by the NSF to document and manage marine biological, chemical, physical, and biogeochemical data, ensuring their discovery and access, and facilitating their reuse. The task of curating and providing access to research data is a collaborative process, with associated actors and critical activities occurring throughout the data’s life cycle. BCO-DMO supports all phases of the data life cycle and works closely with investigators to ensure open access of well-documented project data and information. Supporting this curation process is a flexible cyberinfrastructure that provides the means for data submission, discovery, and access; ultimately enabling reuse. Based upon community feedback, this infrastructure is undergoing evaluation and improvement to better meet oceanographic research needs. This poster will introduce the repository and describe some of the strategic enhancements coming to BCO-DMO, and presents an opportunity for you to provide feedback on enhancements yet to come. We invite you to think about your own research workflow of searching and accessing new data for research, and to provide your feedback through the poster’s interactive sections. Your input can help BCO-DMO improve its service to the research community.

Copley Nancy J.

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