Wiebe Peter H.

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Wiebe

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Peter H.

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0000-0002-6059-4651

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A high-resolution bathymetry map for the Marguerite Bay and adjacent west Antarctic Peninsula shelf for the Southern Ocean GLOBEC Program

(Woods Hole Oceanographic Institution, 2004-05) Bolmer, S. Thompson ; Beardsley, Robert C. ; Pudsey, C. ; Morris, P. ; Wiebe, Peter H. ; Hofmann, Eileen E. ; Anderson, John B. ; Maldonado, A.

One objective of the U.S. Southern Ocean Global Ocean Ecosystems Dynamics (SO GLOBEC) program is to gain a better understanding of the sea floor bathymetry in the program study area. Much of Marguerite Bay and the adjacent shelf west of the Antarctic Peninsula were poorly charted when the SO GLOBEC program started in 2000. Before the first SO GLOBEC cruise, an improved local area version (ETOPO8.2A) was created from the Smith and Sandwell (1997) topo_8.2.img 2-minute digital gridded bathymetry for the study area. The first SO GLOBEC mooring cruise on the R/V Lawrence M. Gould (March 2001) showed that the 2-minute spatial resolution of ETOPO8.2A did not resolve many of the canyons and abrupt changes in topography that characterize Marguerite Bay and the inner- to mid-shelf region. It also was not particularly accurate in the more uniform terrain regions. We then decided to collect as much multibeam bathymetry data as possible during the SO GLOBEC broad-scale survey cruises on the R/VIB Nathaniel B. Palmer and combine these data with all other available multibeam and trackline bathymetry data to construct a digital bathymetry database and map for the study area. The resulting database has high-resolution data over much of the shelf and parts of Marguerite Bay gridded at 2 seconds in latitude and 6 seconds in longitude spacing between 65° to 71° S and 65° to 78° W. This technical report describes the steps taken to assemble and construct this database and how to access the data via the Internet.
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.
Improved parametrization of Antarctic krill target strength models

(Acoustical Society of America, 2006-01) Lawson, Gareth L. ; Wiebe, Peter H. ; Ashjian, Carin J. ; Chu, Dezhang ; Stanton, Timothy K.

There are historical discrepancies between empirical observations of Antarctic krill target strength and predictions using theoretical scattering models. These differences are addressed through improved understanding of key model parameters. The scattering process was modeled using the distorted-wave Born approximation, representing the shape of the animal as a bent and tapered cylinder. Recently published length-based regressions were used to constrain the sound speed and density contrasts between the animal and the surrounding seawater, rather than the earlier approach of using single values for all lengths. To constrain the parameter governing the orientation of the animal relative to the incident acoustic wave, direct measurements of the orientation of krill in situ were made with a video plankton recorder. In contrast to previous indirect and aquarium-based observations, krill were observed to orient themselves mostly horizontally. Averaging predicted scattering over the measured distribution of orientations resulted in predictions of target strength consistent with in situ measurements of target strength of large krill (mean length 40–43 mm) at four frequencies (43–420 kHz), but smaller than expected under the semi-empirical model traditionally used to estimate krill target strength.
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.
Warm core rings : an interdisciplinary study of warm core ring physics, chemistry, and biology; R/V Endeavor, R/V Knorr, R/V Oceanus April 1982 cruise reports

(Woods Hole Oceanographic Institution, 1982) Joyce, Terrence M. ; Kester, Dana R. ; Wiebe, Peter H.
Sound scattering by live zooplankton and micronekton : empirical studies with a dual-beam acoustical system

(Acoustical Society of America, 1990-11) Wiebe, Peter H. ; Greene, Charles H. ; Stanton, Timothy K. ; Burczynski, Janusz

Measurements and analyses are presented of the backscattering of 420-kHz sound by 43 individual animals of representative zooplanktonic and micronektonic taxa. Direct measurements of an individual's target strength were made with a commercial dual-beam sonar system in an enclosure filled with filtered seawater deployed off a dock at Friday Harbor, Washington. The dependence of target stengths upon individual length, wet weight, and dry weight was investigated. In addition, the ``target strength'' and statistical variations of echo amplitude due to variations in shape and orientation of the organism were compared with acoustic scattering models involving different shapes (the general shapes of the sphere, and straight and uniformly bent finite cylinders were used along with attempts to take into account roughness). It was found that: (1) backscattering cross sections are proportional to volume of the organisms rather than area as would be predicted by a sphere scattering model, (2) mean target strength based on average backscattering crossection is best described by the bent cylinder model whose modal series solution is truncated, and (3) the fluctuations of the echo amplitudes are well described by the Rice probability density function whose shape parameter is related to the randomly rough straight cylinder model. These extensive studies showed conclusively that the elongated animals scattered sound more like elongated targets than spherical ones, thus demonstrating the need for models more sophisticated than the spherical ones routinely used to date. The data and model analyses provide a basis for devising future acoustical data acquisition and processing techniques for bioacoustical field studies.
Euphausiid distribution, abundance and succession in North Atlantic warm-core ring 82B

( 2004-11-03) Endo, Yoshinari ; Wiebe, Peter H.

Zooplankton collections were made with a Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS) both day and night in warm-core ring 82B in the North Atlantic Ocean and at night in the Slope Water between March and August 1982. Species succession of euphausiids in 82B was presented during the lifespan of this warm-core ring, aiming at providing basic information on possible response of North Atlantic marine ecosystem to global warming. Species succession of euphausiids (32 species) in this long-lived warm-core ring was investigated. Major physical changes of 82B occurred in March-April by convective mixing and thermostad cooling, in April/May by stratification of the surface waters, and in August by the interaction with Gulf Stream. Substantial changes in species composition were observed that corresponded to these physical changes. Four different patterns were found in temporal change in abundance of warm-water species. There were species that decreased in number from March to August, species that decreased from March to June, but increased in August, species that increased from Match to August, and species that showed no systematic trend. These differences may be attributable to a species tolerance to the thermostad temperature decrease and their vertical distribution. There was also a large change from April to June with ascendance of the transition species, Thysanoessa gregaria. Cold-water species had variable patterns of abundance in 82B and occurred more abundantly in the Slope Water than in the ring. The monthly percentage decrease in the abundance of warm-water species in 82B was high compared with that of cold-water species in cold-core rings as a result of the more rapid changes in the physical structure and the shorter lifetimes of warm-core rings in the Western North Atlantic.
Micronekton biomass distribution, improved estimates across four north Atlantic basins

(Elsevier, 2019-11-27) Klevjer, Thor A. ; Melle, Webjørn ; Knutsen, Tor ; Strand, Espen ; Korneliussen, Rolf J. ; Dupont, Nicolas ; Vea Salvanes, Anne Gro ; Wiebe, Peter

Distribution of micronekton was investigated during early summer of 2013, using data from a cruise covering the central parts of four north Atlantic basins, the Norwegian Sea (NS), Iceland Sea (ICS), Irminger Sea (IRS), and Labrador Sea (LS). Continuous underway acoustics mapped vertical and horizontal distributions, and trawl sampling provided data on biomass and taxonomic composition. The hull mounted acoustics and trawl catches suggested that, among the four basins, biomass of epipelagic, larger nektonic species (>20 cm length) during the cruise was highest in the NS and ICS basins, while mesopelagic non-gelatinous micronekton biomass peaked in the IRS and LS basins. Biomass of Scyphozoa was also about 1 order of magnitude higher in IRS and LS compared to ICS and NS. In ICS and NS, crustaceans made up about 50% of total non-gelatinous micronekton biomass, with fish making up less than 20% of total biomass. In contrast, fish constituted more than 60% of non-gelatinous biomass of catches in IRS and LS. In catches from ICS and NS the myctophid Benthosema glaciale dominated the catches, whereas bathylagids, gonostomatids, barracudinas and stomiids contributed to the high biomass densities of fish in IRS and LS. In addition to the differences in biomass between the basins, the acoustic measurements suggested gradients within the north-eastern basins, and large differences in vertical distribution of biomass between the basins during the cruise.
Collaborative research : EarthCube building blocks, leveraging semantics and linked data for geoscience data sharing and discovery, OceanLink

( 2013-10-28) Wiebe, Peter H. ; Chandler, Cynthia L. ; Raymond, Lisa ; Shepherd, Adam ; Finin, Tim ; Narock, Tom ; Arko, Robert A. ; Carbotte, Suzanne M. ; Hitzler, Pascal ; Cheatham, Michelle ; Krisnadhi, Adila

The OceanLink EarthCube project will apply state-of-the-art Semantic Web Technologies to support data representation, discovery, analysis, sharing, and integration of datasets from the global oceans, and related resources including meeting abstracts and library holdings. Ships are a principal platform from which a wide spectrum of oceanographic data are collected. At the University of Maryland, Baltimore County, semantic relationships will be extracted from text for use in developing methods that efficiently identify relationships across distributed oceanographic datasets. At Wright State University integration of disparate data will occur by refining and applying leading edge technology from the Semantic Web, ontologies, and linked data. From the MBLWHOI Library, DSpace content will be published as Linked Open Data, providing relationships between oceanographic datasets, publications, conference presentations, and funded National Science Foundation projects. Teams of researchers at the Lamont-Doherty Earth Observatory and the Woods Hole Oceanographic Institution will develop Use Cases that represent the needs of the oceanographic research community and will publish oceanographic dataset catalogs as Linked Open Data. A key contribution will be semantically-enabled cyberinfrastructure components capable of automated data integration across distributed repositories. These efforts will ultimately lead to generalized computational techniques applicable to all of EarthCube.
Habitat usage by the cryptic copepods Pseudocalanus moultoni and P. newmani on Georges Bank (Northwest Atlantic)

( 2015-10-04) Bucklin, Ann ; McGillicuddy, Dennis J. ; Wiebe, Peter H. ; Davis, Cabell S.

The cryptic copepod species, Pseudocalanus moultoni and P. newmani, co-occur on Georges Bank and in the Gulf of Maine (Northwest Atlantic); even recent studies have reported results and conclusions based on examination of the combined species. Species-specific PCR (SS-PCR) based on mitochondrial cytochrome oxidase I (COI) sequence divergence was used in this study to discriminate the species. Species-specific descriptions of habitat usage and predicted patterns of transport and retention on Georges Bank were made by mapping distributions and calculating abundances of each species from January to June, 1999 for four vertical strata (0-15 m, 15-40 m, 40-100 m, and 0-100 m) and five regions (Northern Flank, Bank Crest, Northeast Peak, Southern Flank, and Slope Water) identified on the basis of bathymetry and circulation. Patterns of distribution and abundance for the two species during January to June, 1999 were largely consistent with those described based on vertically integrating mapping and analysis for the same period in 1997 by McGillicuddy and Bucklin (2002). The region-specific and depth-stratified analyses allowed further discrimination in habitat usage by the species and confirmed the distinctive patterns for the two species. The observed differences between the species in abundances among the five regions and three depth strata over Georges Bank impact their transport trajectories. The concentration of P. moultoni in deep layers likely explains the higher rates of retention and lower rates of advective loss of this species from the Bank, compared to P. newmani, which may be more subject to wind-driven transport in the surface layer. Accurate identification and discrimination of even closely-related and cryptic species is needed to ensure full understanding and realistic predictions of changes in diversity of zooplankton and the functioning of pelagic ecosystems.
Life cycle of the suctorian ciliate Ephelota plana attached to the krill Euphausia pacifica

( 2016-11) Endo, Yoshinari ; Fujii, Daiki ; Nishitani, Goh ; Wiebe, Peter

The hypothesis that life cycle of an epibiotic suctorian ciliate Ephelota plana is adapted to the molt cycle of the krill Euphausia pacifica collected in Saanich Inlet, Canada was evaluated. The infestation prevalence of E. plana and the number of individuals attached increased from postmolt stage to premolt stage of E. pacifica, and concurrently cell growth of E. plana was observed. Budding individuals of E. plana first appeared at early premolt stage and increased to 21% at late premolt stage. Thus the life cycle of E. plana seems to be adapted to the molt cycle of E. pacifica.
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.
Accounting for biological and physical sources of acoustic backscatter improves estimates of zooplankton biomass

( 2007-09-26) Warren, Joseph D. ; Wiebe, Peter H.

In order to convert measurements of backscattered acoustic energy to estimates of abundance and taxonomic information about the zooplankton community, all of the scattering processes in the water column need to be identified and their scattering contributions quantified. Zooplankton populations in the eastern edge of Wilkinson Basin in the Gulf of Maine in the Northwest Atlantic were surveyed in October 1997. Net tow samples at different depths, temperature and salinity profiles, and multiple frequency acoustic backscatter measurements from the upper 200 meters of the water column were collected. Zooplankton samples were identified, enumerated, and measured. Temperature and salinity profiles were used to estimate the amount of turbulent microstructure in the water column. These data sets were used with theoretical acoustic scattering models to calculate the contributions of both biological and physical scatterers to the overall measured scattering level. The output of these predictions shows that the dominant source of acoustic backscatter varies with depth and acoustic frequency in this region. By quantifying the contributions from multiple scattering sources, acoustic backscatter becomes a better measure of net-collected zooplankton biomass.
Data collected daily along the ship track in JGOFS format from ARSV Laurence M. Gould and RVIB Nathaniel B. Palmer cruises to the Southern Ocean from 2001-2003 as part of the Southern Ocean GLOBEC project.

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-03-27) Beardsley, Robert C ; Costa, Daniel P. ; Limeburner, Richard ; Torres, Joseph J. ; Wiebe, Peter H.

Data collected daily along the ship track in JGOFS format from ARSV Laurence M. Gould and RVIB Nathaniel B. Palmer cruises to the Southern Ocean from 2001-2003 as part of the Southern Ocean GLOBEC project For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/2345
Broad-scale station numbers and locations from the US-GLOBEC Georges Bank project

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-01-23) Wiebe, Peter H.

Broad-scale station numbers and locations from the US-GLOBEC Georges Bank project For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/2329

Wiebe Peter H.

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