OCB Best Practices Collection
https://repository.oceanbestpractices.org/handle/11329/422
2024-03-29T02:02:57ZRoadmap Towards Communitywide Intercalibration and Standardization of Ocean Nucleic Acids ‘Omics Measurements : Ocean Nucleic Acids ‘Omics Intercalibration and Standardization Workshop University of North Carolina, Chapel Hill, NC, USA January 8-11, 2020.
https://repository.oceanbestpractices.org/handle/11329/2159
Roadmap Towards Communitywide Intercalibration and Standardization of Ocean Nucleic Acids ‘Omics Measurements : Ocean Nucleic Acids ‘Omics Intercalibration and Standardization Workshop University of North Carolina, Chapel Hill, NC, USA January 8-11, 2020.
Berube, Paul; Gifford, Scott; Hurwitz, Bonnie; Jenkins, Bethany; Marchetti, Adrian; Santoro, Alyson E.
Maheigan, Mai; Benway, Heather
In January 2020, the US Ocean Carbon & Biogeochemistry (OCB) Project Office funded the Ocean
Nucleic Acids 'omics Intercalibration and Standardization workshop held at the University of
North Carolina in Chapel Hill. Thirty-two participants from across the US, along with guests from
Canada and France, met to develop a framework for standardization and intercalibration (S&I) of
ocean nucleic acid ‘omics (na’omics) approaches (i.e., amplicon sequencing, metagenomics and
metatranscriptomics). During the three-day workshop, participants discussed numerous topics,
including: a) sample biomass collection and nucleic acid preservation for downstream analysis,
b) extraction protocols for nucleic acids, c) addition of standard reference material to nucleic acid
isolation protocols, d) isolation methods unique to RNA, e) sequence library construction, and f )
integration of bioinformatic considerations. This report provides a summary of these and other topics
covered during the workshop and a series of recommendations for future S&I activities for na’omics
approaches.
2022-01-01T00:00:00ZStandards and Best Practices For Reporting Flow Cytometry Observations: a technical manual. Version 1.1.
https://repository.oceanbestpractices.org/handle/11329/2111.2
Standards and Best Practices For Reporting Flow Cytometry Observations: a technical manual. Version 1.1.
Neeley, Aimee; Soto, Inia; Proctor, Christopher
This technical manual guides the user through the detailed process of creating a standardized data table for the submission of taxonomic and morphological information collected by flow cytometry to long-term data repositories. Guidance is provided to produce documentation that describes data collection and processing techniques and outlines the creation of a data file. Field names that are required include scientificName that represents the lowest level taxonomic classification (e.g., genus if not certain of species, family if not certain of genus) and scientificNameID, the unique identifier from a reference database such as the World Register of Marine Species or AlgaeBase. The data table described here also includes the field names volume_analyzed_ul, measurementValue, measurementValueID and abun. The field names measurementValue and measurementValueID are recommended terms developed by NERC to describe morphological properties of cells. Data producers are required to submit their source data (.fcs files) as bundles and may optionally submit data plots as image files. Following these steps for standardization will help optimize the interoperability and reuse of these important data sets.
2023-01-01T00:00:00ZA critical review of the 15N2 tracer method to measure diazotrophic production in pelagic ecosystems.
https://repository.oceanbestpractices.org/handle/11329/1706
A critical review of the 15N2 tracer method to measure diazotrophic production in pelagic ecosystems.
White, Angelicque E.; Granger, Julie; Selden, Corday; Gradoville, Mary R.; Potts, Lindsey; Bourbonnais, Annie; Fulweiler, Robinson W.; Knapp, Angela N.; Mohr, Wiebke; Moisander, Pia H.; Tobias, Craig R.; Caffin, Mathieu; Wilson, Samuel T.; Benavides, Mar; Bonnet, Sophie; Mulholland, Margaret R.; Chang, Bonnie X.
Dinitrogen (N2) fixation is an important source of biologically reactive nitrogen (N) to the global ocean. The
magnitude of this flux, however, remains uncertain, in part because N2 fixation rates have been estimated following
divergent protocols and because associated levels of uncertainty are seldom reported—confounding comparison
and extrapolation of rate measurements. A growing number of reports of relatively low but potentially
significant rates of N2 fixation in regions such as oxygen minimum zones, the mesopelagic water column of the
tropical and subtropical oceans, and polar waters further highlights the need for standardized methodological
protocols for measurements of N2 fixation rates and for calculations of detection limits and propagated error
terms. To this end, we examine current protocols of the 15N2 tracer method used for estimating diazotrophic
rates, present results of experiments testing the validity of specific practices, and describe established metrics for
reporting detection limits. We put forth a set of recommendations for best practices to estimate N2 fixation rates
using 15N2 tracer, with the goal of fostering transparency in reporting sources of uncertainty in estimates, and
to render N2 fixation rate estimates intercomparable among studies.
2020-01-01T00:00:00ZStandards and practices for reporting plankton and other particle observations from images. Technical Manual.
https://repository.oceanbestpractices.org/handle/11329/1705
Standards and practices for reporting plankton and other particle observations from images. Technical Manual.
Neeley, A.; Beaulieu, S.; Proctor, C.; Cetinić, I.; Futrelle, J.; Soto Ramos, I.; Sosik, H.; Devred, E.; Karp-Boss, L.; Picheral, M.; Poulton, N.; Roesler, C.; Shepherd, A.
This technical manual guides the user through the process of creating a data table for the submission
of taxonomic and morphological information for plankton and other particles from images to a
repository. Guidance is provided to produce documentation that should accompany the submission
of plankton and other particle data to a repository, describes data collection and processing
techniques, and outlines the creation of a data file. Field names include scientificName that
represents the lowest level taxonomic classification (e.g., genus if not certain of species, family if not
certain of genus) and scientificNameID, the unique identifier from a reference database such
as the World Register of Marine Species or AlgaeBase. The data table described here includes the
field names associatedMedia, scientificName/ scientificNameID for both automated
and manual identification, biovolume, area_cross_section, length_representation
and width_representation. Additional steps that instruct the user on how to format their data
for a submission to the Ocean Biodiversity Information System (OBIS) are also included. Examples of
documentation and data files are provided for the user to follow. The documentation requirements
and data table format are approved by both NASA’s SeaWiFS Bio-optical Archive and Storage System
(SeaBASS) and the National Science Foundation’s Biological and Chemical Oceanography Data
Management Office (BCO-DMO).
2021-01-01T00:00:00ZProgress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing.
https://repository.oceanbestpractices.org/handle/11329/1397
Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing.
Saito, Mak A.; Bertrand, Erin M.; Duffy, Megan E.; Gaylord, David A.; Held, Noelle A.; Hervey IV, William Judson; Hettich, Robert L.; Jagtap, Pratik D.; Janech, Michael G.; Kinkade, Danie B.; Leary, Dagmar H.; McIlvin, Matthew R.; Moore, Eli K.; Morris, Robert M.; Neely, Benjamin A.; Nunn, Brook L.; Saunders, Jaclyn K.; Shepherd, Adam I.; Symmonds, Nicholas I.; Walsh, David A.
Ocean metaproteomics is an emerging field enabling discoveries about marine microbial communities and their impact on global biogeochemical processes. Recent ocean metaproteomic studies have provided insight into microbial nutrient transport, colimitation of carbon fixation, the metabolism of microbial biofilms, and dynamics of carbon flux in marine ecosystems. Future methodological developments could provide new capabilities such as characterizing long-term ecosystem changes, biogeochemical reaction rates, and in situ stoichiometries. Yet challenges remain for ocean metaproteomics due to the great biological diversity that produces highly complex mass spectra, as well as the difficulty in obtaining and working with environmental samples. This review summarizes the progress and challenges facing ocean metaproteomic scientists and proposes best practices for data sharing of ocean metaproteomic data sets, including the data types and metadata needed to enable intercomparisons of protein distributions and annotations that could foster global ocean metaproteomic capabilities.
2019-01-01T00:00:00ZGlobal Intercomparability in a Changing Ocean: an international time-series methods workshop, November 28-30, 2012 (Bermuda Institute of Ocean Sciences, St. Georges, Bermuda).
https://repository.oceanbestpractices.org/handle/11329/423
Global Intercomparability in a Changing Ocean: an international time-series methods workshop, November 28-30, 2012 (Bermuda Institute of Ocean Sciences, St. Georges, Bermuda).
Lorenzoni, L.; Benway, H.M.
To address methodological approaches and data intercomparability across shipboard time-‐series... This workshop focused specifically on the methods employed by each time-series with the aim of enhancing data comparability between sites. The workshop goals include the following:
• Review current oceanographic time-series core sampling and analytical methodologies and rationale behind protocol differences
• To the extent possible, attempt to define standardized methods applicable across time-series
• Attempt to reconcile differences in variable nomenclature
• Examine new techniques available for more accurate and simplified measurements
• Explore the roles of autonomous sensors in improving and expanding time-series measurements
• Coordinate a best practices publication to facilitate data inter-comparison across time-series site
2013-01-01T00:00:00ZA User’s guide for selected autonomous biogeochemical sensors. An outcome from the 1st IOCCP International Sensors Summer Course, June 22 – July 1, 2015, Kristineberg, Sweden.
https://repository.oceanbestpractices.org/handle/11329/397
A User’s guide for selected autonomous biogeochemical sensors. An outcome from the 1st IOCCP International Sensors Summer Course, June 22 – July 1, 2015, Kristineberg, Sweden.
Lorenzoni, Laura; Telszewski, Maciej; Benway, Heather; Palacz, Artur
Over the last decade, ocean observing technology has risen to the challenge
of scientist by
providing them with cost
-
effective tools that can take measurements of essential
biogeochemical variables autonomously. Yet, despite these options becoming more readily
available, there is still a gap between the technology and the end -
user (investigators and
technicians that deploy these technologies) due to a collective lack of training, in
-
depth
knowledge, and community coordination. There is also a disconnect between data
gathering by autonomous sensors and data quality, which is a major obstacle, as these
sensors are already being deployed on autonomous platforms and in conjunction with
ship
-
based sampling to broaden data coverage in space and time.
2017-01-01T00:00:00Z