GLORIA

GEOMAR Library Ocean Research Information Access

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
  • 1
    facet.materialart.
    Unknown
    Informatics solutions for large ocean optics datasets (2016)
    Details
    Publication Date: 2022-05-25
    Description: Ocean Optics XXI, Glasgow, Scotland October 8-12 2012
    Description: Lack of observations that span the wide range of critical space and time scales continues to limit many aspects of oceanography. As ocean observatories and observing networks mature, the role for optical technologies and approaches in helping to overcome this limitation continues to grow. As a result the quantity and complexity of data produced is increasing at a pace that threatens to overwhelm the capacity of individual researchers who must cope with large high-resolution datasets, complex, multi-stage analyses, and the challenges of preserving sufficient metadata and provenance information to ensure reproducibility and avoid costly reprocessing or data loss. We have developed approaches to address these new challenges in the context of a case study involving very large numbers (~1 billion) of images collected at coastal observatories by Imaging FlowCytobot, an automated submersible flow cytometer that produces high resolution images of plankton and other microscopic particles at rates up to 10 Hz for months to years. By developing partnerships amongst oceanographers generating and using such data and computer scientists focused on improving science outcomes, we have prototyped a replicable system. It provides simple and ubiquitous access to observational data and products via web services in standard formats; accelerates image processing by enabling algorithms developed with desktop applications to be rapidly deployed and evaluated on shared, high-performance servers; and improves data integrity by replacing error-prone manual data management processes with generalized, automated services. The informatics system is currently in operation for multiple Imaging FlowCytobot datasets and being tested with other types of ocean imagery.
    Description: This research was supported by grants from the Gordon and Betty Moore Foundation, NSF, NASA, and ONR (NOPP).
    Repository Name: Woods Hole Open Access Server
    Type: Presentation
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 2
    facet.materialart.
    Unknown
    Environmental metabolomics : databases and tools for data analysis (2016)
    Elsevier
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Marine Chemistry 177 (2015): 366–373, doi:10.1016/j.marchem.2015.06.012.
    Description: Metabolomics is the study of small molecules, or ‘metabolites’, that are the end products of biological processes. While -omics technologies such as genomics, transcriptomics, and proteomics measure the metabolic potential of organisms, metabolomics provides detailed information on the organic compounds produced during metabolism and found within cells and in the environment. Improvements in analytical techniques have expanded our understanding of metabolomics and developments in computational tools have made metabolomics data accessible to a broad segment of the scientific community. Yet, metabolomics methods have only been applied to a limited number of projects in the marine environment. Here, we review analysis techniques for mass spectrometry data and summarize the current state of metabolomics databases. We then describe a boutique database developed in our laboratory for efficient data analysis and selection of mass spectral targets for metabolite identification. The code to implement the database is freely available on GitHub (https://github.com/joefutrelle/domdb). Data organization and analysis are critical, but often under-appreciated, components of metabolomics research. Future advances in environmental metabolomics will take advantage of continued development of new tools that facilitate analysis of large metabolomics datasets.
    Description: The field data populating the database comes from scientific cruises funded by grants from the National Science Foundation to EBK and KL (Atlantic Ocean, OCE-1154320) and E.V. Armbrust (Pacific Ocean, OCE-1205233). The laboratory experiment with coastal seawater was funded by a grant from the Gulf of Mexico Research Initiative to EBK and H.K. White. The laboratory experiments with microbial isolates and the database development are funded by the Gordon and Betty Moore Foundation through Grant GBMF3304 to EBK.
    Keywords: Metabolomics ; Data analysis ; Database design
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 3
    facet.materialart.
    Unknown
    Data Science Training Camp at Woods Hole Oceanographic Institution: Syllabus and slide presentations in 2020 (2020)
    Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-21
    Description: Presented at Data Science Training Camp, Woods Hole, MA, January, 22 - 23, 2020.
    Description: With data and software increasingly recognized as scholarly research products, and aiming towards open science and reproducibility, it is imperative for today's oceanographers to learn foundational practices and skills for data management and research computing, as well as practices specific to the ocean sciences. This educational package was developed as a data science training camp for graduate students and professionals in the ocean sciences and implemented at the Woods Hole Oceanographic Institution (WHOI) in 2019 and 2020. Here we provide materials for the 2020 camp which was delivered in-person during two afternoons (total of 8 hours), with two modules per afternoon. We aimed for ~40 participants per camp, with disciplines spanning Earth and life sciences and engineering. Disciplines at each table were mixed on the first afternoon but similar on the second afternoon. Contents of this package include the syllabus and slide presentations for each of the four modules: 1 "Good enough practices in scientific computing," 2 Data management, 3 Software development and research computing, and 4 Best practices in the ocean sciences. The 3rd module is split into two parts. We also include a poster presented at the 2020 Ocean Science Meeting, which has some results from pre- and post-surveys. Funding: The camp was funded by WHOI Academic Programs Office through a Doherty Chair in Education Award, with additional support from WHOI Ocean Informatics Working Group, WHOI Information Services, MBLWHOI Library, the NSF-funded Biological and Chemical Oceanography Data Management Office (BCO-DMO), and an NSF-funded XSEDE Jetstream Education Allocation TG-OCE190011. We also utilized resources from the NSF-funded Pangeo project.
    Description: The camp was funded by WHOI Academic Programs Office through a Doherty Chair in Education Award, with additional support from WHOI Ocean Informatics Working Group, WHOI Information Services, MBLWHOI Library, the NSF-funded Biological and Chemical Oceanography Data Management Office (BCO-DMO), and an NSF-funded XSEDE Jetstream Education Allocation TG-OCE190011. We also utilized resources from the NSF-funded Pangeo project.
    Keywords: Data science ; Best practices ; Data management ; Scientific computing ; Training ; Workshop ; Professional development ; Curriculum development
    Repository Name: Woods Hole Open Access Server
    Type: Presentation
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 4
    facet.materialart.
    Unknown
    Standards and practices for reporting plankton and other particle observations from images (2021)
    Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-27
    Description: 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).
    Description: This report was an outcome of a working group supported by the Ocean Carbon and Biogeochemistry (OCB) project office, which is funded by the US National Science Foundation (OCE1558412) and the National Aeronautics and Space Administration (NNX17AB17G). AN, SB, and CP conceived and drafted the document. IC, IST, JF and HS contributed to the main body of the document as well as the example files. All members of the working group contributed to the content of the document, including the conceptualization of the data table and metadata format. We would also like thank the external reviewers Cecile Rousseaux (NASA GSFC), Susanne Menden-Deuer (URI) Frank Muller-Karger (USF), and Abigail Benson (USGS) for their valuable feedback.
    Repository Name: Woods Hole Open Access Server
    Type: Working Paper
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    PAPER (OA)
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...