Abstract
The National Science Foundation’s EarthCube End User Workshop was held at USC Wrigley Marine Science Center on Catalina Island, California in August 2013. The workshop was designed to explore and characterize the needs and tools available to the community that is focusing on microbial and physical oceanography research with a particular emphasis on ‘omic research. The assembled researchers outlined the existing concerns regarding the vast data resources that are being generated, and how we will deal with these resources as their volume and diversity increases. Particular attention was focused on the tools for handling and analyzing the existing data, on the need for the construction and curation of diverse federated databases, as well as development of shared, interoperable, “big-data capable” analytical tools. The key outputs from this workshop include (i) critical scientific challenges and cyber infrastructure constraints, (ii) the current and future ocean ‘omics science grand challenges and questions, and (iii) data management, analytical and associated and cyber-infrastructure capabilities required to meet critical current and future scientific challenges. The main thrust of the meeting and the outcome of this report is a definition of the ‘omics tools, technologies and infrastructures that facilitate continued advance in ocean science biology, marine biogeochemistry, and biological oceanography.
Highlights
A large group of ocean scientists and oceanographers are employing “’omics” approaches to characterize and quantify the nature, distribution and function of organisms in ocean ecosystems [1-3]. “’Omics” is defined here as the collective molecular or biochemical characterization of pools of biological molecules, such as genes and genomes, transcripts and transcriptomes, proteins and proteomes, and small molecules, metabolites and metabolomes, that together encode the structure and function of an organism or organisms, and can be used to explore their dynamics and flexibilities
To discuss the ‘omic data challenges for ocean scientists, an NSF EarthCube end user workshop was held at the USC Wrigley Marine Science Center on Catalina Island, California in August 2013
The NSF EarthCube initiative was launched in June 2011 to seek “transformative concepts and approaches to create integrated data management infrastructures across the Geosciences.”
Summary
A large group of ocean scientists and oceanographers are employing “’omics” approaches to characterize and quantify the nature, distribution and function of organisms in ocean ecosystems [1-3]. “’Omics” is defined here as the collective molecular or biochemical characterization of pools of biological molecules, such as genes and genomes, transcripts and transcriptomes, proteins and proteomes, and small molecules, metabolites and metabolomes, that together encode the structure and function of an organism or organisms, and can be used to explore their dynamics and flexibilities. Availability and analyses of these and similar datasets are improving our understanding of ecosystem processes and predicting their future trajectories, the necessary computational and analytical tools and infrastructures to manage, share, analyze and visualize them needs accelerated development and expansion. Workshop participants discussed these current challenges, and identified specific tools, technologies and infrastructures that will be required to continue advancing ‘omics applications in ocean science biology, marine biogeochemistry marine biology, and biological oceanography in the 21st century
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