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Journal of Marine Science and Engineering
Article . 2016 . Peer-reviewed
License: CC BY
Data sources: Crossref
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Dynamic Reusable Workflows for Ocean Science

Authors: Richard Signell; Filipe Fernandes; Kyle Wilcox;

Dynamic Reusable Workflows for Ocean Science

Abstract

Digital catalogs of ocean data have been available for decades, but advances in standardized services and software for catalog searches and data access now make it possible to create catalog-driven workflows that automate—end-to-end—data search, analysis, and visualization of data from multiple distributed sources. Further, these workflows may be shared, reused, and adapted with ease. Here we describe a workflow developed within the US Integrated Ocean Observing System (IOOS) which automates the skill assessment of water temperature forecasts from multiple ocean forecast models, allowing improved forecast products to be delivered for an open water swim event. A series of Jupyter Notebooks are used to capture and document the end-to-end workflow using a collection of Python tools that facilitate working with standardized catalog and data services. The workflow first searches a catalog of metadata using the Open Geospatial Consortium (OGC) Catalog Service for the Web (CSW), then accesses data service endpoints found in the metadata records using the OGC Sensor Observation Service (SOS) for in situ sensor data and OPeNDAP services for remotely-sensed and model data. Skill metrics are computed and time series comparisons of forecast model and observed data are displayed interactively, leveraging the capabilities of modern web browsers. The resulting workflow not only solves a challenging specific problem, but highlights the benefits of dynamic, reusable workflows in general. These workflows adapt as new data enter the data system, facilitate reproducible science, provide templates from which new scientific workflows can be developed, and encourage data providers to use standardized services. As applied to the ocean swim event, the workflow exposed problems with two of the ocean forecast products which led to improved regional forecasts once errors were corrected. While the example is specific, the approach is general, and we hope to see increased use of dynamic notebooks across geoscience domains.

Keywords

ocean forecasting, Naval architecture. Shipbuilding. Marine engineering, Ocean modeling, VM1-989, interoperability, GC1-1581, Oceanography, Data management, Numerical modeling, Catalog services, Data services, ocean modeling, numerical modeling; reproducibility; catalog services; data services; web services; metadata; ocean forecasting; ocean modeling; data management; data system; interoperability; OPeNDAP; THREDDS; CSW; Jupyter Notebooks, CSW, Ocean forecasting, Data system, reproducibility, Web services, data services, Metadata, 020, data system, metadata, Interoperability, Reproducibility, numerical modeling, web services, OPeNDAP, data management, THREDDS, catalog services, Jupyter Notebooks

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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
1
Average
Average
Average
Green
gold