To meet societal needs, modern estuarine science needs to be interdisciplinary and collaborative, combine discovery with hypotheses testing, and be responsive to issues facing both regional and global stakeholders. Such an approach is best conducted with the benefit of data-rich environments, where information from sensors and models is openly accessible within convenient timeframes. Here, we introduce the operational infrastructure of one such data-rich environment, a collaboratory created to support (a) interdisciplinary research in the Columbia River estuary by the multi-institutional team of investigators of the Science and Technology Center for Coastal Margin Observation & Prediction and (b) the integration of scientific knowledge into regional decision making. Core components of the operational infrastructure are an observation network, a modeling system and a cyber-infrastructure, each of which is described. The observation network is anchored on an extensive array of long-term stations, many of them interdisciplinary, and is complemented by on-demand deployment of temporary stations and mobile platforms, often in coordinated field campaigns. The modeling system is based on finiteelement unstructured-grid codes and includes operational and process-oriented simulations of circulation, sediments and ecosystem processes. The flow of information is managed through a dedicated cyber-infrastructure, conversant with regional and national observing systems.
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António M. Baptista has a B.Sc. in Civil Engineering from Academia Militar, Portugal and M.Sc. and Ph.D. degrees in Civil Engineering from the Massachusetts Institute of Technology, United States. He is a Professor at the Oregon Health & Science University, U.S. and serves as the Director of the Center for Coastal Margin Observation & Prediction, a multi-institutional Science and Technology Center funded by the National Science Foundation. Prof. Baptista’s research is broadly interdisciplinary, anchored on a core expertise in estuarine science and in observation & modeling systems. He has published about 70 peerreviewed articles, often collaboratively, in areas including computational science; physical, biogeochemical & microbial oceanography; fisheries; natural hazards; and computer science. He provides scientific and operational coordination for the SATURN collaboratory.
Charles Seaton has a B.Sc. in Botany from the University of Massachusetts at Amherst and a M.S. in Environmental Science and Engineering from the Oregon Graduate Institute of Science & Technology. He is a Research Associate at the Oregon Health & Science University, U.S., and the coordinator of the cyber-infrastructure team for the Center for Coastal Margin Observation & Prediction. Mr. Seaton has published 9 peer-reviewed articles.
Michael P. Wilkin has a B.Sc. in Oceanography from University of Southampton, United Kingdom. With over 25 years of experience in the design and deployment of oceanographic instrumentation, he is a Senior Research Associate at Oregon Health & Science University, U.S., and manages the design, implementation and maintenance of the estuarine and coastal elements of the SATURN observation network from a field station in Astoria, Oregon, U.S. Mr. Wilkin has published 10 peerreviewed articles.
Sarah F. Riseman has a B.Sc. in Zoology from the University of Massachusetts, U.S., and a M.Sc. in Marine Biology from the College of Charleston, U.S. She is a Research Associate at Oregon Health & Science University, U.S., working on quality assurance and quality control of biogeochemical data for the Center for Coastal Margin Observation & Prediction. Before joining the center in 2010, she had over 10 years of oceanographic research experience including operation and maintenance of a diversity of instrumentation for biogeochemical measurements and over 13 cumulative months of research at sea or in remote field locations. She has published 13 peer-reviewed articles.
Joseph A. Needoba has a B.Sc. (Biology) degree and a Ph.D. (Botany) degree from the University of British Columbia, Canada. He is an Assistant Professor at Oregon Health & Science University, U.S, and an Investigator in the Center for Coastal Margin Observation & Prediction. He has published more than 20 peer-reviewed papers in the fields of oceanography and estuarine science.
David Maier is Maseeh Professor of Emerging Technologies in the Department of Computer Science at Portland State University, U.S. His research interests include scientific information management, datastream systems, superimposed information and declarative cloud programming. Prof. Maier has a dual BA (Honors College) in Mathematics and Computer Science from the University of Oregon, U. S. and a Ph.D. in Electrical Engineering and Computer Science from Princeton University, U.S. He is an ACM Fellow, a Senior Member of IEEE and a member of SIAM. He has published 95 peer-reviewed articles in journals and selective conferences. He is a member of the CMOP cyber-infrastructure team.
Paul J. Turner has a B.Sc in Mathematics from Boise State University. He is a Senior Research Assistant at the Oregon Health & Science University, U.S. As a member of the cyber-infrastructure team, he manages operational details of the Virtual Columbia River for the Center for Coastal Margin Observation & Prediction. He has published 9 peerreviewed articles.
Tuomas Kärnä has a M.Sc in Technology from Helsinki University of Technology, Finland and a Ph.D. in Applied Mathematics from Université Catholique de Louvain, Belgium. He is a Post-Doctoral Fellow at the Oregon Health & Science University, U.S. He has published 14 peer-reviewed articles.
Jesse E. Lopez has a B.A. in History from the University ofWashington, U.S. He is a Ph.D. candidate at the Oregon Health & Science University, U.S. and a Department of Energy Computational Science Graduate Fellow.
Lydie Herfort received an undergraduate diplomat (D.E.U.G.) in Biology from the University of Caen, France, and a third year of B.Sc. and a Ph.D. degree in aquatic biology from Queen Mary University London, United Kingdom. She is a Senior Research Associate at the Center for Coastal Margin Observation & Prediction at Oregon Health & Science University, U.S. Dr. Herfort studies the ecology and physiology of aquatic microorganisms—specifically bacteria, archaea and protists— to assess their impacts on biogeochemical cycles. Her work involves many aspects of SATURN’s collaboratory, including traditional vessel-based campaigns and adaptive microbial water sample collection with an Environmental Sample Processor. She has published 23 peerreviewed articles.
V.M. Megler is a Post-Doctoral Fellow in Computer Science at Portland State University, U.S., having received a Ph.D. there in 2015. Megler's most recent industry position was as Executive IT Architect at IBM, publishing more than 20 industry technical papers on applications of emerging technologies to industry problems. Current research centers on applying Information Retrieval techniques to scientific data, ranging from oceanographic to genomic data. General research interests include applications of emerging technologies, scientific information management and spatio-temporal databases. Megler has 11 peer-reviewed research articles and holds 2 patents.
Craig McNeil has a B.Sc. in physics from Heriot-Watt University, Scotland and a Ph.D. from University of Victoria, Canada. He is a Principal Oceanographer at the Applied Physics Laboratory at the University of Washington, U.S. His multi-disciplinary research focuses on upper ocean processes and interactions. He has published more than 20 peer-reviewed articles. He coordinates the CMOP autonomous underwater vehicles program.
Byron C. Crump has a M.S. and Ph.D. in Oceanography from the University of Washington, U.S. He is an Associate Professor in Ocean Ecology and Biogeochemistry at the College of Earth, Ocean and Atmospheric Sciences, Oregon State University, U.S. His research explores the ecology, biodiversity and genomics of microbes in lakes, rivers, estuaries and coastal oceans. He has published 55 peer-reviewed articles and is an editor for the textbook Estuarine Ecology 2nd Ed. (Wiley Interscience).
Tawnya D. Peterson has a B.Sc. in Biology from Mount Allison University (Sackville, Canada) and a Ph.D. in Oceanography from the University of British Columbia (Vancouver, Canada). She is an Assistant Professor at Oregon Health & Science University, U.S., and an Investigator in the Center for Coastal Margin Observation & Prediction. She has published over 30 peer-reviewed papers in the fields of oceanography and environmental science.
Yvette H. Spitz has a B.Sc. in Physics and a M.Sc. in Oceanography from the University of Liège, Belgium, a M.Sc. in Physical Oceanography from Florida State University, U.S., and a Ph.D. in Oceanography from Old Dominion University, U.S. She is a Professor in Ocean Ecology and Biogeochemistry at the College of Earth, Ocean and Atmospheric Sciences at Oregon State University, U.S., and has served for the last two years as co-director of the Center for Coastal Margin Observation & Prediction. Her research includes ecosystem dynamics and physical-biological interactions in the world ocean, with ecosystem modeling spanning tropical microbes to ice algae. She is an expert in data assimilation applied to coupled circulation and ecosystem models. She has published ~45 peer-reviewed articles in areas including circulation and biogeochemical models from coastal to open ocean and ice cover ocean; particle filter and variational adjoint data assimilation.
Holly M. Simon has B.S. (Biology) and B.A. (Chemistry) degrees from the Metropolitan State College of Denver, U.S., and a Ph.D. degree (Bacteriology) from the University ofWisconsin at Madison, U.S. She is an Associate Professor in the Institute of Environmental Health and an Investigator in the Center for Coastal Margin Observation & Prediction at Oregon Health & Science University, U.S. She has published over 20 peer-reviewed articles across diverse areas of environmental microbiology, with emphasis on the application of gene sensing technologies to assess the provisioning of, and perturbations to, microbial ecosystem services.
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Baptista, A.M., Seaton, C., Wilkin, M.P. et al. Infrastructure for collaborative science and societal applications in the Columbia River estuary. Front. Earth Sci. 9, 659–682 (2015). https://doi.org/10.1007/s11707-015-0540-5
- numerical modeling
- Columbia River