Open Science for Synthesis: Gulf Research Program

July 10 - July 28, 2017
NCEAS, Santa Barbara, CA

NCEAS Logo               Training in Open Science Enables Synthetic Science within the Gulf Research Program

Open Science for Synthesis: Gulf Research Program is a hands-on data science course for both early career and established researchers to gain skills in data science, including scientific synthesis, reproducible science, and data management. These skills are critical for understanding the complex environmental, human, and energy systems in the Gulf of Mexico, especially following large disturbance events like the Deepwater Horizon oil spill in 2010. This 3-week intensive training, convening in July 2017 at the National Center for Ecological Analysis and Synthesis (NCEAS) in Santa Barbara, CA, will revolve around scientific computing and scientific software for reproducible science.
 
The course will focus on techniques for data management, scientific programming, synthetic analysis, and collaboration techniques through the use of open-source, community-supported tools. Participants will learn skills for rapid and robust use of open source scientific software. These approaches will be explored and applied to scientific synthesis projects related to the Gulf of Mexico’s human, environmental, and energy systems, and will increase community capability and efficiency in synthesis research. The funding for this project is provided by a grant from the Gulf Research Program, dedicated to improving understanding of the Gulf of Mexico’s human, environmental, and energy systems in response to the Deepwater Horizon oil spill.

Topics

This is a hands-on course that incorporates skill building with group synthesis projects that cement the skills in real-world practice. The course will weave together several core themes which are reinforced – and injected into synthetic scientific research process – through daily work on group synthesis projects relevant to the Gulf Research Program. Core training themes will address:
  • Collaboration modes and technologies, virtual collaboration
  • Data management, preservation, and sharing
  • Data manipulation, integration, and exploration
  • Scientific workflows and reproducible research
  • Programming using agile and sustainable software practices
  • Data analysis and modeling
  • Communicating results to broad communities
Throughout the course participants will receive a solid foundation in computing fundamentals for doing synthetic research in today’s computational- and data-intensive era. This includes:
  • Instruction on languages like R and Python for data manipulation, analysis, and visualization
  • Analytical techniques for synthesis research, including meta-analysis and systematic reviews
  • Survey of general programming constructs, paradigms, and best practices
  • Exposure to the Linux/UNIX command line environment and useful tools
  • Discussion of cyberinfrastructure trends supporting open, networked, reproducible science

Group Synthesis Projects

Participants will form small synthesis teams that focus on utilizing the software skills they learn each day in the context of cross-cutting science research projects. Using an open community engagement process, participants will maximize their success in collaborative research that could potentially lead to publishable results. Project topics will focus on themes relevant to the Gulf Research Program, but will be participant-selected and executed with consultation from instructors.

Instructors

Matthew B. Jones (PI) is the Director of Informatics Research and Development at NCEAS and has expertise in environmental informatics, particularly software for management, integration, analysis, and modeling of data. Jones has taught at over 20 training workshops over a decade on data science topics including analysis in R, GitHub, programming (e.g., Python), data management, quality assessment and reporting, metadata and data infrastructure, scientific workflow systems, and other topics.

Amber Budden (co-PI) is the Director for Community Engagement and Outreach at DataONE. She holds a PhD in Ecology in addition to research experience in bibliometrics. She has coordinated and taught numerous workshops focused on data management for Earth and environmental science. Her skills include data management, science communication and outreach, and training evaluation.

Tracy Teal is a co-founder and the Executive Director of Data Carpentry. As an Assistant Professor at Michigan State University in bioinformatics, she saw that effective data skills have become foundational for research and that data training needs to scale along with data production. She is involved in the open source software and reproducible research communities, including as an Editor at the Journal for Open Source Software.

Mark Schildhauer is Director of Computing at NCEAS. His research interests include informatics, the semantic web, and scientific workflows, with a focus on environmental science. Schildhauer and colleagues developed the extensible observation ontology, OBOE, and a semantic annotation architecture that improves data discovery and re-use. He helped develop Ecological Metadata Language, is a co-founder of the Kepler scientific workflow project, and led the SEEK Knowledge Representation group.

Bryce Mecum is a scientific software engineer with expertise in data analysis and programming and data management systems, including systems like R, GitHub, repository software, Python, and UNIX. He has a background in fisheries modeling and management, and builds software systems supporting environmental synthesis.

Chris Lortie is an integrative scientist with expertise in community theory, sociology, and quantitative methods, specifically systematic reviews, meta-analysis, experimental design, R and statistical analyses. Collaboration and networks are central to his research both conceptually and internationally. As such, his empirical research involves biogeographical comparisons of many forms of community dynamics (plants, animals, & people). He is a Professor at York University in Canada and a Research Associate at NCEAS. He is the Editor in Chief for Oikos for all formal synthesis papers, and an editor for PLOSONE, PeerJ, Gigascience, and Nature Scientific Data.

Leah Wasser is the director of the earth analytics education initiative at Earth Lab, University of Colorado, Boulder and has a background in remote sensing ecology. She has been teaching data-intensive skills for almost 15 years. She is passionate about open, reproducible science and has lead and participated in many courses and data -intensive training events which empower participants to use tools including version control, data bases and scientific programming to work with heterogeneous data.

Julien Brun is a scientific programmer at NCEAS with expertise in data analysis and programming, data management systems, GIS, and analytical modeling. He has worked extensively in systems like R, GitHub, Python, and UNIX. His scientific background is in Ecohydrology and Earth observation techniques (remote sensing and GIS).

 

Participants

Alexander Ilich earned his bachelor’s degree in the Science of Natural and Environmental Systems from Cornell University in 2015. Currently he is a Master’s student concentrating in Marine Resource Assessment at the University of South Florida’s College of Marine Science. His research uses a towed underwater video camera system to study the relationships between habitat and fish communities to provide useful information for fisheries management in the Gulf of Mexico.

Alexander S. Kolker is an Associate Professor at the Louisiana Universities Marine Consortium, and also teaches in the Department of Earth and Environmental Sciences at Tulane University. He is a coastal geologist who has worked in systems around the nation, including the Florida Everglades, the wetlands surrounding Long Island, NY, and the Mississippi River Delta. His work has examined the influence of climatic and meteorological variability on coasts and wetlands, the role that subsidence plays as a driver of wetland loss in the Mississippi River Delta, and the patterns and processes associated with groundwater transport in deltas. Alex Kolker plays an active role in coastal restoration efforts in Louisiana, and has served on the Framework Development Team for the 2017 version of Louisiana’s Coastal Master Plan. He received his Bachelors' degree from the University of California, Santa Cruz and his Masters' and Doctoral degrees from Stony Brook University. He currently lives in New Orleans, LA..

Alexander Sacco is a Conservation Biology Ph.D. student at the University of Central Florida in the Marine Turtle Research Group. His research interests are seascape ecology, marine geophysics, remote sensing, image analysis, Indigenous knowledge, staekholder outreach, and environmental science. He has expertise in data analysis and programming in MATLAB, R, Python, ArcGIS, and image analysis algorithm development. Alex has earned an M.S. in Sea-ice geophysics from the University of Alaska Fairbanks and a B.S. in Applied Mathematics from SUNY: Empire State College. He is currently studying seascape ecology and movement ecology of sea turtles in the Gulf of Mexico, and is also an Adjunct Faculty at SUNY: Empire State College.

Andrea Dell'Apa is the Marine Restoration Specialist in Ocean Conservancy’s Gulf Restoration Program. He is originally from Italy, and holds a PhD in Coastal Resources Management and a MS in Marine Biology and Oceanography. Over the last decade, Andrea has researched on the management of coastal and marine resources, with a particular interest on shark ecology, ecosystem-based management, and restoration of marine resources in the Gulf of Mexico.

Brad Erisman is an Assistant Professor of Fisheries Ecology at the University of Texas at Austin and a National Academy of Sciences Early-Career Research Fellow. He is a co-founder of a bi-national research program (Gulf of California Marine Program), a member of the Species Survival Commission (Grouper-Wrasse Specialist Group) for the IUCN, and he serves on the Coastal Resources Advisory Committee for the Texas Parks and Wildlife Department. His research focuses on the reproductive biology, behavioral ecology, population dynamics, conservation and management of marine fishes.

Brittany Blomberg is a Postdoctoral Researcher at the Dauphin Island Sea Lab in Alabama. She holds a PhD in Coastal and Marine System Science from Texas A&M University-Corpus Christi. Her research focuses on the restoration ecology of coastal ecosystems, with a particular emphasis on oyster reef habitats. Currently, she is leading a team of scientists in an effort to synthesize ecological, social and economic data resulting from the implementation of more than a dozen living shoreline projects in coastal Alabama over the past decade.

Caitlin Young is a National Academies of Sciences, Engineering and Medicine Gulf Research Program Fellow working with the NOAA RESTORE Act Science Program. She has a PhD in Geosciences and her research is focused on biogeochemical reactions during groundwater-surface water exchange. She is involved in collaboration of RESTORE Act programs and is interested in translation of science into environmental management and decision making processes.

Cassandra Glaspie is a postdoctoral scholar at Oregon State University in the Fisheries and Wildlife Department. Cassandra’s research involves marine food webs and predator-prey interactions as they relate to changes in the environment. Her current research involves using bioenergetics and foraging models to quantify habitat quality for a variety of fish species in the Gulf of Mexico and the Pacific Northwest.

Courtney M. Page is a PhD Candidate at Northeastern University. Her expertise is in community resilience and social capital. She has a Master’s in Diplomacy and International Relations and an MPA from Seton Hall University. Her skills include data visualization and statistical and geospatial analysis.

Edward T. Sherwood is Senior Scientist at the Tampa Bay Estuary Program. He fosters partnerships and collaborations among regional scientists and resource managers to more effectively study, manage and restore the Tampa Bay estuarine ecosystem and its watershed. Ed’s past research has focused on monitoring and improving estuarine water quality, fisheries dynamics, and coastal habitat resources within the SW Florida region.

Haorui Wu is a postdoctoral fellow at the University of Calgary, Canada. With the interdisciplinary background of architecture, urban planning, urban design, and social work, he focuses on applying interdisciplinary knowledge and methods into community engaged design and the practice of sustainable development. Given the global context of climate change and disaster, his humanitarian architectural practice examines the post-disaster reconstruction and recovery of built environment through the lens of social and environmental justice, aiming to provide the benefits of architecture to underserved individuals, families, and communities.

Jessica Renee Henkel is an ecosystem science specialist at the Gulf Coast Ecosystem Restoration Council. In this position Jessica works to advance coastal restoration, data management and science coordination across several state and federal agencies. Jessica holds a PhD in Ecology and Evolutionary biology from Tulane University and a MS in Biology from the University of New Orleans. Her PhD dissertation focused on how environmental changes and habitat degradation are impacting the coastal habitats of the U.S. Gulf of Mexico and the effects these changes are having on the bird populations that migrate through them.

Kaitlin Frasier is an assistant project scientist at UC San Diego's Scripps Institution of Oceanography where she develops tools and techniques for using underwater acoustics to understand and manage marine mammal populations. Her expertise includes unsupervised learning, simulations and statistical modeling.

Kathryn Ireland is a research scientist at Montana State University. She holds a PhD in Forest Science and has experience with research into fire-climate-vegetation interactions. Her most recent research has focused on developing management alternatives for high elevation forests in the Greater Yellowstone region under future climate change and applying simulation models to evaluate their effectiveness at maintaining these forests into the future. She is interested in learning more about data science to increase the reproducibility and transparency of science relevant to natural resource management..

Kim de Mutsert is an assistant professor in the Department of Environmental Science and Policy at George Mason University. She received her PhD degree in Oceanography and Coastal Sciences from Louisiana State University. Her research interests include coastal and estuarine fish ecology, and ecosystem-based fisheries management. She studies the effects of environmental factors and fishing on fish abundance, biomass, community structure, and landings using end-to-end model simulations, large existing datasets, field surveys, and lab studies.

Kirsten Dorans is a science policy fellow with the Gulf Research Program of The National Academies of Sciences, Engineering, and Medicine, working with the Gulf Coast Ecosystem Restoration Council. She has a background in epidemiology, chemistry, and science communication and policy. She is interested in environmental health, communicating science to the public, and helping to develop public policies that are rooted in sound science.

Marcus W. Beck is a post-doctorate research fellow with the USEPA Gulf Ecology Division in Gulf Breeze, FL. He has a MSc and PhD in Conservation Biology, including a minor in Statistics from the Conservation Biology Program at the University of Minnesota. His research focuses on the analysis of large datasets to support decision-making in water quality monitoring programs. His current work with the EPA includes analysis of time series data from coastal ecosystems and the development of analytical tools using open-source software.

Mohammad Yassin is a graduate-level professor at Jackson State University. Dr. Yassin’s research interests include: water resources engineering, biological processes in environmental engineering, chemical processes in environmental engineering, and environmental modeling. He is an Administrator at the Mississippi Department of Environmental Quality, with over 25 years of practical engineering experience, enforcing federal environmental law. Dr. Yassin also participates with USAID, the USEPA National Environmental Research Center and the National Science Foundation. Dr. Yassin is a licensed Professional Engineer and Board Certified Environmental Engineer.

Patricia Varlea is a Geological Engineer and a research assistant from the Geotechnical Engineering Division at Texas A&M University. She is a PhD. student and member of the Stochastic Geomechanics Laboratory whose primary mission is the use of probabilistic modeling for risk assessment and informed decision-making. Patricia has conducted research on the integration of GIS and Bayesian Networks as a tool for environmental, social and economic risk assessment. Other interests include integrated geosciences and engineering, remote sensing, and geostatistics for improved policymaking.


Paula Moreno is a research scientist at the University of Southern Mississippi. I believe that multi-, inter-disciplinary research is the best approach to answer complex ecological questions in dynamic systems such as estuaries and oceans. My research goal is to understand the environmental factors (anthropogenic or not) that are key drivers of marine species behavior, distribution and abundance. I’m particularly interested in fisheries-marine mammal interactions and the effects of oil spills on these highly mobile marine top predators. I use GIS and multivariate statistics tools to understand the influence of multiple and cumulative environmental factors on marine species’ behavior, abundance and distribution patterns.

Samendra Sherchan received his BS and MS from Georgia College and his PhD in soil, water and environmental science from the University of Arizona. He is a registered environmental health specialist (REHS). His research program addresses critical issues at the intersection of water quality, environmental health microbiology and public health.His specific research interests include water pollution, environmental bioinformatics, metagenomics, microbial source tracking, fecal contamination, waterborne pathogens, emerging contaminants of concern,mechanisms of pathogen inactivation, risk assessment, water treatment, water reuse and challenges associated with safe drinking water, sanitation and hygiene.

Sunil Nepal is a Ph.D. Student at the School of Forestry and Wildlife Sciences, Auburn University. I am interested in applying spatial and statistical tools in analyzing forest ecology in and around the coastal area of the southeast USA. My research is focused on forest health monitoring and longleaf pine forest ecosystem.

Tingting Tang is a PhD student majoring in applied mathematics at University of Louisiana at Lafayette. Her research focus on the study of population dynamics and their interaction with the environment using continuous and discrete mathematical models.

Uyen Nguyen is a PhD student in Geosciences at Penn State University. She got her bachelor degrees in Geology and Math from the University of Oklahoma. Her interests include environmental sciences and biomass energy. During her PhD, she has been trained mostly in analytical organic chemistry and microbiology techniques and has some experiences in reactive transport modelling with MATLAB.

Vanessa Tobias is a wetland ecologist with expertise in biogeochemistry, plant and fish ecology, and statistical analysis. She holds a PhD in Wildlife and Fisheries Sciences from Louisiana State University. Vanessa is a Senior Environmental Scientist at the California Department of Fish and Wildlife’s Bay Delta Region and is part of the Interagency Ecological Program’s Synthesis Team. Her research focuses on topics that inform natural resource management and restoration practices.