Summer Institute 2013

A three-week intensive training workshop in ecological analysis and synthesis was offered by NCEAS in Santa Barbara from June 19 through July 10, 2013. Participants received hands-on guided experience using best practices in the technical aspects that underlie successful synthesis – from data discovery and integration to analysis and visualization, and special techniques for collaborative scientific research. The Packard Foundation provided generous support for this summer’s institute.

NCEAS Summer Institute, 2013


In a highly competitive application process, twenty-two participants were selected from a pool of nearly 400 international applicants to participate in the 2013 Summer Institute.

Sharon  Baruch-Mordo The Nature Conservancy
Isabella Bertani University of Parma
Jill R. Bourque U.S. Geological Survey
Iain Caldwell University of Hawaii
Jennifer Costanza North Carolina State University
Cristian Dambros University of Vermont
Kristen Dybala University of California, Davis
Xueying (Shirley) Han University of California, Santa Barbara
David J. Harris University of California, Davis
Alison Haupt Northwest Fisheries Science Center
Shalene Jha University of Texas, Austin
Holly Jones Northern Illinois University
A. Michelle Lawing University of Tennessee (NIMBioS)
Jonathan Lefcheck Virginia Institute of Marine Science
Antonin Machac State University of New York, Stony Brook
Michelle McCrackin Washington State University
Erika Mudrak Iowa State University
Sarah H Olson Wildlife Conservation Society, Canada
Steve Powers University of Notre Dame
Narcisa Pricope Southern Oregon University
Sigrid Smith University of Michigan
Brittany Teller Pennsylvania State University



Instructors advised participants in small-group synthesis projects, and also lead daily hands-on exercises that cover a breadth of topics.  2013 Instructors included:

Ben Bolker - A professor in the departments of Mathematics & Statistics and of Biology at McMaster University. His interests range widely in spatial, theoretical, mathematical, computational and statistical ecology, evolution and epidemiology; plant community, ecosystem, and epidemic dynamics

Stephanie Hampton- The Deputy Director of NCEAS. She is a freshwater ecologist whose research focuses primarily on discerning lake ecosystem dynamics through analysis of long-term ecological data. In her role at NCEAS and other highly collaborative efforts, such as DataONE, she is actively engaged in fostering skills for a vibrant community around data-intensive research.

Matt Jones - The Director of Informatics Research and Development at NCEAS. His research focuses on environmental informatics, including the management, integration, analysis, and modeling of heterogeneous environmental data. He is co-PI for the DataONE federated data repository network. He also co-founded the Kepler project, an open source scientific workflow system, and leads other open source research projects for environmental science.

Jim Regetz - The Lead Scientific Programmer at NCEAS with a background in computationally intensive ecology and environmental science, environmental information management, effective use of relevant software and computing resources, statistical analysis and estimation, and ecological modeling and simulation.

Mark Schildhauer - The Director of Computing at NCEAS. His research interests include ecoinformatics, 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.


Course Materials

The Summer Institute coursework wove together several core themes via a mixture of lectures/instruction, discussions, and exercises. These themes were reinforced and injected into the real-time synthetic scientific research process through daily work on group projects.

Core themes included:

  • Collaboration modes and methods
  • Data management, preservation, and sharing
  • Data manipulation, integration, and exploration
  • Scientific workflows and reproducible research
  • Data analysis and modeling
  • Communicating results

Course Schedule and Presentation Materials 

Group Projects

Based on their research interests, Summer Institute participants self-selected into five research groups. Each group defined a specific research topic that would form the basis of the group project they would collaborate on throughout the program. Through the group projects, participants received hands-on guided experience using best practices in the technical aspects that underlie successful synthesis – from data discovery and integration to analysis and visualization, and special techniques for collaborative scientific research. Summer Institute 2013 participants continue to collaborate on their group projects well beyond the close of the three-week program, with the intent to publish their findings and make their derived data sets publicly available.

Group Projects: