News

More than 40 participants from as far away as Scotland, New Zealand, and Alaska gathered for the annual All Hands project meeting of the Science Environment for Ecological Knowledge, known as SEEK, held at the San Diego Supercomputer Center (SDSC) at UC San Diego from October 24 to 28, 2005.

SDSC executive director Vijay Samalam welcomed the researchers to SDSC, highlighting the center's capabilities as the "data place" among NSF centers that provide high performance computing and cyberinfrastructure to the nation's science and engineering enterprise.

"The meeting gave us an opportunity to step back from the details of everyday research and view the 'big picture' of the project" said SEEK project manager Matt Jones of the National Center for Ecological Analysis and Synthesis (NCEAS) at UCSB. "SEEK has been very successful at developing innovative approaches to cyberinfrastructure such as the Kepler scientific workflow system. Our annual meeting builds communication across the project, which is essential for SEEK to continue its pioneering leadership role in cyberinfrastructure for environmental research and observatories."

A five year Information Technology Research (ITR) initiative funded by the National Science Foundation (NSF), SEEK is a pioneering effort to create cyberinfrastructure for ecological, environmental, and biodiversity research, and to educate the ecological community about the benefits and practice of ecoinformatics. The large-scale project brings together researchers from SDSC, NCEAS, the NSF Long-Term Ecological Research Network (LTER) at the University of New Mexico, the University of Kansas Natural History Museum and Biodiversity Research Center (UKNHM), and the UC Davis Genome Center. In addition, the project includes participants from Arizona State University, the University of North Carolina, the University of Vermont, and Napier University in Scotland.

The SEEK participants commented that they had stimulating discussions and identified opportunities for collaboration with colleagues invited to attend from projects in allied disciplines, including CIPRes (CyberInfrastructure for Phylogenetic Research) and NESCent (the National Evolutionary Synthesis Center), as well as GEON "Cyberinfrastructure for the Geosciences." Both CIPRes and GEON have their IT components based at SDSC, which is a recognized leader in providing data cyberinfrastructure for large-scale collaborative science.

By definition, the study of ecosystems involves a system-wide approach to observing and modeling evolving natural communities, and thus inherently requires integrating highly disparate data from a range of disciplines. As ecologists scale up the scope of their research to capture more accurate representations of ecosystems and beyond, the SEEK researchers have identified the integration of data as one of the most challenging and time-consuming tasks the scientists face. For example, as presently done in manual ways, the process of identifying, accessing, and integrating relevant data can require a year or more of preparatory activity before researchers can run computations of an ecological niche model to predict such things as the impact of climate change on species distribution, or the spread of invasive species and diseases.

"To address these challenges, the SEEK project is building a comprehensive three-part system, including a data grid known as EcoGrid for accessing a wide variety of ecological and biodiversity data, along with an analytical workflow tool known as Kepler for efficiently utilizing these data stores to advance ecological and biodiversity science," said Bertram Ludäscher, a SEEK PI and SDSC Fellow from UC Davis. "The third part is an intelligent middleware system, or Semantic Mediation System, which facilitates powerful search, integration, and synthesis of data and models using a semantic approach that includes ontologies."

To guide the infrastructure development, the researchers are engaged in two ecology test cases. One is applying ecological niche modeling to the large-scale problem of predicting the impact of various climate change scenarios on the range of all mammals in the western hemisphere. Niche modeling works by correlating biological, environmental, and topographical data with observed species distributions to develop reliable predictive algorithms. Researchers in the other test case are using advanced SEEK tools to examine the connections between ecosystem biodiversity and productivity.

Other supporting activities include a knowledge representation effort which is building ontologies to support data discovery, integration, and workflows for the test cases; and a taxonomic effort to address problems with evolving taxonomic nomenclature in ecological and museum collections data. In addition to the scientific and technical components of the project, the researchers are also conducting an active education, outreach, and training effort to teach the ecology community about the growing power and benefits of ecoinformatics, and the need to adopt new practices such as metadata standards and rich annotation in order to make data sets broadly usable by other researchers in the interdisciplinary research needed to tackle the pressing questions of today's biocomplexity. -Paul Tooby.