CAREER: Scientific Computing for a New Generation of Ecologists

University Of Chicago, Chicago IL

Investigators

Abstract

Ecology is about to face the data deluge that other biological disciplines have already experienced. With ecological data increasing rapidly in quality and size, new methods are needed to extract the most relevant biological information from massive data-sets. The objective of this project is to develop new mathematical, computational and statistical tools for the analysis of three ecological problems. First, when a species goes extinct, the impact reverberates through the ecological network, possibly causing the extinction of other species. A new method to predict such "secondary extinctions" will be developed. Second, the number and size of published ecological networks is increasing rapidly, making it possible to answer one of the oldest questions in ecology: how many species traits (e.g., body size, swimming speed, metabolic rate) does one need to measure to predict whether two species will interact? A new computational method, coupled with a large dataset will attempt to answer this question. Knowing which are the critical traits determining the possibility of interactions could find application in the study of invasive species. Third, the spatial structure of ecosystems mediates many ecological processes. A new method will be developed to measure the impact of spatial heterogeneity on the structure of ecological networks. The development of these new tools require sophisticated methods, which are not typically included in the curriculum of biologists. The educational goal of the project is to train ecologists in the computational methods that will be needed to advance the discipline in the decades to come. Graduate students will learn how to automate the analysis of biological data, distribute computation over large computer clusters, organize data into relational databases, program in different languages, collaborate on data, code and manuscripts, automatically managing versions and conflicts, and pick the right tool for each task. Outreach activities will be provided through lectures and media interviews and with activities carried out in collaboration with local elementary schools and the Museum of Science and Industry.