Software, Data and Modelling News: CoSBiLab LIME: A language interface for stochastic dynamical modelling in ecology

Authors:
Ozan Kahramanoğulları;Ferenc Jordán;James Lynch
Affiliations:
The Microsoft Research, University of Trento, Centre for Computational and Systems Biology, Piazza Manci 17, Povo, Trento 38123, Italy;The Microsoft Research, University of Trento, Centre for Computational and Systems Biology, Piazza Manci 17, Povo, Trento 38123, Italy;The Microsoft Research, University of Trento, Centre for Computational and Systems Biology, Piazza Manci 17, Povo, Trento 38123, Italy and Clarkson University, Potsdam, NY, USA
Venue:
Environmental Modelling & Software
Year:
2011

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Abstract

We present a simple language tool, CoSBiLab LIME, for building ecosystem models for stochastic dynamic simulation. The LIME language allows the user to give a biologically intuitive model description in a narrative style. After performing static analysis on the model structure, the software tool translates the model description into the BlenX programming language for stochastic dynamical simulation. These features facilitate the analysis of parallel, multiple ecological interactions in metacommunities. The software tool thus allows ecologists with no programming background to perform quite complicated, process-algebra-based simulations.