A web-based application for building, analyzing and sharing rule-based models encoded in the BioNetGen language (BNGL). Tools accessible within the GetBonNie environment include (i) an applet for drawing graphs that correspond to BNGL code; (ii) a network-generation engine for translating a set of rules into a chemical reaction network; (iii) simulation engines that implement generate-first, on-the-fly and network-free methods for simulating rule-based models; and (iv) a database for sharing models, parameter values, annotations, simulation tasks and results.
Department of Biology, University of New Mexico, Albuquerque, NM; Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM; Department of Computer Science, University of New Mexico, Albuquerque, NM; Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA; Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ; Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, USA
GetBonNie funding source(s)
National Institutes of Health (grants GM076570 and CA109552); Department of Energy (contract DE-AC52-06NA25396); and Arizona Biomedical Research Commission