Encoding Neuronal Models in SBML

Abstract

Encoding computational models in a standard format permit to share and re-use them in a variety of contexts. The Systems Biology Markup Language (SBML) is the de facto standard open format for exchanging models between software tools in systems biology. Neuronal models can often be encoded using this format, thus providing the modeler with access to a large variety of software packages that support SBML. We give a brief overview of the main constructs of SBML Level 3 Version 1 Core (the latest version of SBML). We provide practical examples of encoding particular neuronal models using SBML, illustrate the results of using the SBML encoding to simulate the models, and demonstrate the correspondance of results produced by the original modelers and the exchangeable encoding of the model in SBML.