Epithelial cell modeling: standards‐based simulation experiments (1180.4)

Abstract

We have developed a simulation tool, get‐simulator, for performing simulation experiments with user‐defined epithelial cell models. Users are able to define their epithelial cell model de novo or through the assembly of pre‐existing modules. Existing cell models may also be re‐used in new simulation experiments. Cell models are encoded in the CellML format (http://cellml.org) and the SED‐ML format (http://sed‐ml.org) descriptions of the simulation experiments. SED‐ML allows a given collection of models to be instantiated into one or more specific computational tasks to be executed in order to generate unambiguously defined outputs. In addition to the models and simulation experiment descriptions themselves, get‐simulator makes use of relevant annotations of these source data to enable the automatic generation of executable code for each of the required computational tasks. Following the execution of these tasks, the user is presented with the resulting outputs defined in the SED‐ML document. get‐simulator and example models are available from https://bitbucket.org/get under a free and open‐source license.Grant Funding Source: Supported by the Virtual Physiological Rat Project, NIH grant [P50‐GM094503].