iBioSim is a tool that supports learning of genetic circuit models, efficient abstraction-based analysis of these models, and the design of synthetic genetic circuits. iBioSim includes project management features and a graphical user interface that facilitates the development and maintenance of genetic circuit models as well as both experimental and simulation data records.

Models in iBioSim can be created using either an SBML editor or a Genetic Circuit Model (GCM) editor. The SBML editor and the iBioSim simulation engine support virtually all of SBML Level 2 Version 3 including reactions, rules, events, constraints, etc. The GCM editor improves the efficiency of model development by supporting modeling at a higher level of abstraction than the molecular level supported by SBML. Namely, a GCM includes only important species and their influences upon each other. iBioSim can automatically translate from GCM to SBML models for analysis. A GCM can be either manually created or automatically learned from time-series data. iBioSim also includes an efficient simulation engine that supports ODE, stochastic, and Markov chain analysis of these models. This engine utilizes automatic abstraction to improve analysis time, often by one to two orders of magnitude. Finally, iBioSim has a graphical editor for visualizing both time series and event probability analysis results.

iBioSim has been applied successfully to numerous projects including an analysis of the phage lambda decision circuit and the E. coli Fim switch. It has also been applied to the design of a synthetic genetic Muller C-element, an asynchronous state-holding gate. In these and other efforts, the iBioSim tool with its support for automatic abstraction has been shown to greatly improve the productivity of researchers who are analyzing and designing genetic circuits.