Simmune is the name of an integrated set of computational biology modeling tools. The Simmune Modeler is one of the Simmune tools.

The Simmune Modeler provides a graphical user interface for the creation of models of biomolecular reaction networks. The models are based on the specification of molecules, their components, binding sites and the interactions between those binding sites. Using the molecules and their interactions as building blocks the user of the software can define how the formation (or decay) of multi-molecular complexes modifies the state of the molecular components. The Modeler additionally permits the definition of transformations of complexes, for instance of Enzyme:Substrate complexes into Enzyme:Product complexes, and the specification of molecular properties and interactions related to membrane-bound biochemistry. Models created with the Simmune Modeler can be combined with (multi-)cellular geometries defined with the Simmune Cell Designer and can then be simulated with the Simmune Simulator. The Simulator can simulate 3D reaction diffusion processes while providing full access to all molecular and complex properties specified with the Modeler.

The Simmune Modeler moreover provides a software API to the model components that can be used in third party applications independently of the Simmune Cell Designer and Simulator. Models can also be exported into a variety of formats, including SBML 3.1, SBML 2.4 and SBML 2.1. However, export into Matlab (TM) or SBML formats will suppress those of the properties that are not supported by those standards.

This documentation is prepared for the Simmune Modeler version 2.1.1. Some screenshots are reused from version 2.1.0 and they are consistent with version 2.1.1.