The Simmune Modeler visual interface for creating signaling networks based on bi-molecular interactions

摘要

Motivation: Biochemical modeling efforts now frequently take advantage of the possibility to automatically create reaction networks based on the specification of pairwise molecular interactions. Even though a variety of tools exist to visualize the resulting networks, defining the rules for the molecular interactions typically requires writing scripts, which impacts the non-specialist accessibility of those approaches. We introduce the Simmune Modeler that allows users to specify molecular complexesand their interactions as well as the reaction-induced modifications of the molecules through a flexible visual interface. It can take into account the positions of the components of transmembrane complexes relative to the embedding membranes as well assymmetry aspects affecting the reactions of multimeric molecular structures. Models created with this tool can be simulated using the Simmune Simulator or be exported as SBML code or as files describing the reaction networks as systems of ODEs for importinto Matlab.