Simmune

Simmune models and simulates multiscale molecular interactions and cellular processes to investigate immunological phenomena and cell biology.

Key Features:

• Automatic Reaction Network Creation: Simmune Modeler automatically generates reaction networks from specified pairwise molecular interactions and encodes reaction-induced modifications of molecules.
• Multiscale Integration: Integrates multiple hierarchical scales of cellular behavior into cohesive models of cellular systems.
• Trans-Membrane Complexes and Symmetry Considerations: Accounts for spatial positioning of components within trans-membrane complexes relative to embedding membranes and incorporates symmetry effects in multimeric molecular structures that influence reactions.
• Simulation and Export Capabilities: Models can be simulated with the Simmune Simulator and exported as SBML or as files describing reaction networks as systems of ordinary differential equations (ODEs) for import into Matlab.

Scientific Applications:

• Immunological simulation: Simulation of immune responses and immunological phenomena using detailed molecular interaction models.
• Signaling pathway modeling: Modeling of cellular signaling pathways through explicit reaction networks and dynamic simulation.
• Multimeric complex analysis: Analysis of how symmetry and spatial arrangement in multimeric and trans-membrane complexes affect reaction behavior.
• Multiscale cellular behavior analysis: Investigation of cellular behaviors across hierarchical scales by integrating molecular, complex, and cellular-level processes.

Methodology:

Reaction networks are automatically generated from specified molecular interactions; networks incorporate spatial positioning and symmetry of complexes, can be simulated with the Simmune Simulator, and can be exported as SBML or as ODE system files for Matlab.