Simmune is a suite of software tools that guides the user through the multiple hierarchical scales of cellular behavior, facilitating the generation of comprehensive models. It was originally created to simulate immunological phenomena—hence its name, Simmune—but it is applicable to a very broad class of cell biological models.
The development of Simmune started at the Institute for Theoretical Physics of the University of Hamburg, Germany. Now, its development continues as part of the biocomputation effort at the Laboratory of Systems Biology.
Main Areas of Focus
- To provide the computational approaches appropriate for modeling cell biological systems based on data that describe cellular behavior on various scales, from interactions between molecular domains to the behavior of populations of cells
- To make it possible for (experimental) biologists to define the computational equivalents of their biological models without having to deal with scripting languages or the mathematics involved in translating those models into formalized representations that can be (quantitatively) simulated
- To allow the biologists to interact easily with the modeling software by largely eliminating the necessity to follow the classical strategy of first translating a biological model into a simplified version that then can be modeled by a theorist
Simmune consists of five components:
- Modeler: Provides a visual interface for the definition of molecules, their structures (sub-molecular components or domains and binding sites), and the complexes the molecules form through reactions such as associations, dissociation, and transformations.
- Cell Designer: Provides a visual interface for the specification of cellular morphologies as well.
- Simulator: Allows you to combine biochemical models with three-dimensional cell geometries.
- Network Viewer: Renders the information in the model as a visual network showing the interactions among the user-defined molecular complexes in an interactive way.
- Analyzer: Can perform large-scale parameter scans to explore the behavior of the simulated model.
- 2Pisa: Software accompanying the publication ‘Quantifying cellular interaction dynamics in 3D fluorescence microscopy data’, Klauschen et al., Nat Protoc. 2009;4(9):1305-11
- Morphology Modeler (MoMo) : Software accompanying the publication ‘Computational reconstruction of cell and tissue surfaces for modeling and data analysis’, Klauschen et al., Nature Protocols 4, - 1006 - 1012 (2009)