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Source Code Biol Med. 2008 Apr 28;3:6. doi: 10.1186/1751-0473-3-6.

The Multiscale Systems Immunology project: software for cell-based immunological simulation.

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  • 1Center for Computational Immunology, Department of Biostatistics & Bioinformatics, Duke University Medical Center, 2424 Erwin Road, Hock Plaza Suite G06, Durham NC 27705, USA.



Computer simulations are of increasing importance in modeling biological phenomena. Their purpose is to predict behavior and guide future experiments. The aim of this project is to model the early immune response to vaccination by an agent based immune response simulation that incorporates realistic biophysics and intracellular dynamics, and which is sufficiently flexible to accurately model the multi-scale nature and complexity of the immune system, while maintaining the high performance critical to scientific computing.


The Multiscale Systems Immunology (MSI) simulation framework is an object-oriented, modular simulation framework written in C++ and Python. The software implements a modular design that allows for flexible configuration of components and initialization of parameters, thus allowing simulations to be run that model processes occurring over different temporal and spatial scales.


MSI addresses the need for a flexible and high-performing agent based model of the immune system.

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