The Multiscale Systems Immunology project: software for cell-based immunological simulation.
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BACKGROUND: 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. RESULTS: 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. CONCLUSION: MSI addresses the need for a flexible and high-performing agent based model of the immune system.
Published Version (Please cite this version)
Mitha, Faheem, Timothy A Lucas, Feng Feng, Thomas B Kepler and Cliburn Chan (2008). The Multiscale Systems Immunology project: software for cell-based immunological simulation. Source Code Biol Med, 3. p. 6. 10.1186/1751-0473-3-6 Retrieved from https://hdl.handle.net/10161/6936.
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Computational and Systems Immunology, Theoretical and Evolutionary Medicine
Computational immunology (stochastic and spatial models and simulations, T cell signaling, immune regulation)
Statistical methodology for immunological laboratory techniques (flow cytometry, CFSE analysis, receptor-ligand binding and signaling kinetics)
Informatics of the immune system (reference and application ontologies, meta-programming, text mining and machine learning)
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