title: The Multiscale Systems Immunology project: software for cell-based immunological simulation.
abstract: 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.
  
  
  CONCLUSIONS
  MSI addresses the need for a flexible and high-performing agent based model of the immune system.
authors.affiliation: Center for Computational Immunology, Department of Biostatistics & Bioinformatics, Duke University Medical Center, 2424 Erwin Road, Hock Plaza Suite G06, Durham NC 27705, USA. faheem@email.unc.edu.
authors.forename: Faheem
authors.initials: F
authors.lastname: Mitha
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Lucas
authors.forename: Feng
authors.initials: F
authors.lastname: Feng
authors.forename: Thomas B
authors.initials: TB
authors.lastname: Kepler
authors.forename: Cliburn
authors.initials: C
authors.lastname: Chan