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We have implemented an influenza epidemic simulation tool and have made the source code available. The model is based closely on Germann et al 2006. FluTE differs in its implementation (C/C++ instead of C/Python/SPaSM) and several model details to make it more applicable to the novel H1N1 2009 pandemic. |
| FluTE generates text output files, which can be easily processed. In this example, we import the results from a US simulation into ArcGIS to generate a heatmap showing illness prevalence. |  ArcGIS map generated from FluTE output |
A C++ compiler is required to compile the source code. Binaries are not included with the download.
We have found that about 80Mb of RAM are required per 1,000,000 individuals in the simulation. Therefore, to simulate a region with 10 million people, 800Mb are required. Simulating an unmitigated epidemic in a population of 10 million takes about 2 hours. Smaller epidemics (with smaller populations, low R0, and/or effective intervention) can take much less time.
OpenMPI or MPICH is required to compile the parallel version.
The supplied Makefile assumes MPICH.
The parallel version is only used for simulating large populations
(more than one county). In the current version, if you allocate
mpiflute more processors than it can use, it will terminate with
an error. To simulate the entire continental US (about 280 million
people), I use 32 processors.
Publications
D. L. Chao,
M. E. Halloran,
Valerie Obenchain, and
I. M. Longini Jr.
FluTE, a publicly available stochastic influenza epidemic simulation model.
PLoS Computational Biology,
6(1):
e1000656. 2010.
doi:10.1371/journal.pcbi.1000656
Y. Yang, J. D. Sugimoto, M. E. Halloran, N. E. Basta, D. L. Chao, L. Matrajt, G. Potter, E. Kenah, I. M. Longini Jr.
Transmissibility and control of pandemic influenza A (H1N1) virus.
Science,
326(5953),
729-733. 2009.
doi: 10.1126/science.1177373
FluTE was used to simulate pandemic H1N1 epidemics in Los Angeles County and in the USA.
N. E. Basta, D. L. Chao, M. E. Halloran, L. Matrajt, I. M. Longini Jr.
Strategies for pandemic and seasonal influenza vaccination of school children in the US.
American Journal of Epidemiology,
170(6):679-686.
2009.
doi: 10.1093/aje/kwp237
FluTE was used to simulate the effect of vaccinating schoolchildren on the overall attack rates.
D. L. Chao,
L. Matrajt,
N. E. Basta,
J. D. Sugimoto,
B. Dean,
D. A. Bagwell,
B. Oiulfstad,
M. E. Halloran, and
I. M. Longini Jr.
Planning for the control of pandemic influenza H1N1 in Los Angeles County and the United States.
American Journal of Epidemiology. 173(10):1121--30. 2011.
doi:10.1093/aje/kwq497
FluTE was used to simulate the dynamics of pandemic H1N1 in Los Angeles County and the continental United States, both with and without interventions.
Some of the FluTE configuration files for this paper are in this zip archive. Version 1.15 of the software was used.
Supported by NIGMS/MIDAS