EpiFire: An open source C++ library and application for contact network epidemiology

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Hladish, Thomas ^a   Melamud, Eugene ^b   Barrera, Luis A ^a,c   Galvani, Alison ^d   Meyers, Lauren A ^a,e  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b PRINCETON UNIVERSITY   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

^d YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e SANTA FE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APPLICATIONS PROGRAMMING INTERFACES; C++ LIBRARIES; CONTACT NETWORKS; DISEASE TRANSMISSION; EPIDEMIC SIMULATIONS; FLEXIBLE PROGRAMMING; MASS ACTION; NETWORK MODELS; NETWORK-BASED; OPEN SOURCES; OPEN-SOURCE PROGRAMMING; PEDAGOGICAL TOOLS; POINT-AND-CLICK INTERFACE;

DISEASES; EPIDEMIOLOGY; GRAPHICAL USER INTERFACES; SOLVENTS;

COMPUTER SIMULATION;

ARTICLE; COMPUTER PROGRAM; COMPUTER SIMULATION; CONTACT EXAMINATION; DISEASE TRANSMISSION; EVALUATION; HUMAN; STATISTICAL MODEL; STATISTICS;

COMPUTER SIMULATION; CONTACT TRACING; DISEASE TRANSMISSION, INFECTIOUS; HUMANS; MODELS, STATISTICAL; SOFTWARE;

EID: 84860517178     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-76     Document Type: Article

References (48)

1. Kermack WO, McKendrick AG. Contributions to the mathematical theory of epidemics-I. 1927. Bull Math Biol 1991, 53:33-55.
2. Anderson RM, May RM. Infectious diseases of humans 1991, Oxford University Press.
3. Rahmandad H, Sterman J. Heterogeneity and network structure in the dynamics of diffusion: Comparing agent-based and differential equation models. Manag Sci 2008, 54:998-1014.
4. Meyers LA, Pourbohloul B, Newman MEJ, Skowronski DM, Brunham RC. Network theory and SARS: predicting outbreak diversity. J Theor Biol 2005, 232:71-81. 10.1016/j.jtbi.2004.07.026, 15498594.
5. Newman MEJ. Spread of epidemic disease on networks. Phys Rev E 2002, 66:016128.
6. Meyers LA. Contact network epidemiology: Bond percolation applied to infectious disease prediction and control. Bull Am Math Soc 2007, 44:63-86.
7. Bridges CB, Kuehnert MJ, Hall CB. Transmission of influenza: implications for control in health care settings. Clin Infect Dis 2003, 37:1094-1101. 10.1086/378292, 14523774.
8. Li S, Eisenberg JNS, Spicknall IH, Koopman JS. Dynamics and Control of Infections Transmitted From Person to Person Through the Environment. Am J Epidemiol 2009, 170:257-265. 10.1093/aje/kwp116, 19474071.
9. Volz E, Meyers LA. Susceptible-infected-recovered epidemics in dynamic contact networks. Proc Biol Sci 2007, 274:2925-2933. 10.1098/rspb.2007.1159, 2291166, 17878137.
10. WHO | Cumulative Number of Reported Cases (SARS). http://www.who.int/csr/sars/country/2003_03_26/en/index.html.
11. Liljeros F, Edling CR, Amaral LA, Stanley HE, Aberg Y. The web of human sexual contacts. Nature 2001, 411:907-908. 10.1038/35082140, 11418846.
12. Bearman P, Moody J, Stovel K. Chains of affection: The structure of adolescent romantic and sexual networks. AJS 2004, 110:44-91.
13. Bansal S, Pourbohloul B, Meyers LA. A Comparative Analysis of Influenza Vaccination Programs. PLoS Med 2006, 3:e387. 10.1371/journal.pmed.0030387, 1584413, 17020406.
14. Pourbohloul B, Meyers LA, Skowronski DM, Krajden M, Patrick DM, Brunham RC. Modeling control strategies of respiratory pathogens. Emerg Infect Dis 2005, 11:1249-1256. 3320482, 16102315.
15. Dimitrov NB, Goll S, Hupert N, Pourbohloul B, Meyers LA. Optimizing tactics for use of the U.S. antiviral strategic national stockpile for pandemic influenza. PLoS One 2011, 6:e16094. 10.1371/journal.pone.0016094, 3023704, 21283514.
16. Volz E, Frost SDW, Rothenberg R, Meyers LA. Epidemiological bridging by injection drug use drives an early HIV epidemic. Epidemics 2010, 2:155-164. 10.1016/j.epidem.2010.06.003, 21352786.
17. Abbey H. An examination of the Reed-Frost theory of epidemics. Hum Biol 1952, 24:201-233.
18. Ferrari MJ, Bansal S, Meyers LA, Bjornstad ON. Network frailty and the geometry of herd immunity. Proc R Soc B Biol Sci 2006, 273:2743-2748.
19. Leath PL. Cluster size and boundary distribution near percolation threshold. Phys Rev B 1976, 14:5046-5055.
20. Hagberg AA, Schult DA, Swart PJ. Exploring network structure, dynamics, and function using NetworkX. Proceedings of the 7th Python in Science Conference (SciPy2008) 2008, 11-15. Pasadena, CA USA.
21. Csardi G, Nepusz T. The igraph software package for complex network research. InterJournal 2006, Complex Systems:1695.
22. Handcock MS, Hunter DR, Butts CT, Goodreau SM, Morris M. statnet: Software Tools for the Representation, Visualization, Analysis and Simulation of Network Data. J Stat Softw 2008, 24:1-11. 2443947, 18612375.
23. Livnat Y, Gesteland P, Benuzillo J, Pettey W, Bolton D, Drews F, Kramer H, Samore M. Epinome - a novel workbench for epidemic investigation and analysis of search strategies in public health practice. AMIA Annu Symp Proc 2010, 2010:647-651. 3041367, 21347058.
24. Estimation and Projection Package (EPP). http://www.unaids.org/en/dataanalysis/tools/estimationandprojectionpacka geepp/.
25. Chao DL, Halloran ME, Obenchain VJ, Longini IM. FluTE, a Publicly Available Stochastic Influenza Epidemic Simulation Model. PLoS Comput Biol 2010, 6:e1000656. 10.1371/journal.pcbi.1000656, 2813259, 20126529.
26. CDC H1N1 Flu | Preparedness Tools for Professionals. http://www.cdc.gov/h1n1flu/tools/.
27. Del Valle S, Stroud P, Smith J, Mniszewski S, Riese J, Sydoriak S, Kubicek D. EpiSimS: Epidemic Simulation System. Los Alamos Unlimited Release (LAUR) 2006, 06-06714.
28. Ford DA, Kaufman JH, Eiron I. An extensible spatial and temporal epidemiological modelling system. Int J Health Geogr 2006, 5.
29. Bansal S, Grenfell BT, Meyers LA. When individual behaviour matters: homogeneous and network models in epidemiology. J R Soc Interface 2007, 4:879-891. 10.1098/rsif.2007.1100, 2394553, 17640863.
30. Blanchette J. C++ GUI programming with Qt 4 2008, Prentice Hall in association with Trolltech Press, Extensively rev. and expanded. Upper Saddle River NJ, 2.
31. Erdos P, Rényi A. On random graphs. I. Publicationes Mathematicae 1959, 6:290-297.
32. Molloy M, Reed B. A critical point for random graphs with a given degree sequence. Random Struct Algorithm 1995, 6:161-179.
33. Watts DJ, Strogatz SH. Collective dynamics of " small-world" networks. Nature 1998, 393:440-442. 10.1038/30918, 9623998.
34. On the uniform generation of random graphs with prescribed degree sequences. http://arxiv.org/abs/cond-mat/0312028v2.
35. Matsumoto M, Nishimura T. Mersenne Twister: A 623-dimensionally equidistributed uniform pseudo-random number generator. ACM Trans Model Comput Simulat 1998, 8:3-30.
36. EpiFire Chain-binomial Simulator. https://raw.github.com/tjhladish/EpiFire/master/src/ChainBinomial_Sim.h.
37. EpiFire Percolation Simulator. https://raw.github.com/tjhladish/EpiFire/master/src/ChainBinomial_Sim.h.
38. Burden RL, Faires JD. Numerical analysis 1985, Prindle, Weber & Schmidt, Boston, Mass.
39. Newman MEJ, Watts DJ, Strogatz SH. Random graph models of social networks. Proc Natl Acad Sci U S A 2002, 99 Suppl 1:2566-2572. 128577, 11875211.
40. Gillespie DT. Exact stochastic simulation of coupled chemical reactions. J Phys Chem 1977, 81:2340-2361.
41. Keeling MJ, Rohani P. Modeling infectious diseases in humans and animals 2008, Princeton University Press, Princeton.
42. Fruchterman TMJ, Reingold EM. Graph drawing by force-directed placement. Softw Pract Exper 1991, 21:1129-1164.
43. Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson BO. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci 2007, 104:1777-1782. 10.1073/pnas.0610772104, 1794290, 17267599.
44. Nieminen M. Migration of moth species in a network of small islands. Oecologia 1996, 108:643-651.
45. SISMID 2011: Home. http://depts.washington.edu/sismid/.
46. Volz E. SIR dynamics in random networks with heterogeneous connectivity. J Math Biol 2007, 56:293-310. 10.1007/s00285-007-0116-4, 17668212.
47. Miller JC. A note on a paper by Erik Volz: SIR dynamics in random networks. J Math Biol 2010, 62:349-358.
48. EpiFire SEIR Percolation Simulator. https://raw.github.com/tjhladish/EpiFire/master/research/SEIR_Percolatio n_Sim.h.