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I<jats:sc>ndemics<\/jats:sc>can support policy analysts and epidemiologists interested in planning and control of pandemics. I<jats:sc>ndemics<\/jats:sc>goes beyond traditional epidemic simulations by providing a simple and powerful way to represent and analyze policy-based as well as individual-based<jats:italic>adaptive interventions<\/jats:italic>. Users can also stop the simulation at any point, assess the state of the simulated system, and add additional interventions. I<jats:sc>ndemics<\/jats:sc>is available to end-users via a web-based interface.<\/jats:p><jats:p>Detailed performance analysis shows that I<jats:sc>ndemics<\/jats:sc>greatly enhances the capability and productivity of simulating complex intervention strategies with a marginal decrease in performance. We also demonstrate how I<jats:sc>ndemics<\/jats:sc>was applied in some real case studies where complex interventions were implemented.<\/jats:p>","DOI":"10.1145\/2501602","type":"journal-article","created":{"date-parts":[[2014,2,11]],"date-time":"2014-02-11T14:39:42Z","timestamp":1392129582000},"page":"1-32","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":27,"title":["I<scp>ndemics<\/scp>"],"prefix":"10.1145","volume":"24","author":[{"given":"Keith R.","family":"Bisset","sequence":"first","affiliation":[{"name":"NDSSL, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA"}]},{"given":"Jiangzhuo","family":"Chen","sequence":"additional","affiliation":[{"name":"NDSSL, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA"}]},{"given":"Suruchi","family":"Deodhar","sequence":"additional","affiliation":[{"name":"NDSSL, Virginia Bioinformatics Institute, Virginia Tech, Department of Computer Science, Virginia Tech, Blacksburg, VA"}]},{"given":"Xizhou","family":"Feng","sequence":"additional","affiliation":[{"name":"NDSSL, Virginia Bioinformatics Institute, Virginia Tech, Department of Mathematics, Statistics, and Computer Science, Marquette University, Blacksburg, VA"}]},{"given":"Yifei","family":"Ma","sequence":"additional","affiliation":[{"name":"NDSSL, Virginia Bioinformatics Institute, Virginia Tech, Department of Computer Science, Virginia Tech, Blacksburg, VA"}]},{"given":"Madhav V.","family":"Marathe","sequence":"additional","affiliation":[{"name":"NDSSL, Virginia Bioinformatics Institute, Virginia Tech, Department of Computer Science, Virginia Tech, Blacksburg, VA"}]}],"member":"320","published-online":{"date-parts":[[2014,1]]},"reference":[{"key":"e_1_2_1_1_1","doi-asserted-by":"crossref","unstructured":"M. Ajelli B. Gon\u00e7alves D. Balcan V. Colizza H. Hu J. Ramasco S. Merler and A. Vespignani. 2010. Comparing large-scale computational approaches to epidemic modeling: Agent-based versus structured metapopulation models. BMC Infectious Diseases 10 190 (2010). M. Ajelli B. Gon\u00e7alves D. Balcan V. Colizza H. Hu J. Ramasco S. Merler and A. Vespignani. 2010. Comparing large-scale computational approaches to epidemic modeling: Agent-based versus structured metapopulation models. BMC Infectious Diseases 10 190 (2010).","DOI":"10.1186\/1471-2334-10-190"},{"key":"e_1_2_1_2_1","doi-asserted-by":"crossref","unstructured":"R. M. Anderson and R. M. May. 1991. Infectious Diseases of Humans. Oxford University Press Oxford. R. M. Anderson and R. M. May. 1991. Infectious Diseases of Humans. Oxford University Press Oxford.","DOI":"10.1093\/oso\/9780198545996.001.0001"},{"key":"e_1_2_1_3_1","volume-title":"The Mathematical Theory of Infectious Diseases and Its Applications","author":"Bailey N.","unstructured":"N. Bailey . 1975. The Mathematical Theory of Infectious Diseases and Its Applications . Hafner Press , New York . N. Bailey. 1975. The Mathematical Theory of Infectious Diseases and Its Applications. Hafner Press, New York."},{"key":"e_1_2_1_4_1","doi-asserted-by":"crossref","unstructured":"A. Barrat M. Barthelemy and A. Vespignani. 2008. Dynamical Processes in Complex Networks. Cambridge University Press. A. Barrat M. Barthelemy and A. Vespignani. 2008. Dynamical Processes in Complex Networks. Cambridge University Press.","DOI":"10.1017\/CBO9780511791383"},{"key":"e_1_2_1_5_1","volume-title":"Computing: Essays in Honor of Professor Daniel J. Rosenkrantz","author":"Barrett C. L.","year":"2009","unstructured":"C. L. Barrett , K. Bisset , J. Chen , S. Eubank , B. Lewis , V. S. A. Kumar , M. V. Marathe , and H. S. Mortveit . 2009 . Interactions among human behavior, social networks, and societal infrastructures: A case study in computational epidemiology. In Fundamental Problems in Computing: Essays in Honor of Professor Daniel J. Rosenkrantz , Chapter 18, S. S. Ravi and Sandeep K. Shukla (Eds.). Springer , Netherlands, 477--507. C. L. Barrett, K. Bisset, J. Chen, S. Eubank, B. Lewis, V. S. A. Kumar, M. V. Marathe, and H. S. Mortveit. 2009. Interactions among human behavior, social networks, and societal infrastructures: A case study in computational epidemiology. In Fundamental Problems in Computing: Essays in Honor of Professor Daniel J. Rosenkrantz, Chapter 18, S. S. Ravi and Sandeep K. Shukla (Eds.). Springer, Netherlands, 477--507."},{"key":"e_1_2_1_6_1","volume-title":"Proceedings of the ACM\/IEEE Conference on Supercomputing. 290--294","author":"Barrett C. L.","unstructured":"C. L. Barrett , K. R. Bisset , S. G. Eubank , X. Feng , and M. 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Interaction-based HPC modeling of social, biological, and economic contagions over large networks. In Proceedings of Winter Simulation Conference (WSC). 2933--2947."},{"key":"e_1_2_1_8_1","doi-asserted-by":"publisher","DOI":"10.1145\/1542275.1542336"},{"key":"e_1_2_1_9_1","volume-title":"Winter Simulation Conference. 2020--2031","author":"Bisset K. R.","unstructured":"K. R. Bisset , X. Feng , M. V. Marathe , and S. M. Yardi . 2009. Modeling interaction between individuals, social networks and public policy to support public health epidemiology . In Winter Simulation Conference. 2020--2031 . K. R. Bisset, X. Feng, M. V. Marathe, and S. M. Yardi. 2009. Modeling interaction between individuals, social networks and public policy to support public health epidemiology. In Winter Simulation Conference. 2020--2031."},{"key":"e_1_2_1_10_1","volume-title":"Hospitalizations and Deaths in the United States","author":"CDC.","year":"2010","unstructured":"CDC. 2010 . Updated CDC Estimates of 2009 H1N1 Influenza Cases , Hospitalizations and Deaths in the United States , April 2009--April 10, 2010. Retrieved September 29, 2011 from http:\/\/www.cdc.gov\/h1n1flu\/estimates_2009_h1n1.htm. CDC. 2010. Updated CDC Estimates of 2009 H1N1 Influenza Cases, Hospitalizations and Deaths in the United States, April 2009--April 10, 2010. Retrieved September 29, 2011 from http:\/\/www.cdc.gov\/h1n1flu\/estimates_2009_h1n1.htm."},{"key":"e_1_2_1_11_1","doi-asserted-by":"crossref","unstructured":"D. L. Chao M. E. Halloran V. Obenchain and I. M. Longini Jr. 2010. FluTE a publicly available stochastic influenza epidemic simulation model. PLoS Computational Biology 6 1 (2010). D. L. Chao M. E. Halloran V. Obenchain and I. M. Longini Jr. 2010. FluTE a publicly available stochastic influenza epidemic simulation model. PLoS Computational Biology 6 1 (2010).","DOI":"10.1371\/journal.pcbi.1000656"},{"key":"e_1_2_1_12_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pmed.0040013"},{"key":"e_1_2_1_13_1","unstructured":"V. Colizza A. Barrat M. Barthelemy and A. Vespignani. 2005. Prediction and predictability of global epidemics: the role of the airline transportation network. Arxiv preprint q-bio.OT\/0507029 (2005). V. Colizza A. Barrat M. Barthelemy and A. Vespignani. 2005. Prediction and predictability of global epidemics: the role of the airline transportation network. Arxiv preprint q-bio.OT\/0507029 (2005)."},{"key":"e_1_2_1_14_1","doi-asserted-by":"publisher","DOI":"10.1145\/2110363.2110385"},{"key":"e_1_2_1_15_1","unstructured":"R. Dobbs S. Smit J. Remes J. Manyika C. Roxburgh and A. Restrepo. 2011. Urban world: Mapping the economic power of cities McKinsey Global Institute. Retrieved from http:\/\/www.mckinsey.com\/insights\/mgi\/research\/urbanization\/urban_world. R. Dobbs S. Smit J. Remes J. Manyika C. Roxburgh and A. Restrepo. 2011. Urban world: Mapping the economic power of cities McKinsey Global Institute. Retrieved from http:\/\/www.mckinsey.com\/insights\/mgi\/research\/urbanization\/urban_world."},{"key":"e_1_2_1_16_1","doi-asserted-by":"publisher","DOI":"10.1145\/1882992.1883115"},{"key":"e_1_2_1_17_1","doi-asserted-by":"publisher","DOI":"10.1145\/508791.508819"},{"key":"e_1_2_1_18_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature04017"},{"key":"e_1_2_1_19_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature04795"},{"key":"e_1_2_1_20_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature02007"},{"key":"e_1_2_1_21_1","doi-asserted-by":"crossref","unstructured":"H. V. Fineberg and M. E. Wilson. 2009. Epidemic science in real time. Science 324 (May 2009) 987. H. V. Fineberg and M. E. Wilson. 2009. Epidemic science in real time. Science 324 (May 2009) 987.","DOI":"10.1126\/science.1176297"},{"key":"e_1_2_1_22_1","volume-title":"Hanage et al","author":"Fraser C.","year":"2009","unstructured":"C. Fraser , C. A. Donnelly , S. Cauchemez , and W. P. Hanage et al . 2009 . Pandemic potential of a strain of influenza A (H1N1): Early findings. Science 324, 5934 (2009), 1557--1561. C. Fraser, C. A. Donnelly, S. Cauchemez, and W. P. Hanage et al. 2009. Pandemic potential of a strain of influenza A (H1N1): Early findings. Science 324, 5934 (2009), 1557--1561."},{"key":"e_1_2_1_23_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0601266103"},{"key":"e_1_2_1_24_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mbs.2009.06.002"},{"key":"e_1_2_1_25_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0706849105"},{"key":"e_1_2_1_26_1","volume-title":"I: There is life beyond files. CoRR abs\/cs\/0701159","author":"Heber G.","year":"2007","unstructured":"G. Heber and J. Gray . 2007 a. Supporting finite element analysis with a relational database backend, part I: There is life beyond files. CoRR abs\/cs\/0701159 (2007). G. Heber and J. Gray. 2007a. Supporting finite element analysis with a relational database backend, part I: There is life beyond files. CoRR abs\/cs\/0701159 (2007)."},{"key":"e_1_2_1_27_1","volume-title":"II: Database design and access. CoRR abs\/cs\/0701160","author":"Heber G.","year":"2007","unstructured":"G. Heber and J. Gray . 2007 b. Supporting finite element analysis with a relational database backend, part II: Database design and access. CoRR abs\/cs\/0701160 (2007). G. Heber and J. Gray. 2007b. Supporting finite element analysis with a relational database backend, part II: Database design and access. CoRR abs\/cs\/0701160 (2007)."},{"key":"e_1_2_1_28_1","doi-asserted-by":"publisher","DOI":"10.1023\/A:1016599411804"},{"key":"e_1_2_1_29_1","doi-asserted-by":"publisher","DOI":"10.1098\/rsif.2005.0042"},{"key":"e_1_2_1_30_1","doi-asserted-by":"publisher","DOI":"10.1137\/S0036144500371907"},{"key":"e_1_2_1_31_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0308344101"},{"key":"e_1_2_1_32_1","doi-asserted-by":"publisher","DOI":"10.1098\/rsif.2005.0051"},{"key":"e_1_2_1_33_1","doi-asserted-by":"crossref","unstructured":"M. Van Kerkhove and N. Ferguson. 2012. Epidemic and intervention modelling\u2014a scientific rationale for policy decisions&quest; Lessons from the 2009 influenza pandemic. Bull World Health Organ. (2012) 306--10. M. Van Kerkhove and N. Ferguson. 2012. Epidemic and intervention modelling\u2014a scientific rationale for policy decisions&quest; Lessons from the 2009 influenza pandemic. Bull World Health Organ. (2012) 306--10.","DOI":"10.2471\/BLT.11.097949"},{"key":"e_1_2_1_34_1","doi-asserted-by":"publisher","DOI":"10.1098\/rspa.1927.0118"},{"key":"e_1_2_1_35_1","volume-title":"Complex Sciences: Theory and Applications (COMPLEX).","author":"Liao S.","year":"2012","unstructured":"S. Liao , Y. Ma , J. Chen , and A. Marathe . 2012 . Paid sick-leave: Is it a good way to control epidemics&quest; In the 2nd International Conference on Complex Sciences: Theory and Applications (COMPLEX). S. Liao, Y. Ma, J. Chen, and A. Marathe. 2012. Paid sick-leave: Is it a good way to control epidemics&quest; In the 2nd International Conference on Complex Sciences: Theory and Applications (COMPLEX)."},{"key":"e_1_2_1_36_1","first-page":"89","article-title":"Improving the evidence base for decision making during a pandemic: The example of 2009 Influenza A H1N1","volume":"9","author":"Lipsitch M.","year":"2011","unstructured":"M. Lipsitch , L. Finelli , R. T. Heffernan , G. M. Leung , and S. C. Redd . 2011 . Improving the evidence base for decision making during a pandemic: The example of 2009 Influenza A H1N1 . Biosecur Bioterror. 9 , 2 (2011), 89 -- 115 . M. Lipsitch, L. Finelli, R. T. Heffernan, G. M. Leung, and S. C. Redd. 2011. Improving the evidence base for decision making during a pandemic: The example of 2009 Influenza A H1N1. Biosecur Bioterror. 9, 2 (2011), 89--115.","journal-title":"Biosecur Bioterror."},{"key":"e_1_2_1_37_1","volume-title":"Proceedings of the Winter Simulation Conference.","author":"Ma Y.","unstructured":"Y. Ma , K. R. Bisset , J. Chen , S. Deodhar , and M. V. Marathe . 2011. Efficient implmentation of complex interventions in large scale epidemic simulations . In Proceedings of the Winter Simulation Conference. Y. Ma, K. R. Bisset, J. Chen, S. Deodhar, and M. V. Marathe. 2011. Efficient implmentation of complex interventions in large scale epidemic simulations. In Proceedings of the Winter Simulation Conference."},{"key":"e_1_2_1_38_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0025149"},{"key":"e_1_2_1_39_1","doi-asserted-by":"crossref","unstructured":"S. Merler and M. Ajelli. 2010. The role of population heterogeneity and human mobility in the spread of pandemic influenza. Processings of Royal Society 277 1681 (2010) 557--565. S. Merler and M. Ajelli. 2010. The role of population heterogeneity and human mobility in the spread of pandemic influenza. Processings of Royal Society 277 1681 (2010) 557--565.","DOI":"10.1098\/rspb.2009.1605"},{"key":"e_1_2_1_40_1","doi-asserted-by":"publisher","DOI":"10.1090\/S0273-0979-06-01148-7"},{"key":"e_1_2_1_41_1","unstructured":"L. A. Meyers and N. Dimitrov. 2010. Mathematical approaches to infectious disease prediction and control. INFORMS Tutorials in OPerations Research (2010). L. A. Meyers and N. Dimitrov. 2010. Mathematical approaches to infectious disease prediction and control. INFORMS Tutorials in OPerations Research (2010)."},{"key":"e_1_2_1_42_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jtbi.2005.10.004"},{"key":"e_1_2_1_43_1","doi-asserted-by":"publisher","DOI":"10.1145\/347476.347480"},{"key":"e_1_2_1_44_1","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevE.65.021904"},{"key":"e_1_2_1_45_1","doi-asserted-by":"publisher","DOI":"10.1145\/2043635.2043637"},{"key":"e_1_2_1_46_1","doi-asserted-by":"crossref","unstructured":"R. Pastor-Satorras and A. Vespignani. 2002. Epidemics and immunization in scale-free networks. In Handbook of Graphs and Networks S. Bornholdt and H. G. Schuster (Eds.). Wiley-VCH Berlin. R. Pastor-Satorras and A. Vespignani. 2002. Epidemics and immunization in scale-free networks. In Handbook of Graphs and Networks S. Bornholdt and H. G. Schuster (Eds.). Wiley-VCH Berlin.","DOI":"10.1002\/3527602755.ch5"},{"key":"e_1_2_1_47_1","doi-asserted-by":"publisher","DOI":"10.1177\/0037549711413001"},{"key":"e_1_2_1_48_1","doi-asserted-by":"publisher","DOI":"10.1016\/0025-5564(85)90064-1"},{"key":"e_1_2_1_49_1","doi-asserted-by":"publisher","DOI":"10.5555\/1488734.1490064"},{"key":"e_1_2_1_50_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0304-3800(00)00294-5"},{"key":"e_1_2_1_51_1","unstructured":"B. Sowell A. Demers J. Gehrke N. Gupta H. Li and W. White. 2009. From Declarative Languages to Declarative Processing in Computer Games. In CIDR. B. Sowell A. Demers J. Gehrke N. Gupta H. Li and W. White. 2009. From Declarative Languages to Declarative Processing in Computer Games. In CIDR."},{"key":"e_1_2_1_52_1","unstructured":"E. Vynnycky and R. G. White. 2010. An Introduction to Infectious Disease Modelling. Oxford University Press. E. Vynnycky and R. G. White. 2010. An Introduction to Infectious Disease Modelling. Oxford University Press."},{"key":"e_1_2_1_53_1","doi-asserted-by":"publisher","DOI":"10.14778\/1920841.1920962"},{"key":"e_1_2_1_54_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.amc.2006.06.126"},{"key":"e_1_2_1_55_1","doi-asserted-by":"publisher","DOI":"10.1145\/1247480.1247486"},{"key":"e_1_2_1_56_1","unstructured":"WHO. 2004. WHO consultation on priority public health interventions before and during an influenza pandemic. Available at http:\/\/www.who.int\/csr\/disease\/avian_influenza\/consultation\/en\/. WHO. 2004. WHO consultation on priority public health interventions before and during an influenza pandemic. Available at http:\/\/www.who.int\/csr\/disease\/avian_influenza\/consultation\/en\/."},{"key":"e_1_2_1_57_1","doi-asserted-by":"publisher","DOI":"10.1258\/ebm.2010.010271"}],"container-title":["ACM Transactions on Modeling and Computer Simulation"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/2501602","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/2501602","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,18]],"date-time":"2025-06-18T07:28:48Z","timestamp":1750231728000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/2501602"}},"subtitle":["An interactive high-performance computing framework for data-intensive epidemic modeling"],"short-title":[],"issued":{"date-parts":[[2014,1]]},"references-count":57,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2014,1]]}},"alternative-id":["10.1145\/2501602"],"URL":"https:\/\/doi.org\/10.1145\/2501602","relation":{},"ISSN":["1049-3301","1558-1195"],"issn-type":[{"value":"1049-3301","type":"print"},{"value":"1558-1195","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,1]]},"assertion":[{"value":"2011-10-01","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2013-05-01","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2014-01-01","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}