Literature DB >> 24465120

A Distributed Platform for Global-Scale Agent-Based Models of Disease Transmission.

Jon Parker1, Joshua M Epstein1.   

Abstract

The Global-Scale Agent Model (GSAM) is presented. The GSAM is a high-performance distributed platform for agent-based epidemic modeling capable of simulating a disease outbreak in a population of several billion agents. It is unprecedented in its scale, its speed, and its use of Java. Solutions to multiple challenges inherent in distributing massive agent-based models are presented. Communication, synchronization, and memory usage are among the topics covered in detail. The memory usage discussion is Java specific. However, the communication and synchronization discussions apply broadly. We provide benchmarks illustrating the GSAM's speed and scalability.

Entities:  

Keywords:  Design; Epidemiology; Performance; agent behavior; agent-based modeling

Year:  2011        PMID： 24465120      PMCID： PMC3898773          DOI： 10.1145/2043635.2043637

Source DB:  PubMed          Journal:  ACM Trans Model Comput Simul        ISSN： 1049-3301            Impact factor:   1.075


  9 in total

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Authors:  Stephen Eubank; Hasan Guclu; V S Anil Kumar; Madhav V Marathe; Aravind Srinivasan; Zoltán Toroczkai; Nan Wang
Journal:  Nature       Date:  2004-05-13       Impact factor: 49.962

2.  Strategies for containing an emerging influenza pandemic in Southeast Asia.

Authors:  Neil M Ferguson; Derek A T Cummings; Simon Cauchemez; Christophe Fraser; Steven Riley; Aronrag Meeyai; Sopon Iamsirithaworn; Donald S Burke
Journal:  Nature       Date:  2005-08-03       Impact factor: 49.962

3.  Containing pandemic influenza at the source.

Authors:  Ira M Longini; Azhar Nizam; Shufu Xu; Kumnuan Ungchusak; Wanna Hanshaoworakul; Derek A T Cummings; M Elizabeth Halloran
Journal:  Science       Date:  2005-08-03       Impact factor: 47.728

4.  Using Influenza-Like Illness Data to Reconstruct an Influenza Outbreak.

Authors:  Philip Cooley; Laxminarayana Ganapathi; George Ghneim; Scott Holmberg; William Wheaton
Journal:  Math Comput Model       Date:  2008

5.  Individual-based computational modeling of smallpox epidemic control strategies.

Authors:  Donald S Burke; Joshua M Epstein; Derek A T Cummings; Jon I Parker; Kenneth C Cline; Ramesh M Singa; Shubha Chakravarty
Journal:  Acad Emerg Med       Date:  2006-11       Impact factor: 3.451

6.  Containing pandemic influenza with antiviral agents.

Authors:  Ira M Longini; M Elizabeth Halloran; Azhar Nizam; Yang Yang
Journal:  Am J Epidemiol       Date:  2004-04-01       Impact factor: 4.897

7.  Strategies for mitigating an influenza pandemic.

Authors:  Neil M Ferguson; Derek A T Cummings; Christophe Fraser; James C Cajka; Philip C Cooley; Donald S Burke
Journal:  Nature       Date:  2006-04-26       Impact factor: 49.962

8.  Targeted social distancing design for pandemic influenza.

Authors:  Robert J Glass; Laura M Glass; Walter E Beyeler; H Jason Min
Journal:  Emerg Infect Dis       Date:  2006-11       Impact factor: 6.883

9.  Coupled contagion dynamics of fear and disease: mathematical and computational explorations.

Authors:  Joshua M Epstein; Jon Parker; Derek Cummings; Ross A Hammond
Journal:  PLoS One       Date:  2008-12-16       Impact factor: 3.240
  9 in total
  19 in total

1.  Individual-based modeling of potential poliovirus transmission in connected religious communities in North America with low uptake of vaccination.

Authors:  Kasper H Kisjes; Radboud J Duintjer Tebbens; Gregory S Wallace; Mark A Pallansch; Stephen L Cochi; Steven G F Wassilak; Kimberly M Thompson
Journal:  J Infect Dis       Date:  2014-11-01       Impact factor: 5.226

2.  Indemics: An Interactive High-Performance Computing Framework for Data Intensive Epidemic Modeling.

Authors:  Keith R Bisset; Jiangzhuo Chen; Suruchi Deodhar; Xizhou Feng; Yifei Ma; Madhav V Marathe
Journal:  ACM Trans Model Comput Simul       Date:  2014-01       Impact factor: 1.075

3.  An Interactive, Web-based High Performance Modeling Environment for Computational Epidemiology.

Authors:  Suruchi Deodhar; Keith R Bisset; Jiangzhuo Chen; Yifei Ma; Madhav V Marathe
Journal:  ACM Trans Manag Inf Syst       Date:  2014-07

4.  Planning for climate change: The need for mechanistic systems-based approaches to study climate change impacts on diarrheal diseases.

Authors:  Jonathan E Mellor; Karen Levy; Julie Zimmerman; Mark Elliott; Jamie Bartram; Elizabeth Carlton; Thomas Clasen; Rebecca Dillingham; Joseph Eisenberg; Richard Guerrant; Daniele Lantagne; James Mihelcic; Kara Nelson
Journal:  Sci Total Environ       Date:  2016-01-19       Impact factor: 7.963

5.  Agent-based model of fecal microbial transplant effect on bile acid metabolism on suppressing Clostridium difficile infection: an example of agent-based modeling of intestinal bacterial infection.

Authors:  Xavier Peer; Gary An
Journal:  J Pharmacokinet Pharmacodyn       Date:  2014-08-29       Impact factor: 2.745

6.  Synthesis of a high resolution social contact network for Delhi with application to pandemic planning.

Authors:  Huadong Xia; Kalyani Nagaraj; Jiangzhuo Chen; Madhav V Marathe
Journal:  Artif Intell Med       Date:  2015-07-04       Impact factor: 5.326

7.  Web-based GIS: the vector-borne disease airline importation risk (VBD-AIR) tool.

Authors:  Zhuojie Huang; Anirrudha Das; Youliang Qiu; Andrew J Tatem
Journal:  Int J Health Geogr       Date:  2012-08-14       Impact factor: 3.918

8.  An open-access modeled passenger flow matrix for the global air network in 2010.

Authors:  Zhuojie Huang; Xiao Wu; Andres J Garcia; Timothy J Fik; Andrew J Tatem
Journal:  PLoS One       Date:  2013-05-15       Impact factor: 3.240

9.  Introduction of a Framework for Dynamic Knowledge Representation of the Control Structure of Transplant Immunology: Employing the Power of Abstraction with a Solid Organ Transplant Agent-Based Model.

Authors:  Gary An
Journal:  Front Immunol       Date:  2015-11-06       Impact factor: 7.561

10.  FRED (a Framework for Reconstructing Epidemic Dynamics): an open-source software system for modeling infectious diseases and control strategies using census-based populations.

Authors:  John J Grefenstette; Shawn T Brown; Roni Rosenfeld; Jay DePasse; Nathan T B Stone; Phillip C Cooley; William D Wheaton; Alona Fyshe; David D Galloway; Anuroop Sriram; Hasan Guclu; Thomas Abraham; Donald S Burke
Journal:  BMC Public Health       Date:  2013-10-08       Impact factor: 3.295
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