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Gregory R. Madey

EDUCATION

  • Ph.D., Operations Research, Case Institute of Technology, Case Western Reserve University (CWRU)
  • M.S., Operations Research, (CWRU)
  • M.S., Mathematics, Cleveland State University (CSU)
  • B.S., Mathematics, (CSU)

RESEARCH INTERESTS

  • Emergency Operations Management
  • Bioinformatics, Biocomplexity, Modeling Epidemiology, Health Informatics
  • Agent-Based Modeling & Simulation
  • Cyberinfrastructure, Virtual Research and Engineering Organizations, Collaboratories
  • e-Science, e-Engineering  & e-Commerce
  • Chaos and Complexity
  • Open Source Software
  • Data Warehousing, Data Mining & Web Mining
  • Web Services, Service Oriented Architecture
  • Large Scientific Databases

TEACHING

GRADUATE STUDENTS

  • Ryan McCune
  • Casey Ferris
  • Cindy Nikolai

Research Group Summer 2009

RECENT PUBLICATIONS (always out of date!)

Google Scholar

  • Spatial Agent-Based Simulation Modeling in Public Health: Design, Implementation, and Applications for Malaria Epidemiology, John Wiley & Sons, Inc., Hoboken, NJ (in press).
  • "Verification, Validation, and Replication Methods for Agent-Based Modeling and Simulation: Lessons Learned the Hard Way!." In Concepts and Methodologies for Modeling and Simulation, pp. 217-242. Springer International Publishing, 2015.
  • "Thinking like a vertex: a survey of vertex-centric frameworks for large-scale distributed graph processing." ACM Computing Surveys (CSUR) 48.2 (2015): 25
  • "Lessons Learned from Crowdsourcing Complex Engineering Tasks." PloS One 10, no. 9 (2015): e0134978.
  • "Landscape epidemiology modeling using an agent-based model and a geographic information system." Land 4, no. 2 (2015): 378-412.
  • "Modelling sterile insect technique to control the population of Anopheles gambiae." Malaria Journal 14 (2015): 92.
  • "SimEOC: A Distributed Web-Based Virtual Emergency Operations Center Simulator for Training and Research." International Journal of Information Systems for Crisis Response and Management (IJISCRAM) vol. 7, no. 1 (2015): 1-21.
  • "OpenMalaria and EMOD: a case study on model alignment." In Proceedings of the Conference on Summer Computer Simulation, pp. 1-9. Society for Computer Simulation International, 2015
  • "Enhancing the Usability and Utilization of Accelerated Architectures via Docker", IEEE/ACM 8th International Conference on Utility and Cloud Computing, December, 2015.(pdf)
  • VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. Nucleic Acids Research, 43(D1), pp.D707-D713 (2015),
  • "Control of Artificial Swarms with DDDAS." Procedia Computer Science 29 (2014): 1171-1181.
  • "PGMS: A Case Study of Collecting PDA-Based Geo-Tagged Malaria-Related Survey Data." The American Journal of Tropical Medicine and Hygiene (2014): 13-0652.
  • "Investigations of DDDAS for Command and  Control of UAV Swarms with Agent-based Modelling", Proceedings of the 2013 Winter Simulation Conference, Washington, D.C., December 2013
  • "A test of agent-based models as a tool for predicting patterns of pathogen transmission in complex landscapes", BMC Ecology, Vol 13, Issue 1, September 2013 (open access)
  • "Cyberinfrastructure: The Key to Building Successful Science Gateways – VectorBase: A Bioinformatics Resource Center for Infectious Diseases", Science Gateway Institute Workshop - IEEE Cluster 2013, Indianapolis, IN, September 27, 2013 (pdf)
  • "Integrating An Agent-Based Model Of Malaria Mosquitoes With A Geographic Information System", The 25TH European Modeling & Simulation Symposium (EMSS 2013), Athens, September 2013. (pdf)
  • "Examining the impact of larval source management and insecticide-treated nets using a spatial agent-based model of Anopheles gambiae and a landscape generator tool." Malaria Journal 12 (2013): 290. (open access)
  • "A Testbed for Investigating the UAV Swarm Command and Control Problem Using DDDAS". Procedia Computer Science 10 (2013).(open access)
  • "An Operation-time Simulation Framework for UAV Swarm Configuration and Mission Planning". Procedia Computer Science 10 (2013). (open access)
  • "Swarm Control of UAVs for Cooperative Hunting with DDDAS". Procedia Computer Science 10 (2013). (open access)
  • "Agent-based Simulation for UAV Swarm Mission Planning and Execution," In Proceedings of the 2013 Symposium on Agent Directed Simulation (ADS '13/SpringSim 2013). Society for Computer Simulation International, San Diego, CA, 2013.
  • "Multi-hop Communications in a Swarm of UAVs," In Proceedings of the 2013 Symposium on Agent Directed Simulation (ADS '13/SpringSim 2013). Society for Computer Simulation International, San Diego, CA, 2013.
  • "Agent-Based Simulation of Cooperative Hunting with UAVs," In Proceedings of the 2013 Symposium on Agent Directed Simulation (ADS '13/SpringSim 2013). Society for Computer Simulation International, San Diego, CA, 2013.
  • "Design and Evaluation of UAV Swarm Command and Control Strategies," In Proceedings of the 2013 Symposium on Agent Directed Simulation (ADS '13/SpringSim 2013). Society for Computer Simulation International, San Diego, CA, 2013.
  • "Haiti Earthquake Photo Tagging: Lessons on Crowdsourcing In-Depth Image Classifications",  Seventh International Conference on Digital Information Management (ICDIM 2012), August 22-24, 2012, Macau, China
  • "Citizen Engineering: Evolving OSS Practices to Engineering Design and Analysis", 8th International Conference on Open Source Systems, Hammamet, Tunisia – 10-13 September, 2012
  • "Haiti Earthquake Photo Tagging: Lessons on Crowdsourcing In-Depth Image Classifications",  Seventh International Conference on Digital Information Management (ICDIM 2012), August 22-24, 2012, Macau, China
  • "Applying DDDAS Principles to Command, Control and Mission Planning for UAV Swarms". Procedia Computer Science, 9,  1177-1186. (open access)
  • "Crowdsourcing Highly Trustworthy Results", 45th Hawaii International Conference on System Science (HICSS), 2012
  • "Expert-Citizen Engineering: 'Crowdsourcing' Skilled Citizens"  2011 International Conference on Social Computing and its Applications (SCA2011) 12-14 December 2011, Sydney Australia
  • "An automated homology-based approach for identifying transposable elements", BMC Bioinformatics, 12:130, 2011. (online)
  • "Design and implementation of an agent-based simulation for emergency response and crisis management". Journal of Algorithms & Computational Technology, 5(4), 601-622.
  • "Portals for collaborative research communities: two distinguishing case studies", Concurrency and Computation: Practice and Experience, 2: 269-278, 2011.
  • "Dynamic adaptive disaster simulation: developing a predictive model of emergency behavior using cell phone and GIS data". In Proceedings of the 2011 Workshop on Agent-Directed  Simulation (pp. 5-12). Society for Computer Simulation International.
  • VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics, Nucleic Acids Research, Volume 40, Issue D1, Pp. D729-D734, 2011
  • "Divide and conquer: A four-fold  docking experience of agent-based models." In Proceedings of the Winter Simulation Conference, pp. 575-586. Winter Simulation Conference, 2010.
  • "Genome sequences of the  human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle." Proceedings of the National Academy of Sciences 107, no. 27 (2010): 12168-12173.
  • "Discretionary Access Controls for a Collaborative Virtual Environment", The International Journal of Virtual Reality, 9(1) pp 61-71, 2010.
  • "P-SAM: a  post-simulation analysis module for agent-based models." In Proceedings of the 2010 Summer Computer Simulation Conference, pp. 350-357. Society for Computer Simulation International, 2010.
  • Verification & validation by docking: a case study of agent-based models of Anopheles gambiae. In SummerSim (pp. 236-243).
  • "Warehousing and Studying Open Source Versioning Metadata." Open Source Software: New Horizons. Springer Berlin Heidelberg, 2010. 413-418.
  • "Open Source Software Developer and Project Networks." Open Source Software: New Horizons. Springer Berlin Heidelberg, 2010. 407-412.
  • Open Source Software: New Horizons: 6th International IFIP WG 2.13 Conference on Open Source Systems, OSS 2010,  Notre Dame, IN, USA, May  30-June 2, 2010, Proceedings. Vol. 319. Springer, 2010.
  • "The Importance of Social Network Structure in the Open Source Software Developer Community",  HICSS-43, Kauai, Hawaii, January 2010.

Research Group Summer 2006

SERVICE

  • Local host and Chairman for the 17th Annual International Swarm Agent-Based Simulation Meeting (SwarmFest 2014) hosted at the University of Notre Dame, June 2006
  • Organizing Chair and Co-Conference Chair for IFIP WG 2.13 OSS2010 hosted at Notre Dame
  • Local host and Chairman for the Tenth Annual International Swarm Agent-Based Simulation Meeting hosted at the University of Notre Dame, June 2006
  • Local host and Chairman for Annual  North American Association for Computational Social and Organizational Science (NAACSOS 2006) hosted at the University of Notre Dame, June 2006
  • Local host and Chairman for Annual NAACSOS North American Association for Computational Social and Organizational Science) hosted at the University of Notre Dame, June 2005
  • Chairman of the Seventh Annual International Swarm Researchers Meeting hosted at the University of Notre Dame (Swarm2003)
  • Director of Graduate Studies for Computer Science and Engineering (2003-2005)
  • Academic Mentor: EPICS teams on American Red Cross - GIS, Homelessness Prevention, Habitat for Humanity, Michiana Autism Center, Toys Redesign Project for the Handicapped, and Montessori Technology

INDUSTRY: RESEARCH & MANAGEMENT

  • Director - Advanced Projects and Strategic Planning, Defense Systems, Loral Corporation (now part of Lockheed-Martin)
  • Manager - Systems Analysis, Defense Systems Division, Goodyear Aerospace Corporation
  • Engineering Analyst, Goodyear Aerospace Corporation
  • Systems Engineering - Ocean Systems, Gould Corporation (now part of Northop-Grumman)
  • Computer Scientist - Computer and Networking Division, NASA Glenn Research Center

Research Group Summer 2004

Research Group Summer 2003
  • "Project Ensayo: Designing a Virtual Emergency Operations Center", IEEE International Conference on Systems, Man, and Cybernetics - Homeland Security, San Antonio, Texas, October 2009
  • "A GIS Aware Agent-Based Model of Pathogen Transmission," International Journal of Intelligent Control and Systems, Vol. 14, No. 1, March 2009, 51-61..
  • "Feature Clustering for Data Steering in Dynamic Data Driven Application Systems", Allen, G., et al.,  (Eds.): ICCS 2009, Part II, LNCS 5545, Springer-Verlag Berlin/Heidelberg, pp. 460–469, 2009
  • "Tools of the Trade: A Survey of Various Agent Based Modeling Platforms", Journal of Artificial Societies and Social Simulation 12(2)2, 31-Mar-2009 (online)
  • "A Survey of Technologies for Building Collaborative Virtual Environments", The International Journal of Virtual Reality, 8(1): 53-66, 2009.
  • "VectorBase: a data resource for invertebrate vector genomics", Nucleic Acids Research. 2009 January; 37(Database issue): D583–D587
  • "Multiple Organism Algorithm for Finding Ultraconserved Elements", BMC Bioinformatics, Vol. 9, No. 15, January 2008. (pdf)
  • "Anomaly Detection in a Mobile Communication Network", Computational & Mathematical Organization Theory, Vol. 13, No. 4, December 2007
  • "A stochastic model for the synthesis and degradation of natural organic matter part II: molecular property distributions", Biogeochemistry, Vol. 86, No. 3, December 2007
  • "Uncovering individual and collective human dynamics from mobile phone records", Journal of Physics A: Mathematical and Theoretical, October 2007
  • "A stochastic model for the synthesis and degradation of natural organic matter. Part III: Modeling Cu(II) complexation", Applied Geochemistry, Volume 22, Issue 8, August 2007, 1646-1658
  • "Improving the Reuse of Scientific Workflows and Their By-products", IEEE International Conference on Web Services, July 2007, Salt Lake City, UT
  • "VectorBase: a home for invertebrate vectors of human pathogens",  Nucleic Acids Research, 2007, Vol. 35, Database issue
  • "Analysis of activity in the open source software development community". In Proceedings of the 40th Annual Hawaii International Conference on System Sciences. IEEE Computer Society Press, January 3-6 2007
  • "WIPER: Leveraging the Cell Phone Network for Emergency Response", International Journal of Intelligent Control and Systems, Vol. 11, No. 4, Dec. 2006
  • "Application of Social Network Analysis to the Study of Open Source Software", The Economics of Open Source Software Development, eds. Jürgen Bitzer and Philipp J.H. Schröder, Elsevier Press, 2006.
  • "Modeling the Evolution of Natural Organic Matter in the Environment with an Agent-based Stochastic Approach", Natural Resource Modeling Journal, Spring 2006.
  • "Wiper: The integrated wireless phone based emergency response system." in International Conference on Computational Science, ser. Lecture Notes in Computer Science, V. N. Alexandrov, G. D. van Albada, P. M. A. Sloot, and J. Dongarra, Eds., vol. 3993. Springer, 2006, pp. 417–424.
  • "The Knowledge Management Efficacy Of Matching Information Systems Development Methodologies With Application Characteristics - An Experimental Study", Journal of Systems and Software, January 2006.
  • "Designing Flexible Distributed Component Systems", in  The Development of Component-based Information Systems, eds., M. Lycett, S. de Cesare and R. Macredie, M.E. Sharpe Inc, 2005.
  • "A Stochastic Model for the Synthesis and Degradation of Natural Organic Matter. Part I. Data Structures and Reaction Kinetics",  Biogeochemistry, Springer, Volume 76, Number 2, November 2005, pp. 319 - 347.
  • "Agent-based Scientific Simulation", IEEE Computing in Science & Engineering, Jan-Feb 2005, pp. 22-29.
  • "Modeling the F/OSS Community: A Quantitative Investigation",  in Free/Open Source Software Development, ed., Stephan Koch, Idea Publishing, 2004.
  • "A Web Portal for Environmental Research", ed. Arno Scharl, Environmental Online Communication, Springer, London, 2004.
  • "Temporal representation and reasoning for workflow in engineering design change review," IEEE Transactions on Engineering Management,  Vol. 47, No. 4, pp. 485-492, 2000

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University of
Notre Dame

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