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Mathematical and Computer Modelling of Dynamical Systems
Methods, Tools and Applications in Engineering and Related Sciences
Volume 18, 2012 - Issue 1: Modelling the swarm – analysing biological and engineered swarm systems
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Original Articles

Techniques for grounding agent-based simulations in the real domain: a case study in experimental autoimmune encephalomyelitis

Mark Read Department of Electronics, University of York, York, North Yorkshire, YO10 5DD, UKCorrespondence[email protected]
,
Paul S. Andrews Department of Computer Science, University of York, York, North Yorkshire, YO10 5DD, UK
,
Jon Timmis Department of Electronics, University of York, York, North Yorkshire, YO10 5DD, UK; Department of Computer Science, University of York, York, North Yorkshire, YO10 5DD, UK
&
Vipin Kumar Laboratory of Autoimmunity, Torrey Pines Institute of Molecular Studies, San Diego, CA, USA
Pages 67-86 | Received 03 May 2011, Accepted 06 May 2011, Published online: 01 Aug 2011

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Sean L. Barnes, Daniel J. Morgan, Lisa Pineles & Anthony D. Harris. (2018) Significance of multi-site calibration for agent-based transmission models. IISE Transactions on Healthcare Systems Engineering 8:2, pages 131-143.
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Articles from other publishers (36)

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Givanna H. Putri, Jonathan Chung, Davis N. Edwards, Felix Marsh‐Wakefield, Irena Koprinska, Suat Dervish, Nicholas J. C. King, Thomas M. Ashhurst & Mark N. Read. (2022) TrackSOM : Mapping immune response dynamics through clustering of time‐course cytometry data . Cytometry Part A 103:1, pages 54-70.
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Katja Brinkmann, Daniel Kübler, Stefan Liehr & Andreas Buerkert. (2021) Agent-based modelling of the social-ecological nature of poverty traps in southwestern Madagascar. Agricultural Systems 190, pages 103125.
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Richard A. Williams. (2021) User experiences using FLAME: A Case study modelling conflict in large enterprise system implementations. Simulation Modelling Practice and Theory 106, pages 102196.
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Igor Balaz, Tara Petrić, Marina Kovacevic, Michail-Antisthenis Tsompanas & Namid Stillman. (2021) Harnessing adaptive novelty for automated generation of cancer treatments. Biosystems 199, pages 104290.
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Michael A. Yereniuk & Sarah D. Olson. (2020) Computational framework to capture the spatiotemporal density of cells with a cumulative environmental coupling. Journal of Computational and Applied Mathematics 369, pages 112572.
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Simone Cassani & Sarah D. Olson. (2020) A Hybrid Model of Cartilage Regeneration Capturing the Interactions Between Cellular Dynamics and Porosity. Bulletin of Mathematical Biology 82:2.
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Fiona A. C. Polack. 2020. From Astrophysics to Unconventional Computation. From Astrophysics to Unconventional Computation 103 122 .
Marissa Renardy, Caitlin Hult, Stephanie Evans, Jennifer J. Linderman & Denise E. Kirschner. (2019) Global sensitivity analysis of biological multiscale models. Current Opinion in Biomedical Engineering 11, pages 109-116.
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Kieran Alden, Jason Cosgrove, Mark Coles & Jon Timmis. (2019) Using Emulation to Engineer and Understand Simulations of Biological Systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics, pages 1-1.
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Leandro M. T. Garcia, Ana V. Diez Roux, André C. R. Martins, Yong Yang & Alex A. Florindo. (2018) Exploring the emergence and evolution of population patterns of leisure-time physical activity through agent-based modelling. International Journal of Behavioral Nutrition and Physical Activity 15:1.
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James O'Keeffe, Danesh Tarapore, Alan G. Millard & Jon Timmis. (2018) Adaptive Online Fault Diagnosis in Autonomous Robot Swarms. Frontiers in Robotics and AI 5.
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Mark N Read, Kieran Alden, Jon Timmis & Paul S Andrews. (2018) Strategies for calibrating models of biology. Briefings in Bioinformatics.
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Richard A. Williams. (2018) Lessons learned on development and application of agent-based models of complex dynamical systems. Simulation Modelling Practice and Theory 83, pages 201-212.
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Alexander P. Browning, Scott W. McCue, Rachelle N. Binny, Michael J. Plank, Esha T. Shah & Matthew J. Simpson. (2018) Inferring parameters for a lattice-free model of cell migration and proliferation using experimental data. Journal of Theoretical Biology 437, pages 251-260.
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Kieran Alden, Jon Timmis, Paul S. Andrews, Henrique Veiga-Fernandes & Mark Coles. (2017) Extending and Applying Spartan to Perform Temporal Sensitivity Analyses for Predicting Changes in Influential Biological Pathways in Computational Models. IEEE/ACM Transactions on Computational Biology and Bioinformatics 14:2, pages 431-442.
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J Timmis, K Alden, P Andrews, E Clark, A Nellis, B Naylor, M Coles & P Kaye. (2017) Building confidence in quantitative systems pharmacology models: An engineer's guide to exploring the rationale in model design and development. CPT: Pharmacometrics & Systems Pharmacology 6:3, pages 156-167.
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Stephanie Evans, Kieran Alden, Lourdes Cucurull-Sanchez, Christopher Larminie, Mark C. Coles, Marika C. Kullberg & Jon Timmis. (2017) ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour. PLOS Computational Biology 13:2, pages e1005351.
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Mark N. Read, Jacqueline Bailey, Jon Timmis & Tatyana Chtanova. (2016) Leukocyte Motility Models Assessed through Simulation and Multi-objective Optimization-Based Model Selection. PLOS Computational Biology 12:9, pages e1005082.
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Mark N. Read, Kieran Alden, Louis M. Rose & Jon Timmis. (2016) Automated multi-objective calibration of biological agent-based simulations. Journal of The Royal Society Interface 13:122, pages 20160543.
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Nadia S. Taou, David W. Corne & Michael A. Lones. 2016. Applications of Evolutionary Computation. Applications of Evolutionary Computation 351 362 .
J Cosgrove, J Butler, K Alden, M Read, V Kumar, L Cucurull-Sanchez, J Timmis & M Coles. (2015) Agent-Based Modeling in Systems Pharmacology. CPT: Pharmacometrics & Systems Pharmacology 4:11, pages 615-629.
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K.B. Blyuss & L.B. Nicholson. (2015) Understanding the roles of activation threshold and infections in the dynamics of autoimmune disease. Journal of Theoretical Biology 375, pages 13-20.
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Fiona Polack & Alastair Droop. (2014) Principled simulation of cell proliferation dynamics using the CoSMoS approach. Natural Computing 14:1, pages 63-82.
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Fiona Polack. (2014) Filling gaps in simulation of complex systems: the background and motivation for CoSMoS. Natural Computing 14:1, pages 49-62.
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Kieran Alden, Paul S. Andrews, Henrique Veiga-Fernandes, Jon Timmis & Mark Coles. (2014) Utilising a simulation platform to understand the effect of domain model assumptions. Natural Computing 14:1, pages 99-107.
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Mark Read, Paul S. Andrews, Jon Timmis & Vipin Kumar. (2014) Modelling biological behaviours with the unified modelling language: an immunological case study and critique. Journal of The Royal Society Interface 11:99, pages 20140704.
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Zhihui Wang, Thomas S. Deisboeck & Vittorio Cristini. (2014) Development of a sampling‐based global sensitivity analysis workflow for multiscale computational cancer models. IET Systems Biology 8:5, pages 191-197.
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Muaz A Niazi. (2013) Complex Adaptive Systems Modeling: A multidisciplinary Roadmap. Complex Adaptive Systems Modeling 1:1.
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Mark Read, Paul S. Andrews, Jon Timmis, Richard A. Williams, Richard B. Greaves, Huiming Sheng, Mark Coles & Vipin Kumar. (2013) Determining Disease Intervention Strategies Using Spatially Resolved Simulations. PLoS ONE 8:11, pages e80506.
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Marzio Pennisi, Abdul-Mateen Rajput, Luca Toldo & Francesco Pappalardo. (2013) Agent based modeling of Treg-Teff cross regulation in relapsing-remitting multiple sclerosis. BMC Bioinformatics 14:S16.
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Richard B. Greaves, Mark Read, Jon Timmis, Paul S. Andrews, James A. Butler, Bjorn-Ole Gerckens & Vipin Kumar. (2013) In silico investigation of novel biological pathways: The role of CD200 in regulation of T cell priming in experimental autoimmune encephalomyelitis. Biosystems 112:2, pages 107-121.
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Richard A Williams, Richard Greaves, Mark Read, Jon Timmis, Paul S Andrews & Vipin Kumar. (2013) In silico investigation into dendritic cell regulation of CD8Treg mediated killing of Th1 cells in murine experimental autoimmune encephalomyelitis. BMC Bioinformatics 14:S6.
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Kieran Alden, Mark Read, Jon Timmis, Paul S. Andrews, Henrique Veiga-Fernandes & Mark Coles. (2013) Spartan: A Comprehensive Tool for Understanding Uncertainty in Simulations of Biological Systems. PLoS Computational Biology 9:2, pages e1002916.
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Richard B. Greaves, Mark Read, Jon Timmis, Paul S. Andrews & Vipin Kumar. 2012. Information Processign in Cells and Tissues. Information Processign in Cells and Tissues 150 161 .
Richard A. Williams, Mark Read, Jon Timmis, Paul S. Andrews & Vipin Kumar. 2011. Artificial Immune Systems. Artificial Immune Systems 51 54 .

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