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The Use of Organisational Metaphors
Bosse, T., Jonker, C. M. and Treur, J. 2005.
Modelling the dynamics of intracellular processes as an organisation of
multiple agents. In First International Workshop on Multi-Agent Systems for
Medicine, Computational Biology and Bioinformatics. AAMAS '05.
Cannata, N., Corradini, F., Merelli, E.,
Omicini, A. and Ricci, A. 2005. An Agent-oriented conceptual framework for
systems biology. Transactions on Computational Systems Biology 3, 105-122.
Parisey, N., Beurton-Aimar, M., Lales, C.,
Strandh, R. and Mazat, J. P. 2005. Towards modelling the q cycle by multi-agent
systems. In ECAL 2005.
Formalisms for ABM in Systems Biology
Christley, S. and Madey, G. 2006. Abstract
Process Model for Systems Biology. Proceedings of the 2006 Agent-Directed
Simulation Symposium, Huntsville, AL.
Coakley, S., Smallwood, S. and Halcombe, M.
2006. Using X-Machines as a Formal Basis for Describing Agents in Agent-Based
Modelling. Proceedings of the 2006 Agent-Directed Simulation Symposium,
Huntsville, AL.
Walker, D. C., Hill, G., Wood, S. M., Smallwood, R. H. and Southgate, J. 2004. Agent-based computational modelling of epithelial cell monolayers: predicting the effect of exogenous calcium concentrations on the rate of wound closure. IEEE Transactions Nanobioscience 3, 153-163.
Example applications of ABM in biology and
biomedicine
Biological signalling
Ausk, B.J, Gross, T.S., Srinivasan,
S. An Agent Based Model for Real-Time Signaling Induced in Osteocytic
Networks by Mechanical Stimuli, J Biomechanics (2005) .
Walker, DC, Southgate, J, Hill, G,
Halcombe, M., Hose, D. R., Wood, S. M., Mac Neil, S. and Smallwood, R. H. The
epitheliome: agent-based modelling of the social behaviour of cells. Biosystems
76 (1-3): 89-100 (2004).
Bacterial systems
Paton, R, Gregory, R, Vlachos, C,
Saunders, J. and Wu, H. Evolvable social agents for bacterial systems
modelling. IEEE Transactions in Nanobiosci . 3 (3):
208-216 (2004).
Immunology
Melby, N. J. Comparative relative strength artificial immune systems: System wellness. In
Proceedings of the IEEE Southeastcon. 2004: 368-371 (2005).
Gammack, D, Ganguli, S, Marino, S, Segovia-Juarez, J. and Kirschner, D. E. Understanding the immune response in tuberculosis using different mathematical models and biological scales. Multiscale Model Sim. 3 (2): 312-345 (2005).
Robbins, M. J. and Garrett, S. M. 2005.
Evaluating theories of immunological memory using large-scale simulations. In
ICARIS 2005, LNCS 3627, 193-206.
Tay, J. C. and Jhavar, A. 2005. A complex
adaptive framework for immune system simulation. ACM Symposium of Applied
Computing, 158-164.
Tumour growth
Athale, C. A and Deisboeck, TS. The
effects of EGF-receptor density on multiscale tumor growth patterns. J. Theor.
Biol. 238 (4): 771-779 (2006).
Athale, C, Mansury, Y, Deisboeck, TS.
Simulating the impact of a molecular 'decision-process' on cellular phenotype
and multicellular patterns in brain tumors. J. Theor. Biol. 233
(4): 469-481 (2005)
Mansury, Y and Deisboeck, TS. Simulating
the time series of a selected gene expression profile in an agent-based tumor
model. Physica D 196 (1-2): 193-204 (2004).
Mansury, Y and Deisboeck, TS. Simulating
'structure-function' patterns of malignant brain tumors. Physica A
331 (1-2): 219-232 (2004).
Mansury, Y, Kimura, M, Lobo, J, and Deisboeck,
T. S. Emerging patterns in tumor systems: Simulating the dynamics of
multicellular clusters with an agent-based spatial agglomeration model. J.
Theor. Biol. 219 (3): 343-370 (2002).
Stem cells
d'Inverno, M and Prophet, J.
Multidisciplinary investigation into adult stem cell behaviour. Lect. Notes
Comput. Sc. 3737 : 49-64 (2005).
Environment-climate
Bharwani, S, Bithell, M, Downing, TE, New, M., Washington, R. and Ziervogel, G.
Multi-agent modelling of climate outlooks and food security on a community
garden scheme in Limpopo, South Africa. Philos. T. Roy. Soc. B
360 (1463): 2183-2194 NOV 29 (2005).
Zaima, K. Effects of structural and
behavioral strategies toward the environmentally conscious society: agent-based
approach. Agent Based Soc. Syst. 1 : 233-246 (2005)
Vlachos, C, Gregory, R, Paton, R. C, Saunders,
J. R. and Wu, Q. H. Individual-based modelling of bacterial ecologies and
evolution. Comp. Funct. Genom. 5 (1): 100-104 (2004).
Biogeochemistry
Cabaniss, SE, Madey, G, Leff, L, Maurice, P. A.,
and Wetzel, R. A stochastic model for the synthesis and degradation of natural
organic matter. Part I. Data structures and reaction kinetics. Biogeochemistry
76 (2): 319-347 (2005).
Physiology
An G. In-silico experiments of existing
and hypothetical cytokine-directed clinical trials using agent based modeling. Crit.
Care. Med. 32 (10): 2050-2060 (2004).
An G, Lee I. Agent-Based Computer
simulation (ABCS) and the inflammatory response: Building a tool to study
Systemic Inflammatory Response Syndrome (SIRS). Simulation and Gaming
32 (3): 344-361 (2001).
Muller, G, Grebaut, P, Gouteux, JP. An
agent-based model of sleeping sickness: simulation trials of a forest focus in
southern Cameroon. C. R. Biol . 327 (1): 1-11 (2004).
Environmental toxicology
Topping, CJ, Odderskaer, P. Modeling the
influence of temporal and spatial factors on the assessment of impacts of
pesticides on skylarks. Environ. Toxicol. Chem. 23 (2):
509-520 (2004).
Epidemics and bioweapons
Chen, LC, Carley, KM, Fridsma, D, Kaminsky, B.
and Yahja, A. Model alignment of anthrax attack simulations. Decis. Support
Syst. 41 (3): 654-668 (2006).
Carley, KM, Fridsma, DB, Casman, E, Yahja, A.,
Altman, N., Chen, LC., Kaminsky, B. and Nave, D. BioWar: Scalable agent-based
model of bioattacks. IEEE T. Syst. Man. Cy. A. 36 (2):
252-265 (2006).
Eidelson, BM, Lustick, I. VIR-POX: An
agent-based analysis of smallpox preparedness and response policy. J. Artif.
Soc. S. 7 (3) (2004).
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