title: In silico investigation of novel biological pathways: the role of CD200 in regulation of T cell priming in experimental autoimmune encephalomyelitis.
abstract: The use of simulation to investigate biological domains will inevitably lead to the need to extend existing simulations as new areas of these domains become more fully understood. Such simulation extensions can entail the incorporation of additional cell types, molecules or molecular pathways, all of which can exert a profound influence on the simulation behaviour. Where the biological domain is not well characterised, a structured development methodology must be employed to ensure that the extended simulation is well aligned with its predecessor. We develop and discuss such a methodology, relying on iterative simulation development and sensitivity analysis. The utility of this methodology is demonstrated using a case study simulation of experimental autoimmune encephalomyelitis (EAE), a murine T cell-mediated autoimmune disease model of multiple sclerosis, where it is used to investigate the activity of an additional regulatory pathway. We discuss how application of this methodology guards against creating inappropriate simulation representations of the biology when investigating poorly characterised biological mechanisms.
authors.affiliation: Department of Computer Science, Deramore Lane, University of York, UK. richard.greaves@york.ac.uk
authors.forename: Richard B
authors.initials: RB
authors.lastname: Greaves
authors.forename: Mark
authors.initials: M
authors.lastname: Read
authors.forename: Jon
authors.initials: J
authors.lastname: Timmis
authors.forename: Paul S
authors.initials: PS
authors.lastname: Andrews
authors.forename: James A
authors.initials: JA
authors.lastname: Butler
authors.forename: Bjorn-Ole
authors.initials: BO
authors.lastname: Gerckens
authors.forename: Vipin
authors.initials: V
authors.lastname: Kumar
mesh_terms: D000818:Animals; D015703:Antigens, CD / Q000276:immunology* / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D004195:Disease Models, Animal; D004681:Encephalomyelitis, Autoimmune, Experimental / Q000276:immunology* / Q000378:metabolism; D006801:Humans; D051379:Mice; D018448:Models, Immunological; D009103:Multiple Sclerosis / Q000276:immunology / Q000378:metabolism; D015203:Reproducibility of Results; D015398:Signal Transduction / Q000276:immunology*; D013601:T-Lymphocytes / Q000276:immunology* / Q000378:metabolism
chemical_list: D015703:Antigens, CD; C042739:antigens, CD200