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© The Author(s) 2014. This article is published with open access at Springerlink.com. Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited., Computational and mathematical modelling approaches are increasingly being adopted in attempts to further our understanding of complex biological systems. This approach can be subjected to strong criticism as substantial aspects of the biological system being captured are not currently known, meaning assumptions need to be made that could have a critical impact on simulation response. We have utilised the CoSMoS process in the development of an agent-based simulation of the formation of Peyer's patches (PP), gut-associated lymphoid organs that have a key role in the initiation of adaptive immune responses to infection. Although the use of genetic tools, imaging technologies and ex vivo culture systems has provided significant insight into the cellular components and associated pathways involved in PP development, interesting questions remain that cannot be addressed using these approaches, and as such well justified assumptions have been introduced into our model to counter this. Here we focus not on the development of the model itself, but instead demonstrate how the resultant simulation can be used to assess how these assumptions impact the simulation response. For example, we consider the impact of our assumption that the migration rate of lymphoid tissue cells into the gut remains constant throughout PP development. We demonstrate that an analysis of the assumptions made in the construction of the domain model may either increase confidence in the model as a representation of the biological system it captures, or may suggest areas where further biological experimentation is required., This work was funded by the Wellcome Trust [ref:097829] through the Centre for Chronic Diseases and Disorders (C2D2) at the University of York. Paul Andrews is funded by EPSRC grant EP/I005943/1 “Resilient Futures.” Henrique Veiga-Fernandes is funded by Fundação para a Ciência e Tecnologia (PTDC/SAU-MII/100016/2008), Portugal, European Molecular Biology Organisation (Project 1648) and European Research Council (Project 207057). Jon Timmis is part funded by the Royal Society and the Royal Academy of Engineering. Funding for Mark Coles comes from grants from the Human Frontiers Science Program (RGP0006/2009) and the Medical Research Council (G0601156).