Publications

Building Confidence in Quantitative Systems Pharmacology Models: An Engineer’s Guide to Exploring the Rationale in Model Design and Development
J. Timmis, K. Alden, P. Andrews, E. Clark, A. Nellis, R. Naylor, M. Coles, and P. Kaye. To appear in CPT Pharmacometrics Systems Pharmacology (2016)
Virtual Fish Ecotoxicology Laboratory
J. Timmis, M. Coles, J. Snape, S. Owen, L. Gunnarsson and A. Boxall Industrial Pharmacy. Issue 50. (2016)
Using argument notation to engineer biological simulations with increased confidence.
K. Alden, P.S. Andrews, F.A.C. Polack, H. Veiga-Fernandes, M. C. Coles and J. Timmis The Journal of The Royal Society Interface 12: 20141059 http://dx.doi.org/10.1098/rsif.2014.1059
Utilising a Simulation Platform to Understand the Effect of Domain Model Assumptions. K.Alden, P.S. Andrews, H. Veiga-Fernandes, J. Timmis, M.C. Coles. Natural Computing. doi: 10.1007/s11047-014-9428-7
Modelling Biological Behaviours with the Unified Modelling Language: an Immunological Case Study and Critique.
M. Read, P.S. Andrews, J. Timmis, V. Kumar. Journal of The Royal Society Interface. doi: 10.1098/​rsif.2014.0704
A Petri Net Model of Granulomatous Inflammation: Implications for IL-10 Mediated Control of Leishmania donovani Infection L. Albergane, J. Timmis L. Beattie and P. Kaye. PLoS Comput Biol 9(11): e1003334. doi:10.1371/journal.pcbi.1003334
Determining Disease Intervention Strategies Using Spatially Resolved Simulations.
M. Read, P. Andrews, J. Timmis, R. Williams, R. Greaves, H. Sheng, M. Coles and V. Kumar. PLoS ONE 8(11): e80506. doi:10.1371/journal.pone.0080506
SPARTAN: A Comprehensive Tool for Understanding Uncertainty in Simulations of Biological Systems.
K. Alden, M. Read, J. Timmis, P.S. Andrews, H. Veiga-Fernandes, M.C. Coles. PLoS Comput Biol 9(2): e1002916. doi:10.1371/journal.pcbi.1002916
Pairing experimentation and computational modelling to understand the role of tissue inducer cells in the development of lymphoid organs.
K. Alden, J. Timmis, P.S. Andrews, H. Veiga-Fernandes, M.C Coles.Frontiers in Immunology. Volume 3:172. doi: doi: 10.3389/fimmu.2012.00172.
Techniques for Grounding Agent-Based Simulations in the Real Domain: a case study in Experimental Autoimmune Encephalomyelitis.
M. Read, P. Andrews, J. Timmis and V. Kumar. Mathematical and Computer Modelling of Dynamical Systems (MCMDS), 18(1):67-86. doi: 10.1080/13873954.2011.601419