Papers Published


  1. ASPASIA: A Toolkit for Evaluating the Effects of Biological Interventions on SBML Model Behaviour. S.Evans, K.Alden, L.Cucurull-Sanchez , C.Larminie , M.C.Coles, M.C.Kullberg , J.Timmis. Accepted. To appear in PLoS Computational Biology



  1. Extending and Applying Spartan to Perform Temporal Sensitivity Analyses for Predicting Changes in Influential Biological Pathways in Computational Models. K.Alden, J.Timmis, P.S.Andrews, H.Veiga-Fernandes, M.C.Coles. IEEE Transactions on Computational Biology and Bioinformatics. vol.PP, no.99. doi: 10.1109/TCBB.2016.2527654
  2. Automated multi-objective calibration of biological agent-based simulations. M.Read, K.Alden, L.Rose, J.Timmis. Royal Society Interface. 13 doi:



  1. 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, J.Timmis. Journal of the Royal Society Interface. doi: 10.1098/rsif.2014.1059
  2. Agent-Based Modeling in Systems Pharmacology. J Cosgrove, J Butler, K.Alden, M Read, V Kumar, L Cucurull-Sanchez, J Timmis, M Coles. CPT Pharmacometrics Syst. Pharmacol.



  1. 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
  2. Easing Parameter Sensitivity Analysis of Netlogo Simulations using Spartan. K.Alden, J. Timmis, M.C. Coles. Proceedings of the 14th International Conference on the Synthesis and Simulation of Living Systems. MIT Press. doi: 10.7551/978-0-262-32621-6-ch100
  3. Novel Approaches to the Visualisation and Quantification of Biological Simulations by Emulating Experimental Techniques. J.Butler, K.Alden, H.Veiga-Fernandes, J. Timmis, M.C. Coles. Proceedings of the 14th International Conference on the Synthesis and Simulation of Living Systems. MIT Press. doi: 10.7551/978-0-262-32621-6-ch099
  4. Applying spartan to Understand Parameter Uncertainty in Simulations. K.Alden, M.Read, P.S.Andrews, J.Timmis, M.C.Coles. R Journal



  1. 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



  1. Differential RET signaling responses orchestrate lymphoid and nervous enteric system development. A. Patel, N. Harker, L. Moreira-Santos, M. Ferreira, K. Alden, J. Timmis, K. Foster, A. Garefalaki, P. Pachnis, P.S. Andrews, H. Enomoto, J. Milbrandt, V. Pachnis, M.C. Coles, D. Kioussis, H. Veiga-Fernandes. Science Signalling, Volume 5, Issue 235. doi: 10.1126/scisignal.2002734
  2. 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



  1. Towards Argument-Driven Validation of an in silico Model of Immune Tissue Organogenesis. K. Alden, P. Andrews, J. Timmis, H. Veiga-Fernandes and M.C. Coles. Extended Abstract in LNCS 6826, pp:66-70.



  1. dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment. K.Alden, S.Veretnik, P.E.Bourne. BMC Bioinformatics. 11:310