Title: Plant defence model revisions through iterative minimisation of constraint violations

Authors: Dragana Miljkovic; Matjaž Depolli; Tjaša Stare; Igor Mozetič; Marko Petek; Kristina Gruden; Nada Lavrač

Addresses: Department of Knowledge Technologies, Jožef Stefan Institute, Jamova 39, Ljubljana 1000, Slovenia ' Department of Communication Systems, Jožef Stefan Institute, Jamova 39, Ljubljana 1000, Slovenia ' Department of Systems Biology and Biotechnology, National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia ' Department of Knowledge Technologies, Jožef Stefan Institute, Jamova 39, Ljubljana 1000, Slovenia ' Department of Systems Biology and Biotechnology, National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia ' Department of Systems Biology and Biotechnology, National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia ' Department of Knowledge Technologies, Jožef Stefan Institute, Jamova 39, Ljubljana 1000, Slovenia

Abstract: Biologists have been investigating plant defence response to virus infections; however, a comprehensive mathematical model of this complex process has not been developed. One obstacle in developing a dynamic model, useful for simulation, is the lack of kinetic data from which the model parameters could be determined. We address this problem by proposing a methodology for iterative improvement of the model parameters until the simulation results come close to the expectation of biology experts. These expectations are formalised in the form of constraints to be satisfied by the model simulations. In three iterative steps the model converged to satisfy the biology experts. There are two results of our approach: individual simulations and optimised model parameters, which provide a deeper insight into the biological system. Our constraint-driven optimisation approach allows for an efficient exploration of the dynamic behaviour of biological models and, at the same time, increases their reliability.

Keywords: systems biology; dynamic parameters; plant defence response; constraint-driven optimisation; mathematical modelling; constraint violations; virus infections; dynamic modelling; simulation.

DOI: 10.1504/IJCBDD.2014.058588

International Journal of Computational Biology and Drug Design, 2014 Vol.7 No.1, pp.61 - 79

Published online: 08 Jan 2014 *

Full-text access for editors Access for subscribers Purchase this article Comment on this article