title: Plant defence model revisions through iterative minimisation of constraint violations.
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.
authors.affiliation: Department of Knowledge Technologies, Jožef Stefan Institute, Jamova 39, Ljubljana 1000, Slovenia.
authors.forename: Dragana
authors.initials: D
authors.lastname: Miljkovic
authors.affiliation: Department of Communication Systems, Jožef Stefan Institute, Jamova 39, Ljubljana 1000, Slovenia.
authors.forename: Matjaž
authors.initials: M
authors.lastname: Depolli
authors.affiliation: Department of Systems Biology and Biotechnology, National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia.
authors.forename: Tjaša
authors.initials: T
authors.lastname: Stare
authors.affiliation: Department of Knowledge Technologies, Jožef Stefan Institute, Jamova 39, Ljubljana 1000, Slovenia.
authors.forename: Igor
authors.initials: I
authors.lastname: Mozetič
authors.affiliation: Department of Systems Biology and Biotechnology, National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia.
authors.forename: Marko
authors.initials: M
authors.lastname: Petek
authors.affiliation: Department of Systems Biology and Biotechnology, National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia.
authors.forename: Kristina
authors.initials: K
authors.lastname: Gruden
authors.affiliation: Department of Knowledge Technologies, Jožef Stefan Institute, Jamova 39, Ljubljana 1000, Slovenia.
authors.forename: Nada
authors.initials: N
authors.lastname: Lavrač