Biopsy: An Smt-Based Tool For Guaranteed Parameter Set Synthesis Of Biological Models

The parameter set synthesis problem consists of identifying sets of parameter values for which a given system model satisfies a desired behaviour. This paper presents BioPSy, a tool that performs guaranteed parameter set synthesis for ordinary differential equation (ODE) biological models expressed in the Systems Biology Markup Language (SBML) given a desired behaviour expressed by time-series data. Three key features of BioPSy are: (1) BioPSy computes parameter intervals, not just single values; (2) for the identified intervals the model is formally guaranteed to satisfy the desired behaviour; and (3) BioPSy can handle virtually any Lipschitz-continuous ODEs, including nonlinear ones. BioPSy is able to achieve guaranteed synthesis by utilising Satisfiability Modulo Theory (SMT) solvers to determine acceptable parameter intervals. We have successfully applied our tool to several biological models including a prostate cancer therapy model, a human starvation model, and a cell cycle model.