International Conference on Computational Methods in Systems Biology

CMSB 2015: Computational Methods in Systems Biology pp 182-194

BioPSy: An SMT-based Tool for Guaranteed Parameter Set Synthesis of Biological Models

Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9308)

Abstract

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.

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  1. 1.School of Computing ScienceNewcastle UniversityNewcastle upon TyneUK

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