PyBioNetFit and the Biological Property Specification Language

Overview

Journal iScience

Publisher Cell Press

Date 2019 Sep 16

PMID 31522114

Citations 26

Authors

Eshan D Mitra

Ryan Suderman

Joshua Colvin

Alexander Ionkov

Andrew Hu

Herbert M Sauro

Richard G Posner

William S Hlavacek

Affiliations

Soon will be listed here.

Abstract

In systems biology modeling, important steps include model parameterization, uncertainty quantification, and evaluation of agreement with experimental observations. To help modelers perform these steps, we developed the software PyBioNetFit, which in addition supports checking models against known system properties and solving design problems. PyBioNetFit introduces Biological Property Specification Language (BPSL) for the formal declaration of system properties. BPSL allows qualitative data to be used alone or in combination with quantitative data. PyBioNetFit performs parameterization with parallelized metaheuristic optimization algorithms that work directly with existing model definition standards: BioNetGen Language (BNGL) and Systems Biology Markup Language (SBML). We demonstrate PyBioNetFit's capabilities by solving various example problems, including the challenging problem of parameterizing a 153-parameter model of cell cycle control in yeast based on both quantitative and qualitative data. We demonstrate the model checking and design applications of PyBioNetFit and BPSL by analyzing a model of targeted drug interventions in autophagy signaling.

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