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• W2922257415 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. PyBioNetFit is designed for parameterization, and also supports uncertainty quantification, checking models against known system properties, and solving design problems. PyBioNetFit introduces the 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 for parameterization model checking, and design. PyBioNetFit performs parameterization with parallelized metaheuristic optimization algorithms (differential evolution, particle swarm optimization, scatter search) that work directly with existing model definition standards: BioNetGen Language (BNGL) and Systems Biology Markup Language (SBML). We demonstrate PyBioNetFit's capabilities by solving 31 example problems, including the challenging problem of parameterizing a model of cell cycle control in yeast. We benchmark PyBioNetFit's parallelization efficiency on computer clusters, using up to 288 cores. Finally, we demonstrate the model checking and design applications of PyBioNetFit and BPSL by analyzing a model of therapeutic interventions in autophagy signaling." @default.
• W2922257415 created "2019-03-22" @default.
• W2922257415 creator A5011516162 @default.
• W2922257415 creator A5016126519 @default.
• W2922257415 creator A5040458833 @default.
• W2922257415 creator A5044484291 @default.
• W2922257415 creator A5057558587 @default.
• W2922257415 creator A5061748422 @default.
• W2922257415 creator A5064022214 @default.
• W2922257415 creator A5074190993 @default.
• W2922257415 date "2019-03-18" @default.
• W2922257415 modified "2023-09-27" @default.
• W2922257415 title "PyBioNetFit and the Biological Property Specification Language" @default.
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