PyBioNetFit and the Biological Property Specification Language

Eshan D. Mitra, Ryan Suderman, Joshua Colvin, Alexander Ionkov, Andrew Hu, Herbert M. Sauro, Richard G Posner, William S. Hlavacek

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)1012-1036
Number of pages25
JournaliScience
Volume19
DOIs
StatePublished - Sep 27 2019

Fingerprint

Specification languages
Model checking
Parameterization
Markup languages
Yeast
Cells
Systems Biology

Keywords

  • Bioinformatics
  • Biological Sciences
  • Complex Systems
  • Computer Science
  • Parallel System
  • Systems Biology

ASJC Scopus subject areas

  • General

Cite this

Mitra, E. D., Suderman, R., Colvin, J., Ionkov, A., Hu, A., Sauro, H. M., ... Hlavacek, W. S. (2019). PyBioNetFit and the Biological Property Specification Language. iScience, 19, 1012-1036. https://doi.org/10.1016/j.isci.2019.08.045

PyBioNetFit and the Biological Property Specification Language. / Mitra, Eshan D.; Suderman, Ryan; Colvin, Joshua; Ionkov, Alexander; Hu, Andrew; Sauro, Herbert M.; Posner, Richard G; Hlavacek, William S.

In: iScience, Vol. 19, 27.09.2019, p. 1012-1036.

Research output: Contribution to journalArticle

Mitra, ED, Suderman, R, Colvin, J, Ionkov, A, Hu, A, Sauro, HM, Posner, RG & Hlavacek, WS 2019, 'PyBioNetFit and the Biological Property Specification Language', iScience, vol. 19, pp. 1012-1036. https://doi.org/10.1016/j.isci.2019.08.045
Mitra ED, Suderman R, Colvin J, Ionkov A, Hu A, Sauro HM et al. PyBioNetFit and the Biological Property Specification Language. iScience. 2019 Sep 27;19:1012-1036. https://doi.org/10.1016/j.isci.2019.08.045
Mitra, Eshan D. ; Suderman, Ryan ; Colvin, Joshua ; Ionkov, Alexander ; Hu, Andrew ; Sauro, Herbert M. ; Posner, Richard G ; Hlavacek, William S. / PyBioNetFit and the Biological Property Specification Language. In: iScience. 2019 ; Vol. 19. pp. 1012-1036.
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