LAPSE:2019.0662
Published Article
LAPSE:2019.0662
Application of Parameter Optimization to Search for Oscillatory Mass-Action Networks Using Python
July 25, 2019
Biological systems can be described mathematically to model the dynamics of metabolic, protein, or gene-regulatory networks, but locating parameter regimes that induce a particular dynamic behavior can be challenging due to the vast parameter landscape, particularly in large models. In the current work, a Pythonic implementation of existing bifurcation objective functions, which reward systems that achieve a desired bifurcation behavior, is implemented to search for parameter regimes that permit oscillations or bistability. A differential evolution algorithm progressively approximates the specified bifurcation type while performing a global search of parameter space for a candidate with the best fitness. The user-friendly format facilitates integration with systems biology tools, as Python is a ubiquitous programming language. The bifurcation−evolution software is validated on published models from the BioModels Database and used to search populations of randomly-generated mass-action networks for oscillatory dynamics. Results of this search demonstrate the importance of reaction enrichment to provide flexibility and enable complex dynamic behaviors, and illustrate the role of negative feedback and time delays in generating oscillatory dynamics.
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Keywords
biological networks, BioModels Database, bistable switch, differential evolution, evolutionary algorithm, Hopf bifurcation, mass-action networks, oscillator, parameter optimization, turning point bifurcation
Subject
Suggested Citation
Porubsky VL, Sauro HM. Application of Parameter Optimization to Search for Oscillatory Mass-Action Networks Using Python. (2019). LAPSE:2019.0662
Author Affiliations
Journal Name
Processes
Volume
7
Issue
3
Article Number
E163
Year
2019
Publication Date
2019-03-18
Published Version
ISSN
2227-9717
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Original Submission
Other Meta
PII: pr7030163, Publication Type: Journal Article
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LAPSE:2019.0662
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External Link
doi:10.3390/pr7030163
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[v1] (Original Submission)
Jul 25, 2019
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Jul 25, 2019
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https://psecommunity.org/LAPSE:2019.0662
Original Submitter
Calvin Tsay
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