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Method Article
Eric S. McLamore
University of Florida, Agricultural & Biological Engineering
Corresponding Author
ORCiD: https://orcid.org/0000-0002-1662-7372
License:
This work is licensed under a CC BY 4.0 License. Read Full License
This protocol sets out a broadly-applicable framework for empirically reconstructing the dynamics of biosystems from observational data, modeling reconstructed dynamics phenomenologically with systems of ordinary differential equations extracted from the data, and detecting and quantifying causal interactions among system components. The protocol draws from well-established procedures in Nonlinear Time Series Analysis (NLTS) that can be run with existing R packages. The protocol was applied in McLamore et al. (2020)1 to develop a phenomenological digital proxy of a bioreactor (DIYBOT) from real-time sensor data. DIYBOT was used to investigate whether bioreactor dynamics self-corrected in response to contamination spikes of increasing degrees; and consequently, the extent to which corrective human-in-the-loop management might be required.
Keywords
digital proxy, bioreactor, Nonlinear Time Series Analysis, signal processing, phase space reconstruction, surrogate data testing, convergent cross mapping, phenomenological modeling
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This is a list of supplementary files associated with this preprint. Click to download.
- supplement1.png
Singular Spectrum Analysis.
- Table1.png
Singular Spectrum Analysis.
- supplement2.png
Surrogate Data Testing.
- Table2.png
Surrogate Data Testing.
- supplement3.png
Troubleshooting common problems related to the protocol for establishment of a digital proxy based on sensor data.
- Table3.png
Troubleshooting common problems related to the protocol for establishment of a digital proxy based on sensor data.
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Posted 16 Sep, 2020
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Subject Areas
Biotechnology
Computational biology and bioinformatics
Chemical biology
Environmental sciences
Complex networks
Information theory and computation
Engineering
Associated Publications
Digital Proxy of a Bio-Reactor (DIYBOT) combines sensor data and data analytics to improve greywater treatment and wastewater management systems
by Eric S. McLamore, Ray Huffaker, Matthew Shupler, +6
Scientific Reports (15 May, 2020)
An open repository of community-contributed protocols sponsored by Nature Research.
Learn more about Protocol Exchange
Method Article
Eric S. McLamore
University of Florida, Agricultural & Biological Engineering
Corresponding Author
ORCiD: https://orcid.org/0000-0002-1662-7372
Version History
CURRENT STATUS: Posted
Version 1
Posted 16 Sep, 2020
No community comments so far
Metrics
Comments: 0
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
This protocol sets out a broadly-applicable framework for empirically reconstructing the dynamics of biosystems from observational data, modeling reconstructed dynamics phenomenologically with systems of ordinary differential equations extracted from the data, and detecting and quantifying causal interactions among system components. The protocol draws from well-established procedures in Nonlinear Time Series Analysis (NLTS) that can be run with existing R packages. The protocol was applied in McLamore et al. (2020)1 to develop a phenomenological digital proxy of a bioreactor (DIYBOT) from real-time sensor data. DIYBOT was used to investigate whether bioreactor dynamics self-corrected in response to contamination spikes of increasing degrees; and consequently, the extent to which corrective human-in-the-loop management might be required.
Figure 1
Figure 1
Figure 2
Figure 2
Figure 3
Figure 3
Figure 4
Figure 4
Figure 5
Figure 5
Figure 6
Figure 6
Figure 7
Figure 7
This is a list of supplementary files associated with this preprint. Click to download.
- supplement1.png
Singular Spectrum Analysis.
- Table1.png
Singular Spectrum Analysis.
- supplement2.png
Surrogate Data Testing.
- Table2.png
Surrogate Data Testing.
- supplement3.png
Troubleshooting common problems related to the protocol for establishment of a digital proxy based on sensor data.
- Table3.png
Troubleshooting common problems related to the protocol for establishment of a digital proxy based on sensor data.
Loading...
Associated Publications
Digital Proxy of a Bio-Reactor (DIYBOT) combines sensor data and data analytics to improve greywater treatment and wastewater management systems
by Eric S. McLamore, Ray Huffaker, Matthew Shupler, +6
Scientific Reports (15 May, 2020)