Mike's Notes
Pipi has thousands of parameters, which make it challenging to finely adjust for desired system-level emergent properties.
How to Deal With Parameters for Whole-Cell Modelling is a paper published in the Journal of the Royal Society in 2017. I found the paper listed in the publications from the Theoretical Systems Biology Group at Melbourne University, led by Prof. Michael Stumpf. They are dealing with the same issues. This Research Group could be a great resource.
Resources
- https://www.blog.ajabbi.com/p/pipi.html
- https://royalsocietypublishing.org/doi/10.1098/rsif.2017.0237
- https://royalsocietypublishing.org/journal/rsif
- https://www.theosysbio.com/publications
- https://www.theosysbio.com/research/modelling-cells
References
- How to Deal With Parameters for Whole-Cell Modelling
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Last Updated
17/05/2025
Article
Most models in cell biology are either based on simple networks or stoichiometric metabolic models, or deal only with small pathways. Ultimately we will require models of whole cells. We are interested in combining approaches from text-mining, bioinformatics, comparative genomics, statistical inference, machine learning, and mathematical modelling to arrive at models for whole cells. In the first instance, we are focusing on bacteria.
Ultimately, such models are
- the most stringent test of our understanding; and
- an essential prerequisite for applying rational design and engineering approaches to biological systems. Maintaining the balance of model complexity to explanatory power is a conceptually hugely exciting problem, and tackling parameter inference for thousands of parameters is technically equally exciting.
Representative Publications
- How to Deal With Parameters for Whole-Cell Modelling. Babtie, A.C., & Stumpf, M.P.H. (2017). Journal of the Royal Society, Interface / the Royal Society, 14(133), 20170237. (free PDF)
- Systems Biology (Un)Certainties. Kirk, P. D. W., Babtie, A. C., & Stumpf, M. P. H. (2015). Science, 350(6259), 386–388.
- Quantitative Time-Resolved Analysis Reveals Intricate, Differential Regulation of Standard- and Immuno-Proteasome. Liepe, J., Holzhütter, H.-G., Bellavista, E., Kloetzel, P.M., Stumpf, M.P.H., & Mishto, M. (2015). eLife, 4, e07545. (free PDF)
