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Prediction of metabolite concentrations, rate constants and post-translational regulation

What is being modeled?
Central Metabolism
Description & purpose of resource

This tool consists of Jupyter notebooks, contained in the Supplementary Information to the linked article, for a new approach to modeling the mass action kinetics of metabolism. The central metabolism of Neurospora crassa, a filamentous fungi, is used for demonstration purposes.

Spatial scales
molecular
cellular
Temporal scales
<10-6 s (chemical reactions)
10-6 - 10-3 s
This resource is currently
a demonstration or a framework to be built upon (perhaps with a sample implementation)
Has this resource been validated?
N/A
Can this resource be associated with other resources? (e.g.: modular models, linked tools and platforms)
Yes
Which resources?

The eQuilibrator tool for estimating standard free energies of metabolic reactions: http://equilibrator.weizmann.ac.il/.

Key publications (e.g. describing or using resource)

Cannon, W.R., et al., Prediction of metabolite concentrations, rate constants and post-translational regulation using maximum entropy-based simulations with application to central metabolism of Neurospora crassa. Processes, 2018. 6(6).

DOI link to publication describing this resource

https://doi.org/10.3390/pr6060063

Link to resource
Supplementary Material
Collaborators
Bill Cannon
PI contact information
william.cannon@pnnl.gov
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