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• Parallel coordinate plots of CV across time points for different metabolites
• Parallel coordinate plots of mean metabolomics across time points for different metabolites
• Correlation matrix between conditions
• Correlation matrix between metabolites in different time points

The constrain_flux_regulation or CFR algorithm is based off the iMAT algorithm. This uses a list of up- or downregulated genes, and constrains the model fluxes to maximize flux through reactions encoded by upregulated genes, and minimize flux through reactions encoded by downregulated genes.

This algorithm has been written out in MATLAB. However, a Python version would be desirable to perform COBRA analyses using Python. Thus, @ScottCampit has been working on a version of the constrain_flux_regulation algorithm in the PythonCOBRA directory.

TODO:

• Finish the algorithm

• PCA
• Robust PCA
• Non-linear methods

• Hierarchical clustering
• DBSCAN
• Spectral clustering

• Construct arrays using a distribution of CVs ranging from 0.1 to 2
• Compute flux distributions of different models using all data
• See if they correspond to Nelson et al 2020

• Parallel coordinate plots of CV across time points for different metabolites
• Parallel coordinate plots of mean metabolomics across time points for different metabolites
• Correlation matrix between conditions
• Correlation matrix between metabolites in different time points