AUT-574 update

[svevol]

Adding first version of template notebook for FBA, FVA, and Sampling of targeted exo-metabolomics data

Overview of features

• Load the cobrapy model from .csv - csv not added, xml,json and from BiGG database added

• Load the exo-metabolomics rates (.csv) and growth rate data (.csv) - done

• Constrain the model using the growth rate and uptake/secretion rates - done

• Perform growth rate estimations using FBA - done

• Identify constrained reactions (i.e., flux of 0) using FVA - FVA is done. Function that returns the reaction with zero fluxes needed

• Remove any constrained reactions from the model - TODO

• Calculate the 95% confidence intervals from Sampling using OptGpSampler - Use sample(model, NUMBER_OF_SAMPLES) (optgp is used as default) to sample, and calculate CI from sampled data

• Implement unit tests based on an example model and data - TODO