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Model balancing
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Matlab files for model balancing
o Main function: model_balancing.m
o For usage examples, see m-files 'demo_cmb_artificial_data' and 'demo_cmb_experimental_data'
o For algorithm options, see 'cmb_default_options'
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Input data
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Model:
Model structures are read from SBtab or SBML files
Kinetic data:
Kinetic data are read from SBtab files
o Metabolites must carry the same IDs as in the model (or KEGG Compound IDs)
o Reactions and Enzymes must carry the same IDs as in the model (or KEGG Reaction IDs)
Metabolic state data:
Metabolite, flux, and enzyme data are read from SBtab files
o Metabolites must carry the same IDs as in the model (or KEGG Compound IDs)
o Reactions and Enzymes must carry the same IDs as in the model (or KEGG Reaction IDs)
The columns containing the data can carry arbitrary names
(which must be declared within matlab, for parsing the files)
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Output files
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kinetic_model.tsv SBtab - Metabolic network and kinetic constants (optionally: include kinetic rate law formulae)
metabolic_states.tsv SBtab - Predicted metabolite concentrations, enzyme concentrations, Gibbs free energies, fluxes (for all states)
report.txt text - Number of data points / of fitted variables (by category), and calculation time
options.tsv SBtab - Options
results.mat .mat - Results