This program writes a metabolic reaction network to a file suitable for flux balance analysis..

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Can consume

contigs-db reaction-network

Can provide



This program exports a metabolic reaction-network from a contigs-db to a reaction-network-json file suitable for inspection and flux balance analysis.

The required input to this program is a contigs-db in which a reaction-network has been stored by anvi-reaction-network.

The reaction-network-json file output contains sections on the metabolites, reactions, and genes constituting the reaction-network that had been predicted from the genome. An “objective function” representing the biomass composition of metabolites in the “core metabolism” of E. coli is automatically added as the first entry in the “reactions” section of the file and can be deleted as needed. An objective function is needed for flux balance analysis.


anvi-get-metabolic-model-file requires a contigs-db as input and the path to an output reaction-network-json file.

anvi-get-metabolic-model-file -c contigs-db \ -o /path/to/ouput.json

An existing file at the target output location must be explicitly overwritten with the -W flag.

anvi-get-metabolic-model-file -c contigs-db \ -o /path/to/output.json \ -W

The flag, --remove-missing-objective-metabolites must be used to remove metabolites in the E. coli core biomass objective function from the output file if the metabolites are not produced or consumed by the predicted reaction-network. COBRApy, for instance, cannot load the JSON file if metabolites in the objective function are missing from the genomic model.

anvi-get-metabolic-model-file -c contigs-db \ -o /path/to/output.json \ --remove-missing-objective-metabolites

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Additional Resources

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