reaction-network-json

A JSON-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

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Provided by

anvi-get-metabolic-model-file

Required or used by

There are no anvi’o tools that use or require this artifact directly, which means it is most likely an end-product for the user.

Description

This artifact represents a JSON-formatted file derived from a reaction-network.

The program, anvi-get-metabolic-model-file, produces this file from the reaction-network stored in a contigs-db. The genes, reactions, and metabolites predicted to be involved in metabolism can be inspected in this file, which is formatted for compatability with software used for flux balance analysis, such as COBRApy.

anvi-get-metabolic-model-file includes an “objective function” as the first entry of the “reactions” section of the file, a prerequisite for flux balance analysis. The objective function represents the biomass composition of metabolites in the “core metabolism” of E. coli.

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