micom.measures#

Measures calculated based on fluxes.

Module Contents#

Functions#

production_rates(results)

Calculate the production rates for a set of metabolites.

consumption_rates(results)

Calculate the production rates for a set of metabolites.

micom.measures.production_rates(results)[source]#

Calculate the production rates for a set of metabolites.

Note

Production rates are not net fluxes but the flux of a particular metabolite into the external environment independent whether it is taken up by another taxon. The net rates can be obtained directly by inspecting the exchange fluxes in the “medium” compartment. The (transient) production rates reported here are the fluxes other surrounding cells/consumers would have access to. Thus, they are often more interesting for a phenotype than the net rates which are the excess productin rates, even in the absence of another consumer.

Parameters

results (micom.GrowthResults) – A growth results as returned by grow.

Returns

A new flux DataFrame containing the intermediate production rates for each metabolite.

Return type

pandas.DataFrame

micom.measures.consumption_rates(results)[source]#

Calculate the production rates for a set of metabolites.

Note

Consumption rates are not net fluxes but the total consumption of a particular metabolite by all taxa in the community independent whether it is secreted again. The net rates can be obtained directly by inspecting the exchange fluxes in the “medium” compartment. The (transient) consumption rates reported here is the total flux of a metabolite imported/consumed by taxa in the community.

Parameters

results (micom.GrowthResults) – A growth results as returned by grow.

Returns

A new flux DataFrame containing the intermediate production rates for each metabolite.

Return type

pandas.DataFrame