micom.workflows.tradeoff

Workflow to run cooperative tradeoff with various tradeoff values.

Functions

_tradeoff(args)

tradeoff(manifest, model_folder, medium[, tradeoffs, ...])

Run growth rate predictions for varying tradeoff values.

Module Contents

micom.workflows.tradeoff._tradeoff(args)[source]
micom.workflows.tradeoff.tradeoff(manifest, model_folder, medium, tradeoffs=np.arange(0.1, 1.0 + 1e-06, 0.1), threads=1, atol=None, rtol=None, presolve=False)[source]

Run growth rate predictions for varying tradeoff values.

Parameters:

  • manifest (pandas.DataFrame) – The manifest as returned by the build workflow.

  • model_folder (str) – The folder in which to find the files mentioned in the manifest.

  • medium (pandas.DataFrame) – A growth medium. Must have columns “reaction” and “flux” denoting exchnage reactions and their respective maximum flux.

  • tradeoffs (array of floats in (0.0, 1.0]) – An array of tradeoff vaues to be tested. One simulation without a tradeoff (no cooperative tradeoff) will always be run additionally and will have a tradeoff of “NaN”.

  • threads (int >=1) – The number of parallel workers to use when building models. As a rule of thumb you will need around 1GB of RAM for each thread.

  • atol (float) – Absolute tolerance for the growth rates. If None will use the solver tolerance.

  • rtol (float) – Relative tolerqance for the growth rates. If None will use the solver tolerance.

  • presolve (bool) – Whether to use the presolver/scaling. Can improve numerical accuracy in some cases.

Returns:

The predicted growth rates.

Return type:

pandas.DataFrame