Step 3, Part 2: Cleaning the Model

The third part of the refinement aims to clean the model regarding its entities, including:

  • Checking the directionality of reactions using BioCyc.

  • Complete BioCyc/MetaCyc, if only one of the two is present.

  • Find and resolve duplicate metabolites and reactions.

  • Delete unused metabolites.

  • Perform (additional) gap filling.

Except for the complete Bio/MetaCyc annotations all steps are optional.

../../../_images/3_2_cleanup.png

Warning

The gap filling is currently only available in the COBRApy variant.

This part of the workflow is still a working process, stay tuned for future updates.