Issues applying anaerobic media: '' is not a valid SBML 'SId' and compartment misidentification

[vicru93]

Problem description

I'm working with MICOM 0.37.1 to simulate anaerobic growth in a microbial community. The community is constructed from .xml models exported from ModelSEED (via KBase), using compartments c0 and e0. I manually converted all exchange reactions to follow the MICOM convention: EX_xxx_m.

My goal was to:

• Apply a custom anaerobic medium (filtered from minimal_medium() by removing oxygen and adding CO₂, H₂, etc.)
• Evaluate MAG-level growth using slim_optimize() on each individual model before running cooperative_tradeoff()

However, I encountered multiple problems:

---

Observed output

1. Some models raise the following error: '' is not a valid SBML 'SId'.

This appears to happen when the SBML file has elements with empty IDs, possibly caused by export or post-processing errors. MICOM fails when applying the medium to these models.

2. I also get repeated warnings like:
   Since my models use _m as the external compartment, this suggests MICOM/Cobra can't reliably detect it without manual .compartments assignment.

3. When applying the anaerobic medium:

• Some models raise KeyError: 'EX_cpd00305_m' (exchange not found in the model)
• Others return nan from slim_optimize(), even when the medium is filtered to contain only compatible exchanges.

Expected behavior:

• MICOM should provide a more fault-tolerant way to assign media (e.g., ignore missing reactions with a warning)
• External compartments should be clearly detectable or definable
• There could be a utility to pre-validate models before community construction

---

Code Sample

from cobra.io import read_sbml_model
import os

custom_medium = {
 "EX_cpd00027_m": -10,
 "EX_cpd00029_m": -10,
 "EX_cpd00011_m": -10,
 "EX_cpd11640_m": -10,
 "EX_cpd00013_m": -10,
 "EX_cpd00009_m": -10,
 "EX_cpd00048_m": -10,
}

carpeta_modelos = "/ruta/a/modelos"
crecimientos = {}

for archivo in os.listdir(carpeta_modelos):
 if archivo.endswith(".xml"):
     modelo = read_sbml_model(os.path.join(carpeta_modelos, archivo))

     # Filter medium
     reacciones_disponibles = {rxn.id for rxn in modelo.exchanges}
     medio_filtrado = {k: v for k, v in custom_medium.items() if k in reacciones_disponibles}

     # Apply and test
     modelo.medium = medio_filtrado
     tasa = modelo.slim_optimize()
     crecimientos[archivo] = tasa


'' is not a valid SBML 'SId'.
Could not identify an external compartment by name and choosing one with the most boundary reactions.
KeyError: 'EX_cpd00305_m'


python -c "import micom; micom.show_versions()"

System
------
Platform:     Ubuntu 24.04 lts
Python:       3.10.x
Micom:        0.37.1
COBRApy:      0.25.x
optlang:      1.6.x
Solver:       gurobi (academic license).

[cdiener]

Hi, you are mixing MICOM and COBRApy a bit here. So your medium is a MICOM medium and can be applied to MICOM communities. It is not a valid COBRApy medium for a single model though, which is what you are trying to do I think. So there is no need to bring the exchanges into a MICOM format. Because your code does not use MICOM at all I assume those are questions regarding COBRApy usage.

For the specific questions:

1. Sounds like broken models. SBML can't have empty IDs. If those are generated by ModelSEED like this best to report this there so they can fix it.
2. You did not post the warning but usually it can still find it using the heuristic but will warn you that this is just a guess, which is fine. Like said before, there is no need to rename the exchanges, compartments like e and e0 are recognized by COBRApy.