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Dear COBRA Toolbox Team,

I hope this message finds you well. I am currently working on integrating genome-scale metabolic models (GEMs) of an oleaginous fungus generated from two automated pipelines:

CarveMe (template-based reconstruction)

ModelSEED (reaction database-driven)

I aim to merge these models while addressing:

ID discrepancies (e.g., metabolite/reaction naming conventions between BiGG and ModelSEED databases)

Compartmentalization differences (e.g., lipid droplet reactions in CarveMe vs. cytosolic-only in ModelSEED)

GPR rule conflicts (automated vs. curated gene associations)

From your expertise, could you advise on:

Recommended tools/functions within COBRApy or MATLAB COBRA for cross-database ID mapping (e.g., MetaNetX vs. internal mapping tables)?

Best strategies to resolve reaction conflicts (e.g., prioritizing ModelSEED’s thermodynamics or CarveMe’s template-based reactions)?

Any existing scripts or workflows for fungal-specific model merging (e.g., handling lipid metabolism compartments)?

I’ve attempted standardization using COBRApy’s rename/add_annotation functions and manual gap-filling but would appreciate guidance on scaling this for larger models.

Thank you for your time and insights. I’m happy to share example files or clarify further if needed.

Best regards, Yawen Kong Jiangnan University