what about ModelSEED ?

[hariszaf]

Hi there!

Many thanks for this great software!

I was wondering what it would take to support ModelSEED-oriented reconstructions.
I'd be happy to contribute if this feature could be supported and if you would guide me. 👨‍💻

By the way, if I am not mistaken, there is probably an error the .pdf manual:
in the 5.2 Retrieval of data from external data sources section, the third command you have uses again the data_parse_bigg_metabolites_file.py while I assume it's actually the data_parse_brenda_json_for_model.py that one should use.

Thanks a lot!

[Paulocracy]

Hello :D I fixed the issue in the manual, thank you for mentioning it :-) Regarding ModelSEED identifier integration, the complexity of making AutoPACMEN compatible with its identifiers depends on your intended scope:

• Metabolite IDs: These are currently needed as BiGG identifiers - either you could map the SEED compound ID to it (easier) or try to make it work with these IDs as an alternative (much more complicated).
• Reaction IDs: They actually shouldn't matter and should be able to have any name, however, an EC number annotation is still neccessary for reactions
• Gene/Enzyme IDs: Currently, they only work with Uniprot IDs; Here, I'm not sure which ID system ModelSEED reconstructions typically use, but if neccessary either they are mapped to Uniprot IDs or the code is made compatible with the other system.

Feel free to contribute to AutoPACMEN :-) Even though I personally don't plan to add new features as I work on new projects, contributions from others are always welcome :D It might just take a while until I can review it :3