q2-micom, how to get SBML format files?

Hello, I just used q2-micom on 16S data (worked great and everything installed smoothly). I wanted to export the models to try with other software, but qiime tools export gives me pickle files. Is there a way to convert those to SBML .xml files?

On that note, if I were to export these to .xml files, would it be one .xml per sample? Or one per each bacterial species with a key for which samples they are found in?

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No unfortunately not. SBML has no native support for multi-taxon models right now and also does not work well with models that have 100k+ reactions. It’s something we have on our radar but right now there are limitations in the format itself that limit this. Sorry for that.