Mirek Kratochvil

@stelmo btw should we add subsystems to AbstractFBC interface? I recall we talked about that and it might be the case that I killed the idea with some argument that...

> > how to fix this for the SBML models (SBML doesn't specify subsystems, maybe there would be a way to parse them from MIRIAM-style annotations or so?) > >...

Uuuh good I see it in YeastGEM now. That sounds very vital, thanks! For the SBML import/export, can we assume that - only the groups with the SBO 633 are...

tracking: SBML.jl support here: https://github.com/LCSB-BioCore/SBML.jl/pull/260

ah this. We added `grrs` later so this is an avoidable but kinda expected bug. Thanks for report

Hi all! thanks for the links to the papers, this is very helpful. I'll have to carefully read the methods to be able to guess the size of the implementation,...

We're not going to put this into the parsing process directly (storing stuff in notes just....you shouldn't) but we can make a tiny wrapper atop SBMLModel that re-parses the notes...

@htpusa in one other project we found that there's a unitilty to convert these annotations to the "proper" FBC form; you can do it with `reframed`: ```py model=reframed.load_cbmodel('something.xml',flavor='cobra') reframed.save_cbmodel(model,'something_fbc.xml',flavor='bigg') ```...

Perfect, thank you both! I guess this should be more than sufficient :]

The problem with function type annotations is that it results in extra convert() call in the end, which might and might not be what we actually want. (read: it's not...