Thomas Pfau

SBML Modifierspecies, are only indicators that a specific reaction is in some way modified by the indicated Modifierspecies (which itself has to point to a species in the model). So...

I perfectly agree, that removing it is problematic, and yes, I will suggest it for a v4 of the FBC package (I doubt it will go into v3). And wrt...

Sure, and as I said, I agree that removing it is not good. I just see the problem that e.g. when "normalizing" a GPR into e.g. DNF or something else,...

Hi, A few things from my point of view: - `metComps` as a double Vector might be faster but is more prone to model modifications leading to out of sync...

Oh and one more thing: We recently introduced fields for additional Variables/Constraints to prepare for concepts like Enzyme Capacity constraints (as provided by GECKO). Those fields hold information which is...

@edkerk wrt to `xyzMiriams`: If I get this right, what you have is a cell array of structs where each struct has two fields storing the values. Was there a...

@simas232 The 'whats important or not' question is one reason why we don't have a annotation struct. Its simply up to the user what she/he thinks is important and we...

> Regarding `rxnComps`, well, even though they are arbitrary for e.g. antiport reactions, there is a designated field in SBML structure for it, introduced in Level 3, so why not...

> @tpfau would you then advocate for only using `metComps` as compartment identifier, and abandon storing this as part of the `mets` field? Yes, and no. Since we need distinct...

@edkerk wrt `removeFieldEntriesForType`, there are a bunch of functions for dynamic model modifications: `removeFieldEntriesForType` - to remove individual positions `updateFieldOrderForType` - Which allows to update the order of elements in...