Thomas Pfau

Id actually advocate it rather the other way around since there are no restrictions on the values of model.genes and thus a grRules field could have unparsable entries. At least...

Hi @dayena wrt 1. I'm not sure what you mean.. If there is no objective set, there is no objective. and we can't really set one. Does this become a...

Ahh ok, I see. That should not hurt, since the default value for model.c is a all-zero vector but I agree it looks odd. However I would like to only...

How big is the data that you are handling here? I get the impression that you have a lot of helper functions which read/write to folders that may (or may...

This is due to createMultiSpeciesModel building a new extracellular environment, replacing the existing one. As such, there are no longer any uptake constraints, as it is in any instance likely,...

You are welcome to add an option to the `CreateMultiSpeciesModel` functionality to allow existing flux bounds to be carried over between the model.

@almut-heinken Personally, I think that any bounds should be only carried to the model they originate from and not to the overall model. i.e. if model MA has an uptake...

@almut-heinken From my understanding, the exchange fluxes that are set in models are normally measured uptakes, or rather medium depletion measured when an individual microbe is cultured. As such this...

Thats entirely possible, even though we use reaction lists during the tests. Can you write a test where the results using the current version are wrong so that we can...

@rmtfleming The attachment seems to have been lost on conversion of your mail to github.