Eduard Kerkhoven

Which deltaG value should be stored? @feiranl mentions that MetaCyc provides this information at pH 7.3 and ionic strength 0.25. But the standard Gibbs free energy (ΔG°') is normally measured...

It is important to have a clear definition of the condition, as changing any parameter will change the Gibbs free energy. Standard Gibbs free energy (ΔG°') is defined at pH...

Not sure that is possible (or at least I don't know how to do it)? In addition, the function needs expansion to also read annotations and other fields that might...

The human-GEM function `exportYaml` differs from RAVEN's `writeYaml` (which I would like to rename to `exportYaml` for consistency) in the following ways: - `exportYaml` writes empty entries (e.g. ` -...

> As Metabolic Atlas relies on the YAML file to import models, all of the proposed changes would lead to breaking the import of models. Then it's great to get...

> These adjustments of integrating `exportYaml` and `writeYaml` seem reasonable, please go ahead. > > My suggestion is that it might good to merge the two into one as `writeYaml`,...

In #439 I have somewhat changed the reporting of the function progress, as it actually got stock trying to get the first sample. Rerunning your model with the code in...

Same behaviour here: `randomSampling` directly on human-GEM 1.12.0 cannot get any random samples. I also tried with earlier versions: human-GEM 1.9.0 and RAVEN 2.5.0: same behaviour. Not sure if `randomSampling`...

In principle I support this, but please note the following: 1. While documentation in `importModel` is mentioning the "yeast consensus network model", in essence it is about compatibility with COBRA...

Yes, but when COBRA then [reads](https://github.com/opencobra/cobratoolbox/blob/25dbea46f08a9aeebcc24e0253293965d88e4ac6/src/base/io/utilities/readSBML.m#L385) such a model, it removes the prefixes. So when loaded in COBRA there are never such prefixes, but the SBML file _can_ have such...