Hao Wang

> would be nice to preserve the git history when migrating the files @mihai-sysbio can you please help this

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`, and rename `importYaml`...

@manas-kohli thanks for reporting this. Which specific version of Human1 was used in this analysis?

> don't know if that can be causing an issue no, it shouldn't. will then try to duplicate your work

It appears that the COBRA function `writeSBML` adds prefixes only when ID starts with number. While the `exportModel` in RAVEN applies prefixes to all IDs regardless of their format. Therefore,...

@edkerk thanks for the detail explanations! I don't have an immediate solution the _compatibility_ issue, and hope to get an ideal way through further discussion. IMHO: - the import/export functions...

> While scenario 2 breaks compatibility between COBRA and RAVEN by design, as RAVEN will more strictly adhere to the libSBML desire not to use such prefixes as you rightly...

Agree to deprecate the identifier modifications both in `importModel` and `exportModel` > In addition, it would be good to have a checkIDvalidity function (or other name?) that runs a few...

> The idea of having a few regular expressions check whether the IDs are valid appears to be a pragmatic solution for now. A section for validating id format with...

> What if checkModelStruct (that runs in the beginning of exportModel) not only throws a error when it finds invalid identifiers, but let it also suggest to either fix the...