Reviewer 2 comments for JOSS submission

[marouenbg]

yaml2sbml's implementation was executed flawlessly with a complete set of docs and several examples. These are my comments in relation the review process https://github.com/openjournals/joss-reviews/issues/3215

Comments on the paper:

These are a few suggestions for the authors about the main text.

• Currently 9 software toolboxes support PEtab as an input format, among them COPASI, d2d, Would it be possible to complete the list?

• Due to the aforementioned tools, model simulation or parameter estimation has become a matter of a few lines of code or clicks I suggest using Thanks to the aforementioned tools

• Hence ODE model definition is a relevant bottleneck, I would suggest: However, ODE model definition is often a bottleneck

• Python-based model editor that allows one to generate My suggestion: Python-based model editor that allows to generate

• Figure 1 gives an overview over of the typical Figure 1 gives an overview of the typical

  • Building the input format on YAML allows one to easily parse and validate the model Building the input format on YAML allows to parse and validate the model easily

[marouenbg]

Comments on the tool

• specify the dependencies in the first tutorial - finite state projection ( amici package)
• the URL links in the beginning of Format features tutorial are not working

[jvanhoefer]

Dear Marouen,

Thank you for your helpful comments and for reviewing our submission! I addressed your suggestions in two PRs for your comments regarding the tool (#128) and the text (#129). I agree, that your reformulation will improve the manuscript! Regarding

• Currently 9 software toolboxes support PEtab as an input format, among them COPASI, d2d, Would it be possible to complete the list?

I added a link to the PEtab documentation, that gives a dynamically updated list with detailed overview over tools + support (as there are to my knowledge more tools who will have a PEtab support soon).

[marouenbg]

Great! Thank you.