| Reviewer name and names of any other individual's who aided in reviewer | Jeffrey West |
| Do you understand and agree to our policy of having open and named reviews, and having your review included with the published manuscript. (If no, please inform the editor that you cannot review this manuscript.) | Yes |
| Is the language of sufficient quality? | Yes |
| Please add additional comments on language quality to clarify if needed | |
| Is there a clear statement of need explaining what problems the software is designed to solve and who the target audience is? | Yes |
| Additional Comments | |
| Is the source code available, and has an appropriate Open Source Initiative license <a href="https://opensource.org/licenses" target="_blank">(https://opensource.org/licenses)</a> been assigned to the code? | Yes |
| Additional Comments | |
| As Open Source Software are there guidelines on how to contribute, report issues or seek support on the code? | Yes |
| Additional Comments | |
| Is the code executable? | Unable to test |
| Additional Comments | |
| Is installation/deployment sufficiently outlined in the paper and documentation, and does it proceed as outlined? | Unable to test |
| Additional Comments | |
| Is the documentation provided clear and user friendly? | Yes |
| Additional Comments | |
| Is there enough clear information in the documentation to install, run and test this tool, including information on where to seek help if required? | Yes |
| Additional Comments | |
| Is there a clearly-stated list of dependencies, and is the core functionality of the software documented to a satisfactory level? | Yes |
| Additional Comments | |
| Have any claims of performance been sufficiently tested and compared to other commonly-used packages? | Yes |
| Additional Comments | |
| Is test data available, either included with the submission or openly available via cited third party sources (e.g. accession numbers, data DOIs)? | Yes |
| Additional Comments | |
| Are there (ideally real world) examples demonstrating use of the software? | Yes |
| Additional Comments | |
| Is automated testing used or are there manual steps described so that the functionality of the software can be verified? | Yes |
| Additional Comments | |
| Any Additional Overall Comments to the Author | This is a very nice & useful extension to PhysiCell, in order to model PK/PD dynamics in agent-based simulations. Overall, the description of the software is good and easy to follow, but I offer a few suggestions for clarity: 1. In "Statement of Need" -- the phrase "how much gets to the cells and what they then do to the cells" is vague and casual -- maybe use standard terms like drug exposure & response to describe PK/PD relationships 2. Final sentence in "Statement of Need" that says "Substrates can target any cell type with PD dynamics" -- can you elaborate? Does this indicate that every cell type can have unique PD dynamics? 3. In "Implementation" authors refer to Figure 2A and 2B but figure 2 only has one panel -- perhaps this should be figure 1A/B? 4. In "Pharmacodynamics" -- "the list of PK substrates and the list of PDsubstrates need not have any relationship" -- this is slightly confusing. I assume that every substrate can have associated PK dynamics without having an PD dynamic, but is the opposite true? If so, how what is the drug dispersal / decay rate? 5. Finally, the discussion section is focused mainly on future steps. I think it would be helpful for the discussion to focus more on current advantages and functionality. This is the publication record for this software, and as is often the case, future steps may be subject to change. |
| Recommendation | Minor Revisions |