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. 2022 Nov 30;2022:gigabyte72. doi: 10.46471/gigabyte.72
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