editorialbot commented 1 year ago

Submitting author: !--author-handle-->@BobAubouin@ppxasjsm<!--end-editor-- Reviewers: @yumuk1989, @JHartzer Archive: 10.5281/zenodo.8171326

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/61d34ad9ef855a128509b4279e2c9325/status.svg)](https://joss.theoj.org/papers/61d34ad9ef855a128509b4279e2c9325)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@yumuk1989 & @JHartzer, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @ppxasjsm know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @JHartzer

📝 Checklist for @yumuk1989

editorialbot commented 1 year ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.07 s (244.3 files/s, 64307.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          10            410            939           1425
TeX                              1             42              0            667
Jupyter Notebook                 3              0            691            341
Markdown                         2             57              0            113
TOML                             1              2              0             28
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                            18            512           1634           2592
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for PAS_paper.md is 1743

editorialbot commented 1 year ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1213/00000539-200103000-00020 is OK
- 10.1093/bja/aei259 is OK
- 10.1007/s10928-020-09712-1 is OK
- 10.1097/00000542-200406000-00006 is OK
- 10.1213/ANE.0000000000001372 is OK
- 10.1093/bja/aeh293 is OK
- 10.1007/s42452-021-04885-x is OK
- 10.1016/c2017-0-03401-8 is OK
- 10.1093/bja/aew126 is OK
- 10.1097/ALN.0000000000001634 is OK
- 10.1016/j.bja.2018.01.018 is OK
- 10.1093/bja/67.5.618 is OK
- 10.1109/CDC45484.2021.9683368 is OK
- 10.1109/ACCESS.2020.3037725 is OK
- 10.1186/cc9207 is OK
- 10.1155/2017/7432310 is OK
- 10.1109/ACCESS.2021.3049880 is OK
- 10.1109/TBME.2008.923142 is OK
- 10.1093/bja/aeu553 is OK
- 10.1097/00000542-200102000-00023 is OK
- 10.1097/00000542-200308000-00023 is OK
- 10.1097/00000542-200206000-00033 is OK
- 10.1213/ane.0b013e3181a96f9a is OK
- 10.1038/s41598-018-20062-4 is OK
- 10.1093/bja/67.1.41 is OK
- 10.1016/B978-0-12-815975-0.00013-8 is OK
- 10.1016/j.cnsns.2018.12.015 is OK
- 10.1097/00000542-199701000-00004 is OK
- 10.1097/CCM.0b013e318206d2a3 is OK
- 10.1016/j.compchemeng.2022.107747 is OK
- 10.1016/j.jprocont.2022.07.007 is OK
- 10.1213/ANE.0000000000000769 is OK
- 10.1186/cc10562 is OK
- 10.1016/j.jprocont.2021.12.004 is OK
- 10.1016/j.bspc.2021.102476 is OK
- 10.1097/00000542-199906000-00003 is OK
- 10.1097/00000542-200003000-00017 is OK
- 10.1213/ANE.0000000000000386 is OK
- 10.4103/sja.sja_669_21 is OK
- 10.1111/j.1460-9592.2009.03174.x is OK
- 10.1097/00000542-200002000-00021 is OK
- 10.1213/00000539-199909000-00002 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

ppxasjsm commented 1 year ago

@yumuk1989, @JHartzer you can now get started with your review. If you have any questions in the meantime, please let me know.

JHartzer commented 1 year ago

Review checklist for @JHartzer

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/BobAubouin/Python_Anesthesia_Simulator?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@BobAubouin) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

yumuk1989 commented 1 year ago

Review checklist for @yumuk1989

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/BobAubouin/Python_Anesthesia_Simulator?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@BobAubouin) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

JHartzer commented 1 year ago

In addition to the issue above, I also added Issue 17 regarding additional testing and coverage. This could improve the robustness of testing and help indicate the amount of testing coverage.

Lastly, I would suggest linking or mentioning the new ECC 2023 publication in the repository once it is available.

None of these are substantial issues, and I imagine the code quality will only improve moving forward. Therefore, I recommend JOSS acceptance

BobAubouin commented 1 year ago

Hi @JHartzer, thanks for your review and your suggestions!

I will add the future work into your issue and the citation to the ECC23 into the paper.

About the test framework, I'm not familiar with those, but I will consider it for improvement.

ppxasjsm commented 1 year ago

@yumuk1989, how are you getting on with your review?

yumuk1989 commented 1 year ago

Hello Toni,

Sorry for delay. Yes, I started reviewing it but I have not finished yet. I will have finished it by the end of June.

Best,

Erhan

20 Haz 2023 Sal 10:54 tarihinde Toni Mey @.***> şunu yazdı:

@yumuk1989 https://github.com/yumuk1989, how are you getting on with your review?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5480#issuecomment-1598380049, or unsubscribe https://github.com/notifications/unsubscribe-auth/ARSHHV43KEJLLGXJUI3JJUTXMFQM3ANCNFSM6AAAAAAYIXOVPY . You are receiving this because you were mentioned.Message ID: @.***>

ppxasjsm commented 1 year ago

That's great! Thank you 👍

ppxasjsm commented 1 year ago

Thank you @JHartzer for your review and I've noted the recommend accept.

yumuk1989 commented 1 year ago

Hello Toni,

I could not see/reach my checklist as a reviewer. I started reviewing it one month ago. Could you please help me about it? How can reach it?

Erhan YUMUK

Toni Mey @.***>, 23 Haz 2023 Cum, 11:00 tarihinde şunu yazdı:

Thank you @JHartzer https://github.com/JHartzer for your review and I've noted the recommend accept.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5480#issuecomment-1603961867, or unsubscribe https://github.com/notifications/unsubscribe-auth/ARSHHV2BMXTIXCSHDA5ZN33XMVLJPANCNFSM6AAAAAAYIXOVPY . You are receiving this because you were mentioned.Message ID: @.***>

-- Dr. Erhan YUMUK Lecturer Istanbul Technical University Department of Control and Automation Engineering

BobAubouin commented 1 year ago

Hi Erhan,

You can access the review on github here and edit your comment containing the checklist by clicking on the three dots at the top right of your comment.

yumuk1989 commented 1 year ago

Hello,

I have reviewed the code, documentation and paper. The authors give the statement of need clearly on the paper. However, this section is somewhat lacking in the documentation. They should also give it clearly there. But this is not a big issue. I recommend it to accept in JOSS.

BobAubouin commented 1 year ago

Hi Erhan,

Thanks for your feedback! I have been working on the documentation, it is now available online here: https://python-anesthesia-simulator.readthedocs.io. It includes the statement of need as introduction and also the examples.

ppxasjsm commented 1 year ago

Hi @yumuk1989 thank you for the review!

ppxasjsm commented 1 year ago

@BobAubouin can you please check your manuscript and repository one last time. If you are happy with it, I'll have a look too and will proceed with what is needed to move it to recommend accept.

BobAubouin commented 1 year ago

@ppxasjsm I'm good with the repo and the manuscript! I added a tag v1.0.0 to the current git version since it have changed a bit since the submission.

ppxasjsm commented 1 year ago

@editorialbot generate pdf

ppxasjsm commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- 10.1097/00000539-200103000-00020 may be a valid DOI for title: The Determinants of Propofol Induction of Anesthesia Dose
- 10.1093/bja/aei259 may be a valid DOI for title: Norepinephrine Kinetics and Dynamics in Septic Shock and Trauma Patients
- 10.1007/s10928-020-09712-1 may be a valid DOI for title: The Influence of Cardiac Output on Propofol and Fentanyl Pharmacokinetics and Pharmacodynamics in Patients Undergoing Abdominal Aortic Surgery
- 10.1007/s42452-021-04885-x may be a valid DOI for title: AnesthesiaGUIDE: A MATLAB Tool to Control the Anesthesia
- 10.1016/c2017-0-03401-8 may be a valid DOI for title: Automated Drug Delivery in Anesthesia
- 10.1093/bja/67.5.618 may be a valid DOI for title: HAEMODYNAMIC EFFECTS OF PROPOFOL: INDUCTION WITH 2.5 MG KG-1
- 10.1109/cdc45484.2021.9683368 may be a valid DOI for title: The Python Control Systems Library (Python-Control)
- 10.1186/cc9207 may be a valid DOI for title: Early Administration of Norepinephrine Increases Cardiac Preload and Cardiac Output in Septic Patients with Life-Threatening Hypotension
- 10.1155/2017/7432310 may be a valid DOI for title: A Review of Modern Control Strategies for Clinical Evaluation of Propofol Anesthesia Administration Employing Hypnosis Level Regulation
- 10.1109/access.2021.3049880 may be a valid DOI for title: An Open Source Patient Simulator for Design and Evaluation of Computer Based Multiple Drug Dosing Control for Anesthetic and Hemodynamic Variables
- 10.1109/tbme.2008.923142 may be a valid DOI for title: Robust Predictive Control Strategy Applied for Propofol Dosing Using BIS as a Controlled Variable During Anesthesia
- 10.1093/bja/aeu553 may be a valid DOI for title: Pharmacodynamic Response Modelling of Arterial Blood Pressure in Adult Volunteers during Propofol Anaesthesia
- 10.1097/00000542-200206000-00033 may be a valid DOI for title: Influence of Cardiac Output on Plasma Propofol Concentrations during Constant Infusion in Swine
- 10.1213/ane.0b013e3181a96f9a may be a valid DOI for title: The Influence of Hemorrhagic Shock on the Electroencephalographic and Immobilizing Effects of Propofol in a Swine Model
- 10.1038/s41598-018-20062-4 may be a valid DOI for title: Vital Recorder—a Free Research Tool for Automatic Recording of High-Resolution Time-Synchronised Physiological Data from Multiple Anaesthesia Devices
- 10.1093/bja/67.1.41 may be a valid DOI for title: Pharmacokinetic Model Driven Infusion of Propofol in Children
- 10.1016/j.cnsns.2018.12.015 may be a valid DOI for title: Optimized PID Control of Propofol and Remifentanil Coadministration for General Anesthesia
- 10.1016/j.yccm.2012.01.013 may be a valid DOI for title: Norepinephrine Increases Cardiac Preload and Reduces Preload Dependency Assessed by Passive Leg Raising in Septic Shock Patients*
- 10.1016/j.compchemeng.2022.107747 may be a valid DOI for title: Linear MPC for Anesthesia Process with External Predictor
- 10.1016/j.jprocont.2022.07.007 may be a valid DOI for title: Model Predictive Control Using MISO Approach for Drug Co-Administration in Anesthesia
- 10.1186/cc10562 may be a valid DOI for title: Evaluation of a Novel Closed-Loop Fluid-Administration System Based on Dynamic Predictors of Fluid Responsiveness: An in Silico Simulation Study
- 10.1016/j.jprocont.2021.12.004 may be a valid DOI for title: Individualized PID Tuning for Maintenance of General Anesthesia with Propofol and Remifentanil Coadministration
- 10.1016/j.bspc.2021.102476 may be a valid DOI for title: Optimized Feedforward Control of Propofol for Induction of Hypnosis in General Anesthesia
- 10.1097/00000542-199906000-00003 may be a valid DOI for title: The Influence of Age on Propofol Pharmacodynamics
- 10.4103/sja.sja_669_21 may be a valid DOI for title: Artificial Intelligence and Anesthesia: A Narrative Review
- 10.1097/00000542-200002000-00021 may be a valid DOI for title: Comparison of Plasma Compartment versus  Two Methods for Effect Compartment–Controlled Target-controlled Infusion for Propofol
- 10.1213/00000539-199909000-00002 may be a valid DOI for title: Cardiac Output Is a Determinant of the Initial Concentrations of Propofol After Short-Infusion Administration

INVALID DOIs

- None

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

ppxasjsm commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- 10.1097/00000539-200103000-00020 may be a valid DOI for title: The Determinants of Propofol Induction of Anesthesia Dose
- 10.1093/bja/aei259 may be a valid DOI for title: Norepinephrine Kinetics and Dynamics in Septic Shock and Trauma Patients
- 10.1007/s10928-020-09712-1 may be a valid DOI for title: The Influence of Cardiac Output on Propofol and Fentanyl Pharmacokinetics and Pharmacodynamics in Patients Undergoing Abdominal Aortic Surgery
- 10.1007/s42452-021-04885-x may be a valid DOI for title: AnesthesiaGUIDE: A MATLAB Tool to Control the Anesthesia
- 10.1016/c2017-0-03401-8 may be a valid DOI for title: Automated Drug Delivery in Anesthesia
- 10.1093/bja/67.5.618 may be a valid DOI for title: HAEMODYNAMIC EFFECTS OF PROPOFOL: INDUCTION WITH 2.5 MG KG-1
- 10.1109/cdc45484.2021.9683368 may be a valid DOI for title: The Python Control Systems Library (Python-Control)
- 10.1186/cc9207 may be a valid DOI for title: Early Administration of Norepinephrine Increases Cardiac Preload and Cardiac Output in Septic Patients with Life-Threatening Hypotension
- 10.1155/2017/7432310 may be a valid DOI for title: A Review of Modern Control Strategies for Clinical Evaluation of Propofol Anesthesia Administration Employing Hypnosis Level Regulation
- 10.1109/access.2021.3049880 may be a valid DOI for title: An Open Source Patient Simulator for Design and Evaluation of Computer Based Multiple Drug Dosing Control for Anesthetic and Hemodynamic Variables
- 10.1109/tbme.2008.923142 may be a valid DOI for title: Robust Predictive Control Strategy Applied for Propofol Dosing Using BIS as a Controlled Variable During Anesthesia
- 10.1093/bja/aeu553 may be a valid DOI for title: Pharmacodynamic Response Modelling of Arterial Blood Pressure in Adult Volunteers during Propofol Anaesthesia
- 10.1097/00000542-200206000-00033 may be a valid DOI for title: Influence of Cardiac Output on Plasma Propofol Concentrations during Constant Infusion in Swine
- 10.1213/ane.0b013e3181a96f9a may be a valid DOI for title: The Influence of Hemorrhagic Shock on the Electroencephalographic and Immobilizing Effects of Propofol in a Swine Model
- 10.1038/s41598-018-20062-4 may be a valid DOI for title: Vital Recorder—a Free Research Tool for Automatic Recording of High-Resolution Time-Synchronised Physiological Data from Multiple Anaesthesia Devices
- 10.1093/bja/67.1.41 may be a valid DOI for title: Pharmacokinetic Model Driven Infusion of Propofol in Children
- 10.1016/j.cnsns.2018.12.015 may be a valid DOI for title: Optimized PID Control of Propofol and Remifentanil Coadministration for General Anesthesia
- 10.1016/j.yccm.2012.01.013 may be a valid DOI for title: Norepinephrine Increases Cardiac Preload and Reduces Preload Dependency Assessed by Passive Leg Raising in Septic Shock Patients*
- 10.1016/j.compchemeng.2022.107747 may be a valid DOI for title: Linear MPC for Anesthesia Process with External Predictor
- 10.1016/j.jprocont.2022.07.007 may be a valid DOI for title: Model Predictive Control Using MISO Approach for Drug Co-Administration in Anesthesia
- 10.1186/cc10562 may be a valid DOI for title: Evaluation of a Novel Closed-Loop Fluid-Administration System Based on Dynamic Predictors of Fluid Responsiveness: An in Silico Simulation Study
- 10.1016/j.jprocont.2021.12.004 may be a valid DOI for title: Individualized PID Tuning for Maintenance of General Anesthesia with Propofol and Remifentanil Coadministration
- 10.1016/j.bspc.2021.102476 may be a valid DOI for title: Optimized Feedforward Control of Propofol for Induction of Hypnosis in General Anesthesia
- 10.1097/00000542-199906000-00003 may be a valid DOI for title: The Influence of Age on Propofol Pharmacodynamics
- 10.4103/sja.sja_669_21 may be a valid DOI for title: Artificial Intelligence and Anesthesia: A Narrative Review
- 10.1097/00000542-200002000-00021 may be a valid DOI for title: Comparison of Plasma Compartment versus  Two Methods for Effect Compartment–Controlled Target-controlled Infusion for Propofol
- 10.1213/00000539-199909000-00002 may be a valid DOI for title: Cardiac Output Is a Determinant of the Initial Concentrations of Propofol After Short-Infusion Administration

INVALID DOIs

- None

ppxasjsm commented 1 year ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[ ] Double check authors and affiliations (including ORCIDs)
[ ] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[ ] Archive the release on Zenodo/figshare/etc and post the DOI here.
[ ] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[ ] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a PR)
[x] Check the references in the paper for corrections (e.g. capitalization)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

ppxasjsm commented 1 year ago

@BobAubouin I have now gone through your paper version, can you please make the following small fixes:

[ ] first paragraph performances -> performance
[ ] drug names: are they branded? Then capitalised otherwise if they are generic do not capitalise
[ ] Bispectral index, mean arterial pressure, cardiac output, and tol should not be capitalised, the acronyms should be in capital.
[ ] The statement of need is first discussed -> replace the comma with a semicolon

Statement of need:

[ ] which has drawn -> that has attracted
[ ] an arduous work: either an arduous task or arduous work
[ ] propositions -> suggestions
[ ] If this is a first step -> if this is the first step
[ ] are still not -> are not yet
[ ] performances -> performance
[ ] the control community has been historically using -> has historically used
[ ] facilitate -> facilitates
[ ] simulator at the maintenance phase -> in the maintenance phase Pharmacokinetics:
[ ] compartments -> compartment
[ ] 3-compartments -> 3-compartment
[ ] drugs -> drugs'
[ ] made for the Propofol -> made for propofol
[ ] impact the PK system -> affect the PK Pharmacodynamics:
[ ] Then a Hill curve is -> A Hill curve was then used...
[ ] For Propofol the value from [...] are-> For propofol values [...] are
[ ] Thus -> Thus,
[ ] the crude assumption [...] has been made -> was made
[ ] behaviour -> behavior
[ ] assumption however -> assumption, however Conclusion and future work:
[ ] to design and test multidrug -> for designing and testing multidrug controllers in [...]
[ ] The Respiratory system -> respiratory
[ ] MAP effect, and, experimental -> MAP effect, and the experimental

I am not sure what happened with the DOIs, they all appear to be missing but had not been missing previously can you make sure all the DOIs are available please?

ppxasjsm commented 1 year ago

@BobAubouin can you please also check the following:

[ ] Reference Fairfield1991 appears to be in all caps letters

ppxasjsm commented 1 year ago

@BobAubouin, I am not sure what happened with the DOIs, but they all seem to be missing, but weren't in the past. Can you please make sure all the DOIs that can be added to the references will be and none are missing. You can check these with editorialbot check references after you generated a new version of the pdf with editorialbot generate pdf.

BobAubouin commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

BobAubouin commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1213/00000539-200103000-00020 is OK
- 10.1093/bja/aei259 is OK
- 10.1007/s10928-020-09712-1 is OK
- 10.1097/00000542-200406000-00006 is OK
- 10.1213/ANE.0000000000001372 is OK
- 10.1093/bja/aeh293 is OK
- 10.1007/s42452-021-04885-x is OK
- 10.1016/c2017-0-03401-8 is OK
- 10.1093/bja/aew126 is OK
- 10.1097/ALN.0000000000001634 is OK
- 10.1016/j.bja.2018.01.018 is OK
- 10.1093/bja/67.5.618 is OK
- 10.1109/CDC45484.2021.9683368 is OK
- 10.1109/ACCESS.2020.3037725 is OK
- 10.1186/cc9207 is OK
- 10.1155/2017/7432310 is OK
- 10.1109/ACCESS.2021.3049880 is OK
- 10.1109/TBME.2008.923142 is OK
- 10.1093/bja/aeu553 is OK
- 10.1097/00000542-200102000-00023 is OK
- 10.1097/00000542-200308000-00023 is OK
- 10.1097/00000542-200206000-00033 is OK
- 10.1213/ane.0b013e3181a96f9a is OK
- 10.1038/s41598-018-20062-4 is OK
- 10.1093/bja/67.1.41 is OK
- 10.1016/B978-0-12-815975-0.00013-8 is OK
- 10.1016/j.cnsns.2018.12.015 is OK
- 10.1097/00000542-199701000-00004 is OK
- 10.1097/CCM.0b013e318206d2a3 is OK
- 10.1016/j.compchemeng.2022.107747 is OK
- 10.1016/j.jprocont.2022.07.007 is OK
- 10.1213/ANE.0000000000000769 is OK
- 10.1186/cc10562 is OK
- 10.1016/j.jprocont.2021.12.004 is OK
- 10.1016/j.bspc.2021.102476 is OK
- 10.1097/00000542-199906000-00003 is OK
- 10.1097/00000542-200003000-00017 is OK
- 10.1213/ANE.0000000000000386 is OK
- 10.1111/j.1460-9592.2009.03174.x is OK
- 10.1097/00000542-200002000-00021 is OK
- 10.1213/00000539-199909000-00002 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.4103/sja.sja\_669\_21 URL is INVALID

BobAubouin commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

BobAubouin commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1213/00000539-200103000-00020 is OK
- 10.1093/bja/aei259 is OK
- 10.1007/s10928-020-09712-1 is OK
- 10.1097/00000542-200406000-00006 is OK
- 10.1213/ANE.0000000000001372 is OK
- 10.1093/bja/aeh293 is OK
- 10.1007/s42452-021-04885-x is OK
- 10.1016/c2017-0-03401-8 is OK
- 10.1093/bja/aew126 is OK
- 10.1097/ALN.0000000000001634 is OK
- 10.1016/j.bja.2018.01.018 is OK
- 10.1093/bja/67.5.618 is OK
- 10.1109/CDC45484.2021.9683368 is OK
- 10.1109/ACCESS.2020.3037725 is OK
- 10.1186/cc9207 is OK
- 10.1155/2017/7432310 is OK
- 10.1109/ACCESS.2021.3049880 is OK
- 10.1109/TBME.2008.923142 is OK
- 10.1093/bja/aeu553 is OK
- 10.1097/00000542-200102000-00023 is OK
- 10.1097/00000542-200308000-00023 is OK
- 10.1097/00000542-200206000-00033 is OK
- 10.1213/ane.0b013e3181a96f9a is OK
- 10.1038/s41598-018-20062-4 is OK
- 10.1093/bja/67.1.41 is OK
- 10.1016/B978-0-12-815975-0.00013-8 is OK
- 10.1016/j.cnsns.2018.12.015 is OK
- 10.1097/00000542-199701000-00004 is OK
- 10.1097/CCM.0b013e318206d2a3 is OK
- 10.1016/j.compchemeng.2022.107747 is OK
- 10.1016/j.jprocont.2022.07.007 is OK
- 10.1213/ANE.0000000000000769 is OK
- 10.1186/cc10562 is OK
- 10.1016/j.jprocont.2021.12.004 is OK
- 10.1016/j.bspc.2021.102476 is OK
- 10.1097/00000542-199906000-00003 is OK
- 10.1097/00000542-200003000-00017 is OK
- 10.1213/ANE.0000000000000386 is OK
- 10.4103/sja.sja_669_21 is OK
- 10.1111/j.1460-9592.2009.03174.x is OK
- 10.1097/00000542-200002000-00021 is OK
- 10.1213/00000539-199909000-00002 is OK

MISSING DOIs

- None

INVALID DOIs

- None

BobAubouin commented 1 year ago

Hi @ppxasjsm thanks for the feedbacks.

I have completed all the small fixes and the DOI problem seems to be solved!

ppxasjsm commented 1 year ago

@BobAubouin thanks for making the changes and fixing the small things! I am away for a week now, but will process your submission further at the end of next week.

In the meantime can you look at the following things please:

[ ] Double check authors and affiliations (including ORCIDs)
[ ] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[ ] Archive the release on Zenodo/figshare/etc and post the DOI here.
[ ] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[ ] Make sure that the license listed for the archive is the same as the software license.

BobAubouin commented 1 year ago

@ppxasjsm ok, perfect, I will do that!

[x] Double check authors and affiliations (including ORCIDs)
[x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[x] Archive the release on Zenodo/figshare/etc and post the DOI here.
[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[x] Make sure that the license listed for the archive is the same as the software license.

BobAubouin commented 1 year ago

I have made the release of the software, the version number is v1.0.0.

BobAubouin commented 1 year ago

The release have been archive on Zenodo with the following DOI: 10.5281/zenodo.8171326. It is available here.

ppxasjsm commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

ppxasjsm commented 1 year ago

@editorialbot set 10.5281/zenodo.8171326 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.8171326

ppxasjsm commented 1 year ago

@editorialbot set v1.0.0 as version

editorialbot commented 1 year ago

Done! version is now v1.0.0

openjournals / joss-reviews

[REVIEW]: PAS: a Python Anesthesia Simulator for drug control #5480

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Reviewer instructions & questions

Checklists

Review checklist for @JHartzer

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @yumuk1989

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance