[PRE REVIEW]: ACEInhibPKPD: An open-source MATLAB app for a pharmacokinetic/pharmacodynamic model of ACE inhibition

[whedon]

Submitting author: @ashleefv (Ashlee N. Ford Versypt) Repository: https://github.com/ashleefv/ACEInhibPKPD Version: v1.0 Editor: @Kevin-Mattheus-Moerman Reviewer: @sdelandtsheer

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[whedon]

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[arfon]

👋 @labarba - the submitting authors suggested you as a potential editor.

[labarba]

It's quite removed from any expertise of mine. I have no idea how to even begin finding a reviewer for this. (Not to mention it's a GUI app for MATLAB.)

[ashleefv]

The science has already been peer-reviewed and published this spring: http://www.sciencedirect.com/science/article/pii/S009813541730145X. The code also includes stand alone .m files that can be viewed in any editor.

Ashlee N. Ford Versypt, Ph.D. Assistant Professor, School of Chemical Engineering, Oklahoma State University Member, Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center 420 Engineering North, OSU, Stillwater, OK 74078 Ph: 405-744-5280 ashleefv@okstate.edu Ford Versypt Lab Website https://sites.google.com/site/ashleefordversypt/

On Tue, Jun 20, 2017 at 12:24 PM, Lorena A. Barba notifications@github.com wrote:

It's quite removed from any expertise of mine. I have no idea how to even begin finding a reviewer for this. (Not to mention it's a GUI app for MATLAB.)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/297#issuecomment-309829211, or mute the thread https://github.com/notifications/unsubscribe-auth/AMD-NvV7Bd2iMzKjuPTeXTEIoiN0JBTQks5sGABBgaJpZM4N8zvx .

[Kevin-Mattheus-Moerman]

Not my field either but myself and @cMadan are MATLAB experts so perhaps we can have a look here too.

[Kevin-Mattheus-Moerman]

The readme.md and paper.md emphasize "This software is intended to be used by engineering educators working with college freshmen or high school students and by systems biology researchers investigating pharmaceuticals to modulate the renin-angiotensin system.". Can you elaborate on the scientific research applications a bit more in the paper? Also, there is a small typo in the paper "...describe and solve the the dynamics of...".

[ashleefv]

I updated both the readme.md and paper.md with additional statements about the scientific applications. Is further clarification needed?

Ashlee N. Ford Versypt, Ph.D. Assistant Professor, School of Chemical Engineering, Oklahoma State University Member, Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center 420 Engineering North, OSU, Stillwater, OK 74078 Ph: 405-744-5280 ashleefv@okstate.edu Ford Versypt Lab Website https://sites.google.com/site/ashleefordversypt/

On Tue, Jun 20, 2017 at 3:51 PM, Kevin Mattheus Moerman < notifications@github.com> wrote:

The readme.md https://github.com/ashleefv/ACEInhibPKPD/blob/master/README.md and paper.md https://github.com/ashleefv/ACEInhibPKPD/blob/master/paper.md emphasize "This software is intended to be used by engineering educators working with college freshmen or high school students and by systems biology researchers investigating pharmaceuticals to modulate the renin-angiotensin system.". Can you elaborate on the scientific research applications a bit more in the paper? Also, there is a small typo in the paper "...describe and solve the the dynamics of...".

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/297#issuecomment-309887630, or mute the thread https://github.com/notifications/unsubscribe-auth/AMD-NlcFTp10OilrOYD4pYB9tHtQAAeQks5sGDC7gaJpZM4N8zvx .

[Kevin-Mattheus-Moerman]

Thanks for making the changes. I'll review these and let you know. Although I am happy implementing/reviewing MATLAB code this is not my field of study. Can you recommend any reviewers (e.g. researchers that would be interested in your work but were not involved in its creation)?

[Kevin-Mattheus-Moerman]

@arfon @labarba I can take this as editor

[ashleefv]

potential reviewers:

• Fulden Buyukozturk https://www.linkedin.com/in/fulden-buyukozturk-b4384910/
• Gilbert Koch https://www.ukbb.ch/en/personal/personen/koch-gilbert.php

Ashlee N. Ford Versypt, Ph.D. Assistant Professor, School of Chemical Engineering, Oklahoma State University Member, Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center 420 Engineering North, OSU, Stillwater, OK 74078 Ph: 405-744-5280 ashleefv@okstate.edu Ford Versypt Lab Website https://sites.google.com/site/ashleefordversypt/

On Wed, Jun 21, 2017 at 3:16 PM, Kevin Mattheus Moerman < notifications@github.com> wrote:

Thanks for making the changes. I'll review these and let you know. Although I am happy implementing/reviewing MATLAB code this is not my field of study. Can you recommend any reviewers (e.g. researchers that would be interested in your work but were not involved in its creation)?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/297#issuecomment-310192518, or mute the thread https://github.com/notifications/unsubscribe-auth/AMD-NkPK0pyyt00fUcf4UKq5CjjJNWJhks5sGXosgaJpZM4N8zvx .

[Kevin-Mattheus-Moerman]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List all of Whedon's capabilities
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# Assign a GitHub user as the reviewer of this submission
@whedon assign @username as reviewer

# List the GitHub usernames of the JOSS editors
@whedon list editors

# List of JOSS reviewers together with programming language preferences and domain expertise
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# Change editorial assignment
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[Kevin-Mattheus-Moerman]

@whedon assign @Kevin-Mattheus-Moerman as editor

[whedon]

OK, the editor is @Kevin-Mattheus-Moerman

[Kevin-Mattheus-Moerman]

@dpastoor, @ronkeizer, @billdenney, @PavelBal + @TheiBa (or a colleague at Open Systems Pharmacology team) would you willing to review this JOSS submission?

Here is the JOSS website Here is the repository for this project: https://github.com/ashleefv/ACEInhibPKPD Reviewing JOSS submissions generally does not take a lot of time and is largely focused on the claims and functionality of the software. See here for reviewer instructions

Let me know if you have any questions.

[dpastoor]

@Kevin-Mattheus-Moerman Thanks for your interest. First, I would like to commend @ashleefv for putting her research in the open. This is a fantastic first step, however the core functionality is written in matlab, which is not FOSS. Looking at the guidelines, this does not seem to directly violate the journal requirements, however as I do not have a copy of matlab I will not be able to review.

I will encourage @ashleefv to consider using a fully open source implementation, such as using R shiny for the GUI + https://github.com/metrumresearchgroup/mrgsolve for the PKPD solver or something along those lines, at which point I would be happy to review

[Kevin-Mattheus-Moerman]

@dpastoor thanks for your fast reply. I understand your points. We do not exclude works in principle that require proprietary hardware or software (e.g. a runtime like MATLAB). As long as it adheres to the OSI definitions of open source. If we were able to set-up a free to use MATLAB environment (have to inquire), would you consider reviewing this work?

[Kevin-Mattheus-Moerman]

@ashleefv can you briefly inquire if translation to something like octave is easy to achieve? Translation is NOT a requirement but it would be good to state here if you believe it to be achievable in principle.

[dpastoor]

@Kevin-Mattheus-Moerman I have 2 problems reviewing this (I probably could get ahold of matlab myself).

First and foremost, as I a have not written any matlab, I would not feel comfortable evaluating the implementation, which I believe is an important part of any scientific review. I can handle R, python, go, or javascript implementations, if at some point it is translated to any of those languages.

Second, I appreciate that matlab is extremely prevalent in engineering, and certain components, such as a GUI, were previously much more labor intensive to implement in FOSS languages. However, in this day and age, it is not an unreasonable task. To me, the thing that excites me seeing this journal is the ability to provide a "reviewed" piece of software that anyone, anywhere, can immediately pull and start using. To that end, I would be willing to 'donate' my time to support such software efforts, however in tandem with the first point above I cannot justify the bandwidth needed for a "closed" matlab implementation to take the time to properly review. Again, not to take anything from @ashleefv 's willingness to at least put the code in the open, which I think is amazing.

If @ashleefv is willing to do a translation, I would be happy to assist in both the translation and/or review.

[ashleefv]

I looked into octave. Unfortunately, even for the code that doesnt need the GUI, octave cannot handle the .mat files used for storing data and variables for various cases.

On Jun 22, 2017 9:57 AM, "Kevin Mattheus Moerman" notifications@github.com wrote:

@ashleefv https://github.com/ashleefv can you briefly inquire if translation to something like octave https://www.gnu.org/software/octave/ is easy to achieve? Translation is NOT a requirement but it would be good to state here if you believe it to be achievable in principle.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/297#issuecomment-310405524, or mute the thread https://github.com/notifications/unsubscribe-auth/AMD-Njqqvw9KKByxi6_9D24AzJ8n8mGZks5sGoCugaJpZM4N8zvx .

[Kevin-Mattheus-Moerman]

@ashleefv thanks for your reply. I understand.

[Kevin-Mattheus-Moerman]

@dpastoor Thanks for your detailed reply. I understand your points. We would be happy to have you as reviewer on other projects. And here is a list of currently open reviews: https://github.com/openjournals/joss-reviews/issues/

[Kevin-Mattheus-Moerman]

:wave: @tpfau @sdelandtsheer would you willing to review this JOSS submission?

Here is the JOSS website Here is the repository for this project: https://github.com/ashleefv/ACEInhibPKPD Reviewing JOSS submissions generally does not take a lot of time and is largely focused on the claims and functionality of the software. See here for reviewer instructions

Let me know if you have any questions.

[Kevin-Mattheus-Moerman]

@tpfau @sdelandtsheer would you willing to review this JOSS submission?

[Kevin-Mattheus-Moerman]

@ashleefv you suggested reviewers but I have not found them on GitHub. Can you suggest reviewers by posting GitHub handles here?

[ashleefv]

They may not be on Github. If needed because of no reviewers, I can withdraw this submission.

Ashlee N. Ford Versypt, Ph.D. Assistant Professor, School of Chemical Engineering, Oklahoma State University Member, Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center 420 Engineering North, OSU, Stillwater, OK 74078 Ph: 405-744-5280 ashleefv@okstate.edu Ford Versypt Lab Website https://sites.google.com/site/ashleefordversypt/

On Sun, Jul 30, 2017 at 10:57 AM, Kevin Mattheus Moerman < notifications@github.com> wrote:

@ashleefv https://github.com/ashleefv you suggested reviewers but I have not find them on GitHub. Can you suggest reviewers by posting GitHub handles here?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/297#issuecomment-318907174, or mute the thread https://github.com/notifications/unsubscribe-auth/AMD-NqKJsxuwMSmEsNL8XNfVnQkJfyULks5sTJnDgaJpZM4N8zvx .

[danielskatz]

Or you can provide email addresses, and they can be asked to join GitHub to do the review.

[ashleefv]

gilbert.koch@ukbb.ch

@fulden_b on twitter

Ashlee N. Ford Versypt, Ph.D. Assistant Professor, School of Chemical Engineering, Oklahoma State University Member, Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center 420 Engineering North, OSU, Stillwater, OK 74078 Ph: 405-744-5280 ashleefv@okstate.edu Ford Versypt Lab Website https://sites.google.com/site/ashleefordversypt/

On Sun, Jul 30, 2017 at 3:24 PM, Daniel S. Katz notifications@github.com wrote:

Or you can provide email addresses, and they can be asked to join GitHub to do the review.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/297#issuecomment-318923496, or mute the thread https://github.com/notifications/unsubscribe-auth/AMD-NlxoaEX1IIezZ1vn5GArSYgqX5CIks5sTNhngaJpZM4N8zvx .

[Kevin-Mattheus-Moerman]

I've invited @fulden_b via twitter https://twitter.com/KMMoerman/status/891756250589007874

[Kevin-Mattheus-Moerman]

and I've just e-mailed Gilbert Koch, thanks @ashleefv

[sdelandtsheer]

Hi, sorry for the delayed answer. I just read the reviewers guidelines. I can review that software, happy to do it.

[Kevin-Mattheus-Moerman]

Awesome! Thanks @sdelandtsheer

[Kevin-Mattheus-Moerman]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the reviewer of this submission
@whedon assign @username as reviewer

# List the GitHub usernames of the JOSS editors
@whedon list editors

# List of JOSS reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Open the review issue
@whedon start review

:construction: Important :construction:

This is all quite new. Please make sure you check the top of the issue after running a @whedon command (you might also need to refresh the page to see the issue update).

[Kevin-Mattheus-Moerman]

@whedon start review

[whedon]

You didn't say the magic word! Try this:

@whedon start review magic-word=bananas

[Kevin-Mattheus-Moerman]

@whedon start review magic-word=bananas

[Kevin-Mattheus-Moerman]

@whedon assign @sdelandtsheer as reviewer

[whedon]

OK, the reviewer is @sdelandtsheer

[Kevin-Mattheus-Moerman]

@whedon start review magic-word=bananas

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/340. Feel free to close this issue now!

[Kevin-Mattheus-Moerman]

Ok @ashleefv @sdelandtsheer review will happen here #340