[Vp-reproduce-subgroup] [Vp-integration-subgroup] Fwd: Shayn Peirce-Cottler via Frontiers: Manuscript

Thu Oct 21 08:33:40 PDT 2021

This streamlined approach sounds good to me; thanks Jacob for offering to coordinate edits. I think the one month deadline is a good maximum, since Frontiers favors quick turnaround.

I don't insist on participating in the revisions, but I am available to help with cleaning up grammar, typos, and so on - I noticed quite a few minor issues when reviewing the document for submission. However, my son was born a few days ago and I have limited time.

Marcella
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From: Jacob Barhak <jacob.barhak at gmail.com>
Sent: Wednesday, October 20, 2021 11:53:58 PM
To: Alexander Kulesza <alexander.kulesza at novadiscovery.com>
Cc: Hana <h.dobrovolny at tcu.edu>; James Osborne <jmosborne at unimelb.edu.au>; John Rice <john.rice at noboxes.org>; Torres, Marcella <mtorres at richmond.edu>; vp-reproduce-subgroup at lists.simtk.org <vp-reproduce-subgroup at lists.simtk.org>; vp-integration-subgroup at lists.simtk.org <vp-integration-subgroup at lists.simtk.org>; Jonathan Karr <jonrkarr at gmail.com>; John Gennari <gennari at uw.edu>; Winston Garira <Winston.Garira at univen.ac.za>
Subject: Re: [Vp-integration-subgroup] Fwd: Shayn Peirce-Cottler via Frontiers: Manuscript

External Email: Use caution in opening links, attachments, and buying gift cards.

Thanks Alex, Thanks John,

Your contribution is appreciated and since John cleared us to move forward it simplifies things. I hope he will change his mind about authorship since he contributed a lot, yet I will respect his wishes - perhaps after seeing the final version he will change his mind.

If Sheriff gives me a green light I can incorporate his modifications as well. I do ask that if any of the listed authors has any serious concerns and plans to not approve a modified version that addresses the editors requests alone alongside those I mentioned above, to step up before the work is done so we can resolve things before energy is spent.

If there will be no blocks I plan to start work over the weekend if I see no objections by then.

I appreciate the offer to help with bibliography, from experience I know it is perhaps the most time consuming. However, since we have many links and specialized publications in our list - I am not sure if any tool can make it easier - the last time I had to do a lot of manual work to fit a specific format and find all missing links and also fix some errors - no tool would have helped me then. This time I think it will be a bit easier. Yet I ask for no more references to be added - I also want to add more references, yet I am stopping myself. We can always expand the work in another future version if we have new findings.

Again note that I will only try to address the requests of the editor at this point without trying to perfect anything beyond what I wrote above and I want to keep things as traceable as possible. Once I am done,we will see if we can approve this manuscript for publication.

Unless any blockers appear, if anyone wants to actively participate in the editing over the weekend, please let me know so we can communicate better.

            Jacob

On Tue, Oct 19, 2021 at 2:02 AM Alexander Kulesza <alexander.kulesza at novadiscovery.com<mailto:alexander.kulesza at novadiscovery.com>> wrote:
Dear Jacob,
thanks for forwarding and you suggestions, which seems more than reasonable.

My contributions from May 19th, May31st and June 2nd are in https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit?usp=sharing&ouid=113860487708206439519&rtpof=true&sd=true

The other document https://docs.google.com/document/d/1esZvWWVBvpwvuFUi3C3161lthZkEBFyMRrwwozitBi4/edit?usp=sharing I created initially to suggest my edits without editing the core version can be disregarded as I have tranferred all of them into the main document, cited above.

If we were on Latex, I could offer to create the bibliography but unfortunately we lack a bibliography manager integrated in Word/GDoc. If we were to work with Mendeley and someone could create a group for this paper that has a shared library I could offer to transfer citations from the paper into that database too.

Please let me know.
A

On Tue, 19 Oct 2021 at 05:51, Jacob Barhak <jacob.barhak at gmail.com<mailto:jacob.barhak at gmail.com>> wrote:
Greetings white paper contributors,

Below is the response from the editor to my request and my thank you.

The editor grants us the extension by rejecting the paper and allowing time to come up with a better version. There is no time limit now, yet I want to get her a revised version within a month.

The requests are simple and easy to satisfy - and I know there are many of you who want more revisions, yet I suggest we reduce them to only what is manageable and necessary. Otherwise we will never get this paper published despite its importance.

The most time consuming effort would be adhering to the journal format as defined here:
https://www.frontiersin.org/about/author-guidelines

I think the most time consuming task would be dealing with the references - otherwise the format guidelines seem reasonable.

We can also add some revisions we started working on. However, I will personally insist on :
1. traceability - currently there is no traceability in the revised version in the summer
2. non deletion - do not delete any content unless you wrote it originally or unless you announced it beforehand to the group and got no objections within a few days
3. Avoid Adding more material that is not in the existing versions we had - especially references - we don't have time for that and that is not what the editor asked us anyway.

I will also ask for fast responses from all contributors.

To be practical, I marked the submitted version and opened the document to those who requested editing rights in the past.  If you want editing rights, let me know - however, the edits should be minimal and focus on areas you edited in the past and be aware that if your edits will not get approved by everyone, we will revert to the old version we all accepted. The submitted version was marked so we can always get back to it.

If you want editing rights, let me know and I will respond within a day - I cannot promise to be fatter than that these days.

Alex, John, Sheriff, you had other versions you created, I want to merge some of your changes to the manuscript in this version - here are my suggestions:

- Sheriff, I will soften the language as you requested - this was your main request in the past, yet I will go over your list of changes and see what I else can be done without reinventing the paper
- John - I will 1) merge the credibility sections , 2) delete the history related to the working group since it matches with what was requested, and 3) move the model validation barrier section away from the table since we did not suggest a solution there.  Hopefully this will make the paper more appealing to you and you will be willing to add your name to the list
- Alex, your changes were made on May 16, 2021 and shared in a way I can see the differences and trace them back to you - I will try to add your references and see if I can incorporate your text changes as much as I can.

If the 3 of you are ok with me migrating your changes, I can start the work to save time. Yet I want your ok first.

I know Eric and Hana were working on some sections and feel strongly about those - specifically the stochastic modeling part - I am open to your changes, please suggest what you feel strongly about..

I recall Johnathan Karr wanted to make some changes, please let me know if there is anything you feel strongly about - he had a lot of text in the paper ..

If I forgot anyone who had major requests, please remind me. .

I am trying to avoid a never ending revisioning cycle. So I am asking you to trust me and centralize the work in hope I get a better version by the end of the week..

Hopefully most of you will be ok with that.

               Jacob

---------- Forwarded message ---------
From: Jacob Barhak <jacob.barhak at gmail.com<mailto:jacob.barhak at gmail.com>>
Date: Mon, Oct 18, 2021 at 9:34 PM
Subject: Re: Shayn Peirce-Cottler via Frontiers: Manuscript
To: Peirce-Cottler, Shayn (smp6p) <smp6p at virginia.edu<mailto:smp6p at virginia.edu>>
Cc: Shayn Peirce-Cottler (Via FrontiersIn) <shayn at virginia.edu<mailto:shayn at virginia.edu>>, systemsbiology.editorial.office at frontiersin.org<mailto:systemsbiology.editorial.office at frontiersin.org> <systemsbiology.editorial.office at frontiersin.org<mailto:systemsbiology.editorial.office at frontiersin.org>>, Vodovotz, Yoram <vodovotzy at upmc.edu<mailto:vodovotzy at upmc.edu>>

Thanks Shayn,

You will get a revised manuscript targeted at your journal and get back to you with a more polished version and satisfies your requests.

It will also allow us to incorporate newer versions of the text that answer some of your requests. We really wish to publish it fast, yet we need more time for the approval process. So your solution seems correct - I hope you hear back from us within a month or so.

Many thanks for the rapid responses.

                 Jacob

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Sole Proprietor, Software Developer, and Computational Disease Modeler

Jacob Barhak Analytics
701 Brazos St
Suite 548
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Email: jacob.barhak at gmail.com<mailto:jacob.barhak at gmail.com>

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On Mon, Oct 18, 2021 at 7:43 PM Peirce-Cottler, Shayn (smp6p) <smp6p at virginia.edu<mailto:smp6p at virginia.edu>> wrote:

Hi Jacob,

Thank you for your detailed reply. I agree that the issues can be addressed as you have described below, and that you may need more time to do so. Hence, I am going to officially reject this first submission to remove any imposed deadlines, and I certainly encourage you to make the updates listed below, and submit a new manuscript at your earliest convenience.

Please let me know if you have any questions, and thanks again for considering this journal! I think the topic fits very nicely with the scope of the journal, and it is certainly an important topic to our multi-scale modeling community!

-Shayn

Shayn Peirce-Cottler, Ph.D.

Professor of Biomedical Engineering

Harrison Distinguished Teaching Professor

BME Graduate Program Director

University of Virginia

Charlottesville, VA

From: Jacob Barhak <jacob.barhak at gmail.com<mailto:jacob.barhak at gmail.com>>
Date: Monday, October 18, 2021 at 1:57 AM
To: Peirce-Cottler Shayn <shayn at virginia.edu<mailto:shayn at virginia.edu>>
Cc: "systemsbiology.editorial.office at frontiersin.org<mailto:systemsbiology.editorial.office at frontiersin.org>" <systemsbiology.editorial.office at frontiersin.org<mailto:systemsbiology.editorial.office at frontiersin.org>>, "Vodovotz, Yoram" <vodovotzy at upmc.edu<mailto:vodovotzy at upmc.edu>>
Subject: Re: Shayn Peirce-Cottler via Frontiers: Manuscript

Hi Shayn,

Thanks for returning the response quickly. To you comments.

1. This is the list of authors that agreed to submit this manuscript for review - I collected their approvals for this version personally.

  1.  Jonathan Karr, Icahn Institute for Data Science and Genomic Technology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai USA
  2.  Rahuman Sheriff, The European Bioinformatics Institute (EMBL-EBI), UK
  3.  James Osborne, School of Mathematics and Statistics, University of Melbourne, Australia
  4.  Gilberto Gonzalez Parra, Mathematics Department, New Mexico Tech, USA
  5.  Eric Forgoston, Department of Applied Mathematics and Statistics, Montclair State University, USA
  6.  Ruth Bowness, Department of Mathematical Sciences, University of Bath, UK
  7.  Yaling Liu, Department of Mechanical Engineering and Mechanics , Department of Bioengineering, Lehigh University, USA
  8.  Robin Thompson, Mathematics Institute & The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, UK
  9.  Winston Garira - Department Of Mathematics And Applied Mathematics , Modelling Health and Environmental Linkages Research Group. University of Venda, South Africa
  10. Jacob Barhak - Barhak, Jacob, USA
  11. John Rice - Independent Retired Working Group Volunteer, USA
  12. Marcella Torres, School of Arts and Sciences, University of Richmond, USA
  13. Hana M. Dobrovolny , Department of Physics & Astronomy, Texas Christian University, Fort Worth, USA
  14. Tingting Tang, Department of Mathematics and Statistics in San Diego State University (SDSU) and SDSU Imperial Valley, USA
  15. William Waites, Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, UK
  16. James Glazier, Biocomplexity Institute, Indiana University, Bloomington, USA
  17. James R. Faeder, Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, USA

If there is a mismatch of authors in the submission, it can be easily corrected - we kept the paper traceable when we constructed it so we can point to exact texts contributed by each contributor through their google account and versions kept in google docs with few exceptions where I personally added text their wrote and have email conversations supporting that .  I personally collected all those contributions in google docs when I assembled the version you see and made sure it is agreed upon by the contributors. It is important to note that There was one contributor that asked for more revisions and did not approve this manuscript, yet allowed submitting the text without association to it to avoid delays. The entire conversation was documented publicly in our mailing list and we got consent from this contributor to continue and use the text - You can find the conversation  here: https://lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-March/000019.html  -  so there are no copyright issues and the name of the author is not included in the list above at their request. Those included in the list have contributed and approved. If needed, we will correct the list in the journal to match this list. Please note that we kept the entire process as transparent as possible so there will be no issues. If there are any concerns of authorship, I will be happy to dig into the history and pull out details.

2. The reason the manuscript was submitted in this form is to get confirmation on initial fit and to get some initial feedback. We were interested in fast review to get the information quickly out - Also note that we did not intend this to be a final version - we already have some modifications in the work that we would like to introduce where more people contributed , yet we have not reached agreement on those so we cannot formally publish them - however, we did reach agreement on submitting this version for review so the editor can focus us on what is important to change to get published with a 3rd Party - enough of us agreed in a vote that your Journal seems is a suitable 3rd party and hence the submission. We will be happy to spend the time to convert the manuscript to the desired format if you find the content suitable for the journal. So far your requests are reasonable and I will convey them to the group through our mailing list.

3. Please note that after the list of authors there is a disclaimer : "The opinion of the contributors do not reflect the opinions of the entire working group". Initially this paper started as an activity requested by the working group leads. However, by no means it represents all opinions. The introduction in this version of the paper captures some of this history of how the manuscript was created and modified. However, we have other versions of the manuscript in work where this history is deleted - If you prefer, we can easily create a version that detaches from the working group to eliminate all concerns - this is a relatively easy fix. However, whatever fix we do, we will have to approve with all contributors.

4  The revisions can be done in reasonable time. However, the process of collecting approval for all contributors to legally approve the revised manuscript will take more than 14 days. All contributors must approve a manuscript for publication. With this number of authors we will probably not make it in the time you mentioned - only the approval process for collecting all approvals took alone about 3 weeks to approve this version you see.  Hopefully you will understand this and extend this time period beyond 14 days.

In summary:

Making the fixes you asked for towards publication is easy - yet getting the approval from so many people may take us more time than what you provide. If it is possible to get an extension, it will be appreciated.

I will add this conversation to our mailing list so we can start the process of revising the manuscript.  However, if after this email you have more issues with this paper, Please advise on the best course of action you see fit so we can adjust accordingly.

Hopefully we can address your concerns in time to publish the manuscript in a timely manner.

                 Jacob

--
Jacob Barhak Ph.D.
Sole Proprietor, Software Developer, and Computational Disease Modeler

Jacob Barhak Analytics
701 Brazos St
Suite 548
Austin TX, 78701

Email: jacob.barhak at gmail.com<mailto:jacob.barhak at gmail.com>

https://sites.google.com/view/jacob-barhak/home

On Sun, Oct 17, 2021 at 9:56 AM Shayn Peirce-Cottler (Via FrontiersIn) <noreply at frontiersin.org<mailto:noreply at frontiersin.org>> wrote:

Dear Jacob,

Thank you for your manuscript submission. I cannot send it out for review in its current form because I have a few concerns, but if you can address the following issues, I will certainly reconsider a revised manuscript if the following are adequately addressed:

1. The author list that is on the first page differs from the author list that was provided at the time of submission.

2. The manuscript needs to be submitted using the official Frontiers template.

3. The manuscript states that it represents the views of a number of special interest and working groups, and the authors should provide assurances that they have the authority and approval to speak on behalf of the working groups that are listed.

4. There are places throughout the manuscript, and most frequently in the second half, where information is provided as bulleted talking points without context. Those sections should be revised into paragraphs of text or summarized in a table (or figure).

If you wish to submit a revised manuscript, the journal provides a 14-day time window for you to do so. Please let me know if you have any questions.

Thank you,
Shayn

---------------------------------

Manuscript title: Model Integration in Computational Biology: The Role of Reproducibility, Credibility and Utility
Manuscript ID: 793932
Authors: Marcella Torres, Jacob Barhak, Ruth Bowness, Hana Maria Dobrovolny, James Faeder, Eric Forgoston, Winston Garira, Yaling Liu, James Osborne, Gilberto Gonzalez Parra, John Rice, Rahuman Sheriff, Tingting Tang, Robin Thompson, William Waites
Date submitted: 12 Oct 2021
Edited by: Shayn Peirce-Cottler

Research Topic: Insights in Systems Biology: Multiscale Mechanistic Modeling 2021
Review forum direct access link: https://review.frontiersin.org/review/793932/0/0<http://links.email.frontiersin.org/ls/click?upn=AAaFa03elZRFPXQ6ShiKwHJ7IVBhf38O-2BEQWinpomFtULO0Q-2BM19TTRdh7emL5NqrxgHYRG7-2FEazDF-2FJfPddug-3D-3Dkdpa_6U3AlnyvMxxXqGK2YZZvqQDAig2dZVa43D-2BB81ORWCaNWR45ZJ2fDhpaKsTZzRsuCL-2BNJFR2MRucSNQVfNAGmtHQx1gGGhLotkRxEWQuZDre0jQti6pSzF-2Bm1akZB-2FZLJbzjJjEqrnF6c-2BY79oozDKNeyZDGEV7E7qizJmMtyvWGMFEr4JK1z0YPzIbG66EloII5-2FSNkwoWo-2BqqYbe1fAtco01e7-2FlRQb33KpEVuKlNimzGXjW3kPgAYf1R6wsCnLhi7Aow94qLbu0WkYgbBRg-3D-3D>

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