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

Mon Oct 18 07:40:58 PDT 2021

Jacob,

I think you should incorporate the revisions done over the summer (I think what you refer to as John's version) --- many ideas were more properly flushed out and have a better chance making it through the review process, but I'm fine with having you take care of what is needed to satisfy the editor.

Hana

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________________________________
From: Vp-integration-subgroup <vp-integration-subgroup-bounces at lists.simtk.org> on behalf of James Osborne <jmosborne at unimelb.edu.au>
Sent: October 18, 2021 3:32 AM
To: Jacob Barhak
Cc: John Rice; Torres, Marcella; vp-reproduce-subgroup at lists.simtk.org; vp-integration-subgroup at lists.simtk.org; Jonathan Karr; John Gennari; Winston Garira
Subject: Re: [Vp-integration-subgroup] Fwd: Shayn Peirce-Cottler via Frontiers: Manuscript

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Jacob

I'm happy to go ahead to satisfy the editor.

James

On Mon, Oct 18, 2021 at 7:27 PM Jacob Barhak <jacob.barhak at gmail.com<mailto:jacob.barhak at gmail.com>> wrote:
Sure Alex,

The version that was submitted in the only version that was approved by the contributors - since no other version was fully approved, this is the only version we can legally submit:
https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing<https://urldefense.com/v3/__https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing__;!!K6Z8K8YTIA!TQWkwUruvft7_rC2pMk2AG6x6Qt97N8fDBwmWPKO6i9UiU-_dAT0gGCEfX2yrhZCR6E$>

This is the version that we assembled before your modifications were added in the version you created.

My interpretation is that the editor is open to this version provided we address the issues raised.I think this can be done if we all agree on course of action - I even offered my services to merge this with your version as well as Sheriff's version and John's initial version since those are traceable back to author - however, I will do this only if I know I have a green light from all contributors since this means a few days of work for me and I do not want my time to go to waste because of an objection or an idea for a better version that will never get approved.

So I am waiting for a discussion to see the next move - it seems we have a path towards publication, yet we need to gather together and agree on something.

Hopefully we can do it.

             Jacob.

On Mon, Oct 18, 2021 at 3:07 AM Alexander Kulesza <alexander.kulesza at novadiscovery.com<mailto:alexander.kulesza at novadiscovery.com>> wrote:
Dear Jacob, dear all,

to be very honest, I do not really understand what happens here anymore. Could you please point us to the version that has been submitted ?

Best
Alexander

On Mon, 18 Oct 2021 at 08:44, Jacob Barhak <jacob.barhak at gmail.com<mailto:jacob.barhak at gmail.com>> wrote:
Greeting white paper contributors,

Good news. The editor of the topic "Insights in Systems Biology: Multiscale Mechanistic Modeling 2021" from Frontiers in Systems Biology - Multiscale Mechanistic Modeling has returned an answer to our query about the manuscript Marcella Submitted on our behalf.

You can find her concerns and our answer in the forwarded messages below. I think they can be easily fixed if we can find agreement in the group.

Since little time was provided, I ask that the group will answer fast on the desired course of action. We can easily address the concerns she raised fairly quickly. However, I know many of you want more modifications. So each one of the contributors will have to decide if the minimal changes required will be ok for you to approve the manuscript for publication

If this is agreeable to all contributors  I will be happy to spend the time and adapt the manuscript as requested.

Many of you wanted to revise the manuscript - now is a good chance to introduce those new versions. Yet the work has to be done in reasonable time, including the approval process.

To make things easier, I can personally commit time to transforming the manuscript to the desired format and answer all requested changed - However, I will do this only if I know there is no objection to this by any of the listed contributors - so please respond quickly. I am raising this topic for discussion before we start so contributors form their minds. I can also introduce changes from the other 3 versions of the paper that are traceable back to authors if this helps the group move forward  - The 3 versions are from Alex, Sheriff, and John - yet I will personally not introduce any change that is not traceable back to an author on google docs - please see how the editor is specific about authorship in the first concern raised - hence my insistence of traceability.

If anyone else wants to commit time to quickly assemble a revised manuscript that is traceable back to authors and matches the editors comments, it is now time to step forwards and remember we have little time to move forwards unless the editor grants us an extension. And note that collecting approvals from such a large group also takes time - so revisions should be done quickly regardless.

I will wait for a few days before taking any action to see what are the opinions and ideas you may have to move this forward.

Hopefully we can quickly find common agreement.

I thank Marcella for taking the time to submit this to get a response.

              Jacob

---------- Forwarded message ---------
From: Jacob Barhak <jacob.barhak at gmail.com<mailto:jacob.barhak at gmail.com>>
Date: Mon, Oct 18, 2021 at 12:57 AM
Subject: Re: Shayn Peirce-Cottler via Frontiers: Manuscript
To: Shayn Peirce-Cottler (Via FrontiersIn) <shayn at virginia.edu<mailto:shayn at virginia.edu>>
Cc: <systemsbiology.editorial.office at frontiersin.org<mailto:systemsbiology.editorial.office at frontiersin.org>>, Vodovotz, Yoram <vodovotzy at upmc.edu<mailto:vodovotzy at upmc.edu>>

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<https://urldefense.com/v3/__https://lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-March/000019.html__;!!K6Z8K8YTIA!TQWkwUruvft7_rC2pMk2AG6x6Qt97N8fDBwmWPKO6i9UiU-_dAT0gGCEfX2yLYSB55w$>  -  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

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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<https://urldefense.com/v3/__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__;!!K6Z8K8YTIA!TQWkwUruvft7_rC2pMk2AG6x6Qt97N8fDBwmWPKO6i9UiU-_dAT0gGCEfX2yR7OrgEE$>
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