<div dir="ltr"><div>Greetings white paper contributors,</div><div><br></div><div>Below is the response from the editor to my request and my thank you.</div><div><br></div><div>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. </div><div><br></div><div>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. </div><div><br></div><div>The most time consuming effort would be adhering to the journal format as defined here:</div><div><a href="https://www.frontiersin.org/about/author-guidelines" target="_blank">https://www.frontiersin.org/about/author-guidelines</a><br></div><div><br></div><div>I think the most time consuming task would be dealing with the references - otherwise the format guidelines seem reasonable.</div><div><br></div><div>We can also add some revisions we started working on. However, I will personally insist on :</div><div>1. traceability - currently there is no traceability in the revised version in the summer</div><div>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 </div><div>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. </div><div><br></div><div>I will also ask for fast responses from all contributors. </div><div><br></div><div>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. </div><div><br></div><div>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. </div><div><br></div><div>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:</div><div><br></div><div>- 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</div><div>- 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 </div><div>- 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. </div><div><br></div><div>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. </div><div><br></div><div>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..</div><div><br></div><div>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 ..</div><div><br></div><div>If I forgot anyone who had major requests, please remind me. .</div><div><br></div><div>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..</div><div><br></div><div>Hopefully most of you will be ok with that.</div><div><br></div><div> Jacob</div><div><br></div><div><br></div><div><br></div><div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">---------- Forwarded message ---------<br>From: <strong class="gmail_sendername" dir="auto">Jacob Barhak</strong> <span dir="auto"><<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>></span><br>Date: Mon, Oct 18, 2021 at 9:34 PM<br>Subject: Re: Shayn Peirce-Cottler via Frontiers: Manuscript<br>To: Peirce-Cottler, Shayn (smp6p) <<a href="mailto:smp6p@virginia.edu" target="_blank">smp6p@virginia.edu</a>><br>Cc: Shayn Peirce-Cottler (Via FrontiersIn) <<a href="mailto:shayn@virginia.edu" target="_blank">shayn@virginia.edu</a>>, <a href="mailto:systemsbiology.editorial.office@frontiersin.org" target="_blank">systemsbiology.editorial.office@frontiersin.org</a> <<a href="mailto:systemsbiology.editorial.office@frontiersin.org" target="_blank">systemsbiology.editorial.office@frontiersin.org</a>>, Vodovotz, Yoram <<a href="mailto:vodovotzy@upmc.edu" target="_blank">vodovotzy@upmc.edu</a>><br></div><br><br><div dir="ltr">Thanks Shayn,<div><br></div><div>You will get a revised manuscript targeted at your journal and get back to you with a more polished version and satisfies your requests. </div><div><br></div><div>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.</div><div><br></div><div>Many thanks for the rapid responses.</div><div><br></div><div> Jacob</div><div><br></div><div><br></div><div>--<br>Jacob Barhak Ph.D. <br>Sole Proprietor, Software Developer, and Computational Disease Modeler<br><br>Jacob Barhak Analytics<br>701 Brazos St<br>Suite 548<br>Austin TX, 78701<br><br>Email: <a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a></div><div><br><a href="https://sites.google.com/view/jacob-barhak/home" target="_blank">https://sites.google.com/view/jacob-barhak/home</a><br><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Oct 18, 2021 at 7:43 PM Peirce-Cottler, Shayn (smp6p) <<a href="mailto:smp6p@virginia.edu" target="_blank">smp6p@virginia.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div lang="EN-US">
<div>
<p class="MsoNormal"><span style="font-size:12pt;color:black">Hi Jacob, <u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:12pt;color:black"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:12pt;color:black">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. <u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:12pt;color:black"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:12pt;color:black">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!<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:12pt;color:black"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:12pt;color:black">-Shayn<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:12pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:12pt"><u></u> <u></u></span></p>
<div>
<p class="MsoNormal"><span style="color:black">Shayn Peirce-Cottler, Ph.D.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:black">Professor of Biomedical Engineering<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:black">Harrison Distinguished Teaching Professor</span><u></u><u></u></p>
<p class="MsoNormal"><span style="color:black">BME Graduate Program Director<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:black">University of Virginia<u></u><u></u></span></p>
</div>
<p class="MsoNormal"><span style="color:black">Charlottesville, VA</span><span style="font-size:12pt"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:12pt"><u></u> <u></u></span></p>
<div style="border-right:none;border-bottom:none;border-left:none;border-top:1pt solid rgb(181,196,223);padding:3pt 0in 0in">
<p class="MsoNormal"><b><span style="font-size:12pt;color:black">From: </span></b><span style="font-size:12pt;color:black">Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>><br>
<b>Date: </b>Monday, October 18, 2021 at 1:57 AM<br>
<b>To: </b>Peirce-Cottler Shayn <<a href="mailto:shayn@virginia.edu" target="_blank">shayn@virginia.edu</a>><br>
<b>Cc: </b>"<a href="mailto:systemsbiology.editorial.office@frontiersin.org" target="_blank">systemsbiology.editorial.office@frontiersin.org</a>" <<a href="mailto:systemsbiology.editorial.office@frontiersin.org" target="_blank">systemsbiology.editorial.office@frontiersin.org</a>>, "Vodovotz, Yoram" <<a href="mailto:vodovotzy@upmc.edu" target="_blank">vodovotzy@upmc.edu</a>><br>
<b>Subject: </b>Re: Shayn Peirce-Cottler via Frontiers: Manuscript<u></u><u></u></span></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Hi Shayn,<u></u><u></u></p>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Thanks for returning the response quickly. To you comments. <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">1. This is the list of authors that agreed to submit this manuscript for review - I collected their approvals for this version personally. <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<ol style="margin-top:0in" start="1" type="1">
<li style="color:black;margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal">
<span style="font-family:Arial,sans-serif">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<u></u><u></u></span></li><li style="color:black;margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal">
<span style="font-family:Arial,sans-serif">Rahuman Sheriff, The European Bioinformatics Institute (EMBL-EBI), UK<u></u><u></u></span></li><li style="color:black;margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal">
<span style="font-family:Arial,sans-serif">James Osborne, School of Mathematics and Statistics, University of Melbourne, Australia<u></u><u></u></span></li><li style="color:black;margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal">
<span style="font-family:Arial,sans-serif">Gilberto Gonzalez Parra, Mathematics Department, New Mexico Tech, USA<u></u><u></u></span></li><li style="color:black;margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal">
<span style="font-family:Arial,sans-serif">Eric Forgoston, Department of Applied Mathematics and Statistics, Montclair State University, USA<u></u><u></u></span></li><li style="color:black;margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal">
<span style="font-family:Arial,sans-serif">Ruth Bowness, Department of Mathematical Sciences, University of Bath, UK<u></u><u></u></span></li><li style="color:black;margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal">
<span style="font-family:Arial,sans-serif">Yaling Liu, Department of Mechanical Engineering and Mechanics , Department of Bioengineering, Lehigh University, USA<u></u><u></u></span></li><li style="color:black;margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal">
<span style="font-family:Arial,sans-serif">Robin Thompson, Mathematics Institute & The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, UK<u></u><u></u></span></li><li style="color:black;margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal">
<span style="font-family:Arial,sans-serif">Winston Garira - Department Of Mathematics And Applied Mathematics , Modelling Health and Environmental Linkages Research Group. University of Venda, South Africa<u></u><u></u></span></li><li style="color:black;margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal">
<span style="font-family:Arial,sans-serif">Jacob Barhak - Barhak, Jacob, USA<u></u><u></u></span></li><li style="color:black;margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal">
<span style="font-family:Arial,sans-serif">John Rice - Independent Retired Working Group Volunteer, USA<u></u><u></u></span></li><li style="color:black;margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal">
<span style="font-family:Arial,sans-serif">Marcella Torres, School of Arts and Sciences, University of Richmond, USA<u></u><u></u></span></li><li style="color:black;margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal">
<span style="font-family:Arial,sans-serif">Hana M. Dobrovolny , Department of Physics & Astronomy, Texas Christian University, Fort Worth, USA<u></u><u></u></span></li><li style="color:black;margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal">
<span style="font-family:Arial,sans-serif">Tingting Tang, Department of Mathematics and Statistics in San Diego State University (SDSU) and SDSU Imperial Valley, USA<u></u><u></u></span></li><li style="color:black;margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal">
<span style="font-family:Arial,sans-serif">William Waites, Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, UK<u></u><u></u></span></li><li style="color:black;margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal">
<span style="font-family:Arial,sans-serif">James Glazier, Biocomplexity Institute, Indiana University, Bloomington, USA<u></u><u></u></span></li><li style="color:black;margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal">
<span style="font-family:Arial,sans-serif">James R. Faeder, Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, USA<u></u><u></u></span></li></ol>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">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:
<a href="https://lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-March/000019.html" target="_blank">
https://lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-March/000019.html</a> - 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. <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">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. <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">3. Please note that after the list of authors there is a disclaimer : "<span style="font-family:Arial,sans-serif;color:black">The opinion of the contributors do not reflect the opinions of the entire working group". I</span>nitially 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. <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">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. <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">In summary: <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">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. <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">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. <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Hopefully we can address your concerns in time to publish the manuscript in a timely manner. <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal"> Jacob<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12pt">--<br>
Jacob Barhak Ph.D. <br>
Sole Proprietor, Software Developer, and Computational Disease Modeler<br>
<br>
Jacob Barhak Analytics<br>
701 Brazos St<br>
Suite 548<br>
Austin TX, 78701<br>
<br>
Email: <a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a><br>
<br>
<a href="https://sites.google.com/view/jacob-barhak/home" target="_blank">https://sites.google.com/view/jacob-barhak/home</a><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<div>
<p class="MsoNormal">On Sun, Oct 17, 2021 at 9:56 AM Shayn Peirce-Cottler (Via FrontiersIn) <<a href="mailto:noreply@frontiersin.org" target="_blank">noreply@frontiersin.org</a>> wrote:<u></u><u></u></p>
</div>
<blockquote style="border-top:none;border-right:none;border-bottom:none;border-left:1pt solid rgb(204,204,204);padding:0in 0in 0in 6pt;margin-left:4.8pt;margin-right:0in">
<div>
<p class="MsoNormal">Dear Jacob, <br>
<br>
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:<br>
<br>
1. The author list that is on the first page differs from the author list that was provided at the time of submission.
<br>
<br>
2. The manuscript needs to be submitted using the official Frontiers template.<br>
<br>
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.<br>
<br>
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).<br>
<br>
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.
<br>
<br>
Thank you,<br>
Shayn<br>
<br>
<br>
---------------------------------<br>
<br>
Manuscript title: Model Integration in Computational Biology: The Role of Reproducibility, Credibility and Utility<br>
Manuscript ID: 793932<br>
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
<br>
Date submitted: 12 Oct 2021 <br>
Edited by: Shayn Peirce-Cottler<br>
<br>
<br>
Research Topic: Insights in Systems Biology: Multiscale Mechanistic Modeling 2021<br>
Review forum direct access link: <a href="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" target="_blank">
https://review.frontiersin.org/review/793932/0/0</a><span style="border:1pt solid windowtext;padding:0in"><img border="0" width="1" height="1" style="width:0.0104in;height:0.0104in" id="m_3106702485682359377m_-7813573733557270536m_-7842715099430849307gmail-m_622710468663863154_x0000_i1025" alt="Image removed by sender."></span><u></u><u></u></p>
</div>
</blockquote>
</div>
</div>
</div>
</blockquote></div>
</div></div></div>