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Email from Frontiers and question from the editor shared below:</div>
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Dr Torres,</span><br>
<br style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255)">
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in Systems Biology Editorial Office has sent you a message. Please click 'Reply' to send a direct response</span><br style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255)">
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comments were posted by Specialty Chief Editor Shayn Peirce-Cottler. Please visit the review forum using the link below and address these comments within the coming week:</span><br style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255)">
<a href="http://links.email.frontiersin.org/ls/click?upn=99YMbkkQ8WNJiHLectmHSn5XnTmYe57aPeiziTpYNtyfClFbQqFlwPq2nUMZBzQ7srQvkLkPbc-2F-2BZbZ-2BczlOsPrTMbzmmMktcODsIp2h-2Ffj90r8fRFX2WoaacyAq0r1DpdlwAI9E7tBq-2Fy-2F2Oci2ve-2FCfkFNdVsmiG1bos-2FvnrU-3DZcy-_B-2Fy9jbSVGoT8qhSwbw0AFtm6DlDsGMQJjIadnFC13-2FJyATqJzBD73VYfuDTc-2F-2BJaJPaJJ5oSKrMDAr6Ompo1c21QYWQoQgYfAYNEjVnB244sSGd8-2BEkyma7zMD5B9L6sx2V7r1JTwJYDZpx5bqIUznnbkYmAKXcibTaFF47hgopNpnsrFZkqBi6O6g8b4EiWw24vVRZnhel591eZQKRdrLT3faq2B-2F0DXCpdcIRO-2FjNMfVBXwcpPniAJnsg8Tlmf" target="_blank" rel="noopener noreferrer" data-auth="NotApplicable" data-linkindex="0" style="margin:0px;font-size:15px;font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;background-color:rgb(255, 255, 255)">http://www.frontiersin.org/Review/EnterReviewForum.aspx?activationno=ba15539e-1784-4ed3-9969-2aacb1b5b835</a><br style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255)">
<br style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255)">
<span style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255);display:inline !important">Journal:
Frontiers in Systems Biology, section Multiscale Mechanistic Modeling</span><br style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255)">
<span style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255);display:inline !important">Article
type: Review</span><br style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255)">
<span style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255);display:inline !important">Manuscript
title: Model Integration in Computational Biology: the Role of Reproducibility, Credibility and Utility</span><br style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255)">
<span style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255);display:inline !important">Manuscript
ID: 822606</span><br style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255)">
<span style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255);display:inline !important">Authors:
Jonathan Karr, Rahuman S. Malik Sheriff, James Osborne, Gilberto Gonzalez Parra, Eric Forgoston, Ruth Bowness, Yaling Liu, Robin Thompson, Winston Garira, Jacob Barhak, John Rice, Marcella Torres, Hana Maria Dobrovolny, Tingting Tang, William Waites, James
Glazier, James Faeder, Alexander Kulesza</span><br style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255)">
<span style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255);display:inline !important">Submitted
on: 26 Nov 2021</span><br style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255)">
<span style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255);display:inline !important">Edited
by: Shayn Peirce-Cottler</span><br style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255)">
<br style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255)">
<br style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255)">
<span style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255);display:inline !important">Research
Topic: Insights in Systems Biology: Multiscale Mechanistic Modeling 2021</span><br style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255)">
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regards,</span><br style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255)">
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Frontiers in Systems Biology team</span><br style="color:rgb(32, 31, 30);font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:15px;background-color:rgb(255, 255, 255)">
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Marcella Torres, Ph.D.</div>
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Pronouns: she/her</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Vp-reproduce-subgroup <vp-reproduce-subgroup-bounces@lists.simtk.org> on behalf of Jacob Barhak <jacob.barhak@gmail.com><br>
<b>Sent:</b> Wednesday, January 19, 2022 10:24 PM<br>
<b>To:</b> James Glazier <jaglazier@gmail.com><br>
<b>Cc:</b> vp-reproduce-subgroup@lists.simtk.org <vp-reproduce-subgroup@lists.simtk.org>; vp-integration-subgroup@lists.simtk.org <vp-integration-subgroup@lists.simtk.org><br>
<b>Subject:</b> Re: [Vp-reproduce-subgroup] [Vp-integration-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript</font>
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<div style="font-family:Arial,Helvetica,sans-serif; font-size:10pt; border:1pt solid red; padding:2pt; background:yellow">
<span style="color:red"><b>External Email:</b></span><span style="color:black"> Use caution in opening links, attachments, and buying gift cards.</span></div>
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<p>Hi James,</p>
<p><br>
</p>
<p>Here is the text I added to the submission system to correct your name and draw the attention of the editor to the funding issue we discussed. </p>
<p><br>
</p>
<p>Hopefully no other changes will be raised by contributors and we can proceed as approved by all authors. </p>
<p><br>
</p>
<p> Jacob</p>
<p><br>
</p>
<p><br>
</p>
<p>####### Letter to the editor sent in submission system ########</p>
<p> </p>
<p>Another author asked to change their name - adding a middle initial. I cannot do those changes in the manuscript myself through the system since it does not allow making those changes. Here is the proper name with the proper middle initial:</p>
<p>James A. Glazier</p>
<p> </p>
<p>Also, I am making a round of checks that all funding sources and conflict of interests have been submitted properly. Here is the link to the public communications:</p>
<p><a href="https://lists.simtk.org/pipermail/vp-integration-subgroup/2022-January/000388.html">https://lists.simtk.org/pipermail/vp-integration-subgroup/2022-January/000388.html</a></p>
<p>Hopefully no other changes are necessary. </p>
<p> </p>
<p>Thank you for handling this manuscript.</p>
<p> </p>
<p> Jacob</p>
<p> </p>
</div>
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<br>
<div class="x_gmail_quote">
<div dir="ltr" class="x_gmail_attr">On Wed, Jan 19, 2022 at 9:05 PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com">jacob.barhak@gmail.com</a>> wrote:<br>
</div>
<blockquote class="x_gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex">
<div dir="ltr">Thanks James, and all other paper contributors, please read this. <br>
<div><br>
</div>
<div>Your email clarifies things. We did agree long ago that funding sources are at the discretion of the contributor although this was a volunteer effort. A few insisted on adding their funding source and we did add those. Here is some the discussion that
we held:</div>
<div><a href="https://lists.simtk.org/pipermail/vp-integration-subgroup/2021-April/000073.html" target="_blank">https://lists.simtk.org/pipermail/vp-integration-subgroup/2021-April/000073.html</a></div>
<div><br>
</div>
<div>Sheriff's request came in late and should not have been submitted that late in the process, yet I decided to include his funding source because it has legal implications if it is not included - I assume that tax payer money paid for the time he spend on
this manuscript and this requires traceability - I was surprised with his declaration that does not include a traceable source of fund yet to avoid any wrongdoing I decided to include it. I made the email public so that everyone knows and can reciprocate. </div>
<div><br>
</div>
<div>In the manuscript submission form there is a clause about declaration of funding. When I signed it, I knew I was accurate in my statement about how this work was funded. It is important that these declarations are correct since many times taxpayer money
funds this work and that money needs to be traceable for accounting reasons and to avoid misuse of funds. There are legal implications to incorrect declarations on this question. As far as I knew, except from very few that declared funding early on when we
discussed it, this was a volunteer group. And for those who did declare I assumed this was to trace public funds. </div>
<div><br>
</div>
<div>I am sending this email to the entire group to make sure that everyone that approved, knew that they are approving the paper text, the funding sources, the conflict of interest statements, the authorship / ethics statement., license and more elements as
declared in this document: <a href="https://www.frontiersin.org/about/policies-and-publication-ethics" target="_blank">https://www.frontiersin.org/about/policies-and-publication-ethics</a></div>
<div><br>
</div>
<div>If anything was lost through communications I am raising again now so everyone will know what they are signed on. I want to make sure that when I signed in your name I was not misrepresenting anything.</div>
<div><br>
</div>
<div>So if anyone who reads this, and after my explanation believes that they need to correct a funding statement, a conflict of interest statement, or any other detail regarding the manuscript that has legal implications, please announce it NOW and quickly
so changes will be made prior to publication. After publication, such changes may be very complicated and have other implications. </div>
<div><br>
</div>
<div>In simpler words, if your time spent on handling this paper was funded by the taxpayer or by an entity that requires reporting the funding source, you MUST declare it. If you volunteered your own time for this paper, you just have to make sure you have
no other conflict. </div>
<div><br>
</div>
<div>Hopefully I am clear enough now. </div>
<div><br>
</div>
<div>I will write to the editor about adding the middle initial in your name - I can no longer do this though the submission system - it blocked me changing the authors - this is why I wrote to the editor about the request from William Waites to add his second
affiliation.</div>
<div><br>
</div>
<div>I am not sure if there are any more proof stages where we can fix things - the publication process is different from venue to venue and it's important we will be accurate in declarations.</div>
<div><br>
</div>
<div>Hopefully this email will fix things and make sure our delerations are accurate. </div>
<div><br>
</div>
<div><br>
</div>
<div> Jacob</div>
<div><br>
</div>
<div><br>
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<div class="x_gmail_quote">
<div dir="ltr" class="x_gmail_attr">On Wed, Jan 19, 2022 at 12:31 PM James Glazier <<a href="mailto:jaglazier@gmail.com" target="_blank">jaglazier@gmail.com</a>> wrote:<br>
</div>
<blockquote class="x_gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex">
<div dir="ltr">Dear Jacob:
<div><br>
</div>
<div>I sent the minor corrections I did because I saw your response to Rahuman. I had not thought initially that you were listing funding sources, but your response to Rahuman suggested you were. So if you don't want to list funding, it's ok with me. I would
prefer to have the middle initial added if possible, simply because I otherwise get confused with a different James Glazier, but it isn't critical.</div>
<div><br>
</div>
<div>JAG</div>
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<br>
<div class="x_gmail_quote">
<div dir="ltr" class="x_gmail_attr">On Wed, Jan 19, 2022 at 1:22 PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>> wrote:<br>
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<div dir="auto">Well James,
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<div dir="auto">You put me is a difficult position. You all approved the manuscript multiple times. </div>
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<div dir="auto">Sheriff caught it just before I sent it so I added his funding - out of regular process - just to avoid conflict with journal legal requirements.</div>
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<div dir="auto">As for name changes, I am locked outside the system and such a request should be processed through the editor. Similar to what William asked for.</div>
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<div dir="auto">As for funding. We discussed this a long time ago. And the paper was approved multiple times. I can probably spend an hour later to add your funding. Yet there are 18 of us and only a few claimed funding - this was supposed to be a volunteer
effort... If all 18 ask their funding to be included, we will need to reopen this again.</div>
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<div dir="auto">So I ask you on what should I do.</div>
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<div dir="auto">If this funding declaration is necessary for this volunteer work to fulfill the legal requirement of the publisher to disclose funding I must process your request and will do it tonight. If not , I suggest we avoid changes. Please advise on
proper way to proceed.</div>
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<div dir="auto">Hopefully this will settle the matter.</div>
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<div dir="auto"> Jacob</div>
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<div dir="ltr" class="x_gmail_attr">On Wed, Jan 19, 2022, 11:15 James A Glazier <<a href="mailto:jaglazier@gmail.com" target="_blank">jaglazier@gmail.com</a>> wrote:<br>
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<p>Dear Jacob:</p>
<p>Thank you for your heroic efforts on bringing this paper together. I should probably change my name to James A. Glazier, which is my standard listing. I should also acknowledge my funding support:</p>
<p>James A. Glazier acknowledges funding support from grants NSF 188553, NSF 186890, NSF 1720625, NIH U24 EB028887 and NIH R01 GM122424.</p>
<p>JAG<br>
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<div>On 11/17/2021 10:04 PM, Jacob Barhak wrote:<br>
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<div dir="ltr">Hi James Faedar, Hi John Rice,
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<div>Please check the manuscript and declare by REPLY ALL if you APPROVE, DISAPPROVE or ABSTAIN.</div>
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<div>James, if you responded and I did not get the email, I apologize - there are some communication hiccups occasionally. Yet I need your public approval to proceed and use your name.</div>
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<div>John, I know you allowed us to send the paper, yet you need to be specific and declare if you want to be included as an Author or just moved to acknowledgements. You did have a major contribution, so I hope you will APPROVE. </div>
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<div>Once I have your answer I can proceed. Hopefully you will both APPROVE quickly.</div>
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<div> Jacob</div>
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<div dir="ltr" class="x_gmail_attr">On Wed, Nov 17, 2021 at 3:02 PM sheriff <<a href="mailto:sheriff@ebi.ac.uk" rel="noreferrer" target="_blank">sheriff@ebi.ac.uk</a>> wrote:<br>
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<p>Hi Jacob and all,</p>
<p>I approve the submission of the manuscript. </p>
<p>Please update the citation Tiwari et 2020 Preprint to </p>
<p>Tiwari K, Kananathan S, Roberts MG, Meyer JP, Sharif Shohan MU, Xavier A, Maire M, Zyoud A, Men J, Ng S, Nguyen TVN, Glont M, Hermjakob H, Malik-Sheriff RS. Reproducibility in systems biology modelling. Mol Syst Biol. 2021 Feb;17(2):e9982. doi: 10.15252/msb.20209982.
PMID: 33620773; PMCID: PMC7901289.</p>
<p>Also my name and affiliation below</p>
<p>Rahuman S. <span style="text-decoration:underline">Malik Sheriff</span></p>
<p>European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK</p>
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<p>Thanks for pushing this work forward</p>
<p>Best regards</p>
<p>Sheriff</p>
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On 2021-11-17 18:58, Jonathan Karr wrote:</p>
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<div dir="ltr">Hi Jacob,
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<div>Thank you again for spearheading this effort.<br>
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<div>I approve the submission. I think the paper organizes a variety of important issues toward more credible models, and the content is sound.<br>
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<div>My affiliation is Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.</div>
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<div>As others have mentioned, I think the paper would be more impactful with further editing to make the paper easier to read:</div>
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<li>More clearly articulate the goals/motivation for more credible models</li><li>Be more concise and focused</li><li>Remove redundancies by grouping related text</li><li>Fill in the gaps in logic in the introduction with more transitions, less extraneous information, and/or a brief outline.</li><li>Change the title of the "Utility of models" section to something like "Challenges with using multiscale models" (James' suggestion)</li><li>Order the "Utility of models" subsections to be easier to follow, perhaps from model construction through to reuse</li><li>Rephrase the titles of the "Utility of models" subsections to focus on opportunities for improvement rather than current problems</li></ul>
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<div>Regards,</div>
<div>Jonathan</div>
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<div dir="ltr">On Wed, Nov 10, 2021 at 11:25 PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer noreferrer" target="_blank">jacob.barhak@gmail.com</a>> wrote:</div>
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<div dir="ltr">Thanks to all contributors who answered,
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<div>Most contributors approved by now.</div>
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<div>James and Wiliam, I am not sure how many more revisions there will be for this publication. I did not add several important references of my own in this revision. Frankly I wanted to keep reference changes to a minimum and kept it as close as possible
to the origin . However, we are transferring the paper to the publisher under CC license, so it will not be hard to create another derived version with all sorts of additions and modifications in the future where people can edit it as they see fit and add
whatever references they want - so after it gets published you can continue working on other versions as you see fit. For now I ask we focus on publishing this version alone and I really hope the editors will not put us through another revision round since
it makes no sense at this point - any change is not substantial compared to what we have already and any delay is more damaging than productive.</div>
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<div>To be productive I ask that the following people who did not answer so far take the time to APPROVE, DISAPPROVE, or ABSTAIN.:</div>
<div>Robin Thompson</div>
<div>James R. Faeder</div>
<div>Jonathan Karr<br>
Rahuman Sheriff</div>
<div>John Rice</div>
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<div>John Rice - thanks for your support, yet you will have to be specific: You can either choose APPROVE or ABSTAIN - both of these options will move the paper forwards. APPROVE will add your name to the list of authors with all responsibilities and privileges listed
or implied , ABSTAIN will put you in acknowledgements without any obligation. So John, please choose if you want your name on the paper or not in this specific version - any decision you make will be ok. </div>
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<div>I hope we can father all support quickly so I can move forward and submit the paper.</div>
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<div> Jacob</div>
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<div dir="ltr">On Tue, Nov 9, 2021 at 5:46 AM William Waites <<a href="mailto:wwaites@ieee.org" rel="noreferrer noreferrer" target="_blank">wwaites@ieee.org</a>> wrote:</div>
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I'm just chasing down references for use in another context and I notice that the Ke et al paper is still a pre-print after more than a year. There is no problem in my opinion citing preprints but it is suspect in this case: there's been a ton of work on SARS-CoV-2
infectiousness, why didn't this get published? Probably not best to rely on it as an example of practice. Perhaps to fix on revision.<br>
<br>
-w<br>
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<pre cols="72">--
James A. Glazier, PhD
Professor of Intelligent Systems Engineering, Adjunct Professor of Physics
Director, Biocomplexity Institute
Indiana University, Bloomington
(812) 391-2159 (cell)</pre>
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-- <br>
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<div dir="ltr">James A. Glazier, PhD
<div>Professor of Intelligent Systems Engineering, Adjunct Professor of Physics</div>
<div>Director Biocomplexity Institute<br>
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<div>Indiana University, Bloomington</div>
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<div>(812) 391-2159</div>
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