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Hi all,</div>
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Just checking in: am I the only one seeing the reviewer's comments on the manuscript?</div>
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Thanks,</div>
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Marcella</div>
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Marcella Torres, Ph.D.</div>
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Director of Mathematical Studies</div>
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University of Richmond</div>
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Jepson Hall Room 212</div>
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221 Richmond Way</div>
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Richmond, VA 23173</div>
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(804) 289-8081</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> Monday, November 29, 2021 2:39 AM<br>
<b>To:</b> James A Glazier <jaglazier@gmail.com><br>
<b>Cc:</b> Thompson, Robin <Robin.N.Thompson@warwick.ac.uk>; vp-reproduce-subgroup@lists.simtk.org <vp-reproduce-subgroup@lists.simtk.org>; vp-integration-subgroup@lists.simtk.org <vp-integration-subgroup@lists.simtk.org>; Jonathan Karr <jonrkarr@gmail.com>;
John Gennari <gennari@uw.edu>; Winston Garira <Winston.Garira@univen.ac.za>; Faeder, James R <faeder@pitt.edu><br>
<b>Subject:</b> Re: [Vp-reproduce-subgroup] [Vp-integration-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript</font>
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<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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<div dir="ltr">Thanks James, And thanks to all contributors,
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<div>The paper was submitted on Thanksgiving evening and confirmation was received.</div>
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<div>Hopefully it will be processed quickly.</div>
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<div> Jacob</div>
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<div dir="ltr" class="x_gmail_attr">On Wed, Nov 24, 2021 at 12:22 PM James A Glazier <<a href="mailto:jaglazier@gmail.com">jaglazier@gmail.com</a>> wrote:<br>
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<p>Dear Jacob:</p>
<p>Thank you for all your hard work and patience on this paper. I know you have made a lot of effort to integrate so many differing ideas and voices.</p>
<p>JAG<br>
</p>
<div>On 11/24/2021 9:14 AM, Jacob Barhak wrote:<br>
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<div dir="ltr">Thanks James,
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<div>Unless there are any last minute objections, I will submit the paper this holiday weekend.</div>
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<div>I will update you all on progress.</div>
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<div>Hopefully it will be smooth.</div>
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<div>Happy thanksgiving.</div>
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<div> Jacob</div>
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<div dir="ltr" class="x_gmail_attr">On Wed, Nov 24, 2021 at 8:09 AM Faeder, James R <<a href="mailto:faeder@pitt.edu" target="_blank">faeder@pitt.edu</a>> wrote:<br>
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<p class="x_MsoNormal">APPROVE. I apologize for the delay. These messages were being routed to a folder that I do not check frequently. I finally found out from a voicemail message. Thanks everyone for the efforts you have put into this work and especially
Jacob for all of the work organizing on top of it. Good luck with the submission and Happy Thanksgiving!</p>
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<p class="x_MsoNormal">Jim</p>
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<p class="x_MsoNormal" style="margin-bottom:12pt"><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>Wednesday, November 24, 2021 at 6:47 AM<br>
<b>To: </b>John Rice <<a href="mailto:john.rice@noboxes.org" target="_blank">john.rice@noboxes.org</a>>, Jonathan Karr <<a href="mailto:jonrkarr@gmail.com" target="_blank">jonrkarr@gmail.com</a>>, William Waites <<a href="mailto:wwaites@ieee.org" target="_blank">wwaites@ieee.org</a>>,
Tingting Tang <<a href="mailto:ttang2@sdsu.edu" target="_blank">ttang2@sdsu.edu</a>>,
<a href="mailto:vp-reproduce-subgroup@lists.simtk.org" target="_blank">vp-reproduce-subgroup@lists.simtk.org</a> <<a href="mailto:vp-reproduce-subgroup@lists.simtk.org" target="_blank">vp-reproduce-subgroup@lists.simtk.org</a>>, James A Glazier <<a href="mailto:jaglazier@gmail.com" target="_blank">jaglazier@gmail.com</a>>,
<a href="mailto:vp-integration-subgroup@lists.simtk.org" target="_blank">vp-integration-subgroup@lists.simtk.org</a> <<a href="mailto:vp-integration-subgroup@lists.simtk.org" target="_blank">vp-integration-subgroup@lists.simtk.org</a>>, John Gennari <<a href="mailto:gennari@uw.edu" target="_blank">gennari@uw.edu</a>>,
Winston Garira <<a href="mailto:Winston.Garira@univen.ac.za" target="_blank">Winston.Garira@univen.ac.za</a>>, Faeder, James R <<a href="mailto:faeder@pitt.edu" target="_blank">faeder@pitt.edu</a>>, Thompson, Robin <<a href="mailto:Robin.N.Thompson@warwick.ac.uk" target="_blank">Robin.N.Thompson@warwick.ac.uk</a>><br>
<b>Subject: </b>Re: [Vp-integration-subgroup] [Vp-reproduce-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript</span></p>
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<p class="x_MsoNormal">Greetings James Faeder,</p>
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<p class="x_MsoNormal">You are the last one that needs to Approve. DISAPPROVE , or ABSTAIN from submission of the paper. </p>
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<p class="x_MsoNormal"> </p>
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<p class="x_MsoNormal">I apologize if you already sent a response yet I have not located any response from you- it may be my error, yet I need your public response before I can continue to submit the paper.</p>
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<p class="x_MsoNormal">17 of us already approved submission and you are the last one on my list.</p>
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<p class="x_MsoNormal">I tried to contact your department in the last few days and left voice messages to your administrators since I could not locate your direct phone. </p>
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<p class="x_MsoNormal">I will really appreciate it if someone can contact you and make sure you get this message.</p>
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<p class="x_MsoNormal">I really hope we get an answer so I can process the paper by thanksgiving weekend.</p>
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<p class="x_MsoNormal"> Jacob</p>
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<p class="x_MsoNormal">On Fri, Nov 19, 2021 at 12:22 AM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>> wrote:</p>
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<p class="x_MsoNormal">Thanks John, Hi James Faedar, </p>
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<p class="x_MsoNormal">John, with your approval below we only need James Faedar to respond so I can proceed. </p>
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<p class="x_MsoNormal">Can someone contact him to make sure he saw this correspondence? He should receive these messages, yet if someone is in contact with him regularly, please ask him to respond so we can move on.</p>
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<p class="x_MsoNormal">One last thing before submission. If there is anyone who thinks this paper should not be published, I would ask them to write to this mailing list publicly - if there is any error or omission that anyone thinks is important, we want to
know about it before submitting the article. This request is public and not targeted at the authors - if there is something we missed, we want to know it before submission.</p>
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<p class="x_MsoNormal">Hopefully James Feedar will respond quickly and there will be no public objection and we can get this paper published quickly.</p>
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<p class="x_MsoNormal"> Jacob</p>
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<p class="x_MsoNormal">On Thu, Nov 18, 2021 at 4:34 PM John Rice <<a href="mailto:john.rice@noboxes.org" target="_blank">john.rice@noboxes.org</a>> wrote:</p>
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<p class="x_MsoNormal" style="margin-bottom:12pt">I approve submission.</p>
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<p class="x_MsoNormal">Typed with two thumbs on my iPhone. (757) 318-0671</p>
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<p class="x_MsoNormal">“Upon this gifted age, in its dark hour,</p>
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<p class="x_MsoNormal">Rains from the sky a meteoric shower</p>
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<p class="x_MsoNormal">Of facts . . . they lie unquestioned, uncombined.</p>
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<p class="x_MsoNormal">Wisdom enough to leech us of our ill</p>
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<p class="x_MsoNormal">Is daily spun; but there exists no loom</p>
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<p class="x_MsoNormal">To weave it into fabric.”</p>
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<p class="x_MsoNormal">–Edna St. Vincent Millay,</p>
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On Nov 17, 2021, at 22:04, Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>> wrote:</p>
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<p class="x_MsoNormal">Hi James Faedar, Hi John Rice,</p>
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<p class="x_MsoNormal">Please check the manuscript and declare by REPLY ALL if you APPROVE, DISAPPROVE or ABSTAIN.</p>
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<p class="x_MsoNormal">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.</p>
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<p class="x_MsoNormal">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. </p>
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<p class="x_MsoNormal">Once I have your answer I can proceed. Hopefully you will both APPROVE quickly.</p>
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<p class="x_MsoNormal"> Jacob</p>
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<p class="x_MsoNormal">On Wed, Nov 17, 2021 at 3:02 PM sheriff <<a href="mailto:sheriff@ebi.ac.uk" target="_blank">sheriff@ebi.ac.uk</a>> wrote:</p>
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<p><span style="font-size:10pt; font-family:Verdana,sans-serif">Hi Jacob and all,</span></p>
<p><span style="font-size:10pt; font-family:Verdana,sans-serif">I approve the submission of the manuscript. </span></p>
<p><span style="font-size:10pt; font-family:Verdana,sans-serif">Please update the citation Tiwari et 2020 Preprint to </span></p>
<p><span style="font-size:10pt; font-family:Verdana,sans-serif">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.</span></p>
<p><span style="font-size:10pt; font-family:Verdana,sans-serif">Also my name and affiliation below</span></p>
<p><span style="font-size:10pt; font-family:Verdana,sans-serif">Rahuman S. <u>Malik Sheriff</u></span></p>
<p><span style="font-size:10pt; font-family:Verdana,sans-serif">European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK</span></p>
<p><span style="font-size:10pt; font-family:Verdana,sans-serif"> </span></p>
<p><span style="font-size:10pt; font-family:Verdana,sans-serif">Thanks for pushing this work forward</span></p>
<p><span style="font-size:10pt; font-family:Verdana,sans-serif">Best regards</span></p>
<p><span style="font-size:10pt; font-family:Verdana,sans-serif">Sheriff</span></p>
<p><span style="font-size:10pt; font-family:Verdana,sans-serif"> </span></p>
<p id="x_gmail-m_5903472748620074431gmail-m_-816442842227439560gmail-m_-1664506982640354478gmail-m_2983802147113687999gmail-m_3056082822452168104gmail-m_5776642796092585345reply-intro">
<span style="font-size:10pt; font-family:Verdana,sans-serif">On 2021-11-17 18:58, Jonathan Karr wrote:</span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">Hi Jacob,
</span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif"> </span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">Thank you again for spearheading this effort.</span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif"> </span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">I approve the submission. I think the paper organizes a variety of important issues toward more credible models, and the content is sound.</span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif"> </span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">My affiliation is Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.</span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif"> </span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">As others have mentioned, I think the paper would be more impactful with further editing to make the paper easier to read:</span></p>
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<ul type="disc">
<li class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">More clearly articulate the goals/motivation for more credible models</span></li><li class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">Be more concise and focused</span></li><li class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">Remove redundancies by grouping related text</span></li><li class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">Fill in the gaps in logic in the introduction with more transitions, less extraneous information, and/or a brief outline.</span></li><li class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">Change the title of the "Utility of models" section to something like "Challenges with using multiscale models" (James' suggestion)</span></li><li class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">Order the "Utility of models" subsections to be easier to follow, perhaps from model construction through to reuse</span></li><li class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">Rephrase the titles of the "Utility of models" subsections to focus on opportunities for improvement rather than current problems</span></li></ul>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">Regards,</span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">Jonathan</span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif"> </span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">On Wed, Nov 10, 2021 at 11:25 PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>> wrote:</span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">Thanks to all contributors who answered,
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif"> </span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">Most contributors approved by now.</span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif"> </span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">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.</span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">To be productive I ask that the following people who did not answer so far take the time to APPROVE, DISAPPROVE, or ABSTAIN.:</span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">Robin Thompson</span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">James R. Faeder</span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">Jonathan Karr<br>
Rahuman Sheriff</span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">John Rice</span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">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. </span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">I hope we can father all support quickly so I can move forward and submit the paper.</span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif"> Jacob</span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">On Tue, Nov 9, 2021 at 5:46 AM William Waites <<a href="mailto:wwaites@ieee.org" target="_blank">wwaites@ieee.org</a>> wrote:</span></p>
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<p class="x_MsoNormal"><span style="font-size:10pt; font-family:Verdana,sans-serif">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>
<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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