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Update: the manuscript was accepted, and Jacob and I have received an invoice. The acceptance email is copied below:</div>
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Acceptance email copy:</div>
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<blockquote style="margin-top:0;margin-bottom:0"><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">Dear
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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<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">I am
pleased to inform you that your manuscript "Model Integration in Computational Biology: the Role of Reproducibility, Credibility and Utility" has been approved for production and accepted for publication in 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)">
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are being prepared for you to verify before publication. We will also perform final checks to ensure your manuscript meets our criteria for publication (</span><a href="http://links.email.frontiersin.org/ls/click?upn=AAaFa03elZRFPXQ6ShiKwAPsR8oZaO3IEOnZve2aIAWsx1apwBsjG944wpqaUKr3yodx7eEZuuHS6eg2pIQ1vig3q47etShhyRv3y7q5L9peYv31PLstfv8lcz2LY4l3Aeut_B-2Fy9jbSVGoT8qhSwbw0AFtm6DlDsGMQJjIadnFC13-2FJyATqJzBD73VYfuDTc-2F-2BJa2GQAe6lx-2FHbZjn-2F71kv6o6IixqczrgdiPH77O8-2B-2BkhmkDKCINuYgiDYe-2BkgOI85TBxoUrPrhIPoEmFTJ22APZMd5OvPArhiRx5tluYCDV1q7GVCJ9sXxikWD3VW90LNvQRlMuye1lN5-2F9PzQQjn-2FVsZUOx2NhByJcuLAIsAQ9bwChYW9uSDwLhj0ECYwGks-2F" 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)">https://www.frontiersin.org/about/review-system#ManuscriptQualityStandards</a><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">).</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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questions? Please visit our Production Help Center page for more information:<span> </span></span><a href="http://links.email.frontiersin.org/ls/click?upn=AAaFa03elZRFPXQ6ShiKwAYZ6hWsE-2B756OgrJV89Ef3czyG4zquznJAuGCxDlciPm-2FgiGc4AYMnRW2Vlg5ri6r-2BzPQ7Zt3TMURUlbBTxEV8UUhpoezO0IXna9yQfzMZDoROz_B-2Fy9jbSVGoT8qhSwbw0AFtm6DlDsGMQJjIadnFC13-2FJyATqJzBD73VYfuDTc-2F-2BJa2GQAe6lx-2FHbZjn-2F71kv6o6IixqczrgdiPH77O8-2B-2BkhlxhshZYoqXNh-2FoGzKT98QMkVO6Jl0RSX-2BgTCzBeUlT-2BdZvNH-2FoUvmFEW0q6rehlKod3jCttlTuCGctk-2FqMtiZwrpRQ7nR3i6xTpb9M8l50689YjGpD9f4oLg0ky7zHLiw-2BpyauqB4jqHZydNiHJbXs" target="_blank" rel="noopener noreferrer" data-auth="NotApplicable" data-linkindex="1" 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)">https://zendesk.frontiersin.org/hc/en-us/categories/200397292-Article-Production-</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">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">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">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
A. 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">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)">
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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)">
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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> Saturday, January 29, 2022 10:47 PM<br>
<b>To:</b> Ruth Bowness <rb2250@bath.ac.uk><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>
<div> </div>
</div>
<div>
<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>
<br>
<div>
<div dir="ltr">Greetings paper contributors,
<div><br>
</div>
<div>The changes in funding were submitted:</div>
<div><br>
</div>
<div>Below is the message I wrote to the editor.</div>
<div><br>
</div>
<div>Hopefully the paper can be published now.</div>
<div><br>
</div>
<div> Jacob </div>
<div><br>
</div>
<div>####### Copy of message to the editor #####</div>
<div>
<p>Thanks Shayn,</p>
<p> </p>
<p>The group updated funding sources for 2 more individuals - apologies for the delay, yet it's a large group. I appreciate the patience - this delay helps get things in order. </p>
<p> </p>
<p>Also, one more author noticed that his name is not properly written and I corrected it in the text - yet it needs to be corrected in the system. . </p>
<p>Gilberto Gonzalez-Parra is the proper name of the author - with a hyphen between Gonzalez and Parra - Apparently I added his name improperly to the submission system and the system does not allow me to edit this.</p>
<p>I also remind you that William Waites has 2 affiliations as I mentioned in my previous message - I cannot add his second affiliation to the system - the authors list is grayed out. <br>
</p>
<p> </p>
<p>The changes to funding were added and the revised manuscript with proper funding information was uploaded.</p>
<p> </p>
<p>Please proceed with the process. I hope you find it all in order and ready for publication.</p>
<p> </p>
<p> Jacob</p>
</div>
</div>
<br>
<div class="x_gmail_quote">
<div dir="ltr" class="x_gmail_attr">On Thu, Jan 27, 2022 at 9:28 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">Ok Ruth, And the rest of the contributors please pay attention,
<div><br>
</div>
<div>You will find your support acknowledged now. </div>
<div><br>
</div>
<div>The link to the manuscript draft is: </div>
<div><a href="https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing" target="_blank">https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing</a><br>
</div>
<div><br>
</div>
<div>Here are some observations.</div>
<div><br>
</div>
<div>From 18 authors, 4 declared funding - this means that they were working using taxpayer money on this paper rather than volunteering their time and therefore need to report it:</div>
<div>Jonathan Karr . William Waites, Rahuman S. Malik Sheriff, and Ruth Bowness. <br>
</div>
<div>One Author declared conflict of interest - Jacob Barhak</div>
<div><br>
</div>
<div>James A. Glazier mentioned funding from multiple sources fron NSF/NIH yet later agreed to leave those out - if this is correct, James volunteered his own time towards work on this paper. James - correct me if I am wrong - since if you plan to report this
paper in the summary reports for those grants, we must include those grants in the paper which will mean you used taxpayer funds towards this work. So far I am leaving those out since it seems unlikely that multiple grants supported this work and you withdrew
your request after my query.<br>
</div>
<div><br>
</div>
<div>If this is correct, this means that the rest 12 (13 if we count James) are volunteers that have not been paid or have any financial interest in this work.<br>
</div>
<div><br>
</div>
<div>I will wait until the end of Friday 1/27 before uploading a final version to the submission system and notify the editor. I hope my analysis above is correct and there are no more last minute changes - we had over a year to put those changes in and had
multiple approval rounds - hopefully we are really done with this paper and can move forward to other endeavors.</div>
<div><br>
</div>
<div> Jacob</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
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<div class="x_gmail_quote">
<div dir="ltr" class="x_gmail_attr">On Thu, Jan 27, 2022 at 3:54 AM Ruth Bowness <<a href="mailto:rb2250@bath.ac.uk" target="_blank">rb2250@bath.ac.uk</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 lang="EN-GB">
<div>
<p class="x_MsoNormal"><span style="font-size:11pt">Hi Jacob<u></u><u></u></span></p>
<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
<p class="x_MsoNormal"><span style="font-size:11pt">If I can still add my fellowship funding that would be great. I actually thought I had sent this info to you earlier but can’t find the e-mail in my sent mail so apologies for this late edition! Not sure of
the exact format of the funding acknowledgments for this journal but could you add that
</span><span style="font-size:11pt">I was </span><span style="font-size:11pt">supported by a fellowship funded by the
<span style="color:rgb(0,127,170)">Medical Research Council </span>[grant number <span style="color:rgb(0,127,170)">
MR/P014704/1</span>]</span><span style="font-size:8pt; font-family:Gulliver,serif">.</span><span style="font-size:11pt"><br>
<br>
<u></u><u></u></span></p>
<p class="x_MsoNormal"><span style="font-size:11pt">Many thanks<br>
Ruth<u></u><u></u></span></p>
<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
<div>
<div>
<p class="x_MsoNormal"><b><span style="font-size:9pt; font-family:Verdana,sans-serif; color:rgb(127,127,127)">Dr Ruth Bowness</span></b><span style="font-size:12pt; color:black"><u></u><u></u></span></p>
<p class="x_MsoNormal"><b><span style="font-size:9pt; font-family:Verdana,sans-serif; color:rgb(127,127,127)">Lecturer & MRC Research Fellow</span></b><span style="font-size:12pt; color:black"><u></u><u></u></span></p>
<p class="x_MsoNormal"><span style="font-size:10.5pt; color:rgb(127,127,127)">Department of Mathematical Sciences</span><span style="font-size:12pt; color:black"><u></u><u></u></span></p>
<p class="x_MsoNormal"><span style="font-size:9pt; font-family:Verdana,sans-serif; color:rgb(127,127,127)">University of Bath</span><span style="font-size:12pt; color:black"><u></u><u></u></span></p>
<p class="x_MsoNormal"><span style="font-size:10.5pt; color:rgb(127,127,127)"> </span><span style="font-size:12pt; color:black"><u></u><u></u></span></p>
<p class="x_MsoNormal"><span style="font-size:9pt; font-family:Verdana,sans-serif; color:rgb(121,121,121)">E-mail:</span><span style="font-size:9pt; font-family:Verdana,sans-serif; color:rgb(4,50,255)"> </span><span style="font-size:9pt; font-family:Verdana,sans-serif; color:rgb(0,112,192)"><a href="mailto:rb2250@bath.ac.uk" target="_blank"><span style="color:rgb(0,112,192)">rb2250@bath.ac.uk</span></a></span><span style="font-size:12pt; color:black"><u></u><u></u></span></p>
<p class="x_MsoNormal"><span lang="EN-US" style="font-size:9pt; font-family:Verdana,sans-serif; color:rgb(121,121,121)">Website: </span><u><span lang="EN-US" style="font-size:9pt; font-family:Verdana,sans-serif; color:rgb(0,112,192)"><a href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fruthbowness.com%2F&data=04%7C01%7Crb2250%40bath.ac.uk%7C591572838bf74aeb2de108d97776c932%7C377e3d224ea1422db0ad8fcc89406b9e%7C0%7C0%7C637672174320173922%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=UBXYb3UzAIxJJHcD3uPWsot4LOpTTuIlVOZFNfPLbz8%3D&reserved=0" title="Original URL:
https://ruthbowness.com/
Click to follow link." target="_blank"><span style="color:rgb(0,112,192)">https://ruthbowness.com</span></a></span></u><span style="font-size:12pt; color:black"><u></u><u></u></span></p>
<p class="x_MsoNormal"><span style="font-size:9pt; font-family:Verdana,sans-serif; color:rgb(121,121,121)">Twitter:</span><span style="font-size:9pt; color:rgb(4,50,255)"> </span><span lang="EN-US" style="font-size:10.5pt; color:rgb(0,112,192)"><a href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.com%2FRuthBowness&data=04%7C01%7Crb2250%40bath.ac.uk%7C591572838bf74aeb2de108d97776c932%7C377e3d224ea1422db0ad8fcc89406b9e%7C0%7C0%7C637672174320173922%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=KgWid3T4fEBEh9BMHmytt2%2FBuHhBWdNhsapbYIG1EBE%3D&reserved=0" title="Original URL:
https://twitter.com/RuthBowness
Click to follow link." target="_blank"><span style="font-size:9pt; font-family:Verdana,sans-serif; color:rgb(0,112,192)">@RuthBowness</span></a></span><span style="font-size:12pt; color:black"><u></u><u></u></span></p>
<p class="x_MsoNormal"><span style="font-size:9pt; font-family:Verdana,sans-serif; color:rgb(127,127,127)"> </span><span style="font-size:12pt; color:black"><u></u><u></u></span></p>
<p class="x_MsoNormal"><i><span style="font-size:11pt; color:rgb(118,113,113)">Please note that I work part-time hours, usually Monday-Wednesday.<u></u><u></u></span></i></p>
<p class="x_MsoNormal"><i><span style="font-size:11pt; color:rgb(118,113,113)"> </span></i><span style="font-size:12pt; color:black"><u></u><u></u></span></p>
<p class="x_MsoNormal"><i><span style="font-size:11pt; color:rgb(118,113,113)">As I work flexible hours, you may receive this e-mail at a time outside the hours of a ‘normal’ working day. Please be assured that I respect your working pattern and look forward
to your response when it is reasonable for you to reply. <u></u><u></u></span></i></p>
<p class="x_MsoNormal"><i><span style="font-size:11pt; color:rgb(118,113,113)"><u></u> <u></u></span></i></p>
<p class="x_MsoNormal"><a href="https://www.bath.ac.uk/topics/wellbeing/" target="_blank"><span style="font-size:12pt; color:black; text-decoration:none"><img border="0" width="114" height="114" id="x_gmail-m_3507415694907395065gmail-m_-2280567288883846918Picture_x0020_3" alt="A picture containing logo
Description automatically generated" style="width:1.1875in; height:1.1875in" data-outlook-trace="F:1|T:1" src="cid:17e9ea16f4c4ce8e91"></span></a><span style="font-size:12pt; color:black"><u></u><u></u></span></p>
<p class="x_MsoNormal"><span style="font-size:11pt; color:black"> </span><span style="font-size:11pt"> </span><span style="font-size:12pt; color:black"><u></u><u></u></span></p>
</div>
</div>
<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
<p class="x_MsoNormal"><span style="font-size:11pt"><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 0cm 0cm">
<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">Vp-integration-subgroup <<a href="mailto:vp-integration-subgroup-bounces@lists.simtk.org" target="_blank">vp-integration-subgroup-bounces@lists.simtk.org</a>> on behalf of Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>><br>
<b>Date: </b>Thursday, 27 January 2022 at 01:49<br>
<b>To: </b>Torres, Marcella <<a href="mailto:mtorres@richmond.edu" target="_blank">mtorres@richmond.edu</a>><br>
<b>Cc: </b><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 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>><br>
<b>Subject: </b>Re: [Vp-integration-subgroup] [Vp-reproduce-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript<u></u><u></u></span></p>
</div>
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<p class="x_MsoNormal"><strong><span style="font-size:11pt; font-family:"Helvetica Neue"; color:black">CAUTION:
</span></strong><span style="font-size:11pt; font-family:"Helvetica Neue"; color:black"> This email came from outside of the University. To keep your account safe, only click on links and open attachments if you know the person who sent the email, or you expected
to receive this communication.</span><span style="font-size:11pt; font-family:"Helvetica Neue""><u></u><u></u></span></p>
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<p> <u></u><u></u></p>
</div>
<div>
<div>
<p class="x_MsoNormal"><span style="font-size:11pt">Thanks Marcella, and all paper contributors, please pay attention
<u></u><u></u></span></p>
<div>
<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:11pt">It has been a week since the message sent to the group.<u></u><u></u></span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:11pt">So far no one has responded with any changes in funding sources or conflict of interest.<u></u><u></u></span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:11pt">So again, if anyone was funded by a source that requires recognition to do this work, please let me know by friday so we can correct it. <u></u><u></u></span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:11pt">Also, again, if anyone has an objection to this paper being made public, it is the last chance to do so.<u></u><u></u></span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:11pt">Otherwise I will send a letter to the editor that the group is ok with the current version over the weekend and hopefully it gets published quickly.<u></u><u></u></span></p>
</div>
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<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"> Jacob<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">On Wed, Jan 26, 2022, 18:12 Torres, Marcella <<a href="mailto:mtorres@richmond.edu" target="_blank">mtorres@richmond.edu</a>> wrote:<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:12pt; color:black">Email from Frontiers and question from the editor shared below:<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:12pt; color:black"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11.5pt; font-family:"Segoe UI",sans-serif; color:rgb(32,31,30); background:white">Dear Dr Torres,</span><span style="font-size:12pt; color:black"><br>
</span><span style="font-size:11.5pt; font-family:"Segoe UI",sans-serif; color:rgb(32,31,30)"><br>
<span style="background:white">Frontiers in Systems Biology Editorial Office has sent you a message. Please click 'Reply' to send a direct response</span><br>
<br>
<span style="background:white">New 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>
</span><span style="font-size:12pt; color:black"><a href="https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flinks.email.frontiersin.org%2Fls%2Fclick%3Fupn%3D99YMbkkQ8WNJiHLectmHSn5XnTmYe57aPeiziTpYNtyfClFbQqFlwPq2nUMZBzQ7srQvkLkPbc-2F-2BZbZ-2BczlOsPrTMbzmmMktcODsIp2h-2Ffj90r8fRFX2WoaacyAq0r1DpdlwAI9E7tBq-2Fy-2F2Oci2ve-2FCfkFNdVsmiG1bos-2FvnrU-3DZcy-_B-2Fy9jbSVGoT8qhSwbw0AFtm6DlDsGMQJjIadnFC13-2FJyATqJzBD73VYfuDTc-2F-2BJaJPaJJ5oSKrMDAr6Ompo1c21QYWQoQgYfAYNEjVnB244sSGd8-2BEkyma7zMD5B9L6sx2V7r1JTwJYDZpx5bqIUznnbkYmAKXcibTaFF47hgopNpnsrFZkqBi6O6g8b4EiWw24vVRZnhel591eZQKRdrLT3faq2B-2F0DXCpdcIRO-2FjNMfVBXwcpPniAJnsg8Tlmf&data=04%7C01%7Crb2250%40bath.ac.uk%7C2c3f8a4a29544a88f66008d9e13720f7%7C377e3d224ea1422db0ad8fcc89406b9e%7C0%7C0%7C637788449875266880%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=DkMHU9x7U%2BkZegrOZlQunH27aiRH%2F5AnZR%2F%2FLBdht48%3D&reserved=0" target="_blank"><span style="font-size:11.5pt; font-family:"Segoe UI",sans-serif; background:white">http://www.frontiersin.org/Review/EnterReviewForum.aspx?activationno=ba15539e-1784-4ed3-9969-2aacb1b5b835</span></a></span><span style="font-size:11.5pt; font-family:"Segoe UI",sans-serif; color:rgb(32,31,30)"><br>
<br>
<span style="background:white">Journal: Frontiers in Systems Biology, section Multiscale Mechanistic Modeling</span><br>
<span style="background:white">Article type: Review</span><br>
<span style="background:white">Manuscript title: Model Integration in Computational Biology: the Role of Reproducibility, Credibility and Utility</span><br>
<span style="background:white">Manuscript ID: 822606</span><br>
<span style="background:white">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>
<span style="background:white">Submitted on: 26 Nov 2021</span><br>
<span style="background:white">Edited by: Shayn Peirce-Cottler</span><br>
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<span style="background:white">Research Topic: Insights in Systems Biology: Multiscale Mechanistic Modeling 2021</span><br>
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<span style="background:white">Best regards,</span><br>
<br>
<span style="background:white">Your Frontiers in Systems Biology team</span><br>
<br>
<span style="background:white">Frontiers in Systems Biology Editorial Office</span><br>
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<p class="x_MsoNormal"><span style="font-size:12pt; color:black"><img border="0" width="32" height="32" id="x_gmail-m_3507415694907395065gmail-m_-2280567288883846918_x0000_i1026" style="width:0.3333in; height:0.3333in"></span><span style="font-size:11pt"><u></u><u></u></span></p>
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<p class="x_MsoNormal" style="background:white"><span style="font-size:10.5pt; color:rgb(32,31,30)">Marcella Torres, Ph.D.<u></u><u></u></span></p>
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<p class="x_MsoNormal" style="background:white"><span style="font-size:10.5pt; color:rgb(32,31,30)">Director of Mathematical Studies<u></u><u></u></span></p>
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<p class="x_MsoNormal" style="background:white"><span style="font-size:10.5pt; color:rgb(32,31,30)">University of Richmond<u></u><u></u></span></p>
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<p class="x_MsoNormal" style="background:white"><span style="font-size:10.5pt; color:rgb(32,31,30)">Jepson Hall Room 212<u></u><u></u></span></p>
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<p class="x_MsoNormal" style="background:white"><span style="font-size:10.5pt; color:rgb(32,31,30)">221 Richmond Way<u></u><u></u></span></p>
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<p class="x_MsoNormal" style="background:white"><span style="font-size:10.5pt; color:rgb(32,31,30)">Richmond, VA 23173<u></u><u></u></span></p>
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<p class="x_MsoNormal" style="background:white"><span style="font-size:10.5pt; color:rgb(32,31,30)">(804) 289-8081<u></u><u></u></span></p>
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<p class="x_MsoNormal" style="background:white"><span style="font-size:10.5pt; color:rgb(32,31,30)">Pronouns: she/her<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:12pt; color:black"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><b><span style="font-size:11pt; color:black">From:</span></b><span style="font-size:11pt; color:black"> Vp-reproduce-subgroup <<a href="mailto:vp-reproduce-subgroup-bounces@lists.simtk.org" target="_blank">vp-reproduce-subgroup-bounces@lists.simtk.org</a>>
on behalf of Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>><br>
<b>Sent:</b> Wednesday, January 19, 2022 10:24 PM<br>
<b>To:</b> James Glazier <<a href="mailto:jaglazier@gmail.com" target="_blank">jaglazier@gmail.com</a>><br>
<b>Cc:</b> <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>>;
<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>><br>
<b>Subject:</b> Re: [Vp-reproduce-subgroup] [Vp-integration-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript</span><span style="font-size:11pt">
<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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<p class="x_MsoNormal" style="background:yellow"><b><span style="font-family:Arial,sans-serif; color:red">External Email:</span></b><span style="font-family:Arial,sans-serif; color:black"> Use caution in opening links, attachments, and buying gift cards.</span><span style="font-family:Arial,sans-serif"><u></u><u></u></span></p>
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<p>Hi James,<u></u><u></u></p>
<p><u></u> <u></u></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. <u></u><u></u></p>
<p><u></u> <u></u></p>
<p>Hopefully no other changes will be raised by contributors and we can proceed as approved by all authors. <u></u><u></u></p>
<p><u></u> <u></u></p>
<p> Jacob<u></u><u></u></p>
<p><u></u> <u></u></p>
<p><u></u> <u></u></p>
<p>####### Letter to the editor sent in submission system ########<u></u><u></u></p>
<p> <u></u><u></u></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:<u></u><u></u></p>
<p>James A. Glazier<u></u><u></u></p>
<p> <u></u><u></u></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:<u></u><u></u></p>
<p><a href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.simtk.org%2Fpipermail%2Fvp-integration-subgroup%2F2022-January%2F000388.html&data=04%7C01%7Crb2250%40bath.ac.uk%7C2c3f8a4a29544a88f66008d9e13720f7%7C377e3d224ea1422db0ad8fcc89406b9e%7C0%7C0%7C637788449875266880%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=8TwYHyKVg%2FhxpjxluM8NwOgMlGCwM%2Fb%2B%2F7WFM3ukRNo%3D&reserved=0" target="_blank">https://lists.simtk.org/pipermail/vp-integration-subgroup/2022-January/000388.html</a><u></u><u></u></p>
<p>Hopefully no other changes are necessary. <u></u><u></u></p>
<p> <u></u><u></u></p>
<p>Thank you for handling this manuscript.<u></u><u></u></p>
<p> <u></u><u></u></p>
<p> Jacob<u></u><u></u></p>
<p> <u></u><u></u></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">On Wed, Jan 19, 2022 at 9:05 PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>> wrote:<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">Thanks James, and all other paper contributors, please read this. <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">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:<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"><a href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.simtk.org%2Fpipermail%2Fvp-integration-subgroup%2F2021-April%2F000073.html&data=04%7C01%7Crb2250%40bath.ac.uk%7C2c3f8a4a29544a88f66008d9e13720f7%7C377e3d224ea1422db0ad8fcc89406b9e%7C0%7C0%7C637788449875266880%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=haAlRb891OoZ7eyfMKeHw8exrVXjHcjqTLs2of2kPk4%3D&reserved=0" target="_blank">https://lists.simtk.org/pipermail/vp-integration-subgroup/2021-April/000073.html</a><u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">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. <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">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. <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">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://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.frontiersin.org%2Fabout%2Fpolicies-and-publication-ethics&data=04%7C01%7Crb2250%40bath.ac.uk%7C2c3f8a4a29544a88f66008d9e13720f7%7C377e3d224ea1422db0ad8fcc89406b9e%7C0%7C0%7C637788449875266880%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=dpN%2BWhoOTtUH78QTv21RpSqlB7ZChnXAMZTD4ZXEy2Q%3D&reserved=0" target="_blank">https://www.frontiersin.org/about/policies-and-publication-ethics</a><u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">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.<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">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. <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">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. <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">Hopefully I am clear enough now. <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">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.<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">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.<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">Hopefully this email will fix things and make sure our delerations are accurate. <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"> Jacob<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">On Wed, Jan 19, 2022 at 12:31 PM James Glazier <<a href="mailto:jaglazier@gmail.com" target="_blank">jaglazier@gmail.com</a>> wrote:<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">Dear Jacob: <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">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.<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">JAG<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">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:<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">Well James, <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">You put me is a difficult position. You all approved the manuscript multiple times. <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">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.<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">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.<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">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.<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">So I ask you on what should I do.<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">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.<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">Hopefully this will settle the matter.<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"> Jacob<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">On Wed, Jan 19, 2022, 11:15 James A Glazier <<a href="mailto:jaglazier@gmail.com" target="_blank">jaglazier@gmail.com</a>> wrote:<u></u><u></u></span></p>
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<p>Dear Jacob:<u></u><u></u></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:<u></u><u></u></p>
<p>James A. Glazier acknowledges funding support from grants NSF 188553, NSF 186890, NSF 1720625, NIH U24 EB028887 and NIH R01 GM122424.<u></u><u></u></p>
<p>JAG<u></u><u></u></p>
<p><u></u> <u></u></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">On 11/17/2021 10:04 PM, Jacob Barhak wrote:<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">Hi James Faedar, Hi John Rice,
<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<div>
<p class="x_MsoNormal"><span style="font-size:11pt">Please check the manuscript and declare by REPLY ALL if you APPROVE, DISAPPROVE or ABSTAIN.<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<div>
<p class="x_MsoNormal"><span style="font-size:11pt">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.<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">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. <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">Once I have your answer I can proceed. Hopefully you will both APPROVE quickly.<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"> Jacob<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">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:<u></u><u></u></span></p>
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<p><span style="font-size:10pt; font-family:Verdana,sans-serif">Hi Jacob and all,<u></u><u></u></span></p>
<p><span style="font-size:10pt; font-family:Verdana,sans-serif">I approve the submission of the manuscript. <u></u><u></u></span></p>
<p><span style="font-size:10pt; font-family:Verdana,sans-serif">Please update the citation Tiwari et 2020 Preprint to <u></u><u></u></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.<u></u><u></u></span></p>
<p><span style="font-size:10pt; font-family:Verdana,sans-serif">Also my name and affiliation below<u></u><u></u></span></p>
<p><span style="font-size:10pt; font-family:Verdana,sans-serif">Rahuman S. <u>Malik Sheriff</u><u></u><u></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<u></u><u></u></span></p>
<p><span style="font-size:10pt; font-family:Verdana,sans-serif"><u></u> <u></u></span></p>
<p><span style="font-size:10pt; font-family:Verdana,sans-serif">Thanks for pushing this work forward<u></u><u></u></span></p>
<p><span style="font-size:10pt; font-family:Verdana,sans-serif">Best regards<u></u><u></u></span></p>
<p><span style="font-size:10pt; font-family:Verdana,sans-serif">Sheriff<u></u><u></u></span></p>
<p><span style="font-size:10pt; font-family:Verdana,sans-serif"><u></u> <u></u></span></p>
<p id="x_gmail-m_3507415694907395065gmail-m_-2280567288883846918m_-1175316458943692426x_gmail-m_5192713649370760036gmail-m_-2570967256091897635gmail-m_-3522333716438701893m_-6210025431876839483gmail-m_5776642796092585345reply-intro">
<span style="font-size:10pt; font-family:Verdana,sans-serif">On 2021-11-17 18:58, Jonathan Karr wrote:<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif">Hi Jacob, <u>
</u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif"> <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif">Thank you again for spearheading this effort.<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif"> <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="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.<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif"> <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="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.<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif"> <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="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:<u></u><u></u></span></p>
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<ul type="disc">
<li class="x_MsoNormal"><span style="font-family:Verdana,sans-serif">More clearly articulate the goals/motivation for more credible models<u></u><u></u></span></li><li class="x_MsoNormal"><span style="font-family:Verdana,sans-serif">Be more concise and focused<u></u><u></u></span></li><li class="x_MsoNormal"><span style="font-family:Verdana,sans-serif">Remove redundancies by grouping related text<u></u><u></u></span></li><li class="x_MsoNormal"><span style="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.<u></u><u></u></span></li><li class="x_MsoNormal"><span style="font-family:Verdana,sans-serif">Change the title of the "Utility of models" section to something like "Challenges with using multiscale models" (James' suggestion)<u></u><u></u></span></li><li class="x_MsoNormal"><span style="font-family:Verdana,sans-serif">Order the "Utility of models" subsections to be easier to follow, perhaps from model construction through to reuse<u></u><u></u></span></li><li class="x_MsoNormal"><span style="font-family:Verdana,sans-serif">Rephrase the titles of the "Utility of models" subsections to focus on opportunities for improvement rather than current problems<u></u><u></u></span></li></ul>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif">Regards,<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif">Jonathan<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="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:<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif">Thanks to all contributors who answered,
<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif"> <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif">Most contributors approved by now.<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif"> <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="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.<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif"> <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="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.:<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif">Robin Thompson<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif">James R. Faeder<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif">Jonathan Karr<br>
Rahuman Sheriff<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif">John Rice<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif"> <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="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. <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif"> <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif">I hope we can father all support quickly so I can move forward and submit the paper.<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif"> <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif"> Jacob<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif"> <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-family:Verdana,sans-serif"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="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:<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="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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<p><span style="font-size:10pt; font-family:Verdana,sans-serif"><u></u> <u></u></span></p>
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<pre>-- <u></u><u></u></pre>
<pre>James A. Glazier, PhD<u></u><u></u></pre>
<pre>Professor of Intelligent Systems Engineering, Adjunct Professor of Physics<u></u><u></u></pre>
<pre>Director, Biocomplexity Institute<u></u><u></u></pre>
<pre>Indiana University, Bloomington<u></u><u></u></pre>
<pre>(812) 391-2159 (cell)<u></u><u></u></pre>
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<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">-- <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">James A. Glazier, PhD <u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">Professor of Intelligent Systems Engineering, Adjunct Professor of Physics<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">Director Biocomplexity Institute<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">Indiana University, Bloomington<u></u><u></u></span></p>
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<p class="x_MsoNormal"><span style="font-size:11pt">(812) 391-2159<u></u><u></u></span></p>
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