<div dir="ltr">I'm fine with Frontiers. <div><br></div><div>My 2 cents is that the revised version would be more likely to get published. I think we should find time to tidy up what we need. </div><div><br></div><div>James</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Aug 10, 2021 at 5:11 PM Tomas Helikar <<a href="mailto:thelikar2@unl.edu">thelikar2@unl.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>Hi everyone,</p>
<p>I'm also fine with this journal. But we need to finalize the revised version -- lots of work was done on it already.</p>
<p>Perhaps we can recirculate the last version of the google doc version of it and set a deadline for finishing it? I don't believe it would take more than a couple of weeks to finalize.</p>
<p>Best wishes,</p>
<p>T.<br>
</p>
<div>
<div style="line-height:16px;margin:6px 0px;padding:8px;border-top:1px dotted rgb(174,177,166);border-bottom:1px dotted rgb(174,177,166);font-size:11px;color:grey">
<font size="2.5px;" color="#0049FF">Tomas Helikar, Ph.D.</font>
<br>
Susan J Rosowski Associate Professor <br>
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<div>On 8/9/21 5:06 PM, John Gennari wrote:<br>
</div>
<blockquote type="cite">
<div><font face="sans-serif" color="#FF6347">Non-NU Email</font>
<hr>
</div>
<p>I agree with Jon Karr. The venue is fine, but we need at least a quick review for readability before submission.</p>
<p>-John G.<br>
</p>
<div>On 8/9/2021 7:49 AM, Jonathan Karr wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi everyone,
<div><br>
</div>
<div>I think Frontiers is fine. I think the key thing is to edit the paper (for focus and readability by a broader audience) before it is submitted to any journal.</div>
<div><br>
</div>
<div>Regards</div>
<div>Jonathan</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, Aug 9, 2021 at 10:31 AM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="auto">Well Marcella,
<div dir="auto"><br>
</div>
<div dir="auto">If there is no objection raised or an alternative resolution with more support appears, then I see no reason not to proceed. So I think we just need to give enough time for original contributors to raise an objection or propose an alternatives
that will gain more support. In the past we used a week for such processes, I guess that if we wait until next weekend and no objection is raised to the venue or an alternative with more support appears we can proceed. We currently have 5 original contributors
supporting your suggested venue and one contributor than joined later in the revisions.</div>
<div dir="auto"><br>
</div>
<div dir="auto"><br>
</div>
<div dir="auto">Note that in submission you should use the original version we reached consensus for submission, yet note that that we plan to revise the work and add more contributors. You can point to revisions we started. </div>
<div dir="auto"><br>
</div>
<div dir="auto">Lets wait until next week and hope no one objects so we can proceed quickly. </div>
<div dir="auto"><br>
</div>
<div dir="auto"> Jacob</div>
<br>
<br>
<div class="gmail_quote" dir="auto">
<div dir="ltr" class="gmail_attr">On Mon, Aug 9, 2021, 08:52 Torres, Marcella <<a href="mailto:mtorres@richmond.edu" target="_blank">mtorres@richmond.edu</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div lang="EN-US">
<div>
<p class="MsoNormal">Once enough contributors agree, the process for submission is that I’ll confirm interest (I just got an email requesting for this this morning), let them know that we intend to submit 1 manuscript and what the proposed title of the manuscript
is. Once that initial information is submitted, then I will be “emailed information about next steps”. Of course, at any point we can also contact the editorial office, but would it be helpful to get a sense of the process first and then ask for clarification
as needed? At what point will we have enough responses from contributors to begin?</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Best,</p>
<p class="MsoNormal">Marcella</p>
<p class="MsoNormal"> </p>
<div style="border-right:none;border-bottom:none;border-left:none;border-top:1pt solid rgb(181,196,223);padding:3pt 0in 0in">
<p class="MsoNormal" style="margin-bottom:12pt"><b><span style="font-size:12pt;color:black">From:
</span></b><span style="font-size:12pt;color:black">Vp-reproduce-subgroup <<a href="mailto:vp-reproduce-subgroup-bounces@lists.simtk.org" rel="noreferrer" target="_blank">vp-reproduce-subgroup-bounces@lists.simtk.org</a>> on behalf of
John Rice <<a href="mailto:john.rice@noboxes.org" rel="noreferrer" target="_blank">john.rice@noboxes.org</a>><br>
<b>Date: </b>Sunday, August 8, 2021 at 7:23 PM<br>
<b>To: </b>Yaling Liu <<a href="mailto:yal310@lehigh.edu" rel="noreferrer" target="_blank">yal310@lehigh.edu</a>><br>
<b>Cc: </b><a href="mailto:vp-reproduce-subgroup@lists.simtk.org" rel="noreferrer" target="_blank">vp-reproduce-subgroup@lists.simtk.org</a> <<a href="mailto:vp-reproduce-subgroup@lists.simtk.org" rel="noreferrer" target="_blank">vp-reproduce-subgroup@lists.simtk.org</a>>,
<a href="mailto:vp-integration-subgroup@lists.simtk.org" rel="noreferrer" target="_blank">
vp-integration-subgroup@lists.simtk.org</a> <<a href="mailto:vp-integration-subgroup@lists.simtk.org" rel="noreferrer" target="_blank">vp-integration-subgroup@lists.simtk.org</a>>, Jonathan Karr <<a href="mailto:jonrkarr@gmail.com" rel="noreferrer" target="_blank">jonrkarr@gmail.com</a>>,
John Gennari <<a href="mailto:gennari@uw.edu" rel="noreferrer" target="_blank">gennari@uw.edu</a>>, Faeder, James R <<a href="mailto:faeder@pitt.edu" rel="noreferrer" target="_blank">faeder@pitt.edu</a>>, Winston
Garira <<a href="mailto:Winston.Garira@univen.ac.za" rel="noreferrer" target="_blank">Winston.Garira@univen.ac.za</a>><br>
<b>Subject: </b>Re: [Vp-reproduce-subgroup] [Vp-integration-subgroup] White paper revision</span></p>
</div>
<div style="border:1pt solid red;padding:2pt">
<p class="MsoNormal" style="background:yellow"><b><span style="font-size:10pt;font-family:Arial,sans-serif;color:red">External Email:</span></b><span style="font-size:10pt;font-family:Arial,sans-serif;color:black"> Use caution in opening links, attachments,
and buying gift cards.</span><span style="font-size:10pt;font-family:Arial,sans-serif"></span></p>
</div>
<p class="MsoNormal"> </p>
<div>
<p class="MsoNormal" style="margin-bottom:12pt">Me too</p>
<div>
<p class="MsoNormal">Typed with two thumbs on my iPhone. (757) 318-0671 </p>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<div>
<p class="MsoNormal">“Upon this gifted age, in its dark hour,</p>
</div>
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<p class="MsoNormal">Rains from the sky a meteoric shower</p>
</div>
<div>
<p class="MsoNormal">Of facts . . . they lie unquestioned, uncombined.</p>
</div>
<div>
<p class="MsoNormal">Wisdom enough to leech us of our ill</p>
</div>
<div>
<p class="MsoNormal">Is daily spun; but there exists no loom</p>
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<p class="MsoNormal">To weave it into fabric.”</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">–Edna St. Vincent Millay,</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
</div>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12pt"><br>
On Aug 8, 2021, at 19:09, Yaling Liu <<a href="mailto:yal310@lehigh.edu" rel="noreferrer" target="_blank">yal310@lehigh.edu</a>> wrote:</p>
</div>
<div>
<p class="MsoNormal"> </p>
<div>
<p class="MsoNormal">I am fine with the suggested new venue and willing to revise further. We don't need to wait for everyone to reply here - this email chain is way too long and guess a lot of people were busy and ignored them.
</p>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Thanks.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Yaling</p>
</div>
</div>
<p class="MsoNormal"> </p>
<div>
<div>
<p class="MsoNormal">On Sun, Aug 8, 2021 at 4:57 PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer" target="_blank">jacob.barhak@gmail.com</a>> wrote:</p>
</div>
<blockquote style="border-top:none;border-right:none;border-bottom:none;border-left:1pt solid rgb(204,204,204);padding:0in 0in 0in 6pt;margin:5pt 0in 5pt 4.8pt">
<div>
<p class="MsoNormal">Thanks Hana, </p>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">The revised version is far from ready to being submitted anywhere. There is just too much to do there to put it in shape for submission. </p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">We do want to advance in making revisions, yet the attempt here is to accelerate the process by asking a 3rd publishing party to provide proper review for what is actually needed for publication, so you may want to save your efforts until
after we get feedback - they will be more effective then when we have feedback. </p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">However, we do need enough support and no objections to proceed to engage with the new venue suggested. </p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">We have currently 3 of the 17 of the original contributors and 1 who joined later that approves of a new venue. Hopefully others will follow so we can proceed quickly. </p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Thank you for the reply. </p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal"> Jacob</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
</div>
<p class="MsoNormal"> </p>
<div>
<div>
<p class="MsoNormal">On Sat, Aug 7, 2021, 23:46 Dobrovolny, Hana <<a href="mailto:h.dobrovolny@tcu.edu" rel="noreferrer" target="_blank">h.dobrovolny@tcu.edu</a>> wrote:</p>
</div>
<blockquote style="border-top:none;border-right:none;border-bottom:none;border-left:1pt solid rgb(204,204,204);padding:0in 0in 0in 6pt;margin:5pt 0in 5pt 4.8pt">
<div>
<div id="gmail-m_-7038258438093066422gmail-m_6686079875447190907m_-6359702125158232037gmail-m_-3222322118285752855m_2418018346964135372divtagdefaultwrapper">
<p><span style="font-size:12pt;color:black">I'm fine with the suggested venue. I'll double check the sections I was heading sometime this week, but I think all suggestions were incorporated last time I checked.</span></p>
<p><span style="font-size:12pt;color:black">Hana</span></p>
<p><span style="font-size:12pt;color:black"> </span></p>
<div id="gmail-m_-7038258438093066422gmail-m_6686079875447190907m_-6359702125158232037gmail-m_-3222322118285752855m_2418018346964135372Signature">
<div name="divtagdefaultwrapper">
<div>
<div>
<p class="MsoNormal"><span style="font-size:10pt;color:black">*******************************************************<br>
Dr. Hana Dobrovolny<br>
Associate Professor of Biophysics<br>
Texas Christian University<br>
TCU Box 298840<br>
Fort Worth, TX 76129<br>
<br>
phone: (817) 257-6379 fax: (817) 257-7742<br>
email: </span><a href="mailto:h.dobrovolny@tcu.edu" rel="noreferrer" target="_blank"><span style="font-size:10pt">h.dobrovolny@tcu.edu</span></a><span style="font-size:10pt;color:black"><br>
*******************************************************</span></p>
</div>
</div>
</div>
</div>
<p class="MsoNormal" style="margin-bottom:12pt"><span style="font-size:12pt;color:black"> </span></p>
<div>
<div class="MsoNormal" style="text-align:center" align="center"><span style="font-size:12pt;color:black">
<hr width="100%" size="0" align="center">
</span></div>
<div id="gmail-m_-7038258438093066422gmail-m_6686079875447190907m_-6359702125158232037gmail-m_-3222322118285752855m_2418018346964135372divRplyFwdMsg">
<p class="MsoNormal"><b><span style="color:black">From:</span></b><span style="color:black"> Vp-reproduce-subgroup <</span><a href="mailto:vp-reproduce-subgroup-bounces@lists.simtk.org" rel="noreferrer" target="_blank">vp-reproduce-subgroup-bounces@lists.simtk.org</a><span style="color:black">>
on behalf of Jacob Barhak <</span><a href="mailto:jacob.barhak@gmail.com" rel="noreferrer" target="_blank">jacob.barhak@gmail.com</a><span style="color:black">><br>
<b>Sent:</b> August 7, 2021 11:18 AM<br>
<b>To:</b> Torres, Marcella<br>
<b>Cc:</b> </span><a href="mailto:vp-reproduce-subgroup@lists.simtk.org" rel="noreferrer" target="_blank">vp-reproduce-subgroup@lists.simtk.org</a><span style="color:black">;
</span><a href="mailto:vp-integration-subgroup@lists.simtk.org" rel="noreferrer" target="_blank">vp-integration-subgroup@lists.simtk.org</a><span style="color:black">; Jonathan Karr; John Gennari; Winston Garira; Faeder, James R<br>
<b>Subject:</b> Re: [Vp-reproduce-subgroup] [Vp-integration-subgroup] White paper revision</span><span style="font-size:12pt;color:black">
</span></p>
<div>
<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
</div>
</div>
<div>
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<div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;font-family:Arial,sans-serif;color:black">And to all white paper contributors,</span><span style="font-size:12pt;color:black">
</span></p>
<div>
<p class="MsoNormal"><span style="font-size:12pt;font-family:Arial,sans-serif;color:black"> </span></p>
</div>
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<p class="MsoNormal"><span style="font-size:12pt;font-family:Arial,sans-serif;color:black">You are getting this message to raise it to the top of your mailboxes. </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;font-family:Arial,sans-serif;color:black"> </span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;font-family:Arial,sans-serif;color:black">Hopefully enough of you will look at this during the weekend to comment on the best way to move forward while considering the new offer from Marcella. </span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;font-family:Arial,sans-serif;color:black"> </span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;font-family:Arial,sans-serif;color:black">The faster we move, the better. </span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;font-family:Arial,sans-serif;color:black"> </span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;font-family:Arial,sans-serif;color:black"> Jacob</span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;font-family:Arial,sans-serif;color:black"> </span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;font-family:Arial,sans-serif;color:black"> </span></p>
</div>
</div>
<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;color:black">On Tue, Aug 3, 2021, 01:03 Jacob Barhak <</span><a href="mailto:jacob.barhak@gmail.com" rel="noreferrer" target="_blank"><span style="font-size:12pt">jacob.barhak@gmail.com</span></a><span style="font-size:12pt;color:black">>
wrote:</span></p>
</div>
<blockquote style="border-top:none;border-right:none;border-bottom:none;border-left:1pt solid rgb(204,204,204);padding:0in 0in 0in 6pt;margin:5pt 0in 5pt 4.8pt">
<div>
<p class="MsoNormal"><span style="font-size:12pt;color:black">Thanks Marcella, </span>
</p>
<div>
<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;color:black">Your suggestion may be the solution here. </span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;color:black">From what I see, this venue is a good fit. Yet we need to learn the opinion of the other contributors. </span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;color:black">If we collect enough support and no contributor objects, we can approach the editor and ask if the paper will receive proper review to guide revisions. </span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;color:black">I look forward for more responses. </span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;color:black"> Jacob</span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
</div>
</div>
<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;color:black">On Mon, Aug 2, 2021, 11:57 Torres, Marcella <</span><a href="mailto:mtorres@richmond.edu" rel="noreferrer" target="_blank"><span style="font-size:12pt">mtorres@richmond.edu</span></a><span style="font-size:12pt;color:black">>
wrote:</span></p>
</div>
<blockquote style="border-top:none;border-right:none;border-bottom:none;border-left:1pt solid rgb(204,204,204);padding:0in 0in 0in 6pt;margin:5pt 0in 5pt 4.8pt">
<div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;color:black">Hi all and Jacob,</span></p>
<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
<p class="MsoNormal"><span style="font-size:12pt;color:black">I’m interested in getting it circulated, and want to propose Frontiers in Systems Biology as a possible venue – I just joined the editorial board and received notice of a focused issue that includes
challenges in multiscale modeling: </span><a href="https://urldefense.com/v3/__https:/www.frontiersin.org/research-topics/24484/insights-in-systems-biology-multiscale-mechanistic-modeling-2021?utm_source=F-RTM&utm_medium=CFP_E1&utm_campaign=PRD_CFP_T1_RT-TITLE*__;Iw!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WFepwnGQ8$" rel="noreferrer" target="_blank"><span style="font-size:12pt">https://www.frontiersin.org/research-topics/24484/insights-in-systems-biology-multiscale-mechanistic-modeling-2021?utm_source=F-RTM&utm_medium=CFP_E1&utm_campaign=PRD_CFP_T1_RT-TITLE#</span></a><span style="font-size:12pt;color:black">
.</span></p>
<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
<p class="MsoNormal"><span style="font-size:12pt;color:black">The journal is new, and I don’t remember it being proposed previously.
</span></p>
<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
<p class="MsoNormal"><span style="font-size:12pt;color:black">I am also willing to prioritize revision and submission and apologize for not participating more over the summer.</span></p>
<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
<p class="MsoNormal"><span style="font-size:12pt;color:black">Best,</span></p>
<p class="MsoNormal"><span style="font-size:12pt;color:black">Marcella</span></p>
<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
<div style="border-right:none;border-bottom:none;border-left:none;border-top:1pt solid rgb(181,196,223);padding:3pt 0in 0in">
<p class="MsoNormal" style="margin-bottom:12pt"><b><span style="font-size:12pt;color:black">From:
</span></b><span style="font-size:12pt;color:black">Vp-reproduce-subgroup <</span><a href="mailto:vp-reproduce-subgroup-bounces@lists.simtk.org" rel="noreferrer" target="_blank"><span style="font-size:12pt">vp-reproduce-subgroup-bounces@lists.simtk.org</span></a><span style="font-size:12pt;color:black">>
on behalf of Jacob Barhak <</span><a href="mailto:jacob.barhak@gmail.com" rel="noreferrer" target="_blank"><span style="font-size:12pt">jacob.barhak@gmail.com</span></a><span style="font-size:12pt;color:black">><br>
<b>Date: </b>Monday, August 2, 2021 at 11:45 AM<br>
<b>To: </b>Alexander Kulesza <</span><a href="mailto:alexander.kulesza@novadiscovery.com" rel="noreferrer" target="_blank"><span style="font-size:12pt">alexander.kulesza@novadiscovery.com</span></a><span style="font-size:12pt;color:black">><br>
<b>Cc: </b></span><a href="mailto:vp-reproduce-subgroup@lists.simtk.org" rel="noreferrer" target="_blank"><span style="font-size:12pt">vp-reproduce-subgroup@lists.simtk.org</span></a><span style="font-size:12pt;color:black"> <</span><a href="mailto:vp-reproduce-subgroup@lists.simtk.org" rel="noreferrer" target="_blank"><span style="font-size:12pt">vp-reproduce-subgroup@lists.simtk.org</span></a><span style="font-size:12pt;color:black">>,
</span><a href="mailto:vp-integration-subgroup@lists.simtk.org" rel="noreferrer" target="_blank"><span style="font-size:12pt">vp-integration-subgroup@lists.simtk.org</span></a><span style="font-size:12pt;color:black"> <</span><a href="mailto:vp-integration-subgroup@lists.simtk.org" rel="noreferrer" target="_blank"><span style="font-size:12pt">vp-integration-subgroup@lists.simtk.org</span></a><s style="font-size:12pt;color:black">>,
Jonathan Karr <<a href="mailto:jonrkarr@gmail.com" rel="noreferrer" target="_blank"><span style="font-size:12pt">jonrkarr@gmail.com</span></a><span style="font-size:12pt;color:black">>, John Gennari <</span><a href="mailto:gennari@uw.edu" rel="noreferrer" target="_blank"><span style="font-size:12pt">gennari@uw.edu</span></a><span style="font-size:12pt;color:black">>,
Faeder, James R <</span><a href="mailto:faeder@pitt.edu" rel="noreferrer" target="_blank"><span style="font-size:12pt">faeder@pitt.edu</span></a><span style="font-size:12pt;color:black">>, Winston Garira <</span><a href="mailto:Winston.Garira@univen.ac.za" rel="noreferrer" target="_blank"><span style="font-size:12pt">Winston.Garira@univen.ac.za</span></a><span style="font-size:12pt;color:black">><br>
<b>Subject: </b>Re: [Vp-reproduce-subgroup] [Vp-integration-subgroup] White paper revision</span></s></p>
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<p class="MsoNormal" style="background:yellow"><b><span style="font-size:10pt;font-family:Arial,sans-serif;color:red">External Email:</span></b><span style="font-size:10pt;font-family:Arial,sans-serif;color:black"> Use caution in opening links, attachments,
and buying gift cards.</span><span style="font-size:12pt;color:black"></span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Hi Alex, </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Thanks for your response first - it is the first public response. </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">However, I was hoping for a discussion rather than a poll. We already made a vote and the direction it took us all ended up badly so far - there is no activity for a few months now. Perhaps a discussion
is in order before making more decisions. </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">And Alex, time is something you manage to achieve certain goals with certain priorities. </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">The real question is if circulating this paper is on a high priority list for any of the contributors?</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Some contributors publicly declared they have little time, yet we were still able to push though in the past. What has changed?</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Perhaps a discussion will reveal those things.</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> Jacob</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">On Mon, Aug 2, 2021 at 2:00 AM Alexander Kulesza <</span><a href="mailto:alexander.kulesza@novadiscovery.com" rel="noreferrer" target="_blank"><span style="font-size:12pt">alexander.kulesza@novadiscovery.com</span></a><span style="font-size:12pt;color:black">>
wrote:</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Dear all, Dear Jacob,
</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">I hope that I speak for many others from this group wishing that the ideas presented in that paper do get circulated; optimally in form of a reviewed paper. </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">I think that the time of the year impedes many of us (including myself) to spend the time needed to edit the sections. </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">I have created the following poll </span><a href="https://urldefense.com/v3/__https:/doodle.com/poll/ydpgvgi594ubi82d?utm_source=poll&utm_medium=link__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WFaV6WX1c$" rel="noreferrer" target="_blank"><span style="font-size:12pt">https://doodle.com/poll/ydpgvgi594ubi82d?utm_source=poll&utm_medium=link</span></a><span style="font-size:12pt;color:black">
which intends to get agreement or disgreement of the group for the different optuions that exist. </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Please let me know what you think.</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Alexander</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">On Thu, 29 Jul 2021 at 16:54, Jacob Barhak <</span><a href="mailto:jacob.barhak@gmail.com" rel="noreferrer" target="_blank"><span style="font-size:12pt">jacob.barhak@gmail.com</span></a><span style="font-size:12pt;color:black">>
wrote:</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Greetings contributors,
</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Two of the contributors approach me about this message privately. However, there were many more who participated and no one responded publicly in 2 weeks. </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Do you not want this paper be circulated? </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">I am asking those questions publicly since this deserves a public discussion.</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Hopefully this reminder will stir up the group.</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> Jacob</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">On Wed, Jul 14, 2021 at 4:46 PM Jacob Barhak <</span><a href="mailto:jacob.barhak@gmail.com" rel="noreferrer" target="_blank"><span style="font-size:12pt">jacob.barhak@gmail.com</span></a><span style="font-size:12pt;color:black">>
wrote:</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Hi Gilberto, </span>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">As you can see, there was no response to your email - in fact the paper writing stopped - I waited sufficient time to make sure this is the case to prove a point. If there is no one to tend to the
editing, then there will not be any progress and the paper will lose focus - partially because people will pull it in many directions and resolution will take time no one is willing to provide to move it forward. And this is what happened here.</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">I remind you that I wrote what needs to be done to make progress. See the 4 points in this archived email:</span></p>
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<p class="MsoNormal"><a href="https://urldefense.com/v3/__https:/lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-May/000098.html__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WFEHRSJVg$" rel="noreferrer" target="_blank"><span style="font-size:12pt">https://lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-May/000098.html</span></a><span style="font-size:12pt;color:black"></span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">By now it's fairly safe to declare that the group failed to fulfil those points in reasonable time, and the revised version is in a worse condition towards publication than the version we all agreed
to submit before. </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">This situation raises the question.</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Is there more benefit from submitting the findings we had before as they were to a 3rd party for publication than waiting for revisions to end? </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">I personally doubt that any further revisions will allow publication in reasonable time - which as I mentioned before delays science rather than advancing it.</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">I assume that this email will start a debate with different opinions, that may take a long time and this is not my intention. My purpose is practical - I am trying to salvage the paper so it gets
published quickly. It is better than waiting forever...</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">I believe that what we accumulated and summarized in a table is worth publication as we agreed before. We did reach a consensus and I hope individuals will realize this is the most practical course
of action.</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Revisions can continue and information added for future versions, yet I do ask that this paper be submitted quickly to a venue that will accept it in the form we agreed upon. </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">If we do not do this, we will be guilty of delaying science. </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Hopefully contributors will realize this and we can proceed to fix the situation quickly.</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> Jacob</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">On Mon, Jun 21, 2021 at 1:06 PM Gilberto Gonzalez-Parra <</span><a href="mailto:gilberto.gonzalezparra@nmt.edu" rel="noreferrer" target="_blank"><span style="font-size:12pt">gilberto.gonzalezparra@nmt.edu</span></a><span style="font-size:12pt;color:black">>
wrote:</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Dear all, </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">I like Eric's idea i.e. "section heads can look at the technical aspects of their respective sections this week."</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">There are many suggestions and I think the section heads can focus in one section to make the work more manageable. Then we can read the whole manuscript to check the consistency of the manuscript.
Overall, I think we can focus on two main ideas. One to point out the challenges of </span><span style="font-size:12pt;font-family:Arial,sans-serif;color:black">Biosimulation Model Reproducibility and Model Integration, and some initial basic ideas to tackle
these issues. That might be the main message of the article (??)</span><span style="font-size:12pt;color:black"></span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Best,</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"><br clear="all">
</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">***************************************************************************</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Gilberto C. Gonzalez-Parra, </span><span>Ph.D in Applied Mathematics.</span><span style="font-size:12pt;color:black"></span></p>
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<p class="MsoNormal"><span>Faculty of the </span><span style="font-size:12pt;color:black">Mathematics Department
</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">New Mexico Tech, NM, USA.</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">****************************************************************************</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">On Mon, Jun 21, 2021 at 8:16 AM Eric Forgoston <</span><a href="mailto:eric.forgoston@montclair.edu" rel="noreferrer" target="_blank"><span style="font-size:12pt">eric.forgoston@montclair.edu</span></a><span style="font-size:12pt;color:black">>
wrote:</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Dear all, </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">It seems that progress has mostly stalled - there are numerous comments/edits that have been suggested and are waiting to be acted upon by the section heads.</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">I suggest a renewed effort over the next week or so: perhaps section heads can look at the technical aspects of their respective sections this week. Then, if interested, I can set up a poll for a
discussion next week that will serve to resolve and finalise any remaining issues.</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Thoughts?</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Best wishes,</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black"> </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Eric<br clear="all">
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<p class="MsoNormal"><span style="font-size:12pt;color:black">---------------------<br>
Dr. Eric Forgoston<br>
Professor of Applied Mathematics<br>
Chair, Department of Applied Mathematics and Statistics<br>
Montclair State University<br>
Montclair, NJ 07043 USA<br>
+1 973 655-7242 <br>
</span><a href="https://urldefense.com/v3/__https:/eric-forgoston.github.io/__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WF1l-OpF0$" rel="noreferrer" target="_blank"><span style="font-size:12pt">https://eric-forgoston.github.io/</span></a><span style="font-size:12pt;color:black"></span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">On Mon, Jun 21, 2021 at 5:54 AM Alexander Kulesza <</span><a href="mailto:alexander.kulesza@novadiscovery.com" rel="noreferrer" target="_blank"><span style="font-size:12pt">alexander.kulesza@novadiscovery.com</span></a><span style="font-size:12pt;color:black">>
wrote:</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Hello all, </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">regarding the manuscript, what is the deadline for contributions? I try to find another slot for a working session this and next week. Please let me know where help is needed in terms of editing. </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">ALexander </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">On Mon, 24 May 2021 at 18:00, John Gennari <</span><a href="mailto:gennari@uw.edu" rel="noreferrer" target="_blank"><span style="font-size:12pt">gennari@uw.edu</span></a><span style="font-size:12pt;color:black">>
wrote:</span></p>
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<p><span style="font-size:12pt;color:black">Eric: </span></p>
<p><span style="font-size:12pt;color:black">Yes, I do see your changes. Thanks!</span></p>
<p><span style="font-size:12pt;color:black">-John G. </span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">On 5/24/2021 4:47 AM, Eric Forgoston wrote:</span></p>
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<p class="MsoNormal" style="margin-bottom:12pt"><span style="font-size:12pt;color:black">Hi Jacob and all,</span></p>
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<p class="MsoNormal" style="margin-bottom:12pt"><span style="font-size:12pt;color:black">I did rewrite the stochastic section adding in material from me and comments from William and James G. The only material I removed had been written by myself originally.</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Additional comments are welcome.</span></p>
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<p class="MsoNormal" style="margin-bottom:12pt"><span style="font-size:12pt;color:black">Cheers,</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Eric<br clear="all">
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<p class="MsoNormal"><span style="font-size:12pt;color:black">---------------------<br>
Dr. Eric Forgoston<br>
Professor of Applied Mathematics<br>
Chair, Department of Applied Mathematics and Statistics<br>
Montclair State University<br>
Montclair, NJ 07043 USA<br>
+1 973 655-7242 <br>
</span><a href="https://urldefense.com/v3/__https:/eric-forgoston.github.io/__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WF1l-OpF0$" rel="noreferrer" target="_blank"><span style="font-size:12pt">https://eric-forgoston.github.io/</span></a><span style="font-size:12pt;color:black"></span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">On Mon, May 24, 2021 at 6:55 AM William Waites <</span><a href="mailto:wwaites@ieee.org" rel="noreferrer" target="_blank"><span style="font-size:12pt">wwaites@ieee.org</span></a><span style="font-size:12pt;color:black">>
wrote:</span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">> Otherwise, all I saw was …<br>
<br>
There was editing of the section on stochasticity by Eric with some input from myself.
<br>
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<p class="MsoNormal"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(35,35,73)">Alexander Kulesza</span><span style="font-size:12pt;color:black"></span></p>
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<p class="MsoNormal"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(35,35,73)">Alexander Kulesza</span><span style="font-size:12pt;color:black"></span></p>
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<pre>_______________________________________________
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