<div dir="ltr">Thanks James, Thanks Hana,<div><br></div><div>If ok with you I I will just change the abbreviation since adding another department may confuse the journal as happened before with William who has 2 affiliations. I am trying to simplify things. I even dropped my request to change predict to project/forecast, just because it adds more places where we can make mistakes. I don't like the term predict, yet I will live with it - I should have caught this before. </div><div><br></div><div>Hana, I will change the reference as you requested.</div><div><br></div><div>Unless anyone stops me before with another change I will send the proofs below in 4 hours to the Journal. This time I will not request additional proofs - its good enough,</div><div><br></div><div>Thank you all for your help.</div><div><br></div><div> Jacob</div><div><br></div><div><br></div><div><br></div><div>########## Final proofs to be sent #############</div><div><br></div><div>Page 1: Lines 78-89 Affiliations need correction and standardization:<br><br>2. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom<br>should be<br>Rahuman S. Malik-Sheriff, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, UK<br>Add Hinxton and change Cambridge to Cambridgeshire<br><br>3 School of Mathematics and Statistics, University of Melbourne, VIC, Parkville, Australia<br>should be<br>School of Mathematics and Statistics, University of Melbourne, Parkville, VIC, Australia<br>Parkville, VIC should be switched in order<br><br>12 Department of Mathematics and Computer Science, University of Richmond, Richmond, CA, United States<br>should be:<br>Department of Mathematics and Computer Science, University of Richmond, Richmond, VA, United States<br>CA should be VA<br><br>17 Biocomplexity Institute, Indiana University, Bloomington, IND, United States,<br>should be:<br>Biocomplexity Institute, Indiana University, Bloomington, IN, United States,<br>IN Instead of IND since we are using postal abbreviations for all US states<br><br><br><br><br><br>The reference <br><br>Cresta, D., Warren, D. C., Quirouette, C., Smith, A. P., Lane, L. C., Smith, A. M.,<br>et al. (2021). Time to Revisit the Endpoint Dilution Assay and to Replace<br>TCID$_{50}$ and PFU as Measures of a Virus Sample’s Infection<br>Concentration. arXiv:2101.11526 [q-bio]. Available at: <a href="http://arxiv.org/abs/">http://arxiv.org/abs/</a><br>2101.11526 (Accessed October 24, 2021).<br><br>consider changing to:<br><br>Cresta D., Warren D.C., Quirouette C., Smith A.P., Lane L.C., Smith AM, et al. (2021) Time to revisit the endpoint dilution assay and to replace the TCID50 as a measure of a virus sample’s infection concentration. PLoS Comput Biol 17(10): e1009480. <a href="https://doi.org/10.1371/journal.pcbi.1009480">https://doi.org/10.1371/journal.pcbi.1009480</a><br><br><br>TCID$_{50}$ should be subscript for the number also the preprint was published and we provided the proper DOI<br><br><br><br><br>Page 5 - Line 566 <br>fullfills<br><br>should be <br>fulfills<br><br>There are 3 l's the last occurrence double l not 4. Apologies 0 this was a mistake in the last proofs we provided. Please spell check the word and use the American English version.<br><br><br><br><br><br>Page 3 - Line 306<br>Please consider instead of<br>"Therefore we address many issues at lower..."<br>consider:<br>"Therefore, we address many issues at lower..."<br>We ask to consider adding comma after "Therefore" so<br><br><br><br><br>Pages 3-4:<br>Line 341 - 344, please replace 3 hyphens with large hyphens with spaces around them - the hyphens should have been a perpetrator not a connector between words: i.e. <br>"<br>The “promise of<br>modeling” should be fulfilled already, yet we find modelers<br>consistently unable to reproduce basic steps–thus stagnating<br>instead of innovating, or even worse–backtracking progress.<br>The numbers quoted above cannot be ignored or claimed as being<br>normal–thus the term crisis is used.<br>"<br><br>should become:<br><br>"<br>The promise of<br>modeling” should be fulfilled already, yet we find modelers<br>consistently unable to reproduce basic steps - thus stagnating<br>instead of innovating, or even worse - backtracking progress.<br>The numbers quoted above cannot be ignored or claimed as being<br>normal - thus the term crisis is used.<br>"<br>Alternatively, if preferred. just replaces the 3 hyphens with commas to create the separation<br><br><br><br><br>Page 4 line 401 -<br>Again the hyphen represents separation, so please add spaces around them and use a large hyphen. So that <br>"not approved and tested for the anticipated use–because of the"<br>becomes:<br>"not approved and tested for the anticipated use - because of the"<br>alternatively replace with commas around the hyphen to indicate separation instead of the hyphens <br><br><br><br>Page 5 line 519 -<br><br>Again, hyphens are supposed to separate no connect here. i.e.:<br>"<br>While guidelines and concepts of how to establish credibility<br>of models–even for critical applications–do exist, the field is still<br>"<br>should become<br>"<br>While guidelines and concepts of how to establish credibility<br>of models - even for critical applications - do exist, the field is still<br>"<br>Please use a large hyphen or alternatively use commas instead of the hyphens<br><br><br><br><br><br>Page 7 line 768<br>"<br>Fortunately there are standardization efforts among<br>languages.<br>"<br><br>should be <br><br>"<br>Fortunately, there are standardization efforts among<br>languages.<br>"<br>Thus adding a comma.<br><br><br><br><br>Page 8 line 868-869<br><br>Please link this citation to the first reference in the references list:<br><br>"(About using a multi-scale mortality model in<br>the ensemble, Online)"<br><br>It is a link to a discussion - if needed, remove the word Online at the end - yet this is a reference and not just a comment in parenthesis<br><br><br><br><br>Page 9 line 922:<br>please add spaces around the large hyphen<br>"<br>Sometimes models are used (and published) without<br>specifying the units used for simulation parameters—this is a<br>practice that needs to be corrected.<br>"<br>should be:<br>Sometimes models are used (and published) without<br>specifying the units used for simulation parameters — this is a<br>practice that needs to be corrected.<br><br>Alternatively use a comma instead - the hyphen is intended for explanation separating sentences, not connecting words.<br><br> <br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br></div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Feb 24, 2022 at 12:19 PM James A Glazier <<a href="mailto:jaglazier@gmail.com">jaglazier@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>
<p>We normally would show Zip code which is 47408, but if the others
don't that's fine.</p>
<p>My affiliation should probably be:</p>
<p>Biocomplexity Institute and Department of Intelligent Systems
Engineering, Indiana University, Bloomington, IN, United States,</p>
<p>But it's ok if you don't have energy to change it.</p>
<p>JAG<br>
</p>
<div>On 2/24/2022 1:40 AM, Jacob Barhak
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Thanks Marcella,
<div><br>
</div>
<div>Sheriff, James Osborne, Marcella, and James Glazier -
please look carefully since I am making changes related to
your affiliation - should eb ok, yet you should see this. <br>
<div><br>
</div>
<div>This is a much better version and there are very few
issues that I located after reading the manuscript. See
Below. </div>
<div><br>
</div>
<div>I ask that someone with good English grammar knowledge
check the list below:and let me know if there are any
problems with my proposed proofs - especially
punctuation and my replacement of :"predict" with "project"
- if there are any objections to any of those edits, I can
drop them - except from 2 major changes in Marcela's State
and one typo made in the previous proofs, all other issues I
found may be skipped. </div>
<div><br>
</div>
<div>I ask for authors to review sections they wrote and make
sure their affiliation, name, and references are intact.</div>
<div><br>
</div>
<div>Unless I have any objections or changes, those proofs
will go out to the Journal within 24 hours to meet the
deadline and I will not ask for an additional round of
corrections - so this is the last chance to make edits.</div>
<div><br>
</div>
<div>If anyone will want to make edits later, they will be in
the form of Errata which we want to avoid - so please one
last push and let us release this paper to the public.</div>
<div><br>
</div>
<div>Hopefully you will approve.</div>
<div><br>
</div>
<div> Jacob</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>####### List of changes ######</div>
<div><br>
</div>
<div>Page 1: Lines 78-89 Affiliations need correction and
standardization:<br>
<br>
2. European Molecular Biology Laboratory, European
Bioinformatics Institute (EMBL-EBI), Cambridge, United
Kingdom<br>
should be<br>
Rahuman S. Malik-Sheriff, European Molecular Biology
Laboratory, European Bioinformatics Institute (EMBL-EBI),
Hinxton, Cambridgeshire, UK<br>
Add Hinxton and change Cambridge to Cambridgeshire<br>
<br>
3 School of Mathematics and Statistics, University of
Melbourne, VIC, Parkville, Australia<br>
should be<br>
School of Mathematics and Statistics, University of
Melbourne, Parkville, VIC, Australia<br>
Parkville, VIC should be switched in order<br>
<br>
12 Department of Mathematics and Computer Science,
University of Richmond, Richmond, CA, United States<br>
should be:<br>
Department of Mathematics and Computer Science, University
of Richmond, Richmond, VA, United States<br>
CA should be VA<br>
<br>
17 Biocomplexity Institute, Indiana University, Bloomington,
IND, United States,<br>
should be:<br>
Biocomplexity Institute, Indiana University, Bloomington,
IN, United States,<br>
IN Instead of IND since we are using postal abbreviations
for all US states<br>
<br>
<br>
<br>
<br>
<br>
The reference <br>
<br>
Cresta, D., Warren, D. C., Quirouette, C., Smith, A. P.,
Lane, L. C., Smith, A. M.,<br>
et al. (2021). Time to Revisit the Endpoint Dilution Assay
and to Replace<br>
TCID$_{50}$ and PFU as Measures of a Virus Sample’s
Infection<br>
Concentration. arXiv:2101.11526 [q-bio]. Available at: <a href="http://arxiv.org/abs/" target="_blank">http://arxiv.org/abs/</a><br>
2101.11526 (Accessed October 24, 2021).<br>
<br>
consider changing to:<br>
<br>
Cresta, D., Warren, D. C., Quirouette, C., Smith, A. P.,
Lane, L. C., Smith, A. M.,<br>
et al. (2021). Time to Revisit the Endpoint Dilution Assay
and to Replace<br>
TCID50 and PFU as Measures of a Virus Sample’s Infection<br>
Concentration. arXiv:2101.11526 [q-bio]. Available at: <a href="http://arxiv.org/abs/" target="_blank">http://arxiv.org/abs/</a><br>
2101.11526 (Accessed October 24, 2021).<br>
<br>
TCID$_{50}$ should be subscript fro the number - yet if not
allowed in a reference, the $_{} may be better removed<br>
<br>
<br>
<br>
<br>
Page 5 - Line 566 <br>
fullfills<br>
<br>
should be <br>
fulfills<br>
<br>
There are 3 l's the last occurrence double l not 4.
Apologies 0 this was a mistake in the last proofs we
provided. Please spell check the word and use the American
English version.<br>
<br>
<br>
<br>
<br>
page 2 - Line 119<br>
<br>
Please replace "predictions" with "forecasts"<br>
<br>
Page 3 - Line 306<br>
Please consider instead of<br>
"Therefore we address many issues at lower..."<br>
consider:<br>
"Therefore, we address many issues at lower..."<br>
We ask to consider adding comma after "Therefore" so<br>
<br>
<br>
<br>
<br>
Page 3:<br>
Line 341, 342, please replace hyphens with large hyphens
with spaces around them - the hyphens should have been a
perpetrator not a connector between words: i.e. <br>
"<br>
The “promise of<br>
modeling” should be fulfilled already, yet we find modelers<br>
consistently unable to reproduce basic steps–thus stagnating<br>
instead of innovating, or even worse–backtracking progress.<br>
"<br>
<br>
should become:<br>
<br>
"<br>
The promise of<br>
modeling” should be fulfilled already, yet we find modelers<br>
consistently unable to reproduce basic steps - thus
stagnating<br>
instead of innovating, or even worse - backtracking
progress.<br>
"<br>
Alternatively, if preferred. just replaces the hyphens with
commas to create the separation<br>
<br>
<br>
<br>
<br>
Page 4 line 401 -<br>
Again the hyphen represents separation, so please add spaces
around them and use a large hyphen. So that <br>
"not approved and tested for the anticipated use–because of
the"<br>
becomes:<br>
"not approved and tested for the anticipated use - because
of the"<br>
alternatively replace with commas around the hyphen to
indicate separation instead of the hyphens <br>
<br>
<br>
<br>
Page 5 line 519 -<br>
<br>
Again, hyphens are supposed to separate no connect here.
i.e.:<br>
"<br>
While guidelines and concepts of how to establish
credibility<br>
of models–even for critical applications–do exist, the field
is still<br>
"<br>
should become<br>
"<br>
While guidelines and concepts of how to establish
credibility<br>
of models, even for critical applications - do exist, the
field is still<br>
"<br>
Please use a large hyphen or alternatively use commas
instead of the hyphens<br>
<br>
<br>
<br>
<br>
Page 6 line 681:<br>
<br>
Please replace:<br>
"predictions" with "projections"<br>
<br>
<br>
<br>
<br>
<br>
Page 7 line 786<br>
"<br>
Fortunately there are standardization efforts among<br>
languages.<br>
"<br>
<br>
should be <br>
<br>
"<br>
Fortunately, there are standardization efforts among<br>
languages.<br>
"<br>
Thus adding a comma.<br>
<br>
<br>
<br>
<br>
Page 8 line 868-869<br>
<br>
Please link this citation to the first reference in the
references list:<br>
<br>
"(About using a multi-scale mortality model in<br>
the ensemble, Online)"<br>
<br>
It is a link to a discussion - if needed remove the word
online at the end - yet this is a reference and not just a
comment in parenthesis<br>
<br>
<br>
<br>
<br>
Page 9 line 922:<br>
please add spaces around the large hyphen<br>
"<br>
Sometimes models are used (and published) without<br>
specifying the units used for simulation parameters—this is
a<br>
practice that needs to be corrected.<br>
"<br>
should be:<br>
Sometimes models are used (and published) without<br>
specifying the units used for simulation parameters — this
is a<br>
practice that needs to be corrected.<br>
<br>
Alternatively use a comma instead - the hyphen is intended
for explanation separating sentences, not connecting words.<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, Feb 23, 2022 at 8:37
AM 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 dir="ltr">
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Hello
all,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">The
new, (and final?) proof is attached. At this point I
assume we are not requesting additional proofs and any
remaining minor issues will be submitted as comments that
the typesetters can easily address? For example, for my
incorrect affiliation state I would accept and submit
comment:</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">"The
affiliation location state for Marcella Torres is
incorrect (it should be Virginia (VA) rather than
California (CA) and should read "Department of Mathematics
and Computer Science, University of Richmond, Richmond,
VA, United States"" </div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">It
looks like the other issues raised with names and
affiliations have been corrected! </div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Marcella</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</div>
<div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</div>
<div id="gmail-m_8855575149064398953gmail-m_-7359800268447972926Signature">
<div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<div style="margin:0px;font-size:14px;font-family:Calibri,sans-serif;color:rgb(32,31,30);text-align:start;background-color:rgb(255,255,255)">Marcella
Torres, Ph.D.</div>
<div style="margin:0px;font-size:14px;font-family:Calibri,sans-serif;color:rgb(32,31,30);text-align:start;background-color:rgb(255,255,255)">Director
of Mathematical Studies</div>
<div style="margin:0px;font-size:14px;font-family:Calibri,sans-serif;color:rgb(32,31,30);text-align:start;background-color:rgb(255,255,255)">University
of Richmond</div>
<div style="margin:0px;font-size:14px;font-family:Calibri,sans-serif;color:rgb(32,31,30);text-align:start;background-color:rgb(255,255,255)">Jepson
Hall Room 212</div>
<div style="margin:0px;font-size:14px;font-family:Calibri,sans-serif;color:rgb(32,31,30);text-align:start;background-color:rgb(255,255,255)">221
Richmond Way</div>
<div style="margin:0px;font-size:14px;font-family:Calibri,sans-serif;color:rgb(32,31,30);text-align:start;background-color:rgb(255,255,255)">Richmond,
VA 23173</div>
<div style="margin:0px;font-size:14px;font-family:Calibri,sans-serif;color:rgb(32,31,30);text-align:start;background-color:rgb(255,255,255)">(804)
289-8081</div>
<div style="margin:0px;font-size:14px;font-family:Calibri,sans-serif;color:rgb(32,31,30);text-align:start;background-color:rgb(255,255,255)">Pronouns:
she/her</div>
<br>
</div>
</div>
</div>
</div>
<hr style="display:inline-block;width:98%">
<div id="gmail-m_8855575149064398953gmail-m_-7359800268447972926divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri,
sans-serif" color="#000000"><b>From:</b> Jacob Barhak
<<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>><br>
<b>Sent:</b> Monday, February 14, 2022 9:14 PM<br>
<b>To:</b> Torres, Marcella <<a href="mailto:mtorres@richmond.edu" target="_blank">mtorres@richmond.edu</a>><br>
<b>Cc:</b> Rahuman Sheriff <<a href="mailto:sheriff@ebi.ac.uk" target="_blank">sheriff@ebi.ac.uk</a>>;
<a href="mailto:vp-reproduce-subgroup@lists.simtk.org" target="_blank">vp-reproduce-subgroup@lists.simtk.org</a>
<<a href="mailto:vp-reproduce-subgroup@lists.simtk.org" target="_blank">vp-reproduce-subgroup@lists.simtk.org</a>>;
<a href="mailto:vp-integration-subgroup@lists.simtk.org" target="_blank">vp-integration-subgroup@lists.simtk.org</a>
<<a href="mailto:vp-integration-subgroup@lists.simtk.org" target="_blank">vp-integration-subgroup@lists.simtk.org</a>>;
John Gennari <<a href="mailto:gennari@uw.edu" target="_blank">gennari@uw.edu</a>><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">Thanks Marcella,
<div><br>
</div>
<div>This one missed me. And I did go over all of the
author affiliations, yet for some reason I missed
this. </div>
<div><br>
</div>
<div>I asked for another author's proofs - I assumed
that with so many issues, there will be a need for
another proof. </div>
<div><br>
</div>
<div>Once they issue another proof, I will include a
correction for this issue.</div>
<div><br>
</div>
<div>Hopefully it's the last one.</div>
<div><br>
</div>
<div> Jacob</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
<br>
<div>
<div dir="ltr">On Mon, Feb 14, 2022 at 2:14 PM Torres,
Marcella <<a href="mailto:mtorres@richmond.edu" target="_blank">mtorres@richmond.edu</a>>
wrote:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">There
is a typo in my affiliation location: it should
read "Richmond, VA" not "Richmond, CA".</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">I
am happy to collect and comments and post them
if you still cannot access, Jacob.</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Marcella</div>
<div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</div>
<div id="gmail-m_8855575149064398953gmail-m_-7359800268447972926x_gmail-m_-3808040779273801886Signature">
<div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<div style="margin:0px;font-size:14px;font-family:Calibri,sans-serif;color:rgb(32,31,30);text-align:start;background-color:rgb(255,255,255)">Marcella
Torres, Ph.D.</div>
<div style="margin:0px;font-size:14px;font-family:Calibri,sans-serif;color:rgb(32,31,30);text-align:start;background-color:rgb(255,255,255)">Director
of Mathematical Studies</div>
<div style="margin:0px;font-size:14px;font-family:Calibri,sans-serif;color:rgb(32,31,30);text-align:start;background-color:rgb(255,255,255)">University
of Richmond</div>
<div style="margin:0px;font-size:14px;font-family:Calibri,sans-serif;color:rgb(32,31,30);text-align:start;background-color:rgb(255,255,255)">Jepson
Hall Room 212</div>
<div style="margin:0px;font-size:14px;font-family:Calibri,sans-serif;color:rgb(32,31,30);text-align:start;background-color:rgb(255,255,255)">221
Richmond Way</div>
<div style="margin:0px;font-size:14px;font-family:Calibri,sans-serif;color:rgb(32,31,30);text-align:start;background-color:rgb(255,255,255)">Richmond,
VA 23173</div>
<div style="margin:0px;font-size:14px;font-family:Calibri,sans-serif;color:rgb(32,31,30);text-align:start;background-color:rgb(255,255,255)">(804)
289-8081</div>
<div style="margin:0px;font-size:14px;font-family:Calibri,sans-serif;color:rgb(32,31,30);text-align:start;background-color:rgb(255,255,255)">Pronouns:
she/her</div>
<br>
</div>
</div>
</div>
</div>
<hr style="display:inline-block;width:98%">
<div id="gmail-m_8855575149064398953gmail-m_-7359800268447972926x_gmail-m_-3808040779273801886divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b>
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 Rahuman Sheriff <<a href="mailto:sheriff@ebi.ac.uk" target="_blank">sheriff@ebi.ac.uk</a>><br>
<b>Sent:</b> Saturday, February 12, 2022 1:38
PM<br>
<b>To:</b> Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@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>>;
John Gennari <<a href="mailto:gennari@uw.edu" target="_blank">gennari@uw.edu</a>><br>
<b>Subject:</b> Re: [Vp-reproduce-subgroup]
[Vp-integration-subgroup] Shayn Peirce-Cottler
via Frontiers: Manuscript</font>
<div> </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>Dear Jacob and all,
<div>Please find the proof attached.</div>
<div>There are issue that needs attention,</div>
<div>for e.g. Jonathan’s name is missing
from the authors list.</div>
<div><br>
</div>
<div>Quick corrections from my side:</div>
<div><br>
</div>
<div>My last name: Malik-Sheriff</div>
<div><br>
</div>
<div>Citation: Malik-Sheriff RS</div>
<div><br>
</div>
<div>In the acknowledgement, please change
RS -> Rahuman S. Malik Sheriff, to keep
it consistent as you have it for Jonathan
Karr.</div>
<div><br>
</div>
<div>I will read the proof carefully again
and report if I find any typos or so.
Others can do that too.</div>
<div><br>
</div>
<div>Best regards</div>
<div>Sheriff</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
<div>
<div><br>
<div><br>
<blockquote type="cite">
<div>On 12 Feb 2022, at 18:30, Jacob
Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>>
wrote:</div>
<br>
<div>
<div dir="ltr"> Hi Marcella,
<div><br>
</div>
<div>The link you sent brings back
my own loop profile - not the
article - I tried multiple times -
and I did not get such
correspondence myself. So I am
confused as well.</div>
<div><br>
</div>
<div>If the intention is to update
your loop profile, I did this just
now.</div>
<div><br>
</div>
<div>Hopefully this was the request
from the publisher. If you see
some other proof document, please
provide additional details so we
can all respond properly.</div>
<div><br>
</div>
<div> Jacob</div>
<div><br>
</div>
<div><br>
</div>
</div>
<br>
<div>
<div dir="ltr">On Sat, Feb 12, 2022
at 4:46 AM William Waites <<a href="mailto:wwaites@ieee.org" target="_blank">wwaites@ieee.org</a>>
wrote:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
I am disturbed that it’s asking me
to log in with facebook, linkedin
or twitter…<br>
<br>
> On 11 Feb 2022, at 22:29,
Torres, Marcella <<a href="mailto:mtorres@richmond.edu" target="_blank">mtorres@richmond.edu</a>>
wrote:<br>
> <br>
> Proof available for
viewing/acceptance below. We are
asked to check it and respond
within 48 hours:<br>
> <br>
> Dear Marcella Torres,<br>
> <br>
> Systems Biology Production
Office has sent you a message.
Please click 'Reply' to send a
direct response<br>
> <br>
> I just finished preparing the
proof of your article "Model
Integration in Computational
Biology: the Role of
Reproducibility, Credibility and
Utility", DOI:
10.3389/fsysb.2022.822606. Could
you please check it within 48
hours (excluding weekends and
holidays). Make sure to respond in
the system so that I'm notified of
your corrections.<br>
> <br>
> Here's the link:<br>
> <a href="http://www.frontiersin.org/Production/EnterProductionForum.aspx?activationno=886b0bc9-5221-44e7-9475-1aa44986adb5&pagekey=POF_DISCUSSION_FORUM" rel="noreferrer" target="_blank">
http://www.frontiersin.org/Production/EnterProductionForum.aspx?activationno=886b0bc9-5221-44e7-9475-1aa44986adb5&pagekey=POF_DISCUSSION_FORUM</a><br>
> <br>
> P.S. We would recommend that
you assign one author to collect
all changes and to upload the
revised files.<br>
> <br>
> Do you need help? Visit our
Production Help Center for more
information: <a href="https://zendesk.frontiersin.org/hc/en-us/categories/200397292-Article-Production-" rel="noreferrer" target="_blank">
https://zendesk.frontiersin.org/hc/en-us/categories/200397292-Article-Production-</a><br>
> <br>
> Best regards,<br>
> <br>
> Frontiers in Systems Biology
Production Office<br>
> <a href="mailto:systemsbiology.production.office@frontiersin.org" target="_blank">
systemsbiology.production.office@frontiersin.org</a><br>
> <a href="http://www.frontiersin.org/" rel="noreferrer" target="_blank">www.frontiersin.org</a><br>
> <br>
> For technical issues, please
contact Application Support - <a href="mailto:support@frontiersin.org" target="_blank">
support@frontiersin.org</a><br>
> <br>
> ***********<br>
> Do you need help?<br>
> <br>
> -You need to be logged in to
your account to access the proof.<br>
> -the PDF proof is available
in the top right corner, follow
the instructions on the PDF to
submit your corrections.<br>
> -If your article is not
linked to your account contact <a href="mailto:support@frontiersin.org" target="_blank">
support@frontiersin.org</a><br>
> <br>
> Marcella Torres, Ph.D.<br>
> Director of Mathematical
Studies<br>
> University of Richmond<br>
> Jepson Hall Room 212<br>
> 221 Richmond Way<br>
> Richmond, VA 23173<br>
> (804) 289-8081<br>
> Pronouns: she/her<br>
> <br>
> From: Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>><br>
> Sent: Friday, February 4,
2022 8:28 PM<br>
> To: Torres, Marcella <<a href="mailto:mtorres@richmond.edu" target="_blank">mtorres@richmond.edu</a>><br>
> Cc: Ruth Bowness <<a href="mailto:rb2250@bath.ac.uk" target="_blank">rb2250@bath.ac.uk</a>>;
<a href="mailto:vp-reproduce-subgroup@lists.simtk.org" target="_blank">vp-reproduce-subgroup@lists.simtk.org</a>
<<a href="mailto:vp-reproduce-subgroup@lists.simtk.org" target="_blank">vp-reproduce-subgroup@lists.simtk.org</a>>;
<a href="mailto:vp-integration-subgroup@lists.simtk.org" target="_blank">vp-integration-subgroup@lists.simtk.org</a>
<<a href="mailto:vp-integration-subgroup@lists.simtk.org" target="_blank">vp-integration-subgroup@lists.simtk.org</a>>;
John Gennari <<a href="mailto:gennari@uw.edu" target="_blank">gennari@uw.edu</a>><br>
> Subject: Re:
[Vp-reproduce-subgroup]
[Vp-integration-subgroup] Shayn
Peirce-Cottler via Frontiers:
Manuscript<br>
> <br>
> External Email: Use caution
in opening links, attachments, and
buying gift cards.<br>
> <br>
> Thanks Marcella, and thanks
to all contributors,<br>
> <br>
> Marcella is right. The paper
was indeed accepted and I just
paid the publication costs as
promised to accelerate the
publication process.<br>
> <br>
> William and Gilberto, Here is
a communication I got from the
editor:<br>
> <br>
> "<br>
> Thanks, Jacob! I'm going to
accept this but I want to make
sure that your author
name/affiliations are all correct
in the system, so I will reach out
to the Frontiers staff to ensure
that. But please consider this
"accepted"! Congratulations and
thank you for a wonderful
contribution!<br>
> <br>
> "<br>
> <br>
> The editor also sent a more
elaborate letter to the office, so
your name and affiliation changes
should appear properly once
published.<br>
> <br>
> I am delighted that the
publication process has reached a
conclusion. I would have been
happier if John Gennari would have
agreed to join us, yet I could not
convince him. Hopefully he will be
happy with his contributions
reaching a publisher.
<br>
> <br>
> It is now time to work
towards implementing the ideas in
the paper. We should mention it in
the response to the FDA document
we started discussing last week -
so far John and I are discussing
it, I encourage others to join.<br>
> <br>
> Jacob<br>
> <br>
> <br>
> <br>
> <br>
> On Fri, Feb 4, 2022 at 1:25
PM Torres, Marcella <<a href="mailto:mtorres@richmond.edu" target="_blank">mtorres@richmond.edu</a>>
wrote:<br>
> Update: the manuscript was
accepted, and Jacob and I have
received an invoice. The
acceptance email is copied below:<br>
> <br>
> Acceptance email copy:<br>
> <br>
> Dear Dr Torres,<br>
> <br>
> Frontiers in Systems Biology
Editorial Office has sent you a
message. Please click 'Reply' to
send a direct response<br>
> <br>
> 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.<br>
> Proofs are being prepared for
you to verify before publication.
We will also perform final checks
to ensure your manuscript meets
our criteria for publication (<a href="https://www.frontiersin.org/about/review-system#ManuscriptQualityStandards" rel="noreferrer" target="_blank">https://www.frontiersin.org/about/review-system#ManuscriptQualityStandards</a>).<br>
> <br>
> The title, abstract and
author(s) list you provided during
submission is currently online and
will be replaced with the final
version when your article is
published. Please do not
communicate any changes until you
receive your proofs.<br>
> <br>
> Any questions? Please visit
our Production Help Center page
for more information:
<a href="https://zendesk.frontiersin.org/hc/en-us/categories/200397292-Article-Production-" rel="noreferrer" target="_blank">
https://zendesk.frontiersin.org/hc/en-us/categories/200397292-Article-Production-</a><br>
> <br>
> Manuscript title: Model
Integration in Computational
Biology: the Role of
Reproducibility, Credibility and
Utility<br>
> Journal: Frontiers in Systems
Biology, section Multiscale
Mechanistic Modeling<br>
> Article type: Review<br>
> 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<br>
> Manuscript ID: 822606<br>
> Edited by: Shayn
Peirce-Cottler<br>
> <br>
> You can click here to access
the final review reports and
manuscript: <a href="http://www.frontiersin.org/Review/EnterReviewForum.aspx?activationno=176c11a6-62ac-48cd-bc10-66fd193d8aba" rel="noreferrer" target="_blank">
http://www.frontiersin.org/Review/EnterReviewForum.aspx?activationno=176c11a6-62ac-48cd-bc10-66fd193d8aba</a><br>
> <br>
> As an author, it is important
that you keep your Frontiers
research network (Loop) profile up
to date, so that you and your
publications are more
discoverable. You can update your
profile pages (profile picture,
short bio, list of publications)
using this link: <a href="https://loop.frontiersin.org/people/" rel="noreferrer" target="_blank">
https://loop.frontiersin.org/people/</a><br>
> <br>
> ------------------<br>
> Tell us what you think!<br>
> <br>
> At Frontiers we are
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Collaborative Review process and
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https://frontiers.qualtrics.com/jfe/form/SV_8q8kYmXRvxBH5at?survey=author&aid=822606&uid=1393232</a><br>
> <br>
> Thank you very much for
taking the time to share your
thoughts.<br>
> <br>
> Best regards,<br>
> <br>
> Your Frontiers in Systems
Biology team<br>
> <br>
> Frontiers in Systems Biology
Editorial Office<br>
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> For technical issues, please
contact our IT Helpdesk - <a href="mailto:support@frontiersin.org" target="_blank">
support@frontiersin.org</a><br>
> <br>
> <br>
> <br>
> <br>
> <br>
> Marcella Torres, Ph.D.<br>
> Director of Mathematical
Studies<br>
> University of Richmond<br>
> Jepson Hall Room 212<br>
> 221 Richmond Way<br>
> Richmond, VA 23173<br>
> (804) 289-8081<br>
> Pronouns: she/her<br>
> <br>
> From: 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>
> Sent: Saturday, January 29,
2022 10:47 PM<br>
> To: Ruth Bowness <<a href="mailto:rb2250@bath.ac.uk" target="_blank">rb2250@bath.ac.uk</a>><br>
> Cc: <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>
> Subject: Re:
[Vp-reproduce-subgroup]
[Vp-integration-subgroup] Shayn
Peirce-Cottler via Frontiers:
Manuscript<br>
> <br>
> External Email: Use caution
in opening links, attachments, and
buying gift cards.<br>
> <br>
> Greetings paper contributors,<br>
> <br>
> The changes in funding were
submitted:<br>
> <br>
> Below is the message I wrote
to the editor.<br>
> <br>
> Hopefully the paper can be
published now.<br>
> <br>
> Jacob <br>
> <br>
> ####### Copy of message
to the editor #####<br>
> Thanks Shayn,<br>
> <br>
> 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.
<br>
> <br>
> 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. .
<br>
> 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.<br>
> 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>
> <br>
> The changes to funding were
added and the revised manuscript
with proper funding information
was uploaded.<br>
> <br>
> Please proceed with the
process. I hope you find it all in
order and ready for publication.<br>
> <br>
> Jacob<br>
> <br>
> On Thu, Jan 27, 2022 at 9:28
PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>>
wrote:<br>
> Ok Ruth, And the rest of the
contributors please pay attention,
<br>
> <br>
> You will find your support
acknowledged now. <br>
> <br>
> The link to the manuscript
draft is: <br>
> <a href="https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing" rel="noreferrer" target="_blank">
https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing</a><br>
> <br>
> Here are some observations.<br>
> <br>
> 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:<br>
> Jonathan Karr . William
Waites, Rahuman S. Malik Sheriff,
and Ruth Bowness. <br>
> One Author declared conflict
of interest - Jacob Barhak<br>
> <br>
> 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>
> <br>
> 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>
> <br>
> 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.<br>
> <br>
> Jacob<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> <br>
> <br>
> <br>
> 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>
> Hi Jacob<br>
> <br>
> 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 I was
supported by a fellowship funded
by the Medical Research Council
[grant number MR/P014704/1].<br>
> <br>
> Many thanks<br>
> Ruth<br>
> <br>
> Dr Ruth Bowness<br>
> Lecturer & MRC Research
Fellow<br>
> Department of Mathematical
Sciences<br>
> University of Bath<br>
> <br>
> E-mail: <a href="mailto:rb2250@bath.ac.uk" target="_blank">rb2250@bath.ac.uk</a><br>
> Website: <a href="https://ruthbowness.com/" rel="noreferrer" target="_blank">https://ruthbowness.com</a><br>
> Twitter: @RuthBowness<br>
> <br>
> Please note that I work
part-time hours, usually
Monday-Wednesday.<br>
> <br>
> 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.
<br>
> <br>
> <image001.jpg><br>
> <br>
> <br>
> <br>
> <br>
> <br>
> From: 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>
> Date: Thursday, 27 January
2022 at 01:49<br>
> To: Torres, Marcella <<a href="mailto:mtorres@richmond.edu" target="_blank">mtorres@richmond.edu</a>><br>
> Cc: <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>
> Subject: Re:
[Vp-integration-subgroup]
[Vp-reproduce-subgroup] Shayn
Peirce-Cottler via Frontiers:
Manuscript<br>
> <br>
> CAUTION: 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.<br>
> <br>
> Thanks Marcella, and all
paper contributors, please pay
attention <br>
> <br>
> It has been a week since the
message sent to the group.<br>
> <br>
> So far no one has responded
with any changes in funding
sources or conflict of interest.<br>
> <br>
> 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.
<br>
> <br>
> Also, again, if anyone has an
objection to this paper being made
public, it is the last chance to
do so.<br>
> <br>
> <br>
> 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.<br>
> <br>
> Jacob<br>
> <br>
> On Wed, Jan 26, 2022, 18:12
Torres, Marcella <<a href="mailto:mtorres@richmond.edu" target="_blank">mtorres@richmond.edu</a>>
wrote:<br>
> Email from Frontiers and
question from the editor shared
below:<br>
> <br>
> Dear Dr Torres,<br>
> <br>
> Frontiers in Systems Biology
Editorial Office has sent you a
message. Please click 'Reply' to
send a direct response<br>
> <br>
> 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:<br>
> <a href="http://www.frontiersin.org/Review/EnterReviewForum.aspx?activationno=ba15539e-1784-4ed3-9969-2aacb1b5b835" rel="noreferrer" target="_blank">
http://www.frontiersin.org/Review/EnterReviewForum.aspx?activationno=ba15539e-1784-4ed3-9969-2aacb1b5b835</a><br>
> <br>
> Journal: Frontiers in Systems
Biology, section Multiscale
Mechanistic Modeling<br>
> Article type: Review<br>
> Manuscript title: Model
Integration in Computational
Biology: the Role of
Reproducibility, Credibility and
Utility<br>
> Manuscript ID: 822606<br>
> 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<br>
> Submitted on: 26 Nov 2021<br>
> Edited by: Shayn
Peirce-Cottler<br>
> <br>
> <br>
> Research Topic: Insights in
Systems Biology: Multiscale
Mechanistic Modeling 2021<br>
> <br>
> Best regards,<br>
> <br>
> Your Frontiers in Systems
Biology team<br>
> <br>
> Frontiers in Systems Biology
Editorial Office<br>
> <a href="http://www.frontiersin.org/" rel="noreferrer" target="_blank">www.frontiersin.org</a><br>
> Avenue du Tribunal Federal 34<br>
> Lausanne, Switzerland | T
41(0)21 510 17 93<br>
> <br>
> For technical issues, please
contact our IT Helpdesk - <a href="mailto:support@frontiersin.org" target="_blank">
support@frontiersin.org</a><br>
> <br>
> Marcella Torres, Ph.D.<br>
> Director of Mathematical
Studies<br>
> University of Richmond<br>
> Jepson Hall Room 212<br>
> 221 Richmond Way<br>
> Richmond, VA 23173<br>
> (804) 289-8081<br>
> Pronouns: she/her<br>
> <br>
> From: 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>
> Sent: Wednesday, January 19,
2022 10:24 PM<br>
> To: James Glazier <<a href="mailto:jaglazier@gmail.com" target="_blank">jaglazier@gmail.com</a>><br>
> Cc: <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>
> Subject: Re:
[Vp-reproduce-subgroup]
[Vp-integration-subgroup] Shayn
Peirce-Cottler via Frontiers:
Manuscript<br>
> <br>
> External Email: Use caution
in opening links, attachments, and
buying gift cards.<br>
> <br>
> <br>
> Hi James,<br>
> <br>
> 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.
<br>
> <br>
> Hopefully no other changes
will be raised by contributors and
we can proceed as approved by all
authors.
<br>
> <br>
> Jacob<br>
> <br>
> <br>
> ####### Letter to the editor
sent in submission system
########<br>
> <br>
> 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:<br>
> James A. Glazier<br>
> <br>
> 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:<br>
> <a href="https://lists.simtk.org/pipermail/vp-integration-subgroup/2022-January/000388.html" rel="noreferrer" target="_blank">
https://lists.simtk.org/pipermail/vp-integration-subgroup/2022-January/000388.html</a><br>
> Hopefully no other changes
are necessary. <br>
> <br>
> Thank you for handling this
manuscript.<br>
> <br>
> Jacob<br>
> <br>
> <br>
> 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:<br>
> Thanks James, and all other
paper contributors, please read
this. <br>
> <br>
> 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:<br>
> <a href="https://lists.simtk.org/pipermail/vp-integration-subgroup/2021-April/000073.html" rel="noreferrer" target="_blank">
https://lists.simtk.org/pipermail/vp-integration-subgroup/2021-April/000073.html</a><br>
> <br>
> 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.
<br>
> <br>
> 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.
<br>
> <br>
> I am sending this email to
the entire group to make sure that
everyone that approved, knew that
they are approving the paper text,
the funding sources, the conflict
of interest statements, the
authorship / ethics statement.,
license and more elements as
declared in this document: <a href="https://www.frontiersin.org/about/policies-and-publication-ethics" rel="noreferrer" target="_blank">
https://www.frontiersin.org/about/policies-and-publication-ethics</a><br>
> <br>
> 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.<br>
> <br>
> 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.
<br>
> <br>
> 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. <br>
> <br>
> Hopefully I am clear enough
now. <br>
> <br>
> 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.<br>
> <br>
> 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.<br>
> <br>
> Hopefully this email will fix
things and make sure our
delerations are accurate.
<br>
> <br>
> <br>
> Jacob<br>
> <br>
> <br>
> <br>
> <br>
> On Wed, Jan 19, 2022 at 12:31
PM James Glazier <<a href="mailto:jaglazier@gmail.com" target="_blank">jaglazier@gmail.com</a>>
wrote:<br>
> Dear Jacob: <br>
> <br>
> 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.<br>
> <br>
> JAG<br>
> <br>
> On Wed, Jan 19, 2022 at 1:22
PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>>
wrote:<br>
> Well James, <br>
> <br>
> You put me is a difficult
position. You all approved the
manuscript multiple times.
<br>
> <br>
> 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.<br>
> <br>
> 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.<br>
> <br>
> 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.<br>
> <br>
> So I ask you on what should I
do.<br>
> <br>
> 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.<br>
> <br>
> Hopefully this will settle
the matter.<br>
> <br>
> Jacob<br>
> <br>
> <br>
> On Wed, Jan 19, 2022, 11:15
James A Glazier <<a href="mailto:jaglazier@gmail.com" target="_blank">jaglazier@gmail.com</a>>
wrote:<br>
> Dear Jacob:<br>
> 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:<br>
> James A. Glazier acknowledges
funding support from grants NSF
188553, NSF 186890, NSF 1720625,
NIH U24 EB028887 and NIH R01
GM122424.<br>
> JAG<br>
> <br>
> On 11/17/2021 10:04 PM, Jacob
Barhak wrote:<br>
> Hi James Faedar, Hi John
Rice, <br>
> <br>
> Please check the manuscript
and declare by REPLY ALL if you
APPROVE, DISAPPROVE or ABSTAIN.<br>
> <br>
> 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.<br>
> <br>
> 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.
<br>
> <br>
> Once I have your answer I can
proceed. Hopefully you will both
APPROVE quickly.<br>
> <br>
> Jacob<br>
> <br>
> 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:<br>
> Hi Jacob and all,<br>
> I approve the submission of
the manuscript. <br>
> Please update the citation
Tiwari et 2020 Preprint to <br>
> 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.<br>
> Also my name and affiliation
below<br>
> Rahuman S. Malik Sheriff<br>
> European Molecular Biology
Laboratory, European
Bioinformatics Institute
(EMBL-EBI), Wellcome Genome
Campus, Hinxton, Cambridge, UK<br>
> <br>
> Thanks for pushing this work
forward<br>
> Best regards<br>
> Sheriff<br>
> <br>
> On 2021-11-17 18:58, Jonathan
Karr wrote:<br>
> Hi Jacob, <br>
> <br>
> Thank you again for
spearheading this effort.<br>
> <br>
> I approve the submission. I
think the paper organizes a
variety of important issues toward
more credible models, and the
content is sound.<br>
> <br>
> My affiliation is Department
of Genetics and Genomic Sciences,
Icahn School of Medicine at Mount
Sinai, New York, NY, USA.<br>
> <br>
> As others have mentioned, I
think the paper would be more
impactful with further editing to
make the paper easier to read:<br>
> • More clearly
articulate the goals/motivation
for more credible models<br>
> • Be more concise and
focused<br>
> • Remove redundancies
by grouping related text<br>
> • Fill in the gaps in
logic in the introduction with
more transitions, less extraneous
information, and/or a brief
outline.<br>
> • Change the title of
the "Utility of models" section to
something like "Challenges with
using multiscale models" (James'
suggestion)<br>
> • Order the "Utility of
models" subsections to be easier
to follow, perhaps from model
construction through to reuse<br>
> • Rephrase the titles
of the "Utility of models"
subsections to focus on
opportunities for improvement
rather than current problems<br>
> Regards,<br>
> Jonathan<br>
> <br>
> 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:<br>
> Thanks to all contributors
who answered,<br>
> <br>
> Most contributors approved by
now.<br>
> <br>
> 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.<br>
> <br>
> To be productive I ask that
the following people who did not
answer so far take the time to
APPROVE, DISAPPROVE, or ABSTAIN.:<br>
> Robin Thompson<br>
> James R. Faeder<br>
> Jonathan Karr<br>
> Rahuman Sheriff<br>
> John Rice<br>
> <br>
> 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.
<br>
> <br>
> I hope we can father all
support quickly so I can move
forward and submit the paper.<br>
> <br>
> Jacob<br>
> <br>
> <br>
> On Tue, Nov 9, 2021 at 5:46
AM William Waites <<a href="mailto:wwaites@ieee.org" target="_blank">wwaites@ieee.org</a>>
wrote:<br>
> 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>
>
_______________________________________________<br>
> Vp-integration-subgroup
mailing list<br>
> <a href="mailto:Vp-integration-subgroup@lists.simtk.org" target="_blank">Vp-integration-subgroup@lists.simtk.org</a><br>
> <a href="https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup" rel="noreferrer" target="_blank">
https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup</a><br>
> <br>
> -- <br>
> James A. Glazier, PhD<br>
> Professor of Intelligent
Systems Engineering, Adjunct
Professor of Physics<br>
> Director, Biocomplexity
Institute<br>
> Indiana University,
Bloomington<br>
> (812) 391-2159 (cell)<br>
> <br>
> <br>
> -- <br>
> James A. Glazier, PhD <br>
> Professor of Intelligent
Systems Engineering, Adjunct
Professor of Physics<br>
> Director Biocomplexity
Institute<br>
> Indiana University,
Bloomington<br>
> (812) 391-2159<br>
>
_______________________________________________<br>
> Vp-integration-subgroup
mailing list<br>
> <a href="mailto:Vp-integration-subgroup@lists.simtk.org" target="_blank">Vp-integration-subgroup@lists.simtk.org</a><br>
> <a href="https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup" rel="noreferrer" target="_blank">
https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup</a><br>
<br>
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</blockquote>
</div>
<br>
</div>
</div>
</div>
</div>
</blockquote>
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</div>
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</blockquote>
</div>
<br>
<fieldset></fieldset>
<pre>_______________________________________________
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</pre>
</blockquote>
<pre cols="72">--
James A. Glazier, PhD
Professor of Intelligent Systems Engineering, Adjunct Professor of Physics
Director, Biocomplexity Institute
Indiana University, Bloomington
(812) 391-2159 (cell)</pre>
</div>
</blockquote></div>