<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div dir="ltr"></div><div dir="ltr">Jacob, I don’t think this is a big deal. This kind of non-substantive change should be possible (e.g. when we get the proofs and any missing dots and crosses on t’s and I’s are checked)</div><div dir="ltr"><br><blockquote type="cite">On 19 Jan 2022, at 18:22, Jacob Barhak <jacob.barhak@gmail.com> wrote:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr"><div dir="auto">Well James,<div dir="auto"><br></div><div dir="auto">You put me is a difficult position. You all approved the manuscript multiple times. </div><div dir="auto"><br></div><div dir="auto">Sheriff caught it just before I sent it so I added his funding - out of regular process - just to avoid conflict with journal legal requirements.</div><div dir="auto"><br></div><div dir="auto">As for name changes, I am locked outside the system and such a request should be processed through the editor. Similar to what William asked for.</div><div dir="auto"><br></div><div dir="auto">As for funding. We discussed this a long time ago. And the paper was approved multiple times. I can probably spend an hour later to add your funding. Yet there are 18 of us and only a few claimed funding - this was supposed to be a volunteer effort... If all 18 ask their funding to be included, we will need to reopen this again.</div><div dir="auto"><br></div><div dir="auto">So I ask you on what should I do.</div><div dir="auto"><br></div><div dir="auto">If this funding declaration is necessary for this volunteer work to fulfill the legal requirement of the publisher to disclose funding I must process your request and will do it tonight. If not , I suggest we avoid changes. Please advise on proper way to proceed.</div><div dir="auto"><br></div><div dir="auto">Hopefully this will settle the matter.</div><div dir="auto"><br></div><div dir="auto"> Jacob</div><div dir="auto"><br></div><br><div class="gmail_quote" dir="auto"><div dir="ltr" class="gmail_attr">On Wed, Jan 19, 2022, 11:15 James A Glazier <<a href="mailto:jaglazier@gmail.com">jaglazier@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<p>Dear Jacob:</p>
<p>Thank you for your heroic efforts on bringing this paper
together. I should probably change my name to James A. Glazier,
which is my standard listing. I should also acknowledge my funding
support:</p>
<p>James A. Glazier acknowledges funding support from grants NSF
188553, NSF 186890, NSF 1720625, NIH U24 EB028887 and NIH R01
GM122424.</p>
<p>JAG<br>
</p>
<p><br>
</p>
<div>On 11/17/2021 10:04 PM, Jacob Barhak
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi James Faedar, Hi John Rice,
<div><br>
</div>
<div>Please check the manuscript and declare by REPLY ALL if you
APPROVE, DISAPPROVE or ABSTAIN.</div>
<div><br>
</div>
<div>James, if you responded and I did not get the email, I
apologize - there are some communication hiccups occasionally.
Yet I need your public approval to proceed and use your name.</div>
<div><br>
</div>
<div>John, I know you allowed us to send the paper, yet you need
to be specific and declare if you want to be included as an
Author or just moved to acknowledgements. You did have a major
contribution, so I hope you will APPROVE. </div>
<div><br>
</div>
<div>Once I have your answer I can proceed. Hopefully you will
both APPROVE quickly.</div>
<div><br>
</div>
<div> Jacob</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, Nov 17, 2021 at 3:02
PM sheriff <<a href="mailto:sheriff@ebi.ac.uk" target="_blank" rel="noreferrer">sheriff@ebi.ac.uk</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 style="font-size:10pt;font-family:Verdana,Geneva,sans-serif">
<p>Hi Jacob and all,</p>
<p>I approve the submission of the manuscript. </p>
<p>Please update the citation Tiwari et 2020 Preprint to </p>
<p>Tiwari K, Kananathan S, Roberts MG, Meyer JP, Sharif
Shohan MU, Xavier A, Maire M, Zyoud A, Men J, Ng S, Nguyen
TVN, Glont M, Hermjakob H, Malik-Sheriff RS.
Reproducibility in systems biology modelling. Mol Syst
Biol. 2021 Feb;17(2):e9982. doi: 10.15252/msb.20209982.
PMID: 33620773; PMCID: PMC7901289.</p>
<p>Also my name and affiliation below</p>
<p>Rahuman S. <span style="text-decoration:underline">Malik
Sheriff</span></p>
<p>European Molecular Biology Laboratory, European
Bioinformatics Institute (EMBL-EBI), Wellcome Genome
Campus, Hinxton, Cambridge, UK</p>
<p><br>
</p>
<p>Thanks for pushing this work forward</p>
<p>Best regards</p>
<p>Sheriff</p>
<p><br>
</p>
<p id="m_-6210025431876839483gmail-m_5776642796092585345reply-intro">On 2021-11-17
18:58, Jonathan Karr wrote:</p>
<blockquote type="cite" style="padding:0px 0.4em;border-left:2px solid rgb(16,16,255);margin:0px">
<div id="m_-6210025431876839483gmail-m_5776642796092585345replybody1">
<div dir="ltr">Hi Jacob,
<div> </div>
<div>Thank you again for spearheading this effort.<br>
<div> </div>
<div>I approve the submission. I think the paper
organizes a variety of important issues toward
more credible models, and the content is sound.<br>
<div> </div>
<div>My affiliation is Department of Genetics and
Genomic Sciences, Icahn School of Medicine at
Mount Sinai, New York, NY, USA.</div>
<div> </div>
<div>As others have mentioned, I think the paper
would be more impactful with further editing to
make the paper easier to read:</div>
<div>
<ul>
<li>More clearly articulate the
goals/motivation for more credible models</li>
<li>Be more concise and focused</li>
<li>Remove redundancies by grouping related
text</li>
<li>Fill in the gaps in logic in the
introduction with more transitions, less
extraneous information, and/or a brief
outline.</li>
<li>Change the title of the "Utility of
models" section to something like
"Challenges with using multiscale models"
(James' suggestion)</li>
<li>Order the "Utility of models" subsections
to be easier to follow, perhaps from model
construction through to reuse</li>
<li>Rephrase the titles of the "Utility of
models" subsections to focus on
opportunities for improvement rather than
current problems</li>
</ul>
</div>
<div>Regards,</div>
<div>Jonathan</div>
</div>
</div>
</div>
<br>
<div>
<div dir="ltr">On Wed, Nov 10, 2021 at 11:25 PM Jacob
Barhak <<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer noreferrer" target="_blank">jacob.barhak@gmail.com</a>>
wrote:</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Thanks to all contributors who
answered,
<div> </div>
<div>Most contributors approved by now.</div>
<div> </div>
<div>James and Wiliam, I am not sure how many more
revisions there will be for this publication. I
did not add several important references of my
own in this revision. Frankly I wanted to keep
reference changes to a minimum and kept it
as close as possible to the origin . However, we
are transferring the paper to the publisher
under CC license, so it will not be hard to
create another derived version with all sorts of
additions and modifications in the future where
people can edit it as they see fit and add
whatever references they want - so after it gets
published you can continue working on other
versions as you see fit. For now I ask we focus
on publishing this version alone and I really
hope the editors will not put us through another
revision round since it makes no sense at this
point - any change is not substantial compared
to what we have already and any delay is more
damaging than productive.</div>
<div> </div>
<div>To be productive I ask that the following
people who did not answer so far take the time
to APPROVE, DISAPPROVE, or ABSTAIN.:</div>
<div>Robin Thompson</div>
<div>James R. Faeder</div>
<div>Jonathan Karr<br>
Rahuman Sheriff</div>
<div>John Rice</div>
<div> </div>
<div>
<div>John Rice - thanks for your support, yet
you will have to be specific: You can either
choose APPROVE or ABSTAIN - both of these
options will move the paper forwards. APPROVE
will add your name to the list of authors with
all responsibilities and privileges listed or
implied , ABSTAIN will put you in
acknowledgements without any obligation. So
John, please choose if you want your name on
the paper or not in this specific version -
any decision you make will be ok. </div>
<div> </div>
<div>I hope we can father all support quickly so
I can move forward and submit the paper.</div>
</div>
<div> </div>
<div> Jacob</div>
<div> </div>
</div>
<br>
<div>
<div dir="ltr">On Tue, Nov 9, 2021 at 5:46 AM
William Waites <<a href="mailto:wwaites@ieee.org" rel="noreferrer noreferrer" target="_blank">wwaites@ieee.org</a>>
wrote:</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">I'm just
chasing down references for use in another
context and I notice that the Ke et al paper is
still a pre-print after more than a year. There
is no problem in my opinion citing preprints but
it is suspect in this case: there's been a ton
of work on SARS-CoV-2 infectiousness, why didn't
this get published? Probably not best to rely on
it as an example of practice. Perhaps to fix on
revision.<br>
<br>
-w<br>
<br>
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</div>
</blockquote>
</div>
</div>
</blockquote>
<p><br>
</p>
</div>
</blockquote>
</div>
</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></div>
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