<div dir="ltr">Thanks James, and all other paper contributors, please read this. <br><div><br></div><div>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:</div><div><a href="https://lists.simtk.org/pipermail/vp-integration-subgroup/2021-April/000073.html">https://lists.simtk.org/pipermail/vp-integration-subgroup/2021-April/000073.html</a></div><div><br></div><div>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. </div><div><br></div><div>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. </div><div><br></div><div>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">https://www.frontiersin.org/about/policies-and-publication-ethics</a></div><div><br></div><div>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.</div><div><br></div><div>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. </div><div><br></div><div>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. </div><div><br></div><div>Hopefully I am clear enough now. </div><div><br></div><div>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.</div><div><br></div><div>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.</div><div><br></div><div>Hopefully this email will fix things and make sure our delerations are accurate. </div><div><br></div><div><br></div><div> Jacob</div><div><br></div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jan 19, 2022 at 12:31 PM James 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 dir="ltr">Dear Jacob:<div><br></div><div>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.</div><div><br></div><div>JAG</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">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></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 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" target="_blank">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>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" rel="noreferrer" target="_blank">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="gmail-m_-2570967256091897635gmail-m_-3522333716438701893m_-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="gmail-m_-2570967256091897635gmail-m_-3522333716438701893m_-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>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><div dir="ltr">James A. Glazier, PhD<div>Professor of Intelligent Systems Engineering, Adjunct Professor of Physics</div><div>Director Biocomplexity Institute<br><div><div>Indiana University, Bloomington</div></div></div><div>(812) 391-2159</div></div></div>
</blockquote></div>