<div dir="ltr">Hi James,<div><br></div><div>Apologies - I must have missed your email request. If anyone else wants access and did not get it, please let me know - I will do my best to give you access within a day. </div><div><br></div><div>For those who have access. Please no more additions - from now on just corrections of typos, grammer, and grave errors. Anything else, please leave a comment and we can discuss it.</div><div><br></div><div>I really want the paper out quickly - hopefully we can finish this and submit quickly.</div><div><br></div><div> Jacob</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Oct 28, 2021 at 3:17 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>Dear Jacob:</p>
<p>I would like to review the document. I had asked for access a few
weeks ago. Happy to look in the next few days.</p>
<p>JAG<br>
</p>
<div>On 10/24/2021 4:40 AM, Jacob Barhak
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Eric,
<div><br>
</div>
<div>You are the last one I remember who wanted to edit. Please
check the manuscript</div>
<div><a href="https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing" target="_blank">https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing</a><br>
</div>
<div><br>
</div>
<div>I finished editing the references and am almost ready for
transformation to match the guidelines. I finished addressing
the editor requesting for removal of bullet points everywhere
but the stochastic section . </div>
<div><br>
</div>
<div>I ask that you do not add any more references and focus
only on text in the stochastic section. Handling the
references took about 4 hours alone and still needs
inspection. </div>
<div><br>
</div>
<div>However, I will appreciate help with minor proofs - I made
significant changes so there is a chance for typos still.
Some of the changes have been made after more than 12 hours of
consecutive work. So polish will help - yet no more major
changes. </div>
<div><br>
</div>
<div>The tasks left to do are:</div>
<div>- Ask John Gennari to inspect the paper again - it has
major contributions from his version and he should join the
authors list - I must be ask again </div>
<div>- Finish the edits to the stochastic section - Eric - you
asked for this</div>
<div>- Finish formatting to fit the Journal guidelines </div>
<div>- Add a cover letter and split the paper into sections to
be uploaded to the journal web site</div>
<div>- Approve the version with all authors - we must do this
again and get full approval - this may take a while</div>
<div>- Determine who else wants to be listed as
corresponding author - currently I marked Marcell and myself,
yet others may want to correspond. </div>
<div>- Upload the paper to the journal submission system</div>
<div><br>
</div>
<div>I hope for no obstacles and full cooperation to make the
process smooth.</div>
<div><br>
</div>
<div> Jacob</div>
<div><br>
</div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Sat, Oct 23, 2021 at 9:08
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="ltr">So Gilberto,
<div><br>
</div>
<div>The last approved version is the only one we can
continue from - this is unfortunate that there is a need
to back port some modifications - hence the conversation
with Eric and Hana - yet to maintain traceability and
honor all contributors - this is necessary.</div>
<div><br>
</div>
<div>And yes, there will be some differences - it's
unavoidable. Yet I pretty much merged the other traceable
versions by now. If I missed anything - I apologize -
there is a limit to human capabilities. </div>
<div><br>
</div>
<div>We discussed this multiple times on this list, if this
is a stopper for you, let me know immediately so I will
stop work to resolve this issue.</div>
<div><br>
</div>
<div>Otherwise, I will continue - I think I resolved most
points except from references and removal of bullets -
still working on that and I will have to deal with
modifying conclusions at the end. </div>
<div><br>
</div>
<div>And Gilberto, if you want to contribute time towards
changing order of sections and handle references to comply
with the target journal guidelines, please go online on
the Jitsi channel.and I will show you the extent of work
needed. I will be here for at least 3 more hours - until
midnight - yet to be efficient, please join on jitsi if
you want to talk while I continue modifications. </div>
<div><br>
</div>
<div>I hope I can finish most of the work except references
perhaps by midnight. </div>
<div><br>
</div>
<div> Jacob</div>
<div><br>
</div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Sat, Oct 23, 2021 at
8:32 PM Gilberto Gonzalez-Parra <<a href="mailto:gilberto.gonzalezparra@nmt.edu" target="_blank">gilberto.gonzalezparra@nmt.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">Hi Jacob,
<div><br>
</div>
<div>I noticed that we are not using the last version
that has many modifications. Are you using the
previous version that was originally submitted to
cureus ? and trying to incorporate the changes of the
last version ?</div>
<div><br>
</div>
<div>I noticed that the section/challenge <span style="font-size:11pt;line-height:107%;font-family:Arial,sans-serif;color:black"><b>Barriers
to model implementation and real-world use</b> was
removed. I think in one of the emails it says that
there is no solution proposed for this. I can write
some general ideas for this. </span></div>
<div><span style="font-size:11pt;line-height:107%;font-family:Arial,sans-serif;color:black"><br>
</span></div>
<div><span style="font-size:11pt;line-height:107%;font-family:Arial,sans-serif;color:black">In
the current version in the table it appears "</span><span style="background-color:transparent;color:rgb(0,0,0);font-family:Arial;font-size:11pt;white-space:pre-wrap"><b>Model application and implementation barriers</b>" just after "</span><span style="background-color:transparent;color:rgb(0,0,0);font-family:Arial;font-size:11pt;font-weight:700;white-space:pre-wrap">Missing Annotations in Models" </span><span style="background-color:transparent;color:rgb(0,0,0);font-family:Arial;font-size:11pt;white-space:pre-wrap"> but later in the document appears just before stochastic modeling. I think we should keep the same order that is in the table. The article would look better organized.</span></div>
<div><span style="background-color:transparent;color:rgb(0,0,0);font-family:Arial;font-size:11pt;white-space:pre-wrap">
</span></div>
<div><span style="background-color:transparent;color:rgb(0,0,0);font-family:Arial;font-size:11pt;white-space:pre-wrap">Best,</span></div>
<div><br>
</div>
<div>
<div>
<div dir="ltr">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">***************************************************************************</div>
<div dir="ltr">Gilberto C.
Gonzalez-Parra, <span>Ph.D
in Applied Mathematics.</span></div>
<div dir="ltr"><font face="Helvetica
Neue, Helvetica, Arial, Lucida
Grande, sans-serif, serif,
EmojiFont" color="#000000"><span style="font-size:13px">Faculty
of the </span></font>Mathematics
Department
<div>
<div>New Mexico Tech, NM, USA.</div>
</div>
<div>****************************************************************************</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Sat, Oct 23, 2021
at 5:38 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="ltr">Hi Eric, and also greeting for the
other paper contributors
<div>
<div><br>
</div>
<div>Here is a real time update just to give an
idea of current editing status.</div>
<div><br>
</div>
<div>It took almost 6 hours to get the
manuscript to the point that contributions from
Sheriff, Alex, John Gennari, and Hana were
integrated. I assume Eric will add his edits
later - since those are in one section, it
should not cause any conflict. However, Eric,
please be careful when editing the
stochastic section. Pease look at the comments
Hana and I exchanged. I am also adding the chat
between us so it will be easier on you:</div>
<div><br>
</div>
<div>"</div>
<div>Hi Hana<br>
Can you see the chat?<br>
I can. There's just a lot going on around here
right now, so I'm not fast with typing<br>
I put the references in the comments, can you
see them?<br>
Yes I See them - yet you will have to ensure
that this is your text - you see, you copied
text from a document where we do not have
contributor history - this was the main issue -
so you will have not to prove this was your text
and only your text - this is the problem I am
faced with - I have to establish tracability -
in this document I know you added the text - yet
I cannot verify that you did not include text
from anonymous since I already concluded you
added text from Alex - this is how I stumbled on
this - I apologize yet I really am serious about
tracing back authorship..<br>
And thanks fro helping<br>
If you want, you can join jitsi: <a href="https://meet.jit.si/CollaborativePaperEditing" target="_blank">https://meet.jit.si/CollaborativePaperEditing</a>
and we can chat using voice<br>
I just saw your comment - it is public
confirmation - this is good enough thank you <br>
The first two paragraphs are from the original
paper. The third paragraph is from Alex. The
last two are mine. It looks like someone (other
than me) italicized the in vitro and in vivo and
changed the verb on the "Even data that are..."
(I had is), but everything else is mine.<br>
If you can modify things to the original version
you added - it will be better - if someone
manipulated the text I want to remove it - even
if it is small changes <br>
I know you're trying to get things done today,
but I'll be out tonight, so if anything else
comes up, I probably won't get to it until the
morning. <br>
Well, "are" is the correct verb there, so that
should probably stay. I can remove the
italicization.<br>
Do not worry - I am making good progress and may
not need help until I am done - I appreciate the
help and the fact you are working on it over the
weekend - I will later also make this chat
public for transparency. I do believe you have
contributed a lot to this paper - its not the
first time you are going over it - I can only
thank you . <br>
the are was my change today I believe so its not
a problem - yet google suggests is instead I
guess is and are both acceptable with data ....
nevermind that.<br>
"</div>
<div><br>
</div>
<div>I did my best to keep all ideas and other
texts intact and there are many comments to mark
changes - the paper became longer, yet not too
much and I feel it is still reasonable .</div>
<div><br>
</div>
<div>I am now moving to the next part of complying
with the requests of the editor:</div>
<div>1) Determine authorship</div>
<div>2) Converging format to journal guidelines -
this also means references</div>
<div>3) Detach from group - some elements already
marked</div>
<div>4) Revise bullet points into paragraphs</div>
<div><br>
</div>
<div>I plan to continue editing until midnight CST
with a break for dinner - so if anyone has
comments - please feel free to join the open
channel that shows the editing and influence
real-time.</div>
<div><br>
</div>
<div>Hopefully you will find the merged version in
order. </div>
<div><br>
</div>
<div> Jacob</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Sat, Oct 23,
2021 at 2:50 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="ltr">Hi Eric,
<div><br>
</div>
<div>You wanted to edit the stochastic section -
you are welcome to do it. Yet I ask no more
references or deletions - I am overloaded
already. </div>
<div><br>
</div>
<div>The version benign edited is:</div>
<div><a href="https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit" target="_blank">https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit</a><br>
</div>
<div><br>
</div>
<div>You will need to login so that your edits
will be traceable.</div>
<div><br>
</div>
<div>You can join me while editing in:</div>
<div><a href="https://meet.jit.si/CollaborativePaperEditing" target="_blank">https://meet.jit.si/CollaborativePaperEditing</a><br>
</div>
<div><br>
</div>
<div>I am sharing my screen there while
editing. </div>
<div><br>
</div>
<div>You might be able to help me with other
sections as well.</div>
<div><br>
</div>
<div> Jacob</div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Sat, Oct
23, 2021 at 2:44 PM Eric Forgoston <<a href="mailto:eric.forgoston@montclair.edu" target="_blank">eric.forgoston@montclair.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">Hi Jacob,
<div><br>
</div>
<div>If you give me a link to the paper you
are editing and edit access to the paper I
can update the stochastic section.</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Eric<br clear="all">
<div>
<div dir="ltr">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div><span>---------------------<br>
Dr. Eric
Forgoston<br>
Professor of
Applied
Mathematics<br>
Chair,
Department of
</span><span><span><span>Applied
Mathematics
and Statistics</span></span><br>
Montclair
State
University<br>
Montclair, NJ
07043 USA<br>
+1 973
655-7242 <br>
<span><a href="https://eric-forgoston.github.io/" target="_blank">https://eric-forgoston.github.io/</a></span></span><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Sat,
Oct 23, 2021 at 1:39 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="ltr">Greetings Paper
Contributors,
<div><br>
</div>
<div>The paper editing process started
and you can follow it live on:</div>
<div><a href="https://meet.jit.si/CollaborativePaperEditing" target="_blank">https://meet.jit.si/CollaborativePaperEditing</a><br>
</div>
<div><br>
</div>
<div>I will keep the channel open as
long as I am editing so that the
process will be as transparent as
possible. </div>
<div><br>
</div>
<div>The first step would be to
reconcile the differences between
those 4 versions traceable back to
authors:</div>
<div><a href="https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit" target="_blank">https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit</a>
- the submitted version<br>
</div>
<div><a href="https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit" target="_blank">https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit</a>
- first committed version<br>
</div>
<div><a href="https://docs.google.com/document/d/1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh/edit" target="_blank">https://docs.google.com/document/d/1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh/edit</a>
- first committed version<br>
</div>
<div><a href="https://drive.google.com/file/d/1U_lTHrV6STXWNT3GiCepvsLk1WdYgzN5/view" target="_blank">https://drive.google.com/file/d/1U_lTHrV6STXWNT3GiCepvsLk1WdYgzN5/view</a>
- its the first document posted<br>
</div>
<div><br>
</div>
<div>After this step is done I will move
towards adhering to those
instructions:</div>
<div><a href="https://www.frontiersin.org/about/author-guidelines" target="_blank">https://www.frontiersin.org/about/author-guidelines</a><br>
</div>
<div><br>
</div>
<div>I estimate I will be working till
late today with very few breaks and
hopefully make sufficient progress.</div>
<div><br>
</div>
<div>Feel free to visit and perhaps even
help. If you do, please raise your
voice so I can hear you - I am sharing
my screen and not seeing the video
when I edit - so you will have to let
me know you are in the room. </div>
<div><br>
</div>
<div>Hopefully some of you will visit.</div>
<div><br>
</div>
<div> Jacob</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On
Fri, Oct 22, 2021 at 2:52 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">Thanks Sheriff,
<div dir="auto"><br>
</div>
<div dir="auto">With your green
light I can start editing</div>
<div dir="auto"><br>
</div>
<div dir="auto">Eric, the base of
John's version will be merged to
the best of my ability, yet
unfortunately, it has omissions
and later version based on it are
not traceable back to
contributors, so I can only use
some of the base. </div>
<div dir="auto"><br>
</div>
<div dir="auto">If you want to
repeat edits so those will be
traceable it is possible. Yet we
cannot copy verbatim without going
to details. </div>
<div dir="auto"><br>
</div>
<div dir="auto">To make things
easier, I will open a channel
over the weekend during edits
where anyone can join and
communicate while watching the
edits live. </div>
<div dir="auto"><br>
</div>
<div dir="auto">Hopefully it will
make things smoother. </div>
<div dir="auto"><br>
</div>
<div dir="auto"> Jacob</div>
<div dir="auto"><br>
</div>
<div dir="auto"><br>
</div>
<div dir="auto"><br>
</div>
<div dir="auto"><br>
</div>
<div dir="auto"><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On
Fri, Oct 22, 2021, 13:40 Eric
Forgoston <<a href="mailto:eric.forgoston@montclair.edu" target="_blank">eric.forgoston@montclair.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 dir="ltr">Dear Jacob and
all,
<div><br>
</div>
<div>I suggest, as others have
done, to use the John G.
version as structurally it
has already cleaned up most
of the issues raised by the
Editor, and also has many
revised and improved
sections. In particular, the
stochastic section that I
worked on with others is far
superior to the one in the
paper submitted to
Frontiers.</div>
<div><br>
</div>
<div>Best wishes,</div>
<div><br>
</div>
<div>Eric<br clear="all">
<div>
<div dir="ltr">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div><span>---------------------<br>
Dr. Eric
Forgoston<br>
Professor of
Applied
Mathematics<br>
Chair,
Department of
</span><span><span><span>Applied
Mathematics
and Statistics</span></span><br>
Montclair
State
University<br>
Montclair, NJ
07043 USA<br>
+1 973
655-7242 <br>
<span><a href="https://eric-forgoston.github.io/" rel="noreferrer" target="_blank">https://eric-forgoston.github.io/</a></span></span><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri,
Oct 22, 2021 at 12:57 PM
Rahuman 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>Congratulations
Marcella,
<div><br>
</div>
<div>Hi Jacob and all,</div>
<div><br>
</div>
<div>As Tomas mentioned,
John G’s version is bit
more organised. </div>
<div>Although it would be
nice to take that one
forward, I also fine
with you recovering your
version incorporating
requested changes
including mine. </div>
<div>I would prefer this
manuscript progresses
ahead, instead of
another long discussion.
</div>
<div>Green signal from my
side.</div>
<div>Best regards</div>
<div>Sheriff</div>
<div><br>
</div>
<div>
<div>
<div><br>
<blockquote type="cite">
<div>On 22 Oct
2021, at 01:49,
Jacob Barhak
<<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer" target="_blank">jacob.barhak@gmail.com</a>>
wrote:</div>
<br>
<div>
<div dir="auto" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">Congratulations
Marcella,
<div dir="auto"><br>
</div>
<div dir="auto">Indeed
you bring good
news. <br>
<div dir="auto"><br>
</div>
<div dir="auto">You
should not
worry about
the
manuscript.
You have done
plenty and we
can handle if
from now on,
you can focus
on your
family. </div>
<div dir="auto"><br>
</div>
<div dir="auto">
Jacob</div>
</div>
</div>
<br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<div class="gmail_quote" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<div dir="ltr" class="gmail_attr">On Thu, Oct 21, 2021, 10:33 Torres, Marcella <<a href="mailto:mtorres@richmond.edu" rel="noreferrer" 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>
<div dir="auto" style="direction:ltr;margin:0px;padding:0px;font-family:sans-serif;font-size:11pt">This
streamlined
approach
sounds good to
me; thanks
Jacob for
offering to
coordinate
edits. I think
the one month
deadline is a
good maximum,
since
Frontiers
favors quick
turnaround.<span id="gmail-m_-6812091254919142191gmail-m_-2697268861042949202gmail-m_-1689782665546364892gmail-m_454394027104465375gmail-m_1100449795159862914gmail-m_-3690383742767868331gmail-m_208464925022974690gmail-m_-6684231236743761144gmail-m_5330779350599904174m_6811753030514762076gmail-m_-4652177745642668797m_-8816081919050643472ms-outlook-android-cursor"></span><br>
<br>
</div>
<div dir="auto" style="direction:ltr;margin:0px;padding:0px;font-family:sans-serif;font-size:11pt">I
don't insist
on
participating
in the
revisions, but
I am available
to help with
cleaning up
grammar,
typos, and so
on - I noticed
quite a few
minor issues
when reviewing
the document
for
submission.
However, my
son was born a
few days ago
and I have
limited time.<span> </span><br>
<br>
</div>
<div dir="auto" style="direction:ltr;margin:0px;padding:0px;font-family:sans-serif;font-size:11pt">Marcella</div>
<hr style="display:inline-block;width:545.578px">
<div id="gmail-m_-6812091254919142191gmail-m_-2697268861042949202gmail-m_-1689782665546364892gmail-m_454394027104465375gmail-m_1100449795159862914gmail-m_-3690383742767868331gmail-m_208464925022974690gmail-m_-6684231236743761144gmail-m_5330779350599904174m_6811753030514762076gmail-m_-4652177745642668797m_-8816081919050643472divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif"><b>From:</b><span> </span>Jacob
Barhak <<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer noreferrer" target="_blank">jacob.barhak@gmail.com</a>><br>
<b>Sent:</b><span> </span>Wednesday,
October 20,
2021 11:53:58
PM<br>
<b>To:</b><span> </span>Alexander
Kulesza <<a href="mailto:alexander.kulesza@novadiscovery.com" rel="noreferrer
noreferrer" target="_blank">alexander.kulesza@novadiscovery.com</a>><br>
<b>Cc:</b><span> </span>Hana
<<a href="mailto:h.dobrovolny@tcu.edu" rel="noreferrer noreferrer" target="_blank">h.dobrovolny@tcu.edu</a>>;
James Osborne
<<a href="mailto:jmosborne@unimelb.edu.au" rel="noreferrer noreferrer" target="_blank">jmosborne@unimelb.edu.au</a>>;
John Rice <<a href="mailto:john.rice@noboxes.org" rel="noreferrer noreferrer" target="_blank">john.rice@noboxes.org</a>>; Torres, Marcella
<<a href="mailto:mtorres@richmond.edu" rel="noreferrer noreferrer" target="_blank">mtorres@richmond.edu</a>>;<span> </span><a href="mailto:vp-reproduce-subgroup@lists.simtk.org" rel="noreferrer
noreferrer" target="_blank">vp-reproduce-subgroup@lists.simtk.org</a><span> </span><<a href="mailto:vp-reproduce-subgroup@lists.simtk.org" rel="noreferrer
noreferrer" target="_blank">vp-reproduce-subgroup@lists.simtk.org</a>>;<span> </span><a href="mailto:vp-integration-subgroup@lists.simtk.org" rel="noreferrer
noreferrer" target="_blank">vp-integration-subgroup@lists.simtk.org</a><span> </span><<a href="mailto:vp-integration-subgroup@lists.simtk.org" rel="noreferrer
noreferrer" target="_blank">vp-integration-subgroup@lists.simtk.org</a>>;
Jonathan Karr
<<a href="mailto:jonrkarr@gmail.com" rel="noreferrer noreferrer" target="_blank">jonrkarr@gmail.com</a>>;
John Gennari
<<a href="mailto:gennari@uw.edu" rel="noreferrer noreferrer" target="_blank">gennari@uw.edu</a>>;
Winston Garira
<<a href="mailto:Winston.Garira@univen.ac.za" rel="noreferrer noreferrer" target="_blank">Winston.Garira@univen.ac.za</a>><br>
<b>Subject:</b><span> </span>Re:
[Vp-integration-subgroup] Fwd: 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-color:yellow"><span style="color:red"><b>External Email:</b></span><span> Use caution in
opening links,
attachments,
and buying
gift cards.</span></div>
<br>
<div>
<div dir="ltr">Thanks
Alex, Thanks
John,
<div><br>
</div>
<div>Your
contribution
is appreciated
and since John
cleared us to
move
forward it
simplifies
things. I hope
he will change
his mind about
authorship
since he
contributed a
lot, yet I
will respect
his wishes -
perhaps after
seeing the
final version
he will change
his mind. </div>
<div><br>
</div>
<div>If
Sheriff gives
me a green
light I can
incorporate
his
modifications
as well. I do
ask that if
any of the
listed authors
has any
serious
concerns and
plans to not
approve a
modified version
that addresses
the editors
requests alone
alongside
those I
mentioned
above, to step
up before the
work is done
so we can
resolve things
before energy
is spent. </div>
<div><br>
</div>
<div>If there
will be no
blocks I plan
to start work
over the
weekend if I
see no
objections by
then.</div>
<div><br>
</div>
<div>I
appreciate the
offer to help
with
bibliography,
from
experience I
know it is
perhaps the
most time
consuming.
However,
since we have
many links and
specialized
publications
in our list -
I am not sure
if any tool
can make it
easier - the
last time I
had to do a
lot of manual
work to fit a
specific
format and
find all
missing links
and also fix
some errors -
no tool would
have helped me
then. This
time I think
it will be a
bit easier.
Yet I ask for
no more
references to
be added - I
also want to
add more
references,
yet I am
stopping
myself. We can
always expand
the work in
another future
version if we
have new
findings. </div>
<div><br>
</div>
<div>Again
note that I
will only try
to address the
requests of
the editor at
this point
without trying to
perfect
anything
beyond what I
wrote above
and I want to
keep things as
traceable as
possible. Once
I am done,we
will see if we
can approve
this
manuscript for
publication.</div>
<div><br>
</div>
<div>Unless
any blockers
appear, if
anyone wants
to actively
participate in
the editing
over the
weekend,
please let me
know so we can
communicate
better.</div>
<div><br>
</div>
<div>
<span> </span>Jacob</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
<br>
<div>
<div dir="ltr">On
Tue, Oct 19,
2021 at 2:02
AM Alexander
Kulesza <<a href="mailto:alexander.kulesza@novadiscovery.com" rel="noreferrer
noreferrer" target="_blank">alexander.kulesza@novadiscovery.com</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">Dear
Jacob,
<div>thanks
for forwarding
and you
suggestions,
which seems
more than
reasonable. </div>
<div><br>
</div>
<div>My
contributions
from May 19th,
May31st and
June 2nd are
in <a href="https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit?usp=sharing&ouid=113860487708206439519&rtpof=true&sd=true" rel="noreferrer noreferrer" target="_blank">https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit?usp=sharing&ouid=113860487708206439519&rtpof=true&sd=true</a> </div>
<div><br>
</div>
<div>The other
document <a href="https://docs.google.com/document/d/1esZvWWVBvpwvuFUi3C3161lthZkEBFyMRrwwozitBi4/edit?usp=sharing" rel="noreferrer noreferrer" target="_blank">https://docs.google.com/document/d/1esZvWWVBvpwvuFUi3C3161lthZkEBFyMRrwwozitBi4/edit?usp=sharing</a><span> </span>I
created
initially to
suggest my
edits without
editing the
core version
can be
disregarded as
I have
tranferred all
of them into
the main
document,
cited above. </div>
<div><br>
</div>
<div>If we
were on Latex,
I could offer
to create the
bibliography
but
unfortunately
we lack a
bibliography
manager
integrated in
Word/GDoc. If
we were to
work with
Mendeley and
someone could
create a group
for this paper
that has a
shared library
I could offer
to transfer
citations from
the paper into
that database
too. </div>
<div><br>
</div>
<div>Please
let me know.</div>
<div>A</div>
<div><br>
</div>
<div><br>
</div>
</div>
<br>
<div>
<div dir="ltr">On
Tue, 19 Oct
2021 at 05:51,
Jacob Barhak
<<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer noreferrer" target="_blank">jacob.barhak@gmail.com</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>Greetings
white paper
contributors,</div>
<div><br>
</div>
<div>Below is
the response
from the
editor to my
request and my
thank you.</div>
<div><br>
</div>
<div>The
editor grants
us the
extension by
rejecting the
paper and
allowing time
to come up
with a better
version. There
is no time
limit now, yet
I want to get
her a revised
version
within a
month. </div>
<div><br>
</div>
<div>The
requests are
simple and
easy to
satisfy - and
I know there
are many of
you who want
more
revisions, yet
I suggest we
reduce them to
only what is
manageable and
necessary.
Otherwise we
will never get
this paper
published
despite its
importance. </div>
<div><br>
</div>
<div>The most
time consuming
effort
would be
adhering to
the journal
format as
defined here:</div>
<div><a href="https://www.frontiersin.org/about/author-guidelines" rel="noreferrer noreferrer" target="_blank">https://www.frontiersin.org/about/author-guidelines</a><br>
</div>
<div><br>
</div>
<div>I think
the most time
consuming task
would be
dealing with
the references
- otherwise
the format
guidelines seem
reasonable.</div>
<div><br>
</div>
<div>We can
also add some
revisions we
started
working on.
However, I
will
personally
insist on :</div>
<div>1.
traceability -
currently
there is no
traceability
in the revised
version in the
summer</div>
<div>2. non
deletion - do
not delete any
content unless
you wrote it
originally or
unless you
announced it
beforehand to
the group and
got no
objections
within a few
days </div>
<div>3. Avoid
Adding more
material that
is not in the
existing
versions we
had -
especially
references -
we don't have
time for that
and that is
not what the
editor asked
us anyway. </div>
<div><br>
</div>
<div>I will
also ask for
fast responses
from all
contributors. </div>
<div><br>
</div>
<div>To be
practical, I
marked the
submitted
version and
opened the
document to
those who
requested
editing rights
in the past.
If you want
editing
rights, let me
know -
however, the
edits should
be minimal and
focus on areas
you edited in
the past and
be aware that
if your edits
will not get
approved by
everyone, we
will revert to
the old
version we all
accepted. The
submitted
version
was marked so
we can always
get back to
it. </div>
<div><br>
</div>
<div>If you
want editing
rights, let me
know and I
will respond
within a day -
I cannot
promise to be
fatter than
that these
days. </div>
<div><br>
</div>
<div>Alex,
John, Sheriff,
you had other
versions you
created, I
want to merge
some of your
changes to the
manuscript in
this version -
here are my
suggestions:</div>
<div><br>
</div>
<div>-
Sheriff, I
will soften
the language
as you
requested -
this was your
main request
in the past,
yet I will go
over your list
of changes and
see what I
else can be
done without
reinventing
the paper</div>
<div>- John -
I will 1)
merge the
credibility
sections , 2)
delete the
history
related to the
working group
since it
matches with
what was
requested, and
3) move the
model
validation
barrier
section away
from the table
since we did
not suggest a
solution
there.
Hopefully this
will make the
paper more
appealing to
you and you
will be
willing to add
your name to
the list </div>
<div>- Alex,
your changes
were made
on May 16,
2021 and
shared in a
way I can see
the
differences
and trace them
back to you -
I will try to
add your
references and
see if I can
incorporate
your text
changes as
much as I
can. </div>
<div><br>
</div>
<div>If the 3
of you are ok
with me
migrating your
changes, I can
start the work
to save time.
Yet I want
your ok
first. </div>
<div><br>
</div>
<div>I know
Eric and Hana
were
working on
some sections
and feel
strongly about
those -
specifically
the stochastic
modeling part
- I am open to
your changes,
please suggest
what you feel
strongly
about..</div>
<div><br>
</div>
<div>I recall
Johnathan Karr
wanted to make
some changes,
please let me
know if there
is anything
you feel
strongly about
- he had a lot
of text in the
paper ..</div>
<div><br>
</div>
<div>If I
forgot anyone
who had
major requests,
please
remind me. .</div>
<div><br>
</div>
<div>I am
trying to
avoid a never
ending
revisioning
cycle. So I am
asking you to
trust me and
centralize the
work in hope I
get a better
version by the
end of the
week..</div>
<div><br>
</div>
<div>Hopefully
most of you
will be ok
with that.</div>
<div><br>
</div>
<div>
Jacob</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<div>
<div dir="ltr">----------
Forwarded
message
---------<br>
From:<span> </span><strong dir="auto">Jacob
Barhak</strong><span> </span><span dir="auto"><<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer noreferrer" target="_blank">jacob.barhak@gmail.com</a>></span><br>
Date: Mon, Oct
18, 2021 at
9:34 PM<br>
Subject: Re:
Shayn
Peirce-Cottler
via Frontiers:
Manuscript<br>
To:
Peirce-Cottler,
Shayn (smp6p)
<<a href="mailto:smp6p@virginia.edu" rel="noreferrer noreferrer" target="_blank">smp6p@virginia.edu</a>><br>
Cc: Shayn
Peirce-Cottler
(Via
FrontiersIn)
<<a href="mailto:shayn@virginia.edu" rel="noreferrer noreferrer" target="_blank">shayn@virginia.edu</a>>,<a href="mailto:systemsbiology.editorial.office@frontiersin.org" rel="noreferrer
noreferrer" target="_blank">systemsbiology.editorial.office@frontiersin.org</a><span> </span><<a href="mailto:systemsbiology.editorial.office@frontiersin.org" rel="noreferrer
noreferrer" target="_blank">systemsbiology.editorial.office@frontiersin.org</a>>,
Vodovotz,
Yoram <<a href="mailto:vodovotzy@upmc.edu" rel="noreferrer noreferrer" target="_blank">vodovotzy@upmc.edu</a>><br>
</div>
<br>
<br>
<div dir="ltr">Thanks Shayn,
<div><br>
</div>
<div>You will
get a revised
manuscript
targeted at
your journal
and get back
to you with a
more polished
version and
satisfies your
requests. </div>
<div><br>
</div>
<div>It will
also allow us
to incorporate
newer versions
of the text
that answer
some of your
requests. We
really wish to
publish it
fast, yet we
need more
time for the
approval
process. So
your solution
seems correct
- I hope you
hear back from
us within a
month or so.</div>
<div><br>
</div>
<div>Many thanks
for the rapid
responses.</div>
<div><br>
</div>
<div>
Jacob</div>
<div><br>
</div>
<div><br>
</div>
<div>--<br>
Jacob Barhak
Ph.D. <br>
Sole
Proprietor,
Software
Developer, and
Computational
Disease
Modeler<br>
<br>
Jacob Barhak
Analytics<br>
701 Brazos St<br>
Suite 548<br>
Austin TX,
78701<br>
<br>
Email:<span> </span><a href="mailto:jacob.barhak@gmail.com" rel="noreferrer noreferrer" target="_blank">jacob.barhak@gmail.com</a></div>
<div><br>
<a href="https://sites.google.com/view/jacob-barhak/home" rel="noreferrer noreferrer" target="_blank">https://sites.google.com/view/jacob-barhak/home</a><br>
<br>
</div>
<div><br>
</div>
</div>
<br>
<div>
<div dir="ltr">On
Mon, Oct 18,
2021 at 7:43
PM
Peirce-Cottler,
Shayn (smp6p)
<<a href="mailto:smp6p@virginia.edu" rel="noreferrer noreferrer" target="_blank">smp6p@virginia.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 lang="EN-US">
<div>
<p><span style="font-size:12pt">Hi
Jacob,<span> </span></span></p>
<p><span style="font-size:12pt"> </span></p>
<p><span style="font-size:12pt">Thank
you for your
detailed
reply. I agree
that the
issues can be
addressed as
you have
described
below, and
that you may
need more time
to do so.
Hence, I am
going to
officially
reject this
first
submission to
remove any
imposed
deadlines, and
I certainly
encourage you
to make the
updates listed
below, and
submit a new
manuscript at
your earliest
convenience. </span></p>
<p><span style="font-size:12pt"> </span></p>
<p><span style="font-size:12pt">Please
let me know if
you have any
questions, and
thanks again
for
considering
this journal!
I think the
topic fits
very nicely
with the scope
of the
journal, and
it is
certainly an
important
topic to our
multi-scale
modeling
community!</span></p>
<p><span style="font-size:12pt"> </span></p>
<p><span style="font-size:12pt">-Shayn</span></p>
<p><span style="font-size:12pt"> </span></p>
<p><span style="font-size:12pt"> </span></p>
<div>
<p><span>Shayn
Peirce-Cottler, Ph.D.</span></p>
<p><span>Professor
of Biomedical
Engineering</span></p>
<p><span>Harrison
Distinguished
Teaching
Professor</span></p>
<p><span>BME
Graduate
Program
Director</span></p>
<p><span>University
of Virginia</span></p>
</div>
<p><span>Charlottesville,
VA</span><span style="font-size:12pt"></span></p>
<p><span style="font-size:12pt"> </span></p>
<div style="border-style:solid none none;border-top-width:1pt;border-top-color:rgb(181,196,223);padding:3pt 0in 0in">
<p><b><span style="font-size:12pt">From:<span> </span></span></b><span style="font-size:12pt">Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer noreferrer" target="_blank">jacob.barhak@gmail.com</a>><br>
<b>Date:<span> </span></b>Monday,
October 18,
2021 at 1:57
AM<br>
<b>To:<span> </span></b>Peirce-Cottler
Shayn <<a href="mailto:shayn@virginia.edu" rel="noreferrer noreferrer" target="_blank">shayn@virginia.edu</a>><br>
<b>Cc:<span> </span></b>"<a href="mailto:systemsbiology.editorial.office@frontiersin.org" rel="noreferrer
noreferrer" target="_blank">systemsbiology.editorial.office@frontiersin.org</a>"
<<a href="mailto:systemsbiology.editorial.office@frontiersin.org" rel="noreferrer noreferrer" target="_blank">systemsbiology.editorial.office@frontiersin.org</a>>,
"Vodovotz,
Yoram" <<a href="mailto:vodovotzy@upmc.edu" rel="noreferrer noreferrer" target="_blank">vodovotzy@upmc.edu</a>><br>
<b>Subject:<span> </span></b>Re:
Shayn
Peirce-Cottler
via Frontiers:
Manuscript</span></p>
</div>
<div>
<p> </p>
</div>
<div>
<p>Hi Shayn,</p>
<div>
<p> </p>
</div>
<div>
<p>Thanks for
returning the
response
quickly. To
you comments. </p>
</div>
<div>
<p> </p>
</div>
<div>
<p>1. This is
the list of
authors that
agreed to
submit this
manuscript for
review - I
collected
their
approvals for
this version
personally. </p>
</div>
<div>
<p> </p>
</div>
<div>
<ol style="margin-top:0in" type="1" start="1">
<li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal"><span style="font-family:Arial,sans-serif">Jonathan Karr, Icahn Institute for
Data Science
and Genomic
Technology and
Department of
Genetics and
Genomic
Sciences,
Icahn School
of Medicine at
Mount Sinai
USA</span></li>
<li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal"><span style="font-family:Arial,sans-serif">Rahuman Sheriff, The European
Bioinformatics
Institute
(EMBL-EBI), UK</span></li>
<li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal"><span style="font-family:Arial,sans-serif">James Osborne, School of
Mathematics
and
Statistics,
University of
Melbourne,
Australia</span></li>
<li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal"><span style="font-family:Arial,sans-serif">Gilberto Gonzalez Parra,
Mathematics
Department,
New Mexico
Tech, USA</span></li>
<li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal"><span style="font-family:Arial,sans-serif">Eric Forgoston, Department of
Applied
Mathematics
and
Statistics,
Montclair
State
University,
USA</span></li>
<li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal"><span style="font-family:Arial,sans-serif">Ruth Bowness, Department of
Mathematical
Sciences,
University of
Bath, UK</span></li>
<li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal"><span style="font-family:Arial,sans-serif">Yaling Liu, Department of
Mechanical
Engineering
and Mechanics
, Department
of
Bioengineering,
Lehigh
University,
USA</span></li>
<li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal"><span style="font-family:Arial,sans-serif">Robin Thompson, Mathematics
Institute
& The
Zeeman
Institute for
Systems
Biology and
Infectious
Disease
Epidemiology
Research,
University of
Warwick, UK</span></li>
<li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal"><span style="font-family:Arial,sans-serif">Winston Garira - Department Of
Mathematics
And Applied
Mathematics ,
Modelling
Health and
Environmental
Linkages
Research
Group.
University of
Venda, South
Africa</span></li>
<li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal"><span style="font-family:Arial,sans-serif">Jacob Barhak - Barhak, Jacob, USA</span></li>
<li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal"><span style="font-family:Arial,sans-serif">John Rice - Independent Retired
Working Group
Volunteer, USA</span></li>
<li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal"><span style="font-family:Arial,sans-serif">Marcella Torres, School of Arts and
Sciences,
University of
Richmond, USA</span></li>
<li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal"><span style="font-family:Arial,sans-serif">Hana M. Dobrovolny , Department of
Physics &
Astronomy,
Texas
Christian
University,
Fort Worth,
USA</span></li>
<li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal"><span style="font-family:Arial,sans-serif">Tingting Tang, Department of
Mathematics
and Statistics
in San Diego
State
University
(SDSU) and
SDSU Imperial
Valley, USA</span></li>
<li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal"><span style="font-family:Arial,sans-serif">William Waites, Centre for
Mathematical
Modelling of
Infectious
Diseases,
London School
of Hygiene and
Tropical
Medicine, UK</span></li>
<li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal"><span style="font-family:Arial,sans-serif">James Glazier, Biocomplexity
Institute,
Indiana
University,
Bloomington,
USA</span></li>
<li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal"><span style="font-family:Arial,sans-serif">James R. Faeder, Department of
Computational
and Systems
Biology,
University of
Pittsburgh,
Pittsburgh,
USA</span></li>
</ol>
</div>
<div>
<p> </p>
</div>
<div>
<p>If there is
a mismatch of
authors in the
submission, it
can be easily
corrected - we
kept the paper
traceable when
we constructed
it so we can
point to exact
texts
contributed by
each
contributor
through their
google account
and versions
kept in google
docs with few
exceptions
where I
personally
added text
their wrote
and have email
conversations
supporting
that . I
personally
collected all
those
contributions
in google docs
when I
assembled the
version you
see and made
sure it is
agreed upon by
the
contributors.
It is
important to
note that
There was one
contributor
that asked for
more revisions
and did not
approve this
manuscript,
yet allowed
submitting the
text without
association to
it to avoid
delays. The
entire
conversation
was documented
publicly in
our mailing
list and we
got consent
from this
contributor to
continue and
use the text -
You can find
the
conversation
here:<span> </span><a href="https://lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-March/000019.html" rel="noreferrer noreferrer" target="_blank">https://lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-March/000019.html</a> <span> </span>-
so there are
no copyright
issues and the
name of the
author is not
included in
the list above
at their
request. Those
included in
the list have
contributed
and approved.
If needed, we
will correct
the list in
the journal to
match this
list. Please
note that we
kept the
entire process
as transparent
as possible so
there will be
no issues. If
there are any
concerns of
authorship, I
will be happy
to dig into
the history
and pull out
details. </p>
</div>
<div>
<p> </p>
</div>
<div>
<p> </p>
</div>
<div>
<p>2. The
reason the
manuscript was
submitted in
this form is
to get
confirmation
on initial fit
and to get
some initial
feedback. We
were
interested in
fast review to
get the
information
quickly out -
Also note that
we did not
intend this to
be a final
version - we
already have
some
modifications
in the work
that we would
like to
introduce
where more
people
contributed ,
yet we have
not reached
agreement on
those so we
cannot
formally
publish them -
however, we
did reach
agreement on
submitting
this version
for review so
the editor can
focus us on
what is
important to
change to get
published with
a 3rd Party -
enough of us
agreed in a
vote that your
Journal seems
is a suitable
3rd party and
hence the
submission. We
will be happy
to spend the
time to
convert the
manuscript to
the desired
format if you
find the
content
suitable for
the journal.
So far your
requests are
reasonable and
I will convey
them to the
group through
our mailing
list. </p>
</div>
<div>
<p> </p>
</div>
<div>
<p>3. Please
note that
after the list
of authors
there is a
disclaimer : "<span style="font-family:Arial,sans-serif">The opinion of the contributors do
not reflect
the opinions
of the entire
working
group". I</span>nitially
this paper
started as an
activity
requested by
the working
group leads.
However, by no
means it
represents all
opinions. The
introduction
in this
version of the
paper captures
some of this
history of how
the manuscript
was created
and modified.
However, we
have other
versions of
the manuscript
in work where
this history
is deleted -
If you prefer,
we can easily
create a
version that
detaches from
the working
group to
eliminate all
concerns -
this is a
relatively
easy fix.
However,
whatever fix
we do, we will
have to
approve with
all
contributors. </p>
</div>
<div>
<p> </p>
</div>
<div>
<p>4 The
revisions can
be done in
reasonable
time. However,
the process of
collecting
approval for
all
contributors
to legally
approve the
revised
manuscript
will take more
than 14 days.
All
contributors
must approve a
manuscript for
publication.
With this
number of
authors we
will probably
not make it in
the time you
mentioned -
only the
approval
process for
collecting all
approvals took
alone about 3
weeks to
approve this
version you
see.
Hopefully you
will
understand
this and
extend this
time period
beyond 14
days. </p>
</div>
<div>
<p> </p>
</div>
<div>
<p>In
summary: </p>
</div>
<div>
<p>Making the
fixes you
asked for
towards
publication is
easy - yet
getting the
approval from
so many people
may take us
more time than
what you
provide. If it
is possible to
get an
extension, it
will be
appreciated. </p>
</div>
<div>
<p> </p>
</div>
<div>
<p>I will add
this
conversation
to our mailing
list so we can
start the
process of
revising the
manuscript.
However, if
after this
email you have
more issues
with this
paper, Please
advise on the
best course of
action you see
fit so we can
adjust
accordingly. </p>
</div>
<div>
<p> </p>
</div>
<div>
<p>Hopefully
we can address
your concerns
in time to
publish the
manuscript in
a timely
manner. </p>
</div>
<div>
<p> </p>
</div>
<div>
<p>
Jacob</p>
</div>
<div>
<p> </p>
</div>
<div>
<p style="margin-bottom:12pt">--<br>
Jacob Barhak
Ph.D. <br>
Sole
Proprietor,
Software
Developer, and
Computational
Disease
Modeler<br>
<br>
Jacob Barhak
Analytics<br>
701 Brazos St<br>
Suite 548<br>
Austin TX,
78701<br>
<br>
Email:<span> </span><a href="mailto:jacob.barhak@gmail.com" rel="noreferrer noreferrer" target="_blank">jacob.barhak@gmail.com</a><br>
<br>
<a href="https://sites.google.com/view/jacob-barhak/home" rel="noreferrer noreferrer" target="_blank">https://sites.google.com/view/jacob-barhak/home</a></p>
</div>
<div>
<p> </p>
</div>
</div>
<p> </p>
<div>
<div>
<p>On Sun, Oct
17, 2021 at
9:56 AM Shayn
Peirce-Cottler
(Via
FrontiersIn)
<<a href="mailto:noreply@frontiersin.org" rel="noreferrer noreferrer" target="_blank">noreply@frontiersin.org</a>>
wrote:</p>
</div>
<blockquote style="border-style:none none none solid;border-left-width:1pt;border-left-color:rgb(204,204,204);padding:0in 0in 0in 6pt;margin-left:4.8pt;margin-right:0in">
<div>
<p>Dear Jacob,<span> </span><br>
<br>
Thank you for
your
manuscript
submission. I
cannot send it
out for review
in its current
form because I
have a few
concerns, but
if you can
address the
following
issues, I will
certainly
reconsider a
revised
manuscript if
the following
are adequately
addressed:<br>
<br>
1. The author
list that is
on the first
page differs
from the
author list
that was
provided at
the time of
submission.<span> </span><br>
<br>
2. The
manuscript
needs to be
submitted
using the
official
Frontiers
template.<br>
<br>
3. The
manuscript
states that it
represents the
views of a
number of
special
interest and
working
groups, and
the authors
should provide
assurances
that they have
the authority
and approval
to speak on
behalf of the
working groups
that are
listed.<br>
<br>
4. There are
places
throughout the
manuscript,
and most
frequently in
the second
half, where
information is
provided as
bulleted
talking points
without
context. Those
sections
should be
revised into
paragraphs of
text or
summarized in
a table (or
figure).<br>
<br>
If you wish to
submit a
revised
manuscript,
the journal
provides a
14-day time
window for you
to do so.
Please let me
know if you
have any
questions.<span> </span><br>
<br>
Thank you,<br>
Shayn<br>
<br>
<br>
---------------------------------<br>
<br>
Manuscript
title: Model
Integration in
Computational
Biology: The
Role of
Reproducibility,
Credibility
and Utility<br>
Manuscript ID:
793932<br>
Authors:
Marcella
Torres, Jacob
Barhak, Ruth
Bowness, Hana
Maria
Dobrovolny,
James Faeder,
Eric
Forgoston,
Winston
Garira, Yaling
Liu, James
Osborne,
Gilberto
Gonzalez
Parra, John
Rice, Rahuman
Sheriff,
Tingting Tang,
Robin
Thompson,
William Waites<span> </span><br>
Date
submitted: 12
Oct 2021<span> </span><br>
Edited by:
Shayn
Peirce-Cottler<br>
<br>
<br>
Research
Topic:
Insights in
Systems
Biology:
Multiscale
Mechanistic
Modeling 2021<br>
Review forum
direct access
link:<span> </span><a href="http://links.email.frontiersin.org/ls/click?upn=AAaFa03elZRFPXQ6ShiKwHJ7IVBhf38O-2BEQWinpomFtULO0Q-2BM19TTRdh7emL5NqrxgHYRG7-2FEazDF-2FJfPddug-3D-3Dkdpa_6U3AlnyvMxxXqGK2YZZvqQDAig2dZVa43D-2BB81ORWCaNWR45ZJ2fDhpaKsTZzRsuCL-2BNJFR2MRucSNQVfNAGmtHQx1gGGhLotkRxEWQuZDre0jQti6pSzF-2Bm1akZB-2FZLJbzjJjEqrnF6c-2BY79oozDKNeyZDGEV7E7qizJmMtyvWGMFEr4JK1z0YPzIbG66EloII5-2FSNkwoWo-2BqqYbe1fAtco01e7-2FlRQb33KpEVuKlNimzGXjW3kPgAYf1R6wsCnLhi7Aow94qLbu0WkYgbBRg-3D-3D" rel="noreferrer noreferrer" target="_blank">https://review.frontiersin.org/review/793932/0/0</a><span style="border:1pt solid windowtext;padding:0in"><img id="gmail-m_-6812091254919142191gmail-m_-2697268861042949202gmail-m_-1689782665546364892gmail-m_454394027104465375gmail-m_1100449795159862914gmail-m_-3690383742767868331gmail-m_208464925022974690gmail-m_-6684231236743761144gmail-m_5330779350599904174m_6811753030514762076gmail-m_-4652177745642668797m_-8816081919050643472x_gmail-m_1182346046610349769gmail-m_-3593486653867666975m_3106702485682359377m_-7813573733557270536m_-7842715099430849307gmail-m_622710468663863154_x0000_i1025" alt="Image
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</div>
</blockquote>
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</blockquote>
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<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>
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