<div dir="auto">Thanks James, <div dir="auto"><br></div><div dir="auto">This will for sure not be the final version of the paper. We will have revisions and already had discussions. </div><div dir="auto"><br></div><div dir="auto">The attempt here is to get the ball rolling and to we need to start somewhere, so the proper entry point is the last agreement. </div><div dir="auto"><br></div><div dir="auto">If the editor will be positive, I believe we can reach a nice revised version that everyone will be gappy with with augmented list of authors. </div><div dir="auto"><br></div><div dir="auto">For now I just wanted to verify that Marcella is willing to do the initial communications with the editor.</div><div dir="auto"><br></div><div dir="auto">Hopefully its ok with her. </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><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Aug 16, 2021, 11:04 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>I see a lot of progress but the text is still fragmentary. I
think you will have a hard time having it reviewed before you
clean it up some more. <br>
</p>
<p>Frontiers is a reasonable place for it, and it does give you the
opportunity to do multiple rounds of review.</p>
<p>JAG<br>
</p>
<div>On 8/16/2021 11:59 AM, Jacob Barhak
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Marcella,
<div><br>
</div>
<div>So far there were no objections and support in your
suggested venue was provided by 9 out of the 17 original
authors + support by many that joined later.</div>
<div><br>
</div>
<div>I have seen no objection to the venue by anyone. - meaning
that we can probably move on to the new venue and start the
process.</div>
<div><br>
</div>
<div>I suggest you move on and contact the editor and follow the
proper process for the venue and ask for feedback. </div>
<div><br>
</div>
<div>Please indicate that we are seeking review to guide further
revisions that we have already begun, yet not completed, so
there may be changes in title, authors, and text, yet the core
paper has been approved by 17 authors and major arguments will
most probably stay. </div>
<div><br>
</div>
<div>The version we can currently legally submit is this one
that we approved:</div>
<div><a href="https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing" target="_blank" rel="noreferrer">https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing</a><br>
</div>
<div><br>
</div>
<div>I locked that version for changes until the review process
is complete. </div>
<div><br>
</div>
<div>For the many who wanted revisions - we will have them still
- yet since we have not reached agreement on a revised
version, it will have to wait until after review. is provided
and we can incorporate reviewers comments in the revisions. </div>
<div><br>
</div>
<div>Marcella, please let us know if you will handle submission
and communications with the publication venue. - Frontiers in
Systems Biology</div>
<div><br>
</div>
<div>Regarding submission, I suggest starting with doing things
that do not take effort - like communicating with the editor
about this paper and declaring intention to see the response
we get. </div>
<div><br>
</div>
<div>While we wait for responses, we can continue discussion and
give a last chance for objections to Frontiers in Systems
Biology to arrive from the original 17 contributors. If any
objection to the venue appears before we get a response, we
will have to stop the process. </div>
<div><br>
</div>
<div>Hopefully the large support in the new venue will persist.</div>
<div><br>
</div>
<div>I suggest we start a new email thread regarding submission
and that we all get updated on the process to keep things
transparent. </div>
<div><br>
</div>
<div> Jacob</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, Aug 11, 2021 at 1:08
AM Gilberto Gonzalez-Parra <<a href="mailto:gilberto.gonzalezparra@nmt.edu" target="_blank" rel="noreferrer">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 all,
<div><br>
</div>
<div>I think the new version is better, even though it is
not ready. The main points are there, which include the
importance of reproducibility and integration in modeling
biology systems.</div>
<div><br>
</div>
<div>Probably, one or two co-authors need to take the lead
to polish the article and references. I suggest that
these authors take some of the top positions in the list
of authors (in some places author position is taken into
account). </div>
<div><br>
</div>
<div>Venue seems fine.</div>
<div><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">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 Tue, Aug 10, 2021 at
1:24 PM Rahuman 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>I also agree with the venue and the suggestion to
tidy up the manuscript with a strict deadline.
<div>Sheriff</div>
<div><br>
<div><br>
<blockquote type="cite">
<div>On 10 Aug 2021, at 10:43, James Osborne <<a href="mailto:jmosborne@unimelb.edu.au" target="_blank" rel="noreferrer">jmosborne@unimelb.edu.au</a>>
wrote:</div>
<br>
<div>
<div dir="ltr" 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">I'm
fine with Frontiers.
<div><br>
</div>
<div>My 2 cents is that the revised version
would be more likely to get published. I
think we should find time to tidy up what we
need. </div>
<div><br>
</div>
<div>James</div>
</div>
<br 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 Tue, Aug
10, 2021 at 5:11 PM Tomas Helikar <<a href="mailto:thelikar2@unl.edu" target="_blank" rel="noreferrer">thelikar2@unl.edu</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>Hi everyone,</p>
<p>I'm also fine with this journal. But we
need to finalize the revised version --
lots of work was done on it already.</p>
<p>Perhaps we can recirculate the last
version of the google doc version of it
and set a deadline for finishing it? I
don't believe it would take more than a
couple of weeks to finalize.</p>
<p>Best wishes,</p>
<p>T.<br>
</p>
<div>
<div style="line-height:16px;margin:6px 0px;padding:8px;border-top:1px dotted rgb(174,177,166);border-bottom:1px dotted rgb(174,177,166);font-size:11px;color:grey"><font size="2.5px;" color="#0049FF">Tomas
Helikar, Ph.D.</font><span> </span><br>
Susan J Rosowski Associate Professor<span> </span><br>
Department of Biochemistry |
University of Nebraska-Lincoln<span> </span><br>
m: <a href="callto:402-547-8904" style="color:rgb(0,136,204)" target="_blank" rel="noreferrer">402-547-8904</a><span> </span>| o: <a href="callto:402-472-3530" style="color:rgb(0,136,204)" target="_blank" rel="noreferrer">402-472-3530</a><br>
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</div>
<div>On 8/9/21 5:06 PM, John Gennari
wrote:<br>
</div>
<blockquote type="cite">
<div><font face="sans-serif" color="#FF6347">Non-NU Email</font>
<hr></div>
<p>I agree with Jon Karr. The venue is
fine, but we need at least a quick
review for readability before
submission.</p>
<p>-John G.<br>
</p>
<div>On 8/9/2021 7:49 AM, Jonathan Karr
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi everyone,
<div><br>
</div>
<div>I think Frontiers is fine. I
think the key thing is to edit the
paper (for focus and readability
by a broader audience) before it
is submitted to any journal.</div>
<div><br>
</div>
<div>Regards</div>
<div>Jonathan</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On
Mon, Aug 9, 2021 at 10:31 AM Jacob
Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank" rel="noreferrer">jacob.barhak@gmail.com</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="auto">Well Marcella,
<div dir="auto"><br>
</div>
<div dir="auto">If there is no
objection raised or an
alternative resolution with
more support appears, then I
see no reason not to proceed.
So I think we just need to
give enough time for original
contributors to raise an
objection or propose an
alternatives that will gain
more support. In the past we
used a week for such
processes, I guess that if we
wait until next weekend and no
objection is raised to the
venue or an alternative with
more support appears we can
proceed. We currently have 5
original contributors
supporting your suggested
venue and one contributor than
joined later in the revisions.</div>
<div dir="auto"><br>
</div>
<div dir="auto"><br>
</div>
<div dir="auto">Note that in
submission you should use the
original version we reached
consensus for submission, yet
note that that we plan to
revise the work and add more
contributors. You can point to
revisions we started. </div>
<div dir="auto"><br>
</div>
<div dir="auto">Lets wait until
next week and hope no one
objects so we can proceed
quickly. </div>
<div dir="auto"><br>
</div>
<div dir="auto"> Jacob</div>
<br>
<br>
<div class="gmail_quote" dir="auto">
<div dir="ltr" class="gmail_attr">On Mon,
Aug 9, 2021, 08:52 Torres,
Marcella <<a href="mailto:mtorres@richmond.edu" target="_blank" rel="noreferrer">mtorres@richmond.edu</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div lang="EN-US">
<div>
<p class="MsoNormal">Once
enough contributors
agree, the process for
submission is that
I’ll confirm interest
(I just got an email
requesting for this
this morning), let
them know that we
intend to submit 1
manuscript and what
the proposed title of
the manuscript is.
Once that initial
information is
submitted, then I will
be “emailed
information about next
steps”. Of course, at
any point we can also
contact the editorial
office, but would it
be helpful to get a
sense of the process
first and then ask for
clarification as
needed? At what point
will we have enough
responses from
contributors to begin?</p>
<div> <br>
</div>
<p class="MsoNormal">Best,</p>
<p class="MsoNormal">Marcella</p>
<div> <br>
</div>
<div style="border-style:solid none none;border-top-width:1pt;border-top-color:rgb(181,196,223);padding:3pt 0in 0in">
<p class="MsoNormal" style="margin-bottom:12pt"><b><span style="font-size:12pt">From:<span> </span></span></b><span style="font-size:12pt">Vp-reproduce-subgroup
<<a href="mailto:vp-reproduce-subgroup-bounces@lists.simtk.org" rel="noreferrer noreferrer" target="_blank">vp-reproduce-subgroup-bounces@lists.simtk.org</a>>
on behalf of John
Rice <<a href="mailto:john.rice@noboxes.org" rel="noreferrer noreferrer" target="_blank">john.rice@noboxes.org</a>><br>
<b>Date:<span> </span></b>Sunday,
August 8, 2021 at
7:23 PM<br>
<b>To:<span> </span></b>Yaling
Liu <<a href="mailto:yal310@lehigh.edu" rel="noreferrer noreferrer" target="_blank">yal310@lehigh.edu</a>><br>
<b>Cc:<span> </span></b><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>>,
Faeder, James R
<<a href="mailto:faeder@pitt.edu" rel="noreferrer noreferrer" target="_blank">faeder@pitt.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:<span> </span></b>Re:
[Vp-reproduce-subgroup] [Vp-integration-subgroup] White paper revision</span></p>
</div>
<div style="border:1pt solid red;padding:2pt">
<p class="MsoNormal" style="background-color:yellow"><b><span style="font-size:10pt;font-family:Arial,sans-serif;color:red">External
Email:</span></b><span style="font-size:10pt;font-family:Arial,sans-serif"> Use caution in
opening links,
attachments, and
buying gift cards.</span><span style="font-size:10pt;font-family:Arial,sans-serif"></span></p>
</div>
<div> <br>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12pt">Me
too</p>
<div>
<p class="MsoNormal">Typed
with two thumbs on
my iPhone. (757)
318-0671<span> </span></p>
<div>
<div> <br>
</div>
</div>
<div>
<div>
<p class="MsoNormal">“Upon
this gifted
age, in its
dark hour,</p>
</div>
<div>
<p class="MsoNormal">Rains
from the sky a
meteoric
shower</p>
</div>
<div>
<p class="MsoNormal">Of
facts . . .
they lie
unquestioned,
uncombined.</p>
</div>
<div>
<p class="MsoNormal">Wisdom
enough to
leech us of
our ill</p>
</div>
<div>
<p class="MsoNormal">Is
daily spun;
but there
exists no loom</p>
</div>
<div>
<p class="MsoNormal">To
weave it into
fabric.”</p>
</div>
<div>
<div> <br>
</div>
</div>
<div>
<p class="MsoNormal">–Edna
St. Vincent
Millay,</p>
</div>
<div>
<div> <br>
</div>
</div>
<div>
<div> <br>
</div>
</div>
</div>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12pt"><br>
On Aug 8, 2021, at
19:09, Yaling Liu
<<a href="mailto:yal310@lehigh.edu" rel="noreferrer noreferrer" target="_blank">yal310@lehigh.edu</a>> wrote:</p>
</div>
<div>
<p class="MsoNormal"><span> </span></p>
<div>
<p class="MsoNormal">I
am fine with the
suggested new
venue and
willing to
revise further.
We don't need
to wait for
everyone to
reply here -
this email chain
is way too long
and guess a lot
of people were
busy and ignored
them.</p>
<div>
<div> <br>
</div>
</div>
<div>
<p class="MsoNormal">Thanks.</p>
</div>
<div>
<div> <br>
</div>
</div>
<div>
<p class="MsoNormal">Yaling</p>
</div>
</div>
<div> <br>
</div>
<div>
<div>
<p class="MsoNormal">On
Sun, Aug 8,
2021 at 4:57
PM Jacob
Barhak <<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer noreferrer" target="_blank">jacob.barhak@gmail.com</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:5pt 0in 5pt 4.8pt">
<div>
<p class="MsoNormal">Thanks
Hana, <span> </span></p>
<div>
<div> <br>
</div>
</div>
<div>
<p class="MsoNormal">The
revised
version is far
from ready to
being
submitted
anywhere.
There is just
too much to do
there to put
it in shape
for
submission. </p>
</div>
<div>
<div> <br>
</div>
</div>
<div>
<p class="MsoNormal">We
do want to
advance in
making
revisions,
yet the
attempt here
is to
accelerate the
process by
asking a 3rd
publishing
party to
provide proper
review for
what is
actually
needed for
publication,
so you may
want to save
your efforts
until after we
get feedback -
they will be
more effective
then when we
have
feedback. </p>
</div>
<div>
<div> <br>
</div>
</div>
<div>
<p class="MsoNormal">However,
we do need
enough support
and no
objections to
proceed to
engage with
the new venue
suggested. </p>
</div>
<div>
<div> <br>
</div>
</div>
<div>
<p class="MsoNormal">We
have currently
3 of the 17 of
the original
contributors
and 1 who
joined later
that approves
of a new
venue.
Hopefully
others will
follow so we
can proceed
quickly. </p>
</div>
<div>
<div> <br>
</div>
</div>
<div>
<p class="MsoNormal">Thank
you for the
reply. </p>
</div>
<div>
<div> <br>
</div>
</div>
<div>
<p class="MsoNormal">
<span> </span>Jacob</p>
</div>
<div>
<div> <br>
</div>
</div>
</div>
<div> <br>
</div>
<div>
<div>
<p class="MsoNormal">On
Sat, Aug 7,
2021, 23:46
Dobrovolny,
Hana <<a href="mailto:h.dobrovolny@tcu.edu" rel="noreferrer noreferrer" target="_blank">h.dobrovolny@tcu.edu</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:5pt 0in 5pt 4.8pt">
<div>
<div id="m_-7275440222865029721gmail-m_-2501105178215063338gmail-m_-4770028938192598232gmail-m_-8595028391363473299gmail-m_3218733467120122652gmail-m_-7038258438093066422gmail-m_6686079875447190907m_-6359702125158232037gmail-m_-3222322118285752855m_2418018346964135372divtagdefaultwrapper">
<p><span style="font-size:12pt">I'm
fine with the
suggested
venue. I'll
double check
the sections I
was heading
sometime this
week, but I
think all
suggestions
were
incorporated
last time I
checked.</span></p>
<p><span style="font-size:12pt">Hana</span></p>
<div><span style="font-size:12pt"> </span><br>
</div>
<div id="m_-7275440222865029721gmail-m_-2501105178215063338gmail-m_-4770028938192598232gmail-m_-8595028391363473299gmail-m_3218733467120122652gmail-m_-7038258438093066422gmail-m_6686079875447190907m_-6359702125158232037gmail-m_-3222322118285752855m_2418018346964135372Signature">
<div name="divtagdefaultwrapper">
<div>
<div>
<p class="MsoNormal"><span style="font-size:10pt">*******************************************************<br>
Dr. Hana
Dobrovolny<br>
Associate
Professor of
Biophysics<br>
Texas
Christian
University<br>
TCU Box 298840<br>
Fort Worth, TX
76129<br>
<br>
phone: (817)
257-6379 fax:
(817) 257-7742<br>
email:<span> </span></span><a href="mailto:h.dobrovolny@tcu.edu" rel="noreferrer noreferrer" target="_blank"><span style="font-size:10pt">h.dobrovolny@tcu.edu</span></a><span style="font-size:10pt"><br>
*******************************************************</span></p>
</div>
</div>
</div>
</div>
<div style="margin-bottom:12pt"><span style="font-size:12pt"> </span><br>
</div>
<div>
<div class="MsoNormal" style="text-align:center" align="center"><span style="font-size:12pt">
<hr width="100%" size="0" align="center"></span></div>
<div id="m_-7275440222865029721gmail-m_-2501105178215063338gmail-m_-4770028938192598232gmail-m_-8595028391363473299gmail-m_3218733467120122652gmail-m_-7038258438093066422gmail-m_6686079875447190907m_-6359702125158232037gmail-m_-3222322118285752855m_2418018346964135372divRplyFwdMsg">
<p class="MsoNormal"><b><span>From:</span></b><span><span> </span>Vp-reproduce-subgroup
<</span><a href="mailto:vp-reproduce-subgroup-bounces@lists.simtk.org" rel="noreferrer noreferrer" target="_blank">vp-reproduce-subgroup-bounces@lists.simtk.org</a><span>>
on behalf of
Jacob Barhak
<</span><a href="mailto:jacob.barhak@gmail.com" rel="noreferrer noreferrer" target="_blank">jacob.barhak@gmail.com</a><span>><br>
<b>Sent:</b><span> </span>August
7, 2021 11:18
AM<br>
<b>To:</b><span> </span>Torres,
Marcella<br>
<b>Cc:</b><span> </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> </span></span><a href="mailto:vp-integration-subgroup@lists.simtk.org" rel="noreferrer noreferrer" target="_blank">vp-integration-subgroup@lists.simtk.org</a><span>;
Jonathan Karr;
John Gennari;
Winston
Garira;
Faeder, James
R<br>
<b>Subject:</b><span> </span>Re:
[Vp-reproduce-subgroup] [Vp-integration-subgroup] White paper revision</span><span style="font-size:12pt"></span></p>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
</div>
<div>
<p><strong><span style="font-size:12pt;font-family:Calibri,sans-serif;background-color:yellow">[EXTERNAL
EMAIL WARNING]</span></strong><span style="font-size:12pt;background-color:yellow"> DO NOT CLICK LINKS or
open
attachments
unless you
recognize the
sender and
know the
content is
safe.</span><span style="font-size:12pt"></span></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;font-family:Arial,sans-serif">And to all white
paper
contributors,</span><span style="font-size:12pt"></span></p>
<div>
<div><span style="font-size:12pt;font-family:Arial,sans-serif"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;font-family:Arial,sans-serif">You are getting this
message to
raise it to
the top of
your
mailboxes. </span></p>
</div>
<div>
<div><span style="font-size:12pt;font-family:Arial,sans-serif"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;font-family:Arial,sans-serif">Hopefully enough of
you will look
at this during
the weekend to
comment on the
best way to
move forward
while
considering
the new offer
from
Marcella. </span></p>
</div>
<div>
<div><span style="font-size:12pt;font-family:Arial,sans-serif"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;font-family:Arial,sans-serif">The faster we move,
the better. </span></p>
</div>
<div>
<div><span style="font-size:12pt;font-family:Arial,sans-serif"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt;font-family:Arial,sans-serif"> <span> </span>Jacob</span></p>
</div>
<div>
<div><span style="font-size:12pt;font-family:Arial,sans-serif"> </span><br>
</div>
</div>
<div>
<div><span style="font-size:12pt;font-family:Arial,sans-serif"> </span><br>
</div>
</div>
</div>
<div><span style="font-size:12pt"> </span><br>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">On Tue, Aug 3, 2021, 01:03 Jacob Barhak <</span><a href="mailto:jacob.barhak@gmail.com" rel="noreferrer noreferrer" target="_blank"><span style="font-size:12pt">jacob.barhak@gmail.com</span></a><span style="font-size:12pt">>
wrote:</span></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:5pt 0in 5pt 4.8pt">
<div>
<p class="MsoNormal"><span style="font-size:12pt">Thanks Marcella, <span> </span></span></p>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">Your suggestion may be the solution here. </span></p>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">From what I see, this venue is a good fit. Yet
we need to
learn the
opinion of the
other
contributors. </span></p>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">If we collect enough support and no contributor
objects, we
can approach
the editor and
ask if the
paper will
receive proper
review to
guide
revisions. </span></p>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">I look forward for more responses. </span></p>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt"> <span> </span>Jacob</span></p>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
</div>
<div><span style="font-size:12pt"> </span><br>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">On Mon, Aug 2, 2021, 11:57 Torres, Marcella <</span><a href="mailto:mtorres@richmond.edu" rel="noreferrer noreferrer" target="_blank"><span style="font-size:12pt">mtorres@richmond.edu</span></a><span style="font-size:12pt">>
wrote:</span></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:5pt 0in 5pt 4.8pt">
<div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">Hi all and Jacob,</span></p>
<div><span style="font-size:12pt"> </span><br>
</div>
<p class="MsoNormal"><span style="font-size:12pt">I’m interested in getting it circulated, and want
to propose
Frontiers in
Systems
Biology as a
possible venue
– I just
joined the
editorial
board and
received
notice of a
focused issue
that includes
challenges in
multiscale
modeling:<span> </span></span><a href="https://urldefense.com/v3/__https:/www.frontiersin.org/research-topics/24484/insights-in-systems-biology-multiscale-mechanistic-modeling-2021?utm_source=F-RTM&utm_medium=CFP_E1&utm_campaign=PRD_CFP_T1_RT-TITLE*__;Iw!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WFepwnGQ8$" rel="noreferrer noreferrer" target="_blank"><span style="font-size:12pt">https://www.frontiersin.org/research-topics/24484/insights-in-systems-biology-multiscale-mechanistic-modeling-2021?utm_source=F-RTM&utm_medium=CFP_E1&utm_campaign=PRD_CFP_T1_RT-TITLE#</span></a><span style="font-size:12pt"><span> </span>.</span></p>
<div><span style="font-size:12pt"> </span><br>
</div>
<p class="MsoNormal"><span style="font-size:12pt">The journal is new, and I don’t remember it being
proposed
previously.</span></p>
<div><span style="font-size:12pt"> </span><br>
</div>
<p class="MsoNormal"><span style="font-size:12pt">I am also willing to prioritize revision and
submission and
apologize for
not
participating
more over the
summer.</span></p>
<div><span style="font-size:12pt"> </span><br>
</div>
<p class="MsoNormal"><span style="font-size:12pt">Best,</span></p>
<p class="MsoNormal"><span style="font-size:12pt">Marcella</span></p>
<div><span style="font-size:12pt"> </span><br>
</div>
<div style="border-style:solid none none;border-top-width:1pt;border-top-color:rgb(181,196,223);padding:3pt 0in 0in">
<p class="MsoNormal" style="margin-bottom:12pt"><b><span style="font-size:12pt">From:<span> </span></span></b><span style="font-size:12pt">Vp-reproduce-subgroup <</span><a href="mailto:vp-reproduce-subgroup-bounces@lists.simtk.org" rel="noreferrer noreferrer" target="_blank"><span style="font-size:12pt">vp-reproduce-subgroup-bounces@lists.simtk.org</span></a><span style="font-size:12pt">> on behalf of Jacob Barhak <</span><a href="mailto:jacob.barhak@gmail.com" rel="noreferrer noreferrer" target="_blank"><span style="font-size:12pt">jacob.barhak@gmail.com</span></a><span style="font-size:12pt">><br>
<b>Date:<span> </span></b>Monday,
August 2, 2021
at 11:45 AM<br>
<b>To:<span> </span></b>Alexander
Kulesza <</span><a href="mailto:alexander.kulesza@novadiscovery.com" rel="noreferrer noreferrer" target="_blank"><span style="font-size:12pt">alexander.kulesza@novadiscovery.com</span></a><span style="font-size:12pt">><br>
<b>Cc:<span> </span></b></span><a href="mailto:vp-reproduce-subgroup@lists.simtk.org" rel="noreferrer noreferrer" target="_blank"><span style="font-size:12pt">vp-reproduce-subgroup@lists.simtk.org</span></a><span style="font-size:12pt"><span> </span><</span><a href="mailto:vp-reproduce-subgroup@lists.simtk.org" rel="noreferrer noreferrer" target="_blank"><span style="font-size:12pt">vp-reproduce-subgroup@lists.simtk.org</span></a><span style="font-size:12pt">>,<span> </span></span><a href="mailto:vp-integration-subgroup@lists.simtk.org" rel="noreferrer noreferrer" target="_blank"><span style="font-size:12pt">vp-integration-subgroup@lists.simtk.org</span></a><span style="font-size:12pt"><</span><a href="mailto:vp-integration-subgroup@lists.simtk.org" rel="noreferrer noreferrer" target="_blank"><span style="font-size:12pt">vp-integration-subgroup@lists.simtk.org</span></a><s style="font-size:12pt">>, Jonathan Karr <<a href="mailto:jonrkarr@gmail.com" rel="noreferrer noreferrer" target="_blank"><span style="font-size:12pt">jonrkarr@gmail.com</span></a><span style="font-size:12pt">>, John Gennari <</span><a href="mailto:gennari@uw.edu" rel="noreferrer noreferrer" target="_blank"><span style="font-size:12pt">gennari@uw.edu</span></a><span style="font-size:12pt">>, Faeder, James R <</span><a href="mailto:faeder@pitt.edu" rel="noreferrer noreferrer" target="_blank"><span style="font-size:12pt">faeder@pitt.edu</span></a><span style="font-size:12pt">>, Winston Garira <</span><a href="mailto:Winston.Garira@univen.ac.za" rel="noreferrer noreferrer" target="_blank"><span style="font-size:12pt">Winston.Garira@univen.ac.za</span></a><span style="font-size:12pt">><br>
<b>Subject:<span> </span></b>Re:
[Vp-reproduce-subgroup] [Vp-integration-subgroup] White paper revision</span></s></p>
</div>
<div style="border:1pt solid red;padding:2pt">
<p class="MsoNormal" style="background-color:yellow"><b><span style="font-size:10pt;font-family:Arial,sans-serif;color:red">External
Email:</span></b><span style="font-size:10pt;font-family:Arial,sans-serif"> Use caution in
opening links,
attachments,
and buying
gift cards.</span><span style="font-size:12pt"></span></p>
</div>
<div><span style="font-size:12pt"> </span><br>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">Hi Alex,<span> </span></span></p>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">Thanks for your response first - it is the first
public
response. </span></p>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">However, I was hoping for a discussion rather
than a poll.
We already
made a vote
and the
direction it
took us all
ended up badly
so far - there
is no activity
for a few
months now.
Perhaps a
discussion is
in order
before
making more
decisions. </span></p>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">And Alex, time is something you manage to achieve
certain goals
with certain
priorities. </span></p>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">The real question is if circulating this paper is
on a high
priority list
for any of the
contributors?</span></p>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">Some contributors publicly declared they have
little time,
yet we were
still able to
push though in
the past. What
has changed?</span></p>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">Perhaps a discussion will reveal those things.</span></p>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt"> <span> </span>Jacob</span></p>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
</div>
<div><span style="font-size:12pt"> </span><br>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">On Mon, Aug 2, 2021 at 2:00 AM Alexander Kulesza
<</span><a href="mailto:alexander.kulesza@novadiscovery.com" rel="noreferrer noreferrer" target="_blank"><span style="font-size:12pt">alexander.kulesza@novadiscovery.com</span></a><span style="font-size:12pt">> wrote:</span></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:5pt 0in 5pt 4.8pt">
<div>
<p class="MsoNormal"><span style="font-size:12pt">Dear all, Dear Jacob,</span></p>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">I hope that I speak for many others from this
group wishing
that the ideas
presented in
that paper do
get
circulated;
optimally in
form of a
reviewed
paper. </span></p>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">I think that the time of the year impedes many of
us (including
myself) to
spend the time
needed to edit
the sections. </span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">I have created the following poll </span><a href="https://urldefense.com/v3/__https:/doodle.com/poll/ydpgvgi594ubi82d?utm_source=poll&utm_medium=link__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WFaV6WX1c$" rel="noreferrer noreferrer" target="_blank"><span style="font-size:12pt">https://doodle.com/poll/ydpgvgi594ubi82d?utm_source=poll&utm_medium=link</span></a><span style="font-size:12pt"><span> </span>which intends to get agreement or
disgreement of
the group for
the different
optuions that
exist. </span></p>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">Please let me know what you think.</span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">Alexander</span></p>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
</div>
<div><span style="font-size:12pt"> </span><br>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">On Thu, 29 Jul 2021 at 16:54, Jacob Barhak <</span><a href="mailto:jacob.barhak@gmail.com" rel="noreferrer noreferrer" target="_blank"><span style="font-size:12pt">jacob.barhak@gmail.com</span></a><span style="font-size:12pt">>
wrote:</span></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:5pt 0in 5pt 4.8pt">
<div>
<p class="MsoNormal"><span style="font-size:12pt">Greetings contributors,</span></p>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">Two of the contributors approach me about this
message
privately.
However, there
were many more
who
participated
and no one
responded
publicly in 2
weeks. </span></p>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">Do you not want this paper be circulated? </span></p>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">I am asking those questions publicly since this
deserves a
public
discussion.</span></p>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">Hopefully this reminder will stir up the group.</span></p>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt"> <span> </span>Jacob</span></p>
</div>
</div>
<div><span style="font-size:12pt"> </span><br>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">On Wed, Jul 14, 2021 at 4:46 PM Jacob Barhak <</span><a href="mailto:jacob.barhak@gmail.com" rel="noreferrer noreferrer" target="_blank"><span style="font-size:12pt">jacob.barhak@gmail.com</span></a><span style="font-size:12pt">>
wrote:</span></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:5pt 0in 5pt 4.8pt">
<div>
<p class="MsoNormal"><span style="font-size:12pt">Hi Gilberto,<span> </span></span></p>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">As you can see, there was no response to
your email -
in fact the
paper writing
stopped - I
waited
sufficient
time to make
sure this is
the case to
prove a point.
If there is no
one to tend to
the editing,
then there
will not be
any progress
and the paper
will lose
focus -
partially because people
will pull it
in many
directions and
resolution
will take time
no one is
willing to
provide to
move it
forward. And
this is what
happened here.</span></p>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">I remind you that I wrote what needs to be done
to make
progress. See
the 4 points
in this
archived
email:</span></p>
</div>
<div>
<p class="MsoNormal"><a href="https://urldefense.com/v3/__https:/lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-May/000098.html__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WFEHRSJVg$" rel="noreferrer noreferrer" target="_blank"><span style="font-size:12pt">https://lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-May/000098.html</span></a><span style="font-size:12pt"></span></p>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">By now it's fairly safe to declare that the group
failed to
fulfil those
points in
reasonable
time, and the
revised
version is in
a worse
condition
towards
publication
than the
version we all
agreed to
submit
before. </span></p>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">This situation raises the question.</span></p>
</div>
<div>
<div><span style="font-size:12pt"> </span><br>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12pt">Is there more benefit from submitting the
findings we
had before as
they were to a
3rd party for
</span></p></div></div></blockquote></div></blockquote></div></blockquote></div></div></div></div></blockquote></div></blockquote></div></div></div></div></div></div></blockquote></div></blockquote></div></div></div></div></div></blockquote></div></div></blockquote></div></blockquote></blockquote></div></blockquote></div></div></blockquote></div></div></div></blockquote></div></blockquote></div></blockquote></div></blockquote></div>