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<p>Easy-peasy. Attached, find a marked up "differences" version. As
you might guess, it's almost completely "red ink". Fee<br>
</p>
<p>-John G.</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 5/14/2021 4:43 PM, Jacob Barhak
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAM_y+3RT_NE4yb9yJCz2AGrq5PEpwzDhaTmi7ZcuY-9ZDHoDXA@mail.gmail.com">
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<div dir="ltr">Hi John,
<div><br>
</div>
<div>You removed massive parts - can you share the changes made
from the original - there is a reason I opened up the paper
for changes - we need to see what was changed - Can you please
somehow send a differential version with changes highlighted? </div>
<div><br>
</div>
<div>Hopefully this is attainable.</div>
<div><br>
</div>
<div> Jacob</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, May 14, 2021 at 4:48
PM John Gennari <<a href="mailto:gennari@uw.edu"
moz-do-not-send="true">gennari@uw.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><br>
</p>
<p>Potential co-authors: <br>
</p>
<p>As promised, attached find the skeleton of a complete
re-writing and revision of the white paper. This new
version is tentatively titled "A dozen challenges to
biosimulation model reproducibility and integration",
reflecting a new focus to the paper. </p>
<p>I have also placed this document on a shared drive, where
all of you have the ability to comment (not edit):
<a
href="https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit"
target="_blank" moz-do-not-send="true">https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit</a>
(I hope I've done the settings correctly! Let me know if
not.) <br>
</p>
<p>It's important to note that this new draft is just a
skeleton, and not a complete paper yet. I have provided a
new introduction based on Fig 1 and Table 1 as I suggested
in my earlier email. I have not yet adapted or modified
any of the 12 subsections that correspond to the 12
challenges. This is work that could be distributed among
co-authors, of course. <br>
</p>
<p>I also have not yet created any good organization of
these 12 challenges, although I put in one idea (in
yellow, at the end). Others would be very welcome. <br>
</p>
<p>Although I think this provides a much stronger
organization to the paper, I'm aiming to nonetheless be
faithful to the central ideas of the earlier draft, and
thus I view it as a revision, rather than a completely new
paper. <br>
</p>
<p>My main goal for disseminating the attached is to get
feedback -- is this a reasonable direction to head in for
the revision? Are there critical elements or ideas that
I'm missing from the introduction? As you can see below,
Eric has kindly set up a "whenisgood" poll for a potential
meeting on Monday or Tuesday (5/17 or 5/18). Eric, please
let us know if we have a quorum for any particular time.
(The earlier you can let us know, the better!) <br>
</p>
<p>Of course, if you aren't available to chat on Mon/Tues,
email comments and discussion are welcome! <br>
</p>
<p>-John Gennari</p>
<p><br>
</p>
<div>On 5/12/2021 8:04 PM, Eric Forgoston wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">Here is a link to a meeting poll for next
Monday/Tuesday, 17/18 May. Please fill out by Friday,
14 May, so we can set a day/time to discuss the
revision.
<div><br>
</div>
<div><a href="https://whenisgood.net/kdrzmkj"
style="color:blue;font-family:sans-serif;text-align:center"
target="_blank" moz-do-not-send="true">http://whenisgood.net/kdrzmkj</a><br>
<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" moz-do-not-send="true">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>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, May 12, 2021
at 2:09 PM John Gennari <<a
href="mailto:gennari@uw.edu" target="_blank"
moz-do-not-send="true">gennari@uw.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><br>
</p>
<p>This is definitely a good idea. The challenge
might be to schedule a time when a sufficient
quorum of us are available....</p>
<p>My plan over the rest of this week is to draft up
a significant re-working of the paper, and then
distribute that to all. This won't be a complete
revision, but rather some example of the kinds of
things to say, and some outlines of the proposed
re-organization. I should have this done by
Friday, or this weekend at the latest. So then a
Zoom call next week (Monday, May 17?) might make
sense to talk thru the ideas that I send out by
this Friday. <br>
</p>
<p>-John G.</p>
<p><br>
</p>
<div>On 5/11/2021 7:37 PM, Eric Forgoston wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>Dear all,</div>
<div><br>
</div>
It is probably worth having a zoom chat to
discuss the revision so that we are all working
in concert. In particular, John Gennari sent an
email last week on May 3 with some thoughts that
are well-worth discussing.
<div><br>
</div>
<div>Is there interest in doing this?</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Eric<br>
<div>
<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" moz-do-not-send="true">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>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, May
11, 2021 at 10:26 AM Jacob Barhak <<a
href="mailto:jacob.barhak@gmail.com"
target="_blank" moz-do-not-send="true">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 white paper
contributors,<br>
<div><br>
</div>
<div>The voting period is over and the vote
did not change, so it is now time to act.</div>
<div><br>
</div>
<div>The paper will be revised as requested
by 10 voters and the target journal will
be Bioinformatics - James Glazier and
Yaling Liu will share publication costs.</div>
<div><br>
</div>
<div>All those who asked to revise are
requested to make the revisions and
discuss those.</div>
<div><br>
</div>
<div>I ask to reach a revised version by May
25 so that we can finish an approval
round by June 1st.</div>
<div><br>
</div>
<div>So far only Sheriff provided
suggestions for revisions prior to
submission so I suggest we start
discussing those:</div>
<div><a
href="https://docs.google.com/document/d/1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh/edit"
target="_blank" moz-do-not-send="true">https://docs.google.com/document/d/1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh/edit</a><br>
</div>
<div><br>
</div>
<div>However, since it is out of format and
out of date, I suggest that all those who
want to make changes login and request to
access the main document and introduce
changes there:</div>
<div><a
href="https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing"
target="_blank" moz-do-not-send="true">https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing</a><br>
</div>
<div><br>
</div>
<div>I do ask that this will not be delayed
any further and those who asked for
changes give this task priority so it can
be completed in time.</div>
<div><br>
</div>
<div>I look forward to your contributions. </div>
<div><br>
</div>
<div> Jacob</div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Sun,
May 9, 2021 at 4:25 PM Jacob Barhak <<a
href="mailto:jacob.barhak@gmail.com"
target="_blank" moz-do-not-send="true">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 white paper
contributors,
<div><br>
</div>
<div>Allow me to remind you that the
Voting and vote changes are still
possible until 11-May 1am CDT </div>
<div><br>
</div>
<div>The current votes I saw are:</div>
<div><br>
10 votes for revision<br>
Jonathan Karr<br>
Eric Forgoston<br>
William Waites<br>
James Glazier - RS Interface or
Bioinformatics<br>
Rahuman Sheriff<br>
Yaling Liu - Bioinformatics<br>
John Rice<br>
Winston Garira<br>
Gilberto Gonzalez-Parra<br>
James Osborne</div>
<div><br>
It seems 2 people supported
Bioinformatics - James Glazier and
Yaling Liu so if this vote is
accepted, they will split publication
costs and the terget venue for
revisions will be Bioinformatics. <br>
<br>
There is currently 1 minority vote:<br>
Jacob Barhak for direct submission to
Nature - Scientific Reports </div>
<div><br>
</div>
<div>If revision is selected, time will
be limited, so I suggest those who
voted to start working on revisions. </div>
<div><br>
</div>
<div>Hopefully this reminder will move
us forward.</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, May 1, 2021 at 12:18 PM Jacob
Barhak <<a
href="mailto:jacob.barhak@gmail.com"
target="_blank"
moz-do-not-send="true">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 white paper
contributors,
<div><br>
</div>
<div>It is time to vote again for
the target venue. Here are the
options again. </div>
<div>
<div>
<ol>
<li style="margin-left:15px">Cureus
- resubmission after
addressing editor comments</li>
<li style="margin-left:15px">Nature
- if you <span>vote</span> for
this venue please specify
flavour such as Nature
Scientific Reports</li>
<li style="margin-left:15px">Science</li>
<li style="margin-left:15px">Briefings
in Bioinformatics</li>
<li style="margin-left:15px">Trends
in Biotechnology - requires
distilling the paper</li>
<li style="margin-left:15px">Journal
of The Royal Society
Interface<br>
</li>
<li style="margin-left:15px">Annual
Review of Public Health<br>
</li>
<li style="margin-left:15px">BMJ</li>
<li style="margin-left:15px">Annual
Review of Biomedical
Engineering<br>
</li>
<li style="margin-left:15px">F1000research
- if you <span>vote</span> for
this this venue please
specify Gateway /
Collection </li>
<li style="margin-left:15px">bulletin
of mathematical biology<br>
</li>
<li style="margin-left:15px">Bioinformatics.<br>
</li>
<li style="margin-left:15px">Do
not submit now - instead
open for revisions for 2
weeks and then submit. If
you choose this option also
vote for the target venue
after revisions so that we
will not have to delay
further. </li>
</ol>
<div><br>
</div>
</div>
<div>I will ask that
contributors pick one journal
from that list - I ask that you
REPLY ALL so votes will be
transparent and time of vote
will be registered since first
to vote will break ties.</div>
<div><br>
</div>
<div>The voting period will be
until Tuesday 11-May 1am CDT </div>
</div>
<div><br>
</div>
<div>Again, if a journal costs for
open publication, whoever voted,
will split publication costs. If
anyone on this list is funded for
this, please vote. </div>
<div><br>
</div>
<div>I urge contributors to vote -
just so that we will have a
preference order to follow in case
of rejection.</div>
<div><br>
</div>
<div>Looking forward to your votes. </div>
<div><br>
</div>
<div> Jacob</div>
</div>
</blockquote>
</div>
</blockquote>
</div>
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