<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">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">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">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">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">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">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">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">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">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">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">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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</blockquote>
</div>
</blockquote>
</div>
</blockquote>
</div>
</blockquote>
</div>
</blockquote></div>