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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">
      <meta http-equiv="content-type" content="text/html; charset=UTF-8">
      <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>
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                                                        <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>
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                                    </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>
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                                                          <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>
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                                    </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>
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