<div dir="ltr"><div dir="ltr">Dear Jacob, <div>Thanks for your feedback. I thought the poll to be a good indicator of the overall activity of the authors. Also, if there is significant vote on "don't agree" then any discussion (which anyway will be needed before any action or decision is taken) has little chance of being productive. </div><div><br></div><div> As I joined relatively late, I do not feel comfortable to lead the discussion of next steps, as I would not be sure if the interests of the initial and lead authors would be well represented. Currently, I agree that it is hard to anticipate what the timeframe is or what obstacles there might be for the group to reach consensus (or non-objection) for a the current status of the document. </div><div><br></div><div>I personally like the idea of the Frontiers in Systems Biology as venue.<br></div><div><br></div><div>Kind regards </div><div>Alexander </div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, 2 Aug 2021 at 17:45, 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 Alex,<div><br></div><div>Thanks for your response first - it is the first public response. </div><div><br></div><div>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. </div><div><br></div><div>And Alex, time is something you manage to achieve certain goals with certain priorities. </div><div><br></div><div>The real question is if circulating this paper is on a high priority list for any of the contributors?</div><div><br></div><div>Some contributors publicly declared they have little time, yet we were still able to push though in the past. What has changed?</div><div><br></div><div>Perhaps a discussion will reveal those things.</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></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Aug 2, 2021 at 2:00 AM Alexander Kulesza <<a href="mailto:alexander.kulesza@novadiscovery.com" target="_blank">alexander.kulesza@novadiscovery.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">Dear all, Dear Jacob,<div><br></div><div>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. </div><div><br></div><div>I think that the time of the year impedes many of us (including myself) to spend the time needed to edit the sections. </div><div>I have created the following poll <a href="https://doodle.com/poll/ydpgvgi594ubi82d?utm_source=poll&utm_medium=link" target="_blank">https://doodle.com/poll/ydpgvgi594ubi82d?utm_source=poll&utm_medium=link</a> which intends to get agreement or disgreement of the group for the different optuions that exist. </div><div><br></div><div>Please let me know what you think.</div><div>Alexander</div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, 29 Jul 2021 at 16:54, 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 contributors,<div><br></div><div>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. </div><div><br></div><div>Do you not want this paper be circulated? </div><div><br></div><div>I am asking those questions publicly since this deserves a public discussion.</div><div><br></div><div>Hopefully this reminder will stir up the group.</div><div><br></div><div> Jacob</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jul 14, 2021 at 4:46 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 Gilberto,<div><br></div><div>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.</div><div><br></div><div>I remind you that I wrote what needs to be done to make progress. See the 4 points in this archived email:</div><div><a href="https://lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-May/000098.html" target="_blank">https://lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-May/000098.html</a><br></div><div><br></div><div>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. </div><div><br></div><div>This situation raises the question.</div><div><br></div><div>Is there more benefit from submitting the findings we had before as they were to a 3rd party for publication than waiting for revisions to end? </div><div><br></div><div>I personally doubt that any further revisions will allow publication in reasonable time - which as I mentioned before delays science rather than advancing it.</div><div><br></div><div>I assume that this email will start a debate with different opinions, that may take a long time and this is not my intention. My purpose is practical - I am trying to salvage the paper so it gets published quickly. It is better than waiting forever...<br></div><div><br></div><div>I believe that what we accumulated and summarized in a table is worth publication as we agreed before. We did reach a consensus and I hope individuals will realize this is the most practical course of action.</div><div><br></div><div>Revisions can continue and information added for future versions, yet I do ask that this paper be submitted quickly to a venue that will accept it in the form we agreed upon. </div><div><br></div><div>If we do not do this, we will be guilty of delaying science. </div><div><br></div><div>Hopefully contributors will realize this and we can proceed to fix the situation quickly.</div><div><br></div><div> Jacob</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 Mon, Jun 21, 2021 at 1:06 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"><div dir="ltr">Dear all,<div><br></div><div>I like Eric's idea i.e. "section heads can look at the technical aspects of their respective sections this week."<br></div><div><br></div><div>There are many suggestions and I think the section heads can focus in one section to make the work more manageable. Then we can read the whole manuscript to check the consistency of the manuscript. Overall, I think we can focus on two main ideas. One to point out the challenges of <span style="background-color:transparent;color:rgb(0,0,0);font-family:Arial;white-space:pre-wrap">Biosimulation Model Reproducibility and Model Integration, and some initial basic ideas to tackle these issues. That might be the main message of the article (??)</span></div><div><br></div><div>Best,</div><div><br></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 style="color:rgb(0,0,0);font-family:"Helvetica Neue",Helvetica,Arial,"Lucida Grande",sans-serif,serif,EmojiFont;font-size:13px">Ph.D in Applied Mathematics.</span></div><div dir="ltr"><font color="#000000" face="Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif, serif, EmojiFont"><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 Mon, Jun 21, 2021 at 8:16 AM 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">Dear all,<div><br></div><div>It seems that progress has mostly stalled - there are numerous comments/edits that have been suggested and are waiting to be acted upon by the section heads.</div><div><br></div><div>I suggest a renewed effort over the next week or so: perhaps section heads can look at the technical aspects of their respective sections this week. Then, if interested, I can set up a poll for a discussion next week that will serve to resolve and finalise any remaining issues.</div><div><br></div><div>Thoughts?</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/" target="_blank">https://eric-forgoston.github.io/</a></span></span><br><div style="display:inline"></div></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 Mon, Jun 21, 2021 at 5:54 AM Alexander Kulesza <<a href="mailto:alexander.kulesza@novadiscovery.com" target="_blank">alexander.kulesza@novadiscovery.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">Hello all,<div><br></div><div>regarding the manuscript, what is the deadline for contributions? I try to find another slot for a working session this and next week. Please let me know where help is needed in terms of editing. </div><div><br></div><div>ALexander </div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, 24 May 2021 at 18:00, 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>Eric: <br>
</p>
<p>Yes, I do see your changes. Thanks!</p>
<p>-John G. <br>
</p>
<div>On 5/24/2021 4:47 AM, Eric Forgoston
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>
<div>
<div>Hi Jacob and all,<br>
<br>
</div>
I did rewrite the stochastic section adding in material from
me and comments from William and James G. The only material
I removed had been written by myself originally.<br>
<br>
</div>
<div>Additional comments are welcome.<br>
</div>
<div><br>
</div>
Cheers,<br>
<br>
</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">https://eric-forgoston.github.io/</a></span></span><br>
</div>
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<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, May 24, 2021 at 6:55
AM William Waites <<a href="mailto:wwaites@ieee.org" target="_blank">wwaites@ieee.org</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">>
Otherwise, all I saw was …<br>
<br>
There was editing of the section on stochasticity by Eric with
some input from myself. <br>
<br>
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