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<p class="MsoNormal">Hi all and Jacob,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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:
<a href="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#">
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#</a> .<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The journal is new, and I don’t remember it being proposed previously.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am also willing to prioritize revision and submission and apologize for not participating more over the summer.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best,<o:p></o:p></p>
<p class="MsoNormal">Marcella<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Vp-reproduce-subgroup <vp-reproduce-subgroup-bounces@lists.simtk.org> on behalf of Jacob Barhak <jacob.barhak@gmail.com><br>
<b>Date: </b>Monday, August 2, 2021 at 11:45 AM<br>
<b>To: </b>Alexander Kulesza <alexander.kulesza@novadiscovery.com><br>
<b>Cc: </b>vp-reproduce-subgroup@lists.simtk.org <vp-reproduce-subgroup@lists.simtk.org>, vp-integration-subgroup@lists.simtk.org <vp-integration-subgroup@lists.simtk.org>, Jonathan Karr <jonrkarr@gmail.com>, John Gennari <gennari@uw.edu>, Faeder, James R <faeder@pitt.edu>,
Winston Garira <Winston.Garira@univen.ac.za><br>
<b>Subject: </b>Re: [Vp-reproduce-subgroup] [Vp-integration-subgroup] White paper revision<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:yellow"><b><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:red">External Email:</span></b><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black"> Use caution in opening links, attachments,
and buying gift cards.</span><span style="font-size:10.0pt;font-family:"Arial",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi Alex, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Thanks for your response first - it is the first public response. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">And Alex, time is something you manage to achieve certain goals with certain priorities. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The real question is if circulating this paper is on a high priority list for any of the contributors?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Some contributors publicly declared they have little time, yet we were still able to push though in the past. What has changed?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Perhaps a discussion will reveal those things.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> Jacob<o:p></o:p></p>
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<p class="MsoNormal">On Mon, Aug 2, 2021 at 2:00 AM Alexander Kulesza <<a href="mailto:alexander.kulesza@novadiscovery.com">alexander.kulesza@novadiscovery.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">Dear all, Dear Jacob, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I think that the time of the year impedes many of us (including myself) to spend the time needed to edit the sections. <o:p></o:p></p>
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<p class="MsoNormal">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. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Please let me know what you think.<o:p></o:p></p>
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<p class="MsoNormal">Alexander<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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:<o:p></o:p></p>
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<p class="MsoNormal">Greetings contributors, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Do you not want this paper be circulated? <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I am asking those questions publicly since this deserves a public discussion.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hopefully this reminder will stir up the group.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> Jacob<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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:<o:p></o:p></p>
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<p class="MsoNormal">Hi Gilberto, <o:p></o:p></p>
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<p class="MsoNormal">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.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I remind you that I wrote what needs to be done to make progress. See the 4 points in this archived email:<o:p></o:p></p>
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<p class="MsoNormal"><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><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">This situation raises the question.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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? <o:p></o:p></p>
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<p class="MsoNormal">I personally doubt that any further revisions will allow publication in reasonable time - which as I mentioned before delays science rather than advancing it.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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...<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">If we do not do this, we will be guilty of delaying science. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hopefully contributors will realize this and we can proceed to fix the situation quickly.<o:p></o:p></p>
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<p class="MsoNormal"> Jacob<o:p></o:p></p>
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<p class="MsoNormal">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:<o:p></o:p></p>
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<p class="MsoNormal">Dear all, <o:p></o:p></p>
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<p class="MsoNormal">I like Eric's idea i.e. "section heads can look at the technical aspects of their respective sections this week."<o:p></o:p></p>
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<p class="MsoNormal">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="font-family:"Arial",sans-serif;color:black">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><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Best,<o:p></o:p></p>
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<p class="MsoNormal">***************************************************************************<o:p></o:p></p>
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<p class="MsoNormal">Gilberto C. Gonzalez-Parra, <span style="font-size:10.0pt;font-family:"Helvetica Neue";color:black">Ph.D in Applied Mathematics.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica Neue";color:black">Faculty of the </span>Mathematics Department
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<p class="MsoNormal">New Mexico Tech, NM, USA.<o:p></o:p></p>
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<p class="MsoNormal">****************************************************************************<o:p></o:p></p>
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<p class="MsoNormal">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:<o:p></o:p></p>
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<p class="MsoNormal">Dear all, <o:p></o:p></p>
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<p class="MsoNormal">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.<o:p></o:p></p>
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<p class="MsoNormal">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.<o:p></o:p></p>
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<p class="MsoNormal">Thoughts?<o:p></o:p></p>
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<p class="MsoNormal">Best wishes,<o:p></o:p></p>
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<p class="MsoNormal">Eric<br clear="all">
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<p class="MsoNormal">---------------------<br>
Dr. Eric Forgoston<br>
Professor of Applied Mathematics<br>
Chair, Department of Applied Mathematics and Statistics<br>
Montclair State University<br>
Montclair, NJ 07043 USA<br>
+1 973 655-7242 <br>
<a href="https://eric-forgoston.github.io/" target="_blank">https://eric-forgoston.github.io/</a><o:p></o:p></p>
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<p class="MsoNormal">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:<o:p></o:p></p>
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<p class="MsoNormal">Hello all, <o:p></o:p></p>
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<p class="MsoNormal">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. <o:p></o:p></p>
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<p class="MsoNormal">ALexander <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Mon, 24 May 2021 at 18:00, John Gennari <<a href="mailto:gennari@uw.edu" target="_blank">gennari@uw.edu</a>> wrote:<o:p></o:p></p>
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<p>Eric: </p>
<p>Yes, I do see your changes. Thanks!</p>
<p>-John G. </p>
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<p class="MsoNormal">On 5/24/2021 4:47 AM, Eric Forgoston wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Hi Jacob and all,<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">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.<o:p></o:p></p>
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<p class="MsoNormal">Additional comments are welcome.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Cheers,<o:p></o:p></p>
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Dr. Eric Forgoston<br>
Professor of Applied Mathematics<br>
Chair, Department of Applied Mathematics and Statistics<br>
Montclair State University<br>
Montclair, NJ 07043 USA<br>
+1 973 655-7242 <br>
<a href="https://eric-forgoston.github.io/" target="_blank">https://eric-forgoston.github.io/</a><o:p></o:p></p>
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<p class="MsoNormal">On Mon, May 24, 2021 at 6:55 AM William Waites <<a href="mailto:wwaites@ieee.org" target="_blank">wwaites@ieee.org</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">> Otherwise, all I saw was …<br>
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There was editing of the section on stochasticity by Eric with some input from myself.
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