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<p>I'm happy to help with revisions. I think a zoom call is a good idea.</p>
<p>Hana<br>
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<div class="PlainText">*******************************************************<br>
Dr. Hana Dobrovolny<br>
Associate Professor of Biophysics<br>
Texas Christian University<br>
TCU Box 298840<br>
Fort Worth, TX 76129<br>
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phone: (817) 257-6379 fax: (817) 257-7742<br>
email: h.dobrovolny@tcu.edu<br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Vp-reproduce-subgroup <vp-reproduce-subgroup-bounces@lists.simtk.org> on behalf of James Osborne <jmosborne@unimelb.edu.au><br>
<b>Sent:</b> May 11, 2021 10:00 PM<br>
<b>To:</b> Eric Forgoston<br>
<b>Cc:</b> vp-reproduce-subgroup@lists.simtk.org; vp-integration-subgroup@lists.simtk.org; Jonathan Karr; John Gennari; Winston Garira<br>
<b>Subject:</b> Re: [Vp-reproduce-subgroup] [EXT] Re: [Vp-integration-subgroup] White paper submission - vote for venue</font>
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<div dir="ltr">Agreed
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<div>I also think there needs to be an effort to make it more readable and consistent throughout and from experience this can only happen by a small group taking it on.</div>
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<div>James </div>
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<div dir="ltr" class="gmail_attr">On Wed, May 12, 2021 at 12:38 PM Eric Forgoston <<a href="mailto:eric.forgoston@montclair.edu">eric.forgoston@montclair.edu</a>> wrote:<br>
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<td style="color:red"><b>External email: </b>Please exercise caution</td>
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Dear all,</div>
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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.
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<div>Is there interest in doing this?</div>
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<div>Cheers,</div>
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<div>Eric<br>
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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://urldefense.com/v3/__https://eric-forgoston.github.io/__;!!O2_lDA!i7xWzLA1fndcQ6doX4ybaW0PNRoxrRHsEUBOU2CUqnSjaQesOiQYDKsayOqWDvhQ5bs$" target="_blank">https://eric-forgoston.github.io/</a></span></span><br>
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<div dir="ltr" class="gmail_attr">On Tue, May 11, 2021 at 10:26 AM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>> wrote:<br>
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<div dir="ltr">Greetings white paper contributors,<br>
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<div>The voting period is over and the vote did not change, so it is now time to act.</div>
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<div>The paper will be revised as requested by 10 voters and the target journal will be Bioinformatics - James Glazier and Yaling Liu will share publication costs.</div>
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<div>All those who asked to revise are requested to make the revisions and discuss those.</div>
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<div>I ask to reach a revised version by May 25 so that we can finish an approval round by June 1st.</div>
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<div>So far only Sheriff provided suggestions for revisions prior to submission so I suggest we start discussing those:</div>
<div><a href="https://urldefense.com/v3/__https://docs.google.com/document/d/1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh/edit__;!!O2_lDA!i7xWzLA1fndcQ6doX4ybaW0PNRoxrRHsEUBOU2CUqnSjaQesOiQYDKsayOqWjVyCKjU$" target="_blank">https://docs.google.com/document/d/1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh/edit</a><br>
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<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://urldefense.com/v3/__https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing__;!!O2_lDA!i7xWzLA1fndcQ6doX4ybaW0PNRoxrRHsEUBOU2CUqnSjaQesOiQYDKsayOqWNaTv0Sw$" target="_blank">https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing</a><br>
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<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>
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<div>I look forward to your contributions. </div>
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<div> Jacob</div>
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<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>
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<div dir="ltr">Greetings white paper contributors,
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<div>Allow me to remind you that the Voting and vote changes are still possible until 11-May 1am CDT </div>
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<div>The current votes I saw are:</div>
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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>
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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.
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There is currently 1 minority vote:<br>
Jacob Barhak for direct submission to Nature - Scientific Reports </div>
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<div>If revision is selected, time will be limited, so I suggest those who voted to start working on revisions. </div>
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<div>Hopefully this reminder will move us forward.</div>
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<div> Jacob</div>
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<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>
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<div dir="ltr">Greetings white paper contributors,
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<div>It is time to vote again for the target venue. Here are the options again. </div>
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<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>
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<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>
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<div>The voting period will be until Tuesday 11-May 1am CDT </div>
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<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>
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<div>I urge contributors to vote - just so that we will have a preference order to follow in case of rejection.</div>
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<div>Looking forward to your votes. </div>
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<div> Jacob</div>
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