<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Jacob,<div class=""><br class=""></div><div class="">Thanks for this. As per the email below, I also approve :-)</div><div class=""><br class=""></div><div class="">Best wishes,</div><div class="">Robin</div><div class=""><br class=""></div><div class=""><div class="">Begin forwarded message:</div><br class=""><div style="margin: 0px;" class=""><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class=""><b class="">From: </b></span><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class="">Robin Thompson <<a href="mailto:u2070841@live.warwick.ac.uk" target="_blank" class="">u2070841@live.warwick.ac.uk</a>><br class=""></span></div><div style="margin: 0px;" class=""><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class=""><b class="">Subject: </b></span><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class=""><b class="">Re: [Vp-integration-subgroup] [Vp-reproduce-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript</b><br class=""></span></div><div style="margin: 0px;" class=""><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class=""><b class="">Date: </b></span><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class="">8 November 2021 at 12:25:14 GMT<br class=""></span></div><div style="margin: 0px;" class=""><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class=""><b class="">To: </b></span><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class="">Eric Forgoston <<a href="mailto:eric.forgoston@montclair.edu" target="_blank" class="">eric.forgoston@montclair.edu</a>><br class=""></span></div><div style="margin: 0px;" class=""><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class=""><b class="">Cc: </b></span><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class="">James Osborne <<a href="mailto:jmosborne@unimelb.edu.au" target="_blank" class="">jmosborne@unimelb.edu.au</a>>, "<a href="mailto:vp-reproduce-subgroup@lists.simtk.org" target="_blank" class="">vp-reproduce-subgroup@lists.simtk.org</a>" <<a href="mailto:vp-reproduce-subgroup@lists.simtk.org" target="_blank" class="">vp-reproduce-subgroup@lists.simtk.org</a>>, James A Glazier <<a href="mailto:jaglazier@gmail.com" target="_blank" class="">jaglazier@gmail.com</a>>, "<a href="mailto:vp-integration-subgroup@lists.simtk.org" target="_blank" class="">vp-integration-subgroup@lists.simtk.org</a>" <<a href="mailto:vp-integration-subgroup@lists.simtk.org" target="_blank" class="">vp-integration-subgroup@lists.simtk.org</a>>, John Gennari <<a href="mailto:gennari@uw.edu" target="_blank" class="">gennari@uw.edu</a>>, Jonathan Karr <<a href="mailto:jonrkarr@gmail.com" target="_blank" class="">jonrkarr@gmail.com</a>>, Winston Garira <<a href="mailto:Winston.Garira@univen.ac.za" target="_blank" class="">Winston.Garira@univen.ac.za</a>>, "Faeder, James R" <<a href="mailto:faeder@pitt.edu" target="_blank" class="">faeder@pitt.edu</a>><br class=""></span></div><br class=""><div class=""><div style="overflow-wrap: break-word;" class="">Hi Jacob,<div class=""><br class=""></div><div class="">Thanks for this. I approve too.</div><div class=""><br class=""></div><div class="">Best wishes,</div><div class="">Robin<br class=""><div class="">----------------------------------------------------------------------<br class="">Dr Robin Thompson<br class="">Assistant Professor of Mathematical Epidemiology<br class="">Mathematics Institute<br class="">University of Warwick, UK<br class=""><a href="http://www.robin-thompson.co.uk/" target="_blank" class="">www.robin-thompson.co.uk</a><br class="">----------------------------------------------------------------------</div><div class=""><br class=""><blockquote type="cite" class=""><div class="">On 8 Nov 2021, at 00:32, Eric Forgoston <<a href="mailto:eric.forgoston@montclair.edu" target="_blank" class="">eric.forgoston@montclair.edu</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class=""><div class=""><div class="">Hi Jacob,<br class=""><br class=""></div>I approve.<br class=""><br class=""></div>Eric<br clear="all" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class="">---------------------<br class="">Dr. Eric Forgoston<br class="">Professor of Applied Mathematics<br class="">Chair, Department of Applied Mathematics and Statistics<br class="">Montclair State University<br class="">Montclair, NJ 07043 USA<br class="">+1 973 655-7242 <br class=""><a href="https://eric-forgoston.github.io/" target="_blank" class="">https://eric-forgoston.github.io/</a><br class=""><div style="display: inline;" class=""></div></div></div></div></div></div></div></div></div></div></div></div></div></blockquote></div></div><div class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><br class=""></div></div></div></div></div></div></div></div></div></div></div></div></div></div><div><br class=""><blockquote type="cite" class=""><div class="">On 6 Nov 2021, at 22:59, Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" class="">jacob.barhak@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Greetings paper contributors,<div class=""><br class=""></div><div class="">It is time for final approval of our manuscript. Here is the manuscript I ask you to approve towards submission to Frontiers in Systems Biology:</div><div class=""><a href="https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing" class="">https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing</a><br class=""></div><div class=""><br class=""></div><div class="">I disabled all edits to it at this point so it will not change unless I reopen it. </div><div class=""><br class=""></div><div class=""><span id="gmail-docs-internal-guid-2f6de887-7fff-1394-2643-42eda71b0573" class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; background-color: transparent; font-variant-numeric: normal; font-variant-east-asian: normal; vertical-align: baseline; white-space: pre-wrap;" class="">This is the list of contributors in no particular order </span></div><ol style="margin-top:0px;margin-bottom:0px" class=""><li dir="ltr" style="list-style-type: decimal; font-size: 11pt; font-family: Arial; background-color: transparent; font-variant-numeric: normal; font-variant-east-asian: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size:11pt;background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap" class="">Jonathan Karr, Icahn Institute for Data Science and Genomic Technology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA</span></div></li><li dir="ltr" style="list-style-type: decimal; font-size: 11pt; font-family: Arial; background-color: transparent; font-variant-numeric: normal; font-variant-east-asian: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size:11pt;background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap" class="">Rahuman Sheriff, The European Bioinformatics Institute (EMBL-EBI), London, UK</span></div></li><li dir="ltr" style="list-style-type: decimal; font-size: 11pt; font-family: Arial; background-color: transparent; font-variant-numeric: normal; font-variant-east-asian: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size:11pt;background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap" class="">James Osborne, School of Mathematics and Statistics, University of Melbourne, Parkville, Australia</span></div></li><li dir="ltr" style="list-style-type: decimal; font-size: 11pt; font-family: Arial; background-color: transparent; font-variant-numeric: normal; font-variant-east-asian: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size:11pt;background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap" class="">Gilberto Gonzalez Parra, Mathematics Department, New Mexico Tech, Socorro, USA</span></div></li><li dir="ltr" style="list-style-type: decimal; font-size: 11pt; font-family: Arial; background-color: transparent; font-variant-numeric: normal; font-variant-east-asian: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size:11pt;background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap" class="">Eric Forgoston, Department of Applied Mathematics and Statistics, Montclair State University, Montclair, NJ, USA</span></div></li><li dir="ltr" style="list-style-type: decimal; font-size: 11pt; font-family: Arial; background-color: transparent; font-variant-numeric: normal; font-variant-east-asian: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size:11pt;background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap" class="">Ruth Bowness, Department of Mathematical Sciences, University of Bath, Bath, UK</span></div></li><li dir="ltr" style="list-style-type: decimal; font-size: 11pt; font-family: Arial; background-color: transparent; font-variant-numeric: normal; font-variant-east-asian: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size:11pt;background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap" class="">Yaling Liu, Department of Mechanical Engineering and Mechanics , Department of Bioengineering, Lehigh University, Bethlehem, PA, USA</span></div></li><li dir="ltr" style="list-style-type: decimal; font-size: 11pt; font-family: Arial; background-color: transparent; font-variant-numeric: normal; font-variant-east-asian: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size:11pt;background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap" class="">Robin Thompson, Mathematics Institute & The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry , UK</span></div></li><li dir="ltr" style="list-style-type: decimal; font-size: 11pt; font-family: Arial; background-color: transparent; font-variant-numeric: normal; font-variant-east-asian: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size:11pt;background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap" class="">Winston Garira - Department Of Mathematics And Applied Mathematics , Modelling Health and Environmental Linkages Research Group. University of Venda, Limpopo, South Africa</span></div></li><li dir="ltr" style="list-style-type: decimal; font-size: 11pt; font-family: Arial; background-color: transparent; font-variant-numeric: normal; font-variant-east-asian: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size:11pt;background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap" class="">Jacob Barhak* - Jacob Barhak Analytics, Austin, TX, USA</span></div></li><li dir="ltr" style="list-style-type: decimal; font-size: 11pt; font-family: Arial; background-color: transparent; font-variant-numeric: normal; font-variant-east-asian: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size:11pt;background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap" class="">John Rice - Independent Retired Working Group Volunteer, Virginia Beach, VA, USA</span></div></li><li dir="ltr" style="list-style-type: decimal; font-size: 11pt; font-family: Arial; background-color: transparent; font-variant-numeric: normal; font-variant-east-asian: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size:11pt;background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap" class="">Marcella Torres*, School of Arts and Sciences, University of Richmond, Richmond, USA</span></div></li><li dir="ltr" style="list-style-type: decimal; font-size: 11pt; font-family: Arial; background-color: transparent; font-variant-numeric: normal; font-variant-east-asian: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size:11pt;background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap" class="">Hana M. Dobrovolny , Department of Physics & Astronomy, Texas Christian University, Fort Worth, USA</span></div></li><li dir="ltr" style="list-style-type: decimal; font-size: 11pt; font-family: Arial; background-color: transparent; font-variant-numeric: normal; font-variant-east-asian: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size:11pt;background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap" class="">Tingting Tang, Department of Mathematics and Statistics in San Diego State University (SDSU) and SDSU Imperial Valley, Calexico, CA, USA</span></div></li><li dir="ltr" style="list-style-type: decimal; font-size: 11pt; font-family: Arial; background-color: transparent; font-variant-numeric: normal; font-variant-east-asian: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size:11pt;background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap" class="">William Waites, Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK</span></div></li><li dir="ltr" style="list-style-type: decimal; font-size: 11pt; font-family: Arial; background-color: transparent; font-variant-numeric: normal; font-variant-east-asian: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size:11pt;background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap" class="">James Glazier, Biocomplexity Institute, Indiana University, Bloomington, USA</span></div></li><li dir="ltr" style="list-style-type: decimal; font-size: 11pt; font-family: Arial; background-color: transparent; font-variant-numeric: normal; font-variant-east-asian: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size:11pt;background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap" class="">James R. Faeder, Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, USA</span></div></li><li dir="ltr" style="list-style-type: decimal; font-size: 11pt; font-family: Arial; background-color: transparent; font-variant-numeric: normal; font-variant-east-asian: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size:11pt;background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap" class="">Alexander Kulesza, Novadiscovery SA, Lyon, France</span></div></li></ol><div class=""><font face="Arial" class=""><span style="font-size:14.6667px;white-space:pre-wrap" class=""><br class=""></span></font></div><div class=""><font face="Arial" class=""><span style="font-size:14.6667px;white-space:pre-wrap" class="">IF YOU ARE ON THIS LIST - YOU HAVE 3 TASKS DO TO:</span></font></div><div class=""><font face="Arial" class=""><span style="font-size:14.6667px;white-space:pre-wrap" class=""><br class=""></span></font></div><div class=""><font face="Arial" class=""><span style="font-size:14.6667px;white-space:pre-wrap" class="">TASK 1: </span></font></div><div class=""><font face="Arial" class=""><span style="font-size:14.6667px;white-space:pre-wrap" class="">Please go over the paper and the Journal rules here: </span></font></div><div class=""><a href="https://www.frontiersin.org/about/policies-and-publication-ethics" target="_blank" class="">https://www.frontiersin.org/about/policies-and-publication-ethics</a> </div><div class=""><br class=""></div><div class="">Note that the guidelines allow to establish authors levels of contribution according to <a href="https://www.frontiersin.org/about/author-guidelines" class="">https://www.frontiersin.org/about/author-guidelines</a> section 1.9 - however order is not dictated - I suggest to keep this order which is more or less random - I really do not want to discuss order or authors - this is not the purpose of this paper.<br class=""></div><div class="">Also to simplify the process, I detached the manuscript from the working group - we can add it back according to section 1.10 of the guidelines. For simplicity I suggest we just submit the paper as a group of authors - unless someone volunteers their time to do more paperwork. The working group is mentioned in the paper as well as correspondences.<br class=""></div><div class=""><br class=""></div><div class="">TASK 2: </div><div class="">Please check again your name and affiliation is correct. this can be fixed in submission - and apologies in advance for any mistakes. In cases of dual affiliation, I listed only one, so please look at the submission guidelines and give me the correct information according to the guidelines - I will have to enter it manually in the system upon submission. <br class=""></div><div class=""><br class=""></div><div class="">TASK 3: </div><div class="">REPLY TO ALL TO THIS MESSAGE and note one of the following options:</div><div class=""> </div></span></div><div class="">1. APPROVE: this means you agree that the manuscript represents your views correctly You also approve the corresponding author to act on your behalf for the rest of the publication process - currently I am the corresponding author and will add Marcella if possible yet if anyone else wants to volunteer - please do.</div><div class=""><br class=""></div><div class="">2. DISAPPROVE: This means you cannot have your name signed on this manuscript and the group should discuss some matters in further details before submission to properly represent you - this means you are still interested in being an author, yet need your views represented properly - this will delay us all, so if you choose this option, this means you will have to spend time on discussions and explain why you have not acted by now and you are asking to delay now. This option will take a lot of time from you and others, yet you certainly have the right to choose this option. </div><div class=""><br class=""></div><div class="">3. ABSTAIN: This means you are ok with removing your name from the author list and allowing the rest of us to submit the manuscript with your contribution without taking responsibility - your name will be added to acknowledgements instead. In legal terms it means you waive copyright on the text you added so we can legally send this text to the Journal despite your name not listed in the author list. </div><div class=""><br class=""></div><div class="">I also ask John Gennari for the last time to rejoin the group and approve the manuscript as an author sinceI believe he had major contributions - hopefully he will reconsider and accept this responsibility and privilege. Otherwise he makes our lives harder to protect that paper, especially with elements lik SemGen and Annotaions where he is an expert. </div><div class=""><br class=""></div><div class="">I will need a public response from all of you - if you send me a private email I will forward it to the list to become public record - please avoid doing so since you are making me work twice- so PLEASE PRESS REPLY ALL.</div><div class=""><br class=""></div><div class="">Hopefully we can get this approval round done quickly and move forward and submit. </div><div class=""><br class=""></div><div class=""> Jacob</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Nov 4, 2021 at 12:30 AM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" class="">jacob.barhak@gmail.com</a>> wrote:<br class=""></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" class="">Thanks James, And Greetings to all contributors, <div class=""><br class=""></div><div class="">James, your suggestions are almost all accepted - yes we needed American English and modelling is not the American form - thanks for noticing. The reference will stay as is or corrected during proofs I see no better way to reference it other than the automatically generated text. </div><div class=""><br class=""></div><div class="">At this point 3 people went over the manuscript and it seems ready to go.</div><div class=""><br class=""></div><div class="">However, to avoid any misunderstandings I would like formal public approval from all Authors to make sure we are all on the same page. There were several discussions and different voices and I want to make sure this version is something all authors agree on. Here is the manuscript:</div><div class=""><a href="https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing" target="_blank" class="">https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing</a><br class=""></div><div class=""><br class=""></div><div class="">If you want to see the comment history, please send me a request so I can add you as an editor.</div><div class=""><br class=""></div><div class="">Before you rush approving, I would ask you to take a minute and read section 1.3. Authorship and Author Responsibilities in </div><div class=""><a href="https://www.frontiersin.org/about/policies-and-publication-ethics" target="_blank" class="">https://www.frontiersin.org/about/policies-and-publication-ethics</a><br class=""></div><div class=""><br class=""></div><div class="">If you approve this manuscript, this means you are comfortable with releasing this for publication using the CC-BY, version 4.0 license with the terms above. </div><div class=""><br class=""></div><div class="">Please double check your name and affiliation - I will have to copy it - if there is a mistake, let me know. </div><div class=""><br class=""></div><div class="">If after checking all these you are ok, please:</div><div class="">REPLY TO ALL TO THIS MESSAGE WITH THE TEXT "I APPROVE THE MANUSCRIPT"</div><div class=""><br class=""></div><div class="">I ask that you do not send any approve message before Saturday - 6 - Nov - I want to give a last chance for edits or discussions before everyone approves. WE had plenty of time, yet I want to make sure there is no late arrival that is very important so I am giving this two more days. </div><div class=""><br class=""></div><div class="">On Oct 6th I will lock the manuscript and remove all comments and mark them as resolved. </div><div class=""><br class=""></div><div class="">I hope you all find it in good shape.</div><div class=""><br class=""></div><div class=""> Jacob</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Nov 3, 2021 at 5:15 AM James Osborne <<a href="mailto:jmosborne@unimelb.edu.au" target="_blank" class="">jmosborne@unimelb.edu.au</a>> wrote:<br class=""></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" class="">Jacob <br class=""><div class=""><br class=""></div><div class="">I did another readability pass and fixed a few grammatical errors and fixed some British English vs American English inconsistencies (went on the American side). Everything as suggestions so you can leave if you choose.</div><div class=""><br class=""></div><div class="">For what it's worth thank you for your efforts knocking this into shape.</div><div class=""><br class=""></div><div class="">James </div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Nov 3, 2021 at 4:42 PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank" class="">jacob.barhak@gmail.com</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="">
<div dir="ltr" class="">Hi James,
<div class=""><br class="">
</div>
<div class="">Eric Forgoston was kind enough to gp through the paper and made edits - I resolved most issues and only a few comments are left for experts on annotation and to resolve some differences between John Rice and Alex. </div>
<div class=""><br class="">
</div>
<div class="">I ask that we avoid endless edits and start the approval process for submission. We should not drag editing anymore - Eric's last edits were at the level of punctuation and proofs so we should be good. And this is after many edits and checks I made myself
and I know Hana and Alex also made edits. </div>
<div class=""><br class="">
</div>
<div class="">Unless someone shouts, I will start the approval process tomorrow - so I ask contributors to give the papr a last peek before you are asked to say Yes/NO towards submission with your name on it. </div>
<div class=""><br class="">
</div>
<div class="">Hopefully this last warning is sufficient and you will all find the paper in good shape. </div>
<div class=""><br class="">
</div>
<div class=""> Jacob</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, Oct 28, 2021 at 9:26 PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank" class="">jacob.barhak@gmail.com</a>> wrote:<br class="">
</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" class="">Hi James,
<div class=""><br class="">
</div>
<div class="">Apologies - I must have missed your email request. If anyone else wants access and did not get it, please let me know - I will do my best to give you access within a day. </div>
<div class=""><br class="">
</div>
<div class="">For those who have access. Please no more additions - from now on just corrections of typos, grammer, and grave errors. Anything else, please leave a comment and we can discuss it.</div>
<div class=""><br class="">
</div>
<div class="">I really want the paper out quickly - hopefully we can finish this and submit quickly.</div>
<div class=""><br class="">
</div>
<div class=""> Jacob</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, Oct 28, 2021 at 3:17 PM James A Glazier <<a href="mailto:jaglazier@gmail.com" target="_blank" class="">jaglazier@gmail.com</a>> wrote:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class=""><p class="">Dear Jacob:</p><p class="">I would like to review the document. I had asked for access a few weeks ago. Happy to look in the next few days.</p><p class="">JAG<br class="">
</p>
<div class="">On 10/24/2021 4:40 AM, Jacob Barhak wrote:<br class="">
</div>
<blockquote type="cite" class="">
<div dir="ltr" class="">Hi Eric,
<div class=""><br class="">
</div>
<div class="">You are the last one I remember who wanted to edit. Please check the manuscript</div>
<div class=""><a href="https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing" target="_blank" class="">https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing</a><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">I finished editing the references and am almost ready for transformation to match the guidelines. I finished addressing the editor requesting for removal of bullet points everywhere but the stochastic section . </div>
<div class=""><br class="">
</div>
<div class="">I ask that you do not add any more references and focus only on text in the stochastic section. Handling the references took about 4 hours alone and still needs inspection. </div>
<div class=""><br class="">
</div>
<div class="">However, I will appreciate help with minor proofs - I made significant changes so there is a chance for typos still. Some of the changes have been made after more than 12 hours of consecutive work. So polish will help - yet no more major changes. </div>
<div class=""><br class="">
</div>
<div class="">The tasks left to do are:</div>
<div class="">- Ask John Gennari to inspect the paper again - it has major contributions from his version and he should join the authors list - I must be ask again </div>
<div class="">- Finish the edits to the stochastic section - Eric - you asked for this</div>
<div class="">- Finish formatting to fit the Journal guidelines </div>
<div class="">- Add a cover letter and split the paper into sections to be uploaded to the journal web site</div>
<div class="">- Approve the version with all authors - we must do this again and get full approval - this may take a while</div>
<div class="">- Determine who else wants to be listed as corresponding author - currently I marked Marcell and myself, yet others may want to correspond. </div>
<div class="">- Upload the paper to the journal submission system</div>
<div class=""><br class="">
</div>
<div class="">I hope for no obstacles and full cooperation to make the process smooth.</div>
<div class=""><br class="">
</div>
<div class=""> Jacob</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Sat, Oct 23, 2021 at 9:08 PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank" class="">jacob.barhak@gmail.com</a>> wrote:<br class="">
</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" class="">So Gilberto,
<div class=""><br class="">
</div>
<div class="">The last approved version is the only one we can continue from - this is unfortunate that there is a need to back port some modifications - hence the conversation with Eric and Hana - yet to maintain traceability and honor all contributors - this is necessary.</div>
<div class=""><br class="">
</div>
<div class="">And yes, there will be some differences - it's unavoidable. Yet I pretty much merged the other traceable versions by now. If I missed anything - I apologize - there is a limit to human capabilities. </div>
<div class=""><br class="">
</div>
<div class="">We discussed this multiple times on this list, if this is a stopper for you, let me know immediately so I will stop work to resolve this issue.</div>
<div class=""><br class="">
</div>
<div class="">Otherwise, I will continue - I think I resolved most points except from references and removal of bullets - still working on that and I will have to deal with modifying conclusions at the end. </div>
<div class=""><br class="">
</div>
<div class="">And Gilberto, if you want to contribute time towards changing order of sections and handle references to comply with the target journal guidelines, please go online on the Jitsi channel.and I will show you the extent of work needed. I will be here for
at least 3 more hours - until midnight - yet to be efficient, please join on jitsi if you want to talk while I continue modifications. </div>
<div class=""><br class="">
</div>
<div class="">I hope I can finish most of the work except references perhaps by midnight. </div>
<div class=""><br class="">
</div>
<div class=""> Jacob</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Sat, Oct 23, 2021 at 8:32 PM Gilberto Gonzalez-Parra <<a href="mailto:gilberto.gonzalezparra@nmt.edu" target="_blank" class="">gilberto.gonzalezparra@nmt.edu</a>> wrote:<br class="">
</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" class="">Hi Jacob,
<div class=""><br class="">
</div>
<div class="">I noticed that we are not using the last version that has many modifications. Are you using the previous version that was originally submitted to cureus ? and trying to incorporate the changes of the last version ?</div>
<div class=""><br class="">
</div>
<div class="">I noticed that the section/challenge <span style="font-size: 11pt; line-height: 107%; font-family: Arial, sans-serif;" class=""><b class="">Barriers to model implementation and real-world use</b> was removed. I think in one of the emails it says that there is no solution
proposed for this. I can write some general ideas for this. </span></div>
<div class=""><span style="font-size: 11pt; line-height: 107%; font-family: Arial, sans-serif;" class=""><br class="">
</span></div>
<div class=""><span style="font-size: 11pt; line-height: 107%; font-family: Arial, sans-serif;" class="">In the current version in the table it appears "</span><span style="background-color: transparent; font-family: Arial; font-size: 11pt; white-space: pre-wrap;" class=""><b class="">Model
application and implementation barriers</b>" just after "</span><span style="background-color: transparent; font-family: Arial; font-size: 11pt; font-weight: 700; white-space: pre-wrap;" class="">Missing Annotations in Models"
</span><span style="background-color: transparent; font-family: Arial; font-size: 11pt; white-space: pre-wrap;" class="">but later in the document appears just before stochastic modeling. I think we should keep the same order that is in the table. The article
would look better organized.</span></div>
<div class=""><span style="background-color: transparent; font-family: Arial; font-size: 11pt; white-space: pre-wrap;" class=""></span></div>
<div class=""><span style="background-color: transparent; font-family: Arial; font-size: 11pt; white-space: pre-wrap;" class="">Best,</span></div>
<div class=""><br class="">
</div>
<div class="">
<div class="">
<div dir="ltr" class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">***************************************************************************</div>
<div dir="ltr" class="">Gilberto C. Gonzalez-Parra, <span class="">Ph.D in Applied Mathematics.</span></div>
<div dir="ltr" class=""><font face="Helvetica
Neue, Helvetica, Arial, Lucida
Grande, sans-serif, serif,
EmojiFont" class=""><span style="font-size:13px" class="">Faculty
of the </span></font>Mathematics Department
<div class="">
<div class="">New Mexico Tech, NM, USA.</div>
</div>
<div class="">****************************************************************************</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br class="">
</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Sat, Oct 23, 2021 at 5:38 PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank" class="">jacob.barhak@gmail.com</a>> wrote:<br class="">
</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" class="">Hi Eric, and also greeting for the other paper contributors
<div class="">
<div class=""><br class="">
</div>
<div class="">Here is a real time update just to give an idea of current editing status.</div>
<div class=""><br class="">
</div>
<div class="">It took almost 6 hours to get the manuscript to the point that contributions from Sheriff, Alex, John Gennari, and Hana were integrated. I assume Eric will add his edits later - since those are in one section, it should not cause any conflict. However,
Eric, please be careful when editing the stochastic section. Pease look at the comments Hana and I exchanged. I am also adding the chat between us so it will be easier on you:</div>
<div class=""><br class="">
</div>
<div class="">"</div>
<div class="">Hi Hana<br class="">
Can you see the chat?<br class="">
I can. There's just a lot going on around here right now, so I'm not fast with typing<br class="">
I put the references in the comments, can you see them?<br class="">
Yes I See them - yet you will have to ensure that this is your text - you see, you copied text from a document where we do not have contributor history - this was the main issue - so you will have not to prove this was your text and only your text - this is
the problem I am faced with - I have to establish tracability - in this document I know you added the text - yet I cannot verify that you did not include text from anonymous since I already concluded you added text from Alex - this is how I stumbled on this
- I apologize yet I really am serious about tracing back authorship..<br class="">
And thanks fro helping<br class="">
If you want, you can join jitsi: <a href="https://meet.jit.si/CollaborativePaperEditing" target="_blank" class="">
https://meet.jit.si/CollaborativePaperEditing</a> and we can chat using voice<br class="">
I just saw your comment - it is public confirmation - this is good enough thank you
<br class="">
The first two paragraphs are from the original paper. The third paragraph is from Alex. The last two are mine. It looks like someone (other than me) italicized the in vitro and in vivo and changed the verb on the "Even data that are..." (I had is), but everything
else is mine.<br class="">
If you can modify things to the original version you added - it will be better - if someone manipulated the text I want to remove it - even if it is small changes
<br class="">
I know you're trying to get things done today, but I'll be out tonight, so if anything else comes up, I probably won't get to it until the morning.
<br class="">
Well, "are" is the correct verb there, so that should probably stay. I can remove the italicization.<br class="">
Do not worry - I am making good progress and may not need help until I am done - I appreciate the help and the fact you are working on it over the weekend - I will later also make this chat public for transparency. I do believe you have contributed a lot
to this paper - its not the first time you are going over it - I can only thank you .
<br class="">
the are was my change today I believe so its not a problem - yet google suggests is instead I guess is and are both acceptable with data .... nevermind that.<br class="">
"</div>
<div class=""><br class="">
</div>
<div class="">I did my best to keep all ideas and other texts intact and there are many comments to mark changes - the paper became longer, yet not too much and I feel it is still reasonable .</div>
<div class=""><br class="">
</div>
<div class="">I am now moving to the next part of complying with the requests of the editor:</div>
<div class="">1) Determine authorship</div>
<div class="">2) Converging format to journal guidelines - this also means references</div>
<div class="">3) Detach from group - some elements already marked</div>
<div class="">4) Revise bullet points into paragraphs</div>
<div class=""><br class="">
</div>
<div class="">I plan to continue editing until midnight CST with a break for dinner - so if anyone has comments - please feel free to join the open channel that shows the editing and influence real-time.</div>
<div class=""><br class="">
</div>
<div class="">Hopefully you will find the merged version in order. </div>
<div class=""><br class="">
</div>
<div class=""> Jacob</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Sat, Oct 23, 2021 at 2:50 PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank" class="">jacob.barhak@gmail.com</a>> wrote:<br class="">
</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" class="">Hi Eric,
<div class=""><br class="">
</div>
<div class="">You wanted to edit the stochastic section - you are welcome to do it. Yet I ask no more references or deletions - I am overloaded already. </div>
<div class=""><br class="">
</div>
<div class="">The version benign edited is:</div>
<div class=""><a href="https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit" target="_blank" class="">https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit</a><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">You will need to login so that your edits will be traceable.</div>
<div class=""><br class="">
</div>
<div class="">You can join me while editing in:</div>
<div class=""><a href="https://meet.jit.si/CollaborativePaperEditing" target="_blank" class="">https://meet.jit.si/CollaborativePaperEditing</a><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">I am sharing my screen there while editing. </div>
<div class=""><br class="">
</div>
<div class="">You might be able to help me with other sections as well.</div>
<div class=""><br class="">
</div>
<div class=""> Jacob</div>
<div class=""><br class="">
</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Sat, Oct 23, 2021 at 2:44 PM Eric Forgoston <<a href="mailto:eric.forgoston@montclair.edu" target="_blank" class="">eric.forgoston@montclair.edu</a>> wrote:<br class="">
</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" class="">Hi Jacob,
<div class=""><br class="">
</div>
<div class="">If you give me a link to the paper you are editing and edit access to the paper I can update the stochastic section.</div>
<div class=""><br class="">
</div>
<div class="">Cheers,</div>
<div class=""><br class="">
</div>
<div class="">Eric<br clear="all" class="">
<div class="">
<div dir="ltr" class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class=""><span class="">---------------------<br class="">
Dr. Eric Forgoston<br class="">
Professor of Applied Mathematics<br class="">
Chair, Department of </span><span class=""><span class=""><span class="">Applied Mathematics and Statistics</span></span><br class="">
Montclair State University<br class="">
Montclair, NJ 07043 USA<br class="">
+1 973 655-7242 <br class="">
<span class=""><a href="https://eric-forgoston.github.io/" target="_blank" class="">https://eric-forgoston.github.io/</a></span></span><br class="">
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br class="">
</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Sat, Oct 23, 2021 at 1:39 PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank" class="">jacob.barhak@gmail.com</a>> wrote:<br class="">
</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" class="">Greetings Paper Contributors,
<div class=""><br class="">
</div>
<div class="">The paper editing process started and you can follow it live on:</div>
<div class=""><a href="https://meet.jit.si/CollaborativePaperEditing" target="_blank" class="">https://meet.jit.si/CollaborativePaperEditing</a><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">I will keep the channel open as long as I am editing so that the process will be as transparent as possible. </div>
<div class=""><br class="">
</div>
<div class="">The first step would be to reconcile the differences between those 4 versions traceable back to authors:</div>
<div class=""><a href="https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit" target="_blank" class="">https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit</a> - the submitted version<br class="">
</div>
<div class=""><a href="https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit" target="_blank" class="">https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit</a> - first committed version<br class="">
</div>
<div class=""><a href="https://docs.google.com/document/d/1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh/edit" target="_blank" class="">https://docs.google.com/document/d/1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh/edit</a> - first committed version<br class="">
</div>
<div class=""><a href="https://drive.google.com/file/d/1U_lTHrV6STXWNT3GiCepvsLk1WdYgzN5/view" target="_blank" class="">https://drive.google.com/file/d/1U_lTHrV6STXWNT3GiCepvsLk1WdYgzN5/view</a> - its the first document posted<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">After this step is done I will move towards adhering to those instructions:</div>
<div class=""><a href="https://www.frontiersin.org/about/author-guidelines" target="_blank" class="">https://www.frontiersin.org/about/author-guidelines</a><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">I estimate I will be working till late today with very few breaks and hopefully make sufficient progress.</div>
<div class=""><br class="">
</div>
<div class="">Feel free to visit and perhaps even help. If you do, please raise your voice so I can hear you - I am sharing my screen and not seeing the video when I edit - so you will have to let me know you are in the room. </div>
<div class=""><br class="">
</div>
<div class="">Hopefully some of you will visit.</div>
<div class=""><br class="">
</div>
<div class=""> Jacob</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, Oct 22, 2021 at 2:52 PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank" class="">jacob.barhak@gmail.com</a>> wrote:<br class="">
</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="auto" class="">Thanks Sheriff,
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">With your green light I can start editing</div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">Eric, the base of John's version will be merged to the best of my ability, yet unfortunately, it has omissions and later version based on it are not traceable back to contributors, so I can only use some of the base. </div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">If you want to repeat edits so those will be traceable it is possible. Yet we cannot copy verbatim without going to details. </div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">To make things easier, I will open a channel over the weekend during edits where anyone can join and communicate while watching the edits live. </div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">Hopefully it will make things smoother. </div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class=""> Jacob</div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class=""><br class="">
</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, Oct 22, 2021, 13:40 Eric Forgoston <<a href="mailto:eric.forgoston@montclair.edu" target="_blank" class="">eric.forgoston@montclair.edu</a>> wrote:<br class="">
</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" class="">
<div dir="ltr" class="">Dear Jacob and all,
<div class=""><br class="">
</div>
<div class="">I suggest, as others have done, to use the John G. version as structurally it has already cleaned up most of the issues raised by the Editor, and also has many revised and improved sections. In particular, the stochastic section that I worked on with others
is far superior to the one in the paper submitted to Frontiers.</div>
<div class=""><br class="">
</div>
<div class="">Best wishes,</div>
<div class=""><br class="">
</div>
<div class="">Eric<br clear="all" class="">
<div class="">
<div dir="ltr" class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class=""><span class="">---------------------<br class="">
Dr. Eric Forgoston<br class="">
Professor of Applied Mathematics<br class="">
Chair, Department of </span><span class=""><span class=""><span class="">Applied Mathematics and Statistics</span></span><br class="">
Montclair State University<br class="">
Montclair, NJ 07043 USA<br class="">
+1 973 655-7242 <br class="">
<span class=""><a href="https://eric-forgoston.github.io/" rel="noreferrer" target="_blank" class="">https://eric-forgoston.github.io/</a></span></span><br class="">
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br class="">
</div>
</div>
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<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, Oct 22, 2021 at 12:57 PM Rahuman Sheriff <<a href="mailto:sheriff@ebi.ac.uk" rel="noreferrer" target="_blank" class="">sheriff@ebi.ac.uk</a>> wrote:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="">Congratulations Marcella,
<div class=""><br class="">
</div>
<div class="">Hi Jacob and all,</div>
<div class=""><br class="">
</div>
<div class="">As Tomas mentioned, John G’s version is bit more organised. </div>
<div class="">Although it would be nice to take that one forward, I also fine with you recovering your version incorporating requested changes including mine. </div>
<div class="">I would prefer this manuscript progresses ahead, instead of another long discussion. </div>
<div class="">Green signal from my side.</div>
<div class="">Best regards</div>
<div class="">Sheriff</div>
<div class=""><br class="">
</div>
<div class="">
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<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On 22 Oct 2021, at 01:49, Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer" target="_blank" class="">jacob.barhak@gmail.com</a>> wrote:</div>
<br class="">
<div class="">
<div dir="auto" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none" class="">
Congratulations Marcella,
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">Indeed you bring good news. <br class="">
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">You should not worry about the manuscript. You have done plenty and we can handle if from now on, you can focus on your family. </div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class=""> Jacob</div>
</div>
</div>
<br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none" class="">
<div class="gmail_quote" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<div dir="ltr" class="gmail_attr">On Thu, Oct 21, 2021, 10:33 Torres, Marcella <<a href="mailto:mtorres@richmond.edu" rel="noreferrer" target="_blank" class="">mtorres@richmond.edu</a>> wrote:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="">
<div dir="auto" style="direction:ltr;margin:0px;padding:0px;font-family:sans-serif;font-size:11pt" class="">
This streamlined approach sounds good to me; thanks Jacob for offering to coordinate edits. I think the one month deadline is a good maximum, since Frontiers favors quick turnaround.<span id="gmail-m_1532677427832106191gmail-m_-498237080701749994gmail-m_4632830399077047093gmail-m_-283976446094332176gmail-m_-6812091254919142191gmail-m_-2697268861042949202gmail-m_-1689782665546364892gmail-m_454394027104465375gmail-m_1100449795159862914gmail-m_-3690383742767868331gmail-m_208464925022974690gmail-m_-6684231236743761144gmail-m_5330779350599904174m_6811753030514762076gmail-m_-4652177745642668797m_-8816081919050643472ms-outlook-android-cursor" class=""></span><br class="">
<br class="">
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<div dir="auto" style="direction:ltr;margin:0px;padding:0px;font-family:sans-serif;font-size:11pt" class="">
I don't insist on participating in the revisions, but I am available to help with cleaning up grammar, typos, and so on - I noticed quite a few minor issues when reviewing the document for submission. However, my son was born a few days ago and I have limited
time.<span class=""> </span><br class="">
<br class="">
</div>
<div dir="auto" style="direction:ltr;margin:0px;padding:0px;font-family:sans-serif;font-size:11pt" class="">
Marcella</div>
<hr style="display:inline-block;width:545.578px" class="">
<div id="gmail-m_1532677427832106191gmail-m_-498237080701749994gmail-m_4632830399077047093gmail-m_-283976446094332176gmail-m_-6812091254919142191gmail-m_-2697268861042949202gmail-m_-1689782665546364892gmail-m_454394027104465375gmail-m_1100449795159862914gmail-m_-3690383742767868331gmail-m_208464925022974690gmail-m_-6684231236743761144gmail-m_5330779350599904174m_6811753030514762076gmail-m_-4652177745642668797m_-8816081919050643472divRplyFwdMsg" dir="ltr" class="">
<font style="font-size:11pt" face="Calibri, sans-serif" class=""><b class="">From:</b><span class=""> </span>Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer noreferrer" target="_blank" class="">jacob.barhak@gmail.com</a>><br class="">
<b class="">Sent:</b><span class=""> </span>Wednesday, October 20, 2021 11:53:58 PM<br class="">
<b class="">To:</b><span class=""> </span>Alexander Kulesza <<a href="mailto:alexander.kulesza@novadiscovery.com" rel="noreferrer
noreferrer" target="_blank" class="">alexander.kulesza@novadiscovery.com</a>><br class="">
<b class="">Cc:</b><span class=""> </span>Hana <<a href="mailto:h.dobrovolny@tcu.edu" rel="noreferrer noreferrer" target="_blank" class="">h.dobrovolny@tcu.edu</a>>; James Osborne <<a href="mailto:jmosborne@unimelb.edu.au" rel="noreferrer noreferrer" target="_blank" class="">jmosborne@unimelb.edu.au</a>>;
John Rice <<a href="mailto:john.rice@noboxes.org" rel="noreferrer noreferrer" target="_blank" class="">john.rice@noboxes.org</a>>; Torres, Marcella <<a href="mailto:mtorres@richmond.edu" rel="noreferrer noreferrer" target="_blank" class="">mtorres@richmond.edu</a>>;<span class=""> </span><a href="mailto:vp-reproduce-subgroup@lists.simtk.org" rel="noreferrer
noreferrer" target="_blank" class="">vp-reproduce-subgroup@lists.simtk.org</a><span class=""> </span><<a href="mailto:vp-reproduce-subgroup@lists.simtk.org" rel="noreferrer
noreferrer" target="_blank" class="">vp-reproduce-subgroup@lists.simtk.org</a>>;<span class=""> </span><a href="mailto:vp-integration-subgroup@lists.simtk.org" rel="noreferrer
noreferrer" target="_blank" class="">vp-integration-subgroup@lists.simtk.org</a><span class=""> </span><<a href="mailto:vp-integration-subgroup@lists.simtk.org" rel="noreferrer
noreferrer" target="_blank" class="">vp-integration-subgroup@lists.simtk.org</a>>;
Jonathan Karr <<a href="mailto:jonrkarr@gmail.com" rel="noreferrer noreferrer" target="_blank" class="">jonrkarr@gmail.com</a>>; John Gennari <<a href="mailto:gennari@uw.edu" rel="noreferrer noreferrer" target="_blank" class="">gennari@uw.edu</a>>; Winston Garira <<a href="mailto:Winston.Garira@univen.ac.za" rel="noreferrer noreferrer" target="_blank" class="">Winston.Garira@univen.ac.za</a>><br class="">
<b class="">Subject:</b><span class=""> </span>Re: [Vp-integration-subgroup] Fwd: Shayn Peirce-Cottler via Frontiers: Manuscript</font>
<div class=""> </div>
</div>
<div class="">
<div style="font-family:Arial,Helvetica,sans-serif;font-size:10pt;border:1pt solid red;padding:2pt;background-color:yellow" class="">
<span style="color:red" class=""><b class="">External Email:</b></span><span class=""> Use caution in opening links, attachments, and buying gift cards.</span></div>
<br class="">
<div class="">
<div dir="ltr" class="">Thanks Alex, Thanks John,
<div class=""><br class="">
</div>
<div class="">Your contribution is appreciated and since John cleared us to move forward it simplifies things. I hope he will change his mind about authorship since he contributed a lot, yet I will respect his wishes - perhaps after seeing the final version he will
change his mind. </div>
<div class=""><br class="">
</div>
<div class="">If Sheriff gives me a green light I can incorporate his modifications as well. I do ask that if any of the listed authors has any serious concerns and plans to not approve a modified version that addresses the editors requests alone alongside those I mentioned
above, to step up before the work is done so we can resolve things before energy is spent. </div>
<div class=""><br class="">
</div>
<div class="">If there will be no blocks I plan to start work over the weekend if I see no objections by then.</div>
<div class=""><br class="">
</div>
<div class="">I appreciate the offer to help with bibliography, from experience I know it is perhaps the most time consuming. However, since we have many links and specialized publications in our list - I am not sure if any tool can make it easier - the last time I
had to do a lot of manual work to fit a specific format and find all missing links and also fix some errors - no tool would have helped me then. This time I think it will be a bit easier. Yet I ask for no more references to be added - I also want to add more
references, yet I am stopping myself. We can always expand the work in another future version if we have new findings. </div>
<div class=""><br class="">
</div>
<div class="">Again note that I will only try to address the requests of the editor at this point without trying to perfect anything beyond what I wrote above and I want to keep things as traceable as possible. Once I am done,we will see if we can approve this manuscript
for publication.</div>
<div class=""><br class="">
</div>
<div class="">Unless any blockers appear, if anyone wants to actively participate in the editing over the weekend, please let me know so we can communicate better.</div>
<div class=""><br class="">
</div>
<div class=""> <span class=""> </span>Jacob</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
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</div>
<div class=""><br class="">
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<div class="">
<div dir="ltr" class="">On Tue, Oct 19, 2021 at 2:02 AM Alexander Kulesza <<a href="mailto:alexander.kulesza@novadiscovery.com" rel="noreferrer
noreferrer" target="_blank" class="">alexander.kulesza@novadiscovery.com</a>>
wrote:<br class="">
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex" class="">
<div dir="ltr" class="">Dear Jacob,
<div class="">thanks for forwarding and you suggestions, which seems more than reasonable. </div>
<div class=""><br class="">
</div>
<div class="">My contributions from May 19th, May31st and June 2nd are in <a href="https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit?usp=sharing&ouid=113860487708206439519&rtpof=true&sd=true" rel="noreferrer noreferrer" target="_blank" class="">https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit?usp=sharing&ouid=113860487708206439519&rtpof=true&sd=true</a> </div>
<div class=""><br class="">
</div>
<div class="">The other document <a href="https://docs.google.com/document/d/1esZvWWVBvpwvuFUi3C3161lthZkEBFyMRrwwozitBi4/edit?usp=sharing" rel="noreferrer noreferrer" target="_blank" class="">https://docs.google.com/document/d/1esZvWWVBvpwvuFUi3C3161lthZkEBFyMRrwwozitBi4/edit?usp=sharing</a><span class=""> </span>I
created initially to suggest my edits without editing the core version can be disregarded as I have tranferred all of them into the main document, cited above. </div>
<div class=""><br class="">
</div>
<div class="">If we were on Latex, I could offer to create the bibliography but unfortunately we lack a bibliography manager integrated in Word/GDoc. If we were to work with Mendeley and someone could create a group for this paper that has a shared library I could offer
to transfer citations from the paper into that database too. </div>
<div class=""><br class="">
</div>
<div class="">Please let me know.</div>
<div class="">A</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
</div>
<br class="">
<div class="">
<div dir="ltr" class="">On Tue, 19 Oct 2021 at 05:51, Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer noreferrer" target="_blank" class="">jacob.barhak@gmail.com</a>> wrote:<br class="">
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex" class="">
<div dir="ltr" class="">
<div class="">Greetings white paper contributors,</div>
<div class=""><br class="">
</div>
<div class="">Below is the response from the editor to my request and my thank you.</div>
<div class=""><br class="">
</div>
<div class="">The editor grants us the extension by rejecting the paper and allowing time to come up with a better version. There is no time limit now, yet I want to get her a revised version within a month. </div>
<div class=""><br class="">
</div>
<div class="">The requests are simple and easy to satisfy - and I know there are many of you who want more revisions, yet I suggest we reduce them to only what is manageable and necessary. Otherwise we will never get this paper published despite its importance. </div>
<div class=""><br class="">
</div>
<div class="">The most time consuming effort would be adhering to the journal format as defined here:</div>
<div class=""><a href="https://www.frontiersin.org/about/author-guidelines" rel="noreferrer noreferrer" target="_blank" class="">https://www.frontiersin.org/about/author-guidelines</a><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">I think the most time consuming task would be dealing with the references - otherwise the format guidelines seem reasonable.</div>
<div class=""><br class="">
</div>
<div class="">We can also add some revisions we started working on. However, I will personally insist on :</div>
<div class="">1. traceability - currently there is no traceability in the revised version in the summer</div>
<div class="">2. non deletion - do not delete any content unless you wrote it originally or unless you announced it beforehand to the group and got no objections within a few days </div>
<div class="">3. Avoid Adding more material that is not in the existing versions we had - especially references - we don't have time for that and that is not what the editor asked us anyway. </div>
<div class=""><br class="">
</div>
<div class="">I will also ask for fast responses from all contributors. </div>
<div class=""><br class="">
</div>
<div class="">To be practical, I marked the submitted version and opened the document to those who requested editing rights in the past. If you want editing rights, let me know - however, the edits should be minimal and focus on areas you edited in the past and be
aware that if your edits will not get approved by everyone, we will revert to the old version we all accepted. The submitted version was marked so we can always get back to it. </div>
<div class=""><br class="">
</div>
<div class="">If you want editing rights, let me know and I will respond within a day - I cannot promise to be fatter than that these days. </div>
<div class=""><br class="">
</div>
<div class="">Alex, John, Sheriff, you had other versions you created, I want to merge some of your changes to the manuscript in this version - here are my suggestions:</div>
<div class=""><br class="">
</div>
<div class="">- Sheriff, I will soften the language as you requested - this was your main request in the past, yet I will go over your list of changes and see what I else can be done without reinventing the paper</div>
<div class="">- John - I will 1) merge the credibility sections , 2) delete the history related to the working group since it matches with what was requested, and 3) move the model validation barrier section away from the table since we did not suggest a solution there.
Hopefully this will make the paper more appealing to you and you will be willing to add your name to the list </div>
<div class="">- Alex, your changes were made on May 16, 2021 and shared in a way I can see the differences and trace them back to you - I will try to add your references and see if I can incorporate your text changes as much as I can. </div>
<div class=""><br class="">
</div>
<div class="">If the 3 of you are ok with me migrating your changes, I can start the work to save time. Yet I want your ok first. </div>
<div class=""><br class="">
</div>
<div class="">I know Eric and Hana were working on some sections and feel strongly about those - specifically the stochastic modeling part - I am open to your changes, please suggest what you feel strongly about..</div>
<div class=""><br class="">
</div>
<div class="">I recall Johnathan Karr wanted to make some changes, please let me know if there is anything you feel strongly about - he had a lot of text in the paper ..</div>
<div class=""><br class="">
</div>
<div class="">If I forgot anyone who had major requests, please remind me. .</div>
<div class=""><br class="">
</div>
<div class="">I am trying to avoid a never ending revisioning cycle. So I am asking you to trust me and centralize the work in hope I get a better version by the end of the week..</div>
<div class=""><br class="">
</div>
<div class="">Hopefully most of you will be ok with that.</div>
<div class=""><br class="">
</div>
<div class=""> Jacob</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class="">
<div dir="ltr" class="">---------- Forwarded message ---------<br class="">
From:<span class=""> </span><strong dir="auto" class="">Jacob Barhak</strong><span class=""> </span><span dir="auto" class=""><<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer noreferrer" target="_blank" class="">jacob.barhak@gmail.com</a>></span><br class="">
Date: Mon, Oct 18, 2021 at 9:34 PM<br class="">
Subject: Re: Shayn Peirce-Cottler via Frontiers: Manuscript<br class="">
To: Peirce-Cottler, Shayn (smp6p) <<a href="mailto:smp6p@virginia.edu" rel="noreferrer noreferrer" target="_blank" class="">smp6p@virginia.edu</a>><br class="">
Cc: Shayn Peirce-Cottler (Via FrontiersIn) <<a href="mailto:shayn@virginia.edu" rel="noreferrer noreferrer" target="_blank" class="">shayn@virginia.edu</a>>,<a href="mailto:systemsbiology.editorial.office@frontiersin.org" rel="noreferrer
noreferrer" target="_blank" class="">systemsbiology.editorial.office@frontiersin.org</a><span class=""> </span><<a href="mailto:systemsbiology.editorial.office@frontiersin.org" rel="noreferrer
noreferrer" target="_blank" class="">systemsbiology.editorial.office@frontiersin.org</a>>,
Vodovotz, Yoram <<a href="mailto:vodovotzy@upmc.edu" rel="noreferrer noreferrer" target="_blank" class="">vodovotzy@upmc.edu</a>><br class="">
</div>
<br class="">
<br class="">
<div dir="ltr" class="">Thanks Shayn,
<div class=""><br class="">
</div>
<div class="">You will get a revised manuscript targeted at your journal and get back to you with a more polished version and satisfies your requests. </div>
<div class=""><br class="">
</div>
<div class="">It will also allow us to incorporate newer versions of the text that answer some of your requests. We really wish to publish it fast, yet we need more time for the approval process. So your solution seems correct - I hope you hear back from us within a
month or so.</div>
<div class=""><br class="">
</div>
<div class="">Many thanks for the rapid responses.</div>
<div class=""><br class="">
</div>
<div class=""> Jacob</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">--<br class="">
Jacob Barhak Ph.D. <br class="">
Sole Proprietor, Software Developer, and Computational Disease Modeler<br class="">
<br class="">
Jacob Barhak Analytics<br class="">
701 Brazos St<br class="">
Suite 548<br class="">
Austin TX, 78701<br class="">
<br class="">
Email:<span class=""> </span><a href="mailto:jacob.barhak@gmail.com" rel="noreferrer noreferrer" target="_blank" class="">jacob.barhak@gmail.com</a></div>
<div class=""><br class="">
<a href="https://sites.google.com/view/jacob-barhak/home" rel="noreferrer noreferrer" target="_blank" class="">https://sites.google.com/view/jacob-barhak/home</a><br class="">
<br class="">
</div>
<div class=""><br class="">
</div>
</div>
<br class="">
<div class="">
<div dir="ltr" class="">On Mon, Oct 18, 2021 at 7:43 PM Peirce-Cottler, Shayn (smp6p) <<a href="mailto:smp6p@virginia.edu" rel="noreferrer noreferrer" target="_blank" class="">smp6p@virginia.edu</a>> wrote:<br class="">
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex" class="">
<div lang="EN-US" class="">
<div class=""><p class=""><span style="font-size:12pt" class="">Hi Jacob,<span class=""> </span></span></p><div class=""><span style="font-size:12pt" class=""> </span><br class="webkit-block-placeholder"></div><p class=""><span style="font-size:12pt" class="">Thank you for your detailed reply. I agree that the issues can be addressed as you have described below, and that you may need more time to do so. Hence, I am going to officially reject this first submission to remove any imposed
deadlines, and I certainly encourage you to make the updates listed below, and submit a new manuscript at your earliest convenience. </span></p><div class=""><span style="font-size:12pt" class=""> </span><br class="webkit-block-placeholder"></div><p class=""><span style="font-size:12pt" class="">Please let me know if you have any questions, and thanks again for considering this journal! I think the topic fits very nicely with the scope of the journal, and it is certainly an important topic to our multi-scale modeling
community!</span></p><div class=""><span style="font-size:12pt" class=""> </span><br class="webkit-block-placeholder"></div><p class=""><span style="font-size:12pt" class="">-Shayn</span></p><div class=""><span style="font-size:12pt" class=""> </span><br class="webkit-block-placeholder"></div><div class=""><span style="font-size:12pt" class=""> </span><br class="webkit-block-placeholder"></div>
<div class=""><p class=""><span class="">Shayn Peirce-Cottler, Ph.D.</span></p><p class=""><span class="">Professor of Biomedical Engineering</span></p><p class=""><span class="">Harrison Distinguished Teaching Professor</span></p><p class=""><span class="">BME Graduate Program Director</span></p><p class=""><span class="">University of Virginia</span></p>
</div><p class=""><span class="">Charlottesville, VA</span><span style="font-size:12pt" class=""></span></p><div class=""><span style="font-size:12pt" class=""> </span><br class="webkit-block-placeholder"></div>
<div style="border-style:solid none none;border-top-width:1pt;border-top-color:rgb(181,196,223);padding:3pt 0in 0in" class=""><p class=""><b class=""><span style="font-size:12pt" class="">From:<span class=""> </span></span></b><span style="font-size:12pt" class="">Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer noreferrer" target="_blank" class="">jacob.barhak@gmail.com</a>><br class="">
<b class="">Date:<span class=""> </span></b>Monday, October 18, 2021 at 1:57 AM<br class="">
<b class="">To:<span class=""> </span></b>Peirce-Cottler Shayn <<a href="mailto:shayn@virginia.edu" rel="noreferrer noreferrer" target="_blank" class="">shayn@virginia.edu</a>><br class="">
<b class="">Cc:<span class=""> </span></b>"<a href="mailto:systemsbiology.editorial.office@frontiersin.org" rel="noreferrer
noreferrer" target="_blank" class="">systemsbiology.editorial.office@frontiersin.org</a>" <<a href="mailto:systemsbiology.editorial.office@frontiersin.org" rel="noreferrer noreferrer" target="_blank" class="">systemsbiology.editorial.office@frontiersin.org</a>>,
"Vodovotz, Yoram" <<a href="mailto:vodovotzy@upmc.edu" rel="noreferrer noreferrer" target="_blank" class="">vodovotzy@upmc.edu</a>><br class="">
<b class="">Subject:<span class=""> </span></b>Re: Shayn Peirce-Cottler via Frontiers: Manuscript</span></p>
</div>
<div class=""><div class=""> <br class="webkit-block-placeholder"></div>
</div>
<div class=""><p class="">Hi Shayn,</p>
<div class=""><div class=""> <br class="webkit-block-placeholder"></div>
</div>
<div class=""><p class="">Thanks for returning the response quickly. To you comments. </p>
</div>
<div class=""><div class=""> <br class="webkit-block-placeholder"></div>
</div>
<div class=""><p class="">1. This is the list of authors that agreed to submit this manuscript for review - I collected their approvals for this version personally. </p>
</div>
<div class=""><div class=""> <br class="webkit-block-placeholder"></div>
</div>
<div class="">
<ol style="margin-top:0in" type="1" start="1" class="">
<li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal" class="">
<span style="font-family:Arial,sans-serif" class="">Jonathan Karr, Icahn Institute for Data Science and Genomic Technology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai USA</span></li><li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal" class="">
<span style="font-family:Arial,sans-serif" class="">Rahuman Sheriff, The European Bioinformatics Institute (EMBL-EBI), UK</span></li><li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal" class="">
<span style="font-family:Arial,sans-serif" class="">James Osborne, School of Mathematics and Statistics, University of Melbourne, Australia</span></li><li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal" class="">
<span style="font-family:Arial,sans-serif" class="">Gilberto Gonzalez Parra, Mathematics Department, New Mexico Tech, USA</span></li><li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal" class="">
<span style="font-family:Arial,sans-serif" class="">Eric Forgoston, Department of Applied Mathematics and Statistics, Montclair State University, USA</span></li><li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal" class="">
<span style="font-family:Arial,sans-serif" class="">Ruth Bowness, Department of Mathematical Sciences, University of Bath, UK</span></li><li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal" class="">
<span style="font-family:Arial,sans-serif" class="">Yaling Liu, Department of Mechanical Engineering and Mechanics , Department of Bioengineering, Lehigh University, USA</span></li><li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal" class="">
<span style="font-family:Arial,sans-serif" class="">Robin Thompson, Mathematics Institute & The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, UK</span></li><li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal" class="">
<span style="font-family:Arial,sans-serif" class="">Winston Garira - Department Of Mathematics And Applied Mathematics , Modelling Health and Environmental Linkages Research Group. University of Venda, South Africa</span></li><li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal" class="">
<span style="font-family:Arial,sans-serif" class="">Jacob Barhak - Barhak, Jacob, USA</span></li><li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal" class="">
<span style="font-family:Arial,sans-serif" class="">John Rice - Independent Retired Working Group Volunteer, USA</span></li><li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal" class="">
<span style="font-family:Arial,sans-serif" class="">Marcella Torres, School of Arts and Sciences, University of Richmond, USA</span></li><li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal" class="">
<span style="font-family:Arial,sans-serif" class="">Hana M. Dobrovolny , Department of Physics & Astronomy, Texas Christian University, Fort Worth, USA</span></li><li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal" class="">
<span style="font-family:Arial,sans-serif" class="">Tingting Tang, Department of Mathematics and Statistics in San Diego State University (SDSU) and SDSU Imperial Valley, USA</span></li><li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal" class="">
<span style="font-family:Arial,sans-serif" class="">William Waites, Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, UK</span></li><li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal" class="">
<span style="font-family:Arial,sans-serif" class="">James Glazier, Biocomplexity Institute, Indiana University, Bloomington, USA</span></li><li style="margin-top:0in;margin-bottom:0in;vertical-align:baseline;font-variant-numeric:normal;font-variant-east-asian:normal" class="">
<span style="font-family:Arial,sans-serif" class="">James R. Faeder, Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, USA</span></li></ol>
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<div class=""><p class="">If there is a mismatch of authors in the submission, it can be easily corrected - we kept the paper traceable when we constructed it so we can point to exact texts contributed by each contributor through their google account and versions kept in google docs
with few exceptions where I personally added text their wrote and have email conversations supporting that . I personally collected all those contributions in google docs when I assembled the version you see and made sure it is agreed upon by the contributors.
It is important to note that There was one contributor that asked for more revisions and did not approve this manuscript, yet allowed submitting the text without association to it to avoid delays. The entire conversation was documented publicly in our mailing
list and we got consent from this contributor to continue and use the text - You can find the conversation here:<span class=""> </span><a href="https://lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-March/000019.html" rel="noreferrer noreferrer" target="_blank" class="">https://lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-March/000019.html</a> <span class=""> </span>-
so there are no copyright issues and the name of the author is not included in the list above at their request. Those included in the list have contributed and approved. If needed, we will correct the list in the journal to match this list. Please note that
we kept the entire process as transparent as possible so there will be no issues. If there are any concerns of authorship, I will be happy to dig into the history and pull out details. </p>
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<div class=""><p class="">2. The reason the manuscript was submitted in this form is to get confirmation on initial fit and to get some initial feedback. We were interested in fast review to get the information quickly out - Also note that we did not intend this to be a final version
- we already have some modifications in the work that we would like to introduce where more people contributed , yet we have not reached agreement on those so we cannot formally publish them - however, we did reach agreement on submitting this version for
review so the editor can focus us on what is important to change to get published with a 3rd Party - enough of us agreed in a vote that your Journal seems is a suitable 3rd party and hence the submission. We will be happy to spend the time to convert the manuscript
to the desired format if you find the content suitable for the journal. So far your requests are reasonable and I will convey them to the group through our mailing list. </p>
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<div class=""><p class="">3. Please note that after the list of authors there is a disclaimer : "<span style="font-family:Arial,sans-serif" class="">The opinion of the contributors do not reflect the opinions of the entire working group". I</span>nitially this paper started as an activity
requested by the working group leads. However, by no means it represents all opinions. The introduction in this version of the paper captures some of this history of how the manuscript was created and modified. However, we have other versions of the manuscript
in work where this history is deleted - If you prefer, we can easily create a version that detaches from the working group to eliminate all concerns - this is a relatively easy fix. However, whatever fix we do, we will have to approve with all contributors. </p>
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<div class=""><p class="">4 The revisions can be done in reasonable time. However, the process of collecting approval for all contributors to legally approve the revised manuscript will take more than 14 days. All contributors must approve a manuscript for publication. With this
number of authors we will probably not make it in the time you mentioned - only the approval process for collecting all approvals took alone about 3 weeks to approve this version you see. Hopefully you will understand this and extend this time period beyond
14 days. </p>
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<div class=""><p class="">In summary: </p>
</div>
<div class=""><p class="">Making the fixes you asked for towards publication is easy - yet getting the approval from so many people may take us more time than what you provide. If it is possible to get an extension, it will be appreciated. </p>
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<div class=""><p class="">I will add this conversation to our mailing list so we can start the process of revising the manuscript. However, if after this email you have more issues with this paper, Please advise on the best course of action you see fit so we can adjust accordingly. </p>
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<div class=""><p class="">Hopefully we can address your concerns in time to publish the manuscript in a timely manner. </p>
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<div class=""><p class=""> Jacob</p>
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<div class=""><p style="margin-bottom:12pt" class="">--<br class="">
Jacob Barhak Ph.D. <br class="">
Sole Proprietor, Software Developer, and Computational Disease Modeler<br class="">
<br class="">
Jacob Barhak Analytics<br class="">
701 Brazos St<br class="">
Suite 548<br class="">
Austin TX, 78701<br class="">
<br class="">
Email:<span class=""> </span><a href="mailto:jacob.barhak@gmail.com" rel="noreferrer noreferrer" target="_blank" class="">jacob.barhak@gmail.com</a><br class="">
<br class="">
<a href="https://sites.google.com/view/jacob-barhak/home" rel="noreferrer noreferrer" target="_blank" class="">https://sites.google.com/view/jacob-barhak/home</a></p>
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<div class="">
<div class=""><p class="">On Sun, Oct 17, 2021 at 9:56 AM Shayn Peirce-Cottler (Via FrontiersIn) <<a href="mailto:noreply@frontiersin.org" rel="noreferrer noreferrer" target="_blank" class="">noreply@frontiersin.org</a>> wrote:</p>
</div>
<blockquote style="border-style:none none none solid;border-left-width:1pt;border-left-color:rgb(204,204,204);padding:0in 0in 0in 6pt;margin-left:4.8pt;margin-right:0in" class="">
<div class=""><p class="">Dear Jacob,<span class=""> </span><br class="">
<br class="">
Thank you for your manuscript submission. I cannot send it out for review in its current form because I have a few concerns, but if you can address the following issues, I will certainly reconsider a revised manuscript if the following are adequately addressed:<br class="">
<br class="">
1. The author list that is on the first page differs from the author list that was provided at the time of submission.<span class=""> </span><br class="">
<br class="">
2. The manuscript needs to be submitted using the official Frontiers template.<br class="">
<br class="">
3. The manuscript states that it represents the views of a number of special interest and working groups, and the authors should provide assurances that they have the authority and approval to speak on behalf of the working groups that are listed.<br class="">
<br class="">
4. There are places throughout the manuscript, and most frequently in the second half, where information is provided as bulleted talking points without context. Those sections should be revised into paragraphs of text or summarized in a table (or figure).<br class="">
<br class="">
If you wish to submit a revised manuscript, the journal provides a 14-day time window for you to do so. Please let me know if you have any questions.<span class=""> </span><br class="">
<br class="">
Thank you,<br class="">
Shayn<br class="">
<br class="">
<br class="">
---------------------------------<br class="">
<br class="">
Manuscript title: Model Integration in Computational Biology: The Role of Reproducibility, Credibility and Utility<br class="">
Manuscript ID: 793932<br class="">
Authors: Marcella Torres, Jacob Barhak, Ruth Bowness, Hana Maria Dobrovolny, James Faeder, Eric Forgoston, Winston Garira, Yaling Liu, James Osborne, Gilberto Gonzalez Parra, John Rice, Rahuman Sheriff, Tingting Tang, Robin Thompson, William Waites<span class=""> </span><br class="">
Date submitted: 12 Oct 2021<span class=""> </span><br class="">
Edited by: Shayn Peirce-Cottler<br class="">
<br class="">
<br class="">
Research Topic: Insights in Systems Biology: Multiscale Mechanistic Modeling 2021<br class="">
Review forum direct access link:<span class=""> </span><a href="http://links.email.frontiersin.org/ls/click?upn=AAaFa03elZRFPXQ6ShiKwHJ7IVBhf38O-2BEQWinpomFtULO0Q-2BM19TTRdh7emL5NqrxgHYRG7-2FEazDF-2FJfPddug-3D-3Dkdpa_6U3AlnyvMxxXqGK2YZZvqQDAig2dZVa43D-2BB81ORWCaNWR45ZJ2fDhpaKsTZzRsuCL-2BNJFR2MRucSNQVfNAGmtHQx1gGGhLotkRxEWQuZDre0jQti6pSzF-2Bm1akZB-2FZLJbzjJjEqrnF6c-2BY79oozDKNeyZDGEV7E7qizJmMtyvWGMFEr4JK1z0YPzIbG66EloII5-2FSNkwoWo-2BqqYbe1fAtco01e7-2FlRQb33KpEVuKlNimzGXjW3kPgAYf1R6wsCnLhi7Aow94qLbu0WkYgbBRg-3D-3D" rel="noreferrer noreferrer" target="_blank" class="">https://review.frontiersin.org/review/793932/0/0</a><span style="border:1pt solid windowtext;padding:0in" class=""><img id="gmail-m_1532677427832106191gmail-m_-498237080701749994gmail-m_4632830399077047093gmail-m_-283976446094332176gmail-m_-6812091254919142191gmail-m_-2697268861042949202gmail-m_-1689782665546364892gmail-m_454394027104465375gmail-m_1100449795159862914gmail-m_-3690383742767868331gmail-m_208464925022974690gmail-m_-6684231236743761144gmail-m_5330779350599904174m_6811753030514762076gmail-m_-4652177745642668797m_-8816081919050643472x_gmail-m_1182346046610349769gmail-m_-3593486653867666975m_3106702485682359377m_-7813573733557270536m_-7842715099430849307gmail-m_622710468663863154_x0000_i1025" alt="Image
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sender." style="width: 0.0104in; height: 0.0104in;" width="1" height="1" border="0" class=""></span></p>
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<fieldset class=""></fieldset>
<pre class="">_______________________________________________
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<pre cols="72" class="">--
James A. Glazier, PhD
Professor of Intelligent Systems Engineering, Adjunct Professor of Physics
Director, Biocomplexity Institute
Indiana University, Bloomington
(812) 391-2159 (cell)</pre>
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