[Vp-integration-subgroup] [Vp-reproduce-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript
Gilberto Gonzalez-Parra
gilberto.gonzalezparra at nmt.edu
Sun Nov 7 21:15:48 PST 2021
Dear Jacob and colleagues,
Thank you for taking care of this paper and all the details related to it.
I commend your work. The paper has been improved and deals with important
issues discussed in the meetings. I hope reviewers will see the importance
of these topics. I approve the submission.
Best,
***************************************************************************
Gilberto C. Gonzalez-Parra, Ph.D in Applied Mathematics.
Faculty of the Mathematics Department
New Mexico Tech, NM, USA.
****************************************************************************
On Sun, Nov 7, 2021 at 7:07 PM Torres, Marcella <mtorres at richmond.edu>
wrote:
> Dear Jacob and all,
>
> Small correction to affiliation: Department of Mathematics and Computer
> Science, University of Richmond, Richmond, USA.
>
> I approve.
>
> Thank you so much; the manuscript is dramatically improved.
>
> Marcella
>
>
> Get Outlook for Android <https://aka.ms/AAb9ysg>
> ------------------------------
> *From:* Vp-reproduce-subgroup <
> vp-reproduce-subgroup-bounces at lists.simtk.org> on behalf of Eric
> Forgoston <eric.forgoston at montclair.edu>
> *Sent:* Sunday, November 7, 2021 7:32:49 PM
> *To:* James Osborne <jmosborne at unimelb.edu.au>
> *Cc:* vp-reproduce-subgroup at lists.simtk.org <
> vp-reproduce-subgroup at lists.simtk.org>;
> vp-integration-subgroup at lists.simtk.org <
> vp-integration-subgroup at lists.simtk.org>; Yaling Liu <yal310 at lehigh.edu>;
> John Gennari <gennari at uw.edu>; Jonathan Karr <jonrkarr at gmail.com>;
> Winston Garira <Winston.Garira at univen.ac.za>; Faeder, James R <
> faeder at pitt.edu>
> *Subject:* Re: [Vp-reproduce-subgroup] [Vp-integration-subgroup] Shayn
> Peirce-Cottler via Frontiers: Manuscript
>
> *External Email:* Use caution in opening links, attachments, and buying
> gift cards.
>
> Hi Jacob,
>
> I approve.
>
> Eric
> ---------------------
> Dr. Eric Forgoston
> Professor of Applied Mathematics
> Chair, Department of Applied Mathematics and Statistics
> Montclair State University
> Montclair, NJ 07043 USA
> +1 973 655-7242
> https://eric-forgoston.github.io/
>
>
> On Sun, Nov 7, 2021 at 5:33 PM James Osborne <jmosborne at unimelb.edu.au>
> wrote:
>
> I approve the paper for submission
>
> James
>
> On Mon, Nov 8, 2021 at 7:14 AM Yaling Liu <yal310 at lehigh.edu> wrote:
>
> Dear Jacob,
>
> I approve the paper for submission.
>
> Thanks.
>
> Yaling
>
> On Sun, Nov 7, 2021 at 9:59 AM Winston Garira <Winston.Garira at univen.ac.za>
> wrote:
>
> Dear Jacob,
>
> I approve the paper for submission.
>
> Winston
> ------------------------------
> *From:* William Waites <wwaites at ieee.org>
> *Sent:* Sunday, 07 November 2021 12:34
> *To:* Jacob Barhak <jacob.barhak at gmail.com>
> *Cc:* James Osborne <jmosborne at unimelb.edu.au>;
> vp-reproduce-subgroup at lists.simtk.org <
> vp-reproduce-subgroup at lists.simtk.org>; James A Glazier <
> jaglazier at gmail.com>; vp-integration-subgroup at lists.simtk.org <
> vp-integration-subgroup at lists.simtk.org>; Jonathan Karr <
> jonrkarr at gmail.com>; John Gennari <gennari at uw.edu>; Faeder, James R <
> faeder at pitt.edu>; Winston Garira <Winston.Garira at univen.ac.za>
> *Subject:* Re: [Vp-integration-subgroup] [Vp-reproduce-subgroup] Shayn
> Peirce-Cottler via Frontiers: Manuscript
>
> Dear Jacob,
>
> I approve. This version is much better than the earlier one, though it’s a
> little long. I still prefer the tighter structure of the one that John
> started.
>
> Another example of a model that combines within-host immune dynamics and
> between-host transmission we’ve just put out (this is together with Ruchira
> Datta and Veronika Zarnitsyna among others so comes partly out of the MSM
> innate and adaptive immune response subgroup) is here:
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Farxiv.org%2Fabs%2F2111.02510&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727672293%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=iRm%2FUvVD%2Fv%2F4ZwpUVFUltZxa6rkbq4uVWOzNdBqdXDk%3D&reserved=0
> It gets some interesting results where phenomena that are emergent at the
> population level arise from simple dynamics at the individual level. Feel
> free to ignore this though because (a) it’s just a pre-print and (b) this
> is now fairly late in the game.
>
> Could you add a second affiliation for me? School of Informatics,
> University of Edinburgh
>
> Thank you everyone for pulling this together.
>
> Cheers,
> -w
>
>
> > On 6 Nov 2021, at 22:59, Jacob Barhak <jacob.barhak at gmail.com> wrote:
> >
> > Greetings paper contributors,
> >
> > 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:
> >
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM%2Fedit%3Fusp%3Dsharing&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727672293%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=n56Rv%2BYvUgM6I7vvVXKyRUWqf74k6FPR9plverQXDU0%3D&reserved=0
> >
> > I disabled all edits to it at this point so it will not change unless I
> reopen it.
> >
> > This is the list of contributors in no particular order
> > • 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
> > • Rahuman Sheriff, The European Bioinformatics Institute
> (EMBL-EBI), London, UK
> > • James Osborne, School of Mathematics and Statistics, University
> of Melbourne, Parkville, Australia
> > • Gilberto Gonzalez Parra, Mathematics Department, New Mexico
> Tech, Socorro, USA
> > • Eric Forgoston, Department of Applied Mathematics and
> Statistics, Montclair State University, Montclair, NJ, USA
> > • Ruth Bowness, Department of Mathematical Sciences, University
> of Bath, Bath, UK
> > • Yaling Liu, Department of Mechanical Engineering and Mechanics
> , Department of Bioengineering, Lehigh University, Bethlehem, PA, USA
> > • Robin Thompson, Mathematics Institute & The Zeeman Institute
> for Systems Biology and Infectious Disease Epidemiology Research,
> University of Warwick, Coventry , UK
> > • Winston Garira - Department Of Mathematics And Applied
> Mathematics , Modelling Health and Environmental Linkages Research Group.
> University of Venda, Limpopo, South Africa
> > • Jacob Barhak* - Jacob Barhak Analytics, Austin, TX, USA
> > • John Rice - Independent Retired Working Group Volunteer,
> Virginia Beach, VA, USA
> > • Marcella Torres*, School of Arts and Sciences, University of
> Richmond, Richmond, USA
> > • Hana M. Dobrovolny , Department of Physics & Astronomy, Texas
> Christian University, Fort Worth, USA
> > • Tingting Tang, Department of Mathematics and Statistics in San
> Diego State University (SDSU) and SDSU Imperial Valley, Calexico, CA, USA
> > • William Waites, Centre for Mathematical Modelling of Infectious
> Diseases, London School of Hygiene and Tropical Medicine, London, UK
> > • James Glazier, Biocomplexity Institute, Indiana University,
> Bloomington, USA
> > • James R. Faeder, Department of Computational and Systems
> Biology, University of Pittsburgh, Pittsburgh, USA
> > • Alexander Kulesza, Novadiscovery SA, Lyon, France
> >
> > IF YOU ARE ON THIS LIST - YOU HAVE 3 TASKS DO TO:
> >
> > TASK 1:
> > Please go over the paper and the Journal rules here:
> >
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.frontiersin.org%2Fabout%2Fpolicies-and-publication-ethics&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727672293%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=xDeVGPtW3JEBn%2FKKU5GPMpxsI6vEo7HOuteuRiQHxEw%3D&reserved=0
> >
> > Note that the guidelines allow to establish authors levels of
> contribution according to
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.frontiersin.org%2Fabout%2Fauthor-guidelines&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727672293%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=aGORku92DxMHqhJ%2BicF%2BeXULOBQLIjfkFzekQ5XvrU4%3D&reserved=0
> 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.
> > 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.
> >
> > TASK 2:
> > 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.
> >
> > TASK 3:
> > REPLY TO ALL TO THIS MESSAGE and note one of the following options:
> >
> > 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.
> >
> > 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.
> >
> > 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.
> >
> > 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.
> >
> > 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.
> >
> > Hopefully we can get this approval round done quickly and move forward
> and submit.
> >
> > Jacob
> >
> >
> >
> >
> > On Thu, Nov 4, 2021 at 12:30 AM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
> > Thanks James, And Greetings to all contributors,
> >
> > 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.
> >
> > At this point 3 people went over the manuscript and it seems ready to go.
> >
> > 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:
> >
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM%2Fedit%3Fusp%3Dsharing&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727672293%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=n56Rv%2BYvUgM6I7vvVXKyRUWqf74k6FPR9plverQXDU0%3D&reserved=0
> >
> > If you want to see the comment history, please send me a request so I
> can add you as an editor.
> >
> > Before you rush approving, I would ask you to take a minute and read
> section 1.3. Authorship and Author Responsibilities in
> >
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.frontiersin.org%2Fabout%2Fpolicies-and-publication-ethics&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727672293%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=xDeVGPtW3JEBn%2FKKU5GPMpxsI6vEo7HOuteuRiQHxEw%3D&reserved=0
> >
> > 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.
> >
> > Please double check your name and affiliation - I will have to copy it -
> if there is a mistake, let me know.
> >
> > If after checking all these you are ok, please:
> > REPLY TO ALL TO THIS MESSAGE WITH THE TEXT "I APPROVE THE MANUSCRIPT"
> >
> > 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.
> >
> > On Oct 6th I will lock the manuscript and remove all comments and mark
> them as resolved.
> >
> > I hope you all find it in good shape.
> >
> > Jacob
> >
> >
> >
> >
> > On Wed, Nov 3, 2021 at 5:15 AM James Osborne <jmosborne at unimelb.edu.au>
> wrote:
> > Jacob
> >
> > 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.
> >
> > For what it's worth thank you for your efforts knocking this into shape.
> >
> > James
> >
> > On Wed, Nov 3, 2021 at 4:42 PM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
> > Hi James,
> >
> > 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.
> >
> > 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.
> >
> > 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.
> >
> > Hopefully this last warning is sufficient and you will all find the
> paper in good shape.
> >
> > Jacob
> >
> > On Thu, Oct 28, 2021 at 9:26 PM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
> > Hi James,
> >
> > 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.
> >
> > 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.
> >
> > I really want the paper out quickly - hopefully we can finish this and
> submit quickly.
> >
> > Jacob
> >
> > On Thu, Oct 28, 2021 at 3:17 PM James A Glazier <jaglazier at gmail.com>
> wrote:
> > Dear Jacob:
> >
> > I would like to review the document. I had asked for access a few weeks
> ago. Happy to look in the next few days.
> >
> > JAG
> >
> > On 10/24/2021 4:40 AM, Jacob Barhak wrote:
> >> Hi Eric,
> >>
> >> You are the last one I remember who wanted to edit. Please check the
> manuscript
> >>
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM%2Fedit%3Fusp%3Dsharing&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727672293%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=n56Rv%2BYvUgM6I7vvVXKyRUWqf74k6FPR9plverQXDU0%3D&reserved=0
> >>
> >> 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 .
> >>
> >> 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.
> >>
> >> 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.
> >>
> >> The tasks left to do are:
> >> - 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
> >> - Finish the edits to the stochastic section - Eric - you asked for this
> >> - Finish formatting to fit the Journal guidelines
> >> - Add a cover letter and split the paper into sections to be uploaded
> to the journal web site
> >> - Approve the version with all authors - we must do this again and get
> full approval - this may take a while
> >> - Determine who else wants to be listed as corresponding author -
> currently I marked Marcell and myself, yet others may want to correspond.
> >> - Upload the paper to the journal submission system
> >>
> >> I hope for no obstacles and full cooperation to make the process smooth.
> >>
> >> Jacob
> >>
> >>
> >>
> >> On Sat, Oct 23, 2021 at 9:08 PM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
> >> So Gilberto,
> >>
> >> 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.
> >>
> >> 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.
> >>
> >> 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.
> >>
> >> 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.
> >>
> >> 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.
> >>
> >> I hope I can finish most of the work except references perhaps by
> midnight.
> >>
> >> Jacob
> >>
> >>
> >>
> >> On Sat, Oct 23, 2021 at 8:32 PM Gilberto Gonzalez-Parra <
> gilberto.gonzalezparra at nmt.edu> wrote:
> >> Hi Jacob,
> >>
> >> 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 ?
> >>
> >> I noticed that the section/challenge Barriers to model implementation
> and real-world use 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.
> >>
> >> In the current version in the table it appears "
> >> Model
> >> application and implementation barriers
> >> " just after "
> >> Missing Annotations in Models"
> >>
> >> 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.
> >>
> >> Best,
> >>
> >>
> ***************************************************************************
> >> Gilberto C. Gonzalez-Parra, Ph.D in Applied Mathematics.
> >> Faculty of the Mathematics Department
> >> New Mexico Tech, NM, USA.
> >>
> ****************************************************************************
> >>
> >>
> >> On Sat, Oct 23, 2021 at 5:38 PM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
> >> Hi Eric, and also greeting for the other paper contributors
> >>
> >> Here is a real time update just to give an idea of current editing
> status.
> >>
> >> 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:
> >>
> >> "
> >> Hi Hana
> >> Can you see the chat?
> >> I can. There's just a lot going on around here right now, so I'm not
> fast with typing
> >> I put the references in the comments, can you see them?
> >> 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..
> >> And thanks fro helping
> >> If you want, you can join jitsi:
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmeet.jit.si%2FCollaborativePaperEditing&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727672293%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=kxHZrZGrcqae4B9YRD1zyUSnZDw3oie7lAmHMAzQb7Q%3D&reserved=0
> and we can chat using voice
> >> I just saw your comment - it is public confirmation - this is good
> enough thank you
> >> 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.
> >> 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
> >> 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.
> >> Well, "are" is the correct verb there, so that should probably stay. I
> can remove the italicization.
> >> 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 .
> >> 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.
> >> "
> >>
> >> 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 .
> >>
> >> I am now moving to the next part of complying with the requests of the
> editor:
> >> 1) Determine authorship
> >> 2) Converging format to journal guidelines - this also means references
> >> 3) Detach from group - some elements already marked
> >> 4) Revise bullet points into paragraphs
> >>
> >> 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.
> >>
> >> Hopefully you will find the merged version in order.
> >>
> >> Jacob
> >>
> >>
> >>
> >>
> >>
> >>
> >> On Sat, Oct 23, 2021 at 2:50 PM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
> >> Hi Eric,
> >>
> >> 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.
> >>
> >> The version benign edited is:
> >>
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM%2Fedit&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727672293%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=jRu17cEBk1FL0FlwjwNuvx1b5GTWrgBkm0OVXBeVhWE%3D&reserved=0
> >>
> >> You will need to login so that your edits will be traceable.
> >>
> >> You can join me while editing in:
> >>
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmeet.jit.si%2FCollaborativePaperEditing&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727672293%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=kxHZrZGrcqae4B9YRD1zyUSnZDw3oie7lAmHMAzQb7Q%3D&reserved=0
> >>
> >> I am sharing my screen there while editing.
> >>
> >> You might be able to help me with other sections as well.
> >>
> >> Jacob
> >>
> >>
> >> On Sat, Oct 23, 2021 at 2:44 PM Eric Forgoston <
> eric.forgoston at montclair.edu> wrote:
> >> Hi Jacob,
> >>
> >> If you give me a link to the paper you are editing and edit access to
> the paper I can update the stochastic section.
> >>
> >> Cheers,
> >>
> >> Eric
> >> ---------------------
> >> Dr. Eric Forgoston
> >> Professor of Applied Mathematics
> >> Chair, Department of Applied Mathematics and Statistics
> >> Montclair State University
> >> Montclair, NJ 07043 USA
> >> +1 973 655-7242
> >>
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Feric-forgoston.github.io%2F&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727682287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=KiG9WrIyZdyq8WdZIIzMD2GV86jcFjgPzhkKxwChSRM%3D&reserved=0
> >>
> >>
> >> On Sat, Oct 23, 2021 at 1:39 PM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
> >> Greetings Paper Contributors,
> >>
> >> The paper editing process started and you can follow it live on:
> >>
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmeet.jit.si%2FCollaborativePaperEditing&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727682287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=KHnJGERu2bWXaAIOyq8eOupzextaxY7R2rnFh6L9C4Y%3D&reserved=0
> >>
> >> I will keep the channel open as long as I am editing so that the
> process will be as transparent as possible.
> >>
> >> The first step would be to reconcile the differences between those 4
> versions traceable back to authors:
> >>
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM%2Fedit&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727682287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=I6DsF2ivsYWpSZQgJitLeCia%2FSUA8CI%2BqBzIM9FWv0s%3D&reserved=0
> - the submitted version
> >>
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT%2Fedit&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727682287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=KaQhYbqzSI41r7YtAEa5DXbGFKDMCzt0q9zanMv7vpk%3D&reserved=0
> - first committed version
> >>
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh%2Fedit&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727682287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=ZfpwZxECQgRrBzqp5y3Xbl%2FdkFjPdnASuULrlKag36c%3D&reserved=0
> - first committed version
> >>
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1U_lTHrV6STXWNT3GiCepvsLk1WdYgzN5%2Fview&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727682287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=7pp2qxmQKnhvW%2Fplmg9Qv6l%2FfO6nz42Z7GF2ehRu%2Fa8%3D&reserved=0
> - its the first document posted
> >>
> >> After this step is done I will move towards adhering to those
> instructions:
> >>
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.frontiersin.org%2Fabout%2Fauthor-guidelines&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727682287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=qkqzufzA1m6zgRR9gppIq4%2B2LYYByiBhRQAamQntqTM%3D&reserved=0
> >>
> >> I estimate I will be working till late today with very few breaks and
> hopefully make sufficient progress.
> >>
> >> 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.
> >>
> >> Hopefully some of you will visit.
> >>
> >> Jacob
> >>
> >> On Fri, Oct 22, 2021 at 2:52 PM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
> >> Thanks Sheriff,
> >>
> >> With your green light I can start editing
> >>
> >> 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.
> >>
> >> If you want to repeat edits so those will be traceable it is possible.
> Yet we cannot copy verbatim without going to details.
> >>
> >> 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.
> >>
> >> Hopefully it will make things smoother.
> >>
> >> Jacob
> >>
> >>
> >>
> >>
> >>
> >>
> >> On Fri, Oct 22, 2021, 13:40 Eric Forgoston <
> eric.forgoston at montclair.edu> wrote:
> >> Dear Jacob and all,
> >>
> >> 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.
> >>
> >> Best wishes,
> >>
> >> Eric
> >> ---------------------
> >> Dr. Eric Forgoston
> >> Professor of Applied Mathematics
> >> Chair, Department of Applied Mathematics and Statistics
> >> Montclair State University
> >> Montclair, NJ 07043 USA
> >> +1 973 655-7242
> >>
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Feric-forgoston.github.io%2F&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727682287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=KiG9WrIyZdyq8WdZIIzMD2GV86jcFjgPzhkKxwChSRM%3D&reserved=0
> >>
> >>
> >> On Fri, Oct 22, 2021 at 12:57 PM Rahuman Sheriff <sheriff at ebi.ac.uk>
> wrote:
> >> Congratulations Marcella,
> >>
> >> Hi Jacob and all,
> >>
> >> As Tomas mentioned, John G’s version is bit more organised.
> >> Although it would be nice to take that one forward, I also fine with
> you recovering your version incorporating requested changes including mine.
> >> I would prefer this manuscript progresses ahead, instead of another
> long discussion.
> >> Green signal from my side.
> >> Best regards
> >> Sheriff
> >>
> >>
> >>> On 22 Oct 2021, at 01:49, Jacob Barhak <jacob.barhak at gmail.com> wrote:
> >>>
> >>> Congratulations Marcella,
> >>>
> >>> Indeed you bring good news.
> >>>
> >>> 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.
> >>>
> >>> Jacob
> >>>
> >>> On Thu, Oct 21, 2021, 10:33 Torres, Marcella <mtorres at richmond.edu>
> wrote:
> >>> 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.
> >>>
> >>> 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.
> >>>
> >>> Marcella
> >>> From: Jacob Barhak <jacob.barhak at gmail.com>
> >>> Sent: Wednesday, October 20, 2021 11:53:58 PM
> >>> To: Alexander Kulesza <alexander.kulesza at novadiscovery.com>
> >>> Cc: Hana <h.dobrovolny at tcu.edu>; James Osborne <
> jmosborne at unimelb.edu.au>; John Rice <john.rice at noboxes.org>; Torres,
> Marcella <mtorres at richmond.edu>; vp-reproduce-subgroup at lists.simtk.org <
> vp-reproduce-subgroup at lists.simtk.org>;
> vp-integration-subgroup at lists.simtk.org <
> vp-integration-subgroup at lists.simtk.org>; Jonathan Karr <
> jonrkarr at gmail.com>; John Gennari <gennari at uw.edu>; Winston Garira <
> Winston.Garira at univen.ac.za>
> >>> Subject: Re: [Vp-integration-subgroup] Fwd: Shayn Peirce-Cottler via
> Frontiers: Manuscript
> >>>
> >>> External Email: Use caution in opening links, attachments, and buying
> gift cards.
> >>>
> >>> Thanks Alex, Thanks John,
> >>>
> >>> 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.
> >>>
> >>> 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.
> >>>
> >>> If there will be no blocks I plan to start work over the weekend if I
> see no objections by then.
> >>>
> >>> 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.
> >>>
> >>> 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.
> >>>
> >>> 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.
> >>>
> >>> Jacob
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Tue, Oct 19, 2021 at 2:02 AM Alexander Kulesza <
> alexander.kulesza at novadiscovery.com> wrote:
> >>> Dear Jacob,
> >>> thanks for forwarding and you suggestions, which seems more than
> reasonable.
> >>>
> >>> My contributions from May 19th, May31st and June 2nd are in
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT%2Fedit%3Fusp%3Dsharing%26ouid%3D113860487708206439519%26rtpof%3Dtrue%26sd%3Dtrue&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727682287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=5DkphKFgmXWvV4azKVy0EyqJwh3cnPbocnBSE%2BL8CZQ%3D&reserved=0
> >>>
> >>> The other document
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1esZvWWVBvpwvuFUi3C3161lthZkEBFyMRrwwozitBi4%2Fedit%3Fusp%3Dsharing&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727682287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=i69lTB9BmMlCGAivRn4Z5ZXIayBAK9UYcKmumIsr6TY%3D&reserved=0
> 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.
> >>>
> >>> 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.
> >>>
> >>> Please let me know.
> >>> A
> >>>
> >>>
> >>>
> >>> On Tue, 19 Oct 2021 at 05:51, Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
> >>> Greetings white paper contributors,
> >>>
> >>> Below is the response from the editor to my request and my thank you.
> >>>
> >>> 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.
> >>>
> >>> 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.
> >>>
> >>> The most time consuming effort would be adhering to the journal format
> as defined here:
> >>>
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.frontiersin.org%2Fabout%2Fauthor-guidelines&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727682287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=qkqzufzA1m6zgRR9gppIq4%2B2LYYByiBhRQAamQntqTM%3D&reserved=0
> >>>
> >>> I think the most time consuming task would be dealing with the
> references - otherwise the format guidelines seem reasonable.
> >>>
> >>> We can also add some revisions we started working on. However, I will
> personally insist on :
> >>> 1. traceability - currently there is no traceability in the revised
> version in the summer
> >>> 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
> >>> 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.
> >>>
> >>> I will also ask for fast responses from all contributors.
> >>>
> >>> 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.
> >>>
> >>> 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.
> >>>
> >>> 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:
> >>>
> >>> - 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
> >>> - 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
> >>> - 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.
> >>>
> >>> 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.
> >>>
> >>> 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..
> >>>
> >>> 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 ..
> >>>
> >>> If I forgot anyone who had major requests, please remind me. .
> >>>
> >>> 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..
> >>>
> >>> Hopefully most of you will be ok with that.
> >>>
> >>> Jacob
> >>>
> >>>
> >>>
> >>>
> >>> ---------- Forwarded message ---------
> >>> From: Jacob Barhak <jacob.barhak at gmail.com>
> >>> Date: Mon, Oct 18, 2021 at 9:34 PM
> >>> Subject: Re: Shayn Peirce-Cottler via Frontiers: Manuscript
> >>> To: Peirce-Cottler, Shayn (smp6p) <smp6p at virginia.edu>
> >>> Cc: Shayn Peirce-Cottler (Via FrontiersIn) <shayn at virginia.edu>,
> systemsbiology.editorial.office at frontiersin.org <
> systemsbiology.editorial.office at frontiersin.org>, Vodovotz, Yoram <
> vodovotzy at upmc.edu>
> >>>
> >>>
> >>> Thanks Shayn,
> >>>
> >>> You will get a revised manuscript targeted at your journal and get
> back to you with a more polished version and satisfies your requests.
> >>>
> >>> 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.
> >>>
> >>> Many thanks for the rapid responses.
> >>>
> >>> Jacob
> >>>
> >>>
> >>> --
> >>> Jacob Barhak Ph.D.
> >>> Sole Proprietor, Software Developer, and Computational Disease Modeler
> >>>
> >>> Jacob Barhak Analytics
> >>> 701 Brazos St
> >>> Suite 548
> >>> Austin TX, 78701
> >>>
> >>> Email: jacob.barhak at gmail.com
> >>>
> >>>
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsites.google.com%2Fview%2Fjacob-barhak%2Fhome&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727682287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=gOmUYx5pQzFybacMWUfy9v7oUfcEPnCBBOzOQdICYoU%3D&reserved=0
> >>>
> >>>
> >>>
> >>> On Mon, Oct 18, 2021 at 7:43 PM Peirce-Cottler, Shayn (smp6p) <
> smp6p at virginia.edu> wrote:
> >>> Hi Jacob,
> >>>
> >>>
> >>> 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.
> >>>
> >>>
> >>> 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!
> >>>
> >>>
> >>> -Shayn
> >>>
> >>>
> >>>
> >>> Shayn Peirce-Cottler, Ph.D.
> >>>
> >>> Professor of Biomedical Engineering
> >>>
> >>> Harrison Distinguished Teaching Professor
> >>>
> >>> BME Graduate Program Director
> >>>
> >>> University of Virginia
> >>>
> >>> Charlottesville, VA
> >>>
> >>>
> >>> From: Jacob Barhak <jacob.barhak at gmail.com>
> >>> Date: Monday, October 18, 2021 at 1:57 AM
> >>> To: Peirce-Cottler Shayn <shayn at virginia.edu>
> >>> Cc: "systemsbiology.editorial.office at frontiersin.org" <
> systemsbiology.editorial.office at frontiersin.org>, "Vodovotz, Yoram" <
> vodovotzy at upmc.edu>
> >>> Subject: Re: Shayn Peirce-Cottler via Frontiers: Manuscript
> >>>
> >>>
> >>> Hi Shayn,
> >>>
> >>>
> >>> Thanks for returning the response quickly. To you comments.
> >>>
> >>>
> >>> 1. This is the list of authors that agreed to submit this manuscript
> for review - I collected their approvals for this version personally.
> >>>
> >>>
> >>> • 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
> >>> • Rahuman Sheriff, The European Bioinformatics Institute
> (EMBL-EBI), UK
> >>> • James Osborne, School of Mathematics and Statistics, University
> of Melbourne, Australia
> >>> • Gilberto Gonzalez Parra, Mathematics Department, New Mexico
> Tech, USA
> >>> • Eric Forgoston, Department of Applied Mathematics and
> Statistics, Montclair State University, USA
> >>> • Ruth Bowness, Department of Mathematical Sciences, University
> of Bath, UK
> >>> • Yaling Liu, Department of Mechanical Engineering and Mechanics
> , Department of Bioengineering, Lehigh University, USA
> >>> • Robin Thompson, Mathematics Institute & The Zeeman Institute
> for Systems Biology and Infectious Disease Epidemiology Research,
> University of Warwick, UK
> >>> • Winston Garira - Department Of Mathematics And Applied
> Mathematics , Modelling Health and Environmental Linkages Research Group.
> University of Venda, South Africa
> >>> • Jacob Barhak - Barhak, Jacob, USA
> >>> • John Rice - Independent Retired Working Group Volunteer, USA
> >>> • Marcella Torres, School of Arts and Sciences, University of
> Richmond, USA
> >>> • Hana M. Dobrovolny , Department of Physics & Astronomy, Texas
> Christian University, Fort Worth, USA
> >>> • Tingting Tang, Department of Mathematics and Statistics in San
> Diego State University (SDSU) and SDSU Imperial Valley, USA
> >>> • William Waites, Centre for Mathematical Modelling of Infectious
> Diseases, London School of Hygiene and Tropical Medicine, UK
> >>> • James Glazier, Biocomplexity Institute, Indiana University,
> Bloomington, USA
> >>> • James R. Faeder, Department of Computational and Systems
> Biology, University of Pittsburgh, Pittsburgh, USA
> >>>
> >>> 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:
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.simtk.org%2Fpipermail%2Fvp-reproduce-subgroup%2F2021-March%2F000019.html&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727692287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=ia5ARWxyBl%2BY%2B11jfwExOLPPxpbhGaqtktpYk1Cyp3c%3D&reserved=0
> - 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.
> >>>
> >>>
> >>>
> >>> 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.
> >>>
> >>>
> >>> 3. Please note that after the list of authors there is a disclaimer :
> "The opinion of the contributors do not reflect the opinions of the entire
> working group". Initially 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.
> >>>
> >>>
> >>> 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.
> >>>
> >>>
> >>> In summary:
> >>>
> >>> 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.
> >>>
> >>>
> >>> 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.
> >>>
> >>>
> >>> Hopefully we can address your concerns in time to publish the
> manuscript in a timely manner.
> >>>
> >>>
> >>> Jacob
> >>>
> >>>
> >>> --
> >>> Jacob Barhak Ph.D.
> >>> Sole Proprietor, Software Developer, and Computational Disease Modeler
> >>>
> >>> Jacob Barhak Analytics
> >>> 701 Brazos St
> >>> Suite 548
> >>> Austin TX, 78701
> >>>
> >>> Email: jacob.barhak at gmail.com
> >>>
> >>>
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsites.google.com%2Fview%2Fjacob-barhak%2Fhome&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727692287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Ce1AaYV56fay8a5ng%2FtH8OhrVLjo9344eynKrsKrx5I%3D&reserved=0
> >>>
> >>>
> >>>
> >>> On Sun, Oct 17, 2021 at 9:56 AM Shayn Peirce-Cottler (Via FrontiersIn)
> <noreply at frontiersin.org> wrote:
> >>>
> >>> Dear Jacob,
> >>>
> >>> 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:
> >>>
> >>> 1. The author list that is on the first page differs from the author
> list that was provided at the time of submission.
> >>>
> >>> 2. The manuscript needs to be submitted using the official Frontiers
> template.
> >>>
> >>> 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.
> >>>
> >>> 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).
> >>>
> >>> 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.
> >>>
> >>> Thank you,
> >>> Shayn
> >>>
> >>>
> >>> ---------------------------------
> >>>
> >>> Manuscript title: Model Integration in Computational Biology: The Role
> of Reproducibility, Credibility and Utility
> >>> Manuscript ID: 793932
> >>> 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
> >>> Date submitted: 12 Oct 2021
> >>> Edited by: Shayn Peirce-Cottler
> >>>
> >>>
> >>> Research Topic: Insights in Systems Biology: Multiscale Mechanistic
> Modeling 2021
> >>> Review forum direct access link:
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Freview.frontiersin.org%2Freview%2F793932%2F0%2F0&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727692287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=%2B9EkL0eiqOgAgLYJqAVNr%2FM5vaTJvVEqzjjQBqF7RwA%3D&reserved=0
> >>>
> >>> _______________________________________________
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> >>> Vp-integration-subgroup at lists.simtk.org
> >>>
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> >>>
> >>>
> >>> --
> >>>
> >>> Alexander Kulesza
> >>>
> >>> Team leader
> >>>
> >>> Modeling & simulation / Biomodeling
> >>>
> >>> alexander.kulesza at novadiscovery.com
> >>>
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> >>
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> > --
> > James A. Glazier, PhD
> > Professor of Intelligent Systems Engineering, Adjunct Professor of
> Physics
> > Director, Biocomplexity Institute
> > Indiana University, Bloomington
> > (812) 391-2159 (cell)
> >
> > _______________________________________________
> > Vp-integration-subgroup mailing list
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>
>
> --
> -- ------------------
> Yaling Liu, Professor
> Department of Bioengineering, Director of Graduate Studies
> Department of Mechanical Engineering and Mechanics
> Lehigh University
> www.lehigh.edu/~yal310 <http://www.lehigh.edu/%7Eyal310>
>
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