[Vp-reproduce-subgroup] [Vp-integration-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript
James Osborne
jmosborne at unimelb.edu.au
Sun Nov 7 14:32:39 PST 2021
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
>> >>>
>> >>> _______________________________________________
>> >>> Vp-integration-subgroup mailing list
>> >>> Vp-integration-subgroup at lists.simtk.org
>> >>>
>> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.simtk.org%2Fmailman%2Flistinfo%2Fvp-integration-subgroup&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727692287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=O96p1kQNUebcRbGUf7%2BCUYUf2Im%2FszHFAtpx0EJSAeQ%3D&reserved=0
>> >>>
>> >>>
>> >>> --
>> >>>
>> >>> Alexander Kulesza
>> >>>
>> >>> Team leader
>> >>>
>> >>> Modeling & simulation / Biomodeling
>> >>>
>> >>> alexander.kulesza at novadiscovery.com
>> >>>
>> >>> +33 7 82 92 44 62
>> >>>
>> >>> nova
>> >>> DISCOVERY
>> >>>
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>> >>>
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>> >>> This message is intended only for the personal and confidential use
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>> >>
>> >> _______________________________________________
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>> >> _______________________________________________
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>> >>
>> >>
>> >> _______________________________________________
>> >> Vp-reproduce-subgroup mailing list
>> >>
>> >> Vp-reproduce-subgroup at lists.simtk.org
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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
>> > Vp-integration-subgroup at lists.simtk.org
>> >
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>> nknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=O96p1kQNUebcRbGUf7%2BCUYUf2Im%2FszHFAtpx0EJSAeQ%3D&reserved=0
>>
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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
>
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