[Vp-integration-subgroup] [Vp-reproduce-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript
Eric Forgoston
eric.forgoston at montclair.edu
Sun Nov 7 16:32:49 PST 2021
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
>>> >>>
>>> >>> _______________________________________________
>>> >>> Vp-integration-subgroup mailing list
>>> >>> Vp-integration-subgroup at lists.simtk.org
>>> >>>
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>>> >>>
>>> >>>
>>> >>> --
>>> >>>
>>> >>> Alexander Kulesza
>>> >>>
>>> >>> Team leader
>>> >>>
>>> >>> Modeling & simulation / Biomodeling
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>>> >>> +33 7 82 92 44 62
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>>> >>
>>> >> _______________________________________________
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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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>>>
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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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