[Vp-reproduce-subgroup] [Vp-integration-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript
William Waites
wwaites at ieee.org
Sun Nov 7 02:34:09 PST 2021
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://arxiv.org/abs/2111.02510 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://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
>
> 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://www.frontiersin.org/about/policies-and-publication-ethics
>
> Note that the guidelines allow to establish authors levels of contribution according to https://www.frontiersin.org/about/author-guidelines 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://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
>
> 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://www.frontiersin.org/about/policies-and-publication-ethics
>
> 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://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
>>
>> 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://meet.jit.si/CollaborativePaperEditing 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://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit
>>
>> You will need to login so that your edits will be traceable.
>>
>> You can join me while editing in:
>> https://meet.jit.si/CollaborativePaperEditing
>>
>> 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://eric-forgoston.github.io/
>>
>>
>> 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://meet.jit.si/CollaborativePaperEditing
>>
>> 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://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit - the submitted version
>> https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit - first committed version
>> https://docs.google.com/document/d/1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh/edit - first committed version
>> https://drive.google.com/file/d/1U_lTHrV6STXWNT3GiCepvsLk1WdYgzN5/view - its the first document posted
>>
>> After this step is done I will move towards adhering to those instructions:
>> https://www.frontiersin.org/about/author-guidelines
>>
>> 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://eric-forgoston.github.io/
>>
>>
>> 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://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit?usp=sharing&ouid=113860487708206439519&rtpof=true&sd=true
>>>
>>> The other document https://docs.google.com/document/d/1esZvWWVBvpwvuFUi3C3161lthZkEBFyMRrwwozitBi4/edit?usp=sharing 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://www.frontiersin.org/about/author-guidelines
>>>
>>> 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://sites.google.com/view/jacob-barhak/home
>>>
>>>
>>>
>>> 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://lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-March/000019.html - 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://sites.google.com/view/jacob-barhak/home
>>>
>>>
>>>
>>> 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://review.frontiersin.org/review/793932/0/0
>>>
>>> _______________________________________________
>>> Vp-integration-subgroup mailing list
>>> Vp-integration-subgroup at lists.simtk.org
>>> https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup
>>>
>>>
>>> --
>>>
>>> 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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>>>
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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)
>
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