[Vp-reproduce-subgroup] [Vp-integration-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript
Jacob Barhak
jacob.barhak at gmail.com
Sun Oct 24 01:40:33 PDT 2021
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.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> 1. 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
>>>>>>>>>> 2. Rahuman Sheriff, The European Bioinformatics Institute
>>>>>>>>>> (EMBL-EBI), UK
>>>>>>>>>> 3. James Osborne, School of Mathematics and Statistics,
>>>>>>>>>> University of Melbourne, Australia
>>>>>>>>>> 4. Gilberto Gonzalez Parra, Mathematics Department, New
>>>>>>>>>> Mexico Tech, USA
>>>>>>>>>> 5. Eric Forgoston, Department of Applied Mathematics and
>>>>>>>>>> Statistics, Montclair State University, USA
>>>>>>>>>> 6. Ruth Bowness, Department of Mathematical Sciences,
>>>>>>>>>> University of Bath, UK
>>>>>>>>>> 7. Yaling Liu, Department of Mechanical Engineering and
>>>>>>>>>> Mechanics , Department of Bioengineering, Lehigh University, USA
>>>>>>>>>> 8. Robin Thompson, Mathematics Institute & The Zeeman
>>>>>>>>>> Institute for Systems Biology and Infectious Disease Epidemiology Research,
>>>>>>>>>> University of Warwick, UK
>>>>>>>>>> 9. Winston Garira - Department Of Mathematics And Applied
>>>>>>>>>> Mathematics , Modelling Health and Environmental Linkages Research Group.
>>>>>>>>>> University of Venda, South Africa
>>>>>>>>>> 10. Jacob Barhak - Barhak, Jacob, USA
>>>>>>>>>> 11. John Rice - Independent Retired Working Group Volunteer,
>>>>>>>>>> USA
>>>>>>>>>> 12. Marcella Torres, School of Arts and Sciences, University
>>>>>>>>>> of Richmond, USA
>>>>>>>>>> 13. Hana M. Dobrovolny , Department of Physics & Astronomy,
>>>>>>>>>> Texas Christian University, Fort Worth, USA
>>>>>>>>>> 14. Tingting Tang, Department of Mathematics and Statistics
>>>>>>>>>> in San Diego State University (SDSU) and SDSU Imperial Valley, USA
>>>>>>>>>> 15. William Waites, Centre for Mathematical Modelling of
>>>>>>>>>> Infectious Diseases, London School of Hygiene and Tropical Medicine, UK
>>>>>>>>>> 16. James Glazier, Biocomplexity Institute, Indiana
>>>>>>>>>> University, Bloomington, USA
>>>>>>>>>> 17. 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
>>>>>>>>>> <http://links.email.frontiersin.org/ls/click?upn=AAaFa03elZRFPXQ6ShiKwHJ7IVBhf38O-2BEQWinpomFtULO0Q-2BM19TTRdh7emL5NqrxgHYRG7-2FEazDF-2FJfPddug-3D-3Dkdpa_6U3AlnyvMxxXqGK2YZZvqQDAig2dZVa43D-2BB81ORWCaNWR45ZJ2fDhpaKsTZzRsuCL-2BNJFR2MRucSNQVfNAGmtHQx1gGGhLotkRxEWQuZDre0jQti6pSzF-2Bm1akZB-2FZLJbzjJjEqrnF6c-2BY79oozDKNeyZDGEV7E7qizJmMtyvWGMFEr4JK1z0YPzIbG66EloII5-2FSNkwoWo-2BqqYbe1fAtco01e7-2FlRQb33KpEVuKlNimzGXjW3kPgAYf1R6wsCnLhi7Aow94qLbu0WkYgbBRg-3D-3D>[image:
>>>>>>>>>> Image removed by sender.]
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> 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
>>>>>>>>>> www.novadiscovery.com
>>>>>>>>>> 1 Place Verrazzano, 69009 Lyon
>>>>>>>>>> +33 9 72 53 13 01
>>>>>>>>>>
>>>>>>>>>> *This message is intended only for the personal and confidential
>>>>>>>>>> use of the designated recipient(s) named above. If you are not the intended
>>>>>>>>>> recipient of this message you are hereby notified that any review,
>>>>>>>>>> dissemination, distribution or copying of this message is strictly
>>>>>>>>>> prohibited. Email transmission cannot be guaranteed to be secure or
>>>>>>>>>> error-free. Therefore, we do not represent that this information is
>>>>>>>>>> complete or accurate and it should not be relied upon as such. All
>>>>>>>>>> information is subject to change without notice.*
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>> Vp-integration-subgroup mailing list
>>>>>>>>> Vp-integration-subgroup at lists.simtk.org
>>>>>>>>> https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Vp-reproduce-subgroup mailing list
>>>>>>>>> Vp-reproduce-subgroup at lists.simtk.org
>>>>>>>>> https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup
>>>>>>>>>
>>>>>>>> _______________________________________________
>>> Vp-reproduce-subgroup mailing list
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>>> https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup
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>>
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