[Vp-integration-subgroup] [Vp-reproduce-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript
Jacob Barhak
jacob.barhak at gmail.com
Wed Nov 3 22:30:29 PDT 2021
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.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> 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
>>>>>>> Vp-reproduce-subgroup at lists.simtk.org
>>>>>>> https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup
>>>>>>>
>>>>>>
>>>> _______________________________________________
>>>> Vp-reproduce-subgroup mailing listVp-reproduce-subgroup at lists.simtk.orghttps://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup
>>>>
>>>> --
>>>> 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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