[Vp-reproduce-subgroup] [Vp-integration-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript

James Osborne jmosborne at unimelb.edu.au
Sun Oct 24 15:32:01 PDT 2021 

My main suggestion is what I did to the previous version (John Gs) bit
didn't make it over. Which was to have some more levels to the sections.
As it is they are all the same level and therefore there's no break between
the introduction material and the main focus of the paper (in my opinion
the table of difficulties or challenges and subsequent sections)

My very low effort proposal is to.

 * change the section title "Utility of Models" to something like
"Challenges with using multiscale models
 * Then put the difficulties/ challenges listed in the table into
subsections called things like "Challenge 1: Evaluating Model Credibility "

This wouldn't change any content so would not mess up tracking
contributions or the "content" of the paper but would make it more readable
as the reader would have more help identifying the contribution from the
paper.

I believe it will make the papers intent clearer and easier to read.

But if you're against it I rest my case and defer to your opinion.

James


On Mon, Oct 25, 2021 at 8:53 AM Jacob Barhak <jacob.barhak at gmail.com> wrote:
>
> Well James,
>
> You should look at the new version. And please no more suggestions other
than proofs or pointing out errors. We really are not at that stage
anymore. We had many months for suggestions. It is time for finalization
towards what the editor asked for.
>
> I hope you understand.
>
>           Jacob
>
> On Sun, Oct 24, 2021, 03:51 James Osborne <jmosborne at unimelb.edu.au>
wrote:
>>
>> Jacob
>>
>> I was just about to make some suggestions on structure which were added
to the bakers dozen version version.
>>
>> I'll make in suggest mode then  you can decide of they work or not.
>>
>> James
>>
>> On Sun, Oct 24, 2021 at 7:44 PM Jacob Barhak <jacob.barhak at gmail.com>
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
>>>>>>>>>>>>> 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
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