[Vp-reproduce-subgroup] [Vp-integration-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript
Jacob Barhak
jacob.barhak at gmail.com
Sat Oct 23 12:50:32 PDT 2021
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:
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>>>>>>
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>>>>>>
>>>>>>
>>>>>> --
>>>>>> Alexander Kulesza
>>>>>> Team leader
>>>>>> Modeling & simulation / Biomodeling
>>>>>> alexander.kulesza at novadiscovery.com
>>>>>> +33 7 82 92 44 62
>>>>>> nova
>>>>>> DISCOVERY
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