[Vp-reproduce-subgroup] [Vp-integration-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript
Jacob Barhak
jacob.barhak at gmail.com
Fri Oct 22 12:52:24 PDT 2021
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.]
>>>
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>>>
>>>
>>>
>>> --
>>> Alexander Kulesza
>>> Team leader
>>> Modeling & simulation / Biomodeling
>>> alexander.kulesza at novadiscovery.com
>>> +33 7 82 92 44 62
>>> nova
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