[Vp-integration-subgroup] Fwd: Shayn Peirce-Cottler via Frontiers: Manuscript
Jacob Barhak
jacob.barhak at gmail.com
Mon Oct 18 01:26:23 PDT 2021
Sure Alex,
The version that was submitted in the only version that was approved by the
contributors - since no other version was fully approved, this is the
only version we can legally submit:
https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
This is the version that we assembled before your modifications were added
in the version you created.
My interpretation is that the editor is open to this version provided we
address the issues raised.I think this can be done if we all agree on
course of action - I even offered my services to merge this with your
version as well as Sheriff's version and John's initial version since those
are traceable back to author - however, I will do this only if I know I
have a green light from all contributors since this means a few days of
work for me and I do not want my time to go to waste because of an
objection or an idea for a better version that will never get approved.
So I am waiting for a discussion to see the next move - it seems we have a
path towards publication, yet we need to gather together and agree on
something.
Hopefully we can do it.
Jacob.
On Mon, Oct 18, 2021 at 3:07 AM Alexander Kulesza <
alexander.kulesza at novadiscovery.com> wrote:
> Dear Jacob, dear all,
>
> to be very honest, I do not really understand what happens here anymore.
> Could you please point us to the version that has been submitted ?
>
> Best
> Alexander
>
>
>
>
> On Mon, 18 Oct 2021 at 08:44, Jacob Barhak <jacob.barhak at gmail.com> wrote:
>
>> Greeting white paper contributors,
>>
>> Good news. The editor of the topic "Insights in Systems Biology:
>> Multiscale Mechanistic Modeling 2021" from Frontiers in Systems Biology -
>> Multiscale Mechanistic Modeling has returned an answer to our query about
>> the manuscript Marcella Submitted on our behalf.
>>
>> You can find her concerns and our answer in the forwarded messages below.
>> I think they can be easily fixed if we can find agreement in the group.
>>
>> Since little time was provided, I ask that the group will answer fast on
>> the desired course of action. We can easily address the concerns she raised
>> fairly quickly. However, I know many of you want more modifications. So
>> each one of the contributors will have to decide if the minimal changes
>> required will be ok for you to approve the manuscript for publication
>>
>> If this is agreeable to all contributors I will be happy to spend the
>> time and adapt the manuscript as requested.
>>
>> Many of you wanted to revise the manuscript - now is a good chance to
>> introduce those new versions. Yet the work has to be done in reasonable
>> time, including the approval process.
>>
>> To make things easier, I can personally commit time to transforming the
>> manuscript to the desired format and answer all requested changed -
>> However, I will do this only if I know there is no objection to this by any
>> of the listed contributors - so please respond quickly. I am raising this
>> topic for discussion before we start so contributors form their minds. I
>> can also introduce changes from the other 3 versions of the paper that are
>> traceable back to authors if this helps the group move forward - The 3
>> versions are from Alex, Sheriff, and John - yet I will personally not
>> introduce any change that is not traceable back to an author on google docs
>> - please see how the editor is specific about authorship in the first
>> concern raised - hence my insistence of traceability.
>>
>> If anyone else wants to commit time to quickly assemble a revised
>> manuscript that is traceable back to authors and matches the editors
>> comments, it is now time to step forwards and remember we have little time
>> to move forwards unless the editor grants us an extension. And note that
>> collecting approvals from such a large group also takes time - so revisions
>> should be done quickly regardless.
>>
>> I will wait for a few days before taking any action to see what are the
>> opinions and ideas you may have to move this forward.
>>
>> Hopefully we can quickly find common agreement.
>>
>> I thank Marcella for taking the time to submit this to get a response.
>>
>> Jacob
>>
>>
>>
>>
>>
>> ---------- Forwarded message ---------
>> From: Jacob Barhak <jacob.barhak at gmail.com>
>> Date: Mon, Oct 18, 2021 at 12:57 AM
>> Subject: Re: Shayn Peirce-Cottler via Frontiers: Manuscript
>> To: Shayn Peirce-Cottler (Via FrontiersIn) <shayn at virginia.edu>
>> Cc: <systemsbiology.editorial.office at frontiersin.org>, Vodovotz, Yoram <
>> vodovotzy at upmc.edu>
>>
>>
>> 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>
>>>
>> _______________________________________________
>> 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.*
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.simtk.org/pipermail/vp-integration-subgroup/attachments/20211018/6a902ff4/attachment-0001.html>
More information about the Vp-integration-subgroup
mailing list