[Vp-reproduce-subgroup] [Vp-integration-subgroup] Fwd: Shayn Peirce-Cottler via Frontiers: Manuscript
Alexander Kulesza
alexander.kulesza at novadiscovery.com
Mon Oct 18 01:06:52 PDT 2021
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>
>>
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--
Alexander Kulesza
Team leader
Modeling & simulation / Biomodeling
alexander.kulesza at novadiscovery.com
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