[Vp-reproduce-subgroup] [Vp-integration-subgroup] Fwd: Shayn Peirce-Cottler via Frontiers: Manuscript
James Osborne
jmosborne at unimelb.edu.au
Mon Oct 18 01:32:19 PDT 2021
Jacob
I'm happy to go ahead to satisfy the editor.
James
On Mon, Oct 18, 2021 at 7:27 PM Jacob Barhak <jacob.barhak at gmail.com> wrote:
> 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>
>>>>
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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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