[Vp-reproduce-subgroup] Fwd: Shayn Peirce-Cottler via Frontiers: Manuscript
Jacob Barhak
jacob.barhak at gmail.com
Sun Oct 17 23:44:16 PDT 2021
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
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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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