[Vp-integration-subgroup] Fwd: Shayn Peirce-Cottler via Frontiers: Manuscript
Tomas Helikar
thelikar2 at unl.edu
Tue Oct 19 01:46:33 PDT 2021
Hi everyone,
I'm glad to see this manuscript is being revived.
I do think that the best starting point for the revision is indeed the
version started by John G. at the beginning of the summer. That version
has a much improved structure, flow, and content, and many members have
already further contributed to it. It seems to me that finalizing this
document would be fastest route to a better product. The document is
here, and I'm also happy to continue to contribute to it:
https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit
For citations, I would recommend Zotero, which works relatively well
with GDocs, and I can take care of them. The only thing I would ask is
if everyone (in their part of the text) would provide the PMID for their
citations, which will streamline migrating the citations into Zotero.
Best,
Tomas Helikar, Ph.D.
Susan J Rosowski Associate Professor
Department of Biochemistry | University of Nebraska-Lincoln
m: 402-547-8904 <callto:402-547-8904> | o: 402-472-3530
<callto:402-472-3530>
www.helikarlab.org <http://helikarlab.org> | https://cellcollective.org
<https://cellcollective.org>
twitter: @helikarlab <http://twitter.com/helikarlab>, @biocollective
<http://twitter.com/biocollective>
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On 10/19/21 5:51 AM, Jacob Barhak wrote:
> Non-NU Email
> ------------------------------------------------------------------------
> 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
> <https://urldefense.com/v3/__https://www.frontiersin.org/about/author-guidelines__;!!PvXuogZ4sRB2p-tU!REZUbgUiZfj49nu_WmReUcMSEjNwc2495QNd8pDEttJlYIRWXHRY9T8hH8pM1dCE$>
>
> 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
> <mailto: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
> <mailto:smp6p at virginia.edu>>
> Cc: Shayn Peirce-Cottler (Via FrontiersIn) <shayn at virginia.edu
> <mailto:shayn at virginia.edu>>,
> systemsbiology.editorial.office at frontiersin.org
> <mailto:systemsbiology.editorial.office at frontiersin.org>
> <systemsbiology.editorial.office at frontiersin.org
> <mailto:systemsbiology.editorial.office at frontiersin.org>>, Vodovotz,
> Yoram <vodovotzy at upmc.edu <mailto: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 <mailto:jacob.barhak at gmail.com>
>
> https://sites.google.com/view/jacob-barhak/home
> <https://urldefense.com/v3/__https://sites.google.com/view/jacob-barhak/home__;!!PvXuogZ4sRB2p-tU!REZUbgUiZfj49nu_WmReUcMSEjNwc2495QNd8pDEttJlYIRWXHRY9T8hH40MzZkK$>
>
>
>
> On Mon, Oct 18, 2021 at 7:43 PM Peirce-Cottler, Shayn (smp6p)
> <smp6p at virginia.edu <mailto: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
> <mailto:jacob.barhak at gmail.com>>
> *Date: *Monday, October 18, 2021 at 1:57 AM
> *To: *Peirce-Cottler Shayn <shayn at virginia.edu
> <mailto:shayn at virginia.edu>>
> *Cc: *"systemsbiology.editorial.office at frontiersin.org
> <mailto:systemsbiology.editorial.office at frontiersin.org>"
> <systemsbiology.editorial.office at frontiersin.org
> <mailto:systemsbiology.editorial.office at frontiersin.org>>,
> "Vodovotz, Yoram" <vodovotzy at upmc.edu <mailto: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
> <https://urldefense.com/v3/__https://lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-March/000019.html__;!!PvXuogZ4sRB2p-tU!REZUbgUiZfj49nu_WmReUcMSEjNwc2495QNd8pDEttJlYIRWXHRY9T8hHyXaiJMA$>
> - 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 <mailto:jacob.barhak at gmail.com>
>
> https://sites.google.com/view/jacob-barhak/home
> <https://urldefense.com/v3/__https://sites.google.com/view/jacob-barhak/home__;!!PvXuogZ4sRB2p-tU!REZUbgUiZfj49nu_WmReUcMSEjNwc2495QNd8pDEttJlYIRWXHRY9T8hH40MzZkK$>
>
> On Sun, Oct 17, 2021 at 9:56 AM Shayn Peirce-Cottler (Via
> FrontiersIn) <noreply at frontiersin.org
> <mailto: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
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