[Vp-reproduce-subgroup] [Vp-integration-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript
sheriff
sheriff at ebi.ac.uk
Thu Jan 27 00:59:50 PST 2022
Hi Jacob and all, this is also an opportunity for everyone to check the
spelling of their names.
Just to make it easy, @Jacob, could you share the link to the final
manuscript here one last time.
Best regards
Sheriff
On 2022-01-27 01:48, Jacob Barhak wrote:
> Thanks Marcella, and all paper contributors, please pay attention
>
> It has been a week since the message sent to the group.
>
> So far no one has responded with any changes in funding sources or
> conflict of interest.
>
> So again, if anyone was funded by a source that requires recognition to
> do this work, please let me know by friday so we can correct it.
>
> Also, again, if anyone has an objection to this paper being made
> public, it is the last chance to do so.
>
> Otherwise I will send a letter to the editor that the group is ok with
> the current version over the weekend and hopefully it gets published
> quickly.
>
> Jacob
>
> On Wed, Jan 26, 2022, 18:12 Torres, Marcella <mtorres at richmond.edu>
> wrote:
>
> Email from Frontiers and question from the editor shared below:
>
> Dear Dr Torres,
>
> Frontiers in Systems Biology Editorial Office has sent you a message.
> Please click 'Reply' to send a direct response
>
> New comments were posted by Specialty Chief Editor Shayn
> Peirce-Cottler. Please visit the review forum using the link below and
> address these comments within the coming week:
> http://www.frontiersin.org/Review/EnterReviewForum.aspx?activationno=ba15539e-1784-4ed3-9969-2aacb1b5b835
> [1]
>
> Journal: Frontiers in Systems Biology, section Multiscale Mechanistic
> Modeling
> Article type: Review
> Manuscript title: Model Integration in Computational Biology: the Role
> of Reproducibility, Credibility and Utility
> Manuscript ID: 822606
> Authors: Jonathan Karr, Rahuman S. Malik Sheriff, James Osborne,
> Gilberto Gonzalez Parra, Eric Forgoston, Ruth Bowness, Yaling Liu,
> Robin Thompson, Winston Garira, Jacob Barhak, John Rice, Marcella
> Torres, Hana Maria Dobrovolny, Tingting Tang, William Waites, James
> Glazier, James Faeder, Alexander Kulesza
> Submitted on: 26 Nov 2021
> Edited by: Shayn Peirce-Cottler
>
> Research Topic: Insights in Systems Biology: Multiscale Mechanistic
> Modeling 2021
>
> Best regards,
>
> Your Frontiers in Systems Biology team
>
> Frontiers in Systems Biology Editorial Office
> www.frontiersin.org [2]
> Avenue du Tribunal Federal 34
> Lausanne, Switzerland | T 41(0)21 510 17 93
>
> For technical issues, please contact our IT Helpdesk -
> support at frontiersin.org
>
>
> Marcella Torres, Ph.D.
> Director of Mathematical Studies
> University of Richmond
> Jepson Hall Room 212
> 221 Richmond Way
> Richmond, VA 23173
> (804) 289-8081
> Pronouns: she/her
>
> -------------------------
>
> From: Vp-reproduce-subgroup
> <vp-reproduce-subgroup-bounces at lists.simtk.org> on behalf of Jacob
> Barhak <jacob.barhak at gmail.com>
> Sent: Wednesday, January 19, 2022 10:24 PM
> To: James Glazier <jaglazier at gmail.com>
> Cc: vp-reproduce-subgroup at lists.simtk.org
> <vp-reproduce-subgroup at lists.simtk.org>;
> vp-integration-subgroup at lists.simtk.org
> <vp-integration-subgroup at lists.simtk.org>
> Subject: Re: [Vp-reproduce-subgroup] [Vp-integration-subgroup] Shayn
> Peirce-Cottler via Frontiers: Manuscript
>
> External Email: Use caution in opening links, attachments, and buying
> gift cards.
>
> Hi James,
>
> Here is the text I added to the submission system to correct your name
> and draw the attention of the editor to the funding issue we discussed.
>
> Hopefully no other changes will be raised by contributors and we can
> proceed as approved by all authors.
>
> Jacob
>
> ####### Letter to the editor sent in submission system ########
>
> Another author asked to change their name - adding a middle initial. I
> cannot do those changes in the manuscript myself through the system
> since it does not allow making those changes. Here is the proper name
> with the proper middle initial:
>
> James A. Glazier
>
> Also, I am making a round of checks that all funding sources and
> conflict of interests have been submitted properly. Here is the link
> to the public communications:
>
> https://lists.simtk.org/pipermail/vp-integration-subgroup/2022-January/000388.html
>
> Hopefully no other changes are necessary.
>
> Thank you for handling this manuscript.
>
> Jacob
>
> On Wed, Jan 19, 2022 at 9:05 PM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
> Thanks James, and all other paper contributors, please read this.
>
> Your email clarifies things. We did agree long ago that funding sources
> are at the discretion of the contributor although this was a volunteer
> effort. A few insisted on adding their funding source and we did add
> those. Here is some the discussion that we held:
> https://lists.simtk.org/pipermail/vp-integration-subgroup/2021-April/000073.html
>
> Sheriff's request came in late and should not have been submitted that
> late in the process, yet I decided to include his funding source
> because it has legal implications if it is not included - I assume that
> tax payer money paid for the time he spend on this manuscript and this
> requires traceability - I was surprised with his declaration that does
> not include a traceable source of fund yet to avoid any wrongdoing I
> decided to include it. I made the email public so that everyone knows
> and can reciprocate.
>
> In the manuscript submission form there is a clause about declaration
> of funding. When I signed it, I knew I was accurate in my statement
> about how this work was funded. It is important that these declarations
> are correct since many times taxpayer money funds this work and that
> money needs to be traceable for accounting reasons and to avoid misuse
> of funds. There are legal implications to incorrect declarations on
> this question. As far as I knew, except from very few that declared
> funding early on when we discussed it, this was a volunteer group. And
> for those who did declare I assumed this was to trace public funds.
>
> I am sending this email to the entire group to make sure that everyone
> that approved, knew that they are approving the paper text, the funding
> sources, the conflict of interest statements, the authorship / ethics
> statement., license and more elements as declared in this document:
> https://www.frontiersin.org/about/policies-and-publication-ethics
>
> If anything was lost through communications I am raising again now so
> everyone will know what they are signed on. I want to make sure that
> when I signed in your name I was not misrepresenting anything.
>
> So if anyone who reads this, and after my explanation believes that
> they need to correct a funding statement, a conflict of interest
> statement, or any other detail regarding the manuscript that has legal
> implications, please announce it NOW and quickly so changes will be
> made prior to publication. After publication, such changes may be very
> complicated and have other implications.
>
> In simpler words, if your time spent on handling this paper was funded
> by the taxpayer or by an entity that requires reporting the funding
> source, you MUST declare it. If you volunteered your own time for this
> paper, you just have to make sure you have no other conflict.
>
> Hopefully I am clear enough now.
>
> I will write to the editor about adding the middle initial in your name
> - I can no longer do this though the submission system - it blocked me
> changing the authors - this is why I wrote to the editor about the
> request from William Waites to add his second affiliation.
>
> I am not sure if there are any more proof stages where we can fix
> things - the publication process is different from venue to venue and
> it's important we will be accurate in declarations.
>
> Hopefully this email will fix things and make sure our delerations are
> accurate.
>
> Jacob
>
> On Wed, Jan 19, 2022 at 12:31 PM James Glazier <jaglazier at gmail.com>
> wrote:
> Dear Jacob:
>
> I sent the minor corrections I did because I saw your response to
> Rahuman. I had not thought initially that you were listing funding
> sources, but your response to Rahuman suggested you were. So if you
> don't want to list funding, it's ok with me. I would prefer to have the
> middle initial added if possible, simply because I otherwise get
> confused with a different James Glazier, but it isn't critical.
>
> JAG
>
> On Wed, Jan 19, 2022 at 1:22 PM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
> Well James,
>
> You put me is a difficult position. You all approved the manuscript
> multiple times.
>
> Sheriff caught it just before I sent it so I added his funding - out
> of regular process - just to avoid conflict with journal legal
> requirements.
>
> As for name changes, I am locked outside the system and such a request
> should be processed through the editor. Similar to what William asked
> for.
>
> As for funding. We discussed this a long time ago. And the paper was
> approved multiple times. I can probably spend an hour later to add
> your funding. Yet there are 18 of us and only a few claimed funding -
> this was supposed to be a volunteer effort... If all 18 ask their
> funding to be included, we will need to reopen this again.
>
> So I ask you on what should I do.
>
> If this funding declaration is necessary for this volunteer work to
> fulfill the legal requirement of the publisher to disclose funding I
> must process your request and will do it tonight. If not , I suggest we
> avoid changes. Please advise on proper way to proceed.
>
> Hopefully this will settle the matter.
>
> Jacob
>
> On Wed, Jan 19, 2022, 11:15 James A Glazier <jaglazier at gmail.com>
> wrote:
>
> Dear Jacob:
>
> Thank you for your heroic efforts on bringing this paper together. I
> should probably change my name to James A. Glazier, which is my
> standard listing. I should also acknowledge my funding support:
>
> James A. Glazier acknowledges funding support from grants NSF 188553,
> NSF 186890, NSF 1720625, NIH U24 EB028887 and NIH R01 GM122424.
>
> JAG
>
> On 11/17/2021 10:04 PM, Jacob Barhak wrote:
> Hi James Faedar, Hi John Rice,
>
> Please check the manuscript and declare by REPLY ALL if you APPROVE,
> DISAPPROVE or ABSTAIN.
>
> James, if you responded and I did not get the email, I apologize -
> there are some communication hiccups occasionally. Yet I need your
> public approval to proceed and use your name.
>
> John, I know you allowed us to send the paper, yet you need to be
> specific and declare if you want to be included as an Author or just
> moved to acknowledgements. You did have a major contribution, so I hope
> you will APPROVE.
>
> Once I have your answer I can proceed. Hopefully you will both APPROVE
> quickly.
>
> Jacob
>
> On Wed, Nov 17, 2021 at 3:02 PM sheriff <sheriff at ebi.ac.uk> wrote:
>
> Hi Jacob and all,
>
> I approve the submission of the manuscript.
>
> Please update the citation Tiwari et 2020 Preprint to
>
> Tiwari K, Kananathan S, Roberts MG, Meyer JP, Sharif Shohan MU, Xavier
> A, Maire M, Zyoud A, Men J, Ng S, Nguyen TVN, Glont M, Hermjakob H,
> Malik-Sheriff RS. Reproducibility in systems biology modelling. Mol
> Syst Biol. 2021 Feb;17(2):e9982. doi: 10.15252/msb.20209982. PMID:
> 33620773; PMCID: PMC7901289.
>
> Also my name and affiliation below
>
> Rahuman S. Malik Sheriff
>
> European Molecular Biology Laboratory, European Bioinformatics
> Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
>
> Thanks for pushing this work forward
>
> Best regards
>
> Sheriff
>
> On 2021-11-17 18:58, Jonathan Karr wrote:
>
> Hi Jacob,
>
> Thank you again for spearheading this effort.
>
> I approve the submission. I think the paper organizes a variety of
> important issues toward more credible models, and the content is sound.
>
> My affiliation is Department of Genetics and Genomic Sciences, Icahn
> School of Medicine at Mount Sinai, New York, NY, USA.
>
> As others have mentioned, I think the paper would be more impactful
> with further editing to make the paper easier to read:
>
> * More clearly articulate the goals/motivation for more credible models
> * Be more concise and focused
> * Remove redundancies by grouping related text
> * Fill in the gaps in logic in the introduction with more transitions,
> less extraneous information, and/or a brief outline.
> * Change the title of the "Utility of models" section to something like
> "Challenges with using multiscale models" (James' suggestion)
> * Order the "Utility of models" subsections to be easier to follow,
> perhaps from model construction through to reuse
> * Rephrase the titles of the "Utility of models" subsections to focus
> on opportunities for improvement rather than current problems
>
> Regards,
> Jonathan
>
> On Wed, Nov 10, 2021 at 11:25 PM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
> Thanks to all contributors who answered,
>
> Most contributors approved by now.
>
> James and Wiliam, I am not sure how many more revisions there will be
> for this publication. I did not add several important references of my
> own in this revision. Frankly I wanted to keep reference changes to a
> minimum and kept it as close as possible to the origin . However, we
> are transferring the paper to the publisher under CC license, so it
> will not be hard to create another derived version with all sorts of
> additions and modifications in the future where people can edit it as
> they see fit and add whatever references they want - so after it gets
> published you can continue working on other versions as you see fit.
> For now I ask we focus on publishing this version alone and I really
> hope the editors will not put us through another revision round since
> it makes no sense at this point - any change is not substantial
> compared to what we have already and any delay is more damaging than
> productive.
>
> To be productive I ask that the following people who did not answer so
> far take the time to APPROVE, DISAPPROVE, or ABSTAIN.:
> Robin Thompson
> James R. Faeder
> Jonathan Karr
> Rahuman Sheriff
> John Rice
>
> John Rice - thanks for your support, yet you will have to be specific:
> You can either choose APPROVE or ABSTAIN - both of these options will
> move the paper forwards. APPROVE will add your name to the list of
> authors with all responsibilities and privileges listed or implied ,
> ABSTAIN will put you in acknowledgements without any obligation. So
> John, please choose if you want your name on the paper or not in this
> specific version - any decision you make will be ok.
>
> I hope we can father all support quickly so I can move forward and
> submit the paper.
>
> Jacob
>
> On Tue, Nov 9, 2021 at 5:46 AM William Waites <wwaites at ieee.org> wrote:
> I'm just chasing down references for use in another context and I
> notice that the Ke et al paper is still a pre-print after more than a
> year. There is no problem in my opinion citing preprints but it is
> suspect in this case: there's been a ton of work on SARS-CoV-2
> infectiousness, why didn't this get published? Probably not best to
> rely on it as an example of practice. Perhaps to fix on revision.
>
> -w
>
> _______________________________________________
> Vp-integration-subgroup mailing list
> Vp-integration-subgroup at lists.simtk.org
> https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup
--
James A. Glazier, PhD
Professor of Intelligent Systems Engineering, Adjunct Professor of
Physics
Director, Biocomplexity Institute
Indiana University, Bloomington
(812) 391-2159 (cell)
--
James A. Glazier, PhD
Professor of Intelligent Systems Engineering, Adjunct Professor of
Physics
Director Biocomplexity Institute
Indiana University, Bloomington
(812) 391-2159
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