[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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