[Vp-integration-subgroup] [Vp-reproduce-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript
Jacob Barhak
jacob.barhak at gmail.com
Thu Jan 27 19:28:55 PST 2022
Ok Ruth, And the rest of the contributors please pay attention,
You will find your support acknowledged now.
The link to the manuscript draft is:
https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
Here are some observations.
>From 18 authors, 4 declared funding - this means that they were working
using taxpayer money on this paper rather than volunteering their time and
therefore need to report it:
Jonathan Karr . William Waites, Rahuman S. Malik Sheriff, and Ruth Bowness.
One Author declared conflict of interest - Jacob Barhak
James A. Glazier mentioned funding from multiple sources fron NSF/NIH yet
later agreed to leave those out - if this is correct, James volunteered his
own time towards work on this paper. James - correct me if I am wrong -
since if you plan to report this paper in the summary reports for those
grants, we must include those grants in the paper which will mean you used
taxpayer funds towards this work. So far I am leaving those out since it
seems unlikely that multiple grants supported this work and you withdrew
your request after my query.
If this is correct, this means that the rest 12 (13 if we count James) are
volunteers that have not been paid or have any financial interest in this
work.
I will wait until the end of Friday 1/27 before uploading a final version
to the submission system and notify the editor. I hope my analysis above is
correct and there are no more last minute changes - we had over a year to
put those changes in and had multiple approval rounds - hopefully we are
really done with this paper and can move forward to other endeavors.
Jacob
On Thu, Jan 27, 2022 at 3:54 AM Ruth Bowness <rb2250 at bath.ac.uk> wrote:
> Hi Jacob
>
>
>
> If I can still add my fellowship funding that would be great. I actually
> thought I had sent this info to you earlier but can’t find the e-mail in my
> sent mail so apologies for this late edition! Not sure of the exact format
> of the funding acknowledgments for this journal but could you add that I
> was supported by a fellowship funded by the Medical Research Council [grant
> number MR/P014704/1].
>
> Many thanks
> Ruth
>
>
>
> *Dr Ruth Bowness*
>
> *Lecturer & MRC Research Fellow*
>
> Department of Mathematical Sciences
>
> University of Bath
>
>
>
> E-mail: rb2250 at bath.ac.uk
>
> Website: *https://ruthbowness.com
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>
> Twitter: @RuthBowness
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.com%2FRuthBowness&data=04%7C01%7Crb2250%40bath.ac.uk%7C591572838bf74aeb2de108d97776c932%7C377e3d224ea1422db0ad8fcc89406b9e%7C0%7C0%7C637672174320173922%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=KgWid3T4fEBEh9BMHmytt2%2FBuHhBWdNhsapbYIG1EBE%3D&reserved=0>
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> *As I work flexible hours, you may receive this e-mail at a time outside
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> working pattern and look forward to your response when it is reasonable for
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>
> *From: *Vp-integration-subgroup <
> vp-integration-subgroup-bounces at lists.simtk.org> on behalf of Jacob
> Barhak <jacob.barhak at gmail.com>
> *Date: *Thursday, 27 January 2022 at 01:49
> *To: *Torres, Marcella <mtorres at richmond.edu>
> *Cc: *vp-reproduce-subgroup at lists.simtk.org <
> vp-reproduce-subgroup at lists.simtk.org>, James Glazier <jaglazier at gmail.com>,
> vp-integration-subgroup at lists.simtk.org <
> vp-integration-subgroup at lists.simtk.org>
> *Subject: *Re: [Vp-integration-subgroup] [Vp-reproduce-subgroup] Shayn
> Peirce-Cottler via Frontiers: Manuscript
>
> *CAUTION: * This email came from outside of the University. To keep your
> account safe, only click on links and open attachments if you know the
> person who sent the email, or you expected to receive this communication.
>
>
>
> 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
> <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flinks.email.frontiersin.org%2Fls%2Fclick%3Fupn%3D99YMbkkQ8WNJiHLectmHSn5XnTmYe57aPeiziTpYNtyfClFbQqFlwPq2nUMZBzQ7srQvkLkPbc-2F-2BZbZ-2BczlOsPrTMbzmmMktcODsIp2h-2Ffj90r8fRFX2WoaacyAq0r1DpdlwAI9E7tBq-2Fy-2F2Oci2ve-2FCfkFNdVsmiG1bos-2FvnrU-3DZcy-_B-2Fy9jbSVGoT8qhSwbw0AFtm6DlDsGMQJjIadnFC13-2FJyATqJzBD73VYfuDTc-2F-2BJaJPaJJ5oSKrMDAr6Ompo1c21QYWQoQgYfAYNEjVnB244sSGd8-2BEkyma7zMD5B9L6sx2V7r1JTwJYDZpx5bqIUznnbkYmAKXcibTaFF47hgopNpnsrFZkqBi6O6g8b4EiWw24vVRZnhel591eZQKRdrLT3faq2B-2F0DXCpdcIRO-2FjNMfVBXwcpPniAJnsg8Tlmf&data=04%7C01%7Crb2250%40bath.ac.uk%7C2c3f8a4a29544a88f66008d9e13720f7%7C377e3d224ea1422db0ad8fcc89406b9e%7C0%7C0%7C637788449875266880%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=DkMHU9x7U%2BkZegrOZlQunH27aiRH%2F5AnZR%2F%2FLBdht48%3D&reserved=0>
>
> 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
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>
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>
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> ------------------------------
>
> *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
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.simtk.org%2Fpipermail%2Fvp-integration-subgroup%2F2022-January%2F000388.html&data=04%7C01%7Crb2250%40bath.ac.uk%7C2c3f8a4a29544a88f66008d9e13720f7%7C377e3d224ea1422db0ad8fcc89406b9e%7C0%7C0%7C637788449875266880%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=8TwYHyKVg%2FhxpjxluM8NwOgMlGCwM%2Fb%2B%2F7WFM3ukRNo%3D&reserved=0>
>
> 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
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.simtk.org%2Fpipermail%2Fvp-integration-subgroup%2F2021-April%2F000073.html&data=04%7C01%7Crb2250%40bath.ac.uk%7C2c3f8a4a29544a88f66008d9e13720f7%7C377e3d224ea1422db0ad8fcc89406b9e%7C0%7C0%7C637788449875266880%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=haAlRb891OoZ7eyfMKeHw8exrVXjHcjqTLs2of2kPk4%3D&reserved=0>
>
>
>
> 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
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.frontiersin.org%2Fabout%2Fpolicies-and-publication-ethics&data=04%7C01%7Crb2250%40bath.ac.uk%7C2c3f8a4a29544a88f66008d9e13720f7%7C377e3d224ea1422db0ad8fcc89406b9e%7C0%7C0%7C637788449875266880%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=dpN%2BWhoOTtUH78QTv21RpSqlB7ZChnXAMZTD4ZXEy2Q%3D&reserved=0>
>
>
>
> 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
>
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>
>
> --
>
> 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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