[Vp-integration-subgroup] [Vp-reproduce-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript

Jacob Barhak jacob.barhak at gmail.com
Fri Feb 4 17:28:03 PST 2022 

Thanks Marcella, and thanks to all contributors,

Marcella is right. The paper was indeed accepted and I just paid the
publication costs as promised to accelerate the publication process.

William and Gilberto, Here is a communication I got from the editor:

"
Thanks, Jacob! I'm going to accept this but I want to make sure that your
author name/affiliations are all correct in the system, so I will reach out
to the Frontiers staff to ensure that. But please consider this "accepted"!
Congratulations and thank you for a wonderful contribution!

"

The editor also sent a more elaborate letter to the office, so your name
and affiliation changes should appear properly once published.

I am delighted that the publication process has reached a conclusion. I
would have been happier if John Gennari would have agreed to join us, yet I
could not convince him. Hopefully he will be happy with his contributions
reaching a publisher.

It is now time to work towards implementing the ideas in the paper. We
should mention it in the response to the FDA document we started discussing
last week - so far John and I are discussing it, I encourage others to join.

                    Jacob




On Fri, Feb 4, 2022 at 1:25 PM Torres, Marcella <mtorres at richmond.edu>
wrote:

> Update: the manuscript was accepted, and Jacob and I have received an
> invoice. The acceptance email is copied below:
>
> Acceptance email copy:
>
> Dear Dr Torres,
>
> Frontiers in Systems Biology Editorial Office has sent you a message.
> Please click 'Reply' to send a direct response
>
> I am pleased to inform you that your manuscript "Model Integration in
> Computational Biology: the Role of Reproducibility, Credibility and
> Utility" has been approved for production and accepted for publication in
> Frontiers in Systems Biology, section Multiscale Mechanistic Modeling.
> Proofs are being prepared for you to verify before publication. We will
> also perform final checks to ensure your manuscript meets our criteria for
> publication (
> https://www.frontiersin.org/about/review-system#ManuscriptQualityStandards
> <http://links.email.frontiersin.org/ls/click?upn=AAaFa03elZRFPXQ6ShiKwAPsR8oZaO3IEOnZve2aIAWsx1apwBsjG944wpqaUKr3yodx7eEZuuHS6eg2pIQ1vig3q47etShhyRv3y7q5L9peYv31PLstfv8lcz2LY4l3Aeut_B-2Fy9jbSVGoT8qhSwbw0AFtm6DlDsGMQJjIadnFC13-2FJyATqJzBD73VYfuDTc-2F-2BJa2GQAe6lx-2FHbZjn-2F71kv6o6IixqczrgdiPH77O8-2B-2BkhmkDKCINuYgiDYe-2BkgOI85TBxoUrPrhIPoEmFTJ22APZMd5OvPArhiRx5tluYCDV1q7GVCJ9sXxikWD3VW90LNvQRlMuye1lN5-2F9PzQQjn-2FVsZUOx2NhByJcuLAIsAQ9bwChYW9uSDwLhj0ECYwGks-2F>
> ).
>
> The title, abstract and author(s) list you provided during submission is
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>
> Manuscript title: Model Integration in Computational Biology: the Role of
> Reproducibility, Credibility and Utility
> Journal: Frontiers in Systems Biology, section Multiscale Mechanistic
> Modeling
> Article type: Review
> 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 A. Glazier, James Faeder,
> Alexander Kulesza
> Manuscript ID: 822606
> Edited by: Shayn Peirce-Cottler
>
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>
>
>
> 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:* Saturday, January 29, 2022 10:47 PM
> *To:* Ruth Bowness <rb2250 at bath.ac.uk>
> *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.
>
> Greetings paper contributors,
>
> The changes in funding were submitted:
>
> Below is the message I wrote to the editor.
>
> Hopefully the paper can be published now.
>
>               Jacob
>
> #######  Copy of  message  to  the editor #####
>
> Thanks Shayn,
>
>
>
> The group updated  funding sources for 2 more individuals - apologies for
> the delay, yet it's a large group. I appreciate the patience - this delay
> helps get things in order.
>
>
>
> Also, one more author noticed that his name is not properly written and I
> corrected it in the text - yet it needs to be corrected in the system. .
>
> Gilberto Gonzalez-Parra is the proper name of the author - with a hyphen
> between Gonzalez and Parra - Apparently I added his name improperly to the
> submission system and the system does not allow me to edit this.
>
> I also remind you that William Waites has 2 affiliations as I mentioned in
> my previous message - I cannot add his second affiliation to the system -
> the authors list is grayed out.
>
>
>
> The changes to funding were added and the revised manuscript with proper
> funding information was uploaded.
>
>
>
> Please proceed with the process. I hope you find it all in order and ready
> for publication.
>
>
>
>                 Jacob
>
> On Thu, Jan 27, 2022 at 9:28 PM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
>
> 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
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fruthbowness.com%2F&data=04%7C01%7Crb2250%40bath.ac.uk%7C591572838bf74aeb2de108d97776c932%7C377e3d224ea1422db0ad8fcc89406b9e%7C0%7C0%7C637672174320173922%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=UBXYb3UzAIxJJHcD3uPWsot4LOpTTuIlVOZFNfPLbz8%3D&reserved=0>*
>
> 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>
>
>
>
> *Please note that I work part-time hours, usually Monday-Wednesday.*
>
>
>
> *As I work flexible hours, you may receive this e-mail at a time outside
> the hours of a ‘normal’ working day. Please be assured that I respect your
> working pattern and look forward to your response when it is reasonable for
> you to reply. *
>
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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
> <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.frontiersin.org%2F&data=04%7C01%7Crb2250%40bath.ac.uk%7C2c3f8a4a29544a88f66008d9e13720f7%7C377e3d224ea1422db0ad8fcc89406b9e%7C0%7C0%7C637788449875266880%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=ZNxuovJ3W7M3BIKcHLTJl9DQT3t7iGAcFhV%2FLGZ9N%2F8%3D&reserved=0>
> 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
> <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
>
> _______________________________________________
> Vp-integration-subgroup mailing list
> Vp-integration-subgroup at lists.simtk.org
> https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.simtk.org%2Fmailman%2Flistinfo%2Fvp-integration-subgroup&data=04%7C01%7Crb2250%40bath.ac.uk%7C2c3f8a4a29544a88f66008d9e13720f7%7C377e3d224ea1422db0ad8fcc89406b9e%7C0%7C0%7C637788449875266880%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=7YSc85BykfPNVsOkhJ3QA6XySH1YHD%2B2vwnbRBAXc2w%3D&reserved=0>
>
>
>
> --
>
> 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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